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Sample records for matlab mapping toolbox

  1. The GMT/MATLAB Toolbox

    Science.gov (United States)

    Wessel, Paul; Luis, Joaquim F.

    2017-02-01

    The GMT/MATLAB toolbox is a basic interface between MATLAB® (or Octave) and GMT, the Generic Mapping Tools, which allows MATLAB users full access to all GMT modules. Data may be passed between the two programs using intermediate MATLAB structures that organize the metadata needed; these are produced when GMT modules are run. In addition, standard MATLAB matrix data can be used directly as input to GMT modules. The toolbox improves interoperability between two widely used tools in the geosciences and extends the capability of both tools: GMT gains access to the powerful computational capabilities of MATLAB while the latter gains the ability to access specialized gridding algorithms and can produce publication-quality PostScript-based illustrations. The toolbox is available on all platforms and may be downloaded from the GMT website.

  2. DACE - A Matlab Kriging Toolbox

    DEFF Research Database (Denmark)

    2002-01-01

    DACE, Design and Analysis of Computer Experiments, is a Matlab toolbox for working with kriging approximations to computer models.......DACE, Design and Analysis of Computer Experiments, is a Matlab toolbox for working with kriging approximations to computer models....

  3. Accelerator Toolbox for MATLAB

    International Nuclear Information System (INIS)

    Terebilo, Andrei

    2001-01-01

    This paper introduces Accelerator Toolbox (AT)--a collection of tools to model particle accelerators and beam transport lines in the MATLAB environment. At SSRL, it has become the modeling code of choice for the ongoing design and future operation of the SPEAR 3 synchrotron light source. AT was designed to take advantage of power and simplicity of MATLAB--commercially developed environment for technical computing and visualization. Many examples in this paper illustrate the advantages of the AT approach and contrast it with existing accelerator code frameworks

  4. Matlab laser toolbox

    NARCIS (Netherlands)

    Römer, Gerardus Richardus, Bernardus, Engelina; Huis in 't Veld, Bert; Schmidt, M.; Vollertsen, F.; Geiger, M.

    2010-01-01

    Matlab® is a program for numeric computation, simulation and visualization, developed by The Mathworks, Inc. It is used heavily in education, research, and industry, for solving general, as well as application area-specific problems, that arise in various disciplines. For this purpose Matlab has

  5. Channel Access Client Toolbox for Matlab

    International Nuclear Information System (INIS)

    2002-01-01

    This paper reports on MATLAB Channel Access (MCA) Toolbox--MATLAB [1] interface to EPICS Channel Access (CA) client library. We are developing the toolbox for SPEAR3 accelerator controls, but it is of general use for accelerator and experimental physics applications programming. It is packaged as a MATLAB toolbox to allow easy development of complex CA client applications entirely in MATLAB. The benefits include: the ability to calculate and display parameters that use EPICS process variables as inputs, availability of MATLAB graphics tools for user interface design, and integration with the MATLABbased accelerator modeling software - Accelerator Toolbox [2-4]. Another purpose of this paper is to propose a feasible path to a synergy between accelerator control systems and accelerator simulation codes, the idea known as on-line accelerator model

  6. DAFNE: A Matlab toolbox for Bayesian multi-source remote sensing and ancillary data fusion, with application to flood mapping

    Science.gov (United States)

    D'Addabbo, Annarita; Refice, Alberto; Lovergine, Francesco P.; Pasquariello, Guido

    2018-03-01

    High-resolution, remotely sensed images of the Earth surface have been proven to be of help in producing detailed flood maps, thanks to their synoptic overview of the flooded area and frequent revisits. However, flood scenarios can be complex situations, requiring the integration of different data in order to provide accurate and robust flood information. Several processing approaches have been recently proposed to efficiently combine and integrate heterogeneous information sources. In this paper, we introduce DAFNE, a Matlab®-based, open source toolbox, conceived to produce flood maps from remotely sensed and other ancillary information, through a data fusion approach. DAFNE is based on Bayesian Networks, and is composed of several independent modules, each one performing a different task. Multi-temporal and multi-sensor data can be easily handled, with the possibility of following the evolution of an event through multi-temporal output flood maps. Each DAFNE module can be easily modified or upgraded to meet different user needs. The DAFNE suite is presented together with an example of its application.

  7. Accelerator Modeling with MATLAB Accelerator Toolbox

    International Nuclear Information System (INIS)

    2002-01-01

    This paper introduces Accelerator Toolbox (AT)--a collection of tools to model storage rings and beam transport lines in the MATLAB environment. The objective is to illustrate the flexibility and efficiency of the AT-MATLAB framework. The paper discusses three examples of problems that are analyzed frequently in connection with ring-based synchrotron light sources

  8. A Total Factor Productivity Toolbox for MATLAB

    NARCIS (Netherlands)

    B.M. Balk (Bert); J. Barbero (Javier); J.L. Zofío (José)

    2018-01-01

    textabstractTotal Factor Productivity Toolbox is a new package for MATLAB that includes functions to calculate the main Total Factor Productivity (TFP) indices and their decompositions, based on Shephard’s distance functions and using Data Envelopment Analysis (DEA) programming techniques. The

  9. The Matlab Radial Basis Function Toolbox

    Directory of Open Access Journals (Sweden)

    Scott A. Sarra

    2017-03-01

    Full Text Available Radial Basis Function (RBF methods are important tools for scattered data interpolation and for the solution of Partial Differential Equations in complexly shaped domains. The most straight forward approach used to evaluate the methods involves solving a linear system which is typically poorly conditioned. The Matlab Radial Basis Function toolbox features a regularization method for the ill-conditioned system, extended precision floating point arithmetic, and symmetry exploitation for the purpose of reducing flop counts of the associated numerical linear algebra algorithms.

  10. Object-oriented Matlab adaptive optics toolbox

    Science.gov (United States)

    Conan, R.; Correia, C.

    2014-08-01

    Object-Oriented Matlab Adaptive Optics (OOMAO) is a Matlab toolbox dedicated to Adaptive Optics (AO) systems. OOMAO is based on a small set of classes representing the source, atmosphere, telescope, wavefront sensor, Deformable Mirror (DM) and an imager of an AO system. This simple set of classes allows simulating Natural Guide Star (NGS) and Laser Guide Star (LGS) Single Conjugate AO (SCAO) and tomography AO systems on telescopes up to the size of the Extremely Large Telescopes (ELT). The discrete phase screens that make the atmosphere model can be of infinite size, useful for modeling system performance on large time scales. OOMAO comes with its own parametric influence function model to emulate different types of DMs. The cone effect, altitude thickness and intensity profile of LGSs are also reproduced. Both modal and zonal modeling approach are implemented. OOMAO has also an extensive library of theoretical expressions to evaluate the statistical properties of turbulence wavefronts. The main design characteristics of the OOMAO toolbox are object-oriented modularity, vectorized code and transparent parallel computing. OOMAO has been used to simulate and to design the Multi-Object AO prototype Raven at the Subaru telescope and the Laser Tomography AO system of the Giant Magellan Telescope. In this paper, a Laser Tomography AO system on an ELT is simulated with OOMAO. In the first part, we set-up the class parameters and we link the instantiated objects to create the source optical path. Then we build the tomographic reconstructor and write the script for the pseudo-open-loop controller.

  11. PreSurgMapp: a MATLAB Toolbox for Presurgical Mapping of Eloquent Functional Areas Based on Task-Related and Resting-State Functional MRI.

    Science.gov (United States)

    Huang, Huiyuan; Ding, Zhongxiang; Mao, Dewang; Yuan, Jianhua; Zhu, Fangmei; Chen, Shuda; Xu, Yan; Lou, Lin; Feng, Xiaoyan; Qi, Le; Qiu, Wusi; Zhang, Han; Zang, Yu-Feng

    2016-10-01

    The main goal of brain tumor surgery is to maximize tumor resection while minimizing the risk of irreversible postoperative functional sequelae. Eloquent functional areas should be delineated preoperatively, particularly for patients with tumors near eloquent areas. Functional magnetic resonance imaging (fMRI) is a noninvasive technique that demonstrates great promise for presurgical planning. However, specialized data processing toolkits for presurgical planning remain lacking. Based on several functions in open-source software such as Statistical Parametric Mapping (SPM), Resting-State fMRI Data Analysis Toolkit (REST), Data Processing Assistant for Resting-State fMRI (DPARSF) and Multiple Independent Component Analysis (MICA), here, we introduce an open-source MATLAB toolbox named PreSurgMapp. This toolbox can reveal eloquent areas using comprehensive methods and various complementary fMRI modalities. For example, PreSurgMapp supports both model-based (general linear model, GLM, and seed correlation) and data-driven (independent component analysis, ICA) methods and processes both task-based and resting-state fMRI data. PreSurgMapp is designed for highly automatic and individualized functional mapping with a user-friendly graphical user interface (GUI) for time-saving pipeline processing. For example, sensorimotor and language-related components can be automatically identified without human input interference using an effective, accurate component identification algorithm using discriminability index. All the results generated can be further evaluated and compared by neuro-radiologists or neurosurgeons. This software has substantial value for clinical neuro-radiology and neuro-oncology, including application to patients with low- and high-grade brain tumors and those with epilepsy foci in the dominant language hemisphere who are planning to undergo a temporal lobectomy.

  12. VQone MATLAB toolbox: A graphical experiment builder for image and video quality evaluations: VQone MATLAB toolbox.

    Science.gov (United States)

    Nuutinen, Mikko; Virtanen, Toni; Rummukainen, Olli; Häkkinen, Jukka

    2016-03-01

    This article presents VQone, a graphical experiment builder, written as a MATLAB toolbox, developed for image and video quality ratings. VQone contains the main elements needed for the subjective image and video quality rating process. This includes building and conducting experiments and data analysis. All functions can be controlled through graphical user interfaces. The experiment builder includes many standardized image and video quality rating methods. Moreover, it enables the creation of new methods or modified versions from standard methods. VQone is distributed free of charge under the terms of the GNU general public license and allows code modifications to be made so that the program's functions can be adjusted according to a user's requirements. VQone is available for download from the project page (http://www.helsinki.fi/psychology/groups/visualcognition/).

  13. PFA toolbox: a MATLAB tool for Metabolic Flux Analysis.

    Science.gov (United States)

    Morales, Yeimy; Bosque, Gabriel; Vehí, Josep; Picó, Jesús; Llaneras, Francisco

    2016-07-11

    Metabolic Flux Analysis (MFA) is a methodology that has been successfully applied to estimate metabolic fluxes in living cells. However, traditional frameworks based on this approach have some limitations, particularly when measurements are scarce and imprecise. This is very common in industrial environments. The PFA Toolbox can be used to face those scenarios. Here we present the PFA (Possibilistic Flux Analysis) Toolbox for MATLAB, which simplifies the use of Interval and Possibilistic Metabolic Flux Analysis. The main features of the PFA Toolbox are the following: (a) It provides reliable MFA estimations in scenarios where only a few fluxes can be measured or those available are imprecise. (b) It provides tools to easily plot the results as interval estimates or flux distributions. (c) It is composed of simple functions that MATLAB users can apply in flexible ways. (d) It includes a Graphical User Interface (GUI), which provides a visual representation of the measurements and their uncertainty. (e) It can use stoichiometric models in COBRA format. In addition, the PFA Toolbox includes a User's Guide with a thorough description of its functions and several examples. The PFA Toolbox for MATLAB is a freely available Toolbox that is able to perform Interval and Possibilistic MFA estimations.

  14. System design through Matlab, control toolbox and Simulink

    CERN Document Server

    Singh, Krishna K

    2001-01-01

    MATLAB , a software package developed by Math Works, Inc. is powerful, versatile and interactive software for scientific and technical computations including simulations. Specialised toolboxes provided with several built-in functions are a special feature of MATLAB . This book titled System Design through MATLAB , Control Toolbox and SIMULINK aims at getting the reader started with computations and simulations in system engineering quickly and easily and then proceeds to build concepts for advanced computations and simulations that includes the control and compensation of systems. Simulation through SIMULINK has also been described to allow the reader to get the feel of the real world situation. This book is appropriate for undergraduate students undergoing final semester of their project work, postgraduate students who have MATLAB integrated in their course or wish to take up simulation problem in the area of system engineering for their dissertation work and research scholars for whom MATLABÊ

  15. SBEToolbox: A Matlab Toolbox for Biological Network Analysis.

    Science.gov (United States)

    Konganti, Kranti; Wang, Gang; Yang, Ence; Cai, James J

    2013-01-01

    We present SBEToolbox (Systems Biology and Evolution Toolbox), an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and displays the network using different graph layout algorithms. Straightforward implementation and the inclusion of high-level functions allow the functionality to be easily extended or tailored through developing custom plugins. SBEGUI, a menu-driven graphical user interface (GUI) of SBEToolbox, enables easy access to various network and graph algorithms for programmers and non-programmers alike. All source code and sample data are freely available at https://github.com/biocoder/SBEToolbox/releases.

  16. GISMO: A MATLAB toolbox for seismic research, monitoring, & education

    Science.gov (United States)

    Thompson, G.; Reyes, C. G.; Kempler, L. A.

    2017-12-01

    GISMO is an open-source MATLAB toolbox which provides an object-oriented framework to build workflows and applications that read, process, visualize and write seismic waveform, catalog and instrument response data. GISMO can retrieve data from a variety of sources (e.g. FDSN web services, Earthworm/Winston servers) and data formats (SAC, Seisan, etc.). It can handle waveform data that crosses file boundaries. All this alleviates one of the most time consuming part for scientists developing their own codes. GISMO simplifies seismic data analysis by providing a common interface for your data, regardless of its source. Several common plots are built-in to GISMO, such as record section plots, spectrograms, depth-time sections, event count per unit time, energy release per unit time, etc. Other visualizations include map views and cross-sections of hypocentral data. Several common processing methods are also included, such as an extensive set of tools for correlation analysis. Support is being added to interface GISMO with ObsPy. GISMO encourages community development of an integrated set of codes and accompanying documentation, eliminating the need for seismologists to "reinvent the wheel". By sharing code the consistency and repeatability of results can be enhanced. GISMO is hosted on GitHub with documentation both within the source code and in the project wiki. GISMO has been used at the University of South Florida and University of Alaska Fairbanks in graduate-level courses including Seismic Data Analysis, Time Series Analysis and Computational Seismology. GISMO has also been tailored to interface with the common seismic monitoring software and data formats used by volcano observatories in the US and elsewhere. As an example, toolbox training was delivered to researchers at INETER (Nicaragua). Applications built on GISMO include IceWeb (e.g. web-based spectrograms), which has been used by Alaska Volcano Observatory since 1998 and became the prototype for the USGS

  17. MASCOT - MATLAB Stability and Control Toolbox

    Science.gov (United States)

    Kenny, Sean; Crespo, Luis

    2011-01-01

    MASCOT software was created to provide the conceptual aircraft designer accurate predictions of air vehicle stability and control characteristics. The code takes as input mass property data in the form of an inertia tensor, aerodynamic loading data, and propulsion (i.e. thrust) loading data. Using fundamental non-linear equations of motion, MASCOT then calculates vehicle trim and static stability data for any desired flight condition. Common predefined flight conditions are included. The predefined flight conditions include six horizontal and six landing rotation conditions with varying options for engine out, crosswind and sideslip, plus three takeoff rotation conditions. Results are displayed through a unique graphical interface developed to provide stability and control information to the conceptual design engineers using a qualitative scale indicating whether the vehicle has acceptable, marginal, or unacceptable static stability characteristics. This software allows the user to prescribe the vehicle s CG location, mass, and inertia tensor so that any loading configuration between empty weight and maximum take-off weight can be analyzed. The required geometric and aerodynamic data as well as mass and inertia properties may be entered directly, passed through data files, or come from external programs such as Vehicle Sketch Pad (VSP). The current version of MASCOT has been tested with VSP used to compute the required data, which is then passed directly into the program. In VSP, the vehicle geometry is created and manipulated. The aerodynamic coefficients, stability and control derivatives, are calculated using VorLax, which is now available directly within VSP. MASCOT has been written exclusively using the technical computing language MATLAB . This innovation is able to bridge the gap between low-fidelity conceptual design and higher-fidelity stability and control analysis. This new tool enables the conceptual design engineer to include detailed static stability

  18. PSYCHOACOUSTICS: a comprehensive MATLAB toolbox for auditory testing.

    Science.gov (United States)

    Soranzo, Alessandro; Grassi, Massimo

    2014-01-01

    PSYCHOACOUSTICS is a new MATLAB toolbox which implements three classic adaptive procedures for auditory threshold estimation. The first includes those of the Staircase family (method of limits, simple up-down and transformed up-down); the second is the Parameter Estimation by Sequential Testing (PEST); and the third is the Maximum Likelihood Procedure (MLP). The toolbox comes with more than twenty built-in experiments each provided with the recommended (default) parameters. However, if desired, these parameters can be modified through an intuitive and user friendly graphical interface and stored for future use (no programming skills are required). Finally, PSYCHOACOUSTICS is very flexible as it comes with several signal generators and can be easily extended for any experiment.

  19. Matlab Stability and Control Toolbox: Trim and Static Stability Module

    Science.gov (United States)

    Crespo, Luis G.; Kenny, Sean P.

    2006-01-01

    This paper presents the technical background of the Trim and Static module of the Matlab Stability and Control Toolbox. This module performs a low-fidelity stability and control assessment of an aircraft model for a set of flight critical conditions. This is attained by determining if the control authority available for trim is sufficient and if the static stability characteristics are adequate. These conditions can be selected from a prescribed set or can be specified to meet particular requirements. The prescribed set of conditions includes horizontal flight, take-off rotation, landing flare, steady roll, steady turn and pull-up/ push-over flight, for which several operating conditions can be specified. A mathematical model was developed allowing for six-dimensional trim, adjustable inertial properties, asymmetric vehicle layouts, arbitrary number of engines, multi-axial thrust vectoring, engine(s)-out conditions, crosswind and gyroscopic effects.

  20. The Biopsychology-Toolbox: a free, open-source Matlab-toolbox for the control of behavioral experiments.

    Science.gov (United States)

    Rose, Jonas; Otto, Tobias; Dittrich, Lars

    2008-10-30

    The Biopsychology-Toolbox is a free, open-source Matlab-toolbox for the control of behavioral experiments. The major aim of the project was to provide a set of basic tools that allow programming novices to control basic hardware used for behavioral experimentation without limiting the power and flexibility of the underlying programming language. The modular design of the toolbox allows portation of parts as well as entire paradigms between different types of hardware. In addition to the toolbox, this project offers a platform for the exchange of functions, hardware solutions and complete behavioral paradigms.

  1. CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis.

    Science.gov (United States)

    Inoue, Kentaro; Maeda, Kazuhiro; Miyabe, Takaaki; Matsuoka, Yu; Kurata, Hiroyuki

    2014-09-01

    Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.

  2. MATLAB Stability and Control Toolbox Trim and Static Stability Module

    Science.gov (United States)

    Kenny, Sean P.; Crespo, Luis

    2012-01-01

    MATLAB Stability and Control Toolbox (MASCOT) utilizes geometric, aerodynamic, and inertial inputs to calculate air vehicle stability in a variety of critical flight conditions. The code is based on fundamental, non-linear equations of motion and is able to translate results into a qualitative, graphical scale useful to the non-expert. MASCOT was created to provide the conceptual aircraft designer accurate predictions of air vehicle stability and control characteristics. The code takes as input mass property data in the form of an inertia tensor, aerodynamic loading data, and propulsion (i.e. thrust) loading data. Using fundamental nonlinear equations of motion, MASCOT then calculates vehicle trim and static stability data for the desired flight condition(s). Available flight conditions include six horizontal and six landing rotation conditions with varying options for engine out, crosswind, and sideslip, plus three take-off rotation conditions. Results are displayed through a unique graphical interface developed to provide the non-stability and control expert conceptual design engineer a qualitative scale indicating whether the vehicle has acceptable, marginal, or unacceptable static stability characteristics. If desired, the user can also examine the detailed, quantitative results.

  3. RenderToolbox3: MATLAB tools that facilitate physically based stimulus rendering for vision research.

    Science.gov (United States)

    Heasly, Benjamin S; Cottaris, Nicolas P; Lichtman, Daniel P; Xiao, Bei; Brainard, David H

    2014-02-07

    RenderToolbox3 provides MATLAB utilities and prescribes a workflow that should be useful to researchers who want to employ graphics in the study of vision and perhaps in other endeavors as well. In particular, RenderToolbox3 facilitates rendering scene families in which various scene attributes and renderer behaviors are manipulated parametrically, enables spectral specification of object reflectance and illuminant spectra, enables the use of physically based material specifications, helps validate renderer output, and converts renderer output to physical units of radiance. This paper describes the design and functionality of the toolbox and discusses several examples that demonstrate its use. We have designed RenderToolbox3 to be portable across computer hardware and operating systems and to be free and open source (except for MATLAB itself). RenderToolbox3 is available at https://github.com/DavidBrainard/RenderToolbox3.

  4. FIT3D toolbox: multiple view geometry and 3D reconstruction for Matlab

    NARCIS (Netherlands)

    Esteban, I.; Dijk, J.; Groen, F.

    2010-01-01

    FIT3D is a Toolbox built for Matlab that aims at unifying and distributing a set of tools that will allow the researcher to obtain a complete 3D model from a set of calibrated images. In this paper we motivate and present the structure of the toolbox in a tutorial and example based approach. Given

  5. Structural Time Domain Identification (STDI) Toolbox for Use with MATLAB

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning; Andersen, P.; Brincker, Rune

    1997-01-01

    The Structural Time Domain Identification (STDI) toolbox for use with MATLABTM is developed at Aalborg University, Denmark, based on the system identification research performed during recent years. By now, a reliable set of functions offers a wide spectrum of services for all the important steps...

  6. Structural Time Domain Identification (STDI) Toolbox for Use with MATLAB

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning; Andersen, P.; Brincker, Rune

    The Structural Time Domain Identification (STDI) toolbox for use with MATLABTM is developed at Aalborg University, Denmark, based on the system identification research performed during recent years. By now, a reliable set of functions offers a wide spectrum of services for all the important steps...

  7. SIPPI: A Matlab toolbox for sampling the solution to inverse problems with complex prior information

    DEFF Research Database (Denmark)

    Hansen, Thomas Mejer; Cordua, Knud Skou; Caroline Looms, Majken

    2013-01-01

    on the solution. The combined states of information (i.e. the solution to the inverse problem) is a probability density function typically referred to as the a posteriori probability density function. We present a generic toolbox for Matlab and Gnu Octave called SIPPI that implements a number of methods...

  8. SIPPI: A Matlab toolbox for sampling the solution to inverse problems with complex prior information

    DEFF Research Database (Denmark)

    Hansen, Thomas Mejer; Cordua, Knud Skou; Looms, Majken Caroline

    2013-01-01

    We present an application of the SIPPI Matlab toolbox, to obtain a sample from the a posteriori probability density function for the classical tomographic inversion problem. We consider a number of different forward models, linear and non-linear, such as ray based forward models that rely...

  9. CFS MATLAB toolbox: An experiment builder for continuous flash suppression (CFS) task.

    Science.gov (United States)

    Nuutinen, Mikko; Mustonen, Terhi; Häkkinen, Jukka

    2017-09-15

    CFS toolbox is an open-source collection of MATLAB functions that utilizes PsychToolbox-3 (PTB-3). It is designed to allow a researcher to create and run continuous flash suppression experiments using a variety of experimental parameters (i.e., stimulus types and locations, noise characteristics, and experiment window settings). In a CFS experiment, one of the eyes at a time is presented with a dynamically changing noise pattern, while the other eye is concurrently presented with a static target stimulus, such as a Gabor patch. Due to the strong interocular suppression created by the dominant noise pattern mask, the target stimulus is rendered invisible for an extended duration. Very little knowledge of MATLAB is required for using the toolbox; experiments are generated by modifying csv files with the required parameters, and result data are output to text files for further analysis. The open-source code is available on the project page under a Creative Commons License ( http://www.mikkonuutinen.arkku.net/CFS_toolbox/ and https://bitbucket.org/mikkonuutinen/cfs_toolbox ).

  10. MATLAB Toolboxes for Reference Electrode Standardization Technique (REST) of Scalp EEG.

    Science.gov (United States)

    Dong, Li; Li, Fali; Liu, Qiang; Wen, Xin; Lai, Yongxiu; Xu, Peng; Yao, Dezhong

    2017-01-01

    Reference electrode standardization technique (REST) has been increasingly acknowledged and applied as a re-reference technique to transform an actual multi-channels recordings to approximately zero reference ones in electroencephalography/event-related potentials (EEG/ERPs) community around the world in recent years. However, a more easy-to-use toolbox for re-referencing scalp EEG data to zero reference is still lacking. Here, we have therefore developed two open-source MATLAB toolboxes for REST of scalp EEG. One version of REST is closely integrated into EEGLAB, which is a popular MATLAB toolbox for processing the EEG data; and another is a batch version to make it more convenient and efficient for experienced users. Both of them are designed to provide an easy-to-use for novice researchers and flexibility for experienced researchers. All versions of the REST toolboxes can be freely downloaded at http://www.neuro.uestc.edu.cn/rest/Down.html, and the detailed information including publications, comments and documents on REST can also be found from this website. An example of usage is given with comparative results of REST and average reference. We hope these user-friendly REST toolboxes could make the relatively novel technique of REST easier to study, especially for applications in various EEG studies.

  11. An Open-source Toolbox for Analysing and Processing PhysioNet Databases in MATLAB and Octave.

    Science.gov (United States)

    Silva, Ikaro; Moody, George B

    The WaveForm DataBase (WFDB) Toolbox for MATLAB/Octave enables integrated access to PhysioNet's software and databases. Using the WFDB Toolbox for MATLAB/Octave, users have access to over 50 physiological databases in PhysioNet. The toolbox provides access over 4 TB of biomedical signals including ECG, EEG, EMG, and PLETH. Additionally, most signals are accompanied by metadata such as medical annotations of clinical events: arrhythmias, sleep stages, seizures, hypotensive episodes, etc. Users of this toolbox should easily be able to reproduce, validate, and compare results published based on PhysioNet's software and databases.

  12. OXSA: An open-source magnetic resonance spectroscopy analysis toolbox in MATLAB.

    Directory of Open Access Journals (Sweden)

    Lucian A B Purvis

    Full Text Available In vivo magnetic resonance spectroscopy provides insight into metabolism in the human body. New acquisition protocols are often proposed to improve the quality or efficiency of data collection. Processing pipelines must also be developed to use these data optimally. Current fitting software is either targeted at general spectroscopy fitting, or for specific protocols. We therefore introduce the MATLAB-based OXford Spectroscopy Analysis (OXSA toolbox to allow researchers to rapidly develop their own customised processing pipelines. The toolbox aims to simplify development by: being easy to install and use; seamlessly importing Siemens Digital Imaging and Communications in Medicine (DICOM standard data; allowing visualisation of spectroscopy data; offering a robust fitting routine; flexibly specifying prior knowledge when fitting; and allowing batch processing of spectra. This article demonstrates how each of these criteria have been fulfilled, and gives technical details about the implementation in MATLAB. The code is freely available to download from https://github.com/oxsatoolbox/oxsa.

  13. OXSA: An open-source magnetic resonance spectroscopy analysis toolbox in MATLAB.

    Science.gov (United States)

    Purvis, Lucian A B; Clarke, William T; Biasiolli, Luca; Valkovič, Ladislav; Robson, Matthew D; Rodgers, Christopher T

    2017-01-01

    In vivo magnetic resonance spectroscopy provides insight into metabolism in the human body. New acquisition protocols are often proposed to improve the quality or efficiency of data collection. Processing pipelines must also be developed to use these data optimally. Current fitting software is either targeted at general spectroscopy fitting, or for specific protocols. We therefore introduce the MATLAB-based OXford Spectroscopy Analysis (OXSA) toolbox to allow researchers to rapidly develop their own customised processing pipelines. The toolbox aims to simplify development by: being easy to install and use; seamlessly importing Siemens Digital Imaging and Communications in Medicine (DICOM) standard data; allowing visualisation of spectroscopy data; offering a robust fitting routine; flexibly specifying prior knowledge when fitting; and allowing batch processing of spectra. This article demonstrates how each of these criteria have been fulfilled, and gives technical details about the implementation in MATLAB. The code is freely available to download from https://github.com/oxsatoolbox/oxsa.

  14. Numerical solution of multi groups point kinetic equations by simulink toolbox of Matlab software

    International Nuclear Information System (INIS)

    Hadad, K.; Mohamadi, A.; Sabet, H.; Ayobian, N.; Khani, M.

    2004-01-01

    The simulink toolbox of Matlab Software was employed to solve the point kinetics equation with six group delayed neutrons. The method of Adams-Bash ford showed a good convergence in solving the system of simultaneous equations and the obtained results showed good agreements with other numerical schemes. The flexibility of the package in changing the system parameters and the user friendly interface makes this approach a reliable educational package in revealing the affects of reactivity changes on power incursions

  15. Construction of multi-functional open modulized Matlab simulation toolbox for imaging ladar system

    Science.gov (United States)

    Wu, Long; Zhao, Yuan; Tang, Meng; He, Jiang; Zhang, Yong

    2011-06-01

    Ladar system simulation is to simulate the ladar models using computer simulation technology in order to predict the performance of the ladar system. This paper presents the developments of laser imaging radar simulation for domestic and overseas studies and the studies of computer simulation on ladar system with different application requests. The LadarSim and FOI-LadarSIM simulation facilities of Utah State University and Swedish Defence Research Agency are introduced in details. This paper presents the low level of simulation scale, un-unified design and applications of domestic researches in imaging ladar system simulation, which are mostly to achieve simple function simulation based on ranging equations for ladar systems. Design of laser imaging radar simulation with open and modularized structure is proposed to design unified modules for ladar system, laser emitter, atmosphere models, target models, signal receiver, parameters setting and system controller. Unified Matlab toolbox and standard control modules have been built with regulated input and output of the functions, and the communication protocols between hardware modules. A simulation based on ICCD gain-modulated imaging ladar system for a space shuttle is made based on the toolbox. The simulation result shows that the models and parameter settings of the Matlab toolbox are able to simulate the actual detection process precisely. The unified control module and pre-defined parameter settings simplify the simulation of imaging ladar detection. Its open structures enable the toolbox to be modified for specialized requests. The modulization gives simulations flexibility.

  16. MatTAP: A MATLAB toolbox for the control and analysis of movement synchronisation experiments.

    Science.gov (United States)

    Elliott, Mark T; Welchman, Andrew E; Wing, Alan M

    2009-02-15

    Investigating movement timing and synchronisation at the sub-second range relies on an experimental setup that has high temporal fidelity, is able to deliver output cues and can capture corresponding responses. Modern, multi-tasking operating systems make this increasingly challenging when using standard PC hardware and programming languages. This paper describes a new free suite of tools (available from http://www.snipurl.com/mattap) for use within the MATLAB programming environment, compatible with Microsoft Windows and a range of data acquisition hardware. The toolbox allows flexible generation of timing cues with high temporal accuracy, the capture and automatic storage of corresponding participant responses and an integrated analysis module for the rapid processing of results. A simple graphical user interface is used to navigate the toolbox and so can be operated easily by users not familiar with programming languages. However, it is also fully extensible and customisable, allowing adaptation for individual experiments and facilitating the addition of new modules in future releases. Here we discuss the relevance of the MatTAP (MATLAB Timing Analysis Package) toolbox to current timing experiments and compare its use to alternative methods. We validate the accuracy of the analysis module through comparison to manual observation methods and replicate a previous sensorimotor synchronisation experiment to demonstrate the versatility of the toolbox features demanded by such movement synchronisation paradigms.

  17. The NNSYSID Toolbox - A MATLAB Toolbox for System Identification with Neural Networks

    DEFF Research Database (Denmark)

    Nørgård, Peter Magnus; Ravn, Ole; Hansen, Lars Kai

    1996-01-01

    To assist the identification of nonlinear dynamic systems, a set of tools has been developed for the MATLAB(R) environment. The tools include a number of different model structures, highly effective training algorithms, functions for validating trained networks, and pruning algorithms for determi......To assist the identification of nonlinear dynamic systems, a set of tools has been developed for the MATLAB(R) environment. The tools include a number of different model structures, highly effective training algorithms, functions for validating trained networks, and pruning algorithms...

  18. MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution

    Directory of Open Access Journals (Sweden)

    Xia Xuhua

    2005-03-01

    Full Text Available Abstract Background MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. Results We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. Conclusion MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/project/?group_id=454.

  19. Parallel Sequential Monte Carlo for Efficient Density Combination: The Deco Matlab Toolbox

    DEFF Research Database (Denmark)

    Casarin, Roberto; Grassi, Stefano; Ravazzolo, Francesco

    This paper presents the Matlab package DeCo (Density Combination) which is based on the paper by Billio et al. (2013) where a constructive Bayesian approach is presented for combining predictive densities originating from different models or other sources of information. The combination weights...... for standard CPU computing and for Graphical Process Unit (GPU) parallel computing. For the GPU implementation we use the Matlab parallel computing toolbox and show how to use General Purposes GPU computing almost effortless. This GPU implementation comes with a speed up of the execution time up to seventy...... times compared to a standard CPU Matlab implementation on a multicore CPU. We show the use of the package and the computational gain of the GPU version, through some simulation experiments and empirical applications....

  20. iELVis: An open source MATLAB toolbox for localizing and visualizing human intracranial electrode data.

    Science.gov (United States)

    Groppe, David M; Bickel, Stephan; Dykstra, Andrew R; Wang, Xiuyuan; Mégevand, Pierre; Mercier, Manuel R; Lado, Fred A; Mehta, Ashesh D; Honey, Christopher J

    2017-04-01

    Intracranial electrical recordings (iEEG) and brain stimulation (iEBS) are invaluable human neuroscience methodologies. However, the value of such data is often unrealized as many laboratories lack tools for localizing electrodes relative to anatomy. To remedy this, we have developed a MATLAB toolbox for intracranial electrode localization and visualization, iELVis. NEW METHOD: iELVis uses existing tools (BioImage Suite, FSL, and FreeSurfer) for preimplant magnetic resonance imaging (MRI) segmentation, neuroimaging coregistration, and manual identification of electrodes in postimplant neuroimaging. Subsequently, iELVis implements methods for correcting electrode locations for postimplant brain shift with millimeter-scale accuracy and provides interactive visualization on 3D surfaces or in 2D slices with optional functional neuroimaging overlays. iELVis also localizes electrodes relative to FreeSurfer-based atlases and can combine data across subjects via the FreeSurfer average brain. It takes 30-60min of user time and 12-24h of computer time to localize and visualize electrodes from one brain. We demonstrate iELVis's functionality by showing that three methods for mapping primary hand somatosensory cortex (iEEG, iEBS, and functional MRI) provide highly concordant results. COMPARISON WITH EXISTING METHODS: iELVis is the first public software for electrode localization that corrects for brain shift, maps electrodes to an average brain, and supports neuroimaging overlays. Moreover, its interactive visualizations are powerful and its tutorial material is extensive. iELVis promises to speed the progress and enhance the robustness of intracranial electrode research. The software and extensive tutorial materials are freely available as part of the EpiSurg software project: https://github.com/episurg/episurg. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. An Open-source Toolbox for Analysing and Processing PhysioNet Databases in MATLAB and Octave

    Directory of Open Access Journals (Sweden)

    Ikaro Silva

    2014-09-01

    Full Text Available The WaveForm DataBase (WFDB Toolbox for MATLAB/Octave enables  integrated access to PhysioNet's software and databases. Using the WFDB Toolbox for MATLAB/Octave, users have access to over 50 physiological databases in PhysioNet. The toolbox allows direct loading into MATLAB/Octave's workspace of over 4 TB of biomedical signals including ECG, EEG, EMG, and PLETH. Additionally, most signals are accompanied by meta data such as medical annotations of clinical events: arrhythmias, sleep stages, seizures, hypotensive episodes, etc. Users of this toolbox should easily be able to reproduce, validate, and compare results published based on PhysioNet's software and databases.

  2. Introduction to TAFI - A Matlab® toolbox for analysis of flexural isostasy

    Science.gov (United States)

    Jha, S.; Harry, D. L.; Schutt, D.

    2016-12-01

    The isostatic response of vertical tectonic loads emplaced on thin elastic plates overlying inviscid substrate and the corresponding gravity anomalies are commonly modeled using well established theories and methodologies of flexural analysis. However, such analysis requires some mathematical and coding expertise on part of users. With that in mind, we designed a new interactive Matlab® toolbox called Toolbox for Analysis of Flexural Isostasy (TAFI). TAFI allows users to create forward models (2-D and 3-D) of flexural deformation of the lithosphere and resulting gravity anomaly. TAFI computes Green's Functions for flexure of the elastic plate subjected to point or line loads, and analytical solution for harmonic loads. Flexure due to non-impulsive, distributed 2-D or 3-D loads are computed by convolving the appropriate Green's function with a user-supplied spatially discretized load function. The gravity anomaly associated with each density interface is calculated by using the Fourier Transform of flexural deflection of these interfaces and estimating the gravity in the wavenumber domain. All models created in TAFI are based on Matlab's intrinsic functions and do not require any specialized toolbox, function or library except those distributed with TAFI. Modeling functions within TAFI can be called from Matlab workspace, from within user written programs or from the TAFI's graphical user interface (GUI). The GUI enables the user to model the flexural deflection of lithosphere interactively, enabling real time comparison of model fit with observed data constraining the flexural deformation and gravity, facilitating rapid search for best fitting flexural model. TAFI is a very useful teaching and research tool and have been tested rigorously in graduate level teaching and basic research environment.

  3. GPELab, a Matlab toolbox to solve Gross-Pitaevskii equations II: Dynamics and stochastic simulations

    Science.gov (United States)

    Antoine, Xavier; Duboscq, Romain

    2015-08-01

    GPELab is a free Matlab toolbox for modeling and numerically solving large classes of systems of Gross-Pitaevskii equations that arise in the physics of Bose-Einstein condensates. The aim of this second paper, which follows (Antoine and Duboscq, 2014), is to first present the various pseudospectral schemes available in GPELab for computing the deterministic and stochastic nonlinear dynamics of Gross-Pitaevskii equations (Antoine, et al., 2013). Next, the corresponding GPELab functions are explained in detail. Finally, some numerical examples are provided to show how the code works for the complex dynamics of BEC problems.

  4. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

    KAUST Repository

    Klingbeil, G.

    2011-02-25

    Motivation: The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user\\'s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. © The Author 2011. Published by Oxford University Press. All rights reserved.

  5. DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation.

    Science.gov (United States)

    Sherfey, Jason S; Soplata, Austin E; Ardid, Salva; Roberts, Erik A; Stanley, David A; Pittman-Polletta, Benjamin R; Kopell, Nancy J

    2018-01-01

    DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator) or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations. DynaSim also includes a large set of features that simplify exploring model dynamics over parameter spaces, running simulations in parallel using both multicore processors and high-performance computer clusters, and analyzing and plotting large numbers of simulated data sets in parallel. It also includes a graphical user interface (DynaSim GUI) that supports full functionality without requiring user programming. The software has been implemented in MATLAB to enable advanced neural modeling using MATLAB, given its popularity and a growing interest in modeling neural systems. The design of DynaSim incorporates a novel schema for model specification to facilitate future interoperability with other specifications (e.g., NeuroML, SBML), simulators (e.g., NEURON, Brian, NEST), and web-based applications (e.g., Geppetto) outside MATLAB. DynaSim is freely available at http://dynasimtoolbox.org. This tool promises to reduce barriers for investigating dynamics in large neural models, facilitate collaborative modeling, and complement other tools being developed in the neuroinformatics community.

  6. Wind wave analysis in depth limited water using OCEANLYZ, A MATLAB toolbox

    Science.gov (United States)

    Karimpour, Arash; Chen, Qin

    2017-09-01

    There are a number of well established methods in the literature describing how to assess and analyze measured wind wave data. However, obtaining reliable results from these methods requires adequate knowledge on their behavior, strengths and weaknesses. A proper implementation of these methods requires a series of procedures including a pretreatment of the raw measurements, and adjustment and refinement of the processed data to provide quality assurance of the outcomes, otherwise it can lead to untrustworthy results. This paper discusses potential issues in these procedures, explains what parameters are influential for the outcomes and suggests practical solutions to avoid and minimize the errors in the wave results. The procedure of converting the water pressure data into the water surface elevation data, treating the high frequency data with a low signal-to-noise ratio, partitioning swell energy from wind sea, and estimating the peak wave frequency from the weighted integral of the wave power spectrum are described. Conversion and recovery of the data acquired by a pressure transducer, particularly in depth-limited water like estuaries and lakes, are explained in detail. To provide researchers with tools for a reliable estimation of wind wave parameters, the Ocean Wave Analyzing toolbox, OCEANLYZ, is introduced. The toolbox contains a number of MATLAB functions for estimation of the wave properties in time and frequency domains. The toolbox has been developed and examined during a number of the field study projects in Louisiana's estuaries.

  7. EEGVIS: A MATLAB toolbox for browsing, exploring, and viewing large datasets

    Directory of Open Access Journals (Sweden)

    Kay A Robbins

    2012-05-01

    Full Text Available Recent advances in data monitoring and sensor technology have accelerated the acquisition of very large data sets. Streaming data sets from instrumentation such as multi-channel EEG recording usually must undergo substantial pre-processing and artifact removal. Even when using automated procedures, most scientists engage in laborious manual examination and processing to assure high quality data and to indentify interesting or problematic data segments. Researchers also do not have a convenient method of method of visually assessing the effects of applying any stage in a processing pipeline. EEGVIS is a MATLAB toolbox that allows users to quickly explore multi-channel EEG and other large array-based data sets using multi-scale drill-down techniques. Customizable summary views reveal potentially interesting sections of data, which users can explore further by clicking to examine using detailed viewing components. The viewer and a companion browser are built on our MoBBED framework, which has a library of modular viewing components that can be mixed and matched to best reveal structure. Users can easily create new viewers for their specific data without any programming during the exploration process. These viewers automatically support pan, zoom, resizing of individual components, and cursor exploration. The toolbox can be used directly in MATLAB at any stage in a processing pipeline, as a plug in for EEGLAB, or as a standalone precompiled application without MATLAB running. EEGVIS and its supporting packages are freely available under the GNU general public license at http://visual.cs.utsa.edu/ eegvis.

  8. EEGVIS: A MATLAB Toolbox for Browsing, Exploring, and Viewing Large Datasets.

    Science.gov (United States)

    Robbins, Kay A

    2012-01-01

    Recent advances in data monitoring and sensor technology have accelerated the acquisition of very large data sets. Streaming data sets from instrumentation such as multi-channel EEG recording usually must undergo substantial pre-processing and artifact removal. Even when using automated procedures, most scientists engage in laborious manual examination and processing to assure high quality data and to indentify interesting or problematic data segments. Researchers also do not have a convenient method of method of visually assessing the effects of applying any stage in a processing pipeline. EEGVIS is a MATLAB toolbox that allows users to quickly explore multi-channel EEG and other large array-based data sets using multi-scale drill-down techniques. Customizable summary views reveal potentially interesting sections of data, which users can explore further by clicking to examine using detailed viewing components. The viewer and a companion browser are built on our MoBBED framework, which has a library of modular viewing components that can be mixed and matched to best reveal structure. Users can easily create new viewers for their specific data without any programming during the exploration process. These viewers automatically support pan, zoom, resizing of individual components, and cursor exploration. The toolbox can be used directly in MATLAB at any stage in a processing pipeline, as a plug-in for EEGLAB, or as a standalone precompiled application without MATLAB running. EEGVIS and its supporting packages are freely available under the GNU general public license at http://visual.cs.utsa.edu/eegvis.

  9. Robust Correlation Analyses: False Positive and Power Validation Using a New Open Source Matlab Toolbox

    Science.gov (United States)

    Pernet, Cyril R.; Wilcox, Rand; Rousselet, Guillaume A.

    2012-01-01

    Pearson’s correlation measures the strength of the association between two variables. The technique is, however, restricted to linear associations and is overly sensitive to outliers. Indeed, a single outlier can result in a highly inaccurate summary of the data. Yet, it remains the most commonly used measure of association in psychology research. Here we describe a free Matlab(R) based toolbox (http://sourceforge.net/projects/robustcorrtool/) that computes robust measures of association between two or more random variables: the percentage-bend correlation and skipped-correlations. After illustrating how to use the toolbox, we show that robust methods, where outliers are down weighted or removed and accounted for in significance testing, provide better estimates of the true association with accurate false positive control and without loss of power. The different correlation methods were tested with normal data and normal data contaminated with marginal or bivariate outliers. We report estimates of effect size, false positive rate and power, and advise on which technique to use depending on the data at hand. PMID:23335907

  10. SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer.

    Science.gov (United States)

    Li, Jiannong; Smalley, Inna; Schell, Michael J; Smalley, Keiran S M; Chen, Y Ann

    2017-09-15

    Single-cell technologies allow characterization of transcriptomes and epigenomes for individual cells under different conditions and provide unprecedented resolution for researchers to investigate cellular heterogeneity in cancer. The SinCHet ( gle ell erogeneity) toolbox is developed in MATLAB and has a graphical user interface (GUI) for visualization and user interaction. It analyzes both continuous (e.g. mRNA expression) and binary omics data (e.g. discretized methylation data). The toolbox does not only quantify cellular heterogeneity using S hannon P rofile (SP) at different clonal resolutions but also detects heterogeneity differences using a D statistic between two populations. It is defined as the area under the P rofile of S hannon D ifference (PSD). This flexible tool provides a default clonal resolution using the change point of PSD detected by multivariate adaptive regression splines model; it also allows user-defined clonal resolutions for further investigation. This tool provides insights into emerging or disappearing clones between conditions, and enables the prioritization of biomarkers for follow-up experiments based on heterogeneity or marker differences between and/or within cell populations. The SinCHet software is freely available for non-profit academic use. The source code, example datasets, and the compiled package are available at http://labpages2.moffitt.org/chen/software/ . ann.chen@moffitt.org. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  11. Robust correlation analyses: false positive and power validation using a new open source matlab toolbox.

    Science.gov (United States)

    Pernet, Cyril R; Wilcox, Rand; Rousselet, Guillaume A

    2012-01-01

    Pearson's correlation measures the strength of the association between two variables. The technique is, however, restricted to linear associations and is overly sensitive to outliers. Indeed, a single outlier can result in a highly inaccurate summary of the data. Yet, it remains the most commonly used measure of association in psychology research. Here we describe a free Matlab((R)) based toolbox (http://sourceforge.net/projects/robustcorrtool/) that computes robust measures of association between two or more random variables: the percentage-bend correlation and skipped-correlations. After illustrating how to use the toolbox, we show that robust methods, where outliers are down weighted or removed and accounted for in significance testing, provide better estimates of the true association with accurate false positive control and without loss of power. The different correlation methods were tested with normal data and normal data contaminated with marginal or bivariate outliers. We report estimates of effect size, false positive rate and power, and advise on which technique to use depending on the data at hand.

  12. BOLDSync: a MATLAB-based toolbox for synchronized stimulus presentation in functional MRI.

    Science.gov (United States)

    Joshi, Jitesh; Saharan, Sumiti; Mandal, Pravat K

    2014-02-15

    Precise and synchronized presentation of paradigm stimuli in functional magnetic resonance imaging (fMRI) is central to obtaining accurate information about brain regions involved in a specific task. In this manuscript, we present a new MATLAB-based toolbox, BOLDSync, for synchronized stimulus presentation in fMRI. BOLDSync provides a user friendly platform for design and presentation of visual, audio, as well as multimodal audio-visual (AV) stimuli in functional imaging experiments. We present simulation experiments that demonstrate the millisecond synchronization accuracy of BOLDSync, and also illustrate the functionalities of BOLDSync through application to an AV fMRI study. BOLDSync gains an advantage over other available proprietary and open-source toolboxes by offering a user friendly and accessible interface that affords both precision in stimulus presentation and versatility across various types of stimulus designs and system setups. BOLDSync is a reliable, efficient, and versatile solution for synchronized stimulus presentation in fMRI study. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.

    Science.gov (United States)

    Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K

    2011-04-15

    The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user's models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. The software is open source under the GPL v3 and available at http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU. The web site also contains supplementary information. klingbeil@maths.ox.ac.uk Supplementary data are available at Bioinformatics online.

  14. Load forecasting using different architectures of neural networks with the assistance of the MATLAB toolboxes; Previsao de cargas eletricas utilizando diferentes arquiteturas de redes neurais artificiais com o auxilio das toolboxes do MATLAB

    Energy Technology Data Exchange (ETDEWEB)

    Nose Filho, Kenji; Araujo, Klayton A.M.; Maeda, Jorge L.Y.; Lotufo, Anna Diva P. [Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Ilha Solteira, SP (Brazil)], Emails: kenjinose@yahoo.com.br, klayton_ama@hotmail.com, jorge-maeda@hotmail.com, annadiva@dee.feis.unesp.br

    2009-07-01

    This paper presents a development and implementation of a program to electrical load forecasting with data from a Brazilian electrical company, using four different architectures of neural networks of the MATLAB toolboxes: multilayer backpropagation gradient descendent with momentum, multilayer backpropagation Levenberg-Marquardt, adaptive network based fuzzy inference system and general regression neural network. The program presented a satisfactory performance, guaranteeing very good results. (author)

  15. CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation

    Science.gov (United States)

    2013-01-01

    The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening. PMID:23938087

  16. Optimization design of wind turbine drive train based on Matlab genetic algorithm toolbox

    International Nuclear Information System (INIS)

    Li, R N; Liu, X; Liu, S J

    2013-01-01

    In order to ensure the high efficiency of the whole flexible drive train of the front-end speed adjusting wind turbine, the working principle of the main part of the drive train is analyzed. As critical parameters, rotating speed ratios of three planetary gear trains are selected as the research subject. The mathematical model of the torque converter speed ratio is established based on these three critical variable quantity, and the effect of key parameters on the efficiency of hydraulic mechanical transmission is analyzed. Based on the torque balance and the energy balance, refer to hydraulic mechanical transmission characteristics, the transmission efficiency expression of the whole drive train is established. The fitness function and constraint functions are established respectively based on the drive train transmission efficiency and the torque converter rotating speed ratio range. And the optimization calculation is carried out by using MATLAB genetic algorithm toolbox. The optimization method and results provide an optimization program for exact match of wind turbine rotor, gearbox, hydraulic mechanical transmission, hydraulic torque converter and synchronous generator, ensure that the drive train work with a high efficiency, and give a reference for the selection of the torque converter and hydraulic mechanical transmission

  17. Optimization design of wind turbine drive train based on Matlab genetic algorithm toolbox

    Science.gov (United States)

    Li, R. N.; Liu, X.; Liu, S. J.

    2013-12-01

    In order to ensure the high efficiency of the whole flexible drive train of the front-end speed adjusting wind turbine, the working principle of the main part of the drive train is analyzed. As critical parameters, rotating speed ratios of three planetary gear trains are selected as the research subject. The mathematical model of the torque converter speed ratio is established based on these three critical variable quantity, and the effect of key parameters on the efficiency of hydraulic mechanical transmission is analyzed. Based on the torque balance and the energy balance, refer to hydraulic mechanical transmission characteristics, the transmission efficiency expression of the whole drive train is established. The fitness function and constraint functions are established respectively based on the drive train transmission efficiency and the torque converter rotating speed ratio range. And the optimization calculation is carried out by using MATLAB genetic algorithm toolbox. The optimization method and results provide an optimization program for exact match of wind turbine rotor, gearbox, hydraulic mechanical transmission, hydraulic torque converter and synchronous generator, ensure that the drive train work with a high efficiency, and give a reference for the selection of the torque converter and hydraulic mechanical transmission.

  18. Image processing and pattern recognition with CVIPtools MATLAB toolbox: automatic creation of masks for veterinary thermographic images

    Science.gov (United States)

    Mishra, Deependra K.; Umbaugh, Scott E.; Lama, Norsang; Dahal, Rohini; Marino, Dominic J.; Sackman, Joseph

    2016-09-01

    CVIPtools is a software package for the exploration of computer vision and image processing developed in the Computer Vision and Image Processing Laboratory at Southern Illinois University Edwardsville. CVIPtools is available in three variants - a) CVIPtools Graphical User Interface, b) CVIPtools C library and c) CVIPtools MATLAB toolbox, which makes it accessible to a variety of different users. It offers students, faculty, researchers and any user a free and easy way to explore computer vision and image processing techniques. Many functions have been implemented and are updated on a regular basis, the library has reached a level of sophistication that makes it suitable for both educational and research purposes. In this paper, the detail list of the functions available in the CVIPtools MATLAB toolbox are presented and how these functions can be used in image analysis and computer vision applications. The CVIPtools MATLAB toolbox allows the user to gain practical experience to better understand underlying theoretical problems in image processing and pattern recognition. As an example application, the algorithm for the automatic creation of masks for veterinary thermographic images is presented.

  19. TecLines: A MATLAB-Based Toolbox for Tectonic Lineament Analysis from Satellite Images and DEMs, Part 2: Line Segments Linking and Merging

    Directory of Open Access Journals (Sweden)

    Mehdi Rahnama

    2014-11-01

    Full Text Available Extraction and interpretation of tectonic lineaments is one of the routines for mapping large areas using remote sensing data. However, this is a subjective and time-consuming process. It is difficult to choose an optimal lineament extraction method in order to reduce subjectivity and obtain vectors similar to what an analyst would manually extract. The objective of this study is the implementation, evaluation and comparison of Hough transform, segment merging and polynomial fitting methods towards automated tectonic lineament mapping. For this purpose we developed a new MATLAB-based toolbox (TecLines. The proposed toolbox capabilities were validated using a synthetic Digital Elevation Model (DEM and tested along in the Andarab fault zone (Afghanistan where specific fault structures are known. In this study, we used filters in both frequency and spatial domains and the tensor voting framework to produce binary edge maps. We used the Hough transform to extract linear image discontinuities. We used B-spline as a polynomial curve fitting method to eliminate artificial line segments that are out of interest and to link discontinuous segments with similar trends. We performed statistical analyses in order to compare the final image discontinuities maps with existing references map.

  20. a Matlab Toolbox for Basin Scale Fluid Flow Modeling Applied to Hydrology and Geothermal Energy

    Science.gov (United States)

    Alcanie, M.; Lupi, M.; Carrier, A.

    2017-12-01

    Recent boosts in the development of geothermal energy were fostered by the latest oil crises and by the need of reducing CO2 emissions generated by the combustion of fossil fuels. Various numerical codes (e.g. FEHM, CSMP++, HYDROTHERM, TOUGH) have thus been implemented for the simulation and quantification of fluid flow in the upper crust. One possible limitation of such codes is the limited accessibility and the complex structure of the simulators. For this reason, we began to develop a Hydrothermal Fluid Flow Matlab library as part of MRST (Matlab Reservoir Simulation Toolbox). MRST is designed for the simulation of oil and gas problems including carbon capture storage. However, a geothermal module is still missing. We selected the Geneva Basin as a natural laboratory because of the large amount of data available in the region. The Geneva Basin has been intensely investigated in the past with exploration wells, active seismic and gravity surveys. In addition, the energy strategy of Switzerland promotes the development of geothermal energy that lead to recent geophysical prospections. Previous and ongoing projects have shown the geothermal potential of the Geneva Basin but a consistent fluid flow model assessing the deep circulation in the region is yet to be defined. The first step of the study was to create the basin-scale static model. We integrated available active seismic, gravity inversions and borehole data to describe the principal geologic and tectonic features of the Geneva Basin. Petrophysical parameters were obtained from available and widespread well logs. This required adapting MRST to standard text format file imports and outline a new methodology for quick static model creation in an open source environment. We implemented several basin-scale fluid flow models to test the effects of petrophysical properties on the circulation dynamics of deep fluids in the Geneva Basin. Preliminary results allow the identification of preferential fluid flow

  1. User Guide for Compressible Flow Toolbox Version 2.1 for Use With MATLAB(Registered Trademark); Version 7

    Science.gov (United States)

    Melcher, Kevin J.

    2006-01-01

    This report provides a user guide for the Compressible Flow Toolbox, a collection of algorithms that solve almost 300 linear and nonlinear classical compressible flow relations. The algorithms, implemented in the popular MATLAB programming language, are useful for analysis of one-dimensional steady flow with constant entropy, friction, heat transfer, or shock discontinuities. The solutions do not include any gas dissociative effects. The toolbox also contains functions for comparing and validating the equation-solving algorithms against solutions previously published in the open literature. The classical equations solved by the Compressible Flow Toolbox are: isentropic-flow equations, Fanno flow equations (pertaining to flow of an ideal gas in a pipe with friction), Rayleigh flow equations (pertaining to frictionless flow of an ideal gas, with heat transfer, in a pipe of constant cross section.), normal-shock equations, oblique-shock equations, and Prandtl-Meyer expansion equations. At the time this report was published, the Compressible Flow Toolbox was available without cost from the NASA Software Repository.

  2. DETECT: a MATLAB toolbox for event detection and identification in time series, with applications to artifact detection in EEG signals.

    Science.gov (United States)

    Lawhern, Vernon; Hairston, W David; Robbins, Kay

    2013-01-01

    Recent advances in sensor and recording technology have allowed scientists to acquire very large time-series datasets. Researchers often analyze these datasets in the context of events, which are intervals of time where the properties of the signal change relative to a baseline signal. We have developed DETECT, a MATLAB toolbox for detecting event time intervals in long, multi-channel time series. Our primary goal is to produce a toolbox that is simple for researchers to use, allowing them to quickly train a model on multiple classes of events, assess the accuracy of the model, and determine how closely the results agree with their own manual identification of events without requiring extensive programming knowledge or machine learning experience. As an illustration, we discuss application of the DETECT toolbox for detecting signal artifacts found in continuous multi-channel EEG recordings and show the functionality of the tools found in the toolbox. We also discuss the application of DETECT for identifying irregular heartbeat waveforms found in electrocardiogram (ECG) data as an additional illustration.

  3. DETECT: a MATLAB toolbox for event detection and identification in time series, with applications to artifact detection in EEG signals.

    Directory of Open Access Journals (Sweden)

    Vernon Lawhern

    Full Text Available Recent advances in sensor and recording technology have allowed scientists to acquire very large time-series datasets. Researchers often analyze these datasets in the context of events, which are intervals of time where the properties of the signal change relative to a baseline signal. We have developed DETECT, a MATLAB toolbox for detecting event time intervals in long, multi-channel time series. Our primary goal is to produce a toolbox that is simple for researchers to use, allowing them to quickly train a model on multiple classes of events, assess the accuracy of the model, and determine how closely the results agree with their own manual identification of events without requiring extensive programming knowledge or machine learning experience. As an illustration, we discuss application of the DETECT toolbox for detecting signal artifacts found in continuous multi-channel EEG recordings and show the functionality of the tools found in the toolbox. We also discuss the application of DETECT for identifying irregular heartbeat waveforms found in electrocardiogram (ECG data as an additional illustration.

  4. COMETS2: An advanced MATLAB toolbox for the numerical analysis of electric fields generated by transcranial direct current stimulation.

    Science.gov (United States)

    Lee, Chany; Jung, Young-Jin; Lee, Sang Jun; Im, Chang-Hwan

    2017-02-01

    Since there is no way to measure electric current generated by transcranial direct current stimulation (tDCS) inside the human head through in vivo experiments, numerical analysis based on the finite element method has been widely used to estimate the electric field inside the head. In 2013, we released a MATLAB toolbox named COMETS, which has been used by a number of groups and has helped researchers to gain insight into the electric field distribution during stimulation. The aim of this study was to develop an advanced MATLAB toolbox, named COMETS2, for the numerical analysis of the electric field generated by tDCS. COMETS2 can generate any sizes of rectangular pad electrodes on any positions on the scalp surface. To reduce the large computational burden when repeatedly testing multiple electrode locations and sizes, a new technique to decompose the global stiffness matrix was proposed. As examples of potential applications, we observed the effects of sizes and displacements of electrodes on the results of electric field analysis. The proposed mesh decomposition method significantly enhanced the overall computational efficiency. We implemented an automatic electrode modeler for the first time, and proposed a new technique to enhance the computational efficiency. In this paper, an efficient toolbox for tDCS analysis is introduced (freely available at http://www.cometstool.com). It is expected that COMETS2 will be a useful toolbox for researchers who want to benefit from the numerical analysis of electric fields generated by tDCS. Copyright © 2016. Published by Elsevier B.V.

  5. KEGGParser: parsing and editing KEGG pathway maps in Matlab.

    Science.gov (United States)

    Arakelyan, Arsen; Nersisyan, Lilit

    2013-02-15

    KEGG pathway database is a collection of manually drawn pathway maps accompanied with KGML format files intended for use in automatic analysis. KGML files, however, do not contain the required information for complete reproduction of all the events indicated in the static image of a pathway map. Several parsers and editors of KEGG pathways exist for processing KGML files. We introduce KEGGParser-a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment. It also works with Scilab. The source code is available at http://www.mathworks.com/matlabcentral/fileexchange/37561.

  6. ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data.

    Science.gov (United States)

    Minas, Giorgos; Momiji, Hiroshi; Jenkins, Dafyd J; Costa, Maria J; Rand, David A; Finkenstädt, Bärbel

    2017-06-26

    Given the development of high-throughput experimental techniques, an increasing number of whole genome transcription profiling time series data sets, with good temporal resolution, are becoming available to researchers. The ReTrOS toolbox (Reconstructing Transcription Open Software) provides MATLAB-based implementations of two related methods, namely ReTrOS-Smooth and ReTrOS-Switch, for reconstructing the temporal transcriptional activity profile of a gene from given mRNA expression time series or protein reporter time series. The methods are based on fitting a differential equation model incorporating the processes of transcription, translation and degradation. The toolbox provides a framework for model fitting along with statistical analyses of the model with a graphical interface and model visualisation. We highlight several applications of the toolbox, including the reconstruction of the temporal cascade of transcriptional activity inferred from mRNA expression data and protein reporter data in the core circadian clock in Arabidopsis thaliana, and how such reconstructed transcription profiles can be used to study the effects of different cell lines and conditions. The ReTrOS toolbox allows users to analyse gene and/or protein expression time series where, with appropriate formulation of prior information about a minimum of kinetic parameters, in particular rates of degradation, users are able to infer timings of changes in transcriptional activity. Data from any organism and obtained from a range of technologies can be used as input due to the flexible and generic nature of the model and implementation. The output from this software provides a useful analysis of time series data and can be incorporated into further modelling approaches or in hypothesis generation.

  7. Labbtex: Toolbox para generación de informes en LATEX para Matlab

    Directory of Open Access Journals (Sweden)

    José Luis Almazán Gárate

    2012-10-01

    Full Text Available En este artículo se presenta el software desarrollado por el Equipo H3lite dentro del Departamento de Ingeneniería Civil. Transportes de la Escuela de Ingenieros de Caminos, Canales y Puertos de la Universidad Politécnica de Madrid para la generación de informes enLATEX mediante el software Matlab® y la integración en sus rutinas, Labbtex.La librería Labbtex proporciona un marco flexible para mezclar texto y código Matlab® para la generación automática de documentos. Un rchivo fuente simple contiene el texto de documentación y el código Matlab, al correr la aplicación se genera un documento final LATEX que contiene el texto, gráficos y tablas indicados con el formato de un documento LATEX. El código Matlab genera un documento LATEX usando la sintaxis. Así, LATEX (para composición de texto de alta calidad y Matlab® (para cálculo matemático pueden usarse simultáneamente. Esto permite la generación de informes en tiempo real con un uso de recursos mínimo.

  8. A MATLAB toolbox for the analysis of articulatory data in the production of speech.

    Science.gov (United States)

    Nguyen, N

    2000-08-01

    The goal of this paper is to present EMATOOLS, a set of scripts for displaying and annotating acoustic and articulatory data simultaneously in studies on speech production. These scripts were developed with the use of MATLAB, a multiplatform computing environment for numeric computation and visualization. The system is equipped with a mouse-driven graphical interface made up of a number of displays. This interface can be easily customized to speed up routine tasks. The scripts can also be used in a noninteractive way, as stand-alone MATLAB commands. Output data can be imported into any standard spreadsheet. EMATOOLS is freely available from www.lpl.univ-aix.fr/nguyen/ematools.html.

  9. A Simulation Platform To Model, Optimize And Design Wind Turbines. The Matlab/Simulink Toolbox

    Directory of Open Access Journals (Sweden)

    Anca Daniela HANSEN

    2002-12-01

    Full Text Available In the last years Matlab / Simulink® has become the most used software for modeling and simulation of dynamic systems. Wind energy conversion systems are for example such systems, containing subsystems with different ranges of the time constants: wind, turbine, generator, power electronics, transformer and grid. The electrical generator and the power converter need the smallest simulation step and therefore, these blocks decide the simulation speed. This paper presents a new and integrated simulation platform for modeling, optimizing and designing wind turbines. The platform contains different simulation tools: Matlab / Simulink - used as basic modeling tool, HAWC, DIgSilent and Saber.

  10. GCE Data Toolbox for MATLAB - a software framework for automating environmental data processing, quality control and documentation

    Science.gov (United States)

    Sheldon, W.; Chamblee, J.; Cary, R. H.

    2013-12-01

    Environmental scientists are under increasing pressure from funding agencies and journal publishers to release quality-controlled data in a timely manner, as well as to produce comprehensive metadata for submitting data to long-term archives (e.g. DataONE, Dryad and BCO-DMO). At the same time, the volume of digital data that researchers collect and manage is increasing rapidly due to advances in high frequency electronic data collection from flux towers, instrumented moorings and sensor networks. However, few pre-built software tools are available to meet these data management needs, and those tools that do exist typically focus on part of the data management lifecycle or one class of data. The GCE Data Toolbox has proven to be both a generalized and effective software solution for environmental data management in the Long Term Ecological Research Network (LTER). This open source MATLAB software library, developed by the Georgia Coastal Ecosystems LTER program, integrates metadata capture, creation and management with data processing, quality control and analysis to support the entire data lifecycle. Raw data can be imported directly from common data logger formats (e.g. SeaBird, Campbell Scientific, YSI, Hobo), as well as delimited text files, MATLAB files and relational database queries. Basic metadata are derived from the data source itself (e.g. parsed from file headers) and by value inspection, and then augmented using editable metadata templates containing boilerplate documentation, attribute descriptors, code definitions and quality control rules. Data and metadata content, quality control rules and qualifier flags are then managed together in a robust data structure that supports database functionality and ensures data validity throughout processing. A growing suite of metadata-aware editing, quality control, analysis and synthesis tools are provided with the software to support managing data using graphical forms and command-line functions, as well as

  11. Stress, strain, and structural dynamics an interactive handbook of formulas, solutions, and Matlab toolboxes

    CERN Document Server

    Yang, Bingen

    2005-01-01

    Stress, Strain, and Structural Dynamics is a comprehensive and definitive reference to statics and dynamics of solids and structures, including mechanics of materials, structural mechanics, elasticity, rigid-body dynamics, vibrations, structural dynamics, and structural controls. This text integrates the development of fundamental theories, formulas and mathematical models with user-friendly interactive computer programs, written in the powerful and popular MATLAB. This unique merger of technical referencing and interactive computing allows instant solution of a variety of engineering problems

  12. Regensim – Matlab toolbox for renewable energy sources modelling and simulation

    Directory of Open Access Journals (Sweden)

    Cristian Dragoş Dumitru

    2011-12-01

    Full Text Available This paper deals with the implementation and development of a Matlab Simulink library named RegenSim designed for modeling, simulations and analysis of real hybrid solarwind-hydro systems connected to local grids. Blocks like wind generators, hydro generators, solar photovoltaic modules and accumulators are implemented. The main objective is the study of the hybrid power system behavior, which allows employing renewable and variable in time energy sources while providing a continuous supply.

  13. TecLines: A MATLAB-Based Toolbox for Tectonic Lineament Analysis from Satellite Images and DEMs, Part 1: Line Segment Detection and Extraction

    Directory of Open Access Journals (Sweden)

    Mehdi Rahnama

    2014-06-01

    Full Text Available Geological structures, such as faults and fractures, appear as image discontinuities or lineaments in remote sensing data. Geologic lineament mapping is a very important issue in geo-engineering, especially for construction site selection, seismic, and risk assessment, mineral exploration and hydrogeological research. Classical methods of lineaments extraction are based on semi-automated (or visual interpretation of optical data and digital elevation models. We developed a freely available Matlab based toolbox TecLines (Tectonic Lineament Analysis for locating and quantifying lineament patterns using satellite data and digital elevation models. TecLines consists of a set of functions including frequency filtering, spatial filtering, tensor voting, Hough transformation, and polynomial fitting. Due to differences in the mathematical background of the edge detection and edge linking procedure as well as the breadth of the methods, we introduce the approach in two-parts. In this first study, we present the steps that lead to edge detection. We introduce the data pre-processing using selected filters in spatial and frequency domains. We then describe the application of the tensor-voting framework to improve position and length accuracies of the detected lineaments. We demonstrate the robustness of the approach in a complex area in the northeast of Afghanistan using a panchromatic QUICKBIRD-2 image with 1-meter resolution. Finally, we compare the results of TecLines with manual lineament extraction, and other lineament extraction algorithms, as well as a published fault map of the study area.

  14. TecDEM: A MATLAB Based Toolbox for understanding Tectonics from Digital Elevation Models

    Science.gov (United States)

    Shahzad, F.; Mahmood, S. A.; Gloaguen, R.

    2009-04-01

    TecDEM is a MATLAB based tool box for understanding the tectonics from digital elevation models (DEMs) of any area. These DEMs can be derived from data of any spatial resolution (Low, medium and High). In the first step we extract drainage network from the DEMs using flow grid approach. Drainage network is a group of streams having elevation and catchment area information as a function of spatial locations. We implement an array of stream structure to study this drainage network. Knickpoints can be identified on each stream of the drainage network by a graphical user interface and are helpful for understanding stream morphology. Stream profile analysis in steady state condition is applied on all streams to calculate geomorphic parameters and regional uplift rates. Hack index is calculated for all the profiles at a certain interval and over the change of knickpoints. Reports menu of this tool box generates detailed statistics report, complete tabulated report, graphical output of each analyzed stream profile and Hack index profile. All the calculated values are part of stream structure and is saved as .mat file for later use with this tool box. The spatial distribution of geomorphic parameters, uplift rates and knickpoints are exported as a shape files for visualization in professional GIS software. We test this tool box on DEMs from different tectonic settings worldwide and received verifiable results with other studies.

  15. Fission gas bubble identification using MATLAB's image processing toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Collette, R. [Colorado School of Mines, Nuclear Science and Engineering Program, 1500 Illinois St, Golden, CO 80401 (United States); King, J., E-mail: kingjc@mines.edu [Colorado School of Mines, Nuclear Science and Engineering Program, 1500 Illinois St, Golden, CO 80401 (United States); Keiser, D.; Miller, B.; Madden, J.; Schulthess, J. [Nuclear Fuels and Materials Division, Idaho National Laboratory, P.O. Box 1625, Idaho Falls, ID 83415-6188 (United States)

    2016-08-15

    Automated image processing routines have the potential to aid in the fuel performance evaluation process by eliminating bias in human judgment that may vary from person-to-person or sample-to-sample. This study presents several MATLAB based image analysis routines designed for fission gas void identification in post-irradiation examination of uranium molybdenum (U–Mo) monolithic-type plate fuels. Frequency domain filtration, enlisted as a pre-processing technique, can eliminate artifacts from the image without compromising the critical features of interest. This process is coupled with a bilateral filter, an edge-preserving noise removal technique aimed at preparing the image for optimal segmentation. Adaptive thresholding proved to be the most consistent gray-level feature segmentation technique for U–Mo fuel microstructures. The Sauvola adaptive threshold technique segments the image based on histogram weighting factors in stable contrast regions and local statistics in variable contrast regions. Once all processing is complete, the algorithm outputs the total fission gas void count, the mean void size, and the average porosity. The final results demonstrate an ability to extract fission gas void morphological data faster, more consistently, and at least as accurately as manual segmentation methods. - Highlights: •Automated image processing can aid in the fuel qualification process. •Routines are developed to characterize fission gas bubbles in irradiated U–Mo fuel. •Frequency domain filtration effectively eliminates FIB curtaining artifacts. •Adaptive thresholding proved to be the most accurate segmentation method. •The techniques established are ready to be applied to large scale data extraction testing.

  16. SPATIAL DATA MINING TOOLBOX FOR MAPPING SUITABILITY OF LANDFILL SITES USING NEURAL NETWORKS

    Directory of Open Access Journals (Sweden)

    S. K. M. Abujayyab

    2016-09-01

    Full Text Available Mapping the suitability of landfill sites is a complex field and is involved with multidiscipline. The purpose of this research is to create an ArcGIS spatial data mining toolbox for mapping the suitability of landfill sites at a regional scale using neural networks. The toolbox is constructed from six sub-tools to prepare, train, and process data. The employment of the toolbox is straightforward. The multilayer perceptron (MLP neural networks structure with a backpropagation learning algorithm is used. The dataset is mined from the north states in Malaysia. A total of 14 criteria are utilized to build the training dataset. The toolbox provides a platform for decision makers to implement neural networks for mapping the suitability of landfill sites in the ArcGIS environment. The result shows the ability of the toolbox to produce suitability maps for landfill sites.

  17. Analysis of Power Laws, Shape Collapses, and Neural Complexity: New Techniques and MATLAB Support via the NCC Toolbox.

    Science.gov (United States)

    Marshall, Najja; Timme, Nicholas M; Bennett, Nicholas; Ripp, Monica; Lautzenhiser, Edward; Beggs, John M

    2016-01-01

    Neural systems include interactions that occur across many scales. Two divergent methods for characterizing such interactions have drawn on the physical analysis of critical phenomena and the mathematical study of information. Inferring criticality in neural systems has traditionally rested on fitting power laws to the property distributions of "neural avalanches" (contiguous bursts of activity), but the fractal nature of avalanche shapes has recently emerged as another signature of criticality. On the other hand, neural complexity, an information theoretic measure, has been used to capture the interplay between the functional localization of brain regions and their integration for higher cognitive functions. Unfortunately, treatments of all three methods-power-law fitting, avalanche shape collapse, and neural complexity-have suffered from shortcomings. Empirical data often contain biases that introduce deviations from true power law in the tail and head of the distribution, but deviations in the tail have often been unconsidered; avalanche shape collapse has required manual parameter tuning; and the estimation of neural complexity has relied on small data sets or statistical assumptions for the sake of computational efficiency. In this paper we present technical advancements in the analysis of criticality and complexity in neural systems. We use maximum-likelihood estimation to automatically fit power laws with left and right cutoffs, present the first automated shape collapse algorithm, and describe new techniques to account for large numbers of neural variables and small data sets in the calculation of neural complexity. In order to facilitate future research in criticality and complexity, we have made the software utilized in this analysis freely available online in the MATLAB NCC (Neural Complexity and Criticality) Toolbox.

  18. Pareto design of state feedback tracking control of a biped robot via multiobjective PSO in comparison with sigma method and genetic algorithms: modified NSGAII and MATLAB's toolbox.

    Science.gov (United States)

    Mahmoodabadi, M J; Taherkhorsandi, M; Bagheri, A

    2014-01-01

    An optimal robust state feedback tracking controller is introduced to control a biped robot. In the literature, the parameters of the controller are usually determined by a tedious trial and error process. To eliminate this process and design the parameters of the proposed controller, the multiobjective evolutionary algorithms, that is, the proposed method, modified NSGAII, Sigma method, and MATLAB's Toolbox MOGA, are employed in this study. Among the used evolutionary optimization algorithms to design the controller for biped robots, the proposed method operates better in the aspect of designing the controller since it provides ample opportunities for designers to choose the most appropriate point based upon the design criteria. Three points are chosen from the nondominated solutions of the obtained Pareto front based on two conflicting objective functions, that is, the normalized summation of angle errors and normalized summation of control effort. Obtained results elucidate the efficiency of the proposed controller in order to control a biped robot.

  19. KALMTOOL for use with MATLAB

    DEFF Research Database (Denmark)

    Nørgaard, Peter Magnus; Ravn, Ole; Poulsen, Niels Kjølstad

    2003-01-01

    The KALMTOOL toolbox is a set of MATLAB tools for state estimation for nonlinear systems. The toolbox contains functions for extended Kalman filtering as well as for two new filters called the DD1 filter and the DD2 filter. The toolbox specifically addresses the problem of not having observations...... available at all sampling instants. All functions are available as m-functions but for faster (much faster!) execution, the DD1 and DD2 filters are also available as C Mex files for MATLAB under Windows and Linux. The toolbox requires MATLAB 6. No additional toolboxes are required....

  20. Visualizing flow fields using acoustic Doppler current profilers and the Velocity Mapping Toolbox

    Science.gov (United States)

    Jackson, P. Ryan

    2013-01-01

    The purpose of this fact sheet is to provide examples of how the U.S. Geological Survey is using acoustic Doppler current profilers for much more than routine discharge measurements. These instruments are capable of mapping complex three-dimensional flow fields within rivers, lakes, and estuaries. Using the Velocity Mapping Toolbox to process the ADCP data allows detailed visualization of the data, providing valuable information for a range of studies and applications.

  1. Development of a model using the MATLAB System identification toolbox to estimate 222Rn equilibrium factor from CR-39 based passive measurements

    International Nuclear Information System (INIS)

    Abo-Elmagd, M.; Sadek, A.M.

    2014-01-01

    Can and Bare method is a widely used passive method for measuring the equilibrium factor F through the determination of the track density ratio between bare (D) and filtered (D o ) detectors. The dimensions of the used diffusion chamber are altering the deposition ratios of Po-isotopes on the chamber walls as well as the ratios of the existing alpha emitters in air. Then the measured filtered track density and therefore the resultant equilibrium factor is changed according to the diffusion chamber dimensions. For this reason, high uncertainty was expected in the measured F using different diffusion chambers. In the present work, F is derived as a function of both track density ratio (D/D o ) and the dimensions of the used diffusion chambers (its volume to the total internal surface area; V/A). The accuracy of the derived formula was verified using the black-box modeling technique via the MATLAB System identification toolbox. The results show that the uncertainty of the calculated F by using the derived formula of F (D/D o , V/A) is only 5%. The obtained uncertainty ensures the quality of the derived function to calculate F using diffusion chambers with wide range of dimensions. - Highlights: • The manuscript is aimed to develop the Can and Bare method for measuring the equilibrium factor F. • A new formula F (D/D o , V/A) is obtained taking the dimension of the used cup (V/A) into consideration. • The accuracy of the derived formula was verified using the black-box modeling technique via the MATLAB. • The derived function covers the range of the widely used diffusion chambers (r ≤ 3.5 cm and h ≤ 10 cm). • The reproducibility of F estimated using this model is quite good (5% deviation) for different 8 cups

  2. Development of a model using the MATLAB System identification toolbox to estimate (222)Rn equilibrium factor from CR-39 based passive measurements.

    Science.gov (United States)

    Abo-Elmagd, M; Sadek, A M

    2014-12-01

    Can and Bare method is a widely used passive method for measuring the equilibrium factor F through the determination of the track density ratio between bare (D) and filtered (Do) detectors. The dimensions of the used diffusion chamber are altering the deposition ratios of Po-isotopes on the chamber walls as well as the ratios of the existing alpha emitters in air. Then the measured filtered track density and therefore the resultant equilibrium factor is changed according to the diffusion chamber dimensions. For this reason, high uncertainty was expected in the measured F using different diffusion chambers. In the present work, F is derived as a function of both track density ratio (D/Do) and the dimensions of the used diffusion chambers (its volume to the total internal surface area; V/A). The accuracy of the derived formula was verified using the black-box modeling technique via the MATLAB System identification toolbox. The results show that the uncertainty of the calculated F by using the derived formula of F (D/Do, V/A) is only 5%. The obtained uncertainty ensures the quality of the derived function to calculate F using diffusion chambers with wide range of dimensions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. PDB2Graph: A toolbox for identifying critical amino acids map in proteins based on graph theory.

    Science.gov (United States)

    Niknam, Niloofar; Khakzad, Hamed; Arab, Seyed Shahriar; Naderi-Manesh, Hossein

    2016-05-01

    The integrative and cooperative nature of protein structure involves the assessment of topological and global features of constituent parts. Network concept takes complete advantage of both of these properties in the analysis concomitantly. High compatibility to structural concepts or physicochemical properties in addition to exploiting a remarkable simplification in the system has made network an ideal tool to explore biological systems. There are numerous examples in which different protein structural and functional characteristics have been clarified by the network approach. Here, we present an interactive and user-friendly Matlab-based toolbox, PDB2Graph, devoted to protein structure network construction, visualization, and analysis. Moreover, PDB2Graph is an appropriate tool for identifying critical nodes involved in protein structural robustness and function based on centrality indices. It maps critical amino acids in protein networks and can greatly aid structural biologists in selecting proper amino acid candidates for manipulating protein structures in a more reasonable and rational manner. To introduce the capability and efficiency of PDB2Graph in detail, the structural modification of Calmodulin through allosteric binding of Ca(2+) is considered. In addition, a mutational analysis for three well-identified model proteins including Phage T4 lysozyme, Barnase and Ribonuclease HI, was performed to inspect the influence of mutating important central residues on protein activity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Velocity Mapping Toolbox (VMT): a processing and visualization suite for moving-vessel ADCP measurements

    Science.gov (United States)

    Parsons, D.R.; Jackson, P.R.; Czuba, J.A.; Engel, F.L.; Rhoads, B.L.; Oberg, K.A.; Best, J.L.; Mueller, D.S.; Johnson, K.K.; Riley, J.D.

    2013-01-01

    The use of acoustic Doppler current profilers (ADCP) for discharge measurements and three-dimensional flow mapping has increased rapidly in recent years and has been primarily driven by advances in acoustic technology and signal processing. Recent research has developed a variety of methods for processing data obtained from a range of ADCP deployments and this paper builds on this progress by describing new software for processing and visualizing ADCP data collected along transects in rivers or other bodies of water. The new utility, the Velocity Mapping Toolbox (VMT), allows rapid processing (vector rotation, projection, averaging and smoothing), visualization (planform and cross-section vector and contouring), and analysis of a range of ADCP-derived datasets. The paper documents the data processing routines in the toolbox and presents a set of diverse examples that demonstrate its capabilities. The toolbox is applicable to the analysis of ADCP data collected in a wide range of aquatic environments and is made available as open-source code along with this publication.

  5. The EnMAP-Box—A Toolbox and Application Programming Interface for EnMAP Data Processing

    Directory of Open Access Journals (Sweden)

    Sebastian van der Linden

    2015-09-01

    Full Text Available The EnMAP-Box is a toolbox that is developed for the processing and analysis of data acquired by the German spaceborne imaging spectrometer EnMAP (Environmental Mapping and Analysis Program. It is developed with two aims in mind in order to guarantee full usage of future EnMAP data, i.e., (1 extending the EnMAP user community and (2 providing access to recent approaches for imaging spectroscopy data processing. The software is freely available and offers a range of tools and applications for the processing of spectral imagery, including classical processing tools for imaging spectroscopy data as well as powerful machine learning approaches or interfaces for the integration of methods available in scripting languages. A special developer version includes the full open source code, an application programming interface and an application wizard for easy integration and documentation of new developments. This paper gives an overview of the EnMAP-Box for users and developers, explains typical workflows along an application example and exemplifies the concept for making it a frequently used and constantly extended platform for imaging spectroscopy applications.

  6. Development of Airport Noise Mapping using Matlab Software (Case Study: Adi Soemarmo Airport - Boyolali, Indonesia)

    Science.gov (United States)

    Andarani, Pertiwi; Setiyo Huboyo, Haryono; Setyanti, Diny; Budiawan, Wiwik

    2018-02-01

    Noise is considered as one of the main environmental impact of Adi Soemarmo International Airport (ASIA), the second largest airport in Central Java Province, Indonesia. In order to manage the noise of airport, airport noise mapping is necessary. However, a model that requires simple input but still reliable was not available in ASIA. Therefore, the objective of this study are to develop model using Matlab software, to verify its reliability by measuring actual noise exposure, and to analyze the area of noise levels‥ The model was developed based on interpolation or extrapolation of identified Noise-Power-Distance (NPD) data. In accordance with Indonesian Government Ordinance No.40/2012, the noise metric used is WECPNL (Weighted Equivalent Continuous Perceived Noise Level). Based on this model simulation, there are residence area in the region of noise level II (1.912 km2) and III (1.16 km2) and 18 school buildings in the area of noise levels I, II, and III. These land-uses are actually prohibited unless noise insulation is equipped. The model using Matlab in the case of Adi Soemarmo International Airport is valid based on comparison of the field measurement (6 sampling points). However, it is important to validate the model again once the case study (the airport) is changed.

  7. Towards a binaural modelling toolbox

    DEFF Research Database (Denmark)

    Søndergaard, Peter Lempel; Culling, John F.; Dau, Torsten

    2011-01-01

    The Auditory Modelling Toolbox (AMToolbox) is a new Matlab / Octave toolbox for developing and applying auditory perceptual models and in particular binaural models. The philosophy behind the project is that the models should be implemented in a consistent manner, well documented and user...

  8. Perancangan Kendali Pid Dengan Matlab

    OpenAIRE

    Sukamta, Sri

    2010-01-01

    Perancangan PID Controller selama ini menggunakan metoda trial and error dengan perhitungan yangmemakan waktu lama. MatLab yang dilengkapi Control Toolbox, membantu perancang untuk melihatrespon berbagai kombinasi konstanta dengan variasi input yang berbeda. Penggunaan MatLab ini sangatmembantu perancang dalam menentukan kombinasi di antara P, I, dan D Controller untuk menghasilkansistem pengaturan yang baik dan sederhana.

  9. Experiences with Matlab and VRML in Functional Neuroimaging Visualizations

    DEFF Research Database (Denmark)

    Nielsen, Finn Årup; Hansen, Lars Kai

    2000-01-01

    We describe some experiences with Matlab and VRML. We are developing a toolbox for neuroinformatics and describe some of the functionalities we have implemented or will implement and how Matlab and VRML support the implementation....

  10. The simulation of a non-linear unstable system of motion, utilising the Solid-Works and Matlab/Simulink extended libraries/toolboxes

    Directory of Open Access Journals (Sweden)

    Zátopek Jiří

    2016-01-01

    Full Text Available This text discusses the use and integration of various support software tools for the purpose of designing the motion control law governing mechanical structures with strongly non-linear behaviour. The detailed mathematical model is derived using Lagrange Equations of the Second Type. The physical model was designed by using SolidWorks 3D CAD software and a SimMechanics library. It extends Simulink with modelling tools for the simulation of mechanical “multi-domain” physical systems. The visualization of Simulink outputs is performed using the 3D Animation toolbox. Control law - designed on the basis of the mathematical model, is tested for both models (i.e. mathematical and physical and the regulatory processes’ results are compared.

  11. An Accelerator control middle layer using Matlab

    CERN Document Server

    Portmann, G J; Terebilo, Andrei

    2005-01-01

    Matlab is a matrix manipulation language originally developed to be a convenient language for using the LINPACK and EISPACK libraries. What makes Matlab so appealing for accelerator physics is the combination of a matrix oriented programming language, an active workspace for system variables, powerful graphics capability, built-in math libraries, and platform independence. A number of software toolboxes for accelerators have been written in Matlab – the Accelerator Toolbox (AT) for machine simulations, LOCO for accelerator calibration, Matlab Channel Access Toolbox (MCA) for EPICS connections, and the Middle Layer. This paper will describe the MiddleLayer software toolbox that resides between the high-level control applications and the low-level accelerator control system. This software was a collaborative effort between ALS and Spear but was written to easily port. Five accelerators presently use this software – Spear, ALS, CLS, and the X-ray and VUV rings at Brookhaven. The Middle Layer fu...

  12. FRACOR-software toolbox for deterministic mapping of fracture corridors in oil fields on AutoCAD platform

    Science.gov (United States)

    Ozkaya, Sait I.

    2018-03-01

    Fracture corridors are interconnected large fractures in a narrow sub vertical tabular array, which usually traverse entire reservoir vertically and extended for several hundreds of meters laterally. Fracture corridors with their huge conductivities constitute an important element of many fractured reservoirs. Unlike small diffuse fractures, actual fracture corridors must be mapped deterministically for simulation or field development purposes. Fracture corridors can be identified and quantified definitely with borehole image logs and well testing. However, there are rarely sufficient image logs or well tests, and it is necessary to utilize various fracture corridor indicators with varying degrees of reliability. Integration of data from many different sources, in turn, requires a platform with powerful editing and layering capability. Available commercial reservoir characterization software packages, with layering and editing capabilities, can be cost intensive. CAD packages are far more affordable and may easily acquire the versatility and power of commercial software packages with addition of a small software toolbox. The objective of this communication is to present FRACOR, a software toolbox which enables deterministic 2D fracture corridor mapping and modeling on AutoCAD platform. The FRACOR toolbox is written in AutoLISPand contains several independent routines to import and integrate available fracture corridor data from an oil field, and export results as text files. The resulting fracture corridor maps consists mainly of fracture corridors with different confidence levels from combination of static and dynamic data and exclusion zones where no fracture corridor can exist. The exported text file of fracture corridors from FRACOR can be imported into an upscaling programs to generate fracture grid for dual porosity simulation or used for field development and well planning.

  13. Structural Time Domain Identification Toolbox User's Guide

    DEFF Research Database (Denmark)

    Andersen, P.; Kirkegaard, Poul Henning; Brincker, Rune

    This manual describes the Structural Time Domain Identification toolbox for use with MA TLAB. This version of the tool box has been developed using the PC-based MA TLAB version 4.2c, but is compatible with prior versions of MATLAB and UNIX-based versions. The routines of the toolbox are the so...

  14. TecLines: A MATLAB-Based Toolbox for Tectonic Lineament Analysis from Satellite Images and DEMs, Part 1: Line Segment Detection and Extraction

    OpenAIRE

    Rahnama, Mehdi; Gloaguen, Richard

    2014-01-01

    Geological structures, such as faults and fractures, appear as image discontinuities or lineaments in remote sensing data. Geologic lineament mapping is a very important issue in geo-engineering, especially for construction site selection, seismic, and risk assessment, mineral exploration and hydrogeological research. Classical methods of lineaments extraction are based on semi-automated (or visual) interpretation of optical data and digital elevation models. We developed a freely available M...

  15. TecLines: A MATLAB-Based Toolbox for Tectonic Lineament Analysis from Satellite Images and DEMs, Part 2: Line Segments Linking and Merging

    OpenAIRE

    Mehdi Rahnama; Richard Gloaguen

    2014-01-01

    Extraction and interpretation of tectonic lineaments is one of the routines for mapping large areas using remote sensing data. However, this is a subjective and time-consuming process. It is difficult to choose an optimal lineament extraction method in order to reduce subjectivity and obtain vectors similar to what an analyst would manually extract. The objective of this study is the implementation, evaluation and comparison of Hough transform, segment merging and polynomial fitting methods t...

  16. MATLAB - Introduction

    International Nuclear Information System (INIS)

    Jung, Heon Seul

    2005-08-01

    This book introduces MATLAB giving descriptions of analysis and design of this control system like what is control? cases of control system, working environment of MATLAB, signs of MATLAB, commands of MATLAB, and drawing graphs. It also tells of basic use of simulink, mathematical model of physical system like mechanical-electrical analogous system, system analysis in time part, frequency analysis, state space and design such as canonical from and principle of duality and state observer design.

  17. MATLAB syntaksen

    DEFF Research Database (Denmark)

    Skajaa, Anders; Jørgensen, Jakob Heide

    MATLAB er et matematik-program som fokuserer på anvendelsen af matricer og vektorer. Deraf navnet MATrix LABoratory. Denne bog er en praktisk vejledning i at forstår og anvende MATLAB syntaksen og fungerer som en hurtig genvej til dig, der skal i gang med at anvende MATLAB i forbindelse med fx dit...

  18. The Linear Time Frequency Analysis Toolbox

    DEFF Research Database (Denmark)

    Søndergaard, Peter Lempel; Torrésani, Bruno; Balazs, Peter

    2011-01-01

    The Linear Time Frequency Analysis Toolbox is a Matlab/Octave toolbox for computational time-frequency analysis. It is intended both as an educational and computational tool. The toolbox provides the basic Gabor, Wilson and MDCT transform along with routines for constructing windows (lter...... prototypes) and routines for manipulating coe cients. It also provides a bunch of demo scripts devoted either to demonstrating the main functions of the toolbox, or to exemplify their use in specic signal processing applications. In this paper we describe the used algorithms, their mathematical background...

  19. Conception of Repairable Dynamic Fault Trees and resolution by the use of RAATSS, a Matlab® toolbox based on the ATS formalism

    International Nuclear Information System (INIS)

    Manno, G.; Chiacchio, F.; Compagno, L.; D'Urso, D.; Trapani, N.

    2014-01-01

    availability and reliability of complex systems is shown. • A mapping from DFT entity to ATS entity is proposed. • RAATSS, an automated tool for the evaluation of RDFT, is presented

  20. Statistics in Matlab a primer

    CERN Document Server

    Cho, MoonJung

    2014-01-01

    List of Tables Preface MATLAB BasicsDesktop Environment Getting Help and Other Documentation Data Import and Export Data I/O via the Command Line The Import Wizard Examples of Data I/O in MATLAB Data I/O with the Statistics Toolbox More Functions for Data I/O Data in MATLAB Data Objects in Base MATLAB Accessing Data Elements Examples of Joining Data Sets Data Types in the Statistics Toolbox Object-Oriented Programming Miscellaneous Topics File and Workspace Management Punctuation in MATLAB Arithmetic Operators Functions in MATLAB Summary and Further Reading Visualizing DataBasic Plot Functions Plotting 2-D Data Plotting 3-D Data Examples Scatter Plots Basic 2-D and 3-D Scatter Plots Scatter Plot Matrix Examples GUIs for Graphics Simple Plot Editing Plotting Tools Interface PLOTS Tab Summary and Further Reading Descriptive StatisticsMeasures of Location Means, Medians, and Modes Examples Measures of Dispersion Range Variance and Standard Deviation Covariance and Correlation Examples Describing the Distribution...

  1. moviEEG: An animation toolbox for visualization of intracranial electroencephalography synchronization dynamics.

    Science.gov (United States)

    Wong, Simeon M; Ibrahim, George M; Ochi, Ayako; Otsubo, Hiroshi; Rutka, James T; Snead, O Carter; Doesburg, Sam M

    2016-06-01

    We introduce and describe the functions of moviEEG (Multiple Overlay Visualizations for Intracranial ElectroEncephaloGraphy), a novel MATLAB-based toolbox for spatiotemporal mapping of network synchronization dynamics in intracranial electroencephalography (iEEG) data. The toolbox integrates visualizations of inter-electrode phase-locking relationships in peri-ictal epileptogenic networks with signal spectral properties and graph-theoretical network measures overlaid upon operating room images of the electrode grid. Functional connectivity between every electrode pair is evaluated over a sliding window indexed by phase synchrony. Two case studies are presented to provide preliminary evidence for the application of the toolbox to guide network-based mapping of epileptogenic cortex and to distinguish these regions from eloquent brain networks. In both cases, epileptogenic cortex was visually distinct. We introduce moviEEG, a novel toolbox for animation of oscillatory network dynamics in iEEG data, and provide two case studies showing preliminary evidence for utility of the toolbox in delineating the epileptogenic zone. Despite evidence that atypical network synchronization has shown to be altered in epileptogenic brain regions, network based techniques have yet to be incorporated into clinical pre-surgical mapping. moviEEG provides a set of functions to enable easy visualization with network based techniques. Copyright © 2016 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

  2. Aplikasi MATLAB untuk Mengenali Karakter Tulisan Tangan

    Directory of Open Access Journals (Sweden)

    ali mahmudi

    2017-03-01

    Full Text Available Handwriting recognition is one of the very interesting research object in the field of image processing, artificial intelligence and computer vision. This is due to the handwritten characters is varied in every individual. The style, size and orientation of handwriting characters has made every body’s is different, hence handwriting recognition is a very interesting research object. Handwriting recognition application has been used in quite many applications, such as reading the bank deposits, reading the postal code in letters, and helping peolple in managing documents. This paper presents a handwriting recognition application using Matlab. Matlab toolbox that is used in this research are Image Processing and Neural Network Toolbox.

  3. Broadview Radar Altimetry Toolbox

    Science.gov (United States)

    Garcia-Mondejar, Albert; Escolà, Roger; Moyano, Gorka; Roca, Mònica; Terra-Homem, Miguel; Friaças, Ana; Martinho, Fernando; Schrama, Ernst; Naeije, Marc; Ambrózio, Américo; Restano, Marco; Benveniste, Jérôme

    2017-04-01

    The universal altimetry toolbox, BRAT (Broadview Radar Altimetry Toolbox) which can read all previous and current altimetry missions' data, incorporates now the capability to read the upcoming Sentinel3 L1 and L2 products. ESA endeavoured to develop and supply this capability to support the users of the future Sentinel3 SAR Altimetry Mission. BRAT is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2005 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales), and it is freely available at http://earth.esa.int/brat. The tools enable users to interact with the most common altimetry data formats. The BratGUI is the frontend for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with MATLAB/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the dataformatting hassle. BRAT can be used simply to visualise data quickly, or to translate the data into other formats such as NetCDF, ASCII text files, KML (Google Earth) and raster images (JPEG, PNG, etc.). Several kinds of computations can be done within BRAT involving combinations of data fields that the user can save for posterior reuse or using the already embedded formulas that include the standard oceanographic altimetry formulas. The Radar Altimeter Tutorial, that contains a strong introduction to altimetry, shows its applications in different fields such as Oceanography, Cryosphere, Geodesy, Hydrology among others. Included are also "use cases", with step-by-step examples, on how to use the toolbox in the different contexts. The Sentinel3 SAR Altimetry Toolbox shall benefit from the current BRAT version. While developing the toolbox we will revamp of the Graphical User Interface and provide, among other enhancements, support for reading the upcoming S3 datasets and specific

  4. An Accelerator Control Middle Layer Using MATLAB

    International Nuclear Information System (INIS)

    Portmann, Gregory J.; Corbett, Jeff; Terebilo, Andrei

    2005-01-01

    Matlab is a matrix manipulation language originally developed to be a convenient language for using the LINPACK and EISPACK libraries. What makes Matlab so appealing for accelerator physics is the combination of a matrix oriented programming language, an active workspace for system variables, powerful graphics capability, built-in math libraries, and platform independence. A number of software toolboxes for accelerators have been written in Matlab--the Accelerator Toolbox (AT) for machine simulations, LOCO for accelerator calibration, Matlab Channel Access Toolbox (MCA) for EPICS connections, and the Middle Layer. This paper will describe the ''middle layer'' software toolbox that resides between the high-level control applications and the low-level accelerator control system. This software was a collaborative effort between ALS (LBNL) and SPEAR3 (SSRL) but easily ports to other machines. Five accelerators presently use this software. The high-level Middle Layer functionality includes energy ramp, configuration control (save/restore), global orbit correction, local photon beam steering, insertion device compensation, beam-based alignment, tune correction, response matrix measurement, and script-based programs for machine physics studies

  5. Software Toolbox for Low-Frequency Conductivity and Current Density Imaging Using MRI.

    Science.gov (United States)

    Sajib, Saurav Z K; Katoch, Nitish; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

    2017-11-01

    Low-frequency conductivity and current density imaging using MRI includes magnetic resonance electrical impedance tomography (MREIT), diffusion tensor MREIT (DT-MREIT), conductivity tensor imaging (CTI), and magnetic resonance current density imaging (MRCDI). MRCDI and MREIT provide current density and isotropic conductivity images, respectively, using current-injection phase MRI techniques. DT-MREIT produces anisotropic conductivity tensor images by incorporating diffusion weighted MRI into MREIT. These current-injection techniques are finding clinical applications in diagnostic imaging and also in transcranial direct current stimulation (tDCS), deep brain stimulation (DBS), and electroporation where treatment currents can function as imaging currents. To avoid adverse effects of nerve and muscle stimulations due to injected currents, conductivity tensor imaging (CTI) utilizes B1 mapping and multi-b diffusion weighted MRI to produce low-frequency anisotropic conductivity tensor images without injecting current. This paper describes numerical implementations of several key mathematical functions for conductivity and current density image reconstructions in MRCDI, MREIT, DT-MREIT, and CTI. To facilitate experimental studies of clinical applications, we developed a software toolbox for these low-frequency conductivity and current density imaging methods. This MR-based conductivity imaging (MRCI) toolbox includes 11 toolbox functions which can be used in the MATLAB environment. The MRCI toolbox is available at http://iirc.khu.ac.kr/software.html . Its functions were tested by using several experimental datasets, which are provided together with the toolbox. Users of the toolbox can focus on experimental designs and interpretations of reconstructed images instead of developing their own image reconstruction softwares. We expect more toolbox functions to be added from future research outcomes. Low-frequency conductivity and current density imaging using MRI includes

  6. ESA Atmospheric Toolbox

    Science.gov (United States)

    Niemeijer, Sander

    2017-04-01

    The ESA Atmospheric Toolbox (BEAT) is one of the ESA Sentinel Toolboxes. It consists of a set of software components to read, analyze, and visualize a wide range of atmospheric data products. In addition to the upcoming Sentinel-5P mission it supports a wide range of other atmospheric data products, including those of previous ESA missions, ESA Third Party missions, Copernicus Atmosphere Monitoring Service (CAMS), ground based data, etc. The toolbox consists of three main components that are called CODA, HARP and VISAN. CODA provides interfaces for direct reading of data from earth observation data files. These interfaces consist of command line applications, libraries, direct interfaces to scientific applications (IDL and MATLAB), and direct interfaces to programming languages (C, Fortran, Python, and Java). CODA provides a single interface to access data in a wide variety of data formats, including ASCII, binary, XML, netCDF, HDF4, HDF5, CDF, GRIB, RINEX, and SP3. HARP is a toolkit for reading, processing and inter-comparing satellite remote sensing data, model data, in-situ data, and ground based remote sensing data. The main goal of HARP is to assist in the inter-comparison of datasets. By appropriately chaining calls to HARP command line tools one can pre-process datasets such that two datasets that need to be compared end up having the same temporal/spatial grid, same data format/structure, and same physical unit. The toolkit comes with its own data format conventions, the HARP format, which is based on netcdf/HDF. Ingestion routines (based on CODA) allow conversion from a wide variety of atmospheric data products to this common format. In addition, the toolbox provides a wide range of operations to perform conversions on the data such as unit conversions, quantity conversions (e.g. number density to volume mixing ratios), regridding, vertical smoothing using averaging kernels, collocation of two datasets, etc. VISAN is a cross-platform visualization and

  7. The ABRAVIBE toolbox for teaching vibration analysis and structural dynamics

    DEFF Research Database (Denmark)

    Brandt, A.

    2013-01-01

    , a MATLAB toolbox (the ABRAVIBE toolbox) has been developed as an accompanying toolbox for the recent book "Noise and Vibration Analysis" by the author. This free, open software, published under GNU Public License, can be used with GNU Octave, if an entirely free software platform is wanted, with a few...... functional limitations. The toolbox includes functionality for simulation of mechanical models as well as advanced analysis such as time series analysis, spectral analysis, frequency response and correlation function estimation, modal parameter extraction, and rotating machinery analysis (order tracking...

  8. ERPLAB: An Open-Source Toolbox for the Analysis of Event-Related Potentials

    Directory of Open Access Journals (Sweden)

    Javier eLopez-Calderon

    2014-04-01

    Full Text Available ERPLAB Toolbox is a freely available, open-source toolbox for processing and analyzing event-related potential (ERP data in the MATLAB environment. ERPLAB is closely integrated with EEGLAB, a popular open-source toolbox that provides many EEG preprocessing steps and an excellent user interface design. ERPLAB adds to EEGLAB’s EEG processing functions, providing additional tools for filtering, artifact detection, re-referencing, and sorting of events, among others. ERPLAB also provides robust tools for averaging EEG segments together to create averaged ERPs, for creating difference waves and other recombinations of ERP waveforms through algebraic expressions, for filtering and re-referencing the averaged ERPs, for plotting ERP waveforms and scalp maps, and for quantifying several types of amplitudes and latencies. ERPLAB’s tools can be accessed either from an easy-to-learn graphical user interface or from MATLAB scripts, and a command history function makes it easy for users with no programming experience to write scripts. Consequently, ERPLAB provides both ease of use and virtually unlimited power and flexibility, making it appropriate for the analysis of both simple and complex ERP experiments. Several forms of documentation are available, including a detailed user’s guide, a step-by-step tutorial, a scripting guide, and a set of video-based demonstrations.

  9. Wind Turbine Blockset in Matlab/Simulink. General Overview and Description of the Model

    DEFF Research Database (Denmark)

    Iov, Florin; Hansen, A. D.; Soerensen, P.

    This report presents a new developed Matlab/Simulink Toolbox for wind turbine applications. This toolbox has been developed during the research project ?Simulation Platform to model, optimize and design wind turbines? and it has been used as a general developer tool for other three simulation tools......: Saber, DIgSILENT, HAWC. The report provides first a quick overview over Matlab issues and then explains the structure of the developed toolbox. The attention in the report is mainly drawn to the description of the most important mathematical models, which have been developed in the Toolbox. Then, some...

  10. An Accelerator Control Middle Layer Using MATLAB

    International Nuclear Information System (INIS)

    Portmann, Gregory J.; Corbett, Jeff; Terebilo, Andrei

    2005-01-01

    Matlab is an interpretive programming language originally developed for convenient use with the LINPACK and EISPACK libraries. Matlab is appealing for accelerator physics because it is matrix-oriented, provides an active workspace for system variables, powerful graphics capabilities, built-in math libraries, and platform independence. A number of accelerator software toolboxes have been written in Matlab -- the Accelerator Toolbox (AT) for model-based machine simulations, LOCO for on-line model calibration, and Matlab Channel Access (MCA) to connect with EPICS. The function of the MATLAB ''MiddleLayer'' is to provide a scripting language for machine simulations and on-line control, including non-EPICS based control systems. The MiddleLayer has simplified and streamlined development of high-level applications including configuration control, energy ramp, orbit correction, photon beam steering, ID compensation, beam-based alignment, tune correction and response matrix measurement. The database-driven Middle Layer software is largely machine-independent and easy to port. Six accelerators presently use the software package with more scheduled to come on line soon

  11. Practical image and video processing using MATLAB

    CERN Document Server

    Marques, Oge

    2011-01-01

    "The book provides a practical introduction to the most important topics in image and video processing using MATLAB (and its Image Processing Toolbox) as a tool to demonstrate the most important techniques and algorithms. The contents are presented in a clear, technically accurate, objective way, with just enough mathematical detail. Most of the chapters are supported by figures, examples, illustrative problems, MATLAB scripts, suggestions for further reading, bibliographical references, useful Web sites, and exercises and computer projects to extend the understanding of their contents"--

  12. Virtual toolbox

    Science.gov (United States)

    Jacobus, Charles J.; Jacobus, Heidi N.; Mitchell, Brian T.; Riggs, A. J.; Taylor, Mark J.

    1993-04-01

    At least three of the five senses must be fully addressed in a successful virtual reality (VR) system. Sight, sound, and touch are the most critical elements for the creation of the illusion of presence. Since humans depend so much on sight to collect information about their environment, this area has been the focus of much of the prior art in virtual reality, however, it is also crucial that we provide facilities for force, torque, and touch reflection, and sound replay and 3-D localization. In this paper we present a sampling of hardware and software in the virtual environment maker's `toolbox' which can support rapidly building up of customized VR systems. We provide demonstrative examples of how some of the tools work and we speculate about VR applications and future technology needs.

  13. Kinematic simulation and analysis of robot based on MATLAB

    Science.gov (United States)

    Liao, Shuhua; Li, Jiong

    2018-03-01

    The history of industrial automation is characterized by quick update technology, however, without a doubt, the industrial robot is a kind of special equipment. With the help of MATLAB matrix and drawing capacity in the MATLAB environment each link coordinate system set up by using the d-h parameters method and equation of motion of the structure. Robotics, Toolbox programming Toolbox and GUIDE to the joint application is the analysis of inverse kinematics and path planning and simulation, preliminary solve the problem of college students the car mechanical arm positioning theory, so as to achieve the aim of reservation.

  14. CONTINEX: A Toolbox for Continuation in Experiments

    DEFF Research Database (Denmark)

    Schilder, Frank; Bureau, Emil; Santos, Ilmar

    2014-01-01

    CONTINEX is a MATLAB toolbox for bifurcation analysis based on the development platform COCO (computational continuation core). CONTINEX is specifically designed for coupling to experimental test specimen via DSPACE, but provides also interfaces to SIMULINK-, ODE-, and so-called equation-free mod......CONTINEX is a MATLAB toolbox for bifurcation analysis based on the development platform COCO (computational continuation core). CONTINEX is specifically designed for coupling to experimental test specimen via DSPACE, but provides also interfaces to SIMULINK-, ODE-, and so-called equation......-free models. The current version of the interface for experimental set-ups implements an algorithm for tuning control parameters, a robust noise-tolerant covering algorithm, and functions for monitoring (in)stability. In this talk we will report on experiments with an impact oscillator with magnetic actuators...

  15. U.S. Geological Survey groundwater toolbox, a graphical and mapping interface for analysis of hydrologic data (version 1.0): user guide for estimation of base flow, runoff, and groundwater recharge from streamflow data

    Science.gov (United States)

    Barlow, Paul M.; Cunningham, William L.; Zhai, Tong; Gray, Mark

    2015-01-01

    This report is a user guide for the streamflow-hydrograph analysis methods provided with version 1.0 of the U.S. Geological Survey (USGS) Groundwater Toolbox computer program. These include six hydrograph-separation methods to determine the groundwater-discharge (base-flow) and surface-runoff components of streamflow—the Base-Flow Index (BFI; Standard and Modified), HYSEP (Fixed Interval, Sliding Interval, and Local Minimum), and PART methods—and the RORA recession-curve displacement method and associated RECESS program to estimate groundwater recharge from streamflow data. The Groundwater Toolbox is a customized interface built on the nonproprietary, open source MapWindow geographic information system software. The program provides graphing, mapping, and analysis capabilities in a Microsoft Windows computing environment. In addition to the four hydrograph-analysis methods, the Groundwater Toolbox allows for the retrieval of hydrologic time-series data (streamflow, groundwater levels, and precipitation) from the USGS National Water Information System, downloading of a suite of preprocessed geographic information system coverages and meteorological data from the National Oceanic and Atmospheric Administration National Climatic Data Center, and analysis of data with several preprocessing and postprocessing utilities. With its data retrieval and analysis tools, the Groundwater Toolbox provides methods to estimate many of the components of the water budget for a hydrologic basin, including precipitation; streamflow; base flow; runoff; groundwater recharge; and total, groundwater, and near-surface evapotranspiration.

  16. Parallelizing AT with MatlabMPI

    International Nuclear Information System (INIS)

    2011-01-01

    The Accelerator Toolbox (AT) is a high-level collection of tools and scripts specifically oriented toward solving problems dealing with computational accelerator physics. It is integrated into the MATLAB environment, which provides an accessible, intuitive interface for accelerator physicists, allowing researchers to focus the majority of their efforts on simulations and calculations, rather than programming and debugging difficulties. Efforts toward parallelization of AT have been put in place to upgrade its performance to modern standards of computing. We utilized the packages MatlabMPI and pMatlab, which were developed by MIT Lincoln Laboratory, to set up a message-passing environment that could be called within MATLAB, which set up the necessary pre-requisites for multithread processing capabilities. On local quad-core CPUs, we were able to demonstrate processor efficiencies of roughly 95% and speed increases of nearly 380%. By exploiting the efficacy of modern-day parallel computing, we were able to demonstrate incredibly efficient speed increments per processor in AT's beam-tracking functions. Extrapolating from prediction, we can expect to reduce week-long computation runtimes to less than 15 minutes. This is a huge performance improvement and has enormous implications for the future computing power of the accelerator physics group at SSRL. However, one of the downfalls of parringpass is its current lack of transparency; the pMatlab and MatlabMPI packages must first be well-understood by the user before the system can be configured to run the scripts. In addition, the instantiation of argument parameters requires internal modification of the source code. Thus, parringpass, cannot be directly run from the MATLAB command line, which detracts from its flexibility and user-friendliness. Future work in AT's parallelization will focus on development of external functions and scripts that can be called from within MATLAB and configured on multiple nodes, while

  17. Wind Turbine Blockset in Matlab/Simulink - General overview and description of the models

    Energy Technology Data Exchange (ETDEWEB)

    Iov, F.; Hansen, A.D.; Soerensen, P.; Blaabjerg, F.

    2004-03-01

    This report presents a new developed Matlab/Simulink Toolbox for wind turbine applications. This toolbox has been developed during the research project 'Simulation Platform to model, optimize and design wind turbines' and it has been used as a general developer tool for other three simulation tools: Saber, DIgSILENT, HAWC. The report provides first a quick overview over Matlab issues and then explains the structure of the developed toolbox. The attention in the report is mainly drawn to the description of the most important mathematical models, which have been developed in the Toolbox. Then, some simulation results using the developed models are shown. Finally, some general conclusions regarding this new developed Toolbox as well as some directions for future work are made. (au)

  18. Wind turbine blockset in Matlab/Simulink. General overview and description of the models

    Energy Technology Data Exchange (ETDEWEB)

    Iov, F.; Timbus, A.V.; Hansen, A.D.; Soerensen, P.; Blaabjerg, F.

    2004-03-01

    This report presents a new developed Matlab/Simulink Toolbox for wind turbine applications. This toolbox has been developed during the research project 'Simulation Platform to model, optimize and design wind turbines' and it has been used as a general developer tool for other three simulation tools: Saber, DIgSILENT, HAWC. The report provides first a quick overview over Matlab issues and then explains the structure of the developed toolbox. The attention in the report is mainly drawn to the description of the most important mathematical models, which have been developed in the Toolbox. Then, some simulation results using the developed models are shown. Finally, some general conclusions regarding this new developed Toolbox as well as some directions for future work are made. (au)

  19. Matlab for dummies

    CERN Document Server

    Sizemore, Jim

    2014-01-01

    Plot graphs, solve equations, and write code in a flash! If you work in a STEM field, chances are you'll be using MATLAB on a daily basis. MATLAB is a popular and powerful computational tool and this book provides everything you need to start manipulating and plotting your data. MATLAB has rapidly become the premier data tool, and MATLAB For Dummies is a comprehensive guide to the fundamentals. MATLAB For Dummies guides you through this complex computational language from installation to visualization to automation.Learn MATLAB's language fundamentals including syntax, operators, and data type

  20. Particle Swarm Optimization Toolbox

    Science.gov (United States)

    Grant, Michael J.

    2010-01-01

    The Particle Swarm Optimization Toolbox is a library of evolutionary optimization tools developed in the MATLAB environment. The algorithms contained in the library include a genetic algorithm (GA), a single-objective particle swarm optimizer (SOPSO), and a multi-objective particle swarm optimizer (MOPSO). Development focused on both the SOPSO and MOPSO. A GA was included mainly for comparison purposes, and the particle swarm optimizers appeared to perform better for a wide variety of optimization problems. All algorithms are capable of performing unconstrained and constrained optimization. The particle swarm optimizers are capable of performing single and multi-objective optimization. The SOPSO and MOPSO algorithms are based on swarming theory and bird-flocking patterns to search the trade space for the optimal solution or optimal trade in competing objectives. The MOPSO generates Pareto fronts for objectives that are in competition. A GA, based on Darwin evolutionary theory, is also included in the library. The GA consists of individuals that form a population in the design space. The population mates to form offspring at new locations in the design space. These offspring contain traits from both of the parents. The algorithm is based on this combination of traits from parents to hopefully provide an improved solution than either of the original parents. As the algorithm progresses, individuals that hold these optimal traits will emerge as the optimal solutions. Due to the generic design of all optimization algorithms, each algorithm interfaces with a user-supplied objective function. This function serves as a "black-box" to the optimizers in which the only purpose of this function is to evaluate solutions provided by the optimizers. Hence, the user-supplied function can be numerical simulations, analytical functions, etc., since the specific detail of this function is of no concern to the optimizer. These algorithms were originally developed to support entry

  1. The ROC Toolbox: A toolbox for analyzing receiver-operating characteristics derived from confidence ratings.

    Science.gov (United States)

    Koen, Joshua D; Barrett, Frederick S; Harlow, Iain M; Yonelinas, Andrew P

    2017-08-01

    Signal-detection theory, and the analysis of receiver-operating characteristics (ROCs), has played a critical role in the development of theories of episodic memory and perception. The purpose of the current paper is to present the ROC Toolbox. This toolbox is a set of functions written in the Matlab programming language that can be used to fit various common signal detection models to ROC data obtained from confidence rating experiments. The goals for developing the ROC Toolbox were to create a tool (1) that is easy to use and easy for researchers to implement with their own data, (2) that can flexibly define models based on varying study parameters, such as the number of response options (e.g., confidence ratings) and experimental conditions, and (3) that provides optimal routines (e.g., Maximum Likelihood estimation) to obtain parameter estimates and numerous goodness-of-fit measures.The ROC toolbox allows for various different confidence scales and currently includes the models commonly used in recognition memory and perception: (1) the unequal variance signal detection (UVSD) model, (2) the dual process signal detection (DPSD) model, and (3) the mixture signal detection (MSD) model. For each model fit to a given data set the ROC toolbox plots summary information about the best fitting model parameters and various goodness-of-fit measures. Here, we present an overview of the ROC Toolbox, illustrate how it can be used to input and analyse real data, and finish with a brief discussion on features that can be added to the toolbox.

  2. Introduction to fuzzy logic using Matlab

    CERN Document Server

    Sivanandam, SN; Deepa, S N

    2006-01-01

    Fuzzy Logic, at present is a hot topic, among academicians as well various programmers. This book is provided to give a broad, in-depth overview of the field of Fuzzy Logic. The basic principles of Fuzzy Logic are discussed in detail with various solved examples. The different approaches and solutions to the problems given in the book are well balanced and pertinent to the Fuzzy Logic research projects. The applications of Fuzzy Logic are also dealt to make the readers understand the concept of Fuzzy Logic. The solutions to the problems are programmed using MATLAB 6.0 and the simulated results are given. The MATLAB Fuzzy Logic toolbox is provided for easy reference.

  3. OXlearn: a new MATLAB-based simulation tool for connectionist models.

    Science.gov (United States)

    Ruh, Nicolas; Westermann, Gert

    2009-11-01

    OXlearn is a free, platform-independent MATLAB toolbox in which standard connectionist neural network models can be set up, run, and analyzed by means of a user-friendly graphical interface. Due to its seamless integration with the MATLAB programming environment, the inner workings of the simulation tool can be easily inspected and/or extended using native MATLAB commands or components. This combination of usability, transparency, and extendability makes OXlearn an efficient tool for the implementation of basic research projects or the prototyping of more complex research endeavors, as well as for teaching. Both the MATLAB toolbox and a compiled version that does not require access to MATLAB can be downloaded from http://psych.brookes.ac.uk/oxlearn/.

  4. SpaSM: A MATLAB Toolbox for Sparse Statistical Modeling

    DEFF Research Database (Denmark)

    Sjöstrand, Karl; Clemmensen, Line Harder; Larsen, Rasmus

    2018-01-01

    Applications in biotechnology such as gene expression analysis and image processing have led to a tremendous development of statistical methods with emphasis on reliable solutions to severely underdetermined systems. Furthermore, interpretations of such solutions are of importance, meaning...

  5. Multimodal Imaging Brain Connectivity Analysis (MIBCA toolbox

    Directory of Open Access Journals (Sweden)

    Andre Santos Ribeiro

    2015-07-01

    Full Text Available Aim. In recent years, connectivity studies using neuroimaging data have increased the understanding of the organization of large-scale structural and functional brain networks. However, data analysis is time consuming as rigorous procedures must be assured, from structuring data and pre-processing to modality specific data procedures. Until now, no single toolbox was able to perform such investigations on truly multimodal image data from beginning to end, including the combination of different connectivity analyses. Thus, we have developed the Multimodal Imaging Brain Connectivity Analysis (MIBCA toolbox with the goal of diminishing time waste in data processing and to allow an innovative and comprehensive approach to brain connectivity.Materials and Methods. The MIBCA toolbox is a fully automated all-in-one connectivity toolbox that offers pre-processing, connectivity and graph theoretical analyses of multimodal image data such as diffusion-weighted imaging, functional magnetic resonance imaging (fMRI and positron emission tomography (PET. It was developed in MATLAB environment and pipelines well-known neuroimaging softwares such as Freesurfer, SPM, FSL, and Diffusion Toolkit. It further implements routines for the construction of structural, functional and effective or combined connectivity matrices, as well as, routines for the extraction and calculation of imaging and graph-theory metrics, the latter using also functions from the Brain Connectivity Toolbox. Finally, the toolbox performs group statistical analysis and enables data visualization in the form of matrices, 3D brain graphs and connectograms. In this paper the MIBCA toolbox is presented by illustrating its capabilities using multimodal image data from a group of 35 healthy subjects (19–73 years old with volumetric T1-weighted, diffusion tensor imaging, and resting state fMRI data, and 10 subjets with 18F-Altanserin PET data also.Results. It was observed both a high inter

  6. Matlab for engineers explained

    CERN Document Server

    Gustafsson, Fredrik

    2003-01-01

    This book is written for students at bachelor and master programs and has four different purposes, which split the book into four parts: 1. To teach first or early year undergraduate engineering students basic knowledge in technical computations and programming using MATLAB. The first part starts from first principles and is therefore well suited both for readers with prior exposure to MATLAB but lacking a solid foundational knowledge of the capabilities of the system and readers not having any previous experience with MATLAB. The foundational knowledge gained from these interactive guided tours of the system will hopefully be sufficient for an effective utilization of MATLAB in the engineering profession, in education and in research. 2. To explain the foundations of more advanced use of MATLAB using the facilities added the last couple of years, such as extended data structures, object orientation and advanced graphics. 3. To give an introduction to the use of MATLAB in typical undergraduate courses in elec...

  7. Speeding up the MATLAB complex networks package using graphic processors

    International Nuclear Information System (INIS)

    Zhang Bai-Da; Wu Jun-Jie; Li Xin; Tang Yu-Hua

    2011-01-01

    The availability of computers and communication networks allows us to gather and analyse data on a far larger scale than previously. At present, it is believed that statistics is a suitable method to analyse networks with millions, or more, of vertices. The MATLAB language, with its mass of statistical functions, is a good choice to rapidly realize an algorithm prototype of complex networks. The performance of the MATLAB codes can be further improved by using graphic processor units (GPU). This paper presents the strategies and performance of the GPU implementation of a complex networks package, and the Jacket toolbox of MATLAB is used. Compared with some commercially available CPU implementations, GPU can achieve a speedup of, on average, 11.3×. The experimental result proves that the GPU platform combined with the MATLAB language is a good combination for complex network research. (interdisciplinary physics and related areas of science and technology)

  8. Matlab linear algebra

    CERN Document Server

    Lopez, Cesar

    2014-01-01

    MATLAB is a high-level language and environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java. MATLAB Linear Algebra introduces you to the MATLAB language with practical hands-on instructions and results, allowing you to quickly achieve your goals. In addition to giving an introduction to

  9. SRV: an open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metabolic phenotyping datasets.

    Science.gov (United States)

    Navratil, Vincent; Pontoizeau, Clément; Billoir, Elise; Blaise, Benjamin J

    2013-05-15

    Supervised multivariate statistical analyses are often required to analyze the high-density spectral information in metabolic datasets acquired from complex mixtures in metabolic phenotyping studies. Here we present an implementation of the SRV-Statistical Recoupling of Variables-algorithm as an open-source Matlab and GNU Octave toolbox. SRV allows the identification of similarity between consecutive variables resulting from the high-resolution bucketing. Similar variables are gathered to restore the spectral dependency within the datasets and identify metabolic NMR signals. The correlation and significance of these new NMR variables for a given effect under study can then be measured and represented on a loading plot to allow a visual and efficient identification of candidate biomarkers. Further on, correlations between these candidate biomarkers can be visualized on a two-dimensional pseudospectrum, representing a correlation map, helping to understand the modifications of the underlying metabolic network. SRV toolbox is encoded in MATLAB R2008A (Mathworks, Natick, MA) and in GNU Octave. It is available free of charge at http://www.prabi.fr/redmine/projects/srv/repository with a tutorial. benjamin.blaise@chu-lyon.fr or vincent.navratil@univ-lyon1.fr.

  10. Comparison 3 - 386 MATLAB

    DEFF Research Database (Denmark)

    Jensen, Niels

    1992-01-01

    MATLAB is a C-based general tool for mathematical and engineering calculations with limited capabilities for simulation of non-linear equation systems.......MATLAB is a C-based general tool for mathematical and engineering calculations with limited capabilities for simulation of non-linear equation systems....

  11. The Matlab Syntax

    DEFF Research Database (Denmark)

    Jørgensen, Jakob Heide; Skajaa, Anders

    Matlab (MATrix LABoratory) is one of the most widely used programming environments for numerical computations and simulations in the technical sciences. The reason is that Matlab makes it easy to get started as well as to construct advanced programs. This book is a practical guide to understanding...... and using Matlab. It works as a quick reference for anyone who is starting to use Matlab for example while enrolled in university studies. For this reason, the book is limited to covering what is typically used by a university student and is designed as a reference of the syntax including plenty of examples....... While the primary audience of the book is university students, it is well suited for anyone who wants to become acquainted with Matlab....

  12. Air Sensor Toolbox

    Science.gov (United States)

    Air Sensor Toolbox provides information to citizen scientists, researchers and developers interested in learning more about new lower-cost compact air sensor technologies and tools for measuring air quality.

  13. Sentinel-3 SAR Altimetry Toolbox

    Science.gov (United States)

    Benveniste, Jerome; Lucas, Bruno; DInardo, Salvatore

    2015-04-01

    The prime objective of the SEOM (Scientific Exploitation of Operational Missions) element is to federate, support and expand the large international research community that the ERS, ENVISAT and the Envelope programmes have build up over the last 20 years for the future European operational Earth Observation missions, the Sentinels. Sentinel-3 builds directly on a proven heritage of ERS-2 and Envisat, and CryoSat-2, with a dual-frequency (Ku and C band) advanced Synthetic Aperture Radar Altimeter (SRAL) that provides measurements at a resolution of ~300m in SAR mode along track. Sentinel-3 will provide exact measurements of sea-surface height along with accurate topography measurements over sea ice, ice sheets, rivers and lakes. The first of the two Sentinels is expected to be launched in early 2015. The current universal altimetry toolbox is BRAT (Basic Radar Altimetry Toolbox) which can read all previous and current altimetry mission's data, but it does not have the capabilities to read the upcoming Sentinel-3 L1 and L2 products. ESA will endeavour to develop and supply this capability to support the users of the future Sentinel-3 SAR Altimetry Mission. BRAT is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2005 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales), and it is freely available at http://earth.esa.int/brat. The tools enable users to interact with the most common altimetry data formats, the BratGUI is the front-end for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with Matlab/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the data-formatting hassle. BRAT can be used simply to visualise data quickly, or to translate the data into other formats such as netCDF, ASCII text files, KML (Google Earth

  14. HYDRORECESSION: A toolbox for streamflow recession analysis

    Science.gov (United States)

    Arciniega, S.

    2015-12-01

    Streamflow recession curves are hydrological signatures allowing to study the relationship between groundwater storage and baseflow and/or low flows at the catchment scale. Recent studies have showed that streamflow recession analysis can be quite sensitive to the combination of different models, extraction techniques and parameter estimation methods. In order to better characterize streamflow recession curves, new methodologies combining multiple approaches have been recommended. The HYDRORECESSION toolbox, presented here, is a Matlab graphical user interface developed to analyse streamflow recession time series with the support of different tools allowing to parameterize linear and nonlinear storage-outflow relationships through four of the most useful recession models (Maillet, Boussinesq, Coutagne and Wittenberg). The toolbox includes four parameter-fitting techniques (linear regression, lower envelope, data binning and mean squared error) and three different methods to extract hydrograph recessions segments (Vogel, Brutsaert and Aksoy). In addition, the toolbox has a module that separates the baseflow component from the observed hydrograph using the inverse reservoir algorithm. Potential applications provided by HYDRORECESSION include model parameter analysis, hydrological regionalization and classification, baseflow index estimates, catchment-scale recharge and low-flows modelling, among others. HYDRORECESSION is freely available for non-commercial and academic purposes.

  15. ESA BRAT (Broadview Radar Altimetry Toolbox) and GUT (GOCE User Toolbox) toolboxes

    Science.gov (United States)

    Benveniste, J.; Ambrozio, A.; Restano, M.

    2016-12-01

    The Broadview Radar Altimetry Toolbox (BRAT) is a collection of tools designed to facilitate the processing of radar altimetry data from previous and current altimetry missions, including the upcoming Sentinel-3A L1 and L2 products. A tutorial is included providing plenty of use cases. BRAT's future release (4.0.0) is planned for September 2016. Based on the community feedback, the frontend has been further improved and simplified whereas the capability to use BRAT in conjunction with MATLAB/IDL or C/C++/Python/Fortran, allowing users to obtain desired data bypassing the data-formatting hassle, remains unchanged. Several kinds of computations can be done within BRAT involving the combination of data fields, that can be saved for future uses, either by using embedded formulas including those from oceanographic altimetry, or by implementing ad-hoc Python modules created by users to meet their needs. BRAT can also be used to quickly visualise data, or to translate data into other formats, e.g. from NetCDF to raster images. The GOCE User Toolbox (GUT) is a compilation of tools for the use and the analysis of GOCE gravity field models. It facilitates using, viewing and post-processing GOCE L2 data and allows gravity field data, in conjunction and consistently with any other auxiliary data set, to be pre-processed by beginners in gravity field processing, for oceanographic and hydrologic as well as for solid earth applications at both regional and global scales. Hence, GUT facilitates the extensive use of data acquired during GRACE and GOCE missions. In the current 3.0 version, GUT has been outfitted with a graphical user interface allowing users to visually program data processing workflows. Further enhancements aiming at facilitating the use of gradients, the anisotropic diffusive filtering, and the computation of Bouguer and isostatic gravity anomalies have been introduced. Packaged with GUT is also GUT's VCM (Variance-Covariance Matrix) tool for analysing GOCE

  16. R and Matlab

    CERN Document Server

    Hiebeler, David E

    2015-01-01

    The First Book to Explain How a User of R or MATLAB Can Benefit from the OtherIn today's increasingly interdisciplinary world, R and MATLAB® users from different backgrounds must often work together and share code. R and MATLAB® is designed for users who already know R or MATLAB and now need to learn the other platform. The book makes the transition from one platform to the other as quick and painless as possible.Enables R and MATLAB Users to Easily Collaborate and Share CodeThe author covers essential tasks, such as working with matrices and vectors, writing functions and other programming co

  17. Essential Matlab and Octave

    CERN Document Server

    Rogel-Salazar, Jesus

    2014-01-01

    ""This is an excellent book for anyone approaching MATLAB or Octave for the first time. The pleasant language used throughout creates the sensation of having the author by your side. … An interesting feature are the examples used to explain the use of functions and operations. … compared to similar texts on Octave and MATLAB, the author introduces at an early stage how to produce line and surface plots with MATLAB and Octave. It is very attractive to students to be able to quickly produce plots with scientific journal quality. … The margin notes are great as they can also work as virtual bookm

  18. Numerical methods using Matlab

    CERN Document Server

    Lindfield, George

    2012-01-01

    Numerical Methods using MATLAB, 3e, is an extensive reference offering hundreds of useful and important numerical algorithms that can be implemented into MATLAB for a graphical interpretation to help researchers analyze a particular outcome. Many worked examples are given together with exercises and solutions to illustrate how numerical methods can be used to study problems that have applications in the biosciences, chaos, optimization, engineering and science across the board. Numerical Methods using MATLAB, 3e, is an extensive reference offering hundreds of use

  19. Efficient Matlab Programs

    Data.gov (United States)

    National Aeronautics and Space Administration — Matlab has a reputation for running slowly. Here are some pointers on how to speed computations, to an often unexpected degree. Subjects currently covered: Matrix...

  20. Mathematical Modeling Using MATLAB

    National Research Council Canada - National Science Library

    Phillips, Donovan

    1998-01-01

    .... Mathematical Modeling Using MA MATLAB acts as a companion resource to A First Course in Mathematical Modeling with the goal of guiding the reader to a fuller understanding of the modeling process...

  1. MATLAB matrix algebra

    CERN Document Server

    Pérez López, César

    2014-01-01

    MATLAB is a high-level language and environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java. MATLAB Matrix Algebra introduces you to the MATLAB language with practical hands-on instructions and results, allowing you to quickly achieve your goals. Starting with a look at symbolic and numeric variables, with an emphasis on vector and matrix variables, you will go on to examine functions and operations that support vectors and matrices as arguments, including those based on analytic parent functions. Computational methods for finding eigenvalues and eigenvectors of matrices are detailed, leading to various matrix decompositions. Applications such as change of bases, the classification of quadratic forms and ...

  2. An introduction to MATLAB.

    Science.gov (United States)

    Sobie, Eric A

    2011-09-13

    This two-part lecture introduces students to the scientific computing language MATLAB. Prior computer programming experience is not required. The lectures present basic concepts of computer programming logic that tend to cause difficulties for beginners in addition to concepts that relate specifically to the MATLAB language syntax. The lectures begin with a discussion of vectors, matrices, and arrays. Because many types of biological data, such as fluorescence images and DNA microarrays, are stored as two-dimensional objects, processing these data is a form of array manipulation, and MATLAB is especially adept at handling such array objects. The students are introduced to basic commands in MATLAB, as well as built-in functions that provide useful shortcuts. The second lecture focuses on the differences between MATLAB scripts and MATLAB functions and describes when one method of programming organization might be preferable to the other. The principles are illustrated through the analysis of experimental data, specifically measurements of intracellular calcium concentration in live cells obtained using confocal microscopy.

  3. EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis.

    Science.gov (United States)

    Delorme, Arnaud; Makeig, Scott

    2004-03-15

    We have developed a toolbox and graphic user interface, EEGLAB, running under the crossplatform MATLAB environment (The Mathworks, Inc.) for processing collections of single-trial and/or averaged EEG data of any number of channels. Available functions include EEG data, channel and event information importing, data visualization (scrolling, scalp map and dipole model plotting, plus multi-trial ERP-image plots), preprocessing (including artifact rejection, filtering, epoch selection, and averaging), independent component analysis (ICA) and time/frequency decompositions including channel and component cross-coherence supported by bootstrap statistical methods based on data resampling. EEGLAB functions are organized into three layers. Top-layer functions allow users to interact with the data through the graphic interface without needing to use MATLAB syntax. Menu options allow users to tune the behavior of EEGLAB to available memory. Middle-layer functions allow users to customize data processing using command history and interactive 'pop' functions. Experienced MATLAB users can use EEGLAB data structures and stand-alone signal processing functions to write custom and/or batch analysis scripts. Extensive function help and tutorial information are included. A 'plug-in' facility allows easy incorporation of new EEG modules into the main menu. EEGLAB is freely available (http://www.sccn.ucsd.edu/eeglab/) under the GNU public license for noncommercial use and open source development, together with sample data, user tutorial and extensive documentation.

  4. Introduction à MATLAB

    OpenAIRE

    Zenou, Emmanuel

    2013-01-01

    Cette initiation à MatLab a pour objectif de se familiariser à un outil très utilisé par la communauté scientifique dans les laboratoires et dans l'industrie. Il a également pour objectif d'initier (pour ceux qui n'y ont jamais touché) à la programmation et à l'algorithmique, ce qui est indispensable à tout bon ingénieur aujourd'hui. En effet, beaucoup de notions introduites ici ne sont pas propres à MatLab mais à tout langage structuré comme le C/C++, le Java, etc.

  5. MATLAB 3A

    DEFF Research Database (Denmark)

    Freil, Ole; Kristiansen, Heidi; Kaas, Thomas

    MATLAB 3a – Matematiklaboratoriet er en elevbog til første halvdel af 3. klasse. Bogen indeholder fire kapitler: 'Store tal og regnemåder', 'Kan du tegne det?', 'Gange og division', 'Undersøg data og chance'.......MATLAB 3a – Matematiklaboratoriet er en elevbog til første halvdel af 3. klasse. Bogen indeholder fire kapitler: 'Store tal og regnemåder', 'Kan du tegne det?', 'Gange og division', 'Undersøg data og chance'....

  6. Basis and application of MATLAB

    International Nuclear Information System (INIS)

    Shin, Chun Sik; An, Yeong Ju; Byun, Gi Sik; Lee, Hyeong Gi

    1998-01-01

    This book introduces MATLAB, which deals with operation and basic function, MATLAB programming like for, if, else, while and script file, equation, calculation and interpolation, operation of the matrix, file management function, such as basic file management function input-output of internal file of MATLAB input-output of outer file of MATLAB, basic graph function, two-dimensional graph and three-dimensional graph and other graph function debugger of MATLAB program in 4.2 version and debugger of MATLAB in 5.1 version.

  7. MMM: A toolbox for integrative structure modeling.

    Science.gov (United States)

    Jeschke, Gunnar

    2018-01-01

    Structural characterization of proteins and their complexes may require integration of restraints from various experimental techniques. MMM (Multiscale Modeling of Macromolecules) is a Matlab-based open-source modeling toolbox for this purpose with a particular emphasis on distance distribution restraints obtained from electron paramagnetic resonance experiments on spin-labelled proteins and nucleic acids and their combination with atomistic structures of domains or whole protomers, small-angle scattering data, secondary structure information, homology information, and elastic network models. MMM does not only integrate various types of restraints, but also various existing modeling tools by providing a common graphical user interface to them. The types of restraints that can support such modeling and the available model types are illustrated by recent application examples. © 2017 The Protein Society.

  8. ICT: isotope correction toolbox.

    Science.gov (United States)

    Jungreuthmayer, Christian; Neubauer, Stefan; Mairinger, Teresa; Zanghellini, Jürgen; Hann, Stephan

    2016-01-01

    Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences--in particular for complex isotopic systems--is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms. Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/ {christian.jungreuthmayer@boku.ac.at,juergen.zanghellini@boku.ac.at} Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. Matlab Based LOCO

    International Nuclear Information System (INIS)

    Portmann, Greg; Safranek, James; Huang, Xiaobiao

    2011-01-01

    The LOCO algorithm has been used by many accelerators around the world. Although the uses for LOCO vary, the most common use has been to find calibration errors and correct the optics functions. The light source community in particular has made extensive use of the LOCO algorithms to tightly control the beta function and coupling. Maintaining high quality beam parameters requires constant attention so a relatively large effort was put into software development for the LOCO application. The LOCO code was originally written in FORTRAN. This code worked fine but it was somewhat awkward to use. For instance, the FORTRAN code itself did not calculate the model response matrix. It required a separate modeling code such as MAD to calculate the model matrix then one manually loads the data into the LOCO code. As the number of people interested in LOCO grew, it required making it easier to use. The decision to port LOCO to Matlab was relatively easy. It's best to use a matrix programming language with good graphics capability; Matlab was also being used for high level machine control; and the accelerator modeling code AT, (5), was already developed for Matlab. Since LOCO requires collecting and processing a relative large amount of data, it is very helpful to have the LOCO code compatible with the high level machine control, (3). A number of new features were added while porting the code from FORTRAN and new methods continue to evolve, (7)(9). Although Matlab LOCO was written with AT as the underlying tracking code, a mechanism to connect to other modeling codes has been provided.

  10. Photogrammetry Toolbox Reference Manual

    Science.gov (United States)

    Liu, Tianshu; Burner, Alpheus W.

    2014-01-01

    Specialized photogrammetric and image processing MATLAB functions useful for wind tunnel and other ground-based testing of aerospace structures are described. These functions include single view and multi-view photogrammetric solutions, basic image processing to determine image coordinates, 2D and 3D coordinate transformations and least squares solutions, spatial and radiometric camera calibration, epipolar relations, and various supporting utility functions.

  11. Development of Integral Environment in Matlab/Simulink for FPGA

    Directory of Open Access Journals (Sweden)

    Dejan Jokic

    2014-01-01

    Full Text Available In this paper is presented realization of integral environment which consists of software and hardware components for the purpose of programming Altera DE boards. Software component is Toolbox FPGA Real Time which enables simple use of Matlab/Simulink with DSP Builder for the purpose of realization of control structures. Hardware component are Interface cards that make connection of DE board with object of control possible. Simulation and experimental results of DC motor control indicate the usefulness of the proposed concept.

  12. Differential equations with Matlab exploration, applications, and theory

    CERN Document Server

    McKibben, Mark

    2014-01-01

    ORDINARY DIFFERENTIAL EQUATIONS Welcome! Introduction This Book Is a Field Guide. What Does That Mean for YOU? Mired in Jargon - A Quick Language Lesson! Introducing MATLAB A First Look at Some Elementary Mathematical Models A Basic Analysis Toolbox Some Basic Mathematical Shorthand Set Algebra Functions The Space (R; j_j) A Closer Look at Sequences in (R; j_j) The Spaces (RN; k_kRN ) and (MN(R); k_kMN(R)Calculus of RN-valued and MN(R)-valued FunctionsSome Elementary ODEs Looking Ahead A First Wave of Mathematical Models Newton's Law of Heating and Cooling-Revisited Pharmocokinetics Uniform Mi

  13. User's manual for Ecolego Toolbox and the Discretization Block

    International Nuclear Information System (INIS)

    Broed, Robert; Shulan Xu

    2008-03-01

    The CLIMB modelling team (Catchment LInked Models of radiological effects in the Biosphere) was instituted in 2004 to provide SSI with an independent modelling capability when reviewing SKB's assessment of long-term safety for a geological repository. Modelling in CLIMB covers all aspects of performance assessment (PA) from near-field releases to radiological consequences in the surface environment. Software used to implement assessment models has been developed within the project. The software comprises a toolbox based on the commercial packages Matlab and Simulink used to solve compartment based differential equation systems, but with an added user friendly graphical interface. This report documents the new simulation toolbox and a newly developed Discretisation Block, which is a powerful tool for solving problems involving a network of compartments in two dimensions

  14. Spectral imaging toolbox: segmentation, hyperstack reconstruction, and batch processing of spectral images for the determination of cell and model membrane lipid order.

    Science.gov (United States)

    Aron, Miles; Browning, Richard; Carugo, Dario; Sezgin, Erdinc; Bernardino de la Serna, Jorge; Eggeling, Christian; Stride, Eleanor

    2017-05-12

    Spectral imaging with polarity-sensitive fluorescent probes enables the quantification of cell and model membrane physical properties, including local hydration, fluidity, and lateral lipid packing, usually characterized by the generalized polarization (GP) parameter. With the development of commercial microscopes equipped with spectral detectors, spectral imaging has become a convenient and powerful technique for measuring GP and other membrane properties. The existing tools for spectral image processing, however, are insufficient for processing the large data sets afforded by this technological advancement, and are unsuitable for processing images acquired with rapidly internalized fluorescent probes. Here we present a MATLAB spectral imaging toolbox with the aim of overcoming these limitations. In addition to common operations, such as the calculation of distributions of GP values, generation of pseudo-colored GP maps, and spectral analysis, a key highlight of this tool is reliable membrane segmentation for probes that are rapidly internalized. Furthermore, handling for hyperstacks, 3D reconstruction and batch processing facilitates analysis of data sets generated by time series, z-stack, and area scan microscope operations. Finally, the object size distribution is determined, which can provide insight into the mechanisms underlying changes in membrane properties and is desirable for e.g. studies involving model membranes and surfactant coated particles. Analysis is demonstrated for cell membranes, cell-derived vesicles, model membranes, and microbubbles with environmentally-sensitive probes Laurdan, carboxyl-modified Laurdan (C-Laurdan), Di-4-ANEPPDHQ, and Di-4-AN(F)EPPTEA (FE), for quantification of the local lateral density of lipids or lipid packing. The Spectral Imaging Toolbox is a powerful tool for the segmentation and processing of large spectral imaging datasets with a reliable method for membrane segmentation and no ability in programming required. The

  15. Ubuntu Linux toolbox

    CERN Document Server

    Negus, Christopher

    2012-01-01

    This bestseller from Linux guru Chris Negus is packed with an array of new and revised material As a longstanding bestseller, Ubuntu Linux Toolbox has taught you how to get the most out Ubuntu, the world?s most popular Linux distribution. With this eagerly anticipated new edition, Christopher Negus returns with a host of new and expanded coverage on tools for managing file systems, ways to connect to networks, techniques for securing Ubuntu systems, and a look at the latest Long Term Support (LTS) release of Ubuntu, all aimed at getting you up and running with Ubuntu Linux quickly.

  16. Cosmology with MATLAB

    CERN Document Server

    Green, Dan

    2016-01-01

    This volume makes explicit use of the synergy between cosmology and high energy physics, for example, supersymmetry and dark matter, or nucleosynthesis and the baryon-to-photon ratio. In particular the exciting possible connection between the recently discovered Higgs scalar and the scalar field responsible for inflation is explored.The recent great advances in the accuracy of the basic cosmological parameters is exploited in that no free scale parameters such as h appear, rather the basic calculations are done numerically using all sources of energy density simultaneously. Scripts are provided that allow the reader to calculate exact results for the basic parameters. Throughout MATLAB tools such as symbolic math, numerical solutions, plots and 'movies' of the dynamical evolution of systems are used. The GUI package is also shown as an example of the real time manipulation of parameters which is available to the reader.All the MATLAB scripts are made available to the reader to explore examples of the uses of ...

  17. Three-dimensional mapping of mechanical activation patterns, contractile dyssynchrony and dyscoordination by two-dimensional strain echocardiography: Rationale and design of a novel software toolbox

    Directory of Open Access Journals (Sweden)

    Cramer Maarten J

    2008-05-01

    Full Text Available Abstract Background Dyssynchrony of myocardial deformation is usually described in terms of variability only (e.g. standard deviations SD's. A description in terms of the spatio-temporal distribution pattern (vector-analysis of dyssynchrony or by indices estimating its impact by expressing dyscoordination of shortening in relation to the global ventricular shortening may be preferential. Strain echocardiography by speckle tracking is a new non-invasive, albeit 2-D imaging modality to study myocardial deformation. Methods A post-processing toolbox was designed to incorporate local, speckle tracking-derived deformation data into a 36 segment 3-D model of the left ventricle. Global left ventricular shortening, standard deviations and vectors of timing of shortening were calculated. The impact of dyssynchrony was estimated by comparing the end-systolic values with either early peak values only (early shortening reserve ESR or with all peak values (virtual shortening reserve VSR, and by the internal strain fraction (ISF expressing dyscoordination as the fraction of deformation lost internally due to simultaneous shortening and stretching. These dyssynchrony parameters were compared in 8 volunteers (NL, 8 patients with Wolff-Parkinson-White syndrome (WPW, and 7 patients before (LBBB and after cardiac resynchronization therapy (CRT. Results Dyssynchrony indices merely based on variability failed to detect differences between WPW and NL and failed to demonstrate the effect of CRT. Only the 3-D vector of onset of shortening could distinguish WPW from NL, while at peak shortening and by VSR, ESR and ISF no differences were found. All tested dyssynchrony parameters yielded higher values in LBBB compared to both NL and WPW. CRT reduced the spatial divergence of shortening (both vector magnitude and direction, and improved global ventricular shortening along with reductions in ESR and dyscoordination of shortening expressed by ISF. Conclusion Incorporation

  18. Digital speech processing using Matlab

    CERN Document Server

    Gopi, E S

    2014-01-01

    Digital Speech Processing Using Matlab deals with digital speech pattern recognition, speech production model, speech feature extraction, and speech compression. The book is written in a manner that is suitable for beginners pursuing basic research in digital speech processing. Matlab illustrations are provided for most topics to enable better understanding of concepts. This book also deals with the basic pattern recognition techniques (illustrated with speech signals using Matlab) such as PCA, LDA, ICA, SVM, HMM, GMM, BPN, and KSOM.

  19. ElectroMagnetoEncephalography software: overview and integration with other EEG/MEG toolboxes.

    Science.gov (United States)

    Peyk, Peter; De Cesarei, Andrea; Junghöfer, Markus

    2011-01-01

    EMEGS (electromagnetic encephalography software) is a MATLAB toolbox designed to provide novice as well as expert users in the field of neuroscience with a variety of functions to perform analysis of EEG and MEG data. The software consists of a set of graphical interfaces devoted to preprocessing, analysis, and visualization of electromagnetic data. Moreover, it can be extended using a plug-in interface. Here, an overview of the capabilities of the toolbox is provided, together with a simple tutorial for both a standard ERP analysis and a time-frequency analysis. Latest features and future directions of the software development are presented in the final section.

  20. Matlab differential and integral calculus

    CERN Document Server

    Lopez, Cesar

    2014-01-01

    MATLAB is a high-level language and environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java. MATLAB Differential and Integral Calculus introduces you to the MATLAB language with practical hands-on instructions and results, allowing you to quickly achieve your goals. In addition to givi

  1. Matlab programming for numerical analysis

    CERN Document Server

    Lopez, Cesar

    2014-01-01

    MATLAB is a high-level language and environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java. Programming MATLAB for Numerical Analysis introduces you to the MATLAB language with practical hands-on instructions and results, allowing you to quickly achieve your goals. You will first become

  2. Geoplotlib: a Python Toolbox for Visualizing Geographical Data

    OpenAIRE

    Cuttone, Andrea; Lehmann, Sune; Larsen, Jakob Eg

    2016-01-01

    We introduce geoplotlib, an open-source python toolbox for visualizing geographical data. geoplotlib supports the development of hardware-accelerated interactive visualizations in pure python, and provides implementations of dot maps, kernel density estimation, spatial graphs, Voronoi tesselation, shapefiles and many more common spatial visualizations. We describe geoplotlib design, functionalities and use cases.

  3. Conformal mapping and convergence of Krylov iterations

    Energy Technology Data Exchange (ETDEWEB)

    Driscoll, T.A.; Trefethen, L.N. [Cornell Univ., Ithaca, NY (United States)

    1994-12-31

    Connections between conformal mapping and matrix iterations have been known for many years. The idea underlying these connections is as follows. Suppose the spectrum of a matrix or operator A is contained in a Jordan region E in the complex plane with 0 not an element of E. Let {phi}(z) denote a conformal map of the exterior of E onto the exterior of the unit disk, with {phi}{infinity} = {infinity}. Then 1/{vert_bar}{phi}(0){vert_bar} is an upper bound for the optimal asymptotic convergence factor of any Krylov subspace iteration. This idea can be made precise in various ways, depending on the matrix iterations, on whether A is finite or infinite dimensional, and on what bounds are assumed on the non-normality of A. This paper explores these connections for a variety of matrix examples, making use of a new MATLAB Schwarz-Christoffel Mapping Toolbox developed by the first author. Unlike the earlier Fortran Schwarz-Christoffel package SCPACK, the new toolbox computes exterior as well as interior Schwarz-Christoffel maps, making it easy to experiment with spectra that are not necessarily symmetric about an axis.

  4. Matpar: Parallel Extensions for MATLAB

    Science.gov (United States)

    Springer, P. L.

    1998-01-01

    Matpar is a set of client/server software that allows a MATLAB user to take advantage of a parallel computer for very large problems. The user can replace calls to certain built-in MATLAB functions with calls to Matpar functions.

  5. Smoke Ready Toolbox for Wildfires

    Science.gov (United States)

    This site provides an online Smoke Ready Toolbox for Wildfires, which lists resources and tools that provide information on health impacts from smoke exposure, current fire conditions and forecasts and strategies to reduce exposure to smoke.

  6. Invertebrate diversity classification using self-organizing map neural network: with some special topological functions

    Directory of Open Access Journals (Sweden)

    WenJun Zhang

    2014-06-01

    Full Text Available In present study we used self-organizing map (SOM neural network to conduct the non-supervisory clustering of invertebrate orders in rice field. Four topological functions, i.e., cossintopf, sincostopf, acossintopf, and expsintopf, established on the template in toolbox of Matlab, were used in SOM neural network learning. Results showed that clusters were different when using different topological functions because different topological functions will generate different spatial structure of neurons in neural network. We may chose these functions and results based on comparison with the practical situation.

  7. fMRI Artefact Rejection and Sleep Scoring Toolbox

    Directory of Open Access Journals (Sweden)

    Yves Leclercq

    2011-01-01

    Full Text Available We started writing the “fMRI artefact rejection and sleep scoring toolbox”, or “FAST”, to process our sleep EEG-fMRI data, that is, the simultaneous recording of electroencephalographic and functional magnetic resonance imaging data acquired while a subject is asleep. FAST tackles three crucial issues typical of this kind of data: (1 data manipulation (viewing, comparing, chunking, etc. of long continuous M/EEG recordings, (2 rejection of the fMRI-induced artefact in the EEG signal, and (3 manual sleep-scoring of the M/EEG recording. Currently, the toolbox can efficiently deal with these issues via a GUI, SPM8 batching system or hand-written script. The tools developed are, of course, also useful for other EEG applications, for example, involving simultaneous EEG-fMRI acquisition, continuous EEG eye-balling, and manipulation. Even though the toolbox was originally devised for EEG data, it will also gracefully handle MEG data without any problem. “FAST” is developed in Matlab as an add-on toolbox for SPM8 and, therefore, internally uses its SPM8-meeg data format. “FAST” is available for free, under the GNU-GPL.

  8. ERP Reliability Analysis (ERA) Toolbox: An open-source toolbox for analyzing the reliability of event-related brain potentials.

    Science.gov (United States)

    Clayson, Peter E; Miller, Gregory A

    2017-01-01

    Generalizability theory (G theory) provides a flexible, multifaceted approach to estimating score reliability. G theory's approach to estimating score reliability has important advantages over classical test theory that are relevant for research using event-related brain potentials (ERPs). For example, G theory does not require parallel forms (i.e., equal means, variances, and covariances), can handle unbalanced designs, and provides a single reliability estimate for designs with multiple sources of error. This monograph provides a detailed description of the conceptual framework of G theory using examples relevant to ERP researchers, presents the algorithms needed to estimate ERP score reliability, and provides a detailed walkthrough of newly-developed software, the ERP Reliability Analysis (ERA) Toolbox, that calculates score reliability using G theory. The ERA Toolbox is open-source, Matlab software that uses G theory to estimate the contribution of the number of trials retained for averaging, group, and/or event types on ERP score reliability. The toolbox facilitates the rigorous evaluation of psychometric properties of ERP scores recommended elsewhere in this special issue. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Integrated Budget Office Toolbox

    Science.gov (United States)

    Rushing, Douglas A.; Blakeley, Chris; Chapman, Gerry; Robertson, Bill; Horton, Allison; Besser, Thomas; McCarthy, Debbie

    2010-01-01

    The Integrated Budget Office Toolbox (IBOT) combines budgeting, resource allocation, organizational funding, and reporting features in an automated, integrated tool that provides data from a single source for Johnson Space Center (JSC) personnel. Using a common interface, concurrent users can utilize the data without compromising its integrity. IBOT tracks planning changes and updates throughout the year using both phasing and POP-related (program-operating-plan-related) budget information for the current year, and up to six years out. Separating lump-sum funds received from HQ (Headquarters) into separate labor, travel, procurement, Center G&A (general & administrative), and servicepool categories, IBOT creates a script that significantly reduces manual input time. IBOT also manages the movement of travel and procurement funds down to the organizational level and, using its integrated funds management feature, helps better track funding at lower levels. Third-party software is used to create integrated reports in IBOT that can be generated for plans, actuals, funds received, and other combinations of data that are currently maintained in the centralized format. Based on Microsoft SQL, IBOT incorporates generic budget processes, is transportable, and is economical to deploy and support.

  10. Une introduction à MATLAB c

    OpenAIRE

    CREMONA, Christian; LABORATOIRE CENTRAL DES PONTS ET CHAUSSEES - LCPC

    2002-01-01

    MATLAB c présente toutes les fonctionnalités des approches récentes de la programmation : programmation objet basée sur des hiérarchies de classes, programmation événementielle du graphisme. MATLAB c présente une aide en ligne très complète sous format html des différentes fontions accessibles. COMPTE RENDU DE RECHERCHE

  11. GOCE User Toolbox and Tutorial

    Science.gov (United States)

    Knudsen, Per; Benveniste, Jerome

    2017-04-01

    The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products.
GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information
and guidance in how to use the toolbox for a variety of applications. GUT consists of a series of advanced
computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations,
and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT
Install Guide. A set of a-priori data and models are made available as well. Without any doubt the development
of the GOCE user toolbox have played a major role in paving the way to successful use of the GOCE data for
oceanography. The GUT version 2.2 was released in April 2014 and beside some bug-fixes it adds the capability for the computation of Simple Bouguer Anomaly (Solid-Earth). During this fall a new GUT version 3 has been released. GUTv3 was further developed through a collaborative effort where the scientific communities participate aiming
on an implementation of remaining functionalities facilitating a wider span of research in the fields of Geodesy,
Oceanography and Solid earth studies.
Accordingly, the GUT version 3 has:
 - An attractive and easy to use Graphic User Interface (GUI) for the toolbox,
 - Enhance the toolbox with some further software functionalities such as to facilitate the use of gradients,
anisotropic diffusive filtering and computation of Bouguer and isostatic gravity anomalies.
 - An associated GUT VCM tool for analyzing the GOCE variance covariance matrices.

  12. Neural Parallel Engine: A toolbox for massively parallel neural signal processing.

    Science.gov (United States)

    Tam, Wing-Kin; Yang, Zhi

    2018-05-01

    Large-scale neural recordings provide detailed information on neuronal activities and can help elicit the underlying neural mechanisms of the brain. However, the computational burden is also formidable when we try to process the huge data stream generated by such recordings. In this study, we report the development of Neural Parallel Engine (NPE), a toolbox for massively parallel neural signal processing on graphical processing units (GPUs). It offers a selection of the most commonly used routines in neural signal processing such as spike detection and spike sorting, including advanced algorithms such as exponential-component-power-component (EC-PC) spike detection and binary pursuit spike sorting. We also propose a new method for detecting peaks in parallel through a parallel compact operation. Our toolbox is able to offer a 5× to 110× speedup compared with its CPU counterparts depending on the algorithms. A user-friendly MATLAB interface is provided to allow easy integration of the toolbox into existing workflows. Previous efforts on GPU neural signal processing only focus on a few rudimentary algorithms, are not well-optimized and often do not provide a user-friendly programming interface to fit into existing workflows. There is a strong need for a comprehensive toolbox for massively parallel neural signal processing. A new toolbox for massively parallel neural signal processing has been created. It can offer significant speedup in processing signals from large-scale recordings up to thousands of channels. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. A toolbox for European judges

    NARCIS (Netherlands)

    Hesselink, M.W.

    2011-01-01

    The forthcoming instrument on European contract law, be it in the shape of an optional code for cross-border contracts or as an official toolbox for the European legislator, is likely to have a spill-over effect on private law adjudication in Europe. Judges will have no great difficulty in finding

  14. Extend your toolbox with R

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    R seems to be ideal tool for visualising your data as well as practically all other data-related tasks. Learn how to start with R as it is worth to be included not only in statistician's or data scientist's toolboxes.

  15. The Life Cycle Analysis Toolbox

    International Nuclear Information System (INIS)

    Bishop, L.; Tonn, B.E.; Williams, K.A.; Yerace, P.; Yuracko, K.L.

    1999-01-01

    The life cycle analysis toolbox is a valuable integration of decision-making tools and supporting materials developed by Oak Ridge National Laboratory (ORNL) to help Department of Energy managers improve environmental quality, reduce costs, and minimize risk. The toolbox provides decision-makers access to a wide variety of proven tools for pollution prevention (P2) and waste minimization (WMin), as well as ORNL expertise to select from this toolbox exactly the right tool to solve any given P2/WMin problem. The central element of the toolbox is a multiple criteria approach to life cycle analysis developed specifically to aid P2/WMin decision-making. ORNL has developed numerous tools that support this life cycle analysis approach. Tools are available to help model P2/WMin processes, estimate human health risks, estimate costs, and represent and manipulate uncertainties. Tools are available to help document P2/WMin decision-making and implement programs. Tools are also available to help track potential future environmental regulations that could impact P2/WMin programs and current regulations that must be followed. An Internet-site will provide broad access to the tools

  16. GOCE user toolbox and tutorial

    DEFF Research Database (Denmark)

    Knudsen, Per; Benveniste, Jerome

    2011-01-01

    consists of a series of advanced computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations, and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT Install Guide. A set of a-priori data and models are made...

  17. Test Generator for MATLAB Simulations

    Science.gov (United States)

    Henry, Joel

    2011-01-01

    MATLAB Automated Test Tool, version 3.0 (MATT 3.0) is a software package that provides automated tools that reduce the time needed for extensive testing of simulation models that have been constructed in the MATLAB programming language by use of the Simulink and Real-Time Workshop programs. MATT 3.0 runs on top of the MATLAB engine application-program interface to communicate with the Simulink engine. MATT 3.0 automatically generates source code from the models, generates custom input data for testing both the models and the source code, and generates graphs and other presentations that facilitate comparison of the outputs of the models and the source code for the same input data. Context-sensitive and fully searchable help is provided in HyperText Markup Language (HTML) format.

  18. Signals and systems with MATLAB

    CERN Document Server

    Yang, Won Young; Song, Ik H; Cho, Yong S

    2009-01-01

    Covers some of the theoretical foundations and mathematical derivations that can be used in higher-level related subjects such as signal processing, communication, and control, minimizing the mathematical difficulty and computational burden. This book illustrates the usage of MATLAB and Simulink for signal and system analysis and design.

  19. Matlab Software for Spatial Panels

    NARCIS (Netherlands)

    Elhorst, J.Paul

    2014-01-01

    Elhorst provides Matlab routines to estimate spatial panel data models at his website. This article extends these routines to include the bias correction procedure proposed by Lee and Yu if the spatial panel data model contains spatial and/or time-period fixed effects, the direct and indirect

  20. FAST: FAST Analysis of Sequences Toolbox

    Directory of Open Access Journals (Sweden)

    Travis J. Lawrence

    2015-05-01

    Full Text Available FAST (FAST Analysis of Sequences Toolbox provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU’s Not Unix Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics makes FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format. Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought.

  1. mGrid: a load-balanced distributed computing environment for the remote execution of the user-defined Matlab code.

    Science.gov (United States)

    Karpievitch, Yuliya V; Almeida, Jonas S

    2006-03-15

    Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke. mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else). Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server. Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web-based infrastructure of mGrid allows for it to be easily extensible over

  2. mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code

    Directory of Open Access Journals (Sweden)

    Almeida Jonas S

    2006-03-01

    Full Text Available Abstract Background Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke. Results mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else. Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server. Conclusion Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web

  3. PANDA: a pipeline toolbox for analyzing brain diffusion images.

    Science.gov (United States)

    Cui, Zaixu; Zhong, Suyu; Xu, Pengfei; He, Yong; Gong, Gaolang

    2013-01-01

    Diffusion magnetic resonance imaging (dMRI) is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named "Pipeline for Analyzing braiN Diffusion imAges" (PANDA) for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL), Pipeline System for Octave and Matlab (PSOM), Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics [e.g., fractional anisotropy (FA) and mean diffusivity (MD)] that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS)-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI), allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies.

  4. PANDA: a pipeline toolbox for analyzing brain diffusion images

    Directory of Open Access Journals (Sweden)

    Zaixu eCui

    2013-02-01

    Full Text Available Diffusion magnetic resonance imaging (dMRI is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named Pipeline for Analyzing braiN Diffusion imAges (PANDA for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL, Pipeline System for Octave and Matlab (PSOM, Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics (e.g., FA and MD that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI, allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies.

  5. GOCE User Toolbox and Tutorial

    Science.gov (United States)

    Knudsen, P.; Benveniste, J.

    2011-07-01

    The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products. GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information and guidance in how to use the toolbox for a variety of applications. GUT consists of a series of advanced computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations, and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT Install Guide. A set of a-priori data and models are made available as well. GUT has been developed in a collaboration within the GUT Core Group. The GUT Core Group: S. Dinardo, D. Serpe, B.M. Lucas, R. Floberghagen, A. Horvath (ESA), O. Andersen, M. Herceg (DTU), M.-H. Rio, S. Mulet, G. Larnicol (CLS), J. Johannessen, L.Bertino (NERSC), H. Snaith, P. Challenor (NOC), K. Haines, D. Bretherton (NCEO), C. Hughes (POL), R.J. Bingham (NU), G. Balmino, S. Niemeijer, I. Price, L. Cornejo (S&T), M. Diament, I Panet (IPGP), C.C. Tscherning (KU), D. Stammer, F. Siegismund (UH), T. Gruber (TUM),

  6. VoxelStats: A MATLAB Package for Multi-Modal Voxel-Wise Brain Image Analysis.

    Science.gov (United States)

    Mathotaarachchi, Sulantha; Wang, Seqian; Shin, Monica; Pascoal, Tharick A; Benedet, Andrea L; Kang, Min Su; Beaudry, Thomas; Fonov, Vladimir S; Gauthier, Serge; Labbe, Aurélie; Rosa-Neto, Pedro

    2016-01-01

    In healthy individuals, behavioral outcomes are highly associated with the variability on brain regional structure or neurochemical phenotypes. Similarly, in the context of neurodegenerative conditions, neuroimaging reveals that cognitive decline is linked to the magnitude of atrophy, neurochemical declines, or concentrations of abnormal protein aggregates across brain regions. However, modeling the effects of multiple regional abnormalities as determinants of cognitive decline at the voxel level remains largely unexplored by multimodal imaging research, given the high computational cost of estimating regression models for every single voxel from various imaging modalities. VoxelStats is a voxel-wise computational framework to overcome these computational limitations and to perform statistical operations on multiple scalar variables and imaging modalities at the voxel level. VoxelStats package has been developed in Matlab(®) and supports imaging formats such as Nifti-1, ANALYZE, and MINC v2. Prebuilt functions in VoxelStats enable the user to perform voxel-wise general and generalized linear models and mixed effect models with multiple volumetric covariates. Importantly, VoxelStats can recognize scalar values or image volumes as response variables and can accommodate volumetric statistical covariates as well as their interaction effects with other variables. Furthermore, this package includes built-in functionality to perform voxel-wise receiver operating characteristic analysis and paired and unpaired group contrast analysis. Validation of VoxelStats was conducted by comparing the linear regression functionality with existing toolboxes such as glim_image and RMINC. The validation results were identical to existing methods and the additional functionality was demonstrated by generating feature case assessments (t-statistics, odds ratio, and true positive rate maps). In summary, VoxelStats expands the current methods for multimodal imaging analysis by allowing the

  7. Wave data processing toolbox manual

    Science.gov (United States)

    Sullivan, Charlene M.; Warner, John C.; Martini, Marinna A.; Lightsom, Frances S.; Voulgaris, George; Work, Paul

    2006-01-01

    Researchers routinely deploy oceanographic equipment in estuaries, coastal nearshore environments, and shelf settings. These deployments usually include tripod-mounted instruments to measure a suite of physical parameters such as currents, waves, and pressure. Instruments such as the RD Instruments Acoustic Doppler Current Profiler (ADCP(tm)), the Sontek Argonaut, and the Nortek Aquadopp(tm) Profiler (AP) can measure these parameters. The data from these instruments must be processed using proprietary software unique to each instrument to convert measurements to real physical values. These processed files are then available for dissemination and scientific evaluation. For example, the proprietary processing program used to process data from the RD Instruments ADCP for wave information is called WavesMon. Depending on the length of the deployment, WavesMon will typically produce thousands of processed data files. These files are difficult to archive and further analysis of the data becomes cumbersome. More imperative is that these files alone do not include sufficient information pertinent to that deployment (metadata), which could hinder future scientific interpretation. This open-file report describes a toolbox developed to compile, archive, and disseminate the processed wave measurement data from an RD Instruments ADCP, a Sontek Argonaut, or a Nortek AP. This toolbox will be referred to as the Wave Data Processing Toolbox. The Wave Data Processing Toolbox congregates the processed files output from the proprietary software into two NetCDF files: one file contains the statistics of the burst data and the other file contains the raw burst data (additional details described below). One important advantage of this toolbox is that it converts the data into NetCDF format. Data in NetCDF format is easy to disseminate, is portable to any computer platform, and is viewable with public-domain freely-available software. Another important advantage is that a metadata

  8. Solving applied mathematical problems with Matlab

    CERN Document Server

    Xue, Dingyu

    2008-01-01

    Computer Mathematics Language-An Overview. Fundamentals of MATLAB Programming. Calculus Problems. MATLAB Computations of Linear Algebra Problems. Integral Transforms and Complex Variable Functions. Solutions to Nonlinear Equations and Optimization Problems. MATLAB Solutions to Differential Equation Problems. Solving Interpolations and Approximations Problems. Solving Probability and Mathematical Statistics Problems. Nontraditional Solution Methods for Mathematical Problems.

  9. Digital signal processing using MATLAB

    CERN Document Server

    Schilling, Robert L

    2016-01-01

    Focus on the development, implementation, and application of modern DSP techniques with DIGITAL SIGNAL PROCESSING USING MATLAB(R), 3E. Written in an engaging, informal style, this edition immediately captures your attention and encourages you to explore each critical topic. Every chapter starts with a motivational section that highlights practical examples and challenges that you can solve using techniques covered in the chapter. Each chapter concludes with a detailed case study example, a chapter summary with learning outcomes, and practical homework problems cross-referenced to specific chapter sections for your convenience. DSP Companion software accompanies each book to enable further investigation. The DSP Companion software operates with MATLAB(R) and provides intriguing demonstrations as well as interactive explorations of analysis and design concepts.

  10. MatLab 1b

    DEFF Research Database (Denmark)

    Kristiansen, Heidi; Kaas, Thomas; Freil, Ole

    Bogen indeholder fire kapitler: ’Tal i spil’, ’Spejlinger og mønstre’, ’Mønstre med farver, figurer og tal’ og ’Længde og vægt’. MATLAB: •bygger på en undersøgende og problemorienteret tilgang til matematikken •understøtter læringsmålstyret undervisning •har fokus på faglige samtaler og undersøge......Bogen indeholder fire kapitler: ’Tal i spil’, ’Spejlinger og mønstre’, ’Mønstre med farver, figurer og tal’ og ’Længde og vægt’. MATLAB: •bygger på en undersøgende og problemorienteret tilgang til matematikken •understøtter læringsmålstyret undervisning •har fokus på faglige samtaler og...

  11. Computational colour science using MATLAB

    CERN Document Server

    Westland, Stephen; Cheung, Vien

    2012-01-01

    Computational Colour Science Using MATLAB 2nd Edition offers a practical, problem-based approach to colour physics. The book focuses on the key issues encountered in modern colour engineering, including efficient representation of colour information, Fourier analysis of reflectance spectra and advanced colorimetric computation. Emphasis is placed on the practical applications rather than the techniques themselves, with material structured around key topics. These topics include colour calibration of visual displays, computer recipe prediction and models for colour-appearance prediction. Each t

  12. MatLab 1a

    DEFF Research Database (Denmark)

    Kristiansen, Heidi; Kaas, Thomas; Freil, Ole

    Bogen indeholder fire kapitler: ’Tæl og brug tal’, ’Undersøg figurer’, ’Plus- og minusproblemer’ og ’Statistik og chance’. MATLAB: •bygger på en undersøgende og problemorienteret tilgang til matematikken •understøtter læringsmålstyret undervisning •har fokus på faglige samtaler og undersøgelser...

  13. MatLab 0. Matematiklaboratoriet

    DEFF Research Database (Denmark)

    Kristiansen, Heidi; Kaas, Thomas; Freil, Ole

    Bogen indeholder fem kapitler: ’Tælle og tal’, ’Figurer og mønstre’, ’Hvor mange?’, ’Måling’ og ’Data og diagrammer’. MATLAB: •bygger på en undersøgende og problemorienteret tilgang til matematikken •understøtter læringsmålstyret undervisning •har fokus på faglige samtaler og undersøgelser, der...

  14. Robust control design with MATLAB

    CERN Document Server

    Gu, Da-Wei; Konstantinov, Mihail M

    2013-01-01

    Robust Control Design with MATLAB® (second edition) helps the student to learn how to use well-developed advanced robust control design methods in practical cases. To this end, several realistic control design examples from teaching-laboratory experiments, such as a two-wheeled, self-balancing robot, to complex systems like a flexible-link manipulator are given detailed presentation. All of these exercises are conducted using MATLAB® Robust Control Toolbox 3, Control System Toolbox and Simulink®. By sharing their experiences in industrial cases with minimum recourse to complicated theories and formulae, the authors convey essential ideas and useful insights into robust industrial control systems design using major H-infinity optimization and related methods allowing readers quickly to move on with their own challenges. The hands-on tutorial style of this text rests on an abundance of examples and features for the second edition: ·        rewritten and simplified presentation of theoretical and meth...

  15. A toolbox to visually explore cerebellar shape changes in cerebellar disease and dysfunction

    Science.gov (United States)

    Abulnaga, S. Mazdak; Yang, Zhen; Carass, Aaron; Kansal, Kalyani; Jedynak, Bruno M.; Onyike, Chiadi U.; Ying, Sarah H.; Prince, Jerry L.

    2016-03-01

    The cerebellum plays an important role in motor control and is also involved in cognitive processes. Cerebellar function is specialized by location, although the exact topographic functional relationship is not fully understood. The spinocerebellar ataxias are a group of neurodegenerative diseases that cause regional atrophy in the cerebellum, yielding distinct motor and cognitive problems. The ability to study the region-specific atrophy patterns can provide insight into the problem of relating cerebellar function to location. In an effort to study these structural change patterns, we developed a toolbox in MATLAB to provide researchers a unique way to visually explore the correlation between cerebellar lobule shape changes and function loss, with a rich set of visualization and analysis modules. In this paper, we outline the functions and highlight the utility of the toolbox. The toolbox takes as input landmark shape representations of subjects' cerebellar substructures. A principal component analysis is used for dimension reduction. Following this, a linear discriminant analysis and a regression analysis can be performed to find the discriminant direction associated with a specific disease type, or the regression line of a specific functional measure can be generated. The characteristic structural change pattern of a disease type or of a functional score is visualized by sampling points on the discriminant or regression line. The sampled points are used to reconstruct synthetic cerebellar lobule shapes. We showed a few case studies highlighting the utility of the toolbox and we compare the analysis results with the literature.

  16. A toolbox to visually explore cerebellar shape changes in cerebellar disease and dysfunction.

    Science.gov (United States)

    Abulnaga, S Mazdak; Yang, Zhen; Carass, Aaron; Kansal, Kalyani; Jedynak, Bruno M; Onyike, Chiadi U; Ying, Sarah H; Prince, Jerry L

    2016-02-27

    The cerebellum plays an important role in motor control and is also involved in cognitive processes. Cerebellar function is specialized by location, although the exact topographic functional relationship is not fully understood. The spinocerebellar ataxias are a group of neurodegenerative diseases that cause regional atrophy in the cerebellum, yielding distinct motor and cognitive problems. The ability to study the region-specific atrophy patterns can provide insight into the problem of relating cerebellar function to location. In an effort to study these structural change patterns, we developed a toolbox in MATLAB to provide researchers a unique way to visually explore the correlation between cerebellar lobule shape changes and function loss, with a rich set of visualization and analysis modules. In this paper, we outline the functions and highlight the utility of the toolbox. The toolbox takes as input landmark shape representations of subjects' cerebellar substructures. A principal component analysis is used for dimension reduction. Following this, a linear discriminant analysis and a regression analysis can be performed to find the discriminant direction associated with a specific disease type, or the regression line of a specific functional measure can be generated. The characteristic structural change pattern of a disease type or of a functional score is visualized by sampling points on the discriminant or regression line. The sampled points are used to reconstruct synthetic cerebellar lobule shapes. We showed a few case studies highlighting the utility of the toolbox and we compare the analysis results with the literature.

  17. PLDAPS: A Hardware Architecture and Software Toolbox for Neurophysiology Requiring Complex Visual Stimuli and Online Behavioral Control.

    Science.gov (United States)

    Eastman, Kyler M; Huk, Alexander C

    2012-01-01

    Neurophysiological studies in awake, behaving primates (both human and non-human) have focused with increasing scrutiny on the temporal relationship between neural signals and behaviors. Consequently, laboratories are often faced with the problem of developing experimental equipment that can support data recording with high temporal precision and also be flexible enough to accommodate a wide variety of experimental paradigms. To this end, we have developed a MATLAB toolbox that integrates several modern pieces of equipment, but still grants experimenters the flexibility of a high-level programming language. Our toolbox takes advantage of three popular and powerful technologies: the Plexon apparatus for neurophysiological recordings (Plexon, Inc., Dallas, TX, USA), a Datapixx peripheral (Vpixx Technologies, Saint-Bruno, QC, Canada) for control of analog, digital, and video input-output signals, and the Psychtoolbox MATLAB toolbox for stimulus generation (Brainard, 1997; Pelli, 1997; Kleiner et al., 2007). The PLDAPS ("Platypus") system is designed to support the study of the visual systems of awake, behaving primates during multi-electrode neurophysiological recordings, but can be easily applied to other related domains. Despite its wide range of capabilities and support for cutting-edge video displays and neural recording systems, the PLDAPS system is simple enough for someone with basic MATLAB programming skills to design their own experiments.

  18. User's manual for Ecolego Toolbox and the Discretization Block

    Energy Technology Data Exchange (ETDEWEB)

    Broed, Robert (Facilia consulting AB (Sweden)); Shulan Xu (Swedish Radiation Protection Authority, Stockholm (Sweden))

    2008-03-15

    The CLIMB modelling team (Catchment LInked Models of radiological effects in the Biosphere) was instituted in 2004 to provide SSI with an independent modelling capability when reviewing SKB's assessment of long-term safety for a geological repository. Modelling in CLIMB covers all aspects of performance assessment (PA) from near-field releases to radiological consequences in the surface environment. Software used to implement assessment models has been developed within the project. The software comprises a toolbox based on the commercial packages Matlab and Simulink used to solve compartment based differential equation systems, but with an added user friendly graphical interface. This report documents the new simulation toolbox and a newly developed Discretisation Block, which is a powerful tool for solving problems involving a network of compartments in two dimensions

  19. A MATLAB companion for multivariable calculus

    CERN Document Server

    Cooper, Jeffery

    2001-01-01

    Offering a concise collection of MatLab programs and exercises to accompany a third semester course in multivariable calculus, A MatLab Companion for Multivariable Calculus introduces simple numerical procedures such as numerical differentiation, numerical integration and Newton''s method in several variables, thereby allowing students to tackle realistic problems. The many examples show students how to use MatLab effectively and easily in many contexts. Numerous exercises in mathematics and applications areas are presented, graded from routine to more demanding projects requiring some programming. Matlab M-files are provided on the Harcourt/Academic Press web site at http://www.harcourt-ap.com/matlab.html.* Computer-oriented material that complements the essential topics in multivariable calculus* Main ideas presented with examples of computations and graphics displays using MATLAB * Numerous examples of short code in the text, which can be modified for use with the exercises* MATLAB files are used to implem...

  20. Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology.

    Science.gov (United States)

    Markiewicz, Tomasz

    2011-03-30

    The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server

  1. Parallel Computation of the Jacobian Matrix for Nonlinear Equation Solvers Using MATLAB

    Science.gov (United States)

    Rose, Geoffrey K.; Nguyen, Duc T.; Newman, Brett A.

    2017-01-01

    Demonstrating speedup for parallel code on a multicore shared memory PC can be challenging in MATLAB due to underlying parallel operations that are often opaque to the user. This can limit potential for improvement of serial code even for the so-called embarrassingly parallel applications. One such application is the computation of the Jacobian matrix inherent to most nonlinear equation solvers. Computation of this matrix represents the primary bottleneck in nonlinear solver speed such that commercial finite element (FE) and multi-body-dynamic (MBD) codes attempt to minimize computations. A timing study using MATLAB's Parallel Computing Toolbox was performed for numerical computation of the Jacobian. Several approaches for implementing parallel code were investigated while only the single program multiple data (spmd) method using composite objects provided positive results. Parallel code speedup is demonstrated but the goal of linear speedup through the addition of processors was not achieved due to PC architecture.

  2. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

    KAUST Repository

    Klingbeil, G.; Erban, R.; Giles, M.; Maini, P. K.

    2011-01-01

    Motivation: The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new

  3. Matlab Toolbox to Perform Secondary Quality Control (2nd QC) on Hydrographic Data (NCEI Accession 0164484)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — High quality, reference measurements of chemical and physical properties of seawater are of great importance for a wide research community, including the need to...

  4. Visual NNet: An Educational ANN's Simulation Environment Reusing Matlab Neural Networks Toolbox

    Science.gov (United States)

    Garcia-Roselló, Emilio; González-Dacosta, Jacinto; Lado, Maria J.; Méndez, Arturo J.; Garcia Pérez-Schofield, Baltasar; Ferrer, Fátima

    2011-01-01

    Artificial Neural Networks (ANN's) are nowadays a common subject in different curricula of graduate and postgraduate studies. Due to the complex algorithms involved and the dynamic nature of ANN's, simulation software has been commonly used to teach this subject. This software has usually been developed specifically for learning purposes, because…

  5. MOtoNMS : A MATLAB toolbox to process motion data for neuromusculoskeletal modeling and simulation

    NARCIS (Netherlands)

    Mantoan, Alice; Pizzolato, Claudio; Sartori, Massimo; Sawacha, Zimi; Cobelli, Claudio; Reggiani, Monica

    2015-01-01

    Background: Neuromusculoskeletal modeling and simulation enable investigation of the neuromusculoskeletal system and its role in human movement dynamics. These methods are progressively introduced into daily clinical practice. However, a major factor limiting this translation is the lack of robust

  6. The Design and Implementation of a GUI-Based Control Allocation Toolbox in the MATLAB Environment

    OpenAIRE

    Glaze, Michelle L.

    1998-01-01

    Control Allocation addresses the problem of the management of multiple, redundant control effectors. Generally speaking, control allocation is any method that is used to determine how the controls of a system should be positioned to achieve some desired effect. An infinite number of allocation methods exist, from the straight-forward direct allocation technique, to the daisy chaining approach, to the computationally simple generalized inverse method. Because different methods have advantag...

  7. Matlab modeling of ITER CODAC

    International Nuclear Information System (INIS)

    Pangione, L.; Lister, J.B.

    2008-01-01

    The ITER CODAC (COntrol, Data Access and Communication) conceptual design resulted from 2 years of activity. One result was a proposed functional partitioning of CODAC into different CODAC Systems, each of them partitioned into other CODAC Systems. Considering the large size of this project, simple use of human language assisted by figures would certainly be ineffective in creating an unambiguous description of all interactions and all relations between these Systems. Moreover, the underlying design is resident in the mind of the designers, who must consider all possible situations that could happen to each system. There is therefore a need to model the whole of CODAC with a clear and preferably graphical method, which allows the designers to verify the correctness and the consistency of their project. The aim of this paper is to describe the work started on ITER CODAC modeling using Matlab/Simulink. The main feature of this tool is the possibility of having a simple, graphical, intuitive representation of a complex system and ultimately to run a numerical simulation of it. Using Matlab/Simulink, each CODAC System was represented in a graphical and intuitive form with its relations and interactions through the definition of a small number of simple rules. In a Simulink diagram, each system was represented as a 'black box', both containing, and connected to, a number of other systems. In this way it is possible to move vertically between systems on different levels, to show the relation of membership, or horizontally to analyse the information exchange between systems at the same level. This process can be iterated, starting from a global diagram, in which only CODAC appears with the Plant Systems and the external sites, and going deeper down to the mathematical model of each CODAC system. The Matlab/Simulink features for simulating the whole top diagram encourage us to develop the idea of completing the functionalities of all systems in order to finally have a full

  8. ACCEPT: Introduction of the Adverse Condition and Critical Event Prediction Toolbox

    Science.gov (United States)

    Martin, Rodney A.; Santanu, Das; Janakiraman, Vijay Manikandan; Hosein, Stefan

    2015-01-01

    The prediction of anomalies or adverse events is a challenging task, and there are a variety of methods which can be used to address the problem. In this paper, we introduce a generic framework developed in MATLAB (sup registered mark) called ACCEPT (Adverse Condition and Critical Event Prediction Toolbox). ACCEPT is an architectural framework designed to compare and contrast the performance of a variety of machine learning and early warning algorithms, and tests the capability of these algorithms to robustly predict the onset of adverse events in any time-series data generating systems or processes.

  9. The Research of Histogram Enhancement Technique Based on Matlab Software

    Directory of Open Access Journals (Sweden)

    Li Kai

    2014-08-01

    Full Text Available Histogram enhancement technique has been widely applied as a typical pattern in digital image processing. The paper is based on Matlab software, through the two ways of histogram equalization and histogram specification technologies to deal with the darker images, using two methods of partial equilibrium and mapping histogram to transform the original histograms, thereby enhanced the image information. The results show that these two kinds of techniques both can significantly improve the image quality and enhance the image feature.

  10. Synchronization of generalized Henon map using polynomial controller

    International Nuclear Information System (INIS)

    Lam, H.K.

    2010-01-01

    This Letter presents the chaos synchronization of two discrete-time generalized Henon map, namely the drive and response systems. A polynomial controller is proposed to drive the system states of the response system to follow those of the drive system. The system stability of the error system formed by the drive and response systems and the synthesis of the polynomial controller are investigated using the sum-of-squares (SOS) technique. Based on the Lyapunov stability theory, stability conditions in terms of SOS are derived to guarantee the system stability and facilitate the controller synthesis. By satisfying the SOS-based stability conditions, chaotic synchronization is achieved. The solution of the SOS-based stability conditions can be found numerically using the third-party Matlab toolbox SOSTOOLS. A simulation example is given to illustrate the merits of the proposed polynomial control approach.

  11. ECONOMIC MODELING PROCESSES USING MATLAB

    Directory of Open Access Journals (Sweden)

    Anamaria G. MACOVEI

    2008-06-01

    Full Text Available To study economic phenomena and processes using mathem atical modeling, and to determine the approximatesolution to a problem we need to choose a method of calculation and a numerical computer program, namely thepackage of programs MatLab. Any economic process or phenomenon is a mathematical description of h is behavior,and thus draw up an economic and mathematical model that has the following stages: formulation of the problem, theanalysis process modeling, the production model and design verification, validation and implementation of the model.This article is presented an economic model and its modeling is using mathematical equations and software packageMatLab, which helps us approximation effective solution. As data entry is considered the net cost, the cost of direct andtotal cost and the link between them. I presented the basic formula for determining the total cost. Economic modelcalculations were made in MatLab software package and with graphic representation of its interpretation of the resultsachieved in terms of our specific problem.

  12. Menhir: An Environment for High Performance Matlab

    Directory of Open Access Journals (Sweden)

    Stéphane Chauveau

    1999-01-01

    Full Text Available In this paper we present Menhir a compiler for generating sequential or parallel code from the Matlab language. The compiler has been designed in the context of using Matlab as a specification language. One of the major features of Menhir is its retargetability to generate parallel and sequential C or Fortran code. We present the compilation process and the target system description for Menhir. Preliminary performances are given and compared with MCC, the MathWorks Matlab compiler.

  13. Cyclotron beam dynamic simulations in MATLAB

    International Nuclear Information System (INIS)

    Karamysheva, G.A.; Karamyshev, O.V.; Lepkina, O.E.

    2008-01-01

    MATLAB is useful for beam dynamic simulations in cyclotrons. Programming in an easy-to-use environment permits creation of models in a short space of time. Advanced graphical tools of MATLAB give good visualization features to created models. The beam dynamic modeling results with an example of two different cyclotron designs are presented. Programming with MATLAB opens wide possibilities of the development of the complex program, able to perform complete block of calculations for the design of the accelerators

  14. MatLab Script and Functional Programming

    Science.gov (United States)

    Shaykhian, Gholam Ali

    2007-01-01

    MatLab Script and Functional Programming: MatLab is one of the most widely used very high level programming languages for scientific and engineering computations. It is very user-friendly and needs practically no formal programming knowledge. Presented here are MatLab programming aspects and not just the MatLab commands for scientists and engineers who do not have formal programming training and also have no significant time to spare for learning programming to solve their real world problems. Specifically provided are programs for visualization. The MatLab seminar covers the functional and script programming aspect of MatLab language. Specific expectations are: a) Recognize MatLab commands, script and function. b) Create, and run a MatLab function. c) Read, recognize, and describe MatLab syntax. d) Recognize decisions, loops and matrix operators. e) Evaluate scope among multiple files, and multiple functions within a file. f) Declare, define and use scalar variables, vectors and matrices.

  15. What's in Your Teaching Toolbox?

    Science.gov (United States)

    Mormer, Elaine

    2018-02-01

    Educators are faced with an array of tools available to enhance learning outcomes in the classroom and clinic. These tools range from those that are very simple to those that are sufficiently complex to require an investment in learning time. This article summarizes a collection of teaching tools, ordered by the time involved in learning proficient use. Simple tools described include specific online blogs providing support for faculty and student writing and a simple method to capture and download videos from YouTube for classroom use. More complex tools described include a Web-based application for custom-created animated videos and an interactive audience polling system. Readers are encouraged to reflect on the tools most appropriate for use in their own teaching toolbox by considering the requisite time to proficiency and suitability to address desired learner outcomes.

  16. NEMO: A Stellar Dynamics Toolbox

    Science.gov (United States)

    Barnes, Joshua; Hut, Piet; Teuben, Peter

    2010-10-01

    NEMO is an extendible Stellar Dynamics Toolbox, following an Open-Source Software model. It has various programs to create, integrate, analyze and visualize N-body and SPH like systems, following the pipe and filter architecture. In addition there are various tools to operate on images, tables and orbits, including FITS files to export/import to/from other astronomical data reduction packages. A large growing fraction of NEMO has been contributed by a growing list of authors. The source code consist of a little over 4000 files and a little under 1,000,000 lines of code and documentation, mostly C, and some C++ and Fortran. NEMO development started in 1986 in Princeton (USA) by Barnes, Hut and Teuben. See also ZENO (ascl:1102.027) for the version that Barnes maintains.

  17. A comprehensive validation toolbox for regional ocean models - Outline, implementation and application to the Baltic Sea

    Science.gov (United States)

    Jandt, Simon; Laagemaa, Priidik; Janssen, Frank

    2014-05-01

    The systematic and objective comparison between output from a numerical ocean model and a set of observations, called validation in the context of this presentation, is a beneficial activity at several stages, starting from early steps in model development and ending at the quality control of model based products delivered to customers. Even though the importance of this kind of validation work is widely acknowledged it is often not among the most popular tasks in ocean modelling. In order to ease the validation work a comprehensive toolbox has been developed in the framework of the MyOcean-2 project. The objective of this toolbox is to carry out validation integrating different data sources, e.g. time-series at stations, vertical profiles, surface fields or along track satellite data, with one single program call. The validation toolbox, implemented in MATLAB, features all parts of the validation process - ranging from read-in procedures of datasets to the graphical and numerical output of statistical metrics of the comparison. The basic idea is to have only one well-defined validation schedule for all applications, in which all parts of the validation process are executed. Each part, e.g. read-in procedures, forms a module in which all available functions of this particular part are collected. The interface between the functions, the module and the validation schedule is highly standardized. Functions of a module are set up for certain validation tasks, new functions can be implemented into the appropriate module without affecting the functionality of the toolbox. The functions are assigned for each validation task in user specific settings, which are externally stored in so-called namelists and gather all information of the used datasets as well as paths and metadata. In the framework of the MyOcean-2 project the toolbox is frequently used to validate the forecast products of the Baltic Sea Marine Forecasting Centre. Hereby the performance of any new product

  18. Drinking Water Cyanotoxin Risk Communication Toolbox

    Science.gov (United States)

    The drinking water cyanotoxin risk communication toolbox is a ready-to-use, “one-stop-shop” to support public water systems, states, and local governments in developing, as they deem appropriate, their own risk communication materials.

  19. Orthogonal transformations for change detection, Matlab code

    DEFF Research Database (Denmark)

    2005-01-01

    Matlab code to do multivariate alteration detection (MAD) analysis, maximum autocorrelation factor (MAF) analysis, canonical correlation analysis (CCA) and principal component analysis (PCA) on image data.......Matlab code to do multivariate alteration detection (MAD) analysis, maximum autocorrelation factor (MAF) analysis, canonical correlation analysis (CCA) and principal component analysis (PCA) on image data....

  20. A DICOM-RT-based toolbox for the evaluation and verification of radiotherapy plans

    International Nuclear Information System (INIS)

    Spezi, E; Lewis, D G; Smith, C W

    2002-01-01

    The verification of radiotherapy plans is an essential step in the treatment planning process. This is especially important for highly conformal and IMRT plans which produce non-intuitive fluence maps and complex 3D dose distributions. In this work we present a DICOM (Digital Imaging and Communication in Medicine) based toolbox, developed for the evaluation and the verification of radiotherapy treatment plans. The toolbox offers the possibility of importing treatment plans generated with different calculation algorithms and/or different optimization engines and evaluating dose distributions on an independent platform. Furthermore the radiotherapy set-up can be exported to the BEAM Monte Carlo code system for dose verification. This can be done by simulating the irradiation of the patient CT dataset or the irradiation of a software-generated water phantom. We show the application of some of the functions implemented in this toolbox for the evaluation and verification of an IMRT treatment of the head and neck region

  1. Development of a fault test experimental facility model using Matlab

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Iraci Martinez; Moraes, Davi Almeida, E-mail: martinez@ipen.br, E-mail: dmoraes@dk8.com.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2015-07-01

    The Fault Test Experimental Facility was developed to simulate a PWR nuclear power plant and is instrumented with temperature, level and pressure sensors. The Fault Test Experimental Facility can be operated to generate normal and fault data, and these failures can be added initially small, and their magnitude being increasing gradually. This work presents the Fault Test Experimental Facility model developed using the Matlab GUIDE (Graphical User Interface Development Environment) toolbox that consists of a set of functions designed to create interfaces in an easy and fast way. The system model is based on the mass and energy inventory balance equations. Physical as well as operational aspects are taken into consideration. The interface layout looks like a process flowchart and the user can set the input variables. Besides the normal operation conditions, there is the possibility to choose a faulty variable from a list. The program also allows the user to set the noise level for the input variables. Using the model, data were generated for different operational conditions, both under normal and fault conditions with different noise levels added to the input variables. Data generated by the model will be compared with Fault Test Experimental Facility data. The Fault Test Experimental Facility theoretical model results will be used for the development of a Monitoring and Fault Detection System. (author)

  2. Efficient MATLAB computations with sparse and factored tensors.

    Energy Technology Data Exchange (ETDEWEB)

    Bader, Brett William; Kolda, Tamara Gibson (Sandia National Lab, Livermore, CA)

    2006-12-01

    In this paper, the term tensor refers simply to a multidimensional or N-way array, and we consider how specially structured tensors allow for efficient storage and computation. First, we study sparse tensors, which have the property that the vast majority of the elements are zero. We propose storing sparse tensors using coordinate format and describe the computational efficiency of this scheme for various mathematical operations, including those typical to tensor decomposition algorithms. Second, we study factored tensors, which have the property that they can be assembled from more basic components. We consider two specific types: a Tucker tensor can be expressed as the product of a core tensor (which itself may be dense, sparse, or factored) and a matrix along each mode, and a Kruskal tensor can be expressed as the sum of rank-1 tensors. We are interested in the case where the storage of the components is less than the storage of the full tensor, and we demonstrate that many elementary operations can be computed using only the components. All of the efficiencies described in this paper are implemented in the Tensor Toolbox for MATLAB.

  3. Development of a fault test experimental facility model using Matlab

    International Nuclear Information System (INIS)

    Pereira, Iraci Martinez; Moraes, Davi Almeida

    2015-01-01

    The Fault Test Experimental Facility was developed to simulate a PWR nuclear power plant and is instrumented with temperature, level and pressure sensors. The Fault Test Experimental Facility can be operated to generate normal and fault data, and these failures can be added initially small, and their magnitude being increasing gradually. This work presents the Fault Test Experimental Facility model developed using the Matlab GUIDE (Graphical User Interface Development Environment) toolbox that consists of a set of functions designed to create interfaces in an easy and fast way. The system model is based on the mass and energy inventory balance equations. Physical as well as operational aspects are taken into consideration. The interface layout looks like a process flowchart and the user can set the input variables. Besides the normal operation conditions, there is the possibility to choose a faulty variable from a list. The program also allows the user to set the noise level for the input variables. Using the model, data were generated for different operational conditions, both under normal and fault conditions with different noise levels added to the input variables. Data generated by the model will be compared with Fault Test Experimental Facility data. The Fault Test Experimental Facility theoretical model results will be used for the development of a Monitoring and Fault Detection System. (author)

  4. Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB.

    Science.gov (United States)

    Chatziioannou, Aristotelis; Moulos, Panagiotis; Kolisis, Fragiskos N

    2009-10-27

    The microarray data analysis realm is ever growing through the development of various tools, open source and commercial. However there is absence of predefined rational algorithmic analysis workflows or batch standardized processing to incorporate all steps, from raw data import up to the derivation of significantly differentially expressed gene lists. This absence obfuscates the analytical procedure and obstructs the massive comparative processing of genomic microarray datasets. Moreover, the solutions provided, heavily depend on the programming skills of the user, whereas in the case of GUI embedded solutions, they do not provide direct support of various raw image analysis formats or a versatile and simultaneously flexible combination of signal processing methods. We describe here Gene ARMADA (Automated Robust MicroArray Data Analysis), a MATLAB implemented platform with a Graphical User Interface. This suite integrates all steps of microarray data analysis including automated data import, noise correction and filtering, normalization, statistical selection of differentially expressed genes, clustering, classification and annotation. In its current version, Gene ARMADA fully supports 2 coloured cDNA and Affymetrix oligonucleotide arrays, plus custom arrays for which experimental details are given in tabular form (Excel spreadsheet, comma separated values, tab-delimited text formats). It also supports the analysis of already processed results through its versatile import editor. Besides being fully automated, Gene ARMADA incorporates numerous functionalities of the Statistics and Bioinformatics Toolboxes of MATLAB. In addition, it provides numerous visualization and exploration tools plus customizable export data formats for seamless integration by other analysis tools or MATLAB, for further processing. Gene ARMADA requires MATLAB 7.4 (R2007a) or higher and is also distributed as a stand-alone application with MATLAB Component Runtime. Gene ARMADA provides a

  5. A toolbox for the fast information analysis of multiple-site LFP, EEG and spike train recordings

    Directory of Open Access Journals (Sweden)

    Logothetis Nikos K

    2009-07-01

    Full Text Available Abstract Background Information theory is an increasingly popular framework for studying how the brain encodes sensory information. Despite its widespread use for the analysis of spike trains of single neurons and of small neural populations, its application to the analysis of other types of neurophysiological signals (EEGs, LFPs, BOLD has remained relatively limited so far. This is due to the limited-sampling bias which affects calculation of information, to the complexity of the techniques to eliminate the bias, and to the lack of publicly available fast routines for the information analysis of multi-dimensional responses. Results Here we introduce a new C- and Matlab-based information theoretic toolbox, specifically developed for neuroscience data. This toolbox implements a novel computationally-optimized algorithm for estimating many of the main information theoretic quantities and bias correction techniques used in neuroscience applications. We illustrate and test the toolbox in several ways. First, we verify that these algorithms provide accurate and unbiased estimates of the information carried by analog brain signals (i.e. LFPs, EEGs, or BOLD even when using limited amounts of experimental data. This test is important since existing algorithms were so far tested primarily on spike trains. Second, we apply the toolbox to the analysis of EEGs recorded from a subject watching natural movies, and we characterize the electrodes locations, frequencies and signal features carrying the most visual information. Third, we explain how the toolbox can be used to break down the information carried by different features of the neural signal into distinct components reflecting different ways in which correlations between parts of the neural signal contribute to coding. We illustrate this breakdown by analyzing LFPs recorded from primary visual cortex during presentation of naturalistic movies. Conclusion The new toolbox presented here implements fast

  6. A toolbox for the fast information analysis of multiple-site LFP, EEG and spike train recordings.

    Science.gov (United States)

    Magri, Cesare; Whittingstall, Kevin; Singh, Vanessa; Logothetis, Nikos K; Panzeri, Stefano

    2009-07-16

    Information theory is an increasingly popular framework for studying how the brain encodes sensory information. Despite its widespread use for the analysis of spike trains of single neurons and of small neural populations, its application to the analysis of other types of neurophysiological signals (EEGs, LFPs, BOLD) has remained relatively limited so far. This is due to the limited-sampling bias which affects calculation of information, to the complexity of the techniques to eliminate the bias, and to the lack of publicly available fast routines for the information analysis of multi-dimensional responses. Here we introduce a new C- and Matlab-based information theoretic toolbox, specifically developed for neuroscience data. This toolbox implements a novel computationally-optimized algorithm for estimating many of the main information theoretic quantities and bias correction techniques used in neuroscience applications. We illustrate and test the toolbox in several ways. First, we verify that these algorithms provide accurate and unbiased estimates of the information carried by analog brain signals (i.e. LFPs, EEGs, or BOLD) even when using limited amounts of experimental data. This test is important since existing algorithms were so far tested primarily on spike trains. Second, we apply the toolbox to the analysis of EEGs recorded from a subject watching natural movies, and we characterize the electrodes locations, frequencies and signal features carrying the most visual information. Third, we explain how the toolbox can be used to break down the information carried by different features of the neural signal into distinct components reflecting different ways in which correlations between parts of the neural signal contribute to coding. We illustrate this breakdown by analyzing LFPs recorded from primary visual cortex during presentation of naturalistic movies. The new toolbox presented here implements fast and data-robust computations of the most relevant

  7. MATLAB for Engineering and the Life Sciences

    CERN Document Server

    Tranquillo, Joseph

    2011-01-01

    In recent years, the life sciences have embraced simulation as an important tool in biomedical research. Engineers are also using simulation as a powerful step in the design process. In both arenas, Matlab has become the gold standard. It is easy to learn, flexible, and has a large and growing userbase. MATLAB for Engineering and the Life Sciences is a self-guided tour of the basic functionality of MATLAB along with the functions that are most commonly used in biomedical engineering and other life sciences. Although the text is written for undergraduates, graduate students and academics, those

  8. TopoToolbox: using sensor topography to calculate psychologically meaningful measures from event-related EEG/MEG.

    Science.gov (United States)

    Tian, Xing; Poeppel, David; Huber, David E

    2011-01-01

    The open-source toolbox "TopoToolbox" is a suite of functions that use sensor topography to calculate psychologically meaningful measures (similarity, magnitude, and timing) from multisensor event-related EEG and MEG data. Using a GUI and data visualization, TopoToolbox can be used to calculate and test the topographic similarity between different conditions (Tian and Huber, 2008). This topographic similarity indicates whether different conditions involve a different distribution of underlying neural sources. Furthermore, this similarity calculation can be applied at different time points to discover when a response pattern emerges (Tian and Poeppel, 2010). Because the topographic patterns are obtained separately for each individual, these patterns are used to produce reliable measures of response magnitude that can be compared across individuals using conventional statistics (Davelaar et al. Submitted and Huber et al., 2008). TopoToolbox can be freely downloaded. It runs under MATLAB (The MathWorks, Inc.) and supports user-defined data structure as well as standard EEG/MEG data import using EEGLAB (Delorme and Makeig, 2004).

  9. SELANSI: a toolbox for simulation of stochastic gene regulatory networks.

    Science.gov (United States)

    Pájaro, Manuel; Otero-Muras, Irene; Vázquez, Carlos; Alonso, Antonio A

    2018-03-01

    Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort. This work presents SELANSI (SEmi-LAgrangian SImulation of GRNs), a software toolbox for the simulation of stochastic multidimensional gene regulatory networks. SELANSI exploits intrinsic structural properties of gene regulatory networks to accurately approximate the corresponding Chemical Master Equation with a partial integral differential equation that is solved by a semi-lagrangian method with high efficiency. Networks under consideration might involve multiple genes with self and cross regulations, in which genes can be regulated by different transcription factors. Moreover, the validity of the method is not restricted to a particular type of kinetics. The tool offers total flexibility regarding network topology, kinetics and parameterization, as well as simulation options. SELANSI runs under the MATLAB environment, and is available under GPLv3 license at https://sites.google.com/view/selansi. antonio@iim.csic.es. © The Author(s) 2017. Published by Oxford University Press.

  10. SU-E-J-253: The Radiomics Toolbox in the Computational Environment for Radiological Research (CERR)

    Energy Technology Data Exchange (ETDEWEB)

    Apte, A; Veeraraghavan, H; Oh, J; Kijewski, P; Deasy, J [Memorial Sloan Kettering Cancer Center, New York, NY (United States)

    2015-06-15

    Purpose: To present an open source and free platform to facilitate radiomics research — The “Radiomics toolbox” in CERR. Method: There is scarcity of open source tools that support end-to-end modeling of image features to predict patient outcomes. The “Radiomics toolbox” strives to fill the need for such a software platform. The platform supports (1) import of various kinds of image modalities like CT, PET, MR, SPECT, US. (2) Contouring tools to delineate structures of interest. (3) Extraction and storage of image based features like 1st order statistics, gray-scale co-occurrence and zonesize matrix based texture features and shape features and (4) Statistical Analysis. Statistical analysis of the extracted features is supported with basic functionality that includes univariate correlations, Kaplan-Meir curves and advanced functionality that includes feature reduction and multivariate modeling. The graphical user interface and the data management are performed with Matlab for the ease of development and readability of code and features for wide audience. Open-source software developed with other programming languages is integrated to enhance various components of this toolbox. For example: Java-based DCM4CHE for import of DICOM, R for statistical analysis. Results: The Radiomics toolbox will be distributed as an open source, GNU copyrighted software. The toolbox was prototyped for modeling Oropharyngeal PET dataset at MSKCC. The analysis will be presented in a separate paper. Conclusion: The Radiomics Toolbox provides an extensible platform for extracting and modeling image features. To emphasize new uses of CERR for radiomics and image-based research, we have changed the name from the “Computational Environment for Radiotherapy Research” to the “Computational Environment for Radiological Research”.

  11. Matlab/Simulink Implementation of Wave-based Models for Microstrip Structures utilizing Short-circuited and Opened Stubs

    Directory of Open Access Journals (Sweden)

    Biljana P. Stošić

    2011-12-01

    Full Text Available This paper describes modeling and analyzing procedures for microstrip filters based on use of one-dimensional wave digital approach. Different filter structures are observed. One filter is based on quarter-wave length short-circuited stubs and connecting transmission lines. The other one is based on cross-junction opened stubs. Frequency responses are obtained by direct analysis of the block-based networks formed in Simulink toolbox of MATLAB environment. This wave-based method allows an accurate and efficient analysis of different microwave structures.

  12. Implementation and Comparison of the Lifting 5/3 and 9/7 Algorithms in MatLab on GPU

    Directory of Open Access Journals (Sweden)

    Randa Khemiri

    2016-06-01

    Full Text Available In order to accelerate the Discrete Wavelet Transform DWT, we have implemented and compared the lifting "Le Gall5/3" and "Cohen-Daubechies-Feauveau9/7" (CDF9/7 algorithms on a low cost NVIDIA’s GPU. The suggested implementation is realized in MatLab using the in-house parallel computation toolbox (PCT. Our experimental results indicate, that the speedup is proportional to the image size until it attains a maximum at 20482 pixels, beyond these values the curve decreases. The performance with GPU enhances above a factor of 2~3 compared with CPU.

  13. One hundred physics visualizations using Matlab

    CERN Document Server

    Green, Dan

    2014-01-01

    This book provides visualizations of many topics in general physics. The aim is to have an interactive MATLAB script wherein the user can vary parameters in a specific problem and then immediately see the outcome by way of dynamic movies of the response of the system in question. MATLAB tools are used throughout and the software scripts accompany the text in Symbolic Mathematics, Classical Mechanics, Electromagnetism, Waves and Optics, Gases and Fluid Flow, Quantum Mechanics, Special and General Relativity, and Astrophysics and Cosmology. The emphasis is on building up an intuition by running many different parametric choices chosen actively by the user and watching the subsequent behavior of the system. Physics books using MATLAB do not have the range or the intent of this text. They are rather steeped in technical detail. Symbolic math is used extensively and is integral to the aim of using MATLAB tools to accomplish the technical aspects of problem solving.

  14. An introduction to differential equations using MATLAB

    CERN Document Server

    Butt, Rizwan

    2016-01-01

    An Introduction to Differential Equations using MATLAB exploits the symbolic, numerical, and graphical capabilitiesof MATLAB to develop a thorough understanding of differential equations algorithms. This book provides the readerwith numerous applications, m-files, and practical examples to problems. Balancing theoretical concepts withcomputational speed and accuracy, the book includes numerous short programs in MATLAB that can be used to solveproblems involving first-and higher-order differential equations, Laplace transforms, linear systems of differentialequations, numerical solutions of differential equations, computer graphics, and more. The author emphasizes thebasic ideas of analytical and numerical techniques and the uses of modern mathematical software (MATLAB) ratherthan relying only on complex mathematical derivations to engineers, mathematician, computer scientists, andphysicists or for use as a textbook in applied or computational courses.A CD-ROM with all the figures, codes, solutions, appendices...

  15. Learning Matlab a problem solving approach

    CERN Document Server

    Gander, Walter

    2015-01-01

    This comprehensive and stimulating introduction to Matlab, a computer language now widely used for technical computing, is based on an introductory course held at Qian Weichang College, Shanghai University, in the fall of 2014.  Teaching and learning a substantial programming language aren’t always straightforward tasks. Accordingly, this textbook is not meant to cover the whole range of this high-performance technical programming environment, but to motivate first- and second-year undergraduate students in mathematics and computer science to learn Matlab by studying representative problems, developing algorithms and programming them in Matlab. While several topics are taken from the field of scientific computing, the main emphasis is on programming. A wealth of examples are completely discussed and solved, allowing students to learn Matlab by doing: by solving problems, comparing approaches and assessing the proposed solutions.

  16. Linear algebra applications using Matlab software

    Directory of Open Access Journals (Sweden)

    Cornelia Victoria Anghel

    2005-10-01

    Full Text Available The paper presents two ways of special matrix generating using some functions included in the MatLab software package. The MatLab software package contains a set of functions that generate special matrixes used in the linear algebra applications and the signal processing from different activity fields. The paper presents two tipes of special matrixes that can be generated using written sintaxes in the dialog window of the MatLab software and for the command validity we need to press the Enter task. The applications presented in the paper represent eamples of numerical calculus using the MatLab software and belong to the scientific field „Computer Assisted Mathematics” thus creating the symbiosis between mathematics and informatics.

  17. MOCCASIN: converting MATLAB ODE models to SBML.

    Science.gov (United States)

    Gómez, Harold F; Hucka, Michael; Keating, Sarah M; Nudelman, German; Iber, Dagmar; Sealfon, Stuart C

    2016-06-15

    MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challenging-especially for legacy models not written with translation in mind. We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODE-based MATLAB models of biochemical reaction networks into the SBML format. MOCCASIN is available under the terms of the LGPL 2.1 license (http://www.gnu.org/licenses/lgpl-2.1.html). Source code, binaries and test cases can be freely obtained from https://github.com/sbmlteam/moccasin : mhucka@caltech.edu More information is available at https://github.com/sbmlteam/moccasin. © The Author 2016. Published by Oxford University Press.

  18. A Matlab program for stepwise regression

    Directory of Open Access Journals (Sweden)

    Yanhong Qi

    2016-03-01

    Full Text Available The stepwise linear regression is a multi-variable regression for identifying statistically significant variables in the linear regression equation. In present study, we presented the Matlab program of stepwise regression.

  19. Visual media processing using Matlab beginner's guide

    CERN Document Server

    Siogkas, George

    2013-01-01

    Written in a friendly, Beginner's Guide format, showing the user how to use the digital media aspects of Matlab (image, video, sound) in a practical, tutorial-based style.This is great for novice programmers in any language who would like to use Matlab as a tool for their image and video processing needs, and also comes in handy for photographers or video editors with even less programming experience wanting to find an all-in-one tool for their tasks.

  20. A conceptual toolbox for designing CSCW applications

    DEFF Research Database (Denmark)

    Bødker, Susanne; Christiansen, Ellen

    1995-01-01

    This paper presents a conceptual toolbox, developed to support the design of CSCW applications in a large Esprit project, EuroCODE. Here, several groups of designers work to investigate computer support for cooperative work in large use organizations, at the same time as they work to develop...... an open development platform for CSCW applications. The conceptual toolbox has been developed to support communication in and among these design groups, between designers and users and in future use of the open development platform. Rejecting the idea that one may design from a framework describing CSCW......, the toolbox aims to support design by doing and help bridging between work with users, technical design, and insights gained from theoretical and empirical CSCW research....

  1. MATLAB Software Versions and Licenses for the Peregrine System |

    Science.gov (United States)

    High-Performance Computing | NREL MATLAB Software Versions and Licenses for the Peregrine System MATLAB Software Versions and Licenses for the Peregrine System Learn about the MATLAB software Peregrine is R2017b. Licenses MATLAB is proprietary software. As such, users have access to a limited number

  2. Aerospace Toolbox---a flight vehicle design, analysis, simulation ,and software development environment: I. An introduction and tutorial

    Science.gov (United States)

    Christian, Paul M.; Wells, Randy

    2001-09-01

    This paper presents a demonstrated approach to significantly reduce the cost and schedule of non real-time modeling and simulation, real-time HWIL simulation, and embedded code development. The tool and the methodology presented capitalize on a paradigm that has become a standard operating procedure in the automotive industry. The tool described is known as the Aerospace Toolbox, and it is based on the MathWorks Matlab/Simulink framework, which is a COTS application. Extrapolation of automotive industry data and initial applications in the aerospace industry show that the use of the Aerospace Toolbox can make significant contributions in the quest by NASA and other government agencies to meet aggressive cost reduction goals in development programs. The part I of this paper provides a detailed description of the GUI based Aerospace Toolbox and how it is used in every step of a development program; from quick prototyping of concept developments that leverage built-in point of departure simulations through to detailed design, analysis, and testing. Some of the attributes addressed include its versatility in modeling 3 to 6 degrees of freedom, its library of flight test validated library of models (including physics, environments, hardware, and error sources), and its built-in Monte Carlo capability. Other topics to be covered in this part include flight vehicle models and algorithms, and the covariance analysis package, Navigation System Covariance Analysis Tools (NavSCAT). Part II of this paper, to be published at a later date, will conclude with a description of how the Aerospace Toolbox is an integral part of developing embedded code directly from the simulation models by using the Mathworks Real Time Workshop and optimization tools. It will also address how the Toolbox can be used as a design hub for Internet based collaborative engineering tools such as NASA's Intelligent Synthesis Environment (ISE) and Lockheed Martin's Interactive Missile Design Environment

  3. Matlab Geochemistry: An open source geochemistry solver based on MRST

    Science.gov (United States)

    McNeece, C. J.; Raynaud, X.; Nilsen, H.; Hesse, M. A.

    2017-12-01

    The study of geological systems often requires the solution of complex geochemical relations. To address this need we present an open source geochemical solver based on the Matlab Reservoir Simulation Toolbox (MRST) developed by SINTEF. The implementation supports non-isothermal multicomponent aqueous complexation, surface complexation, ion exchange, and dissolution/precipitation reactions. The suite of tools available in MRST allows for rapid model development, in particular the incorporation of geochemical calculations into transport simulations of multiple phases, complex domain geometry and geomechanics. Different numerical schemes and additional physics can be easily incorporated into the existing tools through the object-oriented framework employed by MRST. The solver leverages the automatic differentiation tools available in MRST to solve arbitrarily complex geochemical systems with any choice of species or element concentration as input. Four mathematical approaches enable the solver to be quite robust: 1) the choice of chemical elements as the basis components makes all entries in the composition matrix positive thus preserving convexity, 2) a log variable transformation is used which transfers the nonlinearity to the convex composition matrix, 3) a priori bounds on variables are calculated from the structure of the problem, constraining Netwon's path and 4) an initial guess is calculated implicitly by sequentially adding model complexity. As a benchmark we compare the model to experimental and semi-analytic solutions of the coupled salinity-acidity transport system. Together with the reservoir simulation capabilities of MRST the solver offers a promising tool for geochemical simulations in reservoir domains for applications in a diversity of fields from enhanced oil recovery to radionuclide storage.

  4. The RTMM Toolbox for DMM Applications

    DEFF Research Database (Denmark)

    Sharp, Robin; Todirica, Edward Alexandru

    2002-01-01

    This paper describes an approach to implementing distributed multimedia applications based on the use of a software toolbox. The tools in the box allow the designer to specify which components are to be used, how they are logically connected and what properties the streams of data to be passed...

  5. Intrabeam Scattering Studies for the ILC Damping Rings Using a NewMATLAB Code

    Energy Technology Data Exchange (ETDEWEB)

    Reichel, I.; Wolski, A.

    2006-06-21

    A new code to calculate the effects of intrabeam scattering (IBS) has been developed in MATLAB based on the approximation suggested by K. Bane. It interfaces with the Accelerator Toolbox but can also read in lattice functions from other codes. The code has been benchmarked against results from other codes for the ATF that use this approximation or do the calculation in a different way. The new code has been used to calculate the emittance growth due to intrabeam scattering for the lattices currently proposed for the ILC Damping Rings, as IBS is a concern, especially for the electron ring. A description of the code and its user interface, as well as results for the Damping Rings, will be presented.

  6. Intrabeam Scattering Studies for the ILC Damping Rings Using a New MATLAB Code

    International Nuclear Information System (INIS)

    Reichel, I.; Wolski, A.

    2006-01-01

    A new code to calculate the effects of intrabeam scattering (IBS) has been developed in MATLAB based on the approximation suggested by K. Bane. It interfaces with the Accelerator Toolbox but can also read in lattice functions from other codes. The code has been benchmarked against results from other codes for the ATF that use this approximation or do the calculation in a different way. The new code has been used to calculate the emittance growth due to intrabeam scattering for the lattices currently proposed for the ILC Damping Rings, as IBS is a concern, especially for the electron ring. A description of the code and its user interface, as well as results for the Damping Rings, will be presented

  7. Tolkku - a toolbox for decision support from condition monitoring data

    International Nuclear Information System (INIS)

    Saarela, Olli; Lehtonen, Mikko; Halme, Jari; Aikala, Antti; Raivio, Kimmo

    2012-01-01

    This paper describes a software toolbox (a software library) designed for condition monitoring and diagnosis of machines. This toolbox implements both new methods and prior art and is aimed for practical down-to-earth data analysis work. The target is to improve knowledge of the operation and behaviour of machines and processes throughout their entire life-cycles. The toolbox supports different phases of condition based maintenance with tools that extract essential information and automate data processing. The paper discusses principles that have guided toolbox design and the implemented toolbox structure. Case examples are used to illustrate how condition monitoring applications can be built using the toolbox. In the first case study the toolbox is applied to fault detection of industrial centrifuges based on measured electrical current. The second case study outlines an application for centralized monitoring of a fleet of machines that supports organizational learning.

  8. Switch of Sensitivity Dynamics Revealed with DyGloSA Toolbox for Dynamical Global Sensitivity Analysis as an Early Warning for System's Critical Transition

    Science.gov (United States)

    Baumuratova, Tatiana; Dobre, Simona; Bastogne, Thierry; Sauter, Thomas

    2013-01-01

    Systems with bifurcations may experience abrupt irreversible and often unwanted shifts in their performance, called critical transitions. For many systems like climate, economy, ecosystems it is highly desirable to identify indicators serving as early warnings of such regime shifts. Several statistical measures were recently proposed as early warnings of critical transitions including increased variance, autocorrelation and skewness of experimental or model-generated data. The lack of automatized tool for model-based prediction of critical transitions led to designing DyGloSA – a MATLAB toolbox for dynamical global parameter sensitivity analysis (GPSA) of ordinary differential equations models. We suggest that the switch in dynamics of parameter sensitivities revealed by our toolbox is an early warning that a system is approaching a critical transition. We illustrate the efficiency of our toolbox by analyzing several models with bifurcations and predicting the time periods when systems can still avoid going to a critical transition by manipulating certain parameter values, which is not detectable with the existing SA techniques. DyGloSA is based on the SBToolbox2 and contains functions, which compute dynamically the global sensitivity indices of the system by applying four main GPSA methods: eFAST, Sobol's ANOVA, PRCC and WALS. It includes parallelized versions of the functions enabling significant reduction of the computational time (up to 12 times). DyGloSA is freely available as a set of MATLAB scripts at http://bio.uni.lu/systems_biology/software/dyglosa. It requires installation of MATLAB (versions R2008b or later) and the Systems Biology Toolbox2 available at www.sbtoolbox2.org. DyGloSA can be run on Windows and Linux systems, -32 and -64 bits. PMID:24367574

  9. Switch of sensitivity dynamics revealed with DyGloSA toolbox for dynamical global sensitivity analysis as an early warning for system's critical transition.

    Science.gov (United States)

    Baumuratova, Tatiana; Dobre, Simona; Bastogne, Thierry; Sauter, Thomas

    2013-01-01

    Systems with bifurcations may experience abrupt irreversible and often unwanted shifts in their performance, called critical transitions. For many systems like climate, economy, ecosystems it is highly desirable to identify indicators serving as early warnings of such regime shifts. Several statistical measures were recently proposed as early warnings of critical transitions including increased variance, autocorrelation and skewness of experimental or model-generated data. The lack of automatized tool for model-based prediction of critical transitions led to designing DyGloSA - a MATLAB toolbox for dynamical global parameter sensitivity analysis (GPSA) of ordinary differential equations models. We suggest that the switch in dynamics of parameter sensitivities revealed by our toolbox is an early warning that a system is approaching a critical transition. We illustrate the efficiency of our toolbox by analyzing several models with bifurcations and predicting the time periods when systems can still avoid going to a critical transition by manipulating certain parameter values, which is not detectable with the existing SA techniques. DyGloSA is based on the SBToolbox2 and contains functions, which compute dynamically the global sensitivity indices of the system by applying four main GPSA methods: eFAST, Sobol's ANOVA, PRCC and WALS. It includes parallelized versions of the functions enabling significant reduction of the computational time (up to 12 times). DyGloSA is freely available as a set of MATLAB scripts at http://bio.uni.lu/systems_biology/software/dyglosa. It requires installation of MATLAB (versions R2008b or later) and the Systems Biology Toolbox2 available at www.sbtoolbox2.org. DyGloSA can be run on Windows and Linux systems, -32 and -64 bits.

  10. Eddy current loss analysis of open-slot fault-tolerant permanent-magnet machines based on conformal mapping method

    Science.gov (United States)

    Ji, Jinghua; Luo, Jianhua; Lei, Qian; Bian, Fangfang

    2017-05-01

    This paper proposed an analytical method, based on conformal mapping (CM) method, for the accurate evaluation of magnetic field and eddy current (EC) loss in fault-tolerant permanent-magnet (FTPM) machines. The aim of modulation function, applied in CM method, is to change the open-slot structure into fully closed-slot structure, whose air-gap flux density is easy to calculate analytically. Therefore, with the help of Matlab Schwarz-Christoffel (SC) Toolbox, both the magnetic flux density and EC density of FTPM machine are obtained accurately. Finally, time-stepped transient finite-element method (FEM) is used to verify the theoretical analysis, showing that the proposed method is able to predict the magnetic flux density and EC loss precisely.

  11. LIMO EEG: a toolbox for hierarchical LInear MOdeling of ElectroEncephaloGraphic data.

    Science.gov (United States)

    Pernet, Cyril R; Chauveau, Nicolas; Gaspar, Carl; Rousselet, Guillaume A

    2011-01-01

    Magnetic- and electric-evoked brain responses have traditionally been analyzed by comparing the peaks or mean amplitudes of signals from selected channels and averaged across trials. More recently, tools have been developed to investigate single trial response variability (e.g., EEGLAB) and to test differences between averaged evoked responses over the entire scalp and time dimensions (e.g., SPM, Fieldtrip). LIMO EEG is a Matlab toolbox (EEGLAB compatible) to analyse evoked responses over all space and time dimensions, while accounting for single trial variability using a simple hierarchical linear modelling of the data. In addition, LIMO EEG provides robust parametric tests, therefore providing a new and complementary tool in the analysis of neural evoked responses.

  12. The Basic Radar Altimetry Toolbox for Sentinel 3 Users

    Science.gov (United States)

    Lucas, Bruno; Rosmorduc, Vinca; Niemeijer, Sander; Bronner, Emilie; Dinardo, Salvatore; Benveniste, Jérôme

    2013-04-01

    The Basic Radar Altimetry Toolbox (BRAT) is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2006 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales). The latest version of the software, 3.1, was released on March 2012. The tools enable users to interact with the most common altimetry data formats, being the most used way, the Graphical User Interface (BratGui). This GUI is a front-end for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with Matlab/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the data-formatting hassle. The BratDisplay (graphic visualizer) can be launched from BratGui, or used as a stand-alone tool to visualize netCDF files - it is distributed with another ESA toolbox (GUT) as the visualizer. The most frequent uses of BRAT are teaching remote sensing, altimetry data reading (all missions from ERS-1 to Saral and soon Sentinel-3), quick data visualization/export and simple computation on the data fields. BRAT can be used for importing data and having a quick look at his contents, with several different types of plotting available. One can also use it to translate the data into other formats such as netCDF, ASCII text files, KML (Google Earth) and raster images (JPEG, PNG, etc.). Several kinds of computations can be done within BratGui involving combinations of data fields that the user can save for posterior reuse or using the already embedded formulas that include the standard oceanographic altimetry formulas (MSS, -SSH, MSLA, editing of spurious data, etc.). The documentation collection includes the standard user manual explaining all the ways to interact with the set of software tools but the most important item is the Radar Altimeter Tutorial, that contains a strong introduction to

  13. Radar signal analysis and processing using Matlab

    CERN Document Server

    Mahafza, Bassem R

    2008-01-01

    Offering radar-related software for the analysis and design of radar waveform and signal processing, this book provides comprehensive coverage of radar signals and signal processing techniques and algorithms. It contains numerous graphical plots, common radar-related functions, table format outputs, and end-of-chapter problems. The complete set of MATLAB[registered] functions and routines are available for download online.

  14. How to Interface Fortran with Matlab

    OpenAIRE

    Sagastizábal , Claudia; Vige , Guillaume

    1995-01-01

    Projet PROMATH; We describe the general procedure for interfacing Fortran routines with Matlab. We explain how to write a mex-file and the associated gateway function. In particular, each different type of argument is considered in detail. We finish with an illustrative example

  15. Accelerating MATLAB with GPU computing a primer with examples

    CERN Document Server

    Suh, Jung W

    2013-01-01

    Beyond simulation and algorithm development, many developers increasingly use MATLAB even for product deployment in computationally heavy fields. This often demands that MATLAB codes run faster by leveraging the distributed parallelism of Graphics Processing Units (GPUs). While MATLAB successfully provides high-level functions as a simulation tool for rapid prototyping, the underlying details and knowledge needed for utilizing GPUs make MATLAB users hesitate to step into it. Accelerating MATLAB with GPUs offers a primer on bridging this gap. Starting with the basics, setting up MATLAB for

  16. Improve Data Mining and Knowledge Discovery through the use of MatLab

    Science.gov (United States)

    Shaykahian, Gholan Ali; Martin, Dawn Elliott; Beil, Robert

    2011-01-01

    Data mining is widely used to mine business, engineering, and scientific data. Data mining uses pattern based queries, searches, or other analyses of one or more electronic databases/datasets in order to discover or locate a predictive pattern or anomaly indicative of system failure, criminal or terrorist activity, etc. There are various algorithms, techniques and methods used to mine data; including neural networks, genetic algorithms, decision trees, nearest neighbor method, rule induction association analysis, slice and dice, segmentation, and clustering. These algorithms, techniques and methods used to detect patterns in a dataset, have been used in the development of numerous open source and commercially available products and technology for data mining. Data mining is best realized when latent information in a large quantity of data stored is discovered. No one technique solves all data mining problems; challenges are to select algorithms or methods appropriate to strengthen data/text mining and trending within given datasets. In recent years, throughout industry, academia and government agencies, thousands of data systems have been designed and tailored to serve specific engineering and business needs. Many of these systems use databases with relational algebra and structured query language to categorize and retrieve data. In these systems, data analyses are limited and require prior explicit knowledge of metadata and database relations; lacking exploratory data mining and discoveries of latent information. This presentation introduces MatLab(TradeMark)(MATrix LABoratory), an engineering and scientific data analyses tool to perform data mining. MatLab was originally intended to perform purely numerical calculations (a glorified calculator). Now, in addition to having hundreds of mathematical functions, it is a programming language with hundreds built in standard functions and numerous available toolboxes. MatLab's ease of data processing, visualization and

  17. HERMES: towards an integrated toolbox to characterize functional and effective brain connectivity.

    Science.gov (United States)

    Niso, Guiomar; Bruña, Ricardo; Pereda, Ernesto; Gutiérrez, Ricardo; Bajo, Ricardo; Maestú, Fernando; del-Pozo, Francisco

    2013-10-01

    The analysis of the interdependence between time series has become an important field of research in the last years, mainly as a result of advances in the characterization of dynamical systems from the signals they produce, the introduction of concepts such as generalized and phase synchronization and the application of information theory to time series analysis. In neurophysiology, different analytical tools stemming from these concepts have added to the 'traditional' set of linear methods, which includes the cross-correlation and the coherency function in the time and frequency domain, respectively, or more elaborated tools such as Granger Causality.This increase in the number of approaches to tackle the existence of functional (FC) or effective connectivity (EC) between two (or among many) neural networks, along with the mathematical complexity of the corresponding time series analysis tools, makes it desirable to arrange them into a unified-easy-to-use software package. The goal is to allow neuroscientists, neurophysiologists and researchers from related fields to easily access and make use of these analysis methods from a single integrated toolbox.Here we present HERMES ( http://hermes.ctb.upm.es ), a toolbox for the Matlab® environment (The Mathworks, Inc), which is designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. We believe that this toolbox will be very helpful to all the researchers working in the emerging field of brain connectivity analysis.

  18. FACET - a "Flexible Artifact Correction and Evaluation Toolbox" for concurrently recorded EEG/fMRI data.

    Science.gov (United States)

    Glaser, Johann; Beisteiner, Roland; Bauer, Herbert; Fischmeister, Florian Ph S

    2013-11-09

    In concurrent EEG/fMRI recordings, EEG data are impaired by the fMRI gradient artifacts which exceed the EEG signal by several orders of magnitude. While several algorithms exist to correct the EEG data, these algorithms lack the flexibility to either leave out or add new steps. The here presented open-source MATLAB toolbox FACET is a modular toolbox for the fast and flexible correction and evaluation of imaging artifacts from concurrently recorded EEG datasets. It consists of an Analysis, a Correction and an Evaluation framework allowing the user to choose from different artifact correction methods with various pre- and post-processing steps to form flexible combinations. The quality of the chosen correction approach can then be evaluated and compared to different settings. FACET was evaluated on a dataset provided with the FMRIB plugin for EEGLAB using two different correction approaches: Averaged Artifact Subtraction (AAS, Allen et al., NeuroImage 12(2):230-239, 2000) and the FMRI Artifact Slice Template Removal (FASTR, Niazy et al., NeuroImage 28(3):720-737, 2005). Evaluation of the obtained results were compared to the FASTR algorithm implemented in the EEGLAB plugin FMRIB. No differences were found between the FACET implementation of FASTR and the original algorithm across all gradient artifact relevant performance indices. The FACET toolbox not only provides facilities for all three modalities: data analysis, artifact correction as well as evaluation and documentation of the results but it also offers an easily extendable framework for development and evaluation of new approaches.

  19. Cantera Integration with the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)

    Science.gov (United States)

    Lavelle, Thomas M.; Chapman, Jeffryes W.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

    2014-01-01

    NASA Glenn Research Center (GRC) has recently developed a software package for modeling generic thermodynamic systems called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS). T-MATS is a library of building blocks that can be assembled to represent any thermodynamic system in the Simulink (The MathWorks, Inc.) environment. These elements, along with a Newton Raphson solver (also provided as part of the T-MATS package), enable users to create models of a wide variety of systems. The current version of T-MATS (v1.0.1) uses tabular data for providing information about a specific mixture of air, water (humidity), and hydrocarbon fuel in calculations of thermodynamic properties. The capabilities of T-MATS can be expanded by integrating it with the Cantera thermodynamic package. Cantera is an object-oriented analysis package that calculates thermodynamic solutions for any mixture defined by the user. Integration of Cantera with T-MATS extends the range of systems that may be modeled using the toolbox. In addition, the library of elements released with Cantera were developed using MATLAB native M-files, allowing for quicker prototyping of elements. This paper discusses how the new Cantera-based elements are created and provides examples for using T-MATS integrated with Cantera.

  20. The laboratory test utilization management toolbox.

    Science.gov (United States)

    Baird, Geoffrey

    2014-01-01

    Efficiently managing laboratory test utilization requires both ensuring adequate utilization of needed tests in some patients and discouraging superfluous tests in other patients. After the difficult clinical decision is made to define the patients that do and do not need a test, a wealth of interventions are available to the clinician and laboratorian to help guide appropriate utilization. These interventions are collectively referred to here as the utilization management toolbox. Experience has shown that some tools in the toolbox are weak and other are strong, and that tools are most effective when many are used simultaneously. While the outcomes of utilization management studies are not always as concrete as may be desired, what data is available in the literature indicate that strong utilization management interventions are safe and effective measures to improve patient health and reduce waste in an era of increasing financial pressure.

  1. ESA's Multi-mission Sentinel-1 Toolbox

    Science.gov (United States)

    Veci, Luis; Lu, Jun; Foumelis, Michael; Engdahl, Marcus

    2017-04-01

    The Sentinel-1 Toolbox is a new open source software for scientific learning, research and exploitation of the large archives of Sentinel and heritage missions. The Toolbox is based on the proven BEAM/NEST architecture inheriting all current NEST functionality including multi-mission support for most civilian satellite SAR missions. The project is funded through ESA's Scientific Exploitation of Operational Missions (SEOM). The Sentinel-1 Toolbox will strive to serve the SEOM mandate by providing leading-edge software to the science and application users in support of ESA's operational SAR mission as well as by educating and growing a SAR user community. The Toolbox consists of a collection of processing tools, data product readers and writers and a display and analysis application. A common architecture for all Sentinel Toolboxes is being jointly developed by Brockmann Consult, Array Systems Computing and C-S called the Sentinel Application Platform (SNAP). The SNAP architecture is ideal for Earth Observation processing and analysis due the following technological innovations: Extensibility, Portability, Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory Management, and a Graph Processing Framework. The project has developed new tools for working with Sentinel-1 data in particular for working with the new Interferometric TOPSAR mode. TOPSAR Complex Coregistration and a complete Interferometric processing chain has been implemented for Sentinel-1 TOPSAR data. To accomplish this, a coregistration following the Spectral Diversity[4] method has been developed as well as special azimuth handling in the coherence, interferogram and spectral filter operators. The Toolbox includes reading of L0, L1 and L2 products in SAFE format, calibration and de-noising, slice product assembling, TOPSAR deburst and sub-swath merging, terrain flattening radiometric normalization, and visualization for L2 OCN products. The Toolbox also provides several new tools for

  2. Segmentation Toolbox for Tomographic Image Data

    DEFF Research Database (Denmark)

    Einarsdottir, Hildur

    , techniques to automatically analyze such data becomes ever more important. Most segmentation methods for large datasets, such as CT images, deal with simple thresholding techniques, where intensity values cut offs are predetermined and hard coded. For data where the intensity difference is not sufficient......Motivation: Image acquisition has vastly improved over the past years, introducing techniques such as X-ray computed tomography (CT). CT images provide the means to probe a sample non-invasively to investigate its inner structure. Given the wide usage of this technique and massive data amounts......, and partial volume voxels occur frequently, thresholding methods do not suffice and more advanced methods are required. Contribution: To meet these requirements a toolbox has been developed, combining well known methods within the image analysis field. The toolbox includes cluster-based methods...

  3. First Steps into Practical Engineering for Freshman Students Using MATLAB and LEGO Mindstorms Robots

    Directory of Open Access Journals (Sweden)

    A. Behrens

    2008-01-01

    Full Text Available Besides lectures on basic theoretical topics, contemporary teaching and learning concepts for first semester students give more and more consideration to practically motivated courses. In this context, a new first-year introductory course in practical engineering has been established in the first semester curriculum of Electrical Engineering at RWTH Aachen University, Germany. Based on a threefold learning concept, programming skills in MATLAB are taught to 309 students within a full-time block course laboratory. The students are encouraged to transfer known mathematical basics to program algorithms and real-world applications performed by 100 LEGO Mindstorms robots. A new MATLAB toolbox and twofold project tasks have been developed for this purpose by a small team of supervisors. The students are supervised by over 60 tutors at 23 institutes, and are encouraged to create their own robotics applications. We describe how the laboratory motivates the students to act and think like engineers and to solve real-world issues with limited resources. The evaluation results show that the proposed practical course concept successfully boosts students’ motivation, advances their programming skills, and encourages the peer learning process. 

  4. TMS modeling toolbox for realistic simulation.

    Science.gov (United States)

    Cho, Young Sun; Suh, Hyun Sang; Lee, Won Hee; Kim, Tae-Seong

    2010-01-01

    Transcranial magnetic stimulation (TMS) is a technique for brain stimulation using rapidly changing magnetic fields generated by coils. It has been established as an effective stimulation technique to treat patients suffering from damaged brain functions. Although TMS is known to be painless and noninvasive, it can also be harmful to the brain by incorrect focusing and excessive stimulation which might result in seizure. Therefore there is ongoing research effort to elucidate and better understand the effect and mechanism of TMS. Lately Boundary element method (BEM) and Finite element method (FEM) have been used to simulate the electromagnetic phenomenon of TMS. However, there is a lack of general tools to generate the models of TMS due to some difficulties in realistic modeling of the human head and TMS coils. In this study, we have developed a toolbox through which one can generate high-resolution FE TMS models. The toolbox allows creating FE models of the head with isotropic and anisotropic electrical conductivities in five different tissues of the head and the coils in 3D. The generated TMS model is importable to FE software packages such as ANSYS for further and efficient electromagnetic analysis. We present a set of demonstrative results of realistic simulation of TMS with our toolbox.

  5. Insights into the European Years’ Communication Toolboxes

    Directory of Open Access Journals (Sweden)

    Camelia-Mihaela Cmeciu

    2012-08-01

    Full Text Available Since 1983 the European syntagm “unity in diversity” has been implemented in the European Years’ communication campaigns. Dependent on subsidiarity and decentralization, European Years focus on a specific issue which constitutes the subject of a year-long awareness campaign. Beyond the involvement of Europe’s citizens through their local, regional and national authorities in the implementation of the European Years’ policies, there is a unity at the level of the visual communication of the EU by two important image-building elements: EY logos and communication toolboxes. The European Years’ communication toolboxes can be considered signs of inclusion since every organization is expected to customize the templates in the official campaign design of the European Year. The analysis will focus on the image-building elements of three European Years (2010, 2011, 2012. Having social semiotics as the qualitative research method and the analytical framework based on the distinction between design resources and representational resources, I will analyze the double layers of the high intensity point of inclusion: (1 the European Years’ branding process; (2 the visual deontic modality within the visual guidelines of the EY communication toolbox.

  6. The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services.

    Science.gov (United States)

    Castaño-Díez, Daniel

    2017-06-01

    Dynamo is a package for the processing of tomographic data. As a tool for subtomogram averaging, it includes different alignment and classification strategies. Furthermore, its data-management module allows experiments to be organized in groups of tomograms, while offering specialized three-dimensional tomographic browsers that facilitate visualization, location of regions of interest, modelling and particle extraction in complex geometries. Here, a technical description of the package is presented, focusing on its diverse strategies for optimizing computing performance. Dynamo is built upon mbtools (middle layer toolbox), a general-purpose MATLAB library for object-oriented scientific programming specifically developed to underpin Dynamo but usable as an independent tool. Its structure intertwines a flexible MATLAB codebase with precompiled C++ functions that carry the burden of numerically intensive operations. The package can be delivered as a precompiled standalone ready for execution without a MATLAB license. Multicore parallelization on a single node is directly inherited from the high-level parallelization engine provided for MATLAB, automatically imparting a balanced workload among the threads in computationally intense tasks such as alignment and classification, but also in logistic-oriented tasks such as tomogram binning and particle extraction. Dynamo supports the use of graphical processing units (GPUs), yielding considerable speedup factors both for native Dynamo procedures (such as the numerically intensive subtomogram alignment) and procedures defined by the user through its MATLAB-based GPU library for three-dimensional operations. Cloud-based virtual computing environments supplied with a pre-installed version of Dynamo can be publicly accessed through the Amazon Elastic Compute Cloud (EC2), enabling users to rent GPU computing time on a pay-as-you-go basis, thus avoiding upfront investments in hardware and longterm software maintenance.

  7. Object Oriented Toolbox for Modelling and Simulation of Dynamical Systems

    DEFF Research Database (Denmark)

    Poulsen, Mikael Zebbelin; Wagner, Falko Jens; Thomsen, Per Grove

    1998-01-01

    This paper presents the results of an ongoing project, dealing with design and implementation of a simulation toolbox based on object oriented modelling techniques. The paper describes an experimental implementation of parts of such a toolbox in C++, and discusses the experiences drawn from that ...... that process. Essential to the work is the focus on simulation of complex dynamical systems, from modelling the single components/subsystems to building complete systemssuch a toolbox in C++, and discusses the experiences drawn from that process....

  8. Application of MATLAB in testing digital power supply controllers

    International Nuclear Information System (INIS)

    Ke Xinhua; Chinese Academy of Sciences, Beijing; Lu Songlin; Shen Tianjian

    2008-01-01

    Based on introducing MATLAB SISOTOOL in MATLAB control box and the magnet power supply system in detail, this paper presented the application of MATLAB SISOTOOL in Testing Digital Power Supply controllers. This control tool should be popularized because of its characteristics of convenience and easy-to-use. (authors)

  9. MATLAB tensor classes for fast algorithm prototyping.

    Energy Technology Data Exchange (ETDEWEB)

    Bader, Brett William; Kolda, Tamara Gibson (Sandia National Laboratories, Livermore, CA)

    2004-10-01

    Tensors (also known as mutidimensional arrays or N-way arrays) are used in a variety of applications ranging from chemometrics to psychometrics. We describe four MATLAB classes for tensor manipulations that can be used for fast algorithm prototyping. The tensor class extends the functionality of MATLAB's multidimensional arrays by supporting additional operations such as tensor multiplication. The tensor as matrix class supports the 'matricization' of a tensor, i.e., the conversion of a tensor to a matrix (and vice versa), a commonly used operation in many algorithms. Two additional classes represent tensors stored in decomposed formats: cp tensor and tucker tensor. We descibe all of these classes and then demonstrate their use by showing how to implement several tensor algorithms that have appeared in the literature.

  10. Intelligent traffic lights based on MATLAB

    Science.gov (United States)

    Nie, Ying

    2018-04-01

    In this paper, I describes the traffic lights system and it has some. Through analysis, I used MATLAB technology, transformed the camera photographs into digital signals. Than divided the road vehicle is into three methods: very congestion, congestion, a little congestion. Through the MCU programming, solved the different roads have different delay time, and Used this method, saving time and resources, so as to reduce road congestion.

  11. Nuclear Fuel Depletion Analysis Using Matlab Software

    Science.gov (United States)

    Faghihi, F.; Nematollahi, M. R.

    Coupled first order IVPs are frequently used in many parts of engineering and sciences. In this article, we presented a code including three computer programs which are joint with the Matlab software to solve and plot the solutions of the first order coupled stiff or non-stiff IVPs. Some engineering and scientific problems related to IVPs are given and fuel depletion (production of the 239Pu isotope) in a Pressurized Water Nuclear Reactor (PWR) are computed by the present code.

  12. Directional quantile regression in Octave (and MATLAB)

    Czech Academy of Sciences Publication Activity Database

    Boček, Pavel; Šiman, Miroslav

    2016-01-01

    Roč. 52, č. 1 (2016), s. 28-51 ISSN 0023-5954 R&D Projects: GA ČR GA14-07234S Institutional support: RVO:67985556 Keywords : quantile regression * multivariate quantile * depth contour * Matlab Subject RIV: IN - Informatics, Computer Science Impact factor: 0.379, year: 2016 http://library.utia.cas.cz/separaty/2016/SI/bocek-0458380.pdf

  13. Implementation of Digital Watermarking Using MATLAB Software

    OpenAIRE

    Karnpriya Vyas; Kirti Sethiya; Sonu Jain

    2012-01-01

    Digital watermarking holds significant promise as one of the keys to protecting proprietary digital content in the coming years. It focuses on embedding information inside a digital object such that the embedded information is in separable bound to the object. The proposed scheme has been implemented on MATLAB, as it is a high level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation. We w...

  14. Matlab as a robust control design tool

    Science.gov (United States)

    Gregory, Irene M.

    1994-01-01

    This presentation introduces Matlab as a tool used in flight control research. The example used to illustrate some of the capabilities of this software is a robust controller designed for a single stage to orbit air breathing vehicles's ascent to orbit. The global requirements of the controller are to stabilize the vehicle and follow a trajectory in the presence of atmospheric disturbances and strong dynamic coupling between airframe and propulsion.

  15. Generation of synthetic gamma spectra with MATLAB

    International Nuclear Information System (INIS)

    Palmerio, Julian J.; Coppo, Anibal D.

    2009-01-01

    Objectives: The aim of this work is the simulation of gamma spectra using the MATLAB program to generate the calibration curves in efficiency, which will be used to measure radioactive waste in drums. They are necessary for the proper characterization of these drums. A Monte Carlo simulation was basically developed with the random number generator Mersenne Twister and nuclear data obtained from NIST. This paper shows the results obtained and difficulties encountered until today. The physical correction of the simulated spectra has been the only aspect we have been working, up to this moment. Procedures: A simplified representation of the 'Laboratorio de Verificacion y Control de la Calidad' was chosen. Drums with cemented liquid waste are routinely measured in this laboratory. The commercial program MCNP was also used to get a valid reference in the field of simulation of spectra. We analyzed the spectra obtained by MATLAB in the light of classical literature photon detection and the spectrum obtained by MCNP. Conclusions: Currently the program developed seems adequate to simulate a measurement in the 'Laboratorio de Verificacion y Control de la Calidad'. The spectra obtained by MATLAB seem to physically represent what is observed in real spectra. However, it is a slow program. The current development efforts are directed to improve the speed of simulation. An alternative is to use the CUDA language for NVIDIA video cards to parallelized the simulation. An adequate simulation of the electronic measuring chain is also needed to obtain better representations of the shapes of the peaks. (author)

  16. Transportation channels calculation method in MATLAB

    International Nuclear Information System (INIS)

    Averyanov, G.P.; Budkin, V.A.; Dmitrieva, V.V.; Osadchuk, I.O.; Bashmakov, Yu.A.

    2014-01-01

    Output devices and charged particles transport channels are necessary components of any modern particle accelerator. They differ both in sizes and in terms of focusing elements depending on particle accelerator type and its destination. A package of transport line designing codes for magnet optical channels in MATLAB environment is presented in this report. Charged particles dynamics in a focusing channel can be studied easily by means of the matrix technique. MATLAB usage is convenient because its information objects are matrixes. MATLAB allows the use the modular principle to build the software package. Program blocks are small in size and easy to use. They can be executed separately or commonly. A set of codes has a user-friendly interface. Transport channel construction consists of focusing lenses (doublets and triplets). The main of the magneto-optical channel parameters are total length and lens position and parameters of the output beam in the phase space (channel acceptance, beam emittance - beam transverse dimensions, particles divergence and image stigmaticity). Choice of the channel operation parameters is based on the conditions for satisfying mutually competing demands. And therefore the channel parameters calculation is carried out by using the search engine optimization techniques.

  17. Advanced Dynamics Analytical and Numerical Calculations with MATLAB

    CERN Document Server

    Marghitu, Dan B

    2012-01-01

    Advanced Dynamics: Analytical and Numerical Calculations with MATLAB provides a thorough, rigorous presentation of kinematics and dynamics while using MATLAB as an integrated tool to solve problems. Topics presented are explained thoroughly and directly, allowing fundamental principles to emerge through applications from areas such as multibody systems, robotics, spacecraft and design of complex mechanical devices. This book differs from others in that it uses symbolic MATLAB for both theory and applications. Special attention is given to solutions that are solved analytically and numerically using MATLAB. The illustrations and figures generated with MATLAB reinforce visual learning while an abundance of examples offer additional support. This book also: Provides solutions analytically and numerically using MATLAB Illustrations and graphs generated with MATLAB reinforce visual learning for students as they study Covers modern technical advancements in areas like multibody systems, robotics, spacecraft and des...

  18. Testing adaptive toolbox models: a Bayesian hierarchical approach.

    Science.gov (United States)

    Scheibehenne, Benjamin; Rieskamp, Jörg; Wagenmakers, Eric-Jan

    2013-01-01

    Many theories of human cognition postulate that people are equipped with a repertoire of strategies to solve the tasks they face. This theoretical framework of a cognitive toolbox provides a plausible account of intra- and interindividual differences in human behavior. Unfortunately, it is often unclear how to rigorously test the toolbox framework. How can a toolbox model be quantitatively specified? How can the number of toolbox strategies be limited to prevent uncontrolled strategy sprawl? How can a toolbox model be formally tested against alternative theories? The authors show how these challenges can be met by using Bayesian inference techniques. By means of parameter recovery simulations and the analysis of empirical data across a variety of domains (i.e., judgment and decision making, children's cognitive development, function learning, and perceptual categorization), the authors illustrate how Bayesian inference techniques allow toolbox models to be quantitatively specified, strategy sprawl to be contained, and toolbox models to be rigorously tested against competing theories. The authors demonstrate that their approach applies at the individual level but can also be generalized to the group level with hierarchical Bayesian procedures. The suggested Bayesian inference techniques represent a theoretical and methodological advancement for toolbox theories of cognition and behavior.

  19. Concept Mapping: An "Instagram" of Students' Thinking

    Science.gov (United States)

    Campbell, Laurie O.

    2016-01-01

    Minimal research has been accumulated in the field of social studies education for Novakian concept mapping, yet there are many benefits from adding this learning tool to a teacher's instructional toolbox. The article defines Novakian concept mapping and invites readers to adopt digital Novakian concept mapping into the social studies classroom as…

  20. MODIS phenology image service ArcMap toolbox

    Science.gov (United States)

    Talbert, Colin; Kern, Tim J.; Morisette, Jeff; Brown, Don; James, Kevin

    2013-01-01

    Seasonal change is important to consider when managing conservation areas at landscape scales. The study of such patterns throughout the year is referred to as phenology. Recurring life-cycle events that are initiated and driven by environmental factors include animal migration and plant flowering. Phenological events capture public attention, such as fall color change in deciduous forests, the first flowering in spring, and for those with allergies, the start of the pollen season. These events can affect our daily lives, provide clues to help understand and manage ecosystems, and provide evidence of how climate variability can affect the natural cycle of plants and animals. Phenological observations can be gathered at a range of scales, from plots smaller than an acre to landscapes of hundreds to thousands of acres. Linking these observations to diverse disciplines such as evolutionary biology or climate sciences can help further research in species and ecosystem responses to climate change scenarios at appropriate scales. A cooperative study between the National Park Service (NPS), the U.S. Geological Survey (USGS), and the National Aeronautics and Space Administration (NASA) has been exploring how satellite information can be used to summarize phenological patterns observed at the park or landscape scale and how those summaries can be presented to both park managers and visitors. This study specifically addressed seasonal changes in plants, including the onset of growth, photosynthesis in the spring, and the senescence of deciduous vegetation in the fall. The primary objective of the work is to demonstrate that seasonality even in protected areas changes considerably across years. A major challenge is to decouple natural variability from possible trends—directional change that can lead to a permanent and radically different ecosystem state. Trends can be either a gradual degradation of the landscape (often from external influences) or steady improvement (by implementing long-term conservation plans). In either case, it is important to first grasp the magnitude of natural variation so that it is not confused with actual trends. This work used existing and freely available remote sensing data, specifically the NASA-funded 250-meter (m) spatial resolution land-surface phenology product for North America. This product is calculated from an annual record of vegetation health observed by NASA’s Moderate Resolution Imaging Spectroradiometer (MODIS) instrument. The land-surface phenology product is, in essence, a method to summarize all the observations throughout a year into a few key, ecologically relevant “metrics”.

  1. Rad Toolbox User's Guide

    Energy Technology Data Exchange (ETDEWEB)

    Eckerman, Keith F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sjoreen, Andrea L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2013-05-01

    The Radiological Toolbox software developed by Oak Ridge National Laboratory (ORNL) for U. S. Nuclear Regulatory Commission (NRC) is designed to provide electronic access to the vast and varied data that underlies the field of radiation protection. These data represent physical, chemical, anatomical, physiological, and mathematical parameters detailed in various handbooks which a health physicist might consult while in his office. The initial motivation for the software was to serve the needs of the health physicist away from his office and without access to his handbooks; e.g., NRC inspectors. The earlier releases of the software were widely used and accepted around the world by not only practicing health physicist but also those within educational programs. This release updates the software to accommodate changes in Windows operating systems and, in some aspects, radiation protection. This release has been tested on Windows 7 and 8 and on 32- and 64-bit machines. The nuclear decay data has been updated and thermal neutron capture cross sections and cancer risk coefficients have been included. This document and the software’s user’s guide provide further details and documentation of the information captured within the Radiological Toolbox.

  2. MTpy: A Python toolbox for magnetotellurics

    Science.gov (United States)

    Krieger, Lars; Peacock, Jared R.

    2014-11-01

    We present the software package MTpy that allows handling, processing, and imaging of magnetotelluric (MT) data sets. Written in Python, the code is open source, containing sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides the independent definition of classes and functions, MTpy provides wrappers and convenience scripts to call standard external data processing and modelling software. In its current state, modules and functions of MTpy work on raw and pre-processed MT data. However, opposite to providing a static compilation of software, we prefer to introduce MTpy as a flexible software toolbox, whose contents can be combined and utilised according to the respective needs of the user. Just as the overall functionality of a mechanical toolbox can be extended by adding new tools, MTpy is a flexible framework, which will be dynamically extended in the future. Furthermore, it can help to unify and extend existing codes and algorithms within the (academic) MT community. In this paper, we introduce the structure and concept of MTpy. Additionally, we show some examples from an everyday work-flow of MT data processing: the generation of standard EDI data files from raw electric (E-) and magnetic flux density (B-) field time series as input, the conversion into MiniSEED data format, as well as the generation of a graphical data representation in the form of a Phase Tensor pseudosection.

  3. Distributed Aerodynamic Sensing and Processing Toolbox

    Science.gov (United States)

    Brenner, Martin; Jutte, Christine; Mangalam, Arun

    2011-01-01

    A Distributed Aerodynamic Sensing and Processing (DASP) toolbox was designed and fabricated for flight test applications with an Aerostructures Test Wing (ATW) mounted under the fuselage of an F-15B on the Flight Test Fixture (FTF). DASP monitors and processes the aerodynamics with the structural dynamics using nonintrusive, surface-mounted, hot-film sensing. This aerodynamic measurement tool benefits programs devoted to static/dynamic load alleviation, body freedom flutter suppression, buffet control, improvement of aerodynamic efficiency through cruise control, supersonic wave drag reduction through shock control, etc. This DASP toolbox measures local and global unsteady aerodynamic load distribution with distributed sensing. It determines correlation between aerodynamic observables (aero forces) and structural dynamics, and allows control authority increase through aeroelastic shaping and active flow control. It offers improvements in flutter suppression and, in particular, body freedom flutter suppression, as well as aerodynamic performance of wings for increased range/endurance of manned/ unmanned flight vehicles. Other improvements include inlet performance with closed-loop active flow control, and development and validation of advanced analytical and computational tools for unsteady aerodynamics.

  4. Signals and systems primer with Matlab

    CERN Document Server

    Poularikas, Alexander D

    2006-01-01

    Signals and Systems Primer with MATLAB® equally emphasizes the fundamentals of both analog and digital signals and systems. To ensure insight into the basic concepts and methods, the text presents a variety of examples that illustrate a wide range of applications, from microelectromechanical to worldwide communication systems. It also provides MATLAB functions and procedures for practice and verification of these concepts.Taking a pedagogical approach, the author builds a solid foundation in signal processing as well as analog and digital systems. The book first introduces orthogonal signals,

  5. Computational partial differential equations using Matlab

    CERN Document Server

    Li, Jichun

    2008-01-01

    Brief Overview of Partial Differential Equations The parabolic equations The wave equations The elliptic equations Differential equations in broader areasA quick review of numerical methods for PDEsFinite Difference Methods for Parabolic Equations Introduction Theoretical issues: stability, consistence, and convergence 1-D parabolic equations2-D and 3-D parabolic equationsNumerical examples with MATLAB codesFinite Difference Methods for Hyperbolic Equations IntroductionSome basic difference schemes Dissipation and dispersion errors Extensions to conservation lawsThe second-order hyperbolic PDE

  6. Digital signal processing with Matlab examples

    CERN Document Server

    Giron-Sierra, Jose Maria

    2017-01-01

    This is the first volume in a trilogy on modern Signal Processing. The three books provide a concise exposition of signal processing topics, and a guide to support individual practical exploration based on MATLAB programs. This book includes MATLAB codes to illustrate each of the main steps of the theory, offering a self-contained guide suitable for independent study. The code is embedded in the text, helping readers to put into practice the ideas and methods discussed. The book is divided into three parts, the first of which introduces readers to periodic and non-periodic signals. The second part is devoted to filtering, which is an important and commonly used application. The third part addresses more advanced topics, including the analysis of real-world non-stationary signals and data, e.g. structural fatigue, earthquakes, electro-encephalograms, birdsong, etc. The book’s last chapter focuses on modulation, an example of the intentional use of non-stationary signals.

  7. A DOE Computer Code Toolbox: Issues and Opportunities

    International Nuclear Information System (INIS)

    Vincent, A.M. III

    2001-01-01

    The initial activities of a Department of Energy (DOE) Safety Analysis Software Group to establish a Safety Analysis Toolbox of computer models are discussed. The toolbox shall be a DOE Complex repository of verified and validated computer models that are configuration-controlled and made available for specific accident analysis applications. The toolbox concept was recommended by the Defense Nuclear Facilities Safety Board staff as a mechanism to partially address Software Quality Assurance issues. Toolbox candidate codes have been identified through review of a DOE Survey of Software practices and processes, and through consideration of earlier findings of the Accident Phenomenology and Consequence Evaluation program sponsored by the DOE National Nuclear Security Agency/Office of Defense Programs. Planning is described to collect these high-use codes, apply tailored SQA specific to the individual codes, and implement the software toolbox concept. While issues exist such as resource allocation and the interface among code developers, code users, and toolbox maintainers, significant benefits can be achieved through a centralized toolbox and subsequent standardized applications

  8. A guide to MATLAB for beginners and experienced users

    CERN Document Server

    Hunt, Brian R; Rosenberg, Jonathan M

    2014-01-01

    Now in its third edition, this outstanding textbook explains everything you need to get started using MATLAB®. It contains concise explanations of essential MATLAB commands, as well as easily understood instructions for using MATLAB's programming features, graphical capabilities, simulation models, and rich desktop interface. MATLAB 8 and its new user interface is treated extensively in the book. New features in this edition include: a complete treatment of MATLAB's publish feature; new material on MATLAB graphics, enabling the user to master quickly the various symbolic and numerical plotting routines; and a robust presentation of MuPAD® and how to use it as a stand-alone platform. The authors have also updated the text throughout, reworking examples and exploring new applications. The book is essential reading for beginners, occasional users and experienced users wishing to brush up their skills. Further resources are available from the authors' website at www-math.umd.edu/schol/a-guide-to-matlab.html.

  9. CoSMoMVPA: multi-modal multivariate pattern analysis of neuroimaging datain Matlab / GNU Octave

    Directory of Open Access Journals (Sweden)

    Nikolaas N Oosterhof

    2016-07-01

    Full Text Available Recent years have seen an increase in the popularity of multivariate pattern (MVP analysis of functional magnetic resonance (fMRI data, and, to a much lesser extent, magneto- and electro-encephalography (M/EEG data. We present CoSMoMVPA, a lightweight MVPA (MVP analysis toolbox implemented in the intersection of the Matlab and GNU Octave languages, that treats both fMRI and M/EEG data as first-class citizens.CoSMoMVPA supports all state-of-the-art MVP analysis techniques, including searchlight analyses, classification, correlations, representational similarity analysis, and the time generalization method. These can be used to address both data-driven and hypothesis-driven questions about neural organization and representations, both within and across: space, time, frequency bands, neuroimaging modalities, individuals, and species.It uses a uniform data representation of fMRI data in the volume or on the surface, and of M/EEG data at the sensor and source level. Through various external toolboxes, it directly supports reading and writing a variety of fMRI and M/EEG neuroimaging formats, and, where applicable, can convert between them. As a result, it can be integrated readily in existing pipelines and used with existing preprocessed datasets. CoSMoMVPA overloads the traditional volumetric searchlight concept to support neighborhoods for M/EEG and surface-based fMRI data, which supports localization of multivariate effects of interest across space, time, and frequency dimensions. CoSMoMVPA also provides a generalized approach to multiple comparison correction across these dimensions using Threshold-Free Cluster Enhancement with state-of-the-art clustering and permutation techniques.CoSMoMVPA is highly modular and uses abstractions to provide a uniform interface for a variety of MVP measures. Typical analyses require a few lines of code, making it accessible to beginner users. At the same time, expert programmers can easily extend its functionality

  10. TMSEEG: A MATLAB-Based Graphical User Interface for Processing Electrophysiological Signals during Transcranial Magnetic Stimulation

    Directory of Open Access Journals (Sweden)

    Sravya Atluri

    2016-10-01

    Full Text Available Concurrent recording of electroencephalography (EEG during transcranial magnetic stimulation (TMS is an emerging and powerful tool for studying brain health and function. Despite a growing interest in adaptation of TMS-EEG across neuroscience disciplines, its wide-spread utility is limited by signal processing challenges. These challenges arise due to the nature of TMS and the sensitivity of EEG to artifacts that often mask TMS-evoked potentials (TEPs. With an increase in the complexity of data processing methods and a growing interest in multi-site data integration, analysis of TMS-EEG data requires the development of a standardized method to recover TEPs from various sources of artifacts. This paper introduces TMSEEG, an open-source MATLAB application comprised of multiple algorithms organized to facilitate a step-by-step procedure for TMS-EEG signal processing. Using a modular design and interactive GUIs, this toolbox aims to streamline TMS-EEG signal processing for both novice and experienced users. Specifically, TMSEEG provides (i targeted removal of TMS-induced and general EEG artifacts, (ii a step-by-step modular workflow with flexibility to modify existing algorithms and add customized algorithms, (iii a comprehensive display and quantification of artifacts, (iv quality control check points with visual feedback of TEPs throughout the data processing workflow, and (v capability to label and store a database of artifacts. In addition to these features, the software architecture of TMSEEG ensures minimal user effort in initial setup and configuration of parameters for each processing step. This is partly accomplished through a close integration with EEGLAB, a widely used open-source toolbox for EEG signal processing. In this paper we introduce TMSEEG, validate its features, and demonstrate its application in extracting TEPs across several single- and multi-pulse TMS protocols. As the first open-source GUI-based pipeline for TMS-EEG signal

  11. TMSEEG: A MATLAB-Based Graphical User Interface for Processing Electrophysiological Signals during Transcranial Magnetic Stimulation

    Science.gov (United States)

    Atluri, Sravya; Frehlich, Matthew; Mei, Ye; Garcia Dominguez, Luis; Rogasch, Nigel C.; Wong, Willy; Daskalakis, Zafiris J.; Farzan, Faranak

    2016-01-01

    Concurrent recording of electroencephalography (EEG) during transcranial magnetic stimulation (TMS) is an emerging and powerful tool for studying brain health and function. Despite a growing interest in adaptation of TMS-EEG across neuroscience disciplines, its widespread utility is limited by signal processing challenges. These challenges arise due to the nature of TMS and the sensitivity of EEG to artifacts that often mask TMS-evoked potentials (TEP)s. With an increase in the complexity of data processing methods and a growing interest in multi-site data integration, analysis of TMS-EEG data requires the development of a standardized method to recover TEPs from various sources of artifacts. This article introduces TMSEEG, an open-source MATLAB application comprised of multiple algorithms organized to facilitate a step-by-step procedure for TMS-EEG signal processing. Using a modular design and interactive graphical user interface (GUI), this toolbox aims to streamline TMS-EEG signal processing for both novice and experienced users. Specifically, TMSEEG provides: (i) targeted removal of TMS-induced and general EEG artifacts; (ii) a step-by-step modular workflow with flexibility to modify existing algorithms and add customized algorithms; (iii) a comprehensive display and quantification of artifacts; (iv) quality control check points with visual feedback of TEPs throughout the data processing workflow; and (v) capability to label and store a database of artifacts. In addition to these features, the software architecture of TMSEEG ensures minimal user effort in initial setup and configuration of parameters for each processing step. This is partly accomplished through a close integration with EEGLAB, a widely used open-source toolbox for EEG signal processing. In this article, we introduce TMSEEG, validate its features and demonstrate its application in extracting TEPs across several single- and multi-pulse TMS protocols. As the first open-source GUI-based pipeline

  12. TMSEEG: A MATLAB-Based Graphical User Interface for Processing Electrophysiological Signals during Transcranial Magnetic Stimulation.

    Science.gov (United States)

    Atluri, Sravya; Frehlich, Matthew; Mei, Ye; Garcia Dominguez, Luis; Rogasch, Nigel C; Wong, Willy; Daskalakis, Zafiris J; Farzan, Faranak

    2016-01-01

    Concurrent recording of electroencephalography (EEG) during transcranial magnetic stimulation (TMS) is an emerging and powerful tool for studying brain health and function. Despite a growing interest in adaptation of TMS-EEG across neuroscience disciplines, its widespread utility is limited by signal processing challenges. These challenges arise due to the nature of TMS and the sensitivity of EEG to artifacts that often mask TMS-evoked potentials (TEP)s. With an increase in the complexity of data processing methods and a growing interest in multi-site data integration, analysis of TMS-EEG data requires the development of a standardized method to recover TEPs from various sources of artifacts. This article introduces TMSEEG, an open-source MATLAB application comprised of multiple algorithms organized to facilitate a step-by-step procedure for TMS-EEG signal processing. Using a modular design and interactive graphical user interface (GUI), this toolbox aims to streamline TMS-EEG signal processing for both novice and experienced users. Specifically, TMSEEG provides: (i) targeted removal of TMS-induced and general EEG artifacts; (ii) a step-by-step modular workflow with flexibility to modify existing algorithms and add customized algorithms; (iii) a comprehensive display and quantification of artifacts; (iv) quality control check points with visual feedback of TEPs throughout the data processing workflow; and (v) capability to label and store a database of artifacts. In addition to these features, the software architecture of TMSEEG ensures minimal user effort in initial setup and configuration of parameters for each processing step. This is partly accomplished through a close integration with EEGLAB, a widely used open-source toolbox for EEG signal processing. In this article, we introduce TMSEEG, validate its features and demonstrate its application in extracting TEPs across several single- and multi-pulse TMS protocols. As the first open-source GUI-based pipeline

  13. High resolution orientation mapping of secondary phases in ATI 718Plus® alloy

    Directory of Open Access Journals (Sweden)

    Krakow Robert

    2014-01-01

    Full Text Available The polycrystalline superalloy ATI 718Plus ® (hereafter 718Plus has been developed to replace the established alloy Inconel 718 by offering higher temperature capability for applications in gas turbines. The alloy exhibits two secondary phases in the austenitic matrix; it is strengthened by the γ′-phase with η-phase discontinuously precipitated at the grain boundaries. It can be utilized to control grain growth during forging. Generally, hexagonal η phase has been reported to possess a defined crystallographic orientation with the matrix. However, the material studied here exhibits blocky η-phase that has been precipitated and grown during thermo-mechanical processing. Therefore a measurable change in orientation relationship is expected. The standard technique for orientation mapping is electron back-scattered diffraction with spatial resolution of 100 nm. That is insufficient for studying η-phase in 718Plus. By applying high resolution orientation mapping in the transmission electron microscope (Philips CM 300 FEGTEM equipped with a Nanomegas ASTARTM system a resolution of 3 nm was achieved. The indexed diffraction data was analysed using the Matlab Toolbox Mtex. The analysis included grain reconstruction and exclusion of low confidence measurements. The data set allows generating phase boundary maps indicating interfaces characteristics. Quantitative assessment shows that only 19% of the γ-η-interfaces fulfil the orientation relationship.

  14. Presentation of the International Building Physics Toolbox for Simulink

    DEFF Research Database (Denmark)

    Weitzmann, Peter; Sasic Kalagasidis, Angela; Nielsen, Toke Rammer

    2003-01-01

    The international building physics toolbox (IBPT) is a software library specially constructed for HAM system analysis in building physics. The toolbox is constructed as a modular structure of the standard building elements using the graphical programming language Simulink. Two research groups have...... participated in this project. In order to enable the development of the toolbox, a common modelling platform was defined: a set of unique communication signals, material database and documentation protocol. The IBPT is open source and publicly available on the Internet. Any researcher and student can use...

  15. Digital image processing an algorithmic approach with Matlab

    CERN Document Server

    Qidwai, Uvais

    2009-01-01

    Introduction to Image Processing and the MATLAB EnvironmentIntroduction Digital Image Definitions: Theoretical Account Image Properties MATLAB Algorithmic Account MATLAB CodeImage Acquisition, Types, and File I/OImage Acquisition Image Types and File I/O Basics of Color Images Other Color Spaces Algorithmic Account MATLAB CodeImage ArithmeticIntroduction Operator Basics Theoretical TreatmentAlgorithmic Treatment Coding ExamplesAffine and Logical Operations, Distortions, and Noise in ImagesIntroduction Affine Operations Logical Operators Noise in Images Distortions in ImagesAlgorithmic Account

  16. Expanding the UniFrac Toolbox.

    Directory of Open Access Journals (Sweden)

    Ruth G Wong

    Full Text Available The UniFrac distance metric is often used to separate groups in microbiome analysis, but requires a constant sequencing depth to work properly. Here we demonstrate that unweighted UniFrac is highly sensitive to rarefaction instance and to sequencing depth in uniform data sets with no clear structure or separation between groups. We show that this arises because of subcompositional effects. We introduce information UniFrac and ratio UniFrac, two new weightings that are not as sensitive to rarefaction and allow greater separation of outliers than classic unweighted and weighted UniFrac. With this expansion of the UniFrac toolbox, we hope to empower researchers to extract more varied information from their data.

  17. An Emulator Toolbox to Approximate Radiative Transfer Models with Statistical Learning

    Directory of Open Access Journals (Sweden)

    Juan Pablo Rivera

    2015-07-01

    Full Text Available Physically-based radiative transfer models (RTMs help in understanding the processes occurring on the Earth’s surface and their interactions with vegetation and atmosphere. When it comes to studying vegetation properties, RTMs allows us to study light interception by plant canopies and are used in the retrieval of biophysical variables through model inversion. However, advanced RTMs can take a long computational time, which makes them unfeasible in many real applications. To overcome this problem, it has been proposed to substitute RTMs through so-called emulators. Emulators are statistical models that approximate the functioning of RTMs. Emulators are advantageous in real practice because of the computational efficiency and excellent accuracy and flexibility for extrapolation. We hereby present an “Emulator toolbox” that enables analysing multi-output machine learning regression algorithms (MO-MLRAs on their ability to approximate an RTM. The toolbox is included in the free-access ARTMO’s MATLAB suite for parameter retrieval and model inversion and currently contains both linear and non-linear MO-MLRAs, namely partial least squares regression (PLSR, kernel ridge regression (KRR and neural networks (NN. These MO-MLRAs have been evaluated on their precision and speed to approximate the soil vegetation atmosphere transfer model SCOPE (Soil Canopy Observation, Photochemistry and Energy balance. SCOPE generates, amongst others, sun-induced chlorophyll fluorescence as the output signal. KRR and NN were evaluated as capable of reconstructing fluorescence spectra with great precision. Relative errors fell below 0.5% when trained with 500 or more samples using cross-validation and principal component analysis to alleviate the underdetermination problem. Moreover, NN reconstructed fluorescence spectra about 50-times faster and KRR about 800-times faster than SCOPE. The Emulator toolbox is foreseen to open new opportunities in the use of advanced

  18. FocusStack and StimServer: a new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data.

    Science.gov (United States)

    Muir, Dylan R; Kampa, Björn M

    2014-01-01

    Two-photon calcium imaging of neuronal responses is an increasingly accessible technology for probing population responses in cortex at single cell resolution, and with reasonable and improving temporal resolution. However, analysis of two-photon data is usually performed using ad-hoc solutions. To date, no publicly available software exists for straightforward analysis of stimulus-triggered two-photon imaging experiments. In addition, the increasing data rates of two-photon acquisition systems imply increasing cost of computing hardware required for in-memory analysis. Here we present a Matlab toolbox, FocusStack, for simple and efficient analysis of two-photon calcium imaging stacks on consumer-level hardware, with minimal memory footprint. We also present a Matlab toolbox, StimServer, for generation and sequencing of visual stimuli, designed to be triggered over a network link from a two-photon acquisition system. FocusStack is compatible out of the box with several existing two-photon acquisition systems, and is simple to adapt to arbitrary binary file formats. Analysis tools such as stack alignment for movement correction, automated cell detection and peri-stimulus time histograms are already provided, and further tools can be easily incorporated. Both packages are available as publicly-accessible source-code repositories.

  19. Colour based sorting station with Matlab simulation

    Directory of Open Access Journals (Sweden)

    Constantin Victor

    2017-01-01

    Full Text Available The paper presents the design process and manufacturing elements of a colour-based sorting station. The system is comprised of a gravitational storage, which also contains the colour sensor. Parts are extracted using a linear pneumatic motor and are fed onto an electrically driven conveyor belt. Extraction of the parts is done at 4 points, using two pneumatic motors and a geared DC motor, while the 4th position is at the end of the belt. The mechanical parts of the system are manufactured using 3D printer technology, allowing for easy modification and adaption to the geometry of different parts. The paper shows all of the stages needed to design, optimize, test and implement the proposed solution. System optimization was performed using a graphical Matlab interface which also allows for sorting algorithm optimization.

  20. Scientific computing with MATLAB and Octave

    CERN Document Server

    Quarteroni, Alfio; Gervasio, Paola

    2014-01-01

    This textbook is an introduction to Scientific Computing, in which several numerical methods for the computer-based solution of certain classes of mathematical problems are illustrated. The authors show how to compute the zeros, the extrema, and the integrals of continuous functions, solve linear systems, approximate functions using polynomials and construct accurate approximations for the solution of ordinary and partial differential equations. To make the format concrete and appealing, the programming environments Matlab and Octave are adopted as faithful companions. The book contains the solutions to several problems posed in exercises and examples, often originating from important applications. At the end of each chapter, a specific section is devoted to subjects which were not addressed in the book and contains bibliographical references for a more comprehensive treatment of the material. From the review: ".... This carefully written textbook, the third English edition, contains substantial new developme...

  1. Coded Modulation in C and MATLAB

    Science.gov (United States)

    Hamkins, Jon; Andrews, Kenneth S.

    2011-01-01

    This software, written separately in C and MATLAB as stand-alone packages with equivalent functionality, implements encoders and decoders for a set of nine error-correcting codes and modulators and demodulators for five modulation types. The software can be used as a single program to simulate the performance of such coded modulation. The error-correcting codes implemented are the nine accumulate repeat-4 jagged accumulate (AR4JA) low-density parity-check (LDPC) codes, which have been approved for international standardization by the Consultative Committee for Space Data Systems, and which are scheduled to fly on a series of NASA missions in the Constellation Program. The software implements the encoder and decoder functions, and contains compressed versions of generator and parity-check matrices used in these operations.

  2. Improving student comprehension of the interconnectivity of the hydrologic cycle with a novel 'hydrology toolbox', integrated watershed model, and companion textbook

    Science.gov (United States)

    Huning, L. S.; Margulis, S. A.

    2013-12-01

    Concepts in introductory hydrology courses are often taught in the context of process-based modeling that ultimately is integrated into a watershed model. In an effort to reduce the learning curve associated with applying hydrologic concepts to real-world applications, we developed and incorporated a 'hydrology toolbox' that complements a new, companion textbook into introductory undergraduate hydrology courses. The hydrology toolbox contains the basic building blocks (functions coded in MATLAB) for an integrated spatially-distributed watershed model that makes hydrologic topics (e.g. precipitation, snow, radiation, evaporation, unsaturated flow, infiltration, groundwater, and runoff) more user-friendly and accessible for students. The toolbox functions can be used in a modular format so that students can study individual hydrologic processes and become familiar with the hydrology toolbox. This approach allows such courses to emphasize understanding and application of hydrologic concepts rather than computer coding or programming. While topics in introductory hydrology courses are often introduced and taught independently or semi-independently, they are inherently interconnected. These toolbox functions are therefore linked together at the end of the course to reinforce a holistic understanding of how these hydrologic processes are measured, interconnected, and modeled. They are integrated into a spatially-distributed watershed model or numerical laboratory where students can explore a range of topics such as rainfall-runoff modeling, urbanization, deforestation, watershed response to changes in parameters or forcings, etc. Model output can readily be visualized and analyzed by students to understand watershed response in a real river basin or a simple 'toy' basin. These tools complement the textbook, each of which has been well received by students in multiple hydrology courses with various disciplinary backgrounds. The same governing equations that students have

  3. ARC Code TI: X-Plane Communications Toolbox (XPC)

    Data.gov (United States)

    National Aeronautics and Space Administration — The X-Plane Communications Toolbox (XPC) is an open source research tool used to interact with the commercial flight simulator software X-Plane. XPC allows users to...

  4. iamxt: Max-tree toolbox for image processing and analysis

    Directory of Open Access Journals (Sweden)

    Roberto Souza

    2017-01-01

    Full Text Available The iamxt is an array-based max-tree toolbox implemented in Python using the NumPy library for array processing. It has state of the art methods for building and processing the max-tree, and a large set of visualization tools that allow to view the tree and the contents of its nodes. The array-based programming style and max-tree representation used in the toolbox make it simple to use. The intended audience of this toolbox includes mathematical morphology students and researchers that want to develop research in the field and image processing researchers that need a toolbox simple to use and easy to integrate in their applications.

  5. Managing Fieldwork Data with Toolbox and the Natural Language Toolkit

    Directory of Open Access Journals (Sweden)

    Stuart Robinson

    2007-06-01

    Full Text Available This paper shows how fieldwork data can be managed using the program Toolbox together with the Natural Language Toolkit (NLTK for the Python programming language. It provides background information about Toolbox and describes how it can be downloaded and installed. The basic functionality of the program for lexicons and texts is described, and its strengths and weaknesses are reviewed. Its underlying data format is briefly discussed, and Toolbox processing capabilities of NLTK are introduced, showing ways in which it can be used to extend the functionality of Toolbox. This is illustrated with a few simple scripts that demonstrate basic data management tasks relevant to language documentation, such as printing out the contents of a lexicon as HTML.

  6. Basic Radar Altimetry Toolbox: Tools and Tutorial to Use Cryosat Data

    Science.gov (United States)

    Benveniste, J.; Bronner, E.; Dinardo, S.; Lucas, B. M.; Rosmorduc, V.; Earith, D.; Niemeijer, S.

    2011-12-01

    Radar altimetry is very much a technique expanding its applications. Even If quite a lot of effort has been invested for oceanography users, the use of Altimetry data for cryosphere application, especially with the new ESA CryoSat-2 mission data is still somehow tedious for new Altimetry data products users. ESA and CNES therfore developed the Basic Radar Altimetry Toolbox a few years ago, and are improving and upgrading it to fit new missions and the growing number of altimetry uses. The Basic Radar Altimetry Toolbox is an "all-altimeter" collection of tools, tutorials and documents designed to facilitate the use of radar altimetry data. The software is able: - to read most distributed radar altimetry data, from ERS-1 & 2, Topex/Poseidon, Geosat Follow-on, Jason-1, Envisat, Jason- 2, CryoSat, the future Saral missions and is ready for adaptation to Sentinel-3 products - to perform some processing, data editing and statistic, - and to visualize the results. It can be used at several levels/several ways: - as a data reading tool, with APIs for C, Fortran, Matlab and IDL - as processing/extraction routines, through the on-line command mode - as an educational and a quick-look tool, with the graphical user interface As part of the Toolbox, a Radar Altimetry Tutorial gives general information about altimetry, the technique involved and its applications, as well as an overview of past, present and future missions, including information on how to access data and additional software and documentation. It also presents a series of data use cases, covering all uses of altimetry over ocean, cryosphere and land, showing the basic methods for some of the most frequent manners of using altimetry data. It is an opportunity to teach remote sensing with practical training. It has been available since April 2007, and had been demonstrated during training courses and scientific meetings. About 2000 people downloaded it (Summer 2011), with many "newcomers" to altimetry among them

  7. Basic Radar Altimetry Toolbox: Tools and Tutorial To Use Radar Altimetry For Cryosphere

    Science.gov (United States)

    Benveniste, J. J.; Bronner, E.; Dinardo, S.; Lucas, B. M.; Rosmorduc, V.; Earith, D.

    2010-12-01

    Radar altimetry is very much a technique expanding its applications. If quite a lot of efforts have been made for oceanography users (including easy-to-use data), the use of those data for cryosphere application, especially with the new ESA CryoSat-2 mission data is still somehow tedious, especially for new Altimetry data products users. ESA and CNES thus had the Basic Radar Altimetry Toolbox developed a few years ago, and are improving and upgrading it to fit new missions and the growing number of altimetry uses. The Basic Radar Altimetry Toolbox is an "all-altimeter" collection of tools, tutorials and documents designed to facilitate the use of radar altimetry data. The software is able: - to read most distributed radar altimetry data, from ERS-1 & 2, Topex/Poseidon, Geosat Follow-on, Jason-1, Envisat, Jason- 2, CryoSat and the future Saral missions, - to perform some processing, data editing and statistic, - and to visualize the results. It can be used at several levels/several ways: - as a data reading tool, with APIs for C, Fortran, Matlab and IDL - as processing/extraction routines, through the on-line command mode - as an educational and a quick-look tool, with the graphical user interface As part of the Toolbox, a Radar Altimetry Tutorial gives general information about altimetry, the technique involved and its applications, as well as an overview of past, present and future missions, including information on how to access data and additional software and documentation. It also presents a series of data use cases, covering all uses of altimetry over ocean, cryosphere and land, showing the basic methods for some of the most frequent manners of using altimetry data. It is an opportunity to teach remote sensing with practical training. It has been available from April 2007, and had been demonstrated during training courses and scientific meetings. About 1200 people downloaded it (Summer 2010), with many "newcomers" to altimetry among them, including teachers

  8. The BRAT and GUT Couple: Broadview Radar Altimetry and GOCE User Toolboxes

    Science.gov (United States)

    Benveniste, J.; Restano, M.; Ambrózio, A.

    2017-12-01

    The Broadview Radar Altimetry Toolbox (BRAT) is a collection of tools designed to facilitate the processing of radar altimetry data from previous and current altimetry missions, including Sentinel-3A L1 and L2 products. A tutorial is included providing plenty of use cases. BRAT's next release (4.2.0) is planned for October 2017. Based on the community feedback, the front-end has been further improved and simplified whereas the capability to use BRAT in conjunction with MATLAB/IDL or C/C++/Python/Fortran, allowing users to obtain desired data bypassing the data-formatting hassle, remains unchanged. Several kinds of computations can be done within BRAT involving the combination of data fields, that can be saved for future uses, either by using embedded formulas including those from oceanographic altimetry, or by implementing ad-hoc Python modules created by users to meet their needs. BRAT can also be used to quickly visualise data, or to translate data into other formats, e.g. from NetCDF to raster images. The GOCE User Toolbox (GUT) is a compilation of tools for the use and the analysis of GOCE gravity field models. It facilitates using, viewing and post-processing GOCE L2 data and allows gravity field data, in conjunction and consistently with any other auxiliary data set, to be pre-processed by beginners in gravity field processing, for oceanographic and hydrologic as well as for solid earth applications at both regional and global scales. Hence, GUT facilitates the extensive use of data acquired during GRACE and GOCE missions. In the current 3.1 version, GUT has been outfitted with a graphical user interface allowing users to visually program data processing workflows. Further enhancements aiming at facilitating the use of gradients, the anisotropic diffusive filtering, and the computation of Bouguer and isostatic gravity anomalies have been introduced. Packaged with GUT is also GUT's Variance-Covariance Matrix tool (VCM). BRAT and GUT toolboxes can be freely

  9. Sentinel-3 SAR Altimetry Toolbox - Scientific Exploitation of Operational Missions (SEOM) Program Element

    Science.gov (United States)

    Benveniste, Jérôme; Lucas, Bruno; Dinardo, Salvatore

    2014-05-01

    The prime objective of the SEOM (Scientific Exploitation of Operational Missions) element is to federate, support and expand the large international research community that the ERS, ENVISAT and the Envelope programmes have build up over the last 20 years for the future European operational Earth Observation missions, the Sentinels. Sentinel-3 builds directly on a proven heritage pioneered by ERS-1, ERS-2, Envisat and CryoSat-2, with a dual-frequency (Ku and C band) advanced Synthetic Aperture Radar Altimeter (SRAL) that provides measurements at a resolution of ~300m in SAR mode along track. Sentinel-3 will provide exact measurements of sea-surface height along with accurate topography measurements over sea ice, ice sheets, rivers and lakes. The first of the Sentinel-3 series is planned for launch in early 2015. The current universal altimetry toolbox is BRAT (Basic Radar Altimetry Toolbox) which can read all previous and current altimetry mission's data, but it does not have the capabilities to read the upcoming Sentinel-3 L1 and L2 products. ESA will endeavour to develop and supply this capability to support the users of the future Sentinel-3 SAR Altimetry Mission. BRAT is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2005 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales, the French Space Agency), and it is freely available at http://earth.esa.int/brat. The tools enable users to interact with the most common altimetry data formats, the BratGUI is the front-end for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with Matlab/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the data-formatting hassle. BRAT can be used simply to visualise data quickly, or to translate the data into other formats such as net

  10. III. NIH TOOLBOX COGNITION BATTERY (CB): MEASURING EPISODIC MEMORY

    OpenAIRE

    Bauer, Patricia J.; Dikmen, Sureyya S.; Heaton, Robert K.; Mungas, Dan; Slotkin, Jerry; Beaumont, Jennifer L.

    2013-01-01

    One of the most significant domains of cognition is episodic memory, which allows for rapid acquisition and long-term storage of new information. For purposes of the NIH Toolbox, we devised a new test of episodic memory. The nonverbal NIH Toolbox Picture Sequence Memory Test (TPSMT) requires participants to reproduce the order of an arbitrarily ordered sequence of pictures presented on a computer. To adjust for ability, sequence length varies from 6 to 15 pictures. Multiple trials are adminis...

  11. Introduction to Numerical Computation - analysis and Matlab illustrations

    DEFF Research Database (Denmark)

    Elden, Lars; Wittmeyer-Koch, Linde; Nielsen, Hans Bruun

    In a modern programming environment like eg MATLAB it is possible by simple commands to perform advanced calculations on a personal computer. In order to use such a powerful tool efiiciently it is necessary to have an overview of available numerical methods and algorithms and to know about...... are illustrated by examples in MATLAB....

  12. Flexible missile autopilot design studies with PC-MATLAB/386

    Science.gov (United States)

    Ruth, Michael J.

    1989-01-01

    Development of a responsive, high-bandwidth missile autopilot for airframes which have structural modes of unusually low frequency presents a challenging design task. Such systems are viable candidates for modern, state-space control design methods. The PC-MATLAB interactive software package provides an environment well-suited to the development of candidate linear control laws for flexible missile autopilots. The strengths of MATLAB include: (1) exceptionally high speed (MATLAB's version for 80386-based PC's offers benchmarks approaching minicomputer and mainframe performance); (2) ability to handle large design models of several hundred degrees of freedom, if necessary; and (3) broad extensibility through user-defined functions. To characterize MATLAB capabilities, a simplified design example is presented. This involves interactive definition of an observer-based state-space compensator for a flexible missile autopilot design task. MATLAB capabilities and limitations, in the context of this design task, are then summarized.

  13. Fuzzy logic based control system for fresh water aquaculture: A MATLAB based simulation approach

    Directory of Open Access Journals (Sweden)

    Rana Dinesh Singh

    2015-01-01

    Full Text Available Fuzzy control is regarded as the most widely used application of fuzzy logic. Fuzzy logic is an innovative technology to design solutions for multiparameter and non-linear control problems. One of the greatest advantages of fuzzy control is that it uses human experience and process information obtained from operator rather than a mathematical model for the definition of a control strategy. As a result, it often delivers solutions faster than conventional control design techniques. The proposed system is an attempt to apply fuzzy logic techniques to predict the stress factor on the fish, based on line data and rule base generated using domain expert. The proposed work includes a use of Data acquisition system, an interfacing device for on line parameter acquisition and analysis, fuzzy logic controller (FLC for inferring the stress factor. The system takes stress parameters on the fish as inputs, fuzzified by using FLC with knowledge base rules and finally provides single output. All the parameters are controlled and calibrated by the fuzzy logic toolbox and MATLAB programming.

  14. Effective and versatile software beamformation toolbox

    DEFF Research Database (Denmark)

    Kortbek, Jacob; Nikolov, Svetoslav; Jensen, Jørgen Arendt

    2007-01-01

    Delay-and-sum array beamforming is an essential part of signal processing in ultrasound imaging. Although the principles are simple, there are many implementation details to consider for obtaining a reliable and computational efficient beamforming. Different methods for calculation of time......-delays are used for different waveforms. Various inter-sample interpolation schemes such as FIR-filtering, polynomial, and spline interpolation can be chosen. Apodization can be any preferred window function of fixed size applied on the channel signals or it can be dynamic with an expanding and contracting...... seconds using a transducer of 128 elements, dynamic apodization and 3rd order polynomial interpolation. This is a decrease in computation time of at least a factor of 15 compared to an implementation directly in MATLAB of a similar beamformer....

  15. MATLAB tools for improved characterization and quantification of volcanic incandescence in Webcam imagery; applications at Kilauea Volcano, Hawai'i

    Science.gov (United States)

    Patrick, Matthew R.; Kauahikaua, James P.; Antolik, Loren

    2010-01-01

    . These scripts would require minor to moderate modifications for use elsewhere, primarily to customize directory navigation. If the user has some familiarity with MATLAB, or programming in general, these modifications should be easy. Although we originally anticipated needing the Image Processing Toolbox, the scripts in the appendixes do not require it. Thus, only the base installation of MATLAB is needed. Because fairly basic MATLAB functions are used, we expect that the script can be run successfully by versions earlier than 2009b.

  16. Design of a Toolbox of RNA Thermometers.

    Science.gov (United States)

    Sen, Shaunak; Apurva, Divyansh; Satija, Rohit; Siegal, Dan; Murray, Richard M

    2017-08-18

    Biomolecular temperature sensors can be used for efficient control of large-volume bioreactors, for spatiotemporal imaging and control of gene expression, and to engineer robustness to temperature in biomolecular circuit design. Although RNA-based sensors, called "thermometers", have been investigated in both natural and synthetic contexts, an important challenge is to design diverse responses to temperature differing in sensitivity and threshold. We address this issue by constructing a library of RNA thermometers based on thermodynamic computations and experimentally measuring their activities in cell-free biomolecular "breadboards". Using free energies of the minimum free energy structures as well as melt profile computations, we estimated that a diverse set of temperature responses were possible. We experimentally found a wide range of responses to temperature in the range 29-37 °C with fold-changes varying over 3-fold around the starting thermometer. The sensitivities of these responses ranged over 10-fold around the starting thermometer. We correlated these measurements with computational expectations, finding that although there was no strong correlation for the individual thermometers, overall trends of diversity, fold-changes, and sensitivities were similar. These results present a toolbox of RNA-based circuit elements with diverse temperature responses.

  17. Robotic inspection technology-process an toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Hermes, Markus [ROSEN Group (United States). R and D Dept.

    2005-07-01

    Pipeline deterioration grows progressively with ultimate aging of pipeline systems (on-plot and cross country). This includes both, very localized corrosion as well as increasing failure probability due to fatigue cracking. Limiting regular inspecting activities to the 'scrapable' part of the pipelines only, will ultimately result into a pipeline system with questionable integrity. The confidence level in the integrity of these systems will drop below acceptance levels. Inspection of presently un-inspectable sections of the pipeline system becomes a must. This paper provides information on ROSEN's progress on the 'robotic inspection technology' project. The robotic inspection concept developed by ROSEN is based on a modular toolbox principle. This is mandatory. A universal 'all purpose' robot would not be reliable and efficient in resolving the postulated inspection task. A preparatory Quality Function Deployment (QFD) analysis is performed prior to the decision about the adequate robotic solution. This enhances the serviceability and efficiency of the provided technology. The word 'robotic' can be understood in its full meaning of Recognition - Strategy - Motion - Control. Cooperation of different individual systems with an established communication, e.g. utilizing Bluetooth technology, support the robustness of the ROSEN robotic inspection approach. Beside the navigation strategy, the inspection strategy is also part of the QFD process. Multiple inspection technologies combined on a single carrier or distributed across interacting container must be selected with a clear vision of the particular goal. (author)

  18. Watershed Modeling Applications with the Open-Access Modular Distributed Watershed Educational Toolbox (MOD-WET) and Introductory Hydrology Textbook

    Science.gov (United States)

    Huning, L. S.; Margulis, S. A.

    2014-12-01

    Traditionally, introductory hydrology courses focus on hydrologic processes as independent or semi-independent concepts that are ultimately integrated into a watershed model near the end of the term. When an "off-the-shelf" watershed model is introduced in the curriculum, this approach can result in a potential disconnect between process-based hydrology and the inherent interconnectivity of processes within the water cycle. In order to curb this and reduce the learning curve associated with applying hydrologic concepts to complex real-world problems, we developed the open-access Modular Distributed Watershed Educational Toolbox (MOD-WET). The user-friendly, MATLAB-based toolbox contains the same physical equations for hydrological processes (i.e. precipitation, snow, radiation, evaporation, unsaturated flow, infiltration, groundwater, and runoff) that are presented in the companion e-textbook (http://aqua.seas.ucla.edu/margulis_intro_to_hydro_textbook.html) and taught in the classroom. The modular toolbox functions can be used by students to study individual hydrologic processes. These functions are integrated together to form a simple spatially-distributed watershed model, which reinforces a holistic understanding of how hydrologic processes are interconnected and modeled. Therefore when watershed modeling is introduced, students are already familiar with the fundamental building blocks that have been unified in the MOD-WET model. Extensive effort has been placed on the development of a highly modular and well-documented code that can be run on a personal computer within the commonly-used MATLAB environment. MOD-WET was designed to: 1) increase the qualitative and quantitative understanding of hydrological processes at the basin-scale and demonstrate how they vary with watershed properties, 2) emphasize applications of hydrologic concepts rather than computer programming, 3) elucidate the underlying physical processes that can often be obscured with a complicated

  19. PL-DA-PS: A hardware architecture and software toolbox for neurophysiology requiring complex visual stimuli and online behavioral control

    Directory of Open Access Journals (Sweden)

    Kyler M. Eastman

    2012-01-01

    Full Text Available Neurophysiological studies in awake, behaving primates (both human and nonhuman primates have focused with increasing scrutiny on the temporal relationship between neural signals and behaviors. Consequently, laboratories are often faced with the problem of developing experimental equipment that can support data recording with high temporal precision and also be flexible enough to accommodate a wide variety of experimental paradigms. To this end, we have developed an architecture that integrates several modern pieces of equipment, but still grants experimenters a high degree of flexibility. Our hardware architecture and software tools take advantage of three popular and powerful technologies: the PLexon apparatus for neurophysiological recordings (Plexon, Inc., Dallas TX, a DAtapixx box (Vpixx Technologies, Saint-Bruno, QC, Canada for analog, digital, and video signal input-output control, and the PSychtoolbox MATLAB toolbox for stimulus generation (Brainard, 1997. The PL-DA-PS (Platypus system is designed to support the study of the visual systems of awake, behaving primates during multi-electrode neurophysiological recordings, but can be easily applied to other related domains. Despite its wide range of capabilities and support for cutting-edge video displays and neural recording systems, the PLDAPS system is simple enough for someone with basic MATLAB programming skills to design their own experiments.

  20. Introduction to finite element analysis using MATLAB and Abaqus

    CERN Document Server

    Khennane, Amar

    2013-01-01

    There are some books that target the theory of the finite element, while others focus on the programming side of things. Introduction to Finite Element Analysis Using MATLAB(R) and Abaqus accomplishes both. This book teaches the first principles of the finite element method. It presents the theory of the finite element method while maintaining a balance between its mathematical formulation, programming implementation, and application using commercial software. The computer implementation is carried out using MATLAB, while the practical applications are carried out in both MATLAB and Abaqus. MA

  1. Kinematic analysis of the finger exoskeleton using MATLAB/Simulink.

    Science.gov (United States)

    Nasiłowski, Krzysztof; Awrejcewicz, Jan; Lewandowski, Donat

    2014-01-01

    A paralyzed and not fully functional part of human body can be supported by the properly designed exoskeleton system with motoric abilities. It can help in rehabilitation, or movement of a disabled/paralyzed limb. Both suitably selected geometry and specialized software are studied applying the MATLAB environment. A finger exoskeleton was the base for MATLAB/Simulink model. Specialized software, such as MATLAB/Simulink give us an opportunity to optimize calculation reaching precise results, which help in next steps of design process. The calculations carried out yield information regarding movement relation between three functionally connected actuators and showed distance and velocity changes during the whole simulation time.

  2. Matlab Tools: An Alternative to Planning Systems in Brachytherapy Treatments

    International Nuclear Information System (INIS)

    Herrera, Higmar; Rodriguez, Mercedes; Rodriguez, Miguel

    2006-01-01

    This work proposes the use of the Matlab environment to obtain the treatment dose based on the reported data by Krishnaswamy and Liu et al. The comparison with reported measurements is showed for the Amersham source model. For the 3M source model, measurements with TLDs and a Monte Carlo simulation are compared to the data obtained by Matlab. The difference for the Amersham model is well under the 15% recommended by the IAEA and for the 3M model, although the difference is greater, the results are consistent. The good agreement to the reported data allows the Matlab calculations to be used in daily brachytherapy treatments

  3. A Graphical User Interface to Generalized Linear Models in MATLAB

    Directory of Open Access Journals (Sweden)

    Peter Dunn

    1999-07-01

    Full Text Available Generalized linear models unite a wide variety of statistical models in a common theoretical framework. This paper discusses GLMLAB-software that enables such models to be fitted in the popular mathematical package MATLAB. It provides a graphical user interface to the powerful MATLAB computational engine to produce a program that is easy to use but with many features, including offsets, prior weights and user-defined distributions and link functions. MATLAB's graphical capacities are also utilized in providing a number of simple residual diagnostic plots.

  4. Paleomagnetic dating: Methods, MATLAB software, example

    Science.gov (United States)

    Hnatyshin, Danny; Kravchinsky, Vadim A.

    2014-09-01

    A MATLAB software tool has been developed to provide an easy to use graphical interface for the plotting and interpretation of paleomagnetic data. The tool takes either paleomagnetic directions or paleopoles and compares them to a user defined apparent polar wander path or secular variation curve to determine the age of a paleomagnetic sample. Ages can be determined in two ways, either by translating the data onto the reference curve, or by rotating it about a set location (e.g. sampling location). The results are then compiled in data tables which can be exported as an excel file. This data can also be plotted using variety of built-in stereographic projections, which can then be exported as an image file. This software was used to date the giant Sukhoi Log gold deposit in Russia. Sukhoi Log has undergone a complicated history of faulting, folding, metamorphism, and is the vicinity of many granitic bodies. Paleomagnetic analysis of Sukhoi Log allowed for the timing of large scale thermal or chemical events to be determined. Paleomagnetic analysis from gold mineralized black shales was used to define the natural remanent magnetization recorded at Sukhoi Log. The obtained paleomagnetic direction from thermal demagnetization produced a paleopole at 61.3°N, 155.9°E, with the semi-major axis and semi-minor axis of the 95% confidence ellipse being 16.6° and 15.9° respectively. This paleopole is compared to the Siberian apparent polar wander path (APWP) by translating the paleopole to the nearest location on the APWP. This produced an age of 255.2- 31.0+ 32.0Ma and is the youngest well defined age known for Sukhoi Log. We propose that this is the last major stage of activity at Sukhoi Log, and likely had a role in determining the present day state of mineralization seen at the deposit.

  5. Matlab GUI for a Fluid Mixer

    Science.gov (United States)

    Barbieri, Enrique

    2005-01-01

    The Test and Engineering Directorate at NASA John C. Stennis Space Center developed an interest to study the modeling, evaluation, and control of a liquid hydrogen (LH2) and gas hydrogen (GH2) mixer subsystem of a ground test facility. This facility carries out comprehensive ground-based testing and certification of liquid rocket engines including the Space Shuttle Main engine. A software simulation environment developed in MATLAB/SIMULINK (M/S) will allow NASA engineers to test rocket engine systems at relatively no cost. In the progress report submitted in February 2004, we described the development of two foundation programs, a reverse look-up application using various interpolation algorithms, a variety of search and return methods, and self-checking methods to reduce the error in returned search results to increase the functionality of the program. The results showed that these efforts were successful. To transfer this technology to engineers who are not familiar with the M/S environment, a four-module GUI was implemented allowing the user to evaluate the mixer model under open-loop and closed-loop conditions. The progress report was based on an udergraduate Honors Thesis by Ms. Jamie Granger Austin in the Department of Electrical Engineering and Computer Science at Tulane University, during January-May 2003, and her continued efforts during August-December 2003. In collaboration with Dr. Hanz Richter and Dr. Fernando Figueroa we published these results in a NASA Tech Brief due to appear this year. Although the original proposal in 2003 did not address other components of the test facility, we decided in the last few months to extend our research and consider a related pressurization tank component as well. This report summarizes the results obtained towards a Graphical User Interface (GUI) for the evaluation and control of the hydrogen mixer subsystem model and for the pressurization tank each taken individually. Further research would combine the two

  6. Open Babel: An open chemical toolbox

    Directory of Open Access Journals (Sweden)

    O'Boyle Noel M

    2011-10-01

    Full Text Available Abstract Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language and de facto standards have arisen (for example, SMILES format, the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example, and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.

  7. Open Babel: An open chemical toolbox

    Science.gov (United States)

    2011-01-01

    Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org. PMID:21982300

  8. Introducing Effects in an Image: A MATLAB Approach

    OpenAIRE

    Kumar , Vinay; Sood , Saurabh; Mishra , Shruti

    2008-01-01

    A detailed study of introducing morning, night, and some more effect in an image is discussed, the original image is clicked in the morning. Several examples have also been discussed. MATLAB is used for the processing.

  9. Development and Validation of Reentry Simulation Using MATLAB

    National Research Council Canada - National Science Library

    Jameson, Jr, Robert E

    2006-01-01

    This research effort develops a program using MATLAB to solve the equations of motion for atmospheric reentry and analyzes the validity of the program for use as a tool to expeditiously predict reentry profiles...

  10. Research based on matlab method of digital trapezoidal shaping filter

    International Nuclear Information System (INIS)

    Zhou Qinghua; Zhang Ruanyu; Li Taihua

    2008-01-01

    In order to develop digital shaping system fast and conveniently, the paper presents the method of optimizing the trapezoidal shaping filter's parameters by using MATLAB, and discusses the affections of the parameters to the shaping result by this method. (authors)

  11. Design and fabrication of diffractive optical elements with MATLAB

    National Research Council Canada - National Science Library

    Bhattacharya, Shanti (Professor in Optics); Vijayakumar, Anand

    2017-01-01

    ... their diffraction patterns using MATLAB. The fundamentals of fabrication techniques such as photolithography, electron beam lithography, and focused ion beam lithography with basic instructions for the beginner are presented...

  12. Study of a photovoltaic system with MPPT using Matlab

    Directory of Open Access Journals (Sweden)

    Dumitru Pop

    2012-12-01

    Full Text Available In this paper a photovoltaic (PV system is analyzed using Matlab. First, a Matlab code is written in order to obtain the I-V and P-V curves at different values of solar irradiation and cell temperature. The results were compared with the experimental data of a commercial PV module, USP 150. Then, the code was implemented in Simulink and, along with a MPPT algorithm and a DC-DC converter, the whole system was simulated.

  13. Training course "Porting code from Matlab to Python"

    OpenAIRE

    Diaz, Sandra; Klijn, Wouter; Deepu, Rajalekshmi; Peyser, Alexander; Oden, Lena

    2017-01-01

    Python is becoming a popular language for scientific applications and is increasingly used for high performance computing. In this course we want to introduce Matlab programmers to the usage of Python. Matlab and Python have a comparable language philosophy, but Python can offer better performance using its optimizations and parallelization interfaces. Python also increases the portability and flexibility (interaction with other open source and proprietary software packages) of solutions, and...

  14. Subband/Transform MATLAB Functions For Processing Images

    Science.gov (United States)

    Glover, D.

    1995-01-01

    SUBTRANS software is package of routines implementing image-data-processing functions for use with MATLAB*(TM) software. Provides capability to transform image data with block transforms and to produce spatial-frequency subbands of transformed data. Functions cascaded to provide further decomposition into more subbands. Also used in image-data-compression systems. For example, transforms used to prepare data for lossy compression. Written for use in MATLAB mathematical-analysis environment.

  15. Wheat Rust Toolbox Related to New Initiatives on Yellow Rust

    DEFF Research Database (Denmark)

    Hansen, Jens Grønbech; Lassen, Poul

    ://www.fao.org/agriculture/crops/rust/stem/rust-report/en/). The Wheat rust toolbox is one of several International research platforms hosted by Aarhus University, and it uses the same ICT framework and databases as EuroWheat (www.eurowheat.org) and EuroBlight (www.EuroBlight.net). The Wheat Rust Toolbox will also serve the Global Rust Reference Centre (GRRC) as well...... – 2009), and as soon as possible this will be expanded to cover all global yellow rust data available via the GRRC. The presentation will focus on experiences from the previous work on global databases and web based information systems, as well as propose ideas how the toolbox can be helpful regarding...

  16. CBP TOOLBOX VERSION 2.0: CODE INTEGRATION ENHANCEMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Smith, F.; Flach, G.; BROWN, K.

    2013-06-01

    This report describes enhancements made to code integration aspects of the Cementitious Barriers Project (CBP) Toolbox as a result of development work performed at the Savannah River National Laboratory (SRNL) in collaboration with Vanderbilt University (VU) in the first half of fiscal year 2013. Code integration refers to the interfacing to standalone CBP partner codes, used to analyze the performance of cementitious materials, with the CBP Software Toolbox. The most significant enhancements are: 1) Improved graphical display of model results. 2) Improved error analysis and reporting. 3) Increase in the default maximum model mesh size from 301 to 501 nodes. 4) The ability to set the LeachXS/Orchestra simulation times through the GoldSim interface. These code interface enhancements have been included in a new release (Version 2.0) of the CBP Toolbox.

  17. OMPC: an Open-Source MATLAB-to-Python Compiler.

    Science.gov (United States)

    Jurica, Peter; van Leeuwen, Cees

    2009-01-01

    Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB((R)), the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB((R))-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB((R)) functions into Python programs. The imported MATLAB((R)) modules will run independently of MATLAB((R)), relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB((R)). OMPC is available at http://ompc.juricap.com.

  18. QUALITATIVE ANALYSIS OF OFFICIAL MILK CONTROL IN VALENCIA COMMUNITY (SPAIN BY SELF ORGANIZING MAPS

    Directory of Open Access Journals (Sweden)

    Carlos Javier Fernandez

    2009-06-01

    Full Text Available Breeding programs in dairy goats are mainly based on milk production and composition. Murciano-Granadina goats are located principally in the central and southern regions of Spain. This study is focused in Valencia Community (Spain and the objective is to study the Murciano-Granadina livestock based on the database from Murciano-Granadina Goat Breeders Association of Valencia (AMURVAL.  The aim of this study is to analyze the relationship among different variables related with milk production; milk yield, fat, protein, lactose, SCC, the number of births, lactation number and season. This analysis is carried out by using the Self Organizing Map. This tool allows mapping high-dimensional input spaces into much lower-dimensional spaces, thus making much more straightforward to understand any representation of data. These representations enable to visually extract qualitative relationships among variables (Visual Data Mining. A total of 3221 Murciano-Granadina dairy goats from AMURVAL were chosen. Self Organizing Maps (SOM were used to analyze data with the system identification toolbox of MATLAB v7. Data were obtained from Official Milk Control during 2006 campaign. SOM considered in this study is formed by 21´14 neurons (294 neurons; the chosen architecture is given by the range of the input variables used. The map shown that more than 70% of the goats has milk yield greater than 300 kg per lactation and goat, indicating good performance of farms. Besides, the SOM obtained indicate a group of neurons that included goats with high SSC (2%. The use of Self Organizing Maps in the descriptive analysis of this kind of data sets has proven to be highly valuable in extracting qualitative conclusions and guiding in improving the performance of farms.

  19. NATbox: a network analysis toolbox in R.

    Science.gov (United States)

    Chavan, Shweta S; Bauer, Michael A; Scutari, Marco; Nagarajan, Radhakrishnan

    2009-10-08

    There has been recent interest in capturing the functional relationships (FRs) from high-throughput assays using suitable computational techniques. FRs elucidate the working of genes in concert as a system as opposed to independent entities hence may provide preliminary insights into biological pathways and signalling mechanisms. Bayesian structure learning (BSL) techniques and its extensions have been used successfully for modelling FRs from expression profiles. Such techniques are especially useful in discovering undocumented FRs, investigating non-canonical signalling mechanisms and cross-talk between pathways. The objective of the present study is to develop a graphical user interface (GUI), NATbox: Network Analysis Toolbox in the language R that houses a battery of BSL algorithms in conjunction with suitable statistical tools for modelling FRs in the form of acyclic networks from gene expression profiles and their subsequent analysis. NATbox is a menu-driven open-source GUI implemented in the R statistical language for modelling and analysis of FRs from gene expression profiles. It provides options to (i) impute missing observations in the given data (ii) model FRs and network structure from gene expression profiles using a battery of BSL algorithms and identify robust dependencies using a bootstrap procedure, (iii) present the FRs in the form of acyclic graphs for visualization and investigate its topological properties using network analysis metrics, (iv) retrieve FRs of interest from published literature. Subsequently, use these FRs as structural priors in BSL (v) enhance scalability of BSL across high-dimensional data by parallelizing the bootstrap routines. NATbox provides a menu-driven GUI for modelling and analysis of FRs from gene expression profiles. By incorporating readily available functions from existing R-packages, it minimizes redundancy and improves reproducibility, transparency and sustainability, characteristic of open-source environments

  20. Programming for computations MATLAB/Octave : a gentle introduction to numerical simulations with MATLAB/Octave

    CERN Document Server

    Linge, Svein

    2016-01-01

    This book presents computer programming as a key method for solving mathematical problems. There are two versions of the book, one for MATLAB and one for Python. The book was inspired by the Springer book TCSE 6: A Primer on Scientific Programming with Python (by Langtangen), but the style is more accessible and concise, in keeping with the needs of engineering students. The book outlines the shortest possible path from no previous experience with programming to a set of skills that allows the students to write simple programs for solving common mathematical problems with numerical methods in engineering and science courses. The emphasis is on generic algorithms, clean design of programs, use of functions, and automatic tests for verification.

  1. Versatile Cas9-driven subpopulation selection toolbox for Lactococcus lactis

    NARCIS (Netherlands)

    Els, van der Simon; James, Jennelle K.; Kleerebezem, Michiel; Bron, Peter A.

    2018-01-01

    CRISPR-Cas9 technology has been exploited for the removal or replacement of genetic elements in a wide range of prokaryotes and eukaryotes. Here, we describe the extension of the Cas9 application toolbox to the industrially important dairy species Lactococcus lactis. The Cas9 expression vector

  2. 40 CFR 141.719 - Additional filtration toolbox components.

    Science.gov (United States)

    2010-07-01

    ... taken from a surface water or GWUDI source. A cap, such as GAC, on a single stage of filtration is not... separate stage of filtration if both filtration stages treat entire plant flow taken from a surface water... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Additional filtration toolbox...

  3. Wyrm: A Brain-Computer Interface Toolbox in Python.

    Science.gov (United States)

    Venthur, Bastian; Dähne, Sven; Höhne, Johannes; Heller, Hendrik; Blankertz, Benjamin

    2015-10-01

    In the last years Python has gained more and more traction in the scientific community. Projects like NumPy, SciPy, and Matplotlib have created a strong foundation for scientific computing in Python and machine learning packages like scikit-learn or packages for data analysis like Pandas are building on top of it. In this paper we present Wyrm ( https://github.com/bbci/wyrm ), an open source BCI toolbox in Python. Wyrm is applicable to a broad range of neuroscientific problems. It can be used as a toolbox for analysis and visualization of neurophysiological data and in real-time settings, like an online BCI application. In order to prevent software defects, Wyrm makes extensive use of unit testing. We will explain the key aspects of Wyrm's software architecture and design decisions for its data structure, and demonstrate and validate the use of our toolbox by presenting our approach to the classification tasks of two different data sets from the BCI Competition III. Furthermore, we will give a brief analysis of the data sets using our toolbox, and demonstrate how we implemented an online experiment using Wyrm. With Wyrm we add the final piece to our ongoing effort to provide a complete, free and open source BCI system in Python.

  4. Testing adaptive toolbox models: a Bayesian hierarchical approach

    NARCIS (Netherlands)

    Scheibehenne, B.; Rieskamp, J.; Wagenmakers, E.-J.

    2013-01-01

    Many theories of human cognition postulate that people are equipped with a repertoire of strategies to solve the tasks they face. This theoretical framework of a cognitive toolbox provides a plausible account of intra- and interindividual differences in human behavior. Unfortunately, it is often

  5. Automated processing of thermal infrared images of Osservatorio Vesuviano permanent surveillance network by using Matlab code

    Science.gov (United States)

    Sansivero, Fabio; Vilardo, Giuseppe; Caputo, Teresa

    2017-04-01

    polynomial fit Matlab function - LTFC_SCOREF), c) the export of data in different raster formats (i.e. Surfer grd). An interesting example of elaborations of the data produced by ASIRA Tools is the map of the temperature changing rate, which provide remarkable information about the potential migration of fumarole activity. The high efficiency of Matlab in processing matrix data from IR scenes and the flexibility of this code-developing tool proved to be very useful to produce applications to use in volcanic surveillance aimed to monitor the evolution of surface temperatures field in diffuse degassing volcanic areas.

  6. DeltaProt: a software toolbox for comparative genomics

    Directory of Open Access Journals (Sweden)

    Willassen Nils P

    2010-11-01

    Full Text Available Abstract Background Statistical bioinformatics is the study of biological data sets obtained by new micro-technologies by means of proper statistical methods. For a better understanding of environmental adaptations of proteins, orthologous sequences from different habitats may be explored and compared. The main goal of the DeltaProt Toolbox is to provide users with important functionality that is needed for comparative screening and studies of extremophile proteins and protein classes. Visualization of the data sets is also the focus of this article, since visualizations can play a key role in making the various relationships transparent. This application paper is intended to inform the reader of the existence, functionality, and applicability of the toolbox. Results We present the DeltaProt Toolbox, a software toolbox that may be useful in importing, analyzing and visualizing data from multiple alignments of proteins. The toolbox has been written in MATLAB™ to provide an easy and user-friendly platform, including a graphical user interface, while ensuring good numerical performance. Problems in genome biology may be easily stated thanks to a compact input format. The toolbox also offers the possibility of utilizing structural information from the SABLE or other structure predictors. Different sequence plots can then be viewed and compared in order to find their similarities and differences. Detailed statistics are also calculated during the procedure. Conclusions The DeltaProt package is open source and freely available for academic, non-commercial use. The latest version of DeltaProt can be obtained from http://services.cbu.uib.no/software/deltaprot/. The website also contains documentation, and the toolbox comes with real data sets that are intended for training in applying the models to carry out bioinformatical and statistical analyses of protein sequences. Equipped with the new algorithms proposed here, DeltaProt serves as an auxiliary

  7. MultiElec: A MATLAB Based Application for MEA Data Analysis.

    Science.gov (United States)

    Georgiadis, Vassilis; Stephanou, Anastasis; Townsend, Paul A; Jackson, Thomas R

    2015-01-01

    We present MultiElec, an open source MATLAB based application for data analysis of microelectrode array (MEA) recordings. MultiElec displays an extremely user-friendly graphic user interface (GUI) that allows the simultaneous display and analysis of voltage traces for 60 electrodes and includes functions for activation-time determination, the production of activation-time heat maps with activation time and isoline display. Furthermore, local conduction velocities are semi-automatically calculated along with their corresponding vector plots. MultiElec allows ad hoc signal suppression, enabling the user to easily and efficiently handle signal artefacts and for incomplete data sets to be analysed. Voltage traces and heat maps can be simply exported for figure production and presentation. In addition, our platform is able to produce 3D videos of signal progression over all 60 electrodes. Functions are controlled entirely by a single GUI with no need for command line input or any understanding of MATLAB code. MultiElec is open source under the terms of the GNU General Public License as published by the Free Software Foundation, version 3. Both the program and source code are available to download from http://www.cancer.manchester.ac.uk/MultiElec/.

  8. A 'Toolbox' Equivalent Process for Safety Analysis Software

    International Nuclear Information System (INIS)

    O'Kula, K.R.; Eng, Tony

    2004-01-01

    Defense Nuclear Facilities Safety Board (DNFSB) Recommendation 2002-1 (Quality Assurance for Safety-Related Software) identified a number of quality assurance issues on the use of software in Department of Energy (DOE) facilities for analyzing hazards, and designing and operating controls that prevent or mitigate potential accidents. The development and maintenance of a collection, or 'toolbox', of multiple-site use, standard solution, Software Quality Assurance (SQA)-compliant safety software is one of the major improvements identified in the associated DOE Implementation Plan (IP). The DOE safety analysis toolbox will contain a set of appropriately quality-assured, configuration-controlled, safety analysis codes, recognized for DOE-broad, safety basis applications. Currently, six widely applied safety analysis computer codes have been designated for toolbox consideration. While the toolbox concept considerably reduces SQA burdens among DOE users of these codes, many users of unique, single-purpose, or single-site software may still have sufficient technical justification to continue use of their computer code of choice, but are thwarted by the multiple-site condition on toolbox candidate software. The process discussed here provides a roadmap for an equivalency argument, i.e., establishing satisfactory SQA credentials for single-site software that can be deemed ''toolbox-equivalent''. The process is based on the model established to meet IP Commitment 4.2.1.2: Establish SQA criteria for the safety analysis ''toolbox'' codes. Implementing criteria that establish the set of prescriptive SQA requirements are based on implementation plan/procedures from the Savannah River Site, also incorporating aspects of those from the Waste Isolation Pilot Plant (SNL component) and the Yucca Mountain Project. The major requirements are met with evidence of a software quality assurance plan, software requirements and design documentation, user's instructions, test report, a

  9. Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB.

    Science.gov (United States)

    Ullah, M; Schmidt, H; Cho, K H; Wolkenhauer, O

    2006-03-01

    The analysis of complex biochemical networks is conducted in two popular conceptual frameworks for modelling. The deterministic approach requires the solution of ordinary differential equations (ODEs, reaction rate equations) with concentrations as continuous state variables. The stochastic approach involves the simulation of differential-difference equations (chemical master equations, CMEs) with probabilities as variables. This is to generate counts of molecules for chemical species as realisations of random variables drawn from the probability distribution described by the CMEs. Although there are numerous tools available, many of them free, the modelling and simulation environment MATLAB is widely used in the physical and engineering sciences. We describe a collection of MATLAB functions to construct and solve ODEs for deterministic simulation and to implement realisations of CMEs for stochastic simulation using advanced MATLAB coding (Release 14). The program was successfully applied to pathway models from the literature for both cases. The results were compared to implementations using alternative tools for dynamic modelling and simulation of biochemical networks. The aim is to provide a concise set of MATLAB functions that encourage the experimentation with systems biology models. All the script files are available from www.sbi.uni-rostock.de/ publications_matlab-paper.html.

  10. CoSMoMVPA: Multi-Modal Multivariate Pattern Analysis of Neuroimaging Data in Matlab/GNU Octave.

    Science.gov (United States)

    Oosterhof, Nikolaas N; Connolly, Andrew C; Haxby, James V

    2016-01-01

    Recent years have seen an increase in the popularity of multivariate pattern (MVP) analysis of functional magnetic resonance (fMRI) data, and, to a much lesser extent, magneto- and electro-encephalography (M/EEG) data. We present CoSMoMVPA, a lightweight MVPA (MVP analysis) toolbox implemented in the intersection of the Matlab and GNU Octave languages, that treats both fMRI and M/EEG data as first-class citizens. CoSMoMVPA supports all state-of-the-art MVP analysis techniques, including searchlight analyses, classification, correlations, representational similarity analysis, and the time generalization method. These can be used to address both data-driven and hypothesis-driven questions about neural organization and representations, both within and across: space, time, frequency bands, neuroimaging modalities, individuals, and species. It uses a uniform data representation of fMRI data in the volume or on the surface, and of M/EEG data at the sensor and source level. Through various external toolboxes, it directly supports reading and writing a variety of fMRI and M/EEG neuroimaging formats, and, where applicable, can convert between them. As a result, it can be integrated readily in existing pipelines and used with existing preprocessed datasets. CoSMoMVPA overloads the traditional volumetric searchlight concept to support neighborhoods for M/EEG and surface-based fMRI data, which supports localization of multivariate effects of interest across space, time, and frequency dimensions. CoSMoMVPA also provides a generalized approach to multiple comparison correction across these dimensions using Threshold-Free Cluster Enhancement with state-of-the-art clustering and permutation techniques. CoSMoMVPA is highly modular and uses abstractions to provide a uniform interface for a variety of MVP measures. Typical analyses require a few lines of code, making it accessible to beginner users. At the same time, expert programmers can easily extend its functionality. Co

  11. Integrated system dynamics toolbox for water resources planning.

    Energy Technology Data Exchange (ETDEWEB)

    Reno, Marissa Devan; Passell, Howard David; Malczynski, Leonard A.; Peplinski, William J.; Tidwell, Vincent Carroll; Coursey, Don (University of Chicago, Chicago, IL); Hanson, Jason (University of New Mexico, Albuquerque, NM); Grimsrud, Kristine (University of New Mexico, Albuquerque, NM); Thacher, Jennifer (University of New Mexico, Albuquerque, NM); Broadbent, Craig (University of New Mexico, Albuquerque, NM); Brookshire, David (University of New Mexico, Albuquerque, NM); Chemak, Janie (University of New Mexico, Albuquerque, NM); Cockerill, Kristan (Cockeril Consulting, Boone, NC); Aragon, Carlos (New Mexico Univeristy of Technology and Mining (NM-TECH), Socorro, NM); Hallett, Heather (New Mexico Univeristy of Technology and Mining (NM-TECH), Socorro, NM); Vivoni, Enrique (New Mexico Univeristy of Technology and Mining (NM-TECH), Socorro, NM); Roach, Jesse

    2006-12-01

    Public mediated resource planning is quickly becoming the norm rather than the exception. Unfortunately, supporting tools are lacking that interactively engage the public in the decision-making process and integrate over the myriad values that influence water policy. In the pages of this report we document the first steps toward developing a specialized decision framework to meet this need; specifically, a modular and generic resource-planning ''toolbox''. The technical challenge lies in the integration of the disparate systems of hydrology, ecology, climate, demographics, economics, policy and law, each of which influence the supply and demand for water. Specifically, these systems, their associated processes, and most importantly the constitutive relations that link them must be identified, abstracted, and quantified. For this reason, the toolbox forms a collection of process modules and constitutive relations that the analyst can ''swap'' in and out to model the physical and social systems unique to their problem. This toolbox with all of its modules is developed within the common computational platform of system dynamics linked to a Geographical Information System (GIS). Development of this resource-planning toolbox represents an important foundational element of the proposed interagency center for Computer Aided Dispute Resolution (CADRe). The Center's mission is to manage water conflict through the application of computer-aided collaborative decision-making methods. The Center will promote the use of decision-support technologies within collaborative stakeholder processes to help stakeholders find common ground and create mutually beneficial water management solutions. The Center will also serve to develop new methods and technologies to help federal, state and local water managers find innovative and balanced solutions to the nation's most vexing water problems. The toolbox is an important step toward

  12. Fault detection of sensors in nuclear reactors using self-organizing maps

    Energy Technology Data Exchange (ETDEWEB)

    Barbosa, Paulo Roberto; Tiago, Graziela Marchi [Instituto Federal de Educacao, Ciencia e Tecnologia de Sao Paulo (IFSP), Sao Paulo, SP (Brazil); Bueno, Elaine Inacio [Instituto Federal de Educacao, Ciencia e Tecnologia de Sao Paulo (IFSP), Guarulhos, SP (Brazil); Pereira, Iraci Martinez, E-mail: martinez@ipen.b [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2011-07-01

    In this work a Fault Detection System was developed based on the self-organizing maps methodology. This method was applied to the IEA-R1 research reactor at IPEN using a database generated by a theoretical model of the reactor. The IEA-R1 research reactor is a pool type reactor of 5 MW, cooled and moderated by light water, and uses graphite and beryllium as reflector. The theoretical model was developed using the Matlab Guide toolbox. The equations are based in the IEA-R1 mass and energy inventory balance and physical as well as operational aspects are taken into consideration. In order to test the model ability for fault detection, faults were artificially produced. As the value of the maximum calibration error for special thermocouples is +- 0.5 deg C, it had been inserted faults in the sensor signals with the purpose to produce the database considered in this work. The results show a high percentage of correct classification, encouraging the use of the technique for this type of industrial application. (author)

  13. Fault detection of sensors in nuclear reactors using self-organizing maps

    International Nuclear Information System (INIS)

    Barbosa, Paulo Roberto; Tiago, Graziela Marchi; Bueno, Elaine Inacio; Pereira, Iraci Martinez

    2011-01-01

    In this work a Fault Detection System was developed based on the self-organizing maps methodology. This method was applied to the IEA-R1 research reactor at IPEN using a database generated by a theoretical model of the reactor. The IEA-R1 research reactor is a pool type reactor of 5 MW, cooled and moderated by light water, and uses graphite and beryllium as reflector. The theoretical model was developed using the Matlab Guide toolbox. The equations are based in the IEA-R1 mass and energy inventory balance and physical as well as operational aspects are taken into consideration. In order to test the model ability for fault detection, faults were artificially produced. As the value of the maximum calibration error for special thermocouples is +- 0.5 deg C, it had been inserted faults in the sensor signals with the purpose to produce the database considered in this work. The results show a high percentage of correct classification, encouraging the use of the technique for this type of industrial application. (author)

  14. Piezoelectric Actuator Modeling Using MSC/NASTRAN and MATLAB

    Science.gov (United States)

    Reaves, Mercedes C.; Horta, Lucas G.

    2003-01-01

    This paper presents a procedure for modeling structures containing piezoelectric actuators using MSCMASTRAN and MATLAB. The paper describes the utility and functionality of one set of validated modeling tools. The tools described herein use MSCMASTRAN to model the structure with piezoelectric actuators and a thermally induced strain to model straining of the actuators due to an applied voltage field. MATLAB scripts are used to assemble the dynamic equations and to generate frequency response functions. The application of these tools is discussed using a cantilever aluminum beam with a surface mounted piezoelectric actuator as a sample problem. Software in the form of MSCINASTRAN DMAP input commands, MATLAB scripts, and a step-by-step procedure to solve the example problem are provided. Analysis results are generated in terms of frequency response functions from deflection and strain data as a function of input voltage to the actuator.

  15. Effective approach to spectroscopy and spectral analysis techniques using Matlab

    Science.gov (United States)

    Li, Xiang; Lv, Yong

    2017-08-01

    With the development of electronic information, computer and network, modern education technology has entered new era, which would give a great impact on teaching process. Spectroscopy and spectral analysis is an elective course for Optoelectronic Information Science and engineering. The teaching objective of this course is to master the basic concepts and principles of spectroscopy, spectral analysis and testing of basic technical means. Then, let the students learn the principle and technology of the spectrum to study the structure and state of the material and the developing process of the technology. MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment and fourth-generation programming language. A proprietary programming language developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, Based on the teaching practice, this paper summarizes the new situation of applying Matlab to the teaching of spectroscopy. This would be suitable for most of the current school multimedia assisted teaching

  16. Introduction to multifractal detrended fluctuation analysis in matlab.

    Science.gov (United States)

    Ihlen, Espen A F

    2012-01-01

    Fractal structures are found in biomedical time series from a wide range of physiological phenomena. The multifractal spectrum identifies the deviations in fractal structure within time periods with large and small fluctuations. The present tutorial is an introduction to multifractal detrended fluctuation analysis (MFDFA) that estimates the multifractal spectrum of biomedical time series. The tutorial presents MFDFA step-by-step in an interactive Matlab session. All Matlab tools needed are available in Introduction to MFDFA folder at the website www.ntnu.edu/inm/geri/software. MFDFA are introduced in Matlab code boxes where the reader can employ pieces of, or the entire MFDFA to example time series. After introducing MFDFA, the tutorial discusses the best practice of MFDFA in biomedical signal processing. The main aim of the tutorial is to give the reader a simple self-sustained guide to the implementation of MFDFA and interpretation of the resulting multifractal spectra.

  17. GMDPtoolbox: A Matlab library for designing spatial management policies. Application to the long-term collective management of an airborne disease.

    Science.gov (United States)

    Cros, Marie-Josée; Aubertot, Jean-Noël; Peyrard, Nathalie; Sabbadin, Régis

    2017-01-01

    Designing management policies in ecology and agroecology is complex. Several components must be managed together while they strongly interact spatially. Decision choices must be made under uncertainty on the results of the actions and on the system dynamics. Furthermore, the objectives pursued when managing ecological systems or agroecosystems are usually long term objectives, such as biodiversity conservation or sustainable crop production. The framework of Graph-Based Markov Decision Processes (GMDP) is well adapted to the qualitative modeling of such problems of sequential decision under uncertainty. Spatial interactions are easily modeled and integrated control policies (combining several action levers) can be designed through optimization. The provided policies are adaptive, meaning that management actions are decided at each time step (for instance yearly) and the chosen actions depend on the current system state. This framework has already been successfully applied to forest management and invasive species management. However, up to now, no "easy-to-use" implementation of this framework was available. We present GMDPtoolbox, a Matlab toolbox which can be used both for the design of new management policies and for comparing policies by simulation. We provide an illustration of the use of the toolbox on a realistic crop disease management problem: the design of long term management policy of blackleg of canola using an optimal combination of three possible cultural levers. This example shows how GMDPtoolbox can be used as a tool to support expert thinking.

  18. Elements of matrix modeling and computing with Matlab

    CERN Document Server

    White, Robert E

    2006-01-01

    As discrete models and computing have become more common, there is a need to study matrix computation and numerical linear algebra. Encompassing a diverse mathematical core, Elements of Matrix Modeling and Computing with MATLAB examines a variety of applications and their modeling processes, showing you how to develop matrix models and solve algebraic systems. Emphasizing practical skills, it creates a bridge from problems with two and three variables to more realistic problems that have additional variables. Elements of Matrix Modeling and Computing with MATLAB focuses on seven basic applicat

  19. Rapid BeagleBoard prototyping with MATLAB and Simulink

    CERN Document Server

    Qin, Fei

    2013-01-01

    This book is a fast-paced guide with practical, hands-on recipes which will show you how to prototype Beagleboard-based audio/video applications using Matlab/Simlink and Sourcery Codebench on a Windows host.Beagleboard Embedded Projects is great for students and academic researchers who have practical ideas and who want to build a proof-of-concept system on an embedded hardware platform quickly and efficiently. It is also useful for product design engineers who want to ratify their applications and reduce the time-to-market. It is assumed that you are familiar with Matlab/Simulink and have som

  20. Modelling real solar cell using PSCAD/MATLAB

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, Sergio; Silva, Marco; Fernandes, Filipe; Vale, Zita [Polytechnic of Porto (Portugal). GECAD - Knowledge Engineering and Decision Support Research Center

    2012-07-01

    This paper presents the development of a solar photovoltaic (PV) model based on PSCAD/EMTDC - Power System Computer Aided Design - including a mathematical model study. An additional algorithm has been implemented in MATLAB software in order to calculate several parameters required by the PSCAD developed model. All the simulation study has been performed in PSCAD/MATLAB software simulation tool. A real data base concerning irradiance, cell temperature and PV power generation was used in order to support the evaluation of the implemented PV model. (orig.)

  1. Instruction of pattern recognition by MATLAB practice 1

    International Nuclear Information System (INIS)

    1999-06-01

    This book describes the pattern recognition by MATLAB practice. It includes possibility and limit of AI, introduction of pattern recognition a vector and matrix, basic status and a probability theory, a random variable and probability distribution, statistical decision theory, data-mining, gaussian mixture model, a nerve cell modeling such as Hebb's learning rule, LMS learning rule, genetic algorithm, dynamic programming and DTW, HMN on Markov model and HMM's three problems and solution, introduction of SVM with KKT condition and margin optimum, kernel trick and MATLAB practice.

  2. Estimating aquifer transmissivity from specific capacity using MATLAB.

    Science.gov (United States)

    McLin, Stephen G

    2005-01-01

    Historically, specific capacity information has been used to calculate aquifer transmissivity when pumping test data are unavailable. This paper presents a simple computer program written in the MATLAB programming language that estimates transmissivity from specific capacity data while correcting for aquifer partial penetration and well efficiency. The program graphically plots transmissivity as a function of these factors so that the user can visually estimate their relative importance in a particular application. The program is compatible with any computer operating system running MATLAB, including Windows, Macintosh OS, Linux, and Unix. Two simple examples illustrate program usage.

  3. A pedagogical walkthrough of computational modeling and simulation of Wnt signaling pathway using static causal models in MATLAB.

    Science.gov (United States)

    Sinha, Shriprakash

    2016-12-01

    Simulation study in systems biology involving computational experiments dealing with Wnt signaling pathways abound in literature but often lack a pedagogical perspective that might ease the understanding of beginner students and researchers in transition, who intend to work on the modeling of the pathway. This paucity might happen due to restrictive business policies which enforce an unwanted embargo on the sharing of important scientific knowledge. A tutorial introduction to computational modeling of Wnt signaling pathway in a human colorectal cancer dataset using static Bayesian network models is provided. The walkthrough might aid biologists/informaticians in understanding the design of computational experiments that is interleaved with exposition of the Matlab code and causal models from Bayesian network toolbox. The manuscript elucidates the coding contents of the advance article by Sinha (Integr. Biol. 6:1034-1048, 2014) and takes the reader in a step-by-step process of how (a) the collection and the transformation of the available biological information from literature is done, (b) the integration of the heterogeneous data and prior biological knowledge in the network is achieved, (c) the simulation study is designed, (d) the hypothesis regarding a biological phenomena is transformed into computational framework, and (e) results and inferences drawn using d -connectivity/separability are reported. The manuscript finally ends with a programming assignment to help the readers get hands-on experience of a perturbation project. Description of Matlab files is made available under GNU GPL v3 license at the Google code project on https://code.google.com/p/static-bn-for-wnt-signaling-pathway and https: //sites.google.com/site/shriprakashsinha/shriprakashsinha/projects/static-bn-for-wnt-signaling-pathway. Latest updates can be found in the latter website.

  4. The Generic Mapping Tools 6: Classic versus Modern Mode

    Science.gov (United States)

    Wessel, P.; Uieda, L.; Luis, J. M. F.; Scharroo, R.; Smith, W. H. F.; Wobbe, F.

    2017-12-01

    The Generic Mapping Tools (GMT; gmt.soest.hawaii.edu) is a 25-year old, mature open-source software package for the analysis and display of geoscience data (e.g., interpolate, filter, manipulate, project and plot temporal and spatial data). The GMT "toolbox" includes about 80 core and 40 supplemental modules sharing a common set of command options, file structures, and documentation. GMT5, when released in 2013, introduced an application programming interface (API) to allow programmatic access to GMT from other computing environments. Since then, we have released a GMT/MATLAB toolbox, an experimental GMT/Julia package, and will soon introduce a GMT/Python module. In developing these extensions, we wanted to simplify the GMT learning curve but quickly realized the main stumbling blocks to GMT command-line mastery would be ported to the external environments unless we introduced major changes. With thousands of GMT scripts already in use by scientists around the world, we were acutely aware of the need for backwards compatibility. Our solution, to be released as GMT 6, was to add a modern run mode that complements the classic mode offered so far. Modern mode completely eliminates the top three obstacles for new (and not so new) GMT users: (1) The responsibility to properly stack PostScript layers manually (i.e., the -O -K dance), (2) the responsibility of handling output redirection of PostScript (create versus append), and (3) the need to provide commands with repeated information about regions (-R) and projections (-J). Thus, modern mode results in shorter, simpler scripts with fewer pitfalls, without interfering with classic scripts. Our implementation adds five new commands that begin and end a modern session, simplify figure management, automate the conversion of PostScript to more suitable formats, automate region detection, and offer a new automated subplot environment for multi-panel illustrations. Here, we highlight the GMT modern mode and the

  5. A Series of MATLAB Learning Modules to Enhance Numerical Competency in Applied Marine Sciences

    Science.gov (United States)

    Fischer, A. M.; Lucieer, V.; Burke, C.

    2016-12-01

    Enhanced numerical competency to navigate the massive data landscapes are critical skills students need to effectively explore, analyse and visualize complex patterns in high-dimensional data for addressing the complexity of many of the world's problems. This is especially the case for interdisciplinary, undergraduate applied marine science programs, where students are required to demonstrate competency in methods and ideas across multiple disciplines. In response to this challenge, we have developed a series of repository-based data exploration, analysis and visualization modules in MATLAB for integration across various attending and online classes within the University of Tasmania. The primary focus of these modules is to teach students to collect, aggregate and interpret data from large on-line marine scientific data repositories to, 1) gain technical skills in discovering, accessing, managing and visualising large, numerous data sources, 2) interpret, analyse and design approaches to visualise these data, and 3) to address, through numerical approaches, complex, real-world problems, that the traditional scientific methods cannot address. All modules, implemented through a MATLAB live script, include a short recorded lecture to introduce the topic, a handout that gives an overview of the activities, an instructor's manual with a detailed methodology and discussion points, a student assessment (quiz and level-specific challenge task), and a survey. The marine science themes addressed through these modules include biodiversity, habitat mapping, algal blooms and sea surface temperature change and utilize a series of marine science and oceanographic data portals. Through these modules students, with minimal experience in MATLAB or numerical methods are introduced to array indexing, concatenation, sorting, and reshaping, principal component analysis, spectral analysis and unsupervised classification within the context of oceanographic processes, marine geology and

  6. Vectorized Matlab Codes for Linear Two-Dimensional Elasticity

    Directory of Open Access Journals (Sweden)

    Jonas Koko

    2007-01-01

    Full Text Available A vectorized Matlab implementation for the linear finite element is provided for the two-dimensional linear elasticity with mixed boundary conditions. Vectorization means that there is no loop over triangles. Numerical experiments show that our implementation is more efficient than the standard implementation with a loop over all triangles.

  7. A linear algebra course with PC-MATLAB : some experiences

    NARCIS (Netherlands)

    Smits, J.G.M.M.; Rijpkema, J.J.M.

    1992-01-01

    The authors present their views on the impact that the use of computers and software packages should have on the contents of a first service course on linear algebra. Furthermore they report on their experiences using the software package PC-MATLAB in such a course.

  8. Simulaser, a graphical laser simulator based on Matlab Simulink

    CSIR Research Space (South Africa)

    Jacobs, Cobus

    2016-07-01

    Full Text Available We present a single-element plane-wave laser rate equation model and its implementation as a graphical laser simulation library using Matlab Simulink. Simulink’s graphical interface and vector capabilities provide a unique layer of abstraction...

  9. Introduction of pattern recognition by MATLAB practice 2

    International Nuclear Information System (INIS)

    1999-06-01

    The contents of this book starts introduction and examples of pattern recognition. This book describes a vector and matrix, basic statistics and a probability distribution, statistical decision theory and probability density function, liner shunt, vector quantizing and clustering GMM, PCA and KL conversion, LDA, ID 3, a nerve cell modeling, HMM, SVM and Ada boost. It has direction of MATLAB in the appendix.

  10. MATLAB simulation for an experimental setup of digital feedback control

    International Nuclear Information System (INIS)

    Zheng Lifang; Liu Songqiang

    2005-01-01

    This paper describes the digital feedback simulation using MATLAB for an experimental accelerator control setup. By analyzing the plant characteristic in time-domain and frequency-domain, a guideline for design of digital filter and PID controller is derived. (authors)

  11. NNCTRL - a CANCSD toolkit for MATLAB(R)

    DEFF Research Database (Denmark)

    Nørgård, Peter Magnus; Ravn, Ole; Poulsen, Niels Kjølstad

    1996-01-01

    A set of tools for computer-aided neuro-control system design (CANCSD) has been developed for the MATLAB environment. The tools can be used for construction and simulation of a variety of neural network based control systems. The design methods featured in the toolkit are: direct inverse control...

  12. Benchmark Simulation Model No 2 in Matlab-Simulink

    DEFF Research Database (Denmark)

    Vrecko, Darko; Gernaey, Krist; Rosen, Christian

    2006-01-01

    In this paper, implementation of the Benchmark Simulation Model No 2 (BSM2) within Matlab-Simulink is presented. The BSM2 is developed for plant-wide WWTP control strategy evaluation on a long-term basis. It consists of a pre-treatment process, an activated sludge process and sludge treatment...

  13. III. NIH Toolbox Cognition Battery (CB): measuring episodic memory.

    Science.gov (United States)

    Bauer, Patricia J; Dikmen, Sureyya S; Heaton, Robert K; Mungas, Dan; Slotkin, Jerry; Beaumont, Jennifer L

    2013-08-01

    One of the most significant domains of cognition is episodic memory, which allows for rapid acquisition and long-term storage of new information. For purposes of the NIH Toolbox, we devised a new test of episodic memory. The nonverbal NIH Toolbox Picture Sequence Memory Test (TPSMT) requires participants to reproduce the order of an arbitrarily ordered sequence of pictures presented on a computer. To adjust for ability, sequence length varies from 6 to 15 pictures. Multiple trials are administered to increase reliability. Pediatric data from the validation study revealed the TPSMT to be sensitive to age-related changes. The task also has high test-retest reliability and promising construct validity. Steps to further increase the sensitivity of the instrument to individual and age-related variability are described. © 2013 The Society for Research in Child Development, Inc.

  14. The panacea toolbox of a PhD biomedical student.

    Science.gov (United States)

    Skaik, Younis

    2014-01-01

    Doing a PhD (doctor of philosophy) for the sake of contribution to knowledge should give the student an immense enthusiasm through the PhD period. It is the time in one's life that one spends to "hit the nail on the head" in a specific area and topic of interest. A PhD consists mostly of hard work and tenacity; however, luck and genius might also play a little role. You can pass all PhD phases without having both luck and genius. The PhD student should have pre-PhD and PhD toolboxes, which are "sine quibus non" for getting successfully a PhD degree. In this manuscript, the toolboxes of the PhD student are discussed.

  15. Tadarida: A Toolbox for Animal Detection on Acoustic Recordings

    Directory of Open Access Journals (Sweden)

    Yves Bas

    2017-02-01

    Full Text Available Passive Acoustic Monitoring (PAM recently extended to a very wide range of animals, but no available open software has been sufficiently generic to automatically treat several taxonomic groups. Here we present Tadarida, a software toolbox allowing for the detection and labelling of recorded sound events, and to classify any new acoustic data into known classes. It is made up of three modules handling Detection, Labelling and Classification and running on either Linux or Windows. This development resulted in the first open software (1 allowing generic sound event detection (multi-taxa, (2 providing graphical sound labelling at a single-instance level and (3 covering the whole process from sound detection to classification. This generic and modular design opens numerous reuse opportunities among (bioacoustics researchers, especially for those managing and/or developing PAM schemes. The whole toolbox is openly developed in C++ (Detection and Labelling and R (Classification and stored at https://github.com/YvesBas.

  16. Open Source Power Plant Simulator Development Under Matlab Environment

    International Nuclear Information System (INIS)

    Ratemi, W.M.; Fadilah, S.M.; Abonoor, N

    2008-01-01

    In this paper an open source programming approach is targeted for the development of power plant simulator under Matlab environment. With this approach many individuals can contribute to the development of the simulator by developing different orders of complexities of the power plant components. Such modules can be modeled based on physical principles, or using neural networks or other methods. All of these modules are categorized in Matlab library, of which the user can select and build up his simulator. Many international companies developed its own authoring tool for the development of its simulators, and hence it became its own property available for high costs. Matlab is a general software developed by mathworks that can be used with its toolkits as the authoring tool for the development of components by different individuals, and through the appropriate coordination, different plant simulators, nuclear, traditional , or even research reactors can be computerly assembled. In this paper, power plant components such as a pressurizer, a reactor, a steam generator, a turbine, a condenser, a feedwater heater, a valve, a pump are modeled based on physical principles. Also a prototype modeling of a reactor ( a scram case) based on neural networks is developed. These modules are inserted in two different Matlab libraries one called physical and the other is called neural. Furthermore, during the simulation one can pause and shuffle the modules selected from the two libraries and then proceed the simulation. Also, under the Matlab environment a PID controller is developed for multi-loop plant which can be integrated for the control of the appropriate developed simulator. This paper is an attempt to base the open source approach for the development of power plant simulators or even research reactor simulators. It then requires the coordination among interested individuals or institutions to set it to professionalism. (author)

  17. Cumulative Risk Assessment Toolbox: Methods and Approaches for the Practitioner

    Directory of Open Access Journals (Sweden)

    Margaret M. MacDonell

    2013-01-01

    Full Text Available The historical approach to assessing health risks of environmental chemicals has been to evaluate them one at a time. In fact, we are exposed every day to a wide variety of chemicals and are increasingly aware of potential health implications. Although considerable progress has been made in the science underlying risk assessments for real-world exposures, implementation has lagged because many practitioners are unaware of methods and tools available to support these analyses. To address this issue, the US Environmental Protection Agency developed a toolbox of cumulative risk resources for contaminated sites, as part of a resource document that was published in 2007. This paper highlights information for nearly 80 resources from the toolbox and provides selected updates, with practical notes for cumulative risk applications. Resources are organized according to the main elements of the assessment process: (1 planning, scoping, and problem formulation; (2 environmental fate and transport; (3 exposure analysis extending to human factors; (4 toxicity analysis; and (5 risk and uncertainty characterization, including presentation of results. In addition to providing online access, plans for the toolbox include addressing nonchemical stressors and applications beyond contaminated sites and further strengthening resource accessibility to support evolving analyses for cumulative risk and sustainable communities.

  18. Semi-automated Robust Quantification of Lesions (SRQL Toolbox

    Directory of Open Access Journals (Sweden)

    Kaori Ito

    2017-02-01

    Full Text Available Quantifying lesions in a robust manner is fundamental for studying the effects of neuroanatomical changes in the post-stroke brain on recovery. However, the wide variability in lesion characteristics across individuals makes manual lesion segmentation a challenging and often subjective process. This makes it difficult to combine stroke lesion data across multiple research sites, due to subjective differences in how lesions may be defined. We developed the Semi-automated Robust Quantification of Lesions (SRQL; https://github.com/npnl/SRQL; DOI: 10.5281/zenodo.267213 Toolbox that performs several analysis steps: 1 a white matter intensity correction that removes healthy white matter voxels from the lesion mask, thereby making lesions slightly more robust to subjective errors; 2 an automated report of descriptive statistics on lesions for simplified comparison between or across groups, and 3 an option to perform analyses in both native and standard space to facilitate analyses in either space, or comparisons between spaces. Here, we describe the methods implemented in the toolbox and demonstrate the outputs of the SRQL toolbox.

  19. An Open-Source Toolbox for PEM Fuel Cell Simulation

    Directory of Open Access Journals (Sweden)

    Jean-Paul Kone

    2018-05-01

    Full Text Available In this paper, an open-source toolbox that can be used to accurately predict the distribution of the major physical quantities that are transported within a proton exchange membrane (PEM fuel cell is presented. The toolbox has been developed using the Open Source Field Operation and Manipulation (OpenFOAM platform, which is an open-source computational fluid dynamics (CFD code. The base case results for the distribution of velocity, pressure, chemical species, Nernst potential, current density, and temperature are as expected. The plotted polarization curve was compared to the results from a numerical model and experimental data taken from the literature. The conducted simulations have generated a significant amount of data and information about the transport processes that are involved in the operation of a PEM fuel cell. The key role played by the concentration constant in shaping the cell polarization curve has been explored. The development of the present toolbox is in line with the objectives outlined in the International Energy Agency (IEA, Paris, France Advanced Fuel Cell Annex 37 that is devoted to developing open-source computational tools to facilitate fuel cell technologies. The work therefore serves as a basis for devising additional features that are not always feasible with a commercial code.

  20. Development of Stand Alone Application Tool for Processing and Quality Measurement of Weld Imperfection Image Captured by μ-Focused Digital Radiography Using MATLAB- Based Graphical User Interface

    Directory of Open Access Journals (Sweden)

    PZ Nadila

    2012-12-01

    Full Text Available Digital radiography incresingly is being applied in the fabrication industry. Compared to film- based radiography, digitally radiographed images can be acquired with less time and fewer exposures. However, noises can simply occur on the digital image resulting in a low-quality result. Due to this and the system’s complexity, parameters’ sensitivity, and environmental effects, the results can be difficult to interpret, even for a radiographer. Therefore, the need of an application tool to improve and evaluate the image is becoming urgent. In this research, a user-friendly tool for image processing and image quality measurement was developed. The resulting tool contains important components needed by radiograph inspectors in analyzing defects and recording the results. This tool was written by using image processing and the graphical user interface development environment and compiler (GUIDE toolbox available in Matrix Laboratory (MATLAB R2008a. In image processing methods, contrast adjustment, and noise removal, edge detection was applied. In image quality measurement methods, mean square error (MSE, peak signal-to-noise ratio (PSNR, modulation transfer function (MTF, normalized signal-to-noise ratio (SNRnorm, sensitivity and unsharpness were used to measure the image quality. The graphical user interface (GUI wass then compiled to build a Windows, stand-alone application that enables this tool to be executed independently without the installation of MATLAB.

  1. Configuration and debug of field programmable gate arrays using MATLAB[reg)/SIMULINK[reg

    International Nuclear Information System (INIS)

    Grout, I; Ryan, J; O'Shea, T

    2005-01-01

    Increasingly, the need to seamlessly link high-level behavioural descriptions of electronic hardware for modelling and simulation purposes to the final application hardware highlights the gap between the high-level behavioural descriptions of the required circuit functionality (considering here digital logic) in commonly used mathematical modelling tools, and the hardware description languages such as VHDL and Verilog-HDL. In this paper, the linking of a MATLAB[reg] model for digital algorithm for implementation on a programmable logic device for design synthesis from the MATLAB[reg] model into VHDL is discussed. This VHDL model is itself synthesised and downloaded to the target Field Programmable Gate Array, for normal operation and also for design debug purposes. To demonstrate this, a circuit architecture mapped from a SIMULINK[reg] model is presented. The rationale is for a seamless interface between the initial algorithm development and the target hardware, enabling the hardware to be debugged and compared to the simulated model from a single interface for use with by a non-expert in the programmable logic and hardware description language use

  2. MATLAB as a tool as Analysis and Problem Solving Competency Development in Chemical Engineering Degree using MATLAB

    Directory of Open Access Journals (Sweden)

    Maria-Fernanda López-Pérez

    2016-10-01

    The principal purpose of this work is the students improvement using, as has been mentioned previously, MATLAB in a problem-based learning methodology. This methodology allows a more effective coordination in the degree. The present paper presents a real- world problem and the common elements of most problem-solving contexts and how is designed to function across all disciplines.

  3. FracPaQ: a MATLAB™ toolbox for the quantification of fracture patterns

    Science.gov (United States)

    Healy, David; Rizzo, Roberto; Farrell, Natalie; Watkins, Hannah; Cornwell, David; Gomez-Rivas, Enrique; Timms, Nick

    2017-04-01

    The patterns of fractures in deformed rocks are rarely uniform or random. Fracture orientations, sizes, shapes and spatial distributions often exhibit some kind of order. In detail, there may be relationships among the different fracture attributes e.g. small fractures dominated by one orientation, larger fractures by another. These relationships are important because the mechanical (e.g. strength, anisotropy) and transport (e.g. fluids, heat) properties of rock depend on these fracture patterns and fracture attributes. This presentation describes an open source toolbox to quantify fracture patterns, including distributions in fracture attributes and their spatial variation. Software has been developed to quantify fracture patterns from 2-D digital images, such as thin section micrographs, geological maps, outcrop or aerial photographs or satellite images. The toolbox comprises a suite of MATLAB™ scripts based on published quantitative methods for the analysis of fracture attributes: orientations, lengths, intensity, density and connectivity. An estimate of permeability in 2-D is made using a parallel plate model. The software provides an objective and consistent methodology for quantifying fracture patterns and their variations in 2-D across a wide range of length scales. Our current focus for the application of the software is on quantifying crack and fracture patterns in and around fault zones. There is a large body of published work on the quantification of relatively simple joint patterns, but fault zones present a bigger, and arguably more important, challenge. The methods presented are inherently scale independent, and a key task will be to analyse and integrate quantitative fracture pattern data from micro- to macro-scales. New features in this release include multi-scale analyses based on a wavelet method to look for scale transitions, support for multi-colour traces in the input file processed as separate fracture sets, and combining fracture traces

  4. Simulación del Comportamiento Dinámico de un Pequeño Aerogenerador de Imán Permanente Sin Multiplicador en operación autónoma haciendo uso del MatLab

    Directory of Open Access Journals (Sweden)

    Osley López González

    2011-10-01

    Full Text Available En este trabajo los autores hacen uso del software MATLAB SIMULINK versión 7.7.0.471 R2008b para el análisis del comportamiento de un sistema generación eólico de 2 kW autónomo sin multiplicador con generador de imanes permanentes y batería de Plomo-ácido. Se utilizan para ello los modelos de los generadores de imanes permanentes, batería, convertidores así como otros elementos del sistema eléctrico existente en el toolbox SimPowerSystems de este software y se obtiene y discute el comportamiento dinámico de las variables del conjuntoturbina-generador, las variables del bus de directa, así como también las variables de la carga, ante diferentes condiciones de trabajo del sistema. Los resultados basados en simulaciones muestran el correcto funcionamiento de todas las variables de control que regulan el sistema generador eólico-elemento almacenador-carga eléctrica consumida, cuando se somete a perturbaciones típicas como lo son la variación en racha del viento y variación de la carga repentina. The utilization of the popular software MATLAB SIMULINK 7.7.0.471 in order to analyze a 2kW Direct driven Permanent Magnet generator for wind turbine in autonomous operation, including battery of Lead-acid is exposed by the authors. The existent models of the SimPowerSystems MATLAB toolbox are used in order to obtain and discuss the dynamic behavior of the principal variables under different conditions of work of the system.

  5. A Module for Graphical Display of Model Results with the CBP Toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Smith, F. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-04-21

    This report describes work performed by the Savannah River National Laboratory (SRNL) in fiscal year 2014 to add enhanced graphical capabilities to display model results in the Cementitious Barriers Project (CBP) Toolbox. Because Version 2.0 of the CBP Toolbox has just been released, the graphing enhancements described in this report have not yet been integrated into a new version of the Toolbox. Instead they have been tested using a standalone GoldSim model and, while they are substantially complete, may undergo further refinement before full implementation. Nevertheless, this report is issued to document the FY14 development efforts which will provide a basis for further development of the CBP Toolbox.

  6. CerebroMatic: A Versatile Toolbox for Spline-Based MRI Template Creation.

    Science.gov (United States)

    Wilke, Marko; Altaye, Mekibib; Holland, Scott K

    2017-01-01

    Brain image spatial normalization and tissue segmentation rely on prior tissue probability maps. Appropriately selecting these tissue maps becomes particularly important when investigating "unusual" populations, such as young children or elderly subjects. When creating such priors, the disadvantage of applying more deformation must be weighed against the benefit of achieving a crisper image. We have previously suggested that statistically modeling demographic variables, instead of simply averaging images, is advantageous. Both aspects (more vs. less deformation and modeling vs. averaging) were explored here. We used imaging data from 1914 subjects, aged 13 months to 75 years, and employed multivariate adaptive regression splines to model the effects of age, field strength, gender, and data quality. Within the spm/cat12 framework, we compared an affine-only with a low- and a high-dimensional warping approach. As expected, more deformation on the individual level results in lower group dissimilarity. Consequently, effects of age in particular are less apparent in the resulting tissue maps when using a more extensive deformation scheme. Using statistically-described parameters, high-quality tissue probability maps could be generated for the whole age range; they are consistently closer to a gold standard than conventionally-generated priors based on 25, 50, or 100 subjects. Distinct effects of field strength, gender, and data quality were seen. We conclude that an extensive matching for generating tissue priors may model much of the variability inherent in the dataset which is then not contained in the resulting priors. Further, the statistical description of relevant parameters (using regression splines) allows for the generation of high-quality tissue probability maps while controlling for known confounds. The resulting CerebroMatic toolbox is available for download at http://irc.cchmc.org/software/cerebromatic.php.

  7. Reprocessing Close Range Terrestrial and Uav Photogrammetric Projects with the Dbat Toolbox for Independent Verification and Quality Control

    Science.gov (United States)

    Murtiyoso, A.; Grussenmeyer, P.; Börlin, N.

    2017-11-01

    Photogrammetry has recently seen a rapid increase in many applications, thanks to developments in computing power and algorithms. Furthermore with the democratisation of UAVs (Unmanned Aerial Vehicles), close range photogrammetry has seen more and more use due to the easier capability to acquire aerial close range images. In terms of photogrammetric processing, many commercial software solutions exist in the market that offer results from user-friendly environments. However, in most commercial solutions, a black-box approach to photogrammetric calculations is often used. This is understandable in light of the proprietary nature of the algorithms, but it may pose a problem if the results need to be validated in an independent manner. In this paper, the Damped Bundle Adjustment Toolbox (DBAT) developed for Matlab was used to reprocess some photogrammetric projects that were processed using the commercial software Agisoft Photoscan. Several scenarios were experimented on in order to see the performance of DBAT in reprocessing terrestrial and UAV close range photogrammetric projects in several configurations of self-calibration setting. Results show that DBAT managed to reprocess PS projects and generate metrics which can be useful for project verification.

  8. REPROCESSING CLOSE RANGE TERRESTRIAL AND UAV PHOTOGRAMMETRIC PROJECTS WITH THE DBAT TOOLBOX FOR INDEPENDENT VERIFICATION AND QUALITY CONTROL

    Directory of Open Access Journals (Sweden)

    A. Murtiyoso

    2017-11-01

    Full Text Available Photogrammetry has recently seen a rapid increase in many applications, thanks to developments in computing power and algorithms. Furthermore with the democratisation of UAVs (Unmanned Aerial Vehicles, close range photogrammetry has seen more and more use due to the easier capability to acquire aerial close range images. In terms of photogrammetric processing, many commercial software solutions exist in the market that offer results from user-friendly environments. However, in most commercial solutions, a black-box approach to photogrammetric calculations is often used. This is understandable in light of the proprietary nature of the algorithms, but it may pose a problem if the results need to be validated in an independent manner. In this paper, the Damped Bundle Adjustment Toolbox (DBAT developed for Matlab was used to reprocess some photogrammetric projects that were processed using the commercial software Agisoft Photoscan. Several scenarios were experimented on in order to see the performance of DBAT in reprocessing terrestrial and UAV close range photogrammetric projects in several configurations of self-calibration setting. Results show that DBAT managed to reprocess PS projects and generate metrics which can be useful for project verification.

  9. Spectrum image analysis tool - A flexible MATLAB solution to analyze EEL and CL spectrum images.

    Science.gov (United States)

    Schmidt, Franz-Philipp; Hofer, Ferdinand; Krenn, Joachim R

    2017-02-01

    Spectrum imaging techniques, gaining simultaneously structural (image) and spectroscopic data, require appropriate and careful processing to extract information of the dataset. In this article we introduce a MATLAB based software that uses three dimensional data (EEL/CL spectrum image in dm3 format (Gatan Inc.'s DigitalMicrograph ® )) as input. A graphical user interface enables a fast and easy mapping of spectral dependent images and position dependent spectra. First, data processing such as background subtraction, deconvolution and denoising, second, multiple display options including an EEL/CL moviemaker and, third, the applicability on a large amount of data sets with a small work load makes this program an interesting tool to visualize otherwise hidden details. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Computational mathematics models, methods, and analysis with Matlab and MPI

    CERN Document Server

    White, Robert E

    2004-01-01

    Computational Mathematics: Models, Methods, and Analysis with MATLAB and MPI explores and illustrates this process. Each section of the first six chapters is motivated by a specific application. The author applies a model, selects a numerical method, implements computer simulations, and assesses the ensuing results. These chapters include an abundance of MATLAB code. By studying the code instead of using it as a "black box, " you take the first step toward more sophisticated numerical modeling. The last four chapters focus on multiprocessing algorithms implemented using message passing interface (MPI). These chapters include Fortran 9x codes that illustrate the basic MPI subroutines and revisit the applications of the previous chapters from a parallel implementation perspective. All of the codes are available for download from www4.ncsu.edu./~white.This book is not just about math, not just about computing, and not just about applications, but about all three--in other words, computational science. Whether us...

  11. Integration of Modeling in Solidworks and Matlab/Simulink Environments

    Directory of Open Access Journals (Sweden)

    Cekus Dawid

    2014-03-01

    Full Text Available W pracy opisano tok postepowania podczas budowy modeli symulacyjnych z wykorzystaniem programu SolidWorks i Matlab/Simulink. Tworzenie modelu symulacyjnego przebiega etapami, to znaczy najpierw opracowywany jest model geometryczny w programie SolidWorks, nastepnie dzieki mozliwosci wymiany danych, model CAD jest implementowany w srodowisku obliczeniowym Matlab/Simulink. Modele SimMechanics pozwalaja na sledzenie wielu parametrów, np. trajektorii, predkosci, czy przyspieszen dowolnych elementów układu złozonego. W pracy, jako przykłady modeli symulacyjnych opracowanych zgodnie z zaprezentowana metoda, pokazano modele laboratoryjnego zurawia samochodowego oraz zurawia lesnego. Modele te umozliwiaja wizualizacje zadanego - za pomoca wymuszen kinematycznych - cyklu pracy.

  12. Calcolo scientifico esercizi e problemi risolti con Matlab e Octave

    CERN Document Server

    Quarteroni, Alfio; Gervasio, Paola

    2017-01-01

    Questo testo è concepito per i corsi delle Facoltà di Ingegneria e di Scienze. Esso affronta tutti gli argomenti tipici della Matematica Numerica, spaziando dal problema di risolvere sistemi di equazioni lineari e non lineari a quello di approssimare una funzione, di calcolare i suoi minimi, le sue derivate ed il suo integrale definito fino alla risoluzione di equazioni differenziali ordinarie e alle derivate parziali con metodi alle differenze finite ed agli elementi finiti. Un capitolo iniziale conduce lo studente ad un rapido ripasso degli argomenti dell'Analisi Matematica e dell'Algebra Lineare di uso frequente nel volume e ad una introduzione ai linguaggi MATLAB e Octave. Al fine di rendere maggiormente incisiva la presentazione e fornire un riscontro quantitativo immediato alla teoria vengono implementati in linguaggio MATLAB e Octave tutti gli algoritmi che via via si introducono. Vengono inoltre proposti numerosi esercizi, tutti risolti per esteso, ed esempi, anche con riferimento ad applicazioni in...

  13. AIR Tools - A MATLAB package of algebraic iterative reconstruction methods

    DEFF Research Database (Denmark)

    Hansen, Per Christian; Saxild-Hansen, Maria

    2012-01-01

    We present a MATLAB package with implementations of several algebraic iterative reconstruction methods for discretizations of inverse problems. These so-called row action methods rely on semi-convergence for achieving the necessary regularization of the problem. Two classes of methods are impleme......We present a MATLAB package with implementations of several algebraic iterative reconstruction methods for discretizations of inverse problems. These so-called row action methods rely on semi-convergence for achieving the necessary regularization of the problem. Two classes of methods...... are implemented: Algebraic Reconstruction Techniques (ART) and Simultaneous Iterative Reconstruction Techniques (SIRT). In addition we provide a few simplified test problems from medical and seismic tomography. For each iterative method, a number of strategies are available for choosing the relaxation parameter...

  14. Digital signal processing for wireless communication using Matlab

    CERN Document Server

    Gopi, E S

    2016-01-01

    This book examines signal processing techniques used in wireless communication illustrated by using the Matlab program. The author discusses these techniques as they relate to Doppler spread; delay spread; Rayleigh and Rician channel modeling; rake receiver; diversity techniques; MIMO and OFDM -based transmission techniques; and array signal processing. Related topics such as detection theory, link budget, multiple access techniques, and spread spectrum are also covered.   ·         Illustrates signal processing techniques involved in wireless communication using Matlab ·         Discusses multiple access techniques such as Frequency division multiple access, Time division multiple access, and Code division multiple access ·         Covers band pass modulation techniques such as Binary phase shift keying, Differential phase shift keying, Quadrature phase shift keying, Binary frequency shift keying, Minimum shift keying, and Gaussian minimum shift keying.

  15. A Matlab Tool for Tumor Localization in Parathyroid Sestamibi Scintigraphy

    Directory of Open Access Journals (Sweden)

    M. Đurović

    2015-11-01

    Full Text Available Submarine method for localization of parathyroid tumors (PT has proved to be effective in case of typical pitfalls of conventional scintigraphic methods (combined subtraction and double phase methods. It uses images obtained by standard dynamic parathyroid sestamibi scintigraphy suggested by European Association of Nuclear Medicine. This paper presents: 1 the developed Matlab interface that enables the implementation and evaluation of algorithms for the automatic application of Submarine method; 2 the algorithm for automatic extraction of the entire thyroid region from the background radioactivity using operations from mathematical morphology applied on dynamic scintigrams; 3 the results obtained by algorithm for localization and visualization of PTs based on estimation of exponential decreasing trend of time-activity curves. The algorithm was tested on a group of 20 patients with histopathologically proven PTs using developed Matlab interface.

  16. MATLAB/SIMULINK model of CANDU reactor for control studies

    International Nuclear Information System (INIS)

    Javidnia, H.; Jiang, J.

    2006-01-01

    In this paper a MATLAB/SIMULINK model is developed for a CANDU type reactor. The data for the reactor are taken from an Indian PHWR, which is very similar to CANDU in its design. Among the different feedback mechanisms in the core of the reactor, only xenon has been considered which plays an important role in spatial oscillations. The model is verified under closed loop scenarios with simple PI controller. The results of the simulation show that this model can be used for controller design and simulation of the reactor systems. Adding models of the other components of a CANDU reactor would ultimately result in a complete model of CANDU plant in MATLAB/SIMULINK. (author)

  17. Scientific computing an introduction using Maple and Matlab

    CERN Document Server

    Gander, Walter; Kwok, Felix

    2014-01-01

    Scientific computing is the study of how to use computers effectively to solve problems that arise from the mathematical modeling of phenomena in science and engineering. It is based on mathematics, numerical and symbolic/algebraic computations and visualization. This book serves as an introduction to both the theory and practice of scientific computing, with each chapter presenting the basic algorithms that serve as the workhorses of many scientific codes; we explain both the theory behind these algorithms and how they must be implemented in order to work reliably in finite-precision arithmetic. The book includes many programs written in Matlab and Maple – Maple is often used to derive numerical algorithms, whereas Matlab is used to implement them. The theory is developed in such a way that students can learn by themselves as they work through the text. Each chapter contains numerous examples and problems to help readers understand the material “hands-on”.

  18. Slow Orbit Feedback at the ALS Using Matlab

    International Nuclear Information System (INIS)

    Portmann, G.

    1999-01-01

    The third generation Advanced Light Source (ALS) produces extremely bright and finely focused photon beams using undulatory, wigglers, and bend magnets. In order to position the photon beams accurately, a slow global orbit feedback system has been developed. The dominant causes of orbit motion at the ALS are temperature variation and insertion device motion. This type of motion can be removed using slow global orbit feedback with a data rate of a few Hertz. The remaining orbit motion in the ALS is only 1-3 micron rms. Slow orbit feedback does not require high computational throughput. At the ALS, the global orbit feedback algorithm, based on the singular valued decomposition method, is coded in MATLAB and runs on a control room workstation. Using the MATLAB environment to develop, test, and run the storage ring control algorithms has proven to be a fast and efficient way to operate the ALS

  19. First experience with the MATLAB Middle Layer at ANKA

    International Nuclear Information System (INIS)

    Marsching, S.; Huttel, E.; Klein, M.; Mueller, A.S.; Smale, N.J.

    2012-01-01

    ANKA is a synchrotron radiation facility at the Karlsruhe Institute of Technology. The MATLAB Middle Layer (MML) is a collection of scripts for the MATLAB programming environment, designed to control and measure parameters of an accelerator. MML has been adapted for use at ANKA and the commissioning process was quite simple and would have been even simpler if we had used one of the control systems directly supported by MML. At ANKA MML is used for accelerator physics studies and regular tasks like beam-based alignment and response matrix analysis using LOCO. Furthermore, we intend to study the MML as default orbit correction tool for user operation. We report on the experience made during the commissioning process and present the latest results obtained while using the MML for machine studies. MML simplifies the task of performing a beam-based alignment dramatically compared to our old solution which required the user to copy the measured data into specific files for further evaluation

  20. MATLAB based beam orbit correction system of HLS storage ring

    International Nuclear Information System (INIS)

    Ding Shichuan; Liu Gongfa; Xuan Ke; Li Weimin; Wang Lin; Wang Jigang; Li Chuan; Bao Xun; Guo Weiqun

    2006-01-01

    The distortion of closed orbit usually causes much side effect which is harmful to synchrotron radiation source such as HLS, so it is necessary to correct the distortion of closed orbit. In this paper, the correction principle, development procedure and test of MATLAB based on beam orbit correction system of HLS storage ring are described. The correction system is consisted of the beam orbit measure system, corrector magnet system and the control system, and the beam orbit correction code based on MATLAB is working on the operation interface. The data of the beam orbit are analyzed and calculated firstly, and then the orbit is corrected by changing corrector strength via control system. The test shows that the distortion of closed orbit is from max 4.468 mm before correction to max 0.299 mm after correction as well as SDEV is from 2.986 mm to 0.087 mm. So the correction system reaches the design goal. (authors)

  1. Research Reactor Power Control System Design by MATLAB/SIMULINK

    International Nuclear Information System (INIS)

    Baang, Dane; Suh, Yong Suk; Kim, Young Ki; Im, Ki Hong

    2013-01-01

    In this study it is presented that MATLAB/SIMULINK can be efficiently used for modeling and power control system design for research reactors. The presented power control system deals with various functions including reactivity control, signals processing, reactivity calculation, alarm request generation, etc., thus it is required to test all the software logic using proper model for reactor, control rods, and field instruments. In MATLAB/SIMULINK tool, point kinetics, thermal model, control absorber rod model, and other instrument models were developed based on reactor parameters and known properties of each component or system. The software for power control system was invented and linked to the model to test each function. From the simulation result it is shown that the power control performance and other functions of the system can be easily tested and analyzed in the proposed simulation structure

  2. Processing of hyperspectral medical images applications in dermatology using Matlab

    CERN Document Server

    Koprowski, Robert

    2017-01-01

    This book presents new methods of analyzing and processing hyperspectral medical images, which can be used in diagnostics, for example for dermatological images. The algorithms proposed are fully automatic and the results obtained are fully reproducible. Their operation was tested on a set of several thousands of hyperspectral images and they were implemented in Matlab. The presented source code can be used without licensing restrictions. This is a valuable resource for computer scientists, bioengineers, doctoral students, and dermatologists interested in contemporary analysis methods.

  3. Online design of Matlab/Simulink block schemes

    Directory of Open Access Journals (Sweden)

    Zoltán Janík

    2011-04-01

    Full Text Available The paper presents a new online tool that enables to build a Matlab/Simulink block scheme in the Internet environment. The block scheme can be designed in similar manner as it is offered by local installation of Simulink. The application was created by widely used technologies as XHTML, CSS, JavaScript, PHP together with AJAX approach. The created application can be used as a supporting tool in virtual and remote laboratories.

  4. AIR Tools - A MATLAB Package of Algebraic Iterative Reconstruction Techniques

    DEFF Research Database (Denmark)

    Hansen, Per Christian; Saxild-Hansen, Maria

    This collection of MATLAB software contains implementations of several Algebraic Iterative Reconstruction methods for discretizations of inverse problems. These so-called row action methods rely on semi-convergence for achieving the necessary regularization of the problem. Two classes of methods...... are implemented: Algebraic Reconstruction Techniques (ART) and Simultaneous Iterative Reconstruction Techniques (SIRT). In addition we provide a few simplified test problems from medical and seismic tomography. For each iterative method, a number of strategies are available for choosing the relaxation parameter...

  5. Applied Statistics Using SPSS, STATISTICA, MATLAB and R

    CERN Document Server

    De Sá, Joaquim P Marques

    2007-01-01

    This practical reference provides a comprehensive introduction and tutorial on the main statistical analysis topics, demonstrating their solution with the most common software package. Intended for anyone needing to apply statistical analysis to a large variety of science and enigineering problems, the book explains and shows how to use SPSS, MATLAB, STATISTICA and R for analysis such as data description, statistical inference, classification and regression, factor analysis, survival data and directional statistics. It concisely explains key concepts and methods, illustrated by practical examp

  6. Model of a photovoltaic panel emulator in MATLAB-Simulink

    OpenAIRE

    CAN, Hayrettin

    2014-01-01

    Being able to behave electrically similar to photovoltaic (PV) panels, PV emulator systems make it possible to perform different PV system tests under various operation conditions. In this paper, a model of a PV panel emulator is presented using the Power System Blockset under MATLAB-Simulink. The simulation of the emulator system is developed for testing a controller prior to a real-time implementation. The model can handle the dependence of all of the parameters in the model with ...

  7. Virtual experiment of optical spatial filtering in Matlab environment

    Science.gov (United States)

    Ji, Yunjing; Wang, Chunyong; Song, Yang; Lai, Jiancheng; Wang, Qinghua; Qi, Jing; Shen, Zhonghua

    2017-08-01

    The principle of spatial filtering experiment has been introduced, and the computer simulation platform with graphical user interface (GUI) has been made out in Matlab environment. Using it various filtering processes for different input image or different filtering purpose will be completed accurately, and filtering effect can be observed clearly with adjusting experimental parameters. The physical nature of the optical spatial filtering can be showed vividly, and so experimental teaching effect will be promoted.

  8. Matlab implementation of LASSO, LARS, the elastic net and SPCA

    DEFF Research Database (Denmark)

    2005-01-01

    There are a number of interesting variable selection methods available beside the regular forward selection and stepwise selection methods. Such approaches include LASSO (Least Absolute Shrinkage and Selection Operator), least angle regression (LARS) and elastic net (LARS-EN) regression. There al...... exists a method for calculating principal components with sparse loadings. This software package contains Matlab implementations of these functions. The standard implementations of these functions are available as add-on packages in S-Plus and R....

  9. Introduction to Artificial Vision through Laboratory Guides Using Matlab

    OpenAIRE

    Verónica Londoño-Osorio; Jhovana Marín-Pineda; Eliana I. Arango-Zuluaga

    2013-01-01

    This paper presents the design of two laboratory guides in artificial vision for a course which aims to introduce students to the different areas of specialization of his career. Therefore, the designed practices motivate and provide relevant content to the student, and to encourage research in the area of image processing. The first guide presents an introductory practice that explores the basic commands for image processing by programming a GUI in Matlab, and a second practice in which you ...

  10. Simulasi Teknik Modulasi Ofdm Qpsk Dengan Menggunakan Matlab

    OpenAIRE

    Subrata, Rosalia H; Gozali, Ferrianto

    2015-01-01

    This paper provides a brief explanation of the processing steps involved in Orthogonal Frequency Division Multiplexing (OFDM) with Quadrature Phase Shift Keying (QPSK) modulation technique implemented as a simulation program in MatLab. Input data of the simulation program in the form of random bit stream or text can be selected by users. The process conducted in the simulation is divided into three consecutive steps, processes in the OFDM transmitter, in transmission channel and in the OFDM r...

  11. Nonlinear distortion in wireless systems modeling and simulation with Matlab

    CERN Document Server

    Gharaibeh, Khaled M

    2011-01-01

    This book covers the principles of modeling and simulation of nonlinear distortion in wireless communication systems with MATLAB simulations and techniques In this book, the author describes the principles of modeling and simulation of nonlinear distortion in single and multichannel wireless communication systems using both deterministic and stochastic signals. Models and simulation methods of nonlinear amplifiers explain in detail how to analyze and evaluate the performance of data communication links under nonlinear amplification. The book addresses the analysis of nonlinear systems

  12. Robotics, vision and control fundamental algorithms in Matlab

    CERN Document Server

    Corke, Peter

    2017-01-01

    Robotic vision, the combination of robotics and computer vision, involves the application of computer algorithms to data acquired from sensors. The research community has developed a large body of such algorithms but for a newcomer to the field this can be quite daunting. For over 20 years the author has maintained two open-source MATLAB® Toolboxes, one for robotics and one for vision. They provide implementations of many important algorithms and allow users to work with real problems, not just trivial examples. This book makes the fundamental algorithms of robotics, vision and control accessible to all. It weaves together theory, algorithms and examples in a narrative that covers robotics and computer vision separately and together. Using the latest versions of the Toolboxes the author shows how complex problems can be decomposed and solved using just a few simple lines of code. The topics covered are guided by real problems observed by the author over many years as a practitioner of both robotics and compu...

  13. Matlab enhanced multi-threaded tomography optimization sequence (MEMTOS)

    International Nuclear Information System (INIS)

    Lum, Edward S.; Pope, Chad L.

    2016-01-01

    Highlights: • Monte Carlo simulation of spent nuclear fuel assembly neutron computed tomography. • Optimized parallel calculations conducted from within the MATLAB environment. • Projection difference technique used to identify anomalies in spent nuclear fuel assemblies. - Abstract: One challenge associated with spent nuclear fuel assemblies is the lack of non-destructive analysis techniques to determine if fuel pins have been removed or replaced or if there are significant defects associated with fuel pins deep within a fuel assembly. Neutron computed tomography is a promising technique for addressing these qualitative issues. Monte Carlo simulation of spent nuclear fuel neutron computed tomography allows inexpensive process investigation and optimization. The main purpose of this work is to provide a fully automated advanced simulation framework for the analysis of spent nuclear fuel inspection using neutron computed tomography. The simulation framework, called Matlab Enhanced Multi-Threaded Tomography Optimization Sequence (MEMTOS) not only automates the simulation process, but also generates superior tomography image results. MEMTOS is written in the MATLAB scripting language and addresses file management, parallel Monte Carlo execution, results extraction, and tomography image generation. This paper describes the mathematical basis for neutron computed tomography, the Monte Carlo technique used to simulate neutron computed tomography, and the overall tomography simulation optimization algorithm. Sequence results presented include overall simulation speed enhancement, tomography and image results obtained for Experimental Breeder Reactor II spent fuel assemblies and light water reactor fuel assemblies. Optimization using a projection difference technique are also described.

  14. MATLAB as an incentive for student learning of skills

    Science.gov (United States)

    Bank, C. G.; Ghent, R. R.

    2016-12-01

    Our course "Computational Geology" takes a holistic approach to student learning by using MATLAB as a focal point to increase students' computing, quantitative reasoning, data analysis, report writing, and teamwork skills. The course, taught since 2007 with recent enrollments around 35 and aimed at 2nd to 3rd-year students, is required for the Geology and Earth and Environmental Systems major programs, and can be chosen as elective in our other programs, including Geophysics. The course is divided into five projects: Pacific plate velocity from the Hawaiian hotspot track, predicting CO2 concentration in the atmosphere, volume of Earth's oceans and sea-level rise, comparing wind directions for Vancouver and Squamish, and groundwater flow. Each project is based on real data, focusses on a mathematical concept (linear interpolation, gradients, descriptive statistics, differential equations) and highlights a programming task (arrays, functions, text file input/output, curve fitting). Working in teams of three, students need to develop a conceptional model to explain the data, and write MATLAB code to visualize the data and match it to their conceptional model. The programming is guided, and students work individually on different aspects (for example: reading the data, fitting a function, unit conversion) which they need to put together to solve the problem. They then synthesize their thought process in a paper. Anecdotal evidence shows that students continue using MATLAB in other courses.

  15. Design of high-performance parallelized gene predictors in MATLAB.

    Science.gov (United States)

    Rivard, Sylvain Robert; Mailloux, Jean-Gabriel; Beguenane, Rachid; Bui, Hung Tien

    2012-04-10

    This paper proposes a method of implementing parallel gene prediction algorithms in MATLAB. The proposed designs are based on either Goertzel's algorithm or on FFTs and have been implemented using varying amounts of parallelism on a central processing unit (CPU) and on a graphics processing unit (GPU). Results show that an implementation using a straightforward approach can require over 4.5 h to process 15 million base pairs (bps) whereas a properly designed one could perform the same task in less than five minutes. In the best case, a GPU implementation can yield these results in 57 s. The present work shows how parallelism can be used in MATLAB for gene prediction in very large DNA sequences to produce results that are over 270 times faster than a conventional approach. This is significant as MATLAB is typically overlooked due to its apparent slow processing time even though it offers a convenient environment for bioinformatics. From a practical standpoint, this work proposes two strategies for accelerating genome data processing which rely on different parallelization mechanisms. Using a CPU, the work shows that direct access to the MEX function increases execution speed and that the PARFOR construct should be used in order to take full advantage of the parallelizable Goertzel implementation. When the target is a GPU, the work shows that data needs to be segmented into manageable sizes within the GFOR construct before processing in order to minimize execution time.

  16. A Collection of Nonlinear Aircraft Simulations in MATLAB

    Science.gov (United States)

    Garza, Frederico R.; Morelli, Eugene A.

    2003-01-01

    Nonlinear six degree-of-freedom simulations for a variety of aircraft were created using MATLAB. Data for aircraft geometry, aerodynamic characteristics, mass / inertia properties, and engine characteristics were obtained from open literature publications documenting wind tunnel experiments and flight tests. Each nonlinear simulation was implemented within a common framework in MATLAB, and includes an interface with another commercially-available program to read pilot inputs and produce a three-dimensional (3-D) display of the simulated airplane motion. Aircraft simulations include the General Dynamics F-16 Fighting Falcon, Convair F-106B Delta Dart, Grumman F-14 Tomcat, McDonnell Douglas F-4 Phantom, NASA Langley Free-Flying Aircraft for Sub-scale Experimental Research (FASER), NASA HL-20 Lifting Body, NASA / DARPA X-31 Enhanced Fighter Maneuverability Demonstrator, and the Vought A-7 Corsair II. All nonlinear simulations and 3-D displays run in real time in response to pilot inputs, using contemporary desktop personal computer hardware. The simulations can also be run in batch mode. Each nonlinear simulation includes the full nonlinear dynamics of the bare airframe, with a scaled direct connection from pilot inputs to control surface deflections to provide adequate pilot control. Since all the nonlinear simulations are implemented entirely in MATLAB, user-defined control laws can be added in a straightforward fashion, and the simulations are portable across various computing platforms. Routines for trim, linearization, and numerical integration are included. The general nonlinear simulation framework and the specifics for each particular aircraft are documented.

  17. DSISoft—a MATLAB VSP data processing package

    Science.gov (United States)

    Beaty, K. S.; Perron, G.; Kay, I.; Adam, E.

    2002-05-01

    DSISoft is a public domain vertical seismic profile processing software package developed at the Geological Survey of Canada. DSISoft runs under MATLAB version 5.0 and above and hence is portable between computer operating systems supported by MATLAB (i.e. Unix, Windows, Macintosh, Linux). The package includes processing modules for reading and writing various standard seismic data formats, performing data editing, sorting, filtering, and other basic processing modules. The processing sequence can be scripted allowing batch processing and easy documentation. A structured format has been developed to ensure future additions to the package are compatible with existing modules. Interactive modules have been created using MATLAB's graphical user interface builder for displaying seismic data, picking first break times, examining frequency spectra, doing f- k filtering, and plotting the trace header information. DSISoft modular design facilitates the incorporation of new processing algorithms as they are developed. This paper gives an overview of the scope of the software and serves as a guide for the addition of new modules.

  18. A Compilation of MATLAB Scripts and Functions for MACGMC Analyses

    Science.gov (United States)

    Murthy, Pappu L. N.; Bednarcyk, Brett A.; Mital, Subodh K.

    2017-01-01

    The primary aim of the current effort is to provide scripts that automate many of the repetitive pre- and post-processing tasks associated with composite materials analyses using the Micromechanics Analysis Code with the Generalized Method of Cells. This document consists of a compilation of hundreds of scripts that were developed in MATLAB (The Mathworks, Inc., Natick, MA) programming language and consolidated into 16 MATLAB functions. (MACGMC). MACGMC is a composite material and laminate analysis software code developed at NASA Glenn Research Center. The software package has been built around the generalized method of cells (GMC) family of micromechanics theories. The computer code is developed with a user-friendly framework, along with a library of local inelastic, damage, and failure models. Further, application of simulated thermo-mechanical loading, generation of output results, and selection of architectures to represent the composite material have been automated to increase the user friendliness, as well as to make it more robust in terms of input preparation and code execution. Finally, classical lamination theory has been implemented within the software, wherein GMC is used to model the composite material response of each ply. Thus, the full range of GMC composite material capabilities is available for analysis of arbitrary laminate configurations as well. The pre-processing tasks include generation of a multitude of different repeating unit cells (RUCs) for CMCs and PMCs, visualization of RUCs from MACGMC input and output files and generation of the RUC section of a MACGMC input file. The post-processing tasks include visualization of the predicted composite response, such as local stress and strain contours, damage initiation and progression, stress-strain behavior, and fatigue response. In addition to the above, several miscellaneous scripts have been developed that can be used to perform repeated Monte-Carlo simulations to enable probabilistic

  19. Evaluation Toolbox: Ex-Ante Impact Assessment and Value Network Analysis for SI

    NARCIS (Netherlands)

    Dhondt, S.; Ven, H. van de; Cressey, P.; Kaderabkova, A.; Luna, Á.; Moghadam Saman, S.; Castro Spila, J.; Ziauberyte, R.; Torre, W. van der; Terstriep, J.

    2016-01-01

    This report contains a toolbox for use with the Ex-Ante Impact Assessment for social innovations as was developed in the report D7.1. This toolbox proposes a series of convenient and useful tools to apply in an ex-ante assessment of social innovation within SIMPACT's policy areas unemployment,

  20. Design and Implementation of a Space Environment Simulation Toolbox for Small Satellites

    DEFF Research Database (Denmark)

    Amini, Rouzbeh; Larsen, Jesper A.; Izadi-Zamanabadi, Roozbeh

    This paper presents a developed toolbox for space environment model in SIMULINK that facilitates development and design of Attitude Determination and Control Systems (ADCS) for a Low Earth Orbit (LEO) spacecraft. The toolbox includes, among others, models of orbit propagators, disturbances, Earth...

  1. Adding tools to the open source toolbox: The Internet

    Science.gov (United States)

    Porth, Tricia

    1994-01-01

    The Internet offers researchers additional sources of information not easily available from traditional sources such as print volumes or commercial data bases. Internet tools such as e-mail and file transfer protocol (ftp) speed up the way researchers communicate and transmit data. Mosaic, one of the newest additions to the Internet toolbox, allows users to combine tools such as ftp, gopher, wide area information server, and the world wide web with multimedia capabilities. Mosaic has quickly become a popular means of making information available on the Internet because it is versatile and easily customizable.

  2. Rangeland Brush Estimation Toolbox (RaBET): An Approach for Evaluating Brush Management Conservation Efforts in Western Grazing Lands

    Science.gov (United States)

    Holifield Collins, C.; Kautz, M. A.; Skirvin, S. M.; Metz, L. J.

    2016-12-01

    There are over 180 million hectares of rangelands and grazed forests in the central and western United States. Due to the loss of perennial grasses and subsequent increased runoff and erosion that can degrade the system, woody cover species cannot be allowed to proliferate unchecked. The USDA-Natural Resources Conservation Service (NRCS) has allocated extensive resources to employ brush management (removal) as a conservation practice to control woody species encroachment. The Rangeland-Conservation Effects Assessment Project (CEAP) has been tasked with determining how effective the practice has been, however their land managers lack a cost-effective means to conduct these assessments at the necessary scale. An ArcGIS toolbox for generating large-scale, Landsat-based, spatial maps of woody cover on grazing lands in the western United States was developed through a collaboration with NRCS Rangeland-CEAP. The toolbox contains two main components of operation, image generation and temporal analysis, and utilizes simple interfaces requiring minimum user inputs. The image generation tool utilizes geographically specific algorithms developed from combining moderate-resolution (30-m) Landsat imagery and high-resolution (1-m) National Agricultural Imagery Program (NAIP) aerial photography to produce the woody cover scenes at the Major Land Resource (MLRA) scale. The temporal analysis tool can be used on these scenes to assess treatment effectiveness and monitor woody cover reemergence. RaBET provides rangeland managers an operational, inexpensive decision support tool to aid in the application of brush removal treatments and assessing their effectiveness.

  3. A part toolbox to tune genetic expression in Bacillus subtilis

    Science.gov (United States)

    Guiziou, Sarah; Sauveplane, Vincent; Chang, Hung-Ju; Clerté, Caroline; Declerck, Nathalie; Jules, Matthieu; Bonnet, Jerome

    2016-01-01

    Libraries of well-characterised components regulating gene expression levels are essential to many synthetic biology applications. While widely available for the Gram-negative model bacterium Escherichia coli, such libraries are lacking for the Gram-positive model Bacillus subtilis, a key organism for basic research and biotechnological applications. Here, we engineered a genetic toolbox comprising libraries of promoters, Ribosome Binding Sites (RBS), and protein degradation tags to precisely tune gene expression in B. subtilis. We first designed a modular Expression Operating Unit (EOU) facilitating parts assembly and modifications and providing a standard genetic context for gene circuits implementation. We then selected native, constitutive promoters of B. subtilis and efficient RBS sequences from which we engineered three promoters and three RBS sequence libraries exhibiting ∼14 000-fold dynamic range in gene expression levels. We also designed a collection of SsrA proteolysis tags of variable strength. Finally, by using fluorescence fluctuation methods coupled with two-photon microscopy, we quantified the absolute concentration of GFP in a subset of strains from the library. Our complete promoters and RBS sequences library comprising over 135 constructs enables tuning of GFP concentration over five orders of magnitude, from 0.05 to 700 μM. This toolbox of regulatory components will support many research and engineering applications in B. subtilis. PMID:27402159

  4. SCoT: a Python toolbox for EEG source connectivity.

    Science.gov (United States)

    Billinger, Martin; Brunner, Clemens; Müller-Putz, Gernot R

    2014-01-01

    Analysis of brain connectivity has become an important research tool in neuroscience. Connectivity can be estimated between cortical sources reconstructed from the electroencephalogram (EEG). Such analysis often relies on trial averaging to obtain reliable results. However, some applications such as brain-computer interfaces (BCIs) require single-trial estimation methods. In this paper, we present SCoT-a source connectivity toolbox for Python. This toolbox implements routines for blind source decomposition and connectivity estimation with the MVARICA approach. Additionally, a novel extension called CSPVARICA is available for labeled data. SCoT estimates connectivity from various spectral measures relying on vector autoregressive (VAR) models. Optionally, these VAR models can be regularized to facilitate ill posed applications such as single-trial fitting. We demonstrate basic usage of SCoT on motor imagery (MI) data. Furthermore, we show simulation results of utilizing SCoT for feature extraction in a BCI application. These results indicate that CSPVARICA and correct regularization can significantly improve MI classification. While SCoT was mainly designed for application in BCIs, it contains useful tools for other areas of neuroscience. SCoT is a software package that (1) brings combined source decomposition and connectivtiy estimation to the open Python platform, and (2) offers tools for single-trial connectivity estimation. The source code is released under the MIT license and is available online at github.com/SCoT-dev/SCoT.

  5. SCoT: A Python Toolbox for EEG Source Connectivity

    Directory of Open Access Journals (Sweden)

    Martin eBillinger

    2014-03-01

    Full Text Available Analysis of brain connectivity has become an important research tool in neuroscience. Connectivity can be estimated between cortical sources reconstructed from the electroencephalogram (EEG. Such analysis often relies on trial averaging to obtain reliable results. However, some applications such as brain-computer interfaces (BCIs require single-trial estimation methods.In this paper, we present SCoT – a source connectivity toolbox for Python. This toolbox implements routines for blind source decomposition and connectivity estimation with theMVARICA approach. Additionally, a novel extension called CSPVARICA is available for labeled data. SCoT estimates connectivity from various spectral measures relying on vector autoregressive (VAR models. Optionally, these VAR models can be regularized to facilitate ill posed applications such as single-trial fitting.We demonstrate basic usage of SCoT on motor imagery (MI data. Furthermore, we show simulation results of utilizing SCoT for feature extraction in a BCI application. These results indicate that CSPVARICA and correct regularization can significantly improve MI classification. While SCoT was mainly designed for application in BCIs, it contains useful tools for other areas of neuroscience. SCoT is a software package that (1 brings combined source decomposition and connectivtiy estimation to the open Python platform, and (2 offers tools for single-trial connectivity estimation. The source code is released under the MIT license and is available online at github.com/SCoT-dev/SCoT.

  6. Semi-automated Robust Quantification of Lesions (SRQL Toolbox

    Directory of Open Access Journals (Sweden)

    Kaori L Ito

    2017-05-01

    Full Text Available Quantifying lesions in a reliable manner is fundamental for studying the effects of neuroanatomical changes related to recovery in the post-stroke brain. However, the wide variability in lesion characteristics across individuals makes manual lesion segmentation a challenging and often subjective process. This often makes it difficult to combine stroke lesion data across multiple research sites, due to subjective differences in how lesions may be defined. Thus, we developed the Semi-automated Robust Quantification of Lesions (SRQL; https://github.com/npnl/SRQL; DOI: 10.5281/zenodo.557114 Toolbox that performs several analysis steps: 1 a white matter intensity correction that removes healthy white matter voxels from the lesion mask, thereby making lesions slightly more robust to subjective errors; 2 an automated report of descriptive statistics on lesions for simplified comparison between or across groups, and 3 an option to perform analyses in both native and standard space to facilitate analyses in either space. Here, we describe the methods implemented in the toolbox.

  7. SIGNUM: A Matlab, TIN-based landscape evolution model

    Science.gov (United States)

    Refice, A.; Giachetta, E.; Capolongo, D.

    2012-08-01

    Several numerical landscape evolution models (LEMs) have been developed to date, and many are available as open source codes. Most are written in efficient programming languages such as Fortran or C, but often require additional code efforts to plug in to more user-friendly data analysis and/or visualization tools to ease interpretation and scientific insight. In this paper, we present an effort to port a common core of accepted physical principles governing landscape evolution directly into a high-level language and data analysis environment such as Matlab. SIGNUM (acronym for Simple Integrated Geomorphological Numerical Model) is an independent and self-contained Matlab, TIN-based landscape evolution model, built to simulate topography development at various space and time scales. SIGNUM is presently capable of simulating hillslope processes such as linear and nonlinear diffusion, fluvial incision into bedrock, spatially varying surface uplift which can be used to simulate changes in base level, thrust and faulting, as well as effects of climate changes. Although based on accepted and well-known processes and algorithms in its present version, it is built with a modular structure, which allows to easily modify and upgrade the simulated physical processes to suite virtually any user needs. The code is conceived as an open-source project, and is thus an ideal tool for both research and didactic purposes, thanks to the high-level nature of the Matlab environment and its popularity among the scientific community. In this paper the simulation code is presented together with some simple examples of surface evolution, and guidelines for development of new modules and algorithms are proposed.

  8. Curtain Antenna Array Simulation Research Based on MATLAB

    Directory of Open Access Journals (Sweden)

    Hongbo LIU

    2014-01-01

    Full Text Available For the radiating capacity of curtain antenna array, this paper constructs a three- line-four-column curtain antenna array using cage antenna as the antenna array element and obtains a normalizing 3D radiation patterns through conducting simulation with MATLAB. Meanwhile, the relationships between the antenna spacing and the largest directivity coefficient, as well as the communication frequency and largest directivity coefficient are analyzed in this paper. It turns out that the max value will generate when the antenna spacing is around 18 m and the best communication effect will be achieved when the communication frequency is about 12.4 MHz.

  9. PEM fuel cell modeling and simulation using Matlab

    CERN Document Server

    Spiegel, Colleen

    2011-01-01

    Although, the basic concept of a fuel cell is quite simple, creating new designs and optimizing their performance takes serious work and a mastery of several technical areas. PEM Fuel Cell Modeling and Simulation Using Matlab, provides design engineers and researchers with a valuable tool for understanding and overcoming barriers to designing and building the next generation of PEM Fuel Cells. With this book, engineers can test components and verify designs in the development phase, saving both time and money.Easy to read and understand, this book provides design and modelling tips for

  10. Obtención de curvas de residuo con Matlab

    OpenAIRE

    Barrio García-Parra, Marco Bruno del

    2017-01-01

    Los diagramas de curvas de residuo son una herramienta cualitativa que permite una mejor comprensión de los procesos físicos que se dan en la destilación de sistemas multicomponente. Una curva de residuo representa la evolución de la composición de una mezcla líquida según se va evaporando y retirando el vapor producido resultante de la ebullición. En este trabajo se expone la metodología, resultados y conclusiones que han llevado a la obtención de curvas de residuo con Matlab® en sistema...

  11. ADAMS-MATLAB Co-Simulation of A Serial Manipulator

    Directory of Open Access Journals (Sweden)

    Parthasarathy Tejaswin

    2017-01-01

    Full Text Available This paper presents the dynamic modelling and simulation of a now redundant robot, Mitsubishi RM-501, and proposes a general algorithm for experimental simulation in kinematics, dynamics and control analysis to any such robot. Through reverse engineering, a model as accurate as the real robot was developed in SolidWorks.The simulations of the same were performed in ADAMS (dynamicmodeling software offered by MSC Software Corpalong with MATLAB for motion studies and control dynamics. Finally, with a user-input path the accuracy and precision of the simulator was verified.

  12. Discrete random signal processing and filtering primer with Matlab

    CERN Document Server

    Poularikas, Alexander D

    2013-01-01

    Engineers in all fields will appreciate a practical guide that combines several new effective MATLAB® problem-solving approaches and the very latest in discrete random signal processing and filtering.Numerous Useful Examples, Problems, and Solutions - An Extensive and Powerful ReviewWritten for practicing engineers seeking to strengthen their practical grasp of random signal processing, Discrete Random Signal Processing and Filtering Primer with MATLAB provides the opportunity to doubly enhance their skills. The author, a leading expert in the field of electrical and computer engineering, offe

  13. Image processing tensor transform and discrete tomography with Matlab

    CERN Document Server

    Grigoryan, Artyom M

    2012-01-01

    Focusing on mathematical methods in computer tomography, Image Processing: Tensor Transform and Discrete Tomography with MATLAB(R) introduces novel approaches to help in solving the problem of image reconstruction on the Cartesian lattice. Specifically, it discusses methods of image processing along parallel rays to more quickly and accurately reconstruct images from a finite number of projections, thereby avoiding overradiation of the body during a computed tomography (CT) scan. The book presents several new ideas, concepts, and methods, many of which have not been published elsewhere. New co

  14. Causes of maternal mortality decline in Matlab, Bangladesh.

    Science.gov (United States)

    Chowdhury, Mahbub Elahi; Ahmed, Anisuddin; Kalim, Nahid; Koblinsky, Marge

    2009-04-01

    Bangladesh is distinct among developing countries in achieving a low maternal mortality ratio (MMR) of 322 per 100,000 livebirths despite the very low use of skilled care at delivery (13% nationally). This variation has also been observed in Matlab, a rural area in Bangladesh, where longitudinal data on maternal mortality are available since the mid-1970s. The current study investigated the possible causes of the maternal mortality decline in Matlab. The study analyzed 769 maternal deaths and 215,779 pregnancy records from the Health and Demographic Surveillance System (HDSS) and other sources of safe motherhood data in the ICDDR,B and government service areas in Matlab during 1976-2005. The major interventions that took place in both the areas since the early 1980s were the family-planning programme plus safe menstrual regulation services and safe motherhood interventions (midwives for normal delivery in the ICDDR,B service area from the late 1980s and equal access to comprehensive emergency obstetric care [EmOC] in public facilities for women from both the areas). National programmes for social development and empowerment of women through education and microcredit programmes were implemented in both the areas. The quantitative findings were supplemented by a qualitative study by interviewing local community care providers for their change in practices for maternal healthcare over time. After the introduction of the safe motherhood programme, reduction in maternal mortality was higher in the ICDDR,B service area (68.6%) than in the government service area (50.4%) during 1986-1989 and 2001-2005. Reduction in the number of maternal deaths due to the fertility decline was higher in the government service area (30%) than in the ICDDR,B service area (23%) during 1979-2005. In each area, there has been substantial reduction in abortion-related mortality--86.7% and 78.3%--in the ICDDR,B and government service areas respectively. Education of women was a strong predictor

  15. Automatic analysis of intrinsic positional verification films brachytherapy using MATLAB

    International Nuclear Information System (INIS)

    Quiros Higueras, J. D.; Marco Blancas, N. de; Ruiz Rodriguez, J. C.

    2011-01-01

    One of the essential tests in quality control of brachytherapy equipment is verification auto load intrinsic positional radioactive source. A classic method for evaluation is the use of x-ray film and measuring the distance between the marks left by autoradiography of the source with respect to a reference. In our center has developed an automated method of measurement by the radiochromic film scanning and implementation of a macro developed in Matlab, in order to optimize time and reduce uncertainty in the measurement. The purpose of this paper is to describe the method developed, assess their uncertainty and quantify their advantages over the manual method. (Author)

  16. Efficient topology optimization in MATLAB using 88 lines of code

    DEFF Research Database (Denmark)

    Andreassen, Erik; Clausen, Anders; Schevenels, Mattias

    2011-01-01

    The paper presents an efficient 88 line MATLAB code for topology optimization. It has been developed using the 99 line code presented by Sigmund (Struct Multidisc Optim 21(2):120–127, 2001) as a starting point. The original code has been extended by a density filter, and a considerable improvemen...... of the basic code to include recent PDE-based and black-and-white projection filtering methods. The complete 88 line code is included as an appendix and can be downloaded from the web site www.topopt.dtu.dk....

  17. Digital Signal Processing for Medical Imaging Using Matlab

    CERN Document Server

    Gopi, E S

    2013-01-01

    This book describes medical imaging systems, such as X-ray, Computed tomography, MRI, etc. from the point of view of digital signal processing. Readers will see techniques applied to medical imaging such as Radon transformation, image reconstruction, image rendering, image enhancement and restoration, and more. This book also outlines the physics behind medical imaging required to understand the techniques being described. The presentation is designed to be accessible to beginners who are doing research in DSP for medical imaging. Matlab programs and illustrations are used wherever possible to reinforce the concepts being discussed.  ·         Acts as a “starter kit” for beginners doing research in DSP for medical imaging; ·         Uses Matlab programs and illustrations throughout to make content accessible, particularly with techniques such as Radon transformation and image rendering; ·         Includes discussion of the basic principles behind the various medical imaging tec...

  18. KiT: a MATLAB package for kinetochore tracking.

    Science.gov (United States)

    Armond, Jonathan W; Vladimirou, Elina; McAinsh, Andrew D; Burroughs, Nigel J

    2016-06-15

    During mitosis, chromosomes are attached to the mitotic spindle via large protein complexes called kinetochores. The motion of kinetochores throughout mitosis is intricate and automated quantitative tracking of their motion has already revealed many surprising facets of their behaviour. Here, we present 'KiT' (Kinetochore Tracking)-an easy-to-use, open-source software package for tracking kinetochores from live-cell fluorescent movies. KiT supports 2D, 3D and multi-colour movies, quantification of fluorescence, integrated deconvolution, parallel execution and multiple algorithms for particle localization. KiT is free, open-source software implemented in MATLAB and runs on all MATLAB supported platforms. KiT can be downloaded as a package from http://www.mechanochemistry.org/mcainsh/software.php The source repository is available at https://bitbucket.org/jarmond/kit and under continuing development. Supplementary data are available at Bioinformatics online. jonathan.armond@warwick.ac.uk. © The Author 2016. Published by Oxford University Press.

  19. Solution of the reactor point kinetics equations by MATLAB computing

    Directory of Open Access Journals (Sweden)

    Singh Sudhansu S.

    2015-01-01

    Full Text Available The numerical solution of the point kinetics equations in the presence of Newtonian temperature feedback has been a challenging issue for analyzing the reactor transients. Reactor point kinetics equations are a system of stiff ordinary differential equations which need special numerical treatments. Although a plethora of numerical intricacies have been introduced to solve the point kinetics equations over the years, some of the simple and straightforward methods still work very efficiently with extraordinary accuracy. As an example, it has been shown recently that the fundamental backward Euler finite difference algorithm with its simplicity has proven to be one of the most effective legacy methods. Complementing the back-ward Euler finite difference scheme, the present work demonstrates the application of ordinary differential equation suite available in the MATLAB software package to solve the stiff reactor point kinetics equations with Newtonian temperature feedback effects very effectively by analyzing various classic benchmark cases. Fair accuracy of the results implies the efficient application of MATLAB ordinary differential equation suite for solving the reactor point kinetics equations as an alternate method for future applications.

  20. Interval Coded Scoring: a toolbox for interpretable scoring systems

    Directory of Open Access Journals (Sweden)

    Lieven Billiet

    2018-04-01

    Full Text Available Over the last decades, clinical decision support systems have been gaining importance. They help clinicians to make effective use of the overload of available information to obtain correct diagnoses and appropriate treatments. However, their power often comes at the cost of a black box model which cannot be interpreted easily. This interpretability is of paramount importance in a medical setting with regard to trust and (legal responsibility. In contrast, existing medical scoring systems are easy to understand and use, but they are often a simplified rule-of-thumb summary of previous medical experience rather than a well-founded system based on available data. Interval Coded Scoring (ICS connects these two approaches, exploiting the power of sparse optimization to derive scoring systems from training data. The presented toolbox interface makes this theory easily applicable to both small and large datasets. It contains two possible problem formulations based on linear programming or elastic net. Both allow to construct a model for a binary classification problem and establish risk profiles that can be used for future diagnosis. All of this requires only a few lines of code. ICS differs from standard machine learning through its model consisting of interpretable main effects and interactions. Furthermore, insertion of expert knowledge is possible because the training can be semi-automatic. This allows end users to make a trade-off between complexity and performance based on cross-validation results and expert knowledge. Additionally, the toolbox offers an accessible way to assess classification performance via accuracy and the ROC curve, whereas the calibration of the risk profile can be evaluated via a calibration curve. Finally, the colour-coded model visualization has particular appeal if one wants to apply ICS manually on new observations, as well as for validation by experts in the specific application domains. The validity and applicability

  1. ASAP (Automatic Software for ASL Processing): A toolbox for processing Arterial Spin Labeling images.

    Science.gov (United States)

    Mato Abad, Virginia; García-Polo, Pablo; O'Daly, Owen; Hernández-Tamames, Juan Antonio; Zelaya, Fernando

    2016-04-01

    The method of Arterial Spin Labeling (ASL) has experienced a significant rise in its application to functional imaging, since it is the only technique capable of measuring blood perfusion in a truly non-invasive manner. Currently, there are no commercial packages for processing ASL data and there is no recognized standard for normalizing ASL data to a common frame of reference. This work describes a new Automated Software for ASL Processing (ASAP) that can automatically process several ASL datasets. ASAP includes functions for all stages of image pre-processing: quantification, skull-stripping, co-registration, partial volume correction and normalization. To assess the applicability and validity of the toolbox, this work shows its application in the study of hypoperfusion in a sample of healthy subjects at risk of progressing to Alzheimer's disease. ASAP requires limited user intervention, minimizing the possibility of random and systematic errors, and produces cerebral blood flow maps that are ready for statistical group analysis. The software is easy to operate and results in excellent quality of spatial normalization. The results found in this evaluation study are consistent with previous studies that find decreased perfusion in Alzheimer's patients in similar regions and demonstrate the applicability of ASAP. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. Design and Implementation of a Space Environment Simulation Toolbox for Small Satellites

    DEFF Research Database (Denmark)

    Amini, Rouzbeh; Larsen, Jesper A.; Izadi-Zamanabadi, Roozbeh

    2005-01-01

    This paper presents a developed toolbox for space environment model in SIMULINK that facilitates development and design of Attitude Determination and Control Systems (ADCS) for a Low Earth Orbit (LEO) spacecraft. The toolbox includes, among others, models of orbit propagators, disturbances, Earth...... gravity field, Earth magnetic field and eclipse. The structure and facilities within the toolbox are described and exemplified using a student satellite case (AAUSAT-II). The validity of developed models is confirmed by comparing the simulation results with the realistic data obtained from the Danish...

  3. Development of MATLAB Scripts for the Calculation of Thermal Manikin Regional Resistance Values

    Science.gov (United States)

    2016-01-01

    TECHNICAL NOTE NO. TN16-1 DATE January 2016 ADA DEVELOPMENT OF MATLAB ® SCRIPTS FOR THE...USARIEM TECHNICAL NOTE TN16-1 DEVELOPMENT OF MATLAB ® SCRIPTS FOR THE CALCULATION OF THERMAL MANIKIN REGIONAL RESISTANCE VALUES...EXECUTIVE SUMMARY A software tool has been developed via MATLAB ® scripts to reduce the amount of repetitive and time-consuming calculations that are

  4. DYNAMIC SYSTEM ANALYSIS WITH pplane8.m (MATLAB® toolbox

    Directory of Open Access Journals (Sweden)

    Alejandro Regalado-Méndez

    2013-12-01

    Full Text Available In this work, four dynamic systems were analyzed (physical, chemical, ecological and economical, represented by autonomous systems of two ordinary differential equations. Main objective is proving that pplane8.m is an adequate and efficient computer tool. The analysis of autonomous systems was given by characterization of their critical points according to Coughanowr & LeBlanc (2009, with the MATLAB® toolbox pplane8.m. The main results are that pplane8.m (Polking, 2009 can quickly and precisely draw trajectories of each phase plane, it easily computes each critical point, and correctly characterize each equilibrium point of all autonomous studied systems. Finally, we can say that pplane8.m is a powerful tool to help the teaching-learning process for engineering students.

  5. The influence of industrial applications on a control system toolbox

    International Nuclear Information System (INIS)

    Clout, P.

    1992-01-01

    Vsystem is as an open, advanced software application toolbox for rapidly creating fast, efficient and cost-effective control and data-acquisition systems. Vsystem's modular architecture is designed for single computers, networked computers and workstations running under VAX/VMS or VAX/ELN. At the heart of Vsystem lies Vaccess, a user extendible real-time database and library of access routines. The application database provides the link to the hardware of the application and can be organized as one database or separate database installed in different computers on the network. Vsystem has found application in charged-particle accelerator control, tokamak control, and industrial research, as well as its more recent industrial applications. This paper describes the broad feature of Vsystem and the influence that recent industrial applications have had on the software. (author)

  6. Neuro-QOL and the NIH Toolbox: implications for epilepsy

    Science.gov (United States)

    Nowinski, Cindy J; Victorson, David; Cavazos, Jose E; Gershon, Richard; Cella, David

    2011-01-01

    The impact of neurological disorders on the lives of patients is often far more complex than what is measured in routine examination. Measurement of this impact can be challenging owing to a lack of brief, psychometrically sound and generally accepted instruments. Two NIH-funded initiatives are developing assessment tools, in English and Spanish, which address these issues, and should prove useful to the study and treatment of epilepsy and other neurological conditions. The first, Neuro-QOL, has created a set of health-related quality of life measures that are applicable for people with common neurological disorders. The second, the NIH Toolbox for the Assessment of Neurological and Behavioral Function, is assembling measures of cognitive, emotional, motor and sensory health and function that can be used across all ages, from 3 to 85 years. This article describes both the projects and their potential value to epilepsy treatment and research. PMID:21552344

  7. A fractured rock geophysical toolbox method selection tool

    Science.gov (United States)

    Day-Lewis, F. D.; Johnson, C.D.; Slater, L.D.; Robinson, J.L.; Williams, J.H.; Boyden, C.L.; Werkema, D.D.; Lane, J.W.

    2016-01-01

    Geophysical technologies have the potential to improve site characterization and monitoring in fractured rock, but the appropriate and effective application of geophysics at a particular site strongly depends on project goals (e.g., identifying discrete fractures) and site characteristics (e.g., lithology). No method works at every site or for every goal. New approaches are needed to identify a set of geophysical methods appropriate to specific project goals and site conditions while considering budget constraints. To this end, we present the Excel-based Fractured-Rock Geophysical Toolbox Method Selection Tool (FRGT-MST). We envision the FRGT-MST (1) equipping remediation professionals with a tool to understand what is likely to be realistic and cost-effective when contracting geophysical services, and (2) reducing applications of geophysics with unrealistic objectives or where methods are likely to fail.

  8. Peptide chemistry toolbox - Transforming natural peptides into peptide therapeutics.

    Science.gov (United States)

    Erak, Miloš; Bellmann-Sickert, Kathrin; Els-Heindl, Sylvia; Beck-Sickinger, Annette G

    2018-06-01

    The development of solid phase peptide synthesis has released tremendous opportunities for using synthetic peptides in medicinal applications. In the last decades, peptide therapeutics became an emerging market in pharmaceutical industry. The need for synthetic strategies in order to improve peptidic properties, such as longer half-life, higher bioavailability, increased potency and efficiency is accordingly rising. In this mini-review, we present a toolbox of modifications in peptide chemistry for overcoming the main drawbacks during the transition from natural peptides to peptide therapeutics. Modifications at the level of the peptide backbone, amino acid side chains and higher orders of structures are described. Furthermore, we are discussing the future of peptide therapeutics development and their impact on the pharmaceutical market. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Development of an Ontology-Directed Signal Processing Toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Stephen W. Lang

    2011-05-27

    This project was focused on the development of tools for the automatic configuration of signal processing systems. The goal is to develop tools that will be useful in a variety of Government and commercial areas and useable by people who are not signal processing experts. In order to get the most benefit from signal processing techniques, deep technical expertise is often required in order to select appropriate algorithms, combine them into a processing chain, and tune algorithm parameters for best performance on a specific problem. Therefore a significant benefit would result from the assembly of a toolbox of processing algorithms that has been selected for their effectiveness in a group of related problem areas, along with the means to allow people who are not signal processing experts to reliably select, combine, and tune these algorithms to solve specific problems. Defining a vocabulary for problem domain experts that is sufficiently expressive to drive the configuration of signal processing functions will allow the expertise of signal processing experts to be captured in rules for automated configuration. In order to test the feasibility of this approach, we addressed a lightning classification problem, which was proposed by DOE as a surrogate for problems encountered in nuclear nonproliferation data processing. We coded a toolbox of low-level signal processing algorithms for extracting features of RF waveforms, and demonstrated a prototype tool for screening data. We showed examples of using the tool for expediting the generation of ground-truth metadata, for training a signal recognizer, and for searching for signals with particular characteristics. The public benefits of this approach, if successful, will accrue to Government and commercial activities that face the same general problem - the development of sensor systems for complex environments. It will enable problem domain experts (e.g. analysts) to construct signal and image processing chains without

  10. Expanding access to rheumatology care: the rheumatology general practice toolbox.

    LENUS (Irish Health Repository)

    Conway, R

    2015-02-01

    Management guidelines for many rheumatic diseases are published in specialty rheumatology literature but rarely in general medical journals. Musculoskeletal disorders comprise 14% of all consultations in primary care. Formal post-graduate training in rheumatology is limited or absent for many primary care practitioners. Primary care practitioners can be trained to effectively treat complex diseases and have expressed a preference for interactive educational courses. The Rheumatology General Practice (GP) Toolbox is an intensive one day course designed to offer up to date information to primary care practitioners on the latest diagnostic and treatment guidelines for seven common rheumatic diseases. The course structure involves a short lecture on each topic and workshops on arthrocentesis, joint injection and DXA interpretation. Participants evaluated their knowledge and educational experience before, during and after the course. Thirty-two primary care practitioners attended, who had a median of 13 (IQR 6.5, 20) years experience in their specialty. The median number of educational symposia attended in the previous 5 years was 10 (IQR-5, 22.5), with a median of 0 (IQR 0, 1) in rheumatology. All respondents agreed that the course format was appropriate. Numerical improvements were demonstrated in participant\\'s confidence in diagnosing and managing all seven common rheumatologic conditions, with statistically significant improvements (p < 0.05) in 11 of the 14 aspects assessed. The Rheumatology Toolbox is an effective educational method for disseminating current knowledge in rheumatology to primary care physicians and improved participant\\'s self-assessed competence in diagnosis and management of common rheumatic diseases.

  11. Developing a Conceptual Design Engineering Toolbox and its Tools

    Directory of Open Access Journals (Sweden)

    R. W. Vroom

    2004-01-01

    Full Text Available In order to develop a successful product, a design engineer needs to pay attention to all relevant aspects of that product. Many tools are available, software, books, websites, and commercial services. To unlock these potentially useful sources of knowledge, we are developing C-DET, a toolbox for conceptual design engineering. The idea of C-DET is that designers are supported by a system that provides them with a knowledge portal on one hand, and a system to store their current work on the other. The knowledge portal is to help the designer to find the most appropriate sites, experts, tools etc. at a short notice. Such a toolbox offers opportunities to incorporate extra functionalities to support the design engineering work. One of these functionalities could be to help the designer to reach a balanced comprehension in his work. Furthermore C-DET enables researchers in the area of design engineering and design engineers themselves to find each other or their work earlier and more easily. Newly developed design tools that can be used by design engineers but have not yet been developed up to a commercial level could be linked to by C-DET. In this way these tools can be evaluated in an early stage by design engineers who would like to use them. This paper describes the first prototypes of C-DET, an example of the development of a design tool that enables designers to forecast the use process and an example of the future functionalities of C-DET such as balanced comprehension.

  12. PEANO, a toolbox for real-time process signal validation and estimation

    Energy Technology Data Exchange (ETDEWEB)

    Fantoni, Paolo F.; Figedy, Stefan; Racz, Attila

    1998-02-01

    PEANO (Process Evaluation and Analysis by Neural Operators), a toolbox for real time process signal validation and condition monitoring has been developed. This system analyses the signals, which are e.g. the readings of process monitoring sensors, computes their expected values and alerts if real values are deviated from the expected ones more than limits allow. The reliability level of the current analysis is also produced. The system is based on neuro-fuzzy techniques. Artificial Neural Networks and Fuzzy Logic models can be combined to exploit learning and generalisation capability of the first technique with the approximate reasoning embedded in the second approach. Real-time process signal validation is an application field where the use of this technique can improve the diagnosis of faulty sensors and the identification of outliers in a robust and reliable way. This study implements a fuzzy and possibilistic clustering algorithm to classify the operating region where the validation process has to be performed. The possibilistic approach (rather than probabilistic) allows a ''don't know'' classification that results in a fast detection of unforeseen plant conditions or outliers. Specialised Artificial Neural Networks are used for the validation process, one for each fuzzy cluster in which the operating map has been divided. There are two main advantages in using this technique: the accuracy and generalisation capability is increased compared to the case of a single network working in the entire operating region, and the ability to identify abnormal conditions, where the system is not capable to operate with a satisfactory accuracy, is improved. This model has been tested in a simulated environment on a French PWR, to monitor safety-related reactor variables over the entire power-flow operating map. (author)

  13. PEANO, a toolbox for real-time process signal validation and estimation

    International Nuclear Information System (INIS)

    Fantoni, Paolo F.; Figedy, Stefan; Racz, Attila

    1998-02-01

    PEANO (Process Evaluation and Analysis by Neural Operators), a toolbox for real time process signal validation and condition monitoring has been developed. This system analyses the signals, which are e.g. the readings of process monitoring sensors, computes their expected values and alerts if real values are deviated from the expected ones more than limits allow. The reliability level of the current analysis is also produced. The system is based on neuro-fuzzy techniques. Artificial Neural Networks and Fuzzy Logic models can be combined to exploit learning and generalisation capability of the first technique with the approximate reasoning embedded in the second approach. Real-time process signal validation is an application field where the use of this technique can improve the diagnosis of faulty sensors and the identification of outliers in a robust and reliable way. This study implements a fuzzy and possibilistic clustering algorithm to classify the operating region where the validation process has to be performed. The possibilistic approach (rather than probabilistic) allows a ''don't know'' classification that results in a fast detection of unforeseen plant conditions or outliers. Specialised Artificial Neural Networks are used for the validation process, one for each fuzzy cluster in which the operating map has been divided. There are two main advantages in using this technique: the accuracy and generalisation capability is increased compared to the case of a single network working in the entire operating region, and the ability to identify abnormal conditions, where the system is not capable to operate with a satisfactory accuracy, is improved. This model has been tested in a simulated environment on a French PWR, to monitor safety-related reactor variables over the entire power-flow operating map. (author)

  14. Toolbox for Urban Mobility Simulation: High Resolution Population Dynamics for Global Cities

    Science.gov (United States)

    Bhaduri, B. L.; Lu, W.; Liu, C.; Thakur, G.; Karthik, R.

    2015-12-01

    In this rapidly urbanizing world, unprecedented rate of population growth is not only mirrored by increasing demand for energy, food, water, and other natural resources, but has detrimental impacts on environmental and human security. Transportation simulations are frequently used for mobility assessment in urban planning, traffic operation, and emergency management. Previous research, involving purely analytical techniques to simulations capturing behavior, has investigated questions and scenarios regarding the relationships among energy, emissions, air quality, and transportation. Primary limitations of past attempts have been availability of input data, useful "energy and behavior focused" models, validation data, and adequate computational capability that allows adequate understanding of the interdependencies of our transportation system. With increasing availability and quality of traditional and crowdsourced data, we have utilized the OpenStreetMap roads network, and has integrated high resolution population data with traffic simulation to create a Toolbox for Urban Mobility Simulations (TUMS) at global scale. TUMS consists of three major components: data processing, traffic simulation models, and Internet-based visualizations. It integrates OpenStreetMap, LandScanTM population, and other open data (Census Transportation Planning Products, National household Travel Survey, etc.) to generate both normal traffic operation and emergency evacuation scenarios. TUMS integrates TRANSIMS and MITSIM as traffic simulation engines, which are open-source and widely-accepted for scalable traffic simulations. Consistent data and simulation platform allows quick adaption to various geographic areas that has been demonstrated for multiple cities across the world. We are combining the strengths of geospatial data sciences, high performance simulations, transportation planning, and emissions, vehicle and energy technology development to design and develop a simulation

  15. FZUImageReg: A toolbox for medical image registration and dose fusion in cervical cancer radiotherapy.

    Directory of Open Access Journals (Sweden)

    Qinquan Gao

    Full Text Available The combination external-beam radiotherapy and high-dose-rate brachytherapy is a standard form of treatment for patients with locally advanced uterine cervical cancer. Personalized radiotherapy in cervical cancer requires efficient and accurate dose planning and assessment across these types of treatment. To achieve radiation dose assessment, accurate mapping of the dose distribution from HDR-BT onto EBRT is extremely important. However, few systems can achieve robust dose fusion and determine the accumulated dose distribution during the entire course of treatment. We have therefore developed a toolbox (FZUImageReg, which is a user-friendly dose fusion system based on hybrid image registration for radiation dose assessment in cervical cancer radiotherapy. The main part of the software consists of a collection of medical image registration algorithms and a modular design with a user-friendly interface, which allows users to quickly configure, test, monitor, and compare different registration methods for a specific application. Owing to the large deformation, the direct application of conventional state-of-the-art image registration methods is not sufficient for the accurate alignment of EBRT and HDR-BT images. To solve this problem, a multi-phase non-rigid registration method using local landmark-based free-form deformation is proposed for locally large deformation between EBRT and HDR-BT images, followed by intensity-based free-form deformation. With the transformation, the software also provides a dose mapping function according to the deformation field. The total dose distribution during the entire course of treatment can then be presented. Experimental results clearly show that the proposed system can achieve accurate registration between EBRT and HDR-BT images and provide radiation dose warping and fusion results for dose assessment in cervical cancer radiotherapy in terms of high accuracy and efficiency.

  16. Numerical linear algebra a concise introduction with Matlab and Julia

    CERN Document Server

    Bornemann, Folkmar

    2018-01-01

    This book offers an introduction to the algorithmic-numerical thinking using basic problems of linear algebra. By focusing on linear algebra, it ensures a stronger thematic coherence than is otherwise found in introductory lectures on numerics. The book highlights the usefulness of matrix partitioning compared to a component view, leading not only to a clearer notation and shorter algorithms, but also to significant runtime gains in modern computer architectures. The algorithms and accompanying numerical examples are given in the programming environment MATLAB, and additionally – in an appendix – in the future-oriented, freely accessible programming language Julia. This book is suitable for a two-hour lecture on numerical linear algebra from the second semester of a bachelor's degree in mathematics.

  17. Bifurcation software in Matlab with applications in neuronal modeling.

    Science.gov (United States)

    Govaerts, Willy; Sautois, Bart

    2005-02-01

    Many biological phenomena, notably in neuroscience, can be modeled by dynamical systems. We describe a recent improvement of a Matlab software package for dynamical systems with applications to modeling single neurons and all-to-all connected networks of neurons. The new software features consist of an object-oriented approach to bifurcation computations and the partial inclusion of C-code to speed up the computation. As an application, we study the origin of the spiking behaviour of neurons when the equilibrium state is destabilized by an incoming current. We show that Class II behaviour, i.e. firing with a finite frequency, is possible even if the destabilization occurs through a saddle-node bifurcation. Furthermore, we show that synchronization of an all-to-all connected network of such neurons with only excitatory connections is also possible in this case.

  18. Proper generalized decompositions an introduction to computer implementation with Matlab

    CERN Document Server

    Cueto, Elías; Alfaro, Icíar

    2016-01-01

    This book is intended to help researchers overcome the entrance barrier to Proper Generalized Decomposition (PGD), by providing a valuable tool to begin the programming task. Detailed Matlab Codes are included for every chapter in the book, in which the theory previously described is translated into practice. Examples include parametric problems, non-linear model order reduction and real-time simulation, among others. Proper Generalized Decomposition (PGD) is a method for numerical simulation in many fields of applied science and engineering. As a generalization of Proper Orthogonal Decomposition or Principal Component Analysis to an arbitrary number of dimensions, PGD is able to provide the analyst with very accurate solutions for problems defined in high dimensional spaces, parametric problems and even real-time simulation. .

  19. Numerical simulation of dimples in airfoil using MATLAB

    Science.gov (United States)

    Booma Devi, P.; Shah, Dilip A.

    2017-05-01

    The Aircraft wing is a point of important research which poses greater challenge in terms of aerodynamic efficiency. The flow separation control method is addressed in classical aerodynamics methods. This study focuses on influence of dimples on controlling the flow and also increasing the aerodynamic efficiency. The periodic process of placing the cavities on the wing starting from root to tip controls the flow separation. The linear variation of characteristic curve provides the information about the flow separation and control of flow on upper surface of the airfoil.These different shapes are utilized viz., Square, Rectangle and Triangle. The numerical simulation is carried out in using MATLAB package. Preliminary analysis on the flow separation is carried out focuses on laminar flow separation, which has the influence on the overall lift generation and drag generation.

  20. MATLAB Simulation of RFID Communication Protocol for Sensor Data Acquisition

    Directory of Open Access Journals (Sweden)

    Soumen GHOSH

    2015-05-01

    Full Text Available Data acquisition processes the sampling and conditioning the signals that measure real world physical conditions such as temperature, pressure, flow etc. and convert the signal into in appropriate format for displaying and transmission to remote end. Now a days RFID i.e. Radio Frequency Identification plays a vital role in Data acquisition system. The present article proposes a smart DAS scheme containing RFID reader and Active tag. The data acquisition system is interfaced with tag through I2C bus. The reader communicates with tag following RFID communication protocol requesting to send the logged data which are refreshed and stored into tag memory periodically. The communication is simulated using MATLAB software successfully.

  1. Introduction to Artificial Vision through Laboratory Guides Using Matlab

    Directory of Open Access Journals (Sweden)

    Verónica Londoño-Osorio

    2013-11-01

    Full Text Available This paper presents the design of two laboratory guides in artificial vision for a course which aims to introduce students to the different areas of specialization of his career. Therefore, the designed practices motivate and provide relevant content to the student, and to encourage research in the area of image processing. The first guide presents an introductory practice that explores the basic commands for image processing by programming a GUI in Matlab, and a second practice in which you use an image recognition algorithm, which compares the color characteristics of facial or objects images. The discussion of the results, challenges and recommendations for the development of each practice session are explained. The survey answers of the students are displayed. This survey allows checking their level of acceptance for the design and content of practice and motivation to continue studying in the image processing area. Finally, comparisons with laboratory guides that were designed in other universities are made.

  2. Some selected quantitative methods of thermal image analysis in Matlab.

    Science.gov (United States)

    Koprowski, Robert

    2016-05-01

    The paper presents a new algorithm based on some selected automatic quantitative methods for analysing thermal images. It shows the practical implementation of these image analysis methods in Matlab. It enables to perform fully automated and reproducible measurements of selected parameters in thermal images. The paper also shows two examples of the use of the proposed image analysis methods for the area of ​​the skin of a human foot and face. The full source code of the developed application is also provided as an attachment. The main window of the program during dynamic analysis of the foot thermal image. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. A GUI tool for beta function measurement using MATLAB

    International Nuclear Information System (INIS)

    Chen Guangling; Tian Shunqiang; Liu Guimin; Jiang Bocheng

    2009-01-01

    The beta function measurement is used to detect the shift in the betatron tune as the strength of an individual quadrupole magnet is varied. A GUI (graphic user interface) tool for the beta function measurement is developed using the MATLAB program language in the Linux environment, which facilitates the commissioning of the Shanghai Synchrotron Radiation Facility (SSRF) storage ring. In this paper, we describe the design of the application and give some measuring results and discussions about the definition of the measurement. The program has been optimized to solve some restrictions of the AT tracking code. After the correction with LOCO (linear optics from closed orbits), the horizontal and the vertical root mean square values (rms values) can be reduced to 0.12 and 0.10. (authors)

  4. The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

    Energy Technology Data Exchange (ETDEWEB)

    Aarle, Wim van, E-mail: wim.vanaarle@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Palenstijn, Willem Jan, E-mail: willemjan.palenstijn@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Centrum Wiskunde & Informatica, Science Park 123, NL-1098 XG Amsterdam (Netherlands); De Beenhouwer, Jan, E-mail: jan.debeenhouwer@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Altantzis, Thomas, E-mail: thomas.altantzis@uantwerpen.be [Electron Microscopy for Materials Science, University of Antwerp, Groenenborgerlaan 171, B-2020 Wilrijk (Belgium); Bals, Sara, E-mail: sara.bals@uantwerpen.be [Electron Microscopy for Materials Science, University of Antwerp, Groenenborgerlaan 171, B-2020 Wilrijk (Belgium); Batenburg, K. Joost, E-mail: joost.batenburg@cwi.nl [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Centrum Wiskunde & Informatica, Science Park 123, NL-1098 XG Amsterdam (Netherlands); Mathematical Institute, Leiden University, P.O. Box 9512, NL-2300 RA Leiden (Netherlands); Sijbers, Jan, E-mail: jan.sijbers@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium)

    2015-10-15

    We present the ASTRA Toolbox as an open platform for 3D image reconstruction in tomography. Most of the software tools that are currently used in electron tomography offer limited flexibility with respect to the geometrical parameters of the acquisition model and the algorithms used for reconstruction. The ASTRA Toolbox provides an extensive set of fast and flexible building blocks that can be used to develop advanced reconstruction algorithms, effectively removing these limitations. We demonstrate this flexibility, the resulting reconstruction quality, and the computational efficiency of this toolbox by a series of experiments, based on experimental dual-axis tilt series. - Highlights: • The ASTRA Toolbox is an open platform for 3D image reconstruction in tomography. • Advanced reconstruction algorithms can be prototyped using the fast and flexible building blocks. • This flexibility is demonstrated on a common use case: dual-axis tilt series reconstruction with prior knowledge. • The computational efficiency is validated on an experimentally measured tilt series.

  5. Reinforcement Toolbox, a Parametric Reinforcement Modelling Tool for Curved Surface Structures

    NARCIS (Netherlands)

    Lauppe, J.; Rolvink, A.; Coenders, J.L.

    2013-01-01

    This paper presents a computational strategy and parametric modelling toolbox which aim at enhancing the design- and production process of reinforcement in freeform curved surface structures. The computational strategy encompasses the necessary steps of raising an architectural curved surface model

  6. A microfluidic toolbox for the development of in-situ product removal strategies in biocatalysis

    DEFF Research Database (Denmark)

    Heintz, Søren; Mitic, Aleksandar; Ringborg, Rolf Hoffmeyer

    2016-01-01

    A microfluidic toolbox for accelerated development of biocatalytic processes has great potential. This is especially the case for the development of advanced biocatalytic process concepts, where reactors and product separation methods are closely linked together to intensify the process performan...

  7. A toolbox for safety instrumented system evaluation based on improved continuous-time Markov chain

    Science.gov (United States)

    Wardana, Awang N. I.; Kurniady, Rahman; Pambudi, Galih; Purnama, Jaka; Suryopratomo, Kutut

    2017-08-01

    Safety instrumented system (SIS) is designed to restore a plant into a safe condition when pre-hazardous event is occur. It has a vital role especially in process industries. A SIS shall be meet with safety requirement specifications. To confirm it, SIS shall be evaluated. Typically, the evaluation is calculated by hand. This paper presents a toolbox for SIS evaluation. It is developed based on improved continuous-time Markov chain. The toolbox supports to detailed approach of evaluation. This paper also illustrates an industrial application of the toolbox to evaluate arch burner safety system of primary reformer. The results of the case study demonstrates that the toolbox can be used to evaluate industrial SIS in detail and to plan the maintenance strategy.

  8. Review of Qualitative Approaches for the Construction Industry: Designing a Risk Management Toolbox

    Directory of Open Access Journals (Sweden)

    David M. Zalk

    2011-06-01

    Conclusion: The Construction Toolbox presents a review-generated format to harness multiple solutions-based national programs and publications for controlling construction-related risks with simplified approaches across the occupational safety, health and hygiene professions.

  9. The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

    International Nuclear Information System (INIS)

    Aarle, Wim van; Palenstijn, Willem Jan; De Beenhouwer, Jan; Altantzis, Thomas; Bals, Sara; Batenburg, K. Joost; Sijbers, Jan

    2015-01-01

    We present the ASTRA Toolbox as an open platform for 3D image reconstruction in tomography. Most of the software tools that are currently used in electron tomography offer limited flexibility with respect to the geometrical parameters of the acquisition model and the algorithms used for reconstruction. The ASTRA Toolbox provides an extensive set of fast and flexible building blocks that can be used to develop advanced reconstruction algorithms, effectively removing these limitations. We demonstrate this flexibility, the resulting reconstruction quality, and the computational efficiency of this toolbox by a series of experiments, based on experimental dual-axis tilt series. - Highlights: • The ASTRA Toolbox is an open platform for 3D image reconstruction in tomography. • Advanced reconstruction algorithms can be prototyped using the fast and flexible building blocks. • This flexibility is demonstrated on a common use case: dual-axis tilt series reconstruction with prior knowledge. • The computational efficiency is validated on an experimentally measured tilt series

  10. Non-stationary Condition Monitoring of large diesel engines with the AEWATT toolbox

    DEFF Research Database (Denmark)

    Pontoppidan, Niels Henrik; Larsen, Jan; Sigurdsson, Sigurdur

    2005-01-01

    We are developing a specialized toolbox for non-stationary condition monitoring of large 2-stroke diesel engines based on acoustic emission measurements. The main contribution of this toolbox has so far been the utilization of adaptive linear models such as Principal and Independent Component Ana......, the inversion of those angular timing changes called “event alignment”, has allowed for condition monitoring across operation load settings, successfully enabling a single model to be used with realistic data under varying operational conditions-...

  11. A MATLAB-Aided Method for Teaching Calculus-Based Business Mathematics

    Science.gov (United States)

    Liang, Jiajuan; Pan, William S. Y.

    2009-01-01

    MATLAB is a powerful package for numerical computation. MATLAB contains a rich pool of mathematical functions and provides flexible plotting functions for illustrating mathematical solutions. The course of calculus-based business mathematics consists of two major topics: 1) derivative and its applications in business; and 2) integration and its…

  12. Matlab for electrical and computer engineering students and professionals with Simulink

    CERN Document Server

    Priemer, Roland

    2013-01-01

    This book combines the teaching of the MATLAB#65533; programming language with the presentation and development of carefully selected electrical and computer engineering (ECE) fundamentals. This is what distinguishes it from other books concerned with MATLAB#65533;: it is directed specifically to ECE concerns.

  13. Scilab and MATLAB Interfaces to MUMPS (version 4.6 or greater)

    OpenAIRE

    Fèvre , Aurélia; Pralet , Stéphane; L'Excellent , Jean-Yves

    2006-01-01

    This document describes the Scilab and MATLAB interfaces to MUMPS version 4.6. We describe the differences and similarities between usual Fortran/C MUMPS interfaces and its Scilab/MATLAB interfaces, the calling sequences and functionalities. Examples of use and experimental results are also provided.

  14. A Matlab/Simulink-Based Interactive Module for Servo Systems Learning

    Science.gov (United States)

    Aliane, N.

    2010-01-01

    This paper presents an interactive module for learning both the fundamental and practical issues of servo systems. This module, developed using Simulink in conjunction with the Matlab graphical user interface (Matlab-GUI) tool, is used to supplement conventional lectures in control engineering and robotics subjects. First, the paper introduces the…

  15. Based on matlab 3d visualization programming in the application of the uranium exploration

    International Nuclear Information System (INIS)

    Qi Jianquan

    2012-01-01

    Combined geological theory, geophysical curve and Matlab programming three dimensional visualization applied to the production of uranium exploration. With a simple Matlab programming, numerical processing and graphical visualization of convenient features, and effective in identifying ore bodies, recourse to ore, ore body delineation of the scope of analysis has played the role of sedimentary environment. (author)

  16. Regularization Tools Version 3.0 for Matlab 5.2

    DEFF Research Database (Denmark)

    Hansen, Per Christian

    1999-01-01

    This communication describes Version 3.0 of Regularization Tools, a Matlab package for analysis and solution of discrete ill-posed problems.......This communication describes Version 3.0 of Regularization Tools, a Matlab package for analysis and solution of discrete ill-posed problems....

  17. MatLab Programming for Engineers Having No Formal Programming Knowledge

    Science.gov (United States)

    Shaykhian, Linda H.; Shaykhian, Gholam Ali

    2007-01-01

    MatLab is one of the most widely used very high level programming languages for Scientific and engineering computations. It is very user-friendly and needs practically no formal programming knowledge. Presented here are MatLab programming aspects and not just the MatLab commands for scientists and engineers who do not have formal programming training and also have no significant time to spare for learning programming to solve their real world problems. Specifically provided are programs for visualization. Also, stated are the current limitations of the MatLab, which possibly can be taken care of by Mathworks Inc. in a future version to make MatLab more versatile.

  18. Microcontroller USB interfacing with MATLAB GUI for low cost medical ultrasound scanners

    Directory of Open Access Journals (Sweden)

    Jean Rossario Raj

    2016-06-01

    Full Text Available This paper presents an 8051 microcontroller-based control of ultrasound scanner prototype hardware from a host laptop MATLAB GUI. The hardware control of many instruments is carried out by microcontrollers. These microcontrollers are in turn controlled from a GUI residing in a computing machine that is connected over the USB interface. Conventionally such GUIs are developed using ‘C’ language or its variants. But MATLAB GUI is a better tool, when such GUI programs need to do huge image/video processing. However interfacing MATLAB with the microcontroller is a challenging task. Here, MATLAB interfacing through an intermediate MEX ‘C’ language program is presented. This paper outlines the MEX programming methods for achieving the smooth interfacing of microcontrollers with MATLAB GUI.

  19. Versatile Cas9-Driven Subpopulation Selection Toolbox for Lactococcus lactis.

    Science.gov (United States)

    van der Els, Simon; James, Jennelle K; Kleerebezem, Michiel; Bron, Peter A

    2018-04-15

    CRISPR-Cas9 technology has been exploited for the removal or replacement of genetic elements in a wide range of prokaryotes and eukaryotes. Here, we describe the extension of the Cas9 application toolbox to the industrially important dairy species Lactococcus lactis The Cas9 expression vector pLABTarget, encoding the Streptocccus pyogenes Cas9 under the control of a constitutive promoter, was constructed, allowing plug and play introduction of short guide RNA (sgRNA) sequences to target specific genetic loci. Introduction of a pepN -targeting derivative of pLABTarget into L. lactis strain MG1363 led to a strong reduction in the number of transformants obtained, which did not occur in a pepN deletion derivative of the same strain, demonstrating the specificity and lethality of the Cas9-mediated double-strand breaks in the lactococcal chromosome. Moreover, the same pLABTarget derivative allowed the selection of a pepN deletion subpopulation from its corresponding single-crossover plasmid integrant precursor, accelerating the construction and selection of gene-specific deletion derivatives in L. lactis Finally, pLABTarget, which contained sgRNAs designed to target mobile genetic elements, allowed the effective curing of plasmids, prophages, and integrative conjugative elements (ICEs). These results establish that pLABTarget enables the effective exploitation of Cas9 targeting in L. lactis , while the broad-host-range vector used suggests that this toolbox could readily be expanded to other Gram-positive bacteria. IMPORTANCE Mobile genetic elements in Lactococcus lactis and other lactic acid bacteria (LAB) play an important role in dairy fermentation, having both positive and detrimental effects during the production of fermented dairy products. The pLABTarget vector offers an efficient cloning platform for Cas9 application in lactic acid bacteria. Targeting Cas9 toward mobile genetic elements enabled their effective curing, which is of particular interest in the

  20. European Studies and Public Engagement: A Conceptual Toolbox

    Directory of Open Access Journals (Sweden)

    Andreas Müllerleile

    2014-11-01

    Full Text Available Journal of Contemporary European Research User Username Password Remember me Subscribe... Sign up for issue alerts Follow JCER on Twitter Font Size Make font size smaller Make font size default Make font size larger Journal Content Search Search Scope Browse By Issue By Author By Title Information For Readers For Authors For Librarians Journal Help Keywords CFSP Communication ESDP EU EU enlargement EU trade policy Energy, EU, External Policy Europe European Commission European Parliament European Union European integration Europeanisation First Enlargement Germany Liberty Lisbon Treaty Poland Russia Security teaching European studies The UACES Blog The Commission after the 2014 EP... Power shift? The EU’s pivot to Asia 100 Books on Europe to be Remembered For a Global European Studies? EU Member State Building in the... Open Journal Systems Home About Login Register Search Current Archives Announcements UACES Home > Vol 10, No 4 (2014 > Müllerleile European Studies and Public Engagement: A Conceptual Toolbox Andreas Müllerleile Abstract This article examines public engagement strategies for academics working in the field of European Studies. Should academics engage with the public? What are the most effective outreach strategies? And what are the implications for universities and departments? The article argues that engaging with the public should be considered an integral part for academics working on topics that relate to the European Union or European politics. The article has a theoretical and a practical dimension. The first part of the paper deals with the nature of public engagement, explaining why it is an important issue and how it differs from the mainstream understanding of public engagement. The practical part of the paper presents the idea of building an online presence through which academics can engage with the public debate both during periods of low issue salience and high issue salience. The final section includes a toolbox

  1. ObsPy - A Python Toolbox for Seismology - and Applications

    Science.gov (United States)

    Krischer, L.; Megies, T.; Barsch, R.; MacCarthy, J.; Lecocq, T.; Koymans, M. R.; Carothers, L.; Eulenfeld, T.; Reyes, C. G.; Falco, N.; Sales de Andrade, E.

    2017-12-01

    Recent years witnessed the evolution of Python's ecosystem into one of the most powerful and productive scientific environments across disciplines. ObsPy (https://www.obspy.org) is a fully community driven, open-source project dedicated to provide a bridge for seismology into that ecosystem. It is a Python toolbox offering: Read and write support for essentially every commonly used data format in seismology with a unified interface and automatic format detection. This includes waveform data (MiniSEED, SAC, SEG-Y, Reftek, …) as well as station (SEED, StationXML, SC3ML, …) and event meta information (QuakeML, ZMAP, …). Integrated access to the largest data centers, web services, and real-time data streams (FDSNWS, ArcLink, SeedLink, ...). A powerful signal processing toolbox tuned to the specific needs of seismologists. Utility functionality like travel time calculations with the TauP method, geodetic functions, and data visualizations. ObsPy has been in constant development for more than eight years and is developed and used by scientists around the world with successful applications in all branches of seismology. Additionally it nowadays serves as the foundation for a large number of more specialized packages. Newest features include: Full interoperability of SEED and StationXML/Inventory objects Access to the Nominal Response Library (NRL) for easy and quick creation of station metadata from scratch Support for the IRIS Federated Catalog Service Improved performance of the EarthWorm client Several improvements to MiniSEED read/write module Improved plotting capabilities for PPSD (spectrograms, PSD of discrete frequencies over time, ..) Support for.. Reading ArcLink Inventory XML Reading Reftek data format Writing SeisComp3 ML (SC3ML) Writing StationTXT format This presentation will give a short overview of the capabilities of ObsPy and point out several representative or new use cases and show-case some projects that are based on ObsPy, e.g.: seismo

  2. ALEA: a toolbox for allele-specific epigenomics analysis.

    Science.gov (United States)

    Younesy, Hamid; Möller, Torsten; Heravi-Moussavi, Alireza; Cheng, Jeffrey B; Costello, Joseph F; Lorincz, Matthew C; Karimi, Mohammad M; Jones, Steven J M

    2014-04-15

    The assessment of expression and epigenomic status using sequencing based methods provides an unprecedented opportunity to identify and correlate allelic differences with epigenomic status. We present ALEA, a computational toolbox for allele-specific epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for allele-specific analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. The pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data. The package, test data and usage instructions are available online at http://www.bcgsc.ca/platform/bioinfo/software/alea CONTACT: : mkarimi1@interchange.ubc.ca or sjones@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. ObsPy: A Python Toolbox for Seismology

    Science.gov (United States)

    Krischer, Lion; Megies, Tobias; Sales de Andrade, Elliott; Barsch, Robert; MacCarthy, Jonathan

    2017-04-01

    In recent years the Python ecosystem evolved into one of the most powerful and productive scientific environments across disciplines. ObsPy (https://www.obspy.org) is a fully community-driven, open-source project dedicated to providing a bridge for seismology into that ecosystem. It does so by offering Read and write support for essentially every commonly used data format in seismology with a unified interface and automatic format detection. This includes waveform data (MiniSEED, SAC, SEG-Y, Reftek, …) as well as station (SEED, StationXML, …) and event meta information (QuakeML, ZMAP, …). Integrated access to the largest data centers, web services, and real-time data streams (FDSNWS, ArcLink, SeedLink, ...). A powerful signal processing toolbox tuned to the specific needs of seismologists. Utility functionality like travel time calculations with the TauP method, geodetic functions, and data visualizations. ObsPy has been in constant development for more than seven years and is developed and used by scientists around the world with successful applications in all branches of seismology. Additionally it nowadays serves as the foundation for a large number of more specialized packages. This presentation will give a short overview of the capabilities of ObsPy and point out several representative or new use cases. Additionally we will discuss the road ahead as well as the long-term sustainability of open-source scientific software.

  4. A Statistical Toolbox For Mining And Modeling Spatial Data

    Directory of Open Access Journals (Sweden)

    D’Aubigny Gérard

    2016-12-01

    Full Text Available Most data mining projects in spatial economics start with an evaluation of a set of attribute variables on a sample of spatial entities, looking for the existence and strength of spatial autocorrelation, based on the Moran’s and the Geary’s coefficients, the adequacy of which is rarely challenged, despite the fact that when reporting on their properties, many users seem likely to make mistakes and to foster confusion. My paper begins by a critical appraisal of the classical definition and rational of these indices. I argue that while intuitively founded, they are plagued by an inconsistency in their conception. Then, I propose a principled small change leading to corrected spatial autocorrelation coefficients, which strongly simplifies their relationship, and opens the way to an augmented toolbox of statistical methods of dimension reduction and data visualization, also useful for modeling purposes. A second section presents a formal framework, adapted from recent work in statistical learning, which gives theoretical support to our definition of corrected spatial autocorrelation coefficients. More specifically, the multivariate data mining methods presented here, are easily implementable on the existing (free software, yield methods useful to exploit the proposed corrections in spatial data analysis practice, and, from a mathematical point of view, whose asymptotic behavior, already studied in a series of papers by Belkin & Niyogi, suggests that they own qualities of robustness and a limited sensitivity to the Modifiable Areal Unit Problem (MAUP, valuable in exploratory spatial data analysis.

  5. MATLAB simulation software used for the PhD thesis "Acquisition of Multi-Band Signals via Compressed Sensing

    DEFF Research Database (Denmark)

    2014-01-01

    MATLAB simulation software used for the PhD thesis "Acquisition of Multi-Band Signals via Compressed Sensing......MATLAB simulation software used for the PhD thesis "Acquisition of Multi-Band Signals via Compressed Sensing...

  6. A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels.

    Science.gov (United States)

    Keator, David Bryant; Gadde, Syam; Grethe, Jeffrey S; Taylor, Derek V; Potkin, Steven G

    2006-01-01

    With the increased frequency of multisite, large-scale collaborative neuro-imaging studies, the need for a general, self-documenting framework for the storage and retrieval of activation maps and anatomical labels becomes evident. To address this need, we have developed and extensible markup language (XML) schema and associated tools for the storage of neuro-imaging activation maps and anatomical labels. This schema, as part of the XML-based Clinical Experiment Data Exchange (XCEDE) schema, provides storage capabilities for analysis annotations, activation threshold parameters, and cluster and voxel-level statistics. Activation parameters contain information describing the threshold, degrees of freedom, FWHM smoothness, search volumes, voxel sizes, expected voxels per cluster, and expected number of clusters in the statistical map. Cluster and voxel statistics can be stored along with the coordinates, threshold, and anatomical label information. Multiple threshold types can be documented for a given cluster or voxel along with the uncorrected and corrected probability values. Multiple atlases can be used to generate anatomical labels and stored for each significant voxel or cluter. Additionally, a toolbox for Statistical Parametric Mapping software (http://www. fil. ion.ucl.ac.uk/spm/) was created to capture the results from activation maps using the XML schema that supports both SPM99 and SPM2 versions (http://nbirn.net/Resources/Users/ Applications/xcede/SPM_XMLTools.htm). Support for anatomical labeling is available via the Talairach Daemon (http://ric.uthscsa. edu/projects/talairachdaemon.html) and Automated Anatomical Labeling (http://www. cyceron.fr/freeware/).

  7. Optoelectronic polarimeter controlled by a graphical user interface of Matlab

    International Nuclear Information System (INIS)

    Vilardy, J M; Torres, R; Jimenez, C J

    2017-01-01

    We show the design and implementation of an optical polarimeter using electronic control. The polarimeter has a software with a graphical user interface (GUI) that controls the optoelectronic setup and captures the optical intensity measurement, and finally, this software evaluates the Stokes vector of a state of polarization (SOP) by means of the synchronous detection of optical waves. The proposed optoelectronic polarimeter can determine the Stokes vector of a SOP in a rapid and efficient way. Using the polarimeter proposed in this paper, the students will be able to observe (in an optical bench) and understand the different interactions of the SOP when the optical waves pass through to the linear polarizers and retarder waves plates. The polarimeter prototype could be used as a main tool for the students in order to learn the theory and experimental aspects of the SOP for optical waves via the Stokes vector measurement. The proposed polarimeter controlled by a GUI of Matlab is more attractive and suitable to teach and to learn the polarization of optical waves. (paper)

  8. MATLAB Simulation of Photovoltaic and Photovoltaic/Thermal Systems Performance

    Science.gov (United States)

    Nasir, Farah H. M.; Husaini, Yusnira

    2018-03-01

    The efficiency of the photovoltaic reduces when the photovoltaic cell temperature increased due to solar irradiance. One solution is come up with the cooling system photovoltaic system. This combination is forming the photovoltaic-thermal (PV/T) system. Not only will it generate electricity also heat at the same time. The aim of this research is to focus on the modeling and simulation of photovoltaic (PV) and photovoltaic-thermal (PV/T) electrical performance by using single-diode equivalent circuit model. Both PV and PV/T models are developed in Matlab/Simulink. By providing the cooling system in PV/T, the efficiency of the system can be increased by decreasing the PV cell temperature. The maximum thermal, electrical and total efficiency values of PV/T in the present research are 35.18%, 15.56% and 50.74% at solar irradiance of 400 W/m2, mass flow rate of 0.05kgs-1 and inlet temperature of 25 °C respectively has been obtained. The photovoltaic-thermal shows that the higher efficiency performance compared to the photovoltaic system.

  9. Designing an ultrafast laser virtual laboratory using MATLAB GUIDE

    International Nuclear Information System (INIS)

    Cambronero-López, F; Gómez-Varela, A I; Bao-Varela, C

    2017-01-01

    In this work we present a virtual simulator developed using the MATLAB GUIDE environment based on the numerical resolution of the nonlinear Schrödinger equation (NLS) and using the split step method for the study of the spatial–temporal propagation of nonlinear ultrashort laser pulses. This allows us to study the spatial–temporal propagation of ultrafast pulses as well as the influence of high-order spectral phases such as group delay dispersion and third-order dispersion on pulse compression in time. The NLS can describe several nonlinear effects, in particular in this paper we consider the Kerr effect, cross-polarized wave generation and cubic–quintic propagation in order to highlight the potential of this equation combined with the GUIDE environment. Graphical user interfaces are commonly used in science and engineering teaching due to their educational value, and have proven to be an effective way to engage and motivate students. Specifically, the interactive graphical interfaces presented provide the visualization of some of the most important nonlinear optics phenomena and allows users to vary the values of the main parameters involved. (paper)

  10. Development Of Translational Motion Of Unmanned Aerial Vehicle Using MATLAB

    Directory of Open Access Journals (Sweden)

    Thwe Thwe Htoo

    2015-08-01

    Full Text Available This research work describes the translational motion analysis of unmanned aerial vehicle UAV. Since the center of mass of the receiver is timevarying the equations are written in a reference frame that is geometrically fixed in the aircraft. Due to the fact that aerial vehicle simulation and control deal with the position and orientation of the UAV the equations of motion are derived in terms of the translational and rotational position and velocity with respect to the aircraft location. The formation relative motion control is a challenging problem due to the coupled translational and rotational dynamics. As the translational vector depends on the current attitude and its angular velocity and some of the attitude constraints also couple the position and attitude of the spacecraft it makes the formation control problem high dimensional. This work develops UAV stability conditions including translational vector maneuverability condition and included angle condition between the translational and the rotational motion of UAV system and then presents two methods to calculate the UAV attitude. Both of the two methods need first design the optimal trajectory of the translational vector and then use geometric and nonlinear programming methods to calculate the target trajectory. The validity of the proposed approach is demonstrated in a UAV by using MATLAB. The performance of the translational motion control is evaluated by the simulated results.

  11. Wind power limit calculation basedon frequency deviation using Matlab

    International Nuclear Information System (INIS)

    Santos Fuentefria, Ariel; Salgado Duarte, Yorlandis; MejutoFarray, Davis

    2017-01-01

    The utilization of the wind energy for the production of electricity it’s a technology that has promoted itself in the last years, like an alternative before the environmental deterioration and the scarcity of the fossil fuels. When the power generation of wind energy is integrated into the electrical power systems, maybe take place problems in the frequency stability due to, mainly, the stochastic characteristic of the wind and the impossibility of the wind power control on behalf of the dispatchers. In this work, is make an analysis of frequency deviation when the wind power generation rise in an isolated electrical power system. This analysis develops in a computerized frame with the construction of an algorithm using Matlab, which allowed to make several simulations in order to obtain the frequency behavior for different loads and wind power conditions. Besides, it was determined the wind power limit for minimum, medium and maximum load. The results show that the greatest values on wind power are obtained in maximum load condition. However, the minimum load condition limit the introduction of wind power into the system. (author)

  12. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations.

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules.

  13. A Series of Computational Neuroscience Labs Increases Comfort with MATLAB.

    Science.gov (United States)

    Nichols, David F

    2015-01-01

    Computational simulations allow for a low-cost, reliable means to demonstrate complex and often times inaccessible concepts to undergraduates. However, students without prior computer programming training may find working with code-based simulations to be intimidating and distracting. A series of computational neuroscience labs involving the Hodgkin-Huxley equations, an Integrate-and-Fire model, and a Hopfield Memory network were used in an undergraduate neuroscience laboratory component of an introductory level course. Using short focused surveys before and after each lab, student comfort levels were shown to increase drastically from a majority of students being uncomfortable or with neutral feelings about working in the MATLAB environment to a vast majority of students being comfortable working in the environment. Though change was reported within each lab, a series of labs was necessary in order to establish a lasting high level of comfort. Comfort working with code is important as a first step in acquiring computational skills that are required to address many questions within neuroscience.

  14. Designing an ultrafast laser virtual laboratory using MATLAB GUIDE

    Science.gov (United States)

    Cambronero-López, F.; Gómez-Varela, A. I.; Bao-Varela, C.

    2017-05-01

    In this work we present a virtual simulator developed using the MATLAB GUIDE environment based on the numerical resolution of the nonlinear Schrödinger equation (NLS) and using the split step method for the study of the spatial-temporal propagation of nonlinear ultrashort laser pulses. This allows us to study the spatial-temporal propagation of ultrafast pulses as well as the influence of high-order spectral phases such as group delay dispersion and third-order dispersion on pulse compression in time. The NLS can describe several nonlinear effects, in particular in this paper we consider the Kerr effect, cross-polarized wave generation and cubic-quintic propagation in order to highlight the potential of this equation combined with the GUIDE environment. Graphical user interfaces are commonly used in science and engineering teaching due to their educational value, and have proven to be an effective way to engage and motivate students. Specifically, the interactive graphical interfaces presented provide the visualization of some of the most important nonlinear optics phenomena and allows users to vary the values of the main parameters involved.

  15. Calculus Problem Solution And Simulation Using GUI Of Matlab

    Directory of Open Access Journals (Sweden)

    Syaharuddin

    2017-09-01

    Full Text Available This research aims to develop the project application in teaching and learning Calculus using Grapichal User Interface GUI of Matlab. The scope of the development result includes 1 PreCalculus 2 Function Limit 3 Derivative and its application and 4 Integral and its application. Every aspect of development is presented according to the standards of material competence learning achievement indicators and solutions or settlement steps on each issue presented. This project application can be used by lecturers and students in universities to improve motivation mastery of material and student learning outcomes in the Calculus course. Development of this project application is done through 4 stages called 4-D namely Define Design Development and Dissemination. Based on the data analysis the results obtained at the validation stage of expert validity level average of 3.575 which means quite valid. Then on a limited trial the average student gave a response of 92.00 which means very good. While in the first field trial the average student gave a response of 89.30 which means very good and in the second field trial the average student gave a responded of 90.15 which means very good. Besides that we also solve computational calculus problems in Edwin J. Purcell Dale Varbergs Book of Volume 1 of Edition 5 of 48 questions that are divided into 64 cases.

  16. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson-Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post-analysis of structural and electrical properties of biomolecules.

  17. Comparing mobile robot localisation algorithms using Kalmtool

    DEFF Research Database (Denmark)

    Mogensen, Lars Valdemar; Hansen, Søren; Ravn, Ole

    2009-01-01

    In this paper we present an estimation platform with simulation capabilities to evaluate methods for localisation of a mobile robot using a feature map. The platform is based on the Kalmtool 4 toolbox which is a set of MATLAB tools for state estimation of nonlinear systems. The toolbox contains...

  18. Real-Time Motion Capture Toolbox (RTMocap): an open-source code for recording 3-D motion kinematics to study action-effect anticipations during motor and social interactions.

    Science.gov (United States)

    Lewkowicz, Daniel; Delevoye-Turrell, Yvonne

    2016-03-01

    We present here a toolbox for the real-time motion capture of biological movements that runs in the cross-platform MATLAB environment (The MathWorks, Inc., Natick, MA). It provides instantaneous processing of the 3-D movement coordinates of up to 20 markers at a single instant. Available functions include (1) the setting of reference positions, areas, and trajectories of interest; (2) recording of the 3-D coordinates for each marker over the trial duration; and (3) the detection of events to use as triggers for external reinforcers (e.g., lights, sounds, or odors). Through fast online communication between the hardware controller and RTMocap, automatic trial selection is possible by means of either a preset or an adaptive criterion. Rapid preprocessing of signals is also provided, which includes artifact rejection, filtering, spline interpolation, and averaging. A key example is detailed, and three typical variations are developed (1) to provide a clear understanding of the importance of real-time control for 3-D motion in cognitive sciences and (2) to present users with simple lines of code that can be used as starting points for customizing experiments using the simple MATLAB syntax. RTMocap is freely available (http://sites.google.com/site/RTMocap/) under the GNU public license for noncommercial use and open-source development, together with sample data and extensive documentation.

  19. iSpectra: An Open Source Toolbox For The Analysis of Spectral Images Recorded on Scanning Electron Microscopes.

    Science.gov (United States)

    Liebske, Christian

    2015-08-01

    iSpectra is an open source and system-independent toolbox for the analysis of spectral images (SIs) recorded on energy-dispersive spectroscopy (EDS) systems attached to scanning electron microscopes (SEMs). The aim of iSpectra is to assign pixels with similar spectral content to phases, accompanied by cumulative phase spectra with superior counting statistics for quantification. Pixel-to-phase assignment starts with a threshold-based pre-sorting of spectra to create groups of pixels with identical elemental budgets, similar to a method described by van Hoek (2014). Subsequent merging of groups and re-assignments of pixels using elemental or principle component histogram plots enables the user to generate chemically and texturally plausible phase maps. A variety of standard image processing algorithms can be applied to groups of pixels to optimize pixel-to-phase assignments, such as morphology operations to account for overlapping excitation volumes over pixels located at phase boundaries. iSpectra supports batch processing and allows pixel-to-phase assignments to be applied to an unlimited amount of SIs, thus enabling phase mapping of large area samples like petrographic thin sections.

  20. GuidosToolbox: universal digital image object analysis

    Science.gov (United States)

    Peter Vogt; Kurt Riitters

    2017-01-01

    The increased availability of mapped environmental data calls for better tools to analyze the spatial characteristics and information contained in those maps. Publicly available, userfriendly and universal tools are needed to foster the interdisciplinary development and application of methodologies for the extraction of image object information properties contained in...