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Sample records for python numpy matlab

  1. Python for data analysis data wrangling with Pandas, NumPy, and IPython

    CERN Document Server

    McKinney, Wes

    2017-01-01

    Get complete instructions for manipulating, processing, cleaning, and crunching datasets in Python. Updated for Python 3.6, the second edition of this hands-on guide is packed with practical case studies that show you how to solve a broad set of data analysis problems effectively. You’ll learn the latest versions of pandas, NumPy, IPython, and Jupyter in the process. Written by Wes McKinney, the creator of the Python pandas project, this book is a practical, modern introduction to data science tools in Python. It’s ideal for analysts new to Python and for Python programmers new to data science and scientific computing. Data files and related material are available on GitHub. Use the IPython shell and Jupyter notebook for exploratory computing Learn basic and advanced features in NumPy (Numerical Python) Get started with data analysis tools in the pandas library Use flexible tools to load, clean, transform, merge, and reshape data Create informative visualizations with matplotlib ...

  2. Numpy cookbook

    CERN Document Server

    Idris, Ivan

    2015-01-01

    If you are a Python developer with some experience of working on scientific, mathematical, and statistical applications and want to gain an expert understanding of NumPy programming in relation to science, math, and finance using practical recipes, then this book is for you.

  3. 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...

  4. 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.

  5. Lose Your Loops with Numpy

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    Developing in python is fast. Computation, however, can often be another story. Or at least that is how it may seem. When working with arrays and numerical datasets one can subvert many of python’s computational limitations by utilizing numpy. Numpy is python’s standard matrix computation library. Many python users only use numpy to store and generate arrays, failing to utilize one of python’s most powerful computational tools. By leveraging numpy’s ufuncs, aggregation, broadcasting and slicing/masking/indexing functionality one can cut back on slow python loops and increase the speed of their programs by as much as 100x. This talk aims at teaching attendees how to use these tools through toy examples.

  6. NumPy 1.5 Beginner's Guide

    CERN Document Server

    Idris, Ivan

    2011-01-01

    The book is written in beginner's guide style with each aspect of NumPy demonstrated by real world examples. There is appropriate explained code with the required screenshots thrown in for the novice. This book is for the programmer, scientist or engineer, who has basic Python knowledge and would like to be able to do numerical computations with Python.

  7. IB2d: a Python and MATLAB implementation of the immersed boundary method.

    Science.gov (United States)

    Battista, Nicholas A; Strickland, W Christopher; Miller, Laura A

    2017-03-29

    The development of fluid-structure interaction (FSI) software involves trade-offs between ease of use, generality, performance, and cost. Typically there are large learning curves when using low-level software to model the interaction of an elastic structure immersed in a uniform density fluid. Many existing codes are not publicly available, and the commercial software that exists usually requires expensive licenses and may not be as robust or allow the necessary flexibility that in house codes can provide. We present an open source immersed boundary software package, IB2d, with full implementations in both MATLAB and Python, that is capable of running a vast range of biomechanics models and is accessible to scientists who have experience in high-level programming environments. IB2d contains multiple options for constructing material properties of the fiber structure, as well as the advection-diffusion of a chemical gradient, muscle mechanics models, and artificial forcing to drive boundaries with a preferred motion.

  8. CUDArray: CUDA-based NumPy

    DEFF Research Database (Denmark)

    Larsen, Anders Boesen Lindbo

    This technical report introduces CUDArray – a CUDA-accelerated subset of the NumPy library. The goal of CUDArray is to combine the ease of development from NumPy with the computational power of Nvidia GPUs in a lightweight and extensible framework. Since the motivation behind CUDArray is to facil......This technical report introduces CUDArray – a CUDA-accelerated subset of the NumPy library. The goal of CUDArray is to combine the ease of development from NumPy with the computational power of Nvidia GPUs in a lightweight and extensible framework. Since the motivation behind CUDArray...

  9. Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

    Science.gov (United States)

    Smith, Daniel G A; Burns, Lori A; Sirianni, Dominic A; Nascimento, Daniel R; Kumar, Ashutosh; James, Andrew M; Schriber, Jeffrey B; Zhang, Tianyuan; Zhang, Boyi; Abbott, Adam S; Berquist, Eric J; Lechner, Marvin H; Cunha, Leonardo A; Heide, Alexander G; Waldrop, Jonathan M; Takeshita, Tyler Y; Alenaizan, Asem; Neuhauser, Daniel; King, Rollin A; Simmonett, Andrew C; Turney, Justin M; Schaefer, Henry F; Evangelista, Francesco A; DePrince, A Eugene; Crawford, T Daniel; Patkowski, Konrad; Sherrill, C David

    2018-06-11

    Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

  10. A full-fledged micromagnetic code in fewer than 70 lines of NumPy

    International Nuclear Information System (INIS)

    Abert, Claas; Bruckner, Florian; Vogler, Christoph; Windl, Roman; Thanhoffer, Raphael; Suess, Dieter

    2015-01-01

    We present a complete micromagnetic finite-difference code in fewer than 70 lines of Python. The code makes a large use of the NumPy library and computes the exchange field by finite differences and the demagnetization field with a fast convolution algorithm. Since the magnetization in finite-difference micromagnetics is represented by a multi-dimensional array and the NumPy library features a rich interface for this data structure, the code we present is an ideal starting point for the development of novel algorithms. - Highlights: • A very concise but complete micromagnetic code written in Python is presented. • An introduction to finite-difference micromagnetics is provided. • The code is a perfect starting point for the development of novel algorithms

  11. DeepPy: Pythonic deep learning

    DEFF Research Database (Denmark)

    Larsen, Anders Boesen Lindbo

    This technical report introduces DeepPy – a deep learning framework built on top of NumPy with GPU acceleration. DeepPy bridges the gap between highperformance neural networks and the ease of development from Python/NumPy. Users with a background in scientific computing in Python will quickly...... be able to understand and change the DeepPy codebase as it is mainly implemented using high-level NumPy primitives. Moreover, DeepPy supports complex network architectures by letting the user compose mathematical expressions as directed graphs. The latest version is available at http...

  12. OpenNFT: An open-source Python/Matlab framework for real-time fMRI neurofeedback training based on activity, connectivity and multivariate pattern analysis.

    Science.gov (United States)

    Koush, Yury; Ashburner, John; Prilepin, Evgeny; Sladky, Ronald; Zeidman, Peter; Bibikov, Sergei; Scharnowski, Frank; Nikonorov, Artem; De Ville, Dimitri Van

    2017-08-01

    Neurofeedback based on real-time functional magnetic resonance imaging (rt-fMRI) is a novel and rapidly developing research field. It allows for training of voluntary control over localized brain activity and connectivity and has demonstrated promising clinical applications. Because of the rapid technical developments of MRI techniques and the availability of high-performance computing, new methodological advances in rt-fMRI neurofeedback become possible. Here we outline the core components of a novel open-source neurofeedback framework, termed Open NeuroFeedback Training (OpenNFT), which efficiently integrates these new developments. This framework is implemented using Python and Matlab source code to allow for diverse functionality, high modularity, and rapid extendibility of the software depending on the user's needs. In addition, it provides an easy interface to the functionality of Statistical Parametric Mapping (SPM) that is also open-source and one of the most widely used fMRI data analysis software. We demonstrate the functionality of our new framework by describing case studies that include neurofeedback protocols based on brain activity levels, effective connectivity models, and pattern classification approaches. This open-source initiative provides a suitable framework to actively engage in the development of novel neurofeedback approaches, so that local methodological developments can be easily made accessible to a wider range of users. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  13. Tangent: Automatic Differentiation Using Source Code Transformation in Python

    OpenAIRE

    van Merriënboer, Bart; Wiltschko, Alexander B.; Moldovan, Dan

    2017-01-01

    Automatic differentiation (AD) is an essential primitive for machine learning programming systems. Tangent is a new library that performs AD using source code transformation (SCT) in Python. It takes numeric functions written in a syntactic subset of Python and NumPy as input, and generates new Python functions which calculate a derivative. This approach to automatic differentiation is different from existing packages popular in machine learning, such as TensorFlow and Autograd. Advantages ar...

  14. Parallel Algorithm of Geometrical Hashing Based on NumPy Package and Processes Pool

    Directory of Open Access Journals (Sweden)

    Klyachin Vladimir Aleksandrovich

    2015-10-01

    Full Text Available The article considers the problem of multi-dimensional geometric hashing. The paper describes a mathematical model of geometric hashing and considers an example of its use in localization problems for the point. A method of constructing the corresponding hash matrix by parallel algorithm is considered. In this paper an algorithm of parallel geometric hashing using a development pattern «pool processes» is proposed. The implementation of the algorithm is executed using the Python programming language and NumPy package for manipulating multidimensional data. To implement the process pool it is proposed to use a class Process Pool Executor imported from module concurrent.futures, which is included in the distribution of the interpreter Python since version 3.2. All the solutions are presented in the paper by corresponding UML class diagrams. Designed GeomNash package includes classes Data, Result, GeomHash, Job. The results of the developed program presents the corresponding graphs. Also, the article presents the theoretical justification for the application process pool for the implementation of parallel algorithms. It is obtained condition t2 > (p/(p-1*t1 of the appropriateness of process pool. Here t1 - the time of transmission unit of data between processes, and t2 - the time of processing unit data by one processor.

  15. The Python ARM Radar Toolkit (Py-ART), a Library for Working with Weather Radar Data in the Python Programming Language

    OpenAIRE

    Helmus, Jonathan J; Collis, Scott M

    2016-01-01

    The Python ARM Radar Toolkit is a package for reading, visualizing, correcting and analysing data from weather radars. Development began to meet the needs of the Atmospheric Radiation Measurement Climate Research Facility and has since expanded to provide a general-purpose framework for working with data from weather radars in the Python programming language. The toolkit is built on top of libraries in the Scientific Python ecosystem including NumPy, SciPy, and matplotlib, and makes use of Cy...

  16. Learning Python

    National Research Council Canada - National Science Library

    Lutz, Mark; Ascher, David

    1999-01-01

    ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv Part I. Getting Started 1. A Python Q&A Session Why Do People Use Python? Is Python a Scripting Language? Okay, But What's the Downside? Who Uses Python Today...

  17. Learning Python

    National Research Council Canada - National Science Library

    Lutz, Mark; Ascher, David

    2004-01-01

    ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv Part I. Getting Started 1. A Python Q&A Session Why Do People Use Python? Is Python a Scripting Language? Okay, But What's the Downside? Who Uses Python Today...

  18. Python data science essentials

    CERN Document Server

    Boschetti, Alberto

    2015-01-01

    If you are an aspiring data scientist and you have at least a working knowledge of data analysis and Python, this book will get you started in data science. Data analysts with experience of R or MATLAB will also find the book to be a comprehensive reference to enhance their data manipulation and machine learning skills.

  19. Formula Translation in Blitz++, NumPy and Modern Fortran: A Case Study of the Language Choice Tradeoffs

    Directory of Open Access Journals (Sweden)

    Sylwester Arabas

    2014-01-01

    Full Text Available Three object-oriented implementations of a prototype solver of the advection equation are introduced. The presented programs are based on Blitz++ (C++, NumPy (Python and Fortran's built-in array containers. The solvers constitute implementations of the Multidimensional Positive-Definite Advective Transport Algorithm (MPDATA. The introduced codes serve as examples for how the application of object-oriented programming (OOP techniques and new language constructs from C++11 and Fortran 2008 allow to reproduce the mathematical notation used in the literature within the program code. A discussion on the tradeoffs of the programming language choice is presented. The main angles of comparison are code brevity and syntax clarity (and hence maintainability and auditability as well as performance. All performance tests are carried out using free and open-source compilers. In the case of Python, a significant performance gain is observed when switching from the standard interpreter (CPython to the PyPy implementation of Python. Entire source code of all three implementations is embedded in the text and is licensed under the terms of the GNU GPL license.

  20. Learning scientific programming with Python

    CERN Document Server

    Hill, Christian

    2015-01-01

    Learn to master basic programming tasks from scratch with real-life scientifically relevant examples and solutions drawn from both science and engineering. Students and researchers at all levels are increasingly turning to the powerful Python programming language as an alternative to commercial packages and this fast-paced introduction moves from the basics to advanced concepts in one complete volume, enabling readers to quickly gain proficiency. Beginning with general programming concepts such as loops and functions within the core Python 3 language, and moving onto the NumPy, SciPy and Matplotlib libraries for numerical programming and data visualisation, this textbook also discusses the use of IPython notebooks to build rich-media, shareable documents for scientific analysis. Including a final chapter introducing challenging topics such as floating-point precision and algorithm stability, and with extensive online resources to support advanced study, this textbook represents a targeted package for students...

  1. Python data science handbook essential tools for working with data

    CERN Document Server

    VanderPlas, Jake

    2016-01-01

    For many researchers, Python is a first-class tool mainly because of its libraries for storing, manipulating, and gaining insight from data. Several resources exist for individual pieces of this data science stack, but only with the Python Data Science Handbook do you get them all—IPython, NumPy, Pandas, Matplotlib, Scikit-Learn, and other related tools. Working scientists and data crunchers familiar with reading and writing Python code will find this comprehensive desk reference ideal for tackling day-to-day issues.

  2. 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.

  3. 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...

  4. Jet flavor tagging with Deep Learning using Python

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    Besides the part that implements the resulting deep neural net in the ATLAS C++ software framework, a Python framework has been developed to connect HEP data to standard Data Science Python based libraries for Machine Learning. It makes use of HDF5, JSON and Pickle as intermediate data storage format, pandas and numpy for data handling and calculations, Keras for neural net construction and training as well as testing and matplotlib for plotting. It can be seen as an example of taking advantage of outside-HEP software developments without relying on the HEP standard ROOT.

  5. Pro Python

    CERN Document Server

    Alchin, Marty

    2010-01-01

    You've learned the basics of Python, but how do you take your skills to the next stage? Even if you know enough to be productive, there are a number of features that can take you to the next level in Python. Pro Python explores concepts and features normally left to experimentation, allowing you to be even more productive and creative. In addition to pure code concerns, Pro Python will develop your programming techniques and approaches, which will help make you a better Python programmer. Not only will this book help your code, it will also help you understand and interact with the many establ

  6. SunPy—Python for solar physics

    International Nuclear Information System (INIS)

    Community, The SunPy; Mumford, Stuart J; Freij, Nabil; Bennett, Samuel M; Christe, Steven; Ireland, Jack; Shih, Albert Y; Inglis, Andrew R; Pérez-Suárez, David; Liedtke, Simon; Hewett, Russell J; Mayer, Florian; Hughitt, Keith; Meszaros, Tomas; Malocha, Michael; Evans, John; Agrawal, Ankit; Leonard, Andrew J; Robitaille, Thomas P; Mampaey, Benjamin

    2015-01-01

    This paper presents SunPy (version 0.5), a community-developed Python package for solar physics. Python, a free, cross-platform, general-purpose, high-level programming language, has seen widespread adoption among the scientific community, resulting in the availability of a large number of software packages, from numerical computation (NumPy, SciPy) and machine learning (scikit-learn) to visualization and plotting (matplotlib). SunPy is a data-analysis environment specializing in providing the software necessary to analyse solar and heliospheric data in Python. SunPy is open-source software (BSD licence) and has an open and transparent development workflow that anyone can contribute to. SunPy provides access to solar data through integration with the Virtual Solar Observatory (VSO), the Heliophysics Event Knowledgebase (HEK), and the HELiophysics Integrated Observatory (HELIO) webservices. It currently supports image data from major solar missions (e.g., SDO, SOHO, STEREO, and IRIS), time-series data from missions such as GOES, SDO/EVE, and PROBA2/LYRA, and radio spectra from e-Callisto and STEREO/SWAVES. We describe SunPy's functionality, provide examples of solar data analysis in SunPy, and show how Python-based solar data-analysis can leverage the many existing tools already available in Python. We discuss the future goals of the project and encourage interested users to become involved in the planning and development of SunPy. (paper)

  7. Programming Python

    CERN Document Server

    Lutz, Mark

    2011-01-01

    If you've mastered Python's fundamentals, you're ready to start using it to get real work done. Programming Python will show you how, with in-depth tutorials on the language's primary application domains: system administration, GUIs, and the Web. You'll also explore how Python is used in databases, networking, front-end scripting layers, text processing, and more. This book focuses on commonly used tools and libraries to give you a comprehensive understanding of Python's many roles in practical, real-world programming. You'll learn language syntax and programming techniques in a clear and co

  8. Learning Python

    CERN Document Server

    Lutz, Mark

    2009-01-01

    Google and YouTube use Python because it's highly adaptable, easy to maintain, and allows for rapid development. If you want to write high-quality, efficient code that's easily integrated with other languages and tools, this hands-on book will help you be productive with Python quickly -- whether you're new to programming or just new to Python. It's an easy-to-follow self-paced tutorial, based on author and Python expert Mark Lutz's popular training course. Each chapter contains a stand-alone lesson on a key component of the language, and includes a unique Test Your Knowledge section with p

  9. MEG and EEG data analysis with MNE-Python

    Directory of Open Access Journals (Sweden)

    Alexandre eGramfort

    2013-12-01

    Full Text Available Magnetoencephalography and electroencephalography (M/EEG measure the weakelectromagnetic signals generated by neuronal activity in the brain. Using thesesignals to characterize and locate neural activation in the brain is achallenge that requires expertise in physics, signalprocessing, statistics, and numerical methods. As part of the MNE softwaresuite, MNE-Python is an open-sourcesoftware package that addresses this challenge by providingstate-of-the-art algorithms implemented in Python that cover multiple methods of data preprocessing, source localization, statistical analysis, and estimation offunctional connectivity between distributed brain regions.All algorithms and utility functions are implemented in a consistent manner with well-documented interfaces, enabling users to create M/EEG data analysispipelines by writing Python scripts.Moreover, MNE-Python is tightly integrated with the core Python libraries for scientificcomptutation (Numpy, Scipy and visualization (matplotlib and Mayavi, as wellas the greater neuroimaging ecosystem in Python via the Nibabel package. The code is provided under the new BSD licenseallowing code reuse, even in commercial products. Although MNE-Python has onlybeen under heavy development for a couple of years, it has rapidly evolved withexpanded analysis capabilities and pedagogical tutorials because multiple labs have collaborated during code development to help share best practices.MNE-Python also gives easy access to preprocessed datasets,helping users to get started quickly and facilitating reproducibility ofmethods by other researchers. Full documentation, including dozens ofexamples, is available at http://martinos.org/mne.

  10. Python tutorial

    NARCIS (Netherlands)

    G. van Rossum (Guido)

    1995-01-01

    textabstractPython is a simple, yet powerful programming language that bridges the gap between C and shell programming, and is thus ideally suited for ``throw-away programming'' and rapid prototyping. Its syntax is put together from constructs borrowed from a variety of other languages; most

  11. PyTrilinos: Recent Advances in the Python Interface to Trilinos

    Directory of Open Access Journals (Sweden)

    William F. Spotz

    2012-01-01

    Full Text Available PyTrilinos is a set of Python interfaces to compiled Trilinos packages. This collection supports serial and parallel dense linear algebra, serial and parallel sparse linear algebra, direct and iterative linear solution techniques, algebraic and multilevel preconditioners, nonlinear solvers and continuation algorithms, eigensolvers and partitioning algorithms. Also included are a variety of related utility functions and classes, including distributed I/O, coloring algorithms and matrix generation. PyTrilinos vector objects are compatible with the popular NumPy Python package. As a Python front end to compiled libraries, PyTrilinos takes advantage of the flexibility and ease of use of Python, and the efficiency of the underlying C++, C and Fortran numerical kernels. This paper covers recent, previously unpublished advances in the PyTrilinos package.

  12. Python essential reference

    CERN Document Server

    Beazley, David M

    2009-01-01

    Python Essential Reference is the definitive reference guide to the Python programming language — the one authoritative handbook that reliably untangles and explains both the core Python language and the most essential parts of the Python library. Designed for the professional programmer, the book is concise, to the point, and highly accessible. It also includes detailed information on the Python library and many advanced subjects that is not available in either the official Python documentation or any other single reference source. Thoroughly updated to reflect the significant new programming language features and library modules that have been introduced in Python 2.6 and Python 3, the fourth edition of Python Essential Reference is the definitive guide for programmers who need to modernize existing Python code or who are planning an eventual migration to Python 3. Programmers starting a new Python project will find detailed coverage of contemporary Python programming idioms.

  13. xarray: N-D labeled Arrays and Datasets in Python

    Directory of Open Access Journals (Sweden)

    Stephan Hoyer

    2017-04-01

    Full Text Available xarray is an open source project and Python package that provides a toolkit and data structures for N-dimensional labeled arrays. Our approach combines an application programing interface (API inspired by pandas with the Common Data Model for self-described scientific data. Key features of the xarray package include label-based indexing and arithmetic, interoperability with the core scientific Python packages (e.g., pandas, NumPy, Matplotlib, out-of-core computation on datasets that don’t fit into memory, a wide range of serialization and input/output (I/O options, and advanced multi-dimensional data manipulation tools such as group-by and resampling. xarray, as a data model and analytics toolkit, has been widely adopted in the geoscience community but is also used more broadly for multi-dimensional data analysis in physics, machine learning and finance.

  14. Pythran: enabling static optimization of scientific Python programs

    Science.gov (United States)

    Guelton, Serge; Brunet, Pierrick; Amini, Mehdi; Merlini, Adrien; Corbillon, Xavier; Raynaud, Alan

    2015-01-01

    Pythran is an open source static compiler that turns modules written in a subset of Python language into native ones. Assuming that scientific modules do not rely much on the dynamic features of the language, it trades them for powerful, possibly inter-procedural, optimizations. These optimizations include detection of pure functions, temporary allocation removal, constant folding, Numpy ufunc fusion and parallelization, explicit thread-level parallelism through OpenMP annotations, false variable polymorphism pruning, and automatic vector instruction generation such as AVX or SSE. In addition to these compilation steps, Pythran provides a C++ runtime library that leverages the C++ STL to provide generic containers, and the Numeric Template Toolbox for Numpy support. It takes advantage of modern C++11 features such as variadic templates, type inference, move semantics and perfect forwarding, as well as classical idioms such as expression templates. Unlike the Cython approach, Pythran input code remains compatible with the Python interpreter. Output code is generally as efficient as the annotated Cython equivalent, if not more, but without the backward compatibility loss.

  15. MEG and EEG data analysis with MNE-Python.

    Science.gov (United States)

    Gramfort, Alexandre; Luessi, Martin; Larson, Eric; Engemann, Denis A; Strohmeier, Daniel; Brodbeck, Christian; Goj, Roman; Jas, Mainak; Brooks, Teon; Parkkonen, Lauri; Hämäläinen, Matti

    2013-12-26

    Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals generated by neuronal activity in the brain. Using these signals to characterize and locate neural activation in the brain is a challenge that requires expertise in physics, signal processing, statistics, and numerical methods. As part of the MNE software suite, MNE-Python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in Python that cover multiple methods of data preprocessing, source localization, statistical analysis, and estimation of functional connectivity between distributed brain regions. All algorithms and utility functions are implemented in a consistent manner with well-documented interfaces, enabling users to create M/EEG data analysis pipelines by writing Python scripts. Moreover, MNE-Python is tightly integrated with the core Python libraries for scientific comptutation (NumPy, SciPy) and visualization (matplotlib and Mayavi), as well as the greater neuroimaging ecosystem in Python via the Nibabel package. The code is provided under the new BSD license allowing code reuse, even in commercial products. Although MNE-Python has only been under heavy development for a couple of years, it has rapidly evolved with expanded analysis capabilities and pedagogical tutorials because multiple labs have collaborated during code development to help share best practices. MNE-Python also gives easy access to preprocessed datasets, helping users to get started quickly and facilitating reproducibility of methods by other researchers. Full documentation, including dozens of examples, is available at http://martinos.org/mne.

  16. Learning Python network programming

    CERN Document Server

    Sarker, M O Faruque

    2015-01-01

    If you're a Python developer or a system administrator with Python experience and you're looking to take your first steps in network programming, then this book is for you. Basic knowledge of Python is assumed.

  17. A modern Python interface for the Generic Mapping Tools

    Science.gov (United States)

    Uieda, L.; Wessel, P.

    2017-12-01

    Figures generated by The Generic Mapping Tools (GMT) are present in countless publications across the Earth sciences. The command-line interface of GMT lends the tool its flexibility but also creates a barrier to entry for begginers. Meanwhile, adoption of the Python programming language has grown across the scientific community. This growth is largely due to the simplicity and low barrier to entry of the language and its ecosystem of tools. Thus, it is not surprising that there have been at least three attempts to create Python interfaces for GMT: gmtpy (github.com/emolch/gmtpy), pygmt (github.com/ian-r-rose/pygmt), and PyGMT (github.com/glimmer-cism/PyGMT). None of these projects are currently active and, with the exception of pygmt, they do not use the GMT Application Programming Interface (API) introduced in GMT 5. The two main Python libraries for plotting data on maps are the matplotlib Basemap toolkit (matplotlib.org/basemap) and Cartopy (scitools.org.uk/cartopy), both of which rely on matplotlib (matplotlib.org) as the backend for generating the figures. Basemap is known to have limitations and is being discontinued. Cartopy is an improvement over Basemap but is still bound by the speed and memory constraints of matplotlib. We present a new Python interface for GMT (GMT/Python) that makes use of the GMT API and of new features being developed for the upcoming GMT 6 release. The GMT/Python library is designed according to the norms and styles of the Python community. The library integrates with the scientific Python ecosystem by using the "virtual files" from the GMT API to implement input and output of Python data types (numpy "ndarray" for tabular data and xarray "Dataset" for grids). Other features include an object-oriented interface for creating figures, the ability to display figures in the Jupyter notebook, and descriptive aliases for GMT arguments (e.g., "region" instead of "R" and "projection" instead of "J"). GMT/Python can also serve as a backend

  18. The Python ARM Radar Toolkit (Py-ART, a Library for Working with Weather Radar Data in the Python Programming Language

    Directory of Open Access Journals (Sweden)

    Jonathan J Helmus

    2016-07-01

    Full Text Available The Python ARM Radar Toolkit is a package for reading, visualizing, correcting and analysing data from weather radars. Development began to meet the needs of the Atmospheric Radiation Measurement Climate Research Facility and has since expanded to provide a general-purpose framework for working with data from weather radars in the Python programming language. The toolkit is built on top of libraries in the Scientific Python ecosystem including NumPy, SciPy, and matplotlib, and makes use of Cython for interfacing with existing radar libraries written in C and to speed up computationally demanding algorithms. The source code for the toolkit is available on GitHub and is distributed under a BSD license.

  19. X Python reference manual

    NARCIS (Netherlands)

    K.S. Mullender (Sjoerd)

    1995-01-01

    textabstractThis document describes the built-in types, exceptions, and functions of the X windows extension to Python. It assumes basic knowledge about the Python language and access to the X windows documentation. For an informal introduction to the language, see the Python Tutorial. The Python

  20. pypet: A Python Toolkit for Data Management of Parameter Explorations.

    Science.gov (United States)

    Meyer, Robert; Obermayer, Klaus

    2016-01-01

    pypet (Python parameter exploration toolkit) is a new multi-platform Python toolkit for managing numerical simulations. Sampling the space of model parameters is a key aspect of simulations and numerical experiments. pypet is designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches. pypet collects and stores both simulation parameters and results in a single HDF5 file. This collective storage allows fast and convenient loading of data for further analyses. pypet provides various additional features such as multiprocessing and parallelization of simulations, dynamic loading of data, integration of git version control, and supervision of experiments via the electronic lab notebook Sumatra. pypet supports a rich set of data formats, including native Python types, Numpy and Scipy data, Pandas DataFrames, and BRIAN(2) quantities. Besides these formats, users can easily extend the toolkit to allow customized data types. pypet is a flexible tool suited for both short Python scripts and large scale projects. pypet's various features, especially the tight link between parameters and results, promote reproducible research in computational neuroscience and simulation-based disciplines.

  1. 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.

  2. pypet: A Python Toolkit for Data Management of Parameter Explorations

    Directory of Open Access Journals (Sweden)

    Robert Meyer

    2016-08-01

    Full Text Available pypet (Python parameter exploration toolkit is a new multi-platform Python toolkit for managing numerical simulations. Sampling the space of model parameters is a key aspect of simulations and numerical experiments. pypet is designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches.pypet collects and stores both simulation parameters and results in a single HDF5 file.This collective storage allows fast and convenient loading of data for further analyses.pypet provides various additional features such as multiprocessing and parallelization of simulations, dynamic loading of data, integration of git version control, and supervision of experiments via the electronic lab notebook Sumatra. pypet supports a rich set of data formats, including native Python types, Numpy and Scipy data, Pandas DataFrames, and BRIAN(2 quantities. Besides these formats, users can easily extend the toolkit to allow customized data types. pypet is a flexible tool suited for both short Python scripts and large scale projects. pypet's various features, especially the tight link between parameters and results, promote reproducible research in computational neuroscience and simulation-based disciplines.

  3. The atomic simulation environment-a Python library for working with atoms.

    Science.gov (United States)

    Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D; Jennings, Paul C; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W

    2017-07-12

    The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

  4. 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

  5. Dive Into Python 3

    CERN Document Server

    Pilgrim, Mark

    2009-01-01

    Mark Pilgrim's Dive Into Python 3 is a hands-on guide to Python 3 (the latest version of the Python language) and its differences from Python 2. As in the original book, Dive Into Python, each chapter starts with a real, complete code sample, proceeds to pick it apart and explain the pieces, and then puts it all back together in a summary at the end. This book includes: * Example programs completely rewritten to illustrate powerful new concepts now available in Python 3: sets, iterators, generators, closures, comprehensions, and much more* A detailed case study of porting a major library from

  6. Imbalanced-learn: A Python Toolbox to Tackle the Curse of Imbalanced Datasets in Machine Learning

    OpenAIRE

    Lemaitre , Guillaume; Nogueira , Fernando; Aridas , Christos ,

    2017-01-01

    International audience; imbalanced-learn is an open-source python toolbox aiming at providing a wide range of methods to cope with the problem of imbalanced dataset frequently encountered in machine learning and pattern recognition. The implemented state-of-the-art methods can be categorized into 4 groups: (i) under-sampling, (ii) over-sampling, (iii) combination of over-and under-sampling, and (iv) ensemble learning methods. The proposed toolbox depends only on numpy, scipy, and scikit-learn...

  7. Learning Python testing

    CERN Document Server

    Arbuckle, Daniel

    2014-01-01

    This book is ideal if you want to learn about the testing disciplines and automated testing tools from a hands-on, conversational guide. You should already know Python and be comfortable with Python 3.

  8. Functional Python programming

    CERN Document Server

    Lott, Steven

    2015-01-01

    This book is for developers who want to use Python to write programs that lean heavily on functional programming design patterns. You should be comfortable with Python programming, but no knowledge of functional programming paradigms is needed.

  9. GMES: A Python package for solving Maxwell’s equations using the FDTD method

    Science.gov (United States)

    Chun, Kyungwon; Kim, Huioon; Kim, Hyounggyu; Jung, Kil Su; Chung, Youngjoo

    2013-04-01

    This paper describes GMES, a free Python package for solving Maxwell’s equations using the finite-difference time-domain (FDTD) method. The design of GMES follows the object-oriented programming (OOP) approach and adopts a unique design strategy where the voxels in the computational domain are grouped and then updated according to its material type. This piecewise updating scheme ensures that GMES can adopt OOP without losing its simple structure and time-stepping speed. The users can easily add various material types, sources, and boundary conditions into their code using the Python programming language. The key design features, along with the supported material types, excitation sources, boundary conditions and parallel calculations employed in GMES are also described in detail. Catalog identifier: AEOK_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOK_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3.0 No. of lines in distributed program, including test data, etc.: 17700 No. of bytes in distributed program, including test data, etc.: 89878 Distribution format: tar.gz Programming language: C++, Python. Computer: Any computer with a Unix-like system with a C++ compiler, and a Python interpreter; developed on 2.53 GHz Intel CoreTM i3. Operating system: Any Unix-like system; developed under Ubuntu 12.04 LTS 64 bit. Has the code been vectorized or parallelized?: Yes. Parallelized with MPI directives (optional). RAM: Problem dependent (a simulation with real valued electromagnetic field uses roughly 0.18 KB per Yee cell.) Classification: 10. External routines: SWIG [1], Cython [2], NumPy [3], SciPy [4], matplotlib [5], MPI for Python [6] Nature of problem: Classical electrodynamics Solution method: Finite-difference time-domain (FDTD) method Additional comments: This article describes version 0.9.5. The most recent version can be downloaded at the GMES

  10. VPython: Python plus Animations in Stereo 3D

    Science.gov (United States)

    Sherwood, Bruce

    2004-03-01

    Python is a modern object-oriented programming language. VPython (http://vpython.org) is a combination of Python (http://python.org), the Numeric module from LLNL (http://www.pfdubois.com/numpy), and the Visual module created by David Scherer, all of which have been under continuous development as open source projects. VPython makes it easy to write programs that generate real-time, navigable 3D animations. The Visual module includes a set of 3D objects (sphere, cylinder, arrow, etc.), tools for creating other shapes, and support for vector algebra. The 3D renderer runs in a parallel thread, and animations are produced as a side effect of computations, freeing the programmer to concentrate on the physics. Applications include educational and research visualization. In the Fall of 2003 Hugh Fisher at the Australian National University, John Zelle at Wartburg College, and I contributed to a new stereo capability of VPython. By adding a single statement to an existing VPython program, animations can be viewed in true stereo 3D. One can choose several modes: active shutter glasses, passive polarized glasses, or colored glasses (e.g. red-cyan). The talk will demonstrate the new stereo capability and discuss the pros and cons of various schemes for display of stereo 3D for a large audience. Supported in part by NSF grant DUE-0237132.

  11. Head First Python

    CERN Document Server

    Barry, Paul

    2010-01-01

    Ever wished you could learn Python from a book? Head First Python is a complete learning experience for Python that helps you learn the language through a unique method that goes beyond syntax and how-to manuals, helping you understand how to be a great Python programmer. You'll quickly learn the language's fundamentals, then move onto persistence, exception handling, web development, SQLite, data wrangling, and Google App Engine. You'll also learn how to write mobile apps for Android, all thanks to the power that Python gives you. We think your time is too valuable to waste struggling with

  12. 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...

  13. IRISpy: Analyzing IRIS Data in Python

    Science.gov (United States)

    Ryan, Daniel; Christe, Steven; Mumford, Stuart; Baruah, Ankit; Timothy, Shelbe; Pereira, Tiago; De Pontieu, Bart

    2017-08-01

    IRISpy is a new community-developed open-source software library for analysing IRIS level 2 data. It is written in Python, a free, cross-platform, general-purpose, high-level programming language. A wide array of scientific computing software packages have already been developed in Python, from numerical computation (NumPy, SciPy, etc.), to visualization and plotting (matplotlib), to solar-physics-specific data analysis (SunPy). IRISpy is currently under development as a SunPy-affiliated package which means it depends on the SunPy library, follows similar standards and conventions, and is developed with the support of of the SunPy development team. IRISpy’s has two primary data objects, one for analyzing slit-jaw imager data and another for analyzing spectrograph data. Both objects contain basic slicing, indexing, plotting, and animating functionality to allow users to easily inspect, reduce and analyze the data. As part of this functionality the objects can output SunPy Maps, TimeSeries, Spectra, etc. of relevant data slices for easier inspection and analysis. Work is also ongoing to provide additional data analysis functionality including derivation of systematic measurement errors (e.g. readout noise), exposure time correction, residual wavelength calibration, radiometric calibration, and fine scale pointing corrections. IRISpy’s code base is publicly available through github.com and can be contributed to by anyone. In this poster we demonstrate IRISpy’s functionality and future goals of the project. We also encourage interested users to become involved in further developing IRISpy.

  14. 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

  15. OMPC: an Open-Source MATLAB?-to-Python Compiler

    OpenAIRE

    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...

  16. PySSM: A Python Module for Bayesian Inference of Linear Gaussian State Space Models

    Directory of Open Access Journals (Sweden)

    Christopher Strickland

    2014-04-01

    Full Text Available PySSM is a Python package that has been developed for the analysis of time series using linear Gaussian state space models. PySSM is easy to use; models can be set up quickly and efficiently and a variety of different settings are available to the user. It also takes advantage of scientific libraries NumPy and SciPy and other high level features of the Python language. PySSM is also used as a platform for interfacing between optimized and parallelized Fortran routines. These Fortran routines heavily utilize basic linear algebra and linear algebra Package functions for maximum performance. PySSM contains classes for filtering, classical smoothing as well as simulation smoothing.

  17. 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....

  18. 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

  19. 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....

  20. Python geospatial development essentials

    CERN Document Server

    Bahgat, Karim

    2015-01-01

    This book is ideal for Python programmers who are tasked with or wish to make a special-purpose GIS application. Analysts, political scientists, geographers, and GIS specialists seeking a creative platform to experiment with cutting-edge spatial analysis, but who are still only beginners in Python, will also find this book beneficial. Familiarity with Tkinter application development in Python is preferable but not mandatory.

  1. Learning Python design patterns

    CERN Document Server

    Zlobin, Gennadiy

    2013-01-01

    This book takes a tutorial-based and user-friendly approach to covering Python design patterns. Its concise presentation means that in a short space of time, you will get a good introduction to various design patterns.If you are an intermediate level Python user, this book is for you. Prior knowledge of Python programming is essential. Some knowledge of UML is also required to understand the UML diagrams which are used to describe some design patterns.

  2. Python penetration testing essentials

    CERN Document Server

    Mohit

    2015-01-01

    If you are a Python programmer or a security researcher who has basic knowledge of Python programming and want to learn about penetration testing with the help of Python, this book is ideal for you. Even if you are new to the field of ethical hacking, this book can help you find the vulnerabilities in your system so that you are ready to tackle any kind of attack or intrusion.

  3. Adventures in Python

    CERN Document Server

    Richardson, Craig

    2015-01-01

    The complete beginner's guide to Python, for young people whowant to start today Adventures in Python is designed for 11-to 15-year oldswho want to teach themselves Python programming, but don't knowwhere to start. Even if you have no programming experience at all,this easy to follow format and clear, simple instruction will getyou up and running quickly. The book walks you through nineprojects that teach you the fundamentals of programming in general,and Python in particular, gradually building your skills until youhave the confidence and ability to tackle your own projects. Videoclips accom

  4. Python data visualization cookbook

    CERN Document Server

    Milovanovic, Igor

    2013-01-01

    This book is written in a Cookbook style targeted towards an advanced audience. It covers the advanced topics of data visualization in Python.Python Data Visualization Cookbook is for developers that already know about Python programming in general. If you have heard about data visualization but you don't know where to start, then this book will guide you from the start and help you understand data, data formats, data visualization, and how to use Python to visualize data.You will need to know some general programming concepts, and any kind of programming experience will be helpful, but the co

  5. Python pocket reference

    CERN Document Server

    Lutz, Mark

    2010-01-01

    This is the book to reach for when you're coding on the fly and need an answer now. It's an easy-to-use reference to the core language, with descriptions of commonly used modules and toolkits, and a guide to recent changes, new features, and upgraded built-ins -- all updated to cover Python 3.X as well as version 2.6. You'll also quickly find exactly what you need with the handy index. Written by Mark Lutz -- widely recognized as the world's leading Python trainer -- Python Pocket Reference, Fourth Edition, is the perfect companion to O'Reilly's classic Python tutorials, also written by Mark

  6. Python high performance programming

    CERN Document Server

    Lanaro, Gabriele

    2013-01-01

    An exciting, easy-to-follow guide illustrating the techniques to boost the performance of Python code, and their applications with plenty of hands-on examples.If you are a programmer who likes the power and simplicity of Python and would like to use this language for performance-critical applications, this book is ideal for you. All that is required is a basic knowledge of the Python programming language. The book will cover basic and advanced topics so will be great for you whether you are a new or a seasoned Python developer.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. Python data analysis

    CERN Document Server

    Idris, Ivan

    2014-01-01

    This book is for programmers, scientists, and engineers who have knowledge of the Python language and know the basics of data science. It is for those who wish to learn different data analysis methods using Python and its libraries. This book contains all the basic ingredients you need to become an expert data analyst.

  12. Python for Ecology

    Science.gov (United States)

    Python is a high-level scripting language that is becoming increasingly popular for scientific computing. This all-day workshop is designed to introduce the basics of Python programming to ecologists. Some scripting/programming experience is recommended (e.g. familiarity with R)....

  13. Python requests essentials

    CERN Document Server

    Chandra, Rakesh Vidya

    2015-01-01

    If you are a Python administrator or developer interested in interacting with web APIs and have a passion for creating your own web applications, this is the book for you. Basic knowledge of Python programming, APIs, and web services will be an advantage.

  14. Scraping EDGAR with Python

    Science.gov (United States)

    Ashraf, Rasha

    2017-01-01

    This article presents Python codes that can be used to extract data from Securities and Exchange Commission (SEC) filings. The Python program web crawls to obtain URL paths for company filings of required reports, such as Form 10-K. The program then performs a textual analysis and counts the number of occurrences of words in the filing that…

  15. Python library reference

    NARCIS (Netherlands)

    G. van Rossum (Guido)

    1995-01-01

    textabstractPython is an extensible, interpreted, object-oriented programming language. It supports a wide range of applications, from simple text processing scripts to interactive WWW browsers. While the Python Reference Manual describes the exact syntax and semantics of the language, it does not

  16. 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...

  17. 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...

  18. 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 ...

  19. Python in a nutshell

    CERN Document Server

    Martelli, Alex; Holden, Steve

    2016-01-01

    Useful in many roles, from design and prototyping to testing, deployment, and maintenance, Python is consistently ranked among today’s most popular programming languages. The third edition of this practical book provides a quick reference to the language—including Python 3.5, 2.7, and highlights of 3.6—commonly used areas of its vast standard library, and some of the most useful third-party modules and packages. Ideal for programmers with some Python experience, and those coming to Python from other programming languages, this book covers a wide range of application areas, including web and network programming, XML handling, database interactions, and high-speed numeric computing. Discover how Python provides a unique mix of elegance, simplicity, practicality, and sheer power.

  20. Python to learn programming

    Science.gov (United States)

    Bogdanchikov, A.; Zhaparov, M.; Suliyev, R.

    2013-04-01

    Today we have a lot of programming languages that can realize our needs, but the most important question is how to teach programming to beginner students. In this paper we suggest using Python for this purpose, because it is a programming language that has neatly organized syntax and powerful tools to solve any task. Moreover it is very close to simple math thinking. Python is chosen as a primary programming language for freshmen in most of leading universities. Writing code in python is easy. In this paper we give some examples of program codes written in Java, C++ and Python language, and we make a comparison between them. Firstly, this paper proposes advantages of Python language in relation to C++ and JAVA. Then it shows the results of a comparison of short program codes written in three different languages, followed by a discussion on how students understand programming. Finally experimental results of students' success in programming courses are shown.

  1. Amebiasis in four ball pythons, Python reginus.

    Science.gov (United States)

    Kojimoto, A; Uchida, K; Horii, Y; Okumura, S; Yamaguch, R; Tateyama, S

    2001-12-01

    Between September 13th and November 18th in 1999, four ball pythons, Python reginus kept in the same display, showed anorexia and died one after another. At necropsy, all four snakes had severe hemorrhagic colitis. Microscopically, all snakes had severe necrotizing hemorrhagic colitis, in association with ameba-like protozoa. Some of the protozoa had macrophage-like morphology and others formed protozoal cysts with thickened walls. These protozoa were distributed throughout the wall in the large intestine. Based on the pathological findings, these snakes were infested with a member of Entamoeba sp., presumably with infection by Entamoeba invadens, the most prevalent type of reptilian amoebae.

  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. A Distributed Python HPC Framework: ODIN, PyTrilinos, & Seamless

    Energy Technology Data Exchange (ETDEWEB)

    Grant, Robert [Enthought, Inc., Austin, TX (United States)

    2015-11-23

    Under this grant, three significant software packages were developed or improved, all with the goal of improving the ease-of-use of HPC libraries. The first component is a Python package, named DistArray (originally named Odin), that provides a high-level interface to distributed array computing. This interface is based on the popular and widely used NumPy package and is integrated with the IPython project for enhanced interactive parallel distributed computing. The second Python package is the Distributed Array Protocol (DAP) that enables separate distributed array libraries to share arrays efficiently without copying or sending messages. If a distributed array library supports the DAP, it is then automatically able to communicate with any other library that also supports the protocol. This protocol allows DistArray to communicate with the Trilinos library via PyTrilinos, which was also enhanced during this project. A third package, PyTrilinos, was extended to support distributed structured arrays (in addition to the unstructured arrays of its original design), allow more flexible distributed arrays (i.e., the restriction to double precision data was lifted), and implement the DAP. DAP support includes both exporting the protocol so that external packages can use distributed Trilinos data structures, and importing the protocol so that PyTrilinos can work with distributed data from external packages.

  4. Scoria: a Python module for manipulating 3D molecular data.

    Science.gov (United States)

    Ropp, Patrick; Friedman, Aaron; Durrant, Jacob D

    2017-09-18

    Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with dependencies and compilers. This presents a barrier that can hinder the otherwise broad adoption of new tools. We present Scoria, a Python package for manipulating three-dimensional molecular data. Unlike similar packages, Scoria requires no dependencies, compilation, or system-wide installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g. NumPy, SciPy), if present, to speed and extend its own functionality. To show its utility, we use Scoria to analyze a molecular dynamics trajectory. Our FootPrint script colors the atoms of one chain by the frequency of their contacts with a second chain. We are hopeful that Scoria will be a useful tool for the computational-biology community. A copy is available for download free of charge (Apache License 2.0) at http://durrantlab.com/scoria/ . Graphical abstract .

  5. Pro Python System Administration

    CERN Document Server

    Sileika, R

    2010-01-01

    As time goes on, system administrators are presented with increasingly complicated challenges. In the early days, a team of engineers might have had to look after one or two systems. These days, one engineer can administer hundreds or thousands of systems. System administrators are gradually replacing their tools with more advanced and flexible ones. One of the choices is Python. Structurally, Python is a modern, high-level language with a very clean syntax. Python comes with many built-in libraries that can make automation tasks easier. It also has extensive set of third-party libraries and a

  6. Python geospatial development

    CERN Document Server

    Westra, Erik

    2013-01-01

    This is a tutorial style book that will teach usage of Python tools for GIS using simple practical examples and then show you how to build a complete mapping application from scratch. The book assumes basic knowledge of Python. No knowledge of Open Source GIS is required.Experienced Python developers who want to learn about geospatial concepts, work with geospatial data, solve spatial problems, and build mapbased applications.This book will be useful those who want to get up to speed with Open Source GIS in order to build GIS applications or integrate GeoSpatial features into their existing ap

  7. Parallel programming with Python

    CERN Document Server

    Palach, Jan

    2014-01-01

    A fast, easy-to-follow and clear tutorial to help you develop Parallel computing systems using Python. Along with explaining the fundamentals, the book will also introduce you to slightly advanced concepts and will help you in implementing these techniques in the real world. If you are an experienced Python programmer and are willing to utilize the available computing resources by parallelizing applications in a simple way, then this book is for you. You are required to have a basic knowledge of Python development to get the most of this book.

  8. Python Introduction and Installation

    Directory of Open Access Journals (Sweden)

    William J. Turkel

    2012-07-01

    Full Text Available This first lesson in our section on dealing with Online Sources is designed to get you and your computer set up to start programming. We will focus on installing the relevant software – all free and reputable – and finally we will help you to get your toes wet with some simple programming that provides immediate results. In this opening module you will install the Python programming language, the Beautiful Soup HTML/XML parser, and a text editor. Screencaps provided here come from Komodo Edit, but you can use any text editor capable of working with Python. Here’s a list of other options: Python Editors. Once everything is installed, you will write your first programs, “Hello World” in Python and HTML.

  9. Python for secret agents

    CERN Document Server

    Lott, Steven F

    2014-01-01

    If you are a Python beginner who is looking to learn the language through interesting projects, this book is for you. A basic knowledge of programming and statistics is beneficial to get the most out of the book.

  10. Python profiling 101

    CERN Multimedia

    CERN. Geneva

    2014-01-01

    Python code is much easier to write than C, yet much less efficient. It's often assumed that Python is not performance-oriented and therefore making effort to optimize it doesn't pay off. While in many cases it's true, at a certain moment of a development, especially right before reaching production-ready state, it might turn out that a Python code runs slowly and one needs to find a culprit. In this talk I'll not tell how to make your program faster. Instead, I'll show different techniques to look for the bottlenecks in the code. The presentation will be built around a live demo using real-life Python code.

  11. NEURON and Python.

    Science.gov (United States)

    Hines, Michael L; Davison, Andrew P; Muller, Eilif

    2009-01-01

    The NEURON simulation program now allows Python to be used, alone or in combination with NEURON's traditional Hoc interpreter. Adding Python to NEURON has the immediate benefit of making available a very extensive suite of analysis tools written for engineering and science. It also catalyzes NEURON software development by offering users a modern programming tool that is recognized for its flexibility and power to create and maintain complex programs. At the same time, nothing is lost because all existing models written in Hoc, including graphical user interface tools, continue to work without change and are also available within the Python context. An example of the benefits of Python availability is the use of the xml module in implementing NEURON's Import3D and CellBuild tools to read MorphML and NeuroML model specifications.

  12. Python Switch Statement

    Directory of Open Access Journals (Sweden)

    2008-06-01

    Full Text Available The Python programming language does not have a built in switch/case control structure as found in many other high level programming languages. It is thought by some that this is a deficiency in the language, and the control structure should be added. This paper demonstrates that not only is the control structure not needed, but that the methods available in Python are more expressive than built in case statements in other high level languages.

  13. Manipulating Strings in Python

    Directory of Open Access Journals (Sweden)

    William J. Turkel

    2012-07-01

    Full Text Available This lesson is a brief introduction to string manipulation techniques in Python. Knowing how to manipulate strings plays a crucial role in most text processing tasks. If you’d like to experiment with the following lessons, you can write and execute short programs as we’ve been doing, or you can open up a Python shell / Terminal to try them out on the command line.

  14. 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

  15. 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.

  16. 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'....

  17. Programming for computations Python : a gentle introduction to numerical simulations with Python

    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.

  18. 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.

  19. 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....

  20. Ascaridosis in captive reticulated python( Python reticulatus ) | Taiwo ...

    African Journals Online (AJOL)

    Two captive reticulated pythons, Python reticulatus, in the Zoological Gardens, University of Ibadan, Ibadan, Nigeria died and were submitted for necropsy at the Diagnostic Laboratory of the Department of Veterinary Pathology, University of Ibadan. Both pythons had been infected with Ascaridia galli for a long period of time ...

  1. Python for scientists

    CERN Document Server

    Stewart, John M

    2017-01-01

    Scientific Python is a significant public domain alternative to expensive proprietary software packages. This book teaches from scratch everything the working scientist needs to know using copious, downloadable, useful and adaptable code snippets. Readers will discover how easy it is to implement and test non-trivial mathematical algorithms and will be guided through the many freely available add-on modules. A range of examples, relevant to many different fields, illustrate the language's capabilities. The author also shows how to use pre-existing legacy code (usually in Fortran77) within the Python environment, thus avoiding the need to master the original code. In this new edition, several chapters have been re-written to reflect the IPython notebook style. With an extended index, an entirely new chapter discussing SymPy and a substantial increase in the number of code snippets, researchers and research students will be able to quickly acquire all the skills needed for using Python effectively.

  2. 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.

  3. Python and AWS Cookbook

    CERN Document Server

    Garnaat, Mitch

    2011-01-01

    If you intend to use Amazon Web Services (AWS) for remote computing and storage, Python is an ideal programming language for developing applications and controlling your cloud-based infrastructure. This cookbook gets you started with more than two dozen recipes for using Python with AWS, based on the author's boto library. You'll find detailed recipes for working with the S3 storage service as well as EC2, the service that lets you design and build cloud applications. Each recipe includes a code solution you can use immediately, along with a discussion of why and how the recipe works. You al

  4. Python for finance

    CERN Document Server

    Yan, Yuxing

    2014-01-01

    Python is a free and powerful tool which can be used to build a financial calculator and price options, and can also explain many trading strategies and test various hypotheses. In addition to that, real-world data can be used to run CAPM (Capital Asset Pricing Model), the Fama-French 3-factor model, estimate VaR (Value at Risk), and estimate spread, illiquidity, and liquidity. This book explores the basics of programming in Python. It is a step-by-step tutorial that will teach you, with the help of concise, practical programs, how to run various statistic tests. With this book, you will learn

  5. Practical Maya programming with Python

    CERN Document Server

    Galanakis, Robert

    2014-01-01

    ""Practical Maya Programming with Python"" is a practical tutorial packed with plenty of examples and sample projects which guides you through building reusable, independent modules and handling unexpected errors. If you are a developer looking to build a powerful system using Python and Maya's capabilities, then this book is for you. Practical Maya Programming with Python is perfect for intermediate users with basic experience in Python and Maya who want to better their knowledge and skills.

  6. Developers@CERN Forums: Python

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    The Developers@CERN Forums second edition took place at the end of May on the topic of Python. How do developers at CERN interact with Python? Which cutting-edge projects are using Python? What were the highlights of this most recent forum?

  7. Learning robotics using Python

    CERN Document Server

    Joseph, Lentin

    2015-01-01

    If you are an engineer, a researcher, or a hobbyist, and you are interested in robotics and want to build your own robot, this book is for you. Readers are assumed to be new to robotics but should have experience with Python.

  8. Python and computer vision

    Energy Technology Data Exchange (ETDEWEB)

    Doak, J. E. (Justin E.); Prasad, Lakshman

    2002-01-01

    This paper discusses the use of Python in a computer vision (CV) project. We begin by providing background information on the specific approach to CV employed by the project. This includes a brief discussion of Constrained Delaunay Triangulation (CDT), the Chordal Axis Transform (CAT), shape feature extraction and syntactic characterization, and normalization of strings representing objects. (The terms 'object' and 'blob' are used interchangeably, both referring to an entity extracted from an image.) The rest of the paper focuses on the use of Python in three critical areas: (1) interactions with a MySQL database, (2) rapid prototyping of algorithms, and (3) gluing together all components of the project including existing C and C++ modules. For (l), we provide a schema definition and discuss how the various tables interact to represent objects in the database as tree structures. (2) focuses on an algorithm to create a hierarchical representation of an object, given its string representation, and an algorithm to match unknown objects against objects in a database. And finally, (3) discusses the use of Boost Python to interact with the pre-existing C and C++ code that creates the CDTs and CATS, performs shape feature extraction and syntactic characterization, and normalizes object strings. The paper concludes with a vision of the future use of Python for the CV project.

  9. Python reference manual

    NARCIS (Netherlands)

    G. van Rossum (Guido)

    1995-01-01

    textabstractPython is a simple, yet powerful, interpreted programming language that bridges the gap between C and shell programming, and is thus ideally suited for ``throw-away programming'' and rapid prototyping. Its syntax is put together from constructs borrowed from a variety of other languages;

  10. Python at CERN

    CERN Multimedia

    Witowski, Sebastian

    2017-01-01

    The Large Hadron Collider at CERN is producing 600 million collisions every second. Only 1 in a million collisions is interesting. It requires a fast programming language to analyze and filter this amount of data. Is Python such a language? No, it’s not. Does it mean there is no place for Python in one of the largest scientific facilities in the world? Quite the contrary. The ease of use and a very low learning curve makes Python a perfect programming language for many physicists and other people without the computer science background. CERN does not only produce large amounts of data. The interesting bits of data have to be stored, analyzed, shared and published. Work of many scientists across various research facilities around the world has to be synchronized. This is the area where Python flourishes. And with CERN’s pursuit to create and use open source software, many interesting projects were born. To facilitate the analysis of data, ROOT framework [https://root.cern.ch/] was created. It’s a C++ fra...

  11. 75 FR 38069 - Injurious Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda...

    Science.gov (United States)

    2010-07-01

    ... Python Species, and Four Anaconda Species as Injurious Reptiles AGENCY: Fish and Wildlife Service... regulations to add Indian python (Python molurus, including Burmese python Python molurus bivittatus), reticulated python (Broghammerus reticulatus or Python reticulatus), Northern African python (Python sebae...

  12. A primer on scientific programming with Python

    CERN Document Server

    Langtangen, Hans Petter

    2014-01-01

    The book serves as a first introduction to computer programming of scientific applications, using the high-level Python language. The exposition is example and problem-oriented, where the applications are taken from mathematics, numerical calculus, statistics, physics, biology and finance. The book teaches "Matlab-style" and procedural programming as well as object-oriented programming. High school mathematics is a required background and it is advantageous to study classical and numerical one-variable calculus in parallel with reading this book. Besides learning how to program computers, the reader will also learn how to solve mathematical problems, arising in various branches of science and engineering, with the aid of numerical methods and programming. By blending programming, mathematics and scientific applications, the book lays a solid foundation for practicing computational science. From the reviews: Langtangen … does an excellent job of introducing programming as a set of skills in problem solving. ...

  13. A primer on scientific programming with Python

    CERN Document Server

    Langtangen, Hans Petter

    2016-01-01

    The book serves as a first introduction to computer programming of scientific applications, using the high-level Python language. The exposition is example and problem-oriented, where the applications are taken from mathematics, numerical calculus, statistics, physics, biology and finance. The book teaches "Matlab-style" and procedural programming as well as object-oriented programming. High school mathematics is a required background and it is advantageous to study classical and numerical one-variable calculus in parallel with reading this book. Besides learning how to program computers, the reader will also learn how to solve mathematical problems, arising in various branches of science and engineering, with the aid of numerical methods and programming. By blending programming, mathematics and scientific applications, the book lays a solid foundation for practicing computational science. From the reviews: Langtangen … does an excellent job of introducing programming as a set of skills in problem solving. ...

  14. 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 ...

  15. 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.

  16. 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

  17. 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

  18. Deep learning with Python

    CERN Document Server

    Chollet, Francois

    2018-01-01

    DESCRIPTION Deep learning is applicable to a widening range of artificial intelligence problems, such as image classification, speech recognition, text classification, question answering, text-to-speech, and optical character recognition. Deep Learning with Python is structured around a series of practical code examples that illustrate each new concept introduced and demonstrate best practices. By the time you reach the end of this book, you will have become a Keras expert and will be able to apply deep learning in your own projects. KEY FEATURES • Practical code examples • In-depth introduction to Keras • Teaches the difference between Deep Learning and AI ABOUT THE TECHNOLOGY Deep learning is the technology behind photo tagging systems at Facebook and Google, self-driving cars, speech recognition systems on your smartphone, and much more. AUTHOR BIO Francois Chollet is the author of Keras, one of the most widely used libraries for deep learning in Python. He has been working with deep neural ...

  19. Python algorithms mastering basic algorithms in the Python language

    CERN Document Server

    Hetland, Magnus Lie

    2014-01-01

    Python Algorithms, Second Edition explains the Python approach to algorithm analysis and design. Written by Magnus Lie Hetland, author of Beginning Python, this book is sharply focused on classical algorithms, but it also gives a solid understanding of fundamental algorithmic problem-solving techniques. The book deals with some of the most important and challenging areas of programming and computer science in a highly readable manner. It covers both algorithmic theory and programming practice, demonstrating how theory is reflected in real Python programs. Well-known algorithms and data struc

  20. Installing Python Modules with pip

    OpenAIRE

    Fred Gibbs

    2013-01-01

    This lesson shows you how to download and install Python modules. There are many ways to install external modules, but for the purposes of this lesson, we’re going to use a program called pip. As of Python 2.7.9 and newer, pip is installed by default. This tutorial will be helpful for anyone using older versions of Python (which are still quite common).

  1. Mastering object-oriented Python

    CERN Document Server

    Lott, Steven F

    2014-01-01

    This book follows a standard tutorial approach with approximately 750 code samples spread through the 19 chapters. This amounts to over 5,900 lines of code that illustrate each concept.This book is aimed at programmers who have already learned the basics of object-oriented Python and need to write more sophisticated, flexible code that integrates seamlessly with the rest of Python. This book assumes a computer science background, with experience of common Python design patterns.

  2. 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.

  3. 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.

  4. 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.

  5. Beginning Python using Python 2.6 and Python 3.1

    CERN Document Server

    Payne, James

    2010-01-01

    Beginning Python: Using Python 2.6 and Python 3.1 introduces this open source, portable, interpreted, object-oriented programming language that combines remarkable power with clear syntax. This book enables you to quickly create robust, reliable, and reusable Python applications by teaching the basics so you can quickly develop Web and scientific applications, incorporate databases, and master systems tasks on various operating systems, including Linux, MAC OS, and Windows. You’ll get a comprehensive tutorial that guides you from writing simple, basic Python scripts all the way through complex concepts, and also features a reference of the standard modules with examples illustrating how to implement features in the various modules. Plus, the book covers using Python in specific program development domains, such as XML, databases, scientific applications, network programming, and Web development

  6. Brian: a simulator for spiking neural networks in Python

    Directory of Open Access Journals (Sweden)

    Dan F M Goodman

    2008-11-01

    Full Text Available Brian is a new simulator for spiking neural networks, written in Python (http://brian.di.ens.fr. It is an intuitive and highly flexible tool for rapidly developing new models, especially networks of single-compartment neurons. In addition to using standard types of neuron models, users can define models by writing arbitrary differential equations in ordinary mathematical notation. Python scientific libraries can also be used for defining models and analysing data. Vectorisation techniques allow efficient simulations despite the overheads of an interpreted language. Brian will be especially valuable for working on non-standard neuron models not easily covered by existing software, and as an alternative to using Matlab or C for simulations. With its easy and intuitive syntax, Brian is also very well suited for teaching computational neuroscience.

  7. Brian: a simulator for spiking neural networks in python.

    Science.gov (United States)

    Goodman, Dan; Brette, Romain

    2008-01-01

    "Brian" is a new simulator for spiking neural networks, written in Python (http://brian. di.ens.fr). It is an intuitive and highly flexible tool for rapidly developing new models, especially networks of single-compartment neurons. In addition to using standard types of neuron models, users can define models by writing arbitrary differential equations in ordinary mathematical notation. Python scientific libraries can also be used for defining models and analysing data. Vectorisation techniques allow efficient simulations despite the overheads of an interpreted language. Brian will be especially valuable for working on non-standard neuron models not easily covered by existing software, and as an alternative to using Matlab or C for simulations. With its easy and intuitive syntax, Brian is also very well suited for teaching computational neuroscience.

  8. The spectacle of the ball python (Python regius)

    DEFF Research Database (Denmark)

    Da Silva, Mari-Ann Otkjær; Heegaard, Steffen; Wang, Tobias

    2014-01-01

    A detailed morphological description of the spectacle of the ball python (Python regius) is provided. The eyes of 21 snakes were examined by light microscopy and/or transmission electron microscopy. Additionally, eyes of nine live snakes were examined using optical coherence tomography (OCT...

  9. Python Integration with a Functional DBMS

    OpenAIRE

    Zou, Hanzheng

    2009-01-01

    Python is an Object Oriented programming language and widely used nowadays. This report describes how to extend a functional database system Amos II for integration with Python. Several possibilities are analyzed to combine the Amos II C external interfaces with those of Python. Based on these discussions, new functionality has been added to the Python language by implementing a Python C external module. A basic API called PyAmos, interfacing Python and Amos II, is proposed and implemented in...

  10. Pythons in Burma: Short-tailed python (Reptilia: Squamata)

    Science.gov (United States)

    Zug, George R.; Gotte, Steve W.; Jacobs, Jeremy F.

    2011-01-01

    Short-tailed pythons, Python curtus species group, occur predominantly in the Malayan Peninsula, Sumatra, and Borneo. The discovery of an adult female in Mon State, Myanmar, led to a review of the distribution of all group members (spot-mapping of all localities of confirmed occurrence) and an examination of morphological variation in P. brongersmai. The resulting maps demonstrate a limited occurrence of these pythons within peninsular Malaya, Sumatra, and Borneo with broad absences in these regions. Our small samples limit the recognition of regional differentiation in the morphology of P. brongersmai populations; however, the presence of unique traits in the Myanmar python and its strong allopatry indicate that it is a unique genetic lineage, and it is described as Python kyaiktiyo new species.

  11. Python Introduction and Installation

    OpenAIRE

    William J. Turkel; Adam Crymble

    2012-01-01

    This first lesson in our section on dealing with Online Sources is designed to get you and your computer set up to start programming. We will focus on installing the relevant software – all free and reputable – and finally we will help you to get your toes wet with some simple programming that provides immediate results. In this opening module you will install the Python programming language, the Beautiful Soup HTML/XML parser, and a text editor. Screencaps provided here come from Komodo ...

  12. Python tools for Visual Studio

    CERN Document Server

    Wang, Cathy

    2014-01-01

    This is a hands-on guide that provides exemplary coverage of all the features and concepts related to PTVS.The book is intended for developers who are aiming to enhance their productivity in Python projects with automation tools that Visual Studio provides for the .Net community. Some basic knowledge of Python programming is essential.

  13. 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....

  14. Writing faster Python

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    Did you know that Python preallocates integers from -5 to 257 ? Reusing them 1000 times, instead of allocating memory for a bigger integer, can save you a couple of milliseconds of code’s execution time. If you want to learn more about this kind of optimizations then, … well, probably this presentation is not for you :) Instead of going into such small details, I will talk about more "sane" ideas for writing faster code. After a very brief overview of how to optimize Python code (rule 1: don’t do this; rule 2: don’t do this yet; rule 3: ok, but what if I really want to do this ?), I will show simple and fast ways of measuring the execution time and finally, discuss examples of how some code structures could be improved. You will see: - What is the fastest way of removing duplicates from a list - How much faster your code is when you reuse the built-in functions instead of trying to reinvent the wheel - What is faster than the good ol’ for loop - If the lookup is faster in a list or a set (and w...

  15. EPICS V4 in Python

    International Nuclear Information System (INIS)

    Guobao Shen; Kraimer, M.; Davidsaver, M.

    2012-01-01

    At NSLS-II, Python has been selected as the primary development language for physics applications. Interest in Python as a rapid application development environment continues to grow. Many large experimental scientific facilities have adopted Python for beam commissioning and the operation. The EPICS control system framework has become the de facto standard for the control of large experimental facilities, where it is in use in over 100 facilities. The next version of EPICS (EPICS V4), under active development will extend the support for physics applications, data acquisition, and data analysis. Python support for EPICS V4 will provide an effective framework to address these requirements. This paper presents design, development and status of activities focused on EPICS V4 in Python

  16. Pyphant – A Python Framework for Modelling Reusable Information Processing Tasks

    Directory of Open Access Journals (Sweden)

    2008-06-01

    Full Text Available We are presenting the Python framework “Pyphant” for the creation and application of information flow models. The central idea of this approach is to encapsulate each data processing step in one unit which we call a worker. A worker receives input via sockets and provides the results of its data processing via plugs. These can be connected to other workers' sockets. The resulting directed graph is called a recipe. Classes for these objects comprise the Pyphant core. To implement the actual processing steps, Pyphant relies on third-party plug-ins which extend the basic worker class and can be distributed as Python eggs. On top of the core, Pyphant offers an information exchange layer which facilitates the interoperability of the workers, using Numpy objects. A third layer comprises textual and graphical user interfaces. The former allows for the batch processing of data and the latter allows for the interactive construction of recipes.

    This paper discusses the Pyphant framework and presents an example recipe for determining the length scale of aggregated polymeric phases, building an amphiphilic conetwork from an Atomic Force Microscopy (AFM phase mode image.

  17. Analyzing rasters, vectors and time series using new Python interfaces in GRASS GIS 7

    Science.gov (United States)

    Petras, Vaclav; Petrasova, Anna; Chemin, Yann; Zambelli, Pietro; Landa, Martin; Gebbert, Sören; Neteler, Markus; Löwe, Peter

    2015-04-01

    helps researchers to ensure the robustness of the algorithm, correctness of the results in edge cases as well as the detection of changes in results due to new development. For all modules GRASS GIS automatically creates standardized command line and graphical user interfaces and documentation. Finally, we will show how GRASS GIS can be used together with powerful Python tools such as the NumPy package and the IPython Notebook. References: Gebbert, S., Pebesma, E., 2014. A temporal GIS for field based environmental modeling. Environmental Modelling & Software 53, 1-12. Neteler, M., Bowman, M.H., Landa, M. and Metz, M., 2012. GRASS GIS: a multi-purpose Open Source GIS. Environmental Modelling & Software 31: 124-130. Petras, V., Gebbert, S., 2014. Testing framework for GRASS GIS: ensuring reproducibility of scientific geospatial computing. Poster presented at: AGU Fall Meeting, December 15-19, 2014, San Francisco, USA. Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS International Journal of Geo-Information 2, 201-219.

  18. 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

  19. Endocardial fibrosarcoma in a reticulated python (Python reticularis).

    Science.gov (United States)

    Gumber, Sanjeev; Nevarez, Javier G; Cho, Doo-Youn

    2010-11-01

    A female, reticulated python (Python reticularis) of unknown age was presented with a history of lethargy, weakness, and distended coelom. Physical examination revealed severe dystocia and stomatitis. The reticulated python was euthanized due to a poor clinical prognosis. Postmortem examination revealed marked distention of the reproductive tract with 26 eggs (10-12 cm in diameter), pericardial effusion, and a slightly firm, pale tan mass (3-4 cm in diameter) adhered to the endocardium at the base of aorta. Based on histopathologic and transmission electron microscopic findings, the diagnosis of endocardial fibrosarcoma was made.

  20. QuTiP: An open-source Python framework for the dynamics of open quantum systems

    Science.gov (United States)

    Johansson, J. R.; Nation, P. D.; Nori, Franco

    2012-08-01

    We present an object-oriented open-source framework for solving the dynamics of open quantum systems written in Python. Arbitrary Hamiltonians, including time-dependent systems, may be built up from operators and states defined by a quantum object class, and then passed on to a choice of master equation or Monte Carlo solvers. We give an overview of the basic structure for the framework before detailing the numerical simulation of open system dynamics. Several examples are given to illustrate the build up to a complete calculation. Finally, we measure the performance of our library against that of current implementations. The framework described here is particularly well suited to the fields of quantum optics, superconducting circuit devices, nanomechanics, and trapped ions, while also being ideal for use in classroom instruction. Catalogue identifier: AEMB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 16 482 No. of bytes in distributed program, including test data, etc.: 213 438 Distribution format: tar.gz Programming language: Python Computer: i386, x86-64 Operating system: Linux, Mac OSX, Windows RAM: 2+ Gigabytes Classification: 7 External routines: NumPy (http://numpy.scipy.org/), SciPy (http://www.scipy.org/), Matplotlib (http://matplotlib.sourceforge.net/) Nature of problem: Dynamics of open quantum systems. Solution method: Numerical solutions to Lindblad master equation or Monte Carlo wave function method. Restrictions: Problems must meet the criteria for using the master equation in Lindblad form. Running time: A few seconds up to several tens of minutes, depending on size of underlying Hilbert space.

  1. 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...

  2. DAL Algorithms and Python

    CERN Document Server

    Aydemir, Bahar

    2017-01-01

    The Trigger and Data Acquisition (TDAQ) system of the ATLAS detector at the Large Hadron Collider (LHC) at CERN is composed of a large number of distributed hardware and software components. TDAQ system consists of about 3000 computers and more than 25000 applications which, in a coordinated manner, provide the data-taking functionality of the overall system. There is a number of online services required to configure, monitor and control the ATLAS data taking. In particular, the configuration service is used to provide configuration of above components. The configuration of the ATLAS data acquisition system is stored in XML-based object database named OKS. DAL (Data Access Library) allowing to access it's information by C++, Java and Python clients in a distributed environment. Some information has quite complicated structure, so it's extraction requires writing special algorithms. Algorithms available on C++ programming language and partially reimplemented on Java programming language. The goal of the projec...

  3. Acariasis on pet Burmese python, Python molurus bivittatus in Malaysia.

    Science.gov (United States)

    Mariana, A; Vellayan, S; Halimaton, I; Ho, T M

    2011-03-01

    To identify the acari present on pet Burmese pythons in Malaysia and to determine whether there is any potential public health risk related to handling of the snakes. Two sub-adult Burmese pythons kept as pets for a period of about 6 to 7 months by different owners, were brought to an exotic animal practice for treatment. On a complete medical examination, some ticks and mites (acari) were detected beneath the dorsal and ventral scales along body length of the snakes. Ticks were directly identified and mites were mounted prior to identification. A total of 12 ticks represented by 3 males, 2 females and 7 nymphal stages of Rhipicephalus sanguineus (R. sanguineus) were extracted from the first python while the other one was with 25 female Ophionyssus natricis (O. natricis) mesostigmatid mites. Only adult female mites were found. These mites are common ectoparasites of Burmese pythons. Both the acarine species found on the Burmese pythons are known vectors of pathogens. This is the first record that R. sanguineus has been reported from a pet Burmese python in Malaysia. Copyright © 2011 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

  4. Python for Google app engine

    CERN Document Server

    Pippi, Massimiliano

    2015-01-01

    If you are a Python developer, whether you have experience in web applications development or not, and want to rapidly deploy a scalable backend service or a modern web application on Google App Engine, then this book is for you.

  5. MDSplus objects-Python implementation

    Energy Technology Data Exchange (ETDEWEB)

    Fredian, T., E-mail: twf@psfc.mit.ed [Massachusetts Institute of Technology, Plasma Science and Fusion Center, NW17-268, 175 Albany Street, Cambridge, MA 02139 (United States); Stillerman, J. [Massachusetts Institute of Technology, Plasma Science and Fusion Center, NW17-268, 175 Albany Street, Cambridge, MA 02139 (United States); Manduchi, G. [Consorzio RFX, Euratom-ENEA Association, Corso Stati Uniti 4, Padova 35127 (Italy)

    2010-07-15

    MDSplus is a data acquisition and analysis software package used widely throughout the international fusion research community. During the past year, an important set of enhancements were designed under the project name of 'MDSobjects' which would provide a common, powerful application programming interface (API) to MDSplus in programming languages with object-oriented capabilities. This paper will discuss the Python language implementation of this API and some of the capabilities that this implementation provides for data storage and retrieval using the MDSplus system. We have implemented a new MDSplus Python module which exposes the MDSplus objects features to the language. The internal MDSplus programming language, TDI, has also been enhanced to be able to invoke Python commands from the TDI language. Now that Python is aware of the complex data structures in MDSplus such as Signals, the language becomes a very good candidate for applications ranging from data acquisition device support to analysis and visualization.

  6. MDSplus objects-Python implementation

    International Nuclear Information System (INIS)

    Fredian, T.; Stillerman, J.; Manduchi, G.

    2010-01-01

    MDSplus is a data acquisition and analysis software package used widely throughout the international fusion research community. During the past year, an important set of enhancements were designed under the project name of 'MDSobjects' which would provide a common, powerful application programming interface (API) to MDSplus in programming languages with object-oriented capabilities. This paper will discuss the Python language implementation of this API and some of the capabilities that this implementation provides for data storage and retrieval using the MDSplus system. We have implemented a new MDSplus Python module which exposes the MDSplus objects features to the language. The internal MDSplus programming language, TDI, has also been enhanced to be able to invoke Python commands from the TDI language. Now that Python is aware of the complex data structures in MDSplus such as Signals, the language becomes a very good candidate for applications ranging from data acquisition device support to analysis and visualization.

  7. ObsPy: A Python Toolbox for Seismology - Recent Developments and Applications

    Science.gov (United States)

    Megies, T.; Krischer, L.; Barsch, R.; Sales de Andrade, E.; Beyreuther, M.

    2014-12-01

    ObsPy (http://www.obspy.org) is a community-driven, open-source project dedicated to building a bridge for seismology into the scientific Python ecosystem. It offersa) read and write support for essentially all commonly used waveform, station, and event metadata file formats with a unified interface,b) a comprehensive signal processing toolbox tuned to the needs of seismologists,c) integrated access to all large data centers, web services and databases, andd) convenient wrappers to legacy codes like libtau and evalresp.Python, currently the most popular language for teaching introductory computer science courses at top-ranked U.S. departments, is a full-blown programming language with the flexibility of an interactive scripting language. Its extensive standard library and large variety of freely available high quality scientific modules cover most needs in developing scientific processing workflows. Together with packages like NumPy, SciPy, Matplotlib, IPython, Pandas, lxml, and PyQt, ObsPy enables the construction of complete workflows in Python. These vary from reading locally stored data or requesting data from one or more different data centers through to signal analysis and data processing and on to visualizations in GUI and web applications, output of modified/derived data and the creation of publication-quality figures.ObsPy enjoys a large world-wide rate of adoption in the community. Applications successfully using it include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. All functionality is extensively documented and the ObsPy tutorial and gallery give a good impression of the wide range of possible use cases.We will present the basic features of ObsPy, new developments and applications, and a roadmap for the near future and discuss the sustainability of our open-source development model.

  8. Pynamic: the Python Dynamic Benchmark

    Energy Technology Data Exchange (ETDEWEB)

    Lee, G L; Ahn, D H; de Supinksi, B R; Gyllenhaal, J C; Miller, P J

    2007-07-10

    Python is widely used in scientific computing to facilitate application development and to support features such as computational steering. Making full use of some of Python's popular features, which improve programmer productivity, leads to applications that access extremely high numbers of dynamically linked libraries (DLLs). As a result, some important Python-based applications severely stress a system's dynamic linking and loading capabilities and also cause significant difficulties for most development environment tools, such as debuggers. Furthermore, using the Python paradigm for large scale MPI-based applications can create significant file IO and further stress tools and operating systems. In this paper, we present Pynamic, the first benchmark program to support configurable emulation of a wide-range of the DLL usage of Python-based applications for large scale systems. Pynamic has already accurately reproduced system software and tool issues encountered by important large Python-based scientific applications on our supercomputers. Pynamic provided insight for our system software and tool vendors, and our application developers, into the impact of several design decisions. As we describe the Pynamic benchmark, we will highlight some of the issues discovered in our large scale system software and tools using Pynamic.

  9. 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.

  10. Data processing with Pymicra, the Python tool for Micrometeorological Analyses

    Science.gov (United States)

    Chor, T. L.; Dias, N. L.

    2017-12-01

    With the ever-increasing capability of instrumentation of collecting high-frequency turbulence data, micrometeorological experiments are now generating significant amounts of data. Clearly, data processing -- and not data collection anymore -- has become the limiting factor for those very large data sets. The ability of extracting useful scientific information from those experiments, therefore, hinges on tools that (i) are able to process those data effectively and accurately, (ii) are flexible enough to be adapted to the specific requirements of each investigation, and (iii) are robust enough to make data analysis easily reproducible over different sets of large data sets. We have developed a framework for micrometeorological data analysis called Pymicra which does deliver such capabilities while maintaining proximity of the investigator with the data. It is fully written in an open-source, very high level language, Python, which has been gaining widespread acceptance as a scientific tool. It follows the philosophy of "not reinventing the wheel" and, as a result, relies on existing well-established open-source Python packages such as Numpy and Pandas. Thus, minimum effort is needed to program statistics, array processing, Fourier analysis, etc. Among the things that Pymicra does are reading and organizing data from virtually any format, applying common quality control procedures, extracting fluctuations in a number of ways, correcting for sensor drift, automatic calculation of fluid properties (such as air and dry air density), handling of units, calculation of cross-spectra, calculation of turbulent fluxes and scales, and all other features already provided by Pandas (interpolation, statistical tests, handling of missing data, etc.). Pymicra is freely available on Github and the fact that it makes heavy use of high-level programming makes adding and modifying code considerably easy for any scientific programmer, making it straightforward for other scientists to

  11. Respiratory disease in ball pythons (Python regius) experimentally infected with ball python nidovirus.

    Science.gov (United States)

    Hoon-Hanks, Laura L; Layton, Marylee L; Ossiboff, Robert J; Parker, John S L; Dubovi, Edward J; Stenglein, Mark D

    2018-04-01

    Circumstantial evidence has linked a new group of nidoviruses with respiratory disease in pythons, lizards, and cattle. We conducted experimental infections in ball pythons (Python regius) to test the hypothesis that ball python nidovirus (BPNV) infection results in respiratory disease. Three ball pythons were inoculated orally and intratracheally with cell culture isolated BPNV and two were sham inoculated. Antemortem choanal, oroesophageal, and cloacal swabs and postmortem tissues of infected snakes were positive for viral RNA, protein, and infectious virus by qRT-PCR, immunohistochemistry, western blot and virus isolation. Clinical signs included oral mucosal reddening, abundant mucus secretions, open-mouthed breathing, and anorexia. Histologic lesions included chronic-active mucinous rhinitis, stomatitis, tracheitis, esophagitis and proliferative interstitial pneumonia. Control snakes remained negative and free of clinical signs throughout the experiment. Our findings establish a causal relationship between nidovirus infection and respiratory disease in ball pythons and shed light on disease progression and transmission. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  12. Humoral regulation of heart rate during digestion in pythons (Python molurus and Python regius).

    Science.gov (United States)

    Enok, Sanne; Simonsen, Lasse Stærdal; Pedersen, Signe Vesterskov; Wang, Tobias; Skovgaard, Nini

    2012-05-15

    Pythons exhibit a doubling of heart rate when metabolism increases several times during digestion. Pythons, therefore, represent a promising model organism to study autonomic cardiovascular regulation during the postprandial state, and previous studies show that the postprandial tachycardia is governed by a release of vagal tone as well as a pronounced stimulation from nonadrenergic, noncholinergic (NANC) factors. Here we show that infusion of plasma from digesting donor pythons elicit a marked tachycardia in fasting snakes, demonstrating that the NANC factor resides in the blood. Injections of the gastrin and cholecystokinin receptor antagonist proglumide had no effect on double-blocked heart rate or blood pressure. Histamine has been recognized as a NANC factor in the early postprandial period in pythons, but the mechanism of its release has not been identified. Mast cells represent the largest repository of histamine in vertebrates, and it has been speculated that mast cells release histamine during digestion. Treatment with the mast cell stabilizer cromolyn significantly reduced postprandial heart rate in pythons compared with an untreated group but did not affect double-blocked heart rate. While this study indicates that histamine induces postprandial tachycardia in pythons, its release during digestion is not stimulated by gastrin or cholecystokinin nor is its release from mast cells a stimulant of postprandial tachycardia.

  13. Beginning Python from novice to professional

    CERN Document Server

    Hetland, Magnus Lie

    2005-01-01

    ""Beginning Python: From Novice to Professional"" is the most comprehensive book on the Python ever written. Based on ""Practical Python,"" this newly revised book is both an introduction and practical reference for a swath of Python-related programming topics, including addressing language internals, database integration, network programming, and web services. Advanced topics, such as extending Python and packaging/distributing Python applications, are also covered. Ten different projects illustrate the concepts introduced in the book. You will learn how to create a P2P file-sharing applicati

  14. 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.

  15. 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

  16. Algorithmic synthesis using Python compiler

    Science.gov (United States)

    Cieszewski, Radoslaw; Romaniuk, Ryszard; Pozniak, Krzysztof; Linczuk, Maciej

    2015-09-01

    This paper presents a python to VHDL compiler. The compiler interprets an algorithmic description of a desired behavior written in Python and translate it to VHDL. FPGA combines many benefits of both software and ASIC implementations. Like software, the programmed circuit is flexible, and can be reconfigured over the lifetime of the system. FPGAs have the potential to achieve far greater performance than software as a result of bypassing the fetch-decode-execute operations of traditional processors, and possibly exploiting a greater level of parallelism. This can be achieved by using many computational resources at the same time. Creating parallel programs implemented in FPGAs in pure HDL is difficult and time consuming. Using higher level of abstraction and High-Level Synthesis compiler implementation time can be reduced. The compiler has been implemented using the Python language. This article describes design, implementation and results of created tools.

  17. Accessing the VO with Python

    Science.gov (United States)

    Plante, R.; Fitzpatrick, M.; Graham, M.; Tody, D.; Young, W.

    2014-05-01

    We introduce two products for accessing the VO from Python: PyVO and VOClient. PyVO is built on the widely-used Astropy package and is well suited for integrating automated access to astronomical data into highly customizable scripts and applications for data analysis in Python. VOClient is built on a collection of C-libraries and is well suited for integrating with multi-language analysis packages. It also provides a framework for integrating legacy software into the Python environment. In this demo, we will run through several examples demonstrate basic data discovery and retrieval of data. This includes finding archives containing data of interest (VO registry), retrieving datasets (SIA, SSA), and exploring (Cone Search, SLAP). VOClient features some extended capabilities including the ability to communicate to other desktop applications from a script using the SAMP protocol.

  18. Building machine learning systems with Python

    CERN Document Server

    Coelho, Luis Pedro

    2015-01-01

    This book primarily targets Python developers who want to learn and use Python's machine learning capabilities and gain valuable insights from data to develop effective solutions for business problems.

  19. Anatomy of the python heart.

    Science.gov (United States)

    Jensen, Bjarke; Nyengaard, Jens R; Pedersen, Michael; Wang, Tobias

    2010-12-01

    The hearts of all snakes and lizards consist of two atria and a single incompletely divided ventricle. In general, the squamate ventricle is subdivided into three chambers: cavum arteriosum (left), cavum venosum (medial) and cavum pulmonale (right). Although a similar division also applies to the heart of pythons, this family of snakes is unique amongst snakes in having intracardiac pressure separation. Here we provide a detailed anatomical description of the cardiac structures that confer this functional division. We measured the masses and volumes of the ventricular chambers, and we describe the gross morphology based on dissections of the heart from 13 ball pythons (Python regius) and one Burmese python (P. molurus). The cavum venosum is much reduced in pythons and constitutes approximately 10% of the cavum arteriosum. We suggest that shunts will always be less than 20%, while other studies conclude up to 50%. The high-pressure cavum arteriosum accounted for approximately 75% of the total ventricular mass, and was twice as dense as the low-pressure cavum pulmonale. The reptile ventricle has a core of spongious myocardium, but the three ventricular septa that separate the pulmonary and systemic chambers--the muscular ridge, the bulbuslamelle and the vertical septum--all had layers of compact myocardium. Pythons, however, have unique pads of connective tissue on the site of pressure separation. Because the hearts of varanid lizards, which also are endowed with pressure separation, share many of these morphological specializations, we propose that intraventricular compact myocardium is an indicator of high-pressure systems and possibly pressure separation.

  20. Learning Python with Raspberry Pi

    CERN Document Server

    Bradbury, Alex

    2014-01-01

    The must-have companion guide to the Raspberry Pi User Guide! Raspberry Pi chose Python as its teaching language of choice to encourage a new generation of programmers to learn how to program. This approachable book serves as an ideal resource for anyone wanting to use Raspberry Pi to learn to program and helps you get started with the Python programming language. Aimed at first-time developers with no prior programming language assumed, this beginner book gets you up and running.Covers variables, loops, and functionsAddresses 3D graphics programmingWalks you through programming MinecraftZero

  1. 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.

  2. Infestation of Royal Python (Python regius) with ticks Amblyomma ...

    African Journals Online (AJOL)

    The Python/Boa Family is found in most part of tropics. It is a highly domesticated pet and can easily be handled (Cansdale 1962). Snakes are commonly infected by ticks more importantly the hand bodied ticks (Fowler, 1986).However, under captive condition, ticks usually exert a lot of burden on their hosts being carriers of ...

  3. 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.

  4. 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...

  5. 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

  6. 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...

  7. 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...

  8. Pybus - A Python Software Bus

    International Nuclear Information System (INIS)

    Lavrijsen, Wim T.L.P.

    2004-01-01

    A software bus, just like its hardware equivalent, allows for the discovery, installation, configuration, loading, unloading, and run-time replacement of software components, as well as channeling of inter-component communication. Python, a popular open-source programming language, encourages a modular design on software written in it, but it offers little or no component functionality. However, the language and its interpreter provide sufficient hooks to implement a thin, integral layer of component support. This functionality can be presented to the developer in the form of a module, making it very easy to use. This paper describes a Pythonmodule, PyBus, with which the concept of a ''software bus'' can be realized in Python. It demonstrates, within the context of the ATLAS software framework Athena, how PyBus can be used for the installation and (run-time) configuration of software, not necessarily Python modules, from a Python application in a way that is transparent to the end-user

  9. Imagining a Stata / Python Combination

    Science.gov (United States)

    Fiedler, James

    2012-01-01

    There are occasions when a task is difficult in Stata, but fairly easy in a more general programming language. Python is a popular language for a range of uses. It is easy to use, has many high ]quality packages, and programs can be written relatively quickly. Is there any advantage in combining Stata and Python within a single interface? Stata already offers support for user-written programs, which allow extensive control over calculations, but somewhat less control over graphics. Also, except for specifying output, the user has minimal programmatic control over the user interface. Python can be used in a way that allows more control over the interface and graphics, and in so doing provide a roundabout method for satisfying some user requests (e.g., transparency levels in graphics and the ability to clear the results window). My talk will explore these ideas, present a possible method for combining Stata and Python, and give examples to demonstrate how this combination might be useful.

  10. Python pocket reference, version 2.4

    CERN Document Server

    Lutz, Mark

    2005-01-01

    Python is optimized for quality, productivity, portability, and integration. Hundreds of thousands of Python developers around the world rely on Python for general-purpose tasks, Internet scripting, systems programming, user interfaces, and product customization. Available on all major computing platforms, including commercial versions of Unix, Linux, Windows, and Mac OS X, Python is portable, powerful and remarkable easy to use. With its convenient, quick-reference format, Python Pocket Reference, 3rd Edition is the perfect on-the-job reference. More importantly, it's now been refreshed

  11. 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...

  12. QuTiP 2: A Python framework for the dynamics of open quantum systems

    Science.gov (United States)

    Johansson, J. R.; Nation, P. D.; Nori, Franco

    2013-04-01

    We present version 2 of QuTiP, the Quantum Toolbox in Python. Compared to the preceding version [J.R. Johansson, P.D. Nation, F. Nori, Comput. Phys. Commun. 183 (2012) 1760.], we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch-Redfield and Floquet-Markov master equations. Here we introduce these new features, demonstrate their use, and give a summary of the important backward-incompatible API changes introduced in this version. Catalog identifier: AEMB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 33625 No. of bytes in distributed program, including test data, etc.: 410064 Distribution format: tar.gz Programming language: Python. Computer: i386, x86-64. Operating system: Linux, Mac OSX. RAM: 2+ Gigabytes Classification: 7. External routines: NumPy, SciPy, Matplotlib, Cython Catalog identifier of previous version: AEMB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 1760 Does the new version supercede the previous version?: Yes Nature of problem: Dynamics of open quantum systems Solution method: Numerical solutions to Lindblad, Floquet-Markov, and Bloch-Redfield master equations, as well as the Monte Carlo wave function method. Reasons for new version: Compared to the preceding version we have introduced numerous new features, enhanced performance, and made changes in

  13. 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

  14. Strike kinematics and performance in juvenile ball pythons (Python regius).

    Science.gov (United States)

    Ryerson, William G; Tan, Weimin

    2017-08-01

    The rapid strike of snakes has interested researchers for decades. Although most work has focused on the strike performance of vipers, recent work has shown that other snakes outside of the Viperidae can strike with the same velocities and accelerations. However, to date all of these examples focus on performance in adult snakes. Here, we use high-speed video to measure the strike kinematics and performance of 10 juvenile (pythons, Python regius. We find that juvenile P. regius strike at levels comparable to larger snakes, but with shorter durations and over shorter distances. We conclude that the juvenile P. regius maintain performance likely through manipulation of the axial musculature and accompanying elastic tissues, and that this is a first step to understanding ontogenetic changes in behavior and a potential avenue for understanding how captivity may also impact behavior. © 2017 Wiley Periodicals, Inc.

  15. 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.

  16. Counting Word Frequencies with Python

    Directory of Open Access Journals (Sweden)

    William J. Turkel

    2012-07-01

    Full Text Available Your list is now clean enough that you can begin analyzing its contents in meaningful ways. Counting the frequency of specific words in the list can provide illustrative data. Python has an easy way to count frequencies, but it requires the use of a new type of variable: the dictionary. Before you begin working with a dictionary, consider the processes used to calculate frequencies in a list.

  17. 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.

  18. 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

  19. 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.

  20. Implementing Python for DrRacket

    OpenAIRE

    Ramos, Pedro Palma; Leitão, António Menezes

    2014-01-01

    The Python programming language is becoming increasingly popular in a variety of areas, most notably among novice programmers. On the other hand, Racket and other Scheme dialects are considered excellent vehicles for introducing Computer Science concepts. This paper presents an implementation of Python for Racket and the DrRacket IDE. This allows Python programmers to use Racket libraries and vice versa, as well as using DrRacket's pedagogic features. In particular, it allows architects and d...

  1. Creating and Viewing HTML Files with Python

    Directory of Open Access Journals (Sweden)

    William J. Turkel

    2012-07-01

    Full Text Available This lesson uses Python to create and view an HTML file. If you write programs that output HTML, you can use any browser to look at your results. This is especially convenient if your program is automatically creating hyperlinks or graphic entities like charts and diagrams. Here you will learn how to create HTML files with Python scripts, and how to use Python to automatically open an HTML file in Firefox.

  2. Programming ArcGIS with Python cookbook

    CERN Document Server

    Pimpler, Eric

    2015-01-01

    Programming ArcGIS with Python Cookbook, Second Edition, is written for GIS professionals who wish to revolutionize their ArcGIS workflow with Python. Whether you are new to ArcGIS or a seasoned professional, you almost certainly spend time each day performing various geoprocessing tasks. This book will teach you how to use the Python programming language to automate these geoprocessing tasks and make you a more efficient and effective GIS professional.

  3. Creating and Viewing HTML Files with Python

    OpenAIRE

    William J. Turkel; Adam Crymble

    2012-01-01

    This lesson uses Python to create and view an HTML file. If you write programs that output HTML, you can use any browser to look at your results. This is especially convenient if your program is automatically creating hyperlinks or graphic entities like charts and diagrams. Here you will learn how to create HTML files with Python scripts, and how to use Python to automatically open an HTML file in Firefox.

  4. Python for Unix and Linux system administration

    CERN Document Server

    Gift, Noah

    2007-01-01

    Python is an ideal language for solving problems, especially in Linux and Unix networks. With this pragmatic book, administrators can review various tasks that often occur in the management of these systems, and learn how Python can provide a more efficient and less painful way to handle them. Each chapter in Python for Unix and Linux System Administration presents a particular administrative issue, such as concurrency or data backup, and presents Python solutions through hands-on examples. Once you finish this book, you'll be able to develop your own set of command-line utilities with Pytho

  5. Enhanced OpenModelica Python Interface

    OpenAIRE

    Bajracharya, Sudeep

    2016-01-01

    OMPython is a Python library for OpenModelica, which provides a Python interface to OpenModelica. This thesis significantly improves OMPython by an enhanced, more powerful and easier to use API. It presents how a user can use the Python interface to simulate and access Modelica models using Python objects. The enhanced OMPython includes the list of functions that have been implemented such as getXXXNames(), getXXXValues(), setXXXValues(), getXXXOptions(), setXXXOptions(), and simulate(), etc....

  6. Computed tomography of ball pythons (Python regius) in curled recumbency.

    Science.gov (United States)

    Hedley, Joanna; Eatwell, Kevin; Schwarz, Tobias

    2014-01-01

    Anesthesia and tube restraint methods are often required for computed tomography (CT) of snakes due to their natural tendency to curl up. However, these restraint methods may cause animal stress. The aim of this study was to determine whether the CT appearance of the lungs differs for ball pythons in a curled position vs. tube restraint. Whole body CT was performed on ten clinically healthy ball pythons, first in curled and then in straight positions restrained in a tube. Curved multiplanar reformatted (MPR) lung images from curled position scans were compared with standard MPR lung images from straight position scans. Lung attenuation and thickness were measured at three locations for each scan. Time for positioning and scanning was 12 ± 5 min shorter for curled snakes compared to tube restraint. Lung parenchyma thickness and attenuation declined from cranial to caudal on both straight and curled position images. Mean lung parenchyma thickness was greater in curled images at locations 1 (P = 0.048) and 3 (P = 0.044). Mean lung parenchyma thickness decreased between location 1 and 2 by 86-87% (straight: curled) and between location 1 and 3 by 51-50% (straight: curled). Mean lung attenuation at location 1 was significantly greater on curled position images than tube restraint images (P = 0.043). Findings indicated that CT evaluation of the lungs is feasible for ball pythons positioned in curled recumbency if curved MPR is available. However, lung parenchyma thickness and attenuation in some locations may vary from those acquired using tube restraint. © 2014 American College of Veterinary Radiology.

  7. 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....

  8. 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

  9. 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

  10. SpacePy - a Python-based library of tools for the space sciences

    International Nuclear Information System (INIS)

    Morley, Steven K.; Welling, Daniel T.; Koller, Josef; Larsen, Brian A.; Henderson, Michael G.

    2010-01-01

    Space science deals with the bodies within the solar system and the interplanetary medium; the primary focus is on atmospheres and above - at Earth the short timescale variation in the the geomagnetic field, the Van Allen radiation belts and the deposition of energy into the upper atmosphere are key areas of investigation. SpacePy is a package for Python, targeted at the space sciences, that aims to make basic data analysis, modeling and visualization easier. It builds on the capabilities of the well-known NumPy and MatPlotLib packages. Publication quality output direct from analyses is emphasized. The SpacePy project seeks to promote accurate and open research standards by providing an open environment for code development. In the space physics community there has long been a significant reliance on proprietary languages that restrict free transfer of data and reproducibility of results. By providing a comprehensive, open-source library of widely used analysis and visualization tools in a free, modern and intuitive language, we hope that this reliance will be diminished. SpacePy includes implementations of widely used empirical models, statistical techniques used frequently in space science (e.g. superposed epoch analysis), and interfaces to advanced tools such as electron drift shell calculations for radiation belt studies. SpacePy also provides analysis and visualization tools for components of the Space Weather Modeling Framework - currently this only includes the BATS-R-US 3-D magnetohydrodynamic model and the RAM ring current model - including streamline tracing in vector fields. Further development is currently underway. External libraries, which include well-known magnetic field models, high-precision time conversions and coordinate transformations are wrapped for access from Python using SWIG and f2py. The rest of the tools have been implemented directly in Python. The provision of open-source tools to perform common tasks will provide openness in the

  11. Internationalization and Localization in Python

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    Internationalization and Localization are increasingly important in an interconnected world. Regardless of that, developers tend to treat them as secondary issues, very often choosing to address them properly when it's already too late. The fact that most programming language standard libraries choose to ignore the matter doesn't help either. In this talk we will present some useful Python libraries and tools that can help you internationalize and localize your code with minimal effort. We will also describe some common pitfalls and problems.

  12. [Lecture Games] Python programming game

    OpenAIRE

    Johnsen, Andreas Lyngstad; Ushakov, Georgy

    2011-01-01

    Pythia is a programming game that allows the player to change pieces of theirenvironment through use of the programming language Python. The idea is that thegame could be used as a part of teaching simple programming to first year universitystudents. The game should be fun enough for the students to keep playing, teachenough for it to earn a place as a teaching tool, and it should be usable by allstudents. It should also be possible for a teacher to create their own content for theg...

  13. Python 3 for Absolute Beginners

    CERN Document Server

    Hall, Tim

    2009-01-01

    There are many more people who want to study programming other than aspiring computer scientists with a passing grade in advanced calculus. This guide appeals to your intelligence and ability to solve practical problems, while gently teaching the most recent revision of the programming language Python. You can learn solid software design skills and accomplish practical programming tasks, like extending applications and automating everyday processes, even if you have no programming experience at all. Authors Tim Hall and J-P Stacey use everyday language to decode programming jargon and teach Py

  14. A field test of attractant traps for invasive Burmese pythons (Python molurus bivittatus) in southern Florida

    Science.gov (United States)

    Reed, Robert N.; Hart, Kristen M.; Rodda, Gordon H.; Mazzotti, Frank J.; Snow, Ray W.; Cherkiss, Michael; Rozar, Rondald; Goetz, Scott

    2011-01-01

    Context: Invasive Burmese pythons (Python molurus bivittatus) are established over thousands of square kilometres of southern Florida, USA, and consume a wide range of native vertebrates. Few tools are available to control the python population, and none of the available tools have been validated in the field to assess capture success as a proportion of pythons available to be captured. Aims: Our primary aim was to conduct a trap trial for capturing invasive pythons in an area east of Everglades National Park, where many pythons had been captured in previous years, to assess the efficacy of traps for population control. We also aimed to compare results of visual surveys with trap capture rates, to determine capture rates of non-target species, and to assess capture rates as a proportion of resident pythons in the study area. Methods: We conducted a medium-scale (6053 trap nights) experiment using two types of attractant traps baited with live rats in the Frog Pond area east of Everglades National Park. We also conducted standardised and opportunistic visual surveys in the trapping area. Following the trap trial, the area was disc harrowed to expose pythons and allow calculation of an index of the number of resident pythons. Key results: We captured three pythons and 69 individuals of various rodent, amphibian, and reptile species in traps. Eleven pythons were discovered during disc harrowing operations, as were large numbers of rodents.

  15. Extending and embedding the Python interpreter

    NARCIS (Netherlands)

    G. van Rossum (Guido)

    1995-01-01

    textabstractPython is an interpreted, object-oriented programming language. This document describes how to write modules in C or C++ to extend the Python interpreter with new modules. Those modules can define new functions but also new object types and their methods. The document also describes

  16. On Parallel Software Engineering Education Using Python

    Science.gov (United States)

    Marowka, Ami

    2018-01-01

    Python is gaining popularity in academia as the preferred language to teach novices serial programming. The syntax of Python is clean, easy, and simple to understand. At the same time, it is a high-level programming language that supports multi programming paradigms such as imperative, functional, and object-oriented. Therefore, by default, it is…

  17. Learning selenium testing tools with Python

    CERN Document Server

    Gundecha, Unmesh

    2014-01-01

    If you are a quality testing professional, or a software or web application developer looking to create automation test scripts for your web applications, with an interest in Python, then this is the perfect guide for you. Python developers who need to do Selenium testing need not learn Java, as they can directly use Selenium for testing with this book.

  18. Optics simulations: a Python workshop

    Science.gov (United States)

    Ghalila, H.; Ammar, A.; Varadharajan, S.; Majdi, Y.; Zghal, M.; Lahmar, S.; Lakshminarayanan, V.

    2017-08-01

    Numerical simulations allow teachers and students to indirectly perform sophisticated experiments that cannot be realizable otherwise due to cost and other constraints. During the past few decades there has been an explosion in the development of numerical tools concurrently with open source environments such as Python software. This availability of open source software offers an incredible opportunity for advancing teaching methodologies as well as in research. More specifically it is possible to correlate theoretical knowledge with experimental measurements using "virtual" experiments. We have been working on the development of numerical simulation tools using the Python program package and we have concentrated on geometric and physical optics simulations. The advantage of doing hands-on numerical experiments is that it allows the student learner to be an active participant in the pedagogical/learning process rather than playing a passive role as in the traditional lecture format. Even in laboratory classes because of constraints of space, lack of equipment and often-large numbers of students, many students play a passive role since they work in groups of 3 or more students. Furthermore these new tools help students get a handle on numerical methods as well simulations and impart a "feel" for the physics under investigation.

  19. TEACHING ALGORITHMIZATION AND PROGRAMMING USING PYTHON LANGUAGE

    Directory of Open Access Journals (Sweden)

    M. Lvov

    2014-07-01

    Full Text Available The article describes requirements to educational programming languages and considers the use of Python as the first programming language. The issues of introduction of this programming language into teaching and replacing Pascal by Python are examined. The advantages of such approach are regarded. The comparison of popular programming languages is represented from the point of view of their convenience of use for teaching algorithmization and programming. Python supports lots of programming paradigms: structural, object-oriented, functional, imperative and aspect-oriented, and learning can be started without any preparation. There is one more advantage of the language: all algorithms are written easily and structurally in Python. Therefore, due to all mentioned above, it is possible to affirm that Python pretends to become a decent replacement for educational programming language PASCAL both at schools and on the first courses of higher education establishments.

  20. 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

  1. 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

  2. Development of hemipenes in the ball python snake Python regius.

    Science.gov (United States)

    Leal, Francisca; Cohn, Martin J

    2015-01-01

    Within amniotes, external copulatory organs have undergone extensive morphological diversification. One of the most extreme examples is squamate (lizards and snakes) hemipenes, which are paired copulatory organs that extend from the lateral margins of the cloaca. Here, we describe the development of hemipenes in a basal snake, the ball python (Python regius). Snake hemipenes arise as a pair of lateral swellings on either side of the caudal part of the cloaca, and these paired outgrowths persist to form the left and right hemipenes. In non-squamate amniotes, external genitalia form from paired swellings that arise on the anterior side of the cloaca, which then fuse medially to form a single genital tubercle, the anlagen of the penis or clitoris. Whereas in non-squamate amniotes, Sonic hedgehog (Shh)-expressing cells of the cloacal endoderm form the urethral or sulcus epithelium and are required for phallus outgrowth, the hemipenes of squamates lack an endodermal contribution, and the sulcus does not express Shh. Thus, snake hemipenes differ from the genital tubercles of non-squamate amniotes both in their embryonic origins and in at least part of patterning mechanisms, which raises the possibility that hemipenes may not be direct homologs of the unpaired amniote penis. Nonetheless, we find that some developmental genes show similar expression patterns in snake hemipenes buds and non-squamate genital tubercles, suggesting that homologous developmental mechanisms are involved in aspects of external genital development across amniotes, even when these structures may have different developmental origins and may have arisen independently during evolution.

  3. Python : the holy grail of programming

    CERN Multimedia

    2006-01-01

    From 3 to 5 July, CERN hosted the fifth EuroPython Conference bringing together 300 users of Python, an open source programming language, which is more and more appreciated, especially at CERN. The local organisation of Euopython 2006 was managed by a small team from the PH/SFT group. Above, David Quarrie presenting the use of Python in Atlas analyses. If you visited Building 40 at the beginning of July, you may have come across a long orange and yellow snake. This had no relation with the Football World Championship! It was just the mascot of the fifth EuroPython Conference that saw almost 300 software developers, designers and business people gathering at CERN for the annual meeting of the European Python community. Python is an open source programming language actively used in industry and academia for a wide variety of purposes. As CERN decided to host this conference, it is perhaps not surprising to learn that Python is increasingly used in our Laboratory in both computing and physics application domai...

  4. Reflection-Based Python-C++ Bindings

    International Nuclear Information System (INIS)

    Generowicz, Jacek; Lavrijsen, Wim T.L.P.; Marino, Massimo; Mato, Pere

    2004-01-01

    Python is a flexible, powerful, high-level language with excellent interactive and introspective capabilities and a very clean syntax. As such, it can be a very effective tool for driving physics analysis. Python is designed to be extensible in low-level C-like languages, and its use as a scientific steering language has become quite widespread. To this end, existing and custom-written C or C++ libraries are bound to the Python environment as so-called extension modules. A number of tools for easing the process of creating such bindings exist, such as SWIG and Boost. Python. Yet, the process still requires a considerable amount of effort and expertise. The C++ language has few built-in introspective capabilities, but tools such as LCGDict and CINT add this by providing so-called dictionaries: libraries that contain information about the names, entry points, argument types, etc. of other libraries. The reflection information from these dictionaries can be used for the creation of bindings and so the process can be fully automated, as dictionaries are already provided for many end-user libraries for other purposes, such as object persistency. PyLCGDict is a Python extension module that uses LCG dictionaries, as PyROOT uses CINT reflection information, to allow /cwPython users to access C++ libraries with essentially no preparation on the users' behalf. In addition, and in a similar way, PyROOT gives ROOT users access to Python libraries

  5. 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.

  6. 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...

  7. 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...

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Pyomo optimization modeling in Python

    CERN Document Server

    Hart, William E; Watson, Jean-Paul; Woodruff, David L; Hackebeil, Gabriel A; Nicholson, Bethany L; Siirola, John D

    2017-01-01

    This book provides a complete and comprehensive guide to Pyomo (Python Optimization Modeling Objects) for beginning and advanced modelers, including students at the undergraduate and graduate levels, academic researchers, and practitioners. Using many examples to illustrate the different techniques useful for formulating models, this text beautifully elucidates the breadth of modeling capabilities that are supported by Pyomo and its handling of complex real-world applications. This second edition provides an expanded presentation of Pyomo’s modeling capabilities, providing a broader description of the software that will enable the user to develop and optimize models. Introductory chapters have been revised to extend tutorials; chapters that discuss advanced features now include the new functionalities added to Pyomo since the first edition including generalized disjunctive programming, mathematical programming with equilibrium constraints, and bilevel programming. Pyomo is an open source software package fo...

  13. Test-beam with Python

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    The talk will show the current implementation of the software tool developed by Silab (Bonn) and Oxford University to analyze test beam data with Mimosa telescope. Data collected from the telescope are merged with hits recorded on pixel detectors with a FE-I4 chips, the official read-out chip of the Atlas Pixel Detector. The software tool used to collect data, pyBAR, is developed with Python as well. The test-beam analysis tool parses the data-sets, recreates the tracks, aligns the telescope planes and allows to investigate the detectors spatial properties with high resolution. This has just allowed to study the properties of brand new devices that stand as possible candidate to replace the current pixel detector in Atlas.

  14. 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.

  15. Beginning programming with Python for dummies

    CERN Document Server

    Mueller, John Paul

    2014-01-01

    Learn Python-the fun and easy way-and get in the programming game today! Python is one of the fastest growing programming languages, and no wonder. It requires three to five times less time than developing in Java, is a great building block for learning both procedural and object-oriented programming concepts, and is an ideal language for data analysis. Beginning Programming with Python For Dummies is the perfect guide to this dynamic and powerful programming language-even if you''ve never coded before! Author John Paul Mueller draws on his vast programming knowledge and experience to guide yo

  16. Pyception: Teaching Python with a Serious Game

    OpenAIRE

    Laskemoen, Kristian

    2013-01-01

    This thesis set out to study how an online serious game could affect users? motivation on learning Python. One of the projects core goals is to find out whether learning Python is more motivating when having an effortless start through a web based game. A second goal is to find out if Python as a programming language are well suited for a serious game.After the development and implementation of the game, it was performed a user experiment in order to receive feedback. Data from this user expe...

  17. Python based high-level synthesis compiler

    Science.gov (United States)

    Cieszewski, Radosław; Pozniak, Krzysztof; Romaniuk, Ryszard

    2014-11-01

    This paper presents a python based High-Level synthesis (HLS) compiler. The compiler interprets an algorithmic description of a desired behavior written in Python and map it to VHDL. FPGA combines many benefits of both software and ASIC implementations. Like software, the mapped circuit is flexible, and can be reconfigured over the lifetime of the system. FPGAs therefore have the potential to achieve far greater performance than software as a result of bypassing the fetch-decode-execute operations of traditional processors, and possibly exploiting a greater level of parallelism. Creating parallel programs implemented in FPGAs is not trivial. This article describes design, implementation and first results of created Python based compiler.

  18. Building probabilistic graphical models with Python

    CERN Document Server

    Karkera, Kiran R

    2014-01-01

    This is a short, practical guide that allows data scientists to understand the concepts of Graphical models and enables them to try them out using small Python code snippets, without being too mathematically complicated. If you are a data scientist who knows about machine learning and want to enhance your knowledge of graphical models, such as Bayes network, in order to use them to solve real-world problems using Python libraries, this book is for you. This book is intended for those who have some Python and machine learning experience, or are exploring the machine learning field.

  19. The Profile Envision and Splice Tool (PRESTO): Developing an Atmospheric Wind Analysis Tool for Space Launch Vehicles Using Python

    Science.gov (United States)

    Orcutt, John M.; Barbre, Robert E., Jr.; Brenton, James C.; Decker, Ryan K.

    2017-01-01

    Tropospheric winds are an important driver of the design and operation of space launch vehicles. Multiple types of weather balloons and Doppler Radar Wind Profiler (DRWP) systems exist at NASA's Kennedy Space Center (KSC), co-located on the United States Air Force's (USAF) Eastern Range (ER) at the Cape Canaveral Air Force Station (CCAFS), that are capable of measuring atmospheric winds. Meteorological data gathered by these instruments are being used in the design of NASA's Space Launch System (SLS) and other space launch vehicles, and will be used during the day-of-launch (DOL) of SLS to aid in loads and trajectory analyses. For the purpose of SLS day-of-launch needs, the balloons have the altitude coverage needed, but take over an hour to reach the maximum altitude and can drift far from the vehicle's path. The DRWPs have the spatial and temporal resolutions needed, but do not provide complete altitude coverage. Therefore, the Natural Environments Branch (EV44) at Marshall Space Flight Center (MSFC) developed the Profile Envision and Splice Tool (PRESTO) to combine balloon profiles and profiles from multiple DRWPs, filter the spliced profile to a common wavelength, and allow the operator to generate output files as well as to visualize the inputs and the spliced profile for SLS DOL operations. PRESTO was developed in Python taking advantage of NumPy and SciPy for the splicing procedure, matplotlib for the visualization, and Tkinter for the execution of the graphical user interface (GUI). This paper describes in detail the Python coding implementation for the splicing, filtering, and visualization methodology used in PRESTO.

  20. Elementary mechanics using Matlab a modern course combining analytical and numerical techniques

    CERN Document Server

    Malthe-Sørenssen, Anders

    2015-01-01

    This book – specifically developed as a novel textbook on elementary classical mechanics – shows how analytical and numerical methods can be seamlessly integrated to solve physics problems. This approach allows students to solve more advanced and applied problems at an earlier stage and equips them to deal with real-world examples well beyond the typical special cases treated in standard textbooks. Another advantage of this approach is that students are brought closer to the way physics is actually discovered and applied, as they are introduced right from the start to a more exploratory way of understanding phenomena and of developing their physical concepts. While not a requirement, it is advantageous for the reader to have some prior knowledge of scientific programming with a scripting-type language. This edition of the book uses Matlab, and a chapter devoted to the basics of scientific programming with Matlab is included. A parallel edition using Python instead of Matlab is also available. Last but not...

  1. Python GUI Scripting Interface for Running Atomic Physics Applications

    OpenAIRE

    Tahat, Amani; Tahat, Mofleh

    2011-01-01

    We create a Python GUI scripting interface working under Windows in addition to (UNIX/Linux). The GUI has been built around the Python open-source programming language. We use the Python's GUI library that so called Python Mega Widgets (PMW) and based on Tkinter Python module (http://www.freenetpages.co.uk/hp/alan.gauld/tutgui.htm). The new GUI was motivated primarily by the desire of more updated operations, more flexibility incorporating future and current improvements in producing atomic d...

  2. Python for probability, statistics, and machine learning

    CERN Document Server

    Unpingco, José

    2016-01-01

    This book covers the key ideas that link probability, statistics, and machine learning illustrated using Python modules in these areas. The entire text, including all the figures and numerical results, is reproducible using the Python codes and their associated Jupyter/IPython notebooks, which are provided as supplementary downloads. The author develops key intuitions in machine learning by working meaningful examples using multiple analytical methods and Python codes, thereby connecting theoretical concepts to concrete implementations. Modern Python modules like Pandas, Sympy, and Scikit-learn are applied to simulate and visualize important machine learning concepts like the bias/variance trade-off, cross-validation, and regularization. Many abstract mathematical ideas, such as convergence in probability theory, are developed and illustrated with numerical examples. This book is suitable for anyone with an undergraduate-level exposure to probability, statistics, or machine learning and with rudimentary knowl...

  3. 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

  4. A Python Library for Historical Comparative Linguistics

    OpenAIRE

    Moran , Steven; List , Johann-Mattis

    2012-01-01

    Awarded best paper award; International audience; In this talk we will discuss a European Research Council funded collaborative effort to build a Python library for undertaking academic research in historical-comparative linguistics. Our aim of implementing quantitative methods, specifically in Python, is to transform historical-comparative linguistics from a primarily handcrafted scientific scholarly endeavor, performed by individual researchers, into a quantitative and collaborative field o...

  5. Python 3 Web Development Beginner's Guide

    CERN Document Server

    Anders, Michel

    2011-01-01

    Part of Packt's Beginner's Guide Series, this book follows a sample application, with lots of screenshots, to help you get to grips with the techniques as quickly as possible. Moderately experienced Python programmers who want to learn how to create fairly complex, database-driven, cross browser compatible web apps that are maintainable and look good will find this book of most use. All key technologies except for Python 3 are explained in detail.

  6. Introduction to Python for CMF Authority Users

    Energy Technology Data Exchange (ETDEWEB)

    Pritchett-Sheats, Lori A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-03-14

    This talk is a very broad over view of Python that highlights key features in the language used in the Common Model Framework (CMF). I assume that the audience has some programming experience in a shell scripting language (C shell, Bash, PERL) or other high level language (C/C++/ Fortran). The talk will cover Python data types, classes (objects) and basic programming constructs. The talk concludes with slides describing how I developed the basic classes for a TITANS homework assignment.

  7. Visualization of the CMS python configuration system

    International Nuclear Information System (INIS)

    Erdmann, M; Fischer, R; Klimkovich, T; Mueller, G; Steggemann, J; Hegner, B; Hinzmann, A

    2010-01-01

    The job configuration system of the CMS experiment is based on the Python programming language. Software modules and their order of execution are both represented by Python objects. In order to investigate and verify configuration parameters and dependencies naturally appearing in modular software, CMS employs a graphical tool. This tool visualizes the configuration objects, their dependencies, and the information flow. Furthermore it can be used for documentation purposes. The underlying software concepts as well as the visualization are presented.

  8. Visualization of the CMS python configuration system

    Energy Technology Data Exchange (ETDEWEB)

    Erdmann, M; Fischer, R; Klimkovich, T; Mueller, G; Steggemann, J [RWTH Aachen University, Physikalisches Institut 3A, 52062 Aachen (Germany); Hegner, B [CERN, CH-1211 Geneva 23 (Switzerland); Hinzmann, A, E-mail: andreas.hinzmann@cern.c

    2010-04-01

    The job configuration system of the CMS experiment is based on the Python programming language. Software modules and their order of execution are both represented by Python objects. In order to investigate and verify configuration parameters and dependencies naturally appearing in modular software, CMS employs a graphical tool. This tool visualizes the configuration objects, their dependencies, and the information flow. Furthermore it can be used for documentation purposes. The underlying software concepts as well as the visualization are presented.

  9. Use of EPICS and Python technology for the development of a computational toolkit for high heat flux testing of plasma facing components

    Energy Technology Data Exchange (ETDEWEB)

    Sugandhi, Ritesh, E-mail: ritesh@ipr.res.in; Swamy, Rajamannar, E-mail: rajamannar@ipr.res.in; Khirwadkar, Samir, E-mail: sameer@ipr.res.in

    2016-11-15

    Highlights: • An integrated approach to software development for computational processing and experimental control. • Use of open source, cross platform, robust and advanced tools for computational code development. • Prediction of optimized process parameters for critical heat flux model. • Virtual experimentation for high heat flux testing of plasma facing components. - Abstract: The high heat flux testing and characterization of the divertor and first wall components are a challenging engineering problem of a tokamak. These components are subject to steady state and transient heat load of high magnitude. Therefore, the accurate prediction and control of the cooling parameters is crucial to prevent burnout. The prediction of the cooling parameters is based on the numerical solution of the critical heat flux (CHF) model. In a test facility for high heat flux testing of plasma facing components (PFC), the integration of computations and experimental control is an essential requirement. Experimental physics and industrial control system (EPICS) provides powerful tools for steering controls, data simulation, hardware interfacing and wider usability. Python provides an open source alternative for numerical computations and scripting. We have integrated these two open source technologies to develop a graphical software for a typical high heat flux experiment. The implementation uses EPICS based tools namely IOC (I/O controller) server, control system studio (CSS) and Python based tools namely Numpy, Scipy, Matplotlib and NOSE. EPICS and Python are integrated using PyEpics library. This toolkit is currently under operation at high heat flux test facility at Institute for Plasma Research (IPR) and is also useful for the experimental labs working in the similar research areas. The paper reports the software architectural design, implementation tools and rationale for their selection, test and validation.

  10. On the tradeoffs of programming language choice for numerical modelling in geoscience. A case study comparing modern Fortran, C++/Blitz++ and Python/NumPy.

    Science.gov (United States)

    Jarecka, D.; Arabas, S.; Fijalkowski, M.; Gaynor, A.

    2012-04-01

    The language of choice for numerical modelling in geoscience has long been Fortran. A choice of a particular language and coding paradigm comes with different set of tradeoffs such as that between performance, ease of use (and ease of abuse), code clarity, maintainability and reusability, availability of open source compilers, debugging tools, adequate external libraries and parallelisation mechanisms. The availability of trained personnel and the scale and activeness of the developer community is of importance as well. We present a short comparison study aimed at identification and quantification of these tradeoffs for a particular example of an object oriented implementation of a parallel 2D-advection-equation solver in Python/NumPy, C++/Blitz++ and modern Fortran. The main angles of comparison will be complexity of implementation, performance of various compilers or interpreters and characterisation of the "added value" gained by a particular choice of the language. The choice of the numerical problem is dictated by the aim to make the comparison useful and meaningful to geoscientists. Python is chosen as a language that traditionally is associated with ease of use, elegant syntax but limited performance. C++ is chosen for its traditional association with high performance but even higher complexity and syntax obscurity. Fortran is included in the comparison for its widespread use in geoscience often attributed to its performance. We confront the validity of these traditional views. We point out how the usability of a particular language in geoscience depends on the characteristics of the language itself and the availability of pre-existing software libraries (e.g. NumPy, SciPy, PyNGL, PyNIO, MPI4Py for Python and Blitz++, Boost.Units, Boost.MPI for C++). Having in mind the limited complexity of the considered numerical problem, we present a tentative comparison of performance of the three implementations with different open source compilers including CPython and

  11. Use of EPICS and Python technology for the development of a computational toolkit for high heat flux testing of plasma facing components

    International Nuclear Information System (INIS)

    Sugandhi, Ritesh; Swamy, Rajamannar; Khirwadkar, Samir

    2016-01-01

    Highlights: • An integrated approach to software development for computational processing and experimental control. • Use of open source, cross platform, robust and advanced tools for computational code development. • Prediction of optimized process parameters for critical heat flux model. • Virtual experimentation for high heat flux testing of plasma facing components. - Abstract: The high heat flux testing and characterization of the divertor and first wall components are a challenging engineering problem of a tokamak. These components are subject to steady state and transient heat load of high magnitude. Therefore, the accurate prediction and control of the cooling parameters is crucial to prevent burnout. The prediction of the cooling parameters is based on the numerical solution of the critical heat flux (CHF) model. In a test facility for high heat flux testing of plasma facing components (PFC), the integration of computations and experimental control is an essential requirement. Experimental physics and industrial control system (EPICS) provides powerful tools for steering controls, data simulation, hardware interfacing and wider usability. Python provides an open source alternative for numerical computations and scripting. We have integrated these two open source technologies to develop a graphical software for a typical high heat flux experiment. The implementation uses EPICS based tools namely IOC (I/O controller) server, control system studio (CSS) and Python based tools namely Numpy, Scipy, Matplotlib and NOSE. EPICS and Python are integrated using PyEpics library. This toolkit is currently under operation at high heat flux test facility at Institute for Plasma Research (IPR) and is also useful for the experimental labs working in the similar research areas. The paper reports the software architectural design, implementation tools and rationale for their selection, test and validation.

  12. Elementary mechanics using Python a modern course combining analytical and numerical techniques

    CERN Document Server

    Malthe-Sørenssen, Anders

    2015-01-01

    This book – specifically developed as a novel textbook on elementary classical mechanics – shows how analytical and numerical methods can be seamlessly integrated to solve physics problems. This approach allows students to solve more advanced and applied problems at an earlier stage and equips them to deal with real-world examples well beyond the typical special cases treated in standard textbooks. Another advantage of this approach is that students are brought closer to the way physics is actually discovered and applied, as they are introduced right from the start to a more exploratory way of understanding phenomena and of developing their physical concepts. While not a requirement, it is advantageous for the reader to have some prior knowledge of scientific programming with a scripting-type language. This edition of the book uses Python, and a chapter devoted to the basics of scientific programming with Python is included. A parallel edition using Matlab instead of Python is also available. Last but not...

  13. 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

  14. Uncertainty quantification of surface-water/groundwater exchange estimates in large wetland systems using Python

    Science.gov (United States)

    Hughes, J. D.; Metz, P. A.

    2014-12-01

    Most watershed studies include observation-based water budget analyses to develop first-order estimates of significant flow terms. Surface-water/groundwater (SWGW) exchange is typically assumed to be equal to the residual of the sum of inflows and outflows in a watershed. These estimates of SWGW exchange, however, are highly uncertain as a result of the propagation of uncertainty inherent in the calculation or processing of the other terms of the water budget, such as stage-area-volume relations, and uncertainties associated with land-cover based evapotranspiration (ET) rate estimates. Furthermore, the uncertainty of estimated SWGW exchanges can be magnified in large wetland systems that transition from dry to wet during wet periods. Although it is well understood that observation-based estimates of SWGW exchange are uncertain it is uncommon for the uncertainty of these estimates to be directly quantified. High-level programming languages like Python can greatly reduce the effort required to (1) quantify the uncertainty of estimated SWGW exchange in large wetland systems and (2) evaluate how different approaches for partitioning land-cover data in a watershed may affect the water-budget uncertainty. We have used Python with the Numpy, Scipy.stats, and pyDOE packages to implement an unconstrained Monte Carlo approach with Latin Hypercube sampling to quantify the uncertainty of monthly estimates of SWGW exchange in the Floral City watershed of the Tsala Apopka wetland system in west-central Florida, USA. Possible sources of uncertainty in the water budget analysis include rainfall, ET, canal discharge, and land/bathymetric surface elevations. Each of these input variables was assigned a probability distribution based on observation error or spanning the range of probable values. The Monte Carlo integration process exposes the uncertainties in land-cover based ET rate estimates as the dominant contributor to the uncertainty in SWGW exchange estimates. We will discuss

  15. A Python Geospatial Language Toolkit

    Science.gov (United States)

    Fillmore, D.; Pletzer, A.; Galloy, M.

    2012-12-01

    The volume and scope of geospatial data archives, such as collections of satellite remote sensing or climate model products, has been rapidly increasing and will continue to do so in the near future. The recently launched (October 2011) Suomi National Polar-orbiting Partnership satellite (NPP) for instance, is the first of a new generation of Earth observation platforms that will monitor the atmosphere, oceans, and ecosystems, and its suite of instruments will generate several terabytes each day in the form of multi-spectral images and derived datasets. Full exploitation of such data for scientific analysis and decision support applications has become a major computational challenge. Geophysical data exploration and knowledge discovery could benefit, in particular, from intelligent mechanisms for extracting and manipulating subsets of data relevant to the problem of interest. Potential developments include enhanced support for natural language queries and directives to geospatial datasets. The translation of natural language (that is, human spoken or written phrases) into complex but unambiguous objects and actions can be based on a context, or knowledge domain, that represents the underlying geospatial concepts. This poster describes a prototype Python module that maps English phrases onto basic geospatial objects and operations. This module, along with the associated computational geometry methods, enables the resolution of natural language directives that include geographic regions of arbitrary shape and complexity.

  16. Apprendre à programmer avec Python

    CERN Document Server

    Swinnen, Gérard

    2009-01-01

    Quel meilleur choix pour apprendre la programmation qu'un langage moderne et élégant tel que Python, aussi bon pour le développement d'applications web que pour la réalisation de scripts système ou l'analyse de fichiers textuels ? Un support de cours réputé et adopté par de nombreux enseignants, avec 40 pages d'exercices corrigés Reconnu et utilisé par les enseignants de nombreuses écoles et IUT, complété d'exercices accompagnés de leurs corrigés, cet ouvrage original et érudit est une référence sur tous les fondamentaux de la programmation : choix d'une structure de données, paramétrage, modularité, orientation objet et héritage, conception d'interface, multithreading et gestion d'événements, protocoles de communication et gestion réseau, formulaires web et (GI, bases de données) jusqu'à la désormais indispensable norme Unicode (le format UTF-8).

  17. Unilateral microphthalmia or anophthalmia in eight pythons (Pythonidae)

    DEFF Research Database (Denmark)

    Da Silva, Mari-Ann Otkjær; Berthelsen, MF; Wang, T

    2015-01-01

    OBJECTIVE: To provide morphological descriptions of microphthalmia or anophthalmia in eight pythons using microcomputerized tomography (μCT), magnetic resonance imaging (MRI), and histopathology. ANIMALS STUDIED: Seven Burmese pythons (Python bivittatus) and one ball python (P. regius) with clini......OBJECTIVE: To provide morphological descriptions of microphthalmia or anophthalmia in eight pythons using microcomputerized tomography (μCT), magnetic resonance imaging (MRI), and histopathology. ANIMALS STUDIED: Seven Burmese pythons (Python bivittatus) and one ball python (P. regius...... macroscopic anomalies. CONCLUSIONS: Eight pythons with unilateral left-sided microphthalmia or anophthalmia had one normal eye and a left orbit with malformed or incompletely developed ocular structures along with remnants of fetal structures. These cases lend further information to a condition that is often...

  18. Ultrasonographic anatomy of the coelomic organs of boid snakes (Boa constrictor imperator, Python regius, Python molurus molurus, and Python curtus).

    Science.gov (United States)

    Banzato, Tommaso; Russo, Elisa; Finotti, Luca; Milan, Maria C; Gianesella, Matteo; Zotti, Alessandro

    2012-05-01

    To determine the ultrasonographic features of the coelomic organs of healthy snakes belonging to the Boidae and Pythonidae families. 16 ball pythons (Python regius; 7 males, 8 females, and 1 sexually immature), 10 Indian rock pythons (Python molurus molurus; 5 males, 4 females, and 1 sexually immature), 12 Python curtus (5 males and 7 females), and 8 boa constrictors (Boa constrictor imperator; 4 males and 4 females). All snakes underwent complete ultrasonographic evaluation of the coelomic cavity; chemical restraint was not necessary. A dorsolateral approach to probe placement was chosen to increase image quality and to avoid injury to the snakes and operators. Qualitative and quantitative observations were recorded. The liver, stomach, gallbladder, pancreas, small and large intestines, kidneys, cloaca, and scent glands were identified in all snakes. The hemipenes were identified in 10 of the 21 (48%) male snakes. The spleen was identified in 5 of the 46 (11%) snakes, and ureters were identified in 6 (13%). In 2 sexually immature snakes, the gonads were not visible. One (2%) snake was gravid, and 7 (15%) had small amounts of free fluid in the coelomic cavity. A significant positive correlation was identified between several measurements (diameter and thickness of scent glands, gastric and pyloric walls, and colonic wall) and body length (snout to vent) and body weight. The study findings can be used as an atlas of the ultrasonographic anatomy of the coelomic cavity in healthy boid snakes. Ultrasonography was reasonably fast to perform and was well tolerated in conscious snakes.

  19. Postprandial increase of oleoylethanolamide mobilization in small intestine of the Burmese python (Python molurus)

    DEFF Research Database (Denmark)

    Astarita, Giuseppe; Rourke, Bryan C; Andersen, Johnnie Bremholm

    2006-01-01

    to the induction of between-meal satiety. Here we examined whether feeding-induced OEA mobilization also occurs in Burmese pythons (Python molurus), a species of ambush-hunting snakes that consumes huge meals after months of fasting and undergoes massive feeding-dependent changes in gastrointestinal hormonal...... release and gut morphology. Using liquid-chromatography/mass-spectrometry (LC/MS), we measured OEA levels in the gastrointestinal tract of fasted (28 days) and fed (48h after feeding) pythons. We observed a nearly 300-fold increase in OEA levels in the small intestine of fed compared to fasted animals......-unsaturated, but not polyunsaturated fatty-acid ethanolamides (FAE) in the small intestine of fed pythons. The identification of OEA and other FAEs in the gastrointestinal tract of Python molurus suggests that this class of lipid messengers may be widespread among vertebrate groups and may represent an evolutionarily ancient means...

  20. 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"--

  1. 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.

  2. A Pythonic Approach for Computational Geosciences and Geo-Data Processing

    Science.gov (United States)

    Morra, G.; Yuen, D. A.; Lee, S. M.

    2016-12-01

    Computational methods and data analysis play a constantly increasing role in Earth Sciences however students and professionals need to climb a steep learning curve before reaching a sufficient level that allows them to run effective models. Furthermore the recent arrival and new powerful machine learning tools such as Torch and Tensor Flow has opened new possibilities but also created a new realm of complications related to the completely different technology employed. We present here a series of examples entirely written in Python, a language that combines the simplicity of Matlab with the power and speed of compiled languages such as C, and apply them to a wide range of geological processes such as porous media flow, multiphase fluid-dynamics, creeping flow and many-faults interaction. We also explore ways in which machine learning can be employed in combination with numerical modelling. From immediately interpreting a large number of modeling results to optimizing a set of modeling parameters to obtain a desired optimal simulation. We show that by using Python undergraduate and graduate can learn advanced numerical technologies with a minimum dedicated effort, which in turn encourages them to develop more numerical tools and quickly progress in their computational abilities. We also show how Python allows combining modeling with machine learning as pieces of LEGO, therefore simplifying the transition towards a new kind of scientific geo-modelling. The conclusion is that Python is an ideal tool to create an infrastructure for geosciences that allows users to quickly develop tools, reuse techniques and encourage collaborative efforts to interpret and integrate geo-data in profound new ways.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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

  8. An introduction to Python and computer programming

    CERN Document Server

    Zhang, Yue

    2015-01-01

    This book introduces Python programming language and fundamental concepts in algorithms and computing. Its target audience includes students and engineers with little or no background in programming, who need to master a practical programming language and learn the basic thinking in computer science/programming. The main contents come from lecture notes for engineering students from all disciplines, and has received high ratings. Its materials and ordering have been adjusted repeatedly according to classroom reception. Compared to alternative textbooks in the market, this book introduces the underlying Python implementation of number, string, list, tuple, dict, function, class, instance and module objects in a consistent and easy-to-understand way, making assignment, function definition, function call, mutability and binding environments understandable inside-out. By giving the abstraction of implementation mechanisms, this book builds a solid understanding of the Python programming language.

  9. Hemodynamic consequences of cardiac malformations in two juvenile ball pythons (Python regius).

    Science.gov (United States)

    Jensen, Bjarke; Wang, Tobias

    2009-12-01

    Two cases of bifid ventricles and cardiac malformations in juvenile ball python (Python regius) were investigated by blood pressure measurements and macro- and microscopic sectioning. A study of a normal ball python was included for reference. In both cases, all cardiac chambers were enlarged and abnormally shaped. Internal assessment of the ventricles revealed a pronounced defect of the muscular ridge, which normally is responsible for separating the systemic and pulmonary circuits. Consistent with the small muscular ridge, systolic pressures were identical in the pulmonary and systemic arteries, but, the snakes, nevertheless, lived to reach body weights severalfold of their hatchling weight.

  10. Building machine learning systems with Python

    CERN Document Server

    Richert, Willi

    2013-01-01

    This is a tutorial-driven and practical, but well-grounded book showcasing good Machine Learning practices. There will be an emphasis on using existing technologies instead of showing how to write your own implementations of algorithms. This book is a scenario-based, example-driven tutorial. By the end of the book you will have learnt critical aspects of Machine Learning Python projects and experienced the power of ML-based systems by actually working on them.This book primarily targets Python developers who want to learn about and build Machine Learning into their projects, or who want to pro

  11. Raspberry Pi cookbook for Python programmers

    CERN Document Server

    Cox, Tim

    2014-01-01

    ""Raspberry Pi Cookbook for Python Programmers"" is written in a Cookbook format, presenting examples in the style of recipes.This allows you to go directly to your topic of interest, or follow topics throughout a chapter to gain a thorough in-depth knowledge.The aim of this book is to bring you a broad range of Python 3 examples and practical ideas which you can develop to suit your own requirements. By modifying and combining the examples to create your own projects you learn far more effectively with a much greater understanding. Each chapter is designed to become a foundation for further e

  12. Next-Generation Web Frameworks in Python

    CERN Document Server

    Daly, Liza

    2007-01-01

    With its flexibility, readability, and maturecode libraries, Python is a naturalchoice for developing agile and maintainableweb applications. Severalframeworks have emerged in the last fewyears that share ideas with Ruby on Railsand leverage the expressive nature of Python.This Short Cut will tell you whatyou need to know about the hottest fullstackframeworks: Django, Pylons, andTurboGears. Their philosophies, relativestrengths, and development status aredescribed in detail. What you won't find out is, "Which oneshould I use?" The short answer is thatall of them can be used to build web appl

  13. Python for signal processing featuring IPython notebooks

    CERN Document Server

    Unpingco, José

    2013-01-01

    This book covers the fundamental concepts in signal processing illustrated with Python code and made available via IPython Notebooks, which are live, interactive, browser-based documents that allow one to change parameters, redraw plots, and tinker with the ideas presented in the text. Everything in the text is computable in this format and thereby invites readers to ""experiment and learn"" as they read. The book focuses on the core, fundamental principles of signal processing. The code corresponding to this book uses the core functionality of the scientific Python toolchain that should remai

  14. A 3d game in python

    OpenAIRE

    Xu, Minghui

    2014-01-01

    3D game has widely been accepted and loved by many game players. More and more different kinds of 3D games were developed to feed people’s needs. The most common programming language for development of 3D game is C++ nowadays. Python is a high-level scripting language. It is simple and clear. The concise syntax could speed up the development cycle. This project was to develop a 3D game using only Python. The game is about how a cat lives in the street. In order to live, the player need...

  15. Python passive network mapping P2NMAP

    CERN Document Server

    Hosmer, Chet

    2015-01-01

    Python Passive Network Mapping: P2NMAP is the first book to reveal a revolutionary and open source method for exposing nefarious network activity. The ""Heartbleed"" vulnerability has revealed significant weaknesses within enterprise environments related to the lack of a definitive mapping of network assets. In Python Passive Network Mapping, Chet Hosmer shows you how to effectively and definitively passively map networks. Active or probing methods to network mapping have traditionally been used, but they have many drawbacks - they can disrupt operations, crash systems, and - most important

  16. TensorLy: Tensor Learning in Python

    OpenAIRE

    Kossaifi, Jean; Panagakis, Yannis; Pantic, Maja

    2016-01-01

    Tensors are higher-order extensions of matrices. While matrix methods form the cornerstone of machine learning and data analysis, tensor methods have been gaining increasing traction. However, software support for tensor operations is not on the same footing. In order to bridge this gap, we have developed \\emph{TensorLy}, a high-level API for tensor methods and deep tensorized neural networks in Python. TensorLy aims to follow the same standards adopted by the main projects of the Python scie...

  17. SymPy: symbolic computing in Python

    Directory of Open Access Journals (Sweden)

    Aaron Meurer

    2017-01-01

    Full Text Available SymPy is an open source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and programmatic applications. These characteristics have led SymPy to become a popular symbolic library for the scientific Python ecosystem. This paper presents the architecture of SymPy, a description of its features, and a discussion of select submodules. The supplementary material provide additional examples and further outline details of the architecture and features of SymPy.

  18. Feasibility of Python in teaching programming

    Directory of Open Access Journals (Sweden)

    Rafael Martínez Estévez

    2014-03-01

    Full Text Available Given the diversity of the objectives of the programming courses in the Cuban educational system and the training of teachers, it is not easy to decide the language to be used in each case. The intention of this article is to bring to debate to our context a trend that has been growing in the last decade: Python as a first programming language. The aim of this study is to compile some inter national experiences in the use of Python in introductory programming courses, also analyzing their advantages and disadvantages.

  19. Data Visualization within the Python ecosystem

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    Data analysis is integral to what we do at CERN. Data visualization is at the foundation of this workflow and is also an important part of the python stack. Python's plotting ecosystem offers numerous open source solutions. These solutions can offer ease of use, detailed configuration, interactivity and web readiness. This talk will cover three of the most robust and supported packages, matplotlib, bokeh, and plotly. It aims to provide an overview of these packages. In addition, give suggestions to where these tools might fit in an analysis workflow.

  20. Programming ArcGIS 10.1 with Python cookbook

    CERN Document Server

    Pimpler, Eric

    2013-01-01

    This book is written in a helpful, practical style with numerous hands-on recipes and chapters to help you save time and effort by using Python to power ArcGIS to create shortcuts, scripts, tools, and customizations.""Programming ArcGIS 10.1 with Python Cookbook"" is written for GIS professionals who wish to revolutionize their ArcGIS workflow with Python. Basic Python or programming knowledge is essential(?).

  1. 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....

  2. Python bindings for the open source electromagnetic simulator Meep

    OpenAIRE

    Lambert, Emmanuel; Fiers, Martin; Nizamov, Shavkat; Tassaert, Martijn; Johnson, Steven G; Bienstman, Peter; Bogaerts, Wim

    2011-01-01

    Meep is a broadly used open source package for finite-difference time-domain electromagnetic simulations. Python bindings for Meep make it easier to use for researchers and open promising opportunities for integration with other packages in the Python ecosystem. As this project shows, implementing Python-Meep offers benefits for specific disciplines and for the wider research community.

  3. The zoonotic implications of pentastomiasis in the royal python (python regius).

    Science.gov (United States)

    Ayinmode, Ab; Adedokun, Ao; Aina, A; Taiwo, V

    2010-09-01

    Pentastomes are worm-like endoparasites of the phylum Pentastomida found principally in the respiratory tract of reptiles, birds, and mammals. They cause a zoonotic disease known as pentastomiasis in humans and other mammals. The autopsy of a Nigerian royal python (Python regius) revealed two yellowish-white parasites in the lungs, tissue necrosis and inflammatory lesions. The parasite was confirmed to be Armillifer spp (Pentastomid); this is the first recorded case of pentastomiasis in the royal python (Python regius) in Nigeria. This report may be an alert of the possibility of on-going zoonotic transmission of pentastomiasis from snake to man, especially in the sub-urban/rural areas of Nigeria and other West African countries where people consume snake meat.

  4. 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)

  5. 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.

  6. 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.

  7. Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis

    OpenAIRE

    Ong, Shyue Ping; Richards, William Davidson; Jain, Anubhav; Hautier, Geoffroy; Kocher, Michael; Cholia, Shreyas; Gunter, Dan; Chevrier, Vincent L.; Persson, Kristin A.; Ceder, Gerbrand

    2012-01-01

    We present the Python Materials Genomics (pymatgen) library, a robust, open-source Python library for materials analysis. A key enabler in high-throughput computational materials science efforts is a robust set of software tools to perform initial setup for the calculations (e.g., generation of structures and necessary input files) and post-calculation analysis to derive useful material properties from raw calculated data. The pymatgen library aims to meet these needs by (1) defining core Pyt...

  8. The Zoonotic Implications of Pentastomiasis in the Royal Python (Python Regius)

    OpenAIRE

    Ayinmode, AB; Adedokun, AO; Aina, A; Taiwo, V

    2010-01-01

    Pentastomes are worm-like endoparasites of the phylum Pentastomida found principally in the respiratory tract of reptiles, birds, and mammals. They cause a zoonotic disease known as pentastomiasis in humans and other mammals. The autopsy of a Nigerian royal python (Python regius) revealed two yellowish-white parasites in the lungs, tissue necrosis and inflammatory lesions. The parasite was confirmed to be Armillifer spp (Pentastomid); this is the first recorded case of pentastomiasis in the r...

  9. Julia and Python in Astronomy: Better Together

    OpenAIRE

    Barbary, Kyle

    2016-01-01

    Astronomers love Python because it is open source, easy to learn, and has a tremendous ecosystem for scientific computing. The Julia programming language has many of those same characteristics. In this talk, I discuss Julia, its use in astronomy and the growing ecosystem of astronomy packages, particularly those managed by the JuliaAstro organization (http://JuliaAstro.github.io).

  10. Python scripting in the nengo simulator.

    Science.gov (United States)

    Stewart, Terrence C; Tripp, Bryan; Eliasmith, Chris

    2009-01-01

    Nengo (http://nengo.ca) is an open-source neural simulator that has been greatly enhanced by the recent addition of a Python script interface. Nengo provides a wide range of features that are useful for physiological simulations, including unique features that facilitate development of population-coding models using the neural engineering framework (NEF). This framework uses information theory, signal processing, and control theory to formalize the development of large-scale neural circuit models. Notably, it can also be used to determine the synaptic weights that underlie observed network dynamics and transformations of represented variables. Nengo provides rich NEF support, and includes customizable models of spike generation, muscle dynamics, synaptic plasticity, and synaptic integration, as well as an intuitive graphical user interface. All aspects of Nengo models are accessible via the Python interface, allowing for programmatic creation of models, inspection and modification of neural parameters, and automation of model evaluation. Since Nengo combines Python and Java, it can also be integrated with any existing Java or 100% Python code libraries. Current work includes connecting neural models in Nengo with existing symbolic cognitive models, creating hybrid systems that combine detailed neural models of specific brain regions with higher-level models of remaining brain areas. Such hybrid models can provide (1) more realistic boundary conditions for the neural components, and (2) more realistic sub-components for the larger cognitive models.

  11. MGtoolkit: A python package for implementing metagraphs

    Science.gov (United States)

    Ranathunga, D.; Nguyen, H.; Roughan, M.

    In this paper we present MGtoolkit: an open-source Python package for implementing metagraphs - a first of its kind. Metagraphs are commonly used to specify and analyse business and computer-network policies alike. MGtoolkit can help verify such policies and promotes learning and experimentation with metagraphs. The package currently provides purely textual output for visualising metagraphs and their analysis results.

  12. PyXNAT: XNAT in Python

    Directory of Open Access Journals (Sweden)

    Yannick eSchwartz

    2012-05-01

    Full Text Available As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low level interfaces to databases. We introduce here {PyXNAT}, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT through native Python calls across multiple operating systems. The choice of Python enables {PyXNAT} to expose the XNAT Web Services and unify their features with a higher level and more expressive language. {PyXNAT} provides XNAT users direct access to all the scientific packages in Python. Finally {PyXNAT} aims to be efficient and easy to use, both as a backend library to build XNAT clients and as an alternative frontend from the command line.

  13. PyXNAT: XNAT in Python.

    Science.gov (United States)

    Schwartz, Yannick; Barbot, Alexis; Thyreau, Benjamin; Frouin, Vincent; Varoquaux, Gaël; Siram, Aditya; Marcus, Daniel S; Poline, Jean-Baptiste

    2012-01-01

    As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programmatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low-level interfaces to databases. We introduce here PyXNAT, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems. The choice of Python enables PyXNAT to expose the XNAT Web Services and unify their features with a higher level and more expressive language. PyXNAT provides XNAT users direct access to all the scientific packages in Python. Finally PyXNAT aims to be efficient and easy to use, both as a back-end library to build XNAT clients and as an alternative front-end from the command line.

  14. Python scripting in the Nengo simulator

    Directory of Open Access Journals (Sweden)

    Terrence C Stewart

    2009-03-01

    Full Text Available Nengo is an open-source neural simulator that has been greatly enhanced by the recent addition of a Python script interface. Nengo provides a wide range of features that are useful for physiological simulations, including unique features that facilitate development of population-coding models using the Neural Engineering Framework (NEF. This framework uses information theory, signal processing, and control theory to formalize the development of large-scale neural circuit models. Notably, it can also be used to determine the synaptic weights that underlie observed network dynamics and transformations of represented variables. Nengo provides rich NEF support, and includes customizable models of spike generation, muscle dynamics, synaptic plasticity, and synaptic integration, as well as an intuitive graphical user interface. All aspects of Nengo models are accessible via the Python interface, allowing for programmatic creation of models, inspection and modification of neural parameters, and automation of model evaluation. Since Nengo combines Python and Java, it can also be integrated with any existing Java or 100% Python code libraries. Current work includes connecting neural models in Nengo with existing symbolic cognitive models, creating hybrid systems that combine detailed neural models of specific brain regions with higher-level models of remaining brain areas. Such hybrid models can provide 1 more realistic boundary conditions for the neural components, and 2 more realistic sub-components for the larger cognitive models.

  15. TensorLy: Tensor Learning in Python

    NARCIS (Netherlands)

    Kossaifi, Jean; Panagakis, Yannis; Pantic, Maja

    2016-01-01

    Tensor methods are gaining increasing traction in machine learning. However, there are scant to no resources available to perform tensor learning and decomposition in Python. To answer this need we developed TensorLy. TensorLy is a state of the art general purpose library for tensor learning.

  16. My Journey from Python to R

    OpenAIRE

    Lorgat, Mohamed Wasim

    2018-01-01

    A lightning talk of my personal experiences in programming, from childhood with languages including Game Maker and DarkBASIC, to now with Python and R. I highlight the underlying principle which, I argue, separates the R community from others.See the reference for further reading material along this line.

  17. 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.

  18. 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.

  19. 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

  20. 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...

  1. 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.

  2. 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)

  3. 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.

  4. Challenges to a molecular approach to prey identification in the Burmese python, Python molurus bivittatus

    Science.gov (United States)

    Falk, Bryan; Reed, Robert N.

    2015-01-01

    Molecular approaches to prey identification are increasingly useful in elucidating predator–prey relationships, and we aimed to investigate the feasibility of these methods to document the species identities of prey consumed by invasive Burmese pythons in Florida. We were particularly interested in the diet of young snakes, because visual identification of prey from this size class has proven difficult. We successfully extracted DNA from the gastrointestinal contents of 43 young pythons, as well as from several control samples, and attempted amplification of DNA mini-barcodes, a 130-bp region of COX1. Using a PNA clamp to exclude python DNA, we found that prey DNA was not present in sufficient quality for amplification of this locus in 86% of our samples. All samples from the GI tracts of young pythons contained only hair, and the six samples we were able to identify to species were hispid cotton rats. This suggests that young Burmese pythons prey predominantly on small mammals and that prey diversity among snakes of this size class is low. We discuss prolonged gastrointestinal transit times and extreme gastric breakdown as possible causes of DNA degradation that limit the success of a molecular approach to prey identification in Burmese pythons

  5. Size, but not experience, affects the ontogeny of constriction performance in ball pythons (Python regius).

    Science.gov (United States)

    Penning, David A; Dartez, Schuyler F

    2016-03-01

    Constriction is a prey-immobilization technique used by many snakes and is hypothesized to have been important to the evolution and diversification of snakes. However, very few studies have examined the factors that affect constriction performance. We investigated constriction performance in ball pythons (Python regius) by evaluating how peak constriction pressure is affected by snake size, sex, and experience. In one experiment, we tested the ontogenetic scaling of constriction performance and found that snake diameter was the only significant factor determining peak constriction pressure. The number of loops applied in a coil and its interaction with snake diameter did not significantly affect constriction performance. Constriction performance in ball pythons scaled differently than in other snakes that have been studied, and medium to large ball pythons are capable of exerting significantly higher pressures than those shown to cause circulatory arrest in prey. In a second experiment, we tested the effects of experience on constriction performance in hatchling ball pythons over 10 feeding events. By allowing snakes in one test group to gain constriction experience, and manually feeding snakes under sedation in another test group, we showed that experience did not affect constriction performance. During their final (10th) feedings, all pythons constricted similarly and with sufficiently high pressures to kill prey rapidly. At the end of the 10 feeding trials, snakes that were allowed to constrict were significantly smaller than their non-constricting counterparts. © 2016 Wiley Periodicals, Inc.

  6. A New Python Library for Spectroscopic Analysis with MIDAS Style

    Science.gov (United States)

    Song, Y.; Luo, A.; Zhao, Y.

    2013-10-01

    The ESO MIDAS is a system for astronomers to analyze data which many astronomers are using. Python is a high level script language and there are many applications for astronomical data process. We are releasing a new Python library which realizes some MIDAS commands in Python. People can use it to write a MIDAS style Python code. We call it PydasLib. It is a Python library based on ESO MIDAS functions, which is easily used by astronomers who are familiar with the usage of MIDAS.

  7. VarPy: A python library for volcanology and rock physics data analysis

    Science.gov (United States)

    Filgueira, Rosa; Atkinson, Malcom; Bell, Andrew; Snelling, Brawen; Main, Ian

    2014-05-01

    and rock physics data with the intent of stimulating sharing, collaboration and comparison of methods among the practitioners in the two fields. As such, it offers facilities for running analyses and models either under a researcher's control or periodically as part of an experiment and to compare the skills of predictive methods. The gateway therefore runs code on behalf of volcanology and rock physics researchers. Varpy library is intended to make it much easier for those researchers to set up the code they need to run. The library also makes it easier to arrange that code is in a form suitable for running in the EFFORT computational services. Care has been taken to ensure that the library can also be used outside of EFFORT systems, e.g., on a researcher's own laptop, providing two variants of the library: the gateway version and developer's version, with many of the functions completely identical. The library must fulfill two purposes simultaneously: • by providing a full repertoire of commonly required actions it must make it easy for volcanologist and rock physicists to write the python scripts they need to accomplish their work, and • by wrapping operations it must enable the EFFORT gateway to maintain the integrity of its data. Notice that proposal of VarPy library does not attempt to replace the functions provided by other libraries, such as NumpY and ScipY. VarPy is complementary to them.

  8. 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...

  9. Pyff---A Pythonic Framework for Feedback Applications and Stimulus Presentation in Neuroscience

    Directory of Open Access Journals (Sweden)

    Bastian Venthur

    2010-12-01

    Full Text Available This paper introduces Pyff, the Pythonic Feedback Framework for feedbackapplications and stimulus presentation. Pyff provides a platform independentframework that allows users to develop and run neuroscientific experiments inthe programming language Python. Existing solutions have mostly beenimplemented in C++, which makes for a rather tedious programming task fornon-computer-scientists, or in Matlab, which is not well suited for moreadvanced visual or auditory applications. Pyff was designed to makeexperimental paradigms (i.e. feedback and stimulus applications easilyprogrammable. It includes base classes for various types of common feedbacksand stimuli as well as useful libraries for external hardware such aseyetrackers. Pyff is also equipped with a steadily growing set of ready-to-usefeedbacks and stimuli. It can be used as a standalone application, for instanceproviding stimulus presentation in psychophysics experiments, or within aclosed loop such as in biofeedback or brain-computer interfacing experiments.Pyff communicates with other systems via a standardized communication protocoland is therefore suitable to be used with any system that may be adapted tosend its data in the specified format. Having such a general, open sourceframework will help foster a fruitful exchange of experimental paradigmsbetween research groups. In particular, it will decrease the need ofreprogramming standard paradigms, ease the reproducibility of publishedresults, and naturally entail some standardization of stimulus presentation.

  10. Pyff - a pythonic framework for feedback applications and stimulus presentation in neuroscience.

    Science.gov (United States)

    Venthur, Bastian; Scholler, Simon; Williamson, John; Dähne, Sven; Treder, Matthias S; Kramarek, Maria T; Müller, Klaus-Robert; Blankertz, Benjamin

    2010-01-01

    This paper introduces Pyff, the Pythonic feedback framework for feedback applications and stimulus presentation. Pyff provides a platform-independent framework that allows users to develop and run neuroscientific experiments in the programming language Python. Existing solutions have mostly been implemented in C++, which makes for a rather tedious programming task for non-computer-scientists, or in Matlab, which is not well suited for more advanced visual or auditory applications. Pyff was designed to make experimental paradigms (i.e., feedback and stimulus applications) easily programmable. It includes base classes for various types of common feedbacks and stimuli as well as useful libraries for external hardware such as eyetrackers. Pyff is also equipped with a steadily growing set of ready-to-use feedbacks and stimuli. It can be used as a standalone application, for instance providing stimulus presentation in psychophysics experiments, or within a closed loop such as in biofeedback or brain-computer interfacing experiments. Pyff communicates with other systems via a standardized communication protocol and is therefore suitable to be used with any system that may be adapted to send its data in the specified format. Having such a general, open-source framework will help foster a fruitful exchange of experimental paradigms between research groups. In particular, it will decrease the need of reprogramming standard paradigms, ease the reproducibility of published results, and naturally entail some standardization of stimulus presentation.

  11. Unilateral microphthalmia or anophthalmia in eight pythons (Pythonidae).

    Science.gov (United States)

    Da Silva, Mari-Ann O; Bertelsen, Mads F; Wang, Tobias; Pedersen, Michael; Lauridsen, Henrik; Heegaard, Steffen

    2015-01-01

    To provide morphological descriptions of microphthalmia or anophthalmia in eight pythons using microcomputerized tomography (μCT), magnetic resonance imaging (MRI), and histopathology. Seven Burmese pythons (Python bivittatus) and one ball python (P. regius) with clinically normal right eyes and an abnormal or missing left eye. At the time of euthanasia, four of the eight snakes underwent necropsy. Hereafter, the heads of two Burmese pythons and one ball python were examined using μCT, and another Burmese python was subjected to MRI. Following these procedures, the heads of these four pythons along with the heads of an additional three Burmese pythons were prepared for histology. All eight snakes had left ocular openings seen as dermal invaginations between 0.2 and 2.0 mm in diameter. They also had varying degrees of malformations of the orbital bones and a limited presence of nervous, glandular, and muscle tissue in the posterior orbit. Two individuals had small but identifiable eyes. Furthermore, remnants of the pigmented embryonic framework of the hyaloid vessels were found in the anophthalmic snakes. Necropsies revealed no other macroscopic anomalies. Eight pythons with unilateral left-sided microphthalmia or anophthalmia had one normal eye and a left orbit with malformed or incompletely developed ocular structures along with remnants of fetal structures. These cases lend further information to a condition that is often seen in snakes, but infrequently described. © 2014 American College of Veterinary Ophthalmologists.

  12. Detection of nidoviruses in live pythons and boas.

    Science.gov (United States)

    Marschang, Rachel E; Kolesnik, Ekaterina

    2017-02-09

    Nidoviruses have recently been described as a putative cause of severe respiratory disease in pythons in the USA and Europe. The objective of this study was to establish the use of a conventional PCR for the detection of nidoviruses in samples from live animals and to extend the list of susceptible species. A PCR targeting a portion of ORF1a of python nidoviruses was used to detect nidoviruses in diagnostic samples from live boas and pythons. A total of 95 pythons, 84 boas and 22 snakes of unknown species were included in the study. Samples tested included oral swabs and whole blood. Nidoviruses were detected in 27.4% of the pythons and 2.4% of the boas tested. They were most commonly detected in ball pythons (Python [P.] regius) and Indian rock pythons (P. molurus), but were also detected for the first time in other python species, including Morelia spp. and Boa constrictor. Oral swabs were most commonly tested positive. The PCR described here can be used for the detection of nidoviruses in oral swabs from live snakes. These viruses appear to be relatively common among snakes in captivity in Europe and screening for these viruses should be considered in the clinical work-up. Nidoviruses are believed to be an important cause of respiratory disease in pythons, but can also infect boas. Detection of these viruses in live animals is now possible and can be of interest both in diseased animals as well as in quarantine situations.

  13. 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,

  14. 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.

  15. 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

  16. ParselTongue: AIPS Talking Python

    Science.gov (United States)

    Kettenis, M.; van Langevelde, H. J.; Reynolds, C.; Cotton, B.

    2006-07-01

    After more than 20 years of service, classic AIPS still is the data reduction package of choice for many radio-interferometry projects, especially for VLBI. Its age shows, most prominently in the limited scripting capabilities of its user interface: POPS. ParselTongue is an attempt to make the trusted AIPS algorithms and AIPS data structures available in a modern dynamic programming language: Python. It also provides an environment to do distributed computing to take advantage of modern computing clusters. This makes it suitable for use as a scripting interface for doing complicated data reduction on large data sets. It is also used as a coding platform for the new calibration algorithms that are being developed for the European VLBI Network as part of the ALBUS project. Here we hope to take advantage of Python's extensive support for web-based technologies to automate things like collecting calibration data.

  17. Transliterating non-ASCII characters with Python

    Directory of Open Access Journals (Sweden)

    Seth Bernstein

    2013-10-01

    Full Text Available This lesson shows how to use Python to transliterate automatically a list of words from a language with a non-Latin alphabet to a standardized format using the American Standard Code for Information Interchange (ASCII characters. It builds on readers’ understanding of Python from the lessons “Viewing HTML Files,” “Working with Web Pages,” “From HTML to List of Words (part 1” and “Intro to Beautiful Soup.” At the end of the lesson, we will use the transliteration dictionary to convert the names from a database of the Russian organization Memorial from Cyrillic into Latin characters. Although the example uses Cyrillic characters, the technique can be reproduced with other alphabets using Unicode.

  18. Gala: A Python package for galactic dynamics

    Science.gov (United States)

    Price-Whelan, Adrian M.

    2017-10-01

    Gala is an Astropy-affiliated Python package for galactic dynamics. Python enables wrapping low-level languages (e.g., C) for speed without losing flexibility or ease-of-use in the user-interface. The API for Gala was designed to provide a class-based and user-friendly interface to fast (C or Cython-optimized) implementations of common operations such as gravitational potential and force evaluation, orbit integration, dynamical transformations, and chaos indicators for nonlinear dynamics. Gala also relies heavily on and interfaces well with the implementations of physical units and astronomical coordinate systems in the Astropy package (astropy.units and astropy.coordinates). Gala was designed to be used by both astronomical researchers and by students in courses on gravitational dynamics or astronomy. It has already been used in a number of scientific publications and has also been used in graduate courses on Galactic dynamics to, e.g., provide interactive visualizations of textbook material.

  19. Experimentally derived salinity tolerance of hatchling Burmese pythons (Python molurus bivittatus) from the Everglades, Florida (USA)

    Science.gov (United States)

    Hart, Kristen M.; Schofield, Pamela J.; Gregoire, Denise R.

    2012-01-01

    In a laboratory setting, we tested the ability of 24 non-native, wild-caught hatchling Burmese pythons (Python molurus bivittatus) collected in the Florida Everglades to survive when given water containing salt to drink. After a one-month acclimation period in the laboratory, we grouped snakes into three treatments, giving them access to water that was fresh (salinity of 0, control), brackish (salinity of 10), or full-strength sea water (salinity of 35). Hatchlings survived about one month at the highest marine salinity and about five months at the brackish-water salinity; no control animals perished during the experiment. These results are indicative of a "worst-case scenario", as in the laboratory we denied access to alternate fresh-water sources that may be accessible in the wild (e.g., through rainfall). Therefore, our results may underestimate the potential of hatchling pythons to persist in saline habitats in the wild. Because of the effect of different salinity regimes on survival, predictions of ultimate geographic expansion by non-native Burmese pythons that consider salt water as barriers to dispersal for pythons may warrant re-evaluation, especially under global climate change and associated sea-level-rise scenarios.

  20. PyBus -- A Python Software Bus

    OpenAIRE

    Lavrijsen, W

    2005-01-01

    A software bus, just like its hardware equivalent, allows for the discovery, installation, configuration, loading, unloading, and run-time replacement of software components, as well as channeling of inter-component communication. Python, a popular open-source programming language, encourages a modular design on software written in it, but it offers little or no component functionality. However, the language and its interpreter provide sufficient hooks to implement a thin, integral layer...

  1. Py4Syn: Python for synchrotrons.

    Science.gov (United States)

    Slepicka, H H; Canova, H F; Beniz, D B; Piton, J R

    2015-09-01

    In this report, Py4Syn, an open-source Python-based library for data acquisition, device manipulation, scan routines and other helper functions, is presented. Driven by easy-to-use and scalability ideals, Py4Syn offers control system agnostic solution and high customization level for scans and data output, covering distinct techniques and facilities. Here, most of the library functionalities are described, examples of use are shown and ideas for future implementations are presented.

  2. Scikit-learn: Machine Learning in Python

    OpenAIRE

    Pedregosa, Fabian; Varoquaux, Gaël; Gramfort, Alexandre; Michel, Vincent; Thirion, Bertrand; Grisel, Olivier; Blondel, Mathieu; Prettenhofer, Peter; Weiss, Ron; Dubourg, Vincent; Vanderplas, Jake; Passos, Alexandre; Cournapeau, David; Brucher, Matthieu; Perrot, Matthieu

    2011-01-01

    International audience; Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic ...

  3. Scikit-learn: Machine Learning in Python

    OpenAIRE

    Pedregosa, Fabian; Varoquaux, Gaël; Gramfort, Alexandre; Michel, Vincent; Thirion, Bertrand; Grisel, Olivier; Blondel, Mathieu; Louppe, Gilles; Prettenhofer, Peter; Weiss, Ron; Dubourg, Vincent; Vanderplas, Jake; Passos, Alexandre; Cournapeau, David; Brucher, Matthieu

    2012-01-01

    Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings....

  4. Osteosarcoma in a woma python (Aspidites ramsayi).

    Science.gov (United States)

    Cowan, M L; Monks, D J; Raidal, S R

    2011-12-01

    Osteosarcoma of the axial skeleton in an 18-month-old woma python (Aspidites ramsayi) is described. A subcutaneous mass overlying the costal arches enlarged progressively over a period of 5 months and, in that time, became ulcerated and more invasive of surrounding tissues. A punch biopsy of the lesion under general anaesthesia provided tissue for histopathology and diagnosis of low-grade osteosarcoma. © 2011 The Authors. Australian Veterinary Journal © 2011 Australian Veterinary Association.

  5. MTpy: A Python toolbox for magnetotellurics

    Science.gov (United States)

    Krieger, Lars; Peacock, Jared R.

    2014-01-01

    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.

  6. MGtoolkit: A python package for implementing metagraphs

    Directory of Open Access Journals (Sweden)

    D. Ranathunga

    2017-01-01

    Full Text Available In this paper we present MGtoolkit : an open-source Python package for implementing metagraphs - a first of its kind. Metagraphs are commonly used to specify and analyse business and computer-network policies alike. MGtoolkit can help verify such policies and promotes learning and experimentation with metagraphs. The package currently provides purely textual output for visualising metagraphs and their analysis results.

  7. GIFT-Grab: Real-time C++ and Python multi-channel video capture, processing and encoding API

    Directory of Open Access Journals (Sweden)

    Dzhoshkun Ismail Shakir

    2017-10-01

    Full Text Available GIFT-Grab is an open-source API for acquiring, processing and encoding video streams in real time. GIFT-Grab supports video acquisition using various frame-grabber hardware as well as from standard-compliant network streams and video files. The current GIFT-Grab release allows for multi-channel video acquisition and encoding at the maximum frame rate of supported hardware – 60 frames per second (fps. GIFT-Grab builds on well-established highly configurable multimedia libraries including FFmpeg and OpenCV. GIFT-Grab exposes a simplified high-level API, aimed at facilitating integration into client applications with minimal coding effort. The core implementation of GIFT-Grab is in C++11. GIFT-Grab also features a Python API compatible with the widely used scientific computing packages NumPy and SciPy. GIFT-Grab was developed for capturing multiple simultaneous intra-operative video streams from medical imaging devices. Yet due to the ubiquity of video processing in research, GIFT-Grab can be used in many other areas. GIFT-Grab is hosted and managed on the software repository of the Centre for Medical Image Computing (CMIC at University College London, and is also mirrored on GitHub. In addition it is available for installation from the Python Package Index (PyPI via the pip installation tool. Funding statement: This work was supported through an Innovative Engineering for Health award by the Wellcome Trust [WT101957], the Engineering and Physical Sciences Research Council (EPSRC [NS/A000027/1] and a National Institute for Health Research Biomedical Research Centre UCLH/UCL High Impact Initiative. Sébastien Ourselin receives funding from the EPSRC (EP/H046410/1, EP/J020990/1, EP/K005278 and the MRC (MR/J01107X/1. Luis C. García-Peraza-Herrera is supported by the EPSRC-funded UCL Centre for Doctoral Training in Medical Imaging (EP/L016478/1.

  8. 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.

  9. Saccular lung cannulation in a ball python (Python regius) to treat a tracheal obstruction.

    Science.gov (United States)

    Myers, Debbie A; Wellehan, James F X; Isaza, Ramiro

    2009-03-01

    An adult male ball python (Python regius) presented in a state of severe dyspnea characterized by open-mouth breathing and vertical positioning of the head and neck. The animal had copious discharge in the tracheal lumen acting as an obstruction. A tube was placed through the body wall into the caudal saccular aspect of the lung to allow the animal to breathe while treatment was initiated. The ball python's dyspnea immediately improved. Diagnostics confirmed a bacterial respiratory infection with predominantly Providencia rettgeri. The saccular lung (air sac) tube was removed after 13 days. Pulmonary endoscopy before closure showed minimal damage with a small amount of hemorrhage in the surrounding muscle tissue. Respiratory disease is a common occurrence in captive snakes and can be associated with significant morbidity and mortality. Saccular lung cannulation is a relatively simple procedure that can alleviate tracheal narrowing or obstruction, similar to air sac cannulation in birds.

  10. Predators in training: operant conditioning of novel behavior in wild Burmese pythons (Python molurus bivitattus).

    Science.gov (United States)

    Emer, Sherri A; Mora, Cordula V; Harvey, Mark T; Grace, Michael S

    2015-01-01

    Large pythons and boas comprise a group of animals whose anatomy and physiology are very different from traditional mammalian, avian and other reptilian models typically used in operant conditioning. In the current study, investigators used a modified shaping procedure involving successive approximations to train wild Burmese pythons (Python molurus bivitattus) to approach and depress an illuminated push button in order to gain access to a food reward. Results show that these large, wild snakes can be trained to accept extremely small food items, associate a stimulus with such rewards via operant conditioning and perform a contingent operant response to gain access to a food reward. The shaping procedure produced robust responses and provides a mechanism for investigating complex behavioral phenomena in massive snakes that are rarely studied in learning research.

  11. 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.

  12. Transcriptome Analysis of the Response of Burmese Python to Digestion

    OpenAIRE

    Duan, Jinjie; Sanggaard, Kristian Wejse; Schauser, Leif; Lauridsen, Sanne Enok; Enghild, Jan J.; Schierup, Mikkel Heide; Wang, Tobias

    2017-01-01

    Abstract Exceptional and extreme feeding behaviour makes the Burmese python (Python bivittatus) an interesting model to study physiological remodelling and metabolic adaptation in response to refeeding after prolonged starvation. In this study, we used transcriptome sequencing of 5 visceral organs during fasting as well as 24 hours and 48 hours after ingestion of a large meal to unravel the postprandial changes in Burmese pythons. We first used the pooled data to perform a de novo assembly of...

  13. PyMidas: Interface from Python to Midas

    Science.gov (United States)

    Maisala, Sami; Oittinen, Tero

    2014-01-01

    PyMidas is an interface between Python and MIDAS, the major ESO legacy general purpose data processing system. PyMidas allows a user to exploit both the rich legacy of MIDAS software and the power of Python scripting in a unified interactive environment. PyMidas also allows the usage of other Python-based astronomical analysis systems such as PyRAF.

  14. Interactive game programming with Python (CodeSkulptor)

    OpenAIRE

    Ajayi, Richard Olugbenga

    2014-01-01

    Over the years, several types of gaming platforms have been created to encourage a more organised and friendly atmosphere for game lovers in various works of life, culture, and environment. This thesis focuses on the concept of interactive programming using Python. It encourages the use of Python to create simple interactive games applications based on basic human concept and ideas. CodeSkulptor is a browser-based IDE programming environment and uses the Python programming language. O...

  15. HOPE: Just-in-time Python compiler for astrophysical computations

    Science.gov (United States)

    Akeret, Joel; Gamper, Lukas; Amara, Adam; Refregier, Alexandre

    2014-11-01

    HOPE is a specialized Python just-in-time (JIT) compiler designed for numerical astrophysical applications. HOPE focuses on a subset of the language and is able to translate Python code into C++ while performing numerical optimization on mathematical expressions at runtime. To enable the JIT compilation, the user only needs to add a decorator to the function definition. By using HOPE, the user benefits from being able to write common numerical code in Python while getting the performance of compiled implementation.

  16. Pro Android Python with SL4A Writing Android Native Apps Using Python, Lua, and Beanshell

    CERN Document Server

    Ferrill, Paul

    2011-01-01

    Pro Android Python with SL4A is for programmers and hobbyists who want to write apps for Android devices without having to learn Java first. Paul Ferrill leads you from installing the Scripting Layer for Android (SL4A) to writing small scripts, to more complicated and interesting projects, and finally to uploading and packaging your programs to an Android device. Android runs scripts in many scripting languages, but Python, Lua, and Beanshell are particularly popular. Most programmers know more than one programming language, so that they have the best tool for whatever task they want to accomp

  17. Subspectacular nematodiasis caused by a novel Serpentirhabdias species in ball pythons (Python regius).

    Science.gov (United States)

    Hausmann, J C; Mans, C; Dreyfus, J; Reavill, D R; Lucio-Forster, A; Bowman, D D

    2015-01-01

    Subspectacular nematodiasis was diagnosed in three captive-bred juvenile ball pythons (Python regius) from two unrelated facilities within a 6-month period. The snakes were presented with similar lesions, including swelling of facial, periocular and oral tissues. Bilaterally, the subspectacular spaces were distended and filled with an opaque fluid, which contained nematodes and eggs. Histopathology showed nematodes throughout the periocular tissue, subspectacular space and subcutaneous tissue of the head. The nematodes from both facilities were morphologically indistinguishable and most closely resembled Serpentirhabdias species. Morphological characterization and genetic sequencing indicate this is a previously undescribed rhabdiasid nematode. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. 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

  19. Re-imagining a Stata/Python combination

    OpenAIRE

    James Fiedler

    2013-01-01

    At last year’s Stata Conference, I presented some ideas for combining Stata and Python within a single interface. Two methods were presented; in one, Python was used to automate Stata, and in the other, Python was used to send simulated keystrokes to the Stata GUI. The first method has the drawback of only working in Windows, and the second can be slow and subject to character input limits. In this talk I will demonstrate a method for achieving interaction between Stata and Python which does ...

  20. PRACTICAL APPROACH FOR HYPERSPECTRAL IMAGE PROCESSING IN PYTHON

    OpenAIRE

    Annala, L.; Eskelinen, M. A.; Hämäläinen, J.; Riihinen, A.; Pölönen, I.

    2018-01-01

    Python is a very popular programming language among data scientists around the world. Python can also be used in hyperspectral data analysis. There are some toolboxes designed for spectral imaging, such as Spectral Python and HyperSpy, but there is a need for analysis pipeline, which is easy to use and agile for different solutions. We propose a Python pipeline which is built on packages xarray, Holoviews and scikit-learn. We have developed some of own tools, MaskAccessor, VisualisorAccessor ...

  1. Machine learning in Python essential techniques for predictive analysis

    CERN Document Server

    Bowles, Michael

    2015-01-01

    Learn a simpler and more effective way to analyze data and predict outcomes with Python Machine Learning in Python shows you how to successfully analyze data using only two core machine learning algorithms, and how to apply them using Python. By focusing on two algorithm families that effectively predict outcomes, this book is able to provide full descriptions of the mechanisms at work, and the examples that illustrate the machinery with specific, hackable code. The algorithms are explained in simple terms with no complex math and applied using Python, with guidance on algorithm selection, d

  2. Re-imagining a Stata/Python Combination

    Science.gov (United States)

    Fiedler, James

    2013-01-01

    At last year's Stata Conference, I presented some ideas for combining Stata and the Python programming language within a single interface. Two methods were presented: in one, Python was used to automate Stata; in the other, Python was used to send simulated keystrokes to the Stata GUI. The first method has the drawback of only working in Windows, and the second can be slow and subject to character input limits. In this presentation, I will demonstrate a method for achieving interaction between Stata and Python that does not suffer these drawbacks, and I will present some examples to show how this interaction can be useful.

  3. 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.

  4. 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...

  5. 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.

  6. 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.

  7. A postmortem experience of Indian rock python (Python molurus molurus that swallowed a whole barking deer

    Directory of Open Access Journals (Sweden)

    Amam Zonaed Siddiki

    2013-06-01

    Full Text Available The object of this study was to report a post mortem findings of a female Indian Rock Python with a length of 406 cm (13.32 feet and approximate weight of 60 kg (including a whole deer that was swallowed by the python, that was brought to the Teaching Veterinary Hospital, Chittagong Veterinary and Animal Sciences University (CVASU by the Forest Department of Kumira Range Office, Chittagong. The local inhabitants accidently found the python at the forest area of Kumira and they frightenedly injured and killed the snake eventually. The postmortem (PM examination was performed according to standard protocols. Gross examination revealed bloody discharge was come out through mouth and a couple of skin lacerations observed on the right dorso-lateral part of the abdominal region. The whole barrel-shaped body cavity was opened and whole deer (partially decomposed was recovered from the stomach. Furthermore, three fractured ribs were found on right thorax. The PM examination team believes that the possible cause of python death was traumatic injury inflicted by the local people. [Vet World 2013; 6(3.000: 163-165

  8. Trypanosoma cf. varani in an imported ball python (Python reginus) from Ghana.

    Science.gov (United States)

    Sato, Hiroshi; Takano, Ai; Kawabata, Hiroki; Une, Yumi; Watanabe, Haruo; Mukhtar, Maowia M

    2009-08-01

    Peripheral blood from a ball python (Python reginus) imported from Ghana was cultured in Barbour-Stoenner-Kelly (BSK) medium for Borrelia spp. isolation, resulting in the prominent appearance of free, and clusters of, trypanosomes in a variety of morphological forms. The molecular phylogenetic characterization of these cultured trypanosomes, using the small subunit rDNA, indicated that this python was infected with a species closely related to Trypanosoma varani Wenyon, 1908, originally described in the Nile monitor lizard (Varanus niloticus) from Sudan. Furthermore, nucleotide sequences of glycosomal glyceraldehyde-3-phosphate dehydrogenase gene of both isolates showed few differences. Giemsa-stained blood smears, prepared from the infected python 8 mo after the initial observation of trypanosomes in hemoculture, contained trypomastigotes with a broad body and a short, free flagellum; these most closely resembled the original description of T. varani, or T. voltariae Macfie, 1919 recorded in a black-necked spitting cobra (Naja nigricollis) from Ghana. It is highly possible that lizards and snakes could naturally share an identical trypanosome species. Alternatively, lizards and snakes in the same region might have closely related, but distinct, Trypanosoma species as a result of sympatric speciation. From multiple viewpoints, including molecular phylogenetic analyses, reappraisal of trypanosome species from a wide range of reptiles in Africa is needed to clarify the relationship of recorded species, or to unmask unrecorded species.

  9. Ball python nidovirus: a candidate etiologic agent for severe respiratory disease in Python regius.

    Science.gov (United States)

    Stenglein, Mark D; Jacobson, Elliott R; Wozniak, Edward J; Wellehan, James F X; Kincaid, Anne; Gordon, Marcus; Porter, Brian F; Baumgartner, Wes; Stahl, Scott; Kelley, Karen; Towner, Jonathan S; DeRisi, Joseph L

    2014-09-09

    A severe, sometimes fatal respiratory disease has been observed in captive ball pythons (Python regius) since the late 1990s. In order to better understand this disease and its etiology, we collected case and control samples and performed pathological and diagnostic analyses. Electron micrographs revealed filamentous virus-like particles in lung epithelial cells of sick animals. Diagnostic testing for known pathogens did not identify an etiologic agent, so unbiased metagenomic sequencing was performed. Abundant nidovirus-like sequences were identified in cases and were used to assemble the genome of a previously unknown virus in the order Nidovirales. The nidoviruses, which were not previously known to infect nonavian reptiles, are a diverse order that includes important human and veterinary pathogens. The presence of the viral RNA was confirmed in all diseased animals (n = 8) but was not detected in healthy pythons or other snakes (n = 57). Viral RNA levels were generally highest in the lung and other respiratory tract tissues. The 33.5-kb viral genome is the largest RNA genome yet described and shares canonical characteristics with other nidovirus genomes, although several features distinguish this from related viruses. This virus, which we named ball python nidovirus (BPNV), will likely establish a new genus in Torovirinae subfamily. The identification of a novel nidovirus in reptiles contributes to our understanding of the biology and evolution of related viruses, and its association with lung disease in pythons is a promising step toward elucidating an etiology for this long-standing veterinary disease. Ball pythons are popular pets because of their diverse coloration, generally nonaggressive behavior, and relatively small size. Since the 1990s, veterinarians have been aware of an infectious respiratory disease of unknown cause in ball pythons that can be fatal. We used unbiased shotgun sequencing to discover a novel virus in the order Nidovirales that was

  10. Computational physics problem solving with Python

    CERN Document Server

    Landau, Rubin H; Bordeianu, Cristian C

    2015-01-01

    The use of computation and simulation has become an essential part of the scientific process. Being able to transform a theory into an algorithm requires significant theoretical insight, detailed physical and mathematical understanding, and a working level of competency in programming. This upper-division text provides an unusually broad survey of the topics of modern computational physics from a multidisciplinary, computational science point of view. Its philosophy is rooted in learning by doing (assisted by many model programs), with new scientific materials as well as with the Python progr

  11. Rapid web development using AJAX and Python

    Energy Technology Data Exchange (ETDEWEB)

    Dolgert, A; Gibbons, L; Kuznetsov, V [Cornell University, Ithaca, NY 14853 (United States)], E-mail: vkuznet@gmail.com

    2008-07-15

    We discuss the rapid development of a large scale data discovery service for the CMS experiment using modern AJAX techniques and the Python language. To implement a flexible interface capable of accommodating several different versions of the DBS database, we used a 'stack' approach. Asynchronous JavaScript and XML (AJAX) together with an SQL abstraction layer, template engine, code generation tool and dynamic queries provide powerful tools for constructing interactive interfaces to large amounts of data. We show how the use of these tools, with rapid development in a modern scripting language, improved the scalability and usability of the the search interface for different user communities.

  12. Rapid web development using AJAX and Python

    International Nuclear Information System (INIS)

    Dolgert, A; Gibbons, L; Kuznetsov, V

    2008-01-01

    We discuss the rapid development of a large scale data discovery service for the CMS experiment using modern AJAX techniques and the Python language. To implement a flexible interface capable of accommodating several different versions of the DBS database, we used a 'stack' approach. Asynchronous JavaScript and XML (AJAX) together with an SQL abstraction layer, template engine, code generation tool and dynamic queries provide powerful tools for constructing interactive interfaces to large amounts of data. We show how the use of these tools, with rapid development in a modern scripting language, improved the scalability and usability of the the search interface for different user communities

  13. Scikit-spectra: Explorative Spectroscopy in Python

    Directory of Open Access Journals (Sweden)

    Adam Hughes

    2015-06-01

    Full Text Available Scikit-spectra is an intuitive framework for explorative spectroscopy in Python. Scikit-spectra leverages the Pandas library for powerful data processing to provide datastructures and an API designed for spectroscopy. Utilizing the new IPython Notebook widget system, scikit-spectra is headed towards a GUI when you want it, API when you need it approach to spectral analysis. As an application, analysis is presented of the surface-plasmon resonance shift in a solution of gold nanoparticles induced by proteins binding to the gold’s surface. Please refer to the scikit-spectra website for full documentation and support: http://hugadams.github.io/scikit-spectra/

  14. scikit-image: image processing in Python.

    Science.gov (United States)

    van der Walt, Stéfan; Schönberger, Johannes L; Nunez-Iglesias, Juan; Boulogne, François; Warner, Joshua D; Yager, Neil; Gouillart, Emmanuelle; Yu, Tony

    2014-01-01

    scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org.

  15. scikit-image: image processing in Python

    Directory of Open Access Journals (Sweden)

    Stéfan van der Walt

    2014-06-01

    Full Text Available scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org.

  16. 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....

  17. SpiceyPy, a Python Wrapper for SPICE

    Science.gov (United States)

    Annex, A.

    2017-06-01

    SpiceyPy is an open source Python wrapper for the NAIF SPICE toolkit. It is available for macOS, Linux, and Windows platforms and for Python versions 2.7.x and 3.x as well as Anaconda. SpiceyPy can be installed by running: “pip install spiceypy.”

  18. Cost versus precision for approximate typing for Python

    NARCIS (Netherlands)

    Fritz, Levin; Hage, J.

    2017-01-01

    In this paper we describe a variation of monotone frameworks that enables us to perform approximate typing of Python, in particular for dealing with some of its more dynamic features such as first-class functions and Python's dynamic class system. We additionally introduce a substantial number of

  19. 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.

  20. pupyMPI - MPI implemented in pure Python

    DEFF Research Database (Denmark)

    Bromer, Rune; Hantho, Frederik; Vinter, Brian

    2011-01-01

    As distributed memory systems have become common, the de facto standard for communication is still the Message Passing Interface (MPI). pupyMPI is a pure Python implementation of a broad subset of the MPI 1.3 specifications that allows Python programmers to utilize multiple CPUs with datatypes...

  1. Pyndri: a Python Interface to the Indri Search Engine

    NARCIS (Netherlands)

    Van Gysel, C.; Kanoulas, E.; de Rijke, M.; Jose, J.M.; Hauff, C.; Altıngovde, I.S.; Song, D.; Albakour, D.; Watt, S.; Tait, J.

    2017-01-01

    We introduce pyndri, a Python interface to the Indri search engine. Pyndri allows to access Indri indexes from Python at two levels: (1) dictionary and tokenized document collection, (2) evaluating queries on the index. We hope that with the release of pyndri, we will stimulate reproducible, open

  2. Reimplementing a Multi-Agent System in Python

    DEFF Research Database (Denmark)

    Villadsen, Jørgen; Jensen, Andreas Schmidt; Ettienne, Mikko Berggren

    2012-01-01

    We provide a brief description of our Python-DTU system, including the overall design, the tools and the algorithms that we used in the Multi-Agent Programming Contest 2012, where the scenario was called Agents on Mars like in 2011. Our solution is an improvement of our Python-DTU system from last...

  3. Expyriment: A Python library for cognitive and neuroscientific experiments

    NARCIS (Netherlands)

    Krause, F.; Lindemann, O.

    2014-01-01

    Expyriment is an open-source and platform-independent lightweight Python library for designing and conducting timing-critical behavioral and neuroimaging experiments. The major goal is to provide a well-structured Python library for script-based experiment development, with a high priority being the

  4. Reimplementing a Multi-Agent System in Python

    DEFF Research Database (Denmark)

    Villadsen, Jørgen; Jensen, Andreas Schmidt; Ettienne, Mikko Berggren

    2013-01-01

    We provide a brief description of our Python-DTU system, including the overall design, the tools and the algorithms that we used in the Multi-Agent Programming Contest 2012, where the scenario was called Agents on Mars like in 2011. Our solution is an improvement of our Python-DTU system from last...

  5. 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.

  6. Stimfit: quantifying electrophysiological data with Python

    Directory of Open Access Journals (Sweden)

    Segundo Jose Guzman

    2014-02-01

    Full Text Available Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals.

  7. Writing analytic element programs in Python.

    Science.gov (United States)

    Bakker, Mark; Kelson, Victor A

    2009-01-01

    The analytic element method is a mesh-free approach for modeling ground water flow at both the local and the regional scale. With the advent of the Python object-oriented programming language, it has become relatively easy to write analytic element programs. In this article, an introduction is given of the basic principles of the analytic element method and of the Python programming language. A simple, yet flexible, object-oriented design is presented for analytic element codes using multiple inheritance. New types of analytic elements may be added without the need for any changes in the existing part of the code. The presented code may be used to model flow to wells (with either a specified discharge or drawdown) and streams (with a specified head). The code may be extended by any hydrogeologist with a healthy appetite for writing computer code to solve more complicated ground water flow problems. Copyright © 2009 The Author(s). Journal Compilation © 2009 National Ground Water Association.

  8. A student's guide to Python for physical modeling

    CERN Document Server

    Kinder, Jesse M

    2015-01-01

    Python is a computer programming language that is rapidly gaining popularity throughout the sciences. A Student’s Guide to Python for Physical Modeling aims to help you, the student, teach yourself enough of the Python programming language to get started with physical modeling. You will learn how to install an open-source Python programming environment and use it to accomplish many common scientific computing tasks: importing, exporting, and visualizing data; numerical analysis; and simulation. No prior programming experience is assumed. This tutorial focuses on fundamentals and introduces a wide range of useful techniques, including: Basic Python programming and scripting Numerical arrays Two- and three-dimensional graphics Monte Carlo simulations Numerical methods, including solving ordinary differential equations Image processing Animation Numerous code samples and exercises—with solutions—illustrate new ideas as they are introduced. A website that accompanies this guide provides additional resourc...

  9. A facility for creating Python extensions in C++

    International Nuclear Information System (INIS)

    Dubois, P F

    1998-01-01

    Python extensions are usually created by writing the glue that connects Python to the desired new functionality in the C language. While simple extensions do not require much effort, to do the job correctly with full error checking is tedious and prone to errors in reference counting and to memory leaks, especially when errors occur. The resulting program is difficult to read and maintain. By designing suitable C++ classes to wrap the Python C API, we are able to produce extensions that are correct and which clean up after themselves correctly when errors occur. This facility also integrates the C++ and Python exception facilities. This paper briefly describes our package for this purpose, named CXX. The emphasis is on our design choices and the way these contribute to the construction of accurate Python extensions. We also briefly relate the way CXX's facilities for sequence classes allow use of C++'s Standard Template Library (STL) algorithms on C++ sequences

  10. Report on the observed response of Javan lutungs (Trachypithecus auratus mauritius) upon encountering a reticulated python (Python reticulatus).

    Science.gov (United States)

    Tsuji, Yamato; Prayitno, Bambang; Suryobroto, Bambang

    2016-04-01

    We observed an encounter between a reticulated python (Python reticulatus) and a group of wild Javan lutungs (Trachypithecus auratus mauritius) at the Pangandaran Nature Reserve, West Java, Indonesia. A python (about 2 m in length) moved toward a group of lutungs in the trees. Upon seeing the python, an adult male and several adult female lutungs began to emit alarm calls. As the python approached, two adult and one sub-adult female jumped onto a branch near the python and began mobbing the python by shaking the branch. During the mobbing, other individuals in the group (including an adult lutung male) remained nearby but did not participate. The python then rolled into a ball-like shape and stopped moving, at which point the lutungs moved away. The total duration of the encounter was about 40 min, during which time the lutungs stopped feeding and grooming. Group cohesiveness during and after the encounter was greater than that before the encounter, indicating that lutungs adjust their daily activity in response to potential predation risk.

  11. Lectin histochemical aspects of mucus function in the oesophagus of the reticulated python (Python reticulatus).

    Science.gov (United States)

    Meyer, W; Luz, S; Schnapper, A

    2009-08-01

    Using lectin histochemistry, the study characterizes basic functional aspects of the mucus produced by the oesophageal epithelium of the Reticulated python (Python reticulatus). Reaction staining varied as related to the two epithelium types present, containing goblet cells and ciliary cells. Remarkable intensities were achieved especially in the luminal mucus layer and the fine mucus covering the epithelial ciliary border for Con A (alpha-D-Man; alpha-D-Glc) as part of neutral glycoproteins, Limax flavus agglutinin (NeuNac = NeuNgc), emphasizing that water binding hyaluronan provides a hydrated interface conductive to the passage of material and UEA-I (alpha-L-Fuc), corroborating the view that fucose-rich highly viscous mucus is helpful against mechanical stress during prey transport.

  12. Ultrasonographic diagnosis of an endocarditis valvularis in a Burmese python (Python molurus bivittatus) with pneumonia.

    Science.gov (United States)

    Schroff, Sandra; Schmidt, Volker; Kiefer, Ingmar; Krautwald-Junghanns, Maria-Elisabeth; Pees, Michael

    2010-12-01

    An 11-yr-old Burmese python (Python molurus bivittatus) was presented with a history of respiratory symptoms. Computed tomography and an endoscopic examination of the left lung were performed and revealed severe pneumonia. Microbiologic examination of a tracheal wash sample and an endoscopy-guided sample from the lung confirmed infection with Salmonella enterica ssp. IV, Enterobacter cloacae, and Klebsiella pneumoniae. Computed tomographic examination demonstrated a hyperattenuated structure within the heart. Echocardiographic examination revealed a hyperechoic mass at the pulmonic valve as well as a dilated truncus pulmonalis. As therapy for pneumonia was ineffective, the snake was euthanized. Postmortem examination confirmed pneumonia and infective endocarditis of the pulmonic valve caused by septicemia with Salmonella enterica ssp. IV. Focal arteriosclerosis of the pulmonary trunk was also diagnosed. The case presented here demonstrates the possible connection between respiratory and cardiovascular diseases in snakes.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. PyMOOSE: interoperable scripting in Python for MOOSE

    Directory of Open Access Journals (Sweden)

    Subhasis Ray

    2008-12-01

    Full Text Available Python is emerging as a common scripting language for simulators. This opens up many possibilities for interoperability in the form of analysis, interfaces, and communications between simulators. We report the integration of Python scripting with the Multi-scale Object Oriented Simulation Environment (MOOSE. MOOSE is a general-purpose simulation system for compartmental neuronal models and for models of signaling pathways based on chemical kinetics. We show how the Python-scripting version of MOOSE, PyMOOSE, combines the power of a compiled simulator with the versatility and ease of use of Python. We illustrate this by using Python numerical libraries to analyze MOOSE output online, and by developing a GUI in Python/Qt for a MOOSE simulation. Finally, we build and run a composite neuronal/signaling model that uses both the NEURON and MOOSE numerical engines, and Python as a bridge between the two. Thus PyMOOSE has a high degree of interoperability with analysis routines, with graphical toolkits, and with other simulators.

  18. Python in the NERSC Exascale Science Applications Program for Data

    Energy Technology Data Exchange (ETDEWEB)

    Ronaghi, Zahra; Thomas, Rollin; Deslippe, Jack; Bailey, Stephen; Gursoy, Doga; Kisner, Theodore; Keskitalo, Reijo; Borrill, Julian

    2017-11-12

    We describe a new effort at the National Energy Re- search Scientific Computing Center (NERSC) in performance analysis and optimization of scientific Python applications targeting the Intel Xeon Phi (Knights Landing, KNL) many- core architecture. The Python-centered work outlined here is part of a larger effort called the NERSC Exascale Science Applications Program (NESAP) for Data. NESAP for Data focuses on applications that process and analyze high-volume, high-velocity data sets from experimental/observational science (EOS) facilities supported by the US Department of Energy Office of Science. We present three case study applications from NESAP for Data that use Python. These codes vary in terms of “Python purity” from applications developed in pure Python to ones that use Python mainly as a convenience layer for scientists without expertise in lower level programming lan- guages like C, C++ or Fortran. The science case, requirements, constraints, algorithms, and initial performance optimizations for each code are discussed. Our goal with this paper is to contribute to the larger conversation around the role of Python in high-performance computing today and tomorrow, highlighting areas for future work and emerging best practices

  19. Reduction of blood oxygen levels enhances postprandial cardiac hypertrophy in Burmese python (Python bivittatus).

    Science.gov (United States)

    Slay, Christopher E; Enok, Sanne; Hicks, James W; Wang, Tobias

    2014-05-15

    Physiological cardiac hypertrophy is characterized by reversible enlargement of cardiomyocytes and changes in chamber architecture, which increase stroke volume and via augmented convective oxygen transport. Cardiac hypertrophy is known to occur in response to repeated elevations of O2 demand and/or reduced O2 supply in several species of vertebrate ectotherms, including postprandial Burmese pythons (Python bivittatus). Recent data suggest postprandial cardiac hypertrophy in P. bivittatus is a facultative rather than obligatory response to digestion, though the triggers of this response are unknown. Here, we hypothesized that an O2 supply-demand mismatch stimulates postprandial cardiac enlargement in Burmese pythons. To test this hypothesis, we rendered animals anemic prior to feeding, essentially halving blood oxygen content during the postprandial period. Fed anemic animals had heart rates 126% higher than those of fasted controls, which, coupled with a 71% increase in mean arterial pressure, suggests fed anemic animals were experiencing significantly elevated cardiac work. We found significant cardiac hypertrophy in fed anemic animals, which exhibited ventricles 39% larger than those of fasted controls and 28% larger than in fed controls. These findings support our hypothesis that those animals with a greater magnitude of O2 supply-demand mismatch exhibit the largest hearts. The 'low O2 signal' stimulating postprandial cardiac hypertrophy is likely mediated by elevated ventricular wall stress associated with postprandial hemodynamics. © 2014. Published by The Company of Biologists Ltd.

  20. Effect of laser treatment on first-intention incisional wound healing in ball pythons (Python regius).

    Science.gov (United States)

    Cole, Grayson L; Lux, Cassie N; Schumacher, Juergen P; Seibert, Rachel L; Sadler, Ryan A; Henderson, Andrea L; Odoi, Agricola; Newkirk, Kim M

    2015-10-01

    To evaluate effects of laser treatment on incisional wound healing in ball pythons (Python regius). 6 healthy adult ball pythons. Snakes were sedated, a skin biopsy specimen was collected for histologic examination, and eight 2-cm skin incisions were made in each snake; each incision was closed with staples (day 0). Gross evaluation of all incision sites was performed daily for 30 days, and a wound score was assigned. Four incisions of each snake were treated (5 J/cm(2) and a wavelength of 980 nm on a continuous wave sequence) by use of a class 4 laser once daily for 7 consecutive days; the other 4 incisions were not treated. Two excisional skin biopsy specimens (1 control and 1 treatment) were collected from each snake on days 2, 7, 14, and 30 and evaluated microscopically. Scores were assigned for total inflammation, degree of fibrosis, and collagen maturity. Generalized linear models were used to investigate the effect of treatment on each variable. Wound scores for laser-treated incisions were significantly better than scores for control incisions on day 2 but not at other time points. There were no significant differences in necrosis, fibroplasia, inflammation, granuloma formation, or bacterial contamination between control and treatment groups. Collagen maturity was significantly better for the laser-treated incisions on day 14. Laser treatment resulted in a significant increase in collagen maturity at day 14 but did not otherwise significantly improve healing of skin incisions.

  1. COSMOS: Python library for massively parallel workflows.

    Science.gov (United States)

    Gafni, Erik; Luquette, Lovelace J; Lancaster, Alex K; Hawkins, Jared B; Jung, Jae-Yoon; Souilmi, Yassine; Wall, Dennis P; Tonellato, Peter J

    2014-10-15

    Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  2. A Python Calculator for Supernova Remnant Evolution

    Science.gov (United States)

    Leahy, D. A.; Williams, J. E.

    2017-05-01

    A freely available Python code for modeling supernova remnant (SNR) evolution has been created. This software is intended for two purposes: to understand SNR evolution and to use in modeling observations of SNR for obtaining good estimates of SNR properties. It includes all phases for the standard path of evolution for spherically symmetric SNRs. In addition, alternate evolutionary models are available, including evolution in a cloudy ISM, the fractional energy-loss model, and evolution in a hot low-density ISM. The graphical interface takes in various parameters and produces outputs such as shock radius and velocity versus time, as well as SNR surface brightness profile and spectrum. Some interesting properties of SNR evolution are demonstrated using the program.

  3. galpy: A python LIBRARY FOR GALACTIC DYNAMICS

    International Nuclear Information System (INIS)

    Bovy, Jo

    2015-01-01

    I describe the design, implementation, and usage of galpy, a python package for galactic-dynamics calculations. At its core, galpy consists of a general framework for representing galactic potentials both in python and in C (for accelerated computations); galpy functions, objects, and methods can generally take arbitrary combinations of these as arguments. Numerical orbit integration is supported with a variety of Runge-Kutta-type and symplectic integrators. For planar orbits, integration of the phase-space volume is also possible. galpy supports the calculation of action-angle coordinates and orbital frequencies for a given phase-space point for general spherical potentials, using state-of-the-art numerical approximations for axisymmetric potentials, and making use of a recent general approximation for any static potential. A number of different distribution functions (DFs) are also included in the current release; currently, these consist of two-dimensional axisymmetric and non-axisymmetric disk DFs, a three-dimensional disk DF, and a DF framework for tidal streams. I provide several examples to illustrate the use of the code. I present a simple model for the Milky Way's gravitational potential consistent with the latest observations. I also numerically calculate the Oort functions for different tracer populations of stars and compare them to a new analytical approximation. Additionally, I characterize the response of a kinematically warm disk to an elliptical m = 2 perturbation in detail. Overall, galpy consists of about 54,000 lines, including 23,000 lines of code in the module, 11,000 lines of test code, and about 20,000 lines of documentation. The test suite covers 99.6% of the code. galpy is available at http://github.com/jobovy/galpy with extensive documentation available at http://galpy.readthedocs.org/en/latest

  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. PNet: A Python Library for Petri Net Modeling and Simulation

    OpenAIRE

    Zhu En Chay; Bing Feng Goh; Maurice HT Ling

    2016-01-01

    Petri Net is a formalism to describe changes between 2 or more states across discrete time and has been used to model many systems. We present PNet – a pure Python library for Petri Net modeling and simulation in Python programming language. The design of PNet focuses on reducing the learning curve needed to define a Petri Net by using a text-based language rather than programming constructs to define transition rules. Complex transition rules can be refined as regular Python functions. To de...

  7. Python as First Textual Programming Language in Secondary Education

    Directory of Open Access Journals (Sweden)

    José Carlos GARCÍA MONSÁLVEZ

    2017-07-01

    Full Text Available With the recent introduction of Programming in the K-12 curricula there is an opportunity to include Computer Science fundamental concepts. This paper presents the origin and evolution of Python as well as their main features that configure it as an ideal programming language. We also review and classify some educational tools in the Python ecosystem. Such tools cover a wide-open spectrum of resources from interactive books to libraries which ease the construction of student elaborated software artefacts. This work presents a multidisciplinary proposal to use the Python programming language in all levels of Secondary Stage.

  8. Implementation of quantum game theory simulations using Python

    Science.gov (United States)

    Madrid S., A.

    2013-05-01

    This paper provides some examples about quantum games simulated in Python's programming language. The quantum games have been developed with the Sympy Python library, which permits solving quantum problems in a symbolic form. The application of these methods of quantum mechanics to game theory gives us more possibility to achieve results not possible before. To illustrate the results of these methods, in particular, there have been simulated the quantum battle of the sexes, the prisoner's dilemma and card games. These solutions are able to exceed the classic bottle neck and obtain optimal quantum strategies. In this form, python demonstrated that is possible to do more advanced and complicated quantum games algorithms.

  9. 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

  10. 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)

  11. 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.

  12. 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...

  13. 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)

  14. 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...

  15. Estimating Dbh of Trees Employing Multiple Linear Regression of the best Lidar-Derived Parameter Combination Automated in Python in a Natural Broadleaf Forest in the Philippines

    Science.gov (United States)

    Ibanez, C. A. G.; Carcellar, B. G., III; Paringit, E. C.; Argamosa, R. J. L.; Faelga, R. A. G.; Posilero, M. A. V.; Zaragosa, G. P.; Dimayacyac, N. A.

    2016-06-01

    Diameter-at-Breast-Height Estimation is a prerequisite in various allometric equations estimating important forestry indices like stem volume, basal area, biomass and carbon stock. LiDAR Technology has a means of directly obtaining different forest parameters, except DBH, from the behavior and characteristics of point cloud unique in different forest classes. Extensive tree inventory was done on a two-hectare established sample plot in Mt. Makiling, Laguna for a natural growth forest. Coordinates, height, and canopy cover were measured and types of species were identified to compare to LiDAR derivatives. Multiple linear regression was used to get LiDAR-derived DBH by integrating field-derived DBH and 27 LiDAR-derived parameters at 20m, 10m, and 5m grid resolutions. To know the best combination of parameters in DBH Estimation, all possible combinations of parameters were generated and automated using python scripts and additional regression related libraries such as Numpy, Scipy, and Scikit learn were used. The combination that yields the highest r-squared or coefficient of determination and lowest AIC (Akaike's Information Criterion) and BIC (Bayesian Information Criterion) was determined to be the best equation. The equation is at its best using 11 parameters at 10mgrid size and at of 0.604 r-squared, 154.04 AIC and 175.08 BIC. Combination of parameters may differ among forest classes for further studies. Additional statistical tests can be supplemented to help determine the correlation among parameters such as Kaiser- Meyer-Olkin (KMO) Coefficient and the Barlett's Test for Spherecity (BTS).

  16. 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.

  17. 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.

  18. 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

  19. LinvPy : a Python package for linear inverse problems

    OpenAIRE

    Beaud, Guillaume François Paul

    2016-01-01

    The goal of this project is to make a Python package including the tau-estimator algorithm to solve linear inverse problems. The package must be distributed, well documented, easy to use and easy to extend for future developers.

  20. Usage of the Python programming language in the CMS experiment

    International Nuclear Information System (INIS)

    Wilkinson, R; Hegner, B; Jones, C D

    2010-01-01

    Being a highly dynamic language and allowing reliable programming with quick turnarounds, Python is a widely used programming language in CMS. Most of the tools used in workflow management and the GRID interface tools are written in this language. Also most of the tools used in the context of release management: integration builds, release building and deploying, as well as performance measurements are in Python. With an interface to the CMS data formats, rapid prototyping of analyses and debugging is an additional use case. Finally in 2008 the CMS experiment switched to using Python as its configuration language. This paper will give an overview of the general usage of Python in the CMS experiment and discuss which features of the language make it well-suited for the existing use cases.

  1. PRACTICAL APPROACH FOR HYPERSPECTRAL IMAGE PROCESSING IN PYTHON

    Directory of Open Access Journals (Sweden)

    L. Annala

    2018-04-01

    Full Text Available Python is a very popular programming language among data scientists around the world. Python can also be used in hyperspectral data analysis. There are some toolboxes designed for spectral imaging, such as Spectral Python and HyperSpy, but there is a need for analysis pipeline, which is easy to use and agile for different solutions. We propose a Python pipeline which is built on packages xarray, Holoviews and scikit-learn. We have developed some of own tools, MaskAccessor, VisualisorAccessor and a spectral index library. They also fulfill our goal of easy and agile data processing. In this paper we will present our processing pipeline and demonstrate it in practice.

  2. Practical Approach for Hyperspectral Image Processing in Python

    Science.gov (United States)

    Annala, L.; Eskelinen, M. A.; Hämäläinen, J.; Riihinen, A.; Pölönen, I.

    2018-04-01

    Python is a very popular programming language among data scientists around the world. Python can also be used in hyperspectral data analysis. There are some toolboxes designed for spectral imaging, such as Spectral Python and HyperSpy, but there is a need for analysis pipeline, which is easy to use and agile for different solutions. We propose a Python pipeline which is built on packages xarray, Holoviews and scikit-learn. We have developed some of own tools, MaskAccessor, VisualisorAccessor and a spectral index library. They also fulfill our goal of easy and agile data processing. In this paper we will present our processing pipeline and demonstrate it in practice.

  3. CVXPY: A Python-Embedded Modeling Language for Convex Optimization

    OpenAIRE

    Diamond, Steven; Boyd, Stephen

    2016-01-01

    CVXPY is a domain-specific language for convex optimization embedded in Python. It allows the user to express convex optimization problems in a natural syntax that follows the math, rather than in the restrictive standard form required by solvers. CVXPY makes it easy to combine convex optimization with high-level features of Python such as parallelism and object-oriented design. CVXPY is available at http://www.cvxpy.org/ under the GPL license, along with documentation and examples.

  4. Proceedings of the 7th Python in Science conference

    OpenAIRE

    Varoquaux , Gaël; Vaught , Travis; Millman , Jarrod

    2008-01-01

    International audience; The SciPy conference provides a unique opportunity to learn and affect what is happening in the realm of scientific computing with Python. Attendees have the opportunity to review the available tools and how they apply to specific problems. By providing a forum for developers to share their Python expertise with the wider commercial, academic, and research communities, this conference fosters collaboration and facilitates the sharing of software components, techniques ...

  5. Proceedings of the 8th Python in Science conference

    OpenAIRE

    Varoquaux , Gaël; Van Der Walt , Stefan; Millman , Jarrod

    2009-01-01

    International audience; The SciPy conference provides a unique opportunity to learn and affect what is happening in the realm of scientific computing with Python. Attendees have the opportunity to review the available tools and how they apply to specific problems. By providing a forum for developers to share their Python expertise with the wider commercial, academic, and research communities, this conference fosters collaboration and facilitates the sharing of software components, techniques ...

  6. Introduction into bi-partite networks in python

    OpenAIRE

    Kasberger, Stefan

    2016-01-01

    This essay and the related computation delivers a comprehensive introduction into the concept of bipartite networks, a class of networks whose nodes are divided into two sets and only the connection between two nodes in different sets is allowed (Easley and Kleinberg, 2010). The analysis and visualization is done in the programming language Python and offers easy to understand first steps in both fields, network analyses and python programming. As data a collaboration network of github users ...

  7. CVXPY: A Python-Embedded Modeling Language for Convex Optimization.

    Science.gov (United States)

    Diamond, Steven; Boyd, Stephen

    2016-04-01

    CVXPY is a domain-specific language for convex optimization embedded in Python. It allows the user to express convex optimization problems in a natural syntax that follows the math, rather than in the restrictive standard form required by solvers. CVXPY makes it easy to combine convex optimization with high-level features of Python such as parallelism and object-oriented design. CVXPY is available at http://www.cvxpy.org/ under the GPL license, along with documentation and examples.

  8. Ecological correlates of invasion impact for Burmese pythons in Florida

    Science.gov (United States)

    Reed, R.N.; Willson, J.D.; Rodda, G.H.; Dorcas, M.E.

    2012-01-01

    An invasive population of Burmese pythons (Python molurus bivittatus) is established across several thousand square kilometers of southern Florida and appears to have caused precipitous population declines among several species of native mammals. Why has this giant snake had such great success as an invasive species when many established reptiles have failed to spread? We scored the Burmese python for each of 15 literature-based attributes relative to predefined comparison groups from a diverse range of taxa and provide a review of the natural history and ecology of Burmese pythons relevant to each attribute. We focused on attributes linked to spread and magnitude of impacts rather than establishment success. Our results suggest that attributes related to body size and generalism appeared to be particularly applicable to the Burmese python's success in Florida. The attributes with the highest scores were: high reproductive potential, low vulnerability to predation, large adult body size, large offspring size and high dietary breadth. However, attributes of ectotherms in general and pythons in particular (including predatory mode, energetic efficiency and social interactions) might have also contributed to invasion success. Although establishment risk assessments are an important initial step in prevention of new establishments, evaluating species in terms of their potential for spreading widely and negatively impacting ecosystems might become part of the means by which resource managers prioritize control efforts in environments with large numbers of introduced species.

  9. PyROOT: Seamless Melting of C++ and Python

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    With ROOT it's possible to use any C++ library from Python without writing any bindings nor dictionaries: loading the library and injecting the relevant headers in the ROOT C++ interpreter is enough to guarantee interactive usage from within Python. Just in time (JIT) compilation of C++ code and immediate utilisation of C++ entities from within Python is also supported. Thanks to the ROOT type system and C++ interpreter and JIT compiler, complete Python/C++ interoperability is achieved. In this contribution we explain how this mechanism is general enough to make any library written in C or C++ usable from within Python and how concepts such as template metaprogramming are mapped in Python. We review the basics of the JIT compilation capabilities provided by the Clang based ROOT interpreter, Cling, and the way in which some of the information of the Abstract Syntax Tree (AST) built by Clang is stored by the ROOT type system. The way in which ROOT manages the automatic loading of libraries and parsing of neces...

  10. Introducing Python tools for magnetotellurics: MTpy

    Science.gov (United States)

    Krieger, L.; Peacock, J.; Inverarity, K.; Thiel, S.; Robertson, K.

    2013-12-01

    Within the framework of geophysical exploration techniques, the magnetotelluric method (MT) is relatively immature: It is still not as widely spread as other geophysical methods like seismology, and its processing schemes and data formats are not thoroughly standardized. As a result, the file handling and processing software within the academic community is mainly based on a loose collection of codes, which are sometimes highly adapted to the respective local specifications. Although tools for the estimation of the frequency dependent MT transfer function, as well as inversion and modelling codes, are available, the standards and software for handling MT data are generally not unified throughout the community. To overcome problems that arise from missing standards, and to simplify the general handling of MT data, we have developed the software package "MTpy", which allows the handling, processing, and imaging of magnetotelluric data sets. It is written in Python and the code is open-source. The setup of this package follows the modular approach of successful software packages like GMT or Obspy. It contains sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides pure Python classes and functions, MTpy provides wrappers and convenience scripts to call external software, e.g. modelling and inversion codes. Even though still under development, MTpy already contains ca. 250 functions that work on raw and preprocessed data. However, as our aim is not to produce a static collection of software, we rather introduce MTpy as a flexible framework, which will be dynamically extended in the future. It then has the potential to help standardise processing procedures and at same time be a versatile supplement for existing algorithms. We introduce the concept and structure of MTpy, and we illustrate the workflow of MT data processing utilising MTpy on an example data set collected over a geothermal exploration site in South

  11. 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/).

  12. Hearing with an atympanic ear: good vibration and poor sound-pressure detection in the royal python, Python regius

    DEFF Research Database (Denmark)

    Christensen, Christian Bech; Christensen-Dalsgaard, Jakob; Brandt, Christian

    2012-01-01

    are sensitive to sound pressure and (2) snakes are sensitive to vibrations, but cannot hear the sound pressure per se. Vibration and sound-pressure sensitivities were quantified by measuring brainstem evoked potentials in 11 royal pythons, Python regius. Vibrograms and audiograms showed greatest sensitivity...... at low frequencies of 80-160 Hz, with sensitivities of -54 dB re. 1 m s(-2) and 78 dB re. 20 μPa, respectively. To investigate whether pythons detect sound pressure or sound-induced head vibrations, we measured the sound-induced head vibrations in three dimensions when snakes were exposed to sound...... pressure at threshold levels. In general, head vibrations induced by threshold-level sound pressure were equal to or greater than those induced by threshold-level vibrations, and therefore sound-pressure sensitivity can be explained by sound-induced head vibration. From this we conclude that pythons...

  13. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes.

    Science.gov (United States)

    Castoe, Todd A; de Koning, Jason A P; Hall, Kathryn T; Yokoyama, Ken D; Gu, Wanjun; Smith, Eric N; Feschotte, Cédric; Uetz, Peter; Ray, David A; Dobry, Jason; Bogden, Robert; Mackessy, Stephen P; Bronikowski, Anne M; Warren, Wesley C; Secor, Stephen M; Pollock, David D

    2011-07-28

    The Consortium for Snake Genomics is in the process of sequencing the genome and creating transcriptomic resources for the Burmese python. Here, we describe how this will be done, what analyses this work will include, and provide a timeline.

  14. Renal plasticity in response to feeding in the Burmese python, Python molurus bivittatus.

    Science.gov (United States)

    Esbaugh, A J; Secor, S M; Grosell, M

    2015-10-01

    Burmese pythons are sit-and-wait predators that are well adapted to go long periods without food, yet subsequently consume and digest single meals that can exceed their body weight. These large feeding events result in a dramatic alkaline tide that is compensated by a hypoventilatory response that normalizes plasma pH; however, little is known regarding how plasma HCO3(-) is lowered in the days post-feeding. The current study demonstrated that Burmese pythons contain the cellular machinery for renal acid-base compensation and actively remodel the kidney to limit HCO3(-) reabsorption in the post-feeding period. After being fed a 25% body weight meal plasma total CO2 was elevated by 1.5-fold after 1 day, but returned to control concentrations by 4 days post-feeding (d pf). Gene expression analysis was used to verify the presence of carbonic anhydrase (CA) II, IV and XIII, Na(+) H(+) exchanger 3 (NHE3), the Na(+) HCO3(-) co-transporter (NBC) and V-type ATPase. CA IV expression was significantly down-regulated at 3 dpf versus fasted controls. This was supported by activity analysis that showed a significant decrease in the amount of GPI-linked CA activity in isolated kidney membranes at 3 dpf versus fasted controls. In addition, V-type ATPase activity was significantly up-regulated at 3 dpf; no change in gene expression was observed. Both CA II and NHE3 expression was up-regulated at 3 dpf, which may be related to post-prandial ion balance. These results suggest that Burmese pythons actively remodel their kidney after feeding, which would in part benefit renal HCO3(-) clearance. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Surgical management of maxillary and premaxillary osteomyelitis in a reticulated python (Python reticulatus).

    Science.gov (United States)

    Latney, La'Toya V; McDermott, Colin; Scott, Gregory; Soltero-Rivera, Maria M; Beguesse, Kyla; Sánchez, Melissa D; Lewis, John R

    2016-05-01

    CASE DESCRIPTION A 1-year-old reticulated python (Python reticulatus) was evaluated because of a 2-week history of wheezing and hissing. CLINICAL FINDINGS Rostral facial cellulitis and deep gingival pockets associated with missing rostral maxillary teeth were evident. Tissues of the nares were swollen, resulting in an audible wheeze during respiration. Multiple scars and superficial facial wounds attributed to biting by live prey were apparent. Radiographic examination revealed bilateral, focal, rostral maxillary osteomyelitis. TREATMENT AND OUTCOME Wound irrigation, antimicrobials, and anti-inflammatory drug treatment resulted in reduced cellulitis. A 3-week regimen that included empirical antimicrobial treatment and improved husbandry resulted in resolution of the respiratory sounds and partial healing of bite wounds, but radiographic evaluation revealed progressive maxillary osteomyelitis. Microbial culture of blood yielded scant gram-positive cocci and Bacillus spp, which were suspected sample contaminants. Bilateral partial maxillectomies were performed; microbial culture and histologic examination of resected bone confirmed osteomyelitis with gram-positive cocci. Treatment with trimethoprim-sulfamethoxazole was initiated on the basis of microbial susceptibility tests. Four months later, follow-up radiography revealed premaxillary osteomyelitis; surgery was declined, and treatment with trimethoprim-sulfamethoxazole was reinstituted. Eight months after surgery, the patient was reevaluated because of recurrent clinical signs; premaxillectomy was performed, and treatment with trimethoprim-sulfamethoxazole was prescribed on the basis of microbial culture of bone and microbial susceptibility testing. Resolution of osteomyelitis was confirmed by CT 11 months after the initial surgery. CONCLUSIONS AND CLINICAL RELEVANCE Focal maxillectomies and premaxillectomy were successfully performed in a large python. Surgical management and appropriate antimicrobial treatment

  16. Morphological respiratory diffusion capacity of the lungs of ball pythons (Python regius).

    Science.gov (United States)

    Starck, J Matthias; Aupperle, Heike; Kiefer, Ingmar; Weimer, Isabel; Krautwald-Junghanns, Maria-Elisabeth; Pees, Michael

    2012-08-01

    This study aims at a functional and morphological characterization of the lung of a boid snake. In particular, we were interested to see if the python's lungs are designed with excess capacity as compared to resting and working oxygen demands. Therefore, the morphological respiratory diffusion capacity of ball pythons (Python regius) was examined following a stereological, hierarchically nested approach. The volume of the respiratory exchange tissue was determined using computed tomography. Tissue compartments were quantified using stereological methods on light microscopic images. The tissue diffusion barrier for oxygen transport was characterized and measured using transmission electron micrographs. We found a significant negative correlation between body mass and the volume of respiratory tissue; the lungs of larger snakes had relatively less respiratory tissue. Therefore, mass-specific respiratory tissue was calculated to exclude effects of body mass. The volume of the lung that contains parenchyma was 11.9±5.0mm(3)g(-1). The volume fraction, i.e., the actual pulmonary exchange tissue per lung parenchyma, was 63.22±7.3%; the total respiratory surface was, on average, 0.214±0.129m(2); it was significantly negatively correlated to body mass, with larger snakes having proportionally smaller respiratory surfaces. For the air-blood barrier, a harmonic mean of 0.78±0.05μm was found, with the epithelial layer representing the thickest part of the barrier. Based on these findings, a median diffusion capacity of the tissue barrier ( [Formula: see text] ) of 0.69±0.38ml O(2)min(-1)mmHg(-1) was calculated. Based on published values for blood oxygen concentration, a total oxygen uptake capacity of 61.16mlO(2)min(-1)kg(-1) can be assumed. This value exceeds the maximum demand for oxygen in ball pythons by a factor of 12. We conclude that healthy individuals of P. regius possess a considerable spare capacity for tissue oxygen exchange. Copyright © 2012 Elsevier Gmb

  17. 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.

  18. Matriarch: A Python Library for Materials Architecture.

    Science.gov (United States)

    Giesa, Tristan; Jagadeesan, Ravi; Spivak, David I; Buehler, Markus J

    2015-10-12

    Biological materials, such as proteins, often have a hierarchical structure ranging from basic building blocks at the nanoscale (e.g., amino acids) to assembled structures at the macroscale (e.g., fibers). Current software for materials engineering allows the user to specify polypeptide chains and simple secondary structures prior to molecular dynamics simulation, but is not flexible in terms of the geometric arrangement of unequilibrated structures. Given some knowledge of a larger-scale structure, instructing the software to create it can be very difficult and time-intensive. To this end, the present paper reports a mathematical language, using category theory, to describe the architecture of a material, i.e., its set of building blocks and instructions for combining them. While this framework applies to any hierarchical material, here we concentrate on proteins. We implement this mathematical language as an open-source Python library called Matriarch. It is a domain-specific language that gives the user the ability to create almost arbitrary structures with arbitrary amino acid sequences and, from them, generate Protein Data Bank (PDB) files. In this way, Matriarch is more powerful than commercial software now available. Matriarch can be used in tandem with molecular dynamics simulations and helps engineers design and modify biologically inspired materials based on their desired functionality. As a case study, we use our software to alter both building blocks and building instructions for tropocollagen, and determine their effect on its structure and mechanical properties.

  19. SunPy: Python for Solar Physics

    Science.gov (United States)

    Bobra, M.; Inglis, A. R.; Mumford, S.; Christe, S.; Freij, N.; Hewett, R.; Ireland, J.; Martinez Oliveros, J. C.; Reardon, K.; Savage, S. L.; Shih, A. Y.; Pérez-Suárez, D.

    2017-12-01

    SunPy is a community-developed open-source software library for solar physics. It is written in Python, a free, cross-platform, general-purpose, high-level programming language which is being increasingly adopted throughout the scientific community. SunPy aims to provide the software for obtaining and analyzing solar and heliospheric data. This poster introduces a new major release, SunPy version 0.8. The first major new feature introduced is Fido, the new primary interface to download data. It provides a consistent and powerful search interface to all major data providers including the VSO and the JSOC, as well as individual data sources such as GOES XRS time series. It is also easy to add new data sources as they become available, i.e. DKIST. The second major new feature is the SunPy coordinate framework. This provides a powerful way of representing coordinates, allowing simple and intuitive conversion between coordinate systems and viewpoints of different instruments (i.e., Solar Orbiter and the Parker Solar Probe), including transformation to astrophysical frames like ICRS. Other new features including new timeseries capabilities with better support for concatenation and metadata, updated documentation and example gallery. SunPy is distributed through pip and conda and all of its code is publicly available (sunpy.org).

  20. 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.

  1. Predicting size limit of wild blood python (python brongersmai stull, 1938) harvesting in north sumatera

    Science.gov (United States)

    Mangantar Pardamean Sianturi, Markus; Jumilawaty, Erni; Delvian; Hartanto, Adrian

    2018-03-01

    Blood python (Python brongersmai Stull, 1938) is one of heavily exploited wildlife in Indonesia. The high demands on its skin trade have made its harvesting regulated under quota-based setting by the government to prevent over-harvesting. To gain understanding on the sustainability of P. brongersmai in the wild, biological characters of wild-caught specimens were studied. Samples were collected from two slaughterhouses from Rantau Prapat and Langkat. Parameters measured were morphological (Snout-vent length (SVL), body mass, abdomen width) and anatomical characters (Fat classes). Total samples of P. brongersmai in this research were 541 with 269 male and 272 female snakes. Female snakes had the highest proportion of individuals with the best quality of abdominal fat reserves (Class 3). Linear models are built and tested for its significance in relation between fat classes as anatomical characters and morphological characters. All tested morphological characters were significant in female snakes. By using linear equation models, we generate size limit to prioritize harvesting in the future. We suggest the use of SVL and stomach width ranging between 139,7 – 141,5 cm and 24,72 – 25,71 cm respectively to achieve sustainability of P. brongersmai in the wild.

  2. The spectacle of the ball python (Python regius): a morphological description.

    Science.gov (United States)

    Da Silva, Mari-Ann O; Heegaard, Steffen; Wang, Tobias; Nyengaard, Jens R; Bertelsen, Mads F

    2014-05-01

    A detailed morphological description of the spectacle of the ball python (Python regius) is provided. The eyes of 21 snakes were examined by light microscopy and/or transmission electron microscopy. Additionally, eyes of nine live snakes were examined using optical coherence tomography (OCT) and Scheimpflug scanning (Pentacam). The spectacle consists of three layers: outer epithelium, stroma and inner epithelium. The outer epithelium is made up of flat basal cells overlaid by keratin, the stroma consists of organized layers of collagen fibrils with interweaving nerve fibers and blood vessels, and the inner epithelium holds squamous cells containing vesicles and microvilli. At the rim of the spectacle, there is a transition zone, where the spectacle merges with the epidermis and dermis of the periocular scales. This zone is characterized by a greater height of the basal cells of the outer epithelium and a less orderly organization of the stroma compared with the spectacle proper. The thickness of the spectacle was uniform throughout. It averaged 96 ± 10 µm in histological specimens and 108 ± 13 µm using OCT. The subspectacular space was extremely narrow in the live snakes; however, the space was visible at the periphery of the spectacle with OCT. Copyright © 2013 Wiley Periodicals, Inc.

  3. Python-Assisted MODFLOW Application and Code Development

    Science.gov (United States)

    Langevin, C.

    2013-12-01

    The U.S. Geological Survey (USGS) has a long history of developing and maintaining free, open-source software for hydrological investigations. The MODFLOW program is one of the most popular hydrologic simulation programs released by the USGS, and it is considered to be the most widely used groundwater flow simulation code. MODFLOW was written using a modular design and a procedural FORTRAN style, which resulted in code that could be understood, modified, and enhanced by many hydrologists. The code is fast, and because it uses standard FORTRAN it can be run on most operating systems. Most MODFLOW users rely on proprietary graphical user interfaces for constructing models and viewing model results. Some recent efforts, however, have focused on construction of MODFLOW models using open-source Python scripts. Customizable Python packages, such as FloPy (https://code.google.com/p/flopy), can be used to generate input files, read simulation results, and visualize results in two and three dimensions. Automating this sequence of steps leads to models that can be reproduced directly from original data and rediscretized in space and time. Python is also being used in the development and testing of new MODFLOW functionality. New packages and numerical formulations can be quickly prototyped and tested first with Python programs before implementation in MODFLOW. This is made possible by the flexible object-oriented design capabilities available in Python, the ability to call FORTRAN code from Python, and the ease with which linear systems of equations can be solved using SciPy, for example. Once new features are added to MODFLOW, Python can then be used to automate comprehensive regression testing and ensure reliability and accuracy of new versions prior to release.

  4. 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.

  5. 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

  6. 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.

  7. ETE: a python Environment for Tree Exploration.

    Science.gov (United States)

    Huerta-Cepas, Jaime; Dopazo, Joaquín; Gabaldón, Toni

    2010-01-13

    Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.

  8. ETE: a python Environment for Tree Exploration

    Directory of Open Access Journals (Sweden)

    Gabaldón Toni

    2010-01-01

    Full Text Available Abstract Background Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Results Here we present the Environment for Tree Exploration (ETE, a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. Conclusions ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.

  9. pyam: Python Implementation of YaM

    Science.gov (United States)

    Myint, Steven; Jain, Abhinandan

    2012-01-01

    pyam is a software development framework with tools for facilitating the rapid development of software in a concurrent software development environment. pyam provides solutions for development challenges associated with software reuse, managing multiple software configurations, developing software product lines, and multiple platform development and build management. pyam uses release-early, release-often development cycles to allow developers to integrate their changes incrementally into the system on a continual basis. It facilitates the creation and merging of branches to support the isolated development of immature software to avoid impacting the stability of the development effort. It uses modules and packages to organize and share software across multiple software products, and uses the concepts of link and work modules to reduce sandbox setup times even when the code-base is large. One sidebenefit is the enforcement of a strong module-level encapsulation of a module s functionality and interface. This increases design transparency, system stability, and software reuse. pyam is written in Python and is organized as a set of utilities on top of the open source SVN software version control package. All development software is organized into a collection of modules. pyam packages are defined as sub-collections of the available modules. Developers can set up private sandboxes for module/package development. All module/package development takes place on private SVN branches. High-level pyam commands support the setup, update, and release of modules and packages. Released and pre-built versions of modules are available to developers. Developers can tailor the source/link module mix for their sandboxes so that new sandboxes (even large ones) can be built up easily and quickly by pointing to pre-existing module releases. All inter-module interfaces are publicly exported via links. A minimal, but uniform, convention is used for building modules.

  10. 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

  11. 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.

  12. 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

  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. 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.)

  15. 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.

  16. 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.

  17. Querying and Serving N-gram Language Models with Python

    Directory of Open Access Journals (Sweden)

    2009-06-01

    Full Text Available Statistical n-gram language modeling is a very important technique in Natural Language Processing (NLP and Computational Linguistics used to assess the fluency of an utterance in any given language. It is widely employed in several important NLP applications such as Machine Translation and Automatic Speech Recognition. However, the most commonly used toolkit (SRILM to build such language models on a large scale is written entirely in C++ which presents a challenge to an NLP developer or researcher whose primary language of choice is Python. This article first provides a gentle introduction to statistical language modeling. It then describes how to build a native and efficient Python interface (using SWIG to the SRILM toolkit such that language models can be queried and used directly in Python code. Finally, it also demonstrates an effective use case of this interface by showing how to leverage it to build a Python language model server. Such a server can prove to be extremely useful when the language model needs to be queried by multiple clients over a network: the language model must only be loaded into memory once by the server and can then satisfy multiple requests. This article includes only those listings of source code that are most salient. To conserve space, some are only presented in excerpted form. The complete set of full source code listings may be found in Volume 1 of The Python Papers Source Codes Journal.

  18. Cosmic Microwave Background Anisotropy Measurement from Python V

    Science.gov (United States)

    Coble, K.; Dodelson, S.; Dragovan, M.; Ganga, K.; Knox, L.; Kovac, J.; Ratra, B.; Souradeep, T.

    2003-02-01

    We analyze observations of the microwave sky made with the Python experiment in its fifth year of operation at the Amundsen-Scott South Pole Station in Antarctica. After modeling the noise and constructing a map, we extract the cosmic signal from the data. We simultaneously estimate the angular power spectrum in eight bands ranging from large (l~40) to small (l~260) angular scales, with power detected in the first six bands. There is a significant rise in the power spectrum from large to smaller (l~200) scales, consistent with that expected from acoustic oscillations in the early universe. We compare this Python V map to a map made from data taken in the third year of Python. Python III observations were made at a frequency of 90 GHz and covered a subset of the region of the sky covered by Python V observations, which were made at 40 GHz. Good agreement is obtained both visually (with a filtered version of the map) and via a likelihood ratio test.

  19. Scripting MODFLOW model development using Python and FloPy

    Science.gov (United States)

    Bakker, Mark; Post, Vincent E. A.; Langevin, Christian D.; Hughes, Joseph D.; White, Jeremy; Starn, Jeffrey; Fienen, Michael N.

    2016-01-01

    Graphical user interfaces (GUIs) are commonly used to construct and postprocess numerical groundwater flow and transport models. Scripting model development with the programming language Python is presented here as an alternative approach. One advantage of Python is that there are many packages available to facilitate the model development process, including packages for plotting, array manipulation, optimization, and data analysis. For MODFLOW-based models, the FloPy package was developed by the authors to construct model input files, run the model, and read and plot simulation results. Use of Python with the available scientific packages and FloPy facilitates data exploration, alternative model evaluations, and model analyses that can be difficult to perform with GUIs. Furthermore, Python scripts are a complete, transparent, and repeatable record of the modeling process. The approach is introduced with a simple FloPy example to create and postprocess a MODFLOW model. A more complicated capture-fraction analysis with a real-world model is presented to demonstrate the types of analyses that can be performed using Python and FloPy.

  20. The effects of UV light on calcium metabolism in ball pythons (Python regius).

    Science.gov (United States)

    Hedley, J; Eatwell, K

    2013-10-12

    Despite the popularity of keeping snakes in captivity, there has been limited investigation into the effects of UV radiation on vitamin D levels in snakes. The aim of this study was to investigate the effects of UV-b radiation on plasma 25-hydroxyvitamin D3 levels and ionised calcium concentrations in ball pythons (Python regius). Blood samples were taken from 14 ball pythons, which had never been exposed to UV-b light, to obtain baseline 25-hydroxyvitamin D3 levels and ionised calcium concentrations. Blood samples were then taken again from the same snakes 70 days later after one group (Group 1, n=6 females) were exposed to UV-b radiation daily, and the other group (Group 2, n=5 males and 3 females) were exposed to no UV-b radiation. Mean±sd 25-hydroxyvitamin D3 levels on day 0 in Group 1 were 197±35 nmol/l, and on day 70 were 203.5±13.8 nmol/l. Mean±sd 25-hydroxyvitamin D3 levels in Group 2 on day 0 were 77.7±41.5 nmol/l, and on day 70 were 83.0±41.9 nmol/l. Mean±sd ionised calcium levels at day 0 were 1.84±0.05 mmol/l for Group 1, and on day 70 were 1.78±0.07 mmol/l. Mean±sd ionised calcium levels at day 0 were 1.79±0.07 mmol/l for Group 2, and on day 70 were 1.81±0.05 mmol/l. No association was demonstrated between exposure to UV-b radiation and plasma 25-hydroxyvitamin D3 and ionised calcium concentrations. These results may provide baseline parameters for future studies in this and other snake species to determine ability to utilise UV-b light for vitamin D production.

  1. Leveraging Comparative Genomics to Identify and Functionally Characterize Genes Associated with Sperm Phenotypes in Python bivittatus (Burmese Python

    Directory of Open Access Journals (Sweden)

    Kristopher J. L. Irizarry

    2016-01-01

    Full Text Available Comparative genomics approaches provide a means of leveraging functional genomics information from a highly annotated model organism’s genome (such as the mouse genome in order to make physiological inferences about the role of genes and proteins in a less characterized organism’s genome (such as the Burmese python. We employed a comparative genomics approach to produce the functional annotation of Python bivittatus genes encoding proteins associated with sperm phenotypes. We identify 129 gene-phenotype relationships in the python which are implicated in 10 specific sperm phenotypes. Results obtained through our systematic analysis identified subsets of python genes exhibiting associations with gene ontology annotation terms. Functional annotation data was represented in a semantic scatter plot. Together, these newly annotated Python bivittatus genome resources provide a high resolution framework from which the biology relating to reptile spermatogenesis, fertility, and reproduction can be further investigated. Applications of our research include (1 production of genetic diagnostics for assessing fertility in domestic and wild reptiles; (2 enhanced assisted reproduction technology for endangered and captive reptiles; and (3 novel molecular targets for biotechnology-based approaches aimed at reducing fertility and reproduction of invasive reptiles. Additional enhancements to reptile genomic resources will further enhance their value.

  2. Clinical and histologic effects of intracardiac administration of propofol for induction of anesthesia in ball pythons (Python regius).

    Science.gov (United States)

    McFadden, Michael S; Bennett, R Avery; Reavill, Drury R; Ragetly, Guillaume R; Clark-Price, Stuart C

    2011-09-15

    To assess the clinical differences between induction of anesthesia in ball pythons with intracardiac administration of propofol and induction with isoflurane in oxygen and to assess the histologic findings over time in hearts following intracardiac administration of propofol. Prospective randomized study. 30 hatchling ball pythons (Python regius). Anesthesia was induced with intracardiac administration of propofol (10 mg/kg [4.5 mg/lb]) in 18 ball pythons and with 5% isoflurane in oxygen in 12 ball pythons. Induction time, time of anesthesia, and recovery time were recorded. Hearts from snakes receiving intracardiac administration of propofol were evaluated histologically 3, 7, 14, 30, and 60 days following propofol administration. Induction time with intracardiac administration of propofol was significantly shorter than induction time with 5% isoflurane in oxygen. No significant differences were found in total anesthesia time. Recovery following intracardiac administration of propofol was significantly longer than recovery following induction of anesthesia with isoflurane in oxygen. Heart tissue evaluated histologically at 3, 7, and 14 days following intracardiac administration of propofol had mild inflammatory changes, and no histopathologic lesions were seen 30 and 60 days following propofol administration. Intracardiac injection of propofol in snakes is safe and provides a rapid induction of anesthesia but leads to prolonged recovery, compared with that following induction with isoflurane. Histopathologic lesions in heart tissues following intracardiac injection of propofol were mild and resolved after 14 days.

  3. Development of a technique for contrast radiographic examination of the gastrointestinal tract in ball pythons (Python regius).

    Science.gov (United States)

    Banzato, Tommaso; Russo, Elisa; Finotti, Luca; Zotti, Alessandro

    2012-07-01

    To develop a technique for radiographic evaluation of the gastrointestinal tract in ball pythons (Python regius). 10 ball python cadavers (5 males and 5 females) and 18 healthy adult ball pythons (10 males and 8 females). Live snakes were allocated to 3 groups (A, B, and C). A dose (25 mL/kg) of barium sulfate suspension at 3 concentrations (25%, 35%, and 45% [wt/vol]) was administered through an esophageal probe to snakes in groups A, B, and C, respectively. Each evaluation ended when all the contrast medium had reached the large intestine. Transit times through the esophagus, stomach, and small intestine were recorded. Imaging quality was evaluated by 3 investigators who assigned a grading score on the basis of predetermined criteria. Statistical analysis was conducted to evaluate differences in quality among the study groups. The esophagus and stomach had a consistent distribution pattern of contrast medium, whereas 3 distribution patterns of contrast medium were identified in the small intestine, regardless of barium concentration. Significant differences in imaging quality were detected among the 3 groups. Radiographic procedures were tolerated well by all snakes. The 35% concentration of contrast medium yielded the best imaging quality. Use of contrast medium for evaluation of the cranial portion of the gastrointestinal tract could be a reliable technique for the diagnosis of gastrointestinal diseases in ball pythons. However, results of this study may not translate to other snake species because of variables identified in this group of snakes.

  4. Pharmacokinetics of a long-acting ceftiofur formulation (ceftiofur crystalline free acid) in the ball python (Python regius).

    Science.gov (United States)

    Adkesson, Michael J; Fernandez-Varon, Emilio; Cox, Sherry; Martín-Jiménez, Tomás

    2011-09-01

    The objective of this study was to determine the pharmacokinetics of a long-acting formulation of ceftiofur crystalline-free acid (CCFA) following intramuscular injection in ball pythons (Python regius). Six adult ball pythons received an injection of CCFA (15 mg/kg) in the epaxial muscles. Blood samples were collected by cardiocentesis immediately prior to and at 0.5, 1, 2, 4, 8, 12, 18, 24, 48, 72, 96, 144, 192, 240, 288, 384, 480, 576, 720, and 864 hr after CCFA administration. Plasma ceftiofur concentrations were determined by high-performance liquid chromatography. A noncompartmental pharmacokinetic analysis was applied to the data. Maximum plasma concentration (Cmax) was 7.096 +/- 1.95 microg/ml and occurred at (Tmax) 2.17 +/- 0.98 hr. The area under the curve (0 to infinity) for ceftiofur was 74.59 +/- 13.05 microg x h/ml and the elimination half-life associated with the terminal slope of the concentration-time curve was 64.31 +/- 14.2 hr. Mean residence time (0 to infinity) was 46.85 +/- 13.53 hr. CCFA at 15 mg/kg was well tolerated in all the pythons. Minimum inhibitory concentration (MIC) data for bacterial isolates from snakes are not well established. For MIC values of python. For MICs > or =0.5 microg/ml, more frequent dosing or a higher dosage may be required.

  5. PyCSP - Communicating Sequential Processes for Python

    DEFF Research Database (Denmark)

    Vinter, Brian; Bjørndalen, John Markus; Anshus, Otto Johan

    CSP presently supports the core CSP abstractions. We introduce the PyCSP library, its implementation, a few performance benchmarks, and show example code using PyCSP. An early prototype of PyCSP has been used in this year's Extreme Multiprogramming Class at the CS department, university of Copenhagen......The Python programming language is effective for rapidly specifying programs and experimenting with them. It is increasingly being used in computational sciences, and in teaching computer science. CSP is effective for describing concurrency. It has become especially relevant with the emergence...... of commodity multi-core architectures. We are interested in exploring how a combination of Python and CSP can benefit both the computational sciences and the hands-on teaching of distributed and parallel computing in computer science. To make this possible, we have developed PyCSP, a CSP library for Python. Py...

  6. Tongue worm (Pentastomida) infection in ball pythons (Python regius) – a case report

    Science.gov (United States)

    Gałęcki, Remigiusz; Sokół, Rajmund; Dudek, Agnieszka

    Tongue worms (Pentastomida) are endoparasites causing pentastomiasis, an invasive disease representing a threat to exotic animals and humans. Animals acquire infection via the alimentary tract. In reptiles, the parasite is present in the lungs, resulting in symptoms from the respiratory system. Pentastomiasis may be asymptomatic, but nonspecific symptoms may occur at high parasite concentrations. Due to the harmful effects of many antiparasitic substances, tongue worm invasion in reptiles remains not fully treatable. Although pentasomiasis is rarely diagnosed in Poland, pentastomids were diagnosed in two ball pythons, who were patients of the “Poliklinika Weterynaryjna” veterinary clinic. They demonstrated problems with the respiratory system and a significant deterioration of health. Fenbendazole at a dose of 100 mg/kg b.w., repeated after 7 days was shown to be effective.

  7. The influence of mechanical ventilation on physiological parameters in ball pythons (Python regius).

    Science.gov (United States)

    Jakobsen, Sashia L; Williams, Catherine J A; Wang, Tobias; Bertelsen, Mads F

    2017-05-01

    Mechanical ventilation is widely recommended for reptiles during anesthesia, and while it is well-known that their low ectothermic metabolism requires much lower ventilation than in mammals, very little is known about the influence of ventilation protocol on the recovery from anesthesia. Here, 15 ball pythons (Python regius) were induced and maintained with isoflurane for 60min at one of three ventilation protocols (30, 125, or 250mlmin -1 kg -1 body mass) while an arterial catheter was inserted, and ventilation was then continued on 100% oxygen at the specified rate until voluntary extubation. Mean arterial blood pressure and heart rate (HR) were measured, and arterial blood samples collected at 60, 80, 180min and 12 and 24h after intubation. In all three groups, there was evidence of a metabolic acidosis, and snakes maintained at 30mlmin -1 kg -1 experienced an additional respiratory acidosis, while the two other ventilation protocols resulted in normal or low arterial PCO 2 . In general, normal acid-base status was restored within 12h in all three protocols. HR increased by 143±64% during anesthesia with high mechanical ventilation (250mlmin -1 kg -1 ) in comparison with recovered values. Recovery times after mechanical ventilation at 30, 125, or 250mlmin -1 kg -1 were 289±70, 126±16, and 68±7min, respectively. Mild overventilation may result in a faster recovery, and the associated lowering of arterial PCO 2 normalised arterial pH in the face of metabolic acidosis. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Spectral domain optical coherence tomography imaging of spectacular ecdysis in the royal python (Python regius).

    Science.gov (United States)

    Tusler, Charlotte A; Maggs, David J; Kass, Philip H; Paul-Murphy, Joanne R; Schwab, Ivan R; Murphy, Christopher J

    2015-01-01

    To describe using spectral domain optical coherence tomography (SD-OCT), digital slit-lamp biomicroscopy, and external photography, changes in the ophidian cuticle, spectacle, and cornea during ecdysis. Four normal royal pythons (Python regius). Snakes were assessed once daily throughout a complete shed cycle using nasal, axial, and temporal SD-OCT images, digital slit-lamp biomicroscopy, and external photography. Spectral domain optical coherence tomography (SD-OCT) images reliably showed the spectacular cuticle and stroma, subcuticular space (SCS), cornea, anterior chamber, iris, and Schlemm's canal. When visible, the subspectacular space (SSS) was more distended peripherally than axially. Ocular surface changes throughout ecdysis were relatively conserved among snakes at all three regions imaged. From baseline (7 days following completion of a full cycle), the spectacle gradually thickened before separating into superficial cuticular and deep, hyper-reflective stromal components, thereby creating the SCS. During spectacular separation, the stroma regained original reflectivity, and multiple hyper-reflective foci (likely fragments from the cuticular-stromal interface) were noted within the SCS. The cornea was relatively unchanged in character or thickness throughout all stages of ecdysis. Slit-lamp images did not permit observation of these changes. Spectral domain optical coherence tomography (SD-OCT) provided excellent high-resolution images of the snake anterior segment, and especially the cuticle, spectacle, and cornea of manually restrained normal snakes at all stages of ecdysis and warrants investigation in snakes with anterior segment disease. The peripheral spectacle may be the preferred entry point for diagnostic or therapeutic injections into the SSS and for initiating spectacular surgery. © 2014 American College of Veterinary Ophthalmologists.

  9. 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.

  10. 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.

  11. 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...

  12. 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.

  13. 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)

  14. 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...

  15. 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...

  16. A spent fuel assemblies monitoring device by nondestructive analysis 'PYTHON'

    International Nuclear Information System (INIS)

    Saad, M.; Broeskamp, M.; Hahn, H.; Bignan, G.; Boisset, M.; Silie, P.

    1995-01-01

    The monitoring of spent fuel assemblies (16 x 16 UOX) in KWG-reactor pool with the use of non-destructive methods (total Gamma and neutron counting) allow the control of average burn-up and the extremity burn-up. The measurements allow a safety-criticality control before loading the fuel assemblies into the transport casks. A device called PYTHON has been tested and qualified in France. This paper presents a description of the industrial PYTHON device and the results of the measurements. (orig.)

  17. Python 3 text processing with NLTK 3 cookbook

    CERN Document Server

    Perkins, Jacob

    2014-01-01

    This book is intended for Python programmers interested in learning how to do natural language processing. Maybe you've learned the limits of regular expressions the hard way, or you've realized that human language cannot be deterministically parsed like a computer language. Perhaps you have more text than you know what to do with, and need automated ways to analyze and structure that text. This Cookbook will show you how to train and use statistical language models to process text in ways that are practically impossible with standard programming tools. A basic knowledge of Python and the basi

  18. Solving PDEs in Python the FEniCS tutorial I

    CERN Document Server

    Langtangen, Hans Petter

    2016-01-01

    This book offers a concise and gentle introduction to finite element programming in Python based on the popular FEniCS software library. Using a series of examples, including the Poisson equation, the equations of linear elasticity, the incompressible Navier–Stokes equations, and systems of nonlinear advection–diffusion–reaction equations, it guides readers through the essential steps to quickly solving a PDE in FEniCS, such as how to define a finite variational problem, how to set boundary conditions, how to solve linear and nonlinear systems, and how to visualize solutions and structure finite element Python programs. This book is open access under a CC BY license.

  19. Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius).

    Science.gov (United States)

    Uccellini, Lorenzo; Ossiboff, Robert J; de Matos, Ricardo E C; Morrisey, James K; Petrosov, Alexandra; Navarrete-Macias, Isamara; Jain, Komal; Hicks, Allison L; Buckles, Elizabeth L; Tokarz, Rafal; McAloose, Denise; Lipkin, Walter Ian

    2014-08-08

    Respiratory infections are important causes of morbidity and mortality in reptiles; however, the causative agents are only infrequently identified. Pneumonia, tracheitis and esophagitis were reported in a collection of ball pythons (Python regius). Eight of 12 snakes had evidence of bacterial pneumonia. High-throughput sequencing of total extracted nucleic acids from lung, esophagus and spleen revealed a novel nidovirus. PCR indicated the presence of viral RNA in lung, trachea, esophagus, liver, and spleen. In situ hybridization confirmed the presence of intracellular, intracytoplasmic viral nucleic acids in the lungs of infected snakes. Phylogenetic analysis based on a 1,136 amino acid segment of the polyprotein suggests that this virus may represent a new species in the subfamily Torovirinae. This report of a novel nidovirus in ball pythons may provide insight into the pathogenesis of respiratory disease in this species and enhances our knowledge of the diversity of nidoviruses.

  20. Record length, mass, and clutch size in the nonindigenous Burmese Python, Python bivittatus Kuhl 1820 (Squamata: Pythonidae), in Florida

    Science.gov (United States)

    Krysko, Kenneth L.; Hart, Kristen M.; Smith, Brian J.; Selby, Thomas H.; Cherkiss, Michael S.; Coutu, Nicholas T.; Reichart, Rebecca M.; Nuñez, Leroy P.; Mazzotti, Frank J.; Snow, Ray W.

    2012-01-01

    The Burmese Python, Python bivittatus Kuhl 1820 (Squamata: Pythonidae), is indigenous to northern India,east to southern China, and south to Vietnam and a few islands in Indonesia (Barker and Barker 2008, Reed and Rodda 2009). This species has been introduced since at least 1979 in southern Florida, USA, where it likely began reproducing and became established during the 1980s (Meshaka et al. 2000, Snowet al. 2007b,Kraus 2009, Krysko et al. 2011, Willson et al. 2011). Python bivittatus has been documented in Florida consuming a variety of mammals and birds, and the American Alligator(Alligator mississippiensis) (Snowet al. 2007a, 2007b; Harvey et al. 2008; Rochford et al. 2010b; Holbrook and Chesnes 2011), many of which are protected species. Herein, we provide details on two of the largest known wild P. bivittatus in Florida to date, including current records on length,mass,clutch size, and diet.

  1. 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)

  2. Photodermatitis and photokeratoconjunctivitis in a ball python (Python regius) and a blue-tongue skink (Tiliqua spp.).

    Science.gov (United States)

    Gardiner, David W; Baines, Frances M; Pandher, Karamjeet

    2009-12-01

    A male ball python (Python regius) and a female blue tongue skink (Tiliqua spp.) of unknown age were evaluated for anorexia, lethargy, excessive shedding, corneal opacity (python), and weight loss (skink) of approximately three weeks' duration. These animals represented the worst affected animals from a private herpetarium where many animals exhibited similar signs. At necropsy, the python had bilateral corneal opacity and scattered moderate dysecdysis. The skink had mild dysecdysis, poor body condition, moderate intestinal nematodiasis, and mild liver atrophy. Microscopic evaluation revealed epidermal erosion and ulceration, with severe epidermal basal cell degeneration and necrosis, and superficial dermatitis (python and skink). Severe bilateral ulcerative keratoconjunctivitis with bacterial colonization was noted in the ball python. Microscopic findings within the skin and eyes were suggestive of ultraviolet (UV) radiation damage or of photodermatitis and photokeratoconjunctivitis. Removal of the recently installed new lamps from the terrariums of the surviving reptiles resulted in resolution of clinical signs. Evaluation of a sample lamp of the type associated with these cases revealed an extremely high UV output, including very-short-wavelength UVB, neither found in natural sunlight nor emitted by several other UVB lamps unassociated with photokeratoconjunctivitis. Exposure to high-intensity and/or inappropriate wavelengths of UV radiation may be associated with significant morbidity, and even mortality, in reptiles. Veterinarians who are presented with reptiles with ocular and/or cutaneous disease of unapparent cause should fully evaluate the specifics of the vivarium light sources. Further research is needed to determine the characteristics of appropriate and of toxic UV light for reptiles kept in captivity.

  3. 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.

  4. Double valvular insufficiency in a Burmese python (Python molurus bivittatus, Linnaeus, 1758) suffering from concomitant bacterial pneumonia.

    Science.gov (United States)

    Schilliger, Lionel; Tréhiou-Sechi, Emilie; Petit, Amandine M P; Misbach, Charlotte; Chetboul, Valérie

    2010-12-01

    Ultrasonography, and, to a lesser extent, echocardiography are now well-established, noninvasive, and painless diagnostic tools in herpetologic medicine. Various cardiac lesions have been previously described in reptiles, but valvulopathy is rarely documented in these animals and, consequently, is poorly understood. In this report, sinoatrial and atrioventricular insufficiencies were diagnosed in a 5-yr-old captive dyspneic Burmese python (Python molurus bivittatus) on the basis of echocardiographic and Doppler examination. This case report is the first to document Doppler assessment of valvular regurgitations in a reptile.

  5. Status of parallel Python-based implementation of UEDGE

    Science.gov (United States)

    Umansky, M. V.; Pankin, A. Y.; Rognlien, T. D.; Dimits, A. M.; Friedman, A.; Joseph, I.

    2017-10-01

    The tokamak edge transport code UEDGE has long used the code-development and run-time framework Basis. However, with the support for Basis expected to terminate in the coming years, and with the advent of the modern numerical language Python, it has become desirable to move UEDGE to Python, to ensure its long-term viability. Our new Python-based UEDGE implementation takes advantage of the portable build system developed for FACETS. The new implementation gives access to Python's graphical libraries and numerical packages for pre- and post-processing, and support of HDF5 simplifies exchanging data. The older serial version of UEDGE has used for time-stepping the Newton-Krylov solver NKSOL. The renovated implementation uses backward Euler discretization with nonlinear solvers from PETSc, which has the promise to significantly improve the UEDGE parallel performance. We will report on assessment of some of the extended UEDGE capabilities emerging in the new implementation, and will discuss the future directions. Work performed for U.S. DOE by LLNL under contract DE-AC52-07NA27344.

  6. Fixing the Sorting Algorithm for Android, Java and Python

    NARCIS (Netherlands)

    C.P.T. de Gouw (Stijn); F.S. de Boer (Frank)

    2015-01-01

    htmlabstractTim Peters developed the Timsort hybrid sorting algorithm in 2002. TimSort was first developed for Python, a popular programming language, but later ported to Java (where it appears as java.util.Collections.sort and java.util.Arrays.sort). TimSort is today used as the default sorting

  7. p3d--Python module for structural bioinformatics.

    Science.gov (United States)

    Fufezan, Christian; Specht, Michael

    2009-08-21

    High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

  8. p3d – Python module for structural bioinformatics

    Directory of Open Access Journals (Sweden)

    Fufezan Christian

    2009-08-01

    Full Text Available Abstract Background High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. Results p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files. p3d's strength arises from the combination of a very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP tree, b set theory and c functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. Conclusion p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

  9. Building and documenting workflows with python-based snakemake

    NARCIS (Netherlands)

    J. Köster (Johannes); S. Rahmann (Sven)

    2012-01-01

    textabstractSnakemake is a novel workflow engine with a simple Python-derived workflow definition language and an optimizing execution environment. It is the first system that supports multiple named wildcards (or variables) in input and output filenames of each rule definition. It also allows to

  10. Duplicating MC-15 Output with Python and MCNP

    Energy Technology Data Exchange (ETDEWEB)

    McSpaden, Alexander Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-08-23

    Two Python scripts have been written that process the output files of MCNP6 into a format that mimics the list-mode output of Los Alamos National Laboratory’s MC-15 and NPOD neutron detection systems. This report details the methods implemented in these scripts and instructions on their use.

  11. Cosmic tragedy in Steve Chimombo's The Python | Molande ...

    African Journals Online (AJOL)

    Cosmic tragedy in Steve Chimombo's The Python. Bright Molande. Abstract. No Abstract. Full Text: EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT · AJOL African Journals Online. HOW TO USE AJOL... for Researchers · for Librarians · for Authors · FAQ's · More about ...

  12. Maybe it's not Python that sucks, maybe it's my code

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    Did you know that in Python integers from -5 to 257 are preallocated? Reusing them 1000 times, instead of allocating memory for a bigger integer, saves a whopping 1 millisecond of code's execution time! Isn't that thrilling? Well, before you get that crazy, learn some basic performance tricks that you can start using today.

  13. Write Python instead of SQL - an introduction to SQLAlchemy.

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    SQLAlchemy is the most popular ORM and SQL abstraction layer for Python and used by multiple big projects at CERN such as Indico or Invenio. In my talk I'm going to give a short introduction on how to use it.

  14. Cost versus Precision for Approximate Typing for Python

    NARCIS (Netherlands)

    Fritz, Levin; Hage, J

    2014-01-01

    In this paper we describe a variation of monotone frameworks that enables us to perform approximate typing of Python, in particular for dealing with some of its more dynamic features such as first-class functions and Python’s dynamic class system. We additionally introduce a substantial number of

  15. The ageing body in Monty Python Live (Mostly)

    DEFF Research Database (Denmark)

    Petersen, Line Nybro

    2018-01-01

    This article analyses representations of the ageing body in the live televised show Monty Python Live (Mostly) (2014). The famous satire group performed in the O2 arena in London, and the show was telecast live in cinemas and aired on television across the world. In the show, the group members, now...

  16. Python for Scientific Computing Education: Modeling of Queueing Systems

    Directory of Open Access Journals (Sweden)

    Vladimiras Dolgopolovas

    2014-01-01

    Full Text Available In this paper, we present the methodology for the introduction to scientific computing based on model-centered learning. We propose multiphase queueing systems as a basis for learning objects. We use Python and parallel programming for implementing the models and present the computer code and results of stochastic simulations.

  17. Implementing a Multi-Agent System in Python

    DEFF Research Database (Denmark)

    Ettienne, Mikko Berggren; Vester, Steen; Villadsen, Jørgen

    2012-01-01

    We describe the solution used by the Python-DTU team in the Multi-Agent Programming Contest 2011, where the scenario was called Agents on Mars. We present our auction-based agreement, area controlling and pathfinding algorithms and discuss our chosen strategy and our choice of technology used...

  18. Aura: A Multi-Featured Programming Framework in Python

    Directory of Open Access Journals (Sweden)

    2010-09-01

    Full Text Available This paper puts forward the design, programming and application of innovative educational software, ‘Aura’ made using Python and PyQt Python bindings. The research paper presents a new concept of using a single tool to relate between syntaxes of various programming languages and algorithms. It radically increases their understanding and retaining capacity, since they can correlate between many programming languages. The software is a totally unorthodox attempt towards helping students who have their first tryst with programming languages. The application is designed to help students understand how algorithms work and thus, help them in learning multiple programming languages on a single platform using an interactive graphical user interface. This paper elucidates how using Python and PyQt bindings, a comprehensive feature rich application, that implements an interactive algorithm building technique, a web browser, multiple programming language framework, a code generator and a real time code sharing hub be embedded into a single interface. And also explains, that using Python as building tool, it requires much less coding than conventional feature rich applications coded in other programming languages, and at the same time does not compromise on stability, inter-operability and robustness of the application.

  19. Python Source Code Plagiarism Attacks on Introductory Programming Course Assignments

    Science.gov (United States)

    Karnalim, Oscar

    2017-01-01

    This paper empirically enlists Python plagiarism attacks that have been found on Introductory Programming course assignments for undergraduate students. According to our observation toward 400 plagiarism-suspected cases, there are 35 plagiarism attacks that have been conducted by students. It starts with comment & whitespace modification as…

  20. Teaching CS1 with Python GUI Game Programming

    Science.gov (United States)

    Wang, Hong

    2010-06-01

    Python is becoming a popular programming language in teaching freshman programming courses. The author designed a sequence of game programming labs using Pygame to further help engage students and to improve their programming skills. The class survey showed that the adoption of Pygame is successful.

  1. Monty Python e a inversão do platonismo

    Directory of Open Access Journals (Sweden)

    Flavia Pitaluga

    2008-11-01

    Full Text Available O objetivo deste trabalho é analisar os filmes Monty Python and the holy grail (Em busca do cálice sagrado e Monty Python's life of Brian (A vida de Brian à luz das discussões de Gilles Deleuze sobre o sentido na filosofia dos estóicos. A inversão do platonismo e a ascensão à superfície dos simulacros são problemas centrais para compreendermos o humor do grupo. Ao longo da discussão, as questões sobre o lugar do clichê no cinema, o falso e suas potências e a injeção de temporalidade nas produções cinematográficas, uma das características do cinema moderno, serão abordadas. A hipótese destas articulações é que a morte de Deus (crise da Verdade é inseparável da maneira como o indivíduo moderno experimenta o tempo: o cinema moderno, ao fazer "a apresentação direta do tempo" (DELEUZE, 1990, coloca em questão a linearidade e a própria verdade como representáveis. Palavras-chave: simulacro; nonsense; humor; Monty Python Abstract: Monty Python and the inversion of Platonism — The purpose of this paper is to analyze the films "Monty Python and the Holy Grail" and "Monty Python's Life of Brian" in the light of Gilles Deleuze's reflections about meaning in the philosophy of the Stoics. The inversion of Platonism and the rise of simulacra to the surface are keys to understanding the group's humor. This discussion examines questions relating to the role of clichés in motion pictures, the fake and its powers, and the insertion of temporality in film productions as one of the characteristics of modern moviemaking. The hypothesis underpinning these articulations is that the death of God (the crisis of Truth is inseparable from the way in which modern individuals experience time: modern cinema, in its "direct presentation of time" (DELEUZE, 1990, questions linearity and truth itself as being representable. Keywords: simulacrum; nonsense; humor; Monty Python

  2. Python programming language and the effectiveness of its inclusion in the teaching

    OpenAIRE

    Vitásek, Tomáš

    2009-01-01

    The goal of the first part of this work is to summarize the basics of the Python programming language. Show how to create programs in Python, what are the modules, the basic data types, syntax and the possibility of approach to language. The second part will address the description of the initial programming courses, their objectives and what benefits it brings to teaching Python. Finally, then look at the (in)dependence on the Python platform for running and how to get from Python to another...

  3. C++QEDv2 Milestone 10: A C++/Python application-programming framework for simulating open quantum dynamics

    Science.gov (United States)

    Sandner, Raimar; Vukics, András

    2014-09-01

    ++ libraries, GNU Scientific Library, Blitz++, FLENS, NumPy, SciPy Catalogue identifier of previous version: AELU_v1_0 Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 1381 Does the new version supersede the previous version?: Yes Nature of problem: Definition of (open) composite quantum systems out of elementary building blocks [2,3]. Manipulation of such systems, with emphasis on dynamical simulations such as Master-equation evolution [4] and Monte Carlo wave-function simulation [5]. Solution method: Master equation, Monte Carlo wave-function method Reasons for new version: The new version is mainly a feature release, but it does correct some problems of the previous version, especially as regards the build system. Summary of revisions: We give an example for a typical Python script implementing the ring-cavity system presented in Sec. 3.3 of Ref. [2]: Restrictions: Total dimensionality of the system. Master equation-few thousands. Monte Carlo wave-function trajectory-several millions. Unusual features: Because of the heavy use of compile-time algorithms, compilation of programs written in the framework may take a long time and much memory (up to several GBs). Additional comments: The framework is not a program, but provides and implements an application-programming interface for developing simulations in the indicated problem domain. We use several C++11 features which limits the range of supported compilers (g++ 4.7, clang++ 3.1) Documentation, http://cppqed.sourceforge.net/ Running time: Depending on the magnitude of the problem, can vary from a few seconds to weeks. References: [1] Entry point: http://cppqed.sf.net [2] A. Vukics, C++QEDv2: The multi-array concept and compile-time algorithms in the definition of composite quantum systems, Comp. Phys. Comm. 183(2012)1381. [3] A. Vukics, H. Ritsch, C++QED: an object-oriented framework for wave-function simulations of cavity QED systems, Eur. Phys. J. D 44 (2007) 585. [4] H. J. Carmichael, An Open

  4. Emerge - A Python environment for the modeling of subsurface transfers

    Science.gov (United States)

    Lopez, S.; Smai, F.; Sochala, P.

    2014-12-01

    The simulation of subsurface mass and energy transfers often relies on specific codes that were mainly developed using compiled languages which usually ensure computational efficiency at the expense of relatively long development times and relatively rigid software. Even if a very detailed, possibly graphical, user-interface is developed the core numerical aspects are rarely accessible and the smallest modification will always need a compilation step. Thus, user-defined physical laws or alternative numerical schemes may be relatively difficult to use. Over the last decade, Python has emerged as a popular and widely used language in the scientific community. There already exist several libraries for the pre and post-treatment of input and output files for reservoir simulators (e.g. pytough). Development times in Python are considerably reduced compared to compiled languages, and programs can be easily interfaced with libraries written in compiled languages with several comprehensive numerical libraries that provide sequential and parallel solvers (e.g. PETSc, Trilinos…). The core objective of the Emerge project is to explore the possibility to develop a modeling environment in full Python. Consequently, we are developing an open python package with the classes/objects necessary to express, discretize and solve the physical problems encountered in the modeling of subsurface transfers. We heavily relied on Python to have a convenient and concise way of manipulating potentially complex concepts with a few lines of code and a high level of abstraction. Our result aims to be a friendly numerical environment targeting both numerical engineers and physicist or geoscientists with the possibility to quickly specify and handle geometries, arbitrary meshes, spatially or temporally varying properties, PDE formulations, boundary conditions…

  5. Flexible Environmental Modeling with Python and Open - GIS

    Science.gov (United States)

    Pryet, Alexandre; Atteia, Olivier; Delottier, Hugo; Cousquer, Yohann

    2015-04-01

    Numerical modeling now represents a prominent task of environmental studies. During the last decades, numerous commercial programs have been made available to environmental modelers. These software applications offer user-friendly graphical user interfaces that allow an efficient management of many case studies. However, they suffer from a lack of flexibility and closed-source policies impede source code reviewing and enhancement for original studies. Advanced modeling studies require flexible tools capable of managing thousands of model runs for parameter optimization, uncertainty and sensitivity analysis. In addition, there is a growing need for the coupling of various numerical models associating, for instance, groundwater flow modeling to multi-species geochemical reactions. Researchers have produced hundreds of open-source powerful command line programs. However, there is a need for a flexible graphical user interface allowing an efficient processing of geospatial data that comes along any environmental study. Here, we present the advantages of using the free and open-source Qgis platform and the Python scripting language for conducting environmental modeling studies. The interactive graphical user interface is first used for the visualization and pre-processing of input geospatial datasets. Python scripting language is then employed for further input data processing, call to one or several models, and post-processing of model outputs. Model results are eventually sent back to the GIS program, processed and visualized. This approach combines the advantages of interactive graphical interfaces and the flexibility of Python scripting language for data processing and model calls. The numerous python modules available facilitate geospatial data processing and numerical analysis of model outputs. Once input data has been prepared with the graphical user interface, models may be run thousands of times from the command line with sequential or parallel calls. We

  6. Rapid microsatellite marker development using next generation pyrosequencing to inform invasive Burmese python -- Python molurus bivittatus -- management

    Science.gov (United States)

    Hunter, Margaret E.; Hart, Kristen M.

    2013-01-01

    Invasive species represent an increasing threat to native ecosystems, harming indigenous taxa through predation, habitat modification, cross-species hybridization and alteration of ecosystem processes. Additionally, high economic costs are associated with environmental damage, restoration and control measures. The Burmese python, Python molurus bivittatus, is one of the most notable invasive species in the US, due to the threat it poses to imperiled species and the Greater Everglades ecosystem. To address population structure and relatedness, next generation sequencing was used to rapidly produce species-specific microsatellite loci. The Roche 454 GS-FLX Titanium platform provided 6616 di-, tri- and tetra-nucleotide repeats in 117,516 sequences. Using stringent criteria, 24 of 26 selected tri- and tetra-nucleotide loci were polymerase chain reaction (PCR) amplified and 18 were polymorphic. An additional six cross-species loci were amplified, and the resulting 24 loci were incorporated into eight PCR multiplexes. Multi-locus genotypes yielded an average of 61% (39%–77%) heterozygosity and 3.7 (2–6) alleles per locus. Population-level studies using the developed microsatellites will track the invasion front and monitor population-suppression dynamics. Additionally, cross-species amplification was detected in the invasive Ball, P. regius, and Northern African python, P. sebae. These markers can be used to address the hybridization potential of Burmese pythons and the larger, more aggressive P. sebae.

  7. 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...

  8. 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.

  9. 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...

  10. 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...

  11. 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.

  12. 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.

  13. 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)

  14. 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”.

  15. 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

  16. 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

  17. 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)

  18. 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

  19. An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators

    DEFF Research Database (Denmark)

    Gautier, Laurent

    2010-01-01

    time, Python has matured as a rich and reliable language for the agile development of prototypes or final implementations, as well as for handling large data sets. Results The data structures and functions from Bioconductor can be exposed to Python as a regular library. This allows a fully transparent...... and native use of Bioconductor from Python, without one having to know the R language and with only a small community of translators required to know both. To demonstrate this, we have implemented such Python representations for key infrastructure packages in Bioconductor, letting a Python programmer handle...... annotation data, microarray data, and next-generation sequencing data. Conclusions Bioconductor is now not solely reserved to R users. Building a Python application using Bioconductor functionality can be done just like if Bioconductor was a Python package....

  20. 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.

  1. 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.

  2. 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.

  3. 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...

  4. 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

  5. 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 ...

  6. 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.

  7. 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....

  8. 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 ...

  9. 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...

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. Characterization of carbonic anhydrase XIII in the erythrocytes of the Burmese python, Python molurus bivittatus.

    Science.gov (United States)

    Esbaugh, A J; Secor, S M; Grosell, M

    2015-09-01

    Carbonic anhydrase (CA) is one of the most abundant proteins found in vertebrate erythrocytes with the majority of species expressing a low activity CA I and high activity CA II. However, several phylogenetic gaps remain in our understanding of the expansion of cytoplasmic CA in vertebrate erythrocytes. In particular, very little is known about isoforms from reptiles. The current study sought to characterize the erythrocyte isoforms from two squamate species, Python molurus and Nerodia rhombifer, which was combined with information from recent genome projects to address this important phylogenetic gap. Obtained sequences grouped closely with CA XIII in phylogenetic analyses. CA II mRNA transcripts were also found in erythrocytes, but found at less than half the levels of CA XIII. Structural analysis suggested similar biochemical activity as the respective mammalian isoforms, with CA XIII being a low activity isoform. Biochemical characterization verified that the majority of CA activity in the erythrocytes was due to a high activity CA II-like isoform; however, titration with copper supported the presence of two CA pools. The CA II-like pool accounted for 90 % of the total activity. To assess potential disparate roles of these isoforms a feeding stress was used to up-regulate CO2 excretion pathways. Significant up-regulation of CA II and the anion exchanger was observed; CA XIII was strongly down-regulated. While these results do not provide insight into the role of CA XIII in the erythrocytes, they do suggest that the presence of two isoforms is not simply a case of physiological redundancy. Copyright © 2015. Published by Elsevier Inc.

  19. ConKit: a python interface to contact predictions.

    Science.gov (United States)

    Simkovic, Felix; Thomas, Jens M H; Rigden, Daniel J

    2017-07-15

    Recent advances in protein residue contact prediction algorithms have led to the emergence of many new methods and a variety of file formats. We present ConKit , an open source, modular and extensible Python interface which allows facile conversion between formats and provides an interface to analyses of sequence alignments and sets of contact predictions. ConKit is available via the Python Package Index. The documentation can be found at http://www.conkit.org . ConKit is licensed under the BSD 3-Clause. hlfsimko@liverpool.ac.uk or drigden@liverpool.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  20. Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.

    Science.gov (United States)

    Spielman, Stephanie J; Wilke, Claus O

    2015-01-01

    We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid, and codon sequence evolution. All model parameters are fully customizable. Users can additionally specify custom evolutionary models, with custom rate matrices and/or states to evolve. This flexibility makes Pyvolve a convenient framework not only for simulating sequences under a wide variety of conditions, but also for developing and testing new evolutionary models. Pyvolve is an open-source project under a FreeBSD license, and it is available for download, along with a detailed user-manual and example scripts, from http://github.com/sjspielman/pyvolve.