Metadata-Version: 1.0
Name: axographio
Version: 0.1.1b1
Summary: A python library for reading and writing AxoGraph data files
Home-page: http://code.google.com/p/axographio/
Author: Kendrick Shaw
Author-email: kms15@case.edu
License: BSD License
Description: 
        axographio is a library that makes it easy to read and write binary data files
        in the AxoGraph file format.
        
        AxoGraph X is a commercial software package used for data acquisition and
        analysis that is widely used in electrophysiological research (see
        http://axographx.com for more details).  While it can read and write files in
        text format, its binary format is much smaller and faster to load and save;
        thus many users preferentially use this format.  The company distributes the
        details of the file format along with sample C++ code for reading and writing
        to these files with AxoGraph X.
        
        Python is a powerful and easy to use general purpose programming language (see
        http://python.org for more details).  There are many useful python libraries
        available for scientific data analysis and data visualization such as scipy,
        matplotlib and MayaVI.
        
        This library provides a simple interface for loading AxoGraph data files into
        a python program or interactive session.  If you want to analyze data you
        recorded in AxoGraph using python based tools, this library provides the glue
        code you'll need.
        
        Installation
        ============
        
        Preinstallation Requirements
        ----------------------------
        
        * A working Python installation
        * The setuptools package
        * The NumPy package
        * The Cython package
        
        Note that NumPy takes a bit of work to build, so it may be easiest to install
        it from your linux distribution's repository, or use as pre-built package
        such as the Scipy Superpack (http://macinscience.org/?page_id=6) for the mac.
        Depending on your OS, you may be able to get away with simply typing:
        
        ::
        
        sudo easy_install numpy
        sudo easy_install Cython
        
        
        Installation
        ------------
        
        Once all the preinstallation requirements have been met, you can download and
        install axographio using easy_install by typing the following command in a
        terminal window:
        
        easy_install axographio
        
        
        Usage
        =====
        
        Loading a data file is as easy as calling `read`:
        
        >>> import axographio
        >>>
        >>> f = axographio.read("AxoGraph X File.axgx")
        
        At this point the variable f will contain a file_contents object with the
        column names and data from the file.  For example, you could now plot the first
        two columns using matplotlib:
        
        >>> import matplotlib.pyplot as plt
        >>>
        >>> plt.plot(f.data[0], f.data[1])
        >>> plt.xlabel(f.names[0])
        >>> plt.ylabel(f.names[1])
        >>> plt.show()
        
        (The plt.show() may not be optional depending on your OS.)
        
        Of course, you probably have grander plans than just plotting the data.  The
        column data supports the standard sequence interfaces (i.e. indexing,
        iteration, etc.) and can be converted to a scipy or numpy array using the
        asarray functions in these packages, e.g.:
        
        >>> import scipy as sp
        >>>
        >>> times = sp.asarray(f.data[0])
        
        Writing files is also relatively easy.  You simply create a new file_contents
        object (or use one you loaded earlier), and then call write.  For example, the
        following code creates a file in the current directory called "my60Hz.axgx"
        with two channels with 60 Hz sine waves
        
        >>> import axographio
        >>> import numpy as np
        >>>
        >>> times = np.arange(0,10,0.0001)
        >>> column1 = np.sin(2*np.pi * 60 * times)
        >>> column2 = np.cos(2*np.pi * 60 * times)
        >>> f = axographio.file_contents(
        ...    ['time (s)', 'my recording (V)', 'your recording (V)'],
        ...    [times, column1, column2])
        >>> f.write("my60Hz.axgx")
        
        
        Questions and Support
        =====================
        
        Please post any questions, problems, comments, or suggestions on the axographio
        group on google groups (http://groups.google.com/group/axographio)
        
        
        News
        ====
        
        0.1.1
        -----
        Fixed a rounding error that could create one extra data point in the times
        column.
        
        0.1.0
        -----
        First release
        
        
        Acknowledgments
        ===============
        
        This initial version of this project was written in the
        Chiel Laboratory at Case Western Reserve University, with support from NIH
        grant NS047073, an Ohio Innovation Incentive Award Fellowship, and the
        Case Western Reserve MSTP (NIH T32 GM007250).  This project builds on a
        number of other open source projects, including Python, C++ AxoGraph file
        input/output code from AxoGraph Scientific (placed in the public domain; a
        modified version is included with the project source code), Cython, and many
        others.
        
Keywords: physiology,electrophysiology,axograph
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
