axographio 0.1.1b1

Installation

sudo easy_install numpy
sudo easy_install Cython

easy_install axographio

easy_install -U 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() command may 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

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. Thanks also to Dr. Hillel Chiel for providing testing and helpful suggestions.