Metadata-Version: 1.1
Name: pyabf
Version: 2.1.7
Summary: Python library for reading files in Axon Binary Format (ABF)
Home-page: http://github.com/swharden/pyABF
Author: Scott W Harden
Author-email: SWHarden@gmail.com
License: MIT License
Description: pyABF: a pure-Python ABF file reader
        ====================================
        
        **pyABF** provides a Python interface to electrophysiology files in the Axon Binary Format (ABF).
        pyABF supports Python 2.7 and Python 3.6+ and does not use obscure libraries
        (just the standard libraries plus numpy and matplotlib). pyABF supports reading
        of ABF1 and ABF2 files, and can write ABF1 files.
        
        .. class:: no-web
        
            .. image:: https://raw.githubusercontent.com/swharden/pyABF/master/docs/graphics/2017-11-06-aps.png
                :alt: pyABF electrophysiology data analysis with Python and Matplotlib
                :align: center
        
        
        Links
        =====
        * `pyABF Homepage (GitHub) <https://github.com/swharden/pyABF>`_
        * `Getting Started with pyABF <https://github.com/swharden/pyABF/tree/master/docs/getting-started>`_
        * `Unofficial Guide to the ABF File Format <https://github.com/swharden/pyABF/tree/master/docs/advanced/abf-file-format>`_
        
        Quickstart
        ==========
        
        Install or upgrade pyABF:
        
        .. code-block:: bash
        
            pip install --upgrade pyabf
        
        |
        
        Access ABF sweep data:
        
        .. code-block:: python
        
          import pyabf
          abf = pyabf.ABF("demo.abf")
          abf.setSweep(3)
          print(abf.sweepY) # sweep data (ADC)
          print(abf.sweepC) # sweep command (DAC)
          print(abf.sweepX) # sweep times (seconds)
        
        |
        
        Plot a sweep with Matplotlib:
        
        .. code-block:: python
        
          import matplotlib.pyplot as plt
          import pyabf
          abf = pyabf.ABF("17o05028_ic_steps.abf")
          abf.setSweep(14)
          plt.plot(abf.sweepX, abf.sweepY)
          plt.show()
        
        .. class:: no-web
        
            .. image:: https://raw.githubusercontent.com/swharden/pyABF/master/docs/getting-started/source/demo_02a_plot_matplotlib_sweep.jpg
                :alt: pyABF Example
                :align: center
        
        |
        
        Get fancy with Matplotlib:
        
        .. code-block:: python
        
          import matplotlib.pyplot as plt
          import pyabf
          abf = pyabf.ABF("sample.abf")
        
          plt.figure(figsize=(8, 5))
          for sweepNumber in range(abf.sweepCount)[::5]:
              abf.setSweep(sweepNumber)
              plt.plot(abf.sweepX,abf.sweepY,alpha=.5,label="sweep %d"%(sweepNumber))
        
          plt.legend()
          plt.ylabel(abf.sweepLabelY)
          plt.xlabel(abf.sweepLabelX)
          plt.title("pyABF and Matplotlib are a great pair!")
          plt.show()
        
        .. class:: no-web
        
            .. image:: https://raw.githubusercontent.com/swharden/pyABF/master/docs/getting-started/source/demo_03a_decorate_matplotlib_plot.jpg
                :alt: pyABF Example
                :align: center
        
        |
        
        Additional Examples
        ===================
        Full pyabf API documentation, additional code examples, a pyabf cookbook, 
        and low-level information about the ABF file format can be found at the pyABF 
        project homepage: https://github.com/swharden/pyABF
        
        .. class:: no-web
        
            .. image:: https://raw.githubusercontent.com/swharden/pyABF/master/docs/getting-started/source/advanced_08b_using_plot_module.jpg
                :alt: pyABF Example
                :align: center
        
        |
        
        Citing pyABF
        ============
        
        If the pyABF module facilitated your research, consider citing this project by name so it can benefit others too:
        
            *"Computational analysis of electrophysiological recordings was performed with custom software written for this project using Python 3.6 and the pyABF module."*
        
        |
        
        Feature Requests / Unsupported ABF Files
        ========================================
        If you have ABF files which are unsupported (or read incorrectly) 
        by this software, it is likely due to a use case we have not run 
        across yet, so let us know about it! We can only develop and test 
        this software against ABF files we have access to, so if you're 
        interested in having your ABF file supported send the primary author 
        an email (and the ABF file you are trying to analyze) and we will 
        investigate it. If a solution is reached the pyabf package will be 
        updated so everyone can benefit from the change. 
        We can only develop for (and test against) ABFs we have access to, 
        so we really appreciate your contributions!
        
        |
        
        Author
        ======
        
        | **Scott W Harden, DMD, PhD**
        | `Harden Technologies, LLC <http://tech.SWHarden.com>`_
        | `www.SWHarden.com <http://www.SWHarden.com>`_
        | SWHarden@gmail.com
Platform: any
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Software Development :: Libraries :: Application Frameworks
