pyabf 0.1.11

Python library for reading files in Axon Binary Format (ABF)

pyabf: A portable Python library for reading files in Axon Binary Format (ABF)
==============================================================================

* Project Homepage: `https://github.com/swharden/pyABF <https://github.com/swharden/pyABF>`_
* pyABF Cookbook: `Getting Started <https://github.com/swharden/pyABF/blob/master/cookbook/getting-started.ipynb>`_
* pyABF Cookbook: `Advanced Interactions with ABF Objects <https://github.com/swharden/pyABF/tree/master/cookbook>`_
* `The Unofficial Guide to the ABF File Format <https://github.com/swharden/pyABF/tree/master/doc/abf-file-format>`_






Quickstart
----------

**Display ABF Information:**

.. code-block:: python

import pyabf
abf=pyabf.ABF("filename.abf")
abf.info()

**Access ABF Sweep Data:**

.. code-block:: python

import pyabf
abf=pyabf.ABF("filename.abf")
abf.setSweep(7)
print(abf.dataY, abf.units)
print(abf.dataC, abf.unitsCommand)
print(abf.dataX, abf.unitsTime)

Output:

.. code-block:: text

[-47.729 -47.729 -47.76 ..., -42.542 -42.542 -42.572] mV
[ 0. 0. 0. ..., 0. 0. 0.] pA
[ 0. 0. 0. ..., 3. 3. 3.] seconds

**Plot all sweeps with matplotlib:**

.. code-block:: python
import pyabf
import matplotlib.pyplot as plt

abf=pyabf.ABF("filename.abf")
plt.figure(figsize=(8,4))
for sweepNumber in abf.sweepList:
abf.setSweep(sweepNumber)
plt.plot(abf.dataX,abf.dataY)

plt.ylabel(abf.unitsLong)
plt.xlabel(abf.unitsTimeLong)
plt.margins(0,.1)
plt.show()

Output:

.. image:: demo1.png


**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