pyABF 2.1.5

This release is on pypi.org/project/pyabf

pip install --upgrade pyabf

Need to roll back? If the switch from pyABF 2.0 to 2.1 caused a problem for your code base, you can revert to the final version of pyABF 2.0 version using: pip install --force-reinstall pyabf==2.0.35

Minor Changes

• fixed a bug in setup.py that caused pip installation to fail on Python 2.7 systems
• added a Python 2 test to ensure setup.py (not just the pyabf package itself) remains supported by Python 2.7

pyABF 2.1.4

This release is on pypi.org/project/pyabf

pip install --upgrade pyabf

Need to roll back? If the switch from pyABF 2.0 to 2.1 caused a problem for your code base, you can revert to the final version of pyABF 2.0 version using: pip install --force-reinstall pyabf==2.0.35

Major Changes

• setSweep() now supports baseline subtraction as an argument. abf.setSweep(5, baseline=[1.5, 2.5]) will load the 6th sweep (sweep numbers start at zero) baseline-subtracted between 1.5 and 2.5 seconds. The quickstart guide was updated to reflect this.
• Formatted header text can be accessed from ABF class with abf.headerMarkdown and abf.headerHTML (which compliment abf.headerText and abf.headerLaunch()). Note that abf.getInfoPage() was removed entirely.

Minor/Internal Changes

• sweep.py was removed. Some methods were deleted (sweepArea(), sweepAvg(), sweepBaseline(), sweepMax(), sweepMin(), and sweepStdev()). Important ones (setSweep(), sweepC, and sweepD) are now integrated into abf.py.
• text module (which generates markdown and HTML files) moved to tools folder
• unused modules from 2.0 added to tools folder (AP detection, membrane test calculations, waveform generation)

pyABF 2.1.1

This release is on pypi.org/project/pyabf

pip install --upgrade pyabf

Need to roll back? If the switch from pyABF 2.0 to 2.1 caused a problem, you can revert to the latest version of 2.0 version using: pip install --force-reinstall pyabf==2.0.35

Major Changes

• improved stimulus waveform (abf.sweepC) generation from epoch tables and stimulus files
  • many more ABF files are supported
  • fixed errors in ABFs with "delta" epochs which do not return to holding levels between sweeps
  • access epoch levels for the current channel/sweep using abf.abf.sweepEpochs
  • define alternate file path to look for stimulus waveform files with abf.stimulusFileFolder
  • stimulus waveform caching can be disabled with pyabf.ABF("demo.abf", cacheStimulusFiles=False)
• improved digital output level access and waveform generation (abf.sweepD())
  • digital outputs supported for multi-channel ABFs
  • epoch table chart now shows digital output levels (example)

Minor/Internal Changes

• separate stimulus module and waveform module
• complicated analysis modules removed (membrane test and action potential detection)
• updated getting started guides to reflect new usage
• created script to test stimulus file waveform caching

pyABF 2.0.35

This release is on pypi.org/project/pyabf

pip install --upgrade pyabf

Minor Changes

• added abf.dataLengthSec and abf.dataLengthMin to the ABF class
• improved output of print(abf)
• abf.headerText and abf.headerLaunch() now support Python 2.7

pyABF 2.0.34

This release is on pypi.org/project/pyabf

pip install --upgrade pyabf

Minor Changes

• added abf.launchInClampFit() which launches the default program associated with ABF files (usually ClampFit)
• fixed rare DAC epoch level error (due to floating point conversion of junk bytes in the header)
• improved output of print(abf) which now produces a string like: ABF file (2018_11_16_sh_0006.abf) sampled at 20.00 kHz with 1 channel, 60 sweeps, 1 tag, and a total length of 5.10 min
• better support for ABFs with intersweep intervals greater than the sweep length (abf.sweepX units are correct when abf.setSweep(sweepNumber, absoluteTime=True)) is called
• Intersweep interval (which can be different than sweep length) is now accessable as abf.sweepIntervalSec

pyABF 2.0.32

This release is on pypi.org/project/pyabf

pip install --upgrade pyabf

Minor Changes

• Corrected a change that broke Python 2.7 support (issue #66)
• Added a test to the test suite to ensure future updates don't break Python 2.7 comparability

pyABF 2.0.31

This release is on pypi.org/project/pyabf

pip install --upgrade pyabf

Minor Changes

• You can define units when writing ABF1 files like abf.saveABF1(data, "output.abf", "pA")
• ABF1 file writing uses auto-scaling (so very large data ranges do not crash the saving process)
• non-ASCII characters in protocol or unit strings are ignored
• new data index format

pyABF 2.0.30

This release is on pypi.org/project/pyabf

pip install --upgrade pyabf

Major Changes

• ABF file writing - The ABF class now allows commands like abf.saveABF1("demo.abf") to save any ABF as an ABF1 file. ABF files saved in this way are compatible with MiniAnalysis, allowing pyabf to be used to convert modern ABF1 and ABF2 files into the ABF version 1.3 files it was originally designed to load in 2003.
• Simplified header inspection - The ABF header can now be retrieved as text using print(abf.headerText) or launched in a browser as a formatted HTML document using abf.headerLaunch().
• Sweep synthesis - Intended to aid in development of event detection code, lifelike voltage-clamp and current-clamp sweeps can be generated complete with noise, drift, spontaneous EPSCs and IPSCs, spontaneous EPSPs and IPSPs, and action potentials. See abfWriter.py for details.

pyABF 2.0.28

This release is on pypi.org/project/pyabf

pip install --upgrade pyabf

Major Changes

• Python 2.7 support - this library now supports both Python 2.7 and Python 3.6+ (automatically configured upon import). Advanced features (e.g., calculation of whole cell capacitance from membrane test sweeps) may not be fully supported in Python 2.7, but the core ABF reading features will work. Python 3.6+ will continue to be the officially supported version pyABF is targeted for.

pyABF 2.0.27

This release is on pypi.org/project/pyabf

pip install --upgrade pyabf

Minor Changes

• Improved version checking: pip will only install if Python >=3.6, and if imported in Python <3.6 a simple error is displayed (previously f-strings caused a python interpreter crash).