Convert neuroscience data from binary formats to text formats (ATF).
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bin2txtswps
experimental
.gitignore
README.md
requirements.txt

README.md

bin2txtswps

Convert from common neuroscience binary formats (ABF, WCP) to text formats (ATF). This is useful for analysis programs that require text formats. bin2txtswps uses neo, numpy, wx and quantities. It has GUI entry point (bin2txtswps_run.py).

Before running

Required python modules are listed in requirements.txt (this file was auto-generated with pip)

  • Tested with python 2.7 and python 3.6
  • The program has been tested and is functional on the following operating systems:
    • Windows 7
    • Windows 10
    • Ubuntu 16.04

Usage

To install requirements, do pip install -r requirements.txt Then python bin2txtswps_run.py to start the program

To-do

  • Extended testing - particularly with multiple channels
  • Add more input and output formats

Changelogs

01/Dec/2017

  • Removed '#' from output file headers

  • Added support for igor files (new requirement is igor python package)

  • Added new GUI, unified entry point at bin2txtswps_run.py

    • GUI uses python threading module to delegate tasks
    • Ability to cancel running task
    • New GUI provides scope for clearer/cleaner presentation
  • Code restructure:

    • src folder changed to bin2txtswps, which is now a module
    • file_looper.folder_converter is now a generator
    • Other minor code cleanup

25/Nov/2017

  • Bug in neo 0.5.1 (reading WinWCP data) addressed by updating neo to 0.5.2 in requirements.txt
  • Numpy requirement downgraded to 1.11.1 due to a bug in compatibility with py2exe
  • Added additional headers in ATF_functions.py
  • Updated bin2txtswps_win.py for python3
  • Updated setup.py for py2exe
  • Using read_header() function of axonIO to get additional information for headers

24/Sept/2017

  • Changed code to work with Python 3.6.2
  • Changed write_ATF function in ATF_functions to use numpy.stack instead of vstack
  • Changed build_full_header in ATF_functions to improve code readability