OpenCARP-Analyzer

creates a list of csv-formatted files for each ion channel and current with inbuilt opencarp-analyzer command and then plots them as line graph with opencarp-plotter command.

OpenCARP-Analyzer

Data generation module

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OpenCARP Analyzer
Extracts data and multiple txt files from Trace data created by openCARP at once.
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usage: analyzer.py [-h] [-c COLUMNS [COLUMNS ...]] [-t TRACE] [-i IION [IION ...]] [-s [SUFFIX]] [-v [VERSION]]

optional arguments:
  -h, --help            show this help message and exit
  -c COLUMNS [COLUMNS ...], --columns COLUMNS [COLUMNS ...]
                        Name of files that contain header data
  -t TRACE, --trace TRACE
                        Trace data file, e.g. Trace_0.dat
  -i IION [IION ...], --iion IION [IION ...]
                        Ion you want to visualize, e.g. -i i_Ks
  -s [SUFFIX], --suffix [SUFFIX]
                        Suffix to be added behind every exported file name.
  -v [VERSION], --version [VERSION]
                        Displays current version of the script

OpenCARP-Plotter

Data visualization module

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OpenCARP Plotter
Plots multiple txt files created by opencarp at once.
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usage: plotter.py [-h] [-f FILES [FILES ...]] [-o OUT] [-i IGNORE [IGNORE ...]] [-t TITLE [TITLE ...]]
                  [-l LEGEND [LEGEND ...]] [-xlabel XLABEL [XLABEL ...]] [-ylabel YLABEL [YLABEL ...]]
                  [-xlim XLIM [XLIM ...]] [-ylim YLIM [YLIM ...]] [-custom CUSTOM [CUSTOM ...]] [-v [VERSION]]

optional arguments:
  -h, --help            show this help message and exit
  -f FILES [FILES ...], --files FILES [FILES ...]
                        Files to Plot
  -o OUT, --out OUT     Output image name
  -i IGNORE [IGNORE ...], --ignore IGNORE [IGNORE ...]
                        Ignores a file name if this text exists in file
  -t TITLE [TITLE ...], --title TITLE [TITLE ...]
                        Title of plot
  -l LEGEND [LEGEND ...], --legend LEGEND [LEGEND ...]
                        Legend location in plot. Options: BEST,UPPER RIGHT,UPPER LEFT,LOWER LEFT,LOWER
                        RIGHT,RIGHT,CENTER LEFT,CENTER RIGHT,LOWER CENTER,UPPER CENTER,CENTER
  -xlabel XLABEL [XLABEL ...]
                        Label for x-Axis in plot
  -ylabel YLABEL [YLABEL ...]
                        Label for y-Axis in plot
  -xlim XLIM [XLIM ...]
                        Limit for x-Axis, start and end separated by space.
  -ylim YLIM [YLIM ...]
                        Limit for y-Axis, start and end separated by space.
  -custom CUSTOM [CUSTOM ...]
                        Kwargs for matplotlib
  -v [VERSION], --version [VERSION]
                        Displays current version of the scripts

Installation

Install current version of this toolkit using pip install opencarp-analyzer or using pip install git+https://github.com/regmibijay/opencarp-analyzer

Usage

After installation, make sure your pip installation site is in your PATH. If so, you will be able to use opencarp-analyzer and opencarp-plotter from CLI.

Examples

opencarp-analyzer -c header1.txt header2.txt -t Trace_0.dat -i i_Ks V i_NCX will read header1.txt and header2.txt and combine column names so content of header1.txt is before header2.txt. After that it reads Trace_0.dat and creates a dataframe with given column names. Then the given i_Ks, V and i_NCX files are generated in .txt format with respective values from Trace_0.dat.

opencarp-plotter -f data/i_*.txt data_2/*.txt -i MurineMouse header -t Comparision of voltages in mV -legend upper right will read data folder and extract all the files containing i_ in the name and .txt extension. Then it will search for *.txt files in data2 folder and make a list of all files, from which all files containing either MurineMouse or header in filename are omitted. Now we create a plot with title of Comparision of voltages in mV and legends in upper right corner.

To Do

Current features being considered:

color-palettes to specify custom colors for each line.

If you want certain features, feel free to open a feature request.