Metadata-Version: 2.1
Name: opencarp_analyzer
Version: 1.0.7
Summary: OpenCARP Trace Analyzer
Home-page: https://github.com/regmibijay/opencarp-analyzer
Author: Bijay Regmi
Author-email: opencarp-analyzer@regdelivery.de
License: MIT
Description: # 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
        
        ```
        _____________________________________________________
        OpenCARP Analyzer
        Extracts data and multiple txt files from Trace data created by openCARP at once.
        _____________________________________________________
        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
        ```
        _____________________________________________________
        OpenCARP Plotter
        Plots multiple txt files created by opencarp at once.
        _____________________________________________________
        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](https://github.com/regmibijay/opencarp-analyzer/issues).
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
