opencarp-analyzer 1.0.7
OpenCARP Trace Analyzer
License: MIT
Requires Python: >=3.6

# 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).