This PR introduces a command line interface (CLI) to the application, allowing users to run the calcium imaging analysis pipeline directly from the command line.
The main changes include:
Creation of a new cli.py file in the calcium_analysis directory. This file uses the argparse module to parse command line arguments and calls the run_analysis function with these arguments.
Modification of the run_analysis.py file to call the main function of cli.py when the script is run directly from the command line.
To use the new CLI, users can now run the application with the following command:
This PR introduces a command line interface (CLI) to the application, allowing users to run the calcium imaging analysis pipeline directly from the command line.
The main changes include:
cli.pyfile in thecalcium_analysisdirectory. This file uses theargparsemodule to parse command line arguments and calls therun_analysisfunction with these arguments.run_analysis.pyfile to call the main function ofcli.pywhen the script is run directly from the command line.To use the new CLI, users can now run the application with the following command:
Where
IMAGE_FLDis the path to the image folder,SAVE_FLDis the path to the save folder, andSDis the standard deviation value.Fixes #9.