Command line interface
Generalities
ForSys can be run using its Command Line Interface, by invoking:
python -m forsys
Using the -h option allows for help to be displayed. This is only possible from version 1.1.0 onwards. To check which version you are running, you can use:
python -m forsys -v
Example
Static inference
The following command would execute ForSys in “/path/to/input_folder” using the “nnls” method, using the static modality, in only the first microscopy. Saving the results in “/path/to/save_folder”
python -m forsys -f /path/to/input_folder -m nnls -mt 0 -sf /path/to/save_folder
Dynamic inference
The following command would execute ForSys in “/path/to/input_folder” using the “nnls” method, in the dynamic modality, for the first 5 timepoints. The connections files is located in “/path/to/connections.json” The results are saved in “/path/to/save_folder”
python -m forsys -f /path/to/input_folder -m nnls -mt 5 -sf /path/to/save_folder --dynamic -c /path/to/connections.json