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
Current flags
Flag |
Description |
|---|---|
-h, --help |
Shows help message. |
-f, --folder <FOLDER> |
Path to the folder containing the input images. |
-d, --dynamic |
Whether to use dynamic inference. Default is static. |
-m, --method <METHOD> |
Method to use for inference. Options are: ‘nnls’, ‘lsq’ and ‘lsq_linear. Default is ‘nnls’. |
-vn, --velocity_normalization <NORMALIZATION> |
Velocity normalization factor (only used in dynamic mode). Default is 0.1. |
-mt, --max_time <MAX_TIME> |
Maximum time step to infer. Default is 0. |
-sf, --save_folder <SAVE_FOLDER> |
Path to the folder in which to save the output. Default is the same as the input folder. |
-cc, --composite |
Whether to create composite image with the original microscopies. |
-p, --pngs |
Whether to create forsys output of each frame. |
-pc, --plot_connections |
Whether to plot the connections based on the connections file. |
-c, --connections <CONNECTIONS_FILE> |
Path to the connections file. |
-ar, --aspect_ratio <ASPECT_RATIO> |
Aspect ratio of the PNG images. Default is 1. |
-y, --pressure |
Plot pressure in the PNG images. |
-cb, --colorbar |
Plot colorbar in the PNG images. |
-v, --version |
Show the version of the package. |