crm_fit

Usage of the crm_fit script

crm_fit -h

usage: crm_fit [-h] [-i ITERATION] [-w WORKERS] [-d DATA]
            [-o OUTPUT_FOLDER] [--skip-profiles] [--skip-masks]
            [--skip-param-space] [--skip-distributions]

Fits the Bacterial Rods model to a system of cells.

options:
-h, --help            show this help message and exit
-i, --iteration ITERATION
                        Use existing output folder instead of
                        creating new one
-w, --workers WORKERS
                        Number of threads
-d, --data DATA       Directory containing initial and final
                        snapshots with masks.
-o, --output-folder OUTPUT_FOLDER
                        Folder to store all output in. If left
                        unspecified, the output folder will be
                        generated via OUTPUT_FOLDER='./out/crm_fit/
                        POTENTIAL_TYPE/ITERATION/' where ITERATION
                        is the next number larger than any already
                        existing one and POTENTIAL_TYPE is obtained
                        from the settings.toml file
--skip-profiles       Skips Plotting of profiles for parameters
--skip-masks          Skips Plotting of masks and microscopic
                        images
--skip-param-space    Skips visualization of parameter space
--skip-distributions  Skips plotting of distributions

class Parameter: TODO

class Parameters: TODO

class Optimization: TODO

class Constants: Contains all constants of the numerical simulation

class Settings: Contains all settings required to fit the model to images