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

Warning

It is important that the input files for the masks are named in ascending order. Furthermore, they should be named by the convention 00015-something.csv. The script will infer the spacing between the masks from this naming convention. If we provide the files 00015-mask.csv, 00016-mask.csv and 00019-mask.csv it will deduce that iterations 17 and 18 have been left out for this prediction.

class Settings

Contains all settings required to fit the model to images

domain_height(float)

Obtains the domain height

constants(Constants)

See Constants

parameters(Parameters)

See Parameters

optimization(OptimizationMethod)

See OptimizationParameters

others(Others)

See Others

class Parameters

TODO

class Constants

Contains all constants of the numerical simulation

class OptimizationMethod

Contains settings for the various optimization routines.

class Others(show_progressbar=False)

Other settings which are not related to the outcome of the simulation

class Parameter

This enum has 3 variants:

• SampledFloat Samples the value in the given range

• float Fixes it to the given value

• list Fixes it on a per-agent basis to the given values.

class PotentialType

TODO

class SampledFloat(min, max, initial, individual=False)

TODO

class DifferentialEvolution

TODO

class OptimizationResult

run_optimizer(iterations_images, positions_all, settings, n_workers=Ellipsis)

run_simulation(parameters, initial_positions, settings)