Command Line Interface

Run the workflow

usage: synthesis_workflow [-h] [--version] [-c CONFIG_PATH] [-m]
                          [-ll {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                          [-lf LOG_FILE] [-w WORKERS]
                          [-dg CREATE_DEPENDENCY_GRAPH]
                          [-dgdpi DEPENDENCY_GRAPH_DPI]
                          {ValidateSynthesis,ValidateVacuumSynthesis,ValidateRescaling}
                          ...

Positional Arguments

workflow

Possible choices: ValidateSynthesis, ValidateVacuumSynthesis, ValidateRescaling

Possible workflows

Named Arguments

--version

show program’s version number and exit

-c, --config-path

Path to the Luigi config file.

-m, --master-scheduler

Use Luigi’s master scheduler instead of local scheduler.

Default: False

-ll, --log-level

Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL

Logger level.

Default: 'INFO'

-lf, --log-file

Logger file.

-w, --workers

Number of workers that luigi can summon.

Default: 1

-dg, --create-dependency-graph

Create the dependency graph of a workflow instead of running it. Pass a path to render it as an image (depending on the extension of the given path).

-dgdpi, --dependency-graph-dpi

The DPI used for the dependency graph export.

Sub-commands

ValidateSynthesis

Workflow to validate synthesis.

synthesis_workflow ValidateSynthesis [-h] [--rerun]
                                     [--with-collage [VALIDATESYNTHESIS_WITH_COLLAGE]]
                                     [--with-morphometrics [VALIDATESYNTHESIS_WITH_MORPHOMETRICS]]
                                     [--with-density-profiles [VALIDATESYNTHESIS_WITH_DENSITY_PROFILES]]
                                     [--with-path-distance-fits [VALIDATESYNTHESIS_WITH_PATH_DISTANCE_FITS]]
                                     [--with-scale-statistics [VALIDATESYNTHESIS_WITH_SCALE_STATISTICS]]
                                     [--with-morphology-validation-reports [VALIDATESYNTHESIS_WITH_MORPHOLOGY_VALIDATION_REPORTS]]
                                     [--with-score-matrix-reports [VALIDATESYNTHESIS_WITH_SCORE_MATRIX_REPORTS]]
                                     [--with-trunk-validation]

Named Arguments

--rerun

Trigger to force the task to rerun. Default value: False.

Default: False

--with-collage

(bool) Trigger collage. Default value: True.

--with-morphometrics

(bool) Trigger morphometrics. Default value: True.

--with-density-profiles

(bool) Trigger density profiles. Default value: True.

--with-path-distance-fits

(bool) Trigger path distance fits. Default value: True.

--with-scale-statistics

(bool) Trigger scale statistics. Default value: True.

--with-morphology-validation-reports

(bool) Trigger morphology validation reports. Default value: True.

--with-score-matrix-reports

(bool) Trigger score matrix reports. Default value: True.

--with-trunk-validation

(bool) Trigger trunk validation. Default value: False.

Default: False

ValidateVacuumSynthesis

Workflow to validate vacuum synthesis.

synthesis_workflow ValidateVacuumSynthesis [-h] [--rerun]
                                           [--with-vacuum-morphologies [VALIDATEVACUUMSYNTHESIS_WITH_VACUUM_MORPHOLOGIES]]
                                           [--with-morphometrics [VALIDATEVACUUMSYNTHESIS_WITH_MORPHOMETRICS]]
                                           [--with-density-profiles [VALIDATEVACUUMSYNTHESIS_WITH_DENSITY_PROFILES]]
                                           [--with-score-matrix-reports [VALIDATEVACUUMSYNTHESIS_WITH_SCORE_MATRIX_REPORTS]]
                                           [--with-trunk-validation]

Named Arguments

--rerun

Trigger to force the task to rerun. Default value: False.

Default: False

--with-vacuum-morphologies

(bool) Trigger morphologies. Default value: True.

--with-morphometrics

(bool) Trigger morphometrics. Default value: True.

--with-density-profiles

(bool) Trigger density profiles. Default value: True.

--with-score-matrix-reports

(bool) Trigger score matrix reports. Default value: True.

--with-trunk-validation

(bool) Trigger trunk validation. Default value: False.

Default: False

ValidateRescaling

Workflow to validate rescaling.

synthesis_workflow ValidateRescaling [-h] [--rerun]
                                     [--morphometrics-path VALIDATERESCALING_MORPHOMETRICS_PATH]
                                     [--base-key VALIDATERESCALING_BASE_KEY]
                                     [--comp-key VALIDATERESCALING_COMP_KEY]
                                     [--base-label VALIDATERESCALING_BASE_LABEL]
                                     [--comp-label VALIDATERESCALING_COMP_LABEL]
                                     [--config-features VALIDATERESCALING_CONFIG_FEATURES]
                                     [--normalize]

Named Arguments

--rerun

Trigger to force the task to rerun. Default value: False.

Default: False

--morphometrics-path

(str) Output path. Default value: morphometrics.

--base-key

(str) Column name in the DF. Default value: morphology_path.

--comp-key

(str) Column name in the DF. Default value: morphology_path.

--base-label

(str) Label for the base morphologies. Default value: bio.

--comp-label

(str) Label for the compared morphologies. Default value: substituted.

--config-features

(dict) Mapping of features to plot.

--normalize

(bool) Normalize data if set to True. Default value: False.

Default: False