Command Line Interface

Entry point and global parameters

axon-synthesis

A command line tool for axon-synthesis management.

axon-synthesis [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

-c, --config <config>

Read option defaults from the specified CFG file.

--log-level <log_level>

The logger level.

Options:

debug | info | warning | error | critical

-d, --debug, -nd, --no-debug

Trigger the debug mode.

--seed <seed>

The random seed.

Commands

create-inputs

Generate all the parameters from the Atlas, the White Matter Recipe and the input morphologies

fetch-white-matter-recipe

Fetch the White Matter Recipe file from a given repository

scripts

Subset of commands used to run some useful…

synthesize

Synthesize the axons for the given morphologies

validation

Subset of commands used to validate axon…

Sub-commands

axon-synthesis fetch-white-matter-recipe

Command to fetch the White Matter Recipe from a git repository.

axon-synthesis fetch-white-matter-recipe [OPTIONS]

Options

--url <url>

Required The URL of the repository that contains the target file

--file-path <file_path>

The path of the target file in the target repository

--version-reference <version_reference>

The version that should be used in the repository (can be a tag, a commit hash or a branch name)

-o, --output-path <output_path>

Required The path to the destination file

axon-synthesis create-inputs

The command to create inputs.

axon-synthesis create-inputs [OPTIONS]

Options

--morphology-dir <morphology_dir>

Required The directory containing the input morphologies

--atlas-enable, --atlas-disable

Enable or disable the Atlas

--atlas-path <atlas_path>

Path to the Atlas folder

--atlas-region-filename <atlas_region_filename>

Name of NRRD file containing the brain regions in the Atlas folder

--atlas-layer-names <atlas_layer_names>

Names of the layers given as a JSON list (the atlas folder must contain a file name ‘[PH]<layer_name>.nrrd’ for each given layer)

--atlas-outside-region-id <atlas_outside_region_id>

ID of the ‘outside’ brain region

--atlas-enable-boundary, --atlas-disable-boundary

Enable or disable the boundary conditions

--wmr-path <wmr_path>

Path to the White Matter Recipe file

--wmr-subregion-uppercase

--wmr-subregion-keep-prefix

--wmr-subregion-remove-prefix

--wmr-sub-region-separator <wmr_sub_region_separator>

--clustering-parameters <clustering_parameters>

Required Parameters used for the clustering algorithm

--neuron-density <neuron_density>

The density of neurons in the atlas (we suppose here that this density is uniform). This density should be given in number of neurons by cube atlas-unit (usually micrometer).

--bouton-density <bouton_density>

The density of boutons along the axons (we suppose here that this density is uniform).

-o, --output-dir <output_dir>

Required Output directory

--nb-workers <nb_workers>

The number of workers

--dask-config <dask_config>

The dask configuration given as a JSON string.

--progress-bar, --no-progress-bar

If set to True, a progress bar is displayed during computation

--use-mpi, --no-use-mpi

If set to True, MPI is used for parallel computation

axon-synthesis synthesize

The command to synthesize axons.

axon-synthesis synthesize [OPTIONS]

Options

--input-dir <input_dir>

Required The directory containing the inputs.

--morphology-dir <morphology_dir>

Required The directory containing the input morphologies

--morphology-data-file <morphology_data_file>

Required The MVD3 or SONATA file containing morphology data.

-r, --rebuild-existing-axons, -nr, --no-rebuild-existing-axons

Force rebuilding existing axons.

--axon-grafting-points-file <axon_grafting_points_file>

Path to the HDF5 file containing the section IDs where the axons should be grafted in the input morphologies (axons are grafted to the soma if not provided).

--population-probabilities-file <population_probabilities_file>

Path to the file containing the population probabilities.

--projection-probabilities-file <projection_probabilities_file>

Path to the file containing the projection probabilities.

--population-tuft-number-file <population_tuft_number_file>

Path to the file containing the tuft number distribution for each target population.

--trunk-properties-file <trunk_properties_file>

Path to the file containing the trunk properties.

--tuft-properties-file <tuft_properties_file>

Path to the file containing the tuft barcodes given to NeuroTS.

--tuft-distributions-file <tuft_distributions_file>

Path to the file containing the tuft distributions given to NeuroTS.

--tuft-parameters-file <tuft_parameters_file>

Path to the file containing the tuft parameters given to NeuroTS.

--tuft-boundary-max-distance <tuft_boundary_max_distance>

Maximum distance used for the calculation of the attenuation component near the boundary.

--tuft-boundary-scale-coeff <tuft_boundary_scale_coeff>

Coefficient used in the calculation of the attenuation component near the boundary.

--target-max-tries <target_max_tries>

The maximum number of tries for picking target points.

--output-dir <output_dir>

Required The directory where the outputs will be stored.

--outputs-enable-final-figures, --outputs-disable-final-figures

If enabled, the final figures are exported

--outputs-enable-graph-creation-figures, --outputs-disable-graph-creation-figures

If enabled, the graph creation figures are exported

--outputs-enable-graph-creation-data, --outputs-disable-graph-creation-data

If enabled, the graph creation data are exported

--outputs-enable-main-trunk-figures, --outputs-disable-main-trunk-figures

If enabled, the main trunk figures are exported

--outputs-enable-main-trunk-morphologies, --outputs-disable-main-trunk-morphologies

If enabled, the main trunk morphologies are exported

--outputs-enable-morphologies, --outputs-disable-morphologies

If enabled, the morphologies with new axons are exported

--outputs-enable-morphologies-edges, --outputs-disable-morphologies-edges

If enabled, the morphologies with new axons are exported as edges

--outputs-enable-postprocess-trunk-figures, --outputs-disable-postprocess-trunk-figures

If enabled, the post-process trunk figures are exported

--outputs-enable-postprocess-trunk-morphologies, --outputs-disable-postprocess-trunk-morphologies

If enabled, the post-process trunk morphologies are exported

--outputs-enable-steiner-tree-solutions, --outputs-disable-steiner-tree-solutions

If enabled, the Steiner tree solutions are exported

--outputs-enable-steiner-tree-solution-figures, --outputs-disable-steiner-tree-solution-figures

If enabled, the Steiner tree solution figures are exported

--outputs-enable-target-point-figures, --outputs-disable-target-point-figures

If enabled, the target point figures are exported

--outputs-enable-target-points, --outputs-disable-target-points

If enabled, the target point data are exported

--outputs-enable-tuft-figures, --outputs-disable-tuft-figures

If enabled, the tuft figures are exported

--outputs-enable-tuft-morphologies, --outputs-disable-tuft-morphologies

If enabled, the tuft morphologies are exported

--atlas-enable, --atlas-disable

Enable or disable the Atlas

--atlas-path <atlas_path>

Required Path to the Atlas folder

--atlas-region-filename <atlas_region_filename>

Name of NRRD file containing the brain regions in the Atlas folder

--atlas-layer-names <atlas_layer_names>

Names of the layers given as a JSON list (the atlas folder must contain a file name ‘[PH]<layer_name>.nrrd’ for each given layer)

--atlas-outside-region-id <atlas_outside_region_id>

ID of the ‘outside’ brain region

--atlas-enable-boundary, --atlas-disable-boundary

Enable or disable the boundary conditions

--create-graph-intermediate-number <create_graph_intermediate_number>

The number of intermediate points added before Voronoï process

--create-graph-min-intermediate-distance <create_graph_min_intermediate_distance>

The min distance between two successive intermediate points

--create-graph-min-random-point-distance <create_graph_min_random_point_distance>

The min distance used to add random points

--create-graph-random-max-tries <create_graph_random_max_tries>

The max number of tries to place a new random point

--create-graph-random-point-bbox-buffer <create_graph_random_point_bbox_buffer>

The distance used to add a buffer around the bbox of the points

--create-graph-voronoi-steps <create_graph_voronoi_steps>

The number of Voronoi steps

--create-graph-duplicate_precision <create_graph_duplicate_precision>

The precision used to detect duplicated points

--create-graph-use-orientation-penalty, --create-graph-no-use-orientation-penalty

If set to True, a penalty is added to edges whose direction is not radial

--create-graph-orientation-penalty-exponent <create_graph_orientation_penalty_exponent>

The exponent used for the orientation penalty

--create-graph-orientation-penalty-amplitude <create_graph_orientation_penalty_amplitude>

The amplitude used for the orientation penalty

--create-graph-use-depth-penalty, --create-graph-no-use-depth-penalty

If set to True, a penalty is added to edges whose direction is not parallel to the iso-depth curves

--create-graph-depth-penalty-sigma <create_graph_depth_penalty_sigma>

The sigma used for depth penalty

--create-graph-depth-penalty-amplitude <create_graph_depth_penalty_amplitude>

The amplitude of the depth penalty

--create-graph-preferred-regions <create_graph_preferred_regions>

The list of brain regions in which edge weights are divided by the preferring factor

--create-graph-preferred-region-min-random-point-distance <create_graph_preferred_region_min_random_point_distance>

The min distance used to pick random points in preferred regions

--create-graph-preferring-sigma <create_graph_preferring_sigma>

The sigma used to compute the preferring factor for the given regions

--create-graph-preferring-amplitude <create_graph_preferring_amplitude>

The amplitude used to compute the preferring factor for the given regions

--create-graph-use-terminal-penalty, --create-graph-no-use-terminal-penalty

If enabled, a penalty is added to edges that are connected to a

--post-processing-disable, --post-processing-enable

If disabled, the long-range trunk is not post-processed with random walk

--post-processing-history-path-length <post_processing_history_path_length>

The length used to compute the random walk history

--post-processing-default-history-path-length <post_processing_default_history_path_length>

The coefficient used to compute the history path length when it is not provided

--post-processing-global-target-coeff <post_processing_global_target_coeff>

The coefficient applied to the global target term

--post-processing-global-target-sigma-coeff <post_processing_global_target_sigma_coeff>

The sigma coefficient applied to the global target term

--post-processing-target-coeff <post_processing_target_coeff>

The coefficient applied to the next target term

--post-processing-target-sigma-coeff <post_processing_target_sigma_coeff>

The sigma coefficient applied to the next target term

--post-processing-random-coeff <post_processing_random_coeff>

The coefficient applied to the random term

--post-processing-history-coeff <post_processing_history_coeff>

The coefficient applied to the history term

--post-processing-history-sigma-coeff <post_processing_history_sigma_coeff>

The sigma coefficient applied to the history term

--post-processing-length-coeff <post_processing_length_coeff>

The coefficient applied to step length

--post-processing-max-random-direction-picks <post_processing_max_random_direction_picks>

The maximum number of random direction picks

--nb-workers <nb_workers>

The number of workers

--dask-config <dask_config>

The dask configuration given as a JSON string.

--progress-bar, --no-progress-bar

If set to True, a progress bar is displayed during computation

--use-mpi, --no-use-mpi

If set to True, MPI is used for parallel computation

Validation sub-commands

axon-synthesis validation mimic

The command to synthesize mimicking axons.

axon-synthesis validation mimic [OPTIONS]

Options

--morphology-dir <morphology_dir>

Required The directory containing the input morphologies

--workflows <workflows>

The mimic workflows to synthesize

--voxel-dimensions <voxel_dimensions>

The voxel dimensions used to build the dummy atlas in the ‘preferred_regions’ workflow

--keep-tmp-atlas, --no-keep-tmp-atlas

If set to True, the temporary atlas is not removed at the end of the process

--merge-results, --no-merge-results

If set to True, the temporary atlas is not removed at the end of the process

--tuft-parameters-file <tuft_parameters_file>

Path to the file containing the tuft parameters given to NeuroTS.

--output-dir <output_dir>

Required The directory where the outputs will be stored.

--outputs-enable-final-figures, --outputs-disable-final-figures

If enabled, the final figures are exported

--outputs-enable-graph-creation-figures, --outputs-disable-graph-creation-figures

If enabled, the graph creation figures are exported

--outputs-enable-graph-creation-data, --outputs-disable-graph-creation-data

If enabled, the graph creation data are exported

--outputs-enable-main-trunk-figures, --outputs-disable-main-trunk-figures

If enabled, the main trunk figures are exported

--outputs-enable-main-trunk-morphologies, --outputs-disable-main-trunk-morphologies

If enabled, the main trunk morphologies are exported

--outputs-enable-morphologies, --outputs-disable-morphologies

If enabled, the morphologies with new axons are exported

--outputs-enable-morphologies-edges, --outputs-disable-morphologies-edges

If enabled, the morphologies with new axons are exported as edges

--outputs-enable-postprocess-trunk-figures, --outputs-disable-postprocess-trunk-figures

If enabled, the post-process trunk figures are exported

--outputs-enable-postprocess-trunk-morphologies, --outputs-disable-postprocess-trunk-morphologies

If enabled, the post-process trunk morphologies are exported

--outputs-enable-steiner-tree-solutions, --outputs-disable-steiner-tree-solutions

If enabled, the Steiner tree solutions are exported

--outputs-enable-steiner-tree-solution-figures, --outputs-disable-steiner-tree-solution-figures

If enabled, the Steiner tree solution figures are exported

--outputs-enable-target-point-figures, --outputs-disable-target-point-figures

If enabled, the target point figures are exported

--outputs-enable-target-points, --outputs-disable-target-points

If enabled, the target point data are exported

--outputs-enable-tuft-figures, --outputs-disable-tuft-figures

If enabled, the tuft figures are exported

--outputs-enable-tuft-morphologies, --outputs-disable-tuft-morphologies

If enabled, the tuft morphologies are exported

--clustering-parameters <clustering_parameters>

Required Parameters used for the clustering algorithm

--create-graph-intermediate-number <create_graph_intermediate_number>

The number of intermediate points added before Voronoï process

--create-graph-min-intermediate-distance <create_graph_min_intermediate_distance>

The min distance between two successive intermediate points

--create-graph-min-random-point-distance <create_graph_min_random_point_distance>

The min distance used to add random points

--create-graph-random-max-tries <create_graph_random_max_tries>

The max number of tries to place a new random point

--create-graph-random-point-bbox-buffer <create_graph_random_point_bbox_buffer>

The distance used to add a buffer around the bbox of the points

--create-graph-voronoi-steps <create_graph_voronoi_steps>

The number of Voronoi steps

--create-graph-duplicate_precision <create_graph_duplicate_precision>

The precision used to detect duplicated points

--create-graph-use-orientation-penalty, --create-graph-no-use-orientation-penalty

If set to True, a penalty is added to edges whose direction is not radial

--create-graph-orientation-penalty-exponent <create_graph_orientation_penalty_exponent>

The exponent used for the orientation penalty

--create-graph-orientation-penalty-amplitude <create_graph_orientation_penalty_amplitude>

The amplitude used for the orientation penalty

--create-graph-use-depth-penalty, --create-graph-no-use-depth-penalty

If set to True, a penalty is added to edges whose direction is not parallel to the iso-depth curves

--create-graph-depth-penalty-sigma <create_graph_depth_penalty_sigma>

The sigma used for depth penalty

--create-graph-depth-penalty-amplitude <create_graph_depth_penalty_amplitude>

The amplitude of the depth penalty

--create-graph-preferred-regions <create_graph_preferred_regions>

The list of brain regions in which edge weights are divided by the preferring factor

--create-graph-preferred-region-min-random-point-distance <create_graph_preferred_region_min_random_point_distance>

The min distance used to pick random points in preferred regions

--create-graph-preferring-sigma <create_graph_preferring_sigma>

The sigma used to compute the preferring factor for the given regions

--create-graph-preferring-amplitude <create_graph_preferring_amplitude>

The amplitude used to compute the preferring factor for the given regions

--create-graph-use-terminal-penalty, --create-graph-no-use-terminal-penalty

If enabled, a penalty is added to edges that are connected to a

--post-processing-disable, --post-processing-enable

If disabled, the long-range trunk is not post-processed with random walk

--post-processing-history-path-length <post_processing_history_path_length>

The length used to compute the random walk history

--post-processing-default-history-path-length <post_processing_default_history_path_length>

The coefficient used to compute the history path length when it is not provided

--post-processing-global-target-coeff <post_processing_global_target_coeff>

The coefficient applied to the global target term

--post-processing-global-target-sigma-coeff <post_processing_global_target_sigma_coeff>

The sigma coefficient applied to the global target term

--post-processing-target-coeff <post_processing_target_coeff>

The coefficient applied to the next target term

--post-processing-target-sigma-coeff <post_processing_target_sigma_coeff>

The sigma coefficient applied to the next target term

--post-processing-random-coeff <post_processing_random_coeff>

The coefficient applied to the random term

--post-processing-history-coeff <post_processing_history_coeff>

The coefficient applied to the history term

--post-processing-history-sigma-coeff <post_processing_history_sigma_coeff>

The sigma coefficient applied to the history term

--post-processing-length-coeff <post_processing_length_coeff>

The coefficient applied to step length

--post-processing-max-random-direction-picks <post_processing_max_random_direction_picks>

The maximum number of random direction picks

--nb-workers <nb_workers>

The number of workers

--dask-config <dask_config>

The dask configuration given as a JSON string.

--progress-bar, --no-progress-bar

If set to True, a progress bar is displayed during computation

--use-mpi, --no-use-mpi

If set to True, MPI is used for parallel computation