Command Line Interface

region-grower

A tool for space synthesis management.

region-grower [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

generate-distributions

Generate JSON files containing the TMD distributions for each mtype in input_folder.

INPUT_FOLDER is folder containing the cells.

DAT_FILE is the .dat file with mtype for each cell.

region-grower generate-distributions [OPTIONS] INPUT_FOLDER DAT_FILE

Options

-df, --distribution-filename <distribution_filename>

name of outputted .json file

-dc, --diametrizer-config <diametrizer_config>

config file for diametrizer

-e, --ext <ext>

extension for neuron files

Options:

.h5 | .swc | .asc

Arguments

INPUT_FOLDER

Required argument

DAT_FILE

Required argument

generate-parameters

Generate JSON files containing the TMD parameters for each mtype in input_folder.

INPUT_FOLDER is folder containing the cells.

DAT_FILE is the .dat file with mtype for each cell.

region-grower generate-parameters [OPTIONS] INPUT_FOLDER DAT_FILE

Options

-dc, --diametrizer-config <diametrizer_config>

config file for diametrizer

-tp, --tmd-parameters <tmd_parameters>

tmd_parameter json if different from default generated by TMD

-pf, --parameter-filename <parameter_filename>

name of outputted .json file

-e, --ext <ext>

extension for neuron files

Options:

.h5 | .swc | .asc

Arguments

INPUT_FOLDER

Required argument

DAT_FILE

Required argument

synthesize-morphologies

Synthesize morphologies.

region-grower synthesize-morphologies [OPTIONS]

Options

--input-cells <input_cells>

Required Path to a MVD3/sonata file storing cells collection whose positions are used as new soma locations

--tmd-parameters <tmd_parameters>

Required Path to JSON with TMD parameters

--tmd-distributions <tmd_distributions>

Required Path to JSON with TMD distributions

--morph-axon <morph_axon>

TSV file with axon morphology list (for grafting)

--base-morph-dir <base_morph_dir>

Path to base morphology release folder

--atlas <atlas>

Required Atlas URL

--atlas-cache <atlas_cache>

Atlas cache folder

--seed <seed>

Random number generator seed (default: 0)

--out-cells <out_cells>

Required Path to output cells file.

--out-apical <out_apical>

Path to output YAML apical file containing the coordinates where apical dendrites are tufting

--out-apical-nrn-sections <out_apical_nrn_sections>

Path to output YAML apical file containing the neuron section ids where apical dendrites are tufting

--out-morph-dir <out_morph_dir>

Path to output morphology folder

--out-morph-ext <out_morph_ext>

Morphology export format(s)

Options:

swc | asc | h5

--max-files-per-dir <max_files_per_dir>

Maximum files per level for morphology output folder

--overwrite

Overwrite output morphology folder (default: False)

--max-drop-ratio <max_drop_ratio>

Max drop ratio for any mtype (default: 0)

--scaling-jitter-std <scaling_jitter_std>

Apply scaling jitter to all axon sections with the given std.

--rotational-jitter-std <rotational_jitter_std>

Apply rotational jitter to all axon sections with the given std.

--out-debug-data <out_debug_data>

Export the debug data of each cell to this file.

--nb-processes <nb_processes>

Number of processes when MPI is not used.

--with-mpi

Use MPI for parallel computation.

--log-level <log_level>

The logger level.

Options:

debug | info | warning | error | critical

--min-depth <min_depth>

Minimum depth to use

--skip-write

Skip writing of morphologies

--min-hard-scale <min_hard_scale>

Minimum hard limit scale below which neurite is deleted

--region-structure <region_structure>

Path to region structure file

--container-path <container_path>

Path to container file of all morphologies (if None, not container created)

--hide-progress-bar

Do not display the progress bar during the computation

--dask-config <dask_config>

The Dask configuration given as a file path or a JSON string

--chunksize <chunksize>

The chunk size used by Dask

--show-pip-freeze

Display the versions of all the accessible modules in a logger entry

--synthesize-axons

Use to synthesize axons or not