tasks.config¶

Configurations for luigi tasks.

Classes¶

`GitClone`	Task to clone a git repository.
`GetSynthesisInputs`	Task to get synthesis input files from a folder on git repository.
`DiametrizerConfig`	Diametrizer configuration.
`RunnerConfig`	Runner global configuration.
`SynthesisConfig`	Synthesis global configuration.
`CircuitConfig`	Circuit configuration.
`GetCellComposition`	Get cell_composition with adapted entries.
`PathConfig`	Morphology path configuration.
`AtlasLocalTarget`	Specific target for atlas targets.
`CircuitLocalTarget`	Specific target for circuit targets.
`MorphsDfLocalTarget`	Specific target for morphology dataframe targets.
`SynthesisLocalTarget`	Specific target for synthesis targets.
`ValidationLocalTarget`	Specific target for validation targets.

Functions¶

reset_default_prefixes()

Set default output paths for targets.

Module Contents¶

class GitClone(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Task to clone a git repository.

url¶

Url of repository. If None, git_synthesis_input_path should be an existing folder.

Type:: str

dest¶

Path to the destination directory.

Type:: str

branch¶

class GetSynthesisInputs(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Task to get synthesis input files from a folder on git repository.

If no url is provided, this task will copy an existing folder to the target location given in the ‘local_synthesis_input_path’ parameter of the ‘PathConfig’ task.

url¶

(Optional) Url of repository. If None, git_synthesis_input_path should be an existing folder.

Type:: str

version¶

(Optional) Version of repo to checkout.

Type:: str

git_synthesis_input_path¶

Path to folder in git repo with synthesis files.

Type:: str
Default value:: synthesis_input

branch¶

class DiametrizerConfig(*args, **kwargs)¶

Bases: luigi.Config

Diametrizer configuration.

model¶

Choices:: {simpler, generic}
Default value:: simpler

terminal_threshold¶

taper_min¶

taper_max¶

asymmetry_threshold_basal¶

asymmetry_threshold_apical¶

neurite_types¶

trunk_max_tries¶

n_samples¶

config_model¶

config_diametrizer¶

class RunnerConfig(*args, **kwargs)¶

Bases: luigi.Config

Runner global configuration.

nb_jobs¶

Number of jobs used by parallel tasks.

Type:: int
Default value:: -1

joblib_verbose¶

Verbosity level used by the joblib library.

Type:: int
Permitted values:: int in [0, 50)
Default value:: 0

class SynthesisConfig(*args, **kwargs)¶

Bases: luigi.Config

Synthesis global configuration.

tmd_parameters_path¶

The path to the TMD parameters.

Type:: str
Default value:: neurots_input/tmd_parameters.json

tmd_distributions_path¶

The path to the TMD distributions.

Type:: str
Default value:: neurots_input/tmd_distributions.json

mtypes¶

The list of mtypes to process (default is None, which means that all found mtypes are taken).

Type:: list(str)

axon_method¶

The method used to handle axons.

Type:: str
Choices:: {reconstructed, no_axon, synthesis}
Default value:: no_axon

class CircuitConfig(*args, **kwargs)¶

Bases: luigi.Config

Circuit configuration.

circuit_somata_path¶

Path to the circuit somata.

Type:: str
Default value:: circuit_somata.mvd3

atlas_path¶

(Optional) Path to the atlas directory.

Type:: str

cell_composition_path¶

Path to cell_compoistion.yaml file.

Type:: str
Default value:: cell_composition.yaml

region_structure_path¶

Path to the file containing the layer structure data.

Type:: str
Default value:: region_structure.yaml

region¶

hemisphere¶

The hemisphere side.

Type:: str
Choices:: {right, left}

class GetCellComposition(*args, **kwargs)¶

Bases: luigi.Task

Get cell_composition with adapted entries.

new_cell_composition¶

Filename to the new cell composition file with modified entries.

Type:: str
Default value:: new_cell_composition.yaml

class PathConfig(*args, **kwargs)¶

Bases: luigi.Config

Morphology path configuration.

local_synthesis_input_path¶

Path to the synthesis input directory.

Type:: str
Default value:: synthesis_input

result_path¶

Path to the output directory.

Type:: str
Default value:: out

atlas_subpath¶

Path to output atlas subdirectory.

Type:: str
Default value:: atlas

circuit_subpath¶

Path to output circuit subdirectory.

Type:: str
Default value:: circuit

morphs_df_subpath¶

Path to output morphs_df subdirectory.

Type:: str
Default value:: morphs_df

synthesis_subpath¶

Path to output synthesis subdirectory.

Type:: str
Default value:: synthesis

validation_subpath¶

Path to output validation subdirectory.

Type:: str
Default value:: validation

ext¶

Default extension used.

Type:: str
Default value:: asc

morphology_path¶

Column name in the morphology dataframe to access morphology paths

Default value:: path

morphs_df_path¶

Path to the morphology DataFrame.

Type:: str
Default value:: morphs_df.csv

substituted_morphs_df_path¶

Path to the substituted morphology DataFrame.

Type:: str
Default value:: substituted_morphs_df.csv

synth_morphs_df_path¶

Path to the synthesized morphology DataFrame.

Type:: str
Default value:: synth_morphs_df.csv

synth_output_path¶

Path to the synthesized morphologies.

Type:: str
Default value:: synthesized_morphologies

debug_region_grower_scales_path¶

Path to the log files in which the scaling factors computed in region-grower are stored.

Type:: str
Default value:: region_grower_scales.pkl

class AtlasLocalTarget(*args, prefix=None, create_parent=True, **kwargs)¶

Bases: luigi_tools.target.OutputLocalTarget

Specific target for atlas targets.

class CircuitLocalTarget(*args, prefix=None, create_parent=True, **kwargs)¶

Bases: luigi_tools.target.OutputLocalTarget

Specific target for circuit targets.

class MorphsDfLocalTarget(*args, prefix=None, create_parent=True, **kwargs)¶

Bases: luigi_tools.target.OutputLocalTarget

Specific target for morphology dataframe targets.

class SynthesisLocalTarget(*args, prefix=None, create_parent=True, **kwargs)¶

Bases: luigi_tools.target.OutputLocalTarget

Specific target for synthesis targets.

class ValidationLocalTarget(*args, prefix=None, create_parent=True, **kwargs)¶

Bases: luigi_tools.target.OutputLocalTarget

Specific target for validation targets.

reset_default_prefixes()¶: Set default output paths for targets.