tasks.synthesis¶

Luigi tasks for morphology synthesis.

Classes¶

`BuildMorphsDF`	Generate the list of morphologies with their mtypes and paths.
`ApplySubstitutionRules`	Apply substitution rules to the morphology dataframe.
`GetDefaultParameters`	Build the tmd_parameter.json for synthesis.
`BuildSynthesisParameters`	Build the tmd_parameters.json for synthesis.
`BuildSynthesisDistributions`	Build the tmd_distribution.json for synthesis.
`BuildAxonMorphsDF`	Generate the list of axon morphologies with their mtypes and paths.
`CreateAnnotationsFile`	Task to compact annotations into a single JSON file.
`BuildAxonMorphologies`	Run choose-morphologies to synthesize axon morphologies.
`Synthesize`	Run placement-algorithm to synthesize morphologies.
`AddScalingRulesToParameters`	Add scaling rules to tmd_parameter.json.
`AddTrunkFitToParameters`	Add fits to trunk angles to tmd_parameter.json.
`OverwriteCustomParameters`	Overwrite parameters with custom parameters.
`RescaleMorphologies`	Rescale morphologies.

Module Contents¶

class BuildMorphsDF(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Generate the list of morphologies with their mtypes and paths.

neurondb_path¶

Path to the neuronDB file (XML).

Type:: str

morphology_dirs¶

mapping between column names and paths to each morphology file.

Type:: dict

apical_points_path¶

(Optional) Path to the apical points file (JSON).

Type:: str

class ApplySubstitutionRules(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Apply substitution rules to the morphology dataframe.

substitution_rules_path¶

Path to the file containing the rules to assign duplicated mtypes to morphologies.

Type:: str
Default value:: substitution_rules.yaml

class GetDefaultParameters(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Build the tmd_parameter.json for synthesis.

default_tmd_parameters_path¶

Path to default tmd_parameters.json.

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

class BuildSynthesisParameters(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Build the tmd_parameters.json for synthesis.

tmd_parameters_path¶

The path to the TMD parameters.

Type:: str

class BuildSynthesisDistributions(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Build the tmd_distribution.json for synthesis.

morphology_path¶

Column name in the morphology dataframe to access morphology paths.

Type:: str

nb_jobs¶

Number of workers.

Type:: int

class BuildAxonMorphsDF(*args, **kwargs)¶

Bases: BuildMorphsDF

Generate the list of axon morphologies with their mtypes and paths.

axon_morphs_df_path¶

Path to the CSV file containing axon morphologies.

Type:: str
Default value:: axon_morphs_df.csv

class CreateAnnotationsFile(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Task to compact annotations into a single JSON file.

annotation_dir¶

Path to annotations folder.

Type:: str

morph_db¶

(Optional) Path to MorphDB file.

Type:: str

destination¶

Path to output JSON file.

Type:: str

class BuildAxonMorphologies(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Run choose-morphologies to synthesize axon morphologies.

If no annotation file is given, axons will be randomly chosen from input cells.

axon_morphs_path¶

Path to save .tsv file with list of morphologies for axon grafting.

Type:: str
Default value:: axon_morphs.tsv

annotations_path¶

(Optional) Path to annotations file used by placementAlgorithm.app.choose_morphologies. If None, random axons will be chosen.

Type:: str

neurondb_basename¶

Base name of the neurondb file (without file extension).

Type:: str
Default value:: neuronDB

axon_cells_path¶

Path to the directory where cells with axons are located.

Type:: str

placement_rules_path¶

(Optional) See placementAlgorithm.app.choose_morphologies.

Type:: str

placement_alpha¶

See placementAlgorithm.app.choose_morphologies.

Type:: float
Default value:: 1.0

placement_scales¶

See placementAlgorithm.app.choose_morphologies.

Type:: list

placement_seed¶

See placementAlgorithm.app.choose_morphologies.

Type:: int
Default value:: 0

with_scores¶

Export morphology scores.

Type:: bool
Default value:: False

filter_axons¶

Read the neuronDB.xml file, filter cell with use_axon=True and generate a new neurondb.dat that is then read by placementAlgorithm.app.choose_morphologies.

Type:: bool
Default value:: False

bias_kind¶

Kind of bias used to penalize scores of rescaled morphologies.

Type:: str
Choices:: {linear, gaussian, uniform}
Default value:: linear

with_optional_scores¶

Use or ignore optional rules for morphology choice.

Type:: bool
Default value:: True

nb_jobs¶

Number of workers.

Type:: int
Default value:: 20

get_neuron_db_path(ext)¶: Helper function to fix neuronDB vs neurondb in file names.

class Synthesize(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Run placement-algorithm to synthesize morphologies.

ext¶

Extension for morphology files

Type:: str

morphology_path¶

Column name to use in the DF to compute axon_morphs_base_dir if it is not provided

Type:: str

nb_jobs¶

Number of threads used for synthesis

Type:: int

out_circuit_path¶

Path to circuit with morphology data.

Type:: str
Default value:: circuit.h5

axon_morphs_base_dir¶

(Optional) Base dir for morphology used for axon (.h5 files).

Type:: str

apical_points_path¶

Path to the apical points file (YAML).

Type:: str
Default value:: apical_points.yaml

debug_region_grower_scales¶

Trigger the recording of scaling factors computed by region-grower.

Type:: bool
Default value:: False

max_drop_ratio¶

The maximum drop ratio.

Type:: float
Permitted values:: float in [0, 1]
Default value:: 0.1

apply_jitter¶

Apply jitter to all sections of axons.

Type:: bool
Default value:: False

scaling_jitter_std¶

The std value of the scaling jitter to apply.

Type:: float
Permitted values:: float in (0, inf)
Default value:: 0.2

rotational_jitter_std¶

The std value of the scaling jitter to apply (in degrees).

Type:: float
Permitted values:: float in (0, 180]
Default value:: 10

seed¶

Pseudo-random generator seed.

Type:: int
Default value:: 0

class AddScalingRulesToParameters(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Add scaling rules to tmd_parameter.json.

morphology_path¶

Column name to use in the DF to compute axon_morphs_base_dir if it is not provided.

Type:: str

nb_jobs¶

Number of threads used for synthesis.

Type:: int

scaling_tmd_parameters_path¶

Path to tmd_parameters.json with scaling rules added.

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

scaling_rules_path¶

Path to the file containing the scaling rules.

Type:: str
Default value:: scaling_rules.yaml

class AddTrunkFitToParameters(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Add fits to trunk angles to tmd_parameter.json.

morphology_path¶

Column name to use in the DF to compute axon_morphs_base_dir if it is not provided.

Type:: str

nb_jobs¶

Number of threads used for synthesis.

Type:: int

trunk_tmd_parameters_path¶

Path to tmd_parameters.json with trunk fit added.

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

scaling_rules_path¶

Path to the file containing the scaling rules.

Type:: str
Default value:: scaling_rules.yaml

class OverwriteCustomParameters(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Overwrite parameters with custom parameters.

custom_tmd_parameters_path¶

Path to tmd_parameters.json with custom parameters overwritten.

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

custom_parameters_path¶

Path to the file containing the custom parameters.

Type:: str
Default value:: custom_parameters.csv

class RescaleMorphologies(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Rescale morphologies.

morphology_path¶

Column name to use in the DF to compute axon_morphs_base_dir if it is not provided.

Type:: str

nb_jobs¶

Number of threads used for synthesis.

Type:: int

rescaled_morphology_path¶

Column name with rescaled morphology paths in the morphology DataFrame.

Type:: str
Default value:: rescaled_morphology_path

rescaled_morphology_base_path¶

Base path to rescaled morphologies.

Type:: str
Default value:: rescaled_morphologies

scaling_rules_path¶

Path to the file containing the scaling rules.

Type:: str
Default value:: scaling_rules.yaml

rescaled_morphs_df_path¶

Path to the CSV morphology file.

Type:: str
Default value:: rescaled_morphs_df.csv

scaling_mode¶

Scaling mode used: cells are either rescaled only according the Y axis or all axes.

Type:: str
Choices:: {radial, y}
Default value:: y

skip_rescale¶

Just copy input cells to the output directory.

Type:: bool
Default value:: False