tasks.transform¶

Transformation phase (Optional).

Attributes¶

logger

Classes¶

`CollectSourceDataset`	Collect source dataset to transform.
`CollectTargetDataset`	Collect target dataset to learn the transformation.
`LearnSomaTransform`	Learn how to transform soma from source to target datasets.
`LearnMorphologyTransform`	Learn how to transform morphologies.
`LearnDiameterTransform`	Learn how to transform diameters.
`ApplyTransformation`	Apply the transformation on source dataset.
`CompareTransformed`	Compare the transformed morphologies by simple plots.
`MakeTransformRelease`	Make a morpology release, with only repair.

Module Contents¶

tasks.transform.logger¶

class tasks.transform.CollectSourceDataset(*args, **kwargs)¶

Bases: data_validation_framework.task.ElementValidationTask

Collect source dataset to transform.

class tasks.transform.CollectTargetDataset(*args, **kwargs)¶

Bases: data_validation_framework.task.ElementValidationTask

Collect target dataset to learn the transformation.

class tasks.transform.LearnSomaTransform(*args, **kwargs)¶

Bases: data_validation_framework.task.SetValidationTask

Learn how to transform soma from source to target datasets.

per_mtype¶

method¶

Choices:: {ratio_of_means}
Default value:: ratio_of_means

plot¶

extra_requires()¶: Requirements that should not be considered as validation tasks.

class tasks.transform.LearnMorphologyTransform(*args, **kwargs)¶

Bases: data_validation_framework.task.SetValidationTask

Learn how to transform morphologies.

per_mtype¶

method¶

Choices:: {extents_no_axon, cortical}
Default value:: cortical

extra_data¶

plot¶

extra_requires()¶: Requirements that should not be considered as validation tasks.

class tasks.transform.LearnDiameterTransform(*args, **kwargs)¶

Bases: data_validation_framework.task.SetValidationTask

Learn how to transform diameters.

per_mtype¶

method¶

Choices:: {branch_order}
Default value:: branch_order

plot¶

max_x¶

extra_requires()¶: Requirements that should not be considered as validation tasks.

class tasks.transform.ApplyTransformation(*args, **kwargs)¶

Bases: data_validation_framework.task.ElementValidationTask

Apply the transformation on source dataset.

class tasks.transform.CompareTransformed(*args, **kwargs)¶

Bases: data_validation_framework.task.SetValidationTask

Compare the transformed morphologies by simple plots.

extra_requires()¶: Requirements that should not be considered as validation tasks.

class tasks.transform.MakeTransformRelease(*args, **kwargs)¶

Bases: data_validation_framework.task.SetValidationTask

Make a morpology release, with only repair.

release_path¶

(Optional) Path to the directory in which all the releases will be exported

Type:: str

repair_path¶

Path to repaired morphologies (not created if None)

Type:: str
Default value:: repaired_release

extensions = ['.asc', '.h5', '.swc']¶

ext¶