tasks.repair

Repair tasks.

Module Contents

Classes

CollectAnnotated	Collect annotated dataset to work with on this phase.
FixZeroDiameters	Fix zero diameters.
Unravel	Unravel morphologies.
RepairNeurites	RepairNeurites morphologies.
MakeCollage	Make collage plot of morphologies.
MakeRelease	Make a morpology release, with three possible folders: zero-diameter, unravel or repair.
PlotRepair	Plot the cut leaves on repaired cells.
SmoothDiameters	Smooth diameters with diameter_synthesis.
PlotSmoothDiameters	Plot smoothed diameters versus originals.

Attributes

logger

tasks.repair.logger

class tasks.repair.CollectAnnotated(*args, **kwargs)

Bases: morphology_workflows.utils.StrIndexMixin, data_validation_framework.task.ElementValidationTask

Collect annotated dataset to work with on this phase.

class tasks.repair.FixZeroDiameters(*args, **kwargs)

Bases: morphology_workflows.utils.StrIndexMixin, data_validation_framework.task.ElementValidationTask

Fix zero diameters.

This task applies a fix on zero diameters on dendrites, by calling neuror.zero_diameter_fixer.fix_zero_diameters().

class tasks.repair.Unravel(*args, **kwargs)

Bases: morphology_workflows.utils.StrIndexMixin, data_validation_framework.task.ElementValidationTask

Unravel morphologies.

In-vitro morphologies produce recostruction with too much tortuosity, which is corrected for here, using neuror.unravel.unravel(). As this changes the location of the points, the cut leaves have to be updated, as well as the apical points, if any.

window_half_length

Size in path length of unravel window

Type:

float

Default value:

10

class tasks.repair.RepairNeurites(*args, **kwargs)

Bases: morphology_workflows.utils.StrIndexMixin, data_validation_framework.task.ElementValidationTask

RepairNeurites morphologies.

Using the cut leaves, we recreate missing branches using neuror.main.repair.

Todo

Currently, axons are not repaired, as they need other axons.

Improve repair of dendrite by using all dendrites of same type.

with_plot

Save plots with highlighted repaired branches

Type:

bool

Default value:

False

repair_params

Repair internal parameters (see details in https://neuror.readthedocs.io/en/stable/neuror.main.html#neuror.main.Repair)

Type:

dict

class tasks.repair.MakeCollage(*args, **kwargs)

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(), data_validation_framework.task.SetValidationTask

Make collage plot of morphologies.

collage_path

Path to collage plot

Type:

str

Default value:

collage.pdf

separation

layer_thickness

dpi

n_morph_per_page

class tasks.repair.MakeRelease(*args, **kwargs)

Bases: morphology_workflows.utils.StrIndexMixin, data_validation_framework.task.SetValidationTask

Make a morpology release, with three possible folders: zero-diameter, unravel or repair.

release_path

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

Type:

str

zero_diameter_path

(Optional) Path to zero diameter morphologies (not created if None)

Type:

str

unravel_path

(Optional) Path to unravel morphologies (not created if None)

Type:

str

repair_path

Path to repaired morphologies (not created if None)

Type:

str

Default value:

repaired_release

duplicate_layers

Duplicate entries with mixed layer mtypes, i.e. L23_PC.

Type:

bool

Default value:

True

extensions = ['.asc', '.h5', '.swc']

class tasks.repair.PlotRepair(*args, **kwargs)

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(), data_validation_framework.task.ElementValidationTask

Plot the cut leaves on repaired cells.

with_plotly

Use Plotly for plotting

Type:

bool

Default value:

False

class tasks.repair.SmoothDiameters(*args, **kwargs)

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(True), data_validation_framework.task.ElementValidationTask

Smooth diameters with diameter_synthesis.

We use actual diameters to learn a diameter model used to diametrize the morphology.

By default, this task is skipped.

class tasks.repair.PlotSmoothDiameters(*args, **kwargs)

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(True), data_validation_framework.task.ElementValidationTask

Plot smoothed diameters versus originals.