tasks.repair
¶
Repair tasks.
Module Contents¶
Classes¶
Collect annotated dataset to work with on this phase. |
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Fix zero diameters. |
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Unravel morphologies. |
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RepairNeurites morphologies. |
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Make collage plot of morphologies. |
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Make a morpology release, with three possible folders: zero-diameter, unravel or repair. |
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Plot the cut leaves on repaired cells. |
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Smooth diameters with |
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Plot smoothed diameters versus originals. |
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tasks.repair.
logger
¶
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class
tasks.repair.
CollectAnnotated
(*args, **kwargs)¶ Bases:
data_validation_framework.task.ElementValidationTask
Collect annotated dataset to work with on this phase.
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class
tasks.repair.
FixZeroDiameters
(*args, **kwargs)¶ Bases:
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()
.
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class
tasks.repair.
Unravel
(*args, **kwargs)¶ Bases:
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.
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class
tasks.repair.
RepairNeurites
(*args, **kwargs)¶ Bases:
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.
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class
tasks.repair.
MakeCollage
(*args, **kwargs)¶ Bases:
data_validation_framework.task.SkippableMixin()
,data_validation_framework.task.SetValidationTask
Make collage plot of morphologies.
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separation
¶
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layer_thickness
¶
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dpi
¶
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n_morph_per_page
¶
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class
tasks.repair.
MakeRelease
(*args, **kwargs)¶ Bases:
data_validation_framework.task.SetValidationTask
Make a morpology release, with three possible folders: zero-diameter, unravel or repair.
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repair_path
¶ Path to repaired morphologies (not created if None)
- Type
- Default value
repaired_release
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duplicate_layers
¶ Duplicate entries with mixed layer mtypes, i.e. L23_PC.
- Type
- Default value
True
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extensions
= ['.asc', '.h5', '.swc']¶
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class
tasks.repair.
PlotRepair
(*args, **kwargs)¶ Bases:
data_validation_framework.task.SkippableMixin()
,data_validation_framework.task.ElementValidationTask
Plot the cut leaves on repaired cells.
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class
tasks.repair.
SmoothDiameters
(*args, **kwargs)¶ Bases:
data_validation_framework.task.SkippableMixin()
,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.
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class
tasks.repair.
PlotSmoothDiameters
(*args, **kwargs)¶ Bases:
data_validation_framework.task.SkippableMixin()
,data_validation_framework.task.ElementValidationTask
Plot smoothed diameters versus originals.