`morphology_workflows.repair`¶

Process functions.

Module Contents¶

`write_neuron`(neuron, filename)	Write a NEURON ordered version of the morphology.
`fix_zero_diameters`(row, data_dir)	Assign mtype to morphologies.
`unravel`(row, data_dir[, window_half_length])	Unravel morphologies and update cut plane.
`repair`(row, data_dir[, with_plot, repair_params])	Repair morphologies.
`plot_repair`(row, data_dir[, with_plotly])	Plotting cut leaves on morphologies.
`smooth_diameters`(df, data_dir[, neurite_types, seed])	Smooth diameters using diameter-synthesis simpler algorithm.
`plot_smooth_diameters`(row, data_dir[, shift])	Plot original morphology and smoother one next to each other.
`make_collage`(df, data_dir[, collage_path, separation, ...])	Make collage plot of morphologies per mtype.
`set_layer_column`(df)	Set layer values from mtype name if no layer column is present.
`add_duplicated_layers`(df)	Duplicate entries if layer name has mixed layers, i.e. L23_PC.
`make_release`(df, _, release_path, zero_diameter_path, ...)	Make morphology release.

exception morphology_workflows.repair.RepairError¶

Exception for Repair step.

morphology_workflows.repair.write_neuron(neuron, filename)¶: Write a NEURON ordered version of the morphology.

morphology_workflows.repair.fix_zero_diameters(row, data_dir)¶: Assign mtype to morphologies.

morphology_workflows.repair.unravel(row, data_dir, window_half_length=10)¶: Unravel morphologies and update cut plane.

morphology_workflows.repair.repair(row, data_dir, with_plot=False, repair_params=None)¶

Repair morphologies.

TODO: understand the repair_flag correctly and how to set them.

morphology_workflows.repair.plot_repair(row, data_dir, with_plotly=True)¶: Plotting cut leaves on morphologies.

morphology_workflows.repair.smooth_diameters(df, data_dir, neurite_types=None, seed=42)¶: Smooth diameters using diameter-synthesis simpler algorithm.

morphology_workflows.repair.plot_smooth_diameters(row, data_dir, shift=200)¶: Plot original morphology and smoother one next to each other.

morphology_workflows.repair.make_collage(df, data_dir, collage_path='collage.pdf', separation=500, n_morph_per_page=10, middle_panel_shift=1000, top_panel_shift=2000, layer_thickness=None, rasterized=False, dpi=1000, figsize=None)¶: Make collage plot of morphologies per mtype.

morphology_workflows.repair.set_layer_column(df)¶: Set layer values from mtype name if no layer column is present.

morphology_workflows.repair.add_duplicated_layers(df)¶: Duplicate entries if layer name has mixed layers, i.e. L23_PC.

morphology_workflows.repair.make_release(df, _, release_path, zero_diameter_path, unravel_path, repair_path, extensions, duplicate_layers=True, nb_processes=None)¶: Make morphology release.