morphval.common

Private helper functions of the validation module.

Attributes

COMP_MAP

Functions

pretty_name(name)	Make a pretty name.
add_progress_bar(items, template, description)	Add a progress bar in notebooks.
progress_bar_label(template, description, notebook)	Format progress bar label.
dump2json(data_dir, var_name, data)	Save the dictionary 'data' into a .json file.
load_json(fname)	Load a json file from file with fname into the results dictionary.
find_cells(dir_name)	Return the cells in dir_name.
pyplot_non_interactive()	Suppress pyplot showing blank graphs when in interactive mode.
get_agg_fig()	Yield a figure and close it afterwards.
center_population(population)	Return a new population where all cells have been translated to their soma origins.
truncate_population(population, count)	Return a new population with count elements.
get_components_population(population, component)	Get component of a given population.
compute_bounding_box(*populations)	Get bounding box of a population.
plot_population(output_dir, population, xlim, ylim[, ...])	Plot a population.
plot_normalized_neurons(output_dir, ref_population, ...)	Plot cell examples and store the file in output_dir.
_center_truncate_population(population, cell_figure_count)

Module Contents

COMP_MAP

pretty_name(name)

Make a pretty name.

add_progress_bar(items, template, description)

Add a progress bar in notebooks.

progress_bar_label(template, description, notebook)

Format progress bar label.

dump2json(data_dir, var_name, data)

Save the dictionary ‘data’ into a .json file.

Parameters:

• data_dir – the data directory

• var_name – the name of the dictionary as a string

• data – the data dictionary

load_json(fname)

Load a json file from file with fname into the results dictionary.

Returns:

The results dictionary

find_cells(dir_name)

Return the cells in dir_name.

Parameters:

dir_name (str) – path to the directory containing the cells

Returns:

The list of cell files

pyplot_non_interactive()

Suppress pyplot showing blank graphs when in interactive mode.

This usually happens in the context of jupyter notebooks

get_agg_fig()

Yield a figure and close it afterwards.

center_population(population)

Return a new population where all cells have been translated to their soma origins.

truncate_population(population, count)

Return a new population with count elements.

get_components_population(population, component)

Get component of a given population.

compute_bounding_box(*populations)

Get bounding box of a population.

plot_population(output_dir, population, xlim, ylim, notebook_desc=None)

Plot a population.

plot_normalized_neurons(output_dir, ref_population, test_population, cell_figure_count, components, notebook_desc=None)

Plot cell examples and store the file in output_dir.

Parameters:

• output_dir (str) – path to the output directory

• ref_population (NeuroM morph population) – reference population

• test_population (NeuroM morph population) – test population

• cell_figure_count (int) – number of exemplars to plot

• components (list of str) – components to visualize

• notebook_desc (str) – string used for labelling notebook progress bar

_center_truncate_population(population, cell_figure_count)