tasks.validation¶

Luigi tasks for validation of synthesis.

Classes¶

`ConvertCircuit`	Convert synthesize circuit file to morphs_df.csv file.
`PlotMorphometrics`	Plot cell morphometrics for two groups of cells so they can be easily compared.
`PlotDensityProfiles`	Plot density profiles of neurites in an atlas.
`PlotCollage`	Plot collage for all given mtypes.
`PlotSingleCollage`	Plot collage for a single mtype.
`PlotScales`	Plot scales.
`PlotPathDistanceFits`	Plot fits of path distances as functions of their projection.
`MorphologyValidationReports`	Create morphology validation reports.
`PlotScoreMatrix`	Create score matrix reports.
`TrunkValidation`	Trunk angle validation plots.

Module Contents¶

class ConvertCircuit(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Convert synthesize circuit file to morphs_df.csv file.

ext¶

Extension for morphology files.

Type:: str

class PlotMorphometrics(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Plot cell morphometrics for two groups of cells so they can be easily compared.

The generated images are like the following:

in_atlas¶

Set to True to consider cells in an atlas.

Type:: bool
Default value:: False

config_features¶

The features to plot.

Type:: dict

morphometrics_path¶

Path to output directory (relative from PathConfig.result_path).

Type:: str
Default value:: morphometrics

base_key¶

Base key to use in the morphology DataFrame.

Type:: str
Default value:: path

comp_key¶

Compared key to use in the morphology DataFrame.

Type:: str
Default value:: synth_morphology_path

base_label¶

Label for base morphologies.

Type:: str
Default value:: bio

comp_label¶

Label for compared morphologies.

Type:: str
Default value:: synth

normalize¶

Normalize data if set to True.

Type:: bool
Default value:: False

class PlotDensityProfiles(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Plot density profiles of neurites in an atlas.

nb_jobs¶

Number of joblib workers.

Type:: int

n_cells¶

Number of cells to use. If None, use all cells.

Type:: int

density_profiles_path¶

Path for pdf file.

Type:: str
Default value:: density_profiles.pdf

sample_distance¶

Distance between sampled points along neurites.

Type:: float
Default value:: 10

in_atlas¶

Trigger atlas case.

Type:: bool
Default value:: False

class PlotCollage(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Plot collage for all given mtypes.

Collage reports show the cells in the atlas.

mtypes¶

Mtypes to plot.

Type:: list(str)

nb_jobs¶

Number of joblib workers.

Type:: int

joblib_verbose¶

Verbosity level of joblib.

Type:: int

collage_base_path¶

Path to the output folder.

Type:: str
Default value:: collages

dpi¶

Dpi for pdf rendering (rasterized).

Type:: int
Default value:: 100

sample¶

Number of cells to plot

Type:: int

realistic_diameters¶

Set or unset realistic diameter when NeuroM plot neurons.

Type:: bool
Default value:: True

linewidth¶

Linewidth used by NeuroM to plot neurons.

Type:: float
Permitted values:: float in (0, inf)
Default value:: 0.1

diameter_scale¶

Diameter scale used by NeuroM to plot neurons.

Type:: float
Permitted values:: float in (0, inf)
Default value:: 1.0

class PlotSingleCollage(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Plot collage for a single mtype.

nb_jobs¶

Number of joblib workers.

Type:: int

joblib_verbose¶

Verbosity level of joblib.

Type:: int

collage_base_path¶

Path to the output folder.

Type:: str

sample¶

Number of cells to use, if None, all available.

Type:: float

dpi¶

Dpi for pdf rendering (rasterized).

Type:: int

realistic_diameters¶

Set or unset realistic diameter when NeuroM plot neurons.

Type:: bool

linewidth¶

Linewidth used by NeuroM to plot neurons.

Type:: float

diameter_scale¶

Diameter scale used by NeuroM to plot neurons.

Type:: float

mtype¶

The mtype to plot.

Type:: str

class PlotScales(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Plot scales.

Create images of scaling factors used when the cells are generated.

The generated images are like the following:

mtypes¶

Mtypes to plot.

Type:: list(str)

scales_base_path¶

Path to the output folder.

Type:: str
Default value:: scales

debug_file¶

(Optional) File containing debug data.

Type:: str

extra_stat_cols¶

The extra columns that should be plotted (these columns must exist in the debug data).

Type:: str
Default value:: ()

class PlotPathDistanceFits(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Plot fits of path distances as functions of their projection.

The generated images are like the following:

../../../_images/path_distance_fit-1.png

mtypes¶

Mtypes to plot.

Type:: list(str)

morphology_path¶

Column name to use in the DF from ApplySubstitutionRules.

Type:: str

nb_jobs¶

Number of jobs.

Type:: int

output_path¶

Path to the output file.

Type:: str
Default value:: path_distance_fit.pdf

outlier_percentage¶

Percentage from which the outliers are removed.

Type:: int
Default value:: 90

class MorphologyValidationReports(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Create morphology validation reports.

mtypes¶

List of mtypes to plot.

Type:: list(str)

morphology_path¶

Column name to use in the DF from ApplySubstitutionRules.

Type:: str

nb_jobs¶

Number of jobs.

Type:: int

config_path¶

(Optional) Path to the configuration file. Use default configuration if not provided.

Type:: str

output_path¶

Path to the output file.

Type:: str
Default value:: morphology_validation_reports

cell_figure_count¶

Number of example cells to show.

Type:: int
Default value:: 10

bio_compare¶

Use the bio compare template.

Type:: bool
Default value:: False

class PlotScoreMatrix(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Create score matrix reports.

The generated images are like the following:

../../../_images/score_matrix_reports-1.png

mtypes¶

List of mtypes to plot.

Type:: list(str)

morphology_path¶

Column name to use in the DF from ApplySubstitutionRules.

Type:: str

nb_jobs¶

Number of jobs.

Type:: int

config_path¶

(Optional) Path to the configuration file. Use default configuration if not provided.

Type:: str

output_path¶

Path to the output file.

Type:: str
Default value:: score_matrix_reports.pdf

in_atlas¶

Trigger atlas case.

Type:: bool
Default value:: False

class TrunkValidation(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Trunk angle validation plots.

in_atlas¶

Set to True to consider cells in an atlas.

Type:: bool
Default value:: False

validation_path¶

Path to output directory (relative from PathConfig.result_path).

Type:: str
Default value:: trunk_validation

base_key¶

Base key to use in the morphology DataFrame.

Type:: str
Default value:: path

comp_key¶

Compared key to use in the morphology DataFrame.

Type:: str
Default value:: synth_morphology_path

base_label¶

Label for base morphologies.

Type:: str
Default value:: bio

comp_label¶

Label for compared morphologies.

Type:: str
Default value:: synth