"""Validation of configuration."""
import logging
import os
from pathlib import Path
from schema import And, Optional, Or, Schema, SchemaError
from topostats.logs.logs import LOGGER_NAME
LOGGER = logging.getLogger(LOGGER_NAME)
# pylint: disable=line-too-long
# pylint: disable=too-many-lines
[docs]
def validate_config(config: dict, schema: Schema, config_type: str) -> None:
"""
Validate configuration.
Parameters
----------
config : dict
Config dictionary imported by read_yaml() and parsed through clean_config().
schema : Schema
A schema against which the configuration is to be compared.
config_type : str
Description of of configuration being validated.
"""
try:
schema.validate(config)
LOGGER.info(f"The {config_type} is valid.")
except SchemaError as schema_error:
raise SchemaError(
f"There is an error in your {config_type} configuration. "
"Please refer to the first error message above for details"
) from schema_error
DEFAULT_CONFIG_SCHEMA = Schema(
{
"base_dir": Path,
"output_dir": Path,
"log_level": Or(
"debug",
"info",
"warning",
"error",
error="Invalid value in config for 'log_level', valid values are 'info' (default), 'debug', 'error' or 'warning",
),
"cores": lambda n: 1 <= n <= os.cpu_count(),
"file_ext": Or(
".spm",
".asd",
".jpk",
".ibw",
".gwy",
".topostats",
".stp",
".top",
error="Invalid value in config for 'file_ext', valid values are '.spm', '.jpk', '.ibw', '.gwy', '.topostats', or '.asd'.",
),
"output_stats": Or(
"basic", "full", error="Invalid value for 'output_stats', valid values are 'full' or 'basic'."
),
"loading": {
"channel": str,
"extract": Or(
"all",
"raw",
"filters",
error="Invalid value in config for 'extract', valid values are 'all', 'raw' or 'filters'",
),
},
"filter": {
"run": Or(
True,
False,
error="Invalid value in config for 'filter.run', valid values are 'True' or 'False'",
),
"row_alignment_quantile": lambda n: 0.0 <= n <= 1.0,
"threshold_method": Or(
"absolute",
"otsu",
"std_dev",
error=(
"Invalid value in config for 'filter.threshold_method', valid values "
"are 'absolute', 'otsu' or 'std_dev'"
),
),
"otsu_threshold_multiplier": float,
"threshold_std_dev": {
"below": lambda n: n > 0,
"above": lambda n: n > 0,
},
"threshold_absolute": {
"below": Or(
int,
float,
error=("Invalid value in config for filter.threshold.absolute.below should be type int or float"),
),
"above": Or(
int,
float,
error=("Invalid value in config for filter.threshold.absolute.below should be type int or float"),
),
},
"gaussian_size": float,
"gaussian_mode": Or(
"nearest",
error="Invalid value in config for 'filter.gaussian_mode', valid values are 'nearest'",
),
"remove_scars": {
"run": bool,
"removal_iterations": lambda n: 0 <= n < 10,
"threshold_low": lambda n: n > 0,
"threshold_high": lambda n: n > 0,
"max_scar_width": lambda n: n >= 1,
"min_scar_length": lambda n: n >= 1,
},
},
"grains": {
"run": Or(
True,
False,
error="Invalid value in config for grains.run, valid values are 'True' or 'False'",
),
"grain_crop_padding": int,
"threshold_method": Or(
"absolute",
"otsu",
"std_dev",
error=(
"Invalid value in config for 'grains.threshold_method', valid values "
"are 'absolute', 'otsu' or 'std_dev'"
),
),
"otsu_threshold_multiplier": float,
"threshold_std_dev": {
"below": [lambda n: n > 0],
"above": [
lambda n: n > 0,
],
},
"threshold_absolute": {
"below": [
Or(
int,
float,
error=(
"Invalid value in config for grains.threshold.absolute.below should be type int or float"
),
)
],
"above": [
Or(
int,
float,
error=(
"Invalid value in config for grains.threshold.absolute.above should be type int or float"
),
)
],
},
"area_thresholds": {
"above": [
Or(
int,
None,
error=(
"Invalid value in config for 'grains.area_thresholds.above', valid values are int or null"
),
)
],
"below": [
Or(
int,
None,
error=(
"Invalid value in config for 'grains.area_thresholds.below', valid values are int or null"
),
)
],
},
"direction": Or(
"both",
"below",
"above",
error="Invalid direction for grains.direction valid values are 'both', 'below' or 'above",
),
"remove_edge_intersecting_grains": Or(
True,
False,
error="Invalid value in config for 'grains.remove_edge_intersecting_grains', valid values are 'True' or 'False'",
),
"unet_config": {
"model_path": Or(None, str),
"upper_norm_bound": float,
"lower_norm_bound": float,
"remove_disconnected_grains": bool,
"confidence": float,
},
"vetting": {
"whole_grain_size_thresholds": Or(
None,
[lambda n: n > 0, lambda n: n > 0],
error="Invalid value in config for 'grainstats.vetting.whole_grain_size_thresholds', this needs to"
"be a list of two positive floats",
),
"class_conversion_size_thresholds": Or(
None,
# List of lists of 3 integers and 2 integers
[[[int, int, int], [int, int]]],
error="Invalid value in config for 'grainstats.vetting.class_conversion_size_thresholds', this "
"needs to be a list of lists of 3 integers and 2 integers - [class number, class to convert to "
"if too small, class to convert to if too big] and [minimum size, maximum size]",
),
"class_region_number_thresholds": Or(
None,
# List of lists of 3 integers
[[int, int, int]],
error="Invalid value in config for 'grainstats.vetting.class_region_number_thresholds', this needs"
"to be a list of lists of 3 integers - class number, minimum region number, maximum region number",
),
"class_size_thresholds": Or(
None,
# List of lists of 3 integers
[[int, int, int]],
error="Invalid value in config for 'grainstats.vetting.class_size_thresholds', this needs to be a"
"list of lists of 3 integers - class number, minimum size, maximum size",
),
"nearby_conversion_classes_to_convert": Or(
None,
# List of tuples of two integers
[[int, int]],
error="Invalid value in config for 'grainstats.vetting.nearby_conversion_classes_to_convert', this"
"needs to be a list of tuples of two integers",
),
"class_touching_threshold": lambda n: n >= 0,
"keep_largest_labelled_regions_classes": Or(
None,
# List of integers
[int],
error="Invalid value in config for 'grainstats.vetting.keep_largest_labelled_regions_classes', this"
"needs to be a list of integers",
),
"class_connection_point_thresholds": Or(
None,
# List of tuples: list[tuple[[tuple[int, int], tuple[int, int]]]
[[[int, int], [int, int]]],
error="Invalid value in config for 'grainstats.vetting.class_connection_point_thresholds', this"
"needs to be a list of tuples of two tuples of two integers. Eg [((1, 2), (3, 4))]",
),
},
"classes_to_merge": Or(
None,
[int],
error="Invalid value in config for 'grains.classes_to_merge', this needs to be a list of integers.",
),
},
"grainstats": {
"run": Or(
True,
False,
error="Invalid value in config for 'grainstats.run', valid values are 'True' or 'False'",
),
"edge_detection_method": Or(
"binary_erosion",
"canny",
),
"extract_height_profile": Or(
True,
False,
error="Invalid value in config for 'grainstats.extract_height_profile',"
"valid values are 'True' or 'False'",
),
"class_names": [str],
},
"disordered_tracing": {
"run": Or(
True,
False,
error="Invalid value in config for 'disordered_tracing.run', valid values are 'True' or 'False'",
),
"class_index": int,
"min_skeleton_size": lambda n: n > 0.0,
"mask_smoothing_params": {
"gaussian_sigma": Or(
float,
int,
None,
),
"dilation_iterations": Or(
int,
None,
),
"holearea_min_max": [
Or(
int,
float,
None,
error=(
"Invalid value in config for 'disordered_tracing.mask_smoothing_params.holearea_min_max', valid values "
"are int, float or null"
),
),
],
},
"skeletonisation_params": {
"method": Or(
"zhang",
"lee",
"thin",
"medial_axis",
"topostats",
error="Invalid value in config for 'disordered_tracing.skeletonisation_method',"
"valid values are 'zhang', 'lee', 'thin', 'medial_axis', 'topostats'",
),
"height_bias": lambda n: 0 < n <= 1,
},
"pruning_params": {
"method": Or(
"topostats",
error="Invalid value in config for 'disordered_tracing.pruning_method', valid values are 'topostats'",
),
"max_length": lambda n: n >= 0,
"method_values": Or("min", "median", "mid"),
"method_outlier": Or("abs", "mean_abs", "iqr"),
"height_threshold": Or(int, float, None),
"only_height_prune_endpoints": Or(
True,
False,
error="Invalid value in config for 'disordered_tracing.pruning_params.run', valid values are 'True' or 'False'",
),
},
},
"nodestats": {
"run": Or(
True,
False,
error="Invalid value in config for 'nodestats.run', valid values are 'True' or 'False'",
),
"node_joining_length": float,
"node_extend_dist": float,
"branch_pairing_length": float,
"pair_odd_branches": bool,
},
"ordered_tracing": {
"run": Or(
True,
False,
error="Invalid value in config for 'ordered_tracing.run', valid values are 'True' or 'False'",
),
"ordering_method": Or(
"nodestats",
"original",
error="Invalid value in config for 'ordered_tracing.ordering_method', valid values are 'nodestats' or 'original'",
),
},
"splining": {
"run": Or(
True,
False,
error="Invalid value in config for 'splining.run', valid values are 'True' or 'False'",
),
"method": Or(
"spline",
"rolling_window",
error="Invalid value in config for 'splining.method', valid values are 'spline' or 'rolling_window'",
),
"rolling_window_size": lambda n: n > 0.0,
"rolling_window_resampling": bool,
"rolling_window_resample_regular_spatial_interval": lambda n: n > 0.0,
"spline_step_size": lambda n: n > 0.0,
"spline_linear_smoothing": lambda n: n >= 0.0,
"spline_circular_smoothing": lambda n: n >= 0.0,
"spline_degree": int,
# "cores": lambda n: n > 0.0,
},
"curvature": {
"run": Or(
True,
False,
error="Invalid value in config for 'curvature.run', valid values are 'True' or 'False'",
),
"colourmap_normalisation_bounds": [
Or(
float,
int,
error="Invalid value in config for 'curvature.colourmap_normalisation_bounds', valid values"
"are float or int",
)
],
},
"plotting": {
"run": Or(
True,
False,
error="Invalid value in config for 'plotting.run', valid values are 'True' or 'False'",
),
"style": And(
str,
Or(
"topostats.mplstyle",
str,
Path,
None,
error="Invalid value in config for 'plotting.style', valid values are 'topostats.mplstyle' or None",
),
),
"savefig_format": Or(
None,
str,
error="Invalid value in config for plotting.savefig_formatmust be a value supported by Matplotlib.",
),
"savefig_dpi": Or(
None,
"figure",
lambda n: n > 0,
error="Invalid value in config for plotting.savefig_dpi, validvalues are 'figure' or floats",
),
"image_set": [
Or(
"all",
"core",
"filters",
"grains",
"grain_crops",
"disordered_tracing",
"nodestats",
"ordered_tracing",
"splining",
error="Invalid value in config for 'plotting.image_set', valid values are 'all' or 'core'",
)
],
"pixel_interpolation": Or(
None,
"none",
"bessel",
"bicubic",
"bilinear",
"catrom",
"gaussian",
"hamming",
"hanning",
"hermite",
"kaiser",
"lanczos",
"mitchell",
"nearest",
"quadric",
"sinc",
"spline16",
"spline36",
error="Invalid interpolation value. See https://matplotlib.org/stable/gallery/images_contours_and_fields/interpolation_methods.html for options.",
),
"grain_crop_plot_size_nm": Or(
int,
float,
error=("Invalid value in config for 'grains.grain_crop_plot_size_nm', valid values are int or float"),
),
"zrange": [float, int, None],
"colorbar": Or(
True,
False,
error="Invalid value in config for 'plotting.colorbar', valid values are 'True' or 'False'",
),
"axes": Or(
True,
False,
error="Invalid value in config plotting.for 'axes', valid values are 'True' or 'False'",
),
"num_ticks": Or(
[None, And(int, lambda n: n > 1)],
error="Invalid value in config plotting.for 'num_ticks', valid values are 'null' or integers > 1",
),
"cmap": Or(
None,
str,
error="Invalid value in config for 'plotting.cmap', valid values are 'afmhot', 'nanoscope', "
"'gwyddion' or values supported by Matplotlib",
),
"mask_cmap": str,
"histogram_log_axis": Or(
True,
False,
error=(
"Invalid value in config plotting histogram. For 'log_y_axis', valid values are 'True' or 'False'"
),
),
"number_grains": Or(
True,
False,
error=("Invalid value in config for 'plotting.number_grain_plots', valid values are 'True' or 'False'"),
),
},
"summary_stats": {
"run": Or(
True,
False,
error="Invalid value in config for summary_stats.run, valid values are 'True' or 'False'",
),
"config": Or(
None,
str,
error=(
"Invalid value in config for summary_stats.config, valid values are 'None' or a path to a "
"config file."
),
),
},
}
)
PLOTTING_SCHEMA = Schema(
{
"extracted_channel": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'extracted_channel.image_type', valid values are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": Or(
"filters",
"grains",
"grain_crops",
"disordered_tracing",
"nodestats",
"ordered_tracing",
"splining",
error=(
"Invalid value in config 'extracted_channel.module', valid values "
"are 'filters', 'grains', 'grain_crops', 'disordered_tracing', "
"'nodestats', 'ordered_tracing', or 'splining'"
),
),
},
"pixels": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error="Invalid value in config 'pixels.image_type', valid values are 'binary' or 'non-binary'",
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": Or(
"filters",
"grains",
"grain_crops",
"disordered_tracing",
"nodestats",
"ordered_tracing",
"splining",
error=(
"Invalid value in config 'pixels.module', valid values "
"are 'filters', 'grains', 'grain_crops', 'disordered_tracing', "
"'nodestats', 'ordered_tracing', or 'splining'"
),
),
},
"initial_median_flatten": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'initial_median_flatten.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": Or(
"filters",
"grains",
"grain_crops",
"disordered_tracing",
"nodestats",
"ordered_tracing",
"splining",
error=(
"Invalid value in config 'initial_median_flatten.module', valid values "
"are 'filters', 'grains', 'grain_crops', 'disordered_tracing', "
"'nodestats', 'ordered_tracing', or 'splining'"
),
),
},
"initial_tilt_removal": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'initial_tilt_removal.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": Or(
"filters",
"grains",
"grain_crops",
"disordered_tracing",
"nodestats",
"ordered_tracing",
"splining",
error=(
"Invalid value in config 'initial_tilt_removal.module', valid values "
"are 'filters', 'grains', 'grain_crops', 'disordered_tracing', "
"'nodestats', 'ordered_tracing', or 'splining'"
),
),
},
"initial_quadratic_removal": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'initial_quadratic_removal.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"initial_scar_removal": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'initial_scar_removal.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"initial_zero_average_background": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'initial_zero_average_background.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"initial_nonlinear_polynomial_removal": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'initial_nonlinear_polynomial_removal.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"mask": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error="Invalid value in config 'mask.image_type', valid values are 'binary' or 'non-binary'",
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"masked_median_flatten": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'masked_median_flatten.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"masked_tilt_removal": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'masked_tilt_removal.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"masked_quadratic_removal": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'masked_quadratic_removal.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"masked_nonlinear_polynomial_removal": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'masked_nonlinear_polynomial_removal.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"secondary_scar_removal": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'masked_quadratic_removal.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"scar_mask": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'masked_quadratic_removal.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"final_zero_average_background": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'final_zero_average_background.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"gaussian_filtered": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'gaussian_filtered.image_type', valid values are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"z_threshed": {
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=("Invalid value in config 'z_threshold.image_type', valid values are 'binary' or 'non-binary'"),
),
"core_set": True,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "filters",
},
"thresholded_grains": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=("Invalid value in config 'mask_grains.image_type', valid values are 'binary' or 'non-binary'"),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"mask_cmap": str,
"module": "grains",
},
"tidied_border": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=("Invalid value in config 'tidied_border.image_type', valid values are 'binary' or 'non-binary'"),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"mask_cmap": str,
"module": "grains",
},
"removed_objects_too_small_to_process": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'removed_small_objects.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "grains",
},
"area_thresholded": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'removed_objects_too_small_to_process.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "grains",
},
"unet": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=("Invalid value in config 'unet_tensor.image_type', valid values are 'binary' or 'non-binary'"),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "grains",
},
"vetted": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=("Invalid value in config 'vetted_tensor.image_type', valid values are 'binary' or 'non-binary'"),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "grains",
},
"merged_classes": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'merged_classes_tensor.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "grains",
},
"mask_overlay": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=("Invalid value in config 'mask_overlay.image_type', valid values are 'binary' or 'non-binary'"),
),
"core_set": True,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "grains",
},
"bounding_boxes": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'bounding_boxes.image_type', valid values are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "grains",
},
"grain_image": {
"image_type": Or(
"binary",
"non-binary",
error=("Invalid value in config 'grain_image.image_type', valid values are 'binary' or 'non-binary'"),
),
"core_set": False,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "grain_crops",
},
"grain_mask": {
"image_type": Or(
"binary",
"non-binary",
error=("Invalid value in config 'grain_mask.image_type', valid values are 'binary' or 'non-binary'"),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "grain_crops",
},
"grain_mask_image": {
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'grain_mask_image.image_type', valid values are 'binary' or 'non-binary'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "grain_crops",
},
"orig_grain": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'coloured_boxes.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"module": "disordered_tracing",
},
"smoothed_grain": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'coloured_boxes.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"module": "disordered_tracing",
},
"skeleton": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'coloured_boxes.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": int,
"module": "disordered_tracing",
},
"pruned_skeleton": {
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'coloured_boxes.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": int,
"module": "disordered_tracing",
},
"branch_indexes": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'branch_indexes.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": int,
"module": "disordered_tracing",
},
"branch_types": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'coloured_boxes.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": int,
"module": "disordered_tracing",
},
"convolved_skeletons": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'convolved_skeleton.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": int,
"module": "nodestats",
},
"node_centres": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=("Invalid value in config 'node_centres.image_type', valid values are 'binary' or 'non-binary'"),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": int,
"module": "nodestats",
},
"connected_nodes": {
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'node_branch_mask.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": int,
"module": "nodestats",
},
"node_area_skeleton": {
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'node_area_skeleton.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": int,
"module": "nodestats",
},
"node_branch_mask": {
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'node_branch_mask.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": int,
"module": "nodestats",
},
"node_avg_mask": {
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=("Invalid value in config 'node_avg_mask.image_type', valid values are 'binary' or 'non-binary'"),
),
"mask_cmap": str,
"core_set": bool,
"module": "nodestats",
},
"node_line_trace": {
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'coloured_boxes.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"module": "nodestats",
},
"ordered_traces": {
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'all_molecule_traces.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "ordered_tracing",
},
"trace_segments": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'all_molecule_traces.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "ordered_tracing",
},
"over_under": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'all_molecule_traces.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "ordered_tracing",
},
"all_molecules": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'coloured_boxes.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": int,
"module": "ordered_tracing",
},
"fitted_trace": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'coloured_boxes.image_type', valid values are 'binary' or 'non-binary'"
),
),
"mask_cmap": str,
"core_set": bool,
"savefig_dpi": int,
"module": "ordered_tracing",
},
"splined_trace": {
"image_type": Or(
"binary",
"non-binary",
error=("Invalid value in config 'splined_trace.image_type', valid values are 'binary' or 'non-binary'"),
),
"title": str,
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "splining",
},
"curvature": {
"image_type": Or(
"binary",
"non-binary",
error=("Invalid value in config 'curvature.image_type', valid values are 'binary' or 'non-binary'"),
),
"title": str,
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "splining",
},
"curvature_individual_grains": {
"filename": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'curvature_individual_grains.image_type', valid values "
"are 'binary' or 'non-binary'"
),
),
"title": str,
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
"module": "splining",
},
}
)
SUMMARY_SCHEMA = Schema(
{
"base_dir": Path,
"output_dir": Path,
"csv_file": str,
"savefig_format": Or(
"png",
"pdf",
"svg",
"tiff",
"tif",
error=("Invalid value in config 'savefig_format', valid values are 'png', 'pdf', 'svg', 'tiff' or 'tif'"),
),
"var_to_label": Or(
None,
str,
error="Invalid value in config for 'var_to_label', valid values are 'None' or a str",
),
"image_id": str,
"molecule_id": str,
"hist": Or(
True,
False,
error="Invalid value in config for 'hist', valid values are 'True' or 'False'",
),
"bins": lambda n: n > 0,
"stat": Or(
"count",
"frequency",
"probability",
"percent",
"density",
error=(
"Invalid value in config 'stat', valid values are 'count', 'frequency', "
"'probability', 'percent' or 'density'"
),
),
"kde": Or(
True,
False,
error="Invalid value in config for 'kde', valid values are 'True' or 'False'",
),
"violin": Or(
True,
False,
error="Invalid value in config for 'violin', valid values are 'True' or 'False'",
),
"figsize": [lambda n: n > 0],
"alpha": lambda n: n > 0,
"palette": Or(
"colorblind",
"deep",
"muted",
"pastel",
"bright",
"dark",
"Spectral",
"Set2",
error=(
"Invalid value in config 'palette', valid values are 'colorblind', 'deep', "
"'muted', 'pastel', 'bright', 'dark', 'Spectral' or 'Set2'"
),
),
"stats_to_sum": [
Optional("area"),
Optional("area_cartesian_bbox"),
Optional("aspect_ratio"),
Optional("bending_angle"),
Optional("total_contour_length"),
Optional("average_end_to_end_distance"),
Optional("height_max"),
Optional("height_mean"),
Optional("height_median"),
Optional("height_min"),
Optional("max_feret"),
Optional("min_feret"),
Optional("radius_max"),
Optional("radius_mean"),
Optional("radius_median"),
Optional("radius_min"),
Optional("smallest_bounding_area"),
Optional("smallest_bounding_length"),
Optional("smallest_bounding_width"),
Optional("volume"),
],
}
)