"""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
[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",
error="Invalid value in config for 'file_ext', valid values are '.spm', '.jpk', '.ibw', '.gwy', '.topostats', or '.asd'.",
),
"loading": {"channel": str},
"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'",
),
"smallest_grain_size_nm2": lambda n: n > 0.0,
"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.below " "should be type int or float"
),
),
},
"absolute_area_threshold": {
"above": [
Or(
int,
None,
error=(
"Invalid value in config for 'grains.absolute_area_threshold.above', valid values "
"are int or null"
),
)
],
"below": [
Or(
int,
None,
error=(
"Invalid value in config for 'grains.absolute_area_threshold.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'",
),
},
"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",
),
"cropped_size": Or(
float,
int,
),
},
"dnatracing": {
"run": Or(
True,
False,
error="Invalid value in config for 'dnatracing.run', valid values are 'True' or 'False'",
),
"min_skeleton_size": lambda n: n > 0.0,
"skeletonisation_method": Or(
"zhang",
"lee",
"thin",
"topostats",
error="Invalid value in config for 'dnatracing.skeletonisation_method',"
"valid values are 'zhang' or 'lee', 'thin' or 'topostats'",
),
"spline_step_size": lambda n: n > 0.0,
"spline_linear_smoothing": lambda n: n >= 0.0,
"spline_circular_smoothing": lambda n: n >= 0.0,
"pad_width": lambda n: n > 0.0,
# "cores": lambda n: n > 0.0,
},
"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_format" "must be a value supported by Matplotlib.",
),
"savefig_dpi": Or(
None,
"figure",
lambda n: n > 0,
error="Invalid value in config for plotting.savefig_dpi, valid" "values are 'figure' or floats",
),
"image_set": Or(
"all",
"core",
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.",
),
"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'"
),
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"mask_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.",
),
},
"labelled_regions_01": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'labelled_regions_01.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.",
),
},
"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.",
),
},
"removed_noise": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'removed_noise.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.",
),
},
"removed_small_objects": {
"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'"
),
),
"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_overlay": {
"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.",
),
},
"labelled_regions_02": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'labelled_regions_02.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.",
),
},
"coloured_regions": {
"filename": str,
"title": str,
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'coloured_regions.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.",
),
},
"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.",
),
},
"coloured_boxes": {
"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'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
},
"all_molecule_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'"
),
),
"core_set": bool,
"savefig_dpi": Or(
lambda n: n > 0,
"figure",
error="Invalid value in config for 'dpi', valid values are 'figure' or > 0.",
),
},
"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.",
),
},
"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.",
),
},
"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.",
),
},
"single_molecule_trace": {
"image_type": Or(
"binary",
"non-binary",
error=(
"Invalid value in config 'single_molecule_trace.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.",
),
},
}
)
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'"),
),
"pickle_plots": Or(
True,
False,
error="Invalid value in config for 'pickle_plots', valid values are 'True' or 'False'",
),
"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("contour_length"),
Optional("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"),
],
}
)