Source code for topostats.validation

"""Validation of configuration."""
import logging
import os
from pathlib import Path
from schema import 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 """ 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'", ), "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'", ), "save_format": str, "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": list, "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'", ), "cmap": Or( "afmhot", "nanoscope", "gwyddion", error="Invalid value in config for 'plotting.cmap', valid values are 'afmhot', 'nanoscope' or 'gwyddion'", ), "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'" ), ), "histogram_bins": lambda n: n > 0, }, "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, "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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud 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, "dpi": Or( lambda n: n > 0, "figure", error="Invalid valud in config for 'dpi', valid values are 'figure' or > 0.", ), }, } ) SUMMARY_SCHEMA = Schema( { "base_dir": Path, "output_dir": Path, "csv_file": str, "file_ext": Or( "png", "pdf", "svg", error=("Invalid value in config 'file_ext', valid values are 'png', 'pdf' or 'svg' "), ), "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"), ], } )