misc¶

tiatoolbox . utils . misc

Miscellaneous small functions repeatedly used in tiatoolbox.

Functions

`add_from_dat`	Add annotations from a .dat file to an existing store.
`anns_from_hoverdict`	Helper function to create list of Annotation objects.
`assert_dtype_int`	Generate error if dtype is not int.
`cast_to_min_dtype`	Cast the input array to the minimal data type required to represent its values.
`contrast_enhancer`	Enhance contrast of the input image using intensity adjustment.
`create_smart_array`	Allocate a NumPy or Zarr array depending on available memory and a threshold.
`dict_to_store_patch_predictions`	Converts output of the PatchPredictor engine to AnnotationStore or QuPath json.
`dict_to_store_semantic_segmentor`	Converts output of TIAToolbox SemanticSegmentor engine to AnnotationStore.
`download_data`	Download data from a given URL to location.
`get_bounding_box`	Get bounding box coordinate information.
`get_luminosity_tissue_mask`	Get tissue mask based on the luminosity of the input image.
`get_zarr_array`	Converts a zarr array into a numpy array.
`grab_files_from_dir`	Grab file paths specified by file extensions.
`imread`	Read an image as `numpy.ndarray`.
`imwrite`	Write numpy array to an image.
`load_stain_matrix`	Load a stain matrix as a numpy array.
`make_default_dict`	Helper function to create a default typedict if none is provided.
`make_valid_poly`	Helper function to make a valid polygon.
`parse_cv2_interpolaton`	Convert a string to a OpenCV (cv2) interpolation enum.
`patch_predictions_as_annotations`	Helper function to generate annotation per patch predictions.
`patch_predictions_as_qupath_json`	Helper function to generate QuPath JSON per patch predictions.
`ppu2mpp`	Convert pixels per unit (ppu) to microns per pixel (mpp).
`process_contours`	Process contours and hierarchy to create annotations.
`read_locations`	Read annotations as pandas DataFrame.
`save_annotations`	Saves Annotation Store to disk.
`save_as_json`	Save data to a json file.
`save_qupath_json`	Saves QuPath JSON to disk.
`save_yaml`	Save dictionary as yaml.
`select_cv2_interpolation`	Return appropriate interpolation method for opencv based image resize.
`select_device`	Selects the appropriate device as requested.
`split_path_name_ext`	Split path of a file to directory path, file name and extensions.
`store_from_dat`	Load annotations from a hovernet-style .dat file.
`string_to_tuple`	Splits input string to tuple at ','.
`tqdm_dask_progress_bar`	Helper function for tqdm_dask_progress_bar.
`unzip_data`	Extract data from zip file.
`update_tqdm_desc`	Helper function to update tqdm progress bar description.
`write_probability_heatmap_as_ome_tiff`	Saves output probability maps from segmentation models as heatmaps.