SlidingWindowPatchExtractor

class SlidingWindowPatchExtractor(input_img, patch_size, input_mask=None, resolution=0, units='level', stride=None, pad_mode='constant', pad_constant_values=0, min_mask_ratio=0, *, within_bound=False)[source]

Extract patches using sliding fixed sized window for images and labels.

Parameters:

  • input_img (str, pathlib.Path, numpy.ndarray) – Input image for patch extraction.

  • patch_size (int or tuple(int)) – Patch size tuple (width, height).

  • input_mask (str, pathlib.Path, numpy.ndarray, or WSIReader) – Input mask that is used for position filtering when extracting patches i.e., patches will only be extracted based on the highlighted regions in the input_mask. input_mask can be either path to the mask, a numpy array, VirtualWSIReader, or one of ‘otsu’ and ‘morphological’ options. In case of ‘otsu’ or ‘morphological’, a tissue mask is generated for the input_image using tiatoolbox TissueMasker functionality.

  • resolution (Resolution) – Resolution at which to read the image, default = 0. Either a single number or a sequence of two numbers for x and y are valid. This value is in terms of the corresponding units. For example: resolution=0.5 and units=”mpp” will read the slide at 0.5 microns per-pixel, and resolution=3, units=”level” will read at level at pyramid level / resolution layer 3.

  • units (Units) – The units of resolution, default = “level”.

  • pad_mode (str) – Method for padding at edges of the WSI. Default to ‘constant’. See numpy.pad() for more information.

  • pad_constant_values (int or tuple(int)) – Values to use with constant padding. Defaults to 0. See numpy.pad() for more information.

  • within_bound (bool) – Whether to extract patches beyond the input_image size limits. If False, extracted patches at margins will be padded appropriately based on pad_constant_values and pad_mode. If True, patches at the margins whose bounds would exceed the mother image dimensions would be neglected. Default is False.

  • stride (int or tuple(int)) – Stride in (x, y) direction for patch extraction, default = patch_size.

  • min_mask_ratio (float) – Only patches with positive area percentage above this value are included. Defaults to 0.

stride

Stride in (x, y) direction for patch extraction.

Type:

tuple(int)

Initialize SlidingWindowPatchExtractor.

Methods