:py:mod:`wsinfer.patchlib.patch`
================================

.. py:module:: wsinfer.patchlib.patch


Module Contents
---------------


Functions
~~~~~~~~~

.. autoapisummary::

   wsinfer.patchlib.patch.temporary_recursion_limit
   wsinfer.patchlib.patch.get_multipolygon_from_binary_arr
   wsinfer.patchlib.patch.get_patch_coordinates_within_polygon



Attributes
~~~~~~~~~~

.. autoapisummary::

   wsinfer.patchlib.patch.logger


.. py:data:: logger

   

.. py:function:: temporary_recursion_limit(limit: int) -> Iterator[None]


.. py:function:: get_multipolygon_from_binary_arr(arr: numpy.typing.NDArray[numpy.int_], scale: tuple[float, float] | None = None) -> tuple[shapely.MultiPolygon, Sequence[numpy.typing.NDArray[numpy.int_]], numpy.typing.NDArray[numpy.int_]] | None

   Create a Shapely Polygon from a binary array.

   :param arr: Binary array where non-zero values indicate presence of tissue.
   :type arr: array
   :param scale: If specified, this is the factor by which coordinates are multiplied to recover
                 the coordinates at the base resolution of the whole slide image.
   :type scale: tuple of two floats, optional

   :returns: * *polygon* -- A shapely `MultiPolygon` object representing tissue regions.
             * *contours* -- A sequence of arrays representing unscaled contours of tissue.
             * *hierarchy* -- An array of the hierarchy of contours.


.. py:function:: get_patch_coordinates_within_polygon(slide_width: int, slide_height: int, patch_size: int, half_patch_size: int, polygon: shapely.Polygon, overlap: float = 0.0) -> numpy.typing.NDArray[numpy.int_]

   Get coordinates of patches within a polygon.

   :param slide_width: The width of the slide in pixels at base resolution.
   :type slide_width: int
   :param slide_height: The height of the slide in pixels at base resolution.
   :type slide_height: int
   :param patch_size: The size of a patch in pixels.
   :type patch_size: int
   :param half_patch_size: Half of the length of a patch in pixels.
   :type half_patch_size: int
   :param polygon: A shapely Polygon representing the presence of tissue.
   :type polygon: Polygon
   :param overlap: The proportion of the patch_size to overlap. A value of 0.5
                   would have an overlap of 50%. A value of 0.2 would have an
                   overlap of 20%. Negative values will add space between patches.
                   A value of -1 would skip every other patch. Value must be in (-inf, 1).
                   The default value of 0.0 produces non-overlapping patches.
   :type overlap: float

   :returns: Array with shape (N, 2), where N is the number of tiles. Each row in this array
             contains the coordinates of the top-left of a tile: (minx, miny).
   :rtype: coordinates