aigarmic.process_plate_image
============================

.. py:module:: aigarmic.process_plate_image

.. autoapi-nested-parse::

   Pre-processing of agar plate images to extract individual colonies



Functions
---------

.. autoapisummary::

   aigarmic.process_plate_image.find_threshold_value
   aigarmic.process_plate_image.split_by_grid


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

.. py:function:: find_threshold_value(image: numpy.ndarray, look_for: int, start: int = 20, end: int = 100, by: int = 1, area_lower_bound: int = 1000) -> Optional[tuple[list, int]]

   Find threshold value that correctly splits an agar plate image into colony sub-images. Assumes that a black grid
   overlays the image.
   :param image: Image file loaded using cv2.imread
   :param look_for: target sub-images
   :param start: starting threshold value
   :param end: ending threshold value
   :param by: threshold increment value
   :param area_lower_bound: minimum area for a contour to be considered
   :return: tuple of contours and threshold value


.. py:function:: split_by_grid(image: numpy.ndarray, n_rows: int, n_cols: int, visualise_contours: bool = False, plate_name: Optional[str] = None) -> list[list[numpy.ndarray]]

   Split an agar plate image into individual colony sub-images using a grid overlay.

   :param image: image file loaded using cv2.imread
   :param n_rows: number of rows in the grid
   :param n_cols: number of columns in the grid
   :param visualise_contours: if True, display the contours found (useful for validation)
   :param plate_name: name of plate to display in visualisation (useful for validation)
   :return: matrix of sub-images