topostats.grains
================

.. py:module:: topostats.grains

.. autoapi-nested-parse::

   Find grains in an image.

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Attributes
----------

.. autoapisummary::

   topostats.grains.LOGGER


Classes
-------

.. autoapisummary::

   topostats.grains.Grains


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

.. py:data:: LOGGER

.. py:class:: Grains(image: numpy.ndarray, filename: str, pixel_to_nm_scaling: float, threshold_method: str = None, otsu_threshold_multiplier: float = None, threshold_std_dev: dict = None, threshold_absolute: dict = None, absolute_area_threshold: dict = {'above': [None, None], 'below': [None, None]}, direction: str = None, smallest_grain_size_nm2: float = None, remove_edge_intersecting_grains: bool = True)

   
   Find grains in an image.
















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   .. py:attribute:: image


   .. py:attribute:: filename


   .. py:attribute:: pixel_to_nm_scaling


   .. py:attribute:: threshold_method


   .. py:attribute:: otsu_threshold_multiplier


   .. py:attribute:: threshold_std_dev


   .. py:attribute:: threshold_absolute


   .. py:attribute:: absolute_area_threshold


   .. py:attribute:: direction


   .. py:attribute:: smallest_grain_size_nm2


   .. py:attribute:: remove_edge_intersecting_grains


   .. py:attribute:: thresholds
      :value: None



   .. py:attribute:: images


   .. py:attribute:: directions


   .. py:attribute:: minimum_grain_size
      :value: None



   .. py:attribute:: region_properties


   .. py:attribute:: bounding_boxes


   .. py:attribute:: grainstats
      :value: None



   .. py:method:: tidy_border(image: numpy.array, **kwargs) -> numpy.array

      
      Remove grains touching the border.

      :param image: Numpy array representing image.
      :type image: np.array

      :returns: Numpy array of image with borders tidied.
      :rtype: np.array















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   .. py:method:: label_regions(image: numpy.array) -> numpy.array

      
      Label regions.

      This method is used twice, once prior to removal of small regions, and again afterwards, hence requiring an
      argument of what image to label.

      :param image: Numpy array representing image.
      :type image: np.array

      :returns: Numpy array of image with objects coloured.
      :rtype: np.array















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   .. py:method:: calc_minimum_grain_size(image: numpy.ndarray) -> float

      
      Calculate the minimum grain size in pixels squared.

      Very small objects are first removed via thresholding before calculating the below extreme.















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   .. py:method:: remove_noise(image: numpy.ndarray, **kwargs) -> numpy.ndarray

      
      Removes noise which are objects smaller than the 'smallest_grain_size_nm2'.

      This ensures that the smallest objects ~1px are removed regardless of the size distribution of the grains.

      :param image: 2D Numpy image to be cleaned.
      :type image: np.ndarray

      :returns: 2D Numpy array of image with objects < smallest_grain_size_nm2 removed.
      :rtype: np.ndarray















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   .. py:method:: remove_small_objects(image: numpy.array, **kwargs)

      
      Remove small objects from the input image. Threshold determined by the minimum_grain_size variable of the
      Grains class which is in pixels squared.

      :param image: 2D Numpy image to remove small objects from.
      :type image: np.ndarray

      :returns: 2D Numpy array of image with objects < minimum_grain_size removed.
      :rtype: np.ndarray















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   .. py:method:: area_thresholding(image: numpy.ndarray, area_thresholds: list)

      
      Removes objects larger and smaller than the specified thresholds.

      :param image: Image array where the background == 0 and grains are labelled as integers > 0.
      :type image: np.ndarray
      :param area_thresholds: List of area thresholds (in nanometres squared, not pixels squared), first should be
                              the lower limit for size, and the second should be the upper limit for size.
      :type area_thresholds: list

      :returns: Image where grains outside the thresholds have been removed, as a re-numbered labeled image.
      :rtype: np.ndarray















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   .. py:method:: colour_regions(image: numpy.array, **kwargs) -> numpy.array

      
      Colour the regions.

      :param image: Numpy array representing image.
      :type image: np.array

      :returns: Numpy array of image with objects coloured.
      :rtype: np.array















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   .. py:method:: get_region_properties(image: numpy.array, **kwargs) -> List
      :staticmethod:


      
      Extract the properties of each region.

      :param image: Numpy array representing image
      :type image: np.array

      :returns: List of region property objects.
      :rtype: List















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   .. py:method:: get_bounding_boxes(direction) -> Dict

      
      Derive a list of bounding boxes for each region from the derived region_properties

      :param direction: Direction of threshold for which bounding boxes are being calculated.
      :type direction: str

      :returns: Dictionary of bounding boxes indexed by region area.
      :rtype: dict















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   .. py:method:: find_grains()

      
      Find grains.
















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