smoother.simulation.histology
=============================

.. py:module:: smoother.simulation.histology

.. autoapi-nested-parse::

   Extract spatial patterns from a given histology image



Attributes
----------

.. autoapisummary::

   smoother.simulation.histology.ImageContainer


Functions
---------

.. autoapisummary::

   smoother.simulation.histology.get_features_matrix
   smoother.simulation.histology.extract_features_from_image
   smoother.simulation.histology.cal_membership_value


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

.. py:data:: ImageContainer
   :value: None


.. py:function:: get_features_matrix(crop: squidpy.im.ImageContainer, layer)

   Extract features from a given crop

   :param crop: crop of a image
   :param layer: Image layer in crop that should be processed

   :returns: the extracted features at this crop
   :rtype: df_1


.. py:function:: extract_features_from_image(image: squidpy.im.ImageContainer, crop_size, layer)

   Extract features from a given image

   :param image: squidpy ImageContainer
   :param crop_size: the # of crops wanted [n_row_crops, n_col_crops]
   :param layer: Image layer in image that should be processed

   :returns: the extracted features at all crops
   :rtype: features_df


.. py:function:: cal_membership_value(membership_mat, feature_df, cluster_centers, m)

   Calculate fuzzy-c-means membership values

   :param membership_mat: membership matrix n_location x n_cluster
   :param feature_df: features matrix n_location x n_feature
   :param cluster_centers: center point for clusters n_cluster x n_feature
   :param m: m value required by FCM

   :returns: updated membership matrix n_location x n_cluster
   :rtype: membership_mat