cellects 0.2.7__py3-none-any.whl → 0.3.1__py3-none-any.whl

cellects/image_analysis/one_image_analysis_threads.py

@@ -1,24 +1,19 @@
 #!/usr/bin/env python3
-"""Module containing classes for image processing and saving selected color space combinations.
+"""Module implementing an image processing pipeline for segmentation and analysis.
 
-This module provides two thread-based components for analyzing images and storing results:
-
-ProcessFirstImage handles initial segmentation, thresholding, clustering, and shape validation
-SaveCombinationThread stores processed features in parent objects asynchronously
-The processing pipeline includes Otsu thresholding, k-means clustering, connected component analysis,
-and geometric filtering based on size/shape constraints.
+This module defines functionality to process images using various color space
+combinations, filters, and segmentation techniques like K-means clustering or
+Otsu thresholding. It supports logical operations between images and iterative refinement of
+color space combinations by adding/removing channels based on validation criteria.
+The pipeline evaluates resulting binary masks for blob statistics and spatial relationships.
 
 Classes
-ProcessFirstImage : Processes image data with segmentation techniques and validates shapes.
-SaveCombinationThread : Thread to save combination results while maintaining UI responsiveness.
-
-Functions (in ProcessFirstImage)
-shape_selection : Filters shapes by size thresholds and geometric criteria.
-kmeans : Performs clustering-based image segmentation into specified number of clusters.
-process_binary_image : Validates detected shapes against area constraints and spot count targets.
+ProcessImage : Processes an image according to parameterized instructions, performing color space combination,
+filtering, segmentation, and shape validation.
 
 Notes
-Uses threading.Thread for background operations to maintain application responsiveness during processing.
+Relies on external functions from cellects.image_analysis module for core operations like
+color space combination, filtering, PCA extraction, and segmentation.
 """
 import threading
 import logging
@@ -26,145 +21,299 @@ import numpy as np
 import cv2
 from numpy.typing import NDArray
 from typing import Tuple
-from cellects.image_analysis.image_segmentation import otsu_thresholding, combine_color_spaces
+from numba.typed import Dict, List
+import pandas as pd
+from cellects.image_analysis.image_segmentation import combine_color_spaces, apply_filter, kmeans, extract_first_pc, otsu_thresholding
 from cellects.image_analysis.morphological_operations import shape_selection
 
 
-class ProcessFirstImage:
+class ProcessImage:
     """
-    A class for processing lists.
+    A class for processing an image according to a list of parameters.
     """
     def __init__(self, l):
         """
         Arguments:
             list : list
-
         """
+        self.stats = None
+        self.greyscale = None
         self.start_processing(l)
 
     def start_processing(self, l: list):
         """
+        Begin processing tasks based on the given process type.
 
-        Start the processing based on given list input.
-
-        The method processes the provided list to perform various operations
-        on the image data. It sets up several attributes and performs different
-        image processing tasks like Otsu thresholding or k-means clustering.
+        Parameters
+        ----------
+        l : list
+            A list containing parameters and instructions for processing.
+            Expected structure:
+                - First element: self.parent (object)
+                - Second element: params (dict)
+                - Third element: process type (str) ('one', 'PCA', 'add', 'subtract', or 'logical')
+                - Fourth element (if applicable): additional parameters based on process type.
 
-        The method does not return any value.
+        Notes
+        -----
+        This function modifies instance attributes directly and performs various operations based on the `process` type.
         """
         self.parent = l[0]
-        get_one_channel_result = l[1]
-        combine_channels = l[2]
+        self.fact = pd.DataFrame(np.zeros((1, len(self.parent.factors)), dtype=np.uint32), columns=self.parent.factors)
+        self.params = l[1]
+        process = l[2]
         self.all_c_spaces = self.parent.all_c_spaces
-        self.several_blob_per_arena = l[4]
-        self.sample_number = l[5]
-        self.horizontal_size = l[6]
-        self.spot_shape = l[7]
-        kmeans_clust_nb = l[8]
-        self.biomask = l[9]
-        self.backmask = l[10]
-        if get_one_channel_result:
+        if process == 'one':
             self.csc_dict = l[3]
-            self.image = combine_color_spaces(self.csc_dict, self.all_c_spaces)
-            if kmeans_clust_nb is None:
-                self.binary_image = otsu_thresholding(self.image)
-            else:
-                self.kmeans(kmeans_clust_nb, self.biomask, self.backmask)
-                # self.parent.image = self.image
-                # self.parent.kmeans(kmeans_clust_nb, self.biomask, self.backmask)
-                # self.binary_image = self.parent.binary_image
-            self.unaltered_concomp_nb, shapes = cv2.connectedComponents(self.binary_image)
-            if 1 < self.unaltered_concomp_nb < 10000:
-                self.total_area = np.sum(self.binary_image)
-                inf_lim = np.min((100, np.ceil(self.binary_image.size / 1000)))
-                if inf_lim < self.total_area < self.binary_image.size * 0.9:
-                    self.process_binary_image()
-                    self.parent.save_combination_features(self)
-                    # except RuntimeWarning:
-                    #     Make sure that scaling and spot size are correct
-        if combine_channels:
-            i = l[3]
-            possibilities = l[11]
-            saved_color_space_list = self.parent.saved_color_space_list
-            combination_features = self.parent.combination_features
-            self.csc_dict = saved_color_space_list[i]
-            previous_shape_number = combination_features[i, 4]
-            previous_sum = combination_features[i, 5]
-            for j in possibilities[::-1]:
-                csc_dict2 = saved_color_space_list[j]
-                csc_dict = self.csc_dict.copy()
-                keys = list(csc_dict.keys())
-
-                k2 = list(csc_dict2.keys())[0]
-                v2 = csc_dict2[k2]
-                if np.isin(k2, keys) and np.sum(v2 * csc_dict[k2]) != 0:
-                    break
-                for factor in [2, 1]:
-                    if np.isin(k2, keys):
-                        csc_dict[k2] += v2 * factor
-                    else:
-                        csc_dict[k2] = v2 * factor
-                    self.image = combine_color_spaces(csc_dict, self.all_c_spaces)
-                    if kmeans_clust_nb is None:
-                        self.binary_image = otsu_thresholding(self.image)
-                    else:
-                        self.kmeans(kmeans_clust_nb, self.biomask, self.backmask)
-                    self.process_binary_image()
-                    self.total_area = self.validated_shapes.sum()
-                    if previous_shape_number >= self.shape_number and self.total_area > previous_sum * 0.9:
-                        previous_shape_number = self.shape_number
-                        previous_sum = self.total_area
-                        self.csc_dict = csc_dict.copy()
-                        self.unaltered_concomp_nb = combination_features[i, 3]
-                        self.parent.save_combination_features(self)
-
-    def kmeans(self, cluster_number: int, biomask: NDArray[np.uint8]=None, backmask: NDArray[np.uint8]=None, bio_label=None):
-        """
-
-        Perform k-means clustering on the image to segment it into a specified number of clusters.
-
-        Args:
-            cluster_number (int): The desired number of clusters.
-            biomask (NDArray[np.uint8]): Optional mask for biological regions. Default is None.
-            backmask (NDArray[np.uint8]): Optional mask for background regions. Default is None.
-            bio_label (int): The label assigned to the biological region. Default is None.
-
-        Returns:
-            None
-
-        Note:
-            This method modifies the `binary_image` and `bio_label` attributes of the instance.
-
-        """
-        image = self.image.reshape((-1, 1))
-        image = np.float32(image)
-        criteria = (cv2.TERM_CRITERIA_EPS + cv2.TERM_CRITERIA_MAX_ITER, 10, 1.0)
-        compactness, label, center = cv2.kmeans(image, cluster_number, None, criteria, attempts=10, flags=cv2.KMEANS_RANDOM_CENTERS)
-        kmeans_image = np.uint8(label.flatten().reshape(self.image.shape[:2]))
-        sum_per_label = np.zeros(cluster_number)
-        self.binary_image = np.zeros(self.image.shape[:2], np.uint8)
-        if bio_label is not None:
-            self.binary_image[np.nonzero(kmeans_image == bio_label)] = 1
-            self.bio_label = bio_label
+            self.combine_and_segment()
+            self.evaluate_segmentation()
+        elif process == 'PCA':
+            self.pca_and_segment()
+            self.evaluate_segmentation()
+        elif process == 'add':
+            self.try_adding_channels(l[3])
+        elif process == 'subtract':
+            self.try_subtracting_channels()
+        elif process == 'logical':
+            self.operation = l[3]
+            self.apply_logical_operation()
+
+    def combine_and_segment(self, csc_dict: Dict=None):
+        """
+        Combines color spaces and segments images into binary masks using either K-means clustering or Otsu's thresholding based on specified parameters.
+
+        Parameters
+        ----------
+        csc_dict : dict or None
+            Optional dictionary mapping color space abbreviations (e.g., 'bgr', 'hsv') to their relative contribution coefficients for combination. If not provided, uses the instance's `self.csc_dict` attribute instead.
+
+        """
+        if csc_dict is None:
+            csc_dict = self.csc_dict
+        self.image = combine_color_spaces(csc_dict, self.all_c_spaces)
+        self.apply_filter_and_segment()
+
+    def pca_and_segment(self):
+        """
+        Extract the first principal component and perform segmentation.
+
+        This method extracts the first principal component from the 'bgr' color space
+        and performs k-means clustering or Otsu thresholding to segment the image based on the
+        parameters provided.
+        """
+        self.image, _, first_pc_vector = extract_first_pc(self.all_c_spaces['bgr'])
+        self.csc_dict = Dict()
+        self.csc_dict['bgr'] = first_pc_vector
+        self.apply_filter_and_segment()
+
+    def apply_filter_and_segment(self):
+        self.greyscale = self.image
+        if self.params['filter_spec'] is not None and self.params['filter_spec']["filter1_type"] != "":
+            self.greyscale = apply_filter(self.greyscale, self.params['filter_spec']["filter1_type"], self.params['filter_spec']["filter1_param"])
+
+
+        if self.params['kmeans_clust_nb'] is not None and (self.params['bio_mask'] is not None or self.params['back_mask'] is not None):
+            self.binary_image, _, self.bio_label, _ = kmeans(self.greyscale, None, self.params['kmeans_clust_nb'],
+                                                             self.params['bio_mask'], self.params['back_mask'])
+        else:
+            self.binary_image = otsu_thresholding(self.greyscale)
+        self.validated_shapes = self.binary_image
+
+    def evaluate_segmentation(self):
+        """
+        Use the filtering algorithm based on the kind of image to analyse
+        """
+        if self.params['is_first_image']:
+            self.eval_first_image()
         else:
-            if biomask is not None:
-                all_labels = kmeans_image[biomask[0], biomask[1]]
-                for i in range(cluster_number):
-                    sum_per_label[i] = (all_labels == i).sum()
-                self.bio_label = np.nonzero(sum_per_label == np.max(sum_per_label))
-            elif backmask is not None:
-                all_labels = kmeans_image[backmask[0], backmask[1]]
-                for i in range(cluster_number):
-                    sum_per_label[i] = (all_labels == i).sum()
-                self.bio_label = np.nonzero(sum_per_label == np.min(sum_per_label))
+            self.eval_any_image()
+
+    def eval_first_image(self):
+        """
+        First image filtering process for binary images.
+
+        This method processes the first binary image by identifying connected components, computing
+        the total area of the image and its potential size limits. If the number of blobs and their
+        total area fall within acceptable thresholds, it proceeds with additional processing and saving.
+        """
+        self.fact['unaltered_blob_nb'], shapes = cv2.connectedComponents(self.binary_image)
+        self.fact['unaltered_blob_nb'] -= 1
+        if 1 <= self.fact['unaltered_blob_nb'].values[0] < 10000:
+            self.fact['total_area'] = np.sum(self.binary_image)
+            inf_lim = np.min((20, np.ceil(self.binary_image.size / 1000)))
+            if inf_lim < self.fact['total_area'].values[0] < self.binary_image.size * 0.9:
+                self.process_first_binary_image()
+                self.save_combination()
+
+    def eval_any_image(self):
+        """
+
+        Summarizes the binary image analysis and determines blob characteristics.
+
+        Evaluates a binary image to determine various attributes like surface area,
+        blob number, and their relative positions within specified masks. It also
+        checks for common areas with a reference image and saves the combination if
+        certain conditions are met.
+        """
+        surf = self.binary_image.sum()
+        if surf < self.params['total_surface_area']:
+            self.fact['unaltered_blob_nb'], shapes = cv2.connectedComponents(self.binary_image)
+            self.fact['unaltered_blob_nb'] -= 1
+            test: bool = True
+            if self.params['arenas_mask'] is not None:
+                self.fact['out_of_arenas'] = np.sum(self.binary_image * self.params['out_of_arenas_mask'])
+                self.fact['in_arenas'] = np.sum(self.binary_image * self.params['arenas_mask'])
+                test = self.fact['out_of_arenas'].values[0] < self.fact['in_arenas'].values[0]
+            if test:
+                if self.params['con_comp_extent'][0] <= self.fact['unaltered_blob_nb'].values[0] <= self.params['con_comp_extent'][1]:
+                    if self.params['ref_image'] is not None:
+                        self.fact['common_with_ref'] = np.sum(self.params['ref_image'] * self.binary_image)
+                        test = self.fact['common_with_ref'].values[0] > 0
+                    if test:
+                        self.fact['blob_nb'], shapes, self.stats, centroids = cv2.connectedComponentsWithStats(self.binary_image)
+                        self.fact['blob_nb'] -= 1
+                        if np.all(np.sort(self.stats[:, 4])[:-1] < self.params['max_blob_size']):
+                            self.save_combination()
+
+    def apply_logical_operation(self):
+        """
+        Apply a logical operation between two saved images.
+
+        This method applies a specified logical operation ('And' or 'Or')
+        between two images stored in the parent's saved_images_list. The result
+        is stored as a binary image and validated, with color space information
+        updated accordingly.
+
+        Notes
+        -----
+        This method modifies the following instance attributes:
+        - `binary_image`
+        - `validated_shapes`
+        - `image`
+        - `csc_dict`
+        """
+        im1 = self.parent.saved_images_list[self.operation[0]]
+        im2 = self.parent.saved_images_list[self.operation[1]]
+        if self.operation['logical'] == 'And':
+            self.binary_image = np.logical_and(im1, im2).astype(np.uint8)
+        elif self.operation['logical'] == 'Or':
+            self.binary_image = np.logical_or(im1, im2).astype(np.uint8)
+        self.validated_shapes = self.binary_image
+        self.greyscale = self.parent.converted_images_list[self.operation[0]]
+        csc1 = self.parent.saved_color_space_list[self.operation[0]]
+        csc2 = self.parent.saved_color_space_list[self.operation[1]]
+        self.csc_dict = {}
+        for k, v in csc1.items():
+            self.csc_dict[k] = v
+        for k, v in csc2.items():
+            self.csc_dict[k] = v
+        self.csc_dict['logical'] = self.operation['logical']
+        self.evaluate_segmentation()
+
+    def try_adding_channels(self, i: int):
+        """
+        Try adding channels to the current color space combination.
+
+        Extend the functionality of a selected color space combination by attempting
+        to add channels from other combinations, evaluating the results based on
+        the number of shapes and total area.
+
+        Parameters
+        ----------
+        i : int
+            The index of the saved color space and combination features to start with.
+        """
+        saved_color_space_list = self.parent.saved_color_space_list
+        combination_features = self.parent.combination_features
+        self.csc_dict = saved_color_space_list[i]
+        previous_shape_number = combination_features.loc[i, 'blob_nb']
+        previous_sum = combination_features.loc[i, 'total_area']
+        for j in self.params['possibilities'][::-1]:
+            csc_dict2 = saved_color_space_list[j]
+            csc_dict = self.csc_dict.copy()
+            keys = list(csc_dict.keys())
+
+            k2 = list(csc_dict2.keys())[0]
+            v2 = csc_dict2[k2]
+            if np.isin(k2, keys) and np.sum(v2 * csc_dict[k2]) != 0:
+                break
+            for factor in [2, 1]:
+                if np.isin(k2, keys):
+                    csc_dict[k2] += v2 * factor
+                else:
+                    csc_dict[k2] = v2 * factor
+                self.combine_and_segment(csc_dict)
+                if self.params['is_first_image']:
+                    self.process_first_binary_image()
+                else:
+                    self.fact['blob_nb'], shapes, self.stats, centroids = cv2.connectedComponentsWithStats(self.validated_shapes)
+                    self.fact['blob_nb'] -= 1
+                self.fact['total_area'] = self.validated_shapes.sum()
+                if self.fact['blob_nb'].values[0] < previous_shape_number  and self.fact['total_area'].values[0] > previous_sum * 0.9:
+                    previous_shape_number = self.fact['blob_nb'].values[0]
+                    previous_sum = self.fact['total_area'].values[0]
+                    self.csc_dict = csc_dict.copy()
+                    self.fact['unaltered_blob_nb'] = combination_features.loc[i, 'unaltered_blob_nb']
+                    self.save_combination()
+
+    def try_subtracting_channels(self):
+        """
+        Tries to subtract channels to find the optimal color space combination.
+
+        This method attempts to remove color spaces one by one from the image
+        to find a combination that maintains the majority of areas while reducing
+        the number of color spaces. This process is repeated until no further
+        improvements are possible.
+        """
+        potentials = self.parent.all_combined
+        # Try to remove color space one by one
+        i = 0
+        original_length = len(potentials)
+        # The while loop until one col space remains or the removal of one implies a strong enough area change
+        while np.logical_and(len(potentials) > 1, i < original_length - 1):
+            self.combine_and_segment(potentials)
+            if self.params['is_first_image']:
+                self.process_first_binary_image()
+                previous_blob_nb = self.fact['blob_nb'].values[0]
             else:
-                for i in range(cluster_number):
-                    sum_per_label[i] = (kmeans_image == i).sum()
-                self.bio_label = np.nonzero(sum_per_label == np.min(sum_per_label))
-            self.binary_image[np.nonzero(kmeans_image == self.bio_label)] = 1
+                previous_blob_nb, shapes, self.stats, centroids = cv2.connectedComponentsWithStats(
+                    self.validated_shapes)
+                previous_blob_nb -= 1
+            previous_sum = self.validated_shapes.sum()
+            color_space_to_remove = List()
+            previous_c_space = list(potentials.keys())[-1]
+            for c_space in potentials.keys():
+                try_potentials = potentials.copy()
+                try_potentials.pop(c_space)
+                if i > 0:
+                    try_potentials.pop(previous_c_space)
+                self.combine_and_segment(try_potentials)
+                if self.params['is_first_image']:
+                    self.process_first_binary_image()
+                else:
+                    self.fact['blob_nb'], shapes, self.stats, centroids = cv2.connectedComponentsWithStats(
+                        self.validated_shapes)
+                    self.fact['blob_nb'] -= 1
+                self.fact['total_area'] = self.validated_shapes.sum()
+                if self.fact['blob_nb'].values[0] < previous_blob_nb and self.fact['total_area'].values[0] > previous_sum * 0.9:
+                    previous_blob_nb = self.fact['blob_nb'].values[0]
+                    previous_sum = self.fact['total_area'].values[0]
+                    self.csc_dict = try_potentials.copy()
+                    self.fact['unaltered_blob_nb'] = previous_blob_nb
+                    self.save_combination()
+                    # If removing that color space helps, we remove it from potentials
+                    color_space_to_remove.append(c_space)
+                    if i > 0:
+                        color_space_to_remove.append(previous_c_space)
+                previous_c_space = c_space
+            if len(color_space_to_remove) == 0:
+                break
+            color_space_to_remove = np.unique(color_space_to_remove)
+            for remove_col_space in color_space_to_remove:
+                potentials.pop(remove_col_space)
+            i += 1
 
-    def process_binary_image(self):
+    def process_first_binary_image(self):
         """
         Process the binary image to identify and validate shapes.
 
@@ -174,57 +323,38 @@ class ProcessFirstImage:
         sample number or applies additional filtering if necessary.
 
         """
-        shapes_features = shape_selection(self.binary_image, true_shape_number=self.sample_number, horizontal_size=self.horizontal_size,
-                        spot_shape=self.spot_shape, several_blob_per_arena=self.several_blob_per_arena,
-                        bio_mask=self.biomask, back_mask=self.backmask)
-        self.validated_shapes, self.shape_number, self.stats, self.centroids = shapes_features
-
+        shapes_features = shape_selection(self.binary_image, true_shape_number=self.params['blob_nb'],
+                        horizontal_size=self.params['blob_size'], spot_shape=self.params['blob_shape'],
+                        several_blob_per_arena=self.params['several_blob_per_arena'],
+                        bio_mask=self.params['bio_mask'], back_mask=self.params['back_mask'])
+        self.validated_shapes, self.fact['blob_nb'], self.stats, self.centroids = shapes_features
 
-class SaveCombinationThread(threading.Thread):
-    """
-    SaveCombinationThread
+    def save_combination(self):
+        """
+        Saves the calculated features and masks for a combination of shapes.
 
-    This class represents a thread for saving combinations.
+        This method calculates various statistical properties (std) and sums for the
+        validated shapes, and optionally computes sums for bio and back masks if they are
+        specified in the parameters.
 
-    """
-    def __init__(self, parent=None):
-        """
-        **Args:**
-
-            - `parent`: The parent object that initiated the thread. This is an optional argument and defaults to 'None'.
-
-        """
-        # super(SaveCombinationThread, self).__init__()
-        threading.Thread.__init__(self)
-        self.parent = parent
-
-    def run(self):
-        """
-        Runs the color space combination process and saves the results.
-
-        This method performs several tasks to save intermediate and final
-        results of the color space combination process. It logs messages,
-        updates lists with valid shapes, converts images to a specific format,
-        and updates combination features with various statistics. The method
-        also handles biomask and backmask calculations if they are not None.
-        Finally, it increments the saved color space number counter.
-        """
-        logging.info(f"Saving results from the color space combination: {self.process_i.csc_dict}. {self.process_i.shape_number} distinct specimen(s) detected.")
-        self.parent.saved_images_list.append(self.process_i.validated_shapes)
-        self.parent.converted_images_list.append(np.round(self.process_i.image).astype(np.uint8))
-        self.parent.saved_color_space_list.append(self.process_i.csc_dict)
-        self.parent.combination_features[self.parent.saved_csc_nb, :3] = list(self.process_i.csc_dict.values())[0]
-        self.parent.combination_features[self.parent.saved_csc_nb, 3] = self.process_i.unaltered_concomp_nb - 1  # unaltered_cc_nb
-        self.parent.combination_features[self.parent.saved_csc_nb, 4] = self.process_i.shape_number  # cc_nb
-        self.parent.combination_features[self.parent.saved_csc_nb, 5] = self.process_i.total_area  # area
-        self.parent.combination_features[self.parent.saved_csc_nb, 6] = np.std(self.process_i.stats[1:, 2])  # width_std
-        self.parent.combination_features[self.parent.saved_csc_nb, 7] = np.std(self.process_i.stats[1:, 3])  # height_std
-        self.parent.combination_features[self.parent.saved_csc_nb, 8] = np.std(self.process_i.stats[1:, 4])  # area_std
-        if self.process_i.biomask is not None:
-            self.parent.combination_features[self.parent.saved_csc_nb, 9] = np.sum(
-                self.process_i.validated_shapes[self.process_i.biomask[0], self.process_i.biomask[1]])
-        if self.process_i.backmask is not None:
-            self.parent.combination_features[self.parent.saved_csc_nb, 10] = np.sum(
-                (1 - self.process_i.validated_shapes)[self.process_i.backmask[0], self.process_i.backmask[1]])
-        self.parent.saved_csc_nb += 1
-        logging.info("end")
+        Parameters
+        ----------
+        self : object
+            The instance of the class containing this method. Must have attributes:
+            - ``validated_shapes``: (ndarray) Array of validated shapes.
+            - ``stats``: (ndarray) Statistics array containing width, height, and area.
+            - ``params``: dictionary with parameters including 'bio_mask' and 'back_mask'.
+            - ``fact``: dictionary to store the calculated features.
+            - ``parent``: The parent object containing the method `save_combination_features`.
+        """
+        self.fact['total_area'] = self.validated_shapes.sum()
+        self.fact['width_std'] = np.std(self.stats[1:, 2])
+        self.fact['height_std'] = np.std(self.stats[1:, 3])
+        self.fact['area_std'] = np.std(self.stats[1:, 4])
+        if self.params['bio_mask'] is not None:
+            self.fact['bio_sum'] = self.validated_shapes[self.params['bio_mask'][0], self.params['bio_mask'][1]].sum()
+        if self.params['back_mask'] is not None:
+            self.fact['back_sum'] = (1 - self.validated_shapes)[self.params['back_mask'][0], self.params['back_mask'][1]].sum()
+        self.parent.save_combination_features(self)
+        
+