cellects 0.2.6__tar.gz → 0.3.2__tar.gz

{cellects-0.2.6 → cellects-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: cellects
-Version: 0.2.6
+Version: 0.3.2
 Summary: Cell Expansion Computer Tracking Software.
 Author: Aurèle Boussard
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -730,7 +730,7 @@ Requires-Dist: mkdocs-jupyter; extra == "doc"
 [![Python versions](https://img.shields.io/pypi/pyversions/cellects.svg?style=flat-square)](https://pypi.org/project/cellects/)
 [![License](https://img.shields.io/pypi/l/cellects.svg?style=flat-square)](https://github.com/Aurele-B/cellects/blob/main/LICENSE)
 [![Stars](https://img.shields.io/github/stars/Aurele-B/cellects.svg?style=flat-square)](https://github.com/Aurele-B/cellects/stargazers)
-![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/Aurele-B/Cellects/.github%2Fworkflows%2Fci.yml)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/Aurele-B/Cellects/.github%2Fworkflows%2Frelease.yml)
 ![Coverage](https://raw.githubusercontent.com/Aurele-B/cellects/gh-pages/badges/coverage.svg)
 
 Description

{cellects-0.2.6 → cellects-0.3.2}/README.md

@@ -10,7 +10,7 @@
 [![Python versions](https://img.shields.io/pypi/pyversions/cellects.svg?style=flat-square)](https://pypi.org/project/cellects/)
 [![License](https://img.shields.io/pypi/l/cellects.svg?style=flat-square)](https://github.com/Aurele-B/cellects/blob/main/LICENSE)
 [![Stars](https://img.shields.io/github/stars/Aurele-B/cellects.svg?style=flat-square)](https://github.com/Aurele-B/cellects/stargazers)
-![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/Aurele-B/Cellects/.github%2Fworkflows%2Fci.yml)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/Aurele-B/Cellects/.github%2Fworkflows%2Frelease.yml)
 ![Coverage](https://raw.githubusercontent.com/Aurele-B/cellects/gh-pages/badges/coverage.svg)
 
 Description

{cellects-0.2.6 → cellects-0.3.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cellects"
-version = "0.2.6"
+version = "0.3.2"
 description = "Cell Expansion Computer Tracking Software."
 readme = "README.md"
 license = { file = "LICENSE" }

{cellects-0.2.6 → cellects-0.3.2}/src/cellects/core/cellects_threads.py

@@ -354,26 +354,18 @@ class UpdateImageThread(QtCore.QThread):
             image = self.parent().imageanalysiswindow.drawn_image.copy()
             # 3) The automatically detected video contours
             if self.parent().imageanalysiswindow.delineation_done:  # add a mask of the video contour
+                if self.parent().po.vars['contour_color'] == 255:
+                    arena_contour_col = (240, 232, 202)
+                else:
+                    arena_contour_col = (138, 95, 18)
                 # Draw the delineation mask of each arena
-                for contour_i in range(len(self.parent().po.top)):
-                    min_cy = self.parent().po.top[contour_i]
-                    max_cy = self.parent().po.bot[contour_i]
-                    min_cx = self.parent().po.left[contour_i]
-                    max_cx = self.parent().po.right[contour_i]
-                    text = f"{contour_i + 1}"
-                    position = (self.parent().po.left[contour_i] + 25, self.parent().po.top[contour_i] + (self.parent().po.bot[contour_i] - self.parent().po.top[contour_i]) // 2)
-                    image = cv2.putText(image,  # numpy array on which text is written
-                                    text,  # text
-                                    position,  # position at which writing has to start
-                                    cv2.FONT_HERSHEY_SIMPLEX,  # font family
-                                    1,  # font size
-                                    (138, 95, 18, 255),
-                                    # (209, 80, 0, 255),  # font color
-                                    2)  # font stroke
+                for _i, (min_cy, max_cy, min_cx, max_cx) in enumerate(zip(self.parent().po.top, self.parent().po.bot, self.parent().po.left, self.parent().po.right)):
+                    position = (min_cx + 25, min_cy + (max_cy - min_cy) // 2)
+                    image = cv2.putText(image, f"{_i + 1}", position, cv2.FONT_HERSHEY_SIMPLEX, 1,  arena_contour_col + (255,),2)
                     if (max_cy - min_cy) < 0 or (max_cx - min_cx) < 0:
                         self.parent().imageanalysiswindow.message.setText("Error: the shape number or the detection is wrong")
                     image = draw_img_with_mask(image, dims, (min_cy, max_cy - 1, min_cx, max_cx - 1),
-                                               self.parent().po.vars['arena_shape'], (138, 95, 18), True, contour_width)
+                                               self.parent().po.vars['arena_shape'], arena_contour_col, True, contour_width)
         else: #load
             if user_input:
                 # III/ If this thread runs from user input: update the drawn_image according to the current user input
@@ -391,7 +383,7 @@ class UpdateImageThread(QtCore.QThread):
                     mask_shape = "rectangle"
                 else:
                     color = (0, 0, 0)
-                    mask_shape = self.parent().po.all['arena_shape']
+                    mask_shape = self.parent().po.vars['arena_shape']
                 image = draw_img_with_mask(image, dims, minmax, mask_shape, color)
         self.parent().imageanalysiswindow.display_image.update_image(image)
         self.message_when_thread_finished.emit(True)
@@ -455,67 +447,12 @@ class FirstImageAnalysisThread(QtCore.QThread):
         pixel sizes, and updates various state attributes on the parent object.
         """
         tic = default_timer()
-        biomask = None
-        backmask = None
-        if self.parent().imageanalysiswindow.bio_masks_number != 0:
-            shape_nb, ordered_image = cv2.connectedComponents((self.parent().imageanalysiswindow.bio_mask > 0).astype(np.uint8))
-            shape_nb -= 1
-            biomask = np.nonzero(self.parent().imageanalysiswindow.bio_mask)
-        else:
-            shape_nb = 0
-        if self.parent().imageanalysiswindow.back_masks_number != 0:
-            backmask = np.nonzero(self.parent().imageanalysiswindow.back_mask)
-        if self.parent().po.visualize or len(self.parent().po.first_im.shape) == 2 or shape_nb == self.parent().po.sample_number:
-            self.message_from_thread.emit("Image segmentation, wait")
-            if not self.parent().imageanalysiswindow.asking_first_im_parameters_flag and self.parent().po.all['scale_with_image_or_cells'] == 0 and self.parent().po.all["set_spot_size"]:
-                self.parent().po.get_average_pixel_size()
-            else:
-                self.parent().po.starting_blob_hsize_in_pixels = None
-            self.parent().po.all["bio_mask"] = biomask
-            self.parent().po.all["back_mask"] = backmask
-            self.parent().po.fast_first_image_segmentation()
-            if shape_nb == self.parent().po.sample_number and self.parent().po.first_image.im_combinations[self.parent().po.current_combination_id]['shape_number'] != self.parent().po.sample_number:
-                self.parent().po.first_image.im_combinations[self.parent().po.current_combination_id]['shape_number'] = shape_nb
-                self.parent().po.first_image.shape_number = shape_nb
-                self.parent().po.first_image.validated_shapes = (self.parent().imageanalysiswindow.bio_mask > 0).astype(np.uint8)
-                self.parent().po.first_image.im_combinations[self.parent().po.current_combination_id]['binary_image'] = self.parent().po.first_image.validated_shapes
+        if self.parent().po.visualize or len(self.parent().po.first_im.shape) == 2:
+            self.message_from_thread.emit("Image segmentation, wait...")
         else:
-            self.message_from_thread.emit("Generating analysis options, wait...")
-            if self.parent().po.vars["color_number"] > 2:
-                kmeans_clust_nb = self.parent().po.vars["color_number"]
-                if self.parent().po.basic:
-                    self.message_from_thread.emit("Generating analysis options, wait less than 30 minutes")
-                else:
-                    self.message_from_thread.emit("Generating analysis options, a few minutes")
-            else:
-                kmeans_clust_nb = None
-                if self.parent().po.basic:
-                    self.message_from_thread.emit("Generating analysis options, wait a few minutes")
-                else:
-                    self.message_from_thread.emit("Generating analysis options, around 1 minute")
-            if self.parent().imageanalysiswindow.asking_first_im_parameters_flag:
-                self.parent().po.first_image.find_first_im_csc(sample_number=self.parent().po.sample_number,
-                                                               several_blob_per_arena=None,
-                                                               spot_shape=None, spot_size=None,
-                                                               kmeans_clust_nb=kmeans_clust_nb,
-                                                               biomask=self.parent().po.all["bio_mask"],
-                                                               backmask=self.parent().po.all["back_mask"],
-                                                               color_space_dictionaries=None,
-                                                               basic=self.parent().po.basic)
-            else:
-                if self.parent().po.all['scale_with_image_or_cells'] == 0:
-                    self.parent().po.get_average_pixel_size()
-                else:
-                    self.parent().po.starting_blob_hsize_in_pixels = None
-                self.parent().po.first_image.find_first_im_csc(sample_number=self.parent().po.sample_number,
-                                                                                   several_blob_per_arena=self.parent().po.vars['several_blob_per_arena'],
-                                                                                   spot_shape=self.parent().po.all['starting_blob_shape'],
-                                                               spot_size=self.parent().po.starting_blob_hsize_in_pixels,
-                                                                                   kmeans_clust_nb=kmeans_clust_nb,
-                                                                                   biomask=self.parent().po.all["bio_mask"],
-                                                                                   backmask=self.parent().po.all["back_mask"],
-                                                                                   color_space_dictionaries=None,
-                                                               basic=self.parent().po.basic)
+            self.message_from_thread.emit("Generating segmentation options, wait...")
+        self.parent().po.full_first_image_segmentation(not self.parent().imageanalysiswindow.asking_first_im_parameters_flag,
+                                                       self.parent().imageanalysiswindow.bio_mask, self.parent().imageanalysiswindow.back_mask)
 
         logging.info(f" image analysis lasted {np.floor((default_timer() - tic) / 60).astype(int)} minutes {np.round((default_timer() - tic) % 60).astype(int)} secondes")
         self.message_when_thread_finished.emit(True)
@@ -582,58 +519,11 @@ class LastImageAnalysisThread(QtCore.QThread):
         message_when_thread_finished.emit(success : bool) : signal
             Signal to indicate the completion of the thread.
         """
-        self.parent().po.cropping(False)
-        self.parent().po.get_background_to_subtract()
-        biomask = None
-        backmask = None
-        if self.parent().imageanalysiswindow.bio_masks_number != 0:
-            biomask = np.nonzero(self.parent().imageanalysiswindow.bio_mask)
-        if self.parent().imageanalysiswindow.back_masks_number != 0:
-            backmask = np.nonzero(self.parent().imageanalysiswindow.back_mask)
         if self.parent().po.visualize or (len(self.parent().po.first_im.shape) == 2 and not self.parent().po.network_shaped):
             self.message_from_thread.emit("Image segmentation, wait...")
-            self.parent().po.fast_last_image_segmentation(biomask=biomask, backmask=backmask)
         else:
             self.message_from_thread.emit("Generating analysis options, wait...")
-            arenas_mask = None
-            if self.parent().po.all['are_gravity_centers_moving'] != 1:
-                cr = [self.parent().po.top, self.parent().po.bot, self.parent().po.left, self.parent().po.right]
-                arenas_mask = np.zeros_like(self.parent().po.first_image.validated_shapes)
-                for _i in np.arange(len(self.parent().po.vars['analyzed_individuals'])):
-                    if self.parent().po.vars['arena_shape'] == 'circle':
-                        ellipse = create_ellipse(cr[1][_i] - cr[0][_i], cr[3][_i] - cr[2][_i])
-                        arenas_mask[cr[0][_i]: cr[1][_i], cr[2][_i]:cr[3][_i]] = ellipse
-                    else:
-                        arenas_mask[cr[0][_i]: cr[1][_i], cr[2][_i]:cr[3][_i]] = 1
-            if self.parent().po.network_shaped:
-                self.parent().po.last_image.network_detection(arenas_mask, csc_dict=self.parent().po.vars["convert_for_motion"], biomask=biomask, backmask=backmask)
-            else:
-                if self.parent().po.vars['several_blob_per_arena']:
-                    concomp_nb = [self.parent().po.sample_number, self.parent().po.first_image.size // 50]
-                    max_shape_size = .75 * self.parent().po.first_image.size
-                    total_surfarea = .99 * self.parent().po.first_image.size
-                else:
-                    concomp_nb = [self.parent().po.sample_number, self.parent().po.sample_number * 200]
-                    if self.parent().po.all['are_zigzag'] == "columns":
-                        inter_dist = np.mean(np.diff(np.nonzero(self.parent().po.first_image.y_boundaries)))
-                    elif self.parent().po.all['are_zigzag'] == "rows":
-                        inter_dist = np.mean(np.diff(np.nonzero(self.parent().po.first_image.x_boundaries)))
-                    else:
-                        dist1 = np.mean(np.diff(np.nonzero(self.parent().po.first_image.y_boundaries)))
-                        dist2 = np.mean(np.diff(np.nonzero(self.parent().po.first_image.x_boundaries)))
-                        inter_dist = np.max(dist1, dist2)
-                    if self.parent().po.all['starting_blob_shape'] == "rectangle":
-                        max_shape_size = np.square(2 * inter_dist)
-                    else:
-                        max_shape_size = np.pi * np.square(inter_dist)
-                    total_surfarea = max_shape_size * self.parent().po.sample_number
-                ref_image = self.parent().po.first_image.validated_shapes
-                self.parent().po.first_image.generate_subtract_background(self.parent().po.vars['convert_for_motion'], self.parent().po.vars['drift_already_corrected'])
-                kmeans_clust_nb = None
-                self.parent().po.last_image.find_last_im_csc(concomp_nb, total_surfarea, max_shape_size, arenas_mask,
-                                                             ref_image, self.parent().po.first_image.subtract_background,
-                                                             kmeans_clust_nb, biomask, backmask, color_space_dictionaries=None,
-                                                             basic=self.parent().po.basic)
+        self.parent().po.full_last_image_segmentation(self.parent().imageanalysiswindow.bio_mask, self.parent().imageanalysiswindow.back_mask)
         self.message_when_thread_finished.emit(True)
 
 
@@ -645,7 +535,7 @@ class CropScaleSubtractDelineateThread(QtCore.QThread):
     -------
     message_from_thread : Signal(str)
         Signal emitted when progress messages are available.
-    message_when_thread_finished : Signal(bool)
+    message_when_thread_finished : Signal(dict)
         Signal emitted upon completion of the thread's task.
 
     Notes
@@ -653,7 +543,7 @@ class CropScaleSubtractDelineateThread(QtCore.QThread):
     This class uses `QThread` to manage the process asynchronously.
     """
     message_from_thread = QtCore.Signal(str)
-    message_when_thread_finished = QtCore.Signal(str)
+    message_when_thread_finished = QtCore.Signal(dict)
 
     def __init__(self, parent=None):
         """
@@ -686,8 +576,8 @@ class CropScaleSubtractDelineateThread(QtCore.QThread):
         to perform necessary image processing tasks.
         """
         logging.info("Start cropping if required")
+        analysis_status = {"continue": True, "message": ""}
         self.parent().po.cropping(is_first_image=True)
-        self.parent().po.cropping(is_first_image=False)
         self.parent().po.get_average_pixel_size()
         if os.path.isfile('Data to run Cellects quickly.pkl'):
             os.remove('Data to run Cellects quickly.pkl')
@@ -700,18 +590,22 @@ class CropScaleSubtractDelineateThread(QtCore.QThread):
             nb, shapes, stats, centroids = cv2.connectedComponentsWithStats(self.parent().po.first_image.validated_shapes)
             y_lim = self.parent().po.first_image.y_boundaries
             if ((nb - 1) != self.parent().po.sample_number or np.any(stats[:, 4] == 1)):
-                self.message_from_thread.emit("Image analysis failed to detect the right cell(s) number: restart the analysis.")
+                analysis_status["message"] = "Image analysis failed to detect the right cell(s) number: restart the analysis."
+                analysis_status['continue'] = False
+            elif y_lim is None:
+                analysis_status["message"] = "The shapes detected in the image did not allow automatic arena delineation."
+                analysis_status['continue'] = False
             elif (y_lim == - 1).sum() != (y_lim == 1).sum():
-                self.message_from_thread.emit("Automatic arena delineation cannot work if one cell touches the image border.")
+                analysis_status["message"] = "Automatic arena delineation cannot work if one cell touches the image border."
                 self.parent().po.first_image.y_boundaries = None
-            else:
-                logging.info("Start automatic video delineation")
-                analysis_status = self.parent().po.delineate_each_arena()
-                self.message_when_thread_finished.emit(analysis_status["message"])
-        else:
+                analysis_status['continue'] = False
+        if analysis_status['continue']:
             logging.info("Start automatic video delineation")
             analysis_status = self.parent().po.delineate_each_arena()
-            self.message_when_thread_finished.emit(analysis_status["message"])
+        else:
+            self.parent().po.first_image.validated_shapes = np.zeros(self.parent().po.first_image.image.shape[:2], dtype=np.uint8)
+            logging.info(analysis_status["message"])
+        self.message_when_thread_finished.emit(analysis_status)
 
 
 class SaveManualDelineationThread(QtCore.QThread):
@@ -738,21 +632,18 @@ class SaveManualDelineationThread(QtCore.QThread):
         """
         Do save the coordinates.
         """
-        self.parent().po.left = np.arange(self.parent().po.sample_number)
-        self.parent().po.right = np.arange(self.parent().po.sample_number)
-        self.parent().po.top = np.arange(self.parent().po.sample_number)
-        self.parent().po.bot = np.arange(self.parent().po.sample_number)
-        for arena in np.arange(1, self.parent().po.sample_number + 1):
-            y, x = np.nonzero(self.parent().imageanalysiswindow.arena_mask == arena)
-            self.parent().po.left[arena - 1] = np.min(x)
-            self.parent().po.right[arena - 1] = np.max(x)
-            self.parent().po.top[arena - 1] = np.min(y)
-            self.parent().po.bot[arena - 1] = np.max(y)
-
-        logging.info("Save data to run Cellects quickly")
-        self.parent().po.data_to_save['coordinates'] = True
+        self.parent().po.left = np.zeros(self.parent().po.sample_number)
+        self.parent().po.right = np.zeros(self.parent().po.sample_number)
+        self.parent().po.top = np.zeros(self.parent().po.sample_number)
+        self.parent().po.bot = np.zeros(self.parent().po.sample_number)
+        for arena_i in np.arange(self.parent().po.sample_number):
+            y, x = np.nonzero(self.parent().imageanalysiswindow.arena_mask == arena_i + 1)
+            self.parent().po.left[arena_i] = np.min(x)
+            self.parent().po.right[arena_i] = np.max(x)
+            self.parent().po.top[arena_i] = np.min(y)
+            self.parent().po.bot[arena_i] = np.max(y)
+        self.parent().po.list_coordinates()
         self.parent().po.save_data_to_run_cellects_quickly()
-        self.parent().po.data_to_save['coordinates'] = False
 
         logging.info("Save manual video delineation")
         self.parent().po.vars['analyzed_individuals'] = np.arange(self.parent().po.sample_number) + 1
@@ -816,7 +707,6 @@ class CompleteImageAnalysisThread(QtCore.QThread):
     def run(self):
         self.parent().po.get_background_to_subtract()
         self.parent().po.get_origins_and_backgrounds_lists()
-        self.parent().po.data_to_save['coordinates'] = True
         self.parent().po.data_to_save['exif'] = True
         self.parent().po.save_data_to_run_cellects_quickly()
         self.parent().po.all['bio_mask'] = None
@@ -867,10 +757,8 @@ class PrepareVideoAnalysisThread(QtCore.QThread):
         self.parent().po.find_if_lighter_background()
         logging.info("The current (or the first) folder is ready to run")
         self.parent().po.first_exp_ready_to_run = True
-        self.parent().po.data_to_save['coordinates'] = True
         self.parent().po.data_to_save['exif'] = True
         self.parent().po.save_data_to_run_cellects_quickly()
-        self.parent().po.data_to_save['coordinates'] = False
         self.parent().po.data_to_save['exif'] = False
 
 
@@ -1096,7 +984,7 @@ class OneArenaThread(QtCore.QThread):
         """
         arena = self.parent().po.all['arena']
         i = np.nonzero(self.parent().po.vars['analyzed_individuals'] == arena)[0][0]
-        true_frame_width = self.parent().po.vars['origin_list'][i].shape[1]
+        true_frame_width = self.parent().po.right[i] - self.parent().po.left[i]# self.parent().po.vars['origin_list'][i].shape[1]
         if self.parent().po.all['overwrite_unaltered_videos'] and os.path.isfile(f'ind_{arena}.npy'):
             os.remove(f'ind_{arena}.npy')
         background = None
@@ -1173,16 +1061,7 @@ class OneArenaThread(QtCore.QThread):
             self.parent().po.converted_video = deepcopy(self.parent().po.motion.converted_video)
             if self.parent().po.vars['convert_for_motion']['logical'] != 'None':
                 self.parent().po.converted_video2 = deepcopy(self.parent().po.motion.converted_video2)
-        self.parent().po.motion.get_origin_shape()
-
-        if self.parent().po.motion.dims[0] >= 40:
-            step = self.parent().po.motion.dims[0] // 20
-        else:
-            step = 1
-        if self.parent().po.motion.start >= (self.parent().po.motion.dims[0] - step - 1):
-            self.parent().po.motion.start = None
-        else:
-            self.parent().po.motion.get_covering_duration(step)
+        self.parent().po.motion.assess_motion_detection()
         self.when_loading_finished.emit(save_loaded_video)
 
         if self.parent().po.motion.visu is None:
@@ -1323,8 +1202,7 @@ class OneArenaThread(QtCore.QThread):
 
             while self._isRunning and analysis_i.t < analysis_i.binary.shape[0]:
                 analysis_i.update_shape(False)
-                contours = np.nonzero(
-                    cv2.morphologyEx(analysis_i.binary[analysis_i.t - 1, :, :], cv2.MORPH_GRADIENT, cross_33))
+                contours = np.nonzero(get_contours(analysis_i.binary[analysis_i.t - 1, :, :]))
                 current_image = deepcopy(self.parent().po.motion.visu[analysis_i.t - 1, :, :, :])
                 current_image[contours[0], contours[1], :] = self.parent().po.vars['contour_color']
                 self.image_from_thread.emit(
@@ -1355,7 +1233,6 @@ class OneArenaThread(QtCore.QThread):
         self.when_detection_finished.emit("Post processing done, read to see the result")
 
 
-
 class VideoReaderThread(QtCore.QThread):
     """
     Thread for reading a video in the GUI.
@@ -1427,7 +1304,7 @@ class VideoReaderThread(QtCore.QThread):
                 video_mask = np.cumsum(video_mask.astype(np.uint32), axis=0)
                 video_mask[video_mask > 0] = 1
                 video_mask = video_mask.astype(np.uint8)
-        logging.info(f"sum: {video_mask.sum()}")
+        frame_delay = (8 + np.log10(self.parent().po.motion.dims[0])) / self.parent().po.motion.dims[0]
         for t in np.arange(self.parent().po.motion.dims[0]):
             mask = cv2.morphologyEx(video_mask[t, ...], cv2.MORPH_GRADIENT, cross_33)
             mask = np.stack((mask, mask, mask), axis=2)
@@ -1435,7 +1312,7 @@ class VideoReaderThread(QtCore.QThread):
             current_image[mask > 0] = self.parent().po.vars['contour_color']
             self.message_from_thread.emit(
                 {"current_image": current_image, "message": f"Reading in progress... Image number: {t}"}) #, "time": timings[t]
-            time.sleep(1 / 50)
+            time.sleep(frame_delay)
         self.message_from_thread.emit({"current_image": current_image, "message": ""})#, "time": timings[t]
 
 
@@ -1552,26 +1429,11 @@ class WriteVideoThread(QtCore.QThread):
 
         already_greyscale : bool
             Flag indicating if the video is already in greyscale format.
-            This parameter must be set as a variable named 'already_greyscale' in the instance
-            variables of the parent object.
-
-        Returns
-        -------
-        None
 
         Raises
         ------
         FileNotFoundError
             When the path to write the video is not specified.
-
-        Examples
-        --------
-        >>> self.parent().po.vars['already_greyscale'] = False
-        >>> self.run()
-        >>> # Expects to write a visualization video as 'ind_arena.npy'
-        >>> self.parent().po.vars['already_greyscale'] = True
-        >>> self.run()
-        >>> # Expects to write a converted video as 'ind_arena.npy'
         """
         arena = self.parent().po.all['arena']
         if not self.parent().po.vars['already_greyscale']:

{cellects-0.2.6 → cellects-0.3.2}/src/cellects/core/motion_analysis.py

@@ -151,28 +151,14 @@ class MotionAnalysis:
 
         self.start = None
         if detect_shape:
-            self.start = None
-            # Here to conditional layers allow to detect if an expansion/exploration occured
-            self.get_origin_shape()
-            # The first, user-defined is the 'first_move_threshold' and the second is the detection of the
-            # substantial image: if any of them is not detected, the program considers there is not exp.
-            if self.dims[0] >= 40:
-                step = self.dims[0] // 20
-            else:
-                step = 1
-            if self.dims[0] == 1 or self.start >= (self.dims[0] - step - 1):
-                self.start = None
-            else:
-                self.get_covering_duration(step)
-                if self.start is not None:
-                    self.detection()
-                    self.initialize_post_processing()
-                    self.t = self.start
-                    while self.t < self.dims[0]:  #200:
-                        self.update_shape(show_seg)
+            self.assess_motion_detection()
+            if self.start is not None:
+                self.detection()
+                self.initialize_post_processing()
+                self.t = self.start
+                while self.t < self.dims[0]:  #200:
+                    self.update_shape(show_seg)
                 #
-            if self.start is None:
-                self.binary = np.repeat(np.expand_dims(self.origin, 0), self.converted_video.shape[0], axis=0)
 
             if analyse_shape:
                 self.get_descriptors_from_binary()
@@ -204,8 +190,25 @@ class MotionAnalysis:
 
         """
         logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Load images and videos")
-        self.origin = self.vars['origin_list'][i]  # self.vars['origins_list'][i]
-        true_frame_width = self.origin.shape[1]
+        if 'bb_coord' in self.vars:
+            crop_top, crop_bot, crop_left, crop_right, top, bot, left, right = self.vars['bb_coord']
+        elif videos_already_in_ram is not None:
+            if isinstance(videos_already_in_ram, list):
+                crop_bot, crop_right = videos_already_in_ram[0].shape[1], videos_already_in_ram[0].shape[2]
+            else:
+                crop_bot, crop_right = videos_already_in_ram.shape[1], videos_already_in_ram.shape[2]
+            crop_top, crop_left, top, bot, left, right = 0, 0, [0], [crop_bot], [0], [crop_right]
+        if isinstance(self.vars['origin_list'][i], Tuple):
+            self.origin_idx = self.vars['origin_list'][i]
+            frame_height = bot[i] - top[i]
+            true_frame_width = right[i] - left[i]
+            self.origin = np.zeros((frame_height, true_frame_width), dtype=np.uint8)
+            self.origin[self.origin_idx[0], self.origin_idx[1]] = 1
+        else:
+            self.origin = self.vars['origin_list'][i]
+            frame_height = self.origin.shape[0]
+            true_frame_width = self.origin.shape[1]
+
         vid_name = None
         if self.vars['video_list'] is not None:
             vid_name = self.vars['video_list'][i]
@@ -219,6 +222,18 @@ class MotionAnalysis:
                               self.vars['convert_for_motion'], videos_already_in_ram, true_frame_width, vid_name,
                               self.background, self.background2)
         self.visu, self.converted_video, self.converted_video2 = vids
+        # When the video(s) already exists (not just written as .pny), they need to be sliced:
+        if self.visu is not None:
+            if self.visu.shape[1] != frame_height or self.visu.shape[2] != true_frame_width:
+                self.visu = self.visu[:, crop_top:crop_bot, crop_left:crop_right, ...]
+                self.visu = self.visu[:, top[i]:bot[i], left[i]:right[i], ...]
+                if self.converted_video is not None:
+                    self.converted_video = self.converted_video[:, crop_top:crop_bot, crop_left:crop_right]
+                    self.converted_video = self.converted_video[:, top[i]:bot[i], left[i]:right[i]]
+                    if self.converted_video2 is not None:
+                        self.converted_video2 = self.converted_video2[:, crop_top:crop_bot, crop_left:crop_right]
+                        self.converted_video2 = self.converted_video2[:, top[i]:bot[i], left[i]:right[i]]
+
         if self.converted_video is None:
             logging.info(
                 f"Arena n°{self.one_descriptor_per_arena['arena']}. Convert the RGB visu video into a greyscale image using the color space combination: {self.vars['convert_for_motion']}")
@@ -228,6 +243,26 @@ class MotionAnalysis:
                                                      self.vars['filter_spec'])
             self.converted_video, self.converted_video2 = vids
 
+    def assess_motion_detection(self):
+        """
+        Assess if a motion can be detected using the current parameters.
+
+        Validate the specimen(s) detected in the first frame and evaluate roughly how growth occurs during the video.
+        """
+        # Here to conditional layers allow to detect if an expansion/exploration occured
+        self.get_origin_shape()
+        # The first, user-defined is the 'first_move_threshold' and the second is the detection of the
+        # substantial image: if any of them is not detected, the program considers there is no motion.
+        if self.dims[0] >= 40:
+            step = self.dims[0] // 20
+        else:
+            step = 1
+        if self.dims[0] == 1 or self.start >= (self.dims[0] - step - 1):
+            self.start = None
+            self.binary = np.repeat(np.expand_dims(self.origin, 0), self.converted_video.shape[0], axis=0)
+        else:
+            self.get_covering_duration(step)
+
     def get_origin_shape(self):
         """
         Determine the origin shape and initialize variables based on the state of the current analysis.
@@ -259,25 +294,19 @@ class MotionAnalysis:
                     self.drift_mask_coord[:, 2] == 0) and np.all(self.drift_mask_coord[:, 3] == self.dims[2] - 1):
                 logging.error(f"Drift correction has been wrongly detected. Images do not contain zero-valued pixels")
                 self.vars['drift_already_corrected'] = False
-        if self.vars['origin_state'] == "constant":
-            self.start = 1
-            if self.vars['lighter_background']:
-                # Initialize the covering_intensity matrix as a reference for pixel fading
-                self.covering_intensity[self.origin_idx[0], self.origin_idx[1]] = 200
-        else:
-            self.start = 0
+        self.start = 1
+        if self.vars['origin_state'] == "invisible":
+            self.start += self.vars['first_detection_frame']
             analysisi = self.frame_by_frame_segmentation(self.start, self.origin)
-            while np.logical_and(np.sum(analysisi.binary_image) < self.vars['first_move_threshold'], self.start < self.dims[0]):
-                self.start += 1
-                analysisi = self.frame_by_frame_segmentation(self.start, self.origin)
-
             # Use connected components to find which shape is the nearest from the image center.
             if self.vars['several_blob_per_arena']:
                 self.origin = analysisi.binary_image
             else:
-                nb_components, output, stats, centroids = cv2.connectedComponentsWithStats(analysisi.binary_image,
-                                                                                           connectivity=8)
-                if self.vars['appearance_detection_method'] == 'most_central':
+                if self.vars['appearance_detection_method'] == 'largest':
+                    self.origin = keep_one_connected_component(analysisi.binary_image)
+                elif self.vars['appearance_detection_method'] == 'most_central':
+                    nb_components, output, stats, centroids = cv2.connectedComponentsWithStats(analysisi.binary_image,
+                                                                                               connectivity=8)
                     center = np.array((self.dims[2] // 2, self.dims[1] // 2))
                     stats = np.zeros(nb_components - 1)
                     for shape_i in np.arange(1, nb_components):
@@ -285,10 +314,11 @@ class MotionAnalysis:
                     # The shape having the minimal euclidean distance from the center will be the original shape
                     self.origin = np.zeros((self.dims[1], self.dims[2]), dtype=np.uint8)
                     self.origin[output == (np.argmin(stats) + 1)] = 1
-                elif self.vars['appearance_detection_method'] == 'largest':
-                    self.origin = np.zeros((self.dims[1], self.dims[2]), dtype=np.uint8)
-                    self.origin[output == np.argmax(stats[1:, 4])] = 1
         self.origin_idx = np.nonzero(self.origin)
+        if self.vars['origin_state'] == "constant":
+            if self.vars['lighter_background']:
+                # Initialize the covering_intensity matrix as a reference for pixel fading
+                self.covering_intensity[self.origin_idx[0], self.origin_idx[1]] = 200
         self.substantial_growth = np.min((1.2 * self.origin.sum(), self.origin.sum() + 250))
 
     def get_covering_duration(self, step: int):
@@ -851,7 +881,7 @@ class MotionAnalysis:
             self.pixel_ring_depth = 3
         if self.pixel_ring_depth % 2 == 0:
             self.pixel_ring_depth = self.pixel_ring_depth + 1
-        self.erodila_disk = create_ellipse(self.pixel_ring_depth, self.pixel_ring_depth).astype(np.uint8)
+        self.erodila_disk = create_ellipse(self.pixel_ring_depth, self.pixel_ring_depth, min_size=3).astype(np.uint8)
         self.max_distance = self.pixel_ring_depth * self.vars['detection_range_factor']
 
     def initialize_post_processing(self):
@@ -918,7 +948,7 @@ class MotionAnalysis:
             self.near_periphery = np.zeros(self.dims[1:])
             if self.vars['arena_shape'] == 'circle':
                 periphery_width = self.vars['periphery_width'] * 2
-                elliperiphery = create_ellipse(self.dims[1] - periphery_width, self.dims[2] - periphery_width)
+                elliperiphery = create_ellipse(self.dims[1] - periphery_width, self.dims[2] - periphery_width, min_size=3)
                 half_width = periphery_width // 2
                 if periphery_width % 2 == 0:
                     self.near_periphery[half_width:-half_width, half_width:-half_width] = elliperiphery
@@ -1166,7 +1196,7 @@ class MotionAnalysis:
         `PercentAndTimeTracker` for progress tracking, and other image processing techniques such as connected components analysis.
 
         """
-        ##
+        logging.info(f"Arena n°{self.one_descriptor_per_arena['arena']}. Computing and saving specimen(s) coordinates and required descriptors")
         if release_memory:
             self.substantial_image = None
             self.covering_intensity = None
@@ -1529,7 +1559,6 @@ Extract and analyze graphs from a binary representation of network dynamics, pro
 
             if np.any(self.one_row_per_frame['time'] > 0):
                 position = (5, self.dims[1] - 5)
-                print(self.vars['time_step_is_arbitrary'])
                 if self.vars['time_step_is_arbitrary']:
                     time_unit = ""
                 else:
@@ -1597,7 +1626,7 @@ Extract and analyze graphs from a binary representation of network dynamics, pro
         """
         Manages the saving and updating of CSV files based on data extracted from analyzed
         one arena. Specifically handles three CSV files: "one_row_per_arena.csv",
-        "one_row_per_frame.csv", and "one_row_per_oscillating_cluster.csv".
+        "one_row_per_frame.csv".
         Each file is updated or created based on the presence of existing data.
         The method ensures that each CSV file contains the relevant information for
         the given arena, frame, and oscillator cluster data.