Multi annotation

napari_organoid_counter/_utils.py

@@ -62,20 +62,22 @@ def write_to_json(name, data):
     with open(name, 'w') as outfile:
         json.dump(data, outfile)  
 
-def get_bboxes_as_dict(bboxes, bbox_ids, scores, scales):
-    """ Write all data, boxes, ids and scores and scale, to a dict so we can later save as a json """
+def get_bboxes_as_dict(bboxes, bbox_ids, scores, scales, labels):
+    """ Write all data, boxes, ids and scores, scale and class label, to a dict so we can later save as a json """
     data_json = {} 
     for idx, bbox in enumerate(bboxes):
         x1, y1 = bbox[0]
         x2, y2 = bbox[2]
+
         data_json.update({str(bbox_ids[idx]): {'box_id': str(bbox_ids[idx]),
                                                 'x1': str(x1),
                                                 'x2': str(x2),
                                                 'y1': str(y1),
                                                 'y2': str(y2),
                                                 'confidence': str(scores[idx]),
                                                 'scale_x': str(scales[0]),
-                                                'scale_y': str(scales[1])
+                                                'scale_y': str(scales[1]),
+                                                'class': labels[idx]
                                                 }
                         })
     return data_json

napari_organoid_counter/_widget.py

@@ -3,8 +3,12 @@
 from skimage.io import imsave
 from datetime import datetime
 
+import napari
+
 from napari import layers
-from napari.utils.notifications import show_info
+from napari.utils.notifications import show_info, show_error, show_warning
+
+import numpy as np
 
 from qtpy.QtCore import Qt
 from qtpy.QtWidgets import QWidget, QVBoxLayout, QApplication, QDialog, QFileDialog, QGroupBox, QHBoxLayout, QLabel, QComboBox, QPushButton, QLineEdit, QProgressBar, QSlider
@@ -95,6 +99,10 @@ def __init__(self,
         self.stored_confidences = {}
         self.stored_diameters = {}
 
+        # Initialize multi_annotation_mode to False by default
+        self.multi_annotation_mode = False
+        # self.single_annotation_mode = True  # Initially, it's single annotation mode
+
         # setup gui        
         self.setLayout(QVBoxLayout())
         self.layout().addWidget(self._setup_input_widget())
@@ -112,9 +120,76 @@ def __init__(self,
         self.viewer.layers.events.inserted.connect(self._added_layer)
         self.viewer.layers.events.removed.connect(self._removed_layer)
         self.viewer.layers.selection.events.changed.connect(self._sel_layer_changed)
+
         # setup flags used for changing slider and text of min diameter and confidence threshold
         self.diameter_slider_changed = False 
-        self.confidence_slider_changed = False 
+        self.confidence_slider_changed = False
+
+        # Key binding to change the edge_color of the bounding boxes to green
+        @self.viewer.bind_key('g')
+        def change_edge_color_to_green(viewer: napari.Viewer):
+            if not self.multi_annotation_mode:  # Check if single-annotation mode is active
+                show_error("Cannot change edge color. Change to multi-annotation mode to enable this feature.")
+                return
+            if self.cur_shapes_layer is not None:  # Ensure shapes layer exists
+                selected_shapes = self.cur_shapes_layer.selected_data # Retrieves indices of shapes currently selected, returns a set 
+                if len(selected_shapes) > 0:
+                    # Modify the edge color only for the selected shapes
+                    current_edge_colors = self.cur_shapes_layer.edge_color 
+                    for idx in selected_shapes:
+                        # Save original color
+                        # if idx not in self.original_colors: 
+                            # self.original_colors[idx] = current_edge_colors[idx].copy()
+                        # Update to the new color
+                        current_edge_colors[idx] = settings.COLOR_CLASS_1
+                    self.cur_shapes_layer.edge_color = current_edge_colors  # Apply the changes
+                    show_info(f"Changed edge color of shapes {list(selected_shapes)} to green.")
+                else:
+                    show_warning("No shapes selected to change edge color.")
+
+        # Key binding to change the edge_color of the bounding boxes to blue
+        @self.viewer.bind_key('h')
+        def change_edge_color_to_blue(viewer: napari.Viewer):
+            if not self.multi_annotation_mode:  # Check if single-annotation mode is active
+                show_error("Cannot change edge color. Change to multi-annotation mode to enable this feature.")
+                return         
+            if self.cur_shapes_layer is not None:  # Ensure shapes layer exists
+                selected_shapes = self.cur_shapes_layer.selected_data
+                if len(selected_shapes) > 0:
+                    # Modify the edge color only for the selected shapes
+                    current_edge_colors = self.cur_shapes_layer.edge_color
+                    for idx in selected_shapes:
+                        # Save original color
+                        # if idx not in self.original_colors: 
+                            # self.original_colors[idx] = current_edge_colors[idx].copy()
+                        # Update to the new color
+                        current_edge_colors[idx] = settings.COLOR_CLASS_2
+                    self.cur_shapes_layer.edge_color = current_edge_colors  # Apply the changes
+                    show_info(f"Changed edge color of {list(selected_shapes)} to blue.")
+                else:
+                    show_warning("No shapes selected to change edge color.")
+
+        # Key binding to reset the edge_color of selected bounding boxes to the original magenta color
+        @self.viewer.bind_key('m')
+        def change_to_original_color(viewer: napari.Viewer):
+            if not self.multi_annotation_mode:  # Check if single-annotation mode is active
+                show_info("Cannot change edge color. Change to multi-annotation mode to enable this feature.")
+                return
+            if self.cur_shapes_layer is not None:  # Ensure shapes layer exists
+                selected_shapes = self.cur_shapes_layer.selected_data
+                if len(selected_shapes) > 0:
+                    current_edge_colors = self.cur_shapes_layer.edge_color
+                    # Modify the edge color only for the selected shapes
+                    current_edge_colors = self.cur_shapes_layer.edge_color
+                    for idx in selected_shapes:
+                        # if idx in self.original_colors:
+                            # Revert to the original color
+                            current_edge_colors[idx] = settings.COLOR_DEFAULT
+                    self.cur_shapes_layer.edge_color = current_edge_colors  # Apply the changes
+                    show_info(f"Reset edge color of {list(selected_shapes)} to magenta.")
+                else:
+                    show_warning("No shapes selected to reset edge color.")
+
 
     def handle_progress(self, blocknum, blocksize, totalsize):
         """ When the model is being downloaded, this method is called and th progress of the download
@@ -212,12 +287,13 @@ def _update_vis_bboxes(self, bboxes, scores, box_ids, labels_layer_name):
                                                                face_color='transparent',  
                                                                properties = properties,
                                                                text = text_params,
-                                                               edge_color='magenta',
+                                                               edge_color=settings.COLOR_DEFAULT,
                                                                shape_type='rectangle',
                                                                edge_width=12) # warning generated here
 
             # set current_edge_width so edge width is the same when users annotate - doesnt' fix new preds being added!
             self.viewer.layers[labels_layer_name].current_edge_width = 12
+
 
     def _on_preprocess_click(self):
         """ Is called whenever preprocess button is clicked """
@@ -404,6 +480,17 @@ def _on_screenshot_click(self):
         name,_ = fd.getSaveFileName(self, 'Save File', potential_name, 'Image files (*.png);;(*.tiff)') #, 'CSV Files (*.csv)')
         if name: imsave(name, screenshot)
 
+    def on_annotation_mode_changed(self, index):
+        """Callback for dropdown selection."""
+        if index == 0:  # Single Annotation
+            self.multi_annotation_mode = False
+            # self.single_annotation_mode = True
+            show_info("Switched to Single Annotation mode.")
+        elif index == 1:  # Multi Annotation
+            self.multi_annotation_mode = True
+            # self.single_annotation_mode = False
+            show_info("Switched to Multi Annotation mode.")
+
     def _on_save_csv_click(self): 
         """ Is called whenever Save features button is clicked """
         bboxes = self.viewer.layers[self.save_layer_name].data
@@ -421,16 +508,57 @@ def _on_save_json_click(self):
         """ Is called whenever Save boxes button is clicked """
         bboxes = self.viewer.layers[self.save_layer_name].data
         #scores = #add
-        if not bboxes: show_info('No organoids detected! Please run auto organoid counter or run algorithm first and try again!')
+        if not bboxes: 
+            show_info('No organoids detected! Please run auto organoid counter or run algorithm first and try again!')
+            return
+
+        # Check for multi-annotation mode
+        if self.multi_annotation_mode:
+
+            # Get the edge colors for all bounding boxes
+            edge_colors = self.cur_shapes_layer.edge_color
+            labels = []
+
+            # Check if all bounding boxes have their edge color set (not green or blue)
+            green = np.array(settings.COLOR_CLASS_1)
+            blue = np.array(settings.COLOR_CLASS_2)
+
+            all_colored = True
+            for edge_color in edge_colors:
+                # Compare the colors with a tolerance using np.allclose to account for floating-point errors
+                if not (np.allclose(edge_color[:3], green[:3]) or np.allclose(edge_color[:3], blue[:3])):
+                    all_colored = False
+                    break
+
+            if not all_colored:
+                show_error('Please change the color of all bounding boxes before saving.')
+                return
+
+            # Assign organoid label based on edge_color
+            for edge_color in edge_colors:
+                if np.allclose(edge_color[:3], green[:3]):
+                    labels.append(0)  # Label for green
+                elif np.allclose(edge_color[:3], blue[:3]):
+                    labels.append(1)  # Label for blue
+                else:
+                    raise ValueError(f"Unexpected edge color {edge_color[:3]} encountered.")
+
+        #elif self.single_annotation_mode:
         else:
-            data_json = utils.get_bboxes_as_dict(bboxes, 
-                                           self.viewer.layers[self.save_layer_name].properties['box_id'],
-                                           self.viewer.layers[self.save_layer_name].properties['scores'],
-                                           self.viewer.layers[self.save_layer_name].scale)
-            # write bbox coordinates to json
-            fd = QFileDialog()
-            name,_ = fd.getSaveFileName(self, 'Save File', self.save_layer_name, 'JSON files (*.json)')#, 'CSV Files (*.csv)')
-            if name: utils.write_to_json(name, data_json)
+            # Single annotation mode: all bounding boxes get a default label
+            labels = [0] * len(bboxes)  # Default label for single annotation mode
+
+        data_json = utils.get_bboxes_as_dict(bboxes, 
+                                    self.viewer.layers[self.save_layer_name].properties['box_id'],
+                                    self.viewer.layers[self.save_layer_name].properties['scores'],
+                                    self.viewer.layers[self.save_layer_name].scale,
+                                    labels=labels)
+
+
+        # write bbox coordinates to json
+        fd = QFileDialog()
+        name,_ = fd.getSaveFileName(self, 'Save File', self.save_layer_name, 'JSON files (*.json)')#, 'CSV Files (*.csv)')
+        if name: utils.write_to_json(name, data_json)
 
     def _update_added_image(self, added_items):
         """
@@ -471,7 +599,8 @@ def _update_added_shapes(self, added_items):
         self.organoiDL.update_bboxes_scores(self.cur_shapes_name,
                                             self.cur_shapes_layer.data,
                                             self.cur_shapes_layer.properties['scores'],
-                                            self.cur_shapes_layer.properties['box_id'])
+                                            self.cur_shapes_layer.properties['box_id']
+                                            )
         self.cur_shapes_layer.events.data.connect(self.shapes_event_handler)
 
     def _update_remove_shapes(self, removed_layers):
@@ -507,6 +636,7 @@ def shapes_event_handler(self, event):
                 new_ids[-1] = self.organoiDL.next_id[self.cur_shapes_name]
                 new_scores = self.viewer.layers[self.cur_shapes_name].properties['scores']
                 new_scores[-1] = 1
+
             # set new properties to shapes layer
             self.viewer.layers[self.cur_shapes_name].properties ={'box_id': new_ids,'scores':  new_scores}
             # refresh text displayed
@@ -530,6 +660,7 @@ def _setup_input_widget(self):
         window_sizes_box = self._setup_window_sizes_box()
         downsampling_box = self._setup_downsampling_box()
         run_box = self._setup_run_box()
+        annotation_mode_box = self._setup_annotation_mode_box() # Annotation mode dropdown to select single or multi-annotation
         self._setup_progress_box()
 
         # and add all these to the layout
@@ -540,6 +671,7 @@ def _setup_input_widget(self):
         vbox.addLayout(window_sizes_box)
         vbox.addLayout(downsampling_box)
         vbox.addLayout(run_box)
+        vbox.addLayout(annotation_mode_box)  # Add the annotation dropdown
         vbox.addWidget(self.progress_box)
         input_widget.setLayout(vbox)
         return input_widget
@@ -682,6 +814,24 @@ def _setup_run_box(self):
         hbox.addWidget(run_btn)
         hbox.addStretch(1)
         return hbox
+
+    def _setup_annotation_mode_box(self):
+        """
+        Sets up the GUI part where the annotation mode is selected.
+        """
+        hbox = QHBoxLayout()
+
+        # Label
+        annotation_mode_label = QLabel("Annotation Mode:", self)
+        hbox.addWidget(annotation_mode_label)
+
+        # Dropdown
+        self.annotation_mode_dropdown = QComboBox()
+        self.annotation_mode_dropdown.addItems(["Single Annotation", "Multi Annotation"])
+        self.annotation_mode_dropdown.currentIndexChanged.connect(self.on_annotation_mode_changed)
+        hbox.addWidget(self.annotation_mode_dropdown)
+
+        return hbox
 
     def _setup_progress_box(self):
         """

napari_organoid_counter/settings.py

@@ -38,7 +38,18 @@ def init():
         "rtmdet":  {"source": "https://zenodo.org/records/11388549/files/rtmdet_l_organoid.py",
                     "destination": ".mim/configs/rtmdet/rtmdet_l_organoid.py"
                     }
+
 }
+
+    # Add color definitions
+    global COLOR_CLASS_1
+    COLOR_CLASS_1 = [85 / 255, 1.0, 0, 1.0]  # Green
+
+    global COLOR_CLASS_2
+    COLOR_CLASS_2 = [0, 29 / 255, 1.0, 1.0]  # Blue
+
+    global COLOR_DEFAULT
+    COLOR_DEFAULT = [1., 0, 1., 1.] # Magenta