coralnet-toolbox 0.0.76__py2.py3-none-any.whl → 0.0.77__py2.py3-none-any.whl

coralnet_toolbox/Common/QtGraphicsUtility.py

@@ -1,18 +1,17 @@
 import warnings
 
-warnings.filterwarnings("ignore", category=DeprecationWarning)
-warnings.filterwarnings("ignore", category=UserWarning)
-
-import os 
 
+from PyQt5.QtCore import Qt                
+from PyQt5.QtGui import QPen, QColor
 from PyQt5.QtWidgets import (QVBoxLayout, QLabel, QGroupBox, QFormLayout,
                              QDoubleSpinBox, QComboBox, QSpinBox, QHBoxLayout,
                              QWidget, QStackedWidget, QGridLayout, QMessageBox,
                              QDialog, QListWidget, QPushButton, QFileDialog,
-                             QGraphicsView)
-from PyQt5.QtCore import Qt                           
+                             QGraphicsView, QGraphicsLineItem)
+
 
-from coralnet_toolbox.Icons import get_icon
+warnings.filterwarnings("ignore", category=DeprecationWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
 
 
 # ----------------------------------------------------------------------------------------------------------------------
@@ -161,4 +160,15 @@ class GraphicsUtility:
             
         view_width = round(extent.width())
         view_height = round(extent.height())
-        return max(2, min(5, max(view_width, view_height) // 1000))
+        return max(2, min(5, max(view_width, view_height) // 1000))
+    
+    @staticmethod
+    def create_guide_line(start_point, end_point):
+        """Create a semi-transparent guide line for crosshairs."""
+        line = QGraphicsLineItem(start_point.x(), start_point.y(), end_point.x(), end_point.y())
+        pen = QPen(QColor(255, 255, 255, 180))  # Semi-transparent white
+        pen.setWidth(1)
+        pen.setStyle(Qt.DashLine)
+        line.setPen(pen)
+        line.setZValue(1000)  # Ensure it's drawn on top of other elements
+        return line

coralnet_toolbox/IO/QtExportMaskAnnotations.py

@@ -585,14 +585,53 @@ class ExportMaskAnnotations(QDialog):
         if not has_annotations and not self.include_negative_samples_checkbox.isChecked():
             return
 
-        # Always save as PNG
-        filename = f"{os.path.splitext(os.path.basename(image_path))[0]}.png"
+        # Use the selected file format
+        filename = f"{os.path.splitext(os.path.basename(image_path))[0]}{self.file_format}"
         mask_path = os.path.join(output_path, filename)
 
-        if self.mask_mode == 'rgb':
-            # OpenCV expects BGR, so convert from RGB
-            mask = cv2.cvtColor(mask, cv2.COLOR_RGB2BGR)
-        cv2.imwrite(mask_path, mask)
+        # Check if we need to preserve georeferencing
+        use_georef = has_georef and self.preserve_georef_checkbox.isChecked() and self.file_format.lower() == '.tif'
+        
+        if use_georef:
+            # Save with georeferencing using rasterio
+            if self.mask_mode == 'rgb':
+                # For RGB, we need to convert to the expected channel order for rasterio
+                # rasterio expects (bands, height, width) with R,G,B channel order
+                mask_transposed = np.transpose(mask, (2, 0, 1))
+                with rasterio.open(
+                    mask_path,
+                    'w',
+                    driver='GTiff',
+                    height=height,
+                    width=width,
+                    count=3,
+                    dtype=mask.dtype,
+                    crs=crs,
+                    transform=transform
+                ) as dst:
+                    dst.write(mask_transposed)
+            else:
+                # For single-channel masks
+                with rasterio.open(
+                    mask_path,
+                    'w',
+                    driver='GTiff',
+                    height=height,
+                    width=width,
+                    count=1,
+                    dtype=mask.dtype,
+                    crs=crs,
+                    transform=transform
+                ) as dst:
+                    dst.write(mask, 1)
+        else:
+            # Use cv2 for non-georeferenced output
+            if self.mask_mode == 'rgb':
+                # OpenCV expects BGR, so convert from RGB
+                mask = cv2.cvtColor(mask, cv2.COLOR_RGB2BGR)
+            
+            # Save using the appropriate format
+            cv2.imwrite(mask_path, mask)
 
     def export_metadata(self, output_path):
         if self.mask_mode == 'semantic':

coralnet_toolbox/IO/QtImportImages.py

@@ -50,7 +50,6 @@ class ImportImages:
     
     def _process_image_files(self, file_names):
         """Helper method to process a list of image files with progress tracking."""
-        # Make the cursor busy
         QApplication.setOverrideCursor(Qt.WaitCursor)
 
         progress_bar = ProgressBar(self.image_window, title="Importing Images")
@@ -58,30 +57,24 @@ class ImportImages:
         progress_bar.start_progress(len(file_names))
 
         try:
-            # Keep track of successfully imported images
             imported_paths = []
             
-            # Add images to the image window's raster manager
+            # Add images directly to the manager without emitting signals
             for file_name in file_names:
-                # Check if the image is already in the raster manager
                 if file_name not in self.image_window.raster_manager.image_paths:
-                    try:
-                        # Use the image window's add_image method which handles the raster manager
-                        if self.image_window.add_image(file_name):
-                            imported_paths.append(file_name)
-                    except Exception as e:
-                        print(f"Warning: Could not import image {file_name}. Error: {e}")
+                    # Call the manager directly to add the raster silently,
+                    # bypassing ImageWindow.add_image and its signal handlers.
+                    if self.image_window.raster_manager.add_raster(file_name, emit_signal=False):
+                        imported_paths.append(file_name)
                 else:
-                    # Image already exists
                     imported_paths.append(file_name)
 
-                # Update the progress bar
                 progress_bar.update_progress()
 
-            # Apply filtering to update the view
+            # After the silent loop, manually update the UI exactly once.
+            self.image_window.update_search_bars()
             self.image_window.filter_images()
             
-            # Show the last imported image if any were imported
             if imported_paths:
                 self.image_window.load_image_by_path(imported_paths[-1])
 
@@ -89,7 +82,6 @@ class ImportImages:
         except Exception as e:
             self._show_error_message(str(e))
         finally:
-            # Restore the cursor to the default cursor
             QApplication.restoreOverrideCursor()
             progress_bar.stop_progress()
             progress_bar.close()

coralnet_toolbox/IO/QtOpenProject.py

@@ -163,46 +163,42 @@ class OpenProject(QDialog):
         # Exit
         self.accept()
 
+    # In: QtOpenProject.py
+
     def import_images(self, images_data, legacy_workareas=None):
         """Import images, states, and work areas from the given data."""
         if not images_data:
             return
 
-        # Determine if the format is old (list of strings) or new (list of dicts)
         is_new_format = isinstance(images_data[0], dict)
-        
         image_paths = [img['path'] for img in images_data] if is_new_format else images_data
         
         if not all([os.path.exists(path) for path in image_paths]):
             image_paths, self.updated_paths = UpdateImagePaths.update_paths(image_paths)
         
-        # Start progress bar
         total_images = len(image_paths)
         progress_bar = ProgressBar(self.image_window, title="Importing Images")
         progress_bar.show()
         progress_bar.start_progress(total_images)
 
         try:
-            # Create a map for quick data lookup if using the new format
             image_data_map = {img['path']: img for img in images_data} if is_new_format else {}
 
-            # Add images to the image window's raster manager one by one
+            # Add images directly to the manager without emitting signals
             for path in image_paths:
-                self.image_window.add_image(path)
+                # Call the manager directly to add the raster silently
+                self.image_window.raster_manager.add_raster(path, emit_signal=False) 
+                
                 raster = self.image_window.raster_manager.get_raster(path)
                 if not raster:
+                    progress_bar.update_progress()
                     continue
 
-                # If using the new format, apply saved state and work areas
                 if is_new_format and path in image_data_map:
                     data = image_data_map[path]
                     state = data.get('state', {})
                     work_areas_list = data.get('work_areas', [])
-
-                    # Apply raster state
                     raster.checkbox_state = state.get('checkbox_state', False)
-                    
-                    # Import work areas for this image
                     for work_area_data in work_areas_list:
                         try:
                             work_area = WorkArea.from_dict(work_area_data, path)
@@ -210,10 +206,8 @@ class OpenProject(QDialog):
                         except Exception as e:
                             print(f"Warning: Could not import work area {work_area_data}: {str(e)}")
                 
-                # Update the progress bar
                 progress_bar.update_progress()
-            
-            # Handle backward compatibility for old, top-level work areas
+
             if legacy_workareas:
                 for image_path, work_areas_list in legacy_workareas.items():
                     current_path = self.updated_paths.get(image_path, image_path)
@@ -223,16 +217,18 @@ class OpenProject(QDialog):
                             work_area = WorkArea.from_dict(work_area_data, current_path)
                             raster.add_work_area(work_area)
 
-            # Show the last image if any were imported
-            if self.image_window.raster_manager.image_paths:
-                self.image_window.load_image_by_path(self.image_window.raster_manager.image_paths[-1])
-
         except Exception as e:
             QMessageBox.warning(self.annotation_window,
                                 "Error Importing Image(s)",
                                 f"An error occurred while importing image(s): {str(e)}")
         finally:
-            # Close progress bar
+            # Manually perform the UI updates ONCE for all imported images
+            self.image_window.update_search_bars()
+            self.image_window.filter_images()
+
+            if self.image_window.raster_manager.image_paths:
+                self.image_window.load_image_by_path(self.image_window.raster_manager.image_paths[-1])
+            
             progress_bar.stop_progress()
             progress_bar.close()
 

coralnet_toolbox/MachineLearning/ImportDataset/QtBase.py

@@ -346,6 +346,8 @@ class Base(QDialog):
         self.button_box.rejected.connect(self.reject)
         self.layout.addWidget(self.button_box)
 
+    # In: QtBase.py
+
     def browse_data_yaml(self):
         """Open a file dialog to select the data YAML file and populate advanced options."""
         options = QFileDialog.Options()
@@ -358,22 +360,40 @@ class Base(QDialog):
         try:
             with open(file_path, 'r') as file:
                 data = yaml.safe_load(file)
-            class_names = data.get('names', [])
-            if not class_names:
-                QMessageBox.warning(self, "Warning", "Could not find a 'names' list in the selected YAML file.")
+            
+            names_data = data.get('names')
+            if not names_data:
+                QMessageBox.warning(self, "Warning", "Could not find a 'names' entry in the selected YAML file.")
                 return
 
+            # Handle both dictionary and list formats for class names
+            names_to_display = []
+            if isinstance(names_data, dict):
+                # If it's a dictionary (e.g., {0: 'coral'}), extract the values, sorting by key
+                # to preserve the intended class order.
+                names_to_display = [str(names_data[key]) for key in sorted(names_data.keys())]
+            elif isinstance(names_data, list):
+                # If it's already a list, use it directly.
+                names_to_display = [str(name) for name in names_data]
+            else:
+                # Handle any other unexpected format.
+                QMessageBox.warning(self, "Format Error", 
+                                    f"The 'names' entry in the YAML has an unexpected format: {type(names_data)}.")
+                return
+            
             self.yaml_path_label.setText(file_path)
             yaml_dir = os.path.dirname(file_path)
             self.output_dir_label.setText(yaml_dir)
             self.output_folder_name.setText("data")
 
+            # Clear any existing checkboxes before adding new ones
             for checkbox in self.class_checkboxes:
                 self.class_layout.removeWidget(checkbox)
                 checkbox.deleteLater()
             self.class_checkboxes.clear()
 
-            for name in class_names:
+            # Create checkboxes using the processed list of names
+            for name in names_to_display:
                 checkbox = QCheckBox(name)
                 checkbox.setChecked(True)
                 self.class_layout.addWidget(checkbox)
@@ -504,8 +524,11 @@ class Base(QDialog):
         added_paths = []
         progress_bar.set_title(f"Adding {len(image_paths)} images...")
         progress_bar.start_progress(len(image_paths))
+        
         for path in image_paths:
-            if self.image_window.add_image(path):
+            # Call the manager directly to add the raster silently,
+            # bypassing ImageWindow.add_image and its signal handlers.
+            if self.image_window.raster_manager.add_raster(path, emit_signal=False):
                 added_paths.append(path)
             progress_bar.update_progress()
 
@@ -535,19 +558,21 @@ class Base(QDialog):
                                                self.main_window.get_transparency_value())
 
             self.annotation_window.add_annotation_to_dict(annotation)
-            newly_created_annotations.append(annotation)  # Collect created objects
+            newly_created_annotations.append(annotation)
             
             progress_bar.update_progress()
 
-        # --- Call the restored, correct export function ---
         progress_bar.set_title("Exporting annotations.json...")
         self._export_annotations_to_json(newly_created_annotations, self.output_folder)
         
         progress_bar.finish_progress()
         progress_bar.stop_progress()
         progress_bar.close()
-
+        
+        # Manually perform a full UI update exactly once.
+        self.image_window.update_search_bars()
         self.image_window.filter_images()
+
         if added_paths:
             self.image_window.load_image_by_path(added_paths[-1])
             self.image_window.update_image_annotations(added_paths[-1])

coralnet_toolbox/QtAnnotationWindow.py

@@ -401,6 +401,10 @@ class AnnotationWindow(QGraphicsView):
         self.current_image_path = image_path
         self.active_image = True
 
+        # Automatically mark this image as checked when viewed
+        raster.checkbox_state = True
+        self.main_window.image_window.table_model.update_raster_data(image_path)
+
         self.tools["zoom"].reset_zoom()
         self.scene.addItem(QGraphicsPixmapItem(self.pixmap_image))
         self.fitInView(self.scene.sceneRect(), Qt.KeepAspectRatio)

coralnet_toolbox/QtEventFilter.py

@@ -13,7 +13,7 @@ warnings.filterwarnings("ignore", category=DeprecationWarning)
 
 class GlobalEventFilter(QObject):
     def __init__(self, main_window):
-        super().__init__()
+        super().__init__(main_window)
         self.main_window = main_window
         self.label_window = main_window.label_window
         self.annotation_window = main_window.annotation_window

coralnet_toolbox/QtImageWindow.py

@@ -667,6 +667,10 @@ class ImageWindow(QWidget):
                 # Get the raster
                 raster = self.raster_manager.get_raster(image_path)
                 
+                # Mark as checked when viewed
+                raster.checkbox_state = True
+                self.table_model.update_raster_data(image_path)
+                
                 # Update selection
                 self.selected_image_path = image_path
                 self.table_model.set_selected_path(image_path)

coralnet_toolbox/Rasters/RasterManager.py

@@ -31,7 +31,7 @@ class RasterManager(QObject):
         self.rasters: Dict[str, Raster] = {}
         self.image_paths: List[str] = []
         
-    def add_raster(self, image_path: str) -> bool:
+    def add_raster(self, image_path: str, emit_signal: bool = True) -> bool:
         """
         Add a new raster to the manager.
         
@@ -51,7 +51,10 @@ class RasterManager(QObject):
                 
             self.rasters[image_path] = raster
             self.image_paths.append(image_path)
-            self.rasterAdded.emit(image_path)
+            
+            if emit_signal:
+                self.rasterAdded.emit(image_path)
+                
             return True
             
         except Exception as e: