Updating polyline saving and drawing

src/gui/tabs/annotation_tab.py

@@ -93,6 +93,12 @@ class AnnotationTab(QWidget):
         self.annotation_tools.clear_annotations_requested.connect(
             self._on_clear_annotations
         )
+        self.annotation_tools.process_annotations_requested.connect(
+            self._on_process_annotations
+        )
+        self.annotation_tools.show_annotations_requested.connect(
+            self._on_show_annotations
+        )
         self.right_splitter.addWidget(self.annotation_tools)
 
         # Image loading section
@@ -237,6 +243,140 @@ class AnnotationTab(QWidget):
         self.annotation_canvas.clear_annotations()
         logger.info("Cleared all annotations")
 
+    def _on_process_annotations(self):
+        """Process annotations and save to database."""
+        # Check if we have an image loaded
+        if not self.current_image or not self.current_image_id:
+            QMessageBox.warning(
+                self, "No Image", "Please load an image before processing annotations."
+            )
+            return
+
+        # Get current class
+        current_class = self.annotation_tools.get_current_class()
+        if not current_class:
+            QMessageBox.warning(
+                self,
+                "No Class Selected",
+                "Please select an object class before processing annotations.",
+            )
+            return
+
+        # Compute annotation parameters asbounding boxes and polylines from annotations
+        parameters = self.annotation_canvas.get_annotation_parameters()
+        if not parameters:
+            QMessageBox.warning(
+                self,
+                "No Annotations",
+                "Please draw some annotations before processing.",
+            )
+            return
+
+        # polyline = self.annotation_canvas.get_annotation_polyline()
+
+        for param in parameters:
+            bounds = param["bbox"]
+            polyline = param["polyline"]
+
+            try:
+                # Save annotation to database
+                annotation_id = self.db_manager.add_annotation(
+                    image_id=self.current_image_id,
+                    class_id=current_class["id"],
+                    bbox=bounds,
+                    annotator="manual",
+                    segmentation_mask=polyline,
+                    verified=False,
+                )
+
+                logger.info(
+                    f"Saved annotation (ID: {annotation_id}) for class '{current_class['class_name']}' "
+                    f"Bounding box: ({bounds[0]:.3f}, {bounds[1]:.3f}) to ({bounds[2]:.3f}, {bounds[3]:.3f})\n"
+                    f"with {len(polyline)} polyline points"
+                )
+
+                # QMessageBox.information(
+                #     self,
+                #     "Success",
+                #     f"Annotation saved successfully!\n\n"
+                #     f"Class: {current_class['class_name']}\n"
+                #     f"Bounding box: ({bounds[0]:.3f}, {bounds[1]:.3f}) to ({bounds[2]:.3f}, {bounds[3]:.3f})\n"
+                #     f"Polyline points: {len(polyline)}",
+                # )
+
+            except Exception as e:
+                logger.error(f"Failed to save annotation: {e}")
+                QMessageBox.critical(
+                    self, "Error", f"Failed to save annotation:\n{str(e)}"
+                )
+
+        # Optionally clear annotations after saving
+        reply = QMessageBox.question(
+            self,
+            "Clear Annotations",
+            "Do you want to clear the annotations to start a new one?",
+            QMessageBox.Yes | QMessageBox.No,
+            QMessageBox.Yes,
+        )
+
+        if reply == QMessageBox.Yes:
+            self.annotation_canvas.clear_annotations()
+            logger.info("Cleared annotations after saving")
+
+    def _on_show_annotations(self):
+        """Load and display saved annotations from database."""
+        # Check if we have an image loaded
+        if not self.current_image or not self.current_image_id:
+            QMessageBox.warning(
+                self, "No Image", "Please load an image to view its annotations."
+            )
+            return
+
+        try:
+            # Clear current annotations
+            self.annotation_canvas.clear_annotations()
+
+            # Retrieve annotations from database
+            annotations = self.db_manager.get_annotations_for_image(
+                self.current_image_id
+            )
+
+            if not annotations:
+                QMessageBox.information(
+                    self, "No Annotations", "No saved annotations found for this image."
+                )
+                return
+
+            # Draw each annotation's polyline
+            drawn_count = 0
+            for ann in annotations:
+                if ann.get("segmentation_mask"):
+                    polyline = ann["segmentation_mask"]
+                    color = ann.get("class_color", "#FF0000")
+
+                    # Draw the polyline
+                    self.annotation_canvas.draw_saved_polyline(polyline, color, width=3)
+                    self.annotation_canvas.draw_saved_bbox(
+                        [ann["x_min"], ann["y_min"], ann["x_max"], ann["y_max"]],
+                        color,
+                        width=3,
+                    )
+                    drawn_count += 1
+
+            logger.info(f"Displayed {drawn_count} saved annotations from database")
+
+            QMessageBox.information(
+                self,
+                "Annotations Loaded",
+                f"Successfully loaded and displayed {drawn_count} annotation(s).",
+            )
+
+        except Exception as e:
+            logger.error(f"Failed to load annotations: {e}")
+            QMessageBox.critical(
+                self, "Error", f"Failed to load annotations:\n{str(e)}"
+            )
+
     def _restore_state(self):
         """Restore splitter positions from settings."""
         settings = QSettings("microscopy_app", "object_detection")

src/gui/widgets/annotation_canvas_widget.py

@@ -3,6 +3,8 @@ Annotation canvas widget for drawing annotations on images.
 Supports pen tool with color selection for manual annotation.
 """
 
+import numpy as np
+
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel, QScrollArea
 from PySide6.QtGui import (
     QPixmap,
@@ -15,12 +17,17 @@ from PySide6.QtGui import (
     QPaintEvent,
 )
 from PySide6.QtCore import Qt, QEvent, Signal, QPoint
-from typing import List, Optional, Tuple
+from typing import Any, Dict, List, Optional, Tuple
-import numpy as np
+
+from scipy.ndimage import binary_dilation, label, binary_fill_holes, find_objects
+from skimage.measure import find_contours
 
 from src.utils.image import Image, ImageLoadError
 from src.utils.logger import get_logger
 
+# For debugging visualization
+import pylab as plt
+
 logger = get_logger(__name__)
 
 
@@ -369,6 +376,270 @@ class AnnotationCanvasWidget(QWidget):
         """Get all drawn strokes with metadata."""
         return self.all_strokes
 
+    # def get_annotation_bounds(self) -> Optional[Tuple[float, float, float, float]]:
+    #     """
+    #     Compute bounding box that encompasses all annotation strokes.
+
+    #     Returns:
+    #         Tuple of (x_min, y_min, x_max, y_max) in normalized coordinates (0-1),
+    #         or None if no annotations exist.
+    #     """
+    #     if not self.all_strokes:
+    #         return None
+
+    #     # Find min/max across all strokes
+    #     all_x = []
+    #     all_y = []
+
+    #     for stroke in self.all_strokes:
+    #         for x, y in stroke["points"]:
+    #             all_x.append(x)
+    #             all_y.append(y)
+
+    #     if not all_x:
+    #         return None
+
+    #     x_min = min(all_x)
+    #     y_min = min(all_y)
+    #     x_max = max(all_x)
+    #     y_max = max(all_y)
+
+    #     return (x_min, y_min, x_max, y_max)
+
+    # def get_annotation_polyline(self) -> List[List[float]]:
+    #     """
+    #     Get polyline coordinates representing all annotation strokes.
+
+    #     Returns:
+    #         List of [x, y] coordinate pairs in normalized coordinates (0-1).
+    #     """
+    #     polyline = []
+
+    #     fig = plt.figure()
+    #     ax1 = fig.add_subplot(411)
+    #     ax2 = fig.add_subplot(412)
+    #     ax3 = fig.add_subplot(413)
+    #     ax4 = fig.add_subplot(414)
+
+    #     # Get np.arrays from  annotation_pixmap accoriding to the color of the stroke
+    #     qimage = self.annotation_pixmap.toImage()
+    #     arr = np.ndarray(
+    #         (qimage.height(), qimage.width(), 4),
+    #         buffer=qimage.constBits(),
+    #         strides=[qimage.bytesPerLine(), 4, 1],
+    #         dtype=np.uint8,
+    #     )
+    #     print(arr.shape, arr.dtype, arr.min(), arr.max())
+    #     arr = np.sum(arr, axis=2)
+    #     ax1.imshow(arr)
+
+    #     arr_bin = arr > 0
+    #     ax2.imshow(arr_bin)
+
+    #     arr_bin = binary_fill_holes(arr_bin)
+    #     ax3.imshow(arr_bin)
+
+    #     labels, _number_of_features = label(
+    #         arr_bin,
+    #     )
+
+    #     ax4.imshow(labels)
+
+    #     objects = find_objects(labels)
+    #     bounding_boxes = np.array(
+    #         [[obj[0].start, obj[0].stop, obj[1].start, obj[1].stop] for obj in objects]
+    #     ) / np.array([arr.shape[0], arr.shape[1]])
+
+    #     print(objects)
+    #     print(bounding_boxes)
+    #     print(np.array([arr.shape[0], arr.shape[1]]))
+
+    #     polylines = find_contours(arr_bin, 0.5)
+    #     for pl in polylines:
+    #         ax1.plot(pl[:, 1], pl[:, 0], "k")
+
+    #     print(arr.shape, arr.dtype, arr.min(), arr.max())
+
+    #     plt.show()
+
+    #     return polyline
+
+    def get_annotation_parameters(self) -> Dict[str, Any]:
+        """
+        Get all annotation parameters including bounding box and polyline.
+
+        Returns:
+            Dictionary containing:
+            - 'bbox': Bounding box coordinates (x_min, y_min, x_max, y_max)
+            - 'polyline': List of [x, y] coordinate pairs
+        """
+
+        # Get np.arrays from  annotation_pixmap accoriding to the color of the stroke
+        qimage = self.annotation_pixmap.toImage()
+        arr = np.ndarray(
+            (qimage.height(), qimage.width(), 4),
+            buffer=qimage.constBits(),
+            strides=[qimage.bytesPerLine(), 4, 1],
+            dtype=np.uint8,
+        )
+        arr = np.sum(arr, axis=2)
+        arr_bin = arr > 0
+        arr_bin = binary_fill_holes(arr_bin)
+
+        labels, _number_of_features = label(
+            arr_bin,
+        )
+        if _number_of_features == 0:
+            return None
+
+        objects = find_objects(labels)
+        w, h = arr.shape
+        bounding_boxes = [
+            [obj[0].start / w, obj[1].start / h, obj[0].stop / w, obj[1].stop / h]
+            for obj in objects
+        ]
+
+        polylines = find_contours(arr_bin, 0.5)
+        params = []
+        for i, pl in enumerate(polylines):
+            # pl is in [row, col] format from find_contours
+            # We need to normalize: row/height, col/width
+            # w = height (rows), h = width (cols) from line 510
+            normalized_polyline = (pl[::-1] / np.array([w, h])).tolist()
+
+            logger.debug(f"Polyline {i}: {len(pl)} points")
+            logger.debug(f"  w={w} (height), h={h} (width)")
+            logger.debug(f"  First 3 normalized points: {normalized_polyline[:3]}")
+
+            params.append(
+                {
+                    "bbox": bounding_boxes[i],
+                    "polyline": normalized_polyline,
+                }
+            )
+
+        return params
+
+    def draw_saved_polyline(
+        self, polyline: List[List[float]], color: str, width: int = 3
+    ):
+        """
+        Draw a polyline from database coordinates onto the annotation canvas.
+
+        Args:
+            polyline: List of [x, y] coordinate pairs in normalized coordinates (0-1)
+            color: Color hex string (e.g., '#FF0000')
+            width: Line width in pixels
+        """
+        if not self.annotation_pixmap or not self.original_pixmap:
+            logger.warning("Cannot draw polyline: no image loaded")
+            return
+
+        if len(polyline) < 2:
+            logger.warning("Polyline has less than 2 points, cannot draw")
+            return
+
+        # Convert normalized coordinates to image coordinates
+        # Polyline is stored as [[y_norm, x_norm], ...] (row_norm, col_norm format)
+        img_width = self.original_pixmap.width()
+        img_height = self.original_pixmap.height()
+
+        logger.debug(f"Loading polyline with {len(polyline)} points")
+        logger.debug(f"  Image size: {img_width}x{img_height}")
+        logger.debug(f"  First 3 normalized points from DB: {polyline[:3]}")
+
+        img_coords = []
+        for y_norm, x_norm in polyline:
+            x = int(x_norm * img_width)
+            y = int(y_norm * img_height)
+            img_coords.append((x, y))
+
+        logger.debug(f"  First 3 pixel coords: {img_coords[:3]}")
+
+        # Draw polyline on annotation pixmap
+        painter = QPainter(self.annotation_pixmap)
+        pen_color = QColor(color)
+        pen_color.setAlpha(128)  # Add semi-transparency
+        pen = QPen(pen_color, width, Qt.SolidLine, Qt.RoundCap, Qt.RoundJoin)
+        painter.setPen(pen)
+
+        # Draw lines between consecutive points
+        for i in range(len(img_coords) - 1):
+            x1, y1 = img_coords[i]
+            x2, y2 = img_coords[i + 1]
+            painter.drawLine(x1, y1, x2, y2)
+
+        painter.end()
+
+        # Store in all_strokes for consistency
+        self.all_strokes.append(
+            {"points": polyline, "color": color, "alpha": 128, "width": width}
+        )
+
+        # Update display
+        self._update_display()
+        logger.debug(
+            f"Drew saved polyline with {len(polyline)} points in color {color}"
+        )
+
+    def draw_saved_bbox(self, bbox: List[float], color: str, width: int = 3):
+        """
+        Draw a bounding box from database coordinates onto the annotation canvas.
+
+        Args:
+            bbox: Bounding box as [y_min_norm, x_min_norm, y_max_norm, x_max_norm]
+                  in normalized coordinates (0-1)
+            color: Color hex string (e.g., '#FF0000')
+            width: Line width in pixels
+        """
+        if not self.annotation_pixmap or not self.original_pixmap:
+            logger.warning("Cannot draw bounding box: no image loaded")
+            return
+
+        if len(bbox) != 4:
+            logger.warning(
+                f"Invalid bounding box format: expected 4 values, got {len(bbox)}"
+            )
+            return
+
+        # Convert normalized coordinates to image coordinates
+        # bbox format: [y_min_norm, x_min_norm, y_max_norm, x_max_norm]
+        img_width = self.original_pixmap.width()
+        img_height = self.original_pixmap.height()
+
+        y_min_norm, x_min_norm, y_max_norm, x_max_norm = bbox
+        x_min = int(x_min_norm * img_width)
+        y_min = int(y_min_norm * img_height)
+        x_max = int(x_max_norm * img_width)
+        y_max = int(y_max_norm * img_height)
+
+        logger.debug(f"Drawing bounding box: {bbox}")
+        logger.debug(f"  Image size: {img_width}x{img_height}")
+        logger.debug(f"  Pixel coords: ({x_min}, {y_min}) to ({x_max}, {y_max})")
+
+        # Draw bounding box on annotation pixmap
+        painter = QPainter(self.annotation_pixmap)
+        pen_color = QColor(color)
+        pen_color.setAlpha(128)  # Add semi-transparency
+        pen = QPen(pen_color, width, Qt.SolidLine, Qt.SquareCap, Qt.MiterJoin)
+        painter.setPen(pen)
+
+        # Draw rectangle
+        rect_width = x_max - x_min
+        rect_height = y_max - y_min
+        painter.drawRect(x_min, y_min, rect_width, rect_height)
+
+        painter.end()
+
+        # Store in all_strokes for consistency
+        self.all_strokes.append(
+            {"bbox": bbox, "color": color, "alpha": 128, "width": width}
+        )
+
+        # Update display
+        self._update_display()
+        logger.debug(f"Drew saved bounding box in color {color}")
+
     def keyPressEvent(self, event: QKeyEvent):
         """Handle keyboard events for zooming."""
         if event.key() in (Qt.Key_Plus, Qt.Key_Equal):

src/gui/widgets/annotation_tools_widget.py

@@ -51,6 +51,8 @@ class AnnotationToolsWidget(QWidget):
     pen_width_changed = Signal(int)
     class_selected = Signal(dict)
     clear_annotations_requested = Signal()
+    process_annotations_requested = Signal()
+    show_annotations_requested = Signal()
 
     def __init__(self, db_manager: DatabaseManager, parent=None):
         """
@@ -146,6 +148,20 @@ class AnnotationToolsWidget(QWidget):
         actions_group = QGroupBox("Actions")
         actions_layout = QVBoxLayout()
 
+        self.process_btn = QPushButton("Process Annotations")
+        self.process_btn.clicked.connect(self._on_process_annotations)
+        self.process_btn.setStyleSheet(
+            "QPushButton { background-color: #2196F3; color: white; font-weight: bold; }"
+        )
+        actions_layout.addWidget(self.process_btn)
+
+        self.show_btn = QPushButton("Show Saved Annotations")
+        self.show_btn.clicked.connect(self._on_show_annotations)
+        self.show_btn.setStyleSheet(
+            "QPushButton { background-color: #4CAF50; color: white; }"
+        )
+        actions_layout.addWidget(self.show_btn)
+
         self.clear_btn = QPushButton("Clear All Annotations")
         self.clear_btn.clicked.connect(self._on_clear_annotations)
         actions_layout.addWidget(self.clear_btn)
@@ -335,6 +351,24 @@ class AnnotationToolsWidget(QWidget):
             self.clear_annotations_requested.emit()
             logger.debug("Clear annotations requested")
 
+    def _on_process_annotations(self):
+        """Handle process annotations button."""
+        if not self.current_class:
+            QMessageBox.warning(
+                self,
+                "No Class Selected",
+                "Please select an object class before processing annotations.",
+            )
+            return
+
+        self.process_annotations_requested.emit()
+        logger.debug("Process annotations requested")
+
+    def _on_show_annotations(self):
+        """Handle show annotations button."""
+        self.show_annotations_requested.emit()
+        logger.debug("Show annotations requested")
+
     def get_current_class(self) -> Optional[Dict]:
         """Get currently selected object class."""
         return self.current_class