Adding pen tool for annotation

src/database/db_manager.py

@@ -30,18 +30,48 @@ class DatabaseManager:
         # Create directory if it doesn't exist
         Path(self.db_path).parent.mkdir(parents=True, exist_ok=True)
 
+        conn = self.get_connection()
+        try:
+            # Check if annotations table needs migration
+            self._migrate_annotations_table(conn)
+
             # Read schema file and execute
             schema_path = Path(__file__).parent / "schema.sql"
             with open(schema_path, "r") as f:
                 schema_sql = f.read()
 
-        conn = self.get_connection()
-        try:
             conn.executescript(schema_sql)
             conn.commit()
         finally:
             conn.close()
 
+    def _migrate_annotations_table(self, conn: sqlite3.Connection) -> None:
+        """
+        Migrate annotations table from old schema (class_name) to new schema (class_id).
+        """
+        cursor = conn.cursor()
+
+        # Check if annotations table exists
+        cursor.execute(
+            "SELECT name FROM sqlite_master WHERE type='table' AND name='annotations'"
+        )
+        if not cursor.fetchone():
+            # Table doesn't exist yet, no migration needed
+            return
+
+        # Check if table has old schema (class_name column)
+        cursor.execute("PRAGMA table_info(annotations)")
+        columns = {row[1]: row for row in cursor.fetchall()}
+
+        if "class_name" in columns and "class_id" not in columns:
+            # Old schema detected, need to migrate
+            print("Migrating annotations table to new schema with class_id...")
+
+            # Drop old annotations table (assuming no critical data since this is a new feature)
+            cursor.execute("DROP TABLE IF EXISTS annotations")
+            conn.commit()
+            print("Old annotations table dropped, will be recreated with new schema")
+
     def get_connection(self) -> sqlite3.Connection:
         """Get database connection with proper settings."""
         conn = sqlite3.connect(self.db_path)
@@ -593,25 +623,38 @@ class DatabaseManager:
     def add_annotation(
         self,
         image_id: int,
-        class_name: str,
+        class_id: int,
         bbox: Tuple[float, float, float, float],
         annotator: str,
         segmentation_mask: Optional[List[List[float]]] = None,
         verified: bool = False,
     ) -> int:
-        """Add manual annotation."""
+        """
+        Add manual annotation.
+
+        Args:
+            image_id: ID of the image
+            class_id: ID of the object class (foreign key to object_classes)
+            bbox: Bounding box coordinates (normalized 0-1)
+            annotator: Name of person/tool creating annotation
+            segmentation_mask: Polygon coordinates for segmentation
+            verified: Whether annotation has been verified
+
+        Returns:
+            ID of the inserted annotation
+        """
         conn = self.get_connection()
         try:
             cursor = conn.cursor()
             x_min, y_min, x_max, y_max = bbox
             cursor.execute(
                 """
-                INSERT INTO annotations (image_id, class_name, x_min, y_min, x_max, y_max, segmentation_mask, annotator, verified)
+                INSERT INTO annotations (image_id, class_id, x_min, y_min, x_max, y_max, segmentation_mask, annotator, verified)
                 VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
                 """,
                 (
                     image_id,
-                    class_name,
+                    class_id,
                     x_min,
                     y_min,
                     x_max,
@@ -627,15 +670,178 @@ class DatabaseManager:
             conn.close()
 
     def get_annotations_for_image(self, image_id: int) -> List[Dict]:
-        """Get all annotations for an image."""
+        """
+        Get all annotations for an image with class information.
+
+        Args:
+            image_id: ID of the image
+
+        Returns:
+            List of annotation dictionaries with joined class information
+        """
         conn = self.get_connection()
         try:
             cursor = conn.cursor()
-            cursor.execute("SELECT * FROM annotations WHERE image_id = ?", (image_id,))
+            cursor.execute(
+                """
+                SELECT
+                    a.*,
+                    c.class_name,
+                    c.color as class_color,
+                    c.description as class_description
+                FROM annotations a
+                JOIN object_classes c ON a.class_id = c.id
+                WHERE a.image_id = ?
+                ORDER BY a.created_at DESC
+                """,
+                (image_id,),
+            )
+            annotations = []
+            for row in cursor.fetchall():
+                ann = dict(row)
+                if ann.get("segmentation_mask"):
+                    ann["segmentation_mask"] = json.loads(ann["segmentation_mask"])
+                annotations.append(ann)
+            return annotations
+        finally:
+            conn.close()
+
+    # ==================== Object Class Operations ====================
+
+    def get_object_classes(self) -> List[Dict]:
+        """
+        Get all object classes.
+
+        Returns:
+            List of object class dictionaries
+        """
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute("SELECT * FROM object_classes ORDER BY class_name")
             return [dict(row) for row in cursor.fetchall()]
         finally:
             conn.close()
 
+    def get_object_class_by_id(self, class_id: int) -> Optional[Dict]:
+        """Get object class by ID."""
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute("SELECT * FROM object_classes WHERE id = ?", (class_id,))
+            row = cursor.fetchone()
+            return dict(row) if row else None
+        finally:
+            conn.close()
+
+    def get_object_class_by_name(self, class_name: str) -> Optional[Dict]:
+        """Get object class by name."""
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute(
+                "SELECT * FROM object_classes WHERE class_name = ?", (class_name,)
+            )
+            row = cursor.fetchone()
+            return dict(row) if row else None
+        finally:
+            conn.close()
+
+    def add_object_class(
+        self, class_name: str, color: str, description: Optional[str] = None
+    ) -> int:
+        """
+        Add a new object class.
+
+        Args:
+            class_name: Name of the object class
+            color: Hex color code (e.g., '#FF0000')
+            description: Optional description
+
+        Returns:
+            ID of the inserted object class
+        """
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute(
+                """
+                INSERT INTO object_classes (class_name, color, description)
+                VALUES (?, ?, ?)
+                """,
+                (class_name, color, description),
+            )
+            conn.commit()
+            return cursor.lastrowid
+        except sqlite3.IntegrityError:
+            # Class already exists
+            existing = self.get_object_class_by_name(class_name)
+            return existing["id"] if existing else None
+        finally:
+            conn.close()
+
+    def update_object_class(
+        self,
+        class_id: int,
+        class_name: Optional[str] = None,
+        color: Optional[str] = None,
+        description: Optional[str] = None,
+    ) -> bool:
+        """
+        Update an object class.
+
+        Args:
+            class_id: ID of the class to update
+            class_name: New class name (optional)
+            color: New color (optional)
+            description: New description (optional)
+
+        Returns:
+            True if updated, False otherwise
+        """
+        conn = self.get_connection()
+        try:
+            updates = {}
+            if class_name is not None:
+                updates["class_name"] = class_name
+            if color is not None:
+                updates["color"] = color
+            if description is not None:
+                updates["description"] = description
+
+            if not updates:
+                return False
+
+            set_clauses = [f"{key} = ?" for key in updates.keys()]
+            params = list(updates.values()) + [class_id]
+
+            query = f"UPDATE object_classes SET {', '.join(set_clauses)} WHERE id = ?"
+            cursor = conn.cursor()
+            cursor.execute(query, params)
+            conn.commit()
+            return cursor.rowcount > 0
+        finally:
+            conn.close()
+
+    def delete_object_class(self, class_id: int) -> bool:
+        """
+        Delete an object class.
+
+        Args:
+            class_id: ID of the class to delete
+
+        Returns:
+            True if deleted, False otherwise
+        """
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute("DELETE FROM object_classes WHERE id = ?", (class_id,))
+            conn.commit()
+            return cursor.rowcount > 0
+        finally:
+            conn.close()
+
     @staticmethod
     def calculate_checksum(file_path: str) -> str:
         """Calculate MD5 checksum of a file."""

src/database/schema.sql

@@ -44,11 +44,27 @@ CREATE TABLE IF NOT EXISTS detections (
     FOREIGN KEY (model_id) REFERENCES models (id) ON DELETE CASCADE
 );
 
--- Annotations table: stores manual annotations (future feature)
+-- Object classes table: stores annotation class definitions with colors
+CREATE TABLE IF NOT EXISTS object_classes (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    class_name TEXT NOT NULL UNIQUE,
+    color TEXT NOT NULL,  -- Hex color code (e.g., '#FF0000')
+    created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+    description TEXT
+);
+
+-- Insert default object classes
+INSERT OR IGNORE INTO object_classes (class_name, color, description) VALUES
+    ('cell', '#FF0000', 'Cell object'),
+    ('nucleus', '#00FF00', 'Cell nucleus'),
+    ('mitochondria', '#0000FF', 'Mitochondria'),
+    ('vesicle', '#FFFF00', 'Vesicle');
+
+-- Annotations table: stores manual annotations
 CREATE TABLE IF NOT EXISTS annotations (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     image_id INTEGER NOT NULL,
-    class_name TEXT NOT NULL,
+    class_id INTEGER NOT NULL,
     x_min REAL NOT NULL CHECK(x_min >= 0 AND x_min <= 1),
     y_min REAL NOT NULL CHECK(y_min >= 0 AND y_min <= 1),
     x_max REAL NOT NULL CHECK(x_max >= 0 AND x_max <= 1),
@@ -57,7 +73,8 @@ CREATE TABLE IF NOT EXISTS annotations (
     annotator TEXT,
     created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
     verified BOOLEAN DEFAULT 0,
-    FOREIGN KEY (image_id) REFERENCES images (id) ON DELETE CASCADE
+    FOREIGN KEY (image_id) REFERENCES images (id) ON DELETE CASCADE,
+    FOREIGN KEY (class_id) REFERENCES object_classes (id) ON DELETE CASCADE
 );
 
 -- Create indexes for performance optimization
@@ -69,4 +86,6 @@ CREATE INDEX IF NOT EXISTS idx_detections_confidence ON detections(confidence);
 CREATE INDEX IF NOT EXISTS idx_images_relative_path ON images(relative_path);
 CREATE INDEX IF NOT EXISTS idx_images_added_at ON images(added_at);
 CREATE INDEX IF NOT EXISTS idx_annotations_image_id ON annotations(image_id);
+CREATE INDEX IF NOT EXISTS idx_annotations_class_id ON annotations(class_id);
 CREATE INDEX IF NOT EXISTS idx_models_created_at ON models(created_at);
+CREATE INDEX IF NOT EXISTS idx_object_classes_class_name ON object_classes(class_name);

src/gui/tabs/annotation_tab.py

@@ -1,6 +1,6 @@
 """
 Annotation tab for the microscopy object detection application.
-Future feature for manual annotation.
+Manual annotation with pen tool and object class management.
 """
 
 from PySide6.QtWidgets import (
@@ -21,13 +21,13 @@ from src.database.db_manager import DatabaseManager
 from src.utils.config_manager import ConfigManager
 from src.utils.image import Image, ImageLoadError
 from src.utils.logger import get_logger
-from src.gui.widgets import ImageDisplayWidget
+from src.gui.widgets import AnnotationCanvasWidget, AnnotationToolsWidget
 
 logger = get_logger(__name__)
 
 
 class AnnotationTab(QWidget):
-    """Annotation tab placeholder (future feature)."""
+    """Annotation tab for manual image annotation."""
 
     def __init__(
         self, db_manager: DatabaseManager, config_manager: ConfigManager, parent=None
@@ -37,6 +37,7 @@ class AnnotationTab(QWidget):
         self.config_manager = config_manager
         self.current_image = None
         self.current_image_path = None
+        self.current_image_id = None
 
         self._setup_ui()
 
@@ -52,49 +53,52 @@ class AnnotationTab(QWidget):
         self.left_splitter = QSplitter(Qt.Vertical)
         self.left_splitter.setHandleWidth(10)
 
-        # Image display section
-        display_group = QGroupBox("Image Display")
-        display_layout = QVBoxLayout()
+        # Annotation canvas section
+        canvas_group = QGroupBox("Annotation Canvas")
+        canvas_layout = QVBoxLayout()
 
-        # Use the reusable ImageDisplayWidget
-        self.image_display_widget = ImageDisplayWidget()
-        self.image_display_widget.zoom_changed.connect(self._on_zoom_changed)
-        display_layout.addWidget(self.image_display_widget)
+        # Use the AnnotationCanvasWidget
+        self.annotation_canvas = AnnotationCanvasWidget()
+        self.annotation_canvas.zoom_changed.connect(self._on_zoom_changed)
+        self.annotation_canvas.annotation_drawn.connect(self._on_annotation_drawn)
+        canvas_layout.addWidget(self.annotation_canvas)
 
-        display_group.setLayout(display_layout)
-        self.left_splitter.addWidget(display_group)
+        canvas_group.setLayout(canvas_layout)
+        self.left_splitter.addWidget(canvas_group)
 
-        # Zoom controls info
-        zoom_info = QLabel("Zoom: Mouse wheel or +/- keys to zoom in/out")
-        zoom_info.setStyleSheet("QLabel { color: #888; font-style: italic; }")
-        self.left_splitter.addWidget(zoom_info)
+        # Controls info
+        controls_info = QLabel(
+            "Zoom: Mouse wheel or +/- keys | Drawing: Enable pen and drag mouse"
+        )
+        controls_info.setStyleSheet("QLabel { color: #888; font-style: italic; }")
+        self.left_splitter.addWidget(controls_info)
         # }
 
         # { Right splitter for annotation tools and controls
         self.right_splitter = QSplitter(Qt.Vertical)
         self.right_splitter.setHandleWidth(10)
 
+        # Annotation tools section
+        self.annotation_tools = AnnotationToolsWidget(self.db_manager)
+        self.annotation_tools.pen_enabled_changed.connect(
+            self.annotation_canvas.set_pen_enabled
+        )
+        self.annotation_tools.pen_color_changed.connect(
+            self.annotation_canvas.set_pen_color
+        )
+        self.annotation_tools.pen_width_changed.connect(
+            self.annotation_canvas.set_pen_width
+        )
+        self.annotation_tools.class_selected.connect(self._on_class_selected)
+        self.annotation_tools.clear_annotations_requested.connect(
+            self._on_clear_annotations
+        )
+        self.right_splitter.addWidget(self.annotation_tools)
+
         # Image loading section
         load_group = QGroupBox("Image Loading")
         load_layout = QVBoxLayout()
 
-        # Future features info
-        info_group = QGroupBox("Annotation Tool (Future Feature)")
-        info_layout = QVBoxLayout()
-        info_label = QLabel(
-            "Full annotation functionality will be implemented in future version.\n\n"
-            "Planned Features:\n"
-            "- Drawing tools for bounding boxes\n"
-            "- Class label assignment\n"
-            "- Export annotations to YOLO format\n"
-            "- Annotation verification"
-        )
-        info_label.setWordWrap(True)
-        info_layout.addWidget(info_label)
-        info_group.setLayout(info_layout)
-
-        self.right_splitter.addWidget(info_group)
-
         # Load image button
         button_layout = QHBoxLayout()
         self.load_image_btn = QPushButton("Load Image")
@@ -158,13 +162,22 @@ class AnnotationTab(QWidget):
                 "annotation_tab/last_directory", str(Path(file_path).parent)
             )
 
-            # Display image using the ImageDisplayWidget
-            self.image_display_widget.load_image(self.current_image)
+            # Get or create image in database
+            relative_path = str(Path(file_path).name)  # Simplified for now
+            self.current_image_id = self.db_manager.get_or_create_image(
+                relative_path,
+                Path(file_path).name,
+                self.current_image.width,
+                self.current_image.height,
+            )
+
+            # Display image using the AnnotationCanvasWidget
+            self.annotation_canvas.load_image(self.current_image)
 
             # Update info label
             self._update_image_info()
 
-            logger.info(f"Loaded image: {file_path}")
+            logger.info(f"Loaded image: {file_path} (DB ID: {self.current_image_id})")
 
         except ImageLoadError as e:
             logger.error(f"Failed to load image: {e}")
@@ -181,7 +194,7 @@ class AnnotationTab(QWidget):
             self.image_info_label.setText("No image loaded")
             return
 
-        zoom_percentage = self.image_display_widget.get_zoom_percentage()
+        zoom_percentage = self.annotation_canvas.get_zoom_percentage()
         info_text = (
             f"File: {Path(self.current_image_path).name}\n"
             f"Size: {self.current_image.width}x{self.current_image.height} pixels\n"
@@ -194,9 +207,36 @@ class AnnotationTab(QWidget):
         self.image_info_label.setText(info_text)
 
     def _on_zoom_changed(self, zoom_scale: float):
-        """Handle zoom level changes from the image display widget."""
+        """Handle zoom level changes from the annotation canvas."""
         self._update_image_info()
 
+    def _on_annotation_drawn(self, points: list):
+        """Handle when an annotation stroke is drawn."""
+        current_class = self.annotation_tools.get_current_class()
+
+        if not current_class:
+            logger.warning("Annotation drawn but no object class selected")
+            QMessageBox.warning(
+                self,
+                "No Class Selected",
+                "Please select an object class before drawing annotations.",
+            )
+            return
+
+        logger.info(
+            f"Annotation drawn with {len(points)} points for class: {current_class['class_name']}"
+        )
+        # Future: Save annotation to database or export
+
+    def _on_class_selected(self, class_data: dict):
+        """Handle when an object class is selected."""
+        logger.debug(f"Object class selected: {class_data['class_name']}")
+
+    def _on_clear_annotations(self):
+        """Handle clearing all annotations."""
+        self.annotation_canvas.clear_annotations()
+        logger.info("Cleared all annotations")
+
     def _restore_state(self):
         """Restore splitter positions from settings."""
         settings = QSettings("microscopy_app", "object_detection")

src/gui/widgets/__init__.py

@@ -1,5 +1,7 @@
 """GUI widgets for the microscopy object detection application."""
 
 from src.gui.widgets.image_display_widget import ImageDisplayWidget
+from src.gui.widgets.annotation_canvas_widget import AnnotationCanvasWidget
+from src.gui.widgets.annotation_tools_widget import AnnotationToolsWidget
 
-__all__ = ["ImageDisplayWidget"]
+__all__ = ["ImageDisplayWidget", "AnnotationCanvasWidget", "AnnotationToolsWidget"]

src/gui/widgets/annotation_canvas_widget.py

@@ -0,0 +1,406 @@
+"""
+Annotation canvas widget for drawing annotations on images.
+Supports pen tool with color selection for manual annotation.
+"""
+
+from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel, QScrollArea
+from PySide6.QtGui import (
+    QPixmap,
+    QImage,
+    QPainter,
+    QPen,
+    QColor,
+    QKeyEvent,
+    QMouseEvent,
+    QPaintEvent,
+)
+from PySide6.QtCore import Qt, QEvent, Signal, QPoint
+from typing import List, Optional, Tuple
+import numpy as np
+
+from src.utils.image import Image, ImageLoadError
+from src.utils.logger import get_logger
+
+logger = get_logger(__name__)
+
+
+class AnnotationCanvasWidget(QWidget):
+    """
+    Widget for displaying images and drawing annotations with pen tool.
+
+    Features:
+    - Display images with zoom functionality
+    - Pen tool for drawing annotations
+    - Configurable pen color and width
+    - Mouse-based drawing interface
+    - Zoom in/out with mouse wheel and keyboard
+
+    Signals:
+        zoom_changed: Emitted when zoom level changes (float zoom_scale)
+        annotation_drawn: Emitted when a new stroke is completed (list of points)
+    """
+
+    zoom_changed = Signal(float)
+    annotation_drawn = Signal(list)  # List of (x, y) points in normalized coordinates
+
+    def __init__(self, parent=None):
+        """Initialize the annotation canvas widget."""
+        super().__init__(parent)
+
+        self.current_image = None
+        self.original_pixmap = None
+        self.annotation_pixmap = None  # Overlay for annotations
+        self.zoom_scale = 1.0
+        self.zoom_min = 0.1
+        self.zoom_max = 10.0
+        self.zoom_step = 0.1
+        self.zoom_wheel_step = 0.15
+
+        # Drawing state
+        self.is_drawing = False
+        self.pen_enabled = False
+        self.pen_color = QColor(255, 0, 0, 128)  # Default red with 50% alpha
+        self.pen_width = 3
+        self.current_stroke = []  # Points in current stroke
+        self.all_strokes = []  # All completed strokes
+
+        self._setup_ui()
+
+    def _setup_ui(self):
+        """Setup user interface."""
+        layout = QVBoxLayout()
+        layout.setContentsMargins(0, 0, 0, 0)
+
+        # Scroll area for canvas
+        self.scroll_area = QScrollArea()
+        self.scroll_area.setWidgetResizable(True)
+        self.scroll_area.setMinimumHeight(400)
+
+        self.canvas_label = QLabel("No image loaded")
+        self.canvas_label.setAlignment(Qt.AlignCenter)
+        self.canvas_label.setStyleSheet(
+            "QLabel { background-color: #2b2b2b; color: #888; }"
+        )
+        self.canvas_label.setScaledContents(False)
+        self.canvas_label.setMouseTracking(True)
+
+        self.scroll_area.setWidget(self.canvas_label)
+        self.scroll_area.viewport().installEventFilter(self)
+
+        layout.addWidget(self.scroll_area)
+        self.setLayout(layout)
+
+        self.setFocusPolicy(Qt.StrongFocus)
+
+    def load_image(self, image: Image):
+        """
+        Load and display an image.
+
+        Args:
+            image: Image object to display
+        """
+        self.current_image = image
+        self.zoom_scale = 1.0
+        self.clear_annotations()
+        self._display_image()
+        logger.debug(
+            f"Loaded image into annotation canvas: {image.width}x{image.height}"
+        )
+
+    def clear(self):
+        """Clear the displayed image and all annotations."""
+        self.current_image = None
+        self.original_pixmap = None
+        self.annotation_pixmap = None
+        self.zoom_scale = 1.0
+        self.clear_annotations()
+        self.canvas_label.setText("No image loaded")
+        self.canvas_label.setPixmap(QPixmap())
+
+    def clear_annotations(self):
+        """Clear all drawn annotations."""
+        self.all_strokes = []
+        self.current_stroke = []
+        self.is_drawing = False
+        if self.annotation_pixmap:
+            self.annotation_pixmap.fill(Qt.transparent)
+            self._update_display()
+
+    def _display_image(self):
+        """Display the current image in the canvas."""
+        if self.current_image is None:
+            return
+
+        try:
+            # Get RGB image data
+            if self.current_image.channels == 3:
+                image_data = self.current_image.get_rgb()
+                height, width, channels = image_data.shape
+            else:
+                image_data = self.current_image.get_grayscale()
+                height, width = image_data.shape
+
+            image_data = np.ascontiguousarray(image_data)
+            bytes_per_line = image_data.strides[0]
+
+            qimage = QImage(
+                image_data.data,
+                width,
+                height,
+                bytes_per_line,
+                self.current_image.qtimage_format,
+            )
+
+            self.original_pixmap = QPixmap.fromImage(qimage)
+
+            # Create transparent overlay for annotations
+            self.annotation_pixmap = QPixmap(self.original_pixmap.size())
+            self.annotation_pixmap.fill(Qt.transparent)
+
+            self._apply_zoom()
+
+        except Exception as e:
+            logger.error(f"Error displaying image: {e}")
+            raise ImageLoadError(f"Failed to display image: {str(e)}")
+
+    def _apply_zoom(self):
+        """Apply current zoom level to the displayed image."""
+        if self.original_pixmap is None:
+            return
+
+        scaled_width = int(self.original_pixmap.width() * self.zoom_scale)
+        scaled_height = int(self.original_pixmap.height() * self.zoom_scale)
+
+        # Scale both image and annotations
+        scaled_image = self.original_pixmap.scaled(
+            scaled_width,
+            scaled_height,
+            Qt.KeepAspectRatio,
+            (
+                Qt.SmoothTransformation
+                if self.zoom_scale >= 1.0
+                else Qt.FastTransformation
+            ),
+        )
+
+        scaled_annotations = self.annotation_pixmap.scaled(
+            scaled_width,
+            scaled_height,
+            Qt.KeepAspectRatio,
+            (
+                Qt.SmoothTransformation
+                if self.zoom_scale >= 1.0
+                else Qt.FastTransformation
+            ),
+        )
+
+        # Composite image and annotations
+        combined = QPixmap(scaled_image.size())
+        painter = QPainter(combined)
+        painter.drawPixmap(0, 0, scaled_image)
+        painter.drawPixmap(0, 0, scaled_annotations)
+        painter.end()
+
+        self.canvas_label.setPixmap(combined)
+        self.canvas_label.setScaledContents(False)
+        self.canvas_label.adjustSize()
+
+        self.zoom_changed.emit(self.zoom_scale)
+
+    def _update_display(self):
+        """Update display after drawing."""
+        self._apply_zoom()
+
+    def set_pen_enabled(self, enabled: bool):
+        """Enable or disable pen tool."""
+        self.pen_enabled = enabled
+        if enabled:
+            self.canvas_label.setCursor(Qt.CrossCursor)
+        else:
+            self.canvas_label.setCursor(Qt.ArrowCursor)
+
+    def set_pen_color(self, color: QColor):
+        """Set pen color."""
+        self.pen_color = color
+
+    def set_pen_width(self, width: int):
+        """Set pen width."""
+        self.pen_width = max(1, width)
+
+    def get_zoom_percentage(self) -> int:
+        """Get current zoom level as percentage."""
+        return int(self.zoom_scale * 100)
+
+    def zoom_in(self):
+        """Zoom in on the image."""
+        if self.original_pixmap is None:
+            return
+        new_scale = self.zoom_scale + self.zoom_step
+        if new_scale <= self.zoom_max:
+            self.zoom_scale = new_scale
+            self._apply_zoom()
+
+    def zoom_out(self):
+        """Zoom out from the image."""
+        if self.original_pixmap is None:
+            return
+        new_scale = self.zoom_scale - self.zoom_step
+        if new_scale >= self.zoom_min:
+            self.zoom_scale = new_scale
+            self._apply_zoom()
+
+    def reset_zoom(self):
+        """Reset zoom to 100%."""
+        if self.original_pixmap is None:
+            return
+        self.zoom_scale = 1.0
+        self._apply_zoom()
+
+    def _canvas_to_image_coords(self, pos: QPoint) -> Optional[Tuple[int, int]]:
+        """Convert canvas coordinates to image coordinates, accounting for zoom and centering."""
+        if self.original_pixmap is None or self.canvas_label.pixmap() is None:
+            return None
+
+        # Get the displayed pixmap size (after zoom)
+        displayed_pixmap = self.canvas_label.pixmap()
+        displayed_width = displayed_pixmap.width()
+        displayed_height = displayed_pixmap.height()
+
+        # Calculate offset due to label centering (label might be larger than pixmap)
+        label_width = self.canvas_label.width()
+        label_height = self.canvas_label.height()
+        offset_x = max(0, (label_width - displayed_width) // 2)
+        offset_y = max(0, (label_height - displayed_height) // 2)
+
+        # Adjust position for offset and convert to image coordinates
+        x = (pos.x() - offset_x) / self.zoom_scale
+        y = (pos.y() - offset_y) / self.zoom_scale
+
+        # Check bounds
+        if (
+            0 <= x < self.original_pixmap.width()
+            and 0 <= y < self.original_pixmap.height()
+        ):
+            return (int(x), int(y))
+        return None
+
+    def _image_to_normalized_coords(self, x: int, y: int) -> Tuple[float, float]:
+        """Convert image coordinates to normalized coordinates (0-1)."""
+        if self.original_pixmap is None:
+            return (0.0, 0.0)
+
+        norm_x = x / self.original_pixmap.width()
+        norm_y = y / self.original_pixmap.height()
+        return (norm_x, norm_y)
+
+    def mousePressEvent(self, event: QMouseEvent):
+        """Handle mouse press events for drawing."""
+        if not self.pen_enabled or self.annotation_pixmap is None:
+            super().mousePressEvent(event)
+            return
+
+        if event.button() == Qt.LeftButton:
+            # Get accurate position using global coordinates
+            label_pos = self.canvas_label.mapFromGlobal(event.globalPos())
+            img_coords = self._canvas_to_image_coords(label_pos)
+
+            if img_coords:
+                self.is_drawing = True
+                self.current_stroke = [img_coords]
+
+    def mouseMoveEvent(self, event: QMouseEvent):
+        """Handle mouse move events for drawing."""
+        if (
+            not self.is_drawing
+            or not self.pen_enabled
+            or self.annotation_pixmap is None
+        ):
+            super().mouseMoveEvent(event)
+            return
+
+        # Get accurate position using global coordinates
+        label_pos = self.canvas_label.mapFromGlobal(event.globalPos())
+        img_coords = self._canvas_to_image_coords(label_pos)
+
+        if img_coords and len(self.current_stroke) > 0:
+            # Draw line from last point to current point
+            painter = QPainter(self.annotation_pixmap)
+            pen = QPen(
+                self.pen_color, self.pen_width, Qt.SolidLine, Qt.RoundCap, Qt.RoundJoin
+            )
+            painter.setPen(pen)
+
+            last_point = self.current_stroke[-1]
+            painter.drawLine(last_point[0], last_point[1], img_coords[0], img_coords[1])
+            painter.end()
+
+            self.current_stroke.append(img_coords)
+            self._update_display()
+
+    def mouseReleaseEvent(self, event: QMouseEvent):
+        """Handle mouse release events to complete a stroke."""
+        if not self.is_drawing or event.button() != Qt.LeftButton:
+            super().mouseReleaseEvent(event)
+            return
+
+        self.is_drawing = False
+
+        if len(self.current_stroke) > 1:
+            # Convert to normalized coordinates and save stroke
+            normalized_stroke = [
+                self._image_to_normalized_coords(x, y) for x, y in self.current_stroke
+            ]
+            self.all_strokes.append(
+                {
+                    "points": normalized_stroke,
+                    "color": self.pen_color.name(),
+                    "alpha": self.pen_color.alpha(),
+                    "width": self.pen_width,
+                }
+            )
+
+            # Emit signal with normalized coordinates
+            self.annotation_drawn.emit(normalized_stroke)
+            logger.debug(f"Completed stroke with {len(normalized_stroke)} points")
+
+        self.current_stroke = []
+
+    def get_all_strokes(self) -> List[dict]:
+        """Get all drawn strokes with metadata."""
+        return self.all_strokes
+
+    def keyPressEvent(self, event: QKeyEvent):
+        """Handle keyboard events for zooming."""
+        if event.key() in (Qt.Key_Plus, Qt.Key_Equal):
+            self.zoom_in()
+            event.accept()
+        elif event.key() == Qt.Key_Minus:
+            self.zoom_out()
+            event.accept()
+        elif event.key() == Qt.Key_0 and event.modifiers() == Qt.ControlModifier:
+            self.reset_zoom()
+            event.accept()
+        else:
+            super().keyPressEvent(event)
+
+    def eventFilter(self, obj, event: QEvent) -> bool:
+        """Event filter to capture wheel events for zooming."""
+        if event.type() == QEvent.Wheel:
+            wheel_event = event
+            if self.original_pixmap is not None:
+                delta = wheel_event.angleDelta().y()
+
+                if delta > 0:
+                    new_scale = self.zoom_scale + self.zoom_wheel_step
+                    if new_scale <= self.zoom_max:
+                        self.zoom_scale = new_scale
+                        self._apply_zoom()
+                else:
+                    new_scale = self.zoom_scale - self.zoom_wheel_step
+                    if new_scale >= self.zoom_min:
+                        self.zoom_scale = new_scale
+                        self._apply_zoom()
+
+                return True
+
+        return super().eventFilter(obj, event)

src/gui/widgets/annotation_tools_widget.py

@@ -0,0 +1,352 @@
+"""
+Annotation tools widget for controlling annotation parameters.
+Includes pen tool, color picker, class selection, and annotation management.
+"""
+
+from PySide6.QtWidgets import (
+    QWidget,
+    QVBoxLayout,
+    QHBoxLayout,
+    QLabel,
+    QGroupBox,
+    QPushButton,
+    QComboBox,
+    QSpinBox,
+    QColorDialog,
+    QInputDialog,
+    QMessageBox,
+)
+from PySide6.QtGui import QColor, QIcon, QPixmap, QPainter
+from PySide6.QtCore import Qt, Signal
+from typing import Optional, Dict
+
+from src.database.db_manager import DatabaseManager
+from src.utils.logger import get_logger
+
+logger = get_logger(__name__)
+
+
+class AnnotationToolsWidget(QWidget):
+    """
+    Widget for annotation tool controls.
+
+    Features:
+    - Enable/disable pen tool
+    - Color selection for pen
+    - Object class selection
+    - Add new object classes
+    - Pen width control
+    - Clear annotations
+
+    Signals:
+        pen_enabled_changed: Emitted when pen tool is enabled/disabled (bool)
+        pen_color_changed: Emitted when pen color changes (QColor)
+        pen_width_changed: Emitted when pen width changes (int)
+        class_selected: Emitted when object class is selected (dict)
+        clear_annotations_requested: Emitted when clear button is pressed
+    """
+
+    pen_enabled_changed = Signal(bool)
+    pen_color_changed = Signal(QColor)
+    pen_width_changed = Signal(int)
+    class_selected = Signal(dict)
+    clear_annotations_requested = Signal()
+
+    def __init__(self, db_manager: DatabaseManager, parent=None):
+        """
+        Initialize annotation tools widget.
+
+        Args:
+            db_manager: Database manager instance
+            parent: Parent widget
+        """
+        super().__init__(parent)
+        self.db_manager = db_manager
+        self.pen_enabled = False
+        self.current_color = QColor(255, 0, 0, 128)  # Red with 50% alpha
+        self.current_class = None
+
+        self._setup_ui()
+        self._load_object_classes()
+
+    def _setup_ui(self):
+        """Setup user interface."""
+        layout = QVBoxLayout()
+
+        # Pen Tool Group
+        pen_group = QGroupBox("Pen Tool")
+        pen_layout = QVBoxLayout()
+
+        # Enable/Disable pen
+        button_layout = QHBoxLayout()
+        self.pen_toggle_btn = QPushButton("Enable Pen")
+        self.pen_toggle_btn.setCheckable(True)
+        self.pen_toggle_btn.clicked.connect(self._on_pen_toggle)
+        button_layout.addWidget(self.pen_toggle_btn)
+        pen_layout.addLayout(button_layout)
+
+        # Pen width control
+        width_layout = QHBoxLayout()
+        width_layout.addWidget(QLabel("Pen Width:"))
+        self.pen_width_spin = QSpinBox()
+        self.pen_width_spin.setMinimum(1)
+        self.pen_width_spin.setMaximum(20)
+        self.pen_width_spin.setValue(3)
+        self.pen_width_spin.valueChanged.connect(self._on_pen_width_changed)
+        width_layout.addWidget(self.pen_width_spin)
+        width_layout.addStretch()
+        pen_layout.addLayout(width_layout)
+
+        # Color selection
+        color_layout = QHBoxLayout()
+        color_layout.addWidget(QLabel("Color:"))
+        self.color_btn = QPushButton()
+        self.color_btn.setFixedSize(40, 30)
+        self.color_btn.clicked.connect(self._on_color_picker)
+        self._update_color_button()
+        color_layout.addWidget(self.color_btn)
+        color_layout.addStretch()
+        pen_layout.addLayout(color_layout)
+
+        pen_group.setLayout(pen_layout)
+        layout.addWidget(pen_group)
+
+        # Object Class Group
+        class_group = QGroupBox("Object Class")
+        class_layout = QVBoxLayout()
+
+        # Class selection dropdown
+        self.class_combo = QComboBox()
+        self.class_combo.currentIndexChanged.connect(self._on_class_selected)
+        class_layout.addWidget(self.class_combo)
+
+        # Add class button
+        class_button_layout = QHBoxLayout()
+        self.add_class_btn = QPushButton("Add New Class")
+        self.add_class_btn.clicked.connect(self._on_add_class)
+        class_button_layout.addWidget(self.add_class_btn)
+
+        self.refresh_classes_btn = QPushButton("Refresh")
+        self.refresh_classes_btn.clicked.connect(self._load_object_classes)
+        class_button_layout.addWidget(self.refresh_classes_btn)
+        class_layout.addLayout(class_button_layout)
+
+        # Selected class info
+        self.class_info_label = QLabel("No class selected")
+        self.class_info_label.setWordWrap(True)
+        self.class_info_label.setStyleSheet(
+            "QLabel { color: #888; font-style: italic; }"
+        )
+        class_layout.addWidget(self.class_info_label)
+
+        class_group.setLayout(class_layout)
+        layout.addWidget(class_group)
+
+        # Actions Group
+        actions_group = QGroupBox("Actions")
+        actions_layout = QVBoxLayout()
+
+        self.clear_btn = QPushButton("Clear All Annotations")
+        self.clear_btn.clicked.connect(self._on_clear_annotations)
+        actions_layout.addWidget(self.clear_btn)
+
+        actions_group.setLayout(actions_layout)
+        layout.addWidget(actions_group)
+
+        layout.addStretch()
+        self.setLayout(layout)
+
+    def _update_color_button(self):
+        """Update the color button appearance with current color."""
+        pixmap = QPixmap(40, 30)
+        pixmap.fill(self.current_color)
+
+        # Add border
+        painter = QPainter(pixmap)
+        painter.setPen(Qt.black)
+        painter.drawRect(0, 0, pixmap.width() - 1, pixmap.height() - 1)
+        painter.end()
+
+        self.color_btn.setIcon(QIcon(pixmap))
+        self.color_btn.setStyleSheet(f"background-color: {self.current_color.name()};")
+
+    def _load_object_classes(self):
+        """Load object classes from database and populate combo box."""
+        try:
+            classes = self.db_manager.get_object_classes()
+
+            # Clear and repopulate combo box
+            self.class_combo.clear()
+            self.class_combo.addItem("-- Select Class --", None)
+
+            for cls in classes:
+                self.class_combo.addItem(cls["class_name"], cls)
+
+            logger.debug(f"Loaded {len(classes)} object classes")
+
+        except Exception as e:
+            logger.error(f"Error loading object classes: {e}")
+            QMessageBox.warning(
+                self, "Error", f"Failed to load object classes:\n{str(e)}"
+            )
+
+    def _on_pen_toggle(self, checked: bool):
+        """Handle pen tool enable/disable."""
+        self.pen_enabled = checked
+
+        if checked:
+            self.pen_toggle_btn.setText("Disable Pen")
+            self.pen_toggle_btn.setStyleSheet(
+                "QPushButton { background-color: #4CAF50; }"
+            )
+        else:
+            self.pen_toggle_btn.setText("Enable Pen")
+            self.pen_toggle_btn.setStyleSheet("")
+
+        self.pen_enabled_changed.emit(self.pen_enabled)
+        logger.debug(f"Pen tool {'enabled' if checked else 'disabled'}")
+
+    def _on_pen_width_changed(self, width: int):
+        """Handle pen width changes."""
+        self.pen_width_changed.emit(width)
+        logger.debug(f"Pen width changed to {width}")
+
+    def _on_color_picker(self):
+        """Open color picker dialog with alpha support."""
+        color = QColorDialog.getColor(
+            self.current_color,
+            self,
+            "Select Pen Color",
+            QColorDialog.ShowAlphaChannel,  # Enable alpha channel selection
+        )
+
+        if color.isValid():
+            self.current_color = color
+            self._update_color_button()
+            self.pen_color_changed.emit(color)
+            logger.debug(
+                f"Pen color changed to {color.name()} with alpha {color.alpha()}"
+            )
+
+    def _on_class_selected(self, index: int):
+        """Handle object class selection."""
+        class_data = self.class_combo.currentData()
+
+        if class_data:
+            self.current_class = class_data
+
+            # Update info label
+            info_text = (
+                f"Class: {class_data['class_name']}\n" f"Color: {class_data['color']}"
+            )
+            if class_data.get("description"):
+                info_text += f"\nDescription: {class_data['description']}"
+
+            self.class_info_label.setText(info_text)
+
+            # Update pen color to match class color with semi-transparency
+            class_color = QColor(class_data["color"])
+            if class_color.isValid():
+                # Add 50% alpha for semi-transparency
+                class_color.setAlpha(128)
+                self.current_color = class_color
+                self._update_color_button()
+                self.pen_color_changed.emit(class_color)
+
+            self.class_selected.emit(class_data)
+            logger.debug(f"Selected class: {class_data['class_name']}")
+        else:
+            self.current_class = None
+            self.class_info_label.setText("No class selected")
+
+    def _on_add_class(self):
+        """Handle adding a new object class."""
+        # Get class name
+        class_name, ok = QInputDialog.getText(
+            self, "Add Object Class", "Enter class name:"
+        )
+
+        if not ok or not class_name.strip():
+            return
+
+        class_name = class_name.strip()
+
+        # Check if class already exists
+        existing = self.db_manager.get_object_class_by_name(class_name)
+        if existing:
+            QMessageBox.warning(
+                self, "Class Exists", f"A class named '{class_name}' already exists."
+            )
+            return
+
+        # Get color
+        color = QColorDialog.getColor(self.current_color, self, "Select Class Color")
+
+        if not color.isValid():
+            return
+
+        # Get optional description
+        description, ok = QInputDialog.getText(
+            self, "Class Description", "Enter class description (optional):"
+        )
+
+        if not ok:
+            description = None
+
+        # Add to database
+        try:
+            class_id = self.db_manager.add_object_class(
+                class_name, color.name(), description.strip() if description else None
+            )
+
+            logger.info(f"Added new object class: {class_name} (ID: {class_id})")
+
+            # Reload classes and select the new one
+            self._load_object_classes()
+
+            # Find and select the newly added class
+            for i in range(self.class_combo.count()):
+                class_data = self.class_combo.itemData(i)
+                if class_data and class_data.get("id") == class_id:
+                    self.class_combo.setCurrentIndex(i)
+                    break
+
+            QMessageBox.information(
+                self, "Success", f"Class '{class_name}' added successfully!"
+            )
+
+        except Exception as e:
+            logger.error(f"Error adding object class: {e}")
+            QMessageBox.critical(
+                self, "Error", f"Failed to add object class:\n{str(e)}"
+            )
+
+    def _on_clear_annotations(self):
+        """Handle clear annotations button."""
+        reply = QMessageBox.question(
+            self,
+            "Clear Annotations",
+            "Are you sure you want to clear all annotations?",
+            QMessageBox.Yes | QMessageBox.No,
+            QMessageBox.No,
+        )
+
+        if reply == QMessageBox.Yes:
+            self.clear_annotations_requested.emit()
+            logger.debug("Clear annotations requested")
+
+    def get_current_class(self) -> Optional[Dict]:
+        """Get currently selected object class."""
+        return self.current_class
+
+    def get_pen_color(self) -> QColor:
+        """Get current pen color."""
+        return self.current_color
+
+    def get_pen_width(self) -> int:
+        """Get current pen width."""
+        return self.pen_width_spin.value()
+
+    def is_pen_enabled(self) -> bool:
+        """Check if pen tool is enabled."""
+        return self.pen_enabled