Adding annotation list

src/database/db_manager.py

@@ -658,6 +658,75 @@ class DatabaseManager:
 
     # ==================== Annotation Operations ====================
 
+    def get_annotated_images_summary(
+        self,
+        name_filter: Optional[str] = None,
+        order_by: str = "filename",
+        order_dir: str = "ASC",
+        limit: Optional[int] = None,
+        offset: int = 0,
+    ) -> List[Dict]:
+        """Return images that have at least one manual annotation.
+
+        Args:
+            name_filter: Optional substring filter applied to filename/relative_path.
+            order_by: One of: 'filename', 'relative_path', 'annotation_count', 'added_at'.
+            order_dir: 'ASC' or 'DESC'.
+            limit: Optional max number of rows.
+            offset: Pagination offset.
+
+        Returns:
+            List of dicts: {id, relative_path, filename, added_at, annotation_count}
+        """
+
+        allowed_order_by = {
+            "filename": "i.filename",
+            "relative_path": "i.relative_path",
+            "annotation_count": "annotation_count",
+            "added_at": "i.added_at",
+        }
+        order_expr = allowed_order_by.get(order_by, "i.filename")
+        dir_norm = str(order_dir).upper().strip()
+        if dir_norm not in {"ASC", "DESC"}:
+            dir_norm = "ASC"
+
+        conn = self.get_connection()
+        try:
+            params: List[Any] = []
+            where_sql = ""
+            if name_filter:
+                # Case-insensitive substring search.
+                token = f"%{name_filter}%"
+                where_sql = "WHERE (i.filename LIKE ? OR i.relative_path LIKE ?)"
+                params.extend([token, token])
+
+            limit_sql = ""
+            if limit is not None:
+                limit_sql = " LIMIT ? OFFSET ?"
+                params.extend([int(limit), int(offset)])
+
+            query = f"""
+                SELECT
+                    i.id,
+                    i.relative_path,
+                    i.filename,
+                    i.added_at,
+                    COUNT(a.id) AS annotation_count
+                FROM images i
+                JOIN annotations a ON a.image_id = i.id
+                {where_sql}
+                GROUP BY i.id
+                HAVING annotation_count > 0
+                ORDER BY {order_expr} {dir_norm}
+                {limit_sql}
+            """
+
+            cursor = conn.cursor()
+            cursor.execute(query, params)
+            return [dict(row) for row in cursor.fetchall()]
+        finally:
+            conn.close()
+
     def add_annotation(
         self,
         image_id: int,

src/gui/main_window.py

@@ -199,6 +199,10 @@ class MainWindow(QMainWindow):
                 self.training_tab.refresh()
             if hasattr(self, "results_tab"):
                 self.results_tab.refresh()
+            if hasattr(self, "annotation_tab"):
+                self.annotation_tab.refresh()
+            if hasattr(self, "validation_tab"):
+                self.validation_tab.refresh()
         except Exception as e:
             logger.error(f"Error applying settings: {e}")
 
@@ -215,6 +219,14 @@ class MainWindow(QMainWindow):
         logger.debug(f"Switched to tab: {tab_name}")
         self._update_status(f"Viewing: {tab_name}")
 
+        # Ensure the Annotation tab always shows up-to-date DB-backed lists.
+        try:
+            current_widget = self.tab_widget.widget(index)
+            if hasattr(self, "annotation_tab") and current_widget is self.annotation_tab:
+                self.annotation_tab.refresh()
+        except Exception as exc:
+            logger.debug(f"Failed to refresh annotation tab on selection: {exc}")
+
     def _show_database_stats(self):
         """Show database statistics dialog."""
         try:
@@ -527,6 +539,11 @@ class MainWindow(QMainWindow):
             if hasattr(self, "training_tab"):
                 self.training_tab.shutdown()
             if hasattr(self, "annotation_tab"):
+                # Best-effort refresh so DB-backed UI state is consistent at shutdown.
+                try:
+                    self.annotation_tab.refresh()
+                except Exception:
+                    pass
                 self.annotation_tab.save_state()
 
             logger.info("Application closing")

src/gui/tabs/annotation_tab.py

@@ -13,6 +13,11 @@ from PySide6.QtWidgets import (
     QFileDialog,
     QMessageBox,
     QSplitter,
+    QLineEdit,
+    QTableWidget,
+    QTableWidgetItem,
+    QHeaderView,
+    QAbstractItemView,
 )
 from PySide6.QtCore import Qt, QSettings
 from pathlib import Path
@@ -50,6 +55,32 @@ class AnnotationTab(QWidget):
         self.main_splitter = QSplitter(Qt.Horizontal)
         self.main_splitter.setHandleWidth(10)
 
+        # { Left-most pane: annotated images list
+        annotated_group = QGroupBox("Annotated Images")
+        annotated_layout = QVBoxLayout()
+
+        filter_row = QHBoxLayout()
+        filter_row.addWidget(QLabel("Filter:"))
+        self.annotated_filter_edit = QLineEdit()
+        self.annotated_filter_edit.setPlaceholderText("Type to filter by image name…")
+        self.annotated_filter_edit.textChanged.connect(self._refresh_annotated_images_list)
+        filter_row.addWidget(self.annotated_filter_edit, 1)
+        annotated_layout.addLayout(filter_row)
+
+        self.annotated_images_table = QTableWidget(0, 2)
+        self.annotated_images_table.setHorizontalHeaderLabels(["Image", "Annotations"])
+        self.annotated_images_table.horizontalHeader().setSectionResizeMode(0, QHeaderView.Stretch)
+        self.annotated_images_table.horizontalHeader().setSectionResizeMode(1, QHeaderView.ResizeToContents)
+        self.annotated_images_table.setSelectionBehavior(QAbstractItemView.SelectRows)
+        self.annotated_images_table.setSelectionMode(QAbstractItemView.SingleSelection)
+        self.annotated_images_table.setEditTriggers(QAbstractItemView.NoEditTriggers)
+        self.annotated_images_table.setSortingEnabled(True)
+        self.annotated_images_table.itemSelectionChanged.connect(self._on_annotated_image_selected)
+        annotated_layout.addWidget(self.annotated_images_table, 1)
+
+        annotated_group.setLayout(annotated_layout)
+        # }
+
         # { Left splitter for image display and zoom info
         self.left_splitter = QSplitter(Qt.Vertical)
         self.left_splitter.setHandleWidth(10)
@@ -120,12 +151,13 @@ class AnnotationTab(QWidget):
         self.right_splitter.addWidget(load_group)
         # }
 
-        # Add both splitters to the main horizontal splitter
+        # Add list + both splitters to the main horizontal splitter
+        self.main_splitter.addWidget(annotated_group)
         self.main_splitter.addWidget(self.left_splitter)
         self.main_splitter.addWidget(self.right_splitter)
 
-        # Set initial sizes: 75% for left (image), 25% for right (controls)
+        # Set initial sizes: list (left), canvas (middle), controls (right)
-        self.main_splitter.setSizes([750, 250])
+        self.main_splitter.setSizes([320, 650, 280])
 
         layout.addWidget(self.main_splitter)
         self.setLayout(layout)
@@ -133,6 +165,9 @@ class AnnotationTab(QWidget):
         # Restore splitter positions from settings
         self._restore_state()
 
+        # Populate list on startup.
+        self._refresh_annotated_images_list()
+
     def _load_image(self):
         """Load and display an image file."""
         # Get last opened directory from QSettings
@@ -166,7 +201,21 @@ class AnnotationTab(QWidget):
             settings.setValue("annotation_tab/last_directory", str(Path(file_path).parent))
 
             # Get or create image in database
-            relative_path = str(Path(file_path).name)  # Simplified for now
+            repo_root = self.config_manager.get_image_repository_path()
+            relative_path: str
+            try:
+                if repo_root:
+                    repo_root_path = Path(repo_root).expanduser().resolve()
+                    file_resolved = Path(file_path).expanduser().resolve()
+                    if file_resolved.is_relative_to(repo_root_path):
+                        relative_path = file_resolved.relative_to(repo_root_path).as_posix()
+                    else:
+                        # Fallback: store filename only to avoid leaking absolute paths.
+                        relative_path = file_resolved.name
+                else:
+                    relative_path = str(Path(file_path).name)
+            except Exception:
+                relative_path = str(Path(file_path).name)
             self.current_image_id = self.db_manager.get_or_create_image(
                 relative_path,
                 Path(file_path).name,
@@ -180,6 +229,9 @@ class AnnotationTab(QWidget):
             # Load and display any existing annotations for this image
             self._load_annotations_for_current_image()
 
+            # Update annotated images list (newly annotated image added/selected).
+            self._refresh_annotated_images_list(select_image_id=self.current_image_id)
+
             # Update info label
             self._update_image_info()
 
@@ -275,6 +327,9 @@ class AnnotationTab(QWidget):
             # Reload annotations from DB and redraw (respecting current class filter)
             self._load_annotations_for_current_image()
 
+            # Update list counts.
+            self._refresh_annotated_images_list(select_image_id=self.current_image_id)
+
         except Exception as e:
             logger.error(f"Failed to save annotation: {e}")
             QMessageBox.critical(self, "Error", f"Failed to save annotation:\n{str(e)}")
@@ -405,6 +460,9 @@ class AnnotationTab(QWidget):
             self.annotation_tools.set_has_selected_annotation(False)
             self._load_annotations_for_current_image()
 
+            # Update list counts.
+            self._refresh_annotated_images_list(select_image_id=self.current_image_id)
+
         except Exception as e:
             logger.error(f"Failed to delete annotations: {e}")
             QMessageBox.critical(
@@ -521,4 +579,164 @@ class AnnotationTab(QWidget):
 
     def refresh(self):
         """Refresh the tab."""
-        pass
+        self._refresh_annotated_images_list(select_image_id=self.current_image_id)
+
+    # ==================== Annotated images list ====================
+
+    def _refresh_annotated_images_list(self, select_image_id: int | None = None) -> None:
+        """Reload annotated-images list from the database."""
+        if not hasattr(self, "annotated_images_table"):
+            return
+
+        # Preserve selection if possible
+        desired_id = select_image_id if select_image_id is not None else self.current_image_id
+
+        name_filter = ""
+        if hasattr(self, "annotated_filter_edit"):
+            name_filter = self.annotated_filter_edit.text().strip()
+
+        try:
+            rows = self.db_manager.get_annotated_images_summary(name_filter=name_filter)
+        except Exception as exc:
+            logger.error(f"Failed to load annotated images summary: {exc}")
+            rows = []
+
+        sorting_enabled = self.annotated_images_table.isSortingEnabled()
+        self.annotated_images_table.setSortingEnabled(False)
+        self.annotated_images_table.blockSignals(True)
+        try:
+            self.annotated_images_table.setRowCount(len(rows))
+            for r, entry in enumerate(rows):
+                image_name = str(entry.get("filename") or "")
+                count = int(entry.get("annotation_count") or 0)
+                rel_path = str(entry.get("relative_path") or "")
+
+                name_item = QTableWidgetItem(image_name)
+                # Tooltip shows full path of the image (best-effort: repository_root + relative_path)
+                full_path = rel_path
+                repo_root = self.config_manager.get_image_repository_path()
+                if repo_root and rel_path and not Path(rel_path).is_absolute():
+                    try:
+                        full_path = str((Path(repo_root) / rel_path).resolve())
+                    except Exception:
+                        full_path = str(Path(repo_root) / rel_path)
+                name_item.setToolTip(full_path)
+                name_item.setData(Qt.UserRole, int(entry.get("id")))
+                name_item.setData(Qt.UserRole + 1, rel_path)
+
+                count_item = QTableWidgetItem()
+                # Use EditRole to ensure numeric sorting.
+                count_item.setData(Qt.EditRole, count)
+                count_item.setData(Qt.UserRole, int(entry.get("id")))
+                count_item.setData(Qt.UserRole + 1, rel_path)
+
+                self.annotated_images_table.setItem(r, 0, name_item)
+                self.annotated_images_table.setItem(r, 1, count_item)
+
+            # Re-select desired row
+            if desired_id is not None:
+                for r in range(self.annotated_images_table.rowCount()):
+                    item = self.annotated_images_table.item(r, 0)
+                    if item and item.data(Qt.UserRole) == desired_id:
+                        self.annotated_images_table.selectRow(r)
+                        break
+        finally:
+            self.annotated_images_table.blockSignals(False)
+            self.annotated_images_table.setSortingEnabled(sorting_enabled)
+
+    def _on_annotated_image_selected(self) -> None:
+        """When user clicks an item in the list, load that image in the annotation canvas."""
+        selected = self.annotated_images_table.selectedItems()
+        if not selected:
+            return
+
+        # Row selection -> take the first column item
+        row = self.annotated_images_table.currentRow()
+        item = self.annotated_images_table.item(row, 0)
+        if not item:
+            return
+
+        image_id = item.data(Qt.UserRole)
+        rel_path = item.data(Qt.UserRole + 1) or ""
+        if not image_id:
+            return
+
+        image_path = self._resolve_image_path_for_relative_path(rel_path)
+        if not image_path:
+            QMessageBox.warning(
+                self,
+                "Image Not Found",
+                "Unable to locate image on disk for:\n"
+                f"{rel_path}\n\n"
+                "Tip: set Settings → Image repository path to the folder containing your images.",
+            )
+            return
+
+        try:
+            self.current_image = Image(image_path)
+            self.current_image_path = image_path
+            self.current_image_id = int(image_id)
+            self.annotation_canvas.load_image(self.current_image)
+            self._load_annotations_for_current_image()
+            self._update_image_info()
+        except ImageLoadError as exc:
+            logger.error(f"Failed to load image '{image_path}': {exc}")
+            QMessageBox.critical(self, "Error Loading Image", f"Failed to load image:\n{exc}")
+        except Exception as exc:
+            logger.error(f"Unexpected error loading image '{image_path}': {exc}")
+            QMessageBox.critical(self, "Error", f"Unexpected error:\n{exc}")
+
+    def _resolve_image_path_for_relative_path(self, relative_path: str) -> str | None:
+        """Best-effort conversion from a DB relative_path to an on-disk file path."""
+
+        rel = (relative_path or "").strip()
+        if not rel:
+            return None
+
+        candidates: list[Path] = []
+
+        # 1) Repository root + relative
+        repo_root = (self.config_manager.get_image_repository_path() or "").strip()
+        if repo_root:
+            candidates.append(Path(repo_root) / rel)
+
+        # 2) If the DB path is absolute, try it directly.
+        candidates.append(Path(rel))
+
+        # 3) Try the directory of the currently loaded image (helps when DB stores only filenames)
+        if self.current_image_path:
+            try:
+                candidates.append(Path(self.current_image_path).expanduser().resolve().parent / Path(rel).name)
+            except Exception:
+                pass
+
+        # 4) Try the last directory used by the annotation file picker
+        try:
+            settings = QSettings("microscopy_app", "object_detection")
+            last_dir = settings.value("annotation_tab/last_directory", None)
+            if last_dir:
+                candidates.append(Path(str(last_dir)) / Path(rel).name)
+        except Exception:
+            pass
+
+        for p in candidates:
+            try:
+                expanded = p.expanduser()
+                if expanded.exists() and expanded.is_file():
+                    return str(expanded.resolve())
+            except Exception:
+                continue
+
+        # 5) Fallback: search by filename within repository root.
+        filename = Path(rel).name
+        if repo_root and filename:
+            root = Path(repo_root).expanduser()
+            try:
+                if root.exists():
+                    for match in root.rglob(filename):
+                        if match.is_file():
+                            return str(match.resolve())
+            except Exception as exc:
+                logger.debug(f"Search for {filename} under {root} failed: {exc}")
+
+        return None