Merge pull request #116 from Cephla-Lab/feature/save-load-coordinates

feat: Add save/load scan coordinates to CSV in the GUI

software/control/widgets.py

@@ -3441,11 +3441,15 @@ def __init__(
         self.setFrameStyle(QFrame.Panel | QFrame.Raised)
         self.set_default_scan_size()
 
+        # Add state tracking for coordinates
+        self.has_loaded_coordinates = False
+
     def add_components(self):
         self.entry_well_coverage = QDoubleSpinBox()
         self.entry_well_coverage.setRange(1, 999.99)
         self.entry_well_coverage.setValue(100)
         self.entry_well_coverage.setSuffix("%")
+        self.entry_well_coverage.setDecimals(0)
         btn_width = self.entry_well_coverage.sizeHint().width()
 
         self.btn_setSavingDir = QPushButton("Browse")
@@ -3547,6 +3551,9 @@ def add_components(self):
         self.combobox_shape.setFixedWidth(btn_width)
         # self.combobox_shape.currentTextChanged.connect(self.on_shape_changed)
 
+        self.btn_save_scan_coordinates = QPushButton("Save Coordinates")
+        self.btn_load_scan_coordinates = QPushButton("Load Coordinates")
+
         self.checkbox_genAFMap = QCheckBox("Generate Focus Map")
         self.checkbox_genAFMap.setChecked(False)
 
@@ -3595,25 +3602,25 @@ def add_components(self):
         saving_path_layout.addWidget(self.btn_setSavingDir)
         main_layout.addLayout(saving_path_layout)
 
-        # Experiment ID and Scan Shape
+        # Experiment ID
         row_1_layout = QHBoxLayout()
         row_1_layout.addWidget(QLabel("Experiment ID"))
         row_1_layout.addWidget(self.lineEdit_experimentID)
-        row_1_layout.addWidget(QLabel("Well Shape"))
-        row_1_layout.addWidget(self.combobox_shape)
         main_layout.addLayout(row_1_layout)
 
-        # Well Coverage, Scan Size, and Overlap
-        row_4_layout = QHBoxLayout()
-        row_4_layout.addWidget(QLabel("Size"))
-        row_4_layout.addWidget(self.entry_scan_size)
-        # row_4_layout.addStretch(1)
-        row_4_layout.addWidget(QLabel("FOV Overlap"))
-        row_4_layout.addWidget(self.entry_overlap)
-        # row_4_layout.addStretch(1)
-        row_4_layout.addWidget(QLabel("Well Coverage"))
-        row_4_layout.addWidget(self.entry_well_coverage)
-        main_layout.addLayout(row_4_layout)
+        # Scan Shape, FOV overlap, and Save / Load Scan Coordinates
+        row_2_layout = QGridLayout()
+        row_2_layout.addWidget(QLabel("Scan Shape"), 0, 0)
+        row_2_layout.addWidget(self.combobox_shape, 0, 1)
+        row_2_layout.addWidget(QLabel("Scan Size"), 0, 2)
+        row_2_layout.addWidget(self.entry_scan_size, 0, 3)
+        row_2_layout.addWidget(QLabel("Coverage"), 0, 4)
+        row_2_layout.addWidget(self.entry_well_coverage, 0, 5)
+        row_2_layout.addWidget(QLabel("FOV Overlap"), 1, 0)
+        row_2_layout.addWidget(self.entry_overlap, 1, 1)
+        row_2_layout.addWidget(self.btn_save_scan_coordinates, 1, 2, 1, 2)
+        row_2_layout.addWidget(self.btn_load_scan_coordinates, 1, 4, 1, 2)
+        main_layout.addLayout(row_2_layout)
 
         grid = QGridLayout()
 
@@ -3725,6 +3732,10 @@ def add_components(self):
         self.entry_NZ.valueChanged.connect(self.signal_stitcher_z_levels.emit)
         # self.combobox_z_stack.currentIndexChanged.connect(self.signal_z_stacking.emit)
 
+        # Connect save/clear coordinates button
+        self.btn_save_scan_coordinates.clicked.connect(self.on_save_or_clear_coordinates_clicked)
+        self.btn_load_scan_coordinates.clicked.connect(self.on_load_coordinates_clicked)
+
     def enable_manual_ROI(self, enable):
         self.combobox_shape.model().item(3).setEnabled(enable)
         if not enable:
@@ -3851,7 +3862,9 @@ def set_default_scan_size(self):
         self.set_default_shape()
 
         if "glass slide" in self.navigationViewer.sample:
-            self.entry_scan_size.setValue(1.0)  # init to 1mm when switching to 'glass slide'
+            self.entry_scan_size.setValue(
+                0.1
+            )  # init to 0.1mm when switching to 'glass slide' (for imaging a single FOV by default)
             self.entry_scan_size.setEnabled(True)
             self.entry_well_coverage.setEnabled(False)
         else:
@@ -4169,6 +4182,133 @@ def emit_selected_channels(self):
     def display_stitcher_widget(self, checked):
         self.signal_stitcher_widget.emit(checked)
 
+    def toggle_coordinate_controls(self, has_coordinates: bool):
+        """Toggle button text and control states based on whether coordinates are loaded"""
+        if has_coordinates:
+            self.btn_save_scan_coordinates.setText("Clear Coordinates")
+            # Disable scan controls when coordinates are loaded
+            self.combobox_shape.setEnabled(False)
+            self.entry_scan_size.setEnabled(False)
+            self.entry_well_coverage.setEnabled(False)
+            self.entry_overlap.setEnabled(False)
+            # Disable well selector
+            self.parent.wellSelectionWidget.setEnabled(False)
+        else:
+            self.btn_save_scan_coordinates.setText("Save Coordinates")
+            # Re-enable scan controls when coordinates are cleared
+            self.combobox_shape.setEnabled(True)
+            self.entry_scan_size.setEnabled(True)
+            if "glass slide" in self.navigationViewer.sample:
+                self.entry_well_coverage.setEnabled(False)
+            else:
+                self.entry_well_coverage.setEnabled(True)
+            self.entry_overlap.setEnabled(True)
+            # Re-enable well selector
+            self.parent.wellSelectionWidget.setEnabled(True)
+
+        self.has_loaded_coordinates = has_coordinates
+
+    def on_save_or_clear_coordinates_clicked(self):
+        """Handle save/clear coordinates button click"""
+        if self.has_loaded_coordinates:
+            # Clear coordinates
+            self.scanCoordinates.clear_regions()
+            self.toggle_coordinate_controls(has_coordinates=False)
+            # Update display/coordinates as needed
+            self.update_coordinates()
+        else:
+            # Save coordinates (existing save functionality)
+            self.save_coordinates()
+
+    def on_load_coordinates_clicked(self):
+        """Open file dialog and load coordinates from selected CSV file"""
+        file_path, _ = QFileDialog.getOpenFileName(
+            self, "Load Scan Coordinates", "", "CSV Files (*.csv);;All Files (*)"  # Default directory
+        )
+
+        if file_path:
+            print("loading coordinates from", file_path)
+            self.load_coordinates(file_path)
+
+    def load_coordinates(self, file_path: str):
+        """Load scan coordinates from a CSV file.
+
+        Args:
+            file_path: Path to CSV file containing coordinates
+        """
+        try:
+            # Read coordinates from CSV
+            import pandas as pd
+
+            df = pd.read_csv(file_path)
+
+            # Validate CSV format
+            required_columns = ["Region", "X_mm", "Y_mm"]
+            if not all(col in df.columns for col in required_columns):
+                raise ValueError("CSV file must contain 'Region', 'X_mm', and 'Y_mm' columns")
+
+            # Clear existing coordinates
+            self.scanCoordinates.clear_regions()
+
+            # Load coordinates into scanCoordinates
+            for region_id in df["Region"].unique():
+                region_points = df[df["Region"] == region_id]
+                coords = list(zip(region_points["X_mm"], region_points["Y_mm"]))
+                self.scanCoordinates.region_fov_coordinates[region_id] = coords
+
+                # Calculate and store region center (average of points)
+                center_x = region_points["X_mm"].mean()
+                center_y = region_points["Y_mm"].mean()
+                self.scanCoordinates.region_centers[region_id] = (center_x, center_y)
+
+                # Register FOVs with navigation viewer
+                for x, y in coords:
+                    self.navigationViewer.register_fov_to_image(x, y)
+
+            self._log.info(f"Loaded {len(df)} coordinates from {file_path}")
+
+            # Update UI state
+            self.toggle_coordinate_controls(has_coordinates=True)
+
+        except Exception as e:
+            self._log.error(f"Failed to load coordinates: {str(e)}")
+            QMessageBox.warning(self, "Load Error", f"Failed to load coordinates from {file_path}\nError: {str(e)}")
+
+    def save_coordinates(self):
+        """Save scan coordinates to a CSV file.
+
+        Opens a file dialog for the user to choose save location and filename.
+        Coordinates are saved in CSV format with headers.
+        """
+        # Open file dialog for user to select save location and filename
+        file_path, _ = QFileDialog.getSaveFileName(
+            self, "Save Scan Coordinates", "", "CSV Files (*.csv);;All Files (*)"  # Default directory
+        )
+
+        if file_path:
+            # Add .csv extension if not present
+            if not file_path.lower().endswith(".csv"):
+                file_path += ".csv"
+
+            try:
+                # Get coordinates from scanCoordinates
+                coordinates = []
+                for region_id, fov_coords in self.scanCoordinates.region_fov_coordinates.items():
+                    for x, y in fov_coords:
+                        coordinates.append([region_id, x, y])
+
+                # Save to CSV with headers
+                import pandas as pd
+
+                df = pd.DataFrame(coordinates, columns=["Region", "X_mm", "Y_mm"])
+                df.to_csv(file_path, index=False)
+
+                self._log.info(f"Saved scan coordinates to {file_path}")
+
+            except Exception as e:
+                self._log.error(f"Failed to save coordinates: {str(e)}")
+                QMessageBox.warning(self, "Save Error", f"Failed to save coordinates to {file_path}\nError: {str(e)}")
+
 
 class FocusMapWidget(QFrame):
     """Widget for managing focus map points and surface fitting"""