import os import traceback # --- ImageJ/Java Libraries --- from ij import IJ from ij.plugin.frame import RoiManager from javax.swing import (JDialog, JPanel, JList, JScrollPane, JTextField, JLabel, JCheckBox, JButton, DefaultListModel, ListSelectionModel, BorderFactory, JOptionPane) from java.awt import BorderLayout, GridLayout from java.awt.event import WindowAdapter class ROIEditor(WindowAdapter): """ Creates a JFrame with tools for creating, modifying, and managing ROIs for a single image using a "commit on action" model. """ def __init__(self, parent_gui, project, project_image): self.parent_gui = parent_gui self.project = project self.image_obj = project_image self.win = None self.unsaved_changes = False self.updating_fields = False # Flag to prevent event cascades self.last_selected_index = -1 # Track the last selected ROI index # Open Image and create canvas and imagewindow to hold it self.imp = IJ.openImage(self.image_obj.full_path) if not self.imp: IJ.error("Failed to open image:", self.image_obj.full_path) return self.imp.show() self.win = self.imp.getWindow() # Open a local ROI manager instance self.rm = RoiManager(True) self.rm.reset() if self.image_obj.has_roi(): self.rm.runCommand("Open", self.image_obj.roi_path) self.rm.runCommand("Show All") # Build GUI self.base_title = "ROI Editor: " + self.image_obj.filename self.frame = JDialog(self.win, self.base_title, False) self.frame.setSize(350, 650) self.frame.addWindowListener(self) self.frame.setLayout(BorderLayout(5, 5)) # --- GUI Components --- # ROI list self.roi_list_model = DefaultListModel() self.roi_list = JList(self.roi_list_model) self.update_roi_list_from_manager() self.roi_list.setSelectionMode(ListSelectionModel.SINGLE_SELECTION) self.roi_list.addListSelectionListener(self._on_roi_select) list_pane = JScrollPane(self.roi_list) list_pane.setBorder(BorderFactory.createTitledBorder("ROIs")) # Edit Panel for selected ROI edit_panel = JPanel(GridLayout(0, 2, 5, 5)) edit_panel.setBorder(BorderFactory.createTitledBorder("Edit Selected ROI")) self.roi_name_field = JTextField() self.bregma_field = JTextField() edit_panel.add(JLabel("ROI Name:")) edit_panel.add(self.roi_name_field) edit_panel.add(JLabel("Bregma Value:")) edit_panel.add(self.bregma_field) self.show_all_checkbox = JCheckBox("Show All ROIs", True) self.show_all_checkbox.addActionListener(self._toggle_show_all) edit_panel.add(self.show_all_checkbox) # Button panel for actions button_panel = JPanel(GridLayout(0, 1, 10, 10)) button_panel.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10)) create_button = JButton("Create New From Selection", actionPerformed=self._create_new_roi) update_button = JButton("Update Selected ROI", actionPerformed=self._update_selected_roi) delete_button = JButton("Delete Selected ROI", actionPerformed=self._delete_selected_roi) self.ready_checkbox = JCheckBox("Mark as 'ROIs completed'", True) is_ready = (self.image_obj.status == "ROIs completed") self.ready_checkbox.setSelected(is_ready) self.ready_checkbox.addActionListener(self._toggle_ready_status) save_button = JButton("Save All ROIs & Close", actionPerformed=self._save_and_close) button_panel.add(create_button) button_panel.add(update_button) button_panel.add(delete_button) button_panel.add(self.ready_checkbox) button_panel.add(save_button) # Main layout south_panel = JPanel(BorderLayout()) south_panel.add(edit_panel, BorderLayout.NORTH) south_panel.add(button_panel, BorderLayout.CENTER) self.frame.add(list_pane, BorderLayout.CENTER) self.frame.add(south_panel, BorderLayout.SOUTH) def show(self): if not self.frame or not self.win: return img_win_x = self.win.getX() img_win_width = self.win.getWidth() img_win_y = self.win.getY() self.frame.setLocation(img_win_x + img_win_width, img_win_y) self.frame.setVisible(True) # -------------------------------------------------------------------------- # Core Logic and Event Handling # -------------------------------------------------------------------------- def _commit_changes_for_index(self, index, commit_geometry=True): """ A single, unified method to save changes for the ROI at a given index. The commit_geometry flag prevents overwriting geometry during new ROI creation. Returns True if the ROI name was changed. """ if index < 0 or index >= self.rm.getCount(): return False name_was_changed = False try: manager_roi = self.rm.getRoi(index) if not manager_roi: return False # Part 1: Commit metadata (text fields) new_name = self.roi_name_field.getText().strip() new_bregma = self.bregma_field.getText().strip() current_bregma = str(manager_roi.getProperty("comment") or "") if manager_roi.getName() != new_name and new_name: self.rm.rename(index, new_name) self._set_unsaved_changes(True) name_was_changed = True if new_bregma != current_bregma: if new_bregma: try: float(new_bregma) manager_roi.setProperty("comment", new_bregma) except ValueError: JOptionPane.showMessageDialog(self.frame, "Bregma must be a number.", "Invalid Input", JOptionPane.WARNING_MESSAGE) self.bregma_field.setText(current_bregma) else: manager_roi.setProperty("comment", None) self._set_unsaved_changes(True) # Part 2: Commit geometry (shape on canvas) if commit_geometry: image_roi = self.imp.getRoi() if image_roi: updated_roi = image_roi.clone() # Preserve the name and properties from the manager ROI current_manager_roi = self.rm.getRoi(index) updated_roi.setName(current_manager_roi.getName()) updated_roi.setProperty("comment", current_manager_roi.getProperty("comment")) self.rm.setRoi(updated_roi, index) self._set_unsaved_changes(True) except Exception as e: IJ.log("Error during commit for index {}: {}".format(index, str(e))) traceback.print_exc() return name_was_changed def _on_roi_select(self, event): """ Handles a user manually selecting an ROI in the list. """ if event.getValueIsAdjusting() or self.updating_fields: return # Don't commit changes when switching ROIs - we only want to commit # when explicitly saving or when the user is editing an existing ROI # (not when creating new ones) selected_index = self.roi_list.getSelectedIndex() if selected_index != -1: self.updating_fields = True try: self._refresh_roi_display(selected_index) selected_roi = self.rm.getRoi(selected_index) if selected_roi: self.roi_name_field.setText(selected_roi.getName() or "") bregma_prop = selected_roi.getProperty("comment") if bregma_prop is not None: self.bregma_field.setText(str(bregma_prop)) else: self.bregma_field.setText("") finally: self.updating_fields = False else: self.roi_name_field.setText("") self.bregma_field.setText("") self.last_selected_index = selected_index # -------------------------------------------------------------------------- # GUI Actions (Buttons & Checkboxes) # -------------------------------------------------------------------------- def _create_new_roi(self, event): """ Handles the entire ROI creation process as a self-contained transaction, preventing event listener conflicts. """ # Step 1: Validate that a new ROI can be created. current_roi = self.imp.getRoi() if not current_roi: JOptionPane.showMessageDialog(self.frame, "Please draw a selection on the image first.", "No Selection", JOptionPane.WARNING_MESSAGE) return new_name = self.roi_name_field.getText().strip() if not new_name: JOptionPane.showMessageDialog(self.frame, "Please enter a name in the 'ROI Name' field.", "No Name Provided", JOptionPane.WARNING_MESSAGE) return # Step 2: Save the current selection and create the new ROI object roi_clone = current_roi.clone() roi_clone.setName(new_name) bregma_value = self.bregma_field.getText().strip() if bregma_value: try: float(bregma_value) roi_clone.setProperty("comment", bregma_value) except ValueError: pass # Step 3: DON'T commit changes to the previous ROI # The text fields now contain data for the NEW roi, not the old one # So committing would overwrite the old ROI's name/bregma with the new ROI's data # Step 4: Add the new ROI to the manager self.rm.addRoi(roi_clone) new_index = self.rm.getCount() - 1 # Step 5: Update the UI to reflect the new ROI try: self.updating_fields = True # Update the list display self.update_roi_list_from_manager() # Select the newly created ROI self.roi_list.setSelectedIndex(new_index) # Clear the text fields for the next ROI entry self.roi_name_field.setText("") self.bregma_field.setText("") # Update the tracking index self.last_selected_index = new_index # Refresh the display to show the new ROI self._refresh_roi_display(new_index) finally: self.updating_fields = False # Step 6: Finalize the creation process self._set_unsaved_changes(True) def _update_selected_roi(self, event): """Updates the currently selected ROI with values from the text fields.""" selected_index = self.roi_list.getSelectedIndex() if selected_index == -1: JOptionPane.showMessageDialog(self.frame, "Please select an ROI from the list to update.", "No ROI Selected", JOptionPane.WARNING_MESSAGE) return # Commit both metadata and geometry changes if self._commit_changes_for_index(selected_index, commit_geometry=True): self.update_roi_list_from_manager() # Refresh to show the updated ROI self._refresh_roi_display(selected_index) def _delete_selected_roi(self, event): """Deletes the selected ROI from the manager.""" selected_index = self.roi_list.getSelectedIndex() if selected_index == -1: JOptionPane.showMessageDialog(self.frame, "Please select an ROI from the list to delete.", "No ROI Selected", JOptionPane.WARNING_MESSAGE) return roi_name = self.rm.getRoi(selected_index).getName() or "Untitled" result = JOptionPane.showConfirmDialog(self.frame, "Delete ROI '{}'?".format(roi_name), "Confirm Deletion", JOptionPane.YES_NO_OPTION) if result != JOptionPane.YES_OPTION: return self.rm.select(selected_index) self.rm.runCommand("Delete") self.last_selected_index = -1 self.update_roi_list_from_manager() self.roi_name_field.setText("") self.bregma_field.setText("") self._set_unsaved_changes(True) self.imp.deleteRoi() def _toggle_ready_status(self, event): """Updates the image's status in the project object.""" self.image_obj.status = "ROIs completed" if self.ready_checkbox.isSelected() else "In Progress" self._set_unsaved_changes(True) def _save_and_close(self, event=None): """Saves all changes, updates project, and closes the editor.""" # No need to commit individual ROI changes - all ROIs are already in the manager # and will be saved to the file if not self._save_all_rois_to_file(): return if not self.project.sync_project_db(): JOptionPane.showMessageDialog(self.frame, "Could not save project databases.", "Database Sync Failed", JOptionPane.ERROR_MESSAGE) return self.parent_gui.update_view_for_image(self.image_obj) self.parent_gui.set_unsaved_changes(True) self._set_unsaved_changes(False) self.cleanup() # -------------------------------------------------------------------------- # Helper & Utility Methods # -------------------------------------------------------------------------- def update_roi_list_from_manager(self): """Syncs the JList with the IJ ROI manager without triggering selection events.""" listeners = self.roi_list.getListSelectionListeners() for l in listeners: self.roi_list.removeListSelectionListener(l) try: current_selection = self.roi_list.getSelectedIndex() self.roi_list_model.clear() for i, roi in enumerate(self.rm.getRoisAsArray()): self.roi_list_model.addElement("{}. {}".format(i + 1, roi.getName() or "Untitled")) if -1 < current_selection < self.roi_list_model.getSize(): self.roi_list.setSelectedIndex(current_selection) finally: for l in listeners: self.roi_list.addListSelectionListener(l) def _refresh_roi_display(self, selected_index): """Loads and displays the selected ROI using the Manager's native select method.""" # Enforce "Show All" state if self.show_all_checkbox.isSelected(): self.rm.runCommand("Show All") else: self.rm.runCommand("Show None") # Then select the specific ROI to make it active and editable if -1 < selected_index < self.rm.getCount(): self.rm.select(selected_index) else: self.imp.deleteRoi() def _save_all_rois_to_file(self): """Validates and saves ROI data to a .zip file.""" rois = self.rm.getRoisAsArray() for i, roi in enumerate(rois): if not roi.getName() or not roi.getName().strip(): JOptionPane.showMessageDialog(self.frame, "ROI #{} has no name. Please name all ROIs.".format(i+1), "Validation Error", JOptionPane.WARNING_MESSAGE) return False self.image_obj.rois = [{'roi_name': r.getName(), 'bregma': r.getProperty("comment") or 'N/A'} for r in rois] roi_dir = os.path.dirname(self.image_obj.roi_path) if not os.path.exists(roi_dir): os.makedirs(roi_dir) self.rm.runCommand("Save", self.image_obj.roi_path) return True def _toggle_show_all(self, event): """Toggles visibility of all ROIs.""" self._refresh_roi_display(self.roi_list.getSelectedIndex()) def _set_unsaved_changes(self, state): """Updates the UI to show if there are unsaved changes.""" self.unsaved_changes = state self.frame.setTitle(self.base_title + (" *" if state else "")) def cleanup(self): """Closes all associated windows and resources.""" if self.imp: self.imp.close() if self.rm: self.rm.close() if self.frame: self.frame.dispose() def windowClosing(self, event): """Handles the window 'X' button with a save confirmation.""" if self.unsaved_changes: result = JOptionPane.showConfirmDialog(self.frame, "You have unsaved changes. Save before closing?", "Unsaved Changes", JOptionPane.YES_NO_CANCEL_OPTION) if result == JOptionPane.YES_OPTION: self._save_and_close() elif result == JOptionPane.NO_OPTION: self.cleanup() else: self.cleanup()