import os import json import csv from ij import IJ from ij.gui import Overlay from ij.plugin.frame import RoiManager from javax.swing import JDialog, JPanel, JCheckBox, JLabel, BorderFactory from javax.swing.border import EmptyBorder from java.awt import GridLayout, BorderLayout from java.awt.event import WindowAdapter class ResultsViewer(WindowAdapter): """ A self-contained dialog for viewing an image with toggleable overlays for analysis ROIs and quantified cell outlines. """ def __init__(self, parent_frame, project_image): self.image_obj = project_image 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.image_window = self.imp.getWindow() # Load both sets of ROIs into memory self.analysis_rois = self._load_rois_from_zip(self.image_obj.roi_path) self.outline_rois = self._load_rois_from_zip(self.image_obj.outline_path) # Build the control dialog self.dialog = JDialog(self.image_window, "Results Viewer: " + self.image_obj.filename, False) self.dialog.setSize(300, 150) self.dialog.addWindowListener(self) self.image_window.addWindowListener(ImageWindowListener(self.dialog)) panel = JPanel(GridLayout(0, 1, 10, 10)) panel.setBorder(EmptyBorder(10, 10, 10, 10)) # Create checkboxes self.analysis_checkbox = JCheckBox("Show Analysis ROIs", True) self.outlines_checkbox = JCheckBox("Show Cell Outlines", True) # Enable checkboxes only if their corresponding ROIs were found self.analysis_checkbox.setEnabled(bool(self.analysis_rois)) self.outlines_checkbox.setEnabled(bool(self.outline_rois)) # Add a single action listener to both action_listener = self._update_overlay self.analysis_checkbox.addActionListener(action_listener) self.outlines_checkbox.addActionListener(action_listener) panel.add(self.analysis_checkbox) panel.add(self.outlines_checkbox) # Load and display processing metadata metadata = self._load_metadata_for_image() if metadata: info_panel = JPanel(GridLayout(0, 1, 5, 5)) info_panel.setBorder(BorderFactory.createTitledBorder("Processing Info")) workflow_name = metadata.get('workflow_name', 'Unknown') processed_date = metadata.get('processed_date', 'Unknown') # Format date nicely if in ISO format if 'T' in processed_date: processed_date = processed_date.replace('T', ' ').split('.')[0] info_panel.add(JLabel("Workflow: " + workflow_name)) info_panel.add(JLabel("Processed: " + processed_date)) # Show all workflow settings dynamically (excluding non-display values) settings = metadata.get('workflow_settings', {}) exclude_keys = ['workflow', 'workflow_name', 'images', 'show_images'] for key, value in sorted(settings.items()): if key in exclude_keys: continue # Format key nicely: apply_watershed -> Apply watershed display_key = key.replace('_', ' ').capitalize() # Format boolean values as Yes/No if isinstance(value, bool) or value in (0, 1, '0', '1', 'True', 'False'): if value in (True, 1, '1', 'True'): display_value = 'Yes' else: display_value = 'No' else: display_value = str(value) info_panel.add(JLabel("{}: {}".format(display_key, display_value))) panel.add(info_panel) self.dialog.add(panel) self.dialog.pack() self.dialog.setSize(max(300, self.dialog.getWidth()), self.dialog.getHeight()) # Initial display self._update_overlay() def _load_rois_from_zip(self, zip_path): """Helper function to load all ROIs from a zip file into a list.""" if not os.path.exists(zip_path): return [] rm = RoiManager(True) rm.open(zip_path) rois = rm.getRoisAsArray() rm.close() return list(rois) def _load_metadata_for_image(self): """ Load processing metadata for this image by: 1. Finding the processing_run_id from Results_DB.csv 2. Looking up that run in processing_log.json """ try: # Derive paths from image location # Image is in Images/, CSV and JSON are in project root project_dir = os.path.dirname(os.path.dirname(self.image_obj.full_path)) csv_path = os.path.join(project_dir, 'Results_DB.csv') metadata_path = os.path.join(project_dir, 'processing_log.json') if not os.path.exists(metadata_path): return None # Find this image's run_id from the CSV run_id = None if os.path.exists(csv_path): with open(csv_path, 'r') as f: reader = csv.DictReader(f) for row in reader: if row.get('filename') == self.image_obj.filename: run_id = row.get('processing_run_id') break if not run_id: return None # Load metadata log and get this run's entry with open(metadata_path, 'r') as f: all_metadata = json.load(f) return all_metadata.get(run_id) except Exception as e: IJ.log("Could not load processing metadata: " + str(e)) return None def _update_overlay(self, event=None): """Builds and applies a new overlay based on checkbox states.""" overlay = Overlay() if self.analysis_checkbox.isSelected() and self.analysis_rois: for roi in self.analysis_rois: overlay.add(roi) if self.outlines_checkbox.isSelected() and self.outline_rois: for roi in self.outline_rois: overlay.add(roi) self.imp.setOverlay(overlay) self.imp.updateAndDraw() def show(self): """Positions and shows the dialog.""" if not self.dialog: return # Position control dialog next to the image window self.dialog.setLocation(self.imp.getWindow().getX() + self.imp.getWindow().getWidth(), self.imp.getWindow().getY()) self.dialog.setVisible(True) def windowClosing(self, event): """Cleans up when the dialog is closed.""" if self.imp: self.imp.close() class ImageWindowListener(WindowAdapter): """A listener that closes the control dialog when its image window is closed.""" def __init__(self, viewer_dialog): self.viewer_dialog = viewer_dialog def windowClosing(self, event): # When the image window is closed by the user, # programmatically close and dispose of our control dialog. if self.viewer_dialog: self.viewer_dialog.dispose()