def makeCropUI(imp, images, tgtDir, panel=None, cropContinuationFn=None): """ imp: the ImagePlus to work on. images: the list of ImgLib2 images, one per frame, not original but already isotropic. (These are views that use a nearest neighbor interpolation using the calibration to scale to isotropy.) tgtDir: the target directory where e.g. CSV files will be stored, for ROI, features, pointmatches. panel: optional, a JPanel controlled by a GridBagLayout. cropContinuationFn: optional, a function to execute after cropping, which is given as arguments the original images, minC, maxC (both define a ROI), and the cropped images. """ independent = None == panel if not panel: panel = JPanel() panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10)) gb = GridBagLayout() gc = GBC() else: gb = panel.getLayout() # Constraints of the last component gc = gb.getConstraints(panel.getComponent(panel.getComponentCount() - 1)) # Horizontal line to separate prior UI components from crop UI gc.gridx = 0 gc.gridy += 1 gc.gridwidth = 4 gc.anchor = GBC.WEST gc.fill = GBC.HORIZONTAL sep = JSeparator() sep.setMinimumSize(Dimension(200, 10)) gb.setConstraints(sep, gc) panel.add(sep) # ROI UI header title = JLabel("ROI controls:") gc.gridy +=1 gc.anchor = GBC.WEST gc.gridwidth = 4 gb.setConstraints(title, gc) panel.add(title) # Column labels for the min and max coordinates gc.gridy += 1 gc.gridwidth = 1 for i, title in enumerate(["", "X", "Y", "Z"]): gc.gridx = i gc.anchor = GBC.CENTER label = JLabel(title) gb.setConstraints(label, gc) panel.add(label) textfields = [] rms = [] # Load stored ROI if any roi_path = path = os.path.join(tgtDir, "crop-roi.csv") if os.path.exists(roi_path): with open(roi_path, 'r') as csvfile: reader = csv.reader(csvfile, delimiter=',', quotechar="\"") reader.next() # header minC = map(int, reader.next()[1:]) maxC = map(int, reader.next()[1:]) # Place the ROI over the ImagePlus imp.setRoi(Roi(minC[0], minC[1], maxC[0] + 1 - minC[0], maxC[1] + 1 - minC[1])) else: # Use whole image dimensions minC = [0, 0, 0] maxC = [v -1 for v in Intervals.dimensionsAsLongArray(images[0])] # Text fields for the min and max coordinates for rowLabel, coords in izip(["min coords: ", "max coords: "], [minC, maxC]): gc.gridx = 0 gc.gridy += 1 label = JLabel(rowLabel) gb.setConstraints(label, gc) panel.add(label) for i in xrange(3): gc.gridx += 1 tf = JTextField(str(coords[i]), 10) gb.setConstraints(tf, gc) panel.add(tf) textfields.append(tf) listener = RoiMaker(imp, textfields, len(textfields) -1) rms.append(listener) tf.addKeyListener(listener) tf.addMouseWheelListener(listener) # Listen to changes in the ROI of imp rfl = RoiFieldListener(imp, textfields) Roi.addRoiListener(rfl) # ... and enable cleanup ImagePlus.addImageListener(FieldDisabler(rfl, rms)) # Functions for cropping images cropped = None cropped_imp = None def storeRoi(minC, maxC): if os.path.exists(roi_path): # Load ROI with open(path, 'r') as csvfile: reader = csv.reader(csvfile, delimiter=',', quotechar="\"") reader.next() # header same = True for a, b in izip(minC + maxC, map(int, reader.next()[1:] + reader.next()[1:])): if a != b: same = False # Invalidate any CSV files for features and pointmatches: different cropping for filename in os.listdir(tgtDir): if filename.endswith("features.csv") or filename.endswith("pointmatches.csv"): os.remove(os.path.join(tgtDir, filename)) break if same: return # Store the ROI as crop-roi.csv with open(roi_path, 'w') as csvfile: w = csv.writer(csvfile, delimiter=',', quotechar="\"", quoting=csv.QUOTE_NONNUMERIC) w.writerow(["coords", "x", "y", "z"]) w.writerow(["min"] + map(int, minC)) w.writerow(["max"] + map(int, maxC)) def crop(event): global cropped, cropped_imp coords = [int(float(tf.getText())) for tf in textfields] minC = [max(0, c) for c in coords[0:3]] maxC = [min(d -1, c) for d, c in izip(Intervals.dimensionsAsLongArray(images[0]), coords[3:6])] storeRoi(minC, maxC) print "ROI min and max coordinates" print minC print maxC cropped = [Views.zeroMin(Views.interval(img, minC, maxC)) for img in images] cropped_imp = showAsStack(cropped, title="cropped") cropped_imp.setDisplayRange(imp.getDisplayRangeMin(), imp.getDisplayRangeMax()) if cropContinuationFn: cropContinuationFn(images, minC, maxC, cropped, cropped_imp) # Buttons to create a ROI and to crop to ROI, # which when activated enables the fine registration buttons crop_button = JButton("Crop to ROI") crop_button.addActionListener(crop) gc.gridx = 0 gc.gridy += 1 gc.gridwidth = 4 gc.anchor = GBC.WEST buttons_panel = JPanel() buttons_panel.add(crop_button) gb.setConstraints(buttons_panel, gc) panel.add(buttons_panel) if independent: frame = JFrame("Crop by ROI") frame.getContentPane().add(panel) frame.pack() frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE) frame.addWindowListener(CloseControl(destroyables=rms + [rfl])) frame.setVisible(True) else: # Re-pack the JFrame parent = panel.getParent() while not isinstance(parent, JFrame) and parent is not None: parent = parent.getParent() if parent: frame = parent frame.pack() found = False for wl in frame.getWindowListeners(): if isinstance(wl, CloseControl): wl.addDestroyables(rms + [rfl]) found = True break if not found: frame.addWindowListener(CloseControl(destroyables=rms + [rfl])) frame.setVisible(True) return panel