def viewAligned(filepaths, csvDir, params, paramsSIFT, paramsTileConfiguration, properties, cropInterval): matrices = align(filepaths, csvDir, params, paramsSIFT, paramsTileConfiguration, properties) def loadImg(filepath): return loadUnsignedShort(filepath, invert=properties["invert"], CLAHE_params=properties["CLAHE_params"]) cellImg, cellGet = makeImg(filepaths, properties["pixelType"], loadImg, properties["img_dimensions"], matrices, cropInterval, properties.get('preload', 0)) print cellImg comp = showStack(cellImg, title=properties["srcDir"].split('/')[-2], proper=True) # Add the SourcePanning KeyListener as the first one canvas = comp.getWindow().getCanvas() kls = canvas.getKeyListeners() for kl in kls: canvas.removeKeyListener(kl) canvas.addKeyListener(SourcePanning(cellGet, comp)) for kl in kls: canvas.addKeyListener(kl) ImagePlus.addImageListener(OnClosing(comp, cellGet)) return comp
def __init__(self): self.imp = None self.preview = None self.createMainWindow() self.cells = None self.files = [] self.results = ResultsTable() ImagePlus.addImageListener(self) self.selectInputDir() self.selectOutputDir() self.pairs = [] self.methods = [] self.processNextFile()
def viewAligned(filepaths, csvDir, params, paramsTileConfiguration, img_dimensions, cropInterval): matrices = align(filepaths, csvDir, params, paramsTileConfiguration) cellImg, cellGet = makeImg(filepaths, loadUnsignedShort, img_dimensions, matrices, cropInterval, 1, 5) print cellImg comp = showStack(cellImg, title=srcDir.split('/')[-2], proper=False) # Add the SourcePanning KeyListener as the first one canvas = comp.getWindow().getCanvas() kls = canvas.getKeyListeners() for kl in kls: canvas.removeKeyListener(kl) canvas.addKeyListener(SourcePanning(cellGet, comp)) for kl in kls: canvas.addKeyListener(kl) ImagePlus.addImageListener(OnClosing(comp, cellGet))
# A listener to react to images being opened via an ij.io.Opener from e.g. "File - Open" class OpenImageListener(ImageListener): def imageClosed(self, imp): pass def imageUpdated(self, imp): pass def imageOpened(self, imp): addOrUpdateEntry(imp) open_imp_listener = OpenImageListener( ) # keep a reference for unregistering on window closing ImagePlus.addImageListener(open_imp_listener) # A listener to detect whether there have been any edits to the text note class TypingListener(KeyAdapter): def keyPressed(self, event): rowIndex = getSelectedRowIndex() if event.getSource().getText() != table_entries[rowIndex][-1]: note_status.setText("Unsaved changes.") textarea.addKeyListener(TypingListener()) # React to a row being selected by showing the corresponding note # in the textarea to the right
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
roi = PointRoi() # Style: large, red dots roi.setSize(4) # ranges 1-4 roi.setPointType(2) # 2 is a dot (filled circle) roi.setFillColor(Color.red) roi.setStrokeColor(Color.red) # Add points for point in points: # points are floats roi.addPoint(self.imp, int(point[0]), int(point[1])) self.imp.setRoi(roi) except: IJ.error(sys.exc_info()) listener = PointRoiRefresher(com, nuclei_detections) ImagePlus.addImageListener(listener) # Visualization 2: with a 2nd channel where each each detection is painted as a sphere from net.imglib2 import KDTree, RealPoint, RealRandomAccess, RealRandomAccessible, FinalInterval from net.imglib2.neighborsearch import NearestNeighborSearchOnKDTree from net.imglib2.type.numeric.integer import UnsignedShortType # A KDTree is a data structure for fast lookup of e.g. neareast spatial coordinates # Here, we create a KDTree for each timepoint 3D volume # ('i' is the timepoint index kdtrees = { i: KDTree(peaks, peaks) for i, peaks in nuclei_detections.iteritems() }
def perform_user_qc(in_imp, edges, alt_edges, fixed_anchors_list, params): """allow the user to intervene to fix erroneously identified membrane edges""" n_frames = in_imp.getNFrames(); n_channels = in_imp.getNChannels(); output_folder = params.output_path; current_edges = edges; rgbstack = ImageStack(in_imp.getWidth(), in_imp.getHeight()); if n_frames > 1: for tidx in range(n_frames): in_imp.setT(tidx+1); ip = in_imp.getProcessor(); rgbip = ip.convertToRGB(); rgbstack.addSlice(rgbip); else: for cidx in range(n_channels): in_imp.setC(cidx+1); ip = in_imp.getProcessor(); rgbip = ip.convertToRGB(); rgbstack.addSlice(rgbip); imp = ImagePlus(("RGB " + in_imp.getTitle()), rgbstack); IJ.run("Colors...", "foreground=red background=white selection=yellow"); for tidx in range(imp.getNSlices()): imp.setSlice(tidx+1); for anchor in params.manual_anchor_positions: imp.setRoi(PointRoi(anchor[0], anchor[1])); IJ.run(imp, "Draw", "slice"); imp.show(); autoset_zoom(imp); imp.setPosition(1); imp.setRoi(current_edges[0]); if n_frames > 1: listener = UpdateRoiImageListener(current_edges); imp.addImageListener(listener); IJ.setTool("freeline"); do_flip = True; while do_flip: dialog = NonBlockingGenericDialog("User quality control"); dialog.enableYesNoCancel("Continue", "Flip all edges"); dialog.setCancelLabel("Cancel analysis"); dialog.addMessage("Please redraw the membrane edges as necessary, \n" + "making sure to draw beyond anchor points at either end...\n" + "Click OK when done. "); p = Panel(); but = Button("Flip this edge"); al = Listener(edges, alt_edges, imp); but.addActionListener(al); p.add(but); dialog.addPanel(p); dialog.showDialog(); if dialog.wasCanceled(): raise KeyboardInterrupt("Run canceled"); elif dialog.wasOKed(): do_flip = False; else: print("flip edges"); do_flip = True; if n_frames > 1: imp.removeImageListener(listener); current_edges = alt_edges if (current_edges == edges) else edges; imp.setPosition(1); imp.setRoi(current_edges[0]); if n_frames > 1: listener = UpdateRoiImageListener(current_edges); imp.addImageListener(listener); last_roi = imp.getRoi(); if n_frames > 1: qcd_edges = listener.getRoiList(); if imp.getNFrames() > imp.getNSlices(): qcd_edges[imp.getT() - 1] = last_roi; else: qcd_edges[imp.getZ() - 1] = last_roi; imp.removeImageListener(listener); else: qcd_edges = [last_roi]; mbio.save_qcd_edges2(qcd_edges, output_folder); # next four lines are a quick and dirty hack... if n_frames > 1: nframes = imp.getNFrames() if imp.getNFrames()>imp.getNSlices() else imp.getNSlices(); else: nframes = n_frames; for fridx in range(0, nframes): if (qcd_edges[fridx].getType()==Roi.FREELINE) or (qcd_edges[fridx].getType()==Roi.POLYLINE): if (fridx == 0) or params.constrain_anchors: anchors = params.manual_anchor_positions; else: anchors = fixed_anchors_list[fridx - 1]; fixed_anchors = mb.fix_anchors_to_membrane(anchors, qcd_edges[fridx], params); fixed_anchors = mb.order_anchors(fixed_anchors, params.manual_anchor_midpoint); fixed_anchors_list[fridx] = fixed_anchors; poly = qcd_edges[fridx].getInterpolatedPolygon(0.25, False); polypoints = [(x,y) for x,y in zip(poly.xpoints, poly.ypoints)]; idx = [polypoints.index(fixed_anchors[0]), polypoints.index(fixed_anchors[1])]; idx.sort(); polypoints = polypoints[idx[0]:idx[1]]; newedge = PolygonRoi([x for (x,y) in polypoints], [y for (x,y) in polypoints], Roi.POLYLINE); newedge = mb.check_edge_order(anchors, newedge); imp.setPosition(fridx + 1); imp.setRoi(newedge); IJ.run(imp, "Interpolate", "interval=1.0 smooth adjust"); IJ.run(imp, "Fit Spline", ""); qcd_edges[fridx] = imp.getRoi(); mbio.save_qcd_edges2(qcd_edges, output_folder); imp.changes = False; imp.close(); return qcd_edges, fixed_anchors_list;
from ij import ImageListener, ImagePlus # Function to be used for all methods of the implemented interface def spyImageEvents(self, imp): print "Event on image:", imp # New class definition spying_class = type( 'Spying', # the name of the class (ImageListener, ), # the tuple of interfaces to implement { "imageOpened": spyImageEvents, # the methods of the interfaces "imageUpdated": spyImageEvents, "imageClosed": spyImageEvents }) # Create a new instance instance = spying_class() ImagePlus.addImageListener(instance)