def qc_background_regions(intensity_imp, bg_rois): """allow the user to view and correct automatically-determined background regions""" imp = Duplicator().run(intensity_imp); imp.setTitle("Background region QC"); imp.show(); imp.setPosition(1); autoset_zoom(imp); imp.setRoi(bg_rois[0]); IJ.setTool("freehand"); notOK = True; while notOK: listener = UpdateRoiImageListener(bg_rois, is_area=True); imp.addImageListener(listener); dialog = NonBlockingGenericDialog("Background region quality control"); dialog.enableYesNoCancel("Continue", "Use this region for all t"); dialog.setCancelLabel("Cancel analysis"); dialog.addMessage("Please redraw background regions as necessary...") dialog.showDialog(); if dialog.wasCanceled(): raise KeyboardInterrupt("Run canceled"); elif not(dialog.wasOKed()): this_roi = imp.getRoi(); bg_rois = [this_roi for _ in listener.getRoiList()]; imp.removeImageListener(listener); else: last_roi = imp.getRoi(); qcd_bg_rois = listener.getRoiList(); if imp.getNFrames() > imp.getNSlices(): qcd_bg_rois[imp.getT() - 1] = last_roi; else: qcd_bg_rois[imp.getZ() - 1] = last_roi; notOK = False; imp.removeImageListener(listener); imp.changes = False; imp.close(); return qcd_bg_rois;
def generate_background_rois(input_mask_imp, params, membrane_edges, dilations=5, threshold_method=None, membrane_imp=None): """automatically identify background region based on auto-thresholded image, existing membrane edges and position of midpoint anchor""" if input_mask_imp is None and membrane_imp is not None: segmentation_imp = Duplicator().run(membrane_imp) # do thresholding using either previous method if threhsold_method is None or using (less conservative?) threshold method if (threshold_method is None or not (threshold_method in params.listThresholdMethods())): mask_imp = make_and_clean_binary(segmentation_imp, params.threshold_method) else: mask_imp = make_and_clean_binary(segmentation_imp, threshold_method) segmentation_imp.close() else: input_mask_imp.killRoi() mask_imp = Duplicator().run(input_mask_imp) rois = [] IJ.setForegroundColor(0, 0, 0) roim = RoiManager(True) rt = ResultsTable() for fridx in range(mask_imp.getNFrames()): mask_imp.setT(fridx + 1) # add extra bit to binary mask from loaded membrane in case user refined edges... # flip midpoint anchor across the line joining the two extremes of the membrane, # and fill in the triangle made by this new point and those extremes poly = membrane_edges[fridx].getPolygon() l1 = (poly.xpoints[0], poly.ypoints[0]) l2 = (poly.xpoints[-1], poly.ypoints[-1]) M = (0.5 * (l1[0] + l2[0]), 0.5 * (l1[1] + l2[1])) Mp1 = (params.manual_anchor_midpoint[0][0] - M[0], params.manual_anchor_midpoint[0][1] - M[1]) p2 = (M[0] - Mp1[0], M[1] - Mp1[1]) new_poly_x = list(poly.xpoints) new_poly_x.append(p2[0]) new_poly_y = list(poly.ypoints) new_poly_y.append(p2[1]) mask_imp.setRoi(PolygonRoi(new_poly_x, new_poly_y, PolygonRoi.POLYGON)) IJ.run(mask_imp, "Fill", "slice") mask_imp.killRoi() # now dilate the masked image and identify the unmasked region closest to the midpoint anchor ip = mask_imp.getProcessor() dilations = 5 for d in range(dilations): ip.dilate() ip.invert() mask_imp.setProcessor(ip) mxsz = mask_imp.getWidth() * mask_imp.getHeight() pa = ParticleAnalyzer( ParticleAnalyzer.ADD_TO_MANAGER | ParticleAnalyzer.SHOW_PROGRESS, ParticleAnalyzer.CENTROID, rt, 0, mxsz) pa.setRoiManager(roim) pa.analyze(mask_imp) ds_to_anchor = [ math.sqrt((x - params.manual_anchor_midpoint[0][0])**2 + (y - params.manual_anchor_midpoint[0][1])**2) for x, y in zip( rt.getColumn(rt.getColumnIndex("X")).tolist(), rt.getColumn(rt.getColumnIndex("Y")).tolist()) ] if len(ds_to_anchor) > 0: roi = roim.getRoi(ds_to_anchor.index(min(ds_to_anchor))) rois.append(roi) else: rois.append(None) roim.reset() rt.reset() roim.close() mask_imp.close() return rois
def ColMigBud(): def setupDialog(imp): gd = GenericDialog("Collective migration buddy options") gd.addMessage("Collective migration buddy 2.0, you are analyzing: " + imp.getTitle()) calibration = imp.getCalibration() if (calibration.frameInterval > 0): default_interval = calibration.frameInterval default_timeunit = calibration.getTimeUnit() else: default_interval = 8 default_timeunit = "min" gd.addNumericField("Frame interval:", default_interval, 2) # show 2 decimals gd.addCheckbox("Do you want to use a gliding window?", True) gd.addCheckbox( "Project hyperStack? (defaluts to projecting current channel only)", False) gd.addStringField("time unit", default_timeunit, 3) gd.addSlider("Start compacting at frame:", 1, imp.getNFrames(), 1) gd.addSlider("Stop compacting at frame:", 1, imp.getNFrames(), imp.getNFrames()) gd.addNumericField("Number of frames to project in to one:", 3, 0) # show 0 decimals gd.addChoice('Method to use for frame projection:', methods_as_strings, methods_as_strings[5]) gd.showDialog() if gd.wasCanceled(): IJ.log("User canceled dialog!") return return gd #Start by getting the active image window and get the current active channel and other stats imp = WindowManager.getCurrentImage() cal = imp.getCalibration() nSlices = 1 #TODO fix this in case you want to do Z-stacks title = imp.getTitle() current_channel = imp.getChannel() #zp = ZProjector(imp) #Make a dict containg method_name:const_fieled_value pairs for the projection methods methods_as_strings = [ 'Average Intensity', 'Max Intensity', 'Min Intensity', 'Sum Slices', 'Standard Deviation', 'Median' ] methods_as_const = [ ZProjector.AVG_METHOD, ZProjector.MAX_METHOD, ZProjector.MIN_METHOD, ZProjector.SUM_METHOD, ZProjector.SD_METHOD, ZProjector.MEDIAN_METHOD ] medthod_dict = dict(zip(methods_as_strings, methods_as_const)) # Run the setupDialog, read out and store the options gd = setupDialog(imp) frame_interval = gd.getNextNumber() time_unit = gd.getNextString() glidingFlag = gd.getNextBoolean() hyperstackFlag = gd.getNextBoolean() #Set the frame interval and unit, and store it in the ImagePlus calibration cal.frameInterval = frame_interval cal.setTimeUnit(time_unit) imp.setCalibration(cal) start_frame = int(gd.getNextNumber()) stop_frame = int(gd.getNextNumber()) #If a subset of the image is to be projected, these lines of code handle that if (start_frame > stop_frame): IJ.showMessage("Start frame > Stop frame, can't go backwards in time!") raise RuntimeException("Start frame > Stop frame!") if ((start_frame != 1) or (stop_frame != imp.getNFrames())): imp = Duplicator().run(imp, 1, nChannels, 1, nSlices, start_frame, stop_frame) no_frames_per_integral = int(gd.getNextNumber()) #the doHyperstackProjection method can't project past the end of the stack if hyperstackFlag: total_no_frames_to_project = imp.getNFrames() - no_frames_per_integral #the doProjection method can project past the end, it just adds black frames at the end #When not projecting hyperstacks, just copy the current active channel from the active image else: total_no_frames_to_project = imp.getNFrames() imp = Duplicator().run(imp, current_channel, current_channel, 1, nSlices, start_frame, stop_frame) #The Z-Projection magic happens here through a ZProjector object zp = ZProjector(imp) projection_method = gd.getNextChoice() chosen_method = medthod_dict[projection_method] zp.setMethod(chosen_method) outstack = imp.createEmptyStack() if glidingFlag: frames_to_advance_per_step = 1 else: frames_to_advance_per_step = no_frames_per_integral for frame in range(1, total_no_frames_to_project, frames_to_advance_per_step): zp.setStartSlice(frame) zp.setStopSlice(frame + no_frames_per_integral) if hyperstackFlag: zp.doHyperStackProjection(False) projected_stack = zp.getProjection().getStack() for channel in range(projected_stack.getSize()): outstack.addSlice(projected_stack.getProcessor(channel + 1)) else: zp.doProjection() outstack.addSlice(zp.getProjection().getProcessor()) #Create an image processor from the newly created Z-projection stack nChannels = imp.getNChannels() nFrames = outstack.getSize() / nChannels imp2 = ImagePlus( title + '_' + projection_method + '_' + str(no_frames_per_integral) + '_frames', outstack) imp2 = HyperStackConverter.toHyperStack(imp2, nChannels, nSlices, nFrames) imp2.show() Startmenu()