def new_Table(): """Creates a new ResultsTable padded with float("nan"), ie, all empty cells will be filled with Java's String.valueOf(Double.NaN) """ new_rt = RT() new_rt.setNaNEmptyCells(True); new_rt.showRowNumbers(False); return new_rt
def measure(self): imp = IJ.openImage(self.filename) IJ.log("Input file: %s" % self.filename) ImageConverter(imp).convertToGray8() res = Auto_Threshold().exec(imp, self.myMethod, self.noWhite, self.noBlack, self.doIwhite, self.doIset, self.doIlog, self.doIstackHistogram) rt = ResultsTable() rt.showRowNumbers(False) pa = PA(self.options, PA.AREA + PA.PERIMETER + PA.CIRCULARITY, rt, self.MINSIZE, self.MAXSIZE) pa.analyze(imp) self.result = self.rtToResult(rt) self.mask = imp
def measure(stack, cells, nuclei): time = [ (t-1)*cal.frameInterval for t in range(T+1) ] cellValues0 = [ 0.0 for t in range(T+1) ] cellValues1 = [ 0.0 for t in range(T+1) ] cellAreas0 = [ 0.0 for t in range(T+1) ] cellAreas1 = [ 0.0 for t in range(T+1) ] nucleusValues0 = [ 0.0 for t in range(T+1) ] nucleusValues1 = [ 0.0 for t in range(T+1) ] nucleusAreas0 = [ 0.0 for t in range(T+1) ] nucleusAreas1 = [ 0.0 for t in range(T+1) ] nonNucleusValues0 = [ 0.0 for t in range(T+1) ] nonNucleusValues1 = [ 0.0 for t in range(T+1) ] for t in range(1,T+1): ip = stack.getProcessor(t) if cells[t] is None: continue #subtract background Z from all intensity Z measurements if cells [t] is None: print("Nocellsfound" + str(t)) bothCells = ShapeRoi(cells[t][0]).or(ShapeRoi(cells[t][1])) backRoi = ShapeRoi(Rectangle(0,0,imp.getWidth(),imp.getHeight())).not( bothCells ) ip.setRoi(backRoi) backMean = ip.getStatistics().mean ip.setRoi( cells[t][0] ) stats0 = ip.getStatistics() cellValues0[t] = stats0.mean - backMean cellAreas0[t] = stats0.area * cal.pixelWidth * cal.pixelHeight nuc0 = None for nuc in nuclei[t]: rect = nuc.getBounds() nx = int(rect.x+(rect.width/2.0)) ny = int(rect.y+(rect.height/2.0)) if cells[t][0].contains(nx,ny): nuc0 = nuc break if nuc0 is not None: ip.setRoi( nuc0 ) nucStats0 = ip.getStatistics() nucleusValues0[t] = nucStats0.mean - backMean nucleusAreas0[t] = nucStats0.area * cal.pixelWidth * cal.pixelHeight nuc0.setPosition(0,0,t) nuc0.setStrokeColor(Color.CYAN) ol.add(nuc0) nonnucRoi0 = ShapeRoi(cells[t][0]).not( ShapeRoi(nuc0) ) ip.setRoi( nonnucRoi0 ) nonNucleusValues0[t] = ip.getStatistics().mean - backMean ip.setRoi( cells[t][1] ) stats1 = ip.getStatistics() cellValues1[t] = stats1.mean - backMean cellAreas1[t] = stats1.area * cal.pixelWidth * cal.pixelHeight nuc1 = None for nuc in nuclei[t]: rect = nuc.getBounds() nx = int(rect.x+(rect.width/2.0)) ny = int(rect.y+(rect.height/2.0)) if cells[t][1].contains(nx,ny): nuc1 = nuc break if nuc1 is not None: ip.setRoi( nuc1 ) nucStats1 = ip.getStatistics() nucleusValues1[t] = nucStats1.mean - backMean nucleusAreas1[t] = nucStats1.area * cal.pixelWidth * cal.pixelHeight nuc1.setPosition(0,0,t) nuc1.setStrokeColor(Color.CYAN) ol.add(nuc1) nonnucRoi1 = ShapeRoi(cells[t][1]).not( ShapeRoi(nuc1) ) ip.setRoi( nonnucRoi1 ) nonNucleusValues1[t] = ip.getStatistics().mean - backMean rt = ResultsTable() rt.showRowNumbers(False) for t in range(1,T+1): rt.setValue("Time ("+cal.getTimeUnit()+")", t-1, IJ.d2s(time[t],1)) areaRatio = cellAreas0[t] / cellAreas1[t] if cellAreas0[t]>0 and cellAreas1[t]>0 else 0.0 rt.setValue("Cell 0:Cell 1 Area Ratio", t-1, areaRatio) nucleusRatio = nucleusValues0[t] / nucleusValues1[t] if nucleusValues0[t]>0 and nucleusValues1[t]>0 else 0.0 rt.setValue("Cell 0:Cell 1 Nucleus Ratio", t-1, nucleusRatio) nonNucleusRatio = nonNucleusValues0[t] / nonNucleusValues1[t] if nonNucleusValues0[t]>0 and nonNucleusValues1[t]>0 else 0.0 rt.setValue("Cell 0:Cell 1 Non-Nucleus Ratio", t-1, nonNucleusRatio) nnnRatio0 = nucleusValues0[t] / nonNucleusValues0[t] if nucleusValues0[t]>0 and nonNucleusValues0[t]>0 else 0.0 rt.setValue("Cell 0 Nucleus:Non-Nucleus Ratio", t-1, nnnRatio0) nnnRatio1 = nucleusValues1[t] / nonNucleusValues1[t] if nucleusValues1[t]>0 and nonNucleusValues1[t]>0 else 0.0 rt.setValue("Cell 1 Nucleus:Non-Nucleus Ratio", t-1, nnnRatio1) rt.setValue("Cell 0 (red) Area ("+cal.getUnit()+u"\u00b2"+")", t-1, cellAreas0[t]) rt.setValue("Cell 0 Nucleus Area ("+cal.getUnit()+u"\u00b2"+")", t-1, nucleusAreas0[t]) rt.setValue("Cell 0 All", t-1, cellValues0[t]) rt.setValue("Cell 0 Nucleus", t-1, nucleusValues0[t]) rt.setValue("Cell 0 Non-Nucleus", t-1, nonNucleusValues0[t]) rt.setValue("Cell 1 (green) Area ("+cal.getUnit()+u"\u00b2"+")", t-1, cellAreas1[t]) rt.setValue("Cell 1 Nucleus Area ("+cal.getUnit()+u"\u00b2"+")", t-1, nucleusAreas1[t]) rt.setValue("Cell 1 All", t-1, cellValues1[t]) rt.setValue("Cell 1 Nucleus", t-1, nucleusValues1[t]) rt.setValue("Cell 1 Non-Nucleus", t-1, nonNucleusValues1[t]) rt.show(imp.getTitle()+"-Results") dataset = DefaultXYDataset() dataset.addSeries( "Cell 0", [time[1:], cellValues0[1:]] ) dataset.addSeries( "Cell 1", [time[1:], cellValues1[1:]] ) dataset.addSeries( "Nucleus 0", [time[1:], nucleusValues0[1:]] ) dataset.addSeries( "Nucleus 1", [time[1:], nucleusValues1[1:]] ) dataset.addSeries( "Non-Nucleus 0", [time[1:], nonNucleusValues0[1:]] ) dataset.addSeries( "Non-Nucleus 1", [time[1:], nonNucleusValues1[1:]] ) chart = ChartFactory.createScatterPlot( imp.getTitle(), "Time ("+cal.getTimeUnit()+")", "Intensity Z", dataset, PlotOrientation.VERTICAL, True,True,False ) plot = chart.getPlot() plot.setBackgroundPaint(Color(64, 128, 255)) plot.setDomainGridlinePaint(Color.BLACK) plot.setRangeGridlinePaint(Color.BLACK) renderer = plot.getRenderer() legend = LegendItemCollection() shapeR = 2.0 nucShape = Ellipse2D.Float(-shapeR,-shapeR,shapeR*2,shapeR*2) nonNucShape = Path2D.Float() nonNucShape.moveTo(-shapeR,-shapeR) nonNucShape.lineTo(shapeR,shapeR) nonNucShape.moveTo(shapeR,-shapeR) nonNucShape.lineTo(-shapeR,shapeR) for s in range(dataset.getSeriesCount()): if s == 0: renderer.setSeriesLinesVisible(s, True) renderer.setSeriesShapesVisible(s, False) renderer.setSeriesStroke(s, BasicStroke(1)) renderer.setSeriesPaint(s, Color.RED) legend.add( LegendItem("Cell 0", Color.RED) ) elif s == 1: renderer.setSeriesLinesVisible(s, True) renderer.setSeriesShapesVisible(s, False) renderer.setSeriesStroke(s, BasicStroke(1)) renderer.setSeriesPaint(s, Color.GREEN) legend.add( LegendItem("Cell 1", Color.GREEN) ) elif s == 2: renderer.setSeriesLinesVisible(s, False) renderer.setSeriesShapesVisible(s, True) renderer.setSeriesShape(s, nucShape) renderer.setSeriesPaint(s, Color.RED) elif s == 3: renderer.setSeriesLinesVisible(s, False) renderer.setSeriesShapesVisible(s, True) renderer.setSeriesShape(s, nucShape) renderer.setSeriesPaint(s, Color.GREEN) elif s == 4: renderer.setSeriesLinesVisible(s, False) renderer.setSeriesShapesVisible(s, True) renderer.setSeriesShape(s, nonNucShape) renderer.setSeriesPaint(s, Color.RED) elif s == 5: renderer.setSeriesLinesVisible(s, False) renderer.setSeriesShapesVisible(s, True) renderer.setSeriesShape(s, nonNucShape) renderer.setSeriesPaint(s, Color.GREEN) plot.setFixedLegendItems(legend) frame = ChartFrame(imp.getTitle()+" Z-Normalised Intensity", chart) frame.pack() frame.setSize( Dimension(800, 800) ) frame.setLocationRelativeTo(None) frame.setVisible(True)
try: image = IJ.openImage(options['inputFile']) except Exception: images = BF.openImagePlus(options['inputFile']) image = images[0] if options['oneShot']: results.append(runSimulation(options, image)) else: parameters = makeParameters(options) for index in range(0, len(parameters)): options.update(parameters[index]) results.append(runSimulation(options, image)) resultsTable = ResultsTable() resultsTable.showRowNumbers(False) for i in range(0, len(results)): if options['oneShot']: localBackground = options['localBackground'] seedRadius = options['seedRadius'] gaussXY = options['gaussXY'] gaussZ = options['gaussZ'] else: localBackground = parameters[i]['localBackground'] seedRadius = parameters[i]['seedRadius'] gaussXY = parameters[i]['gaussXY'] gaussZ = parameters[i]['gaussZ'] resultsTable.incrementCounter() resultsTable.addValue("Threshold", localBackground)
def main(): rt = RT.open2(table_file.getAbsolutePath()) if not rt: return log(" --- --- --- ") log("Loaded %s" % table_file.getAbsolutePath()) log("Loading column lists...") # Get column indices from imported file headings = getColumnHeadings(rt) id_col = getColumnIndex(headings, "TID") t_col = getColumnIndex(headings, "t [") d2p_col = getColumnIndex(headings, "D2P [") angle_col = getColumnIndex(headings, u'\u03B1 [deg]') delta_col = getColumnIndex(headings, u'\u0394\u03B1 [deg]') if angle_col == RT.COLUMN_NOT_FOUND: log("Failed to detect index for angle column. Re-trying...") angle_col = getColumnIndex(headings, u'? [deg]') if delta_col == RT.COLUMN_NOT_FOUND: log("Failed to detect index for delta angle column. Re-trying...") delta_col = getColumnIndex(headings, u'?? [deg]') log("Last column index is %s" % rt.getLastColumn()) if RT.COLUMN_NOT_FOUND in (id_col, d2p_col, delta_col, angle_col): uiservice.showDialog("Error: Some key columns were not found!", "Invalid Table?") return log("Settings: BOUT_WINDOW= %s, MIN_D2P= %s, DEF_FRAME_INTERVAL= %s" % (BOUT_WINDOW, '{0:.4f}'.format(MIN_D2P), DEF_FRAME_INTERVAL)) # Store all data on dedicated lists track_id_rows = rt.getColumnAsDoubles(id_col) d2p_rows = rt.getColumnAsDoubles(d2p_col) angle_rows = rt.getColumnAsDoubles(angle_col) delta_rows = rt.getColumnAsDoubles(delta_col) t_rows = rt.getColumnAsDoubles(t_col) # Assess n of data points and extract unique path ids n_rows = len(track_id_rows) row_indices = range(n_rows) track_ids = set(track_id_rows) n_tracks = len(track_ids) log("Table has %g rows" % n_rows) log("Table has %g tracks" % n_tracks) log("Parsing tracks...") for track_id in track_ids: for row, next_row in zip(row_indices, row_indices[1:]): if track_id_rows[row] != track_id: continue if not isNumber(angle_rows[row]): rt.setValue("FLAG", row, "NA") continue lower_bound = max(0, row - BOUT_WINDOW + 1) upper_bound = min(n_rows - 1, row + BOUT_WINDOW) win_d2p = [] for _ in range(lower_bound, upper_bound): win_d2p.append(d2p_rows[row]) if sum(win_d2p) <= MIN_D2P * len(win_d2p): rt.setValue("FLAG", row, 0) else: current_angle = angle_rows[row] next_angle = angle_rows[next_row] current_delta = delta_rows[row] flag = -1 if current_angle < 0 else 1 delta_change = (abs(current_delta) > 90) same_sign = ((current_angle < 0) == (next_angle < 0)) if delta_change and not same_sign: flag *= -1 rt.setValue("FLAG", row, flag) if next_row == n_rows - 1: rt.setValue("FLAG", next_row, flag) if rt.save(table_file.getAbsolutePath()): log("Processed table successfully saved (file overwritten)") else: log("Could not override input file. Displaying it...") rt.show(table_file.name) log("Creating onset table...") onset_rt = RT() onset_rt.showRowNumbers(False) frame_int = DEF_FRAME_INTERVAL if "table" in frame_rate_detection: frame_int = getFrameIntervalFromTable(row_indices, track_id_rows, t_rows) elif "image" in frame_rate_detection: frame_int = getFrameIntervalFromImage(image_file.getAbsolutePath()) else: log("Using default frame rate") for track_id in track_ids: for prev_row, row in zip(row_indices, row_indices[1:]): if not track_id in (track_id_rows[prev_row], track_id_rows[row]): continue flag = rt.getValue("FLAG", row) if not isNumber(flag): continue flag = int(flag) if flag == 0: continue if flag == 1 or flag == -1: srow = onset_rt.getCounter() onset_rt.incrementCounter() onset_rt.setValue("TID", srow, track_id) from_frame = int(t_rows[prev_row] / frame_int) + 1 to_frame = int(t_rows[row] / frame_int) + 1 onset_rt.setValue("First disp. [t]", srow, "%s to %s" % (t_rows[prev_row], t_rows[row])) onset_rt.setValue("First disp. [frames]", srow, "%s to %s" % (from_frame, to_frame)) onset_rt.setValue("ManualTag", srow, "") break out_path = suffixed_path(table_file.getAbsolutePath(), "ManualTagging") if onset_rt.save(out_path): log("Summary table successfully saved: %s" % out_path) else: log("File not saved... Displaying onset table") onset_rt.show("Onsets %s" % table_file.name)
roisBF = getRois(maskBF) ipTomato = stack.getProcessor(imp.getStackIndex(3, z, 1)).duplicate() sub = ipTomato.duplicate() ipTomato.blurGaussian(5) sub.blurGaussian(20) ipTomato.copyBits(sub, 0, 0, Blitter.SUBTRACT) maskTomato = getMask(ipTomato, AutoThresholder.Method.MaxEntropy) roisTomato = getRois(maskTomato) bfMeasure = stack.getProcessor(imp.getStackIndex(2, z, 1)) tomatoMeasure = stack.getProcessor(imp.getStackIndex(3, z, 1)) gfpMeasure = stack.getProcessor(imp.getStackIndex(1, z, 1)) ol = Overlay() rt = ResultsTable() rt.showRowNumbers(False) for bf in roisBF: bfMeasure.setRoi(bf) roiStatsBF = bfMeasure.getStatistics() if roiStatsBF.area * cal.pixelWidth * cal.pixelHeight < BFminA: continue bounds = bf.getBounds() cXbf = int(bounds.x + (bounds.width / 2.0)) cYbf = int(bounds.y + (bounds.height / 2.0)) bf.setStrokeColor(Color.YELLOW) bf.setPosition(0, z, 1) ol.add(bf) tomatoA = 0 for tomato in roisTomato:
def main(): rt = RT.open2(table_file.getAbsolutePath()) if not rt: return log(" --- --- --- ") log("Loaded %s" % table_file.getAbsolutePath()) log("Loading column lists...") # Get column indices from imported file headings = getColumnHeadings(rt) id_col = getColumnIndex(headings, "TID") t_col = getColumnIndex(headings, "t [") d2p_col = getColumnIndex(headings, "D2P [") angle_col = getColumnIndex(headings, u'\u03B1 [deg]') delta_col = getColumnIndex(headings, u'\u0394\u03B1 [deg]') if angle_col == RT.COLUMN_NOT_FOUND: log("Failed to detect index for angle column. Re-trying...") angle_col = getColumnIndex(headings, u'? [deg]') if delta_col == RT.COLUMN_NOT_FOUND: log("Failed to detect index for delta angle column. Re-trying...") delta_col = getColumnIndex(headings, u'?? [deg]') log("Last column index is %s" % rt.getLastColumn()) if RT.COLUMN_NOT_FOUND in (id_col, d2p_col, delta_col, angle_col): uiservice.showDialog("Error: Some key columns were not found!", "Invalid Table?") return log("Settings: BOUT_WINDOW= %s, MIN_D2P= %s, DEF_FRAME_INTERVAL= %s" % (BOUT_WINDOW, '{0:.4f}'.format(MIN_D2P), DEF_FRAME_INTERVAL)) # Store all data on dedicated lists track_id_rows = rt.getColumnAsDoubles(id_col) d2p_rows = rt.getColumnAsDoubles(d2p_col) angle_rows = rt.getColumnAsDoubles(angle_col) delta_rows = rt.getColumnAsDoubles(delta_col) t_rows = rt.getColumnAsDoubles(t_col) # Assess n of data points and extract unique path ids n_rows = len(track_id_rows) row_indices = range(n_rows) track_ids = set(track_id_rows) n_tracks = len(track_ids) log("Table has %g rows" % n_rows) log("Table has %g tracks" % n_tracks) log("Parsing tracks...") for track_id in track_ids: for row, next_row in zip(row_indices, row_indices[1:]): if track_id_rows[row] != track_id: continue if not isNumber(angle_rows[row]): rt.setValue("FLAG", row, "NA") continue lower_bound = max(0, row - BOUT_WINDOW + 1) upper_bound = min(n_rows-1, row + BOUT_WINDOW) win_d2p = [] for _ in range(lower_bound, upper_bound): win_d2p.append(d2p_rows[row]) if sum(win_d2p) <= MIN_D2P * len(win_d2p): rt.setValue("FLAG", row, 0) else: current_angle = angle_rows[row] next_angle = angle_rows[next_row] current_delta = delta_rows[row] flag = -1 if current_angle < 0 else 1 delta_change = (abs(current_delta) > 90) same_sign = ((current_angle<0) == (next_angle<0)) if delta_change and not same_sign: flag *= -1 rt.setValue("FLAG", row, flag) if next_row == n_rows - 1: rt.setValue("FLAG", next_row, flag) if rt.save(table_file.getAbsolutePath()): log("Processed table successfully saved (file overwritten)") else: log("Could not override input file. Displaying it...") rt.show(table_file.name) log("Creating onset table...") onset_rt = RT() onset_rt.showRowNumbers(False) frame_int = DEF_FRAME_INTERVAL if "table" in frame_rate_detection: frame_int = getFrameIntervalFromTable(row_indices, track_id_rows, t_rows) elif "image" in frame_rate_detection: frame_int = getFrameIntervalFromImage(image_file.getAbsolutePath()) else: log("Using default frame rate") for track_id in track_ids: for prev_row, row in zip(row_indices, row_indices[1:]): if not track_id in (track_id_rows[prev_row], track_id_rows[row]): continue flag = rt.getValue("FLAG", row) if not isNumber(flag): continue flag = int(flag) if flag == 0: continue if flag == 1 or flag == -1: srow = onset_rt.getCounter() onset_rt.incrementCounter() onset_rt.setValue("TID", srow, track_id) from_frame = int(t_rows[prev_row]/frame_int) + 1 to_frame = int(t_rows[row]/frame_int) + 1 onset_rt.setValue("First disp. [t]", srow, "%s to %s" % (t_rows[prev_row], t_rows[row])) onset_rt.setValue("First disp. [frames]", srow, "%s to %s" % (from_frame, to_frame)) onset_rt.setValue("ManualTag", srow, "") break out_path = suffixed_path(table_file.getAbsolutePath(), "ManualTagging") if onset_rt.save(out_path): log("Summary table successfully saved: %s" % out_path) else: log("File not saved... Displaying onset table") onset_rt.show("Onsets %s" % table_file.name)