def plot(title, x_label, y_label, *curves):
dataset = XYSeriesCollection()
for legend, curve in curves:
series = XYSeries(legend)
for x, y in curve:
series.add(x, y)
dataset.addSeries(series)
chart = ChartFactory.createXYLineChart(title, x_label, y_label, dataset,
PlotOrientation.VERTICAL, True,
True, False)
frame = ChartFrame(title, chart)
frame.setVisible(True)
frame.setSize(400, 300)
def plot2D(points, Ca, Cb): maxIntensity = 255.0 dataset = XYSeriesCollection() seriesNN = XYSeries(channels[Ca+1]+" -ve "+channels[Cb+1]+" -ve") seriesPP = XYSeries(channels[Ca+1]+" +ve "+channels[Cb+1]+" +ve") seriesNP = XYSeries(channels[Ca+1]+" -ve "+channels[Cb+1]+" +ve") seriesPN = XYSeries(channels[Ca+1]+" +ve "+channels[Cb+1]+" -ve") for p in points: posA = channels[Ca+1] in thresholds and p[Ca]>thresholds[ channels[Ca+1] ] posB = channels[Cb+1] in thresholds and p[Cb]>thresholds[ channels[Cb+1] ] if posA and posB: seriesPP.add(p[Cb], p[Ca]) elif posA: seriesPN.add(p[Cb], p[Ca]) elif posB: seriesNP.add(p[Cb], p[Ca]) else: seriesNN.add(p[Cb], p[Ca]) dataset.addSeries(seriesNN) dataset.addSeries(seriesPN) dataset.addSeries(seriesNP) dataset.addSeries(seriesPP) chart = ChartFactory.createScatterPlot( title+" - "+channels[Cb+1]+" vs "+channels[Ca+1], channels[Cb+1], channels[Ca+1], dataset, PlotOrientation.VERTICAL, False,True,False ) plot = chart.getPlot() plot.getDomainAxis().setRange(Range(0.00, maxIntensity), True, False) plot.getRangeAxis().setRange(Range(0.00, maxIntensity), True, False) renderer = chart.getPlot().getRenderer() renderer.setSeriesPaint(0, Color(64,64,64)) #NN renderer.setSeriesPaint(1, Color(0,255,0)) #PN renderer.setSeriesPaint(2, Color(0,0,255)) #NP renderer.setSeriesPaint(3, Color(0,255,255)) #PP shape = Ellipse2D.Float(-1,-1,3,3) renderer.setSeriesShape(0, shape ) renderer.setSeriesShape(1, shape ) renderer.setSeriesShape(2, shape ) renderer.setSeriesShape(3, shape ) frame = ChartFrame(title+" - "+channels[Cb+1]+" vs "+channels[Ca+1], chart) frame.setSize(800, 800) frame.setLocationRelativeTo(None) frame.setVisible(True)
def histogram(title, values):
dataset = HistogramDataset()
dataset.setType(HistogramType.RELATIVE_FREQUENCY)
#NBINS = int(maths.sqrt(len(values)))
#NBINS = int( (max(values)-min(values))/binW )
NBINS = 64
dataset.addSeries(title, values, NBINS)
chart = ChartFactory.createHistogram(title, "Distance (nm)",
"Relative Frequency", dataset,
PlotOrientation.VERTICAL, False, True,
False)
plot = chart.getXYPlot()
renderer = plot.getRenderer()
renderer.setSeriesPaint(0, Colour.BLUE)
painter = StandardXYBarPainter()
renderer.setBarPainter(painter)
frame = ChartFrame(title, chart)
frame.setSize(1200, 800)
frame.setLocationRelativeTo(None)
frame.setVisible(True)
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)
