def testAutoThreshold(self): """Test that the auto thresholding gives the same results""" for key, data in ThresholdingResults.items(): ch1 = getChannel(key, 0) ch2 = getChannel(key, 1) th1, th2 = data autothreshold = vtk.vtkImageAutoThresholdColocalization() autothreshold.AddInput(ch1) autothreshold.AddInput(ch2) autothreshold.Update() resultth1 = autothreshold.GetCh1ThresholdMax() resultth2 = autothreshold.GetCh2ThresholdMax() self.assertEqual((th1, th2), (resultth1, resultth2), "Our autothresholding produces different results than ImageJ's (%d, %d != %d, %d)" % (resultth1, resultth2, th1, th2))
def testAutoThreshold(self):
"""Test that the auto thresholding gives the same results"""
for key, data in ThresholdingResults.items():
ch1 = getChannel(key, 0)
ch2 = getChannel(key, 1)
th1, th2 = data
autothreshold = vtk.vtkImageAutoThresholdColocalization()
autothreshold.AddInput(ch1)
autothreshold.AddInput(ch2)
autothreshold.Update()
resultth1 = autothreshold.GetCh1ThresholdMax()
resultth2 = autothreshold.GetCh2ThresholdMax()
self.assertEqual((th1, th2), (
resultth1, resultth2
), "Our autothresholding produces different results than ImageJ's (%d, %d != %d, %d)"
% (resultth1, resultth2, th1, th2))
reader2.SetUpdateTimePoint(5)
reader2.Update()
ch2=reader2.GetOutput()
#w1=vtk.vtkXMLImageDataWriter()
#w1.SetFileName("Ch1.vti")
#w1.SetInput(ch1)
#w1.Write()
#w2=vtk.vtkXMLImageDataWriter()
#w2.SetFileName("Ch2.vti")
#w2.SetInput(ch2)
#w2.Write()
coloc=vtk.vtkImageAutoThresholdColocalization()
coloc.AddInput(ch1)
coloc.AddInput(ch2)
coloc.Update()
print coloc
data=coloc.GetOutput(0)
plotdata=coloc.GetOutput(1)
print "Plot data=",plotdata
i=0
writer=vtk.vtkXMLImageDataWriter()
pdata=data.GetPointData()
name=None
if pdata:
name=pdata.GetScalars().GetName()
reader2.SetFileName("/home/kalpaha/BioImageXD/Data/sample2.lsm")
reader2.SetUpdateChannel(1)
reader2.SetUpdateTimePoint(5)
reader2.Update()
ch2 = reader2.GetOutput()
#w1=vtk.vtkXMLImageDataWriter()
#w1.SetFileName("Ch1.vti")
#w1.SetInput(ch1)
#w1.Write()
#w2=vtk.vtkXMLImageDataWriter()
#w2.SetFileName("Ch2.vti")
#w2.SetInput(ch2)
#w2.Write()
coloc = vtk.vtkImageAutoThresholdColocalization()
coloc.AddInput(ch1)
coloc.AddInput(ch2)
coloc.Update()
print coloc
data = coloc.GetOutput(0)
plotdata = coloc.GetOutput(1)
print "Plot data=", plotdata
i = 0
writer = vtk.vtkXMLImageDataWriter()
pdata = data.GetPointData()
name = None
if pdata:
name = pdata.GetScalars().GetName()
