maskedCentromeres = itk.LabelMapMaskImageFilter.LM3IUC3.New(nucleusLM, unflattenCentromeres)
centromeresLM = itk.LabelImageToStatisticsLabelMapFilter.IUC3IUC3LM3.New(maskedCentromeres, unflattenCentromeresInt)
posCentromeresLM = itk.StatisticsPositionLabelMapFilter.LM3.New(centromeresLM, Attribute="CenterOfGravity")
aggrCentromeresLM = itk.AggregateLabelMapFilter.LM3.New(posCentromeresLM, InPlace=False)
shapeAggrCentromeresLM = itk.ShapeLabelMapFilter.LM3.New(aggrCentromeresLM)
simCentromeresLM = itk.LabelMap._3.New()
shapeSimCentromeresLM = itk.ShapeLabelMapFilter.LM3.New(simCentromeresLM)
simCentromeresLM2 = itk.LabelMap._3.New()
shapeSimCentromeresLM2 = itk.ShapeLabelMapFilter.LM3.New(simCentromeresLM2)
extra = ExtraData(defaults={"nucleus-ext": "-nuclei.nrrd",
"spots-ext": "-CENP.nrrd",
"spots-are-labeled": "true",
"rawspots-ext": "",
"rawspots-channel": "0",
"number-of-simulations": "500"})
nf = extra.printer(file(sys.argv[1].replace("::","-")+".txt", "w"))
nf.printHeader("image", "label", "size", "centromeres", "flatness", "cdist", "rdist", "ncdist", "nrdist", "pvalue")
for (nucleusName, centromeresName, centromeresIntName) in extra.iterate(["nucleus-ext", "spots-ext", "rawspots-ext"]):
try:
nbSims = extra.getint("number-of-simulations")
nucleusReader(FileName=nucleusName)
centromeresReader(FileName=centromeresName)
centromeresIntReader(FileName=centromeresIntName)
for flatNucleus in li2lm()[0]:
idx, size, spacing, spacing2 = computeRegion(flatNucleus, nucleusReader)
singleNucleusLM = itk.LabelSelectionLabelMapFilter.LM3.New(nucleusLM, InPlace=False)
binaryNucleus = itk.LabelMapToBinaryImageFilter.LM3IUC3.New(singleNucleusLM, ForegroundValue=0, BackgroundValue=255)
maurerSingleNucleus = itk.SignedMaurerDistanceMapImageFilter.IUC3IF3.New(binaryNucleus, UseImageSpacing=True, SquaredDistance=False)
evfSingleNucleus = itk.ErodedVolumeFractionMapImageFilter.IF3IF3.New(maurerSingleNucleus)
maskedCentromeres = itk.LabelMapMaskImageFilter.LM3IUC3.New(nucleusLM, centromeresReader)
centromeresLM = itk.LabelImageToStatisticsLabelMapFilter.IUC3IUC3LM3.New(maskedCentromeres, centromeresIntReader)
def interpolate(image, pos):
li = itk.LinearInterpolateImageFunction.IF3D.New(image)
return li.Evaluate( pos )
extra = ExtraData(sys.argv[1], sys.argv[2:],
{"nucleus-ext": "-nuclei.nrrd",
"spots-ext": "-CENP.nrrd",
"spots-are-labeled": "true",
"rawspots-ext": "",
"rawspots-channel": "0"})
cf = extra.printer(file(sys.argv[1].replace("::","-")+".txt", "w"))
cf.printHeader("image", "label", "clabel", "mdist", "evf")
for (nucleusName, centromeresName, centromeresIntName) in extra.iterate(["nucleus-ext", "spots-ext", "rawspots-ext"]):
try:
nucleusReader(FileName=nucleusName)
centromeresReader(FileName=centromeresName)
centromeresIntReader(FileName=centromeresIntName, Channel=extra.getint("rawspots-channel"))
for nucleus in nucleusLM()[0]:
singleNucleusLM.SetLabel(nucleus.GetLabel())
maskedCentromeres.SetLabel(nucleus.GetLabel())
