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evf.py
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evf.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import itk, sys, traceback
from ExtraData import ExtraData
itk.auto_not_in_place()
nucleusReader = itk.ImageFileReader.IUC3.New()
centromeresReader = itk.ImageFileReader.IUC3.New()
centromeresIntReader = itk.bioformats()
nucleusLM = itk.LabelImageToShapeLabelMapFilter.IUC3LM3.New(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())
# les mesures sur chaque centromere
evfSingleNucleus()
for cent in centromeresLM()[0]:
cog = cent.GetCenterOfGravity()
evf = interpolate(evfSingleNucleus, cog)
d = interpolate(maurerSingleNucleus, cog)
cf.printData(nucleusName, nucleus.GetLabel(), cent.GetLabel(), d, evf)
# flush every nucleus to be able to check the result quickly
cf.flush()
except Exception, e:
print >> sys.stderr, "Error with", nucleusName
print >> sys.stderr, e
traceback.print_exc(file=sys.stderr)
centromeresLM.ResetPipeline()
evfSingleNucleus.ResetPipeline()