imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/l5c1_350_CLAHE.tif'
#imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/L1CH2_maxp_300-374sampleframe.tif'
#imgpath = '/Users/miura/Dropbox/people/julia/NucSegmentStudy/l5c1_CLAHE.tif'
imp = IJ.openImage(imgpath)
ntd = NucToDots(imp);
#ntd.run()
imp2 = ntd.preprocessCoreStack(imp) # for imp that is already stackCLAHEed.
#for i in ntd.getXcoordA():
# print i
imp2.show()
print "Extracting Nucleus ..."
#subwwhh = 110 # this must be guessed in the pre-run, by doing particle analysis and get the approximate sizes.
en = NucleusExtractor(imp)
#en.constructNodesByPA(imp2)
ns = en.getPerNucleusBinImgProcessors(imp, imp2)
# for i in range(10):
# ImagePlus(str(i), ns.get(i).getBinip()).show()
#print "x", ns.get(i).getOrgroi().getBounds().x, "y", ns.get(i).getOrgroi().getBounds().y
#print "w", ns.get(i).getOrgroi().getBounds().width, "h", ns.get(i).getOrgroi().getBounds().height
en.reassignNodes(ns);
'''
#print 'node length before filtering: ' + str(en.getNodes().size())
#en.analyzeDotsandBinImages()
#print 'node length after filtering: ' + str(en.getNodes().size())
#imgpath = '/Volumes/D/Julia20130201-/almfscreen/samples_112712/l3/l3c1.tif'
#imgpath = '/Volumes/D/Julia20130201-/almfscreen/samples_112712/l4/l4c1.tif'
imgpath = '/Volumes/D/Julia20130201-/almfscreen/samples_112712/l5/l5c1.tif'
imp = IJ.openImage(imgpath)
ntd = NucToDots(imp);
ntd.run() # runs CLAHE first, takes a bit of time.
#ntd.runmain() # for imp that is already stackCLAHEed.
#for i in ntd.getXcoordA():
# print i
print "Extracting Nucleus ..."
subwwhh = 130 # this must be guessed in the pre-run, by doing particle analysis and get the approximate sizes.
WATERSHED_THRESHOLD = 0.10;
en = NucleusExtractor(imp, ntd.getXcoordA(), ntd.getYcoordA(), ntd.getFrameA())
en.constructNodesByDots(subwwhh, WATERSHED_THRESHOLD)
print 'node length before filtering: ' + str(en.getNodes().size())
en.analyzeDotsandBinImages()
print 'node length after filtering: ' + str(en.getNodes().size())
nodes = en.getNodes()
'''
stk = ImageStack(subwwhh, subwwhh)
for n in nodes:
binip = n.getBinip()
stk.addSlice(binip)
ImagePlus("tt", stk).show()
'''
#maximp = NucToDots(imp).run()
#maximp.show()
ntd = NucToDots(imp);
ntd.run()
subwwhh = 120 # size of sub image
# from here is the extraction
'''
nrp = NRP()
nrp.getPerNucleusBinImgProcessors(imp, subwwhh, ntd.getXcoordA(), ntd.getYcoordA(), ntd.getFrameA())
stk = nrp.getBinStack();
'''
en = NucleusExtractor(imp, ntd.getXcoordA(), ntd.getYcoordA(), ntd.getFrameA())
en.constructNodes(subwwhh)
en.analyzeDotsandBinImages()
nodes = en.getNodes()
stk = ImageStack(subwwhh, subwwhh)
for n in nodes:
binip = n.getBinip()
stk.addSlice(binip)
'''
stk = ImageStack(subwwhh, subwwhh)
for i, f in enumerate(ntd.getFrameA()):
ip = imp.getStack().getProcessor(f)
roi = nrp.makeRoi(ip, ntd.getXcoordA()[i], ntd.getYcoordA()[i], subwwhh, subwwhh)
subip = nrp.extract(ip, roi)
binip = nrp.binarize(subip)
