#ntd = NucToDots(imp)
#ntd.stackCLAHE(imp)
#imp.show()
#ppimp =ntd.preprocess(imp)
#ppimp.show()
#maximp = NucToDots(imp).run()
#maximp.show()
ntd = NucToDots(imp);
ntd.run()
for i in ntd.getXcoordA():
print i
IJ.log('test ')
dlh = DLH(imp, 2, 15) # linkrange, distance
# becareful with the swapped X and Y axis
#dlh.setData(jarray.array(ntd.getXcoords(), 'i'), jarray.array(ntd.getYcoords(), 'i'), jarray.array(ntd.getFrame(), 'i'))
dlh.setData(ntd.getXcoordA(), ntd.getYcoordA(), ntd.getFrameA())
nearestneighbor = LinkCostsOnlyDistance()
dlh.doLinking(nearestneighbor, False)
# convert to Tracks object
tracks = VecTrajectoryToTracks().runsimple(dlh.getAll_traj())
tracks.accept(TrackReLinker())
# plotting part
vd = VD(imp)
#img2path = '/Volumes/D/Julia20130201-/NucleusSegmentationStudy/20130312/out_bernsen45.tif'
#outimp = IJ.openImage(img2path)
#vd.plotTracks(outimp)
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()
'''
IJ.log('Linking ...')
dlh = DLH(imp, 3, 10) # linkrange, distance
#dlh.setData(ntd.getXcoordA(), ntd.getYcoordA(), ntd.getFrameA())
dlh.setData(nodes) # a new way, 20130321
nearestneighbor = LinkCostsOnlyDistance()
dlh.doLinking(nearestneighbor, False)
# convert to Tracks object
vttt = VecTrajectoryToTracks()
#vttt.run(dlh.getAll_traj())
vttt.run(dlh.getAll_traj(), nodes)
tracks = vttt.getTracks()
print "tracks", str(tracks.size())
for t in tracks.values():
#print t.getTrackID(), t.getNodes().get(0).getX(), t.getNodes().size(), t.getFrameStart()
print t.getNodes().get(0).getOrgroi()
tracks.accept(TrackReLinker())
for i in range(len(xpA)):
# frame number starts from 1
fulltA.append(j+1)
# from here is just to test.
pointlist = []
for i in range(len(xpA)):
pointlist.append(Point(i, xpA[i], ypA[i], j))
#pointlist.append(Nuc2D(xpA[i], ypA[i], j, i))
if j < 4:
print str(j), len(pointlist)
#print pointlist[3].x
frames.append(pointlist)
IJ.log('test ')
dlh = DLH(imp, 2, 15) # linkrange, distance
# becareful with the swapped X and Y axis
dlh.setData(jarray.array(fullxA, 'i'), jarray.array(fullyA, 'i'), jarray.array(fulltA, 'i'))
nearestneighbor = LinkCostsOnlyDistance()
dlh.doLinking(nearestneighbor, False)
# convert to Tracks object
tracks = VecTrajectoryToTracks().runsimple(dlh.getAll_traj())
tracks.accept(TrackReLinker())
# plotting part
vd = VD(imp)
img2path = '/Volumes/D/Julia20130201-/NucleusSegmentationStudy/20130312/out_bernsen45.tif'
outimp = IJ.openImage(img2path)
#vd.plotTracks(outimp)
vd.plotTracks(tracks, outimp)
