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#!/usr/bin/python
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#-*- coding: utf-8 -*-
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# To define the path:
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from morphee import *
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import sys, os
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pjoin = os.path.join
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# To use Morphee
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sys.path.append(pjoin(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))),"Common","python"))
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from morphee import *
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def ImDisplay3d(im3d, start,M,N,value,filename):
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xsize = im3d.getXSize()
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ysize = im3d.getYSize()
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zsize = im3d.getZSize()
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xsize2 = im3d.getXSize()+2
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ysize2 = im3d.getYSize()+2
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imd = ImCreate(xsize2*M,ysize2*N,1,"UINT8")
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ImSetConstant(imd,value)
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type(imd)
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time = start
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for i in range(N):
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for j in range (M):
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if(time < zsize):
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imd.setActiveWindow(j*xsize2,i*ysize2,0, xsize, ysize, 1)
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im3d.setActiveWindow(0,0, time, xsize, ysize, 1)
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print ';',type(imd)
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ImCopy(im3d,imd)
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time = time + 1
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imd.resetActiveWindow()
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im3d.resetActiveWindow()
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ImDisplayX(imd,filename)
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#--- SOLUTIONS
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def Exercice2(nb_frames):
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"""
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Segment a 3D grey level image with graphs
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"""
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print "II. Segment a 3D grey image"
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# Allocate images
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im = fileRead(pjoin(images_dir,"3D","brain.vis"))
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xsize = im.getXSize()
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ysize = im.getYSize()
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im2= ImCreate(xsize,ysize,nb_frames,"UINT8")
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im.setActiveWindow(0,0,0,xsize,ysize,nb_frames)
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ImCopy(im,im2)
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im = ImCreateSame(im2)
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ImCopy(im2,im)
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pdb.set_trace()
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ImDisplay3d(im,0,6,4,255,"ori")
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imFil = getSame(im)
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imTemp = getSame(im)
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imGrad = getSame(im)
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imLabel = getSameOf(im,dataCategory.dtScalar,scalarDataType.sdtUINT32)
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imFineSeg = getSame(imLabel)
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imOut = getSame(imLabel)
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# Choice of the neighborhood graph
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nl = NeighborList.neighborsCubic63D
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# Alternate Sequential Filtering
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ImASFCloseOpen(im,nl,1,imFil)
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ImDisplay3d(imFil,0,6,4,255,"fil")
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# Gradient
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ImMorphoGradient(imFil,nl,imGrad)
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ImDisplay3d(imGrad,0,6,5,255,"gra")
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# Minima labelisation
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imMini = getSame(imGrad)
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ImMinima(imGrad,nl,imMini)
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ImLabel(imMini,nl,imLabel)
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ImDisplay3d(imLabel,0,6,4,255,"label")
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# Hierarchical segmentation:
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segmType = HierarchicalSegmentationType.Volumic
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graph = ImHierarchicalSegmentation(imGrad,imLabel,nl,segmType,imFineSeg)
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ImDisplay3d(imFineSeg,0,6,4,255,"fineseg")
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# Choice of a level in the hierarchy
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numberOfRegions = 2
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ImDisplayHierarchyLevel(imFineSeg,graph,numberOfRegions,imOut)
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imSeg = ImCreateSame(imOut)
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imSeg8 = ImCreateSame(imOut,"UINT8")
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ImLabelFlatZones(imOut,nl,imSeg)
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ImCopy(imSeg,imSeg8)
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ImDisplay3d(imSeg8,0,6,4,255,"seg")
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pdb.set_trace()
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#--- GLOBAL SCRIPT
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if __name__=='__main__':
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print "3D segmentation and tracking"
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nb_frames = 10
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Exercice2(nb_frames)
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