def show(T,A,IND,VERTS,scale): r=fvtk.ren() fvtk.clear(r) fvtk.add(r,fvtk.line(T,fvtk.red)) fvtk.show(r) Td=[downsample(t,20) for t in T] C=local_skeleton_clustering(Td,3) fvtk.clear(r) lent=float(len(T)) for c in C: color=np.random.rand(3) virtual=C[c]['hidden']/float(C[c]['N']) if length(virtual)> virtual_thr: linewidth=100*len(C[c]['indices'])/lent if linewidth<1.: linewidth=1 #fvtk.add(r,fvtk.line(virtual,color,linewidth=linewidth)) #fvtk.add(r,fvtk.label(r,str(len(C[c]['indices'])),pos=virtual[0],scale=3,color=color )) #print C[c]['hidden'].shape print A.shape print IND.shape print VERTS.shape all,allo=fvtk.crossing(A,IND,VERTS,scale,True) colors=np.zeros((len(all),3)) for (i,a) in enumerate(all): if allo[i][0]==0 and allo[i][1]==0 and allo[i][2]==1: pass else: colors[i]=cm.boys2rgb(allo[i]) fvtk.add(r,fvtk.line(all,colors)) fvtk.show(r)
dcross_shift = [c + np.array([3, 8, 6]) for c in dcross] fvtk.add(r, fvtk.line(no_cross_shift, fvtk.blue, linewidth=5.)) fvtk.add(r, fvtk.line(cross_shift, fvtk.indigo, linewidth=5.)) fvtk.add(r, fvtk.line(dcross_shift, fvtk.red, linewidth=5.)) from dipy.viz import colormap as cm all_shift = [c + np.array([10, 0, 0]) for c in all] all_shift2 = [c + np.array([20, 0, 0]) for c in all] colors = np.zeros((len(all), 3)) colors2 = np.zeros((len(all), 3)) for (i, a) in enumerate(all): #print a[0] colors[i] = cm.boys2rgb(allo[i]) colors2[i] = cm.orient2rgb(allo[i]) fvtk.add(r, fvtk.line(all_shift, colors, linewidth=1.)) fvtk.add(r, fvtk.line(all_shift2, colors2, linewidth=2.)) """ .. figure:: visualize_cross1000000.png :align: center **The crossings of a region of interest shown with one color, or boy2rgb or standard orient2rgb colormap**. .. include:: ../links_names.inc """
dcross_shift=[c+np.array([3,8,6]) for c in dcross] fvtk.add(r,fvtk.line(no_cross_shift,fvtk.blue,linewidth=5.)) fvtk.add(r,fvtk.line(cross_shift,fvtk.indigo,linewidth=5.)) fvtk.add(r,fvtk.line(dcross_shift,fvtk.red,linewidth=5.)) from dipy.viz import colormap as cm all_shift=[c+np.array([10,0,0]) for c in all] all_shift2=[c+np.array([20,0,0]) for c in all] colors=np.zeros((len(all),3)) colors2=np.zeros((len(all),3)) for (i,a) in enumerate(all): #print a[0] colors[i]=cm.boys2rgb(allo[i]) colors2[i]=cm.orient2rgb(allo[i]) fvtk.add(r,fvtk.line(all_shift,colors,linewidth=1.)) fvtk.add(r,fvtk.line(all_shift2,colors2,linewidth=2.)) """ .. figure:: visualize_cross1000000.png :align: center **The crossings of a region of interest shown with one color, or boy2rgb or standard orient2rgb colormap**. .. include:: ../links_names.inc
#3,8,6 double crossing dcross=fvtk.crossing(QA[3,8,6],IN[3,8,6],verts,1) all=fvtk.crossing(QA,IN,verts,1) fvtk.add(r,fvtk.line(all,fvtk.azure,linewidth=1.)) no_cross_shift=[c+np.array([3,8,4]) for c in no_cross] cross_shift=[c+np.array([3,8,5]) for c in cross] dcross_shift=[c+np.array([3,8,6]) for c in dcross] fvtk.add(r,fvtk.line(no_cross_shift,fvtk.blue,linewidth=5.)) fvtk.add(r,fvtk.line(cross_shift,fvtk.indigo,linewidth=5.)) fvtk.add(r,fvtk.line(dcross_shift,fvtk.red,linewidth=5.)) from dipy.viz import colormap as cm all_shift=[c+np.array([10,0,0]) for c in all] all_shift2=[c+np.array([20,0,0]) for c in all] colors=np.zeros((len(all),3)) colors2=np.zeros((len(all),3)) for (i,a) in enumerate(all): #print a[0] colors[i]=cm.boys2rgb(a[0]) colors2[i]=cm.orient2rgb(a[0]) fvtk.add(r,fvtk.line(all_shift,colors,linewidth=1.)) fvtk.add(r,fvtk.line(all_shift2,colors2,linewidth=2.)) fvtk.show(r)