def see_spherical_intersections(fdpy,fsr):
dpr=Dpy(fdpy,'r')
T=dpr.read_tracks()
dpr.close()
SR=load_pickle(fsr)
r=fvtk.ren()
for key in SR:
ind=SR[key]['indices']
intersT=[T[i] for i in ind]
fvtk.add(r,fvtk.line(intersT,np.random.rand(3)))
centerw=SR[key]['centerw']
radius=SR[key]['radiusw']
fvtk.add(r,fvtk.sphere(position=centerw,radius=radius))
fvtk.show(r)
mapping12_best = load_pickle(map_best_fn)
mapping12_coregistration_1nn = load_pickle(map_1nn_fn)
mapped_tract = extract_mapped_tract(s_idx, tractography2, mapping12_best)#[:-num_pro])
ROIs = ROIs_subject[t_sub]
#only for converting from LPS to LAS
#ROIs = [[r[0],128.-r[1],r[2]] for r in ROIs]
common = intersec_ROIs(mapped_tract, ROIs, Rs, vis=True)
print "\t The number of fibers through the ROIs ", len(common)
#print "Done evaluate using ROIs"
#visualize target cst and mapped source cst - yellow and blue
if (args.inputVisualize==1):
ren1 = fvtk.ren()
#target_cst_only = load_tract_trk(t_file,t_cst)
target_cst_only = load_tract(t_file,t_cst)
ren1 = visualize_tract(ren1, target_cst_only, fvtk.yellow)
#ren1 = visualize_mapped(ren1, tractography2, mapping12_best[:- num_pro], fvtk.blue)
ren1 = visualize_mapped(ren1, tractography2, mapping12_best[:-50], fvtk.blue)
fvtk.add(ren1, fvtk.sphere(ROIs[0],Rs[0],color = fvtk.red, opacity=1.0))
fvtk.add(ren1, fvtk.sphere(ROIs[1],Rs[1],color = fvtk.blue, opacity=1.0))
fvtk.show(ren1)
#s_tracts = '/home/bao/tiensy/Tractography_Mapping/data/' + source + '_tracks_dti_3M_linear.dpy'
s_tracts = '/home/bao/tiensy/Tractography_Mapping/data/' + source + '_tracks_dti_3M.dpy'
s_idx = '/home/bao/tiensy/Tractography_Mapping/data/' + source + '_corticospinal_L_3M.pkl'
#s_cst = load_tract_trk(s_tracts,s_idx)
s_cst = load_tract(s_tracts,s_idx)
#t_tracts = '/home/bao/tiensy/Tractography_Mapping/data/' + target + '_tracks_dti_3M_linear.dpy'
t_tracts = '/home/bao/tiensy/Tractography_Mapping/data/' + target + '_tracks_dti_3M.dpy'
t_idx = '/home/bao/tiensy/Tractography_Mapping/data/' + target + '_corticospinal_L_3M.pkl'
#t_cst = load_tract_trk(t_tracts,t_idx)
t_cst = load_tract(t_tracts,t_idx)
print d1, sphere_inter_1, d2, sphere_inter_2
ren = fvtk.ren()
ren = visualize_tract(ren,s_cst,fvtk.red)
fvtk.add(ren, fvtk.sphere(s_ROIs[0],Rs[0],color = fvtk.yellow, opacity=1.0))
fvtk.add(ren, fvtk.sphere(s_ROIs[1],Rs[1],color = fvtk.white, opacity=1.0))
ren = visualize_tract(ren, t_cst, fvtk.blue)
fvtk.add(ren, fvtk.sphere(t_ROIs[0],Rs[0],color = fvtk.blue, opacity=1.0))
fvtk.add(ren, fvtk.sphere(t_ROIs[1],Rs[1],color = fvtk.blue, opacity=1.0))
fvtk.show(ren)
else:
print ' '
#print np.array(dis_1,dtype=np.float)
#print np.array(intersec_1,dtype=np.float)
#print np.array(dis_2,dtype=np.float)
#print np.array(intersec_2,dtype=np.float)
#print dis_1
#print intersec_1
#print dis_2
#print intersec_2