def show_simulated_multiple_crossings(): ''' S=np.array([[-1,0,0],[0,1,0],[0,0,1]]) #T=np.array([[1,0,0],[0,0,]]) T=np.array([[1,0,0],[-0.76672114, 0.26105963, -0.58650369]]) print 'yo ',compare_orientation_sets(S,T) ''' btable=np.loadtxt(get_data('dsi515btable')) bvals=btable[:,0] bvecs=btable[:,1:] """ path='/home/eg309/Data/PROC_MR10032/subj_03/101_32/1312211075232351192010121313490254679236085ep2dadvdiffDSI10125x25x25STs004a001' #path='/home/eg309/Data/101_32/1312211075232351192010121313490254679236085ep2dadvdiffDSI10125x25x25STs004a001' bvals=np.loadtxt(path+'.bval') bvecs=np.loadtxt(path+'.bvec').T bvals=np.append(bvals.copy(),bvals[1:].copy()) bvecs=np.append(bvecs.copy(),-bvecs[1:].copy(),axis=0) """ #bvals=np.load('/tmp/bvals.npy') #bvecs=np.load('/tmp/bvecs.npy') #data=create_data(bvals,bvecs,d=0.00075,S0=100,snr=None) #dvals=[0.0003, 0.0006, 0.0012, 0.0024, 0.0048] dvals=[0.0003, 0.0005, 0.0010, 0.0015, 0.0020, 0.0025, 0.0030] data = multi_d_isotropic_data(bvals,bvecs,dvals=dvals,S0=100,snr=None) dn=DiffusionNabla(data,bvals,bvecs,odf_sphere='symmetric362', auto=False,save_odfs=True,fast=False,rotation=None) #rotation=np.array([[0,0,1],[np.sqrt(0.5),np.sqrt(0.5),0.],[np.sqrt(0.5),-np.sqrt(0.5),0.]]) dn.peak_thr=.4 dn.iso_thr=.05 dn.radius=np.arange(0,6,0.2) dn.radiusn=len(dn.radius) dn.create_qspace(bvals,bvecs,16,8) dn.radon_params(64) dn.precompute_interp_coords() dn.precompute_fast_coords() dn.precompute_equator_indices(5.) dn.precompute_angular(0.01) dn.fit() ''' ds=DiffusionSpectrum(data,bvals,bvecs,odf_sphere='symmetric642',auto=True,save_odfs=True) gq=GeneralizedQSampling(data,bvals,bvecs,1.2,odf_sphere='symmetric642',squared=False,auto=False,save_odfs=True) gq.peak_thr=.6 gq.iso_thr=.7 gq.fit() gq2=GeneralizedQSampling(data,bvals,bvecs,2.,odf_sphere='symmetric642',squared=True,auto=False,save_odfs=True) gq2.peak_thr=.6 gq2.iso_thr=.7 gq2.fit() ''' dn_odfs=dn.odfs() #blobs=np.zeros((1,19,4,dn.odfn)) blobs=np.zeros((1,len(dvals),1,dn.odfn)) #blobs=np.zeros((1,19,1,dn.odfn)) #blobs[0,:,0]=dn.odfs() for i,d in enumerate(dvals): blobs[0,i,0]=dn.ODF[i]/dn.ODF[i].mean() ''' blobs[0,:,1]=ds.odfs() blobs[0,:,2]=gq.odfs() gq2odfs=gq2.odfs() gq2odfs[gq2odfs<0]=0 print 'gq2',gq2odfs.min(),gq2odfs.max() blobs[0,:,3]=gq2odfs ''' ''' peaknos=np.array([0,1,2,3,3,3,3,3,3,2,2,1,1,2,3,0,3,3,3]) print peaknos print np.sum(dn.pk()>0,axis=1),np.sum(np.sum(dn.pk()>0,axis=1)-peaknos),len(peaknos) ''' ''' print np.sum(ds.qa()>0,axis=1),np.sum(np.sum(ds.qa()>0,axis=1)-peaknos),len(peaknos) print np.sum(gq.qa()>0,axis=1),np.sum(np.sum(gq.qa()>0,axis=1)-peaknos),len(peaknos) print np.sum(gq2.qa()>0,axis=1),np.sum(np.sum(gq2.qa()>0,axis=1)-peaknos),len(peaknos) ''' show_blobs(blobs,dn.odf_vertices,dn.odf_faces,colormap='jet') for i, d in enumerate(dvals): m = dn.ODF[i].min() M = dn.ODF[i].max() vM = np.argmax(dn.ODF[i]) print i, d, 50*(M-m)/(M+m), dn.odf_vertices[vM] #odf=dn.fast_odf(data[0]) #r=fvtk.ren() #fvtk.add(r,fvtk.volume(dn.Eq)) #fvtk.show(r) """ blobs2=np.zeros((1,1,3,dn.odfn)) blobs2[0,:,0]=dn.log_fast_odf(data[15]) blobs2[0,:,1]=dn.fast_odf(data[15]) blobs2[0,:,2]=dn.log_slow_odf(data[15]) show_blobs(blobs2,dn.odf_vertices,dn.odf_faces) e=data[15]/data[15,0] ne=np.sqrt(-np.log(e)) norm=np.sum(dn.qtable**2,axis=1) """ """
def show_simulated_2fiber_crossings(): btable=np.loadtxt(get_data('dsi515btable')) bvals=btable[:,0] bvecs=btable[:,1:] data=create_data_2fibers(bvals,bvecs,d=0.0015,S0=100,angles=np.arange(0,47,5),snr=None) #data=create_data_2fibers(bvals,bvecs,d=0.0015,S0=100,angles=np.arange(0,92,5),snr=None) print data.shape #stop #""" dn=DiffusionNabla(data,bvals,bvecs,odf_sphere='symmetric642', auto=False,save_odfs=True,fast=True) dn.peak_thr=.4 dn.iso_thr=.05 dn.radius=np.arange(0,5,0.1) dn.radiusn=len(dn.radius) dn.create_qspace(bvals,bvecs,16,8) dn.radon_params(64) dn.precompute_interp_coords() dn.precompute_fast_coords() dn.precompute_equator_indices(5.) dn.precompute_angular(None)#0.01) dn.fit() dn2=DiffusionNabla(data,bvals,bvecs,odf_sphere='symmetric642', auto=False,save_odfs=True,fast=False) dn2.peak_thr=.4 dn2.iso_thr=.05 dn2.radius=np.arange(0,5,0.1) dn2.radiusn=len(dn.radius) dn2.create_qspace(bvals,bvecs,16,8) dn2.radon_params(64) dn2.precompute_interp_coords() dn2.precompute_fast_coords() dn2.precompute_equator_indices(5.) dn2.precompute_angular(None)#0.01) dn2.fit() #""" eis=EquatorialInversion(data,bvals,bvecs,odf_sphere='symmetric642', auto=False,save_odfs=True,fast=True) #eis.radius=np.arange(0,6,0.2) eis.radius=np.arange(0,5,0.1) eis.gaussian_weight=None eis.set_operator('signal')#'laplap') eis.update() eis.fit() eil=EquatorialInversion(data,bvals,bvecs,odf_sphere='symmetric642', auto=False,save_odfs=True,fast=True) #eil.radius=np.arange(0,6,0.2) eil.radius=np.arange(0,5,0.1) eil.gaussian_weight=None eil.set_operator('laplacian')#'laplap') eil.update() eil.fit() eil2=EquatorialInversion(data,bvals,bvecs,odf_sphere='symmetric642', auto=False,save_odfs=True,fast=True) #eil2.radius=np.arange(0,6,0.2) eil2.radius=np.arange(0,5,0.1) eil2.gaussian_weight=None eil2.set_operator('laplap') eil2.update() eil2.fit() ds=DiffusionSpectrum(data,bvals,bvecs,odf_sphere='symmetric642',auto=True,save_odfs=True) gq=GeneralizedQSampling(data,bvals,bvecs,1.2,odf_sphere='symmetric642',squared=False,auto=False,save_odfs=True) gq.fit() gq2=GeneralizedQSampling(data,bvals,bvecs,3.,odf_sphere='symmetric642',squared=True,auto=False,save_odfs=True) gq2.fit() #blobs=np.zeros((19,1,8,dn.odfn)) blobs=np.zeros((10,1,6,dn.odfn)) """ blobs[:,0,0]=dn.odfs() blobs[:,0,1]=dn2.odfs() blobs[:,0,2]=eis.odfs() blobs[:,0,3]=eil.odfs() blobs[:,0,4]=eil2.odfs() blobs[:,0,5]=ds.odfs() blobs[:,0,6]=gq.odfs() blobs[:,0,7]=gq2.odfs() """ blobs[:,0,0]=dn2.odfs() blobs[:,0,1]=eil.odfs() eo=eil2.odfs() #eo[eo<0.05*eo.max()]=0 blobs[:,0,2]=eo blobs[:,0,3]=ds.odfs() blobs[:,0,4]=gq.odfs() blobs[:,0,5]=gq2.odfs() show_blobs(blobs,dn.odf_vertices,dn.odf_faces,scale=0.5)
dvals=[0.0003, 0.0005, 0.0010, 0.0015, 0.0020, 0.0025, 0.0030] data = multi_d_isotropic_data(bvals,bvecs,dvals=dvals,S0=100,snr=None) dn=DiffusionNabla(data,bvals,bvecs,odf_sphere='symmetric362', auto=False,save_odfs=True,fast=False,rotation=None) #rotation=np.array([[0,0,1],[np.sqrt(0.5),np.sqrt(0.5),0.],[np.sqrt(0.5),-np.sqrt(0.5),0.]]) dn.peak_thr=.4 dn.iso_thr=.05 dn.radius=np.arange(0,6,0.2) dn.radiusn=len(dn.radius) dn.create_qspace(bvals,bvecs,16,8) dn.radon_params(64) dn.precompute_interp_coords() dn.precompute_fast_coords() dn.precompute_equator_indices(5.) dn.precompute_angular(0.01) dn.fit() ''' ds=DiffusionSpectrum(data,bvals,bvecs,odf_sphere='symmetric642',auto=True,save_odfs=True) gq=GeneralizedQSampling(data,bvals,bvecs,1.2,odf_sphere='symmetric642',squared=False,auto=False,save_odfs=True) gq.peak_thr=.6 gq.iso_thr=.7 gq.fit() gq2=GeneralizedQSampling(data,bvals,bvecs,20,odf_sphere='symmetric642',squared=True,auto=False,save_odfs=True) gq2.peak_thr=.6 gq2.iso_thr=.7 gq2.fit()