def skeletonize(fdpy,flsc,points=3):
dpr=Dpy(fdpy,'r')
T=dpr.read_tracks()
dpr.close()
print len(T)
Td=[downsample(t,points) for t in T]
C=local_skeleton_clustering(Td,d_thr=10.,points=points)
#Tobject=np.array(T,dtype=np.object)
#'''
#r=fvtk.ren()
skeleton=[]
for c in C:
#color=np.random.rand(3)
if C[c]['N']>0:
Ttmp=[]
for i in C[c]['indices']:
Ttmp.append(T[i])
si,s=most_similar_track_mam(Ttmp,'avg')
print si,C[c]['N']
C[c]['most']=Ttmp[si]
#fvtk.add(r,fvtk.line(Ttmp[si],color))
print len(skeleton)
#r=fos.ren()
#fos.add(r,fos.line(skeleton,color))
#fos.add(r,fos.line(T,fos.red))
#fvtk.show(r)
#'''
save_pickle(flsc,C)
def spherical_rois(fdpy,fsr,sq_radius=4):
R=atlantic_points()
dpr=Dpy(fdpy,'r')
T=dpr.read_tracks()
dpr.close()
center=R['BCC']
refimg=nib.load(fref)
aff=refimg.get_affine()
SR={}
for key in R:
center=R[key]
#back to world space
centerw=np.dot(aff,np.array(center+(1,)))[:3]
centerw.shape=(1,)+centerw.shape
centerw=centerw.astype(np.float32)
res= [track_roi_intersection_check(t,centerw,sq_radius) for t in T]
res= np.array(res,dtype=np.int)
ind=np.where(res>0)[0]
SR[key]={}
SR[key]['center']=center
SR[key]['centerw']=tuple(np.squeeze(centerw))
SR[key]['radiusw']=np.sqrt(sq_radius)
SR[key]['indices']=ind
save_pickle(fsr,SR)
def bloat_bundle(self,tracks):
tracksn=[]
#c=np.array([0,0,0],np.float32)
import dipy.core.track_performance as pf
#c=tracks[0][-4]
ct=tracks[pf.most_similar_track_mam(tracks,'avg')[0]]
c=ct[len(ct)/2]
#tracks2=[tm.downsample(t,200) for t in tracks]
for X in tracks2:
Xn = X + np.multiply(10/np.sum((X-c)**2,axis=1).reshape(len(X),1),X-c)
#Xn = X + 2*(X-c)
tracksn.append(Xn)
from dipy.io import pickles as pkl
pkl.save_pickle('bundles.pkl',{'init':tracks[10],'after':tracksn[10]})
return tracksn
def a_few_phantoms():
#fibres_1_SNR_100_angle_00_l1_1.4_l2_0.35_l3_0.35_iso_0_diso_00
table={}
#sd=['fibres_1_SNR_60_angle_00_l1_1.4_l2_0.35_l3_0.35_iso_0_diso_00']
#sd=['fibres_1_SNR_20_angle_00_l1_1.4_l2_0.35_l3_0.35_iso_0_diso_00']
sd=['fibres_2_SNR_100_angle_90_l1_1.4_l2_0.35_l3_0.35_iso_0_diso_00']
#for simfile in simdata:
for simfile in sd:
data=np.loadtxt(simdir+simfile)
sf=simfile.split('_')
print sf
print sf[1],sf[3],sf[5],sf[7],sf[9],sf[11],sf[13],sf[15]
b_vals_dirs=np.loadtxt(simdir+'Dir_and_bvals_DSI_marta.txt')
bvals=b_vals_dirs[:,0]*1000
gradients=b_vals_dirs[:,1:]
data2=data[::1000,:]
table={'fibres':sf[1],'snr':sf[3],'angle':sf[5],'l1':sf[7],'l2':sf[9],\
'l3':sf[11],'iso':sf[13],'diso':sf[15],\
'data':data2,'bvals':bvals,'gradients':gradients}
#print table
print table['data'].shape
pkl.save_pickle('test0.pkl',table)
break
def gq_tn_calc_save():
for simfile in simdata:
dataname = simfile
print dataname
sim_data=np.loadtxt(simdir+dataname)
marta_table_fname='/home/ian/Data/SimData/Dir_and_bvals_DSI_marta.txt'
b_vals_dirs=np.loadtxt(marta_table_fname)
bvals=b_vals_dirs[:,0]*1000
gradients=b_vals_dirs[:,1:]
gq = dgqs.GeneralizedQSampling(sim_data,bvals,gradients)
gqfile = simdir+'gq/'+dataname+'.pkl'
pkl.save_pickle(gqfile,gq)
'''
gq.IN gq.__doc__ gq.glob_norm_param
gq.QA gq.__init__ gq.odf
gq.__class__ gq.__module__ gq.q2odf_params
'''
tn = ddti.Tensor(sim_data,bvals,gradients)
tnfile = simdir+'tn/'+dataname+'.pkl'
pkl.save_pickle(tnfile,tn)
'''
tn.ADC tn.__init__ tn._getevals
tn.B tn.__module__ tn._getevecs
tn.D tn.__new__ tn._getndim
tn.FA tn.__reduce__ tn._getshape
tn.IN tn.__reduce_ex__ tn._setevals
tn.MD tn.__repr__ tn._setevecs
tn.__class__ tn.__setattr__ tn.adc
tn.__delattr__ tn.__sizeof__ tn.evals
tn.__dict__ tn.__str__ tn.evecs
tn.__doc__ tn.__subclasshook__ tn.fa
tn.__format__ tn.__weakref__ tn.md
tn.__getattribute__ tn._evals tn.ndim
tn.__getitem__ tn._evecs tn.shape
tn.__hash__ tn._getD
'''
''' file has one row for every voxel, every voxel is repeating 1000
def gq_tn_calc_save():
for simfile in simdata:
dataname = simfile
print dataname
sim_data=np.loadtxt(simdir+dataname)
marta_table_fname='/home/ian/Data/SimData/Dir_and_bvals_DSI_marta.txt'
b_vals_dirs=np.loadtxt(marta_table_fname)
bvals=b_vals_dirs[:,0]*1000
gradients=b_vals_dirs[:,1:]
gq = dp.GeneralizedQSampling(sim_data,bvals,gradients)
gqfile = simdir+'gq/'+dataname+'.pkl'
pkl.save_pickle(gqfile,gq)
'''
gq.IN gq.__doc__ gq.glob_norm_param
gq.QA gq.__init__ gq.odf
gq.__class__ gq.__module__ gq.q2odf_params
'''
tn = dp.Tensor(sim_data,bvals,gradients)
tnfile = simdir+'tn/'+dataname+'.pkl'
pkl.save_pickle(tnfile,tn)
'''
tn.ADC tn.__init__ tn._getevals
tn.B tn.__module__ tn._getevecs
tn.D tn.__new__ tn._getndim
tn.FA tn.__reduce__ tn._getshape
tn.IN tn.__reduce_ex__ tn._setevals
tn.MD tn.__repr__ tn._setevecs
tn.__class__ tn.__setattr__ tn.adc
tn.__delattr__ tn.__sizeof__ tn.evals
tn.__dict__ tn.__str__ tn.evecs
tn.__doc__ tn.__subclasshook__ tn.fa
tn.__format__ tn.__weakref__ tn.md
tn.__getattribute__ tn._evals tn.ndim
tn.__getitem__ tn._evecs tn.shape
tn.__hash__ tn._getD
'''
''' file has one row for every voxel, every voxel is repeating 1000
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='Given the DWI data, the corresponding b-value and b-vecs files\n\
and the type of fODF model. This scripts\n\
computes the fODF for every voxel.'
)
parser.add_argument('-d', '--dwi', required=True, metavar='<dwi>',
help='Path to the diffusion weighted image file (4D in NIFTI format).')
parser.add_argument('-bvals', required=True, metavar='<bvals>',
help='Path to the b-value file (FSL format).')
parser.add_argument('-bvecs', required=True, metavar='<bvecs>',
help='Path to the b-vectors file (FSL format).')
parser.add_argument('-m','--mask', metavar='<mask_file>',
help='Path to the brain mask file.')
parser.add_argument('-t', '--type', metavar='<type>', default='dti', choices=['dti','csd','csa'],
help='The type of the fODF model (default dti).')
parser.add_argument('-b0', metavar='<b0>', type=float, default=0.,
help='Threshold to use for defining b0 images.')
parser.add_argument('--order', type=int, metavar='<order>', default=4,
help='Order of fODF (not used for DTI).')
parser.add_argument('-o','--output', required=True, metavar='<output>',
help='Specifies the output file.')
#parse command line arguments
args = parser.parse_args()
#read DWI
img = nib.load(args.dwi)
data = img.get_data()
#read mask
if args.mask:
img = nib.load(args.mask)
mask = img.get_data().astype(bool)
mask = np.logical_not(mask)
#apply mask to data
data[mask,:] = 0
sys.stdout.write('Data read.\n')
start = time()
#fit the model
if args.mask:
model_fit = reconstruction(data, args.bvals, args.bvecs, mask=np.logical_not(mask), type=args.type, b0=args.b0, order=args.order)
else:
model_fit = reconstruction(data, args.bvals, args.bvecs, type=args.type, b0=args.b0, order=args.order)
sys.stdout.write('Fitted %s model with order %i in %.2f sec.\n' % (args.type,args.order,time()-start))
sys.stdout.flush()
#save the fODF fit, depends on chosen model
if args.type == 'dti':
save_pickle(args.output+'.fit',model_fit.model_params)
elif args.type == 'csd':
save_pickle(args.output+'.fit',model_fit.fit_array)
elif args.type == 'csa':
save_pickle(args.output+'.fit',model_fit.shm_coeff)
#save the model
save_pickle(args.output+'.model',model_fit.model)
def plot_timings():
#dir='/home/eg309/Data/LSC_limits/full_1M'
dir='/tmp/full_1M'
fs=['.npy','_2.npy','_3.npy','_4.npy','_5.npy']#,'_6.npy','_7.npy','_8.npy','_9.npy','_10.npy']
T=[]
for f in fs:
fs1=dir+f
T+=change_dtype(list(np.load(fs1)))
#return T
T=T[:100000]
print len(T)
#dists=[4.,6.,8.,10.]
dists=[8.]
#pts=[3,6,12,18]
pts=[12]
#sub=10**5
sub=10**3
res={}
for p in pts:
print p
res[p]={}
for d in dists:
print d
res[p][d]={}
res[p][d]['time']=[]
res[p][d]['len']=[]
step=0
while step <= len(T):
print step
Td=[downsample(t,p) for t in T[0:step+sub]]
t1=time()
C=local_skeleton_clustering(Td,d)
t2=time()
res[p][d]['time'].append(t2-t1)
res[p][d]['len'].append(len(C))
step=step+sub
save_pickle('/tmp/res.pkl',res)
print('Result saved in /tmp/res.pkl')
#return res
save_pickle('/tmp/res.pkl',res)
def gq_tn_calc_save():
for simfile in simdata:
dataname = simfile
print dataname
sim_data=np.loadtxt(simdir+dataname)
marta_table_fname=simdir+'Dir_and_bvals_DSI_marta.txt'
b_vals_dirs=np.loadtxt(marta_table_fname)
bvals=b_vals_dirs[:,0]*1000
gradients=b_vals_dirs[:,1:]
gq = GeneralizedQSampling(sim_data,bvals,gradients)
gqfile = '/tmp/gq'+dataname+'.pkl'
pkl.save_pickle(gqfile,gq)
tn = Tensor(sim_data,bvals,gradients)
tnfile = '/tmp/tn'+dataname+'.pkl'
pkl.save_pickle(tnfile,tn)
''' file has one row for every voxel, every voxel is repeating 1000
def training_check(dres, prefix):
seeds_per_vox = 5
num_of_cpus = 6
cmd = 'python ~/Devel/scilpy/scripts/stream_local.py -odf ' + dres + prefix + 'odf_sh.nii.gz -m data/training-data_mask.nii.gz -s data/training-data_rois.nii.gz -n -' + str(
seeds_per_vox) + ' -process ' + str(num_of_cpus) + ' -o ' + dres + prefix + 'streams.trk'
pipe(cmd)
mat, conn_mats, diffs, ratio = streams_to_connmat(dres + prefix + 'streams.trk', seeds_per_vox)
save_pickle(dres + prefix + 'conn_mats.pkl', {'mat': mat, 'conn_mats': conn_mats, 'diffs': diffs, 'ratio':ratio})
print dres + prefix + 'conn_mats.pkl'
return diffs
def load_pbc_data(id=None):
if id is None:
path = "/home/eg309/Data/PBC/pbc2009icdm/brain1/"
streams, hdr = tv.read(path + "brain1_scan1_fiber_track_mni.trk")
streamlines = [s[0] for s in streams]
return streamlines
if not osp.exists("/tmp/" + str(id) + ".pkl"):
path = "/home/eg309/Data/PBC/pbc2009icdm/brain1/"
streams, hdr = tv.read(path + "brain1_scan1_fiber_track_mni.trk")
streamlines = [s[0] for s in streams]
labels = np.loadtxt(path + "brain1_scan1_fiber_labels.txt")
labels = labels[:, 1]
mask_cst = labels == id
cst_streamlines = [s for (i, s) in enumerate(streamlines) if mask_cst[i]]
save_pickle("/tmp/" + str(id) + ".pkl", cst_streamlines)
return cst_streamlines
# return [approx_polygon_track(s, 0.7853) for s in cst_streamlines]
else:
return load_pickle("/tmp/" + str(id) + ".pkl")
def generate_skeletons():
img=nib.load(fbet)
data=img.get_data()
affine=img.get_affine()
bvals=np.loadtxt(fbvals)
bvecs=np.loadtxt(fbvecs).T
t=time()
gqs=GeneralizedQSampling(data,bvals,bvecs)
print 'gqs time',time()-t,'s'
for (i,sds) in enumerate(seeds):
print i,sds
t=time()
eu=EuDX(gqs.qa(),gqs.ind(),seeds=sds,a_low=0.0239)
T=[downsample(e,12) for e in eu]
#np.save(dout+outs[i]+'.npy',np.array(T,dtype=np.object))
C=local_skeleton_clustering(T,4.)
save_pickle(dout+outs[i]+'.skl',C)
print time()-t
del T
print outs
def save_id_tract_plus_sff(tracks_filename, id_file, num_proto, distance, out_fname):
if (tracks_filename[-3:]=='dpy'):
dpr_tracks = Dpy(tracks_filename, 'r')
all_tracks=dpr_tracks.read_tracks()
dpr_tracks.close()
else:
all_tracks = load_whole_tract_trk(tracks_filename)
tracks_id = load_pickle(id_file)
tract = [all_tracks[i] for i in tracks_id]
not_tract_fil = []
id_not_tract_fil = []
min_len = min(len(i) for i in tract)
#print 'min_len of cst', min_len
min_len = min_len*2.2/3#2./3.2# - 20
for i in np.arange(len(all_tracks)):
if (i not in tracks_id) and (length(all_tracks[i]) > min_len):
not_tract_fil.append(all_tracks[i])
id_not_tract_fil.append(i)
not_tract_fil = np.array(not_tract_fil,dtype=np.object)
sff_pro_id = sff(not_tract_fil, num_proto, distance)
tract_sff_id = []
for i in tracks_id:
tract_sff_id.append(i)
for idx in sff_pro_id:
tract_sff_id.append(id_not_tract_fil[idx])
#tract_sff_id.append(id_not_tract_fil[i] for i in sff_pro_id)
print len(tract), len(tract_sff_id)
save_pickle(out_fname, tract_sff_id)
return tract_sff_id
def save_id_tract_plus_sff_in_ext(tracks_filename, id_file, num_proto, distance, out_fname_ext , out_fname_sff_in_ext, thres_len= 2.2/3., thres_vol = 1.4 , thres_dis = 3./2.):
tract_ext_id = save_id_tract_ext1(tracks_filename,id_file, distance, out_fname_ext, thres_len, thres_vol , thres_dis)
if (tracks_filename[-3:]=='dpy'):
dpr_tracks = Dpy(tracks_filename, 'r')
all_tracks=dpr_tracks.read_tracks()
dpr_tracks.close()
else:
all_tracks = load_whole_tract_trk(tracks_filename)
tracks_id = load_pickle(id_file)
ext_not_tract_id = []
ext_not_tract = []
for idx in tract_ext_id:
if idx not in tracks_id:
ext_not_tract.append(all_tracks[idx])
ext_not_tract_id.append(idx)
ext_not_tract = np.array(ext_not_tract,dtype=np.object)
sff_pro_id = sff(ext_not_tract, num_proto, distance)
tract_sff_in_ext_id = []
for i in tracks_id:
tract_sff_in_ext_id.append(i)
for k in sff_pro_id:
tract_sff_in_ext_id.append(ext_not_tract_id[k])
#tract_sff_id.append(id_not_tract_fil[i] for i in sff_pro_id)
print len(tracks_id), len(tract_sff_in_ext_id), len(tract_ext_id)
save_pickle( out_fname_sff_in_ext, tract_sff_in_ext_id)
return tract_sff_in_ext_id
def multiple_comparisons(T,samplesize = 10**4, lscdist = 4., replications = 2,subj='1'):
labels1 = np.random.permutation(np.arange(len(T)))[:samplesize]
#labels1 = np.arange(0*samplesize,1*samplesize)
T1=T[labels1]
print 'Number of tracks is %d' % (len(T1))
lists = {}
C = {}
results = {}
C_size = {}
for replication in np.arange(replications):
print '... preparing LSC(%d)' % (replication)
rearrangement = np.random.permutation(np.arange(samplesize))
#print '... min %d, max %d, len %d' % (np.min(rearrangement), np.max(rearrangement), len(rearrangement))
rearrangement = list(rearrangement)
C[replication] = local_skeleton_clustering(T1[rearrangement],lscdist)
print '... skeleton size %d' % (len(C[replication]))
lists[replication] = rearrangement
C_size[replication] = len(C[replication])
save_pickle('labels'+str(samplesize)+'_'+subj+'.pkl',labels1)
save_pickle('C'+str(samplesize)+'_'+subj+'.pkl',C)
save_pickle('lists'+str(samplesize)+'_'+subj+'.pkl',lists)
save_pickle('C_size'+str(samplesize)+'_'+subj+'.pkl',C_size)
for rep1 in np.arange(replications-1):
for rep2 in np.arange(rep1+1,replications):
#report_comparisons(C[rep1],lists[rep1],C[rep2],lists[rep2])
print 'comparing %d and %d' % (rep1,rep2)
results[(rep1,rep2)] = return_comparisons(C[rep1],lists[rep1],C[rep2],lists[rep2])
'''
labels2 = np.arange(1*samplesize,2*samplesize)
T2=T[labels2]
list21 = np.random.permutation(np.arange(samplesize))
C21=local_skeleton_clustering(T2[list21],lscdist)
list22 = np.random.permutation(np.arange(samplesize))
C22=local_skeleton_clustering(T2[list22],lscdist)
'''
#print 'C11 vs C12'
'''
print 'C21 vs C22'
report_comparisons(C21,list21,C22,list22)
'''
return results
print base_dir + "../MPRAGE_1/T1_flirt_out.nii.gz"
img = nib.load(base_dir + "../MPRAGE_1/T1_flirt_out.nii.gz")
data = img.get_data()
for i in range(len(tracks_filename_arr)):
print ">>>>"
print base_dir2 + tracks_filename_arr[i]
tracks = load_tracks(base_dir2 + tracks_filename_arr[i])
print len(tracks)
# tracks = [downsample(t, 12) - np.array(data.shape[:3])/2. for t in tracks]
tracks = [downsample(t, 12) - np.array(data.shape) / 2.0 for t in tracks]
# shift in the center of the volume
# tracks=[t-np.array(data.shape)/2. for t in tracks]
# 1/0
print base_dir2 + qb_filename_15[i]
qb = QuickBundles(tracks, 15.0, 12)
save_pickle(base_dir2 + qb_filename_15[i], qb)
print base_dir2 + qb_filename_20[i]
qb = QuickBundles(tracks, 20.0, 12)
save_pickle(base_dir2 + qb_filename_20[i], qb)
print base_dir2 + qb_filename_30[i]
qb = QuickBundles(tracks, 30.0, 12)
save_pickle(base_dir2 + qb_filename_30[i], qb)
# ================ quick bundles ==============================================
print ("Done")
print (linear_filename)
# stop
scene.SetBackground(1, 1, 1)
scene.add(actor.streamtube(streamlines, window.colors.white))
window.record(scene, out_path=outpath + 'fornix_initial.png', size=(600, 600))
if interactive:
window.show(scene)
colormap = actor.create_colormap(np.arange(len(clusters)))
scene.clear()
scene.SetBackground(1, 1, 1)
scene.add(actor.streamtube(streamlines, window.colors.white, opacity=0.05))
scene.add(actor.streamtube(clusters.centroids, colormap, linewidth=0.4))
window.record(scene,
out_path=outpath + 'fornix_centroids.png',
size=(600, 600))
if interactive:
window.show(scene)
colormap_full = np.ones((len(streamlines), 3))
for cluster, color in zip(clusters, colormap):
colormap_full[cluster.indices] = color
scene.clear()
scene.SetBackground(1, 1, 1)
scene.add(actor.streamtube(streamlines, colormap_full))
window.record(scene, out_path=outpath + 'fornix_clusters.png', size=(600, 600))
if interactive:
window.show(scene)
save_pickle(outpath + 'QB.pkl', clusters)
fvtk.label(r, text=str(len(bundle)), pos=(bundle[si][-1]), scale=(2, 2, 2))
fvtk.add(r, fvtk.line(skeleton, colors, opacity=1))
#fvtk.show(r)
fvtk.record(r, n_frames=1, out_path='fornix_most', size=(600, 600))
"""
.. figure:: fornix_most1000000.png
:align: center
**Showing skeleton with the most representative tracks as the skeletal representation**.
The numbers are depicting the number of tracks in each cluster. This is a very compact way to see the underlying
structures an alternative would be to draw the representative tracks with different widths.
"""
"""
Save the skeleton information in the dictionary. Now try to play with different thresholds LSC and check the different results.
Try it with your datasets and gives us some feedback.
"""
for (i, c) in enumerate(C):
C[c]['most'] = skeleton[i]
for c in C:
print('Keys in bundle %d' % c)
print(C[c].keys())
print('Shape of skeletal track (%d, %d) ' % C[c]['most'].shape)
pkl.save_pickle('skeleton_fornix.pkl', C)
#tracks=tracks[:1000]
#print 'Deleting unnecessary data...'
del streams#,hdr
if not os.path.isfile(C_fname):
print 'Starting LARCH ...'
tim=time.clock()
C,atracks=tl.larch(tracks,[50.**2,20.**2,5.**2],True,True)
#tracks=[tm.downsample(t,3) for t in tracks]
#C=pf.local_skeleton_clustering(tracks,20.)
print 'Done in total of ',time.clock()-tim,'seconds.'
print 'Saving result...'
pkl.save_pickle(C_fname,C)
streams=[(i,None,None)for i in atracks]
tv.write(appr_fname,streams,hdr)
else:
print 'Loading result...'
C=pkl.load_pickle(C_fname)
skel=[]
for c in C:
skel.append(C[c]['repz'])
print 'Showing dataset after clustering...'
r=fos.ren()
def loss_function(mapping12):
"""Computes the loss function of a given mapping.
This is the 'energy_function' of simulated annealing.
"""
global dm1, dm2
loss = np.linalg.norm(dm1[np.triu_indices(size1)] - dm2[mapping12[:,None], mapping12][np.triu_indices(size1)])
return loss
#mapping12_coregistration_1nn, loss_coregistration_1nn, mapping12_best, energy_best = tracts_mapping1(tractography1, tractography2, loss_function,neighbour4, iterations_anneal, pre_map_fn)
mapping12_coregistration_1nn, loss_coregistration_1nn, mapping12_best, energy_best = tracts_mapping(tractography1, tractography2, loss_function,neighbour4, iterations_anneal)
print "Best enegery of annealing: ", energy_best
from dipy.io.pickles import save_pickle
save_pickle(map_best_fn,mapping12_best)
save_pickle(map_1nn_fn,mapping12_coregistration_1nn)
print 'Saved ', map_best_fn
print 'Saved ', map_1nn_fn
'''
#visualize source and mapped source - red and blue
ren3 = fvtk.ren()
ren3 = visualize_source_mappedsource(ren3, tractography1[:- num_pro], tractography2, mapping12_best[:-num_pro])
fvtk.show(ren3)
#visualize target cst and mapped source cst - yellow and blue
ren4 = fvtk.ren()
target_cst_only = load_tract(t_file,t_cst)
ren4 = visualize_tract(ren4, target_cst_only, fvtk.yellow)
ren4 = visualize_mapped(ren4, tractography2, mapping12_best[:- num_pro], fvtk.blue)
fvtk.show(ren4)
''' marta_table_fname = '/home/ian/Data/SimData/Dir_and_bvals_DSI_marta.txt' sim_data = np.loadtxt(fname) #bvalsf='/home/eg01/Data_Backup/Data/Marta/DSI/SimData/bvals101D_float.txt' b_vals_dirs = np.loadtxt(marta_table_fname) bvals = b_vals_dirs[:, 0] * 1000 gradients = b_vals_dirs[:, 1:] gq = dp.GeneralizedQSampling(sim_data, bvals, gradients) tn = dp.Tensor(sim_data, bvals, gradients) #''' gqfile = '/home/ian/Data/SimData/gq_SNR030_1fibre.pkl' pkl.save_pickle(gqfile, gq) tnfile = '/home/ian/Data/SimData/tn_SNR030_1fibre.pkl' pkl.save_pickle(tnfile, tn) ''' print tn.evals.shape print tn.evecs.shape evals=tn.evals[0] evecs=tn.evecs[0] print evecs.shape first_directions = tn.evecs[:,:,0] first1000 = first_directions[:1000,:] cross = np.dot(first1000.T,first1000) np.linalg.eig(cross)
img_mask = nib.load(brain_mask_file)
img, gtab = dwi.get_dwi_img_gtab(dwi_data_file, dwi_bval_file,
dwi_bvec_file)
data_mask = img_mask.get_data()
affine = img.get_affine()
data = img.get_data()
model = TensorModel(gtab)
ten = model.fit(data, mask=data_mask)
sphere = get_sphere('symmetric724')
ind = quantize_evecs(ten.evecs, sphere.vertices)
p = Struct()
p.affine = affine
p.sphere = sphere
p.ten = ten
p.ind = ind
return p
if __name__ == '__main__':
import sys
print(sys.argv)
if len(sys.argv) == 5:
brain_mask = sys.argv[1]
dwi_data = sys.argv[2]
dwi_bval = sys.argv[3]
dwi_bvec = sys.argv[4]
outp = track_gen_model(brain_mask, dwi_data, dwi_bval, dwi_bvec)
pickles.save_pickle('track_gen_model.pickle', outp)
for i in np.arange(size1):
print 'sum row ', i , np.sum(prb_map12[i,:])
#compare to mapping results
if t==0:
pre_map12 = np.copy(prb_map12_init)
norm = np.linalg.norm(prb_map12 - pre_map12)
print "Norm of results - with previous: ", norm
pre_map12 = np.copy(prb_map12)
#print L
plot_smooth(plt, np.arange(len(L)), L, False)
if save:
save_pickle(map_prob, prb_map12)
plt.title('Loss function ')
plt.xlabel('Gradient evaluations')
if save:
#plt.savefig(os.path.join(os.path.curdir, 'objective_function_'+ str(num_pro) + '_' + str(num_pro) + '_sparse_density_' + str(nearest) + '_neighbors.pdf'))
plt.savefig(obj_func_file)
plt.show()
#end of optimize with slsqp
for data_id in data_ids:
print 'Subject/Control: ', data_id
#data = load_data('big_dataset',data_id)
#X = compute_disimilarity(data, bundles_distances_mam, 'random', num_prototype,len(data))
#file_name_dis = 'Results/'+str(data_id)+'/'+str(data_id)+'_data_disimilarity_full_tracks_' + str(num_prototype) + '_prototyes_random_modified_ward_full_tree_130524.dis'
file_name_dis = 'Results/'+str(data_id)+'/'+str(data_id)+'_data_disimilarity_full_tracks_40_prototyes_random_130516.dis'
#save_pickle(file_name_dis,X)
#print 'Saving data_disimilarity: ',file_name_dis,' - done'
X = load_pickle(file_name_dis)
for num_neigh in num_neighbors:
print "\tGenerating at ", num_neigh, " neighbor"
file_name = str(data_id)+'_full_tracks_' + str(num_neigh) + '_neighbors_modified_ward_full_tree_130516_new.tree'
connectivity = kneighbors_graph(X, n_neighbors=num_neigh)
st = cpu_time()#time.clock()
ward = Ward(n_clusters=num_cluster, compute_full_tree=True, connectivity=connectivity).fit(X)
#t = time.clock() - st
t = cpu_time() - st
#-----------------------------------------------------------------------------
# saving the result
save_pickle(file_name,ward)
print '\tSaving tree: ',file_name,' - done'
''' marta_table_fname='/home/ian/Data/SimData/Dir_and_bvals_DSI_marta.txt' sim_data=np.loadtxt(fname) #bvalsf='/home/eg01/Data_Backup/Data/Marta/DSI/SimData/bvals101D_float.txt' b_vals_dirs=np.loadtxt(marta_table_fname) bvals=b_vals_dirs[:,0]*1000 gradients=b_vals_dirs[:,1:] gq = dp.GeneralizedQSampling(sim_data,bvals,gradients) tn = dp.Tensor(sim_data,bvals,gradients) #''' gqfile = '/home/ian/Data/SimData/gq_SNR030_1fibre.pkl' pkl.save_pickle(gqfile,gq) tnfile = '/home/ian/Data/SimData/tn_SNR030_1fibre.pkl' pkl.save_pickle(tnfile,tn) ''' print tn.evals.shape print tn.evecs.shape evals=tn.evals[0] evecs=tn.evecs[0] print evecs.shape first_directions = tn.evecs[:,:,0] first1000 = first_directions[:1000,:]
def save_id_tract_ext1(tracks_filename, id_file, distance, out_fname, thres_len= 2.2/3., thres_vol = 1.2 , thres_dis = 2.8/2.):
print thres_len, thres_vol, thres_dis
if (tracks_filename[-3:]=='dpy'):
dpr_tracks = Dpy(tracks_filename, 'r')
all_tracks=dpr_tracks.read_tracks()
dpr_tracks.close()
else:
all_tracks = load_whole_tract_trk(tracks_filename)
tracks_id = load_pickle(id_file)
tract = [all_tracks[i] for i in tracks_id]
not_tract_fil = []
id_not_tract_fil = []
min_len = min(len(i) for i in tract)
#print 'min_len of cst', min_len
min_len = min_len*thres_len
for i in np.arange(len(all_tracks)):
if (i not in tracks_id) and (length(all_tracks[i]) > min_len):
not_tract_fil.append(all_tracks[i])
id_not_tract_fil.append(i)
k = np.round(len(tract) * thres_vol )
from dipy.segment.quickbundles import QuickBundles
qb = QuickBundles(tract,200,18)
medoid_tract = qb.centroids[0]
med_nottract_dm = distance([medoid_tract], not_tract_fil)
med_tract_dm = distance([medoid_tract], tract)
tract_rad = med_tract_dm[0][np.argmax(med_tract_dm[0])]
len_dis = tract_rad * thres_dis# 2.8/2.
#k_indices which close to the medoid
sort = np.argsort(med_nottract_dm,axis = 1)[0]
#print sort[:k+1]
while (k>0 and med_nottract_dm[0][sort[k]]>=len_dis):
k = k - 1
#print k
close_indices = sort[0:k]
#for idx in close_indices:
# tract_ext.append(not_tract_fil[idx])
#print 'close indices', len(close_indices)
tract_ext_id = []
for i in tracks_id:
tract_ext_id.append(i)
#print 'Before', len(tract_ext_id)
for idx in close_indices:
tract_ext_id.append(id_not_tract_fil[idx])
# print idx, id_not_tract_fil[idx]
#print 'After', len(tract_ext_id)
#tract_ext_id = [i for i in tracks_id]
#tract_ext_id.append(id_not_tract_fil[i] for i in close_indices)
save_pickle(out_fname, tract_ext_id)
return tract_ext_id
"""
.. figure:: fornix_most1000000.png
:align: center
**Showing skeleton with the most representative tracks as the skeletal representation**.
The numbers are depicting the number of tracks in each cluster. This is a very compact way to see the underlying
structures an alternative would be to draw the representative tracks with different widths.
"""
"""
Save the skeleton information in the dictionary. Now try to play with different thresholds LSC and check the different results.
Try it with your datasets and gives us some feedback.
"""
for (i,c) in enumerate(C):
C[c]['most']=skeleton[i]
for c in C:
print('Keys in bundle %d' % c)
print(C[c].keys())
print('Shape of skeletal track (%d, %d) ' % C[c]['most'].shape)
pkl.save_pickle('skeleton_fornix.pkl',C)
"""
"""
Show the labeled *Fornix* (colors from centroids):
"""
colormap_full = np.ones((len(tracks), 3))
for i, centroid in enumerate(centroids):
inds=qb.label2tracksids(i)
colormap_full[inds]=colormap[i]
fvtk.add(r, fvtk.line(tracks, colormap_full, opacity=1., linewidth=3))
#fvtk.show(r)
fvtk.record(r,n_frames=1,out_path='fornix_clust',size=(600,600))
"""
.. figure:: fornix_clust1000000.png
:align: center
**Showing the different clusters with random colors**.
"""
"""
It is also possible to save the QuickBundles object with pickling.
"""
save_pickle('QB.pkl',qb)
#tracks=tracks[:1000]
#print 'Deleting unnecessary data...'
del streams #,hdr
if not os.path.isfile(C_fname):
print 'Starting LARCH ...'
tim = time.clock()
C, atracks = tl.larch(tracks, [50.**2, 20.**2, 5.**2], True, True)
#tracks=[tm.downsample(t,3) for t in tracks]
#C=pf.local_skeleton_clustering(tracks,20.)
print 'Done in total of ', time.clock() - tim, 'seconds.'
print 'Saving result...'
pkl.save_pickle(C_fname, C)
streams = [(i, None, None) for i in atracks]
tv.write(appr_fname, streams, hdr)
else:
print 'Loading result...'
C = pkl.load_pickle(C_fname)
skel = []
for c in C:
skel.append(C[c]['repz'])
print 'Showing dataset after clustering...'
diffs.append(np.sum(np.abs(conn_mat-golden_mat)))
return mat, conn_mats, diffs
Np = 100
Ni = 50
for NC in [1, 2, 3]:
for iso in [0, 1]:
for fr in [0, 1]:
for snr in [30, 10]:
for typ in [0, 1, 2, 3]:
for ang_t in [20,23,25, 30,33,35]:
for category in ['dti']:#, 'hardi']:
filename = '{}_pso_track_sel={}_NC={}_iso={}_fr={}_Np={}_Ni={}_snr={}_type={}'.format(category, ang_t, NC, iso, fr, Np, Ni, snr, typ)
filepath = '/media/Data/work/isbi2013/pso_track/' + filename + '.trk'
if os.path.exists(filepath):
mat, conn_mats, diffs = streams_to_connmat(filepath, seeds_per_voxel=5, thr=[0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9])#thr=[0.25, 0.5, 0.75])
print(filename, diffs)
filename2 = '{}_pso_conn_mat_sel={}_NC={}_iso={}_fr={}_Np={}_Ni={}_snr={}_type={}'.format(category, ang_t, NC, iso, fr, Np, Ni, snr, typ)
save_pickle('/media/Data/work/isbi2013/pso_conn_mat/' + filename2 + '.pkl', {'mat':mat, 'conn_mats':conn_mats, 'diffs':diffs})
def humans():
no_seeds=10**6
visualize = False
save_odfs = False
dirname = "data/"
for root, dirs, files in os.walk(dirname):
if root.endswith('101_32'):
base_dir = root+'/'
filename = 'raw'
base_filename = base_dir + filename
nii_filename = base_filename + 'bet.nii.gz'
bvec_filename = base_filename + '.bvec'
bval_filename = base_filename + '.bval'
flirt_mat = base_dir + 'DTI/flirt.mat'
fa_filename = base_dir + 'DTI/fa.nii.gz'
fsl_ref = '/usr/share/fsl/data/standard/FMRIB58_FA_1mm.nii.gz'
dpy_filename = base_dir + 'DTI/res_tracks_dti.dpy'
print bvec_filename
img = nib.load(nii_filename)
data = img.get_data()
affine = img.get_affine()
bvals = np.loadtxt(bval_filename)
gradients = np.loadtxt(bvec_filename).T # this is the unitary direction of the gradient
tensors = Tensor(data, bvals, gradients, thresh=50)
FA = tensors.fa()
FA = tensors.fa()
famask=FA>=.2
ds=DiffusionSpectrum(data,bvals,gradients,odf_sphere='symmetric642',mask=famask,half_sphere_grads=True,auto=True,save_odfs=save_odfs)
gq=GeneralizedQSampling(data,bvals,gradients,1.2,odf_sphere='symmetric642',mask=famask,squared=False,save_odfs=save_odfs)
ei=EquatorialInversion(data,bvals,gradients,odf_sphere='symmetric642',mask=famask,half_sphere_grads=True,auto=False,save_odfs=save_odfs,fast=True)
ei.radius=np.arange(0,5,0.4)
ei.gaussian_weight=0.05
ei.set_operator('laplacian')
ei.update()
ei.fit()
ds.PK[FA<.2]=np.zeros(5)
ei.PK[FA<.2]=np.zeros(5)
gq.PK[FA<.2]=np.zeros(5)
print 'create seeds'
x,y,z,g=ei.PK.shape
seeds=np.zeros((no_seeds,3))
sid=0
while sid<no_seeds:
rx=(x-1)*np.random.rand()
ry=(y-1)*np.random.rand()
rz=(z-1)*np.random.rand()
seed=np.ascontiguousarray(np.array([rx,ry,rz]),dtype=np.float64)
seeds[sid]=seed
sid+=1
euler = EuDX(a=FA, ind=tensors.ind(), seeds=seeds, a_low=.2)
dt_tracks = [track for track in euler]
euler2 = EuDX(a=ds.PK, ind=ds.IN, seeds=seeds, odf_vertices=ds.odf_vertices, a_low=.2)
ds_tracks = [track for track in euler2]
euler3 = EuDX(a=gq.PK, ind=gq.IN, seeds=seeds, odf_vertices=gq.odf_vertices, a_low=.2)
gq_tracks = [track for track in euler3]
euler4 = EuDX(a=ei.PK, ind=ei.IN, seeds=seeds, odf_vertices=ei.odf_vertices, a_low=.2)
ei_tracks = [track for track in euler4]
if visualize:
renderer = fvtk.ren()
fvtk.add(renderer, fvtk.line(tensor_tracks, fvtk.red, opacity=1.0))
fvtk.show(renderer)
print 'Load images to be used for registration'
img_fa =nib.load(fa_filename)
img_ref =nib.load(fsl_ref)
mat=flirt2aff(np.loadtxt(flirt_mat),img_fa,img_ref)
del img_fa
del img_ref
print 'transform the tracks'
dt_linear = transform_tracks(dt_tracks,mat)
ds_linear = transform_tracks(ds_tracks,mat)
gq_linear = transform_tracks(gq_tracks,mat)
ei_linear = transform_tracks(ei_tracks,mat)
print 'save tensor tracks'
dpy_filename = base_dir + 'DTI/dt_linear.dpy'
print dpy_filename
dpr_linear = Dpy(dpy_filename, 'w')
dpr_linear.write_tracks(dt_linear)
dpr_linear.close()
print 'save ei tracks'
dpy_filename = base_dir + 'DTI/ei_linear.dpy'
print dpy_filename
dpr_linear = Dpy(dpy_filename, 'w')
dpr_linear.write_tracks(ei_linear)
dpr_linear.close()
print 'save ds tracks'
dpy_filename = base_dir + 'DTI/ds_linear.dpy'
print dpy_filename
dpr_linear = Dpy(dpy_filename, 'w')
dpr_linear.write_tracks(ds_linear)
dpr_linear.close()
print 'save gq tracks'
dpy_filename = base_dir + 'DTI/gq_linear.dpy'
print dpy_filename
dpr_linear = Dpy(dpy_filename, 'w')
dpr_linear.write_tracks(gq_linear)
dpr_linear.close()
print 'save lengths'
pkl_filename = base_dir + 'DTI/dt_lengths.pkl'
save_pickle(pkl_filename,lengths(dt_linear))
pkl_filename = base_dir + 'DTI/ei_lengths.pkl'
save_pickle(pkl_filename,lengths(ei_linear))
pkl_filename = base_dir + 'DTI/gq_lengths.pkl'
save_pickle(pkl_filename,lengths(gq_linear))
pkl_filename = base_dir + 'DTI/ds_lengths.pkl'
save_pickle(pkl_filename,lengths(ds_linear))
xdata = np.zeros(len(x.keys()))
ydata = np.zeros(len(y.keys()))
for i,k in enumerate(x.keys()):
xdata[i]=x[k]
ydata[i]=y[k]
#maxKappa(xdata,ydata)
#maxkappa, maxorder = maxKappa(xdata,ydata)
#print 'maxkappa ', maxkappa
#print 'max order', maxorder
'''
"""
fsolid='/home/eg309/Data/LSC_limits/solid_1M.npy'
#fsolid='/home/ian/Data/LSC_stability/solid_1M.npy'
T=np.load(fsolid)
print 'Before',len(T)
T=np.array([t for t in list(T) if length(t)>= 40. and length(t)< 120.],dtype=np.object) # 100mm - 200mm
print 'After',len(T)
results = multiple_comparisons(samplesize=len(T), replications=3)
save_pickle('results_full.pkl', results)
"""
"""
results = multiple_comparisons(samplesize=25*10**3, replications=12)
save_pickle('results25k.pkl', results)
clusters = qb.cluster(streamlines)
# extract > 100
# print len(clusters) # 89
for c in clusters:
if len(c) < 100:
clusters.remove_cluster(c)
out_path = '/home/brain/workingdir/data/dwi/hcp/' \
'preprocessed/response_dhollander/101006/result/CC_fib_length1_2.png'
show(imgtck, clusters, out_path)
metric = CosineMetric()
qb = QuickBundles(threshold=0.1, metric=metric)
clusters = qb.cluster(streamlines)
# extract > 100
# print len(clusters) # 41
for c in clusters:
if len(c) < 100:
clusters.remove_cluster(c)
out_path = '/home/brain/workingdir/data/dwi/hcp/' \
'preprocessed/response_dhollander/101006/result/CC_fib_length2_2.png'
show(imgtck, clusters, out_path)
# save the complete ClusterMap object with picking
save_pickle(
'/home/brain/workingdir/data/dwi/hcp/preprocessed/'
'response_dhollander/101006/result/CC_fib_length_2.pk2', clusters)
from common_functions import init_prb_state_sparse
prb_map12_init, cs_idxs = init_prb_state_sparse(s_cst_sff,t_cst_ext,nn)
#aang lam do den fan nay
#load cai map va chon cai co prob cao nhat
#-------------------------------------------------------
#only for saving the higest prob map
cst_sff_len = len(s_cst_sff)
map_idxs_all = [map_all[i].argsort()[-1] for i in np.arange(cst_sff_len)]
mapped_all = [cs_idxs[i][map_idxs_all[i]] for i in np.arange(cst_sff_len)]
save_pickle(map_file+'choose_highest.txt',mapped_all)
stop
# end only for saving the higest prob map
#-------------------------------------------------------
cst_len = len(s_cst)
map_tmp = map_all[:cst_len]
map_idxs = [map_tmp[i].argsort()[-1] for i in np.arange(cst_len)]
mapped = [cs_idxs[i][map_idxs[i]] for i in np.arange(cst_len)]
#print map_tmp[:10], map_idxs[:10], cs_idxs[:10], mapped[:10]
colormap_full = np.ones((len(streamlines), 3))
for i, centroid in enumerate(centroids):
inds = qb.label2tracksids(i)
colormap_full[inds] = colormap[i]
fvtk.clear(r)
fvtk.add(r, fvtk.line(streamlines, colormap_full, opacity=1.0, linewidth=3))
fvtk.record(r, n_frames=1, out_path="fornix_clust.png", size=(600, 600))
"""
.. figure:: fornix_clust.png
:align: center
**Showing the different clusters with random colors**.
It is also possible to save the complete QuickBundles object with pickling.
"""
save_pickle("QB.pkl", qb)
"""
Finally, here is a video of QuickBundles applied on a larger dataset.
.. raw:: html
<iframe width="420" height="315" src="http://www.youtube.com/embed/kstL7KKqu94" frameborder="0" allowfullscreen></iframe>
.. include:: ../links_names.inc
"""
source = source_ext[:len(s_cst_idx)]
t_cst_idx = load_pickle(t_cst_idx_file)
target = target_ext[:len(t_cst_idx)]
#print len(source), len(target)
tractography1 = source
tractography2 = target_ext
map_all = mapping_nn(tractography1, tractography2)
if save:
#print 'Saving 1-NN tract based: ', out_file
save_pickle(out_file, map_all)
s_cst = source
t_cst = target
t_cst_ext = target_ext
cst_len = len(s_cst)
mapped = map_all[:cst_len]
mapped_s_cst = [t_cst_ext[idx] for idx in mapped]
#jac0, bfn0 = Jac_BFN(s_cst, t_cst, vol_dims, disp=False)
#jac1, bfn1 = Jac_BFN(mapped_s_cst, t_cst, vol_dims, disp=False)
#jac0, bfn0 = Jac_BFN2(s_cst, t_cst, vol_dims, disp=False)
colormap_full[inds] = colormap[i]
fvtk.clear(ren)
ren.SetBackground(1, 1, 1)
fvtk.add(ren, fvtk.streamtube(streamlines, colormap_full))
fvtk.record(ren, n_frames=1, out_path='fornix_clust.png', size=(600, 600))
"""
.. figure:: fornix_clust.png
:align: center
**Showing the different clusters with random colors**.
It is also possible to save the complete QuickBundles object with pickling.
"""
save_pickle('QB.pkl', qb)
"""
Finally, here is a video of QuickBundles applied on a larger dataset.
.. raw:: html
<iframe width="420" height="315" src="http://www.youtube.com/embed/kstL7KKqu94" frameborder="0" allowfullscreen></iframe>
.. include:: ../links_names.inc
.. [Garyfallidis12] Garyfallidis E. et al., QuickBundles a method for
tractography simplification, Frontiers in Neuroscience, vol
6, no 175, 2012.
"""
ren.SetBackground(1, 1, 1)
ren.add(actor.streamtube(streamlines, colormap_full))
window.record(ren, out_path='fornix_clusters.png', size=(600, 600))
if interactive:
window.show(ren)
"""
.. figure:: fornix_clusters.png
:align: center
Showing the different clusters.
It is also possible to save the complete `ClusterMap` object with pickling.
"""
save_pickle('QB.pkl', clusters)
"""
Finally, here is a video of QuickBundles applied on a larger dataset.
.. raw:: html
<iframe width="420" height="315" src="http://www.youtube.com/embed/kstL7KKqu94" frameborder="0" allowfullscreen></iframe>
.. include:: ../links_names.inc
References
----------
.. [Garyfallidis12] Garyfallidis E. et al., QuickBundles a method for
tractography simplification, Frontiers in Neuroscience, vol
def track_gen_net(trackpickle, templatepath):
tracks = dwi.load_streamlines_from_trk(trackpickle)
img_template = nib.load(templatepath)
p = track_gen_net_work(tracks, img_template)
pickles.save_pickle('net_gen_net.pickle', p)
# Display streamlines
ren = window.Renderer()
ren.add(actor.streamtube(streamlines, window.colors.white))
window.show(ren)
window.record(ren, out_path=filename + '_stream_lines_eu.png', size=(600, 600))
# Display centroids
window.clear(ren)
colormap = actor.create_colormap(np.arange(qb.total_clusters))
ren.add(actor.streamtube(streamlines, window.colors.white, opacity=0.1))
ren.add(actor.streamtube(qb.centroids, colormap, linewidth=0.5))
window.show(ren)
window.record(ren, out_path=filename + '_centroids_eu.png', size=(600, 600))
# Display tracks
window.clear(ren)
colormap_full = np.ones((len(streamlines), 3))
for cluster, color in zip(clusters.items(), colormap):
colormap_full[cluster[1]['indices']] = color
ren.add(actor.streamtube(streamlines, colormap_full))
window.show(ren)
window.record(ren,
out_path=filename + '_stream_line_cluster_eu.png',
size=(600, 600))
# Save Streamline files
save_trk(filename + "_stream_line_eu.trk",
streamlines=streamlines,
affine=np.eye(4))
save_pickle(filename + '_qb_eu.pkl', clusters)
ren.SetBackground(1, 1, 1)
fvtk.add(ren, fvtk.streamtube(streamlines, fvtk.colors.white, opacity=0.05))
fvtk.add(ren, fvtk.streamtube(clusters.centroids, colormap, linewidth=0.4))
fvtk.record(
ren,
n_frames=1,
out_path='/home/brain/workingdir/data/dwi/hcp/preprocessed/'
'response_dhollander/100206/result/CC_fib1_remove_non_cc_z-10_x-min_10_jet.png',
size=(600, 600))
# fvtk.show(ren)
# show the label CC (colors form centroids)
colormap_full = np.ones((len(streamlines)), np.float64(3))
for clusters, color in zip(clusters, colormap):
colormap_full[clusters.indices] = color
fvtk.clear(ren)
ren.SetBackground(1, 1, 1)
fvtk.add(ren, fvtk.streamtube(streamlines, colormap_full))
fvtk.record(
ren,
n_frames=1,
out_path='/home/brain/workingdir/data/dwi/hcp/preprocessed/'
'response_dhollander/100206/result/CC_fib2_remove_non_cc_z-10_x-min_10_jet.png',
size=(600, 600))
# fvtk.show(ren)
# save the complete ClusterMap object with picking
save_pickle(
'/home/brain/workingdir/data/dwi/hcp/preprocessed/response_dhollander/'
'100206/result/CC_fib_remove_non_cc_z-10_x-min_10_jet.pk2', clusters)