def run_comparisons(sample_data=35):
for simfile in [simdata[sample_data]]:
dataname = simfile
print (dataname)
gqfile = simdir+'gq/'+dataname+'.pkl'
gq = pkl.load_pickle(gqfile)
tnfile = simdir+'tn/'+dataname+'.pkl'
tn = pkl.load_pickle(tnfile)
dt_first_directions_in=odf_vertices[tn.IN]
dt_indices = tn.IN.reshape((100,1000))
dt_results = analyze_maxima(dt_indices, dt_first_directions_in.reshape((100,1000,3)),range(10,90))
gq_indices = np.array(gq.IN[:,0],dtype='int').reshape((100,1000))
gq_first_directions_in=odf_vertices[np.array(gq.IN[:,0],dtype='int')]
#print gq_first_directions_in.shape
gq_results = analyze_maxima(gq_indices, gq_first_directions_in.reshape((100,1000,3)),range(10,90))
np.set_printoptions(precision=3, suppress=True, linewidth=200, threshold=5000)
out = open('/home/ian/Data/SimVoxels/Out/'+'***_'+dataname,'w')
results = np.hstack((np.vstack(dt_results), np.vstack(gq_results)))
print >> out, results[:,:]
out.close()
def read_reconstruction(model_file,fit_file,mask,type='dti'):
""" Reads in an ODF for each voxel reconstructed using DiPy.
Parameters
----------
model_file: string (mandatory)
Path to the pickled model used for ODF reconstruction.
fit_file: string (mandatory)
Path to the pickled, fitted ODFs reconstructed by DiPy.
mask: numpy array (mandatory)
Logical array defining the brain mask.
type: string \in {'dti','csd','csa'} (default = 'dti')
The type of the ODF reconstruction.
Returns
-----------
model_fit: Dipy Object (depends on the type)
Represents the fitted ODF for each voxel.
"""
model = load_pickle(model_file)
if type == 'dti':
model_params = load_pickle(fit_file)
model_fit = TensorFit(model,model_params)
elif type == 'csd':
fit_array = load_pickle(fit_file)
model_fit = MultiVoxelFit(model,fit_array,mask)
elif type == 'csa':
shm_coeff = load_pickle(fit_file)
model_fit = SphHarmFit(model,shm_coeff,mask)
return model_fit
def bench_time():
bench = load_pickle("bench_qbx_vs_qb.pkl")
nbs = []
qb_times = []
qbx_times = []
for nb_streamlines in np.sort(bench.keys()):
nbs.append(nb_streamlines)
qb_times.append(bench[nb_streamlines]["QB time"])
qbx_times.append(bench[nb_streamlines]["QBX time"])
fig = plt.figure()
# fig.suptitle('Time comparison of QB vs QBX', fontsize=14)
ax = fig.add_subplot(1, 1, 1)
ax.set_title("QB vs QBX (execution time)")
linewidth = 5.0
ax.plot(nbs, qb_times, "r", linewidth=linewidth, alpha=0.6)
ax.plot(nbs, qbx_times, "g", linewidth=linewidth, alpha=0.6)
for i in [1, 2, 3]:
ax.plot([nbs[i], nbs[i]], [qbx_times[i], qb_times[i]], "k--")
ax.text(x=nbs[i], y=qb_times[i] / 2.0, s=" " + str(int(np.round(bench[nbs[i]]["Speedup"]))) + "X")
ax.legend(["QB", "QBX"], loc=2)
ax.set_xticks(nbs)
ax.set_xticklabels(["1M", "2M", "3M", "4M", "5M"])
ax.set_xlabel("# streamlines in millions (M)")
ax.set_ylabel("# seconds")
plt.savefig("speed.png", dpi=300, bbox_inches="tight")
def tracts_mapping1(tractography1, tractography2, loss_function, neighbour, iterations_anneal_now,pre_map_file):
ann = [100, 200, 400, 600, 800, 1000]
iterations_anneal_pre = 0
if iterations_anneal_now<=100:
dm12 = bundles_distances_mam(tractography1, tractography2)
mapping12_coregistration_1nn = np.argmin(dm12, axis=1)
else:
k = (iterations_anneal_now/200) - 1
iterations_anneal_pre = ann[k]
from dipy.io.pickles import load_pickle
mapping12_coregistration_1nn = load_pickle(pre_map_file)
iterations_anneal = iterations_anneal_now - iterations_anneal_pre
print "Iteration: ", iterations_anneal_now, iterations_anneal_pre, iterations_anneal
print "The previous coregistration gives a mapping12 with the following loss:"
loss_coregistration_1nn = loss_function(mapping12_coregistration_1nn)
print "loss =", loss_coregistration_1nn
#iterations_anneal = 100
print "Simulated Annealing"
np.random.seed(1)
initial_state = mapping12_coregistration_1nn.copy()
mapping12_best, energy_best = anneal(initial_state=initial_state, energy_function=loss_function, neighbour=neighbour, transition_probability=transition_probability, temperature=temperature_boltzmann, max_steps=iterations_anneal, energy_max=0.0, T0=200.0, log_every=1000)
return mapping12_coregistration_1nn, loss_coregistration_1nn, mapping12_best, energy_best
def load_ward_tree(data_id,num_neigh=50):
#file_name = 'Results/' + str(data_id) + '/' + str(data_id)+'_full_tracks_' + str(num_neigh) + '_neighbors_original_ward_stop_50_clusters.tree'
file_name = 'Results/' + str(data_id) + '/' + str(data_id)+'_full_tracks_' + str(num_neigh) + '_neighbors_original_ward.tree'
print "Loading ward tree "
ward = load_pickle(file_name)
return ward
def converging_lsc(inp):
C0=load_pickle(dout+outs[inp]+'.skl')
print len(C0)
v0,i0,l0=bring_virtuals(C0)
v=v0
#print len(v0)
not_converged=1
Cs=[]
while not_converged:
lv_before=len(v)
C=local_skeleton_clustering(v,4.)
v,i,l=bring_virtuals(C)
#print '=',len(v)
#for (i,v_) in enumerate(v):
# if length(v_)<50.:
# del v[i]
#c=[v_ for v_ in v if length(v_)>50.]
lv=len(v)
#print lv
if len(v)==lv_before:
not_converged=0
else:
Cs.append(C)
return Cs
def run_on_multi_subjects():
k1 = 15
iterations = 25
fig = plt.figure()
#subjects =['101','109','201','205','210']
#colors = ['ko--', 'kx:', 'k^-','k*-','v-.' ]
subjects =['109','205']
colors = [ 'k^:','ko-' ]
for m, sub_id in enumerate(subjects):
#tree_name = 'Results/' + str(sub_id) + '/' + str(sub_id) +'_full_tracks_50_neighbors_modified_ward_full_tree.tree'
tree_name = 'Results/' + str(sub_id) + '/' + str(sub_id) +'_full_tracks_50_neighbors_modified_ward_full_tree_130516.tree'
tree = load_pickle(tree_name)
cut = tree.best_cut()
print 'origin cut', cut
remove_valley(cut)
print 'after remove valley', cut
cut_scales_ori = [s[0] for s in cut]
temp_scales = heuristic_modified_cuts(cut_scales_ori[:4],3)
temp_scales_1 = heuristic_modified_cuts(cut_scales_ori[4:],4,temp_scales[len(temp_scales)-1])
cut_scales = np.concatenate((temp_scales,temp_scales_1))
#print cut_scales_ori
#print cut_scales
#cut_scales = cut_scales_ori
#cut_scales = heuristic_modified_cuts(cut_scales,4)
cut_scales = cut_scales_ori
split = np.zeros((len(cut_scales),iterations))
for j in np.arange(len(cut_scales)):
#run from the top cut to the bottom cut
i = len(cut_scales) - j - 1
height = cut_scales[i]
guillotines = tree.cut(height)
#the heigh of the next cut
if i==0:
h = 0.
else:
h = cut_scales[i-1]
for k in np.arange(iterations):
random_nodes = random_elements(guillotines, k1)
split[i,k] = split_factor_setnodes(tree,random_nodes,h)
plot_results(plt, split, cut_scales, colors[m], sub_id)
print sub_id, ' : ', cut_scales
plt.legend(loc='upper right')
plt.xlabel("cut scales with a base unit of 1/h", fontsize=17)
plt.ylabel("split factor ", fontsize=17)
#fig.suptitle ("\n Evaluating the cut based on split factor", fontsize=20)
plt.show()
def load_cst(tracks_filename, cst_index_file, ext):
from dipy.io.dpy import Dpy
from dipy.io.pickles import load_pickle
dpr_tracks = Dpy(tracks_filename, 'r')
all_tracks=dpr_tracks.read_tracks()
dpr_tracks.close()
tracks_id = load_pickle(cst_index_file)
cst = [all_tracks[i] for i in tracks_id]
cst_ext = [all_tracks[i] for i in tracks_id]
medoid_cst = []
#len_dis = 250
if ext:
k = np.round(len(cst)*1.2)
not_cst_fil = []
min_len = min(len(i) for i in cst)
#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_cst_fil.append(all_tracks[i])
#for st in all_tracks:
# if (length(st)>=min_len) and (st not in cst):
# not_cst_fil.append(st)
from dipy.segment.quickbundles import QuickBundles
qb = QuickBundles(cst,200,18)
medoid_cst = qb.centroids[0]
med_notcst_dm = bundles_distances_mam([medoid_cst], not_cst_fil)
med_cst_dm = bundles_distances_mam([medoid_cst], cst)
cst_rad = med_cst_dm[0][np.argmax(med_cst_dm[0])]
len_dis = cst_rad * 2.8/2.
#print med_cst_dm
#print cst_rad
#print len_dis
#k_indices which close to the medoid
sort = np.argsort(med_notcst_dm,axis = 1)[0]
#print sort[:k+1]
while (k>0 and med_notcst_dm[0][sort[k]]>=len_dis):
k = k - 1
#print med_notcst_dm[0][sort[0:k]]
#print k
#close_indices = np.argsort(cst_dm,axis = 1)[:,0:k][0]
close_indices = sort[0:k]
for idx in close_indices:
cst_ext.append(not_cst_fil[idx])
return cst, cst_ext, medoid_cst
return cst
def bench_complexity():
bench = load_pickle("bench_qbx_vs_qb_complexity.pkl")
nbs = []
qb_mdfs = []
qbx_mdfs = []
qbx_1 = []
qbx_2 = []
qbx_3 = []
qbx_4 = []
for nb_streamlines in np.sort(bench.keys()):
nbs.append(nb_streamlines)
tmp = bench[nb_streamlines]["QB stats"]["nb_mdf_calls"] / 2
print("QB {}".format(tmp))
qb_mdfs.append(tmp)
tmpx = 0
tmpx_1 = bench[nb_streamlines]["QBX stats"]["stats_per_level"][0]["nb_mdf_calls"] / 2
tmpx_2 = bench[nb_streamlines]["QBX stats"]["stats_per_level"][1]["nb_mdf_calls"] / 2
tmpx_3 = bench[nb_streamlines]["QBX stats"]["stats_per_level"][2]["nb_mdf_calls"] / 2
tmpx_4 = bench[nb_streamlines]["QBX stats"]["stats_per_level"][3]["nb_mdf_calls"] / 2
tmpx = tmpx_1 + tmpx_2 + tmpx_3 + tmpx_4
print("QBX {}".format(tmpx))
print("QB/QBX {}".format(tmp / float(tmpx)))
qbx_mdfs.append(tmpx)
qbx_1.append(tmpx_1)
qbx_2.append(tmpx_2)
qbx_3.append(tmpx_3)
qbx_4.append(tmpx_4)
fig = plt.figure()
# fig.suptitle('Time comparison of QB vs QBX', fontsize=14)
ax = fig.add_subplot(1, 1, 1)
ax.set_title("QB vs QBX (MDF calls)")
linewidth = 5.0
# ax.plot(nbs, qb_mdfs, 'r--', linewidth=linewidth, alpha=0.5)
ax.plot(nbs, qbx_mdfs, "g--", linewidth=linewidth, alpha=0.5)
ax.plot(nbs, qbx_1, "g-", linewidth=linewidth, alpha=0.6)
ax.plot(nbs, qbx_2, linewidth=linewidth, alpha=0.7)
ax.plot(nbs, qbx_3, linewidth=linewidth, alpha=0.8)
ax.plot(nbs, qbx_4, linewidth=linewidth, alpha=0.9)
# for i in [1, 2, 3]:
# ax.plot([nbs[i], nbs[i]], [qbx_times[i], qb_times[i]], 'k--')
# ax.text(x=nbs[i], y=qb_times[i]/2., s=' ' + str(int(np.round(bench[nbs[i]]['Speedup']))) + 'X')
ax.legend(["QBX", "QBX1", "QBX2", "QBX3", "QBX4"], loc=2)
ax.set_xticks(nbs)
ax.set_xticklabels(["1K", "2K", "3K", "4K", "5K"])
ax.set_xlabel("# streamlines in millions (M)")
ax.set_ylabel("# MDF calls")
plt.savefig("complexity.png", dpi=300, bbox_inches="tight")
def see_skeletons(fskel):
C=load_pickle(fskel)
tracks=[C[c]['most'] for c in C if C[c]['N'] > 10 ]
r=fvtk.ren()
colors=np.array([t[0]-t[-1] for t in tracks])
colors=colormap.orient2rgb(colors)
fvtk.add(r,fvtk.line(tracks,colors))
fvtk.show(r)
def show_timings():
res=load_pickle('/home/eg309/Data/LSC_limits/timings_100K_1M.pkl')
#[ 3, 6, 12, 18]
dists=[ 4., 6., 8., 10.]
plt.subplots_adjust(hspace=0.4)
ax1=plt.subplot(221)
plt.title('3 point tracks')
for d in dists:
ax1.plot(res[3][d]['time'][:-2],label=str(d*2.5)+' mm')
ax1.set_ylim((0,6000))
ax1.set_xlim((0,9))
ax1.set_xticklabels(['100K','200K','300K','400K','500K','600K','700K','800K','900K','1M'])
ax1.set_ylabel('Seconds')
ax1.set_xlabel('Number of tracks')
plt.legend()
ax2=plt.subplot(222)
plt.title('6 point tracks')
for d in dists:
ax2.plot(res[6][d]['time'][:-2],label=str(d*2.5)+' mm')
ax2.set_ylim((0,6000))
ax2.set_xlim((0,9))
ax2.set_xticklabels(['100K','200K','300K','400K','500K','600K','700K','800K','900K','1M'])
ax2.set_ylabel('Seconds')
ax2.set_xlabel('Number of tracks')
plt.legend()
ax3=plt.subplot(223)
plt.title('12 point tracks')
for d in dists:
ax3.plot(res[12][d]['time'][:-2],label=str(d*2.5)+' mm')
ax3.set_ylim((0,6000))
ax3.set_xlim((0,9))
ax3.set_xticklabels(['100K','200K','300K','400K','500K','600K','700K','800K','900K','1M'])
ax3.set_ylabel('Seconds')
ax3.set_xlabel('Number of tracks')
plt.legend()
ax4=plt.subplot(224)
plt.title('18 point tracks')
for d in dists:
ax4.plot(res[18][d]['time'][:-2],label=str(d*2.5)+' mm')
ax4.set_ylim((0,6000))
ax4.set_xlim((0,9))
ax4.set_xticklabels(['100K','200K','300K','400K','500K','600K','700K','800K','900K','1M'])
ax4.set_ylabel('Seconds')
ax4.set_xlabel('Number of tracks')
plt.legend(loc=2)
plt.show()
def gen_net_csv():
netpickle = 'net_gen_net.pickle'
net = pickles.load_pickle(netpickle)
M = net.M
atlasdir = os.path.dirname(os.getcwd())
atlasname = os.path.basename(atlasdir)
atlasobj = atlas.get(atlasname)
idx = atlasobj.regions
realM = M[idx][:, idx]
save_csvmat('dwinetraw.csv', realM)
save_csvmat('dwinet.csv', np.log1p(realM))
return realM
def get_luigi_SLFI():
fseg1 = "/home/eg309/Devel/segmented_bundles/luigi_s1_for_eleftherios/S1_SLFI"
# fseg2='/home/eg309/Devel/segmented_bundles/luigi_s1_for_eleftherios/S1_SLFII'
subject = "01"
fdpyw = "data/subj_" + subject + "/101_32/DTI/tracks_gqi_3M_linear.dpy"
dpr = Dpy(fdpyw, "r")
T = dpr.read_tracks()
dpr.close()
seg_inds = load_pickle(fseg1)
T1 = [T[i] for i in seg_inds]
# seg_inds=load_pickle(fseg2)
# T2=[T[i] for i in seg_inds]
return T1
def load_data_dis(data_id, num_prototype=40):
filename = (
"Results/"
+ str(data_id)
+ "/"
+ str(data_id)
+ "_data_disimilarity_full_tracks_"
+ str(num_prototype)
+ "_prototyes_random_130516.dis"
)
print "Loading tracks dissimilarity"
dis = load_pickle(filename)
return dis
def combine_results():
subs=['subj_01','subj_02','subj_03','subj_04','subj_05','subj_06','subj_07','subj_08','subj_09','subj_10','subj_11','subj_12']
categ=['64','64_32','101','101_32','118','118_32']
methods=['DTI','GQI','SDI','NPA']
RES={}
for sub in subs:
RES[sub]={}
for cat in categ:
RES[sub][cat]={}
for meth in methods:
RES[sub][cat][meth]={}
for root, dirs, files in os.walk(dname+sub+'/'+cat+'/'+meth):
for file in files:
if file.endswith('FAW_len.npy'):
print pjoin(root,file)
track_lengths=np.load(pjoin(root,file))
RES[sub][cat][meth]['track_no']=len(track_lengths)
RES[sub][cat][meth]['total_length']=np.sum(track_lengths)
#RES[sub][cat][meth]['lenghts']=track_lengths
if file.startswith('FAW_LSC_ref_'):
if file.endswith('3.pkl'):
RES[sub][cat][meth]['len_lsc_3']=len(load_pickle(pjoin(root,file)))
if file.endswith('6.pkl'):
RES[sub][cat][meth]['len_lsc_6']=len(load_pickle(pjoin(root,file)))
if file.endswith('9.pkl'):
RES[sub][cat][meth]['len_lsc_9']=len(load_pickle(pjoin(root,file)))
if file.endswith('12.pkl'):
RES[sub][cat][meth]['len_lsc_12']=len(load_pickle(pjoin(root,file)))
if file.endswith('_SR.pkl'):
RES[sub][cat][meth]['sr']=load_pickle(pjoin(root,file))
return RES
def load_tract_trk(tracks_filename, id_file):
'''
load tract from trackvis format
'''
import nibabel as nib
streams,hdr=nib.trackvis.read(tracks_filename,points_space='voxel')
all_tracks = np.array([s[0] for s in streams], dtype=np.object)
from dipy.io.pickles import load_pickle
tracks_id = load_pickle(id_file)
tract = [all_tracks[i] for i in tracks_id]
tract = np.array(tract,dtype=np.object)
return tract
def analyze_humans():
#if __name__ == '__main__':
dirname = "data/"
for root, dirs, files in os.walk(dirname):
if root.endswith('101_32'):
base_dir = root+'/'
#filename = 'raw'
#dpy_filename = base_dir + 'DTI/tensor_linear.dpy'
#print dpy_filename
#dpr_linear = Dpy(dpy_filename, 'r')
#tensor_tracks=dpr_linear.read_tracks()
#dpr_linear.close()
pkl_filename = base_dir + 'DTI/dt_lengths.pkl'
dt_lengths=load_pickle(pkl_filename)
pkl_filename = base_dir + 'DTI/ei_lengths.pkl'
ei_lengths=load_pickle(pkl_filename)
pkl_filename = base_dir + 'DTI/gq_lengths.pkl'
gq_lengths=load_pickle(pkl_filename)
pkl_filename = base_dir + 'DTI/ds_lengths.pkl'
ds_lengths=load_pickle(pkl_filename)
d=np.zeros(6)
p=np.zeros(6)
np.set_printoptions(3)
d[0],p[0]=ks_2samp(dt_lengths,ei_lengths)
d[1],p[1]=ks_2samp(dt_lengths,ds_lengths)
d[2],p[2]=ks_2samp(dt_lengths,gq_lengths)
d[3],p[3]=ks_2samp(ei_lengths,ds_lengths)
d[4],p[4]=ks_2samp(ei_lengths,gq_lengths)
d[5],p[5]=ks_2samp(ds_lengths,gq_lengths)
print 'KS statistic ',d,'P-value ',p
print np.median(dt_lengths),np.median(ei_lengths),\
np.median(ds_lengths),np.median(gq_lengths)
#break
stop
def see_combined_spherical_intersections():
subs=['subj_01','subj_02','subj_03','subj_04','subj_05','subj_06','subj_07','subj_08','subj_09','subj_10','subj_11','subj_12']
categ=['64','64_32','101','101_32','118','118_32']
methods=['DTI','GQI','SDI','NPA']
centers=['GCC', 'CSTL', 'FX', 'CGCR', 'SCC', 'BCC', 'CGCL', 'UNCL?', 'CSTR', 'UNCR?']
RES=load_pickle('/home/eg309/Data/PROC_MR10032/results/res_tmp.pkl')
#print RES['subj_03']['64_32']['DTI']
SR_combined={}
for cent in centers:
SR_combined[cent]={}
for cat in categ:
SR_combined[cent][cat]=[]
for sub in subs:
try:
SR_combined[cent][cat].append(len(RES[sub][cat]['DTI']['sr'][cent]['indices']))
except KeyError:
pass
#return SR_combined
#RES['subj_03']['64_32']['DTI']['sr']['GCC']['indices']
width=0.2
for cent in SR_combined:
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title(cent)
mean_=[]
std_=[]
ind=np.arange(6)
for cat in categ:
mean_.append(np.array(SR_combined[cent][cat]).mean())
std_.append(np.array(SR_combined[cent][cat]).std())
rects = ax.bar(ind+width, mean_ , width, color='m', yerr= std_)
ax.set_xticks(ind+width)
ax.set_xticklabels(categ)
plt.show()
"""
def test_sltensor():
fname=pjoin(os.path.dirname(__file__),'data/eg_3voxels.pkl')
dix=pkls.load_pickle(fname)
b=dix['bs']
g=dix['gs']
data=np.array(dix['data']).T
yield assert_equal(b[0],0.)
slt=ten.STensorL(b,g)
yield assert_equal(slt.A.shape[0],len(b)-1)
slt.fit(data)
print 'data coeff',slt.coeff
print 'tensors',slt.tensors
print 'fa',slt.fa
print 'adc',slt.adc
data2=100*np.ones((3,3,3,len(b)))
slt.fit(data2)
print 'data2 coeff',slt.coeff
print 'tensors',slt.tensors
print 'fa',slt.fa
print 'adc',slt.adc
yield assert_array_equal(slt.fa,np.zeros((3,3,3)))
data2[:,:,:,0]=250
slt.fit(data2)
print 'data2 coeff bigger S0',slt.coeff
print 'tensors',slt.tensors
print 'fa',slt.fa
print 'adc',slt.adc
data2[:,:,:,0]=50
slt.fit(data2)
print 'data2 coeff smaller S0',slt.coeff
print 'tensors',slt.tensors
print 'fa',slt.fa
print 'adc',slt.adc
def test_sltensor():
fname = pjoin(os.path.dirname(__file__), 'data/eg_3voxels.pkl')
dix = pkls.load_pickle(fname)
b = dix['bs']
g = dix['gs']
data = np.array(dix['data']).T
yield assert_equal(b[0], 0.)
slt = ten.STensorL(b, g)
yield assert_equal(slt.A.shape[0], len(b) - 1)
slt.fit(data)
print 'data coeff', slt.coeff
print 'tensors', slt.tensors
print 'fa', slt.fa
print 'adc', slt.adc
data2 = 100 * np.ones((3, 3, 3, len(b)))
slt.fit(data2)
print 'data2 coeff', slt.coeff
print 'tensors', slt.tensors
print 'fa', slt.fa
print 'adc', slt.adc
yield assert_array_equal(slt.fa, np.zeros((3, 3, 3)))
data2[:, :, :, 0] = 250
slt.fit(data2)
print 'data2 coeff bigger S0', slt.coeff
print 'tensors', slt.tensors
print 'fa', slt.fa
print 'adc', slt.adc
data2[:, :, :, 0] = 50
slt.fit(data2)
print 'data2 coeff smaller S0', slt.coeff
print 'tensors', slt.tensors
print 'fa', slt.fa
print 'adc', slt.adc
def run_one_subject(subject_id):
#tree_name = 'Results/' + str(subject_id) + '/' + str(subject_id) +'_full_tracks_50_neighbors_modified_ward_full_tree.tree'
tree_name = 'Results/' + str(subject_id) + '/' + str(subject_id) +'_full_tracks_50_neighbors_modified_ward_full_tree_130516.tree'
#'Result/210/210_full_tracks_50_neighbors_modified_ward_full_tree.tree'
tree = load_pickle(tree_name)
k1 = 15
iterations = 50
cut = tree.best_cut()
#print 'origin cut', cut
remove_valley(cut)
#print 'after remove valley', cut
cut_scales_ori = [s[0] for s in cut]
temp_scales = heuristic_modified_cuts(cut_scales_ori[:4],3)
temp_scales_1 = heuristic_modified_cuts(cut_scales_ori[4:],4,temp_scales[len(temp_scales)-1])
cut_scales = np.concatenate((temp_scales,temp_scales_1))
split = np.zeros((len(cut_scales),iterations))
for j in np.arange(len(cut_scales)):
#run from the top cut to the bottom cut
i = len(cut_scales) - j - 1
height = cut_scales[i]
t0 = time.time()
guillotines = tree.cut(height)
t_cut = time.time() - t0
print 'Time for cutting at height ',height, ' : ',t_cut
#the heigh of the next cut
if i==0:
h = 0.
else:
h = cut_scales[i-1]
print 'Compute split factor of ', height,' to scale', h
for k in np.arange(iterations):
random_nodes = random_elements(guillotines, k1)
print '\t trial ', k, ': ', random_nodes
split[i,k] = split_factor_setnodes(tree,random_nodes,h)
title = '\nSplit factor for cutting time of ' + tree_name
plot_result(split, cut_scales, '-kx', '210', title)
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)
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 load_tract(tracks_filename, id_file):
from dipy.io.pickles import load_pickle
if (tracks_filename[-3:]=='dpy'):
from dipy.io.dpy import Dpy
dpr_tracks = Dpy(tracks_filename, 'r')
all_tracks=dpr_tracks.read_tracks()
dpr_tracks.close()
else:
import nibabel as nib
streams,hdr=nib.trackvis.read(tracks_filename,points_space='voxel')
all_tracks = np.array([s[0] for s in streams], dtype=np.object)
tracks_id = load_pickle(id_file)
tract = [all_tracks[i] for i in tracks_id]
tract = np.array(tract,dtype=np.object)
return tract
def show_timing_vs_others():
res=load_pickle('/home/eg309/Data/LSC_limits/timings_1K_100K.pkl')
ax=plt.subplot(111)
times=res[12][8]['time'][:-1]
print len(times)
x=np.arange(10**3,10**5+10**3,10**3)
print len(x)
#ax.set_xticklabels(['1K','20K','40K','60K','70K','80K','90K','100K'])
ax.plot(x,times,label='LSC')
ax.plot([1000,60000],[30,14400],"*",label='Wang')
#ax.set_ylim((0,40))
#ax.set_xlim((1000,100000))
plt.legend(loc=0)
plt.show()
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 show_conn_mat(filename):
d = load_pickle(filename)
method = filename.split('__')[1].split('_')[0]
subplot(2, 2, 1)
title(method + ' full')
imshow(d['mat'])
subplot(2, 2, 2)
title(method + ' 0.5')
imshow(d['conn_mats'][0])
subplot(2, 2, 3)
title(method + ' 1.')
imshow(d['conn_mats'][1])
subplot(2, 2, 4)
title(method + ' 1.5')
imshow(d['conn_mats'][2])
print 'Diffs: ', d['diffs']
try:
print 'Ratio: ', d['ratio']
except KeyError:
print 'KeyError: ratio does not exist'
def check_bigger_clusters():
avirtuals={}
for (i,out) in enumerate(outs):
C=load_pickle(dout+out+'.skl')
cinds=np.zeros(len(C))
for c in C:
cinds[c]=len(C[c]['indices'])
descend=np.argsort(cinds)[::-1]
desc=descend[:400]
virtuals=[]
for c in desc:
v=C[c]['hidden']/float(C[c]['N'])
virtuals.append(v)
avirtuals[i]=virtuals
r=fvtk.ren()
fvtk.add(r,fvtk.line(avirtuals[0],fvtk.red))
fvtk.add(r,fvtk.line(avirtuals[9],fvtk.yellow))
fvtk.add(r,fvtk.line(avirtuals[5],fvtk.green))
fvtk.show(r)
[2*(b*c + a*d), a*a + c*c - b*b - d*d, 2*(c*d - a*b)],
[2*(b*d - a*c), 2*(c*d + a*b), a*a + d*d - b*b - c*c]])
if __name__ == '__main__':
root = Tkinter.Tk()
root.withdraw()
dir_name = 'ALS/ALS_Segmentation'
tracks_chosen_filename = tkFileDialog.askopenfilename(parent=root,initialdir=dir_name)
num_seeds = 3 #1M 3M
#tracks_chosen_filename = 'ALS/ALS_Segmentation/s201_corticospinal_left_3M_Nivedita.pkl'
#subj = 201
tracks_id=load_pickle(tracks_chosen_filename)
root = Tkinter.Tk()
root.wm_title('Subject Selection')
subsel = SubjectSelector(root, default_value=1)
root.wait_window()
mapping = [0,101,201,102,202,103,203,104,204,105,205,106,206,107,207,109,208,110,209,111,210,112,212,113,213]
subj = mapping[subsel.value]
#load the tracks
tracks_filename = 'ALS/ALS_Data/'+str(subj)+'/DIFF2DEPI_EKJ_64dirs_14/DTI/tracks_dti_'+str(num_seeds)+'M_linear.dpy'
dpr_tracks = Dpy(tracks_filename, 'r')
tensor_all_tracks=dpr_tracks.read_tracks();
dpr_tracks.close()
T = [tensor_all_tracks[i] for i in tracks_id]
to_be_deleted[i] = 1
for i in np.where(to_be_deleted > 0)[0]:
del C[k[i]]
return C
def most(C):
for c in C:
pass # pf.most_similar_track_mam()
T = pkl.load_pickle(fname)
print 'Reducing the number of points...'
T = [pf.approx_polygon_track(t) for t in T]
print 'Reducing further to tracks with 3 pts...'
T2 = [tm.downsample(t, 3) for t in T]
print 'LARCH ...'
print 'Splitting ...'
t = time.clock()
C = pf.larch_3split(T2, None, 5.)
print time.clock() - t, len(C)
for c in C:
print c, C[c]['rep3'] / C[c]['N']
#t_cst_ext_file = '/home/bao/tiensy/Lauren_registration/data_compare_mapping/pairwise_reg_cstext2cstext/CST_ROI_trkvis_Right/' + source_sub + '_' + target_sub + '/out_reg/iteration_4/' + target_sub + '_cst_R_tvis_ext_reg.trk'
#out_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/Lauren_pair_CSText2CSText/Lauren_pair_CSText2CSText_f300_l75_1NN/map_1nn_pairwise_reg_CST_R_ext_' + source_sub + '_aligned_to_CST_R_ext_' + target_sub + '_Lauren_f300_l75.txt'
s_cst_ext_file = '/home/bao/tiensy/Lauren_registration/data_compare_mapping/pairwise_reg_cstext2cstext/CST_ROI_trkvis_Right/' + source_sub + '_' + target_sub + '/out_reg_f100_l25/iteration_4/' + source_sub + '_cst_R_tvis_ext_reg.trk'
t_cst_ext_file = '/home/bao/tiensy/Lauren_registration/data_compare_mapping/pairwise_reg_cstext2cstext/CST_ROI_trkvis_Right/' + source_sub + '_' + target_sub + '/out_reg_f100_l25/iteration_4/' + target_sub + '_cst_R_tvis_ext_reg.trk'
out_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/Lauren_pair_CSText2CSText/Lauren_pair_CSText2CSText_f100_l25_1NN/map_1nn_pairwise_reg_CST_R_ext_' + source_sub + '_aligned_to_CST_R_ext_' + target_sub + '_Lauren_f100_l25.txt'
s_cst_idx_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis/ROI_seg_tvis_native/' + source_sub + '_corticospinal_R_tvis.pkl'
t_cst_idx_file = '/home/bao/tiensy/Tractography_Mapping/data/trackvis_tractography/ROI_seg_tvis/ROI_seg_tvis_native/' + target_sub + '_corticospinal_R_tvis.pkl'
'''
source_ext = load_whole_tract(s_cst_ext_file)
target_ext = load_whole_tract(t_cst_ext_file)
s_cst_idx = load_pickle(s_cst_idx_file)
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
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()
fos.clear(r)
colors = np.zeros((len(skel), 3))
for (i, s) in enumerate(skel):
color = np.random.rand(1, 3)
colors[i] = color
def track_eudx(trackmodelpickle):
trackmodel = pickles.load_pickle(trackmodelpickle)
tracks = track_eudx_work(trackmodel)
with open('raw_track.trk', 'wb') as ftrkout:
dwi.save_streamlines_to_trk(tracks, trackmodel.affine, ftrkout)
if __name__ == '__main__':
#load T1 volume registered in MNI space
#img = nib.load('data/subj_05/MPRAGE_32/T1_flirt_out.nii.gz')
#data = img.get_data()
#affine = img.get_affine()
#load the tracks registered in MNI space
fdpyw = 'data/subj_05/101_32/DTI/tracks_gqi_1M_linear.dpy'
dpr = Dpy(fdpyw, 'r')
T = dpr.read_tracks()
dpr.close()
#load initial QuickBundles with threshold 30mm
fpkl = 'data/subj_05/101_32/DTI/qb_gqi_1M_linear_30.pkl'
#qb=QuickBundles(T,30.,12)
#save_pickle(fpkl,qb)
qb = load_pickle(fpkl)
#create the interaction system for tracks
tl = TrackLabeler('Bundle Picker',
qb,
qb.downsampled_tracks(),
vol_shape=(182, 218, 182),
tracks_alpha=1)
#add a interactive slicing/masking tool
#sl = Slicer(affine,data)
#add one way communication between tl and sl
#tl.slicer=sl
title = 'Bundle Picking'
w = Window(caption=title, width=1200, height=800, bgcolor=(0., 0., 0.2))
def load_data_dis(data_id,num_prototype=40):
filename = 'Results/' + str(data_id) + '/' + str(data_id)+'_data_disimilarity_full_tracks_' + str(num_prototype) + '_prototyes_random.dis'
print "Loading tracks dissimilarity"
dis = load_pickle(filename)
return dis