def create_prob_seg_iteration3(template_grays,templates,image,naming):
base='/data/henry10-w/jjuwono/bayesion_masks_'+naming
a=nb.load(image)
adat_raw=a.get_data()
adat=quantile_transform(a.get_data())
print(adat.dtype)
#input()
distributions_raw=[]
distributions=[]
fgs=[]
data_dict={}
for i in template_grays:
print(c.get_ms(os.path.basename(i)),i)
data_dict[c.get_ms(os.path.basename(i))]=i
for i in templates:
temp=nb.load(i).get_data()
temp=quantile_transform(temp)
print('here')
try:
z=z_score(temp)
except:
print(sys.exc_info())
continue
try:
print(data_dict[c.get_ms(os.path.basename(i))],i)
fg=nb.load(data_dict[c.get_ms(os.path.basename(i))]).get_data()
except:
print(sys.exc_info())
continue
distributions.append(z)
fgs.append(fg)
return fgs,distributions,a,adat,adat_raw
def create_prob_seg_iteration3(template_grays, templates, image, file_handl):
a = nb.load(image)
adat_raw = a.get_data()
adat = quantile_transform(a.get_data())
#print(adat.dtype)
#input()
distributions_raw = []
distributions = []
fgs = []
data_dict = {}
for i in template_grays:
#print(c.get_ms(os.path.basename(i)),i)
data_dict[c.get_ms(os.path.basename(i))] = i
for i in templates:
temp = nb.load(i).get_data()
temp = quantile_transform(temp)
#print('here')
try:
z = z_score(temp)
except:
print(sys.exc_info())
file_handl.write(str(sys.exc_info()) + '\n')
continue
try:
#print(data_dict[c.get_ms(os.path.basename(i))],i)
fg = nb.load(data_dict[c.get_ms(os.path.basename(i))]).get_data()
except:
print(sys.exc_info())
file_handl.write(str(sys.exc_info()) + '\n')
continue
distributions.append(z)
fgs.append(fg)
return fgs, distributions, a, adat, adat_raw
print(sys.exc_info())
continue
distributions.append(z)
fgs.append(fg)
return fgs,distributions,a,adat,adat_raw
prefix='test_retest_PSIR'
#glob for images to segment#
glob_path=glob('/data/henry8/nico/SC_ATROPHY_RAP/*/*/*/*C2*/ms*only_cord.nii.gz')+glob('/data/henry8/nico/SC_ATROPHY_RAP/*/*/*/*C2*/vol*only_cord.nii.gz')
glob_path=glob('/data/henry8/nico/SC_ATROPHY_RAP/*/SKYRA/PSIR/C23_retest/*only_cord.nii.gz')
errors=[]
pass_on=[]
for static in glob_path:
if 'retest' in static:
mse_static=c.get_ms(static)+'PSIR_retest'+scanner(static)
else:
mse_static=c.get_ms(static)+'PSIR_'+scanner(static)
try:
os.remove('/data/henry4/jjuwono/data/henry4/jjuwono/'+prefix+'/'+mse_static+'/warped/synslice_avggmsegs.nii.gz')
except:
pass
if os.path.isdir('/data/henry4/jjuwono/new_GM_method/'+mse_static):
continue
output_path='/data/henry4/jjuwono/data/henry4/jjuwono/'+prefix+'/'+mse_static+'/'
files=sorted(glob('/data/henry6/esha/Data/Interp_10/Current_Data/sharpened/*'))
files2=sorted(glob('/data/henry6/esha/Data/Masks_interp10/butterfly/all/*'))
pth='/data/henry6/esha/Data/Interp_10/Current_Data/sharpened/'
pth2='/data/henry6/esha/Data/Masks_interp10/butterfly/all/'
dim=2