def orientation(im, ori=None, set=False, get=False, set_data=False, verbose=1, fname_out=''):
verbose = 0 if get else verbose
printv('Get dimensions of data...', verbose)
nx, ny, nz, nt, px, py, pz, pt = get_dimension(im)
printv(str(nx) + ' x ' + str(ny) + ' x ' + str(nz) + ' x ' + str(nt), verbose)
# if data are 2d or 3d, get orientation from header using fslhd
if (nz == 1 or nt == 1) and len(im.data.shape) < 5:
if get:
try:
printv('Get orientation...', verbose)
im_out = None
ori = get_orientation(im)
except Exception, e:
printv('ERROR: an error occurred: ' + str(e), verbose, 'error')
return ori
elif set:
# set orientation
printv('Change orientation...', verbose)
im_out = set_orientation(im, ori)
elif set_data:
im_out = set_orientation(im, ori, True)
else:
im_out = None
def orientation(im, ori=None, set=False, get=False, set_data=False, verbose=1, fname_out=''):
verbose = 0 if get else verbose
printv('\nGet dimensions of data...', verbose)
nx, ny, nz, nt, px, py, pz, pt = get_dimension(im)
printv(str(nx) + ' x ' + str(ny) + ' x ' + str(nz)+ ' x ' + str(nt), verbose)
# if data are 2d or 3d, get orientation from header using fslhd
if (nz == 1 or nt==1) and len(im.data.shape)<5:
if get:
try:
printv('\nGet orientation...', verbose)
im_out = None
ori = get_orientation(im)
except Exception, e:
printv('ERROR: an error occurred: \n'+str(e), verbose,'error')
return ori
elif set:
# set orientation
printv('\nChange orientation...', verbose)
im_out = set_orientation(im, ori)
elif set_data:
im_out = set_orientation(im, ori, True)
else:
im_out = None
def compute_dist_2im_2d(self):
nx1, ny1, nz1, nt1, px1, py1, pz1, pt1 = get_dimension(self.im1)
nx2, ny2, nz2, nt2, px2, py2, pz2, pt2 = get_dimension(self.im2)
assert px1 == px2 and py1 == py2 and px1 == py1
self.dim_pix = py1
if self.param.thinning:
dat1 = self.thinning1.thinned_image.data
dat2 = self.thinning2.thinned_image.data
else:
dat1 = bin_data(self.im1.data)
dat2 = bin_data(self.im2.data)
self.distances = HausdorffDistance(dat1, dat2, self.param.verbose)
self.res = 'Hausdorff\'s distance : ' + str(self.distances.H * self.dim_pix) + ' mm\n\n' \
'First relative Hausdorff\'s distance : ' + str(self.distances.h1 * self.dim_pix) + ' mm\n' \
'Second relative Hausdorff\'s distance : ' + str(self.distances.h2 * self.dim_pix) + ' mm'
def compute_dist_2im_3d(self):
nx1, ny1, nz1, nt1, px1, py1, pz1, pt1 = get_dimension(self.im1)
nx2, ny2, nz2, nt2, px2, py2, pz2, pt2 = get_dimension(self.im2)
# assert round(pz1, 5) == round(pz2, 5) and round(py1, 5) == round(py2, 5)
assert nx1 == nx2
self.dim_pix = py1
if self.param.thinning:
dat1 = self.thinning1.thinned_image.data
dat2 = self.thinning2.thinned_image.data
else:
dat1 = bin_data(self.im1.data)
dat2 = bin_data(self.im2.data)
self.distances = []
for slice1, slice2 in zip(dat1, dat2):
self.distances.append(HausdorffDistance(slice1, slice2, self.param.verbose))
def compute_dist_2im_2d(self):
nx1, ny1, nz1, nt1, px1, py1, pz1, pt1 = get_dimension(self.im1)
nx2, ny2, nz2, nt2, px2, py2, pz2, pt2 = get_dimension(self.im2)
assert px1 == px2 and py1 == py2 and px1 == py1
self.dim_pix = py1
if self.param.thinning:
dat1 = self.thinning1.thinned_image.data
dat2 = self.thinning2.thinned_image.data
else:
dat1 = bin_data(self.im1.data)
dat2 = bin_data(self.im2.data)
self.distances = HausdorffDistance(dat1, dat2, self.param.verbose)
self.res = 'Hausdorff\'s distance : ' + str(self.distances.H*self.dim_pix) + ' mm\n\n' \
'First relative Hausdorff\'s distance : ' + str(self.distances.h1*self.dim_pix) + ' mm\n' \
'Second relative Hausdorff\'s distance : ' + str(self.distances.h2*self.dim_pix) + ' mm'
def compute_dist_2im_3d(self):
nx1, ny1, nz1, nt1, px1, py1, pz1, pt1 = get_dimension(self.im1)
nx2, ny2, nz2, nt2, px2, py2, pz2, pt2 = get_dimension(self.im2)
# assert round(pz1, 5) == round(pz2, 5) and round(py1, 5) == round(py2, 5)
assert nx1 == nx2
self.dim_pix = py1
if self.param.thinning:
dat1 = self.thinning1.thinned_image.data
dat2 = self.thinning2.thinned_image.data
else:
dat1 = bin_data(self.im1.data)
dat2 = bin_data(self.im2.data)
self.distances = []
for slice1, slice2 in zip(dat1, dat2):
self.distances.append(HausdorffDistance(slice1, slice2, self.param.verbose))
def compute_dist_1im_3d(self):
nx1, ny1, nz1, nt1, px1, py1, pz1, pt1 = get_dimension(self.im1)
self.dim_pix = py1
if self.param.thinning:
dat1 = self.thinning1.thinned_image.data
else:
dat1 = bin_data(self.im1.data)
self.distances = []
for i, dat_slice in enumerate(dat1[:-1]):
self.distances.append(HausdorffDistance(bin_data(dat_slice), bin_data(dat1[i+1]), self.param.verbose))
def compute_dist_1im_3d(self):
nx1, ny1, nz1, nt1, px1, py1, pz1, pt1 = get_dimension(self.im1)
self.dim_pix = py1
if self.param.thinning:
dat1 = self.thinning1.thinned_image.data
else:
dat1 = bin_data(self.im1.data)
self.distances = []
for i, dat_slice in enumerate(dat1[:-1]):
self.distances.append(HausdorffDistance(bin_data(dat_slice), bin_data(dat1[i + 1]), self.param.verbose))
def orientation(im, ori=None, set=False, get=False, set_data=False, verbose=1):
verbose = 0 if get else verbose
printv('\nGet dimensions of data...', verbose)
nx, ny, nz, nt, px, py, pz, pt = get_dimension(im)
printv(str(nx) + ' x ' + str(ny) + ' x ' + str(nz)+ ' x ' + str(nt), verbose)
# if data are 3d, directly set or get orientation
if nt == 1:
if get:
# get orientation
printv('\nGet orientation...', verbose)
im_out = None
return get_orientation(im)
elif set:
# set orientation
printv('\nChange orientation...', verbose)
im_out = set_orientation(im, ori)
elif set_data:
im_out = set_orientation(im, ori, True)
else:
im_out = None
else:
# 4D data: split along T dimension
printv('\nSplit along T dimension...', verbose)
im_split_list = split_data(im, 3)
for im_s in im_split_list:
im_s.save(verbose=verbose)
if get:
# get orientation
printv('\nGet orientation...', verbose)
im_out=None
return get_orientation(im_split_list[0])
elif set:
# set orientation
printv('\nChange orientation...', verbose)
im_changed_ori_list = []
for im_s in im_split_list:
im_set = set_orientation(im_s, ori)
im_changed_ori_list.append(im_set)
printv('\nMerge file back...', verbose)
im_out = concat_data(im_changed_ori_list, 3)
elif set_data:
printv('\nSet orientation of the data only is not compatible with 4D data...', verbose, 'error')
else:
im_out = None
im_out.setFileName(im.file_name+'_'+ori+im.ext)
return im_out
def orientation(im,
ori=None,
set=False,
get=False,
set_data=False,
verbose=1,
fname_out=None):
"""
:param fname_out: when set is True, where to save the output file
(default: in cwd, named basename_orientation.ext)
:returns: when get, the orientation; when set, the changed image data (not saved)
"""
verbose = 0 if get else verbose
if fname_out is None:
fname_out = "{}_{}{}".format(im.file_name, ori, im.ext)
printv('Get dimensions of data...', verbose)
nx, ny, nz, nt, px, py, pz, pt = get_dimension(im)
printv(
str(nx) + ' x ' + str(ny) + ' x ' + str(nz) + ' x ' + str(nt), verbose)
# if data are 2d or 3d, get orientation from header using fslhd
if (nz == 1 or nt == 1) and len(im.data.shape) < 5:
if get:
try:
printv('Get orientation...', verbose)
im_out = None
ori = get_orientation(im)
except Exception as e:
printv('ERROR: an error occurred: ' + str(e), verbose, 'error')
return ori
elif set:
# set orientation
printv('Change orientation...', verbose)
tmp_folder = tmp_create(verbose)
curdir = os.getcwd()
os.chdir(tmp_folder)
im_out = set_orientation(im, ori)
os.chdir(curdir)
sct.rmtree(tmp_folder)
elif set_data:
tmp_folder = tmp_create(verbose)
curdir = os.getcwd()
os.chdir(tmp_folder)
im_out = set_orientation(im, ori, True)
os.chdir(curdir)
sct.rmtree(tmp_folder)
else:
im_out = None
else:
# 4D data: split along T dimension
# or 5D data: split along 5th dimension
# Create a temporary directory and go in it
tmp_folder = tmp_create(verbose)
curdir = os.getcwd()
os.chdir(tmp_folder)
if len(im.data.shape) == 5 and im.data.shape[-1] not in [0, 1]:
# 5D data
printv('Split along 5th dimension...', verbose)
im_split_list = multicomponent_split(im)
dim = 5
else:
# 4D data
printv('Split along T dimension...', verbose)
im_split_list = split_data(im, 3)
dim = 4
for im_s in im_split_list:
im_s.save(verbose=verbose)
if get:
# get orientation
printv('Get orientation...', verbose)
im_out = None
ori = get_orientation(im_split_list[0])
os.chdir(curdir)
sct.rmtree(tmp_folder)
return ori
elif set:
# set orientation
printv('Change orientation...', verbose)
im_changed_ori_list = []
for im_s in im_split_list:
im_set = set_orientation(im_s, ori)
im_changed_ori_list.append(im_set)
printv('Merge file back...', verbose)
if dim == 4:
im_out = concat_data(im_changed_ori_list, 3)
elif dim == 5:
fname_changed_ori_list = [
im_ch_ori.absolutepath for im_ch_ori in im_changed_ori_list
]
im_out = multicomponent_merge(fname_changed_ori_list)
elif set_data:
# set orientation
printv('Change orientation of data...', verbose)
im_changed_ori_list = []
for im_s in im_split_list:
im_set = set_orientation(im_s, ori, True)
im_changed_ori_list.append(im_set)
printv('Merge file back...', verbose)
if dim == 4:
im_out = concat_data(im_changed_ori_list, 3)
elif dim == 5:
printv(
'Set data orientation on 5D data is not supported. Sorry.',
verbose, 'error')
else:
im_out = None
# Go back to previous directory:
os.chdir(curdir)
sct.rmtree(tmp_folder)
if im_out is not None:
im_out.setFileName(fname_out)
return im_out
