def compute(self):
fname_data = self.fmri
# # create temporary folder
# sct.printv('\nCreate temporary folder...', self.param.verbose)
# path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S/")
# status, output = sct.run('mkdir '+path_tmp, self.param.verbose)
# # motion correct the fmri data
# # sct.printv('\nMotion correct the fMRI data...', self.param.verbose, 'normal')
# path_fmri, fname_fmri, ext_fmri = sct.extract_fname(self.fmri)
# fname_fmri_moco = fname_fmri
# # print sct.slash_at_the_end(path_fmri) + fname_fmri
# # sct.run('mcflirt -in ' + sct.slash_at_the_end(path_fmri, 1) + fname_fmri + ' -out ' + fname_fmri_moco)
# compute tsnr
sct.printv('\nCompute the tSNR...', self.param.verbose, 'normal')
fname_data_mean = sct.add_suffix(fname_data, '_mean')
sct.run('fslmaths ' + fname_data + ' -Tmean ' + fname_data_mean)
fname_data_std = sct.add_suffix(fname_data, '_std')
sct.run('fslmaths ' + fname_data + ' -Tstd ' + fname_data_std)
fname_tsnr = sct.add_suffix(fname_data, '_tsnr')
sct.run('fslmaths ' + fname_data_mean + ' -div ' + fname_data_std + ' ' + fname_tsnr)
# Remove temp files
sct.printv('\nRemove temporary files...', self.param.verbose, 'normal')
sct.run('rm ' + fname_data_std)
# to view results
sct.printv('\nDone! To view results, type:', self.param.verbose, 'normal')
sct.printv('fslview '+fname_tsnr+' &\n', self.param.verbose, 'info')
def _call_viewer_centerline(fname_in, interslice_gap=20.0):
from spinalcordtoolbox.gui.base import AnatomicalParams
from spinalcordtoolbox.gui.centerline import launch_centerline_dialog
im_data = Image(fname_in)
# Get the number of slice along the (IS) axis
im_tmp = msct_image.change_orientation(im_data, 'RPI')
_, _, nz, _, _, _, pz, _ = im_tmp.dim
del im_tmp
params = AnatomicalParams()
# setting maximum number of points to a reasonable value
params.num_points = np.ceil(nz * pz / interslice_gap) + 2
params.interval_in_mm = interslice_gap
params.starting_slice = 'top'
im_mask_viewer = msct_image.zeros_like(im_data)
im_mask_viewer.absolutepath = sct.add_suffix(fname_in, '_viewer')
controller = launch_centerline_dialog(im_data, im_mask_viewer, params)
fname_labels_viewer = sct.add_suffix(fname_in, '_viewer')
if not controller.saved:
sct.log.error(
'The viewer has been closed before entering all manual points. Please try again.'
)
sys.exit(1)
# save labels
controller.as_niftii(fname_labels_viewer)
return fname_labels_viewer
def pad_im(fname_im, nx_full, ny_full, nz_full, xi, xf, yi, yf, zi, zf):
fname_im_pad = sct.add_suffix(fname_im, "_pad")
pad_xi = str(xi)
pad_xf = str(nx_full - (xf + 1))
pad_yi = str(yi)
pad_yf = str(ny_full - (yf + 1))
pad_zi = str(zi)
pad_zf = str(nz_full - (zf + 1))
pad = ",".join([pad_xi, pad_xf, pad_yi, pad_yf, pad_zi, pad_zf])
if len(Image(fname_im).data.shape) == 5:
status, output = sct.run("sct_image -i " + fname_im + " -mcs")
s = "Created file(s):\n-->"
output_fnames = output[output.find(s) + len(s) :].split("\n")[0].split("'")
fname_comp_list = [output_fnames[i] for i in range(1, len(output_fnames), 2)]
fname_comp_pad_list = []
for fname_comp in fname_comp_list:
fname_comp_pad = sct.add_suffix(fname_comp, "_pad")
sct.run("sct_image -i " + fname_comp + " -pad-asym " + pad + " -o " + fname_comp_pad)
fname_comp_pad_list.append(fname_comp_pad)
components = ",".join(fname_comp_pad_list)
sct.run("sct_image -i " + components + " -omc -o " + fname_im_pad)
sct.check_file_exist(fname_im_pad, verbose=1)
else:
sct.run("sct_image -i " + fname_im + " -pad-asym " + pad + " -o " + fname_im_pad)
return fname_im_pad
def pad_im(fname_im, nx_full, ny_full, nz_full, xi, xf, yi, yf, zi, zf):
fname_im_pad = sct.add_suffix(fname_im, '_pad')
pad_xi = str(xi)
pad_xf = str(nx_full - (xf + 1))
pad_yi = str(yi)
pad_yf = str(ny_full - (yf + 1))
pad_zi = str(zi)
pad_zf = str(nz_full - (zf + 1))
pad = ','.join([pad_xi, pad_xf, pad_yi, pad_yf, pad_zi, pad_zf])
if len(Image(fname_im).data.shape) == 5:
status, output = sct.run('sct_image -i ' + fname_im + ' -mcs')
s = 'Created file(s):\n-->'
output_fnames = output[output.find(s) +
len(s):].split('\n')[0].split("'")
fname_comp_list = [
output_fnames[i] for i in range(1, len(output_fnames), 2)
]
fname_comp_pad_list = []
for fname_comp in fname_comp_list:
fname_comp_pad = sct.add_suffix(fname_comp, '_pad')
sct.run('sct_image -i ' + fname_comp + ' -pad-asym ' + pad +
' -o ' + fname_comp_pad)
fname_comp_pad_list.append(fname_comp_pad)
components = ','.join(fname_comp_pad_list)
sct.run('sct_image -i ' + components + ' -omc -o ' + fname_im_pad)
sct.check_file_exist(fname_im_pad, verbose=1)
else:
sct.run('sct_image -i ' + fname_im + ' -pad-asym ' + pad + ' -o ' +
fname_im_pad)
return fname_im_pad
def reorient_data(self):
for f in self.fname_metric_lst:
os.rename(self.fname_metric_lst[f], add_suffix(''.join(extract_fname(self.param.fname_im)[1:]), '_2reorient'))
im = Image(add_suffix(''.join(extract_fname(self.param.fname_im)[1:]), '_2reorient'))
im = set_orientation(im, self.orientation_im)
im.setFileName(self.fname_metric_lst[f])
im.save()
def segment(self):
self.copy_data_to_tmp()
# go to tmp directory
os.chdir(self.tmp_dir)
# load model
self.model.load_model()
self.target_im, self.info_preprocessing = pre_processing(self.param_seg.fname_im, self.param_seg.fname_seg, self.param_seg.fname_level, new_res=self.param_data.axial_res, square_size_size_mm=self.param_data.square_size_size_mm, denoising=self.param_data.denoising, verbose=self.param.verbose, rm_tmp=self.param.rm_tmp)
printv('\nRegister target image to model data...', self.param.verbose, 'normal')
# register target image to model dictionary space
path_warp = self.register_target()
if self.param_data.normalization:
printv('\nNormalize intensity of target image...', self.param.verbose, 'normal')
self.normalize_target()
printv('\nProject target image into the model reduced space...', self.param.verbose, 'normal')
self.project_target()
printv('\nCompute similarities between target slices and model slices using model reduced space...', self.param.verbose, 'normal')
list_dic_indexes_by_slice = self.compute_similarities()
printv('\nLabel fusion of model slices most similar to target slices...', self.param.verbose, 'normal')
self.label_fusion(list_dic_indexes_by_slice)
printv('\nWarp back segmentation into image space...', self.param.verbose, 'normal')
self.warp_back_seg(path_warp)
printv('\nPost-processing...', self.param.verbose, 'normal')
self.im_res_gmseg, self.im_res_wmseg = self.post_processing()
if (self.param_seg.path_results != './') and (not os.path.exists('../' + self.param_seg.path_results)):
# create output folder
printv('\nCreate output folder ...', self.param.verbose, 'normal')
os.chdir('..')
os.mkdir(self.param_seg.path_results)
os.chdir(self.tmp_dir)
if self.param_seg.fname_manual_gmseg is not None:
# compute validation metrics
printv('\nCompute validation metrics...', self.param.verbose, 'normal')
self.validation()
if self.param_seg.ratio is not '0':
printv('\nCompute GM/WM CSA ratio...', self.param.verbose, 'normal')
self.compute_ratio()
# go back to original directory
os.chdir('..')
printv('\nSave resulting GM and WM segmentations...', self.param.verbose, 'normal')
self.fname_res_gmseg = self.param_seg.path_results + add_suffix(''.join(extract_fname(self.param_seg.fname_im)[1:]), '_gmseg')
self.fname_res_wmseg = self.param_seg.path_results + add_suffix(''.join(extract_fname(self.param_seg.fname_im)[1:]), '_wmseg')
self.im_res_gmseg.setFileName(self.fname_res_gmseg)
self.im_res_wmseg.setFileName(self.fname_res_wmseg)
self.im_res_gmseg.save()
self.im_res_wmseg.save()
def segment(self):
self.copy_data_to_tmp()
# go to tmp directory
curdir = os.getcwd()
os.chdir(self.tmp_dir)
# load model
self.model.load_model()
self.target_im, self.info_preprocessing = pre_processing(self.param_seg.fname_im, self.param_seg.fname_seg, self.param_seg.fname_level, new_res=self.param_data.axial_res, square_size_size_mm=self.param_data.square_size_size_mm, denoising=self.param_data.denoising, verbose=self.param.verbose, rm_tmp=self.param.rm_tmp)
printv('\nRegister target image to model data...', self.param.verbose, 'normal')
# register target image to model dictionary space
path_warp = self.register_target()
if self.param_data.normalization:
printv('\nNormalize intensity of target image...', self.param.verbose, 'normal')
self.normalize_target()
printv('\nProject target image into the model reduced space...', self.param.verbose, 'normal')
self.project_target()
printv('\nCompute similarities between target slices and model slices using model reduced space...', self.param.verbose, 'normal')
list_dic_indexes_by_slice = self.compute_similarities()
printv('\nLabel fusion of model slices most similar to target slices...', self.param.verbose, 'normal')
self.label_fusion(list_dic_indexes_by_slice)
printv('\nWarp back segmentation into image space...', self.param.verbose, 'normal')
self.warp_back_seg(path_warp)
printv('\nPost-processing...', self.param.verbose, 'normal')
self.im_res_gmseg, self.im_res_wmseg = self.post_processing()
if (self.param_seg.path_results != './') and (not os.path.exists(os.path.join(curdir, self.param_seg.path_results))):
# create output folder
printv('\nCreate output folder ...', self.param.verbose, 'normal')
os.chdir(curdir)
os.mkdir(self.param_seg.path_results)
os.chdir(self.tmp_dir)
if self.param_seg.fname_manual_gmseg is not None:
# compute validation metrics
printv('\nCompute validation metrics...', self.param.verbose, 'normal')
self.validation()
# go back to original directory
os.chdir(curdir)
printv('\nSave resulting GM and WM segmentations...', self.param.verbose, 'normal')
self.fname_res_gmseg = os.path.join(self.param_seg.path_results, add_suffix(''.join(extract_fname(self.param_seg.fname_im)[1:]), '_gmseg'))
self.fname_res_wmseg = os.path.join(self.param_seg.path_results, add_suffix(''.join(extract_fname(self.param_seg.fname_im)[1:]), '_wmseg'))
self.im_res_gmseg.absolutepath = self.fname_res_gmseg
self.im_res_wmseg.absolutepath = self.fname_res_wmseg
self.im_res_gmseg.save()
self.im_res_wmseg.save()
def reorient_data(self):
for f in self.fname_metric_lst:
os.rename(
self.fname_metric_lst[f],
sct.add_suffix(
''.join(sct.extract_fname(self.param.fname_im)[1:]),
'_2reorient'))
im = Image(sct.add_suffix(''.join(sct.extract_fname(self.param.fname_im)[1:]), '_2reorient')) \
.change_orientation(self.orientation_im) \
.save(self.fname_metric_lst[f])
def compute(self):
fname_data = self.fmri
# # create temporary folder
# sct.printv('\nCreate temporary folder...', self.param.verbose)
# path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S/")
# status, output = sct.run('mkdir '+path_tmp, self.param.verbose)
# # motion correct the fmri data
# # sct.printv('\nMotion correct the fMRI data...', self.param.verbose, 'normal')
# path_fmri, fname_fmri, ext_fmri = sct.extract_fname(self.fmri)
# fname_fmri_moco = fname_fmri
# # print sct.slash_at_the_end(path_fmri) + fname_fmri
# # sct.run('mcflirt -in ' + sct.slash_at_the_end(path_fmri, 1) + fname_fmri + ' -out ' + fname_fmri_moco)
# compute tsnr
sct.printv('\nCompute the tSNR...', self.param.verbose, 'normal')
fname_data_mean = sct.add_suffix(fname_data, '_mean.nii')
sct.run('sct_maths -i ' + fname_data + ' -o ' + fname_data_mean +
' -mean t')
# if not average_data_across_dimension(fname_data, fname_data_mean, 3):
# sct.printv('ERROR in average_data_across_dimension', 1, 'error')
# sct.run('fslmaths ' + fname_data + ' -Tmean ' + fname_data_mean)
fname_data_std = sct.add_suffix(fname_data, '_std.nii')
sct.run('sct_maths -i ' + fname_data + ' -o ' + fname_data_std +
' -mean t')
# if not average_data_across_dimension(fname_data, fname_data_std, 3, 1):
# sct.printv('ERROR in average_data_across_dimension', 1, 'error')
# sct.run('fslmaths ' + fname_data + ' -Tstd ' + fname_data_std)
fname_tsnr = sct.add_suffix(fname_data, '_tsnr')
from msct_image import Image
nii_mean = Image(fname_data_mean)
data_mean = nii_mean.data
data_std = Image(fname_data_std).data
data_tsnr = data_mean / data_std
nii_tsnr = nii_mean
nii_tsnr.data = data_tsnr
nii_tsnr.setFileName(fname_tsnr)
nii_tsnr.save()
# sct.run('fslmaths ' + fname_data_mean + ' -div ' + fname_data_std + ' ' + fname_tsnr)
# Remove temp files
sct.printv('\nRemove temporary files...', self.param.verbose, 'normal')
import os
os.remove(fname_data_mean)
os.remove(fname_data_std)
# to view results
sct.printv('\nDone! To view results, type:', self.param.verbose,
'normal')
sct.printv('fslview ' + fname_tsnr + ' &\n', self.param.verbose,
'info')
def compute(self):
fname_data = self.fmri
# # create temporary folder
# sct.printv('\nCreate temporary folder...', self.param.verbose)
# path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S/")
# status, output = sct.run('mkdir '+path_tmp, self.param.verbose)
# # motion correct the fmri data
# # sct.printv('\nMotion correct the fMRI data...', self.param.verbose, 'normal')
# path_fmri, fname_fmri, ext_fmri = sct.extract_fname(self.fmri)
# fname_fmri_moco = fname_fmri
# # print sct.slash_at_the_end(path_fmri) + fname_fmri
# # sct.run('mcflirt -in ' + sct.slash_at_the_end(path_fmri, 1) + fname_fmri + ' -out ' + fname_fmri_moco)
# compute mean
fname_data_mean = sct.add_suffix(fname_data, '_mean')
sct_maths.main(
args=['-i', fname_data, '-o', fname_data_mean, '-mean', 't'])
# compute STD
fname_data_std = sct.add_suffix(fname_data, '_std')
sct_maths.main(
args=['-i', fname_data, '-o', fname_data_std, '-std', 't'])
# compute tSNR
fname_tsnr = sct.add_suffix(fname_data, '_tsnr')
from msct_image import Image
nii_mean = Image(fname_data_mean)
data_mean = nii_mean.data
data_std = Image(fname_data_std).data
data_tsnr = data_mean / data_std
nii_tsnr = nii_mean
nii_tsnr.data = data_tsnr
nii_tsnr.setFileName(fname_tsnr)
nii_tsnr.save()
# Remove temp files
sct.printv('\nRemove temporary files...', self.param.verbose, 'normal')
import os
os.remove(fname_data_mean)
os.remove(fname_data_std)
# to view results
sct.printv('\nDone! To view results, type:', self.param.verbose,
'normal')
sct.printv('fslview ' + fname_tsnr + ' &\n', self.param.verbose,
'info')
def compute(self):
fname_data = self.fmri
# # create temporary folder
# sct.printv('\nCreate temporary folder...', self.param.verbose)
# path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S/")
# status, output = sct.run('mkdir '+path_tmp, self.param.verbose)
# # motion correct the fmri data
# # sct.printv('\nMotion correct the fMRI data...', self.param.verbose, 'normal')
# path_fmri, fname_fmri, ext_fmri = sct.extract_fname(self.fmri)
# fname_fmri_moco = fname_fmri
# # print sct.slash_at_the_end(path_fmri) + fname_fmri
# # sct.run('mcflirt -in ' + sct.slash_at_the_end(path_fmri, 1) + fname_fmri + ' -out ' + fname_fmri_moco)
# compute tsnr
sct.printv('\nCompute the tSNR...', self.param.verbose, 'normal')
fname_data_mean = sct.add_suffix(fname_data, '_mean')
sct.run('sct_maths -i '+fname_data+' -o '+fname_data_mean+' -mean t')
# if not average_data_across_dimension(fname_data, fname_data_mean, 3):
# sct.printv('ERROR in average_data_across_dimension', 1, 'error')
# sct.run('fslmaths ' + fname_data + ' -Tmean ' + fname_data_mean)
fname_data_std = sct.add_suffix(fname_data, '_std')
sct.run('sct_maths -i '+fname_data+' -o '+fname_data_std+' -mean t')
# if not average_data_across_dimension(fname_data, fname_data_std, 3, 1):
# sct.printv('ERROR in average_data_across_dimension', 1, 'error')
# sct.run('fslmaths ' + fname_data + ' -Tstd ' + fname_data_std)
fname_tsnr = sct.add_suffix(fname_data, '_tsnr')
from msct_image import Image
nii_mean = Image(fname_data_mean)
data_mean = nii_mean.data
data_std = Image(fname_data_std).data
data_tsnr = data_mean/data_std
nii_tsnr = nii_mean
nii_tsnr.data = data_tsnr
nii_tsnr.setFileName(fname_tsnr)
nii_tsnr.save()
# sct.run('fslmaths ' + fname_data_mean + ' -div ' + fname_data_std + ' ' + fname_tsnr)
# Remove temp files
sct.printv('\nRemove temporary files...', self.param.verbose, 'normal')
import os
os.remove(fname_data_mean)
os.remove(fname_data_std)
# to view results
sct.printv('\nDone! To view results, type:', self.param.verbose, 'normal')
sct.printv('fslview '+fname_tsnr+' &\n', self.param.verbose, 'info')
def test_integrity(param_test):
"""
Test integrity of function
"""
fname_src = param_test.dict_args_with_path["-i"]
fname_ref = param_test.dict_args_with_path["-d"]
fname_dst = sct.add_suffix(os.path.basename(fname_src), "_reg")
#fname_dst = "output.nii.gz"
img_src = msct_image.Image(fname_src)
img_ref = msct_image.Image(fname_ref)
img_dst = msct_image.Image(fname_dst)
if img_dst.orientation != img_ref.orientation:
param_test.output += "\nImage has wrong orientation (%s -> %s)" \
% (img_ref.orientation, img_dst.orientation)
param_test.status = 1
if len(img_src.data.shape) > 3:
# Allowed failure for now
return param_test
if not (img_dst.data != 0).any():
param_test.output += "\nImage is garbage (all zeros)"
param_test.status = 1
return param_test
def multicomponent_merge(fname_list):
from numpy import zeros
# WARNING: output multicomponent is not optimal yet, some issues may be related to the use of this function
im_0 = Image(fname_list[0])
new_shape = list(im_0.data.shape)
if len(new_shape) == 3:
new_shape.append(1)
new_shape.append(len(fname_list))
new_shape = tuple(new_shape)
data_out = zeros(new_shape)
for i, fname in enumerate(fname_list):
im = Image(fname)
dat = im.data
if len(dat.shape) == 2:
data_out[:, :, 0, 0, i] = dat.astype('float32')
elif len(dat.shape) == 3:
data_out[:, :, :, 0, i] = dat.astype('float32')
elif len(dat.shape) == 4:
data_out[:, :, :, :, i] = dat.astype('float32')
del im
del dat
im_out = im_0.copy()
im_out.data = data_out.astype('float32')
im_out.hdr.set_intent('vector', (), '')
im_out.absolutepath = sct.add_suffix(im_out.absolutepath, '_multicomponent')
return im_out
def resample_file(fname_data, fname_out, new_size, new_size_type,
interpolation, verbose):
"""This function will resample the specified input
image file to the target size.
Can deal with 2d, 3d or 4d image objects.
:param fname_data: The input image filename.
:param fname_out: The output image filename.
:param new_size: The target size, i.e. 0.25x0.25
:param new_size_type: Unit of resample (mm, vox, factor)
:param interpolation: The interpolation type
:param verbose: verbosity level
"""
# Load data
sct.printv('\nLoad data...', verbose)
nii = nipy.load_image(fname_data)
nii_r = resample_image(nii, new_size, new_size_type, interpolation,
verbose)
# build output file name
if fname_out == '':
fname_out = sct.add_suffix(fname_data, '_r')
else:
fname_out = fname_out
# save data
nipy.save_image(nii_r, fname_out)
# to view results
sct.display_viewer_syntax([fname_out], verbose=verbose)
return nii_r
def multicomponent_merge(fname_list):
from numpy import zeros
# WARNING: output multicomponent is not optimal yet, some issues may be related to the use of this function
im_0 = Image(fname_list[0])
new_shape = list(im_0.data.shape)
if len(new_shape) == 3:
new_shape.append(1)
new_shape.append(len(fname_list))
new_shape = tuple(new_shape)
data_out = zeros(new_shape)
for i, fname in enumerate(fname_list):
im = Image(fname)
dat = im.data
if len(dat.shape) == 2:
data_out[:, :, 0, 0, i] = dat.astype('float32')
elif len(dat.shape) == 3:
data_out[:, :, :, 0, i] = dat.astype('float32')
elif len(dat.shape) == 4:
data_out[:, :, :, :, i] = dat.astype('float32')
del im
del dat
im_out = im_0.copy()
im_out.data = data_out.astype('float32')
im_out.hdr.set_intent('vector', (), '')
im_out.absolutepath = sct.add_suffix(im_out.absolutepath,
'_multicomponent')
return im_out
def load_manual_gmseg(list_slices_target,
list_fname_manual_gmseg,
tmp_dir,
im_sc_seg_rpi,
new_res,
square_size_size_mm,
for_model=False,
fname_mask=None):
if isinstance(list_fname_manual_gmseg, str):
# consider fname_manual_gmseg as a list of file names to allow multiple manual GM segmentation
list_fname_manual_gmseg = [list_fname_manual_gmseg]
for fname_manual_gmseg in list_fname_manual_gmseg:
os.chdir('..')
shutil.copy(fname_manual_gmseg, tmp_dir)
# change fname level to only file name (path = tmp dir now)
path_gm, file_gm, ext_gm = extract_fname(fname_manual_gmseg)
fname_manual_gmseg = file_gm + ext_gm
os.chdir(tmp_dir)
im_manual_gmseg = Image(fname_manual_gmseg)
# reorient to RPI
im_manual_gmseg = set_orientation(im_manual_gmseg, 'RPI')
if fname_mask is not None:
fname_gmseg_crop = add_suffix(im_manual_gmseg.absolutepath,
'_pre_crop')
crop_im = ImageCropper(input_file=im_manual_gmseg.absolutepath,
output_file=fname_gmseg_crop,
mask=fname_mask)
im_manual_gmseg_crop = crop_im.crop()
im_manual_gmseg = im_manual_gmseg_crop
# assert gmseg has the right number of slices
assert im_manual_gmseg.data.shape[2] == len(
list_slices_target
), 'ERROR: the manual GM segmentation has not the same number of slices than the image.'
# interpolate gm to reference image
nz_gmseg, nx_gmseg, ny_gmseg, nt_gmseg, pz_gmseg, px_gmseg, py_gmseg, pt_gmseg = im_manual_gmseg.dim
list_im_gm = interpolate_im_to_ref(im_manual_gmseg,
im_sc_seg_rpi,
new_res=new_res,
sq_size_size_mm=square_size_size_mm,
interpolation_mode=0)
# load gm seg in list of slices
n_poped = 0
for im_gm, slice_im in zip(list_im_gm, list_slices_target):
if im_gm.data.max() == 0 and for_model:
list_slices_target.pop(slice_im.id - n_poped)
n_poped += 1
else:
slice_im.gm_seg.append(im_gm.data)
wm_slice = (slice_im.im > 0) - im_gm.data
slice_im.wm_seg.append(wm_slice)
return list_slices_target
def change_orientation(self,
orientation,
inverse=False,
generate_path=False):
"""
Change orientation on image (in-place).
:param orientation: orientation string (SCT "from" convention)
:param inverse: if you think backwards, use this to specify that you actually
want to transform *from* the specified orientation, not *to*
it.
:param generate_path: whether to create a derived path name from the
original absolutepath (note: while it will generate
a file suffix, don't expect the suffix but rather
use the Image's absolutepath.
If not set, the absolutepath is voided.
"""
if orientation is not None:
change_orientation(self, orientation, self, inverse=inverse)
if generate_path and self._path is not None:
self._path = sct.add_suffix(self._path,
"_{}".format(orientation.lower()))
else:
# safe option: remove path to avoid overwrites
self._path = None
return self
def compute(self):
fname_data = self.fmri
# open data
nii_data = Image(fname_data)
data = nii_data.data
# compute mean
data_mean = np.mean(data, 3)
# compute STD
data_std = np.std(data, 3, ddof=1)
# compute TSNR
data_tsnr = data_mean / data_std
# save TSNR
fname_tsnr = sct.add_suffix(fname_data, '_tsnr')
nii_tsnr = nii_data
nii_tsnr.data = data_tsnr
nii_tsnr.setFileName(fname_tsnr)
nii_tsnr.save(type='float32')
# to view results
sct.printv('\nDone! To view results, type:', self.param.verbose, 'normal')
sct.printv('fslview ' + fname_tsnr + ' &\n', self.param.verbose, 'info')
def viewer_centerline(image_fname, interslice_gap, verbose):
image_input_reoriented = Image(image_fname)
nx, ny, nz, nt, px, py, pz, pt = image_input_reoriented.dim
viewer = ClickViewerPropseg(image_input_reoriented)
viewer.gap_inter_slice = int(
interslice_gap /
px) # px because the image is supposed to be SAL orientation
viewer.number_of_slices = 0
viewer.calculate_list_slices()
# start the viewer that ask the user to enter a few points along the spinal cord
mask_points = viewer.start()
if not mask_points and viewer.closed:
mask_points = viewer.list_points_useful_notation
if mask_points:
# create the mask containing either the three-points or centerline mask for initialization
mask_filename = sct.add_suffix(image_fname, "_mask_viewer")
sct.run("sct_label_utils -i " + image_fname + " -create " +
mask_points + " -o " + mask_filename,
verbose=False)
fname_output = mask_filename
else:
sct.printv(
'\nERROR: the viewer has been closed before entering all manual points. Please try again.',
1,
type='error')
fname_output = None
return fname_output
def func_rescale_header(fname_data, rescale_factor, verbose=0):
"""
Rescale the voxel dimension by modifying the NIFTI header qform. Write the output file in a temp folder.
:param fname_data:
:param rescale_factor:
:return: fname_data_rescaled
"""
import nibabel as nib
img = nib.load(fname_data)
# get qform
qform = img.header.get_qform()
# multiply by scaling factor
qform[0:3, 0:3] *= rescale_factor
# generate a new nifti file
header_rescaled = img.header.copy()
header_rescaled.set_qform(qform)
# the data are the same-- only the header changes
img_rescaled = nib.nifti1.Nifti1Image(img.get_data(),
None,
header=header_rescaled)
path_tmp = sct.tmp_create(basename="propseg", verbose=verbose)
fname_data_rescaled = os.path.join(
path_tmp, os.path.basename(sct.add_suffix(fname_data, "_rescaled")))
nib.save(img_rescaled, fname_data_rescaled)
return fname_data_rescaled
def resample_file(fname_data, fname_out, new_size, new_size_type,
interpolation, verbose):
"""This function will resample the specified input
image file to the target size.
:param fname_data: The input image filename.
:param fname_out: The output image filename.
:param new_size: The target size, i.e. 0.25x0.25
:param new_size_type: Unit of resample (mm, vox, factor)
:param interpolation: The interpolation type
:param verbose: verbosity level
"""
# Load data
sct.printv('\nLoad data...', verbose)
nii = nipy.load_image(fname_data)
nii_r = resample_image(nii, new_size, new_size_type, interpolation,
verbose)
# build output file name
if fname_out == '':
fname_out = sct.add_suffix(fname_data, '_r')
else:
fname_out = fname_out
# save data
nipy.save_image(nii_r, fname_out)
# to view results
sct.printv('\nDone! To view results, type:', verbose)
sct.printv('fslview ' + fname_out + ' &', verbose, 'info')
return nii_r
def test_integrity(param_test):
"""
Test integrity of function
"""
dice_segmentation = float('nan')
# extract name of output segmentation: data_seg.nii.gz
file_seg = os.path.join(param_test.path_output,
sct.add_suffix(param_test.file_input, '_seg'))
# open output segmentation
im_seg = Image(file_seg)
# open ground truth
im_seg_manual = Image(param_test.fname_gt)
# compute dice coefficient between generated image and image from database
dice_segmentation = compute_dice(im_seg,
im_seg_manual,
mode='3d',
zboundaries=False)
# display
param_test.output += 'Computed dice: ' + str(dice_segmentation)
param_test.output += '\nDice threshold (if computed Dice smaller: fail): ' + str(
param_test.dice_threshold)
if dice_segmentation < param_test.dice_threshold:
param_test.status = 99
param_test.output += '\n--> FAILED'
else:
param_test.output += '\n--> PASSED'
# update Panda structure
param_test.results['dice'] = dice_segmentation
return param_test
def apply_transfo(im_src, im_dest, warp, interp='spline', rm_tmp=True):
# create tmp dir and go in it
tmp_dir = sct.tmp_create()
# copy warping field to tmp dir
sct.copy(warp, tmp_dir)
warp = ''.join(extract_fname(warp)[1:])
# go to tmp dir
curdir = os.getcwd()
os.chdir(tmp_dir)
# save image and seg
fname_src = 'src.nii.gz'
im_src.save(fname_src)
fname_dest = 'dest.nii.gz'
im_dest.save(fname_dest)
# apply warping field
fname_src_reg = add_suffix(fname_src, '_reg')
sct_apply_transfo.main(
args=['-i', fname_src, '-d', fname_dest, '-w', warp, '-x', interp])
im_src_reg = Image(fname_src_reg)
# get out of tmp dir
os.chdir(curdir)
if rm_tmp:
# remove tmp dir
sct.rmtree(tmp_dir)
# return res image
return im_src_reg
def test_integrity(param_test):
"""
Test integrity of function
"""
fname_src = param_test.dict_args_with_path["-i"]
fname_ref = param_test.dict_args_with_path["-d"]
fname_dst = sct.add_suffix(os.path.basename(fname_src), "_reg")
#fname_dst = "output.nii.gz"
img_src = msct_image.Image(fname_src)
img_ref = msct_image.Image(fname_ref)
img_dst = msct_image.Image(fname_dst)
if img_dst.orientation != img_ref.orientation:
param_test.output += "\nImage has wrong orientation (%s -> %s)" \
% (img_ref.orientation, img_dst.orientation)
param_test.status = 1
if len(img_src.data.shape) > 3:
# Allowed failure for now
return param_test
if not (img_dst.data != 0).any():
param_test.output += "\nImage is garbage (all zeros)"
param_test.status = 1
return param_test
def test_integrity(param_test):
"""
Test integrity of function
"""
dice_segmentation = float('nan')
# extract name of output segmentation: data_seg.nii.gz
file_seg = os.path.join(param_test.path_output, sct.add_suffix(param_test.file_input, '_seg'))
# open output segmentation
im_seg = Image(file_seg)
# open ground truth
im_seg_manual = Image(param_test.fname_gt)
# compute dice coefficient between generated image and image from database
dice_segmentation = compute_dice(im_seg, im_seg_manual, mode='3d', zboundaries=False)
# display
param_test.output += 'Computed dice: '+str(dice_segmentation)
param_test.output += '\nDice threshold (if computed Dice smaller: fail): '+str(param_test.dice_threshold)
if dice_segmentation < param_test.dice_threshold:
param_test.status = 99
param_test.output += '\n--> FAILED'
else:
param_test.output += '\n--> PASSED'
# update Panda structure
param_test.results['dice'] = dice_segmentation
return param_test
def change_shape(self, shape, generate_path=False):
"""
Change data shape (in-place)
:param generate_path: whether to create a derived path name from the
original absolutepath (note: while it will generate
a file suffix, don't expect the suffix but rather
use the Image's absolutepath.
If not set, the absolutepath is voided.
This is mostly useful for adding/removing a fourth dimension,
you probably don't want to use this function.
"""
if shape is not None:
change_shape(self, shape, self)
if generate_path and self._path is not None:
self._path = sct.add_suffix(
self._path,
"_shape-{}".format("-".join([str(x) for x in shape])))
else:
# safe option: remove path to avoid overwrites
self._path = None
return self
def register_data(im_src, im_dest, param_reg, path_copy_warp=None, rm_tmp=True):
'''
Parameters
----------
im_src: class Image: source image
im_dest: class Image: destination image
param_reg: str: registration parameter
path_copy_warp: path: path to copy the warping fields
Returns: im_src_reg: class Image: source image registered on destination image
-------
'''
# im_src and im_dest are already preprocessed (in theory: im_dest = mean_image)
# binarize images to get seg
im_src_seg = binarize(im_src, thr_min=1, thr_max=1)
im_dest_seg = binarize(im_dest)
# create tmp dir and go in it
tmp_dir = tmp_create()
os.chdir(tmp_dir)
# save image and seg
fname_src = 'src.nii.gz'
im_src.setFileName(fname_src)
im_src.save()
fname_src_seg = 'src_seg.nii.gz'
im_src_seg.setFileName(fname_src_seg)
im_src_seg.save()
fname_dest = 'dest.nii.gz'
im_dest.setFileName(fname_dest)
im_dest.save()
fname_dest_seg = 'dest_seg.nii.gz'
im_dest_seg.setFileName(fname_dest_seg)
im_dest_seg.save()
# do registration using param_reg
sct_register_multimodal.main(args=['-i', fname_src,
'-d', fname_dest,
'-iseg', fname_src_seg,
'-dseg', fname_dest_seg,
'-param', param_reg])
# get registration result
fname_src_reg = add_suffix(fname_src, '_reg')
im_src_reg = Image(fname_src_reg)
# get out of tmp dir
os.chdir('..')
# copy warping fields
if path_copy_warp is not None and os.path.isdir(os.path.abspath(path_copy_warp)):
path_copy_warp = os.path.abspath(path_copy_warp)
file_src = extract_fname(fname_src)[1]
file_dest = extract_fname(fname_dest)[1]
fname_src2dest = 'warp_' + file_src +'2' + file_dest +'.nii.gz'
fname_dest2src = 'warp_' + file_dest +'2' + file_src +'.nii.gz'
shutil.copy(tmp_dir +'/' + fname_src2dest, path_copy_warp + '/')
shutil.copy(tmp_dir + '/' + fname_dest2src, path_copy_warp + '/')
if rm_tmp:
# remove tmp dir
shutil.rmtree(tmp_dir)
# return res image
return im_src_reg, fname_src2dest, fname_dest2src
def apply_transfo(im_src, im_dest, warp, interp='spline', rm_tmp=True):
# create tmp dir and go in it
tmp_dir = tmp_create()
# copy warping field to tmp dir
shutil.copy(warp, tmp_dir)
warp = ''.join(extract_fname(warp)[1:])
# go to tmp dir
os.chdir(tmp_dir)
# save image and seg
fname_src = 'src.nii.gz'
im_src.setFileName(fname_src)
im_src.save()
fname_dest = 'dest.nii.gz'
im_dest.setFileName(fname_dest)
im_dest.save()
# apply warping field
fname_src_reg = add_suffix(fname_src, '_reg')
sct_apply_transfo.main(args=['-i', fname_src,
'-d', fname_dest,
'-w', warp,
'-x', interp])
im_src_reg = Image(fname_src_reg)
# get out of tmp dir
os.chdir('..')
if rm_tmp:
# remove tmp dir
shutil.rmtree(tmp_dir)
# return res image
return im_src_reg
def resample_file(fname_data, fname_out, new_size, new_size_type, interpolation, verbose, fname_ref=None):
"""This function will resample the specified input
image file to the target size.
Can deal with 2d, 3d or 4d image objects.
:param fname_data: The input image filename.
:param fname_out: The output image filename.
:param new_size: The target size, i.e. 0.25x0.25
:param new_size_type: Unit of resample (mm, vox, factor)
:param interpolation: The interpolation type
:param verbose: verbosity level
:param fname_ref: Reference image to resample input image to
"""
# Load data
logger.info('load data...')
nii = nib.load(fname_data)
if fname_ref is not None:
nii_ref = nib.load(fname_ref)
else:
nii_ref = None
nii_r = resample_nib(nii, new_size.split('x'), new_size_type, img_dest=nii_ref, interpolation=interpolation)
# build output file name
if fname_out == '':
fname_out = sct.add_suffix(fname_data, '_r')
else:
fname_out = fname_out
# save data
nib.save(nii_r, fname_out)
# to view results
sct.display_viewer_syntax([fname_out], verbose=verbose)
return nii_r
def main(fname_anat, fname_centerline, degree_poly, centerline_fitting, interp,
remove_temp_files, verbose):
# load input image
im_anat = Image(fname_anat)
nx, ny, nz, nt, px, py, pz, pt = im_anat.dim
# re-oriente to RPI
orientation_native = im_anat.orientation
im_anat.change_orientation("RPI")
# load centerline
im_centerline = Image(fname_centerline).change_orientation("RPI")
# smooth centerline and return fitted coordinates in voxel space
x_centerline_fit, y_centerline_fit, z_centerline, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = smooth_centerline(
im_centerline,
algo_fitting=centerline_fitting,
type_window='hanning',
window_length=50,
nurbs_pts_number=3000,
phys_coordinates=False,
verbose=verbose,
all_slices=True)
# compute translation for each slice, such that the flattened centerline is centered in the medial plane (R-L) and
# avoid discontinuity in slices where there is no centerline (in which case, simply copy the translation of the
# closest Z).
# first, get zmin and zmax spanned by the centerline (i.e. with non-zero values)
indz_centerline = np.where(
[np.sum(im_centerline.data[:, :, iz]) for iz in range(nz)])[0]
zmin, zmax = indz_centerline[0], indz_centerline[-1]
# then, extend the centerline by copying values below zmin and above zmax
x_centerline_extended = np.concatenate([
np.ones(zmin) * x_centerline_fit[0], x_centerline_fit,
np.ones(nz - zmax) * x_centerline_fit[-1]
])
# loop across slices and apply translation
im_anat_flattened = msct_image.change_type(im_anat, np.float32)
# change type to float32 because of subsequent conversion (img_as_float). See #1790
for iz in range(nz):
# compute translation along x (R-L)
translation_x = x_centerline_extended[iz] - np.round(nx / 2.0)
# apply transformation to 2D image with linear interpolation
# tform = tf.SimilarityTransform(scale=1, rotation=0, translation=(translation_x, 0))
tform = transform.SimilarityTransform(translation=(0, translation_x))
# important to force input in float to skikit image, because it will output float values
img = img_as_float(im_anat.data[:, :, iz])
img_reg = transform.warp(img, tform)
im_anat_flattened.data[:, :, iz] = img_reg # img_as_uint(img_reg)
# change back to native orientation
im_anat_flattened.change_orientation(orientation_native)
# save output
fname_out = sct.add_suffix(fname_anat, '_flatten')
im_anat_flattened.save(fname_out)
sct.display_viewer_syntax([fname_anat, fname_out])
def savePredictions(predictions, path_output, list_images, segmentation_image_size):
number_of_images = len(list_images)
predictions = numpy.reshape(predictions, [number_of_images, segmentation_image_size, segmentation_image_size, NUM_LABELS])
predictions = predictions[:, :, :, 1]
for i, pref in enumerate(predictions):
im_pred = Image(pref)
im_pred.setFileName(path_output+sct.add_suffix(list_images[i], '_pred'))
im_pred.save()
def prepare(list_images):
fname_images, orientation_images = [], []
for fname_im in list_images:
from sct_image import orientation
orientation_images.append(orientation(Image(fname_im), get=True, verbose=False))
path_fname, file_fname, ext_fname = sct.extract_fname(fname_im)
reoriented_image_filename = 'tmp.' + sct.add_suffix(file_fname + ext_fname, "_SAL")
sct.run('sct_image -i ' + fname_im + ' -o ' + reoriented_image_filename + ' -setorient SAL -v 0', verbose=False)
fname_images.append(reoriented_image_filename)
return fname_images, orientation_images
def compute_texture(self):
offset = int(self.param_glcm.distance)
printv('\nCompute texture metrics...', self.param.verbose, 'normal')
# open image and re-orient it to RPI if needed
im_tmp = Image(self.param.fname_im)
if self.orientation_im != self.orientation_extraction:
im_tmp = set_orientation(im_tmp, self.orientation_extraction)
dct_metric = {}
for m in self.metric_lst:
im_2save = im_tmp.copy()
im_2save.changeType(type='float64')
im_2save.data *= 0
dct_metric[m] = im_2save
# dct_metric[m] = Image(self.fname_metric_lst[m])
timer = Timer(number_of_iteration=len(self.dct_im_seg['im']))
timer.start()
for im_z, seg_z, zz in zip(self.dct_im_seg['im'], self.dct_im_seg['seg'], range(len(self.dct_im_seg['im']))):
for xx in range(im_z.shape[0]):
for yy in range(im_z.shape[1]):
if not seg_z[xx, yy]:
continue
if xx < offset or yy < offset:
continue
if xx > (im_z.shape[0] - offset - 1) or yy > (im_z.shape[1] - offset - 1):
continue # to check if the whole glcm_window is in the axial_slice
if False in np.unique(seg_z[xx - offset: xx + offset + 1, yy - offset: yy + offset + 1]):
continue # to check if the whole glcm_window is in the mask of the axial_slice
glcm_window = im_z[xx - offset: xx + offset + 1, yy - offset: yy + offset + 1]
glcm_window = glcm_window.astype(np.uint8)
dct_glcm = {}
for a in self.param_glcm.angle.split(','): # compute the GLCM for self.param_glcm.distance and for each self.param_glcm.angle
dct_glcm[a] = greycomatrix(glcm_window,
[self.param_glcm.distance], [radians(int(a))],
symmetric=self.param_glcm.symmetric,
normed=self.param_glcm.normed)
for m in self.metric_lst: # compute the GLCM property (m.split('_')[0]) of the voxel xx,yy,zz
dct_metric[m].data[xx, yy, zz] = greycoprops(dct_glcm[m.split('_')[2]], m.split('_')[0])[0][0]
timer.add_iteration()
timer.stop()
for m in self.metric_lst:
fname_out = add_suffix(''.join(extract_fname(self.param.fname_im)[1:]), '_' + m)
dct_metric[m].setFileName(fname_out)
dct_metric[m].save()
self.fname_metric_lst[m] = fname_out
def label_segmentation(fname_seg, list_disc_z, list_disc_value, verbose=1):
"""
Label segmentation image
:param fname_seg: fname of the segmentation, no orientation expected
:param list_disc_z: list of z that correspond to a disc
:param list_disc_value: list of associated disc values
:param verbose:
:return:
"""
# open segmentation
seg = Image(fname_seg)
init_orientation = seg.orientation
seg.change_orientation("RPI")
dim = seg.dim
ny = dim[1]
nz = dim[2]
# loop across z
for iz in range(nz):
# get index of the disc right above iz
try:
ind_above_iz = max(
[i for i in range(len(list_disc_z)) if list_disc_z[i] > iz])
except ValueError:
# if ind_above_iz is empty, attribute value 0
vertebral_level = 0
else:
# assign vertebral level (add one because iz is BELOW the disk)
vertebral_level = list_disc_value[ind_above_iz] + 1
# sct.printv(vertebral_level)
# get voxels in mask
ind_nonzero = np.nonzero(seg.data[:, :, iz])
seg.data[ind_nonzero[0], ind_nonzero[1], iz] = vertebral_level
# if verbose == 2:
# # move to OO. No time to finish... (JCA)
# from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
# from matplotlib.figure import Figure
# fig = Figure()
# FigureCanvas(fig)
# ax = fig.add_subplot(111)
# ax.scatter(int(np.round(ny / 2)), iz, c=vertebral_level, vmin=min(list_disc_value),
# vmax=max(list_disc_value), cmap='prism', marker='_', s=200)
#
# # TODO: the thing below crashes with the py3k move. Fix it when i have time...
# import matplotlib
# matplotlib.use('Agg')
# import matplotlib.pyplot as plt
# plt.figure(50)
# plt.scatter(int(np.round(ny / 2)), iz, c=vertebral_level, vmin=min(list_disc_value), vmax=max(list_disc_value), cmap='prism', marker='_', s=200)
# write file
seg.change_orientation(init_orientation).save(
sct.add_suffix(fname_seg, '_labeled'))
def project_labels_on_spinalcord(fname_label, fname_seg):
"""
Project labels orthogonally on the spinal cord centerline. The algorithm works by finding the smallest distance
between each label and the spinal cord center of mass.
:param fname_label: file name of labels
:param fname_seg: file name of cord segmentation (could also be of centerline)
:return: file name of projected labels
"""
# build output name
fname_label_projected = sct.add_suffix(fname_label, "_projected")
# open labels and segmentation
im_label = Image(fname_label).change_orientation("RPI")
im_seg = Image(fname_seg)
native_orient = im_seg.orientation
im_seg.change_orientation("RPI")
# smooth centerline and return fitted coordinates in voxel space
_, arr_ctl, _ = get_centerline(im_seg, algo_fitting='bspline')
x_centerline_fit, y_centerline_fit, z_centerline = arr_ctl
# convert pixel into physical coordinates
centerline_xyz_transposed = \
[im_seg.transfo_pix2phys([[x_centerline_fit[i], y_centerline_fit[i], z_centerline[i]]])[0]
for i in range(len(x_centerline_fit))]
# transpose list
centerline_phys_x = [i[0] for i in centerline_xyz_transposed]
centerline_phys_y = [i[1] for i in centerline_xyz_transposed]
centerline_phys_z = [i[2] for i in centerline_xyz_transposed]
# get center of mass of label
labels = im_label.getCoordinatesAveragedByValue()
# initialize image of projected labels. Note that we use the space of the seg (not label).
im_label_projected = msct_image.zeros_like(im_seg, dtype=np.uint8)
# loop across label values
for label in labels:
# convert pixel into physical coordinates for the label
label_phys_x, label_phys_y, label_phys_z = im_label.transfo_pix2phys([[label.x, label.y, label.z]])[0]
# calculate distance between label and each point of the centerline
distance_centerline = [np.linalg.norm([centerline_phys_x[i] - label_phys_x,
centerline_phys_y[i] - label_phys_y,
centerline_phys_z[i] - label_phys_z])
for i in range(len(x_centerline_fit))]
# get the index corresponding to the min distance
ind_min_distance = np.argmin(distance_centerline)
# get centerline coordinate (in physical space)
[min_phy_x, min_phy_y, min_phy_z] = [centerline_phys_x[ind_min_distance],
centerline_phys_y[ind_min_distance],
centerline_phys_z[ind_min_distance]]
# convert coordinate to voxel space
minx, miny, minz = im_seg.transfo_phys2pix([[min_phy_x, min_phy_y, min_phy_z]])[0]
# use that index to assign projected label in the centerline
im_label_projected.data[minx, miny, minz] = label.value
# re-orient projected labels to native orientation and save
im_label_projected.change_orientation(native_orient).save(fname_label_projected)
return fname_label_projected
def pad_image(im,
pad_x_i=0,
pad_x_f=0,
pad_y_i=0,
pad_y_f=0,
pad_z_i=0,
pad_z_f=0):
nx, ny, nz, nt, px, py, pz, pt = im.dim
pad_x_i, pad_x_f, pad_y_i, pad_y_f, pad_z_i, pad_z_f = int(pad_x_i), int(
pad_x_f), int(pad_y_i), int(pad_y_f), int(pad_z_i), int(pad_z_f)
if len(im.data.shape) == 2:
new_shape = list(im.data.shape)
new_shape.append(1)
im.data = im.data.reshape(new_shape)
# initialize padded_data, with same type as im.data
padded_data = np.zeros((nx + pad_x_i + pad_x_f, ny + pad_y_i + pad_y_f,
nz + pad_z_i + pad_z_f),
dtype=im.data.dtype)
if pad_x_f == 0:
pad_x_f = None
elif pad_x_f > 0:
pad_x_f *= -1
if pad_y_f == 0:
pad_y_f = None
elif pad_y_f > 0:
pad_y_f *= -1
if pad_z_f == 0:
pad_z_f = None
elif pad_z_f > 0:
pad_z_f *= -1
padded_data[pad_x_i:pad_x_f, pad_y_i:pad_y_f, pad_z_i:pad_z_f] = im.data
im_out = im.copy()
# TODO: Do not copy the Image(), because the dim field and hdr.get_data_shape() will not be updated properly.
# better to just create a new Image() from scratch.
im_out.data = padded_data # done after the call of the function
im_out.absolutepath = sct.add_suffix(im_out.absolutepath, "_pad")
# adapt the origin in the sform and qform matrix
new_origin = np.dot(im_out.hdr.get_qform(),
[-pad_x_i, -pad_y_i, -pad_z_i, 1])
im_out.hdr.structarr['qoffset_x'] = new_origin[0]
im_out.hdr.structarr['qoffset_y'] = new_origin[1]
im_out.hdr.structarr['qoffset_z'] = new_origin[2]
im_out.hdr.structarr['srow_x'][-1] = new_origin[0]
im_out.hdr.structarr['srow_y'][-1] = new_origin[1]
im_out.hdr.structarr['srow_z'][-1] = new_origin[2]
return im_out
def project_labels_on_spinalcord(fname_label, fname_seg, param_centerline):
"""
Project labels orthogonally on the spinal cord centerline. The algorithm works by finding the smallest distance
between each label and the spinal cord center of mass.
:param fname_label: file name of labels
:param fname_seg: file name of cord segmentation (could also be of centerline)
:return: file name of projected labels
"""
# build output name
fname_label_projected = sct.add_suffix(fname_label, "_projected")
# open labels and segmentation
im_label = Image(fname_label).change_orientation("RPI")
im_seg = Image(fname_seg)
native_orient = im_seg.orientation
im_seg.change_orientation("RPI")
# smooth centerline and return fitted coordinates in voxel space
_, arr_ctl, _, _ = get_centerline(im_seg, param_centerline)
x_centerline_fit, y_centerline_fit, z_centerline = arr_ctl
# convert pixel into physical coordinates
centerline_xyz_transposed = \
[im_seg.transfo_pix2phys([[x_centerline_fit[i], y_centerline_fit[i], z_centerline[i]]])[0]
for i in range(len(x_centerline_fit))]
# transpose list
centerline_phys_x = [i[0] for i in centerline_xyz_transposed]
centerline_phys_y = [i[1] for i in centerline_xyz_transposed]
centerline_phys_z = [i[2] for i in centerline_xyz_transposed]
# get center of mass of label
labels = im_label.getCoordinatesAveragedByValue()
# initialize image of projected labels. Note that we use the space of the seg (not label).
im_label_projected = msct_image.zeros_like(im_seg, dtype=np.uint8)
# loop across label values
for label in labels:
# convert pixel into physical coordinates for the label
label_phys_x, label_phys_y, label_phys_z = im_label.transfo_pix2phys([[label.x, label.y, label.z]])[0]
# calculate distance between label and each point of the centerline
distance_centerline = [np.linalg.norm([centerline_phys_x[i] - label_phys_x,
centerline_phys_y[i] - label_phys_y,
centerline_phys_z[i] - label_phys_z])
for i in range(len(x_centerline_fit))]
# get the index corresponding to the min distance
ind_min_distance = np.argmin(distance_centerline)
# get centerline coordinate (in physical space)
[min_phy_x, min_phy_y, min_phy_z] = [centerline_phys_x[ind_min_distance],
centerline_phys_y[ind_min_distance],
centerline_phys_z[ind_min_distance]]
# convert coordinate to voxel space
minx, miny, minz = im_seg.transfo_phys2pix([[min_phy_x, min_phy_y, min_phy_z]])[0]
# use that index to assign projected label in the centerline
im_label_projected.data[minx, miny, minz] = label.value
# re-orient projected labels to native orientation and save
im_label_projected.change_orientation(native_orient).save(fname_label_projected)
return fname_label_projected
def __init__(self, im, v=1):
sct.printv('Thinning ... ', v, 'normal')
self.image = im
self.image.data = bin_data(self.image.data)
self.dim_im = len(self.image.data.shape)
if self.dim_im == 2:
self.thinned_image = msct_image.empty_like(self.image)
self.thinned_image.data = self.zhang_suen(self.image.data)
self.thinned_image.absolutepath = sct.add_suffix(self.image.absolutepath, "_thinned")
elif self.dim_im == 3:
if not self.image.orientation == 'IRP':
sct.printv('-- changing orientation ...')
self.image.change_orientation('IRP')
thinned_data = np.asarray([self.zhang_suen(im_slice) for im_slice in self.image.data])
self.thinned_image = msct_image.empty_like(self.image)
self.thinned_image.data = thinned_data
self.thinned_image.absolutepath = sct.add_suffix(self.image.absolutepath, "_thinned")
def __init__(self, im, v=1):
sct.printv('Thinning ... ', v, 'normal')
self.image = im
self.image.data = bin_data(self.image.data)
self.dim_im = len(self.image.data.shape)
if self.dim_im == 2:
self.thinned_image = msct_image.empty_like(self.image)
self.thinned_image.data = self.zhang_suen(self.image.data)
self.thinned_image.absolutepath = sct.add_suffix(self.image.absolutepath, "_thinned")
elif self.dim_im == 3:
if not self.image.orientation == 'IRP':
sct.printv('-- changing orientation ...')
self.image.change_orientation('IRP')
thinned_data = np.asarray([self.zhang_suen(im_slice) for im_slice in self.image.data])
self.thinned_image = msct_image.empty_like(self.image)
self.thinned_image.data = thinned_data
self.thinned_image.absolutepath = sct.add_suffix(self.image.absolutepath, "_thinned")
def resample_image(fname, suffix='_resampled.nii.gz', binary=False, npx=0.3, npy=0.3, thr=0.0, interpolation='spline'):
"""
Resampling function: add a padding, resample, crop the padding
:param fname: name of the image file to be resampled
:param suffix: suffix added to the original fname after resampling
:param binary: boolean, image is binary or not
:param npx: new pixel size in the x direction
:param npy: new pixel size in the y direction
:param thr: if the image is binary, it will be thresholded at thr (default=0) after the resampling
:param interpolation: type of interpolation used for the resampling
:return: file name after resampling (or original fname if it was already in the correct resolution)
"""
im_in = Image(fname)
orientation = im_in.orientation
if orientation != 'RPI':
fname = im_in.change_orientation(im_in, 'RPI', generate_path=True).save().absolutepath
nx, ny, nz, nt, px, py, pz, pt = im_in.dim
if np.round(px, 2) != np.round(npx, 2) or np.round(py, 2) != np.round(npy, 2):
name_resample = sct.extract_fname(fname)[1] + suffix
if binary:
interpolation = 'nn'
if nz == 1:
# when data is 2d: we convert it to a 3d image in order to avoid conversion problem with 2d data
# TODO: check if this above problem is still present (now that we are using nibabel instead of nipy)
sct.run(['sct_image', '-i', ','.join([fname, fname]), '-concat', 'z', '-o', fname])
sct.run(['sct_resample', '-i', fname, '-mm', str(npx) + 'x' + str(npy) + 'x' + str(pz), '-o', name_resample, '-x', interpolation])
if nz == 1: # when input data was 2d: re-convert data 3d-->2d
sct.run(['sct_image', '-i', name_resample, '-split', 'z'])
im_split = Image(name_resample.split('.nii.gz')[0] + '_Z0000.nii.gz')
im_split.save(name_resample)
if binary:
sct.run(['sct_maths', '-i', name_resample, '-bin', str(thr), '-o', name_resample])
if orientation != 'RPI':
name_resample = Image(name_resample) \
.change_orientation(orientation, generate_path=True) \
.save() \
.absolutepath
return name_resample
else:
if orientation != 'RPI':
fname = sct.add_suffix(fname, "_RPI")
im_in = msct_image.change_orientation(im_in, orientation).save(fname)
sct.printv('Image resolution already ' + str(npx) + 'x' + str(npy) + 'xpz')
return fname
def main(args=None):
parser = get_parser()
param = Param()
arguments = parser.parse(sys.argv[1:])
fname_src = arguments['-i']
fname_dst = arguments.get("-o", sct.add_suffix(fname_src, "_tsnr"))
verbose = int(arguments['-v'])
# call main function
tsnr = Tsnr(param=param, fmri=fname_src, out=fname_dst)
tsnr.compute()
def crop_im(fname_im, fname_mask):
fname_im_crop = sct.add_suffix(fname_im, "_crop")
status, output_crop = sct.run("sct_crop_image -i " + fname_im + " -m " + fname_mask + " -o " + fname_im_crop)
output_list = output_crop.split("\n")
xi, xf, yi, yf, zi, zf = 0, 0, 0, 0, 0, 0
for line in output_list:
if "Dimension 0" in line:
dim, i, xi, xf = line.split(" ")
if "Dimension 1" in line:
dim, i, yi, yf = line.split(" ")
if "Dimension 2" in line:
dim, i, zi, zf = line.split(" ")
return fname_im_crop, int(xi), int(xf), int(yi), int(yf), int(zi), int(zf)
def crop_im(fname_im, fname_mask):
fname_im_crop = sct.add_suffix(fname_im, '_crop')
status, output_crop = sct.run(['sct_crop_image', '-i', fname_im, '-m', fname_mask, '-o', fname_im_crop])
output_list = output_crop.split('\n')
xi, xf, yi, yf, zi, zf = 0, 0, 0, 0, 0, 0
for line in output_list:
if 'Dimension 0' in line:
dim, i, xi, xf = line.split(' ')
if 'Dimension 1' in line:
dim, i, yi, yf = line.split(' ')
if 'Dimension 2' in line:
dim, i, zi, zf = line.split(' ')
return fname_im_crop, int(xi), int(xf), int(yi), int(yf), int(zi), int(zf)
def resample_image(fname, suffix='_resampled.nii.gz', binary=False, npx=0.3, npy=0.3, thr=0.0, interpolation='spline'):
"""
Resampling function: add a padding, resample, crop the padding
:param fname: name of the image file to be resampled
:param suffix: suffix added to the original fname after resampling
:param binary: boolean, image is binary or not
:param npx: new pixel size in the x direction
:param npy: new pixel size in the y direction
:param thr: if the image is binary, it will be thresholded at thr (default=0) after the resampling
:param interpolation: type of interpolation used for the resampling
:return: file name after resampling (or original fname if it was already in the correct resolution)
"""
im_in = Image(fname)
orientation = im_in.orientation
if orientation != 'RPI':
fname = im_in.change_orientation(im_in, 'RPI', generate_path=True).save().absolutepath
nx, ny, nz, nt, px, py, pz, pt = im_in.dim
if np.round(px, 2) != np.round(npx, 2) or np.round(py, 2) != np.round(npy, 2):
name_resample = sct.extract_fname(fname)[1] + suffix
if binary:
interpolation = 'nn'
if nz == 1: # when data is 2d: we convert it to a 3d image in order to avoid nipy problem of conversion nifti-->nipy with 2d data
sct.run(['sct_image', '-i', ','.join([fname, fname]), '-concat', 'z', '-o', fname])
sct.run(['sct_resample', '-i', fname, '-mm', str(npx) + 'x' + str(npy) + 'x' + str(pz), '-o', name_resample, '-x', interpolation])
if nz == 1: # when input data was 2d: re-convert data 3d-->2d
sct.run(['sct_image', '-i', name_resample, '-split', 'z'])
im_split = Image(name_resample.split('.nii.gz')[0] + '_Z0000.nii.gz')
im_split.save(name_resample)
if binary:
sct.run(['sct_maths', '-i', name_resample, '-bin', str(thr), '-o', name_resample])
if orientation != 'RPI':
name_resample = Image(name_resample) \
.change_orientation(orientation, generate_path=True) \
.save() \
.absolutepath
return name_resample
else:
if orientation != 'RPI':
fname = sct.add_suffix(fname, "_RPI")
im_in = msct_image.change_orientation(im_in, orientation).save(fname)
sct.printv('Image resolution already ' + str(npx) + 'x' + str(npy) + 'xpz')
return fname
def change_type(self, dtype, generate_path=False):
"""
Change data type on image.
Note: the image path is voided.
"""
if dtype is not None:
change_type(self, dtype, self)
if generate_path and self._path is not None:
self._path = sct.add_suffix(self._path, "_{}".format(dtype.name))
else:
# safe option: remove path to avoid overwrites
self._path = None
return self
def compute_texture(self):
offset = int(self.param_glcm.distance)
sct.printv('\nCompute texture metrics...', self.param.verbose, 'normal')
# open image and re-orient it to RPI if needed
im_tmp = Image(self.param.fname_im)
if self.orientation_im != self.orientation_extraction:
im_tmp.change_orientation(self.orientation_extraction)
dct_metric = {}
for m in self.metric_lst:
im_2save = msct_image.zeros_like(im_tmp, dtype='float64')
dct_metric[m] = im_2save
# dct_metric[m] = Image(self.fname_metric_lst[m])
with tqdm.tqdm() as pbar:
for im_z, seg_z, zz in zip(self.dct_im_seg['im'], self.dct_im_seg['seg'], range(len(self.dct_im_seg['im']))):
for xx in range(im_z.shape[0]):
for yy in range(im_z.shape[1]):
if not seg_z[xx, yy]:
continue
if xx < offset or yy < offset:
continue
if xx > (im_z.shape[0] - offset - 1) or yy > (im_z.shape[1] - offset - 1):
continue # to check if the whole glcm_window is in the axial_slice
if False in np.unique(seg_z[xx - offset: xx + offset + 1, yy - offset: yy + offset + 1]):
continue # to check if the whole glcm_window is in the mask of the axial_slice
glcm_window = im_z[xx - offset: xx + offset + 1, yy - offset: yy + offset + 1]
glcm_window = glcm_window.astype(np.uint8)
dct_glcm = {}
for a in self.param_glcm.angle.split(','): # compute the GLCM for self.param_glcm.distance and for each self.param_glcm.angle
dct_glcm[a] = greycomatrix(glcm_window,
[self.param_glcm.distance], [np.radians(int(a))],
symmetric=self.param_glcm.symmetric,
normed=self.param_glcm.normed)
for m in self.metric_lst: # compute the GLCM property (m.split('_')[0]) of the voxel xx,yy,zz
dct_metric[m].data[xx, yy, zz] = greycoprops(dct_glcm[m.split('_')[2]], m.split('_')[0])[0][0]
pbar.set_postfix(pos="{}/{}".format(zz, len(self.dct_im_seg["im"])))
pbar.update(1)
for m in self.metric_lst:
fname_out = sct.add_suffix(''.join(sct.extract_fname(self.param.fname_im)[1:]), '_' + m)
dct_metric[m].save(fname_out)
self.fname_metric_lst[m] = fname_out
def load_manual_gmseg(list_slices_target, list_fname_manual_gmseg, tmp_dir, im_sc_seg_rpi, new_res, square_size_size_mm, for_model=False, fname_mask=None):
if isinstance(list_fname_manual_gmseg, str):
# consider fname_manual_gmseg as a list of file names to allow multiple manual GM segmentation
list_fname_manual_gmseg = [list_fname_manual_gmseg]
curdir = os.getcwd()
for fname_manual_gmseg in list_fname_manual_gmseg:
sct.copy(fname_manual_gmseg, tmp_dir)
# change fname level to only file name (path = tmp dir now)
path_gm, file_gm, ext_gm = extract_fname(fname_manual_gmseg)
fname_manual_gmseg = file_gm + ext_gm
os.chdir(tmp_dir)
im_manual_gmseg = Image(fname_manual_gmseg).change_orientation("RPI")
if fname_mask is not None:
fname_gmseg_crop = add_suffix(im_manual_gmseg.absolutepath, '_pre_crop')
crop_im = ImageCropper(input_file=im_manual_gmseg.absolutepath, output_file=fname_gmseg_crop,
mask=fname_mask)
im_manual_gmseg_crop = crop_im.crop()
im_manual_gmseg = im_manual_gmseg_crop
# assert gmseg has the right number of slices
assert im_manual_gmseg.data.shape[2] == len(list_slices_target), 'ERROR: the manual GM segmentation has not the same number of slices than the image.'
# interpolate gm to reference image
nz_gmseg, nx_gmseg, ny_gmseg, nt_gmseg, pz_gmseg, px_gmseg, py_gmseg, pt_gmseg = im_manual_gmseg.dim
list_im_gm = interpolate_im_to_ref(im_manual_gmseg, im_sc_seg_rpi, new_res=new_res, sq_size_size_mm=square_size_size_mm, interpolation_mode=0)
# load gm seg in list of slices
n_poped = 0
for im_gm, slice_im in zip(list_im_gm, list_slices_target):
if im_gm.data.max() == 0 and for_model:
list_slices_target.pop(slice_im.id - n_poped)
n_poped += 1
else:
slice_im.gm_seg.append(im_gm.data)
wm_slice = (slice_im.im > 0) - im_gm.data
slice_im.wm_seg.append(wm_slice)
os.chdir(curdir)
return list_slices_target
def pad_image(im, pad_x_i=0, pad_x_f=0, pad_y_i=0, pad_y_f=0, pad_z_i=0, pad_z_f=0):
nx, ny, nz, nt, px, py, pz, pt = im.dim
pad_x_i, pad_x_f, pad_y_i, pad_y_f, pad_z_i, pad_z_f = int(pad_x_i), int(pad_x_f), int(pad_y_i), int(pad_y_f), int(pad_z_i), int(pad_z_f)
if len(im.data.shape) == 2:
new_shape = list(im.data.shape)
new_shape.append(1)
im.data = im.data.reshape(new_shape)
# initialize padded_data, with same type as im.data
padded_data = np.zeros((nx + pad_x_i + pad_x_f, ny + pad_y_i + pad_y_f, nz + pad_z_i + pad_z_f), dtype=im.data.dtype)
if pad_x_f == 0:
pad_x_f = None
elif pad_x_f > 0:
pad_x_f *= -1
if pad_y_f == 0:
pad_y_f = None
elif pad_y_f > 0:
pad_y_f *= -1
if pad_z_f == 0:
pad_z_f = None
elif pad_z_f > 0:
pad_z_f *= -1
padded_data[pad_x_i:pad_x_f, pad_y_i:pad_y_f, pad_z_i:pad_z_f] = im.data
im_out = im.copy()
# TODO: Do not copy the Image(), because the dim field and hdr.get_data_shape() will not be updated properly.
# better to just create a new Image() from scratch.
im_out.data = padded_data # done after the call of the function
im_out.absolutepath = sct.add_suffix(im_out.absolutepath, "_pad")
# adapt the origin in the sform and qform matrix
new_origin = np.dot(im_out.hdr.get_qform(), [-pad_x_i, -pad_y_i, -pad_z_i, 1])
im_out.hdr.structarr['qoffset_x'] = new_origin[0]
im_out.hdr.structarr['qoffset_y'] = new_origin[1]
im_out.hdr.structarr['qoffset_z'] = new_origin[2]
im_out.hdr.structarr['srow_x'][-1] = new_origin[0]
im_out.hdr.structarr['srow_y'][-1] = new_origin[1]
im_out.hdr.structarr['srow_z'][-1] = new_origin[2]
return im_out
def main(fname_anat, fname_centerline, verbose):
"""
Main function
:param fname_anat:
:param fname_centerline:
:param verbose:
:return:
"""
# load input images
im_anat = Image(fname_anat)
im_centerline = Image(fname_centerline)
# flatten sagittal
im_anat_flattened = flatten_sagittal(im_anat, im_centerline, verbose)
# save output
fname_out = sct.add_suffix(fname_anat, '_flatten')
im_anat_flattened.save(fname_out)
sct.display_viewer_syntax([fname_anat, fname_out])
def run_main():
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
input_filename = arguments["-i"]
try:
output_filename = arguments["-o"]
except KeyError:
output_filename = sct.add_suffix(input_filename, '_gmseg')
use_tta = "-t" in arguments
model_name = arguments["-m"]
threshold = arguments['-thr']
verbose = int(arguments.get('-v'))
sct.init_sct(log_level=verbose, update=True) # Update log level
if threshold > 1.0 or threshold < 0.0:
raise RuntimeError("Threshold should be between 0.0 and 1.0.")
# Threshold zero means no thresholding
if threshold == 0.0:
threshold = None
from spinalcordtoolbox.deepseg_gm import deepseg_gm
deepseg_gm.check_backend()
out_fname = deepseg_gm.segment_file(input_filename, output_filename,
model_name, threshold, int(verbose),
use_tta)
path_qc = arguments.get("-qc", None)
qc_dataset = arguments.get("-qc-dataset", None)
qc_subject = arguments.get("-qc-subject", None)
if path_qc is not None:
generate_qc(fname_in1=input_filename, fname_seg=out_fname, args=sys.argv[1:], path_qc=os.path.abspath(path_qc),
dataset=qc_dataset, subject=qc_subject, process='sct_deepseg_gm')
sct.display_viewer_syntax([input_filename, format(out_fname)],
colormaps=['gray', 'red'],
opacities=['1', '0.7'],
verbose=verbose)
def func_rescale_header(fname_data, rescale_factor, verbose=0):
"""
Rescale the voxel dimension by modifying the NIFTI header qform. Write the output file in a temp folder.
:param fname_data:
:param rescale_factor:
:return: fname_data_rescaled
"""
import nibabel as nib
img = nib.load(fname_data)
# get qform
qform = img.header.get_qform()
# multiply by scaling factor
qform[0:3, 0:3] *= rescale_factor
# generate a new nifti file
header_rescaled = img.header.copy()
header_rescaled.set_qform(qform)
# the data are the same-- only the header changes
img_rescaled = nib.nifti1.Nifti1Image(img.get_data(), None, header=header_rescaled)
path_tmp = sct.tmp_create(basename="propseg", verbose=verbose)
fname_data_rescaled = os.path.join(path_tmp, os.path.basename(sct.add_suffix(fname_data, "_rescaled")))
nib.save(img_rescaled, fname_data_rescaled)
return fname_data_rescaled
def visualize_warp(fname_warp, fname_grid=None, step=3, rm_tmp=True):
if fname_grid is None:
from numpy import zeros
tmp_dir = sct.tmp_create()
im_warp = Image(fname_warp)
os.chdir(tmp_dir)
assert len(im_warp.data.shape) == 5, "ERROR: Warping field does bot have 5 dimensions..."
nx, ny, nz, nt, ndimwarp = im_warp.data.shape
# nx, ny, nz, nt, px, py, pz, pt = im_warp.dim
# This does not work because dimensions of a warping field are not correctly read : it would be 1,1,1,1,1,1,1,1
sq = zeros((step, step))
sq[step - 1] = 1
sq[:, step - 1] = 1
dat = zeros((nx, ny, nz))
for i in range(0, dat.shape[0], step):
for j in range(0, dat.shape[1], step):
for k in range(dat.shape[2]):
if dat[i : i + step, j : j + step, k].shape == (step, step):
dat[i : i + step, j : j + step, k] = sq
fname_grid = "grid_" + str(step) + ".nii.gz"
im_grid = Image(param=dat)
grid_hdr = im_warp.hdr
im_grid.hdr = grid_hdr
im_grid.setFileName(fname_grid)
im_grid.save()
fname_grid_resample = sct.add_suffix(fname_grid, "_resample")
sct.run("sct_resample -i " + fname_grid + " -f 3x3x1 -x nn -o " + fname_grid_resample)
fname_grid = tmp_dir + fname_grid_resample
os.chdir("..")
path_warp, file_warp, ext_warp = sct.extract_fname(fname_warp)
grid_warped = path_warp + "grid_warped_gm" + ext_warp
sct.run("sct_apply_transfo -i " + fname_grid + " -d " + fname_grid + " -w " + fname_warp + " -o " + grid_warped)
if rm_tmp:
sct.run("rm -rf " + tmp_dir, error_exit="warning")
return grid_warped
def visualize_warp(fname_warp, fname_grid=None, step=3, rm_tmp=True):
if fname_grid is None:
from numpy import zeros
tmp_dir = tmp_create()
im_warp = Image(fname_warp)
status, out = run('fslhd '+fname_warp)
from os import chdir
chdir(tmp_dir)
dim1 = 'dim1 '
dim2 = 'dim2 '
dim3 = 'dim3 '
nx = int(out[out.find(dim1):][len(dim1):out[out.find(dim1):].find('\n')])
ny = int(out[out.find(dim2):][len(dim2):out[out.find(dim2):].find('\n')])
nz = int(out[out.find(dim3):][len(dim3):out[out.find(dim3):].find('\n')])
sq = zeros((step, step))
sq[step-1] = 1
sq[:, step-1] = 1
dat = zeros((nx, ny, nz))
for i in range(0, dat.shape[0], step):
for j in range(0, dat.shape[1], step):
for k in range(dat.shape[2]):
if dat[i:i+step, j:j+step, k].shape == (step, step):
dat[i:i+step, j:j+step, k] = sq
fname_grid = 'grid_'+str(step)+'.nii.gz'
im_grid = Image(param=dat)
grid_hdr = im_warp.hdr
im_grid.hdr = grid_hdr
im_grid.setFileName(fname_grid)
im_grid.save()
fname_grid_resample = add_suffix(fname_grid, '_resample')
run('sct_resample -i '+fname_grid+' -f 3x3x1 -x nn -o '+fname_grid_resample)
fname_grid = tmp_dir+fname_grid_resample
chdir('..')
path_warp, file_warp, ext_warp = extract_fname(fname_warp)
grid_warped = path_warp+extract_fname(fname_grid)[1]+'_'+file_warp+ext_warp
run('sct_apply_transfo -i '+fname_grid+' -d '+fname_grid+' -w '+fname_warp+' -o '+grid_warped)
if rm_tmp:
run('rm -rf '+tmp_dir, error_exit='warning')
def visualize_warp(fname_warp, fname_grid=None, step=3, rm_tmp=True):
if fname_grid is None:
from numpy import zeros
tmp_dir = sct.tmp_create()
im_warp = Image(fname_warp)
status, out = sct.run(['fslhd', fname_warp])
curdir = os.getcwd()
os.chdir(tmp_dir)
dim1 = 'dim1 '
dim2 = 'dim2 '
dim3 = 'dim3 '
nx = int(out[out.find(dim1):][len(dim1):out[out.find(dim1):].find('\n')])
ny = int(out[out.find(dim2):][len(dim2):out[out.find(dim2):].find('\n')])
nz = int(out[out.find(dim3):][len(dim3):out[out.find(dim3):].find('\n')])
sq = zeros((step, step))
sq[step - 1] = 1
sq[:, step - 1] = 1
dat = zeros((nx, ny, nz))
for i in range(0, dat.shape[0], step):
for j in range(0, dat.shape[1], step):
for k in range(dat.shape[2]):
if dat[i:i + step, j:j + step, k].shape == (step, step):
dat[i:i + step, j:j + step, k] = sq
fname_grid = 'grid_' + str(step) + '.nii.gz'
im_grid = Image(param=dat)
grid_hdr = im_warp.hdr
im_grid.hdr = grid_hdr
im_grid.absolutepath = fname_grid
im_grid.save()
fname_grid_resample = sct.add_suffix(fname_grid, '_resample')
sct.run(['sct_resample', '-i', fname_grid, '-f', '3x3x1', '-x', 'nn', '-o', fname_grid_resample])
fname_grid = os.path.join(tmp_dir, fname_grid_resample)
os.chdir(curdir)
path_warp, file_warp, ext_warp = sct.extract_fname(fname_warp)
grid_warped = os.path.join(path_warp, sct.extract_fname(fname_grid)[1] + '_' + file_warp + ext_warp)
sct.run(['sct_apply_transfo', '-i', fname_grid, '-d', fname_grid, '-w', fname_warp, '-o', grid_warped])
if rm_tmp:
sct.rmtree(tmp_dir)
def test_integrity(param_test):
"""
Test integrity of function
"""
# initializations
distance_detection = float('nan')
# extract name of output centerline: data_centerline_optic.nii.gz
file_pmj = os.path.join(param_test.path_output, sct.add_suffix(param_test.file_input, '_pmj'))
# open output segmentation
im_pmj = Image(file_pmj)
# open ground truth
im_pmj_manual = Image(param_test.fname_gt)
# compute Euclidean distance between predicted and GT PMJ label
x_true, y_true, z_true = np.where(im_pmj_manual.data == 50)
x_pred, y_pred, z_pred = np.where(im_pmj.data == 50)
x_true, y_true, z_true = im_pmj_manual.transfo_pix2phys([[x_true[0], y_true[0], z_true[0]]])[0]
x_pred, y_pred, z_pred = im_pmj.transfo_pix2phys([[x_pred[0], y_pred[0], z_pred[0]]])[0]
distance_detection = math.sqrt(((x_true - x_pred))**2 + ((y_true - y_pred))**2 + ((z_true - z_pred))**2)
param_test.output += 'Computed distance: ' + str(distance_detection)
param_test.output += 'Distance threshold (if computed Distance higher: fail): ' + str(param_test.dist_threshold)
if distance_detection > param_test.dist_threshold:
param_test.status = 99
param_test.output += '--> FAILED'
else:
param_test.output += '--> PASSED'
# update Panda structure
param_test.results['distance_detection'] = distance_detection
return param_test
def test_integrity(param_test):
"""
Test integrity of function
"""
# open ground truth
im_seg_manual = Image(param_test.fname_gt).change_orientation("RPI")
# Compute center of mass of the SC seg on each axial slice.
center_of_mass_x_y_z_lst = [[int(center_of_mass(im_seg_manual.data[:, :, zz])[0]),
int(center_of_mass(im_seg_manual.data[:, :, zz])[1]),
zz] for zz in range(im_seg_manual.dim[2])]
im_ctr_manual = msct_image.zeros_like(im_seg_manual)
for x_y_z in center_of_mass_x_y_z_lst:
im_ctr_manual.data[x_y_z[0], x_y_z[1], x_y_z[2]] = 1
# open output segmentation
path_in, file_in, _ = sct.extract_fname(param_test.file_input)
file_ctr = os.path.join(param_test.path_data, 't2s', sct.add_suffix(param_test.file_input, '_centerline'))
im_ctr = Image(file_ctr).change_orientation("RPI")
# compute MSE between generated ctr and ctr from database
mse_detection = compute_mse(im_ctr, im_ctr_manual)
param_test.output += 'Computed MSE: ' + str(mse_detection)
param_test.output += 'MSE threshold (if computed MSE higher: fail): ' + str(param_test.mse_threshold)
if mse_detection > param_test.mse_threshold:
param_test.status = 99
param_test.output += '--> FAILED'
else:
param_test.output += '--> PASSED'
# update Panda structure
param_test.results['mse_detection'] = mse_detection
return param_test
def change_shape(self, shape, generate_path=False):
"""
Change data shape (in-place)
:param generate_path: whether to create a derived path name from the
original absolutepath (note: while it will generate
a file suffix, don't expect the suffix but rather
use the Image's absolutepath.
If not set, the absolutepath is voided.
This is mostly useful for adding/removing a fourth dimension,
you probably don't want to use this function.
"""
if shape is not None:
change_shape(self, shape, self)
if generate_path and self._path is not None:
self._path = sct.add_suffix(self._path, "_shape-{}".format("-".join([str(x) for x in shape])))
else:
# safe option: remove path to avoid overwrites
self._path = None
return self
def multicomponent_split(im):
"""
Convert composite image (e.g., ITK warping field, 5dim) into several 3d volumes.
Replaces "c3d -mcs warp_comp.nii -oo warp_vecx.nii warp_vecy.nii warp_vecz.nii"
:param im:
:return:
"""
data = im.data
assert len(data.shape) == 5
data_out = []
for i in range(data.shape[-1]):
dat_out = data[:, :, :, :, i]
'''
while dat_out.shape[-1] == 1:
dat_out = reshape(dat_out, dat_out.shape[:-1])
'''
data_out.append(dat_out) # .astype('float32'))
im_out = [im.copy() for j in range(len(data_out))]
for i, im in enumerate(im_out):
im.data = data_out[i]
im.hdr.set_intent('vector', (), '')
im.absolutepath = sct.add_suffix(im.absolutepath, "_{}".format(i))
return im_out
def split_data(im_in, dim, squeeze_data=True):
"""
Split data
:param im_in: input image.
:param dim: dimension: 0, 1, 2, 3.
:return: list of split images
"""
dim_list = ['x', 'y', 'z', 't']
# Parse file name
# Open first file.
data = im_in.data
# in case input volume is 3d and dim=t, create new axis
if dim + 1 > len(np.shape(data)):
data = data[..., np.newaxis]
# in case splitting along the last dim, make sure to remove the last dim to avoid singleton
if dim + 1 == len(np.shape(data)):
if squeeze_data:
do_reshape = True
else:
do_reshape = False
else:
do_reshape = False
# Split data into list
data_split = np.array_split(data, data.shape[dim], dim)
# Write each file
im_out_list = []
for idx_img, dat in enumerate(data_split):
im_out = msct_image.empty_like(im_in)
if do_reshape:
im_out.data = dat.reshape(tuple([ x for (idx_shape, x) in enumerate(data.shape) if idx_shape != dim]))
else:
im_out.data = dat
im_out.absolutepath = sct.add_suffix(im_in.absolutepath, "_{}{}".format(dim_list[dim].upper(), str(idx_img).zfill(4)))
im_out_list.append(im_out)
return im_out_list