def main(args=None):
parser = get_parser()
if args:
arguments = parser.parse_args(args)
else:
arguments = parser.parse_args(
args=None if sys.argv[1:] else ['--help'])
fname_in = arguments.bvec
fname_out = arguments.o
verbose = int(arguments.v)
init_sct(log_level=verbose, update=True) # Update log level
# get bvecs in proper orientation
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(None, fname_in)
# # Transpose bvecs
# printv('Transpose bvecs...', verbose)
# # from numpy import transpose
# bvecs = bvecs.transpose()
# Write new file
if fname_out == '':
path_in, file_in, ext_in = extract_fname(fname_in)
fname_out = path_in + file_in + ext_in
fid = open(fname_out, 'w')
for iLine in range(bvecs.shape[0]):
fid.write(' '.join(str(i) for i in bvecs[iLine, :]) + '\n')
fid.close()
# display message
printv('Created file:\n--> ' + fname_out + '\n', verbose, 'info')
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_global_loglevel(verbose=verbose)
# initialization
file_mask = ''
# Get parser info
parser = get_parser()
arguments = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
fname_in = arguments.i
fname_bvals = arguments.bval
fname_bvecs = arguments.bvec
prefix = arguments.o
method = arguments.method
evecs = arguments.evecs
if arguments.m is not None:
file_mask = arguments.m
# compute DTI
if not compute_dti(fname_in, fname_bvals, fname_bvecs, prefix, method,
evecs, file_mask, verbose):
printv('ERROR in compute_dti()', 1, 'error')
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_loglevel(verbose=verbose)
fname_in = arguments.bvec
fname_out = arguments.o
# get bvecs in proper orientation
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(None, fname_in)
# # Transpose bvecs
# printv('Transpose bvecs...', verbose)
# # from numpy import transpose
# bvecs = bvecs.transpose()
# Write new file
if fname_out == '':
path_in, file_in, ext_in = extract_fname(fname_in)
fname_out = path_in + file_in + ext_in
fid = open(fname_out, 'w')
for iLine in range(bvecs.shape[0]):
fid.write(' '.join(str(i) for i in bvecs[iLine, :]) + '\n')
fid.close()
# display message
printv('Created file:\n--> ' + fname_out + '\n', verbose, 'info')
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv if argv else ['--help'])
verbose = arguments.v
set_global_loglevel(verbose=verbose)
printv('Load data...', verbose)
nii_mt = Image(arguments.mt)
nii_pd = Image(arguments.pd)
nii_t1 = Image(arguments.t1)
if arguments.b1map is None:
nii_b1map = None
else:
nii_b1map = Image(arguments.b1map)
if arguments.trmt is None:
arguments.trmt = fetch_metadata(
get_json_file_name(arguments.mt, check_exist=True),
'RepetitionTime')
if arguments.trpd is None:
arguments.trpd = fetch_metadata(
get_json_file_name(arguments.pd, check_exist=True),
'RepetitionTime')
if arguments.trt1 is None:
arguments.trt1 = fetch_metadata(
get_json_file_name(arguments.t1, check_exist=True),
'RepetitionTime')
if arguments.famt is None:
arguments.famt = fetch_metadata(
get_json_file_name(arguments.mt, check_exist=True), 'FlipAngle')
if arguments.fapd is None:
arguments.fapd = fetch_metadata(
get_json_file_name(arguments.pd, check_exist=True), 'FlipAngle')
if arguments.fat1 is None:
arguments.fat1 = fetch_metadata(
get_json_file_name(arguments.t1, check_exist=True), 'FlipAngle')
# compute MTsat
nii_mtsat, nii_t1map = compute_mtsat(nii_mt,
nii_pd,
nii_t1,
arguments.trmt,
arguments.trpd,
arguments.trt1,
arguments.famt,
arguments.fapd,
arguments.fat1,
nii_b1map=nii_b1map)
# Output MTsat and T1 maps
printv('Generate output files...', verbose)
nii_mtsat.save(arguments.omtsat)
nii_t1map.save(arguments.ot1map)
display_viewer_syntax([arguments.omtsat, arguments.ot1map],
colormaps=['gray', 'gray'],
minmax=['-10,10', '0, 3'],
opacities=['1', '1'],
verbose=verbose)
def convert(fname_in, fname_out, squeeze_data=True, dtype=None, verbose=1):
"""
Convert data
:return True/False
"""
printv('sct_convert -i ' + fname_in + ' -o ' + fname_out, verbose, 'code')
img = image.Image(fname_in)
img = image.convert(img, squeeze_data=squeeze_data, dtype=dtype)
img.save(fname_out, mutable=True, verbose=verbose)
def fs_ok(sig_a, sig_b, exclude=()):
errors = list()
for path, data in sig_b.items():
if path not in sig_a:
errors.append((path, "added: {}".format(path)))
continue
if sig_a[path] != data:
errors.append((path, "modified: {}".format(path)))
errors = [(x, y) for (x, y) in errors if not x.startswith(exclude)]
if errors:
for error in errors:
printv("Error: %s", 1, type='error')
raise RuntimeError()
def downloaddata(param):
"""
Download testing data from internet.
Parameters
----------
param
Returns
-------
None
"""
printv('\nDownloading testing data...', param.verbose)
sct_download_data.main(['-d', 'sct_testing_data'])
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv if argv else ['--help'])
verbose = arguments.v
set_global_loglevel(verbose=verbose)
param.fname_data = arguments.i
arg = 0
if arguments.f is not None:
param.new_size = arguments.f
param.new_size_type = 'factor'
arg += 1
elif arguments.mm is not None:
param.new_size = arguments.mm
param.new_size_type = 'mm'
arg += 1
elif arguments.vox is not None:
param.new_size = arguments.vox
param.new_size_type = 'vox'
arg += 1
elif arguments.ref is not None:
param.ref = arguments.ref
arg += 1
else:
printv(
parser.error(
'ERROR: you need to specify one of those three arguments : -f, -mm or -vox'
))
if arg > 1:
printv(
parser.error(
'ERROR: you need to specify ONLY one of those three arguments : -f, -mm or -vox'
))
if arguments.o is not None:
param.fname_out = arguments.o
if arguments.x is not None:
if len(arguments.x) == 1:
param.interpolation = int(arguments.x)
else:
param.interpolation = arguments.x
spinalcordtoolbox.resampling.resample_file(param.fname_data,
param.fname_out,
param.new_size,
param.new_size_type,
param.interpolation,
param.verbose,
fname_ref=param.ref)
def run_main():
parser = get_parser()
arguments = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
param.fname_data = arguments.i
arg = 0
if arguments.f is not None:
param.new_size = arguments.f
param.new_size_type = 'factor'
arg += 1
elif arguments.mm is not None:
param.new_size = arguments.mm
param.new_size_type = 'mm'
arg += 1
elif arguments.vox is not None:
param.new_size = arguments.vox
param.new_size_type = 'vox'
arg += 1
elif arguments.ref is not None:
param.ref = arguments.ref
arg += 1
else:
printv(
parser.error(
'ERROR: you need to specify one of those three arguments : -f, -mm or -vox'
))
if arg > 1:
printv(
parser.error(
'ERROR: you need to specify ONLY one of those three arguments : -f, -mm or -vox'
))
if arguments.o is not None:
param.fname_out = arguments.o
if arguments.x is not None:
if len(arguments.x) == 1:
param.interpolation = int(arguments.x)
else:
param.interpolation = arguments.x
param.verbose = int(arguments.v)
init_sct(log_level=param.verbose, update=True) # Update log level
spinalcordtoolbox.resampling.resample_file(param.fname_data,
param.fname_out,
param.new_size,
param.new_size_type,
param.interpolation,
param.verbose,
fname_ref=param.ref)
def main():
parser = get_parser()
arguments = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
# initialization
verbose = 1
# Get parser info
di = arguments.di
da = arguments.da
db = arguments.db
# Compute MSCC
MSCC = mscc(di, da, db)
# Display results
printv('\nMSCC = ' + str(MSCC) + '\n', verbose, 'info')
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_global_loglevel(verbose=verbose)
fname_mtr = arguments.o
# compute MTR
printv('\nCompute MTR...', verbose)
nii_mtr = compute_mtr(nii_mt1=Image(arguments.mt1), nii_mt0=Image(arguments.mt0), threshold_mtr=arguments.thr)
# save MTR file
nii_mtr.save(fname_mtr, dtype='float32')
display_viewer_syntax([arguments.mt0, arguments.mt1, fname_mtr])
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_loglevel(verbose=verbose)
# Get parser info
di = arguments.di
da = arguments.da
db = arguments.db
# Compute MSCC
MSCC = mscc(di, da, db)
# Display results
printv('\nMSCC = ' + str(MSCC) + '\n', verbose, 'info')
def main():
# Check input parameters
parser = get_parser()
args = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
fname_mtr = args.o
verbose = args.v
# compute MTR
printv('\nCompute MTR...', verbose)
nii_mtr = compute_mtr(nii_mt1=Image(args.mt1),
nii_mt0=Image(args.mt0),
threshold_mtr=args.thr)
# save MTR file
nii_mtr.save(fname_mtr, dtype='float32')
display_viewer_syntax([args.mt0, args.mt1, fname_mtr])
def main(argv=None):
"""
Main function
:param argv:
:return:
"""
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_global_loglevel(verbose=verbose)
# check number of input args
if not len(arguments.i) == len(arguments.order):
raise Exception(
"Number of items between flags '-i' and '-order' should be the same."
)
if not len(arguments.bval) == len(arguments.bvec):
raise Exception(
"Number of files for bval and bvec should be the same.")
# Concatenate NIFTI files
im_list = [Image(fname) for fname in arguments.i]
im_concat = concat_data(im_list, dim=3, squeeze_data=False)
im_concat.save(arguments.o)
printv("Generated file: {}".format(arguments.o))
# Concatenate bvals and bvecs
bvals_concat = ''
bvecs_concat = ['', '', '']
i_dwi = 0 # counter for DWI files, to read in bvec/bval files
for i_item in range(len(arguments.order)):
if arguments.order[i_item] == 'b0':
# count number of b=0
n_b0 = Image(arguments.i[i_item]).dim[3]
bval = np.array([0.0] * n_b0)
bvec = np.array([[0.0, 0.0, 0.0]] * n_b0)
elif arguments.order[i_item] == 'dwi':
# read bval/bvec files
bval, bvec = read_bvals_bvecs(arguments.bval[i_dwi],
arguments.bvec[i_dwi])
i_dwi += 1
# Concatenate bvals
bvals_concat += ' '.join(str(v) for v in bval)
bvals_concat += ' '
# Concatenate bvecs
for i in (0, 1, 2):
bvecs_concat[i] += ' '.join(
str(v) for v in map(lambda n: '%.16f' % n, bvec[:, i]))
bvecs_concat[i] += ' '
bvecs_concat = '\n'.join(
str(v) for v in bvecs_concat) # transform list into lines of strings
# Write files
new_f = open(arguments.obval, 'w')
new_f.write(bvals_concat)
new_f.close()
printv("Generated file: {}".format(arguments.obval))
new_f = open(arguments.obvec, 'w')
new_f.write(bvecs_concat)
new_f.close()
printv("Generated file: {}".format(arguments.obvec))
def main(args=None):
# initialization
file_mask = ''
# Get parser info
parser = get_parser()
arguments = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
fname_in = arguments.i
fname_bvals = arguments.bval
fname_bvecs = arguments.bvec
prefix = arguments.o
method = arguments.method
evecs = arguments.evecs
if arguments.m is not None:
file_mask = arguments.m
param.verbose = arguments.v
init_sct(log_level=param.verbose, update=True) # Update log level
# compute DTI
if not compute_dti(fname_in, fname_bvals, fname_bvecs, prefix, method,
evecs, file_mask):
printv('ERROR in compute_dti()', 1, 'error')
def main(script_name=''):
script_name = ''
try:
opts, args = getopt.getopt(sys.argv[1:], 'hi:')
except getopt.GetoptError:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in '-i':
script_name = arg
try:
script_tested = importlib.import_module(script_name)
print(script_tested)
except IOError:
printv(
"\nException caught: IOerror, can not import " + script_name +
'\n', 1, 'warning')
sys.exit(2)
except ImportError as e:
printv("\nException caught: ImportError in " + script_name + '\n', 1,
'warning')
print(e)
sys.exit(2)
else:
try:
sct = script_tested.Param()
except AttributeError:
# except IOError:
print('\nno class param found in script ' + script_name + '\n')
sys.exit(0)
else:
if hasattr(sct, 'debug'):
if sct.debug == 1:
print('\nWarning debug mode on in script ' + script_name +
'\n')
sys.exit(2)
def display_voxel(img: Image, verbose: int = 1) -> Sequence[Coordinate]:
"""
Display all the labels that are contained in the input image.
:param img: source image
:param verbose: verbosity level
"""
coordinates_input = img.getNonZeroCoordinates(sorting='value')
useful_notation = ''
for coord in coordinates_input:
printv('Position=(' + str(coord.x) + ',' + str(coord.y) + ',' + str(coord.z) + ') -- Value= ' + str(coord.value), verbose=verbose)
if useful_notation:
useful_notation = useful_notation + ':'
useful_notation += str(coord)
printv('All labels (useful syntax):', verbose=verbose)
printv(useful_notation, verbose=verbose)
def main(argv: Sequence[str]):
"""
Main function. When this script is run via CLI, the main function is called using main(sys.argv[1:]).
:param argv: A list of unparsed arguments, which is passed to ArgumentParser.parse_args()
"""
for i, arg in enumerate(argv):
if arg == '-create-seg' and len(argv) > i+1 and '-1,' in argv[i+1]:
raise DeprecationWarning("The use of '-1' for '-create-seg' has been deprecated. Please use "
"'-create-seg-mid' instead.")
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_global_loglevel(verbose=verbose)
input_filename = arguments.i
output_fname = arguments.o
img = Image(input_filename)
dtype = None
if arguments.add is not None:
value = arguments.add
out = sct_labels.add(img, value)
elif arguments.create is not None:
labels = arguments.create
out = sct_labels.create_labels_empty(img, labels)
elif arguments.create_add is not None:
labels = arguments.create_add
out = sct_labels.create_labels(img, labels)
elif arguments.create_seg is not None:
labels = arguments.create_seg
out = sct_labels.create_labels_along_segmentation(img, labels)
elif arguments.create_seg_mid is not None:
labels = [(-1, arguments.create_seg_mid)]
out = sct_labels.create_labels_along_segmentation(img, labels)
elif arguments.cubic_to_point:
out = sct_labels.cubic_to_point(img)
elif arguments.display:
display_voxel(img, verbose)
return
elif arguments.increment:
out = sct_labels.increment_z_inverse(img)
elif arguments.disc is not None:
ref = Image(arguments.disc)
out = sct_labels.labelize_from_discs(img, ref)
elif arguments.vert_body is not None:
levels = arguments.vert_body
if len(levels) == 1 and levels[0] == 0:
levels = None # all levels
out = sct_labels.label_vertebrae(img, levels)
elif arguments.vert_continuous:
out = sct_labels.continuous_vertebral_levels(img)
dtype = 'float32'
elif arguments.MSE is not None:
ref = Image(arguments.MSE)
mse = sct_labels.compute_mean_squared_error(img, ref)
printv(f"Computed MSE: {mse}")
return
elif arguments.remove_reference is not None:
ref = Image(arguments.remove_reference)
out = sct_labels.remove_missing_labels(img, ref)
elif arguments.remove_sym is not None:
# first pass use img as source
ref = Image(arguments.remove_reference)
out = sct_labels.remove_missing_labels(img, ref)
# second pass use previous pass result as reference
ref_out = sct_labels.remove_missing_labels(ref, out)
ref_out.save(path=ref.absolutepath)
elif arguments.remove is not None:
labels = arguments.remove
out = sct_labels.remove_labels_from_image(img, labels)
elif arguments.keep is not None:
labels = arguments.keep
out = sct_labels.remove_other_labels_from_image(img, labels)
elif arguments.create_viewer is not None:
msg = "" if arguments.msg is None else f"{arguments.msg}\n"
if arguments.ilabel is not None:
input_labels_img = Image(arguments.ilabel)
out = launch_manual_label_gui(img, input_labels_img, parse_num_list(arguments.create_viewer), msg)
else:
out = launch_sagittal_viewer(img, parse_num_list(arguments.create_viewer), msg)
printv("Generating output files...")
out.save(path=output_fname, dtype=dtype)
display_viewer_syntax([input_filename, output_fname])
if arguments.qc is not None:
generate_qc(fname_in1=input_filename, fname_seg=output_fname, args=argv,
path_qc=os.path.abspath(arguments.qc), dataset=arguments.qc_dataset,
subject=arguments.qc_subject, process='sct_label_utils')
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_global_loglevel(verbose=verbose)
# Default params
param = Param()
# Get parser info
fname_data = arguments.i
if arguments.m is not None:
fname_mask = arguments.m
else:
fname_mask = ''
method = arguments.method
if arguments.vol is not None:
index_vol_user = arguments.vol
else:
index_vol_user = ''
# Check parameters
if method == 'diff':
if not fname_mask:
printv('You need to provide a mask with -method diff. Exit.',
1,
type='error')
# Load data and orient to RPI
im_data = Image(fname_data).change_orientation('RPI')
data = im_data.data
if fname_mask:
mask = Image(fname_mask).change_orientation('RPI').data
# Retrieve selected volumes
if index_vol_user:
index_vol = parse_num_list(index_vol_user)
else:
index_vol = range(data.shape[3])
# Make sure user selected 2 volumes with diff method
if method == 'diff':
if not len(index_vol) == 2:
printv(
'Method "diff" should be used with exactly two volumes (specify with flag "-vol").',
1, 'error')
# Compute SNR
# NB: "time" is assumed to be the 4th dimension of the variable "data"
if method == 'mult':
# Compute mean and STD across time
data_mean = np.mean(data[:, :, :, index_vol], axis=3)
data_std = np.std(data[:, :, :, index_vol], axis=3, ddof=1)
# Generate mask where std is different from 0
mask_std_nonzero = np.where(data_std > param.almost_zero)
snr_map = np.zeros_like(data_mean)
snr_map[mask_std_nonzero] = data_mean[mask_std_nonzero] / data_std[
mask_std_nonzero]
# Output SNR map
fname_snr = add_suffix(fname_data, '_SNR-' + method)
im_snr = empty_like(im_data)
im_snr.data = snr_map
im_snr.save(fname_snr, dtype=np.float32)
# Output non-zero mask
fname_stdnonzero = add_suffix(fname_data, '_mask-STD-nonzero' + method)
im_stdnonzero = empty_like(im_data)
data_stdnonzero = np.zeros_like(data_mean)
data_stdnonzero[mask_std_nonzero] = 1
im_stdnonzero.data = data_stdnonzero
im_stdnonzero.save(fname_stdnonzero, dtype=np.float32)
# Compute SNR in ROI
if fname_mask:
mean_in_roi = np.average(data_mean[mask_std_nonzero],
weights=mask[mask_std_nonzero])
std_in_roi = np.average(data_std[mask_std_nonzero],
weights=mask[mask_std_nonzero])
snr_roi = mean_in_roi / std_in_roi
# snr_roi = np.average(snr_map[mask_std_nonzero], weights=mask[mask_std_nonzero])
elif method == 'diff':
data_2vol = np.take(data, index_vol, axis=3)
# Compute mean in ROI
data_mean = np.mean(data_2vol, axis=3)
mean_in_roi = np.average(data_mean, weights=mask)
data_sub = np.subtract(data_2vol[:, :, :, 1], data_2vol[:, :, :, 0])
_, std_in_roi = weighted_avg_and_std(data_sub, mask)
# Compute SNR, correcting for Rayleigh noise (see eq. 7 in Dietrich et al.)
snr_roi = (2 / np.sqrt(2)) * mean_in_roi / std_in_roi
# Display result
if fname_mask:
printv('\nSNR_' + method + ' = ' + str(snr_roi) + '\n', type='info')
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_loglevel(verbose=verbose)
# Default params
param = Param()
# Get parser info
fname_data = arguments.i
fname_mask = arguments.m
fname_mask_noise = arguments.m_noise
method = arguments.method
file_name = arguments.o
rayleigh_correction = arguments.rayleigh
# Check parameters
if method in ['diff', 'single']:
if not fname_mask:
raise parser.error(
f"Argument '-m' must be specified when using '-method {method}'."
)
# Load data
im_data = Image(fname_data)
data = im_data.data
dim = len(data.shape)
nz = data.shape[2]
if fname_mask:
mask = Image(fname_mask).data
# Check dimensionality
if method in ['diff', 'mult']:
if dim != 4:
raise ValueError(
f"Input data dimension: {dim}. Input dimension for this method should be 4."
)
if method in ['single']:
if dim not in [3, 4]:
raise ValueError(
f"Input data dimension: {dim}. Input dimension for this method should be 3 or 4."
)
# Check dimensionality of mask
if fname_mask:
if len(mask.shape) != 3:
raise ValueError(
f"Mask should be a 3D image, but the input mask has shape '{mask.shape}'."
)
# Retrieve selected volumes
index_vol = parse_num_list(arguments.vol)
if not index_vol:
if method == 'mult':
index_vol = range(data.shape[3])
elif method == 'diff':
index_vol = [0, 1]
elif method == 'single':
index_vol = [0]
# Compute SNR
# NB: "time" is assumed to be the 4th dimension of the variable "data"
if method == 'mult':
# Compute mean and STD across time
data_mean = np.mean(data[:, :, :, index_vol], axis=3)
data_std = np.std(data[:, :, :, index_vol], axis=3, ddof=1)
# Generate mask where std is different from 0
mask_std_nonzero = np.where(data_std > param.almost_zero)
snr_map = np.zeros_like(data_mean)
snr_map[mask_std_nonzero] = data_mean[mask_std_nonzero] / data_std[
mask_std_nonzero]
# Output SNR map
fname_snr = add_suffix(fname_data, '_SNR-' + method)
im_snr = empty_like(im_data)
im_snr.data = snr_map
im_snr.save(fname_snr, dtype=np.float32)
# Output non-zero mask
fname_stdnonzero = add_suffix(fname_data, '_mask-STD-nonzero' + method)
im_stdnonzero = empty_like(im_data)
data_stdnonzero = np.zeros_like(data_mean)
data_stdnonzero[mask_std_nonzero] = 1
im_stdnonzero.data = data_stdnonzero
im_stdnonzero.save(fname_stdnonzero, dtype=np.float32)
# Compute SNR in ROI
if fname_mask:
snr_roi = np.average(snr_map[mask_std_nonzero],
weights=mask[mask_std_nonzero])
elif method == 'diff':
# Check user selected exactly 2 volumes for this method.
if not len(index_vol) == 2:
raise ValueError(
f"Number of selected volumes: {len(index_vol)}. The method 'diff' should be used with "
f"exactly 2 volumes. You can specify the number of volumes with the flag '-vol'."
)
data_2vol = np.take(data, index_vol, axis=3)
# Compute mean across the two volumes
data_mean = np.mean(data_2vol, axis=3)
# Compute mean in ROI for each z-slice, if the slice in the mask is not null
mean_in_roi = [
np.average(data_mean[..., iz], weights=mask[..., iz])
for iz in range(nz) if np.any(mask[..., iz])
]
data_sub = np.subtract(data_2vol[:, :, :, 1], data_2vol[:, :, :, 0])
# Compute STD in the ROI for each z-slice. The "np.sqrt(2)" results from the variance of the subtraction of two
# distributions: var(A-B) = var(A) + var(B).
# More context in: https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3481
std_in_roi = [
weighted_std(data_sub[..., iz] / np.sqrt(2), weights=mask[..., iz])
for iz in range(nz) if np.any(mask[..., iz])
]
# Compute SNR
snr_roi_slicewise = [m / s for m, s in zip(mean_in_roi, std_in_roi)]
snr_roi = sum(snr_roi_slicewise) / len(snr_roi_slicewise)
elif method == 'single':
# Check that the input volume is 3D, or if it is 4D, that the user selected exactly 1 volume for this method.
if dim == 3:
data3d = data
elif dim == 4:
if not len(index_vol) == 1:
raise ValueError(
f"Selected volumes: {index_vol}. The method 'single' should be used with "
f"exactly 1 volume. You can specify the index of the volume with the flag '-vol'."
)
data3d = np.squeeze(data[..., index_vol])
# Check that input noise mask is provided
if fname_mask_noise:
mask_noise = Image(fname_mask_noise).data
else:
raise parser.error(
"A noise mask is mandatory with '-method single'.")
# Check dimensionality of the noise mask
if len(mask_noise.shape) != 3:
raise ValueError(
f"Input noise mask dimension: {dim}. Input dimension for the noise mask should be 3."
)
# Check that non-null slices are consistent between mask and mask_noise.
for iz in range(nz):
if not np.any(mask[..., iz]) == np.any(mask_noise[..., iz]):
raise ValueError(
f"Slice {iz} is empty in either mask or mask_noise. Non-null slices should be "
f"consistent between mask and mask_noise.")
# Compute mean in ROI for each z-slice, if the slice in the mask is not null
mean_in_roi = [
np.average(data3d[..., iz], weights=mask[..., iz])
for iz in range(nz) if np.any(mask[..., iz])
]
std_in_roi = [
weighted_std(data3d[..., iz], weights=mask_noise[..., iz])
for iz in range(nz) if np.any(mask_noise[..., iz])
]
# Compute SNR
snr_roi_slicewise = [m / s for m, s in zip(mean_in_roi, std_in_roi)]
snr_roi = sum(snr_roi_slicewise) / len(snr_roi_slicewise)
if rayleigh_correction:
# Correcting for Rayleigh noise (see eq. A12 in Dietrich et al.)
snr_roi *= np.sqrt((4 - np.pi) / 2)
# Display result
if fname_mask:
printv('\nSNR_' + method + ' = ' + str(snr_roi) + '\n', type='info')
# Added function for text file
if file_name is not None:
with open(file_name, "w") as f:
f.write(str(snr_roi))
printv('\nFile saved to ' + file_name)
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.verbose
set_global_loglevel(verbose=verbose)
# initializations
param = Param()
param.download = int(arguments.download)
param.path_data = arguments.path
functions_to_test = arguments.function
param.remove_tmp_file = int(arguments.remove_temps)
jobs = arguments.jobs
param.verbose = verbose
start_time = time.time()
# get absolute path and add slash at the end
param.path_data = os.path.abspath(param.path_data)
# check existence of testing data folder
if not os.path.isdir(param.path_data) or param.download:
downloaddata(param)
# display path to data
printv('\nPath to testing data: ' + param.path_data, param.verbose)
# create temp folder that will have all results
path_tmp = os.path.abspath(arguments.execution_folder or tmp_create())
# go in path data (where all scripts will be run)
curdir = os.getcwd()
os.chdir(param.path_data)
functions_parallel = list()
functions_serial = list()
if functions_to_test:
for f in functions_to_test:
if f in get_functions_parallelizable():
functions_parallel.append(f)
elif f in get_functions_nonparallelizable():
functions_serial.append(f)
else:
printv(
'Command-line usage error: Function "%s" is not part of the list of testing functions'
% f,
type='error')
jobs = min(jobs, len(functions_parallel))
else:
functions_parallel = get_functions_parallelizable()
functions_serial = get_functions_nonparallelizable()
if arguments.continue_from:
first_func = arguments.continue_from
if first_func in functions_parallel:
functions_serial = []
functions_parallel = functions_parallel[functions_parallel.
index(first_func):]
elif first_func in functions_serial:
functions_serial = functions_serial[functions_serial.
index(first_func):]
if arguments.check_filesystem and jobs != 1:
print("Check filesystem used -> jobs forced to 1")
jobs = 1
print("Will run through the following tests:")
if functions_serial:
print("- sequentially: {}".format(" ".join(functions_serial)))
if functions_parallel:
print("- in parallel with {} jobs: {}".format(
jobs, " ".join(functions_parallel)))
list_status = []
for name, functions in (
("serial", functions_serial),
("parallel", functions_parallel),
):
if not functions:
continue
if any([s for (f, s) in list_status]) and arguments.abort_on_failure:
break
try:
if functions == functions_parallel and jobs != 1:
pool = multiprocessing.Pool(processes=jobs)
results = list()
# loop across functions and run tests
for f in functions:
func_param = copy.deepcopy(param)
func_param.path_output = f
res = pool.apply_async(process_function_multiproc, (
f,
func_param,
))
results.append(res)
else:
pool = None
for idx_function, f in enumerate(functions):
print_line('Checking ' + f)
if functions == functions_serial or jobs == 1:
if arguments.check_filesystem:
if os.path.exists(os.path.join(path_tmp, f)):
shutil.rmtree(os.path.join(path_tmp, f))
sig_0 = fs_signature(path_tmp)
func_param = copy.deepcopy(param)
func_param.path_output = f
res = process_function(f, func_param)
if arguments.check_filesystem:
sig_1 = fs_signature(path_tmp)
fs_ok(sig_0, sig_1, exclude=(f, ))
else:
res = results[idx_function].get()
list_output, list_status_function = res
# manage status
if any(list_status_function):
if 1 in list_status_function:
print_fail()
status = (f, 1)
else:
print_warning()
status = (f, 99)
for output in list_output:
for line in output.splitlines():
print(" %s" % line)
else:
print_ok()
if param.verbose:
for output in list_output:
for line in output.splitlines():
print(" %s" % line)
status = (f, 0)
# append status function to global list of status
list_status.append(status)
if any([s for (f, s) in list_status
]) and arguments.abort_on_failure:
break
except KeyboardInterrupt:
raise
finally:
if pool:
pool.terminate()
pool.join()
print('status: ' + str([s for (f, s) in list_status]))
if any([s for (f, s) in list_status]):
print("Failures: {}".format(" ".join(
[f for (f, s) in list_status if s])))
# display elapsed time
elapsed_time = time.time() - start_time
printv('Finished! Elapsed time: ' + str(int(np.round(elapsed_time))) +
's\n')
# come back
os.chdir(curdir)
# remove temp files
if param.remove_tmp_file and arguments.execution_folder is None:
printv('\nRemove temporary files...', 0)
rmtree(path_tmp)
e = 0
if any([s for (f, s) in list_status]):
e = 1
# print(e)
sys.exit(e)
def compute_dti(fname_in, fname_bvals, fname_bvecs, prefix, method, evecs,
file_mask, verbose):
"""
Compute DTI.
:param fname_in: input 4d file.
:param bvals: bvals txt file
:param bvecs: bvecs txt file
:param prefix: output prefix. Example: "dti_"
:param method: algo for computing dti
:param evecs: bool: output diffusion tensor eigenvectors and eigenvalues
:return: True/False
"""
# Open file.
from spinalcordtoolbox.image import Image
nii = Image(fname_in)
data = nii.data
printv('data.shape (%d, %d, %d, %d)' % data.shape)
# open bvecs/bvals
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(fname_bvals, fname_bvecs)
from dipy.core.gradients import gradient_table
gtab = gradient_table(bvals, bvecs)
# mask and crop the data. This is a quick way to avoid calculating Tensors on the background of the image.
if not file_mask == '':
printv('Open mask file...', verbose)
# open mask file
nii_mask = Image(file_mask)
mask = nii_mask.data
# fit tensor model
printv('Computing tensor using "' + method + '" method...', verbose)
import dipy.reconst.dti as dti
if method == 'standard':
tenmodel = dti.TensorModel(gtab)
if file_mask == '':
tenfit = tenmodel.fit(data)
else:
tenfit = tenmodel.fit(data, mask)
elif method == 'restore':
import dipy.denoise.noise_estimate as ne
sigma = ne.estimate_sigma(data)
dti_restore = dti.TensorModel(gtab, fit_method='RESTORE', sigma=sigma)
if file_mask == '':
tenfit = dti_restore.fit(data)
else:
tenfit = dti_restore.fit(data, mask)
# Compute metrics
printv('Computing metrics...', verbose)
# FA
nii.data = tenfit.fa
nii.save(prefix + 'FA.nii.gz', dtype='float32')
# MD
nii.data = tenfit.md
nii.save(prefix + 'MD.nii.gz', dtype='float32')
# RD
nii.data = tenfit.rd
nii.save(prefix + 'RD.nii.gz', dtype='float32')
# AD
nii.data = tenfit.ad
nii.save(prefix + 'AD.nii.gz', dtype='float32')
if evecs:
data_evecs = tenfit.evecs
data_evals = tenfit.evals
# output 1st (V1), 2nd (V2) and 3rd (V3) eigenvectors as 4d data
for idim in range(3):
nii.data = data_evecs[:, :, :, :, idim]
nii.save(prefix + 'V' + str(idim + 1) + '.nii.gz', dtype="float32")
nii.data = data_evals[:, :, :, idim]
nii.save(prefix + 'E' + str(idim + 1) + '.nii.gz', dtype="float32")
return True
def print_ok():
printv("[" + bcolors.OKGREEN + "OK" + bcolors.ENDC + "]")
def print_warning():
printv("[" + bcolors.WARNING + "WARNING" + bcolors.ENDC + "]")
def print_fail():
printv("[" + bcolors.FAIL + "FAIL" + bcolors.ENDC + "]")
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_loglevel(verbose=verbose)
GYRO = float(42.576 * 10**6) # gyromagnetic ratio (in Hz.T^-1)
gradamp = []
bigdelta = []
smalldelta = []
gradamp = arguments.g
bigdelta = arguments.b
smalldelta = arguments.d
# printv(arguments)
printv('\nCheck parameters:')
printv(' gradient amplitude ..... ' + str(gradamp) + ' mT/m')
printv(' big delta .............. ' + str(bigdelta) + ' ms')
printv(' small delta ............ ' + str(smalldelta) + ' ms')
printv(' gyromagnetic ratio ..... ' + str(GYRO) + ' Hz/T')
printv('')
bvalue = (2 * math.pi * GYRO * gradamp * 0.001 * smalldelta *
0.001)**2 * (bigdelta * 0.001 - smalldelta * 0.001 / 3)
printv('b-value = ' + str(bvalue / 10**6) + ' mm^2/s\n')
return bvalue
def main(args=None):
parser = get_parser()
if args:
arguments = parser.parse_args(args)
else:
arguments = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
verbosity = arguments.v
init_sct(log_level=verbosity, update=True) # Update log level
input_filename = arguments.i
output_fname = arguments.o
img = Image(input_filename)
dtype = None
if arguments.add is not None:
value = arguments.add
out = sct_labels.add(img, value)
elif arguments.create is not None:
labels = arguments.create
out = sct_labels.create_labels_empty(img, labels)
elif arguments.create_add is not None:
labels = arguments.create_add
out = sct_labels.create_labels(img, labels)
elif arguments.create_seg is not None:
labels = arguments.create_seg
out = sct_labels.create_labels_along_segmentation(img, labels)
elif arguments.cubic_to_point:
out = sct_labels.cubic_to_point(img)
elif arguments.display:
display_voxel(img, verbosity)
return
elif arguments.increment:
out = sct_labels.increment_z_inverse(img)
elif arguments.disc is not None:
ref = Image(arguments.disc)
out = sct_labels.labelize_from_discs(img, ref)
elif arguments.vert_body is not None:
levels = arguments.vert_body
if len(levels) == 1 and levels[0] == 0:
levels = None # all levels
out = sct_labels.label_vertebrae(img, levels)
elif arguments.vert_continuous:
out = sct_labels.continuous_vertebral_levels(img)
dtype = 'float32'
elif arguments.MSE is not None:
ref = Image(arguments.MSE)
mse = sct_labels.compute_mean_squared_error(img, ref)
printv(f"Computed MSE: {mse}")
return
elif arguments.remove_reference is not None:
ref = Image(arguments.remove_reference)
out = sct_labels.remove_missing_labels(img, ref)
elif arguments.remove_sym is not None:
# first pass use img as source
ref = Image(arguments.remove_reference)
out = sct_labels.remove_missing_labels(img, ref)
# second pass use previous pass result as reference
ref_out = sct_labels.remove_missing_labels(ref, out)
ref_out.save(path=ref.absolutepath)
elif arguments.remove is not None:
labels = arguments.remove
out = sct_labels.remove_labels_from_image(img, labels)
elif arguments.keep is not None:
labels = arguments.keep
out = sct_labels.remove_other_labels_from_image(img, labels)
elif arguments.create_viewer is not None:
msg = "" if arguments.msg is None else f"{arguments.msg}\n"
if arguments.ilabel is not None:
input_labels_img = Image(arguments.ilabel)
out = launch_manual_label_gui(img, input_labels_img, parse_num_list(arguments.create_viewer), msg)
else:
out = launch_sagittal_viewer(img, parse_num_list(arguments.create_viewer), msg)
printv("Generating output files...")
out.save(path=output_fname, dtype=dtype)
display_viewer_syntax([input_filename, output_fname])
if arguments.qc is not None:
generate_qc(fname_in1=input_filename, fname_seg=output_fname, args=args,
path_qc=os.path.abspath(arguments.qc), dataset=arguments.qc_dataset,
subject=arguments.qc_subject, process='sct_label_utils')
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_loglevel(verbose=verbose)
model = arguments.model
if "," in arguments.radius:
patch_radius = list_type(",", int)(arguments.radius)
else:
patch_radius = int(arguments.radius)
file_to_denoise = arguments.i
bval_file = arguments.b
output_file_name = arguments.o
path, file, ext = extract_fname(file_to_denoise)
img = nib.load(file_to_denoise)
bvals = np.loadtxt(bval_file)
hdr_0 = img.get_header()
data = img.get_data()
printv('Applying Patch2Self Denoising...')
den = patch2self(data,
bvals,
patch_radius=patch_radius,
model=model,
verbose=True)
if verbose == 2:
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1, 3)
axial_middle = int(data.shape[2] / 2)
middle_vol = int(data.shape[3] / 2)
before = data[:, :, axial_middle, middle_vol].T
ax[0].imshow(before, cmap='gray', origin='lower')
ax[0].set_title('before')
after = den[:, :, axial_middle, middle_vol].T
ax[1].imshow(after, cmap='gray', origin='lower')
ax[1].set_title('after')
difference = np.absolute(after.astype('f8') - before.astype('f8'))
ax[2].imshow(difference, cmap='gray', origin='lower')
ax[2].set_title('difference')
for i in range(3):
ax[i].set_axis_off()
plt.show()
# Save files
img_denoise = nib.Nifti1Image(den, None, hdr_0)
diff_4d = np.absolute(den.astype('f8') - data.astype('f8'))
img_diff = nib.Nifti1Image(diff_4d, None, hdr_0)
if output_file_name is not None:
output_file_name_den = output_file_name
output_file_name_diff = add_suffix(output_file_name, "_difference")
else:
output_file_name_den = file + '_patch2self_denoised' + ext
output_file_name_diff = file + '_patch2self_difference' + ext
nib.save(img_denoise, output_file_name_den)
nib.save(img_diff, output_file_name_diff)
printv('\nDone! To view results, type:', verbose)
printv('fsleyes ' + file_to_denoise + ' ' + output_file_name + ' & \n',
verbose, 'info')
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv if argv else ['--help'])
verbose = arguments.v
set_global_loglevel(verbose=verbose)
fname_bvecs = arguments.bvec
# Read bvecs
bvecs = read_bvals_bvecs(fname_bvecs, None)
bvecs = bvecs[0]
# if first dimension is not equal to 3 (x,y,z), transpose bvecs file
if not bvecs.shape[0] == 3:
bvecs = bvecs.transpose()
x, y, z = bvecs[0], bvecs[1], bvecs[2]
# Get total number of directions
n_dir = len(x)
# Get effective number of directions
bvecs_eff = []
n_b0 = 0
for i in range(0, n_dir):
add_direction = True
# check if b=0
if abs(x[i]) < bzero and abs(x[i]) < bzero and abs(x[i]) < bzero:
n_b0 += 1
add_direction = False
else:
# loop across bvecs_eff
for j in range(0, len(bvecs_eff)):
# if bvalue already present, then do not add to bvecs_eff
if bvecs_eff[j] == [x[i], y[i], z[i]]:
add_direction = False
if add_direction:
bvecs_eff.append([x[i], y[i], z[i]])
n_dir_eff = len(bvecs_eff)
# Display scatter plot
fig = plt.figure(facecolor='white', figsize=(9, 8))
fig.suptitle('Number of b=0: ' + str(n_b0) + ', Number of b!=0: ' + str(n_dir - n_b0) + ', Number of effective directions (without duplicates): ' + str(n_dir_eff))
# plt.ion()
# Display three views
plot_2dscatter(fig_handle=fig, subplot=221, x=bvecs[0][:], y=bvecs[1][:], xlabel='X', ylabel='Y')
plot_2dscatter(fig_handle=fig, subplot=222, x=bvecs[0][:], y=bvecs[2][:], xlabel='X', ylabel='Z')
plot_2dscatter(fig_handle=fig, subplot=223, x=bvecs[1][:], y=bvecs[2][:], xlabel='Y', ylabel='Z')
# 3D
ax = fig.add_subplot(224, projection='3d')
# ax.auto_scale_xyz([-1, 1], [-1, 1], [-1, 1])
for i in range(0, n_dir):
# x, y, z = bvecs[0], bvecs[1], bvecs[2]
# if b=0, do not plot
if not(abs(x[i]) < bzero and abs(x[i]) < bzero and abs(x[i]) < bzero):
ax.scatter(x[i], y[i], z[i])
ax.set_xlim3d(-1, 1)
ax.set_ylim3d(-1, 1)
ax.set_zlim3d(-1, 1)
plt.title('3D view (use mouse to rotate)')
plt.axis('off')
# plt.draw()
# Save image
printv("Saving figure: bvecs.png\n")
plt.savefig('bvecs.png')
plt.show()
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_loglevel(verbose=verbose)
fname_bvecs = arguments.bvec
fname_bvals = arguments.bval
# Read bvals and bvecs files (if arguments.bval is not passed, bvals will be None)
bvals, bvecs = read_bvals_bvecs(fname_bvals, fname_bvecs)
# if first dimension is not equal to 3 (x,y,z), transpose bvecs file
if bvecs.shape[0] != 3:
bvecs = bvecs.transpose()
# if bvals file was not passed, create dummy unit bvals array (necessary fot scatter plots)
if bvals is None:
bvals = np.repeat(1, bvecs.shape[1])
# multiply unit b-vectors by b-values
x, y, z = bvecs[0] * bvals, bvecs[1] * bvals, bvecs[2] * bvals
# Set different color for each shell (bval)
shell_colors = {}
# Create iterator with different colors from brg palette
colors = iter(cm.nipy_spectral(np.linspace(0, 1, len(np.unique(bvals)))))
for unique_bval in np.unique(bvals):
# skip b=0
if unique_bval < BZERO_THRESH:
continue
shell_colors[unique_bval] = next(colors)
# Get total number of directions
n_dir = len(x)
# Get effective number of directions
bvecs_eff = []
n_b0 = 0
for i in range(0, n_dir):
add_direction = True
# check if b=0
if abs(x[i]) < BZERO_THRESH and abs(x[i]) < BZERO_THRESH and abs(
x[i]) < BZERO_THRESH:
n_b0 += 1
add_direction = False
else:
# loop across bvecs_eff
for j in range(0, len(bvecs_eff)):
# if bvalue already present, then do not add to bvecs_eff
if bvecs_eff[j] == [x[i], y[i], z[i]]:
add_direction = False
if add_direction:
bvecs_eff.append([x[i], y[i], z[i]])
n_dir_eff = len(bvecs_eff)
# Display scatter plot
fig = plt.figure(facecolor='white', figsize=(9, 8))
fig.suptitle('Number of b=0: ' + str(n_b0) + ', Number of b!=0: ' +
str(n_dir - n_b0) +
', Number of effective directions (without duplicates): ' +
str(n_dir_eff))
# Display three views
plot_2dscatter(fig_handle=fig,
subplot=221,
x=x,
y=y,
xlabel='X',
ylabel='Y',
bvals=bvals,
colors=shell_colors)
plot_2dscatter(fig_handle=fig,
subplot=222,
x=x,
y=z,
xlabel='X',
ylabel='Z',
bvals=bvals,
colors=shell_colors)
plot_2dscatter(fig_handle=fig,
subplot=223,
x=y,
y=z,
xlabel='Y',
ylabel='Z',
bvals=bvals,
colors=shell_colors)
# 3D
ax = fig.add_subplot(224, projection='3d')
# ax.auto_scale_xyz([-1, 1], [-1, 1], [-1, 1])
for i in range(0, n_dir):
# x, y, z = bvecs[0], bvecs[1], bvecs[2]
# if b=0, do not plot
if not (abs(x[i]) < BZERO_THRESH and abs(x[i]) < BZERO_THRESH
and abs(x[i]) < BZERO_THRESH):
ax.scatter(x[i],
y[i],
z[i],
color=shell_colors[bvals[i]],
alpha=0.7)
ax.set_xlim3d(-max(bvals), max(bvals))
ax.set_ylim3d(-max(bvals), max(bvals))
ax.set_zlim3d(-max(bvals), max(bvals))
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
plt.title('3D view (use mouse to rotate)')
plt.axis('on')
# plt.draw()
plt.tight_layout()
# add legend with b-values if bvals file was passed
if arguments.bval is not None:
create_custom_legend(fig, shell_colors, bvals)
# Save image
printv("Saving figure: bvecs.png\n")
plt.savefig('bvecs.png')
