def run_centernifti(
input_dir: PathLike, output_dir: PathLike, ref_dir: PathLike
) -> None:
from clinica.iotools.utils.data_handling import center_all_nifti
output_dir = output_dir / "bids_centered"
bids_dir = input_dir / "bids"
all_modalities = [
"t1w",
"pet",
"dwi",
"magnitude",
"bold",
"flair",
"t2",
"phasediff",
]
center_all_nifti(
fspath(bids_dir),
fspath(output_dir),
all_modalities,
center_all_files=True,
)
hashes_out = create_list_hashes(
fspath(output_dir), extensions_to_keep=(".nii.gz", ".nii")
)
hashes_ref = create_list_hashes(
fspath(ref_dir / "bids_centered"), extensions_to_keep=(".nii.gz", ".nii")
)
assert hashes_out == hashes_ref
if hashes_out != hashes_ref:
raise RuntimeError("Hashes of nii* files are different between out and ref")
def test_run_CenterNifti(cmdopt):
from clinica.iotools.utils.data_handling import center_all_nifti
from os.path import dirname, join, abspath
root = dirname(abspath(join(abspath(__file__), pardir)))
root = join(root, 'data', 'CenterNifti')
clean_folder(join(root, 'out', 'bids_centered'), recreate=True)
bids_dir = join(root, 'in', 'bids')
output_dir = join(root, 'out', 'bids_centered')
all_modalities = [
't1w', 'pet', 'dwi', 'magnitude', 'bold', 'flair', 't2', 'phasediff'
]
center_all_nifti(bids_dir,
output_dir,
all_modalities,
center_all_files=True)
hashes_out = create_list_hashes(output_dir,
extensions_to_keep=('.nii.gz', '.nii'))
hashes_ref = create_list_hashes(join(root, 'ref', 'bids_centered'),
extensions_to_keep=('.nii.gz', '.nii'))
if hashes_out != hashes_ref:
raise RuntimeError(
'Hashes of nii* files are different between out and ref')
clean_folder(join(root, 'out', 'bids_centered'), recreate=False)
def test_run_CenterNifti(cmdopt):
from os.path import abspath, dirname, join
from clinica.iotools.utils.data_handling import center_all_nifti
root = dirname(abspath(join(abspath(__file__), pardir, pardir)))
root = join(root, "data", "CenterNifti")
clean_folder(join(root, "out", "bids_centered"), recreate=True)
bids_dir = join(root, "in", "bids")
output_dir = join(root, "out", "bids_centered")
all_modalities = [
"t1w",
"pet",
"dwi",
"magnitude",
"bold",
"flair",
"t2",
"phasediff",
]
center_all_nifti(bids_dir,
output_dir,
all_modalities,
center_all_files=True)
hashes_out = create_list_hashes(output_dir,
extensions_to_keep=(".nii.gz", ".nii"))
hashes_ref = create_list_hashes(join(root, "ref", "bids_centered"),
extensions_to_keep=(".nii.gz", ".nii"))
if hashes_out != hashes_ref:
raise RuntimeError(
"Hashes of nii* files are different between out and ref")
clean_folder(join(root, "out", "bids_centered"), recreate=False)
def center_nifti(
bids_directory: str,
output_bids_directory: str,
modalities: Optional[List[str]] = None,
center_all_files: bool = False,
) -> None:
"""Center NIfTI files in a BIDS dataset.
This tool is mainly useful as a preprocessing step of SPM. In some cases, SPM is not able to segment T1 volumes
because their respective center is not aligned with the origin of the world coordinate system. By default, only
images detected as problematic are converted from INPUT_BIDS_DIRECTORY to OUTPUT_BIDS_DIRECTORY, whilst the others
are copied verbatim.
"""
import sys
import time
from os import listdir, makedirs
from os.path import isfile, join
from clinica.iotools.utils.data_handling import (
center_all_nifti,
write_list_of_files,
)
from clinica.utils.stream import cprint
# check that output_folder does not exist, or is an empty folder
try:
makedirs(output_bids_directory)
except FileExistsError:
file_list = [
file for file in listdir(output_bids_directory)
if not file.startswith(".")
]
if file_list:
click.echo(
"Target BIDS directory is not empty. Existing files may be overwritten."
)
if not click.confirm("Do you wish to continue?"):
click.echo("Clinica will now exit...")
sys.exit(0)
cprint("Clinica is now centering the requested images.")
centered_files = center_all_nifti(
bids_directory,
output_bids_directory,
modalities,
center_all_files,
)
# Write list of created files
timestamp = time.strftime("%Y%m%d-%H%M%S", time.localtime(time.time()))
log_file = join(output_bids_directory,
"centered_nifti_list_" + timestamp + ".txt")
# If an error happen while creating the file, the function returns Nan
if not write_list_of_files(centered_files, log_file):
cprint("Could not create log file.")
# Final message
cprint(
f"{str(len(centered_files))} NIfTI files/images of BIDS folder:\n"
f"\t{bids_directory}\n"
f"for the modalities {modalities} have been centered in output folder:\n"
f"\t{output_bids_directory}")
if isfile(log_file):
cprint(
f"The list of centered NIfTI files is available here: {log_file}.")
cprint(
"Please note that the rest of the input BIDS folder has also been copied to the output folder."
)
def run_command(self, args):
import sys
import time
from os import listdir, makedirs
from os.path import abspath, isdir, isfile, join
from colorama import Fore
from clinica.iotools.utils.data_handling import (
center_all_nifti,
write_list_of_files,
)
from clinica.utils.stream import cprint
# check that output_folder does not exist, or is an empty folder
if isdir(args.output_bids_directory):
file_list = [
file for file in listdir(args.output_bids_directory)
if not file.startswith(".")
]
if len(file_list) > 0:
error_str = (
f"{Fore.YELLOW}[Warning] Some files or directory have been found "
f"in {{abspath(args.output_bids_directory)}}: \n")
for f in file_list:
error_str += "\t" + f + "\n"
error_str += "Do you wish to continue ? (If yes, this may overwrite the files mentioned above)."
error_str += Fore.RESET
cprint(error_str)
while True:
cprint("Your answer [yes/no]:")
answer = input()
if answer.lower() in ["yes", "no"]:
break
else:
cprint(
f"{Fore.RED}You must answer yes or no{Fore.RESET}")
if answer.lower() == "no":
cprint(f"{Fore.RED}Clinica will now exit...{Fore.RESET}")
sys.exit(0)
else:
makedirs(args.output_bids_directory)
split_modality = args.modality.split(" ")
# Remove empty str in list
split_modality = [element for element in split_modality if element]
cprint("Clinica is now centering the requested images.")
centered_files = center_all_nifti(
abspath(args.bids_directory),
abspath(args.output_bids_directory),
split_modality,
center_all_files=args.center_all_files,
)
# Write list of created files
timestamp = time.strftime("%Y%m%d-%H%M%S", time.localtime(time.time()))
log_file = abspath(
join(args.output_bids_directory,
"centered_nifti_list_" + timestamp + ".txt"))
# If an error happen while creating the file, the function returns Nan
if not write_list_of_files(centered_files, log_file):
cprint(
f"{Fore.YELLOW}[Warning] Could not create log file.{Fore.RESET}"
)
# Final message
cprint(
f"{Fore.GREEN}{str(len(centered_files))} NIfTI files/images of BIDS folder:\n\t "
f"{Fore.BLUE}{abspath(args.bids_directory)}"
f"{Fore.GREEN}\n for the modalities "
f"{Fore.YELLOW}{args.modality}"
f"{Fore.GREEN} have been centered in output folder:\n\t"
f"{Fore.BLUE}{abspath(args.output_bids_directory)}{Fore.RESET}")
if isfile(log_file):
cprint(
f"{Fore.GREEN}The list of centered NIfTI files is available here: {Fore.BLUE}{log_file}{Fore.RESET}"
)
cprint(
"Please note that the rest of the input BIDS folder has also been copied to the output folder."
)
def run_command(self, args):
from colorama import Fore
from os.path import isdir, abspath, join, isfile
from os import listdir
from os import makedirs
from clinica.iotools.utils.data_handling import center_all_nifti, write_list_of_files
from clinica.utils.stream import cprint
import sys
import time
# check that output_folder does not exist, or is an empty folder
if isdir(args.output_bids_directory):
file_list = [
file for file in listdir(args.output_bids_directory)
if not file.startswith('.')
]
if len(file_list) > 0:
error_str = Fore.YELLOW + '[Warning] Some files or directory have been found in ' \
+ abspath(args.output_bids_directory) + ': \n'
for f in file_list:
error_str += '\t' + f + '\n'
error_str += 'Do you wish to continue ? (If yes, this may overwrite the files mentioned above).'
error_str += Fore.RESET
cprint(error_str)
while True:
cprint('Your answer [yes/no]:')
answer = input()
if answer.lower() in ['yes', 'no']:
break
else:
cprint(Fore.RED + 'You must answer yes or no' +
Fore.RESET)
if answer.lower() == 'no':
cprint(Fore.RED + 'Clinica will now exit...' + Fore.RESET)
sys.exit(0)
else:
makedirs(args.output_bids_directory)
split_modality = args.modality.split(' ')
# Remove empty str in list
split_modality = [element for element in split_modality if element]
cprint('Clinica is now centering the requested images.')
centered_files = center_all_nifti(
abspath(args.bids_directory),
abspath(args.output_bids_directory),
split_modality,
center_all_files=args.center_all_files)
# Write list of created files
timestamp = time.strftime("%Y%m%d-%H%M%S", time.localtime(time.time()))
log_file = abspath(
join(args.output_bids_directory,
'centered_nifti_list_' + timestamp + '.txt'))
# If an error happen while creating the file, the function returns Nan
if not write_list_of_files(centered_files, log_file):
cprint(Fore.YELLOW + '[Warning] Could not create log file' +
Fore.RESET)
# Final message
cprint(Fore.GREEN + str(len(centered_files)) +
' NIfTI files/images of BIDS folder:\n\t ' + Fore.BLUE +
abspath(args.bids_directory) + Fore.GREEN +
'\n for the modalities ' + Fore.YELLOW + args.modality +
Fore.GREEN + ' have been centered in output folder:\n\t' +
Fore.BLUE + abspath(args.output_bids_directory) + Fore.RESET)
if isfile(log_file):
cprint(Fore.GREEN +
'The list of centered NIfTI files is available here : ' +
Fore.BLUE + log_file + Fore.RESET)
cprint(
'Please note that the rest of the input BIDS folder has also been copied to the output folder.'
)