def execute():
import os
import argparse
from colorama import Fore
import warnings
import logging
# Suppress potential warnings
warnings.filterwarnings("ignore")
# Remove warnings from duecredit package in order to silent
# "Assuming non interactive session since isatty found missing" message
logging.getLogger("duecredit.utils").setLevel(logging.ERROR)
# Add warning message if PYTHONPATH is not empty
# cf https://groups.google.com/forum/#!topic/clinica-user/bVgifEdkg20
python_path = os.environ.get('PYTHONPATH', '')
if python_path:
print(
'%s[Warning] The PYTHONPATH environment variable is not empty.'
' Make sure there is no interference with Clinica (content of PYTHONPATH: %s).%s'
% (Fore.YELLOW, python_path, Fore.RESET))
# Nice traceback when clinica crashes
sys.excepthook = custom_traceback
MANDATORY_TITLE = (Fore.YELLOW + 'Mandatory arguments' + Fore.RESET)
OPTIONAL_TITLE = (Fore.YELLOW + 'Optional arguments' + Fore.RESET)
"""
Define and parse the command line argument
"""
parser = ArgumentParser(add_help=False)
parser.add_argument('-h',
'--help',
action='help',
default=argparse.SUPPRESS,
help=argparse.SUPPRESS)
parser._positionals.title = (
Fore.YELLOW + 'clinica expects one of the following keywords' +
Fore.RESET)
parser._optionals.title = OPTIONAL_TITLE
sub_parser = parser.add_subparsers(metavar='')
parser.add_argument("-v",
"--verbose",
dest='verbose',
action='store_true',
default=False,
help='Verbose: print all messages to the console')
parser.add_argument("-l",
"--logname",
dest='logname',
default="clinica.log",
metavar=('file.log'),
help='Define the log file name (default: clinica.log)')
"""
run category: run one of the available pipelines
"""
from clinica.engine import CmdParser
from clinica.pipelines.t1_freesurfer.t1_freesurfer_cli import T1FreeSurferCLI
from clinica.pipelines.t1_freesurfer_longitudinal.t1_freesurfer_longitudinal_cli import T1FreeSurferLongitudinalCLI
from clinica.pipelines.t1_freesurfer_longitudinal.t1_freesurfer_template_cli import T1FreeSurferTemplateCLI
from clinica.pipelines.t1_freesurfer_longitudinal.t1_freesurfer_longitudinal_correction_cli import T1FreeSurferLongitudinalCorrectionCLI
from clinica.pipelines.t1_volume_tissue_segmentation.t1_volume_tissue_segmentation_cli import T1VolumeTissueSegmentationCLI
from clinica.pipelines.t1_volume_create_dartel.t1_volume_create_dartel_cli import T1VolumeCreateDartelCLI
from clinica.pipelines.t1_volume_register_dartel.t1_volume_register_dartel_cli import T1VolumeRegisterDartelCLI
from clinica.pipelines.t1_volume_dartel2mni.t1_volume_dartel2mni_cli import T1VolumeDartel2MNICLI
from clinica.pipelines.t1_volume.t1_volume_cli import T1VolumeCLI
from clinica.pipelines.t1_volume_existing_template.t1_volume_existing_template_cli import T1VolumeExistingTemplateCLI
from clinica.pipelines.t1_volume_parcellation.t1_volume_parcellation_cli import T1VolumeParcellationCLI
from clinica.pipelines.t1_linear.t1_linear_cli import T1LinearCLI
from clinica.pipelines.dwi_preprocessing_using_phasediff_fieldmap.dwi_preprocessing_using_phasediff_fieldmap_cli import DwiPreprocessingUsingPhaseDiffFieldmapCli
from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_cli import DwiPreprocessingUsingT1Cli
from clinica.pipelines.dwi_dti.dwi_dti_cli import DwiDtiCli
from clinica.pipelines.dwi_connectome.dwi_connectome_cli import DwiConnectomeCli
from clinica.pipelines.fmri_preprocessing.fmri_preprocessing_cli import fMRIPreprocessingCLI
from clinica.pipelines.pet_volume.pet_volume_cli import PETVolumeCLI
from clinica.pipelines.pet_surface.pet_surface_cli import PetSurfaceCLI
from clinica.pipelines.pet_surface.pet_surface_longitudinal_cli import PetSurfaceLongitudinalCLI
from clinica.pipelines.machine_learning_spatial_svm.spatial_svm_cli import SpatialSVMCLI
from clinica.pipelines.statistics_surface.statistics_surface_cli import StatisticsSurfaceCLI
from clinica.pipelines.statistics_volume.statistics_volume_cli import StatisticsVolumeCLI
from clinica.pipelines.statistics_volume_correction.statistics_volume_correction_cli import StatisticsVolumeCorrectionCLI
pipelines = ClinicaClassLoader(baseclass=CmdParser,
extra_dir="pipelines").load()
# The order in pipelines var will the same when typing `clinica run`
# Pipelines are sorted by main / advanced pipelines then by modality
pipelines += [
# Main pipelines:
T1FreeSurferCLI(),
T1VolumeCLI(),
# T1FreeSurferLongitudinalCLI(),
T1LinearCLI(),
DwiPreprocessingUsingPhaseDiffFieldmapCli(),
DwiPreprocessingUsingT1Cli(),
DwiDtiCli(),
DwiConnectomeCli(),
fMRIPreprocessingCLI(),
PETVolumeCLI(),
PetSurfaceCLI(),
# PetSurfaceLongitudinalCLI(),
SpatialSVMCLI(),
StatisticsSurfaceCLI(),
StatisticsVolumeCLI(),
StatisticsVolumeCorrectionCLI(),
# Advanced pipelines:
T1VolumeExistingTemplateCLI(),
T1VolumeTissueSegmentationCLI(),
T1VolumeCreateDartelCLI(),
T1VolumeRegisterDartelCLI(),
T1VolumeDartel2MNICLI(),
T1VolumeParcellationCLI(),
# T1FreeSurferTemplateCLI(),
# T1FreeSurferLongitudinalCorrectionCLI(),
]
run_parser = sub_parser.add_parser(
'run',
add_help=False,
formatter_class=argparse.RawTextHelpFormatter,
help='To run pipelines on BIDS/CAPS datasets.')
run_parser.description = '%sRun pipelines on BIDS/CAPS datasets.%s' % \
(Fore.GREEN, Fore.RESET)
run_parser._positionals.title = '%sclinica run expects one of the following pipelines%s' % \
(Fore.GREEN, Fore.RESET)
init_cmdparser_objects(parser,
run_parser.add_subparsers(metavar='', dest='run'),
pipelines)
"""
convert category: convert one of the supported datasets into BIDS hierarchy
"""
from clinica.iotools.converters.aibl_to_bids.aibl_to_bids_cli import AiblToBidsCLI
from clinica.iotools.converters.adni_to_bids.adni_to_bids_cli import AdniToBidsCLI
from clinica.iotools.converters.oasis_to_bids.oasis_to_bids_cli import OasisToBidsCLI
from clinica.iotools.converters.nifd_to_bids.nifd_to_bids_cli import NifdToBidsCLI # noga
converters = ClinicaClassLoader(baseclass=CmdParser,
extra_dir="iotools/converters").load()
converters += [
AdniToBidsCLI(),
AiblToBidsCLI(),
OasisToBidsCLI(),
NifdToBidsCLI(),
]
convert_parser = sub_parser.add_parser(
'convert',
add_help=False,
help='To convert unorganized datasets into a BIDS hierarchy.',
)
convert_parser.description = '%sTools to convert unorganized datasets into a BIDS hierarchy.%s' % \
(Fore.GREEN, Fore.RESET)
convert_parser._positionals.title = '%sclinica convert expects one of the following datasets%s' % \
(Fore.YELLOW, Fore.RESET)
convert_parser._optionals.title = OPTIONAL_TITLE
init_cmdparser_objects(
parser, convert_parser.add_subparsers(metavar='', dest='convert'),
converters)
"""
iotools category
"""
from clinica.iotools.utils.data_handling_cli import CmdParserSubjectsSessions
from clinica.iotools.utils.data_handling_cli import CmdParserMergeTsv
from clinica.iotools.utils.data_handling_cli import CmdParserMissingModalities
from clinica.iotools.utils.data_handling_cli import CmdParserCenterNifti
io_tools = [
CmdParserSubjectsSessions(),
CmdParserMergeTsv(),
CmdParserMissingModalities(),
CmdParserCenterNifti()
]
HELP_IO_TOOLS = 'Tools to handle BIDS/CAPS datasets.'
io_parser = sub_parser.add_parser(
'iotools',
add_help=False,
help=HELP_IO_TOOLS,
)
io_parser.description = '%s%s%s' % (Fore.GREEN, HELP_IO_TOOLS, Fore.RESET)
io_parser._positionals.title = '%sclinica iotools expects one of the following BIDS/CAPS utilities%s' % \
(Fore.YELLOW, Fore.RESET)
io_parser._optionals.title = OPTIONAL_TITLE
init_cmdparser_objects(
parser, io_parser.add_subparsers(metavar='', dest='iotools'), io_tools)
"""
visualize category: run one of the available pipelines
"""
from clinica.engine import CmdParser
from clinica.pipelines.t1_freesurfer.t1_freesurfer_visualizer import T1FreeSurferVisualizer
visualizers = ClinicaClassLoader(baseclass=CmdParser,
extra_dir="pipelines").load()
visualizers += [
T1FreeSurferVisualizer(),
]
visualize_parser = sub_parser.add_parser(
'visualize',
add_help=False,
formatter_class=argparse.RawTextHelpFormatter,
help='To visualize outputs of Clinica pipelines.')
visualize_parser.description = '%sVisualize outputs of Clinica pipelines.%s' % \
(Fore.GREEN, Fore.RESET)
visualize_parser._positionals.title = '%sclinica visualize expects one of the following pipelines%s' % \
(Fore.YELLOW, Fore.RESET)
init_cmdparser_objects(
parser, visualize_parser.add_subparsers(metavar='', dest='visualize'),
visualizers)
"""
generate category: template
"""
generate_parser = sub_parser.add_parser(
'generate',
add_help=False,
help=('To generate pre-filled files when creating '
'new pipelines (for developers).'),
)
generate_parser.description = '%sGenerate pre-filled files when creating new pipelines (for developers).%s' % \
(Fore.GREEN, Fore.RESET)
generate_parser._positionals.title = '%sclinica generate expects one of the following tools%s' % \
(Fore.YELLOW, Fore.RESET)
generate_parser._optionals.title = OPTIONAL_TITLE
from clinica.engine.template import CmdGenerateTemplates
init_cmdparser_objects(
parser, generate_parser.add_subparsers(metavar='', dest='generate'),
[CmdGenerateTemplates()])
"""
Silent all sub-parser errors methods except the one which is called
otherwise the output console will display useless messages
"""
def silent_help():
pass
def single_error_message(p):
def error(x):
from colorama import Fore
print('%sError %s%s\n' % (Fore.RED, x, Fore.RESET))
p.print_help()
parser.print_help = silent_help
exit(-1)
return error
for p in [run_parser, io_parser, convert_parser, generate_parser]:
p.error = single_error_message(p)
# Do not want stderr message
def silent_msg(x):
pass
parser.error = silent_msg
"""
Parse the command and check that everything went fine
"""
args = None
unknown_args = None
try:
argcomplete.autocomplete(parser)
args, unknown_args = parser.parse_known_args()
if unknown_args:
if ('--verbose' in unknown_args) or ('-v' in unknown_args):
cprint("Verbose detected")
args.verbose = True
unknown_args = [i for i in unknown_args if i != '-v']
unknown_args = [i for i in unknown_args if i != '--verbose']
if unknown_args:
print(
'%s[Warning] Unknown flag(s) detected: %s. This will be ignored by Clinica%s'
% (Fore.YELLOW, unknown_args, Fore.RESET))
except SystemExit:
exit(0)
except Exception:
print(
"%s\n[Error] You wrote wrong arguments on the command line. Clinica will now exit.\n%s"
% (Fore.RED, Fore.RESET))
parser.print_help()
exit(-1)
if 'run' in args and hasattr(args, 'func') is False:
# Case when we type `clinica run` on the terminal
run_parser.print_help()
exit(0)
elif 'convert' in args and hasattr(args, 'func') is False:
# Case when we type `clinica convert` on the terminal
convert_parser.print_help()
exit(0)
elif 'iotools' in args and hasattr(args, 'func') is False:
# Case when we type `clinica iotools` on the terminal
io_parser.print_help()
exit(0)
elif 'visualize' in args and hasattr(args, 'func') is False:
# Case when we type `clinica visualize` on the terminal
visualize_parser.print_help()
exit(0)
elif 'generate' in args and hasattr(args, 'func') is False:
# Case when we type `clinica generate` on the terminal
generate_parser.print_help()
exit(0)
elif args is None or hasattr(args, 'func') is False:
# Case when we type `clinica` on the terminal
parser.print_help()
exit(0)
import clinica.utils.stream as var
var.clinica_verbose = args.verbose
if args.verbose is False:
"""
Enable only cprint(msg) --> clinica print(msg)
- All the print() will be ignored!
- All the logging will be redirect to the log file.
"""
from clinica.utils.stream import FilterOut
sys.stdout = FilterOut(sys.stdout)
import logging as python_logging
from logging import Filter, ERROR
import os
from nipype import config, logging
# Configure Nipype logger for our needs
config.update_config({
'logging': {
'workflow_level': 'INFO',
'log_directory': os.getcwd(),
'log_to_file': True
},
'execution': {
'stop_on_first_crash': False,
'hash_method': 'content'
}
})
logging.update_logging(config)
# Define the LogFilter for ERROR detection
class LogFilter(Filter):
"""
The LogFilter class ables to monitor if an ERROR log signal is sent
from Clinica/Nipype. If detected, the user will be warned.
"""
def filter(self, record):
if record.levelno >= ERROR:
import datetime
now = datetime.datetime.now().strftime('%H:%M:%S')
cprint(
'%s[%s]%s An error was found: please check the log file (%s) or crash file '
'(nipypecli crash <pklz_file>) for details. Clinica is still running.'
% (Fore.RED, now, Fore.RESET, args.logname))
return True
if args.verbose:
logger = logging.getLogger('nipype.workflow')
logger.addFilter(LogFilter())
# Remove all handlers associated with the root logger object
for handler in python_logging.root.handlers[:]:
python_logging.root.removeHandler(handler)
logging.disable_file_logging()
# Enable file logging using a filename
def enable_file_logging(self, filename):
"""
Hack to define a filename for the log file! It overloads the
'enable_file_logging' method in 'nipype/utils/logger.py' file.
"""
import logging
from logging.handlers import RotatingFileHandler as RFHandler
config = self._config
LOG_FILENAME = os.path.join(config.get('logging', 'log_directory'),
filename)
hdlr = RFHandler(LOG_FILENAME,
maxBytes=int(config.get('logging', 'log_size')),
backupCount=int(
config.get('logging', 'log_rotate')))
formatter = logging.Formatter(fmt=self.fmt, datefmt=self.datefmt)
hdlr.setFormatter(formatter)
self._logger.addHandler(hdlr)
self._fmlogger.addHandler(hdlr)
self._iflogger.addHandler(hdlr)
self._hdlr = hdlr
enable_file_logging(logging, args.logname)
class Stream:
def write(self, text):
print(text)
sys.stdout.flush()
python_logging.basicConfig(format=logging.fmt,
datefmt=logging.datefmt,
stream=Stream())
# Finally, run the command
args.func(args)
def execute():
import argparse
from colorama import Fore
import warnings
# Suppress potential warnings
warnings.filterwarnings("ignore")
# Nice traceback when clinica crashes
sys.excepthook = custom_traceback
MANDATORY_TITLE = (Fore.YELLOW + 'Mandatory arguments' + Fore.RESET)
OPTIONAL_TITLE = (Fore.YELLOW + 'Optional arguments' + Fore.RESET)
"""
Define and parse the command line argument
"""
parser = ArgumentParser(add_help=False)
parser.add_argument('-h',
'--help',
action='help',
default=argparse.SUPPRESS,
help=argparse.SUPPRESS)
parser._positionals.title = (
Fore.YELLOW + 'clinica expects one of the following keywords' +
Fore.RESET)
parser._optionals.title = OPTIONAL_TITLE
sub_parser = parser.add_subparsers(metavar='')
parser.add_argument("-v",
"--verbose",
dest='verbose',
action='store_true',
default=False,
help='Verbose: print all messages to the console')
parser.add_argument("-l",
"--logname",
dest='logname',
default="clinica.log",
metavar=('file.log'),
help='Define the log file name (default: clinica.log)')
"""
run category: run one of the available pipelines
"""
from clinica.engine import CmdParser
from clinica.pipelines.t1_freesurfer_cross_sectional.t1_freesurfer_cross_sectional_cli import T1FreeSurferCrossSectionalCLI # noqa
from clinica.pipelines.t1_volume_tissue_segmentation.t1_volume_tissue_segmentation_cli import T1VolumeTissueSegmentationCLI # noqa
from clinica.pipelines.t1_volume_create_dartel.t1_volume_create_dartel_cli import T1VolumeCreateDartelCLI # noqa
from clinica.pipelines.t1_volume_existing_dartel.t1_volume_existing_dartel_cli import T1VolumeExistingDartelCLI # noqa
from clinica.pipelines.t1_volume_dartel2mni.t1_volume_dartel2mni_cli import T1VolumeDartel2MNICLI # noqa
from clinica.pipelines.t1_volume_new_template.t1_volume_new_template_cli import T1VolumeNewTemplateCLI # noqa
from clinica.pipelines.t1_volume_existing_template.t1_volume_existing_template_cli import T1VolumeExistingTemplateCLI # noqa
from clinica.pipelines.t1_volume_parcellation.t1_volume_parcellation_cli import T1VolumeParcellationCLI
from clinica.pipelines.dwi_preprocessing_using_phasediff_fieldmap.dwi_preprocessing_using_phasediff_fieldmap_cli import DwiPreprocessingUsingPhaseDiffFieldmapCli # noqa
from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_cli import DwiPreprocessingUsingT1Cli # noqa
from clinica.pipelines.dwi_dti.dwi_dti_cli import DwiDtiCli # noqa
# from clinica.pipelines.dwi_connectome.dwi_connectome_cli import DwiConnectomeCli # noqa
from clinica.pipelines.fmri_preprocessing.fmri_preprocessing_cli import fMRIPreprocessingCLI # noqa
from clinica.pipelines.pet_volume.pet_volume_cli import PETVolumeCLI # noqa
from clinica.pipelines.pet_surface.pet_surface_cli import PetSurfaceCLI # noqa
from clinica.pipelines.machine_learning_spatial_svm.spatial_svm_cli import SpatialSVMCLI # noqa
from clinica.pipelines.statistics_surface.statistics_surface_cli import StatisticsSurfaceCLI # noqa
pipelines = ClinicaClassLoader(baseclass=CmdParser,
extra_dir="pipelines").load()
pipelines += [
T1FreeSurferCrossSectionalCLI(),
T1VolumeNewTemplateCLI(),
DwiPreprocessingUsingPhaseDiffFieldmapCli(),
DwiPreprocessingUsingT1Cli(),
DwiDtiCli(),
# DwiConnectomeCli(),
fMRIPreprocessingCLI(),
PETVolumeCLI(),
PetSurfaceCLI(),
SpatialSVMCLI(),
StatisticsSurfaceCLI(),
T1VolumeExistingTemplateCLI(),
T1VolumeTissueSegmentationCLI(),
T1VolumeCreateDartelCLI(),
T1VolumeExistingDartelCLI(),
T1VolumeDartel2MNICLI(),
T1VolumeParcellationCLI()
]
run_parser = sub_parser.add_parser(
'run',
add_help=False,
formatter_class=argparse.RawTextHelpFormatter,
help='To run pipelines on BIDS/CAPS datasets.')
run_parser.description = (Fore.GREEN +
'Run pipelines on BIDS/CAPS datasets.' +
Fore.RESET)
run_parser._positionals.title = (
Fore.YELLOW + 'clinica run expects one of the following pipelines' +
Fore.RESET)
init_cmdparser_objects(parser,
run_parser.add_subparsers(metavar='', dest='run'),
pipelines)
"""
convert category: convert one of the supported datasets into BIDS hierarchy
"""
from clinica.iotools.converters.aibl_to_bids.aibl_to_bids_cli import AiblToBidsCLI # noqa
from clinica.iotools.converters.adni_to_bids.adni_to_bids_cli import AdniToBidsCLI # noqa
from clinica.iotools.converters.oasis_to_bids.oasis_to_bids_cli import OasisToBidsCLI # noqa
converters = ClinicaClassLoader(baseclass=CmdParser,
extra_dir="iotools/converters").load()
converters += [
AdniToBidsCLI(),
AiblToBidsCLI(),
OasisToBidsCLI(),
]
convert_parser = sub_parser.add_parser(
'convert',
add_help=False,
help='To convert unorganized datasets into a BIDS hierarchy.',
)
convert_parser.description = (
Fore.GREEN +
'Tools to convert unorganized datasets into a BIDS hierarchy.' +
Fore.RESET)
convert_parser._positionals.title = (
Fore.YELLOW + 'clinica convert expects one of the following datasets' +
Fore.RESET)
convert_parser._optionals.title = OPTIONAL_TITLE
init_cmdparser_objects(
parser, convert_parser.add_subparsers(metavar='', dest='convert'),
converters)
"""
iotools category
"""
from clinica.iotools.utils.data_handling_cli import CmdParserSubjectsSessions
from clinica.iotools.utils.data_handling_cli import CmdParserMergeTsv
from clinica.iotools.utils.data_handling_cli import CmdParserMissingModalities
io_tools = [
CmdParserSubjectsSessions(),
CmdParserMergeTsv(),
CmdParserMissingModalities(),
]
HELP_IO_TOOLS = 'Tools to handle BIDS/CAPS datasets.'
io_parser = sub_parser.add_parser(
'iotools',
add_help=False,
help=HELP_IO_TOOLS,
)
io_parser.description = (Fore.GREEN + HELP_IO_TOOLS + Fore.RESET)
io_parser._positionals.title = (
Fore.YELLOW +
'clinica iotools expects one of the following BIDS/CAPS utilities' +
Fore.RESET)
io_parser._optionals.title = OPTIONAL_TITLE
init_cmdparser_objects(
parser, io_parser.add_subparsers(metavar='', dest='iotools'), io_tools)
"""
visualize category: run one of the available pipelines
"""
from clinica.engine import CmdParser
from clinica.pipelines.t1_freesurfer_cross_sectional.t1_freesurfer_cross_sectional_visualizer import T1FreeSurferVisualizer
visualizers = ClinicaClassLoader(baseclass=CmdParser,
extra_dir="pipelines").load()
visualizers += [
T1FreeSurferVisualizer(),
]
visualize_parser = sub_parser.add_parser(
'visualize',
add_help=False,
formatter_class=argparse.RawTextHelpFormatter,
help='To visualize outputs of Clinica pipelines.')
visualize_parser.description = (Fore.GREEN +
'Visualize outputs of Clinica pipelines.' +
Fore.RESET)
visualize_parser._positionals.title = (
Fore.YELLOW +
'clinica visualize expects one of the following pipelines' +
Fore.RESET)
init_cmdparser_objects(
parser, visualize_parser.add_subparsers(metavar='', dest='visualize'),
visualizers)
"""
generate category: template
"""
generate_parser = sub_parser.add_parser(
'generate',
add_help=False,
help=('To generate pre-filled files when creating '
'new pipelines (for developers).'),
)
generate_parser.description = (
Fore.GREEN + ('Generate pre-filled files when creating new pipelines '
'(for developers).') + Fore.RESET)
generate_parser._positionals.title = (
Fore.YELLOW + 'clinica generate expects one of the following tools' +
Fore.RESET)
generate_parser._optionals.title = OPTIONAL_TITLE
from clinica.engine.template import CmdGenerateTemplates
init_cmdparser_objects(
parser, generate_parser.add_subparsers(metavar='', dest='generate'),
[CmdGenerateTemplates()])
"""
Silent all sub-parser errors methods except the one which is called
otherwise the output console will display useless messages
"""
def silent_help():
pass
def single_error_message(p):
def error(x):
from colorama import Fore
print('%sError %s%s\n' % (Fore.RED, x, Fore.RESET))
p.print_help()
parser.print_help = silent_help
exit(-1)
return error
for p in [run_parser, io_parser, convert_parser, generate_parser]:
p.error = single_error_message(p)
# Do not want stderr message
def silent_msg(x):
pass
parser.error = silent_msg
"""
Parse the command and check that everything went fine
"""
args = None
unknown_args = None
try:
argcomplete.autocomplete(parser)
args, unknown_args = parser.parse_known_args()
except SystemExit:
exit(0)
except Exception:
parser.print_help()
exit(-1)
# if unknown_args:
# if '--verbose' or '-v' in unknown_args:
# cprint('Verbose flag detected')
# raise ValueError('Unknown flag detected: %s' % unknown_args)
if 'run' in args and hasattr(args, 'func') is False:
# Case when we type `clinica run` on the terminal
run_parser.print_help()
exit(0)
elif 'convert' in args and hasattr(args, 'func') is False:
# Case when we type `clinica convert` on the terminal
convert_parser.print_help()
exit(0)
elif 'iotools' in args and hasattr(args, 'func') is False:
# Case when we type `clinica iotools` on the terminal
io_parser.print_help()
exit(0)
elif 'visualize' in args and hasattr(args, 'func') is False:
# Case when we type `clinica visualize` on the terminal
visualize_parser.print_help()
exit(0)
elif 'generate' in args and hasattr(args, 'func') is False:
# Case when we type `clinica generate` on the terminal
generate_parser.print_help()
exit(0)
elif args is None or hasattr(args, 'func') is False:
# Case when we type `clinica` on the terminal
parser.print_help()
exit(0)
import clinica.utils.stream as var
var.clinica_verbose = args.verbose
if args.verbose is False:
"""
Enable only cprint(msg) --> clinica print(msg)
- All the print() will be ignored!
- All the logging will be redirect to the log file.
"""
from clinica.utils.stream import FilterOut
sys.stdout = FilterOut(sys.stdout)
import logging as python_logging
from logging import Filter, ERROR
import os
# Resolve bug
# "Assuming non interactive session since isatty found missing"
# at the begining of any pipeline caused by logger in duecredit package
# (utils.py)
# Deactivate stdout, then reactivate it
sys.stdout = open(os.devnull, 'w')
from nipype import config
sys.stdout = sys.__stdout__
from nipype import logging
# Configure Nipype logger for our needs
config.update_config({
'logging': {
'workflow_level': 'INFO',
'log_directory': os.getcwd(),
'log_to_file': True
},
'execution': {
'stop_on_first_crash': False,
'hash_method': 'content'
}
})
logging.update_logging(config)
# Define the LogFilter for ERROR detection
class LogFilter(Filter):
"""
The LogFilter class ables to monitor if an ERROR log signal is sent
from Clinica/Nipype. If detected, the user will be warned.
"""
def filter(self, record):
if record.levelno >= ERROR:
cprint(
"An ERROR was generated: please check the log file for more information"
)
return True
logger = logging.getLogger('nipype.workflow')
logger.addFilter(LogFilter())
# Remove all handlers associated with the root logger object
for handler in python_logging.root.handlers[:]:
python_logging.root.removeHandler(handler)
logging.disable_file_logging()
# Enable file logging using a filename
def enable_file_logging(self, filename):
"""
Hack to define a filename for the log file! It overloads the
'enable_file_logging' method in 'nipype/utils/logger.py' file.
"""
import logging
from logging.handlers import RotatingFileHandler as RFHandler
config = self._config
LOG_FILENAME = os.path.join(config.get('logging', 'log_directory'),
filename)
hdlr = RFHandler(LOG_FILENAME,
maxBytes=int(config.get('logging', 'log_size')),
backupCount=int(
config.get('logging', 'log_rotate')))
formatter = logging.Formatter(fmt=self.fmt, datefmt=self.datefmt)
hdlr.setFormatter(formatter)
self._logger.addHandler(hdlr)
self._fmlogger.addHandler(hdlr)
self._iflogger.addHandler(hdlr)
self._hdlr = hdlr
enable_file_logging(logging, args.logname)
class Stream:
def write(self, text):
print(text)
sys.stdout.flush()
python_logging.basicConfig(format=logging.fmt,
datefmt=logging.datefmt,
stream=Stream())
# Finally, run the pipelines
args.func(args)
def execute():
import argparse
import logging
import os
import warnings
from colorama import Fore
# Suppress potential warnings
warnings.filterwarnings("ignore")
# Remove warnings from duecredit package in order to silent
# "Assuming non interactive session since isatty found missing" message
logging.getLogger("duecredit.utils").setLevel(logging.ERROR)
# Add warning message if PYTHONPATH is not empty
# cf https://groups.google.com/forum/#!topic/clinica-user/bVgifEdkg20
python_path = os.environ.get("PYTHONPATH", "")
if python_path:
print(
f"{Fore.YELLOW}[Warning] The PYTHONPATH environment variable is not empty."
f" Make sure there is no interference with Clinica "
f"(content of PYTHONPATH: {python_path}).{Fore.RESET}")
# Nice traceback when clinica crashes
sys.excepthook = custom_traceback
OPTIONAL_TITLE = f"{Fore.YELLOW}Optional arguments{Fore.RESET}"
"""
Define and parse the command line argument
"""
parser = ArgumentParser(add_help=False)
parser.add_argument("-h",
"--help",
action="help",
default=argparse.SUPPRESS,
help=argparse.SUPPRESS)
parser._positionals.title = (
f"{Fore.YELLOW}clinica expects one of the following keywords{Fore.RESET}"
)
parser._optionals.title = OPTIONAL_TITLE
sub_parser = parser.add_subparsers(metavar="")
parser.add_argument(
"-V",
"--version",
dest="version",
action="store_true",
default=False,
help="Clinica's installed version",
)
parser.add_argument(
"-v",
"--verbose",
dest="verbose",
action="store_true",
default=False,
help="Verbose: print all messages to the standard output",
)
parser.add_argument(
"-l",
"--logname",
dest="logname",
default="clinica.log",
metavar=("file.log"),
help="Define the log file name (default: clinica.log)",
)
"""
run category: run one of the available pipelines
"""
# fmt: off
from clinica.engine import CmdParser
from clinica.pipelines.deeplearning_prepare_data.deeplearning_prepare_data_cli import (
DeepLearningPrepareDataCLI, )
from clinica.pipelines.dwi_connectome.dwi_connectome_cli import DwiConnectomeCli
from clinica.pipelines.dwi_dti.dwi_dti_cli import DwiDtiCli
from clinica.pipelines.dwi_preprocessing_using_phasediff_fieldmap.dwi_preprocessing_using_phasediff_fieldmap_cli import (
DwiPreprocessingUsingPhaseDiffFieldmapCli, )
from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_cli import (
DwiPreprocessingUsingT1Cli, )
from clinica.pipelines.machine_learning_spatial_svm.spatial_svm_cli import (
SpatialSVMCLI, )
from clinica.pipelines.pet_linear.pet_linear_cli import PETLinearCLI
from clinica.pipelines.pet_surface.pet_surface_cli import PetSurfaceCLI
from clinica.pipelines.pet_surface.pet_surface_longitudinal_cli import (
PetSurfaceLongitudinalCLI, )
from clinica.pipelines.pet_volume.pet_volume_cli import PETVolumeCLI
from clinica.pipelines.statistics_surface.statistics_surface_cli import (
StatisticsSurfaceCLI, )
from clinica.pipelines.statistics_volume.statistics_volume_cli import (
StatisticsVolumeCLI, )
from clinica.pipelines.statistics_volume_correction.statistics_volume_correction_cli import (
StatisticsVolumeCorrectionCLI, )
from clinica.pipelines.t1_freesurfer.t1_freesurfer_cli import T1FreeSurferCLI
from clinica.pipelines.t1_freesurfer_longitudinal.t1_freesurfer_longitudinal_cli import (
T1FreeSurferLongitudinalCLI, )
from clinica.pipelines.t1_freesurfer_longitudinal.t1_freesurfer_longitudinal_correction_cli import (
T1FreeSurferLongitudinalCorrectionCLI, )
from clinica.pipelines.t1_freesurfer_longitudinal.t1_freesurfer_template_cli import (
T1FreeSurferTemplateCLI, )
from clinica.pipelines.t1_linear.t1_linear_cli import T1LinearCLI
from clinica.pipelines.t1_volume.t1_volume_cli import T1VolumeCLI
from clinica.pipelines.t1_volume_create_dartel.t1_volume_create_dartel_cli import (
T1VolumeCreateDartelCLI, )
from clinica.pipelines.t1_volume_dartel2mni.t1_volume_dartel2mni_cli import (
T1VolumeDartel2MNICLI, )
from clinica.pipelines.t1_volume_existing_template.t1_volume_existing_template_cli import (
T1VolumeExistingTemplateCLI, )
from clinica.pipelines.t1_volume_parcellation.t1_volume_parcellation_cli import (
T1VolumeParcellationCLI, )
from clinica.pipelines.t1_volume_register_dartel.t1_volume_register_dartel_cli import (
T1VolumeRegisterDartelCLI, )
from clinica.pipelines.t1_volume_tissue_segmentation.t1_volume_tissue_segmentation_cli import (
T1VolumeTissueSegmentationCLI, )
# fmt: on
pipelines = ClinicaClassLoader(baseclass=CmdParser,
extra_dir="pipelines").load()
# The order in pipelines var will the same when typing `clinica run`
# Pipelines are sorted by main / advanced pipelines then by modality
pipelines += [
# Main pipelines:
T1FreeSurferCLI(),
T1VolumeCLI(),
T1FreeSurferLongitudinalCLI(),
T1LinearCLI(),
DwiPreprocessingUsingPhaseDiffFieldmapCli(),
DwiPreprocessingUsingT1Cli(),
DwiDtiCli(),
DwiConnectomeCli(),
PETLinearCLI(),
PETVolumeCLI(),
PetSurfaceCLI(),
PetSurfaceLongitudinalCLI(),
DeepLearningPrepareDataCLI(),
SpatialSVMCLI(),
StatisticsSurfaceCLI(),
StatisticsVolumeCLI(),
StatisticsVolumeCorrectionCLI(),
# Advanced pipelines:
T1VolumeExistingTemplateCLI(),
T1VolumeTissueSegmentationCLI(),
T1VolumeCreateDartelCLI(),
T1VolumeRegisterDartelCLI(),
T1VolumeDartel2MNICLI(),
T1VolumeParcellationCLI(),
T1FreeSurferTemplateCLI(),
T1FreeSurferLongitudinalCorrectionCLI(),
]
run_parser = sub_parser.add_parser(
"run",
add_help=False,
formatter_class=argparse.RawTextHelpFormatter,
help="To run pipelines on BIDS/CAPS datasets.",
)
run_parser.description = (
f"{Fore.GREEN}Run pipelines on BIDS/CAPS datasets.{Fore.RESET}")
run_parser._positionals.title = (
f"{Fore.GREEN}clinica run expects one of the following pipelines{Fore.RESET}"
)
init_cmdparser_objects(parser,
run_parser.add_subparsers(metavar="", dest="run"),
pipelines)
"""
convert category: convert one of the supported datasets into BIDS hierarchy
"""
# fmt: off
from clinica.iotools.converters.adni_to_bids.adni_to_bids_cli import AdniToBidsCLI
from clinica.iotools.converters.aibl_to_bids.aibl_to_bids_cli import AiblToBidsCLI
from clinica.iotools.converters.nifd_to_bids.nifd_to_bids_cli import NifdToBidsCLI
from clinica.iotools.converters.oasis_to_bids.oasis_to_bids_cli import (
OasisToBidsCLI, )
# fmt: on
converters = ClinicaClassLoader(baseclass=CmdParser,
extra_dir="iotools/converters").load()
converters += [
AdniToBidsCLI(),
AiblToBidsCLI(),
OasisToBidsCLI(),
NifdToBidsCLI(),
]
convert_parser = sub_parser.add_parser(
"convert",
add_help=False,
help="To convert unorganized datasets into a BIDS hierarchy.",
)
convert_parser.description = f"{Fore.GREEN}Tools to convert unorganized datasets into a BIDS hierarchy.{Fore.RESET}"
convert_parser._positionals.title = f"{Fore.YELLOW}clinica convert expects one of the following datasets{Fore.RESET}"
convert_parser._optionals.title = OPTIONAL_TITLE
init_cmdparser_objects(
parser, convert_parser.add_subparsers(metavar="", dest="convert"),
converters)
"""
iotools category
"""
from clinica.iotools.utils.data_handling_cli import (
CmdParserCenterNifti,
CmdParserMergeTsv,
CmdParserMissingModalities,
CmdParserMissingProcessing,
CmdParserSubjectsSessions,
)
io_tools = [
CmdParserSubjectsSessions(),
CmdParserMergeTsv(),
CmdParserMissingProcessing(),
CmdParserMissingModalities(),
CmdParserCenterNifti(),
]
HELP_IO_TOOLS = "Tools to handle BIDS/CAPS datasets."
io_parser = sub_parser.add_parser(
"iotools",
add_help=False,
help=HELP_IO_TOOLS,
)
io_parser.description = f"{Fore.GREEN}{HELP_IO_TOOLS}{Fore.RESET}"
io_parser._positionals.title = f"{Fore.YELLOW}clinica iotools expects one of the following BIDS/CAPS utilities{Fore.RESET}"
io_parser._optionals.title = OPTIONAL_TITLE
init_cmdparser_objects(
parser, io_parser.add_subparsers(metavar="", dest="iotools"), io_tools)
"""
visualize category: run one of the available pipelines
"""
from clinica.engine import CmdParser
from clinica.pipelines.t1_freesurfer.t1_freesurfer_visualizer import (
T1FreeSurferVisualizer, )
visualizers = ClinicaClassLoader(baseclass=CmdParser,
extra_dir="pipelines").load()
visualizers += [
T1FreeSurferVisualizer(),
]
visualize_parser = sub_parser.add_parser(
"visualize",
add_help=False,
formatter_class=argparse.RawTextHelpFormatter,
help="To visualize outputs of Clinica pipelines.",
)
visualize_parser.description = (
f"{Fore.GREEN}Visualize outputs of Clinica pipelines.{Fore.RESET}")
visualize_parser._positionals.title = f"{Fore.YELLOW}clinica visualize expects one of the following pipelines{Fore.RESET}"
init_cmdparser_objects(
parser,
visualize_parser.add_subparsers(metavar="", dest="visualize"),
visualizers,
)
"""
generate category: template
"""
generate_parser = sub_parser.add_parser(
"generate",
add_help=False,
help=
("To generate pre-filled files when creating new pipelines (for developers)."
),
)
generate_parser.description = f"{Fore.GREEN}Generate pre-filled files when creating new pipelines (for developers).{Fore.RESET}"
generate_parser._positionals.title = (
f"{Fore.YELLOW}clinica generate expects one of the following tools{Fore.RESET}"
)
generate_parser._optionals.title = OPTIONAL_TITLE
from clinica.engine.template import CmdGenerateTemplates
init_cmdparser_objects(
parser,
generate_parser.add_subparsers(metavar="", dest="generate"),
[CmdGenerateTemplates()],
)
"""
Silent all sub-parser errors methods except the one which is called
otherwise the output console will display useless messages
"""
def silent_help():
pass
def single_error_message(p):
def error(x):
from colorama import Fore
print(f"{Fore.RED}Error {x}{Fore.RESET}\n")
p.print_help()
parser.print_help = silent_help
exit(-1)
return error
for p in [run_parser, io_parser, convert_parser, generate_parser]:
p.error = single_error_message(p)
# Do not want stderr message
def silent_msg(x):
pass
parser.error = silent_msg
"""
Parse the command and check that everything went fine
"""
args = None
unknown_args = None
try:
argcomplete.autocomplete(parser)
args, unknown_args = parser.parse_known_args()
if args.version:
import clinica
print(f"Clinica version is: {clinica.__version__}")
exit(0)
if unknown_args:
if ("--verbose" in unknown_args) or ("-v" in unknown_args):
cprint("Verbose detected")
args.verbose = True
unknown_args = [i for i in unknown_args if i != "-v"]
unknown_args = [i for i in unknown_args if i != "--verbose"]
if unknown_args:
print(
f"{Fore.YELLOW}[Warning] Unknown flag(s) detected: {unknown_args}. "
f"This will be ignored by Clinica{Fore.RESET}")
except SystemExit:
exit(0)
except Exception:
print(
f"{Fore.RED}\n[Error] You wrote wrong arguments on the command line. "
f"Clinica will now exit.\n{Fore.RESET}")
parser.print_help()
exit(-1)
if "run" in args and hasattr(args, "func") is False:
# Case when we type `clinica run` on the terminal
run_parser.print_help()
exit(0)
elif "convert" in args and hasattr(args, "func") is False:
# Case when we type `clinica convert` on the terminal
convert_parser.print_help()
exit(0)
elif "iotools" in args and hasattr(args, "func") is False:
# Case when we type `clinica iotools` on the terminal
io_parser.print_help()
exit(0)
elif "visualize" in args and hasattr(args, "func") is False:
# Case when we type `clinica visualize` on the terminal
visualize_parser.print_help()
exit(0)
elif "generate" in args and hasattr(args, "func") is False:
# Case when we type `clinica generate` on the terminal
generate_parser.print_help()
exit(0)
elif args is None or hasattr(args, "func") is False:
# Case when we type `clinica` on the terminal
parser.print_help()
exit(0)
import clinica.utils.stream as var
var.clinica_verbose = args.verbose
if args.verbose is False:
"""
Enable only cprint(msg) --> clinica print(msg)
- All the print() will be ignored!
- All the logging will be redirect to the log file.
"""
from clinica.utils.stream import FilterOut
sys.stdout = FilterOut(sys.stdout)
import logging as python_logging
import os
from logging import ERROR, Filter
from nipype import config, logging
# Configure Nipype logger for our needs
config.update_config({
"logging": {
"workflow_level": "INFO",
"log_directory": os.getcwd(),
"log_to_file": True,
},
"execution": {
"stop_on_first_crash": False,
"hash_method": "content"
},
})
logging.update_logging(config)
# Define the LogFilter for ERROR detection
class LogFilter(Filter):
"""Monitor if an ERROR log signal is sent from Clinica/Nipype.
If detected, the user will be warned.
"""
def filter(self, record):
if record.levelno >= ERROR:
import datetime
now = datetime.datetime.now().strftime("%H:%M:%S")
cprint(
f"{Fore.RED}[{now}]{Fore.RESET} An error was found: please "
f"check the log file ({args.logname}) or crash file "
f"(nipypecli crash <pklz_file>) for details. Clinica is still running."
)
return True
if args.verbose:
logger = logging.getLogger("nipype.workflow")
logger.addFilter(LogFilter())
# Remove all handlers associated with the root logger object
for handler in python_logging.root.handlers[:]:
python_logging.root.removeHandler(handler)
logging.disable_file_logging()
# Enable file logging using a filename
def enable_file_logging(self, filename):
"""Hack to define a filename for the log file.
It overloads the 'enable_file_logging' method in 'nipype/utils/logger.py' file.
"""
import logging
from logging.handlers import RotatingFileHandler as RFHandler
config = self._config
LOG_FILENAME = os.path.join(config.get("logging", "log_directory"),
filename)
hdlr = RFHandler(
LOG_FILENAME,
maxBytes=int(config.get("logging", "log_size")),
backupCount=int(config.get("logging", "log_rotate")),
)
formatter = logging.Formatter(fmt=self.fmt, datefmt=self.datefmt)
hdlr.setFormatter(formatter)
self._logger.addHandler(hdlr)
self._fmlogger.addHandler(hdlr)
self._iflogger.addHandler(hdlr)
self._hdlr = hdlr
enable_file_logging(logging, args.logname)
class Stream:
def write(self, text):
print(text)
sys.stdout.flush()
python_logging.basicConfig(format=logging.fmt,
datefmt=logging.datefmt,
stream=Stream())
# Finally, run the command
args.func(args)