def check_requirements(config,
software,
configFileName=None,
softwareFileName=None):
"""Verifying that all options and software paths are set."""
log = logging.getLogger(__name__)
result_dir = config.result_dir
required_field = [
'reference_im_fn', 'result_dir', 'selection',
'num_of_iterations_per_level', 'num_of_levels', 'ants_params'
]
pyLAR.containsRequirements(config, required_field, configFileName)
required_software = [
'EXE_BRAINSFit', 'EXE_AverageImages', 'EXE_antsRegistration',
'EXE_WarpImageMultiTransform'
]
pyLAR.containsRequirements(software, required_software, softwareFileName)
if not hasattr(config, "histogram_matching"):
config.histogram_matching = False
if config.histogram_matching:
log.info("Script will perform histogram matching.")
if not config.num_of_iterations_per_level >= 0:
raise Exception(
"'num_of_iterations_per_level' must be a positive integer (>=0).")
if not config.num_of_levels >= 1:
raise Exception(
"''num_of_levels' must be a strictly positive integer (>=1).")
if len(config.selection) < 2:
raise Exception("'selection' must contain at least two values.")
log.info('Results will be stored in:' + result_dir)
if not os.path.exists(result_dir):
os.makedirs(result_dir)
def main(argv=None):
"""Parsing command line arguments and reading input files."""
if argv is None:
argv = sys.argv
parser = argparse.ArgumentParser(prog=argv[0], description=__doc__)
parser.add_argument('-c',
"--configFN",
required=True,
help="Parameter configuration file")
parser.add_argument('-s',
"--configSoftware",
required=True,
help="Software configuration file")
parser.add_argument('-a',
"--algorithm",
required=True,
choices=['lr', 'uab', 'nglra'],
help="Software configuration file")
args = parser.parse_args(argv[1:])
# Assign parameters from the input config txt file
configFN = args.configFN
config = pyLAR.loadConfiguration(configFN, 'config')
# Load software paths from file
configSoftware = args.configSoftware
software = pyLAR.loadConfiguration(configSoftware, 'software')
pyLAR.containsRequirements(config, ['file_list_file_name', 'result_dir'],
configFN)
result_dir = config.result_dir
file_list_file_name = config.file_list_file_name
im_fns = pyLAR.readTxtIntoList(file_list_file_name)
# 'clean' needs to be done before configuring the logger that creates a file in the output directory
if hasattr(config, "clean") and config.clean:
shutil.rmtree(result_dir)
# configure logger
logger = logging.getLogger()
logger.setLevel(logging.INFO)
pyLAR.configure_logger(logger, config, configFN)
try:
pyLAR.run(args.algorithm, config, software, im_fns, result_dir,
configFN, configSoftware, file_list_file_name)
val = 0
except:
logger.exception('Error while processing', exc_info=True)
val = 1
finally:
pyLAR.close_handlers(logger)
return val
def check_requirements(config, software, configFileName=None, softwareFileName=None):
"""Verifying that all options and software paths are set."""
log = logging.getLogger(__name__)
pyLAR.containsRequirements(software, ['EXE_BRAINSFit'], softwareFileName)
required_field = ['reference_im_fn', 'result_dir', 'selection', 'lamda', 'sigma', 'registration']
pyLAR.containsRequirements(config, required_field, configFileName)
result_dir = config.result_dir
if not hasattr(config, "histogram_matching"):
config.histogram_matching = False
if config.histogram_matching:
log.info("Script will perform histogram matching.")
if len(config.selection) < 1:
error_message = '\'selection\' must contain at least one value.'
raise Exception(error_message)
log.info('Results will be stored in: ' + result_dir)
if not os.path.exists(result_dir):
os.makedirs(result_dir)
def check_requirements(config,
software,
configFileName=None,
softwareFileName=None):
"""Verifying that all options and software paths are set."""
log = logging.getLogger(__name__)
required_field = [
'use_healthy_atlas', 'reference_im_fn', 'result_dir', 'selection',
'lamda', 'sigma', 'num_of_iterations_per_level', 'num_of_levels',
'registration_type'
]
pyLAR.containsRequirements(config, required_field, configFileName)
result_dir = config.result_dir
registration_type = config.registration_type
required_software = ['EXE_BRAINSFit']
if not hasattr(config, "histogram_matching"):
config.histogram_matching = False
if config.histogram_matching:
log.info("Script will perform histogram matching.")
if not config.use_healthy_atlas:
required_software.append('EXE_AverageImages')
if registration_type == 'BSpline':
required_software.extend([
'EXE_InvertDeformationField', 'EXE_BRAINSResample',
'EXE_BSplineToDeformationField'
])
pyLAR.containsRequirements(config, ['gridSize'], configFileName)
elif registration_type == 'Demons':
required_software.extend([
'EXE_BRAINSDemonWarp', 'EXE_BRAINSResample',
'EXE_InvertDeformationField'
])
elif registration_type == 'ANTS':
required_software.extend(
['EXE_antsRegistration', 'EXE_WarpImageMultiTransform'])
pyLAR.containsRequirements(config, ['ants_params'], configFileName)
if not config.num_of_iterations_per_level >= 0:
raise Exception(
'Error in configuration file: "num_of_iterations_per_level"\
must be a positive integer (>=0).')
if not config.num_of_levels >= 1:
raise Exception(
'Error in configuration file: "num_of_levels" must be a strictly positive integer (>=1).'
)
pyLAR.containsRequirements(software, required_software, softwareFileName)
if len(config.selection) < 2:
raise Exception(
'Error in configuration file: "selection" must contain at least two values.'
)
log.info('Results will be stored in:' + result_dir)
if not os.path.exists(result_dir):
os.makedirs(result_dir)
def main(argv=None):
"""Parsing command line arguments and reading input files."""
if argv is None:
argv = sys.argv
parser = argparse.ArgumentParser(
prog=argv[0],
description=__doc__
)
parser.add_argument('-c', "--configFN", required=True, help="Parameter configuration file")
parser.add_argument('-s', "--configSoftware", required=True, help="Software configuration file")
parser.add_argument('-a', "--algorithm", required=True, choices=['lr', 'uab', 'nglra'],
help="Software configuration file")
args = parser.parse_args(argv[1:])
# Assign parameters from the input config txt file
configFN = args.configFN
config = pyLAR.loadConfiguration(configFN, 'config')
# Load software paths from file
configSoftware = args.configSoftware
software = pyLAR.loadConfiguration(configSoftware, 'software')
pyLAR.containsRequirements(config, ['file_list_file_name', 'result_dir'], configFN)
result_dir = config.result_dir
file_list_file_name = config.file_list_file_name
im_fns = pyLAR.readTxtIntoList(file_list_file_name)
# 'clean' needs to be done before configuring the logger that creates a file in the output directory
if hasattr(config, "clean") and config.clean:
shutil.rmtree(result_dir)
# configure logger
logger = logging.getLogger()
logger.setLevel(logging.INFO)
pyLAR.configure_logger(logger, config, configFN)
try:
pyLAR.run(args.algorithm, config, software, im_fns, result_dir,
configFN, configSoftware, file_list_file_name)
val = 0
except:
logger.exception('Error while processing', exc_info=True)
val = 1
finally:
pyLAR.close_handlers(logger)
return val
def check_requirements(config,
software,
configFileName=None,
softwareFileName=None):
"""Verifying that all options and software paths are set."""
log = logging.getLogger(__name__)
pyLAR.containsRequirements(software, ['EXE_BRAINSFit'], softwareFileName)
required_field = [
'reference_im_fn', 'result_dir', 'selection', 'lamda', 'sigma',
'registration'
]
pyLAR.containsRequirements(config, required_field, configFileName)
result_dir = config.result_dir
if not hasattr(config, "histogram_matching"):
config.histogram_matching = False
if config.histogram_matching:
log.info("Script will perform histogram matching.")
if len(config.selection) < 1:
error_message = '\'selection\' must contain at least one value.'
raise Exception(error_message)
log.info('Results will be stored in: ' + result_dir)
if not os.path.exists(result_dir):
os.makedirs(result_dir)
def check_requirements(config, software, configFileName=None, softwareFileName=None):
"""Verifying that all options and software paths are set."""
log = logging.getLogger(__name__)
result_dir = config.result_dir
required_field = ['reference_im_fn', 'result_dir', 'selection',
'num_of_iterations_per_level', 'num_of_levels', 'ants_params']
pyLAR.containsRequirements(config, required_field, configFileName)
required_software = ['EXE_BRAINSFit', 'EXE_AverageImages', 'EXE_antsRegistration', 'EXE_WarpImageMultiTransform']
pyLAR.containsRequirements(software, required_software, softwareFileName)
if not hasattr(config, "histogram_matching"):
config.histogram_matching = False
if config.histogram_matching:
log.info("Script will perform histogram matching.")
if not config.num_of_iterations_per_level >= 0:
raise Exception("'num_of_iterations_per_level' must be a positive integer (>=0).")
if not config.num_of_levels >= 1:
raise Exception("''num_of_levels' must be a strictly positive integer (>=1).")
if len(config.selection) < 2:
raise Exception("'selection' must contain at least two values.")
log.info('Results will be stored in:' + result_dir)
if not os.path.exists(result_dir):
os.makedirs(result_dir)
def check_requirements(config, software, configFileName=None, softwareFileName=None):
"""Verifying that all options and software paths are set."""
log = logging.getLogger(__name__)
required_field = ['use_healthy_atlas', 'reference_im_fn', 'result_dir', 'selection', 'lamda', 'sigma',
'num_of_iterations_per_level', 'num_of_levels', 'registration_type']
pyLAR.containsRequirements(config, required_field, configFileName)
result_dir = config.result_dir
registration_type = config.registration_type
required_software = ['EXE_BRAINSFit']
if not hasattr(config, "histogram_matching"):
config.histogram_matching = False
if config.histogram_matching:
log.info("Script will perform histogram matching.")
if not config.use_healthy_atlas:
required_software.append('EXE_AverageImages')
if registration_type == 'BSpline':
required_software.extend(['EXE_InvertDeformationField', 'EXE_BRAINSResample', 'EXE_BSplineToDeformationField'])
pyLAR.containsRequirements(config, ['gridSize'], configFileName)
elif registration_type == 'Demons':
required_software.extend(['EXE_BRAINSDemonWarp', 'EXE_BRAINSResample','EXE_InvertDeformationField'])
elif registration_type == 'ANTS':
required_software.extend(['EXE_antsRegistration', 'EXE_WarpImageMultiTransform'])
pyLAR.containsRequirements(config, ['ants_params'], configFileName)
if not config.num_of_iterations_per_level >= 0:
raise Exception('Error in configuration file: "num_of_iterations_per_level"\
must be a positive integer (>=0).')
if not config.num_of_levels >= 1:
raise Exception('Error in configuration file: "num_of_levels" must be a strictly positive integer (>=1).')
pyLAR.containsRequirements(software, required_software, softwareFileName)
if len(config.selection) < 2:
raise Exception('Error in configuration file: "selection" must contain at least two values.')
log.info('Results will be stored in:' + result_dir)
if not os.path.exists(result_dir):
os.makedirs(result_dir)
def configure_logger(logger, config, config_file_name):
_stream_logger(config, logger)
pyLAR.containsRequirements(config, ['result_dir'], config_file_name)
result_dir = config.result_dir
_file_logger(result_dir, logger)
def configure_logger(logger, config, config_file_name):
_stream_logger(config, logger)
pyLAR.containsRequirements(config, ['result_dir'], config_file_name)
result_dir = config.result_dir
_file_logger(result_dir, logger)
