def test_path_contains_whitespace():
assert path_contains_whitespace(os.path.join("path", "with spaces", "to"),
"study")
assert path_contains_whitespace(os.path.join("path", "to"),
"study with spaces")
assert path_contains_whitespace(os.path.join("path", "with spaces", "to"),
"study with spaces")
assert not path_contains_whitespace(os.path.join("path", "to"), "study")
def main_scan():
"""
Parser from terminal with
$ python2 bruker2nifti_scan -h
$ python2 bruker2nifti_scan -i input_file_path -o output_file_path
"""
parser = argparse.ArgumentParser()
# pfo_input_scan
parser.add_argument(
"-i",
"--input_scan_folder",
dest="pfo_input",
type=str,
required=True,
help="Bruker scan folder.",
)
# pfo_output
parser.add_argument(
"-o",
"--output_scan_folder",
dest="pfo_output",
type=str,
required=True,
help="Output folder where the study will be saved.",
)
# fin_output = None
parser.add_argument("--fin_output", dest="fin_output", type=str, default=None)
# nifti_version = 1,
parser.add_argument("-nifti_version", dest="nifti_version", type=int, default=1)
# qform = 1,
parser.add_argument("-qform_code", dest="qform_code", type=int, default=1)
# sform = 2,
parser.add_argument("-sform_code", dest="sform_code", type=int, default=2)
# do_not_save_human_readable = False,
parser.add_argument(
"-do_not_save_human_readable",
dest="do_not_save_human_readable",
action="store_true",
)
# correct_slope = False,
parser.add_argument("-correct_slope", dest="correct_slope", action="store_true")
# correct_offset = False,
parser.add_argument("-correct_offset", dest="correct_offset", action="store_true")
# sample_upside_down = False,
parser.add_argument(
"-sample_upside_down", dest="sample_upside_down", action="store_true"
)
# frame_body_as_frame_head = False,
parser.add_argument(
"-frame_body_as_frame_head",
dest="frame_body_as_frame_head",
action="store_true",
)
# verbose = 1
parser.add_argument("-verbose", "-v", dest="verbose", type=int, default=1)
args = parser.parse_args()
# instantiate a converter:
bruconv = Bruker2Nifti(os.path.dirname(args.pfo_input), args.pfo_output)
# get the attributes
bruconv.nifti_version = args.nifti_version
bruconv.qform_code = args.qform_code
bruconv.sform_code = args.sform_code
bruconv.save_human_readable = not args.do_not_save_human_readable
bruconv.correct_slope = args.correct_slope
bruconv.correct_offset = args.correct_offset
bruconv.verbose = args.verbose
# Sample position
bruconv.sample_upside_down = args.sample_upside_down
bruconv.frame_body_as_frame_head = args.frame_body_as_frame_head
if parser.add_argument > 0:
print("\nConverter parameters: ")
print("-------------------------------------------------------- ")
print("Study Folder : {}".format(os.path.dirname(args.pfo_input)))
print("Scan to convert : {}".format(os.path.basename(args.pfo_input)))
print("List of scans : {}".format(bruconv.scans_list))
print("Output NifTi version : {}".format(bruconv.nifti_version))
print("Output NifTi q-form : {}".format(bruconv.qform_code))
print("Output NifTi s-form : {}".format(bruconv.sform_code))
print("Save human readable : {}".format(bruconv.save_human_readable))
print("Correct the slope : {}".format(bruconv.correct_slope))
print("Correct the offset : {}".format(bruconv.correct_offset))
print("-------------------------------------------------------- ")
print("Sample upside down : {}".format(bruconv.sample_upside_down))
print(
"Frame body as frame head : {}".format(bruconv.frame_body_as_frame_head)
)
print("-------------------------------------------------------- ")
# convert the single:
bruconv.convert_scan(
args.pfo_input,
args.pfo_output,
nifti_file_name=args.fin_output,
create_output_folder_if_not_exists=True,
)
# Print a warning message for paths with whitespace as it may interfere
# with subsequent steps in an image analysis pipeline
if utils.path_contains_whitespace(
bruconv.pfo_study_nifti_output, bruconv.study_name
):
print("INFO: Output path/filename contains whitespace")
def main():
"""
Parser from terminal with:
$ python2 bruker2nifti -h
$ python2 bruker2nifti -i input_file_path -o output_file_path
"""
parser = argparse.ArgumentParser()
# The action to be taken
# 'convert': Convert images to nifti format (default)
# 'list': List scans without converting
parser.add_argument('command',
type=str,
nargs='?',
default='convert',
choices=['convert', 'list'],
help='Action to take: ' +
'convert - convert to nifti, ' +
'list - list studies and exit')
# custom helper
parser.add_argument('-what',
dest='what',
action='store_true',
required=False,
help='Get more information about the software')
# pfo_study_bruker_input
parser.add_argument('-i',
'--input_study_folder',
dest='pfo_input',
type=str,
required=False,
help='Bruker study folder.')
# pfo_study_nifti_output
parser.add_argument('-o',
'--output_study_folder',
dest='pfo_output',
type=str,
required=False,
help='Output folder where the study will be saved.')
# study_name = None,
parser.add_argument('-study_name', dest='study_name', default=None)
# scans_list = None
# Accepts a list of single digit numbers without any separators. Unable to
# specify multi-digit scan numbers this way. The --scans argument specified
# below supersedes this but --scans_list is left in for backwards
# compatibility. If --scans is also supplied, this paramater is ignored.
parser.add_argument('-scans_list', dest='scans_list', default=None)
# A comma or space/tab separated list of scans to operate on
parser.add_argument('--scans', dest='scans', default=None)
# list_new_name_each_scan = None,
parser.add_argument('-list_new_name_each_scan',
dest='list_new_name_each_scan',
default=None)
# nifti_version = 1,
parser.add_argument('-nifti_version',
dest='nifti_version',
type=int,
default=1)
# qform = 2,
parser.add_argument('-qform_code', dest='qform_code', type=int, default=1)
# sform= 1,
parser.add_argument('-sform_code', dest='sform_code', type=int, default=2)
# do_not_save_human_readable = False,
parser.add_argument('-do_not_save_human_readable',
dest='do_not_save_human_readable',
action='store_true')
# correct_slope = True,
parser.add_argument('-correct_slope',
dest='correct_slope',
action='store_true')
# correct_offset = True,
parser.add_argument('-correct_offset',
dest='correct_offset',
action='store_true')
# correct_offset = True,
parser.add_argument('-sample_upside_down',
dest='sample_upside_down',
action='store_false')
# correct_offset = True,
parser.add_argument('-frame_body_as_frame_head',
dest='frame_body_as_frame_head',
action='store_false')
# verbose = 1
parser.add_argument('-verbose', '-v', dest='verbose', type=int, default=1)
# ------ Parsing user's input ------ #
args = parser.parse_args()
if args.scans:
scan_list = re.split(r"[^\d]+", args.scans)
elif args.scans_list:
scan_list = list(args.scans_list)
else:
scan_list = None
# Check input:
if args.command == 'list':
list_scans(args.pfo_input)
sys.exit(0)
if args.what:
msg = 'Code repository : {} \n' \
'Documentation : {}'.format('https://github.com/SebastianoF/bruker2nifti',
'https://github.com/SebastianoF/bruker2nifti/wiki')
sys.exit(msg)
if not args.pfo_input or not args.pfo_output:
sys.exit('Input bruker study [-i] and output folder [-o] required')
# Instantiate a converter:
bruconv = Bruker2Nifti(args.pfo_input,
args.pfo_output,
study_name=args.study_name)
if scan_list is not None:
bruconv.scans_list = scan_list
if args.list_new_name_each_scan is not None:
bruconv.list_new_name_each_scan = args.list_new_name_each_scan
elif scan_list is not None:
# This list of output scan names is populated during object instantiation
# which causes problems when updating the list of scans to convert after
# object instantiation (the only way to do it). The following work-around
# replaces the list of output file names if a list is not explicitly provided.
# TODO: Restructure the Bruker2Nifti class so that this is not necessary.
bruconv.list_new_name_each_scan = [
bruconv.study_name + '_' + ls for ls in scan_list
]
# Basics
bruconv.nifti_version = args.nifti_version
bruconv.qform_code = args.qform_code
bruconv.sform_code = args.sform_code
bruconv.save_human_readable = not args.do_not_save_human_readable
bruconv.correct_slope = args.correct_slope
bruconv.correct_offset = args.correct_offset
bruconv.verbose = args.verbose
# Sample position
bruconv.sample_upside_down = args.sample_upside_down
bruconv.frame_body_as_frame_head = args.frame_body_as_frame_head
print('\nConverter input parameters: ')
print('-------------------------------------------------------- ')
print('Study name : {}'.format(bruconv.study_name))
print('List of scans : {}'.format(bruconv.scans_list))
print('List of scans names : {}'.format(bruconv.list_new_name_each_scan))
print('Output NifTi version : {}'.format(bruconv.nifti_version))
print('Output NifTi q-form : {}'.format(bruconv.qform_code))
print('Output NifTi s-form : {}'.format(bruconv.sform_code))
print('Save human readable : {}'.format(bruconv.save_human_readable))
print('Correct the slope : {}'.format(bruconv.correct_slope))
print('Correct the offset : {}'.format(bruconv.correct_offset))
print('-------------------------------------------------------- ')
print('Sample upside down : {}'.format(bruconv.sample_upside_down))
print('Frame body as frame head : {}'.format(
bruconv.frame_body_as_frame_head))
print('-------------------------------------------------------- ')
bruconv.convert()
# Print a warning message for paths with whitespace as it may interfere
# with subsequent steps in an image analysis pipeline
if utils.path_contains_whitespace(bruconv.pfo_study_nifti_output,
bruconv.study_name):
print("INFO: Output path/filename contains whitespace")