def main():
parser = buildArgsParser()
args = parser.parse_args()
in_filename = args.input
out_filename = args.output
anat_filename = args.anat
isForcing = args.isForce
isVerbose = args.isVerbose
if isVerbose:
logging.basicConfig(level=logging.DEBUG)
if not os.path.isfile(in_filename):
parser.error('"{0}" must be an existing file!'.format(in_filename))
if not tractconverter.is_supported(in_filename):
parser.error('Input file must be one of {0}!'.format(",".join(
FORMATS.keys())))
if not tractconverter.is_supported(out_filename):
parser.error('Output file must be one of {0}!'.format(",".join(
FORMATS.keys())))
if os.path.isfile(out_filename):
if isForcing:
if out_filename == in_filename:
parser.error(
'Cannot use the same name for input and output files. Conversion would fail.'
)
else:
logging.info('Overwriting "{0}".'.format(out_filename))
else:
parser.error('"{0}" already exist! Use -f to overwrite it.'.format(
out_filename))
inFormat = tractconverter.detect_format(in_filename)
outFormat = tractconverter.detect_format(out_filename)
#if inFormat == outFormat:
# parser.error('Input and output must be from different types!'.format(",".join(FORMATS.keys())))
if anat_filename is not None:
if not any(map(anat_filename.endswith, EXT_ANAT.split('|'))):
if isForcing:
logging.info('Reading "{0}" as a {1} file.'.format(
anat_filename.split("/")[-1], EXT_ANAT))
else:
parser.error(
'Anatomy file must be one of {1}!'.format(EXT_ANAT))
if not os.path.isfile(anat_filename):
parser.error(
'"{0}" must be an existing file!'.format(anat_filename))
#Convert input to output
input = inFormat(in_filename, anat_filename)
output = outFormat.create(out_filename, input.hdr, anat_filename)
tractconverter.convert(input, output)
def main():
parser = buildArgsParser()
args = parser.parse_args()
in_filename = args.input
out_filename = args.output
anat_filename = args.anat
isForcing = args.isForce
isVerbose = args.isVerbose
if isVerbose:
logging.basicConfig(level=logging.DEBUG)
if not os.path.isfile(in_filename):
parser.error('"{0}" must be an existing file!'.format(in_filename))
if not tractconverter.is_supported(in_filename):
parser.error("Input file must be one of {0}!".format(",".join(FORMATS.keys())))
if not tractconverter.is_supported(out_filename):
parser.error("Output file must be one of {0}!".format(",".join(FORMATS.keys())))
if os.path.isfile(out_filename):
if isForcing:
if out_filename == in_filename:
parser.error("Cannot use the same name for input and output files. Conversion would fail.")
else:
logging.info('Overwriting "{0}".'.format(out_filename))
else:
parser.error('"{0}" already exist! Use -f to overwrite it.'.format(out_filename))
inFormat = tractconverter.detect_format(in_filename)
outFormat = tractconverter.detect_format(out_filename)
# if inFormat == outFormat:
# parser.error('Input and output must be from different types!'.format(",".join(FORMATS.keys())))
if anat_filename is not None:
if not any(map(anat_filename.endswith, EXT_ANAT.split("|"))):
if isForcing:
logging.info('Reading "{0}" as a {1} file.'.format(anat_filename.split("/")[-1], EXT_ANAT))
else:
parser.error("Anatomy file must be one of {1}!".format(EXT_ANAT))
if not os.path.isfile(anat_filename):
parser.error('"{0}" must be an existing file!'.format(anat_filename))
# Convert input to output
input = inFormat(in_filename, anat_filename)
output = outFormat.create(out_filename, input.hdr, anat_filename)
tractconverter.convert(input, output)
def main():
parser = buildArgsParser()
args = parser.parse_args()
input = args.input
output = args.output
anat = args.anat
vtk2tck = args.vtk2tck
vtk2trk = args.vtk2trk
vtk2fib = args.vtk2fib
fib2tck = args.fib2tck
fib2trk = args.fib2trk
fib2vtk = args.fib2vtk
trk2tck = args.trk2tck
trk2fib = args.trk2fib
trk2vtk = args.trk2vtk
tck2trk = args.tck2trk
tck2fib = args.tck2fib
tck2vtk = args.tck2vtk
isRecursive = args.isRecursive
isForcing = args.isForce
isVerbose = args.isVerbose
if isVerbose:
logging.basicConfig(level=logging.DEBUG)
if not os.path.isdir(input):
parser.error('"{0}" must be a folder!'.format(input))
if output is not None:
if not os.path.isdir(output):
if isForcing:
logging.info('Creating "{0}".'.format(output))
os.makedirs(output)
else:
parser.error("Can't find the output folder")
#TODO: Warn if duplicate conversion (i.e. tck2X, tck2Y)
#TODO: Find better way to add multiple conversions.
conversions = {}
if vtk2tck:
conversions['vtk'] = 'tck'
if vtk2trk:
conversions['vtk'] = 'trk'
if vtk2fib:
conversions['vtk'] = 'fib'
if fib2tck:
conversions['fib'] = 'tck'
if fib2trk:
conversions['fib'] = 'trk'
if fib2vtk:
conversions['fib'] = 'vtk'
if trk2tck:
conversions['trk'] = 'tck'
if trk2fib:
conversions['trk'] = 'fib'
if trk2vtk:
conversions['trk'] = 'vtk'
if tck2trk:
conversions['tck'] = 'trk'
if tck2fib:
conversions['tck'] = 'fib'
if tck2vtk:
conversions['tck'] = 'vtk'
if len(conversions) == 0:
parser.error('Nothing to convert! Please specify at least one conversion.')
if anat is not None:
if not any(map(anat.endswith, EXT_ANAT.split('|'))):
if isForcing:
logging.info('Reading "{0}" as a {1} file.'.format(anat.split("/")[-1], EXT_ANAT))
else:
parser.error('Anatomy file must be one of {0}!'.format(EXT_ANAT))
if not os.path.isfile(anat):
parser.error('"{0}" must be an existing file!'.format(anat))
walkAndConvert(input, conversions, output, anat, isRecursive, isForcing)