def test_conversion():
#Load test data
ref = DATA_DIR + "uncinate"
anat_filename = DATA_DIR + "anat.nii.gz"
#Test every possible conversions
for k1, ref_format in FORMATS.items():
for k2, out_format in FORMATS.items():
print "Testing {0}2{1}".format(k1, k2)
f, out = tempfile.mkstemp('_{0}2{1}'.format(k1, k2))
os.remove(out)
ref_filename = ref + "." + k1
out_filename = out + "." + k2
input = ref_format(ref_filename, anat_filename)
output = out_format.create(out_filename, input.hdr, anat_filename)
tractconverter.convert(input, output)
f, bak = tempfile.mkstemp('_{0}2{1}'.format(k2, k1))
bak_filename = bak + "." + k1
output = out_format(out_filename, anat_filename)
backup = ref_format.create(bak_filename, input.hdr, anat_filename)
tractconverter.convert(output, backup)
input = ref_format(ref_filename, anat_filename)
output = out_format(out_filename, anat_filename)
compare_data(input, output)
os.remove(out_filename)
input = ref_format(ref_filename, anat_filename)
backup = ref_format(bak_filename, anat_filename)
compare_data(input, backup)
os.remove(bak_filename)
def main():
parser = buildArgsParser()
args = parser.parse_args()
in_filenames = args.input
out_filename = args.output
#anat_filename = args.anat
isForcing = args.isForce
isVerbose = args.isVerbose
if isVerbose:
logging.basicConfig(level=logging.DEBUG)
for in_filename in in_filenames:
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:
logging.info('Overwriting "{0}".'.format(out_filename))
else:
parser.error('"{0}" already exist! Use -f to overwrite it.'.format(
out_filename))
inFormats = [
tractconverter.detect_format(in_filename)
for in_filename in in_filenames
]
outFormat = tractconverter.detect_format(out_filename)
# 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))
#TODO: Consider different anat, space.
hdr = {}
hdr[Header.DIMENSIONS] = (1, 1, 1)
hdr[Header.ORIGIN] = (1, 1, 1)
hdr[Header.
NB_FIBERS] = 0 # The actual number of streamlines will be added later.
#Merge inputs to output
inputs = (in_format(in_filename)
for in_filename, in_format in zip(in_filenames, inFormats))
output = outFormat.create(out_filename, hdr)
tractconverter.merge(inputs, output)
def buildArgsParser():
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument(
"-i",
action="store",
dest="input",
metavar="FILE",
required=True,
help="input track file ({0})".format(",".join(FORMATS.keys())),
)
p.add_argument(
"-o",
action="store",
dest="output",
metavar="FILE",
required=True,
help="output track file ({0})".format(",".join(FORMATS.keys())),
)
p.add_argument(
"-a",
action="store",
dest="anat",
metavar="FILE",
required=False,
help="input anatomy file ({0})".format(EXT_ANAT),
)
p.add_argument(
"-f", action="store_true", dest="isForce", help="force (pass extension check; overwrite output file)"
)
p.add_argument("-v", action="store_true", dest="isVerbose", help="produce verbose output")
return p
def buildArgsParser():
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument(
"-i",
action="store",
dest="input",
nargs="+",
metavar="FILE",
required=True,
help="input streamlines file ({0})".format(",".join(FORMATS.keys())),
)
p.add_argument(
"-o",
action="store",
dest="output",
metavar="FILE",
required=True,
help="merged streamline file ({0})".format(",".join(FORMATS.keys())),
)
# p.add_argument('-a', action='store', dest='anat',
# metavar='FILE', required=False,
# help='input anatomy file ({0})'.format(EXT_ANAT))
p.add_argument(
"-f", action="store_true", dest="isForce", help="force (pass extension check; overwrite output file)"
)
p.add_argument("-v", action="store_true", dest="isVerbose", help="produce verbose output")
return p
def buildArgsParser():
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument('-i',
action='store',
dest='input',
nargs='+',
metavar='FILE',
required=True,
help='input streamlines file ({0})'.format(",".join(
FORMATS.keys())))
p.add_argument('-o',
action='store',
dest='output',
metavar='FILE',
required=True,
help='merged streamline file ({0})'.format(",".join(
FORMATS.keys())))
# p.add_argument('-a', action='store', dest='anat',
# metavar='FILE', required=False,
# help='input anatomy file ({0})'.format(EXT_ANAT))
p.add_argument('-f',
action='store_true',
dest='isForce',
help='force (pass extension check; overwrite output file)')
p.add_argument('-v',
action='store_true',
dest='isVerbose',
help='produce verbose output')
return p
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_filenames = args.input
out_filename = args.output
#anat_filename = args.anat
isForcing = args.isForce
isVerbose = args.isVerbose
if isVerbose:
logging.basicConfig(level=logging.DEBUG)
for in_filename in in_filenames:
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 any(in_name == out_filename for in_name in in_filenames):
parser.error('Cannot output to a file which is also an input file ({0}).'.format(out_filename))
else:
logging.info('Overwriting "{0}".'.format(out_filename))
else:
parser.error('"{0}" already exist! Use -f to overwrite it.'.format(out_filename))
inFormats = [tractconverter.detect_format(in_filename) for in_filename in in_filenames]
outFormat = tractconverter.detect_format(out_filename)
# 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))
#TODO: Consider different anat, space.
hdr = {}
hdr[Header.DIMENSIONS] = (1,1,1)
hdr[Header.ORIGIN] = (1,1,1)
hdr[Header.NB_FIBERS] = 0 # The actual number of streamlines will be added later.
#Merge inputs to output
inputs = (in_format(in_filename) for in_filename, in_format in zip(in_filenames, inFormats))
output = outFormat.create(out_filename, hdr)
tractconverter.merge(inputs, 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 buildArgsParser():
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument('-i', action='store', dest='input',
metavar='FILE', required=True,
help='input track file ({0})'.format(",".join(FORMATS.keys())))
p.add_argument('-o', action='store', dest='output',
metavar='FILE', required=True,
help='output track file ({0})'.format(",".join(FORMATS.keys())))
p.add_argument('-a', action='store', dest='anat',
metavar='FILE', required=False,
help='input anatomy file ({0})'.format(EXT_ANAT))
p.add_argument('-f', action='store_true', dest='isForce',
help='force (pass extension check; overwrite output file)')
p.add_argument('-v', action='store_true', dest='isVerbose',
help='produce verbose output')
return p
def buildArgsParser():
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument('-i',
action='store',
dest='input',
metavar='FILE',
required=True,
help='input track file ({0})'.format(",".join(
FORMATS.keys())))
return p
def main():
parser = buildArgsParser()
args = parser.parse_args()
in_filename = args.input
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())))
inFormat = tractconverter.detect_format(in_filename)
#Print info about the input file.
print inFormat(in_filename, None)
def main():
parser = buildArgsParser()
args = parser.parse_args()
in_filename = args.input
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())))
inFormat = tractconverter.detect_format(in_filename)
#Print info about the input file.
print inFormat(in_filename, None)
def buildArgsParser():
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument('-i', action='store', dest='input',
metavar='FILE', required=True,
help='input track file ({0})'.format(",".join(FORMATS.keys())))
return p
import logging
import os
import tractconverter.info as info
import tractconverter
from tractconverter import FORMATS
from tractconverter import EXT_ANAT
from tractconverter.formats.header import Header
# Script description
DESCRIPTION = """
TractMerger {0}.
Merge streamlines files.
Supported formats are {1}
""".format(info.__version__, ",".join(FORMATS.keys()))
#####
# Script part
###
def buildArgsParser():
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument('-i',
action='store',
dest='input',
nargs='+',
metavar='FILE',
required=True,
help='input streamlines file ({0})'.format(",".join(
FORMATS.keys())))
output = FORMATS[v].create(outFile, input.hdr, p_anatFile)
tractconverter.convert(input, output)
logging.info(inFile)
logging.info('{0} skipped (none track files)'.format(len(allFiles) - nbFiles))
if not p_isRecursive:
break
logging.info("Conversion finished!")
#####
# Script part
###
#Script description
DESCRIPTION = 'Convert track files while walking down a path. ({0})'.format(",".join(FORMATS.keys()))
def buildArgsParser():
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument('-i', action='store', dest='input',
metavar='DIR', required=True,
help='path to walk')
p.add_argument('-o', action='store', dest='output',
metavar='DIR',
help='output folder (if omitted, the walking folder is used)')
p.add_argument('-a', action='store', dest='anat',
metavar='FILE', required=False,
help='anatomy file ({0})'.format(EXT_ANAT))
#VTK
logging.info(
'{0} skipped (none track files)'.format(len(allFiles) - nbFiles))
if not p_isRecursive:
break
logging.info("Conversion finished!")
#####
# Script part
###
#Script description
DESCRIPTION = 'Convert streamlines files while walking down a path. ({0})'.format(
",".join(FORMATS.keys()))
def buildArgsParser():
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument('-i',
action='store',
dest='input',
metavar='DIR',
required=True,
help='path to walk')
p.add_argument(
'-o',
action='store',
dest='output',
metavar='DIR',
import argparse
import logging
import os
import tractconverter.info as info
import tractconverter
from tractconverter import FORMATS
from tractconverter import EXT_ANAT
# Script description
DESCRIPTION = """
TractConverter {0}.
Convert track files.
Supported formats are {1}
""".format(info.__version__,
",".join(FORMATS.keys()))
#####
# Script part
###
def buildArgsParser():
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument('-i', action='store', dest='input',
metavar='FILE', required=True,
help='input track file ({0})'.format(",".join(FORMATS.keys())))
p.add_argument('-o', action='store', dest='output',
metavar='FILE', required=True,
help='output track file ({0})'.format(",".join(FORMATS.keys())))
p.add_argument('-a', action='store', dest='anat',
metavar='FILE', required=False,
import copy
import tractconverter.info as info
import tractconverter
from tractconverter import FORMATS
from tractconverter import EXT_ANAT
from tractconverter.formats.header import Header
# Script description
DESCRIPTION = """
TractMerger {0}.
Merge streamlines files.
Supported formats are {1}
""".format(
info.__version__, ",".join(FORMATS.keys())
)
#####
# Script part
###
def buildArgsParser():
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument(
"-i",
action="store",
dest="input",
nargs="+",
metavar="FILE",
required=True,
def main():
parser = buildArgsParser()
args = parser.parse_args()
in_filenames = glob.glob(os.path.join(args.input[0], "*.trk"))
out_filename = args.output
#anat_filename = args.anat
isForcing = args.isForce
isVerbose = args.isVerbose
if isVerbose:
logging.basicConfig(level=logging.DEBUG)
for in_filename in in_filenames:
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 any(in_name == out_filename for in_name in in_filenames):
parser.error(
'Cannot output to a file which is also an input file ({0}).'
.format(out_filename))
else:
logging.info('Overwriting "{0}".'.format(out_filename))
else:
parser.error('"{0}" already exist! Use -f to overwrite it.'.format(
out_filename))
inFormats = [
tractconverter.detect_format(in_filename)
for in_filename in in_filenames
]
outFormat = tractconverter.detect_format(out_filename)
# 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))
#TODO: Consider streamlines files with different anat/space ?
# Use information from the first streamlines file to create the header.
hdr = copy.deepcopy(inFormats[0](in_filenames[0]).hdr)
hdr[Header.
NB_FIBERS] = 0 # The actual number of streamlines will be added later (as we add the streamlines).
#Merge inputs to output
inputs = (in_format(in_filename)
for in_filename, in_format in zip(in_filenames, inFormats))
output = outFormat.create(out_filename, hdr)
tractconverter.merge(inputs, output)