diff --git a/fsl/scripts/fsl_convert_x5.py b/fsl/scripts/fsl_convert_x5.py
index 5dc220cf021e8c967054cb465a6e9f733801815f..4cf94ceb183ba6ea6beb5cc635907ef1c6665f60 100644
--- a/fsl/scripts/fsl_convert_x5.py
+++ b/fsl/scripts/fsl_convert_x5.py
@@ -9,47 +9,64 @@ transformation file formats.
"""
-import os.path as op
-import sys
-import shutil
-import logging
-import argparse
+import os.path as op
+import sys
+import shutil
+import logging
+import argparse
+from collections import OrderedDict
-import fsl.data.image as fslimage
-import fsl.transform as transform
+import fsl.data.image as fslimage
+import fsl.transform.flirt as flirt
+import fsl.transform.fnirt as fnirt
+import fsl.transform.x5 as x5
log = logging.getLogger(__name__)
def parseArgs(args):
+ """Create an argument parser and parse the given ``args``.
+
+ :arg args: Sequence of commane line arguments.
+ :return: An ``argparse.Namespace`` object containing parsed arguments.
+ """
+
+ helps = {
+ 'input' : 'Input file',
+ 'output' : 'Output file',
+ 'source' : 'Source image',
+ 'reference' : 'Reference image',
+ 'input_format' : 'Input format - if not provided, the input format '
+ 'is automatically inferred from the input file '
+ 'name.',
+ 'output_format' : 'Output format - if not provided, the output format '
+ 'is automatically inferred from the output file '
+ 'name.',
+ }
parser = argparse.ArgumentParser('fsl_convert_x5')
subparsers = parser.add_subparsers(dest='ctype')
flirt = subparsers.add_parser('flirt')
fnirt = subparsers.add_parser('fnirt')
-
- flirt.add_argument('input')
- flirt.add_argument('output')
- flirt.add_argument('-s', '--source')
- flirt.add_argument('-r', '--reference')
- flirt.add_argument('-if', '--input_format', choices=('x5', 'mat'))
- flirt.add_argument('-of', '--output_format', choices=('x5', 'mat'))
-
- intype = fnirt.add_mutually_exclusive_group()
- outtype = fnirt.add_mutually_exclusive_group()
-
- fnirt .add_argument('input')
- fnirt .add_argument('output')
- fnirt .add_argument('-s', '--source')
- fnirt .add_argument('-r', '--reference')
- fnirt .add_argument('-if', '--input_format', choices=('x5', 'nii'))
- fnirt .add_argument('-of', '--output_format', choices=('x5', 'nii'))
- intype .add_argument('-ai', '--absin', action='store_const', const='absolute', dest='inDispType')
- intype .add_argument('-ri', '--relin', action='store_const', const='relative', dest='inDispType')
- outtype.add_argument('-ao', '--absout', action='store_const', const='absolute', dest='outDispType')
- outtype.add_argument('-ro', '--relout', action='store_const', const='relative', dest='outDispType')
+ flirt.add_argument('input', help=helps['input'])
+ flirt.add_argument('output', help=helps['output'])
+ flirt.add_argument('-s', '--source', help=helps['source'])
+ flirt.add_argument('-r', '--reference', help=helps['reference'])
+ flirt.add_argument('-if', '--input_format', help=helps['input_format'],
+ choices=('x5', 'mat'))
+ flirt.add_argument('-of', '--output_format', help=helps['output_format'],
+ choices=('x5', 'mat'))
+
+ fnirt .add_argument('input', help=helps['input'])
+ fnirt .add_argument('output', help=helps['output'])
+ fnirt .add_argument('-s', '--source', help=helps['source'])
+ fnirt .add_argument('-r', '--reference', help=helps['reference'])
+ fnirt .add_argument('-if', '--input_format', help=helps['input_format'],
+ choices=('x5', 'nii'))
+ fnirt .add_argument('-of', '--output_format', help=helps['output_format'],
+ choices=('x5', 'nii'))
args = parser.parse_args(args)
@@ -57,34 +74,54 @@ def parseArgs(args):
parser.print_help()
sys.exit(0)
- def getfmt(arg, fname):
+ # If input/output formats were not
+ # specified, infer them from the
+ # file names
+ def getfmt(arg, fname, exist):
ext = op.splitext(fname)[1]
if ext in ('.mat', '.x5'):
return ext[1:]
- if fslimage.looksLikeImage(fslimage.fixExt(fname)):
+
+ fname = fslimage.addExt(fname, mustExist=exist)
+
+ # TODO broken
+ if fslimage.looksLikeImage(fname):
return 'nii'
parser.error('Could not infer format from '
'filename: {}'.format(args.input))
- if args.input_format is None: args.input_format = getfmt('input', args.input)
- if args.output_format is None: args.output_format = getfmt('output', args.output)
+ if args.input_format is None:
+ args.input_format = getfmt('input', args.input, True)
+ if args.output_format is None:
+ args.output_format = getfmt('output', args.output, False)
+
+ # The source and reference arguments are
+ # required if the input is a FLIRT matrix
+ # or a FNIRT displacement/coefficient field.
+ if args.input_format in ('mat', 'nii') and \
+ (args.source is None or args.reference is None):
+ parser.error('You must specify a source and reference '
+ 'when the input is not an X5 file!')
return args
def flirtToX5(args):
+ """Convert a linear FLIRT transformation matrix to an X5 transformation
+ file.
+ """
src = fslimage.Image(args.source, loadData=False)
ref = fslimage.Image(args.reference, loadData=False)
- xform = transform.readFlirt(args.input)
- xform = transform.fromFlirt(xform, src, ref, 'world', 'world')
- transform.writeLinearX5(args.output, xform, src, ref)
+ xform = flirt.readFlirt(args.input)
+ xform = flirt.fromFlirt(xform, src, ref, 'world', 'world')
+ x5.writeLinearX5(args.output, xform, src, ref)
def X5ToFlirt(args):
"""Convert a linear X5 transformation file to a FLIRT matrix. """
- xform, src, ref = transform.readLinearX5(args.input)
- xform = transform.toFlirt(xform, src, ref, 'world', 'world')
- transform.writeFlirt(xform, args.output)
+ xform, src, ref = x5.readLinearX5(args.input)
+ xform = flirt.toFlirt(xform, src, ref, 'world', 'world')
+ flirt.writeFlirt(xform, args.output)
def fnirtToX5(args):
@@ -93,21 +130,17 @@ def fnirtToX5(args):
"""
src = fslimage.Image(args.source, loadData=False)
ref = fslimage.Image(args.reference, loadData=False)
- field = transform.readFnirt(args.input,
- src=src,
- ref=ref,
- dispType=args.inDispType)
- field = transform.fromFnirt(field, 'world', 'world')
- transform.writeNonLinearX5(args.output, field)
+ field = fnirt.readFnirt(args.input, src=src, ref=ref)
+ x5.writeNonLinearX5(args.output, field)
def X5ToFnirt(args):
"""Convert a non-linear X5 transformation file to a FNIRT-style
transformation file.
"""
- field = transform.readNonLinearX5(args.input)
- field = transform.toFnirt(field, 'world', 'world')
- transform.writeFnirt(field, args.output)
+ field = x5.readNonLinearX5(args.input)
+ field = fnirt.toFnirt(field)
+ field.save(args.output)
def doFlirt(args):
diff --git a/fsl/transform/fnirt.py b/fsl/transform/fnirt.py
index 30db64fd34e7d82dbc915859025388ff97822628..74589fa0793a079d7ed9917a9af373fc099de31e 100644
--- a/fsl/transform/fnirt.py
+++ b/fsl/transform/fnirt.py
@@ -247,7 +247,7 @@ def toFnirt(field):
field.data,
src=field.src,
ref=field.ref,
- fieldType=field.fieldType,
+ xform=field.voxToWorldMat,
dispType=field.displacementType)
# Otherwise we have to adjust the