diff --git a/fsl/wrappers/bet.py b/fsl/wrappers/bet.py
index ab72ea9ca9315235d0aba5bf8a91f0ac415b3666..93f1e9ed8375081871ce917d250cd8ca5729d77e 100644
--- a/fsl/wrappers/bet.py
+++ b/fsl/wrappers/bet.py
@@ -16,10 +16,8 @@ from . import wrapperutils as wutils
@wutils.fileOrImage('input', 'output')
def bet(input, output, **kwargs):
- """Delete non-brain tissue from an image of the whole head.
+ """Wrapper for the ``bet`` command.
- :arg input: Image to be brain-extracted
- :arg output: Output image
:arg mask: Generate a brain mask
:arg seg: If ``False``, a brain extracted image is not
generated.
@@ -45,7 +43,7 @@ def bet(input, output, **kwargs):
}
cmd = ['bet', input, output]
- cmd += wutils.applyArgStyle('-', argmap, valmap, **kwargs)
+ cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs)
return run.runfsl(*cmd)
diff --git a/fsl/wrappers/flirt.py b/fsl/wrappers/flirt.py
index f637affb6860694a5cdb6c556d7daae7472123dd..b571aa3d6eeb010a050625c2ff37b12abbe2b5f1 100644
--- a/fsl/wrappers/flirt.py
+++ b/fsl/wrappers/flirt.py
@@ -28,7 +28,7 @@ from . import wrapperutils as wutils
@wutils.fileOrImage('src', 'ref', 'out', 'wmseg', 'fieldmap', 'fieldmapmask')
@wutils.fileOrArray('init', 'omat', 'wmcoords', 'wmnorms')
def flirt(src, ref, **kwargs):
- """Wrapper around the ``flirt`` command. """
+ """Wrapper for the ``flirt`` command. """
asrt.assertIsNifti(src, ref)
@@ -43,8 +43,6 @@ def flirt(src, ref, **kwargs):
'noresampblur' : wutils.SHOW_IF_TRUE,
'2D' : wutils.SHOW_IF_TRUE,
'v' : wutils.SHOW_IF_TRUE,
- 'version' : wutils.SHOW_IF_TRUE,
- 'help' : wutils.SHOW_IF_TRUE,
}
cmd = ['flirt', '-in', src, '-ref', ref]
@@ -93,7 +91,7 @@ def concatxfm(inmat1, inmat2, outmat):
@wutils.fileOrImage('infile', 'out', 'reffile')
@wutils.fileOrArray('init')
def mcflirt(infile, **kwargs):
- """Wrapper around the ``mcflirt`` command."""
+ """Wrapper for the ``mcflirt`` command."""
asrt.assertIsNifti(infile)
diff --git a/fsl/wrappers/fnirt.py b/fsl/wrappers/fnirt.py
index 17c42b036eb181b3d4df7f8daf98641055dd94b7..3abcd51c97e11f88abcf59fd605f76a3638ef5d1 100644
--- a/fsl/wrappers/fnirt.py
+++ b/fsl/wrappers/fnirt.py
@@ -19,182 +19,90 @@ non-linear registration of 3D images.
"""
-import os.path as op
-import glob
-
-
import fsl.utils.run as run
import fsl.utils.assertions as asrt
+from . import wrapperutils as wutils
+
+@wutils.fileOrImage('src', 'ref', 'inwarp', 'cout', 'iout', 'fout', 'jout',
+ 'refout', 'refmask', 'inmask')
+@wutils.fileOrArray('aff')
+def fnirt(src, ref, **kwargs):
+ """Wrapper for the ``fnirt`` command."""
-def fnirt(src, ref, aff=None, imprefm=None, impinm=None, applyrefmask=None,
- applyinmask=None, subsamp=None, miter=None, infwhm=None,
- reffwhm=None, lmbda=None, estint=None, warpres=None, ssqlambda=None,
- regmod=None, intmod=None, intorder=None, biasres=None,
- biaslambda=None, refderiv=None, cout=None, intout=None, refout=None,
- iout=None, interp=None, inwarp=None, minmet=None, verbose=False,
- intin=None, jout=None):
- """Do nonlinear image registration."""
- cmd = 'fnirt --in={0} --ref={1}'.format(src, ref)
-
- if aff is not None:
- cmd += " --aff={0}".format(aff)
- if imprefm is not None:
- cmd += " --imprefm={0}".format(imprefm)
- if impinm is not None:
- cmd += " --impinm={0}".format(impinm)
- if applyrefmask is not None:
- cmd += " --applyrefmask={0}".format(applyrefmask)
- if applyinmask is not None:
- cmd += " --applyinmask={0}".format(applyinmask)
- if subsamp is not None:
- cmd += " --subsamp={0}".format(subsamp)
- if miter is not None:
- cmd += " --miter={0}".format(miter)
- if infwhm is not None:
- cmd += " --infwhm={0}".format(infwhm)
- if reffwhm is not None:
- cmd += " --reffwhm={0}".format(reffwhm)
- if lmbda is not None:
- cmd += " --lambda={0}".format(lmbda)
- if estint is not None:
- cmd += " --estint={0}".format(estint)
- if warpres is not None:
- cmd += " --warpres={0}".format(warpres)
- if ssqlambda is not None:
- cmd += " --ssqlambda={0}".format(ssqlambda)
- if regmod is not None:
- cmd += " --regmod={0}".format(regmod)
- if intmod is not None:
- cmd += " --intmod={0}".format(intmod)
- if intorder is not None:
- cmd += " --intorder={0}".format(intorder)
- if biasres is not None:
- cmd += " --biasres={0}".format(biasres)
- if biaslambda is not None:
- cmd += " --biaslambda={0}".format(biaslambda)
- if refderiv is not None:
- cmd += " --refderiv={0}".format(refderiv)
- if cout is not None:
- cmd += " --cout={0}".format(cout)
- if intout is not None:
- cmd += " --intout={0}".format(intout)
- if refout is not None:
- cmd += " --refout={0}".format(refout)
- if iout is not None:
- cmd += " --iout={0}".format(iout)
- if interp is not None:
- cmd += " --interp={0}".format(interp)
- if inwarp is not None:
- cmd += " --inwarp={0}".format(inwarp)
- if minmet is not None:
- cmd += " --minmet={0}".format(minmet)
- if intin is not None:
- cmd += " --intin={0}".format(intin)
- if jout is not None:
- cmd += " --jout={0}".format(jout)
- if verbose:
- cmd += " --verbose"
+ asrt.assertIsNifti(src, ref)
+
+ cmd = ['fnirt', '--in={}'.format(src), '--ref={}'.format(ref)]
+ cmd += wutils.applyArgStyle('--=', **kwargs)
return run.runfsl(cmd)
-def applywarp(src, ref, out, warp=None, premat=None, prematdir=None,
- postmat=None, postmatdir=None, interp="spline",
- paddingsize=None, abs=False, rel=False):
- """Tool for applying FSL warps.
-
- The ``prematdir`` and ``postmatdir`` arguments can be used when warping a
- 4D image. You can specify a directory containing multiple affines, named
- ``MAT_????`` (as output by e.g. ``mcflirt``). Each file will be applied to
- one volume (in order) of the image.
- """
- assert (warp or premat or postmat or prematdir or postmatdir), \
- "either a warp or mat (premat, postmat or prematdir) must be supplied"
- assert not (premat and prematdir), \
- "cannot use premat and prematdir arguments together"
- assert not (postmat and postmatdir), \
- "cannot use postmat and postmatdir arguments together"
-
- def catmats(matdir, out):
- """Concatenate FSL trasformations files into a single file."""
- mats = sorted(glob.glob(op.join(matdir, "MAT_????")))
- with open(out, 'w') as outfile:
- for fname in mats:
- with open(fname) as infile:
- outfile.write(infile.read())
-
- cmd = "--in={0} --ref={1} --out={2} --interp={3}".format(src, ref, out,
- interp)
- cmd = "applywarp " + cmd
-
- if prematdir:
- premat = op.join(prematdir, 'allmats.txt')
- catmats(prematdir, premat)
- if postmatdir:
- postmat = op.join(postmatdir, 'allmats.txt')
- catmats(postmatdir, postmat)
- if warp:
- cmd += " --warp={0}".format(warp)
- if premat:
- cmd += " --premat={0}".format(premat)
- if postmat:
- cmd += " --postmat={0}".format(postmat)
- if paddingsize:
- cmd += " --paddingsize={0}".format(paddingsize)
- if abs:
- cmd += " --abs"
- if rel:
- cmd += " --rel"
+@wutils.fileOrImage('src', 'ref', 'out', 'warp', 'mask')
+@wutils.fileOrArray('premat', 'postmat')
+def applywarp(src, ref, out, warp, **kwargs):
+ """Wrapper for the ``applywarp`` command. """
+
+ valmap = {
+ 'abs' : wutils.SHOW_IF_TRUE,
+ 'rel' : wutils.SHOW_IF_TRUE,
+ 'super' : wutils.SHOW_IF_TRUE,
+ 'debug' : wutils.SHOW_IF_TRUE,
+ 'verbose' : wutils.SHOW_IF_TRUE,
+ }
+
+ cmd = ['applywarp',
+ '--in={}'.format(src),
+ '--ref={}'.format(ref),
+ '--out={}'.format(out),
+ '--warp={}'.format(warp)]
+
+ cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return run.runfsl(cmd)
-def invwarp(inwarp, ref, outwarp):
- """Tool for inverting FSL warps."""
+@wutils.fileOrImage('warp', 'ref', 'out')
+def invwarp(warp, ref, out, **kwargs):
+ """Wrapper for the ``invwarp`` command."""
+
+ valmap = {
+ 'abs' : wutils.SHOW_IF_TRUE,
+ 'rel' : wutils.SHOW_IF_TRUE,
+ 'noconstraint' : wutils.SHOW_IF_TRUE,
+ 'debug' : wutils.SHOW_IF_TRUE,
+ 'verbose' : wutils.SHOW_IF_TRUE,
+ }
+
+ asrt.assertIsNifti(warp, ref, out)
- asrt.assertFileExists(inwarp, ref)
- asrt.assertIsNifti(inwarp, ref, outwarp)
+ cmd = ['invwarp',
+ '--warp={}'.format(warp),
+ '--ref={}'.format(ref),
+ '--out={}'.format(out)]
- cmd = 'invwarp'
- cmd += ' --warp={}'.format(inwarp)
- cmd += ' --out={}'.format(outwarp)
- cmd += ' --ref={}'.format(ref)
+ cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return run.runfsl(cmd)
-def convertwarp(out, ref, warp1=None, warp2=None, premat=None, midmat=None,
- postmat=None, shiftmap=None, shiftdir=None, absout=False,
- abs=False, rel=False, relout=False):
- """Tool for converting FSL warps."""
-
- assert (warp1 or warp2 or premat or midmat or postmat), \
- "either a warp (warp1 or warp2) or mat (premat, midmat, or " + \
- "postmat) must be supplied"
-
- cmd = "convertwarp --ref={0} --out={1}".format(ref, out)
- if warp1:
- cmd = cmd + " --warp1={0}".format(warp1)
- if warp2:
- cmd = cmd + " --warp2={0}".format(warp2)
- if premat:
- cmd = cmd + " --premat={0}".format(premat)
- if midmat:
- cmd = cmd + " --midmat={0}".format(midmat)
- if postmat:
- cmd = cmd + " --postmat={0}".format(postmat)
- if shiftmap:
- cmd = cmd + " --shiftmap={0}".format(shiftmap)
- if shiftdir:
- cmd = cmd + " --shiftdir={0}".format(shiftdir)
- if absout:
- cmd = cmd + " --absout"
- if relout:
- cmd = cmd + " --relout"
- if abs:
- cmd = cmd + " --abs"
- if rel:
- cmd = cmd + " --rel"
+@wutils.fileOrImage('out', 'ref', 'warp1', 'warp2', 'shiftmap')
+@wutils.fileOrArray('premat', 'midmat', 'postmat')
+def convertwarp(out, ref, **kwargs):
+ """Wrapper for the ``convertwarp`` command."""
+
+ valmap = {
+ 'abs' : wutils.SHOW_IF_TRUE,
+ 'rel' : wutils.SHOW_IF_TRUE,
+ 'absout' : wutils.SHOW_IF_TRUE,
+ 'relout' : wutils.SHOW_IF_TRUE,
+ 'jacobian' : wutils.SHOW_IF_TRUE,
+ 'jstats' : wutils.SHOW_IF_TRUE,
+ 'constrainj' : wutils.SHOW_IF_TRUE,
+ 'verbose' : wutils.SHOW_IF_TRUE,
+ }
+
+ cmd = ['convertwarp', '--ref={}'.format(ref), '--out={}'.format(out)]
+ cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return run.runfsl(cmd)