Skip to content
Snippets Groups Projects
Commit 82083da2 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
Browse files

Cleaned up eddy and fugue modules. Add sean as author.

parent eea41c8e
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
fsl/wrappers/bet.py
+ 1
− 0
View file @ 82083da2
......@@ -2,6 +2,7 @@
#
# bet.py - Wrapper for the FSL bet command.
#
# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides the :func:`bet` function, a wrapper for the FSL
......
fsl/wrappers/eddy.py
+ 67
− 101
View file @ 82083da2
#!/usr/bin/env python
#
# eddy.py -
# eddy.py - Wrappers for topup and eddy.
#
# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides wrapper functions for the FSL `TOPUP
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup>`_ and `EDDY
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy>`_ tools, for field map
estimation and eddy-current distortion correction.
.. autosummary::
:nosignatures:
eddy_cuda
topup
"""
import fsl.utils.run as run
import fsl.utils.assertions as asrt
from . import wrapperutils as wutils
@wutils.fileOrImage('imain', 'mask', 'field')
@wutils.fileOrArray('index', 'acqp', 'bvecs', 'bvals', 'field_mat')
def eddy_cuda(imain, mask, index, acqp, bvecs, bvals, out, **kwargs):
"""Wrapper for the ``eddy_cuda`` command."""
valmap = {
'fep' : wutils.SHOW_IF_TRUE,
'initrand' : wutils.SHOW_IF_TRUE,
'repol' : wutils.SHOW_IF_TRUE,
'ol_pos' : wutils.SHOW_IF_TRUE,
'ol_sqr' : wutils.SHOW_IF_TRUE,
'dont_sep_offs_move' : wutils.SHOW_IF_TRUE,
'dont_peas' : wutils.SHOW_IF_TRUE,
'data_is_shelled' : wutils.SHOW_IF_TRUE,
'b0_only' : wutils.SHOW_IF_TRUE,
'dont_mask_output' : wutils.SHOW_IF_TRUE,
'cnr_maps' : wutils.SHOW_IF_TRUE,
'residuals' : wutils.SHOW_IF_TRUE,
'estimate_move_by_susceptibility' : wutils.SHOW_IF_TRUE,
'verbose' : wutils.SHOW_IF_TRUE,
'very_verbose' : wutils.SHOW_IF_TRUE,
}
def eddy_cuda(imain, mask, index, acqp, bvecs, bvals, out, very_verbose=False,
niter=None, fwhm=None, s2v_niter=None, mporder=None, nvoxhp=None,
slspec=None, b0_only=False, topup=None, field=None,
field_mat=None, debug=None, s2v_fwhm=None, interp=None,
dont_mask_output=False, s2v_interp=None, ref_scan_no=None,
data_is_shelled=False, estimate_move_by_susceptibility=False,
mbs_niter=None, mbs_lambda=None, mbs_ksp=None, s2v_lambda=None,
cnr_maps=False, residuals=False):
"""Correct eddy current-induced distortions and subject movements."""
asrt.assertFileExists(imain, mask, index, acqp, bvecs, bvals)
asrt.assertIsNifti(imain, mask)
assert not (topup and field), "topup and field arguments are incompatible"
out = img.splitext(out)[0]
opts = " --imain={0} --mask={1} --index={2} --bvals={3} " \
"--bvecs={4} --acqp={5} --out={6}".format(imain, mask, index, bvals,
bvecs, acqp, out)
cmd = op.join(os.getenv('DHCP_EDDY_PATH', ''), 'eddy_cuda')
# cmd = 'eddy_cuda'
cmd = cmd + opts
if very_verbose:
cmd += " --very_verbose"
if estimate_move_by_susceptibility:
cmd += " --estimate_move_by_susceptibility"
if data_is_shelled:
cmd += " --data_is_shelled"
if mbs_niter is not None:
cmd += " --mbs_niter={0}".format(mbs_niter)
if mbs_lambda is not None:
cmd += " --mbs_lambda={0}".format(mbs_lambda)
if mbs_ksp is not None:
cmd += " --mbs_ksp={0}".format(mbs_ksp)
if niter is not None:
cmd += " --niter={0}".format(niter)
if fwhm is not None:
cmd += " --fwhm={0}".format(fwhm)
if s2v_fwhm is not None:
cmd += " --s2v_fwhm={0}".format(s2v_fwhm)
if s2v_niter is not None:
cmd += " --s2v_niter={0}".format(s2v_niter)
if s2v_interp is not None:
cmd += " --s2v_interp={0}".format(s2v_interp)
if interp is not None:
cmd += " --interp={0}".format(interp)
if mporder is not None:
cmd += " --mporder={0}".format(mporder)
if nvoxhp is not None:
cmd += " --nvoxhp={0}".format(nvoxhp)
if slspec is not None:
cmd += " --slspec={0}".format(slspec)
if topup is not None:
cmd += " --topup={0}".format(topup)
if field is not None:
field = img.splitext(field)[0]
cmd += " --field={0}".format(field)
if b0_only:
cmd += " --b0_only"
if field_mat is not None:
cmd += " --field_mat={0}".format(field_mat)
if debug is not None:
cmd += " --debug={0}".format(debug)
if dont_mask_output:
cmd += " --dont_mask_output"
if ref_scan_no is not None:
cmd += " --ref_scan_no={0}".format(ref_scan_no)
if s2v_lambda is not None:
cmd += " --s2v_lambda={0}".format(s2v_lambda)
if cnr_maps:
cmd += " --cnr_maps"
if residuals:
cmd += " --residuals"
shops.run(cmd)
def topup(imain, datain, config=None, fout=None, iout=None, out=None,
verbose=False, subsamp=None, logout=None):
"""Estimate and correct susceptibility induced distortions."""
asrt.assertFileExists(imain, datain)
kwargs.update({'imain' : imain,
'mask' : mask,
'index' : index,
'acqp' : acqp,
'bvecs' : bvecs,
'bvals' : bvals,
'out' : out})
cmd = ['eddy_cuda'] + wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return run.runfsl(cmd)
@wutils.fileOrImage('imain', 'fout', 'iout')
@wutils.fileOrArray('datain')
def topup(imain, datain, **kwargs):
"""Wrapper for the ``topup`` command."""
valmap = {
'verbose' : wutils.SHOW_IF_TRUE
}
asrt.assertFileExists(datain)
asrt.assertIsNifti(imain)
cmd = "topup --imain={0} --datain={1}".format(imain, datain)
if config is not None:
cmd += " --config={0}".format(config)
if fout is not None:
cmd += " --fout={0}".format(fout)
if iout is not None:
cmd += " --iout={0}".format(iout)
if out is not None:
cmd += " --out={0}".format(out)
if subsamp is not None:
cmd += " --subsamp={0}".format(subsamp)
if logout is not None:
cmd += " --logout={0}".format(logout)
if verbose:
cmd += " -v"
shops.run(cmd)
cmd = ['topup', '--imain={}'.format(imain), '--datain={}'.format(datain)]
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return run.runfsl(cmd)
fsl/wrappers/flirt.py
+ 1
− 0
View file @ 82083da2
......@@ -2,6 +2,7 @@
#
# flirt.py - Wrappers for FLIRT commands.
#
# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides wrapper functions for the FSL `FLIRT
......
fsl/wrappers/fugue.py
+ 35
− 24
View file @ 82083da2
#!/usr/bin/env python
#
# fugue.py -
# fugue.py - Wrappers for fugue/field map tools.
#
# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""
"""This module contains wrappers for the FSL `FUGUE
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE>`_ tools, for EPI field map
processing and distortion correction.
"""
import fsl.utils.run as run
import fsl.utils.run as run
from . import wrapperutils as wutils
@wutils.fileOrImage('in', 'unwarp', 'warp', 'phasemap', 'savefmap',
'loadfmap', 'saveshift', 'loadshift', 'mask')
def fugue(**kwargs):
"""FMRIB's Utility for Geometric Unwarping of EPIs."""
cmd = "fugue"
if kwargs.pop('unmaskshift', False):
cmd += " --unmaskshift"
if kwargs.pop('despike', False):
cmd += " --despike"
if kwargs.pop('unmaskfmap', False):
cmd += " --unmaskfmap"
cmd += ' '.join(['--{}={}'.format(k, v) for k, v in kwargs.items()])
"""Wrapper for the ``fugue`` command."""
valmap = {
'dwelltoasym' : wutils.SHOW_IF_TRUE,
'median' : wutils.SHOW_IF_TRUE,
'despike' : wutils.SHOW_IF_TRUE,
'nofill' : wutils.SHOW_IF_TRUE,
'noextend' : wutils.SHOW_IF_TRUE,
'pava' : wutils.SHOW_IF_TRUE,
'phaseconj' : wutils.SHOW_IF_TRUE,
'icorr' : wutils.SHOW_IF_TRUE,
'icorronly' : wutils.SHOW_IF_TRUE,
'unmaskfmap' : wutils.SHOW_IF_TRUE,
'unmaskshift' : wutils.SHOW_IF_TRUE,
'nokspace' : wutils.SHOW_IF_TRUE,
'nocheck' : wutils.SHOW_IF_TRUE,
'verbose' : wutils.SHOW_IF_TRUE,
}
cmd = ['fugue'] + wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return run.runfsl(cmd)
def sigloss(input, output, te=None, slicedir=None, mask=None):
"""Estimate signal loss from a field map (in rad/s)."""
cmd = "sigloss -i {0} -s {1}".format(input, output)
def sigloss(input, sigloss, **kwargs):
"""Wrapper for the ``sigloss`` command."""
valmap = {'verbose' : wutils.SHOW_IF_TRUE}
if te is not None:
cmd += " --te={0}".format(te)
if slicedir is not None:
cmd += " --slicedir={0}".format(slicedir)
if mask is not None:
cmd += " --mask={0}".format(mask)
cmd = ['sigloss', '--in', input, '--sigloss', sigloss]
cmd += wutils.applyArgStyle('--', valmap=valmap, **kwargs)
return run.runfsl(cmd)
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment