From 82083da262a532a3c2d8959559a60901ca98decf Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 2 Mar 2018 15:56:38 +0000
Subject: [PATCH] Cleaned up eddy and fugue modules. Add sean as author.
---
fsl/wrappers/bet.py | 1 +
fsl/wrappers/eddy.py | 168 +++++++++++++++++-------------------------
fsl/wrappers/flirt.py | 1 +
fsl/wrappers/fugue.py | 59 +++++++++------
4 files changed, 104 insertions(+), 125 deletions(-)
diff --git a/fsl/wrappers/bet.py b/fsl/wrappers/bet.py
index 93f1e9ed8..1eadd23d8 100644
--- a/fsl/wrappers/bet.py
+++ b/fsl/wrappers/bet.py
@@ -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
diff --git a/fsl/wrappers/eddy.py b/fsl/wrappers/eddy.py
index 1081edb6d..c5d272ad2 100644
--- a/fsl/wrappers/eddy.py
+++ b/fsl/wrappers/eddy.py
@@ -1,113 +1,79 @@
#!/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)
diff --git a/fsl/wrappers/flirt.py b/fsl/wrappers/flirt.py
index b571aa3d6..7d3ef4769 100644
--- a/fsl/wrappers/flirt.py
+++ b/fsl/wrappers/flirt.py
@@ -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
diff --git a/fsl/wrappers/fugue.py b/fsl/wrappers/fugue.py
index 298493beb..7a4cf8e5f 100644
--- a/fsl/wrappers/fugue.py
+++ b/fsl/wrappers/fugue.py
@@ -1,42 +1,53 @@
#!/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)
--
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