From 51abe03114cf7cc6f08071fb3f2de5d7cea3cfd9 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 2 Mar 2018 16:40:35 +0000
Subject: [PATCH] Clean up melodic module. Add alternate for flirt 2D option
---
fsl/wrappers/flirt.py | 12 ++++-
fsl/wrappers/melodic.py | 97 ++++++++++++++++++++++++++---------------
2 files changed, 71 insertions(+), 38 deletions(-)
diff --git a/fsl/wrappers/flirt.py b/fsl/wrappers/flirt.py
index 7d3ef4769..dd4dadbf6 100644
--- a/fsl/wrappers/flirt.py
+++ b/fsl/wrappers/flirt.py
@@ -29,10 +29,18 @@ 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 for the ``flirt`` command. """
+ """Wrapper for the ``flirt`` command.
+
+ The ``twod`` argument may be used in place of the ``2D`` command line
+ option.
+ """
asrt.assertIsNifti(src, ref)
+ argmap = {
+ 'twod' : '2D'
+ }
+
valmap = {
'usesqform' : wutils.SHOW_IF_TRUE,
'displayinit' : wutils.SHOW_IF_TRUE,
@@ -47,7 +55,7 @@ def flirt(src, ref, **kwargs):
}
cmd = ['flirt', '-in', src, '-ref', ref]
- cmd += wutils.applyArgStyle('-', valmap=valmap, **kwargs)
+ cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs)
return run.runfsl(cmd)
diff --git a/fsl/wrappers/melodic.py b/fsl/wrappers/melodic.py
index 82bf28844..16887284d 100644
--- a/fsl/wrappers/melodic.py
+++ b/fsl/wrappers/melodic.py
@@ -1,57 +1,82 @@
#!/usr/bin/env python
#
-# melodic.py -
+# melodic.py - Wrappers for melodic.
#
+# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+"""This module provides wrapper functions for the FSL `MELODIC
+<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC>`_ tool, and other
+related utilities.
+
+.. autosummary::
+ :nosignatures:
+
+ melodic
+ fsl_regfilt
+"""
+
import fsl.utils.run as run
import fsl.utils.assertions as asrt
+from . import wrapperutils as wutils
-def melodic(input, outdir, dim=None, tr=None, mmthresh=None, report=True,
- prefix=None, nomask=False, updatemask=False, nobet=False,
- mask=None):
+@wutils.fileOrArray('mix', 'Tdes', 'Tcon', 'Sdes', 'Scon')
+@wutils.fileOrImage('input', 'mask', 'ICs', 'bgimage')
+def melodic(input, **kwargs):
"""Multivariate Exploratory Linear Optimised ICA."""
+
+ valmap = {
+ 'Oall' : wutils.SHOW_IF_TRUE,
+ 'Ounmix' : wutils.SHOW_IF_TRUE,
+ 'Ostats' : wutils.SHOW_IF_TRUE,
+ 'Opca' : wutils.SHOW_IF_TRUE,
+ 'Owhite' : wutils.SHOW_IF_TRUE,
+ 'Oorig' : wutils.SHOW_IF_TRUE,
+ 'Omean' : wutils.SHOW_IF_TRUE,
+ 'verbose' : wutils.SHOW_IF_TRUE,
+ 'debug' : wutils.SHOW_IF_TRUE,
+ 'report' : wutils.SHOW_IF_TRUE,
+ 'CIFTI' : wutils.SHOW_IF_TRUE,
+ 'varnorm' : wutils.SHOW_IF_TRUE,
+ 'nomask' : wutils.SHOW_IF_TRUE,
+ 'nobet' : wutils.SHOW_IF_TRUE,
+ 'sep_vn' : wutils.SHOW_IF_TRUE,
+ 'disableMigp' : wutils.SHOW_IF_TRUE,
+ 'update_mask' : wutils.HIDE_IF_TRUE,
+ 'migp_shuffle' : wutils.HIDE_IF_TRUE,
+ 'no_mm' : wutils.SHOW_IF_TRUE,
+ 'logPower' : wutils.SHOW_IF_TRUE,
+ }
+
asrt.assertIsNifti(input)
- cmd = "melodic -i {0} -v --Oall --outdir={1}".format(input, outdir)
-
- if mmthresh:
- cmd += " --mmthresh={0}".format(mmthresh)
- if dim:
- cmd += " -d -{0}".format(dim)
- if report:
- cmd += " --report"
- if tr:
- cmd += " --tr={0}".format(tr)
- if nomask:
- cmd += " --nomask"
- if updatemask:
- cmd += " --update_mask"
- if nobet:
- cmd += " --nobet"
- if prefix:
- cmd = prefix + " " + cmd
- if mask is not None:
- cmd += " --mask={0}".format(mask)
+ cmd = ['melodic', '--in', input]
+ cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
+
return run.runfsl(cmd)
-def fsl_regfilt(infile, outfile, mix, ics):
- """Data de-noising by regression.
+@wutils.fileOrImage('input', 'out', 'mask', 'out_data')
+@wutils.fileOrArray('design', 'out_mix')
+def fsl_regfilt(input, out, design, **kwargs):
+ """Wrapper for the ``fsl_regfilt``command. """
+
+ asrt.assertIsNifti(input, out)
- Data de-noising by regressing out part of a design matrix
- using simple OLS regression on 4D images
- """
- asrt.assertIsNifti(infile, outfile)
+ valmap = {
+ 'freqfilt' : wutils.SHOW_IF_TRUE,
+ 'freq_ic' : wutils.HIDE_IF_TRUE,
+ 'vn' : wutils.SHOW_IF_TRUE,
+ 'v' : wutils.SHOW_IF_TRUE,
+ }
- icstr = '"'
- for i in range(0, len(ics) - 1):
- icstr = icstr + '{0},'.format(ics[i] + 1)
- icstr = icstr + '{0}"'.format(ics[-1] + 1)
+ cmd = ['fsl_regfilt',
+ '--in={}'.format(input),
+ '--out={}'.format(out),
+ '--design={}'.format(design)]
+ cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
- cmd = "fsl_regfilt -i {0} -o {1} -d {2} -f {3}".format(infile, outfile,
- mix, icstr)
return run.runfsl(cmd)
--
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