From 16bf5ddcf9d197e8e82bda20b20c26708b67298e Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 2 Mar 2018 13:42:46 +0000
Subject: [PATCH] Cleaned up flirt module
---
fsl/wrappers/flirt.py | 65 +++++++++++++++++++------------------------
1 file changed, 29 insertions(+), 36 deletions(-)
diff --git a/fsl/wrappers/flirt.py b/fsl/wrappers/flirt.py
index 4c777a61f..3bce5b0ff 100644
--- a/fsl/wrappers/flirt.py
+++ b/fsl/wrappers/flirt.py
@@ -1,17 +1,19 @@
#!/usr/bin/env python
#
-# flirt.py -
+# flirt.py - Wrappers for FLIRT commands.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-"""
+"""This module provides wrapper functions for the FSL `FLIRT
+<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT>`_ tool, and other related
+tools.
.. autosummary::
:nosignatures:
flirt
- invxfm
applyxfm
+ invxfm
concatxfm
mcflirt
"""
@@ -19,7 +21,6 @@
import fsl.utils.run as run
import fsl.utils.assertions as asrt
-import fsl.data.image as fslimage
from . import wrapperutils as wutils
@@ -27,7 +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):
- """FLIRT (FMRIB's Linear Image Registration Tool)."""
+ """Wrapper around the ``flirt`` command. """
asrt.assertIsNifti(src, ref)
@@ -52,30 +53,30 @@ def flirt(src, ref, **kwargs):
return run.runfsl(cmd)
+@wutils.fileOrImage('src', 'ref', 'out')
+@wutils.fileOrArray('mat')
+def applyxfm(src, ref, mat, out, interp='spline'):
+ """Convenience function which runs ``flirt -applyxfm ...``."""
+ return flirt(src,
+ ref,
+ out=out,
+ applyxfm=True,
+ init=mat,
+ interp=interp)
+
+
+@wutils.fileOrArray
def invxfm(inmat, omat):
- """Tool for inverting FSL transformation matrices."""
+ """Use ``convert_xfm`` to invert an affine."""
asrt.assertFileExists(inmat)
- cmd = "convert_xfm -omat {0} -inverse {1}".format(omat, inmat)
+ cmd = 'convert_xfm -omat {} -inverse {}'.format(omat, inmat)
return run.runfsl(cmd)
-def applyxfm(src, ref, mat, out, interp='spline'):
- """Tool for applying FSL transformation matrices."""
- asrt.assertFileExists(src, ref)
- asrt.assertIsNifti(src, ref)
-
- cmd = "flirt -init {0} -in {1} -ref {2} -applyxfm -out {3} -interp {4}"
- return run.runfsl(cmd.format(mat, src, ref, out, interp))
-
-@wutils.required( 'inmat1', 'inmat2', 'outmat')
@wutils.fileOrArray('inmat1', 'inmat2', 'outmat')
def concatxfm(inmat1, inmat2, outmat):
- """Tool to concatenate two FSL transformation matrices."""
-
- print('inmat1', inmat1)
- print('inmat2', inmat2)
- print('outmat', outmat)
+ """Use ``convert_xfm`` to concatenate two affines."""
asrt.assertFileExists(inmat1, inmat2)
@@ -89,22 +90,14 @@ def concatxfm(inmat1, inmat2, outmat):
return run.runfsl(cmd)
-def mcflirt(infile, outfile, reffile=None, spline_final=True, plots=True,
- mats=True, refvol=None):
- """Rigid-body motion correction using mcflirt."""
+@wutils.fileOrImage('infile', 'out', 'reffile')
+@wutils.fileOrArary('init')
+def mcflirt(infile, **kwargs):
+ """Wrapper around the ``mcflirt`` command."""
- outfile = fslimage.removeExt(outfile)
- cmd = "mcflirt -in {0} -out {1} -rmsrel -rmsabs".format(infile, outfile)
+ asrt.assertIsNifti(infile)
- if reffile is not None:
- cmd += " -reffile {0}".format(reffile)
- if refvol is not None:
- cmd += " -refvol {0}".format(refvol)
- if spline_final:
- cmd += " -spline_final"
- if plots:
- cmd += " -plots"
- if mats:
- cmd += " -mats"
+ cmd = ['mcflirt', '-in', infile]
+ cmd += wutils.applyArgStyle('-', **kwargs)
return run.runfsl(cmd)
--
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