From c0d35dc935f86524aa9f57be2c4dba2bcfd6efdc Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 9 Jul 2018 12:08:48 +0100
Subject: [PATCH] RF, STY: Improved mcflirt wrapper.
---
fsl/wrappers/fast.py | 5 ++---
fsl/wrappers/flirt.py | 20 +++++++++++++++++---
2 files changed, 19 insertions(+), 6 deletions(-)
diff --git a/fsl/wrappers/fast.py b/fsl/wrappers/fast.py
index 1c12a363f..a944ea77a 100644
--- a/fsl/wrappers/fast.py
+++ b/fsl/wrappers/fast.py
@@ -19,7 +19,7 @@ from . import wrapperutils as wutils
@wutils.fileOrImage('imgs', 'A', 's', 'manualseg', outprefix='out')
@wutils.fileOrArray('a')
@wutils.fslwrapper
-def fast(imgs, out="fast", **kwargs):
+def fast(imgs, out='fast', **kwargs):
"""Wrapper for the ``fast`` command.
:arg imgs: Input image(s)
@@ -31,8 +31,7 @@ def fast(imgs, out="fast", **kwargs):
if isinstance(imgs, six.string_types):
imgs = [imgs]
- for i in imgs:
- asrt.assertIsNifti(imgs)
+ asrt.assertIsNifti(*imgs)
argmap = {
'n_classes' : 'class',
diff --git a/fsl/wrappers/flirt.py b/fsl/wrappers/flirt.py
index dac853992..cac769bf2 100644
--- a/fsl/wrappers/flirt.py
+++ b/fsl/wrappers/flirt.py
@@ -94,15 +94,29 @@ def concatxfm(inmat1, inmat2, outmat):
return cmd
-@wutils.fileOrImage('infile', 'out', 'reffile')
-@wutils.fileOrArray('init')
+@wutils.fileOrImage('infile', 'out', 'reffile', outprefix='out')
+@wutils.fileOrArray('init', outprefix='out')
@wutils.fslwrapper
def mcflirt(infile, **kwargs):
"""Wrapper for the ``mcflirt`` command."""
asrt.assertIsNifti(infile)
+ argmap = {
+ 'twod' : '2d',
+ }
+
+ valmap = {
+ '2d' : wutils.SHOW_IF_TRUE,
+ 'gdt' : wutils.SHOW_IF_TRUE,
+ 'meanvol' : wutils.SHOW_IF_TRUE,
+ 'stats' : wutils.SHOW_IF_TRUE,
+ 'mats' : wutils.SHOW_IF_TRUE,
+ 'plots' : wutils.SHOW_IF_TRUE,
+ 'report' : wutils.SHOW_IF_TRUE,
+ }
+
cmd = ['mcflirt', '-in', infile]
- cmd += wutils.applyArgStyle('-', **kwargs)
+ cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs)
return cmd
--
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