From 971a2b69900be3bda50445d40a0bd0eb422ae71e Mon Sep 17 00:00:00 2001
From: Fidel Alfaro Almagro <falmagro@fmrib.ox.ac.uk>
Date: Tue, 12 Jul 2022 16:26:14 +0100
Subject: [PATCH] Modifications to standard_space for consistency
---
fsl/wrappers/__init__.py | 31 +++++++++++++++---------------
fsl/wrappers/standard_space_roi.py | 31 +++++++++++++++++++++---------
2 files changed, 38 insertions(+), 24 deletions(-)
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
index a27daebbf..1ab959245 100755
--- a/fsl/wrappers/__init__.py
+++ b/fsl/wrappers/__init__.py
@@ -97,39 +97,40 @@ decorators.
"""
-from fsl.wrappers.wrapperutils import (LOAD,)
-from fsl.wrappers.bet import (bet,
+from fsl.wrappers.wrapperutils import (LOAD,)
+from fsl.wrappers.bet import (bet,
robustfov)
-from fsl.wrappers.eddy import (eddy,
+from fsl.wrappers.eddy import (eddy,
eddy_cuda,
topup,
applytopup)
-from fsl.wrappers.fast import (fast,)
-from fsl.wrappers.fsl_anat import (fsl_anat,)
-from fsl.wrappers.fsl_sub import (fsl_sub,)
-from fsl.wrappers.flirt import (flirt,
+from fsl.wrappers.fast import (fast,)
+from fsl.wrappers.fsl_anat import (fsl_anat,)
+from fsl.wrappers.fsl_sub import (fsl_sub,)
+from fsl.wrappers.flirt import (flirt,
invxfm,
applyxfm,
applyxfm4D,
concatxfm,
mcflirt)
-from fsl.wrappers.fnirt import (fnirt,
+from fsl.wrappers.fnirt import (fnirt,
applywarp,
invwarp,
convertwarp)
-from fsl.wrappers.fslmaths import (fslmaths,)
-from fsl.wrappers.fslstats import (fslstats,)
-from fsl.wrappers.fugue import (fugue,
+from fsl.wrappers.fslmaths import (fslmaths,)
+from fsl.wrappers.fslstats import (fslstats,)
+from fsl.wrappers.fugue import (fugue,
prelude,
sigloss,
fsl_prepare_fieldmap)
-from fsl.wrappers.melodic import (melodic,
+from fsl.wrappers.melodic import (melodic,
fsl_regfilt)
-from fsl.wrappers.misc import (fslreorient2std,
+from fsl.wrappers.misc import (fslreorient2std,
fslorient,
fslroi,
slicer,
cluster,
gps)
-from fsl.wrappers.epi_reg import epi_reg
-from fsl.wrappers import tbss
+from fsl.wrappers.epi_reg import epi_reg
+from fsl.wrappers import tbss
+from fsl.wrappers.standard_space_roi import standard_space_roi
diff --git a/fsl/wrappers/standard_space_roi.py b/fsl/wrappers/standard_space_roi.py
index bc0e584c1..4b402ec69 100644
--- a/fsl/wrappers/standard_space_roi.py
+++ b/fsl/wrappers/standard_space_roi.py
@@ -11,7 +11,7 @@ the FSL `standard_space_roi`_ command.
import fsl.utils.assertions as asrt
from . import wrapperutils as wutils
-@wutils.fileOrImage('input', 'maskMASK', 'roiMASK', 'ssref', 'altinput',outprefix='output')
+@wutils.fileOrImage('input', 'output', 'maskMASK', 'roiMASK', 'ssref', 'altinput')
@wutils.fslwrapper
def standard_space_roi(input, output, **kwargs):
"""Wrapper for the ``standard_space_roi`` command.
@@ -33,17 +33,30 @@ def standard_space_roi(input, output, **kwargs):
"""
asrt.assertIsNifti(input)
+ argmap = {
+ 'twod' : '2D'
+ }
+
valmap = {
- 'maskFOV' : wutils.SHOW_IF_TRUE,
- 'maskNONE' : wutils.SHOW_IF_TRUE,
- 'roiFOV' : wutils.SHOW_IF_TRUE,
- 'roiNONE' : wutils.SHOW_IF_TRUE,
- 'd' : wutils.SHOW_IF_TRUE,
- 'b' : wutils.SHOW_IF_TRUE,
+ 'maskFOV' : wutils.SHOW_IF_TRUE,
+ 'maskNONE' : wutils.SHOW_IF_TRUE,
+ 'roiFOV' : wutils.SHOW_IF_TRUE,
+ 'roiNONE' : wutils.SHOW_IF_TRUE,
+ 'd' : wutils.SHOW_IF_TRUE,
+ 'b' : wutils.SHOW_IF_TRUE,
+ 'usesqform' : wutils.SHOW_IF_TRUE,
+ 'displayinit' : wutils.SHOW_IF_TRUE,
+ 'noresample' : wutils.SHOW_IF_TRUE,
+ 'forcescaling' : wutils.SHOW_IF_TRUE,
+ 'applyxfm' : wutils.SHOW_IF_TRUE,
+ 'nosearch' : wutils.SHOW_IF_TRUE,
+ 'noclamp' : wutils.SHOW_IF_TRUE,
+ 'noresampblur' : wutils.SHOW_IF_TRUE,
+ '2D' : wutils.SHOW_IF_TRUE,
+ 'v' : wutils.SHOW_IF_TRUE
}
cmd = ['standard_space_roi', input, output]
-
- cmd += wutils.applyArgStyle('-', valmap=valmap, **kwargs)
+ cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs)
return cmd
--
GitLab