MNT: move standard_space_roi wrapper into the flirt module

fsl/wrappers/__init__.py

@@ -121,7 +121,8 @@ from fsl.wrappers.flirt              import (flirt,
                                              applyxfm4D,
                                              concatxfm,
                                              fixscaleskew,
-                                             mcflirt)
+                                             mcflirt,
+                                             standard_space_roi)
 from fsl.wrappers.fnirt              import (fnirt,
                                              applywarp,
                                              invwarp,
@@ -143,4 +144,8 @@ from fsl.wrappers.misc               import (fslreorient2std,
                                              slicer,
                                              cluster,
                                              gps)
-from fsl.wrappers.standard_space_roi import  standard_space_roi
+from fsl.wrappers.bianca             import (bianca,
+                                             bianca_cluster_stats,
+                                             bianca_overlap_measures,
+                                             bianca_perivent_deep,
+                                             make_bianca_mask)

fsl/wrappers/flirt.py

@@ -4,6 +4,7 @@
 #
 # Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
 # Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
 #
 """This module provides wrapper functions for the FSL `FLIRT
 <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT>`_ tool, and other related
@@ -17,7 +18,9 @@ tools.
    applyxfm4D
    invxfm
    concatxfm
+   fixscaleskew
    mcflirt
+   standard_space_roi
 """
 
 
@@ -175,3 +178,43 @@ def mcflirt(infile, **kwargs):
     cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs)
 
     return cmd
+
+
+@wutils.fileOrImage('input', 'output', 'maskMASK', 'roiMASK',
+                    'ssref', 'altinput')
+@wutils.fslwrapper
+def standard_space_roi(input, output, **kwargs):
+    """Wrapper for the ``standard_space_roi`` command.
+
+    Refer to the ``standard_space_roi`` command-line help for details on all
+    arguments.
+    """
+    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,
+        '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('-', argmap=argmap, valmap=valmap, **kwargs)
+
+    return cmd

fsl/wrappers/standard_space_roi.py

-#!/usr/bin/env python
-#
-# standard_space_roi.py - Wrapper for the standard_space_roi command.
-#
-# Author: Fidel Alfaro Almagro
-#
-"""This module provides the :func:`standard_space_roi` function, a wrapper for
-the FSL `standard_space_roi`_ command.
-"""
-
-import fsl.utils.assertions as asrt
-from . import wrapperutils  as wutils
-
-@wutils.fileOrImage('input', 'output', 'maskMASK', 'roiMASK', 'ssref', 'altinput')
-@wutils.fslwrapper
-def standard_space_roi(input, output, **kwargs):
-    """Wrapper for the ``standard_space_roi`` command.
-
-    :arg maskFOV:   Mask output using transformed standard space FOV (default)
-    :arg maskMASK:  Mask output using transformed standard space mask
-    :arg maskNONE:  Do not mask output
-
-    :arg roiFOV:    Cut down input FOV using bounding box of the transformed standard space FOV (default)
-    :arg roiMASK:   Cut down input FOV using nonbackground bounding box of the transformed standard space mask
-    :arg roiNONE:   Co not cut down input FOV
-
-    :arg ssref      Standard space reference image to use (default $FSLDIR/data/standard/MNI152_T1)
-    :arg altinput   Alternative input image to apply the ROI to (instead of the one used to register to the reference)
-    :arg d          Debug (don't delete intermediate files)
-    :arg b          Betpremask, equivalent to: -maskMASK $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil -roiNONE
-
-    Refer to the ``standard_space_roi`` command-line help for details on all arguments.
-    """
-    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,
-        '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('-', argmap=argmap, valmap=valmap, **kwargs)
-
-    return cmd