Merge branch 'enh/new_bedpostx_wrapper' into 'main'

Adding a new wrapper for bedpostx

See merge request fsl/fslpy!454

CHANGELOG.rst

@@ -2,6 +2,17 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+3.19.0 (Under development)
+--------------------------
+
+
+Added
+^^^^^
+
+
+* New :func:`.bedpostx_postproc` wrapper function (!454).
+
+
 3.18.3 (Saturday 4th May 2024)
 ------------------------------
 

fsl/tests/test_wrappers/test_wrappers.py

@@ -578,6 +578,15 @@ def test_split_parts_gpu():
         assert res.stdout[0] == exp
 
 
+def test_bedpostx_postproc():
+    with testenv('bedpostx_postproc.sh') as bpg:
+        res = fw.bedpostx_postproc('data', 'mask', 'bvecs', 'bvals',
+                                   100, 10, 'subdir', 'bindir', nf=20)
+        exp = f'{bpg} --data=data --mask=mask --bvecs=bvecs --bvals=bvals ' \
+               '--nf=20 100 10 subdir bindir'
+        assert res.stdout[0] == exp
+
+
 def test_bedpostx_postproc_gpu():
     with testenv('bedpostx_postproc_gpu.sh') as bpg:
         res = fw.bedpostx_postproc_gpu('data', 'mask', 'bvecs', 'bvals',

fsl/wrappers/__init__.py

@@ -166,6 +166,7 @@ from fsl.wrappers.bedpostx           import (xfibres,
                                              xfibres_gpu,
                                              split_parts_gpu,
                                              bedpostx_postproc_gpu,
+                                             bedpostx_postproc,
                                              probtrackx,
                                              probtrackx2,
                                              probtrackx2_gpu)

fsl/wrappers/bedpostx.py

@@ -14,6 +14,7 @@ commands.
    xfibres
    xfibres_gpu
    split_parts_gpu
+   bedpostx_postproc
    bedpostx_postproc_gpu
    probtrackx
    probtrackx2
@@ -160,6 +161,27 @@ def bedpostx_postproc_gpu(data, mask, bvecs, bvals, TotalNumVoxels,
     return cmd
 
 
+@wutils.fileOrImage('data', 'mask',)
+@wutils.fileOrArray('bvecs', 'bvals')
+@wutils.fslwrapper
+def bedpostx_postproc(data, mask, bvecs, bvals, TotalNumVoxels,
+                      TotalNumParts, SubjectDir, bindir, **kwargs):
+    """Wrapper for the ``bedpostx_postproc`` command."""
+
+    asrt.assertFileExists(data, bvecs, bvals)
+    asrt.assertIsNifti(mask)
+
+    cmd = ['bedpostx_postproc.sh',
+           '--data='  + data,
+           '--mask='  + mask,
+           '--bvecs=' + bvecs,
+           '--bvals=' + bvals]
+
+    cmd += wutils.applyArgStyle('--=', valmap=XFIBRES_VALMAP, **kwargs)
+    cmd += [str(TotalNumVoxels), str(TotalNumParts), SubjectDir, bindir]
+    return cmd
+
+
 @wutils.fileOrImage('mask', 'seed')
 @wutils.fslwrapper
 def probtrackx(samples, mask, seed, **kwargs):