TEST: Add doctests to new interfaces, fake data

Author: mgxd

smriprep/conftest.py

@@ -13,4 +13,4 @@ def populate_namespace(doctest_namespace, tmp_path):
     doctest_namespace['os'] = os
     doctest_namespace['np'] = numpy
     doctest_namespace['load'] = load_resource
-    doctest_namespace['testdir'] = tmp_path
+    doctest_namespace['testdir'] = tmp_path

smriprep/interfaces/msm.py

@@ -124,6 +124,23 @@ class MSM(CommandLine):
     optimisation framework (FastPD Komodakis 2007), which significantly reduces the search
     space of possible deformations for each vertex, and allows flexibility with regards to the
     choice of similarity metric used to match the images.
+
+    >>> msm = MSM(
+    ...   config_file=load('msm/MSMSulcStrainFinalconf'),
+    ...   in_mesh='sub-01_hemi-L_sphere.surf.gii',
+    ...   reference_mesh='tpl-fsaverage_hemi-L_den-164k_desc-std_sphere.surf.gii',
+    ...   in_data='sub-01_hemi-L_sulc.shape.gii',
+    ...   reference_data='tpl-fsaverage_hemi-L_den-164k_sulc.shape.gii',
+    ...   out_base='L.',
+    ... )
+    >>> msm.cmdline  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
+    'msm --conf=.../MSMSulcStrainFinalconf \
+    --indata=sub-01_hemi-L_sulc.shape.gii \
+    --inmesh=sub-01_hemi-L_sphere.surf.gii \
+    --out=L. \
+    --refdata=tpl-fsaverage_hemi-L_den-164k_sulc.shape.gii \
+    --refmesh=tpl-fsaverage_hemi-L_den-164k_desc-std_sphere.surf.gii'
+
     """
 
     input_spec = MSMInputSpec

smriprep/interfaces/tests/data/sub-01_desc-warped_T1w.nii.gz

@@ -185,6 +185,15 @@ class SurfaceAffineRegression(WBCommand):
     warped source surface. Note that this has a bias to shrink the surface
     that is being warped. The output is written as a NIFTI 'world' matrix,
     see -convert-affine to convert it for use in other software.
+
+    >>> sar = SurfaceAffineRegression()
+    >>> sar.inputs.in_surface = 'sub-01_hemi-L_sulc.shape.gii'
+    >>> sar.inputs.target_surface = 'tpl-fsaverage_hemi-L_den-164k_sulc.shape.gii'
+    >>> sar.cmdline
+    'wb_command -surface-affine-regression \
+    sub-01_hemi-L_sulc.shape.gii \
+    tpl-fsaverage_hemi-L_den-164k_sulc.shape.gii \
+    sub-01_hemi-L_sulc.shape_xfm'
     """
     input_spec = SurfaceAffineRegressionInputSpec
     output_spec = SurfaceAffineRegressionOutputSpec
@@ -250,6 +259,25 @@ class SurfaceApplyAffine(WBCommand):
     represent.  If the -flirt option is not present, the affine must be a
     nifti 'world' affine, which can be obtained with the -convert-affine
     command, or aff_conv from the 4dfp suite.
+
+    .. testsetup::
+
+    >>> np.savetxt('affine.txt', np.eye(4), delimiter='\t')
+
+    .. doctest::
+
+    >>> saa = SurfaceApplyAffine()
+    >>> saa.inputs.in_surface = 'sub-01_hemi-L_sphere.surf.gii'
+    >>> saa.inputs.in_affine = 'affine.txt'
+    >>> saa.cmdline
+    'wb_command -surface-apply-affine \
+    sub-01_hemi-L_sphere.surf.gii \
+    affine.txt \
+    sub-01_hemi-L_sphere.surf_xformed.surf.gii'
+
+    .. testcleanup::
+
+    >>> os.unlink('affine.txt')
     """
     input_spec = SurfaceApplyAffineInputSpec
     output_spec = SurfaceApplyAffineOutputSpec
@@ -309,6 +337,15 @@ class SurfaceApplyWarpfield(WBCommand):
     If the -fnirt option is not present, the warpfield must be a nifti
     'world' warpfield, which can be obtained with the -convert-warpfield
     command.
+
+    >>> saw = SurfaceApplyWarpfield()
+    >>> saw.inputs.in_surface = 'sub-01_hemi-L_sphere.surf.gii'
+    >>> saw.inputs.warpfield = 'sub-01_desc-warped_T1w.nii.gz'
+    >>> saw.cmdline
+    'wb_command -surface-apply-warpfield \
+    sub-01_hemi-L_sphere.surf.gii \
+    sub-01_desc-warped_T1w.nii.gz \
+    sub-01_hemi-L_sphere.surf_warped.surf.gii'
     """
     input_spec = SurfaceApplyWarpfieldInputSpec
     output_spec = SurfaceApplyWarpfieldOutputSpec