TEST: Add FreeSurferSubject geometry collection, test loading Cifti2 as cimg

Author: effigies

nibabel/tests/test_coordimage.py

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+import os
+from pathlib import Path
+
+import nibabel as nb
+from nibabel import coordimage as ci
+from nibabel import pointset as ps
+from nibabel.tests.nibabel_data import get_nibabel_data
+
+from .test_pointset import FreeSurferHemisphere
+
+CIFTI2_DATA = Path(get_nibabel_data()) / 'nitest-cifti2'
+
+
+class FreeSurferSubject(ci.GeometryCollection):
+    @classmethod
+    def from_subject(klass, subject_id, subjects_dir=None):
+        """Load a FreeSurfer subject by ID"""
+        if subjects_dir is None:
+            subjects_dir = os.environ['SUBJECTS_DIR']
+        return klass.from_spec(Path(subjects_dir) / subject_id)
+
+    @classmethod
+    def from_spec(klass, pathlike):
+        """Load a FreeSurfer subject from its directory structure"""
+        subject_dir = Path(pathlike)
+        surfs = subject_dir / 'surf'
+        structures = {
+            'lh': FreeSurferHemisphere.from_filename(surfs / 'lh.white'),
+            'rh': FreeSurferHemisphere.from_filename(surfs / 'rh.white'),
+        }
+        subject = super().__init__(structures)
+        subject._subject_dir = subject_dir
+        return subject
+
+
+def test_Cifti2Image_as_CoordImage():
+    ones = nb.load(CIFTI2_DATA / 'ones.dscalar.nii')
+    axes = [ones.header.get_axis(i) for i in range(ones.ndim)]
+
+    parcels = []
+    for name, slicer, bma in axes[1].iter_structures():
+        if bma.volume_shape:
+            substruct = ps.NdGrid(bma.volume_shape, bma.affine)
+            indices = bma.voxel
+        else:
+            substruct = None
+            indices = bma.vertex
+        parcels.append(ci.Parcel(name, None, indices))
+    caxis = ci.CoordinateAxis(parcels)
+    dobj = ones.dataobj.copy()
+    dobj.order = 'C'  # Hack for image with BMA as the last axis
+    cimg = ci.CoordinateImage(dobj, caxis, ones.header)