ENH: Add from_image/from_header methods to bring logic out of tests

Author: effigies

nibabel/coordimage.py

@@ -1,4 +1,6 @@
+import nibabel as nib
 from nibabel.fileslice import fill_slicer
+import nibabel.pointset as ps
 
 
 class CoordinateImage:
@@ -14,6 +16,22 @@ def __init__(self, data, coordaxis, header=None):
         self.coordaxis = coordaxis
         self.header = header
 
+    @classmethod
+    def from_image(klass, img):
+        coordaxis = CoordinateAxis.from_header(img.header)
+        if isinstance(img, nib.Cifti2Image):
+            if img.ndim != 2:
+                raise ValueError("Can only interpret 2D images")
+            for i in img.header.mapped_indices:
+                if isinstance(img.header.get_axis(i), nib.cifti2.BrainModelAxis):
+                    break
+            # Reinterpret data ordering based on location of coordinate axis
+            data = img.dataobj.copy()
+            data.order = ['F', 'C'][i]
+            if i == 1:
+                data._shape = data._shape[::-1]
+        return klass(data, coordaxis, img.header)
+
 
 class CoordinateAxis:
     """
@@ -81,6 +99,28 @@ def get_indices(self, parcel, indices=None):
     def __len__(self):
         return sum(len(parcel) for parcel in self.parcels)
 
+    # Hacky factory method for now
+    @classmethod
+    def from_header(klass, hdr):
+        parcels = []
+        if isinstance(hdr, nib.Cifti2Header):
+            axes = [hdr.get_axis(i) for i in hdr.mapped_indices]
+            for ax in axes:
+                if isinstance(ax, nib.cifti2.BrainModelAxis):
+                    break
+            else:
+                raise ValueError("No BrainModelAxis, cannot create CoordinateAxis")
+            for name, slicer, struct in ax.iter_structures():
+                if struct.volume_shape:
+                    substruct = ps.NdGrid(struct.volume_shape, struct.affine)
+                    indices = struct.voxel
+                else:
+                    substruct = None
+                    indices = struct.vertex
+                parcels.append(Parcel(name, substruct, indices))
+
+        return klass(parcels)
+
 
 class Parcel:
     """

nibabel/tests/test_coordimage.py

@@ -49,22 +49,12 @@ def from_spec(klass, pathlike):
 
 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)
+    assert ones.shape == (1, 91282)
+    cimg = ci.CoordinateImage.from_image(ones)
+    assert cimg.shape == (91282, 1)
 
+    caxis = cimg.coordaxis
+    assert len(caxis) == 91282
     assert caxis[...] is caxis
     assert caxis[:] is caxis