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Co-authored-by: Mathias Goncalves <[email protected]>
Co-authored-by: Chris Markiewicz <[email protected]>

sdcflows/utils/tools.py

@@ -21,9 +21,16 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Image processing tools."""
+import nibabel as nb
 
 
-def deoblique_and_zooms(in_reference, oblique, factor=4, padding=1):
+def deoblique_and_zooms(
+    in_reference: nb.spatialimages.SpatialImage,
+    oblique: nb.spatialimages.SpatialImage,
+    factor: int = 4,
+    padding: int = 1,
+    factor_tol: float = 1e-4,
+):
     """
     Generate a sampling reference aligned with in_reference fully covering oblique.
 
@@ -39,6 +46,8 @@ def deoblique_and_zooms(in_reference, oblique, factor=4, padding=1):
     padding : :obj:`int`
         Number of additional voxels around the most extreme positions of the projection of
         oblique on to the reference.
+    factor_tol : :obj:`float`
+        Absolute tolerance to determine whether factor is one.
 
     """
     from itertools import product
@@ -54,24 +63,23 @@ def deoblique_and_zooms(in_reference, oblique, factor=4, padding=1):
     _, qcode = in_reference.get_qform(coded=True)
 
     # Calculate the 8 most extreme coordinates of oblique in in_reference space
-    extent = apply_affine(
-        oblique.affine,
-        np.array(list(product((0, 1), repeat=3))) * (np.array(oblique.shape[:3]) - 1),
+    corners = np.array(list(product((0, 1), repeat=3))) * (
+        np.array(oblique.shape[:3]) - 1
     )
-    extent_ijk = apply_affine(np.linalg.inv(affine), extent)
+    extent_ijk = apply_affine(np.linalg.inv(affine) @ oblique.affine, corners)
 
     underflow = np.clip(extent_ijk.min(0) - padding, None, 0).astype(int)
     overflow = np.ceil(
         np.clip(extent_ijk.max(0) + padding + 1 - ref_shape, 0, None)
     ).astype(int)
     if np.any(underflow < 0) or np.any(overflow > 0):
         # Add under/overflow voxels
-        ref_shape += np.abs(underflow) + overflow
+        ref_shape += overflow - underflow
         # Consistently update origin
         affine[:-1, -1] = apply_affine(affine, underflow)
 
     # Make grid denser
-    if abs(1.0 - factor) > 1e-4:
+    if abs(1.0 - factor) > factor_tol:
         new_shape = np.rint(ref_shape * factor)
         affine = rescale_affine(affine, ref_shape, ref_zooms / factor, new_shape)
         ref_shape = new_shape
@@ -81,7 +89,7 @@ def deoblique_and_zooms(in_reference, oblique, factor=4, padding=1):
     hdr.set_qform(affine, qcode)
 
     return in_reference.__class__(
-        np.zeros(ref_shape.astype(int), dtype=hdr.get_data_dtype()),
+        nb.fileslice.strided_scalar(ref_shape.astype(int)),
         affine,
         hdr,
     )