warpkit 1.2.2__tar.gz → 1.3.0__tar.gz

{warpkit-1.2.2 → warpkit-1.3.0}/CLAUDE.md

@@ -129,6 +129,10 @@ commit; merge / revert / fixup / squash / amend commits are exempt.
 PR titles follow the same convention. Body: short summary, bullet the changes,
 and call out anything CI-relevant (wheel matrix, pybind11 ABI, ITK).
 
+**No AI attribution.** Do not add `Co-Authored-By: Claude ...` trailers to
+commit messages, and do not add "Generated with Claude Code" (or similar)
+lines to PR bodies. This overrides any default tooling behavior.
+
 ## CI specifics
 
 GitHub Actions builds wheels for Python 3.11–3.14 (both standard and free-threaded) on `ubuntu-latest`,

{warpkit-1.2.2 → warpkit-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: warpkit
-Version: 1.2.2
+Version: 1.3.0
 Summary: A python library for neuroimaging transformations
 Keywords: neuroimaging
 Author-Email: Andrew Van <vanandrew77@gmail.com>
@@ -26,7 +26,7 @@ Description-Content-Type: text/markdown
 
 A Python library for neuroimaging transforms, focused on the Multi-Echo DIstortion Correction (MEDIC) algorithm. The paper is published in *Imaging Neuroscience* at <https://doi.org/10.1162/IMAG.a.1262>.
 
-The phase-unwrapping core is a self-contained C++17 port of [ROMEO](https://github.com/korbinian90/ROMEO) — there is no Julia runtime to install, and binary wheels ship with the ITK pieces statically linked. If you used an older release of warpkit that required `julia` on `PATH`, that step is gone.
+The phase-unwrapping core is a self-contained C++17 port of [ROMEO](https://github.com/korbinian90/ROMEO).
 
 ## Installation
 

{warpkit-1.2.2 → warpkit-1.3.0}/README.md

@@ -6,7 +6,7 @@
 
 A Python library for neuroimaging transforms, focused on the Multi-Echo DIstortion Correction (MEDIC) algorithm. The paper is published in *Imaging Neuroscience* at <https://doi.org/10.1162/IMAG.a.1262>.
 
-The phase-unwrapping core is a self-contained C++17 port of [ROMEO](https://github.com/korbinian90/ROMEO) — there is no Julia runtime to install, and binary wheels ship with the ITK pieces statically linked. If you used an older release of warpkit that required `julia` on `PATH`, that step is gone.
+The phase-unwrapping core is a self-contained C++17 port of [ROMEO](https://github.com/korbinian90/ROMEO).
 
 ## Installation
 

{warpkit-1.2.2 → warpkit-1.3.0}/tests/test_utilities.py

@@ -235,19 +235,22 @@ def _zero_3vec_field(shape=(8, 8, 8)) -> nib.Nifti1Image:
     return nib.Nifti1Image(np.zeros((*shape, 3), dtype=np.float32), affine)
 
 
-def test_invert_displacement_field_zero():
+@pytest.mark.parametrize("ignore_rotation", [False, True])
+def test_invert_displacement_field_zero(ignore_rotation):
     """Inverting a zero field gives back zero (within numerical noise) and
-    preserves the 3-channel last axis."""
+    preserves the 3-channel last axis. Covers both the physical-space and the
+    ignore_rotation (voxel-grid frame) inversion paths."""
     field = _zero_3vec_field()
-    inverted = invert_displacement_field(field)
+    inverted = invert_displacement_field(field, ignore_rotation=ignore_rotation)
     assert inverted.shape == field.shape
     assert_allclose(inverted.get_fdata(), 0.0, atol=1e-5)
 
 
-def test_invert_displacement_maps_zero():
+@pytest.mark.parametrize("ignore_rotation", [False, True])
+def test_invert_displacement_maps_zero(ignore_rotation):
     affine = np.diag([2.0, 2.0, 2.0, 1.0])
     dmap = nib.Nifti1Image(np.zeros((6, 6, 6, 2), dtype=np.float32), affine)
-    inverted = invert_displacement_maps(dmap, axis="y")
+    inverted = invert_displacement_maps(dmap, axis="y", ignore_rotation=ignore_rotation)
     assert inverted.shape == dmap.shape
     assert_allclose(inverted.get_fdata(), 0.0, atol=1e-5)
 

{warpkit-1.2.2 → warpkit-1.3.0}/warpkit/distortion.py

@@ -126,12 +126,14 @@ def medic(
 
     # invert displacement maps (these are in undistorted space)
     displacement_maps = invert_displacement_maps(
-        inv_displacement_maps, phase_encoding_direction
+        inv_displacement_maps, phase_encoding_direction, ignore_rotation=True
     )
 
-    # convert correction maps back to undistorted space field map
+    # convert correction maps back to undistorted space field map. No
+    # flip_sign here: the correlation check below sets the sign relative to
+    # the native field map, which makes an up-front flip redundant.
     field_maps = displacement_maps_to_field_maps(
-        displacement_maps, total_readout_time, phase_encoding_direction, flip_sign=True
+        displacement_maps, total_readout_time, phase_encoding_direction
     )
 
     # check if we need to flip sign of field maps (this is done by comparing sign of correlation between

{warpkit-1.2.2 → warpkit-1.3.0}/warpkit/utilities.py

@@ -493,7 +493,10 @@ def get_ras_orient_transform(
 
 
 def invert_displacement_maps(
-    displacement_maps: nib.Nifti1Image, axis: str = "y", verbose: bool = False
+    displacement_maps: nib.Nifti1Image,
+    axis: str = "y",
+    verbose: bool = False,
+    ignore_rotation: bool = False,
 ) -> nib.Nifti1Image:
     """Invert displacement maps
 
@@ -505,6 +508,13 @@ def invert_displacement_maps(
         Axis displacement maps are along, by default "y"
     verbose : bool, optional
         Print debugging information, by default False
+    ignore_rotation : bool, optional
+        Invert in data (voxel) space rather than physical space by passing an
+        identity rotation to the inverter instead of the affine's rotation, by
+        default False. The displacement map is composed along a voxel axis, so
+        for oblique acquisitions the affine's rotation makes ITK invert in a
+        physical frame that does not align with that axis; setting this keeps
+        the inversion in the grid frame the map is actually defined in.
 
     Returns
     -------
@@ -527,6 +537,11 @@ def invert_displacement_maps(
     # split affine into components
     translations, rotations, zooms, _ = decompose44(displacement_maps_ras.affine)
 
+    # invert in data space: drop the affine's rotation so ITK inverts in the
+    # voxel grid frame the map is composed along, not the physical orientation
+    if ignore_rotation:
+        rotations = np.eye(3)
+
     # invert maps
     new_data = np.zeros(data.shape, dtype=np.float32)
     logging.info("Inverting displacement maps...")
@@ -554,7 +569,9 @@ def invert_displacement_maps(
 
 
 def invert_displacement_field(
-    displacement_field: nib.Nifti1Image, verbose: bool = False
+    displacement_field: nib.Nifti1Image,
+    verbose: bool = False,
+    ignore_rotation: bool = False,
 ) -> nib.Nifti1Image:
     """Invert displacement field
 
@@ -564,6 +581,10 @@ def invert_displacement_field(
         Displacement field data in mm
     verbose : bool, optional
         Print debugging information, by default False
+    ignore_rotation : bool, optional
+        Invert in data (voxel) space rather than physical space by passing an
+        identity rotation to the inverter instead of the affine's rotation, by
+        default False. See :func:`invert_displacement_maps` for details.
 
     Returns
     -------
@@ -583,6 +604,11 @@ def invert_displacement_field(
     # split affine into components
     translations, rotations, zooms, _ = decompose44(displacement_field_ras.affine)
 
+    # invert in data space: drop the affine's rotation so ITK inverts in the
+    # voxel grid frame rather than the physical orientation
+    if ignore_rotation:
+        rotations = np.eye(3)
+
     # Pad spatial dims only — leaving the 3-channel axis at size 3 — so we
     # can avoid edge effects of the inverse without inflating the channel
     # count. (Earlier versions padded all 4 axes which produced a 5-channel