fix: in reality, there's nothing we must do :D

Author: oesteban

docs/notebooks/02_afni_deoblique.ipynb

@@ -2,6 +2,8 @@
 from math import pi
 import numpy as np
 from nibabel.affines import (
+    append_diag,
+    apply_affine,
     from_matvec,
     obliquity,
     voxel_sizes,
@@ -205,14 +207,18 @@ def _afni_warpdrive(nii, forward=True, ras=False):
 
     """
     oblique = nii.affine
-    plumb = oblique[:3, :3] / np.abs(oblique[:3, :3]).max(0)
-    plumb[np.abs(plumb) < 1.0] = 0
-    plumb *= voxel_sizes(oblique)
-
-    R = from_matvec(plumb @ np.linalg.inv(oblique[:3, :3]), (0, 0, 0))
-    plumb_orig = np.linalg.inv(R[:3, :3]) @ oblique[:3, 3]
-    print(plumb_orig)
-    R[:3, 3] = R[:3, :3] @ (plumb_orig - oblique[:3, 3])
+    shape = np.array(nii.shape[:3])
+    plumb_r = oblique[:3, :3] / np.abs(oblique[:3, :3]).max(0)
+    plumb_r[np.abs(plumb_r) < 1.0] = 0
+    plumb_r *= voxel_sizes(oblique)
+    plumb = np.eye(4)
+    plumb[:3, :3] = plumb_r
+    obliq_o = apply_affine(oblique, 0.5 * (shape - 1))
+    plumb_c = apply_affine(plumb, 0.5 * (shape - 1))
+    plumb[:3, 3] = -plumb_c + obliq_o
+    print(obliq_o, apply_affine(plumb, 0.5 * (shape - 1)))
+
+    R = plumb @ np.linalg.inv(oblique)
     if not ras:
         # Change sign to match AFNI's warpdrive_matvec signs
         B = np.ones((2, 2))
@@ -228,5 +234,8 @@ def _afni_header(nii, field="WARPDRIVE_MATVEC_FOR_000000"):
         root.find(f".//*[@atr_name='{field}']").text,
         sep="\n",
         dtype="float32"
-    ).reshape((3, 4))
-    return np.vstack((retval, (0, 0, 0, 1)))
+    )
+    if retval.size == 12:
+        return np.vstack((retval.reshape((3, 4)), (0, 0, 0, 1)))
+
+    return retval

nitransforms/io/afni.py

@@ -0,0 +1 @@
+affine-RAS.afni