antspymm 1.5.6__py3-none-any.whl → 1.5.7__py3-none-any.whl

antspymm/__init__.py

@@ -140,5 +140,7 @@ from .mm import pet3d_summary
 from .mm import deformation_gradient_optimized
 from .mm import efficient_dwi_fit_voxelwise
 from .mm import generate_voxelwise_bvecs
+from .mm import distortion_correct_bvecs
+
 
 

antspymm/mm.py

@@ -2138,6 +2138,40 @@ def bvec_reorientation( motion_parameters, bvecs, rebase=None ):
                     bvecs[myidx,:] = np.dot( rebase, bvecs[myidx,:] )
     return bvecs
 
+
+def distortion_correct_bvecs(bvecs, def_grad, A_img, A_ref):
+    """
+    Vectorized computation of voxel-wise distortion corrected b-vectors.
+
+    Parameters
+    ----------
+    bvecs : ndarray (N, 3)
+    def_grad : ndarray (X, Y, Z, 3, 3) containing rotations derived from the deformation gradient
+    A_img : ndarray (3, 3) direction matrix of the fixed image (target undistorted space)
+    A_ref : ndarray (3, 3) direction matrix of the moving image (being corrected)
+
+    Returns
+    -------
+    bvecs_5d : ndarray (X, Y, Z, N, 3)
+    """
+    X, Y, Z = def_grad.shape[:3]
+    N = bvecs.shape[0]
+    # Combined rotation: R_voxel = A_ref.T @ A_img @ def_grad
+    A = A_ref.T @ A_img
+    R_voxel = np.einsum('ij,xyzjk->xyzik', A, def_grad)  # (X, Y, Z, 3, 3)
+    # Apply R_voxel.T @ bvecs
+    # First, reshape R_voxel: (X*Y*Z, 3, 3)
+    R_voxel_reshaped = R_voxel.reshape(-1, 3, 3)
+    # Rotate all bvecs for each voxel
+    # Output: (X*Y*Z, N, 3)
+    rotated = np.einsum('vij,nj->vni', R_voxel_reshaped, bvecs)
+    # Normalize
+    norms = np.linalg.norm(rotated, axis=2, keepdims=True)
+    rotated /= np.clip(norms, 1e-8, None)
+    # Reshape back to (X, Y, Z, N, 3)
+    bvecs_5d = rotated.reshape(X, Y, Z, N, 3)
+    return bvecs_5d    
+
 def get_dti( reference_image, tensormodel, upper_triangular=True, return_image=False ):
     """
     extract DTI data from a dipy tensormodel

{antspymm-1.5.6.dist-info → antspymm-1.5.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: antspymm
-Version: 1.5.6
+Version: 1.5.7
 Summary: multi-channel/time-series medical image processing with antspyx
 Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache-2.0

antspymm-1.5.7.dist-info/RECORD

@@ -0,0 +1,6 @@
+antspymm/__init__.py,sha256=cTcqtGO0J5T2I0Chxe-Sy25QDlnHLDEQK8QEnJkkFRs,4900
+antspymm/mm.py,sha256=eqMcRxQt03AbC3qRrubYBxGsbkKNfrS0dd9VgqXavCE,544991
+antspymm-1.5.7.dist-info/METADATA,sha256=c-2SVYUIR2RGZ_XJXE8M1nxG94CpF9-fYBiRERaCHhQ,26007
+antspymm-1.5.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+antspymm-1.5.7.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
+antspymm-1.5.7.dist-info/RECORD,,

antspymm-1.5.6.dist-info/RECORD

@@ -1,6 +0,0 @@
-antspymm/__init__.py,sha256=50wAFf04ZlF7wYg1h07dFLKebGOGFwKCJfAcdyHhSXw,4858
-antspymm/mm.py,sha256=mtkFJi0ZwLFw32vCrBdZcGa4ITgIOSn_Vfwq1SXLdqE,543752
-antspymm-1.5.6.dist-info/METADATA,sha256=0H4Olfd04VZNR56ErUfVd0hEo8DppIsDrWWbks0JgHs,26007
-antspymm-1.5.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-antspymm-1.5.6.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
-antspymm-1.5.6.dist-info/RECORD,,