antspymm 1.5.1__py3-none-any.whl → 1.5.3__py3-none-any.whl

antspymm/mm.py

@@ -2198,9 +2198,10 @@ def dti_numpy_to_image( reference_image, tensorarray, upper_triangular=True):
 def transform_and_reorient_dti( fixed, moving_dti, composite_transform, py_based=True, verbose=False, **kwargs):
     """
     apply a transform to DTI in the style of ants.apply_transforms. this function
-        expects a pre-computed composite transform which it will use to reorient 
-        the DTI using preservation of principle directions.
-    
+        expects a pre-computed composite transform which it will use to reorient
+        the DTI using preservation of principle directions.  BUG fix by cookpa 2025 
+        06 18.
+
     fixed : antsImage reference space
 
     moving_dti : antsImage DTI in upper triangular format
@@ -2224,34 +2225,36 @@ def transform_and_reorient_dti( fixed, moving_dti, composite_transform, py_based
     dtiw = []
     for k in range(len(dtsplit)):
         dtiw.append( ants.apply_transforms( fixed, dtsplit[k], composite_transform ) )
-    dtiw=ants.merge_channels(dtiw)
+    dtiw=ants.merge_channels(dtiw) # resampled into fixed space but still based in moving index space
     if verbose:
         print("reorient tensors locally: compose and get reo image")
-    locrot = ants.deformation_gradient( ants.image_read(composite_transform), 
+    locrot = ants.deformation_gradient( ants.image_read(composite_transform),
         to_rotation = True, py_based=py_based ).numpy()
-    rebaser = np.dot( np.transpose( fixed.direction  ), moving_dti.direction )
+    # rebases from moving index to fixed index space. Not quite what we need here
+    # rebaser = np.dot( np.transpose( fixed.direction  ), moving_dti.direction )
     if verbose:
         print("convert UT to full tensor")
     dtiw2tensor = triangular_to_tensor( dtiw )
     if verbose:
-        print("rebase tensors to new space via iterator")
+        print("rebase tensors to new space and apply reorientation via iterator")
     it = np.ndindex( fixed.shape )
     for i in it:
-        # direction * dt * direction.transpose();
         mmm = dtiw2tensor[i]
-        # transform rebase
+        # Rebase mmm to physical space
+        mmm = np.dot( mmm, np.transpose( moving_dti.direction ) )
+        mmm = np.dot( moving_dti.direction, mmm )
+        # Now apply local rotation
         locrotx = np.reshape( locrot[i], [3,3] )
         mmm = np.dot( mmm, np.transpose( locrotx ) )
         mmm = np.dot( locrotx, mmm )
-        # physical space rebase
-        mmm = np.dot( mmm, np.transpose( rebaser ) )
-        mmm = np.dot( rebaser, mmm )
+        # Now rebase to fixed index space
+        mmm = np.dot( mmm, np.transpose( fixed.direction ) )
+        mmm = np.dot( fixed.direction, mmm )
         dtiw2tensor[i] = mmm
     if verbose:
         print("done with rebasing")
     return dti_numpy_to_image( fixed, dtiw2tensor )
 
-
 def dti_reg(
     image,
     avg_b0,
@@ -3655,8 +3658,8 @@ def efficient_tensor_fit( gtab, fit_method, imagein, maskin, diffusion_model='DT
 
 
 def efficient_dwi_fit(gtab, diffusion_model, imagein, maskin,
-                  model_params=None, bvals_to_use=None,
-                  chunk_size=10, num_threads=1, verbose=True):
+                      model_params=None, bvals_to_use=None,
+                      chunk_size=1024, num_threads=1, verbose=True):
     """
     Efficient and optionally parallelized diffusion model reconstruction using DiPy.
 
@@ -3675,7 +3678,7 @@ def efficient_dwi_fit(gtab, diffusion_model, imagein, maskin,
     bvals_to_use : list of int, optional
         Subset of b-values to use for the fit (e.g., [0, 1000, 2000]).
     chunk_size : int, optional
-        Z-axis slice chunk size.
+        Maximum number of voxels per chunk (default 1024).
     num_threads : int, optional
         Number of parallel threads.
     verbose : bool, optional
@@ -3707,23 +3710,25 @@ def efficient_dwi_fit(gtab, diffusion_model, imagein, maskin,
     img_data = imagein.numpy()
     mask = maskin.numpy().astype(bool)
     X, Y, Z, N = img_data.shape
+    inplane_size = X * Y
+
+    # Convert chunk_size from voxel count to number of slices
+    slices_per_chunk = max(1, chunk_size // inplane_size)
 
     if verbose:
         print(f"[INFO] Image shape: {img_data.shape}")
         print(f"[INFO] Using model: {diffusion_model}")
-        print(f"[INFO] Chunk size: {chunk_size} | Threads: {num_threads}")
+        print(f"[INFO] Max voxels per chunk: {chunk_size} (→ {slices_per_chunk} slices) | Threads: {num_threads}")
 
-    # Filter shells if specified
     if bvals_to_use is not None:
         bvals_to_use = set(bvals_to_use)
         sel = np.isin(gtab.bvals, list(bvals_to_use))
         img_data = img_data[..., sel]
-        gtab = gradient_table(gtab.bvals[sel], gtab.bvecs[sel])
+        gtab = gradient_table(gtab.bvals[sel], bvecs=gtab.bvecs[sel])
         if verbose:
             print(f"[INFO] Selected b-values: {sorted(bvals_to_use)}")
             print(f"[INFO] Selected volumes: {sel.sum()} / {N}")
 
-    # Choose model
     def get_model(name, gtab, **params):
         if name == 'DTI':
             return dti.TensorModel(gtab, **params)
@@ -3736,14 +3741,13 @@ def efficient_dwi_fit(gtab, diffusion_model, imagein, maskin,
 
     model = get_model(diffusion_model, gtab, **model_params)
 
-    # Output volumes initialized to zero
     FA_vol = np.zeros((X, Y, Z), dtype=np.float32)
     MD_vol = np.zeros((X, Y, Z), dtype=np.float32)
     RGB_vol = np.zeros((X, Y, Z, 3), dtype=np.float32)
     has_tensor_metrics = diffusion_model in ['DTI', 'FreeWater']
 
     def process_chunk(z_start):
-        z_end = min(Z, z_start + chunk_size)
+        z_end = min(Z, z_start + slices_per_chunk)
         local_data = img_data[:, :, z_start:z_end, :]
         local_mask = mask[:, :, z_start:z_end]
         masked_data = local_data * local_mask[..., None]
@@ -3758,8 +3762,7 @@ def efficient_dwi_fit(gtab, diffusion_model, imagein, maskin,
             return z_start, z_end, FA, MD, RGB
         return z_start, z_end, None, None, None
 
-    # Run processing
-    chunks = range(0, Z, chunk_size)
+    chunks = range(0, Z, slices_per_chunk)
     if num_threads > 1:
         with ThreadPoolExecutor(max_workers=num_threads) as executor:
             futures = {executor.submit(process_chunk, z): z for z in chunks}
@@ -4455,7 +4458,7 @@ def dwi_deterministic_tracking(
     gtab = gradient_table(bvals, bvecs=bvecs, atol=2.0 )
     if mask is None:
         mask = ants.threshold_image( fa, fa_thresh, 2.0 ).iMath("GetLargestComponent")
-    dwi_data = dwi.numpy() # dwi_img.get_fdata()
+    dwi_data = dwi.numpy()
     dwi_mask = mask.numpy() == 1
     dti_model = dti.TensorModel(gtab,fit_method=fit_method)
     if verbose:

{antspymm-1.5.1.dist-info → antspymm-1.5.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: antspymm
-Version: 1.5.1
+Version: 1.5.3
 Summary: multi-channel/time-series medical image processing with antspyx
 Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache-2.0

antspymm-1.5.3.dist-info/RECORD

@@ -0,0 +1,7 @@
+antspymm/__init__.py,sha256=DnkidUfEu3Dl0tuWNTA-9VOUkBtH_cROKiPGNNXNagU,4637
+antspymm/mm.py,sha256=8iZxrWenPeLhwc1dxDgvAhgNGZHOahTi1LegOhmHkL8,527319
+antspymm-1.5.3.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+antspymm-1.5.3.dist-info/METADATA,sha256=pfNoP9vDefzKmOfRYk5z68qAJXXSmY2ELLLaRioiSHs,25939
+antspymm-1.5.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+antspymm-1.5.3.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
+antspymm-1.5.3.dist-info/RECORD,,

antspymm-1.5.1.dist-info/RECORD

@@ -1,7 +0,0 @@
-antspymm/__init__.py,sha256=DnkidUfEu3Dl0tuWNTA-9VOUkBtH_cROKiPGNNXNagU,4637
-antspymm/mm.py,sha256=oPHhV70IhFXCKI26rP5HgKpkb2OjqCWkqoy4cSxJXqA,526866
-antspymm-1.5.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-antspymm-1.5.1.dist-info/METADATA,sha256=_I4UmZGWLM6KkmTJc21wKW1DrjT2TY723C1jr7LA3Fw,25939
-antspymm-1.5.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-antspymm-1.5.1.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
-antspymm-1.5.1.dist-info/RECORD,,