antspymm 1.5.4__py3-none-any.whl → 1.5.6__py3-none-any.whl

antspymm/__init__.py

@@ -65,6 +65,8 @@ from .mm import mc_denoise
 from .mm import mc_reg
 from .mm import dti_reg
 from .mm import timeseries_reg
+from .mm import timeseries_transform
+from .mm import copy_spatial_metadata_from_3d_to_4d
 from .mm import concat_dewarp
 from .mm import mc_resample_image_to_target
 from .mm import trim_dti_mask
@@ -136,5 +138,7 @@ from .mm import segment_timeseries_by_bvalue
 from .mm import shorten_pymm_names
 from .mm import pet3d_summary
 from .mm import deformation_gradient_optimized
+from .mm import efficient_dwi_fit_voxelwise
+from .mm import generate_voxelwise_bvecs
 
 

antspymm/mm.py

@@ -1794,6 +1794,89 @@ def merge_timeseries_data( img_LR, img_RL, allow_resample=True ):
         mimg.append( temp )
     return ants.list_to_ndimage( img_LR, mimg )
 
+def copy_spatial_metadata_from_3d_to_4d(spatial_img, timeseries_img):
+    """
+    Copy spatial metadata (origin, spacing, direction) from a 3D image to the
+    spatial dimensions (first 3) of a 4D image, preserving the 4th dimension's metadata.
+
+    Parameters
+    ----------
+    spatial_img : ants.ANTsImage
+        A 3D ANTsImage with the desired spatial metadata.
+    timeseries_img : ants.ANTsImage
+        A 4D ANTsImage to update.
+
+    Returns
+    -------
+    ants.ANTsImage
+        A 4D ANTsImage with updated spatial metadata.
+    """
+    if spatial_img.dimension != 3:
+        raise ValueError("spatial_img must be a 3D ANTsImage.")
+    if timeseries_img.dimension != 4:
+        raise ValueError("timeseries_img must be a 4D ANTsImage.")
+    # Get 3D metadata
+    spatial_origin = list(spatial_img.origin)
+    spatial_spacing = list(spatial_img.spacing)
+    spatial_direction = spatial_img.direction  # 3x3
+    # Get original 4D metadata
+    ts_spacing = list(timeseries_img.spacing)
+    ts_origin = list(timeseries_img.origin)
+    ts_direction = timeseries_img.direction  # 4x4
+    # Replace only the first 3 entries for origin and spacing
+    new_origin = spatial_origin + [ts_origin[3]]
+    new_spacing = spatial_spacing + [ts_spacing[3]]
+    # Replace top-left 3x3 block of direction matrix, preserve last row/column
+    new_direction = ts_direction.copy()
+    new_direction[:3, :3] = spatial_direction
+    # Create updated image
+    updated_img = ants.from_numpy(
+        timeseries_img.numpy(),
+        origin=new_origin,
+        spacing=new_spacing,
+        direction=new_direction
+    )
+    return updated_img
+
+def timeseries_transform(transform, image, reference, interpolation='linear'):
+    """
+    Apply a spatial transform to each 3D volume in a 4D time series image.
+
+    Parameters
+    ----------
+    transform : ants transform object
+        Path(s) to ANTs-compatible transform(s) to apply.
+    image : ants.ANTsImage
+        4D input image with shape (X, Y, Z, T).
+    reference : ants.ANTsImage
+        Reference image to match in space.
+    interpolation : str
+        Interpolation method: 'linear', 'nearestNeighbor', etc.
+
+    Returns
+    -------
+    ants.ANTsImage
+        4D transformed image.
+    """
+    if image.dimension != 4:
+        raise ValueError("Input image must be 4D (X, Y, Z, T).")
+    n_volumes = image.shape[3]
+    transformed_volumes = []
+    for t in range(n_volumes):
+        vol = ants.slice_image( image, 3, t )
+        transformed = ants.apply_ants_transform_to_image(
+            transform=transform,
+            image=vol,
+            reference=reference,
+            interpolation=interpolation
+        )
+        transformed_volumes.append(transformed.numpy())
+    # Stack along time axis and convert to ANTsImage
+    transformed_array = np.stack(transformed_volumes, axis=-1)
+    out_image = ants.from_numpy(transformed_array)
+    out_image = ants.copy_image_info(image, out_image)
+    out_image = copy_spatial_metadata_from_3d_to_4d(reference, out_image)
+    return out_image
 
 def timeseries_reg(
     image,
@@ -3932,6 +4015,135 @@ def efficient_dwi_fit(gtab, diffusion_model, imagein, maskin,
     return full_fit, FA_img, MD_img, RGB_img
 
 
+def efficient_dwi_fit_voxelwise(imagein, maskin, bvals, bvecs_5d, model_params=None,
+                                bvals_to_use=None, num_threads=1, verbose=True):
+    """
+    Voxel-wise diffusion model fitting with individual b-vectors per voxel.
+
+    Parameters
+    ----------
+    imagein : ants.ANTsImage
+        4D DWI image (X, Y, Z, N).
+    maskin : ants.ANTsImage
+        3D binary mask.
+    bvals : (N,) array-like
+        Common b-values across volumes.
+    bvecs_5d : (X, Y, Z, N, 3) ndarray
+        Voxel-specific b-vectors.
+    model_params : dict
+        Extra arguments for model.
+    bvals_to_use : list[int]
+        Subset of b-values to include.
+    num_threads : int
+        Number of threads to use.
+    verbose : bool
+        Whether to print status.
+
+    Returns
+    -------
+    FA_img : ants.ANTsImage
+        Fractional anisotropy.
+    MD_img : ants.ANTsImage
+        Mean diffusivity.
+    RGB_img : ants.ANTsImage
+        RGB FA image.
+    """
+    import numpy as np
+    import ants
+    import dipy.reconst.dti as dti
+    from dipy.core.gradients import gradient_table
+    from dipy.reconst.dti import fractional_anisotropy, color_fa, mean_diffusivity
+    from concurrent.futures import ThreadPoolExecutor
+    from tqdm import tqdm
+
+    model_params = model_params or {}
+    img = imagein.numpy()
+    mask = maskin.numpy().astype(bool)
+    X, Y, Z, N = img.shape
+
+    if bvals_to_use is not None:
+        sel = np.isin(bvals, bvals_to_use)
+        img = img[..., sel]
+        bvals = bvals[sel]
+        bvecs_5d = bvecs_5d[..., sel, :]
+
+    FA = np.zeros((X, Y, Z), dtype=np.float32)
+    MD = np.zeros((X, Y, Z), dtype=np.float32)
+    RGB = np.zeros((X, Y, Z, 3), dtype=np.float32)
+
+    def fit_voxel(ix, iy, iz):
+        if not mask[ix, iy, iz]:
+            return
+        sig = img[ix, iy, iz, :]
+        if np.all(sig == 0):
+            return
+        bv = bvecs_5d[ix, iy, iz, :, :]
+        gtab = gradient_table(bvals, bv)
+        try:
+            model = dti.TensorModel(gtab, **model_params)
+            fit = model.fit(sig)
+            evals = fit.evals
+            evecs = fit.evecs
+            FA[ix, iy, iz] = fractional_anisotropy(evals)
+            MD[ix, iy, iz] = mean_diffusivity(evals)
+            RGB[ix, iy, iz, :] = color_fa(FA[ix, iy, iz], evecs)
+        except Exception as e:
+            if verbose:
+                print(f"Voxel ({ix},{iy},{iz}) fit failed: {e}")
+
+    coords = np.argwhere(mask)
+    if verbose:
+        print(f"[INFO] Fitting {len(coords)} voxels using {num_threads} threads...")
+
+    if num_threads > 1:
+        with ThreadPoolExecutor(max_workers=num_threads) as executor:
+            list(tqdm(executor.map(lambda c: fit_voxel(*c), coords), total=len(coords)))
+    else:
+        for c in tqdm(coords):
+            fit_voxel(*c)
+
+    ref = ants.slice_image(imagein, axis=3, idx=0)
+    return (
+        ants.copy_image_info(ref, ants.from_numpy(FA)),
+        ants.copy_image_info(ref, ants.from_numpy(MD)),
+        ants.merge_channels([ants.copy_image_info(ref, ants.from_numpy(RGB[..., i])) for i in range(3)])
+    )
+
+
+def generate_voxelwise_bvecs(global_bvecs, voxel_rotations, transpose=False):
+    """
+    Generate voxel-wise b-vectors from a global bvec and voxel-wise rotation field.
+
+    Parameters
+    ----------
+    global_bvecs : ndarray of shape (N, 3)
+        Global diffusion gradient directions.
+    voxel_rotations : ndarray of shape (X, Y, Z, 3, 3)
+        3x3 rotation matrix for each voxel (can come from Jacobian of deformation field).
+    transpose : bool, optional
+        If True, transpose the rotation matrices before applying them to the b-vectors.
+
+
+    Returns
+    -------
+    bvecs_5d : ndarray of shape (X, Y, Z, N, 3)
+        Voxel-specific b-vectors.
+    """
+    X, Y, Z, _, _ = voxel_rotations.shape
+    N = global_bvecs.shape[0]
+    bvecs_5d = np.zeros((X, Y, Z, N, 3), dtype=np.float32)
+
+    for n in range(N):
+        bvec = global_bvecs[n]
+        for i in range(X):
+            for j in range(Y):
+                for k in range(Z):
+                    R = voxel_rotations[i, j, k]
+                    if transpose:
+                        R = R.T  # Use transpose if needed
+                    bvecs_5d[i, j, k, n, :] = R @ bvec
+    return bvecs_5d
+
 def dipy_dti_recon(
     image,
     bvalsfn,
@@ -7434,7 +7646,7 @@ def mm(
     if do_kk:
         if verbose:
             print('kk')
-        output_dict['kk'] = antspyt1w.kelly_kapowski_thickness( hier['brain_n4_dnz'],
+        output_dict['kk'] = antspyt1w.kelly_kapowski_thickness( t1atropos,
             labels=hier['dkt_parc']['dkt_cortex'], iterations=45 )
     if perfusion_image is not None:
         if perfusion_image.shape[3] > 1: # FIXME - better heuristic?

{antspymm-1.5.4.dist-info → antspymm-1.5.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: antspymm
-Version: 1.5.4
+Version: 1.5.6
 Summary: multi-channel/time-series medical image processing with antspyx
 Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache-2.0
@@ -9,20 +9,18 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
-License-File: LICENSE
 Requires-Dist: h5py>=2.10.0
 Requires-Dist: numpy>=1.19.4
 Requires-Dist: pandas>=1.0.1
 Requires-Dist: antspyx>=0.4.2
-Requires-Dist: antspynet>=0.2.8
-Requires-Dist: antspyt1w>=0.9.3
+Requires-Dist: antspynet>=0.2.9
+Requires-Dist: antspyt1w>=0.9.8
 Requires-Dist: pathlib
 Requires-Dist: dipy
 Requires-Dist: nibabel
 Requires-Dist: scipy
 Requires-Dist: siq
 Requires-Dist: scikit-learn
-Dynamic: license-file
 
 # ANTsPyMM
 

antspymm-1.5.6.dist-info/RECORD

@@ -0,0 +1,6 @@
+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,,

antspymm-1.5.4.dist-info/RECORD

@@ -1,7 +0,0 @@
-antspymm/__init__.py,sha256=hynrdvZDlPQ0Wam8tU6mBtbEk0Worwz_bLZk9N7N1CM,4684
-antspymm/mm.py,sha256=e4BTBarPnlk3RlqMAPOp6wcGZxv5ufSA1GxuKi3oiJw,536471
-antspymm-1.5.4.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-antspymm-1.5.4.dist-info/METADATA,sha256=2NNkAHHTSMIhla6KURkKU39w9CqxWrDshuHzOI2kMdc,26051
-antspymm-1.5.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-antspymm-1.5.4.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
-antspymm-1.5.4.dist-info/RECORD,,

antspymm-1.5.4.dist-info/licenses/LICENSE

@@ -1,201 +0,0 @@
-                                 Apache License
-                           Version 2.0, January 2004
-                        http://www.apache.org/licenses/
-
-   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
-
-   1. Definitions.
-
-      "License" shall mean the terms and conditions for use, reproduction,
-      and distribution as defined by Sections 1 through 9 of this document.
-
-      "Licensor" shall mean the copyright owner or entity authorized by
-      the copyright owner that is granting the License.
-
-      "Legal Entity" shall mean the union of the acting entity and all
-      other entities that control, are controlled by, or are under common
-      control with that entity. For the purposes of this definition,
-      "control" means (i) the power, direct or indirect, to cause the
-      direction or management of such entity, whether by contract or
-      otherwise, or (ii) ownership of fifty percent (50%) or more of the
-      outstanding shares, or (iii) beneficial ownership of such entity.
-
-      "You" (or "Your") shall mean an individual or Legal Entity
-      exercising permissions granted by this License.
-
-      "Source" form shall mean the preferred form for making modifications,
-      including but not limited to software source code, documentation
-      source, and configuration files.
-
-      "Object" form shall mean any form resulting from mechanical
-      transformation or translation of a Source form, including but
-      not limited to compiled object code, generated documentation,
-      and conversions to other media types.
-
-      "Work" shall mean the work of authorship, whether in Source or
-      Object form, made available under the License, as indicated by a
-      copyright notice that is included in or attached to the work
-      (an example is provided in the Appendix below).
-
-      "Derivative Works" shall mean any work, whether in Source or Object
-      form, that is based on (or derived from) the Work and for which the
-      editorial revisions, annotations, elaborations, or other modifications
-      represent, as a whole, an original work of authorship. For the purposes
-      of this License, Derivative Works shall not include works that remain
-      separable from, or merely link (or bind by name) to the interfaces of,
-      the Work and Derivative Works thereof.
-
-      "Contribution" shall mean any work of authorship, including
-      the original version of the Work and any modifications or additions
-      to that Work or Derivative Works thereof, that is intentionally
-      submitted to Licensor for inclusion in the Work by the copyright owner
-      or by an individual or Legal Entity authorized to submit on behalf of
-      the copyright owner. For the purposes of this definition, "submitted"
-      means any form of electronic, verbal, or written communication sent
-      to the Licensor or its representatives, including but not limited to
-      communication on electronic mailing lists, source code control systems,
-      and issue tracking systems that are managed by, or on behalf of, the
-      Licensor for the purpose of discussing and improving the Work, but
-      excluding communication that is conspicuously marked or otherwise
-      designated in writing by the copyright owner as "Not a Contribution."
-
-      "Contributor" shall mean Licensor and any individual or Legal Entity
-      on behalf of whom a Contribution has been received by Licensor and
-      subsequently incorporated within the Work.
-
-   2. Grant of Copyright License. Subject to the terms and conditions of
-      this License, each Contributor hereby grants to You a perpetual,
-      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
-      copyright license to reproduce, prepare Derivative Works of,
-      publicly display, publicly perform, sublicense, and distribute the
-      Work and such Derivative Works in Source or Object form.
-
-   3. Grant of Patent License. Subject to the terms and conditions of
-      this License, each Contributor hereby grants to You a perpetual,
-      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
-      (except as stated in this section) patent license to make, have made,
-      use, offer to sell, sell, import, and otherwise transfer the Work,
-      where such license applies only to those patent claims licensable
-      by such Contributor that are necessarily infringed by their
-      Contribution(s) alone or by combination of their Contribution(s)
-      with the Work to which such Contribution(s) was submitted. If You
-      institute patent litigation against any entity (including a
-      cross-claim or counterclaim in a lawsuit) alleging that the Work
-      or a Contribution incorporated within the Work constitutes direct
-      or contributory patent infringement, then any patent licenses
-      granted to You under this License for that Work shall terminate
-      as of the date such litigation is filed.
-
-   4. Redistribution. You may reproduce and distribute copies of the
-      Work or Derivative Works thereof in any medium, with or without
-      modifications, and in Source or Object form, provided that You
-      meet the following conditions:
-
-      (a) You must give any other recipients of the Work or
-          Derivative Works a copy of this License; and
-
-      (b) You must cause any modified files to carry prominent notices
-          stating that You changed the files; and
-
-      (c) You must retain, in the Source form of any Derivative Works
-          that You distribute, all copyright, patent, trademark, and
-          attribution notices from the Source form of the Work,
-          excluding those notices that do not pertain to any part of
-          the Derivative Works; and
-
-      (d) If the Work includes a "NOTICE" text file as part of its
-          distribution, then any Derivative Works that You distribute must
-          include a readable copy of the attribution notices contained
-          within such NOTICE file, excluding those notices that do not
-          pertain to any part of the Derivative Works, in at least one
-          of the following places: within a NOTICE text file distributed
-          as part of the Derivative Works; within the Source form or
-          documentation, if provided along with the Derivative Works; or,
-          within a display generated by the Derivative Works, if and
-          wherever such third-party notices normally appear. The contents
-          of the NOTICE file are for informational purposes only and
-          do not modify the License. You may add Your own attribution
-          notices within Derivative Works that You distribute, alongside
-          or as an addendum to the NOTICE text from the Work, provided
-          that such additional attribution notices cannot be construed
-          as modifying the License.
-
-      You may add Your own copyright statement to Your modifications and
-      may provide additional or different license terms and conditions
-      for use, reproduction, or distribution of Your modifications, or
-      for any such Derivative Works as a whole, provided Your use,
-      reproduction, and distribution of the Work otherwise complies with
-      the conditions stated in this License.
-
-   5. Submission of Contributions. Unless You explicitly state otherwise,
-      any Contribution intentionally submitted for inclusion in the Work
-      by You to the Licensor shall be under the terms and conditions of
-      this License, without any additional terms or conditions.
-      Notwithstanding the above, nothing herein shall supersede or modify
-      the terms of any separate license agreement you may have executed
-      with Licensor regarding such Contributions.
-
-   6. Trademarks. This License does not grant permission to use the trade
-      names, trademarks, service marks, or product names of the Licensor,
-      except as required for reasonable and customary use in describing the
-      origin of the Work and reproducing the content of the NOTICE file.
-
-   7. Disclaimer of Warranty. Unless required by applicable law or
-      agreed to in writing, Licensor provides the Work (and each
-      Contributor provides its Contributions) on an "AS IS" BASIS,
-      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
-      implied, including, without limitation, any warranties or conditions
-      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
-      PARTICULAR PURPOSE. You are solely responsible for determining the
-      appropriateness of using or redistributing the Work and assume any
-      risks associated with Your exercise of permissions under this License.
-
-   8. Limitation of Liability. In no event and under no legal theory,
-      whether in tort (including negligence), contract, or otherwise,
-      unless required by applicable law (such as deliberate and grossly
-      negligent acts) or agreed to in writing, shall any Contributor be
-      liable to You for damages, including any direct, indirect, special,
-      incidental, or consequential damages of any character arising as a
-      result of this License or out of the use or inability to use the
-      Work (including but not limited to damages for loss of goodwill,
-      work stoppage, computer failure or malfunction, or any and all
-      other commercial damages or losses), even if such Contributor
-      has been advised of the possibility of such damages.
-
-   9. Accepting Warranty or Additional Liability. While redistributing
-      the Work or Derivative Works thereof, You may choose to offer,
-      and charge a fee for, acceptance of support, warranty, indemnity,
-      or other liability obligations and/or rights consistent with this
-      License. However, in accepting such obligations, You may act only
-      on Your own behalf and on Your sole responsibility, not on behalf
-      of any other Contributor, and only if You agree to indemnify,
-      defend, and hold each Contributor harmless for any liability
-      incurred by, or claims asserted against, such Contributor by reason
-      of your accepting any such warranty or additional liability.
-
-   END OF TERMS AND CONDITIONS
-
-   APPENDIX: How to apply the Apache License to your work.
-
-      To apply the Apache License to your work, attach the following
-      boilerplate notice, with the fields enclosed by brackets "[]"
-      replaced with your own identifying information. (Don't include
-      the brackets!)  The text should be enclosed in the appropriate
-      comment syntax for the file format. We also recommend that a
-      file or class name and description of purpose be included on the
-      same "printed page" as the copyright notice for easier
-      identification within third-party archives.
-
-   Copyright [yyyy] [name of copyright owner]
-
-   Licensed under the Apache License, Version 2.0 (the "License");
-   you may not use this file except in compliance with the License.
-   You may obtain a copy of the License at
-
-       http://www.apache.org/licenses/LICENSE-2.0
-
-   Unless required by applicable law or agreed to in writing, software
-   distributed under the License is distributed on an "AS IS" BASIS,
-   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-   See the License for the specific language governing permissions and
-   limitations under the License.