[ENH] Update to dipy 1.13 - DO NOT MERGE -

.python-version

@@ -1,2 +1,2 @@
 3.12
->=3.10, < 3.13
+>=3.11, < 3.13

pyproject.toml

@@ -9,11 +9,11 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "scilpy"
-version = "2.2.2"
+version = "2.3.0"
 description = "Scilpy: diffusion MRI tools and utilities"
 authors = [{ name = "SCIL Team" }]
 readme = "README.md"
-requires-python = ">=3.10, <3.13"
+requires-python = ">=3.11, <3.13"
 license-files = ["LICENSE"]
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -31,7 +31,7 @@ dependencies = [
 "cvxpy==1.6.*",
 "cycler==0.12.*",
 "deepdiff>=8.1,<8.7",
-"dipy==1.11.*",
+"dipy==1.12.*",
 "dmri-amico==2.1.*",
 "dmri-commit>=2.4.2,<2.5.0",
 "docopt==0.6.*",

src/scilpy/cli/scil_denoising_nlmeans.py

@@ -187,7 +187,10 @@ def main():
     if args.sigma is not None:
         logging.info('User supplied noise standard deviation is {}'
                      .format(args.sigma))
-        sigma = np.ones(vol_data.shape[:3]) * args.sigma
+        if nb_volumes > 1:
+            sigma = np.full(nb_volumes, args.sigma, dtype=np.float32)
+        else:
+            sigma = float(args.sigma)
     elif args.basic_sigma:
         if args.mask_sigma:
             mask_sigma = get_data_as_mask(nib.load(args.mask_sigma))
@@ -206,8 +209,8 @@ def main():
         sigma = np.median(sigma)  # Managing 4D data.
         logging.info('The median noise is: {}'.format(sigma))
 
-        # Broadcast the single value to a whole 3D volume for nlmeans
-        sigma = np.ones(vol_data.shape) * sigma
+        if nb_volumes > 1:
+            sigma = np.full(nb_volumes, sigma, dtype=np.float32)
     else:  # --piesno
         logging.info("Computing sigma: one value per slice.")
         sigma, mask_noise = estimate_piesno_sigma(vol_data, args.number_coils)
@@ -219,14 +222,22 @@ def main():
                                      header=vol.header),
                      args.save_piesno_mask)
 
-        # Broadcast the values per slice to a whole 3D volume for nlmeans
+        # Keep a 3D sigma map (one value per slice) for PIESNO.
         sigma = np.ones(vol_data.shape[:3]) * sigma[None, None, :]
 
     with warnings.catch_warnings():
         warnings.simplefilter("ignore", category=DeprecationWarning)
-        data_denoised = nlmeans(
-            vol_data, sigma, mask=mask_denoise, rician=not args.gaussian,
-            num_threads=args.nbr_processes)
+        if vol_data.ndim == 4 and np.ndim(sigma) == 3:
+            data_denoised = np.empty_like(vol_data)
+            for vol_idx in range(vol_data.shape[-1]):
+                data_denoised[..., vol_idx] = nlmeans(
+                    vol_data[..., vol_idx], sigma,
+                    mask=mask_denoise, rician=not args.gaussian,
+                    num_threads=args.nbr_processes)
+        else:
+            data_denoised = nlmeans(
+                vol_data, sigma, mask=mask_denoise, rician=not args.gaussian,
+                num_threads=args.nbr_processes)
 
     # Saving
     nib.save(nib.Nifti1Image(data_denoised, vol.affine, header=vol.header),

src/scilpy/cli/tests/test_tractogram_convert.py

@@ -19,10 +19,10 @@ def test_help_option(script_runner):
 
 def test_execution_surface_vtk_fib(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_fib = os.path.join(SCILPY_HOME, 'surface_vtk_fib',
-                          'gyri_fanning.fib')
+    in_trk = os.path.join(SCILPY_HOME, 'surface_vtk_fib',
+                          'gyri_fanning.trk')
     in_fa = os.path.join(SCILPY_HOME, 'surface_vtk_fib',
                          'fa.nii.gz')
-    ret = script_runner.run(['scil_tractogram_convert', in_fib,
-                            'gyri_fanning.trk', '--reference', in_fa])
+    ret = script_runner.run(['scil_tractogram_convert', in_trk,
+                            'gyri_fanning converted.fib', '--reference', in_fa])
     assert ret.success

src/scilpy/cli/tests/test_tractogram_flip.py

@@ -19,10 +19,10 @@ def test_help_option(script_runner):
 
 def test_execution_surface_vtk_fib(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_fib = os.path.join(SCILPY_HOME, 'surface_vtk_fib',
-                          'gyri_fanning.fib')
+    in_trk = os.path.join(SCILPY_HOME, 'surface_vtk_fib',
+                          'gyri_fanning.trk')
     in_fa = os.path.join(SCILPY_HOME, 'surface_vtk_fib',
                          'fa.nii.gz')
-    ret = script_runner.run(['scil_tractogram_flip', in_fib,
-                             'gyri_fanning.tck', 'x', '--reference', in_fa])
+    ret = script_runner.run(['scil_tractogram_flip', in_trk,
+                             'gyri_fanning_fliped.tck', 'x', '--reference', in_fa])
     assert ret.success

src/scilpy/tractanalysis/tests/test_voxel_boundary_intersection.py

@@ -38,3 +38,18 @@ def test_subdivide():
 
     # streamline 3 should be split into 11 (12 points)
     assert split[2].shape[0] == 12
+
+
+def test_subdivide_float64_streamlines():
+    streamline = np.asarray([[0.0, 0.0, 0.0],
+                             [1.2, 0.5, 0.0]], dtype=np.float64)
+
+    fake_ref = nib.Nifti1Image(np.zeros((3, 3, 3)), affine=np.eye(4))
+    sft = StatefulTractogram([streamline], reference=fake_ref,
+                             origin=Origin('corner'), space=Space('vox'))
+
+    split = subdivide_streamlines_at_voxel_faces(sft.streamlines)
+
+    assert split[0].dtype == np.float32
+    assert np.allclose(split[0][0], streamline[0])
+    assert np.allclose(split[0][-1], streamline[-1])

src/scilpy/tractanalysis/voxel_boundary_intersection.pyx

@@ -45,13 +45,16 @@ def subdivide_streamlines_at_voxel_faces(streamlines):
         Updated streamline coordinates with added coordinate points
         at voxel boundaries.
     """
+    streamlines_data = np.ascontiguousarray(streamlines._data,
+                                            dtype=np.float32)
+
     cdef:
         cnp.npy_intp nb_streamlines = len(streamlines._lengths)
         cnp.npy_intp at_point = 0
 
         # Multiplying by 6 is simply a heuristic to avoiding resizing too many
         # times. In my bundles tests, I had either 0 or 1 resize.
-        cnp.npy_intp max_points = (streamlines.get_data().size // 6) * 12
+        cnp.npy_intp max_points = (streamlines_data.size // 6) * 12
 
     new_array_sequence = nib.streamlines.array_sequence.ArraySequence()
     new_array_sequence._lengths.resize(nb_streamlines)
@@ -61,7 +64,7 @@ def subdivide_streamlines_at_voxel_faces(streamlines):
     cdef:
         cnp.npy_intp[:] lengths_view_in = streamlines._lengths
         cnp.npy_intp[:] offsets_view_in = streamlines._offsets
-        float[:, :] data_view_in = streamlines._data
+        float[:, :] data_view_in = streamlines_data
         cnp.npy_intp[:] lengths_view_out = new_array_sequence._lengths
         cnp.npy_intp[:] offsets_view_out = new_array_sequence._offsets
         cnp.float32_t[:] data_view_out = new_array_sequence._data