Make changes to follow latest scilpy architecture

scil-vital · Jan 17, 2024 · 99d3139 · 99d3139
1 parent c9d2185
commit 99d3139
Show file tree

Hide file tree

Showing 6 changed files with 12 additions and 10 deletions.
diff --git a/dwi_ml/data/processing/dwi/dwi.py b/dwi_ml/data/processing/dwi/dwi.py
@@ -5,8 +5,9 @@
 from dipy.reconst.shm import sph_harm_lookup
 import nibabel as nib
 import numpy as np
+
 from scilpy.io.utils import validate_sh_basis_choice
-from scilpy.reconst.raw_signal import compute_sh_coefficients
+from scilpy.reconst.sh import compute_sh_coefficients
 
 eps = 1e-6
 

diff --git a/dwi_ml/data/processing/streamlines/data_augmentation.py b/dwi_ml/data/processing/streamlines/data_augmentation.py
@@ -8,7 +8,8 @@
 from nibabel.streamlines.tractogram import (PerArrayDict, PerArraySequenceDict)
 import numpy as np
 
-from scilpy.tracking.tools import resample_streamlines_step_size
+from scilpy.tractograms.streamline_operations import \
+    resample_streamlines_step_size
 from scilpy.utils.streamlines import compress_sft
 
 

diff --git a/dwi_ml/data/processing/streamlines/post_processing.py b/dwi_ml/data/processing/streamlines/post_processing.py
@@ -6,7 +6,7 @@
 
 from scilpy.tractanalysis.tools import \
     extract_longest_segments_from_profile as segmenting_func
-from scilpy.tractanalysis.uncompress import uncompress
+from scilpy.tractograms.uncompress import uncompress
 
 # We could try using nan instead of zeros for non-existing previous dirs...
 DEFAULT_UNEXISTING_VAL = torch.zeros((1, 3), dtype=torch.float32)

diff --git a/dwi_ml/testing/projects/transformer_visualisation_utils.py b/dwi_ml/testing/projects/transformer_visualisation_utils.py
@@ -10,7 +10,8 @@
 
 from scilpy.io.streamlines import load_tractogram_with_reference
 from scilpy.io.utils import add_reference_arg, add_overwrite_arg, add_bbox_arg
-from scilpy.tracking.tools import resample_streamlines_step_size
+from scilpy.tractograms.streamline_operations import \
+    resample_streamlines_step_size
 from scilpy.utils.streamlines import compress_sft
 
 from dwi_ml.io_utils import add_logging_arg

diff --git a/dwi_ml/tracking/io_utils.py b/dwi_ml/tracking/io_utils.py
@@ -129,18 +129,18 @@ def prepare_seed_generator(parser, args, hdf_handle):
     seed_generator = SeedGenerator(seed_data, seed_res, space=ALWAYS_VOX_SPACE,
                                    origin=ALWAYS_CORNER)
 
-    if len(seed_generator.seeds_vox) == 0:
+    if len(seed_generator.seeds_vox_corner) == 0:
         parser.error('Seed mask "{}" does not have any voxel with value > 0.'
                      .format(args.in_seed))
 
     if args.npv:
         # Note. Not really nb seed per voxel, just in average.
-        nbr_seeds = len(seed_generator.seeds_vox) * args.npv
+        nbr_seeds = len(seed_generator.seeds_vox_corner) * args.npv
     elif args.nt:
         nbr_seeds = args.nt
     else:
         # Setting npv = 1.
-        nbr_seeds = len(seed_generator.seeds_vox)
+        nbr_seeds = len(seed_generator.seeds_vox_corner)
 
     seed_header = nib.Nifti1Image(seed_data, affine).header
 

diff --git a/dwi_ml/tracking/tracker.py b/dwi_ml/tracking/tracker.py
@@ -399,10 +399,9 @@ def _gpu_simultaneous_tracking(self):
                 if seed_count + nb_next_seeds > self.nbr_seeds:
                     nb_next_seeds = self.nbr_seeds - seed_count
 
-                next_seeds = np.arange(seed_count, seed_count + nb_next_seeds)
-
                 n_seeds = self.seed_generator.get_next_n_pos(
-                    random_generator, indices, next_seeds)
+                    random_generator, indices, which_seed_start=seed_count,
+                    n=nb_next_seeds)
 
                 tmp_lines, tmp_seeds = \
                     self._get_multiple_lines_both_directions(n_seeds)