Merge pull request #224 from EmmaRenauld/back_to_master_scilpy

Back to master scilpy

.gitignore

@@ -71,4 +71,5 @@ target/
 *.swo
 
 # dwi_ml stuff
-.ipynb_config/
+.ipynb_config/
+.ipynb_checkpoints/

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
 

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
 
 

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)

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

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
 

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)

requirements.txt

@@ -1,30 +1,38 @@
 # Supported for python 3.10
 # Should work for python > 3.8.
 
-# Scilpy and comet_ml both require requests. In comet: >=2.18.*,
-# which installs a version >2.28. Adding request version explicitely.
+# -------
+# Main dependency: scilpy
+#    Scilpy and comet_ml both require requests. In comet: >=2.18.*,
+#    which installs a version >2.28. Adding request version explicitely.
+# -------
 requests==2.28.*
+scilpy @ git+https://github.com/scilus/[email protected]
+
+
+# -------
+# Other important dependencies
+# -------
 bertviz~=1.4.0  # For transformer's visu
 torch==1.13.*
 tqdm==4.64.*
 comet-ml==3.21.*
 contextlib2==21.6.0
 jupyterlab>=3.6.2  # For transformer's visu
 IProgress>=0.4     # For jupyter with tdqm
-nested_lookup==0.2.25
-nose==1.3.*
-scilpy==1.5.post2
+nested_lookup==0.2.25  # For lists management
 
-## Necessary but should be installed with scilpy (Last check: 09/2023):
+# -------
+# Necessary but should be installed with scilpy (Last check: 01/2024):
+# -------
 future==0.18.*
 h5py==3.7.*   # h5py must absolutely be >2.4: that's when it became thread-safe
 matplotlib==3.6.*   # Hint: If matplotlib fails, you may try to install pyQt5.
-nibabel==4.0.*
+nibabel==5.2.*
 numpy==1.23.*
 scipy==1.9.*
 
 
-
 # --------------- Notes to developers
 # If we upgrade torch, verify if code copied in
 #     models.projects.transformers_from_torch has changed.