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Fix the streamline_id wrong size, harmonize double quote #1315

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Merged
arnaudbore merged 1 commit into from
Mar 5, 2026
Merged

Fix the streamline_id wrong size, harmonize double quote #1315

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92 changes: 46 additions & 46 deletions src/scilpy/segment/voting_scheme.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
import warnings

from dipy.io.streamline import save_tractogram, load_tractogram
from dipy.io.stateful_tractogram import StatefulTractogram
from dipy.segment.clustering import qbx_and_merge
from dipy.tracking.streamline import transform_streamlines
import nibabel as nib
Expand All @@ -21,7 +22,7 @@
from scilpy.segment.bundleseg import BundleSeg
from scilpy.utils import get_duration

logger = logging.getLogger('BundleSeg')
logger = logging.getLogger("BundleSeg")

# These parameters are leftovers from Recobundles.
# Now with BundleSeg, they do not need to be modified.
Expand Down Expand Up @@ -94,8 +95,8 @@ def _load_bundles_dictionary(self):
if len(tmp_list) > 0:
bundles_filepath.append(tmp_list)

logger.info(f'{len(self.atlas_dir)} sub-model directories were found. '
f'with {len(bundle_names)} model bundles total')
logger.info(f"{len(self.atlas_dir)} sub-model directories were found. "
f"with {len(bundle_names)} model bundles total")

model_bundles_dict = {}
bundle_counts = []
Expand Down Expand Up @@ -193,23 +194,34 @@ def _save_recognized_bundles(self, input_tractograms_path, reference,

if len(streamlines_id) == 0:
streamlines_id = np.array([], dtype=np.uint32)
logger.info(f'{bundle_names[bundle_id]} final recognition got '
f'{len(streamlines_id)} streamlines')
logger.info(f"{bundle_names[bundle_id]} final recognition got "
f"{len(streamlines_id)} streamlines")

scores = np.array([], dtype=np.float16)
if len(streamlines_id) > 0:
scores = bundles_wise_score[bundle_id,
streamlines_id].flatten()

results_dict[basename] = {"indices": streamlines_id.tolist(),
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@frheault frheault Mar 5, 2026

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This is where the important change is.

"scores": scores.tolist()}
else:
streamlines_id = np.array(
results_dict[basename]['indices'])
results_dict[basename]["indices"])

# Need to make sure the indices are valid for this sft
# Convert back to local indices (for this sft)
if len(sft) and len(streamlines_id):
# Convert back to local indices (for this sft)
streamlines_id = streamlines_id[streamlines_id >= tot_sft_len]
streamlines_id = streamlines_id[streamlines_id < tot_sft_len + curr_sft_len]
streamlines_id = streamlines_id[streamlines_id <
tot_sft_len + curr_sft_len]
else:
continue

# If the user asked to ignore metadata, remove it (simpler)
new_sft = sft[streamlines_id - tot_sft_len]
if self.ignore_metadata:
new_sft.data_per_point = {}
new_sft.data_per_streamline = {}
if len(streamlines_id) > 0:
new_sft = sft[streamlines_id - tot_sft_len]
else:
new_sft = StatefulTractogram.from_sft([], sft)

if basename in results_sft:
try:
Expand All @@ -221,18 +233,6 @@ def _save_recognized_bundles(self, input_tractograms_path, reference,
f"try --ignore_metadata.")
else:
results_sft[basename] = new_sft

# Populate the results dictionary (will be saved as json)
curr_results_dict = {}
curr_results_dict['indices'] = streamlines_id.tolist()

if len(streamlines_id) > 0:
scores = bundles_wise_score[bundle_id,
streamlines_id].flatten()
else:
scores = np.array([], dtype=np.float16)
curr_results_dict['scores'] = scores.tolist()
results_dict[basename] = curr_results_dict
tot_sft_len += len(sft)

# Once everything is done, save all bundles, at the moment only
Expand All @@ -242,10 +242,10 @@ def _save_recognized_bundles(self, input_tractograms_path, reference,
if len(sft) > 0 or self.save_empty:
sft.remove_invalid_streamlines()
save_tractogram(sft, os.path.join(self.output_directory,
basename + extension))
basename + extension))

out_logfile = os.path.join(self.output_directory, 'results.json')
with open(out_logfile, 'w') as outfile:
out_logfile = os.path.join(self.output_directory, "results.json")
with open(out_logfile, "w") as outfile:
json.dump(results_dict, outfile)

def __call__(self, input_tractograms_path, nbr_processes=1, seed=None,
Expand Down Expand Up @@ -273,9 +273,9 @@ def __call__(self, input_tractograms_path, nbr_processes=1, seed=None,
nib.streamlines.load(in_tractogram).streamlines)
len_wb_streamlines = len(wb_streamlines)

logger.debug(f'Tractogram {input_tractograms_path} with '
f'{len_wb_streamlines} streamlines '
f'is loaded in {get_duration(load_timer)} seconds')
logger.debug(f"Tractogram {input_tractograms_path} with "
f"{len_wb_streamlines} streamlines "
f"is loaded in {get_duration(load_timer)} seconds")

total_timer = time()
# Each type of bundle is processed separately
Expand All @@ -298,12 +298,12 @@ def __call__(self, input_tractograms_path, nbr_processes=1, seed=None,
clusters_indices = ArraySequence(clusters_indices)
clusters_indices._data = clusters_indices._data.astype(np.uint32)

logger.info(f'QBx with seed {seed} at {TCT}mm took '
f'{get_duration(cluster_timer)}sec. gave '
f'{len(cluster_map.centroids)} centroids')
logger.info(f"QBx with seed {seed} at {TCT}mm took "
f"{get_duration(cluster_timer)}sec. gave "
f"{len(cluster_map.centroids)} centroids")

tmp_dir, tmp_memmap_filenames = streamlines_to_memmap(wb_streamlines,
'float16')
"float16")

# Memory cleanup (before multiprocessing)
cluster_map.refdata = None
Expand Down Expand Up @@ -331,8 +331,8 @@ def __call__(self, input_tractograms_path, nbr_processes=1, seed=None,
pool.close()
pool.join()

logger.info(f'BundleSeg took {get_duration(total_timer)} sec. for '
f'{len(bundle_names)} bundles from {len(self.atlas_dir)} atlas')
logger.info(f"BundleSeg took {get_duration(total_timer)} sec. for "
f"{len(bundle_names)} bundles from {len(self.atlas_dir)} atlas")

bundles_wise_vote = np.zeros((len(bundle_names),
len_wb_streamlines),
Expand Down Expand Up @@ -369,10 +369,10 @@ def __call__(self, input_tractograms_path, nbr_processes=1, seed=None,
minimum_vote, ext)
tmp_dir.cleanup()
saved_bundles = [f for f in os.listdir(self.output_directory)
if os.path.splitext(f)[1] in ['.trk', '.tck']]
logger.info(f'Saving of {len(saved_bundles)} files in '
f'{self.output_directory} took '
f'{get_duration(save_timer)} sec.')
if os.path.splitext(f)[1] in [".trk", ".tck"]]
logger.info(f"Saving of {len(saved_bundles)} files in "
f"{self.output_directory} took "
f"{get_duration(save_timer)} sec.")


def single_recognize_parallel(args):
Expand Down Expand Up @@ -427,7 +427,7 @@ def single_recognize(args):
shorter_tag, ext = os.path.splitext(os.path.basename(model_filepath))

# Now hardcoded (not useful with FSS from Etienne)
slr_transform_type = 'similarity'
slr_transform_type = "similarity"

recognize_timer = time()
results = bsg.recognize(model_bundle,
Expand All @@ -438,11 +438,11 @@ def single_recognize(args):
recognized_indices, recognized_scores = results
del model_bundle._data, model_bundle

logger.info(f'Model {shorter_tag} recognized {len(recognized_indices)} '
'streamlines')
logger.debug(f'Model {model_filepath} with parameters tct={TCT}, mct={MCT}, '
f'bpt={bundle_pruning_thr} '
f'took {get_duration(recognize_timer)} sec.')
logger.info(f"Model {shorter_tag} recognized {len(recognized_indices)} "
"streamlines")
logger.debug(f"Model {model_filepath} with parameters tct={TCT}, mct={MCT}, "
f"bpt={bundle_pruning_thr} "
f"took {get_duration(recognize_timer)} sec.")

bundle_id = bundle_names.index(shorter_tag+ext)
return bundle_id, recognized_indices, recognized_scores