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Bug fixes to re-release 0.4.3 #85

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Merged
francois-drielsma merged 3 commits into from
May 2, 2025
Merged

Bug fixes to re-release 0.4.3 #85

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a6a4725
Local DBSCAN does not play well with DDP (not picklable)
francois-drielsma May 2, 2025
7bf92fd
Bad cdist call in GNN cluster utils
francois-drielsma May 2, 2025
073b802
Flip end point direction to align with particle travel direction
francois-drielsma May 2, 2025
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11 changes: 7 additions & 4 deletions spine/io/parse/cluster.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@

import numpy as np

from spine.math.cluster import DBSCAN
from spine.math.distance import METRICS
from spine.math.cluster import dbscan

from spine.data import Meta

Expand Down Expand Up @@ -190,8 +191,8 @@ def __init__(self, dtype, particle_event=None, add_particle_info=False,

# Intialize DBSCAN if the clusters are to be broken up
self.break_clusters = break_clusters
if break_clusters:
self.dbscan = DBSCAN(break_eps, min_samples=1, metric=break_metric)
self.break_eps = break_eps
self.break_metric_id = METRICS[break_metric]

# Intialize the sparse and particle parsers
self.sparse_parser = Sparse3DParser(dtype, sparse_event='dummy')
Expand Down Expand Up @@ -337,7 +338,9 @@ def process(self, cluster_event, particle_event=None,

# If requested, break cluster into detached pieces
if self.break_clusters:
frag_labels = self.dbscan.fit_predict(voxels)
frag_labels = dbscan(
voxels, eps=self.break_eps, min_samples=1,
metric_id=self.break_metric_id)
features[1] = id_offset + frag_labels
id_offset += max(frag_labels) + 1

Expand Down
5 changes: 4 additions & 1 deletion spine/post/reco/direction.py
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Expand Up @@ -91,4 +91,7 @@ def process(self, data):

# Assign directions to the appropriate particles
for i, part_id in enumerate(part_ids):
setattr(data[k][part_id], attrs[i], dirs[i])
if attrs[i].startswith('start'):
setattr(data[k][part_id], attrs[i], dirs[i])
else:
setattr(data[k][part_id], attrs[i], -dirs[i])
2 changes: 1 addition & 1 deletion spine/utils/gnn/cluster.py
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Expand Up @@ -635,7 +635,7 @@ def _get_cluster_closest_primary_label(data: nb.float64[:,:],
# Minimize the point-cluster distances
dists = np.empty(len(group_index), dtype=data.dtype)
for i, c in enumerate(group_index):
dists[i] = np.min(sm.cdist(start_point, voxels[clusts[c]]))
dists[i] = np.min(sm.distance.cdist(start_point, voxels[clusts[c]]))

# Label the closest cluster as the only primary cluster
labels[group_index] = 0
Expand Down
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