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Fixing princeton_mouse atlas mesh #253

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merged 3 commits into from
Mar 11, 2024
Merged

Fixing princeton_mouse atlas mesh #253

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9751b33
removing rotated_annotations to fix mesh orientation
viktorpm Mar 6, 2024
7338e45
set mesh scaling to True
viktorpm Mar 7, 2024
4cbc10c
remove unnecessary line
alessandrofelder Mar 11, 2024
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8 changes: 4 additions & 4 deletions brainglobe_atlasapi/atlas_generation/atlas_scripts/princeton_mouse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,9 +127,8 @@ def add_parent_id(child_id):
meshes_dir_path.mkdir(exist_ok=True)

tree = get_structures_tree(structs_dict)
rotated_annotations = np.rot90(annotated_volume, axes=(0, 2))

labels = np.unique(rotated_annotations).astype(np.int32)
labels = np.unique(annotated_volume).astype(np.int32)
for key, node in tree.nodes.items():
if key in labels:
is_label = True
Expand All @@ -153,7 +152,7 @@ def add_parent_id(child_id):
node,
tree,
labels,
rotated_annotations,
annotated_volume,
ROOT_ID,
closing_n_iters,
decimate_fraction,
Expand All @@ -177,7 +176,7 @@ def add_parent_id(child_id):
node,
tree,
labels,
rotated_annotations,
annotated_volume,
ROOT_ID,
closing_n_iters,
decimate_fraction,
Expand Down Expand Up @@ -232,6 +231,7 @@ def add_parent_id(child_id):
hemispheres_stack=None,
cleanup_files=False,
compress=True,
scale_meshes=True,
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Love a one-line fix 😁

)

return output_filename
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