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Cleanup unused code - #791
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ProposalGraph.__init__ accepted use_anisotropy via **kwargs but never passed it to FragmentsGraph, and ProofreadPipeline.load_graph did not forward GraphConfig.use_anisotropy either. The flag was therefore silently ignored and SWC coordinates were always scaled by the anisotropy on load, which is wrong for SWCs already in world coordinates such as pipeline outputs. Callers reading voxel-space SWCs must now pass use_anisotropy=True (the default) explicitly in their GraphConfig to keep scaling. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
SparseSearchDataset.estimate_iterations returned every branching node in the graph, but the dataset only visits fragments longer than min_search_size. The tqdm total was therefore inflated (45k vs 28k visited on one whole-brain graph) and the ETA pessimistic. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Move patch-loader construction, search_mode, and default step_size into class attributes handled by SearchDataset.__init__, and define the patch + rooted-subgraph input once as get_patch_and_subgraph (renamed from get_patch_and_arborist). The base class now defaults prefetch to 64. Co-Authored-By: Claude <noreply@anthropic.com>
…setConfig - Remove the old vision_models.py and gnn_models.py and promote new_vision_models.py / new_gnn_models.py to those names. - Move file, zip, GCS and S3 I/O from utils/util.py into utils/io_util.py and update callers. - Add DatasetConfig (brain_id, segmentation_id, img_path, fragments_path) and give ProposalsConfig a name so every config can be saved. Co-Authored-By: Claude <noreply@anthropic.com>
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