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Update parameter name for get_v1_merfish_cells function
1 parent 9755161 commit 24471ac

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Lines changed: 2 additions & 2 deletions

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src/xenium_analysis_tools/map_xenium/map_dataset_sections.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -109,7 +109,7 @@ def map_sections(dataset_name: str, config_path: str=None, select_sections: list
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v1_types_path = Path(paths['scratch_root']) / v1_types_df_name
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else:
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v1_types_path = None
112-
v1_merfish_cells = get_v1_merfish_cells(abc_cache, output_path=v1_types_path)
112+
v1_merfish_cells = get_v1_merfish_cells(abc_cache, df_path=v1_types_path)
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v1_nodes_to_drop = get_nodes_to_drop(v1_merfish_cells, abc_cache, h_level=h_level, min_cells=min_cells)
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logger.info(f"Dropping {len(v1_nodes_to_drop)} {h_level} nodes not present in V1 MERFISH data with at least {min_cells} cells.")
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nodes_to_drop.extend(v1_nodes_to_drop)
@@ -195,4 +195,4 @@ def map_sections(dataset_name: str, config_path: str=None, select_sections: list
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for name, error in failed_sections:
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print(f" - {name}: {error}")
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198-
logger.info(f"Pipeline completed. Success: {len(successful_sections)}, Failed: {len(failed_sections)}")
198+
logger.info(f"Pipeline completed. Success: {len(successful_sections)}, Failed: {len(failed_sections)}")

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