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Fix save path for v1 types df
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Lines changed: 2 additions & 2 deletions

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src/xenium_analysis_tools/map_xenium/map_sections.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -53,15 +53,15 @@ def get_v1_merfish_cells(abc_cache=None, df_path=None):
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# Get MERFISH CCF metadata
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print('V1 cell df not found, generating new one...')
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if abc_cache is None:
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raise ValueError("abc_cache must be provided if output_path does not exist")
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raise ValueError("abc_cache must be provided if path to df does not exist")
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merfish_ccf_metadata = abc_cache.get_metadata_dataframe(
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directory='MERFISH-C57BL6J-638850-CCF',
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file_name='cell_metadata_with_parcellation_annotation'
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).set_index('cell_label')
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v1_merfish_cells = merfish_ccf_metadata.loc[merfish_ccf_metadata['parcellation_structure']=='VISp']
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# Save created df
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print(f"Saving df to: {df_path}")
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v1_merfish_cells.to_csv(output_path)
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v1_merfish_cells.to_csv(df_path)
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return v1_merfish_cells
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def get_nodes_to_drop(cells_df, abc_cache, h_level='subclass', min_cells=0):

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