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Is any mapping from patch index to spot index? #83

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windygoo opened this issue Dec 31, 2024 · 0 comments

windygoo commented Dec 31, 2024 •

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with h5py.File(f'patches/{lung_files[0][:-5]}.h5') as f:
    img = f['img'][:]
    coords = f['coords'][:]
    downsample = dict(f['img'].attrs)['downsample']
    
with h5py.File(f'st/{lung_files[0][:-5]}.h5ad') as f:
    gene_names = f['var']['_index']
    spot_coords = f['obsm']['spatial']

np.where(np.all(spot_coords == (coords[[0]] + 224 * downsample // 2).astype(int), axis=1))

The last line in the codes seems a solution but I am worried about its universality.

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