Distance table generation without segmentation masks #1159
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srivarra
approved these changes
Oct 2, 2024
| centroid_labels = [prop.label for prop in props] | ||
| # get centroid and label info | ||
| centroids = [(row[centroid_ids[0]], row[centroid_ids[1]]) for indx, row in fov_table.iterrows()] | ||
| centroid_labels = list(fov_table[label_id]) | ||
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| # generate the distance matrix, then assign centroid_labels as coords | ||
| dist_matrix = cdist(centroids, centroids).astype(np.float32) | ||
| dist_mat_xarr = xr.DataArray(dist_matrix, coords=[centroid_labels, centroid_labels]) | ||
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| # save the distance matrix to save_path | ||
| dist_mat_xarr.to_netcdf( |
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Didn't know this was netcdf, do you want to keep it as that file format, or switch it to zarr?
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Let's keep it for now, since storing the individual dist mats isn't necessary anyways once we switch to anndata for the spatial outputs.
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What is the purpose of this PR?
Closes #1154. Calculate the distance matrices for the spatial scripts using just the cell table as input.
How did you implement your changes
Pull the cell centroids from the cell table and feed them into
cdist().Remaining issues
N/A