Export table of z-stack patch files and annotations

extensions/chaeo/workflows.py

@@ -244,15 +244,17 @@ def transfer_ecotaxa_labels_to_patch_stacks(
     stack_meta = []
     for fi, pl in enumerate(df_tr.itertuples(name='PatchFile')):
         fn = pl._asdict()['patch_filename']
-        ac = pl._asdict()['annotation_class_id']
-        stack_meta.append({'zi': fi, 'patch_filename': fn, 'annotation_class_id': ac})
+        ac = pl._asdict()['annotation_class']
+        aci = pl._asdict()['annotation_class_id']
+
+        stack_meta.append({'zi': fi, 'patch_filename': fn, 'annotation_class': ac, 'annotation_class_id': aci})
         acc_bm = generate_file_accessor(Path(where_masks) / fn)
         assert acc_bm.hw == patch_size, f'Unexpected patch size {patch_size}'
         assert acc_bm.chroma == 1
         assert acc_bm.nz == 1
         mask = acc_bm.data[:, :, 0, 0]
         zstacks['mask'][:, :, 0, fi] = mask
-        zstacks['label'][:, :, 0, fi] = (mask == 255) * ac
+        zstacks['label'][:, :, 0, fi] = (mask == 255) * aci
 
         acc_pa = generate_file_accessor(Path(where_patches) / fn)
         zstacks['raw'][:, :, :, fi] = acc_pa.data[:, :, :, 0]