From a7d1a71781bcf82283d03236c0521b0b5d667664 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 13 Oct 2023 13:46:29 +0200
Subject: [PATCH] Export table of z-stack patch files and annotations
---
extensions/chaeo/workflows.py | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 71103d84..da0bdf36 100644
--- a/extensions/chaeo/workflows.py
+++ b/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]
--
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