Fix merging annotations with compressed fallback layers (#1191)

* tests: Add failing test * bugfix: Extend output layer bounding box to prevent concurrent writes to properties * doc: Add changelog message * rf: Change formatting --------- Co-authored-by: Norman Rzepka <[email protected]> Co-authored-by: Tom Herold <[email protected]>
scalableminds · Oct 24, 2024 · 0fc495a · 0fc495a
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diff --git a/webknossos/Changelog.md b/webknossos/Changelog.md
@@ -20,6 +20,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Changed
 
 ### Fixed
+- Fixed an issue with merging annotations with compressed fallback layers.
 
 
 ## [0.15.6](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.6) - 2024-10-16

diff --git a/webknossos/tests/test_cli.py b/webknossos/tests/test_cli.py
@@ -542,7 +542,10 @@ def test_export_tiff_stack_tiles_per_dimension(tmp_path: Path) -> None:
                 )
 
 
-def test_merge_fallback_no_fallback_layer(tmp_path: Path) -> None:
+@pytest.mark.parametrize("use_compression", [True, False])
+def test_merge_fallback_no_fallback_layer(
+    tmp_path: Path, use_compression: bool
+) -> None:
     from zipfile import ZIP_DEFLATED, ZipFile
     from zlib import Z_BEST_SPEED
 
@@ -558,7 +561,12 @@ def test_merge_fallback_no_fallback_layer(tmp_path: Path) -> None:
             SEGMENTATION_CATEGORY,
             dtype_per_channel=fallback_layer_data.dtype,
         )
-        .add_mag(1, chunk_shape=(32,) * 3, chunks_per_shard=(1,) * 3)
+        .add_mag(
+            1,
+            chunk_shape=(32,) * 3,
+            chunks_per_shard=(1,) * 3,
+            compress=use_compression,
+        )
     )
 
     fallback_mag.write(absolute_offset=(0,) * 3, data=fallback_layer_data)

diff --git a/webknossos/webknossos/dataset/mag_view.py b/webknossos/webknossos/dataset/mag_view.py
@@ -491,6 +491,13 @@ def merge_with_view(
             bboxes, Mag(self.info.shard_shape * self.mag)
         )
 
+        new_bbox = self.bounding_box
+        for shard_bbox in shards_with_bboxes.keys():
+            new_bbox = new_bbox.extended_by(shard_bbox)
+
+        logging.info(f"Set mag layer bounding box to {new_bbox}")
+        self.layer.bounding_box = new_bbox
+
         args = [(other, shard, bboxes) for shard, bboxes in shards_with_bboxes.items()]
 
         logging.info("Merging %s shards.", len(args))