fixes compression of downsampled mags (#667)

* fixes compression of downsampled mags
* changelog
* changelog
* types

Author: normanrz

webknossos/Changelog.md

@@ -18,8 +18,10 @@ For upgrade instructions, please check the respective *Breaking Changes* section
 ### Added
 
 ### Changed
+- `MagView.compress` now skips in-place compression of already compressed mags. [#667](https://github.com/scalableminds/webknossos-libs/pull/667)
 
 ### Fixed
+- Fixed compression of downsampled mags for layers with arbitrary and potentially mag-unaligned bounding boxes. [#667](https://github.com/scalableminds/webknossos-libs/pull/667)
 
 
 ## [0.9.12](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.9.12) - 2022-03-18

webknossos/tests/test_dataset.py

@@ -2155,3 +2155,19 @@ def test_warn_outdated_properties(tmp_path: Path) -> None:
         # Changing ds1 should raise a warning, since ds1
         # does not know about the change in ds2
         ds1.add_layer("color", COLOR_CATEGORY)
+
+
+def test_can_compress_mag8(tmp_path: Path) -> None:
+    ds = Dataset(tmp_path / "ds", scale=(1, 1, 1))
+
+    layer = ds.add_layer("color", COLOR_CATEGORY)
+    layer.bounding_box = BoundingBox((0, 0, 0), (12240, 12240, 685))
+    for mag in ["1", "2-2-1", "4-4-1", "8-8-2"]:
+        layer.add_mag(mag)
+
+    assert layer.bounding_box == BoundingBox((0, 0, 0), (12240, 12240, 685))
+
+    mag_view = layer.get_mag("8-8-2")
+    data_to_write = (np.random.rand(1, 10, 10, 10) * 255).astype(np.uint8)
+    mag_view.write(data_to_write, absolute_offset=(11264, 11264, 0))
+    mag_view.compress()

webknossos/webknossos/dataset/mag_view.py

@@ -269,6 +269,10 @@ def compress(
 
         from webknossos.dataset.dataset import Dataset
 
+        if target_path is None and self._is_compressed():
+            logging.info(f"Mag {self.name} is already compressed")
+            return
+
         if target_path is not None:
             target_path = Path(target_path)
 
@@ -308,6 +312,7 @@ def compress(
             for bbox in self.get_bounding_boxes_on_disk():
                 bbox = bbox.intersected_with(self.layer.bounding_box, dont_assert=True)
                 if not bbox.is_empty():
+                    bbox = bbox.align_with_mag(self.mag, ceil=True)
                     source_view = self.get_view(
                         absolute_offset=bbox.topleft, size=bbox.size
                     )