adds durations to AnnotationInfo (#914)

* adds durations to AnnotationInfo

* re-generate client

* changelog

* fixes a bug with upsampling a dataset that has a non-aligned bounding… (#915)

* fixes a bug with upsampling a dataset that has a non-aligned bounding box

* changelog

* assert

Author: normanrz

webknossos/Changelog.md

@@ -15,6 +15,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Breaking Changes
 
 ### Added
+- Added `duration_in_seconds` and `modified` to `AnnotationInfo`. [#914](https://github.com/scalableminds/webknossos-libs/pull/914)
 
 ### Changed
 - Integrated the `wkcuber` CLI tool into `webknossos` package. [#903](https://github.com/scalableminds/webknossos-libs/pull/903)
@@ -37,6 +38,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
     - `python -m wkcuber.recubing`
 
 ### Fixed
+- Fixed a bug where upsampling of a layer would fail, if the layer had a bounding box that doesn't align with the from_mag mag. [#915](https://github.com/scalableminds/webknossos-libs/pull/915)
 
 
 ## [0.12.6](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.12.6) - 2023-06-09

webknossos/__generate_client.py

@@ -294,6 +294,7 @@ def iterate_request_ids_with_responses() -> Iterable[Tuple[str, bytes]]:
     "firstName",
     "lastName",
     "created",
+    "modified",
     "lastActivity",
     # "teams", added 2022-07, optional for backwards-compatibility
     "experiences",

webknossos/tests/dataset/test_upsampling.py

@@ -2,7 +2,14 @@
 
 import numpy as np
 
-from webknossos import COLOR_CATEGORY, Dataset, Mag, Vec3Int
+from webknossos import (
+    COLOR_CATEGORY,
+    SEGMENTATION_CATEGORY,
+    BoundingBox,
+    Dataset,
+    Mag,
+    Vec3Int,
+)
 from webknossos.dataset._upsampling_utils import upsample_cube, upsample_cube_job
 from webknossos.dataset.sampling_modes import SamplingModes
 
@@ -125,3 +132,21 @@ def test_upsample_multi_channel(tmp_path: Path) -> None:
     target_buffer = l.get_mag("1").read()
     assert np.any(target_buffer != 0)
     assert np.all(target_buffer == joined_buffer)
+
+
+def test_upsampling_non_aligned(tmp_path: Path) -> None:
+    ds = Dataset(tmp_path / "test", (50, 50, 50))
+    l = ds.add_layer(
+        "color", SEGMENTATION_CATEGORY, dtype_per_channel="uint8", largest_segment_id=0
+    )
+    l.bounding_box = BoundingBox(topleft=(0, 0, 0), size=(8409, 10267, 5271))
+    l.add_mag(32)
+
+    l.upsample(
+        from_mag=Mag(32),
+        finest_mag=Mag(8),
+        sampling_mode=SamplingModes.ISOTROPIC,
+        compress=True,
+    )
+    # The original bbox should be unchanged
+    assert l.bounding_box == BoundingBox(topleft=(0, 0, 0), size=(8409, 10267, 5271))

webknossos/webknossos/annotation/annotation_info.py

@@ -25,6 +25,8 @@ class AnnotationInfo:
     description: str
     type: AnnotationType
     state: AnnotationState
+    duration_in_seconds: Optional[int]
+    modified: Optional[int]
 
     def download_annotation(self) -> Annotation:
         """Downloads and returns the annotation that is discribed by this AnnotationInfo object"""
@@ -46,6 +48,11 @@ def _from_generated_response(
             description=response.description,
             type=AnnotationType(response.typ),
             state=AnnotationState(response.state),
+            duration_in_seconds=response.tracing_time // 1000
+            if response.tracing_time is not None
+            and not isinstance(response.tracing_time, Unset)
+            else None,
+            modified=response.modified,
         )
 
     @property

webknossos/webknossos/client/_generated/api/default/annotation_info.py

@@ -37,11 +37,11 @@ def _get_kwargs(
 def _parse_response(
     *, response: httpx.Response
 ) -> Optional[Union[AnnotationInfoResponse200, Any]]:
-    if response.status_code == 200:
+    if response.status_code == HTTPStatus.OK:
         response_200 = AnnotationInfoResponse200.from_dict(response.json())
 
         return response_200
-    if response.status_code == 400:
+    if response.status_code == HTTPStatus.BAD_REQUEST:
         response_400 = cast(Any, None)
         return response_400
     return None

webknossos/webknossos/client/_generated/api/default/annotation_infos_by_task_id.py

@@ -32,7 +32,7 @@ def _get_kwargs(
 def _parse_response(
     *, response: httpx.Response
 ) -> Optional[Union[Any, List["AnnotationInfosByTaskIdResponse200Item"]]]:
-    if response.status_code == 200:
+    if response.status_code == HTTPStatus.OK:
         response_200 = []
         _response_200 = response.json()
         for response_200_item_data in _response_200:
@@ -43,7 +43,7 @@ def _parse_response(
             response_200.append(response_200_item)
 
         return response_200
-    if response.status_code == 400:
+    if response.status_code == HTTPStatus.BAD_REQUEST:
         response_400 = cast(Any, None)
         return response_400
     return None

webknossos/webknossos/client/_generated/api/default/build_info.py

@@ -29,11 +29,11 @@ def _get_kwargs(
 def _parse_response(
     *, response: httpx.Response
 ) -> Optional[Union[Any, BuildInfoResponse200]]:
-    if response.status_code == 200:
+    if response.status_code == HTTPStatus.OK:
         response_200 = BuildInfoResponse200.from_dict(response.json())
 
         return response_200
-    if response.status_code == 400:
+    if response.status_code == HTTPStatus.BAD_REQUEST:
         response_400 = cast(Any, None)
         return response_400
     return None

webknossos/webknossos/client/_generated/api/default/current_user_info.py

@@ -29,7 +29,7 @@ def _get_kwargs(
 def _parse_response(
     *, response: httpx.Response
 ) -> Optional[CurrentUserInfoResponse200]:
-    if response.status_code == 200:
+    if response.status_code == HTTPStatus.OK:
         response_200 = CurrentUserInfoResponse200.from_dict(response.json())
 
         return response_200

webknossos/webknossos/client/_generated/api/default/dataset_info.py

@@ -40,11 +40,11 @@ def _get_kwargs(
 def _parse_response(
     *, response: httpx.Response
 ) -> Optional[Union[Any, DatasetInfoResponse200]]:
-    if response.status_code == 200:
+    if response.status_code == HTTPStatus.OK:
         response_200 = DatasetInfoResponse200.from_dict(response.json())
 
         return response_200
-    if response.status_code == 400:
+    if response.status_code == HTTPStatus.BAD_REQUEST:
         response_400 = cast(Any, None)
         return response_400
     return None

webknossos/webknossos/client/_generated/api/default/dataset_list.py

@@ -63,7 +63,7 @@ def _get_kwargs(
 def _parse_response(
     *, response: httpx.Response
 ) -> Optional[Union[Any, List["DatasetListResponse200Item"]]]:
-    if response.status_code == 200:
+    if response.status_code == HTTPStatus.OK:
         response_200 = []
         _response_200 = response.json()
         for response_200_item_data in _response_200:
@@ -74,7 +74,7 @@ def _parse_response(
             response_200.append(response_200_item)
 
         return response_200
-    if response.status_code == 400:
+    if response.status_code == HTTPStatus.BAD_REQUEST:
         response_400 = cast(Any, None)
         return response_400
     return None