spatialdata 0.2.2__tar.gz → 0.2.3__tar.gz

spatialdata-0.2.3/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,53 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ""
+labels: ""
+assignees: ""
+---
+
+**Recommendation: attach a minimal working example**
+Generally, the easier it is for us to reproduce the issue, the faster we can work on it. It is not required, but if you can, please:
+
+1. Reproduce using the [`blobs` dataset](https://spatialdata.scverse.org/en/latest/generated/spatialdata.datasets.blobs.html)
+
+    ```python
+    from spatialdata.datasets import blobs
+
+    sdata = blobs()
+    ```
+
+    You can also use [`blobs_annotating_element`](https://spatialdata.scverse.org/en/latest/generated/spatialdata.datasets.blobs_annotating_element.html) for more control:
+
+    ```
+    from spatialdata.datasets import blobs_annotating_element
+    sdata = blobs_annotating_element('blobs_labels')
+    ```
+
+2. If the above is not possible, reproduce using a public dataset and explain how we can download the data.
+3. If the data is private, consider sharing an anonymized version/subset via a [Zulip private message](https://scverse.zulipchat.com/#user/480560), or provide screenshots/GIFs showing the behavior.
+
+**Describe the bug**
+A clear and concise description of what the bug is; please report only one bug per issue.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (optional):**
+
+-   OS: [e.g. macOS, Windows, Linux]
+-   Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

spatialdata-0.2.3/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,19 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ""
+labels: ""
+assignees: ""
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

{spatialdata-0.2.2 → spatialdata-0.2.3}/.pre-commit-config.yaml

@@ -21,13 +21,13 @@ repos:
       hooks:
           - id: blacken-docs
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.11.1
+      rev: v1.11.2
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.5.6
+      rev: v0.6.3
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

{spatialdata-0.2.2 → spatialdata-0.2.3}/CHANGELOG.md

@@ -8,20 +8,29 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-## [0.x.x] - 2024-xx-xx
+## [0.2.3] - 2024-09-25
+
+### Minor
+
+-   Added `clip: bool = False` parameter to `polygon_query()` #670
+-   Add `sort` parameter to `PointsModel.parse()` #672
+
+### Fixed
+
+-   Fix interpolation artifact multiscale computation for labels #697
 
 ## [0.2.2] - 2024-08-07
 
-# Major
+### Major
 
 -   New disk format for shapes using `GeoParquet` (the change is backward compatible) #542
 
-# Minor
+### Minor
 
 -   Add `return_background` as argument to `get_centroids` and `get_element_instances` #621
 -   Ability to save data using older disk formats #542
 
-# Fixed
+### Fixed
 
 -   Circles validation now checks for inf or nan radii #653
 -   Bug with table name in torch dataset #654 @LLehner

{spatialdata-0.2.2 → spatialdata-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: spatialdata
-Version: 0.2.2
+Version: 0.2.3
 Summary: Spatial data format.
 Project-URL: Documentation, https://spatialdata.scverse.org/en/latest
 Project-URL: Source, https://github.com/scverse/spatialdata.git

{spatialdata-0.2.2 → spatialdata-0.2.3}/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.2'
-__version_tuple__ = version_tuple = (0, 2, 2)
+__version__ = version = '0.2.3'
+__version_tuple__ = version_tuple = (0, 2, 3)

{spatialdata-0.2.2 → spatialdata-0.2.3}/src/spatialdata/_core/operations/rasterize.py

@@ -336,7 +336,7 @@ def rasterize(
             element_name = data if isinstance(data, str) else None
             kwargs = {"sdata": sdata, "element_name": element_name} if element_name is not None else {"element": data}
             values = get_values(value_key, table_name=table_name, **kwargs).iloc[:, 0]  # type: ignore[arg-type, union-attr]
-            max_index = np.max(values.index)
+            max_index: int = np.max(values.index)
             assigner = np.zeros(max_index + 1, dtype=values.dtype)
             assigner[values.index] = values
             # call-arg is ignored because model is never TableModel (the error is that the transformation param is not

{spatialdata-0.2.2 → spatialdata-0.2.3}/src/spatialdata/_core/operations/rasterize_bins.py

@@ -14,6 +14,7 @@ from skimage.transform import estimate_transform
 from xarray import DataArray
 
 from spatialdata._core.query.relational_query import get_values
+from spatialdata._types import ArrayLike
 from spatialdata.models import Image2DModel, get_table_keys
 from spatialdata.transformations import Affine, Sequence, get_transformation
 
@@ -113,8 +114,9 @@ def rasterize_bins(
     if value_key is None:
         shape = (n_rows, n_cols)
 
-        def channel_rasterization(block_id: tuple[int, int, int] | None) -> np.ndarray:  # type: ignore[type-arg]
-            image = np.zeros((1, *shape), dtype=dtype)
+        def channel_rasterization(block_id: tuple[int, int, int] | None) -> ArrayLike:
+
+            image: ArrayLike = np.zeros((1, *shape), dtype=dtype)
 
             if block_id is None:
                 return image

{spatialdata-0.2.2 → spatialdata-0.2.3}/src/spatialdata/_core/operations/transform.py

@@ -49,11 +49,11 @@ def _transform_raster(
     v: ArrayLike = np.hstack(c_channel + [binary, np.ones(len(binary)).reshape((-1, 1))])
     matrix = transformation.to_affine_matrix(input_axes=axes, output_axes=axes)
     inverse_matrix = transformation.inverse().to_affine_matrix(input_axes=axes, output_axes=axes)
-    new_v = (matrix @ v.T).T
+    new_v: ArrayLike = (matrix @ v.T).T
     c_shape: tuple[int, ...]
     c_shape = (data.shape[0],) if "c" in axes else ()
     new_spatial_shape = tuple(
-        int(np.max(new_v[:, i]) - np.min(new_v[:, i])) for i in range(len(c_shape), n_spatial_dims + len(c_shape))
+        int(np.max(new_v[:, i]) - np.min(new_v[:, i])) for i in range(len(c_shape), n_spatial_dims + len(c_shape))  # type: ignore[operator]
     )
     output_shape = c_shape + new_spatial_shape
     translation_vector = np.min(new_v[:, :-1], axis=0)

{spatialdata-0.2.2 → spatialdata-0.2.3}/src/spatialdata/_core/query/relational_query.py

@@ -220,8 +220,8 @@ def _filter_table_by_elements(
         merged = pd.merge(table_df, pd.DataFrame(index=instances), left_on=instance_key, right_index=True, how="right")
         matched_positions = merged["position"].to_numpy()
         table = table[matched_positions, :]
-    _inplace_fix_subset_categorical_obs(subset_adata=table, original_adata=original_table)
     table = table.copy()
+    _inplace_fix_subset_categorical_obs(subset_adata=table, original_adata=original_table)
     table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY] = table.obs[region_key].unique().tolist()
     return table
 
@@ -623,6 +623,11 @@ def join_spatialelement_table(
         If the provided join type is not supported.
     ValueError
         If an incorrect value is given for `match_rows`.
+
+    See Also
+    --------
+    match_element_to_table : Function to match elements to a table.
+    join_spatialelement_table : Function to join spatial elements with a table.
     """
     if spatial_element_names is None:
         raise ValueError("`spatial_element_names` must be provided.")
@@ -698,6 +703,11 @@ def match_table_to_element(sdata: SpatialData, element_name: str, table_name: st
     Returns
     -------
     Table with the rows matching the instances of the element
+
+    See Also
+    --------
+    match_element_to_table : Function to match a spatial element to a table.
+    join_spatialelement_table : General function, to join spatial elements with a table with more control.
     """
     if table_name is None:
         warnings.warn(
@@ -731,6 +741,11 @@ def match_element_to_table(
     Returns
     -------
     A tuple containing the joined elements as a dictionary and the joined table as an AnnData object.
+
+    See Also
+    --------
+    match_table_to_element : Function to match a table to a spatial element.
+    join_spatialelement_table : General function, to join spatial elements with a table with more control.
     """
     element_dict, table = join_spatialelement_table(
         sdata=sdata, spatial_element_names=element_name, table_name=table_name, how="right", match_rows="right"

{spatialdata-0.2.2 → spatialdata-0.2.3}/src/spatialdata/_core/query/spatial_query.py

@@ -13,7 +13,7 @@ import numpy as np
 from dask.dataframe import DataFrame as DaskDataFrame
 from datatree import DataTree
 from geopandas import GeoDataFrame
-from shapely.geometry import MultiPolygon, Polygon
+from shapely.geometry import MultiPolygon, Point, Polygon
 from xarray import DataArray
 
 from spatialdata import to_polygons
@@ -758,6 +758,7 @@ def polygon_query(
     polygon: Polygon | MultiPolygon,
     target_coordinate_system: str,
     filter_table: bool = True,
+    clip: bool = False,
     shapes: bool = True,
     points: bool = True,
     images: bool = True,
@@ -777,6 +778,12 @@ def polygon_query(
     filter_table
         Specifies whether to filter the tables to only include tables that annotate elements in the retrieved
         SpatialData object of the query.
+    clip
+        If `True`, the shapes are clipped to the polygon. This behavior is implemented only when querying
+        polygons/multipolygons or circles, and it is ignored for other types of elements (images, labels, points).
+        Importantly, when clipping is enabled, the circles will be converted to polygons before the clipping. This may
+        affect downstream operations that rely on the circle radius or on performance, so it is recommended to disable
+        clipping when querying circles or when querying a `SpatialData` object that contains circles.
     shapes [Deprecated]
         This argument is now ignored and will be removed. Please filter the SpatialData object before calling this
         function.
@@ -810,6 +817,7 @@ def _(
     polygon: Polygon | MultiPolygon,
     target_coordinate_system: str,
     filter_table: bool = True,
+    clip: bool = False,
     shapes: bool = True,
     points: bool = True,
     images: bool = True,
@@ -825,6 +833,7 @@ def _(
             polygon_query,
             polygon=polygon,
             target_coordinate_system=target_coordinate_system,
+            clip=clip,
         )
         new_elements[element_type] = queried_elements
 
@@ -891,6 +900,7 @@ def _(
     element: GeoDataFrame,
     polygon: Polygon | MultiPolygon,
     target_coordinate_system: str,
+    clip: bool = False,
     **kwargs: Any,
 ) -> GeoDataFrame | None:
     from spatialdata.transformations import get_transformation, set_transformation
@@ -912,9 +922,18 @@ def _(
     queried_shapes = element[indices]
     queried_shapes.index = buffered[indices][OLD_INDEX]
     queried_shapes.index.name = None
+
+    if clip:
+        if isinstance(element.geometry.iloc[0], Point):
+            queried_shapes = buffered[indices]
+            queried_shapes.index = buffered[indices][OLD_INDEX]
+            queried_shapes.index.name = None
+        queried_shapes = queried_shapes.clip(polygon_gdf, keep_geom_type=True)
+
     del buffered[OLD_INDEX]
     if OLD_INDEX in queried_shapes.columns:
         del queried_shapes[OLD_INDEX]
+
     transformation = get_transformation(buffered, target_coordinate_system)
     queried_shapes = ShapesModel.parse(queried_shapes)
     set_transformation(queried_shapes, transformation, target_coordinate_system)

{spatialdata-0.2.2 → spatialdata-0.2.3}/src/spatialdata/_core/spatialdata.py

@@ -628,7 +628,7 @@ class SpatialData:
         found_element_name: list[str] = []
         for element_type in ["images", "labels", "points", "shapes", "tables"]:
             for element_name, element_value in getattr(self, element_type).items():
-                if id(element_value) == id(element):
+                if element_value is element:
                     found.append(element_value)
                     found_element_type.append(element_type)
                     found_element_name.append(element_name)
@@ -2225,6 +2225,7 @@ class QueryManager:
         polygon: Polygon | MultiPolygon,
         target_coordinate_system: str,
         filter_table: bool = True,
+        clip: bool = False,
     ) -> SpatialData:
         """
         Perform a polygon query on the SpatialData object.
@@ -2239,6 +2240,7 @@ class QueryManager:
             polygon=polygon,
             target_coordinate_system=target_coordinate_system,
             filter_table=filter_table,
+            clip=clip,
         )
 
     def __call__(self, request: BaseSpatialRequest, **kwargs) -> SpatialData:  # type: ignore[no-untyped-def]

{spatialdata-0.2.2 → spatialdata-0.2.3}/src/spatialdata/_io/io_zarr.py

@@ -128,8 +128,8 @@ def read_zarr(store: Union[str, Path, zarr.Group], selection: Optional[tuple[str
 
     if "table" in selector and "table" in f:
         warnings.warn(
-            f"Table group found in zarr store at location {f_store_path}. Please update the zarr store"
-            f"to use tables instead.",
+            f"Table group found in zarr store at location {f_store_path}. Please update the zarr store to use tables "
+            f"instead.",
             DeprecationWarning,
             stacklevel=2,
         )

{spatialdata-0.2.2 → spatialdata-0.2.3}/src/spatialdata/_types.py

@@ -6,7 +6,7 @@ import numpy as np
 from datatree import DataTree
 from xarray import DataArray
 
-__all__ = ["ArrayLike", "DTypeLike", "Raster_T"]
+__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T"]
 
 try:
     from numpy.typing import DTypeLike, NDArray
@@ -17,3 +17,4 @@ except (ImportError, TypeError):
     DTypeLike = np.dtype  # type: ignore[misc]
 
 Raster_T = Union[DataArray, DataTree]
+ColorLike = Union[tuple[float, ...], str]

{spatialdata-0.2.2 → spatialdata-0.2.3}/src/spatialdata/datasets.py

@@ -63,8 +63,7 @@ def blobs(
 
     Returns
     -------
-    SpatialData
-        SpatialData object with blobs dataset.
+    SpatialData object with blobs dataset.
     """
     return BlobsDataset(
         length=length,
@@ -355,6 +354,19 @@ BlobsTypes = Literal[
 
 
 def blobs_annotating_element(name: BlobsTypes) -> SpatialData:
+    """
+    Return the blobs dataset with the desired element annotated by the table.
+
+    Parameters
+    ----------
+    name
+        Name of the element to annotate. One of "blobs_labels", "blobs_multiscale_labels", "blobs_circles",
+        "blobs_polygons", "blobs_multipolygons".
+
+    Returns
+    -------
+    SpatialData object with the desired element annotated by the table.
+    """
     sdata = blobs(length=50)
     if name in ["blobs_labels", "blobs_multiscale_labels"]:
         instance_id = get_element_instances(sdata[name]).tolist()

{spatialdata-0.2.2 → spatialdata-0.2.3}/src/spatialdata/models/models.py

@@ -255,6 +255,17 @@ class Labels2DModel(RasterSchema):
             **kwargs,
         )
 
+    @classmethod
+    def parse(  # noqa: D102
+        self,
+        *args: Any,
+        **kwargs: Any,
+    ) -> DataArray | DataTree:
+        if kwargs.get("scale_factors") is not None and kwargs.get("method") is None:
+            # Override default scaling method to preserve labels
+            kwargs["method"] = Methods.DASK_IMAGE_NEAREST
+        return super().parse(*args, **kwargs)
+
 
 class Labels3DModel(RasterSchema):
     dims = DimsSchema((Z, Y, X))
@@ -270,6 +281,13 @@ class Labels3DModel(RasterSchema):
             **kwargs,
         )
 
+    @classmethod
+    def parse(self, *args: Any, **kwargs: Any) -> DataArray | DataTree:  # noqa: D102
+        if kwargs.get("scale_factors") is not None and kwargs.get("method") is None:
+            # Override default scaling method to preserve labels
+            kwargs["method"] = Methods.DASK_IMAGE_NEAREST
+        return super().parse(*args, **kwargs)
+
 
 class Image2DModel(RasterSchema):
     dims = DimsSchema((C, Y, X))
@@ -656,14 +674,18 @@ class PointsModel:
                 )
         ndim = len(coordinates)
         axes = [X, Y, Z][:ndim]
-        index_monotonically_increasing = data.index.is_monotonic_increasing
-        if not isinstance(index_monotonically_increasing, bool):
-            index_monotonically_increasing = index_monotonically_increasing.compute()
-        if not index_monotonically_increasing:
+        if "sort" not in kwargs:
+            index_monotonically_increasing = data.index.is_monotonic_increasing
+            if not isinstance(index_monotonically_increasing, bool):
+                index_monotonically_increasing = index_monotonically_increasing.compute()
+            sort = index_monotonically_increasing
+        else:
+            sort = kwargs["sort"]
+        if not sort:
             warnings.warn(
                 "The index of the dataframe is not monotonic increasing. It is recommended to sort the data to "
-                "adjust the order of the index before calling .parse() to avoid possible problems due to unknown "
-                "divisions",
+                "adjust the order of the index before calling .parse() (or call `parse(sort=True)`) to avoid possible "
+                "problems due to unknown divisions.",
                 UserWarning,
                 stacklevel=2,
             )
@@ -671,16 +693,16 @@ class PointsModel:
             table: DaskDataFrame = dd.from_pandas(  # type: ignore[attr-defined]
                 pd.DataFrame(data[[coordinates[ax] for ax in axes]].to_numpy(), columns=axes, index=data.index),
                 # we need to pass sort=True also when the index is sorted to ensure that the divisions are computed
-                sort=index_monotonically_increasing,
+                sort=sort,
                 **kwargs,
             )
             # we cannot compute the divisions whne the index is not monotonically increasing and npartitions > 1
-            if not table.known_divisions and (index_monotonically_increasing or table.npartitions == 1):
+            if not table.known_divisions and (sort or table.npartitions == 1):
                 table.divisions = table.compute_current_divisions()
             if feature_key is not None:
                 feature_categ = dd.from_pandas(
                     data[feature_key].astype(str).astype("category"),
-                    sort=index_monotonically_increasing,
+                    sort=sort,
                     **kwargs,
                 )  # type: ignore[attr-defined]
                 table[feature_key] = feature_categ

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/conftest.py

@@ -21,6 +21,8 @@ from scipy import ndimage as ndi
 from shapely import linearrings, polygons
 from shapely.geometry import MultiPolygon, Point, Polygon
 from skimage import data
+from xarray import DataArray
+
 from spatialdata._core._deepcopy import deepcopy
 from spatialdata._core.spatialdata import SpatialData
 from spatialdata._types import ArrayLike
@@ -34,7 +36,6 @@ from spatialdata.models import (
     ShapesModel,
     TableModel,
 )
-from xarray import DataArray
 
 SEED = 0
 RNG = default_rng(seed=SEED)

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/core/operations/test_aggregations.py

@@ -8,6 +8,7 @@ from anndata import AnnData
 from anndata.tests.helpers import assert_equal
 from geopandas import GeoDataFrame
 from numpy.random import default_rng
+
 from spatialdata import aggregate, to_polygons
 from spatialdata._core._deepcopy import deepcopy as _deepcopy
 from spatialdata._core.spatialdata import SpatialData
@@ -366,7 +367,7 @@ def test_aggregate_requiring_alignment(sdata_blobs: SpatialData, values, by) ->
         raise pytest.skip("Aggregation mixing raster and vector data is not currently supported.")
     values = sdata_blobs[values]
     by = sdata_blobs[by]
-    if id(values) == id(by):
+    if values is by:
         # warning: this will give problems when aggregation labels by labels (not supported yet), because of this: https://github.com/scverse/spatialdata/issues/269
         by = _deepcopy(by)
         assert by.attrs["transform"] is not values.attrs["transform"]

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/core/operations/test_map.py

@@ -2,9 +2,10 @@ import re
 
 import numpy as np
 import pytest
+from xarray import DataArray
+
 from spatialdata._core.operations.map import map_raster
 from spatialdata.transformations import Translation, get_transformation, set_transformation
-from xarray import DataArray
 
 
 def _multiply(arr, parameter=10):

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/core/operations/test_rasterize_bins.py

@@ -8,6 +8,7 @@ from numpy.random import default_rng
 from pandas import DataFrame
 from scipy.sparse import csr_matrix
 from shapely.geometry import Polygon
+
 from spatialdata._core.data_extent import are_extents_equal, get_extent
 from spatialdata._core.operations.rasterize_bins import rasterize_bins
 from spatialdata._core.spatialdata import SpatialData

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/core/operations/test_spatialdata_operations.py

@@ -5,6 +5,7 @@ import math
 import numpy as np
 import pytest
 from anndata import AnnData
+
 from spatialdata._core.concatenate import _concatenate_tables, concatenate
 from spatialdata._core.data_extent import are_extents_equal, get_extent
 from spatialdata._core.operations._utils import transform_to_data_extent
@@ -21,7 +22,6 @@ from spatialdata.transformations.transformations import (
     Sequence,
     Translation,
 )
-
 from tests.conftest import _get_table
 
 
@@ -296,7 +296,7 @@ def test_locate_spatial_element(full_sdata: SpatialData) -> None:
 
 
 def test_get_item(points: SpatialData) -> None:
-    assert id(points["points_0"]) == id(points.points["points_0"])
+    assert points["points_0"] is points.points["points_0"]
 
     # removed this test after this change: https://github.com/scverse/spatialdata/pull/145#discussion_r1133122720
     # to be uncommented/removed/modified after this is closed: https://github.com/scverse/spatialdata/issues/186

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/core/operations/test_transform.py

@@ -6,6 +6,8 @@ import numpy as np
 import pytest
 from datatree import DataTree
 from geopandas.testing import geom_almost_equals
+from xarray import DataArray
+
 from spatialdata import transform
 from spatialdata._core.data_extent import are_extents_equal, get_extent
 from spatialdata._core.spatialdata import SpatialData
@@ -28,7 +30,6 @@ from spatialdata.transformations.transformations import (
     Sequence,
     Translation,
 )
-from xarray import DataArray
 
 
 class TestElementsTransform:

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/core/operations/test_vectorize.py

@@ -4,6 +4,7 @@ import numpy as np
 import pytest
 from geopandas import GeoDataFrame
 from shapely import MultiPoint, Point
+
 from spatialdata._core.operations.vectorize import to_circles, to_polygons
 from spatialdata.datasets import blobs
 from spatialdata.models.models import ShapesModel

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/core/query/test_relational_query.py

@@ -2,6 +2,7 @@ import numpy as np
 import pandas as pd
 import pytest
 from anndata import AnnData
+
 from spatialdata import get_values, match_table_to_element
 from spatialdata._core.query.relational_query import (
     _locate_value,

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/core/query/test_spatial_query.py

@@ -11,6 +11,9 @@ from dask.dataframe import DataFrame as DaskDataFrame
 from datatree import DataTree
 from geopandas import GeoDataFrame
 from shapely import MultiPolygon, Point, Polygon
+from xarray import DataArray
+
+from spatialdata._core.data_extent import get_extent
 from spatialdata._core.query.spatial_query import (
     BaseSpatialRequest,
     BoundingBoxRequest,
@@ -29,8 +32,6 @@ from spatialdata.models import (
 )
 from spatialdata.testing import assert_spatial_data_objects_are_identical
 from spatialdata.transformations import Identity, MapAxis, set_transformation
-from xarray import DataArray
-
 from tests.conftest import _make_points, _make_squares
 
 
@@ -686,3 +687,37 @@ def test_spatial_query_different_axes(full_sdata, name: str):
         return
 
     raise RuntimeError(f"Unexpected type {type(original)}")
+
+
+def test_query_with_clipping(sdata_blobs):
+    circles = sdata_blobs["blobs_circles"]
+    circles.index = [10, 100, 1]
+    polygons = sdata_blobs["blobs_polygons"]
+    polygons.index = [10, 100, 1]
+
+    # define square to use as query geometry
+    minx = 120
+    maxx = 170
+    miny = 150
+    maxy = 210
+    x_coords = [minx, maxx, maxx, minx, minx]
+    y_coords = [miny, miny, maxy, maxy, miny]
+    polygon = Polygon(zip(x_coords, y_coords))
+
+    queried_circles = polygon_query(circles, polygon=polygon, target_coordinate_system="global", clip=True)
+    queried_polygons = polygon_query(polygons, polygon=polygon, target_coordinate_system="global", clip=True)
+
+    assert queried_circles.index.tolist() == [100]
+    assert queried_polygons.index.tolist() == [100]
+
+    extent_circles = get_extent(queried_circles)
+    extent_polygons = get_extent(queried_polygons)
+
+    def query_polyon_contains_queried_data(extent: dict[str, tuple[float, float]]) -> None:
+        assert extent["x"][0] >= minx
+        assert extent["x"][1] <= maxx
+        assert extent["y"][0] >= miny
+        assert extent["y"][1] <= maxy
+
+    query_polyon_contains_queried_data(extent_circles)
+    query_polyon_contains_queried_data(extent_polygons)

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/core/test_centroids.py

@@ -5,6 +5,7 @@ import pandas as pd
 import pytest
 from anndata import AnnData
 from numpy.random import default_rng
+
 from spatialdata._core.centroids import get_centroids
 from spatialdata._core.query.relational_query import get_element_instances
 from spatialdata.models import Labels2DModel, Labels3DModel, PointsModel, TableModel, get_axes_names

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/core/test_data_extent.py

@@ -6,6 +6,7 @@ import pytest
 from geopandas import GeoDataFrame
 from numpy.random import default_rng
 from shapely.geometry import MultiPolygon, Point, Polygon
+
 from spatialdata import SpatialData, get_extent, transform
 from spatialdata._core._deepcopy import deepcopy as _deepcopy
 from spatialdata.datasets import blobs

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/core/test_deepcopy.py

@@ -1,4 +1,5 @@
 from pandas.testing import assert_frame_equal
+
 from spatialdata._core._deepcopy import deepcopy as _deepcopy
 from spatialdata.testing import assert_spatial_data_objects_are_identical
 

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/dataloader/test_datasets.py

@@ -1,5 +1,6 @@
 import numpy as np
 import pytest
+
 from spatialdata.dataloader import ImageTilesDataset
 from spatialdata.datasets import blobs_annotating_element
 

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/io/test_format.py

@@ -2,6 +2,7 @@ from typing import Any, Optional
 
 import pytest
 from shapely import GeometryType
+
 from spatialdata._io.format import CurrentPointsFormat, CurrentShapesFormat, ShapesFormatV01
 from spatialdata.models import PointsModel, ShapesModel
 

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/io/test_metadata.py

@@ -3,6 +3,7 @@ import os
 import tempfile
 
 import pytest
+
 from spatialdata import SpatialData, read_zarr
 from spatialdata._io._utils import _is_element_self_contained
 from spatialdata._logging import logger

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/io/test_utils.py

@@ -2,6 +2,7 @@ import os
 import tempfile
 
 import dask.dataframe as dd
+
 from spatialdata import read_zarr
 from spatialdata._io._utils import get_dask_backing_files
 

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/models/test_models.py

@@ -22,6 +22,8 @@ from numpy.random import default_rng
 from shapely.geometry import MultiPolygon, Point, Polygon
 from shapely.io import to_ragged_array
 from spatial_image import to_spatial_image
+from xarray import DataArray
+
 from spatialdata._core.spatialdata import SpatialData
 from spatialdata._types import ArrayLike
 from spatialdata.models._utils import (
@@ -51,8 +53,6 @@ from spatialdata.transformations.operations import (
     set_transformation,
 )
 from spatialdata.transformations.transformations import Identity, Scale
-from xarray import DataArray
-
 from tests.conftest import (
     MULTIPOLYGON_PATH,
     POINT_PATH,
@@ -195,6 +195,27 @@ class TestModels:
             with pytest.raises(ValueError):
                 model.parse(image, **kwargs)
 
+    @pytest.mark.parametrize("model", [Labels2DModel, Labels3DModel])
+    def test_labels_model_with_multiscales(self, model):
+        # Passing "scale_factors" should generate multiscales with a "method" appropriate for labels
+        dims = np.array(model.dims.dims).tolist()
+        n_dims = len(dims)
+
+        # A labels image with one label value 4, that partially covers 2×2 blocks.
+        # Downsampling with interpolation would produce values 1, 2, 3, 4.
+        image: ArrayLike = np.array([[0, 0, 0, 0], [0, 4, 4, 4], [4, 4, 4, 4], [0, 4, 4, 4]], dtype=np.uint16)
+        if n_dims == 3:
+            image = np.stack([image] * image.shape[0])
+        actual = model.parse(image, scale_factors=(2,))
+        assert isinstance(actual, DataTree)
+        assert actual.children.keys() == {"scale0", "scale1"}
+        assert actual.scale0.image.dtype == image.dtype
+        assert actual.scale1.image.dtype == image.dtype
+        assert set(np.unique(image)) == set(np.unique(actual.scale0.image)), "Scale0 should be preserved"
+        assert set(np.unique(image)) >= set(
+            np.unique(actual.scale1.image)
+        ), "Subsequent scales should not have interpolation artifacts"
+
     @pytest.mark.parametrize("model", [ShapesModel])
     @pytest.mark.parametrize("path", [POLYGON_PATH, MULTIPOLYGON_PATH, POINT_PATH])
     def test_shapes_model(self, model: ShapesModel, path: Path) -> None:

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/transformations/ngff/test_ngff_coordinate_system.py

@@ -2,6 +2,7 @@ import copy
 import json
 
 import pytest
+
 from spatialdata.transformations.ngff.ngff_coordinate_system import (
     NgffAxis,
     NgffCoordinateSystem,

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/transformations/test_transformations.py

@@ -4,6 +4,8 @@ from copy import deepcopy
 import numpy as np
 import pytest
 import xarray.testing
+from xarray import DataArray
+
 from spatialdata import transform
 from spatialdata.datasets import blobs
 from spatialdata.models import Image2DModel, PointsModel
@@ -32,7 +34,6 @@ from spatialdata.transformations.transformations import (
     _decompose_transformation,
     _get_affine_for_element,
 )
-from xarray import DataArray
 
 
 def test_identity():

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/utils/test_element_utils.py

@@ -4,10 +4,11 @@ import dask_image.ndinterp
 import pytest
 import xarray
 from datatree import DataTree
+from xarray import DataArray
+
 from spatialdata._utils import unpad_raster
 from spatialdata.models import get_model
 from spatialdata.transformations import Affine
-from xarray import DataArray
 
 
 def _pad_raster(data: DataArray, axes: tuple[str, ...]) -> DataArray:

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/utils/test_testing.py

@@ -3,6 +3,8 @@ import copy
 import numpy as np
 import pytest
 from datatree import DataTree
+from xarray import DataArray
+
 from spatialdata import SpatialData, deepcopy
 from spatialdata.models import (
     Image2DModel,
@@ -16,7 +18,6 @@ from spatialdata.models import (
 )
 from spatialdata.testing import assert_elements_are_identical, assert_spatial_data_objects_are_identical
 from spatialdata.transformations import Scale, set_transformation
-from xarray import DataArray
 
 scale = Scale([1.0], axes=("x",))
 

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/core/operations/test_rasterize.py

@@ -11,6 +11,8 @@ from geopandas import GeoDataFrame
 from multiscale_spatial_image import MultiscaleSpatialImage
 from shapely import MultiPolygon, box
 from spatial_image import SpatialImage
+from xarray import DataArray
+
 from spatialdata import SpatialData, get_extent
 from spatialdata._core.operations.rasterize import rasterize
 from spatialdata._core.query.relational_query import get_element_instances
@@ -18,8 +20,6 @@ from spatialdata._io._utils import _iter_multiscale
 from spatialdata.models import PointsModel, ShapesModel, TableModel, get_axes_names
 from spatialdata.models._utils import get_spatial_axes
 from spatialdata.transformations import MapAxis
-from xarray import DataArray
-
 from tests.conftest import _get_images, _get_labels
 
 

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/io/test_multi_table.py

@@ -4,9 +4,9 @@ import pandas as pd
 import pytest
 from anndata import AnnData
 from anndata.tests.helpers import assert_equal
+
 from spatialdata import SpatialData, concatenate
 from spatialdata.models import TableModel
-
 from tests.conftest import _get_shapes, _get_table
 
 # notes on paths: https://github.com/orgs/scverse/projects/17/views/1?pane=issue&itemId=44066734

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/io/test_readwrite.py

@@ -8,6 +8,7 @@ import numpy as np
 import pytest
 from anndata import AnnData
 from numpy.random import default_rng
+
 from spatialdata import SpatialData, deepcopy, read_zarr
 from spatialdata._io._utils import _are_directories_identical, get_dask_backing_files
 from spatialdata.datasets import blobs
@@ -19,7 +20,6 @@ from spatialdata.transformations.operations import (
     set_transformation,
 )
 from spatialdata.transformations.transformations import Identity, Scale
-
 from tests.conftest import _get_images, _get_labels, _get_points, _get_shapes
 
 RNG = default_rng(0)

{spatialdata-0.2.2 → spatialdata-0.2.3}/tests/transformations/ngff/test_ngff_transformations.py

@@ -4,6 +4,7 @@ import json
 
 import numpy as np
 import pytest
+
 from spatialdata._types import ArrayLike
 from spatialdata.models import C, X, Y, Z
 from spatialdata.transformations.ngff._utils import get_default_coordinate_system
@@ -19,7 +20,6 @@ from spatialdata.transformations.ngff.ngff_transformations import (
     NgffSequence,
     NgffTranslation,
 )
-
 from tests.transformations.ngff.conftest import (
     c_cs,
     cyx_cs,