Fix scaling and shape issues in spatialdata reader (#50)

Author: Mr-Milk

pyproject.toml

@@ -74,7 +74,6 @@ include = [
 packages = ["wsidata", "README.md", "LICENSE", "pyproject.toml"]
 
 [tool.ruff]
-lint.ignore = ["F401"]
 lint.extend-select = ["I"]
 line-length = 88
 

wsidata/_model/__init__.py

@@ -1 +1,3 @@
 from .core import TileSpec, WSIData
+
+__all__ = ["TileSpec", "WSIData"]

wsidata/accessors/__init__.py

@@ -2,3 +2,10 @@
 from .fetch import FetchAccessor
 from .iter import IterAccessor
 from .register import register_wsidata_accessor
+
+__all__ = [
+    "DatasetAccessor",
+    "FetchAccessor",
+    "IterAccessor",
+    "register_wsidata_accessor",
+]

wsidata/dataset/__init__.py

@@ -2,3 +2,10 @@
 from .graph import graph_data
 from .image import TileImagesDataset
 from .multislides import FeaturesDatasetBuilder
+
+__all__ = [
+    "TileFeatureDataset",
+    "TileImagesDataset",
+    "FeaturesDatasetBuilder",
+    "graph_data",
+]

wsidata/dataset/disk.py

@@ -1,2 +1,9 @@
 from .builder import FeaturesDatasetBuilder
 from .sampler import InSlideUnderSampler, NoBalance, RandomUnderSampler
+
+__all__ = [
+    "FeaturesDatasetBuilder",
+    "InSlideUnderSampler",
+    "NoBalance",
+    "RandomUnderSampler",
+]

wsidata/dataset/multislides/__init__.py

@@ -10,3 +10,18 @@
     update_shapes_data,
 )
 from ._wsi import agg_wsi, concat_feature_anndata, open_wsi
+
+__all__ = [
+    "add_tiles",
+    "add_table",
+    "add_shapes",
+    "add_tissues",
+    "add_features",
+    "agg_wsi",
+    "add_agg_features",
+    "concat_feature_anndata",
+    "open_wsi",
+    "subset_tiles",
+    "sync_tile_spec",
+    "update_shapes_data",
+]

wsidata/io/__init__.py

@@ -17,3 +17,18 @@
     from ._reader_datatree_zarr_v3 import to_datatree
 else:
     from ._reader_datatree_zarr_v2 import to_datatree
+
+__all__ = [
+    "version",
+    "Version",
+    "READERS",
+    "ReaderBase",
+    "OpenSlideReader",
+    "SlideProperties",
+    "BioFormatsReader",
+    "CuCIMReader",
+    "FastSlideReader",
+    "SpatialDataImage2DReader",
+    "TiffSlideReader",
+    "to_datatree",
+]

wsidata/reader/__init__.py

@@ -1,9 +1,8 @@
-from pathlib import Path
-from typing import TYPE_CHECKING, Union
+from typing import TYPE_CHECKING
 
 import cv2
 
-from .base import AssociatedImages, ReaderBase, SlideProperties, convert_image
+from .base import ReaderBase, SlideProperties
 
 if TYPE_CHECKING:
     from spatialdata.models import Image2DModel
@@ -112,17 +111,16 @@ def get_region(
             img = self.img
 
         downsample_factor = self.properties.level_downsample[level]
-        # SpatialData coordinates must be translated to the respective level
-        x = x / downsample_factor
-        y = y / downsample_factor
-        width = width / downsample_factor
-        height = height / downsample_factor
         if self.is_multiscale:
             data = img.sel(
-                y=slice(y, y + height), x=slice(x, x + width)
+                y=slice(y, y + height * downsample_factor),
+                x=slice(x, x + width * downsample_factor),
             ).image.data.compute()
         else:
-            data = img.sel(y=slice(y, y + height), x=slice(x, x + width)).data.compute()
+            data = img.sel(
+                y=slice(y, y + height * downsample_factor),
+                x=slice(x, x + width * downsample_factor),
+            ).data.compute()
         return data.transpose(1, 2, 0)
 
     def get_thumbnail(self, size, **kwargs):