src/spatialexperiment/SpatialExperiment.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -919,7 +919,7 @@ def img_source( @@
             sample_id: Union[str, bool, None] = None,
             image_id: Union[str, bool, None] = None,
             path=False,
-        ):
+        ) -> Union[str, Path, None, List[Union[str, Path]]]:
             """Retrieve the source(s) for images stored in the SpatialExperiment object.
             Args:
@@ Expand Down Expand Up / @@ -958,9 +958,42 @@ def img_source( @@
             return img_sources
-        def img_raster(self, sample_id=None, image_id=None):
-            # NOTE: this function seems redundant, might be an artifact of the different subclasses of SpatialImage in the R implementation? just call `get_img()` for now
-            self.get_img(sample_id=sample_id, image_id=image_id)
+        def img_raster(self, sample_id=None, image_id=None) -> Union[Image.Image, List[Image.Image], None]:
+            """Retrieve and load (if necessary) the images stored in the SpatialExperiment object.
+            Args:
+                sample_id:
+                    - `sample_id=True`: Matches all samples.
+                    - `sample_id=None`: Matches the first sample.
+                    - `sample_id="<str>"`: Matches a sample by its id.
+                image_id:
+                    - `image_id=True`: Matches all images for the specified sample(s).
+                    - `image_id=None`: Matches the first image for the sample(s).
+                    - `image_id="<str>"`: Matches image(s) by its(their) id.
+            Returns:
+                The loaded image(s) for the matching criteria. Returns `None` if `img_data` is `None`.
+                When a single image matches, returns its loaded image.
+                When multiple images match, returns a list of loaded images.
+            Raises:
+                ValueError: If no row matches the provided sample_id and image_id pair.
+            Note:
+                See :py:meth:`~get_img` for detailed behavior regarding sample_id and image_id parameters.
+            """
+            spis = self.get_img(sample_id=sample_id, image_id=image_id)
+            if spis is None:
+                return None
+            if isinstance(spis, VirtualSpatialImage):
+                return spis.img_raster()
+            img_rasters = [spi.img_raster() for spi in spis]
+            return img_rasters
         def rotate_img(self, sample_id=None, image_id=None, degrees=90):
             raise NotImplementedError()
@@ Expand Down @@

tests/test_img_raster.py

-Original file line number
+Diff line change
@@ -0,0 +1,148 @@
+    import pytest
+    from copy import deepcopy
+    from PIL import Image
+    import numpy as np
+    from spatialexperiment import construct_spatial_image_class
+    from spatialexperiment.SpatialImage import (
+        LoadedSpatialImage,
+        StoredSpatialImage,
+        RemoteSpatialImage
+    )
+    def test_loaded_spatial_image_img_raster():
+        image = Image.open("tests/images/sample_image2.png")
+        spi_loaded = construct_spatial_image_class(image, is_url=False)
+        raster = spi_loaded.img_raster()
+        assert isinstance(spi_loaded, LoadedSpatialImage)
+        assert isinstance(raster, Image.Image)
+        np_image = np.zeros((100, 100, 3), dtype=np.uint8)
+        spi_loaded_np = construct_spatial_image_class(np_image)
+        raster_np = spi_loaded_np.img_raster()
+        assert isinstance(spi_loaded_np, LoadedSpatialImage)
+        assert isinstance(raster_np, Image.Image)
+    def test_stored_spatial_image_img_raster():
+        image_path = "tests/images/sample_image1.jpg"
+        spi_stored = construct_spatial_image_class(image_path, is_url=False)
+        raster = spi_stored.img_raster()
+        assert isinstance(spi_stored, StoredSpatialImage)
+        assert isinstance(raster, Image.Image)
+    def test_remote_spatial_image_img_raster(monkeypatch):
+        image_url = "https://example.com/test_image.jpg"
+        spi_remote = construct_spatial_image_class(image_url, is_url=True)
+        # Mock the _download_image method to return an image
+        mock_path = "tests/images/sample_image1.jpg"
+        monkeypatch.setattr(spi_remote, "_download_image", lambda: mock_path)
+        raster = spi_remote.img_raster()
+        assert isinstance(spi_remote, RemoteSpatialImage)
+        assert isinstance(raster, Image.Image)
+        # Test LRU cache works as expected
+        num_calls = 0
+        def mock_download():
+            num_calls += 1
+            return mock_path
+        monkeypatch.setattr(spi_remote, "_download_image", mock_download)
+        raster2 = spi_remote.img_raster()
+        assert num_calls == 0
+        assert raster2 is raster
+    def test_img_raster_no_img_data(spe):
+        tspe = deepcopy(spe)
+        tspe.img_data = None
+        assert not tspe.img_raster()
+    def test_img_raster_no_matches(spe):
+        with pytest.raises(ValueError):
+            res = spe.img_raster(sample_id="foo", image_id="foo")
+    def test_img_raster_both_str(spe):
+        res = spe.img_raster(sample_id="sample_1", image_id="dice")
+        expected_raster = spe.get_img(sample_id="sample_1", image_id="dice").img_raster()
+        assert isinstance(res, Image.Image)
+        assert res == expected_raster
+    def test_img_raster_both_true(spe):
+        res = spe.img_raster(sample_id=True, image_id=True)
+        images = spe.get_img(sample_id=True, image_id=True)
+        expected_rasters = [img.img_raster() for img in images]
+        assert isinstance(res, list)
+        assert res == expected_rasters
+    def test_img_raster_both_none(spe):
+        res = spe.img_raster(sample_id=None, image_id=None)
+        expected_raster = spe.get_img(sample_id=None, image_id=None).img_raster()
+        assert isinstance(res, Image.Image)
+        assert res == expected_raster
+    def test_img_raster_sample_str_image_true(spe):
+        res = spe.img_raster(sample_id="sample_1", image_id=True)
+        images = spe.get_img(sample_id="sample_1", image_id=True)
+        expected_rasters = [img.img_raster() for img in images]
+        assert isinstance(res, list)
+        assert res == expected_rasters
+    def test_img_raster_sample_true_image_str(spe):
+        res = spe.img_raster(sample_id=True, image_id="desert")
+        expected_raster = spe.get_img(sample_id=True, image_id="desert").img_raster()
+        assert isinstance(res, Image.Image)
+        assert res == expected_raster
+    def test_img_raster_sample_str_image_none(spe):
+        res = spe.img_raster(sample_id="sample_1", image_id=None)
+        expected_raster = spe.get_img(sample_id="sample_1", image_id=None).img_raster()
+        assert isinstance(res, Image.Image)
+        assert res == expected_raster
+    def test_img_raster_sample_none_image_str(spe):
+        res = spe.img_raster(sample_id=None, image_id="aurora")
+        expected_raster = spe.get_img(sample_id=None, image_id="aurora").img_raster()
+        assert isinstance(res, Image.Image)
+        assert res == expected_raster
+    def test_img_raster_sample_true_image_none(spe):
+        res = spe.img_raster(sample_id=True, image_id=None)
+        images = spe.get_img(sample_id=True, image_id=None)
+        expected_rasters = [img.img_raster() for img in images]
+        assert isinstance(res, list)
+        assert res == expected_rasters
+    def test_img_raster_sample_none_image_true(spe):
+        res = spe.img_raster(sample_id=None, image_id=True)
+        images = spe.get_img(sample_id=None, image_id=True)
+        expected_rasters = [img.img_raster() for img in images]
+        assert isinstance(res, list)
+        assert res == expected_rasters

Implement `img_raster` in `SpatialExperiment` class #41

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Merged

keviny2 merged 6 commits into main from img-raster

Apr 11, 2025

-Original file line number
+Diff line change
@@ Expand Up / @@ -919,7 +919,7 @@ def img_source( @@
             sample_id: Union[str, bool, None] = None,
             image_id: Union[str, bool, None] = None,
             path=False,
-        ):
+        ) -> Union[str, Path, None, List[Union[str, Path]]]:
             """Retrieve the source(s) for images stored in the SpatialExperiment object.
             Args:
@@ Expand Down Expand Up / @@ -958,9 +958,42 @@ def img_source( @@
             return img_sources
-        def img_raster(self, sample_id=None, image_id=None):
-            # NOTE: this function seems redundant, might be an artifact of the different subclasses of SpatialImage in the R implementation? just call `get_img()` for now
-            self.get_img(sample_id=sample_id, image_id=image_id)
+        def img_raster(self, sample_id=None, image_id=None) -> Union[Image.Image, List[Image.Image], None]:
+            """Retrieve and load (if necessary) the images stored in the SpatialExperiment object.
+            Args:
+                sample_id:
+                    - `sample_id=True`: Matches all samples.
+                    - `sample_id=None`: Matches the first sample.
+                    - `sample_id="<str>"`: Matches a sample by its id.
+                image_id:
+                    - `image_id=True`: Matches all images for the specified sample(s).
+                    - `image_id=None`: Matches the first image for the sample(s).
+                    - `image_id="<str>"`: Matches image(s) by its(their) id.
+            Returns:
+                The loaded image(s) for the matching criteria. Returns `None` if `img_data` is `None`.
+                When a single image matches, returns its loaded image.
+                When multiple images match, returns a list of loaded images.
+            Raises:
+                ValueError: If no row matches the provided sample_id and image_id pair.
+            Note:
+                See :py:meth:`~get_img` for detailed behavior regarding sample_id and image_id parameters.
+            """
+            spis = self.get_img(sample_id=sample_id, image_id=image_id)
+            if spis is None:
+                return None
+            if isinstance(spis, VirtualSpatialImage):
+                return spis.img_raster()
+            img_rasters = [spi.img_raster() for spi in spis]
+            return img_rasters
         def rotate_img(self, sample_id=None, image_id=None, degrees=90):
             raise NotImplementedError()
@@ Expand Down @@

-Original file line number
+Diff line change
@@ -0,0 +1,148 @@
+    import pytest
+    from copy import deepcopy
+    from PIL import Image
+    import numpy as np
+    from spatialexperiment import construct_spatial_image_class
+    from spatialexperiment.SpatialImage import (
+        LoadedSpatialImage,
+        StoredSpatialImage,
+        RemoteSpatialImage
+    )
+    def test_loaded_spatial_image_img_raster():
+        image = Image.open("tests/images/sample_image2.png")
+        spi_loaded = construct_spatial_image_class(image, is_url=False)
+        raster = spi_loaded.img_raster()
+        assert isinstance(spi_loaded, LoadedSpatialImage)
+        assert isinstance(raster, Image.Image)
+        np_image = np.zeros((100, 100, 3), dtype=np.uint8)
+        spi_loaded_np = construct_spatial_image_class(np_image)
+        raster_np = spi_loaded_np.img_raster()
+        assert isinstance(spi_loaded_np, LoadedSpatialImage)
+        assert isinstance(raster_np, Image.Image)
+    def test_stored_spatial_image_img_raster():
+        image_path = "tests/images/sample_image1.jpg"
+        spi_stored = construct_spatial_image_class(image_path, is_url=False)
+        raster = spi_stored.img_raster()
+        assert isinstance(spi_stored, StoredSpatialImage)
+        assert isinstance(raster, Image.Image)
+    def test_remote_spatial_image_img_raster(monkeypatch):
+        image_url = "https://example.com/test_image.jpg"
+        spi_remote = construct_spatial_image_class(image_url, is_url=True)
+        # Mock the _download_image method to return an image
+        mock_path = "tests/images/sample_image1.jpg"
+        monkeypatch.setattr(spi_remote, "_download_image", lambda: mock_path)
+        raster = spi_remote.img_raster()
+        assert isinstance(spi_remote, RemoteSpatialImage)
+        assert isinstance(raster, Image.Image)
+        # Test LRU cache works as expected
+        num_calls = 0
+        def mock_download():
+            num_calls += 1
+            return mock_path
+        monkeypatch.setattr(spi_remote, "_download_image", mock_download)
+        raster2 = spi_remote.img_raster()
+        assert num_calls == 0
+        assert raster2 is raster
+    def test_img_raster_no_img_data(spe):
+        tspe = deepcopy(spe)
+        tspe.img_data = None
+        assert not tspe.img_raster()
+    def test_img_raster_no_matches(spe):
+        with pytest.raises(ValueError):
+            res = spe.img_raster(sample_id="foo", image_id="foo")
+    def test_img_raster_both_str(spe):
+        res = spe.img_raster(sample_id="sample_1", image_id="dice")
+        expected_raster = spe.get_img(sample_id="sample_1", image_id="dice").img_raster()
+        assert isinstance(res, Image.Image)
+        assert res == expected_raster
+    def test_img_raster_both_true(spe):
+        res = spe.img_raster(sample_id=True, image_id=True)
+        images = spe.get_img(sample_id=True, image_id=True)
+        expected_rasters = [img.img_raster() for img in images]
+        assert isinstance(res, list)
+        assert res == expected_rasters
+    def test_img_raster_both_none(spe):
+        res = spe.img_raster(sample_id=None, image_id=None)
+        expected_raster = spe.get_img(sample_id=None, image_id=None).img_raster()
+        assert isinstance(res, Image.Image)
+        assert res == expected_raster
+    def test_img_raster_sample_str_image_true(spe):
+        res = spe.img_raster(sample_id="sample_1", image_id=True)
+        images = spe.get_img(sample_id="sample_1", image_id=True)
+        expected_rasters = [img.img_raster() for img in images]
+        assert isinstance(res, list)
+        assert res == expected_rasters
+    def test_img_raster_sample_true_image_str(spe):
+        res = spe.img_raster(sample_id=True, image_id="desert")
+        expected_raster = spe.get_img(sample_id=True, image_id="desert").img_raster()
+        assert isinstance(res, Image.Image)
+        assert res == expected_raster
+    def test_img_raster_sample_str_image_none(spe):
+        res = spe.img_raster(sample_id="sample_1", image_id=None)
+        expected_raster = spe.get_img(sample_id="sample_1", image_id=None).img_raster()
+        assert isinstance(res, Image.Image)
+        assert res == expected_raster
+    def test_img_raster_sample_none_image_str(spe):
+        res = spe.img_raster(sample_id=None, image_id="aurora")
+        expected_raster = spe.get_img(sample_id=None, image_id="aurora").img_raster()
+        assert isinstance(res, Image.Image)
+        assert res == expected_raster
+    def test_img_raster_sample_true_image_none(spe):
+        res = spe.img_raster(sample_id=True, image_id=None)
+        images = spe.get_img(sample_id=True, image_id=None)
+        expected_rasters = [img.img_raster() for img in images]
+        assert isinstance(res, list)
+        assert res == expected_rasters
+    def test_img_raster_sample_none_image_true(spe):
+        res = spe.img_raster(sample_id=None, image_id=True)
+        images = spe.get_img(sample_id=None, image_id=True)
+        expected_rasters = [img.img_raster() for img in images]
+        assert isinstance(res, list)
+        assert res == expected_rasters

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