fix: update to support RGBA/JPEG and updated structure (#7103)

backend/layers/processing/utils/spatial.py

@@ -64,9 +64,11 @@ def _fetch_image(self, content):
             np.ndarray: The prepared image array.
         """
         resolution = "fullres" if "fullres" in content["images"] else "hires"
+
         image_array = content["images"][resolution]
-        image_array_uint8 = np.uint8(image_array * 255)
-        return image_array_uint8
+        image_array_uint8 = np.uint8(image_array)
+
+        return image_array_uint8, resolution
 
     def _process_and_flip_image(self, image_array_uint8):
         """
@@ -81,10 +83,21 @@ def _process_and_flip_image(self, image_array_uint8):
         Image.MAX_IMAGE_PIXELS = None  # Disable the image size limit
         try:
             with Image.fromarray(image_array_uint8) as img:
-                cropped_img = img.crop(self._calculate_aspect_ratio_crop(img.size))  # Crop the image
-                cropped_img.save(io.BytesIO(), format="JPEG", quality=100)  # Save or manipulate as needed
+                # #####
+                # Convert RGBA to RGB if needed for JPEG compatibility:
+                # bake the alpha channel into the image by pasting it onto
+                # a white background
+                # #####
+                if img.mode == "RGBA":
+                    background = Image.new("RGB", img.size, (255, 255, 255))
+                    background.paste(img, (0, 0), img)
+                    img = background
+                cropped_img = img.crop(self._calculate_aspect_ratio_crop(img.size))
+                cropped_img.save(io.BytesIO(), format="JPEG", quality=100)
+
                 # Flip the image vertically due to explorer client rendering images upside down
                 flipped_img = cropped_img.transpose(Image.FLIP_TOP_BOTTOM)
+
                 return np.array(flipped_img)
         except Exception:
             logger.exception("Error processing image")
@@ -101,7 +114,7 @@ def _generate_deep_zoom_assets(self, image_array, assets_folder):
         h, w, bands = image_array.shape
         linear = image_array.reshape(w * h * bands)
         image = pyvips.Image.new_from_memory(linear.data, w, h, bands, "uchar")
-        image.dzsave(os.path.join(assets_folder, "spatial"), suffix=".webp")
+        image.dzsave(os.path.join(assets_folder, "spatial"), suffix=".jpeg")
 
     def _upload_assets(self, assets_folder):
         """
@@ -126,7 +139,7 @@ def create_deep_zoom_assets(self, container_name, content):
                 assets_folder = os.path.join(temp_dir, container_name.replace(".cxg", ""))
                 os.makedirs(assets_folder)
 
-                image_array = self._fetch_image(content)
+                image_array, _ = self._fetch_image(content)
                 processed_image = self._process_and_flip_image(image_array)
                 self._generate_deep_zoom_assets(processed_image, assets_folder)
                 self._upload_assets(assets_folder)
@@ -145,8 +158,19 @@ def filter_spatial_data(self, content, library_id):
         Returns:
             dict: The filtered spatial data.
         """
+        image_array_uint8, resolution = self._fetch_image(content)
+        with Image.fromarray(image_array_uint8) as img:
+            width, height = img.size
+            width = height = min(width, height)
+            crop_coords = self._calculate_aspect_ratio_crop(img.size)
         return {
             library_id: {
+                "image_properties": {
+                    "resolution": resolution,
+                    "crop_coords": crop_coords,
+                    "width": width,
+                    "height": height,
+                },
                 "images": {"hires": content["images"]["hires"], "fullres": []},
                 "scalefactors": {
                     "spot_diameter_fullres": content["scalefactors"]["spot_diameter_fullres"],

tests/unit/processing/test_spatial_assets_utils.py

@@ -79,9 +79,14 @@ def test__valid_input_metadata_copy(spatial_processor, valid_spatial_data, libra
     """
     Test case for verifying the required metadata is present
     """
-    # Expected output based on the input data
     expected_output = {
         library_id: {
+            "image_properties": {
+                "resolution": "fullres",
+                "crop_coords": (0, 0, 20, 20),
+                "width": 20,
+                "height": 20,
+            },
             "images": {"hires": valid_spatial_data["images"]["hires"], "fullres": []},
             "scalefactors": {
                 "spot_diameter_fullres": valid_spatial_data["scalefactors"]["spot_diameter_fullres"],
@@ -107,8 +112,9 @@ def test__fetch_image_fullres(spatial_processor, valid_spatial_data):
     """
     Test that _fetch_image returns the fullres image when present.
     """
-    image_array = spatial_processor._fetch_image(valid_spatial_data)
+    image_array, resolution = spatial_processor._fetch_image(valid_spatial_data)
     assert image_array.shape == (20, 20, 3), "Expected fullres image to be returned."
+    assert resolution == "fullres", "Expected fullres resolution to be returned."
 
 
 def test__fetch_image_hires(spatial_processor, valid_spatial_data):
@@ -118,8 +124,9 @@ def test__fetch_image_hires(spatial_processor, valid_spatial_data):
     valid_spatial_data_without_fullres = valid_spatial_data.copy()
     del valid_spatial_data_without_fullres["images"]["fullres"]
 
-    image_array = spatial_processor._fetch_image(valid_spatial_data_without_fullres)
+    image_array, resolution = spatial_processor._fetch_image(valid_spatial_data_without_fullres)
     assert image_array.shape == (10, 10, 3), "Expected hires image to be returned."
+    assert resolution == "hires", "Expected hires resolution to be returned."
 
 
 def test__fetch_image_key_error(spatial_processor, valid_spatial_data):
@@ -206,7 +213,7 @@ def test__generate_deep_zoom_assets(spatial_processor, output_folder, mocker):
 
         # verify dzsave was called correctly on the mock_image object
         expected_output_path = os.path.join(assets_folder, "spatial")
-        mock_image.dzsave.assert_called_once_with(expected_output_path, suffix=".webp")
+        mock_image.dzsave.assert_called_once_with(expected_output_path, suffix=".jpeg")
 
 
 def test__upload_assets(spatial_processor, output_folder, mocker):
@@ -248,7 +255,7 @@ def test__create_deep_zoom_assets(spatial_processor, cxg_container, valid_spatia
     mock_temp_dir.return_value.__enter__.return_value = temp_dir_name
 
     # mock return values for the internal methods
-    mock_fetch_image.return_value = np.random.randint(0, 255, (100, 100, 3), dtype=np.uint8)
+    mock_fetch_image.return_value = (np.random.randint(0, 255, (100, 100, 3), dtype=np.uint8), "fullres")
     mock_process_and_flip_image.return_value = np.random.randint(0, 255, (100, 100, 3), dtype=np.uint8)
 
     # call the method under test
@@ -258,7 +265,7 @@ def test__create_deep_zoom_assets(spatial_processor, cxg_container, valid_spatia
 
     # assertions to ensure each step is called
     mock_fetch_image.assert_called_once_with(valid_spatial_data)
-    mock_process_and_flip_image.assert_called_once_with(mock_fetch_image.return_value)
+    mock_process_and_flip_image.assert_called_once_with(mock_fetch_image.return_value[0])
     mock_generate_deep_zoom_assets.assert_called_once_with(mock_process_and_flip_image.return_value, assets_folder)
     mock_upload_assets.assert_called_once_with(assets_folder)