aignostics 0.2.22__tar.gz → 0.2.23__tar.gz

{aignostics-0.2.22 → aignostics-0.2.23}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.22
+Version: 0.2.23
 Summary: 🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library.
 Project-URL: Homepage, https://aignostics.readthedocs.io/en/latest/
 Project-URL: Documentation, https://aignostics.readthedocs.io/en/latest/

{aignostics-0.2.22 → aignostics-0.2.23}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.22",
+#     "aignostics==0.2.23",
 # ]
 # ///
 

{aignostics-0.2.22 → aignostics-0.2.23}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.22"
+version = "0.2.23"
 description = "🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library."
 readme = "README.md"
 authors = [
@@ -355,7 +355,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.22"
+current_version = "0.2.23"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.22 → aignostics-0.2.23}/src/aignostics/wsi/_gui.py

@@ -2,7 +2,8 @@
 
 from pathlib import Path
 
-from fastapi import HTTPException, Response
+from fastapi import Response
+from fastapi.responses import RedirectResponse
 
 from aignostics.utils import BasePageBuilder, get_logger
 
@@ -16,6 +17,8 @@ class PageBuilder(BasePageBuilder):
     def register_pages() -> None:
         from nicegui import app  # noqa: PLC0415
 
+        app.add_static_files("/wsi_assets", Path(__file__).parent / "assets")
+
         @app.get("/thumbnail")
         def thumbnail(source: str) -> Response:
             """Serve a thumbnail for a given source reference.
@@ -24,21 +27,16 @@ class PageBuilder(BasePageBuilder):
                 source (str): The source of the slide pointing to a file on the filesystem.
 
             Returns:
-                fastapi.Response: HTTP response containing the thumbnail image.
-
-            Raises:
-                HTTPException: If the file does not exist or if thumbnail generation fails.
+                fastapi.Response: HTTP response containing the thumbnail or fallback image.
             """
             try:
                 return Response(content=Service().get_thumbnail_bytes(Path(source)), media_type="image/png")
-            except ValueError as e:
+            except ValueError:
                 logger.warning("Error generating thumbnail on bad request or invalid image input")
-                raise HTTPException(status_code=400, detail=f"Bad request or invalid image input: {e!s}") from e
-            except RuntimeError as e:
+                return RedirectResponse("/wsi_assets/fallback.png")
+            except RuntimeError:
                 logger.exception("Internal server error when generating thumbnail")
-                raise HTTPException(
-                    status_code=500, detail=f"Internal server error when generating thumbnail: {e!s}"
-                ) from e
+                return RedirectResponse("/wsi_assets/fallback.png")
 
         @app.get("/tiff")
         def tiff(url: str) -> Response:
@@ -48,16 +46,13 @@ class PageBuilder(BasePageBuilder):
                 url (str): The URL of the tiff.
 
             Returns:
-                fastapi.Response: HTTP response containing the thumbnail image.
-
-            Raises:
-                HTTPException: If the file does not exist or if thumbnail generation fails.
+                fastapi.Response: HTTP response containing the converted tiff or fallback image
             """
             try:
                 return Response(content=Service().get_tiff_as_jpg(url), media_type="image/jpeg")
-            except ValueError as e:
+            except ValueError:
                 logger.warning("Error generating jpeg on bad request or invalid tiff input")
-                raise HTTPException(status_code=400, detail=f"Bad request or invalid tiff input: {e!s}") from e
-            except RuntimeError as e:
+                return RedirectResponse("/wsi_assets/fallback.png")
+            except RuntimeError:
                 logger.exception("Internal server error when generating jpeg")
-                raise HTTPException(status_code=500, detail=f"Internal server error when generating jpeg: {e!s}") from e
+                return RedirectResponse("/wsi_assets/fallback.png")

{aignostics-0.2.22 → aignostics-0.2.23}/src/aignostics/wsi/_openslide_handler.py

@@ -5,6 +5,7 @@ from pathlib import Path
 from typing import Any
 
 import openslide
+from openslide import ImageSlide, OpenSlide, open_slide
 from PIL.Image import Image
 
 TIFF_IMAGE_DESCRIPTION = "tiff.ImageDescription"
@@ -15,10 +16,21 @@ class OpenSlideHandler:
 
     def __init__(self, path: str) -> None:
         self.path = Path(path)
-        self.slide = openslide.OpenSlide(str(path))
+        self.slide: OpenSlide | ImageSlide = open_slide(str(path))
 
     @classmethod
     def from_file(cls, path: str | Path) -> "OpenSlideHandler":
+        """Create an OpenSlideHandler from a file path.
+
+        Args:
+            path (str | Path): The path to the WSI file.
+
+        Returns:
+            OpenSlideHandler: An instance of OpenSlideHandler initialized with the given path.
+
+        Raises:
+            OpenSlideError: If the file cannot be opened as a WSI.
+        """
         return cls(str(path))
 
     def _detect_format(self) -> str | None:
@@ -55,6 +67,9 @@ class OpenSlideHandler:
 
         Returns:
             Image: Thumbnail image of the slide.
+
+        Raises:
+            OpenSlideError: If the slide cannot be opened or if thumbnail generation fails.
         """
         return self.slide.get_thumbnail((256, 256))
 

{aignostics-0.2.22 → aignostics-0.2.23}/src/aignostics/wsi/_service.py

@@ -12,6 +12,8 @@ logger = get_logger(__name__)
 
 TIMEOUT = 60  # 1 minutes
 
+FILE_TYPES_SUPPORTED = {".dcm", ".tiff", ".tif", ".svs"}
+
 
 class Service(BaseService):
     """Service of the application module."""
@@ -34,58 +36,8 @@ class Service(BaseService):
             status=Health.Code.UP,
         )
 
-    def _get_openslide_metadata(self, path: Path) -> dict[str, Any]:  # noqa: PLR6301
-        """Get metadata of a wsi file via OpenSlide.
-
-        Args:
-            path (Path): Path to the wsi file.
-
-        Returns:
-            dict[str, Any]: Metadata of the wsi file.
-        """
-        from ._openslide_handler import OpenSlideHandler  # noqa: PLC0415
-
-        handler = OpenSlideHandler.from_file(path)
-        return handler.get_metadata()
-
-    def _get_openslide_thumbnail(self, path: Path) -> "PIL.Image.Image":  # type: ignore # noqa: F821, PLR6301
-        """Get thumbnail of a wsi file via OpenSlide.
-
-        Args:
-            path (Path): Path to the wsi file.
-
-        Returns:
-            PIL.Image.Image: Thumbnail of the wsi file.
-
-        Raises:
-            OpenSlideError: If there is an error processing the wsi file with OpenSlide.
-        """
-        from openslide import OpenSlideError, OpenSlideUnsupportedFormatError  # noqa: PLC0415
-        from PIL import Image as PILImage  # noqa: PLC0415
-
-        from ._openslide_handler import OpenSlideHandler  # noqa: PLC0415
-
-        try:
-            handler = OpenSlideHandler.from_file(path)
-            return handler.get_thumbnail()
-        except OpenSlideUnsupportedFormatError:
-            # If OpenSlide fails, try using PIL directly
-            img_file = PILImage.open(path)
-            # Create a thumbnail with max size 256x256 while maintaining aspect ratio
-            img_file.thumbnail((256, 256))
-            # Convert to RGB mode if needed (for PNG compatibility)
-            return img_file.convert("RGB") if img_file.mode not in {"RGB", "RGBA"} else img_file.copy()
-        except OpenSlideError as e:
-            if str(e) == "No pyramid levels found":
-                # If regular OpenSlide fails, try using PIL directly
-                img_file = PILImage.open(path)
-                # Create a thumbnail with max size 256x256 while maintaining aspect ratio
-                img_file.thumbnail((256, 256))
-                # Convert to RGB mode if needed (for PNG compatibility)
-                return img_file.convert("RGB") if img_file.mode not in {"RGB", "RGBA"} else img_file.copy()
-            raise
-
-    def get_thumbnail(self, path: Path) -> "PIL.Image.Image":  # type: ignore # noqa: F821
+    @staticmethod
+    def get_thumbnail(path: Path) -> "PIL.Image.Image":  # type: ignore # noqa: F821
         """Get thumbnail as PIL image.
 
         Args:
@@ -96,18 +48,27 @@ class Service(BaseService):
 
         Raises:
             ValueError: If the file type is not supported (.dcm, .tiff, or .tif).
+            RuntimeError: If there is an error generating the thumbnail.
         """
+        from ._openslide_handler import OpenSlideHandler  # noqa: PLC0415
+
         if path.exists() is False:
             message = f"File does not exist: {path}"
             logger.warning(message)
             raise ValueError(message)
-        if path.suffix.lower() in {".dcm", ".tiff", ".tif", ".svs"}:
-            return self._get_openslide_thumbnail(path)
-        message = f"Unsupported file type: {path.suffix}. Supported types are .dcm, .tiff, and .tif."
-        logger.warning(message)
-        raise ValueError(message)
+        if path.suffix.lower() not in FILE_TYPES_SUPPORTED:
+            message = f"Unsupported file type: {path.suffix}. Supported types are .dcm, .tiff, and .tif."
+            logger.warning(message)
+            raise ValueError(message)
+        try:
+            return OpenSlideHandler.from_file(path).get_thumbnail()
+        except Exception as e:
+            message = f"Error processing file {path}: {e!s}"
+            logger.exception(message)
+            raise RuntimeError(message) from e
 
-    def get_thumbnail_bytes(self, path: Path) -> bytes:
+    @staticmethod
+    def get_thumbnail_bytes(path: Path) -> bytes:
         """Get thumbnail of a image as bytes.
 
         Args:
@@ -117,14 +78,16 @@ class Service(BaseService):
             bytes: Thumbnail of the image.
 
         Raises:
-            ValueError: If the file type is not supported (.dcm, .tiff, or .tif).
+            ValueError: If the file type is not supported.
+            RuntimeError: If there is an error processing the file.
         """
-        thumbnail_image = self.get_thumbnail(path)
+        thumbnail_image = Service.get_thumbnail(path)
         buffer = io.BytesIO()
         thumbnail_image.save(buffer, format="PNG")
         return buffer.getvalue()
 
-    def get_metadata(self, path: Path) -> dict[str, Any]:
+    @staticmethod
+    def get_metadata(path: Path) -> dict[str, Any]:
         """Get metadata from a TIFF file.
 
         Args:
@@ -132,10 +95,30 @@ class Service(BaseService):
 
         Returns:
             dict[str, Any]: Metadata of the TIFF file.
+
+        Raises:
+            ValueError: If the file type is not supported.
+            RuntimeError: If there is an error processing the file.
         """
-        return self._get_openslide_metadata(path)
+        from ._openslide_handler import OpenSlideHandler  # noqa: PLC0415
+
+        if path.exists() is False:
+            message = f"File does not exist: {path}"
+            logger.warning(message)
+            raise ValueError(message)
+        if path.suffix.lower() not in FILE_TYPES_SUPPORTED:
+            message = f"Unsupported file type: {path.suffix}. Supported types are .dcm, .tiff, and .tif."
+            logger.warning(message)
+            raise ValueError(message)
+        try:
+            return OpenSlideHandler.from_file(path).get_metadata()
+        except Exception as e:
+            error_msg = f"Error processing file {path}: {e!s}"
+            logger.exception(error_msg)
+            raise RuntimeError(error_msg) from e
 
-    def get_tiff_as_jpg(self, url: str) -> bytes:  # noqa: PLR6301
+    @staticmethod
+    def get_tiff_as_jpg(url: str) -> bytes:
         """Get a TIFF image from a URL and convert it to JPG format.
 
         Args: