aignostics 0.2.22__tar.gz → 0.2.27__tar.gz

{aignostics-0.2.22 → aignostics-0.2.27}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.22
+Version: 0.2.27
 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-0.2.27}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.22",
+#     "aignostics==0.2.27",
 # ]
 # ///
 

{aignostics-0.2.22 → aignostics-0.2.27}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.22"
+version = "0.2.27"
 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 = "0.2.27"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.22 → aignostics-0.2.27}/src/aignostics/application/_gui/_page_application_run_describe.py

@@ -4,7 +4,7 @@ from importlib.util import find_spec
 from multiprocessing import Manager
 from pathlib import Path
 from typing import Any
-from urllib.parse import quote as urlencode
+from urllib.parse import quote
 
 from nicegui import run as nicegui_run
 from nicegui import ui  # noq
@@ -87,7 +87,7 @@ async def _page_application_run_describe(application_run_id: str) -> None:  # no
             return False
 
     @ui.refreshable
-    def download_run_dialog_content(qupath_project: bool = False) -> None:  # noqa: C901, PLR0915
+    def download_run_dialog_content(qupath_project: bool = False, marimo: bool = False) -> None:  # noqa: C901, PLR0915
         if qupath_project:
             ui.markdown(
                 "##### Visualize results in QuPath with one click \n"
@@ -97,6 +97,13 @@ async def _page_application_run_describe(application_run_id: str) -> None:  # no
                 "4. The QuPath project will reference the input slides and resulting image heatmaps. \n"
                 "5. Detected cells will be added as annotations to input slides. \n"
             )
+        elif marimo:
+            ui.markdown(
+                "##### Open results in Marimo with one click \n"
+                "1. Use data directory of Launchpad or select a custom folder. \n"
+                "2. A subfolder with the application run will be created and all results downloaded there. \n"
+                "3. A Marimo notebook will be started pointing to the subfolder. \n"
+            )
         else:
             ui.markdown(
                 "##### Download all results with one click \n"
@@ -223,6 +230,10 @@ async def _page_application_run_describe(application_run_id: str) -> None:  # no
                     ui.notify("Download and QuPath project creation completed.", type="positive")
                     download_item_status.set_text("Opening QuPath ...")
                     await open_qupath(project=results_folder / "qupath", button=download_button)
+                elif marimo:
+                    ui.notify("Download and Notebook preparation completed.", type="positive")
+                    download_item_status.set_text("Opening Notebook ...")
+                    open_marimo(results_folder=results_folder, button=download_button)
                 else:
                     ui.notify("Download completed.", type="positive")
                 show_in_file_manager(str(results_folder))
@@ -238,10 +249,20 @@ async def _page_application_run_describe(application_run_id: str) -> None:  # no
 
         ui.separator()
         with ui.row(align_items="end").classes("w-full justify-end"):
+            if qupath_project:
+                label = "Visualize with QuPath"
+                icon = "zoom_in"
+            elif marimo:
+                label = "Analyze with Notebook"
+                icon = "analytics"
+            else:
+                label = "Download all results"
+                icon = "cloud_download"
+
             download_button = (
                 ui.button(
-                    "Download all results" if not qupath_project else "Visualize with QuPath",
-                    icon="cloud_download" if not qupath_project else "zoom_in",
+                    label,
+                    icon=icon,
                     on_click=start_download,
                 )
                 .props("color=primary")
@@ -254,9 +275,9 @@ async def _page_application_run_describe(application_run_id: str) -> None:  # no
     with ui.dialog() as download_run_dialog, ui.card().style(WIDTH_1200px):
         download_run_dialog_content()
 
-    def download_run_dialog_open(qupath_project: bool = False) -> None:
+    def download_run_dialog_open(qupath_project: bool = False, marimo: bool = False) -> None:
         """Open the CSV dialog."""
-        download_run_dialog_content.refresh(qupath_project=qupath_project)
+        download_run_dialog_content.refresh(qupath_project=qupath_project, marimo=marimo)
         download_run_dialog.open()
 
     @ui.refreshable
@@ -315,7 +336,7 @@ async def _page_application_run_describe(application_run_id: str) -> None:  # no
         if url:
             try:
                 with ui.scroll_area().classes("w-full h-[calc(100vh-2rem)]"):
-                    ui.image("/tiff?url=" + urlencode(url))
+                    ui.image("/tiff?url=" + quote(url))
             except Exception as e:  # noqa: BLE001
                 ui.notify(f"Failed to load CSV: {e!s}", type="negative")
 
@@ -361,11 +382,11 @@ async def _page_application_run_describe(application_run_id: str) -> None:  # no
             button.enable()
             button.props(remove="loading")
 
-    def open_marimo() -> None:
-        marimo_button.disable()
-        marimo_button.props(add="loading")
-        ui.navigate.to(f"/notebook/{run.application_run_id}")
-        marimo_button.enable()
+    def open_marimo(results_folder: Path, button: ui.button | None = None) -> None:
+        if button:
+            button.disable()
+            button.props(add="loading")
+        ui.navigate.to(f"/notebook/{run.application_run_id}?results_folder={quote(results_folder.as_posix())}")
 
     if run_data:  # noqa: PLR1702
         with ui.row().classes("w-full justify-center"):
@@ -399,11 +420,15 @@ async def _page_application_run_describe(application_run_id: str) -> None:  # no
                             ):
                                 ui.tooltip("Open results in QuPath Microscopy Viewer")
                         if find_spec("marimo"):
-                            with ui.button(
-                                "Marimo",
-                                icon="analytics",
-                                on_click=open_marimo,
-                            ).props("push") as marimo_button:
+                            with (
+                                ui.button(
+                                    "Marimo",
+                                    icon="analytics",
+                                    on_click=lambda _: download_run_dialog_open(qupath_project=False, marimo=True),
+                                )
+                                .mark("BUTTON_OPEN_NOTEBOOK")
+                                .props("push")
+                            ):
                                 ui.tooltip("Open results in Python Notebook served by Marimo")
                 if run_data.status.value == ApplicationRunStatus.RUNNING:
                     ui.button(
@@ -434,7 +459,7 @@ async def _page_application_run_describe(application_run_id: str) -> None:  # no
                     ):
                         image_file: Path | None = Path(item.reference).resolve()
                         if image_file and image_file.is_file():
-                            image_url = "/thumbnail?source=" + urlencode(image_file.as_posix())
+                            image_url = "/thumbnail?source=" + quote(image_file.as_posix())
                         else:
                             image_file = None
                             image_url = "/application_assets/image-not-found.png"

{aignostics-0.2.22 → aignostics-0.2.27}/src/aignostics/notebook/_gui.py

@@ -1,8 +1,10 @@
 """Notebook GUI."""
 
 from pathlib import Path
+from urllib.parse import quote
 
 from aignostics.gui import frame, theme
+from aignostics.system import Service as SystemService
 from aignostics.utils import BasePageBuilder, get_logger
 
 logger = get_logger(__name__)
@@ -24,6 +26,14 @@ class PageBuilder(BasePageBuilder):
                 # Nothing to do here, just to show the page
                 pass
 
+            def launch_marimo() -> None:
+                """Launch QuPath."""
+                launch_button.props(add="loading")
+                ui.notify("Launching Python Notebook...", color="blue")
+                ui.navigate.to(
+                    f"/notebook/all?results_folder={quote(SystemService.get_user_data_directory('results').as_posix())}"
+                )
+
             ui.markdown(
                 """
                     ### Manage your Marimo Extension
@@ -36,7 +46,12 @@ class PageBuilder(BasePageBuilder):
                             "Marimo is installed and ready to execute. "
                             "Go to a completed application result and click the Notebook button."
                         )
-
+                        with ui.row().classes("w-full justify-between items-center"):
+                            launch_button = ui.button(
+                                "Open",
+                                on_click=launch_marimo,
+                                icon="visibility",
+                            ).mark("BUTTON_NOTEBOOK_LAUNCH")
                     ui.markdown(
                         """
                             ###### What is Marimo?
@@ -73,23 +88,25 @@ class PageBuilder(BasePageBuilder):
                     ui.space()
 
         @ui.page("/notebook/{application_run_id}")
-        def page_application_run_marimo(application_run_id: str) -> None:
+        def page_application_run_marimo(application_run_id: str, results_folder: str) -> None:
             """Inspect Application Run in Marimo."""
             theme()
 
             with ui.row().classes("w-full justify-end"):
                 ui.button(
-                    "Back to Application Run",
+                    "Back to Application Run" if application_run_id != "all" else "Back to Marimo Extension",
                     icon="arrow_back",
                     on_click=lambda _, application_run_id=application_run_id: ui.navigate.to(
-                        f"/application/run/{application_run_id}"
+                        f"/application/run/{application_run_id}" if application_run_id != "all" else "/notebook"
                     ),
-                )
+                ).mark("BUTTON_NOTEBOOK_BACK")
 
             try:
                 server_url = Service().start()
                 ui.html(
-                    f'<iframe src="{server_url}?run_id={application_run_id}" width="100%" height="100%"></iframe>'
+                    f'<iframe src="{server_url}?application_run_id={application_run_id}'
+                    f'&results_folder={quote(results_folder)}" '
+                    'width="100%" height="100%"></iframe>'
                 ).classes("w-full h-[calc(100vh-5rem)]")
             except Exception:
                 message = "Failed to start Marimo server."

{aignostics-0.2.22 → aignostics-0.2.27}/src/aignostics/notebook/_notebook.py

@@ -8,22 +8,13 @@
 
 import marimo
 
-__generated_with = "0.13.10"
+__generated_with = "0.13.15"
 app = marimo.App(width="full")
 
 
-@app.cell
-def _(mo):
-    query_params = mo.query_params()
-    print(query_params)
-
-    print("Hallo Test Omid")
-    return
-
-
 @app.cell
 def _():
-    """E2E Demo using DICOM data from National Cancer Institute
+    """Aignostics Notebook
 
     Notes:
     - See https://colab.research.google.com/github/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/pathomics/microscopy_dicom_ann_intro.ipynb#scrollTo=fMRsnFlzinO5
@@ -39,14 +30,6 @@ def _():
     from aignostics import dataset
     from wsidicom import WsiDicom
 
-    load_dotenv()
-
-    os.environ
-
-    print(os.environ.get("GOOGLE_APPLICATION_CREDENTIALS", "default"))
-
-    print(Path.cwd())
-
     mo.sidebar([
         mo.md("# aignostics"),
         mo.nav_menu(
@@ -61,23 +44,17 @@ def _():
             orientation="vertical",
         ),
     ])
-
-    mo.vstack([
-        mo.ui.file_browser( # type: ignore
-            GSPath("gs://aignx-storage-service-dev/sample_data_formatted"), # type: ignore
-            filetypes=[".dcm", ".tif", ".tiff", ".svs", ".json"],
-            multiple=True,
-            restrict_navigation=True,
-        )
-    ])  # type: ignore
     return Path, WsiDicom, dataset, mo, plt
-ex
+
 
 @app.cell
 def _(Path, mo):
+    query_params = mo.query_params()
+    application_run_id = query_params["application_run_id"]
+    print(f"Application run id '{application_run_id}'")
     mo.vstack([
         mo.ui.file_browser(
-            Path("tmp"),
+            Path(query_params["results_folder"]),
             filetypes=[".dcm", ".tif", ".tiff", ".svs"],
             multiple=True,
             restrict_navigation=True,

{aignostics-0.2.22 → aignostics-0.2.27}/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-0.2.27}/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-0.2.27}/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: