Merge branch 'develop' into dev-define-engines-abc

Author: shaneahmed

.github/workflows/python-package.yml

@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.4.1 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.4.3 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

.pre-commit-config.yaml

@@ -60,7 +60,7 @@ repos:
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.4.1
+    rev: v0.4.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

examples/inference-pipelines/idars.ipynb

@@ -11,7 +11,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.4.1  # This will be updated by pre-commit bot to latest version
+ruff==0.4.3  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

requirements/requirements_dev.txt

@@ -120,6 +120,26 @@ def sample_ome_tiff(remote_sample: Callable) -> Path:
     return remote_sample("ome-brightfield-pyramid-1-small")
 
 
+@pytest.fixture(scope="session")
+def sample_ventana_tif(remote_sample: Callable) -> Path:
+    """Sample pytest fixture for non-tiled tif Ventana images.
+
+    Download Ventana tif image for pytest.
+
+    """
+    return remote_sample("ventana-tif")
+
+
+@pytest.fixture(scope="session")
+def sample_regular_tif(remote_sample: Callable) -> Path:
+    """Sample pytest fixture for non-tiled tif Ventana images.
+
+    Download Ventana tif image for pytest.
+
+    """
+    return remote_sample("regular-tif")
+
+
 @pytest.fixture(scope="session")
 def sample_jp2(remote_sample: Callable) -> Path:
     """Sample pytest fixture for JP2 images.

tests/conftest.py

@@ -33,7 +33,8 @@
 def cell_grid() -> list[Polygon]:
     """Generate a grid of fake cell boundary polygon annotations."""
     return [
-        cell_polygon(((i + 0.5) * 100, (j + 0.5) * 100)) for i, j in np.ndindex(5, 5)
+        cell_polygon(((i + 0.5) * 100, (j + 0.5) * 100), radius=13)
+        for i, j in np.ndindex(5, 5)
     ]
 
 
@@ -168,7 +169,7 @@ def test_filter_by_expression(fill_store: Callable, tmp_path: Path) -> None:
     tg = AnnotationTileGenerator(wsi.info, store, renderer, tile_size=256)
     thumb = tg.get_thumb_tile()
     _, num = label(np.array(thumb)[:, :, 1])
-    assert num == 25  # expect 25 cell objects, as the added one is too small
+    assert num == 25  # expect 25 cell objects
 
 
 def test_zoomed_out_rendering(fill_store: Callable, tmp_path: Path) -> None:
@@ -190,7 +191,7 @@ def test_zoomed_out_rendering(fill_store: Callable, tmp_path: Path) -> None:
 
     thumb = tg.get_tile(1, 0, 0)
     _, num = label(np.array(thumb)[:, :, 1])  # default color is green
-    assert num == 25  # expect 25 cells in top left quadrant
+    assert num == 25  # expect 25 cells in top left quadrant (added one too small)
 
 
 def test_decimation(fill_store: Callable, tmp_path: Path) -> None:
@@ -434,7 +435,7 @@ def test_unfilled_polys(fill_store: Callable, tmp_path: Path) -> None:
     renderer = AnnotationRenderer(thickness=1)
     tg = AnnotationTileGenerator(wsi.info, store, renderer, tile_size=256)
     tile_outline = np.array(tg.get_tile(1, 0, 0))
-    tg.renderer.edge_thickness = -1
+    tg.renderer.thickness = -1
     tile_filled = np.array(tg.get_tile(1, 0, 0))
     # expect sum of filled polys to be much greater than sum of outlines
     assert np.sum(tile_filled) > 2 * np.sum(tile_outline)

tests/test_annotation_tilerendering.py

@@ -1472,6 +1472,8 @@ def test_wsireader_open(
     sample_ndpi: Path,
     sample_jp2: Path,
     sample_ome_tiff: Path,
+    sample_ventana_tif: Path,
+    sample_regular_tif: Path,
     source_image: Path,
     tmp_path: pytest.TempPathFactory,
 ) -> None:
@@ -1494,6 +1496,12 @@ def test_wsireader_open(
     wsi = WSIReader.open(sample_ome_tiff)
     assert isinstance(wsi, wsireader.TIFFWSIReader)
 
+    wsi = WSIReader.open(sample_ventana_tif)
+    assert isinstance(wsi, wsireader.OpenSlideWSIReader)
+
+    wsi = WSIReader.open(sample_regular_tif)
+    assert isinstance(wsi, wsireader.VirtualWSIReader)
+
     wsi = WSIReader.open(Path(source_image))
     assert isinstance(wsi, wsireader.VirtualWSIReader)
 
@@ -2540,6 +2548,11 @@ def test_jp2_no_header(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
             "sample_key": "ome-brightfield-pyramid-1-small",
             "kwargs": {},
         },
+        {
+            "reader_class": OpenSlideWSIReader,
+            "sample_key": "ventana-tif",
+            "kwargs": {},
+        },
         {
             "reader_class": DICOMWSIReader,
             "sample_key": "dicom-1",
@@ -2565,6 +2578,7 @@ def test_jp2_no_header(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
         "AnnotationReaderOverlaid",
         "AnnotationReaderMaskOnly",
         "TIFFReader",
+        "OpenSlideReader (Ventana non-tiled tif)",
         "DICOMReader",
         "NGFFWSIReader",
         "OpenSlideWSIReader (Small SVS)",

tests/test_wsireader.py

@@ -29,6 +29,10 @@ files:
     url: [*wsis, "CMU-1-Small-Region.ome.tiff"]
   two-tiled-pages:
     url: [*wsis, "two-tiled-pages.tiff"]
+  ventana-tif:
+    url: [*wsis, "ventana-sample.tif"]
+  regular-tif:
+    url: [*wsis, "sample-regular.tif"]
   jp2-omnyx-small:
     url: [*wsis, "CMU-1-Small-Region.omnyx.jp2"]
   jp2-omnyx-1:

tiatoolbox/data/remote_samples.yaml

@@ -661,7 +661,10 @@ def to_tile_coords(
                 Array of coordinates in tile space in the form [x, y].
 
         """
-        return ((np.reshape(coords, (-1, 2)) - top_left) / scale).astype(np.int32)
+        return [
+            ((np.reshape(ring, (-1, 2)) - top_left) / scale).astype(np.int32)
+            for ring in coords
+        ]
 
     def get_color(
         self: AnnotationRenderer,
@@ -756,19 +759,26 @@ def render_poly(
             scale,
         )
         if self.thickness > -1:
-            cv2.drawContours(
+            cv2.polylines(
                 tile,
-                [cnt],
-                0,
-                col,
-                self.edge_thickness,
+                cnt,
+                isClosed=True,
+                color=col,
+                thickness=self.edge_thickness,
                 lineType=cv2.LINE_8,
             )
         else:
-            cv2.drawContours(tile, [cnt], 0, col, self.thickness, lineType=cv2.LINE_8)
+            cv2.fillPoly(tile, cnt, col)
         if self.thickness == -1 and self.edge_thickness > 0:
             edge_col = self.get_color(annotation, edge=True)
-            cv2.drawContours(tile, [cnt], 0, edge_col, 1, lineType=cv2.LINE_8)
+            cv2.polylines(
+                tile,
+                cnt,
+                isClosed=True,
+                color=edge_col,
+                thickness=1,
+                lineType=cv2.LINE_8,
+            )
 
     def render_multipoly(
         self: AnnotationRenderer,
@@ -782,7 +792,7 @@ def render_multipoly(
         geoms = annotation.coords
         for poly in geoms:
             cnt = self.to_tile_coords(poly, top_left, scale)
-            cv2.drawContours(tile, [cnt], 0, col, self.thickness, lineType=cv2.LINE_8)
+            cv2.fillPoly(tile, cnt, col)
 
     def render_pt(
         self: AnnotationRenderer,
@@ -811,7 +821,7 @@ def render_pt(
                 annotation.coords,
                 top_left,
                 scale,
-            )[0],
+            )[0][0],
             np.maximum(self.edge_thickness, 1),
             col,
             thickness=self.thickness,
@@ -838,15 +848,14 @@ def render_line(
 
         """
         col = self.get_color(annotation, edge=False)
+        cnt = self.to_tile_coords(
+            list(annotation.coords),
+            top_left,
+            scale,
+        )
         cv2.polylines(
             tile,
-            [
-                self.to_tile_coords(
-                    list(annotation.coords),
-                    top_left,
-                    scale,
-                ),
-            ],
+            [np.array(cnt)],
             isClosed=False,
             color=col,
             thickness=3,

tiatoolbox/utils/visualization.py

@@ -205,6 +205,90 @@ def is_ngff(  # noqa: PLR0911
     return is_zarr(path)
 
 
+def _handle_virtual_wsi(
+    last_suffix: str,
+    input_path: Path,
+    mpp: tuple[Number, Number] | None,
+    power: Number | None,
+) -> VirtualWSIReader | None:
+    """Handle virtual WSI cases.
+
+    Args:
+        last_suffix (str):
+            Suffix of the file to read.
+        input_path (Path):
+             Input path to virtual WSI.
+        mpp (:obj:`tuple` or :obj:`list` or :obj:`None`, optional):
+            The MPP of the WSI. If not provided, the MPP is approximated
+            from the objective power.
+        power (:obj:`float` or :obj:`None`, optional):
+            The objective power of the WSI. If not provided, the power
+            is approximated from the MPP.
+
+    Returns:
+        VirtualWSIReader | None:
+            :class:`VirtualWSIReader` if input_path is valid path to virtual WSI
+            otherwise None.
+
+    """
+
+    # Handle homogeneous cases (based on final suffix)
+    def np_virtual_wsi(
+        input_path: np.ndarray,
+        *args: Number | tuple | str | WSIMeta | None,
+        **kwargs: dict,
+    ) -> VirtualWSIReader:
+        """Create a virtual WSI from a numpy array."""
+        return VirtualWSIReader(input_path, *args, **kwargs)
+
+    suffix_to_reader = {
+        ".npy": np_virtual_wsi,
+        ".jp2": JP2WSIReader,
+        ".jpeg": VirtualWSIReader,
+        ".jpg": VirtualWSIReader,
+        ".png": VirtualWSIReader,
+        ".tif": VirtualWSIReader,
+        ".tiff": VirtualWSIReader,
+    }
+
+    if last_suffix in suffix_to_reader:
+        return suffix_to_reader[last_suffix](input_path, mpp=mpp, power=power)
+
+    return None
+
+
+def _handle_tiff_wsi(
+    input_path: Path, mpp: tuple[Number, Number] | None, power: Number | None
+) -> TIFFWSIReader | OpenSlideWSIReader | None:
+    """Handle TIFF WSI cases.
+
+    Args:
+        input_path (Path):
+             Input path to virtual WSI.
+        mpp (:obj:`tuple` or :obj:`list` or :obj:`None`, optional):
+            The MPP of the WSI. If not provided, the MPP is approximated
+            from the objective power.
+        power (:obj:`float` or :obj:`None`, optional):
+            The objective power of the WSI. If not provided, the power
+            is approximated from the MPP.
+
+    Returns:
+        OpenSlideWSIReader | TIFFWSIReader | None:
+            :class:`OpenSlideWSIReader` or :class:`TIFFWSIReader` if input_path is
+            valid path to tiff WSI otherwise None.
+
+    """
+    if openslide.OpenSlide.detect_format(input_path) is not None:
+        try:
+            return OpenSlideWSIReader(input_path, mpp=mpp, power=power)
+        except openslide.OpenSlideError:
+            pass
+    if is_tiled_tiff(input_path):
+        return TIFFWSIReader(input_path, mpp=mpp, power=power)
+
+    return None
+
+
 class WSIReader:
     """Base whole slide image (WSI) reader class.
 
@@ -279,7 +363,6 @@ def open(  # noqa: PLR0911
         WSIReader.verify_supported_wsi(input_path)
 
         # Handle special cases first (DICOM, Zarr/NGFF, OME-TIFF)
-
         if is_dicom(input_path):
             return DICOMWSIReader(input_path, mpp=mpp, power=power)
 
@@ -300,33 +383,17 @@ def open(  # noqa: PLR0911
         if suffixes[-2:] in ([".ome", ".tiff"],):
             return TIFFWSIReader(input_path, mpp=mpp, power=power)
 
-        if last_suffix in (".tif", ".tiff") and is_tiled_tiff(input_path):
-            try:
-                return OpenSlideWSIReader(input_path, mpp=mpp, power=power)
-            except openslide.OpenSlideError:
-                return TIFFWSIReader(input_path, mpp=mpp, power=power)
-
-        # Handle homogeneous cases (based on final suffix)
-        def np_virtual_wsi(
-            input_path: np.ndarray,
-            *args: Number | tuple | str | WSIMeta | None,
-            **kwargs: dict,
-        ) -> VirtualWSIReader:
-            """Create a virtual WSI from a numpy array."""
-            return VirtualWSIReader(input_path, *args, **kwargs)
-
-        suffix_to_reader = {
-            ".npy": np_virtual_wsi,
-            ".jp2": JP2WSIReader,
-            ".jpeg": VirtualWSIReader,
-            ".jpg": VirtualWSIReader,
-            ".png": VirtualWSIReader,
-            ".tif": VirtualWSIReader,
-            ".tiff": VirtualWSIReader,
-        }
+        if last_suffix in (".tif", ".tiff"):
+            tiff_wsi = _handle_tiff_wsi(input_path, mpp=mpp, power=power)
+            if tiff_wsi is not None:
+                return tiff_wsi
+
+        virtual_wsi = _handle_virtual_wsi(
+            last_suffix=last_suffix, input_path=input_path, mpp=mpp, power=power
+        )
 
-        if last_suffix in suffix_to_reader:
-            return suffix_to_reader[last_suffix](input_path, mpp=mpp, power=power)
+        if virtual_wsi is not None:
+            return virtual_wsi
 
         # Try openslide last
         return OpenSlideWSIReader(input_path, mpp=mpp, power=power)