🐛 Fix Code Complexity in wsireader (#814)

Fix Code Complexity in `wsireader`
- Fixes `PLR0912`, `C901`
- Improves coverage to include cases with regular tiff files.

Author: shaneahmed

tests/conftest.py

@@ -130,6 +130,16 @@ def sample_ventana_tif(remote_sample: Callable) -> Path:
     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/test_wsireader.py

@@ -1473,6 +1473,7 @@ def test_wsireader_open(
     sample_jp2: Path,
     sample_ome_tiff: Path,
     sample_ventana_tif: Path,
+    sample_regular_tif: Path,
     source_image: Path,
     tmp_path: pytest.TempPathFactory,
 ) -> None:
@@ -1498,6 +1499,9 @@ def test_wsireader_open(
     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)
 

tiatoolbox/data/remote_samples.yaml

@@ -30,7 +30,9 @@ files:
   two-tiled-pages:
     url: [*wsis, "two-tiled-pages.tiff"]
   ventana-tif:
-    url: [*wsis, "ventana_sample.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/wsicore/wsireader.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.
 
@@ -228,7 +312,7 @@ class WSIReader:
     """
 
     @staticmethod
-    def open(  # noqa: PLR0911, PLR0912, C901
+    def open(  # noqa: PLR0911
         input_img: str | Path | np.ndarray | WSIReader,
         mpp: tuple[Number, Number] | None = None,
         power: Number | None = None,
@@ -279,7 +363,6 @@ def open(  # noqa: PLR0911, PLR0912, C901
         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)
 
@@ -301,35 +384,16 @@ def open(  # noqa: PLR0911, PLR0912, C901
             return TIFFWSIReader(input_path, mpp=mpp, power=power)
 
         if last_suffix in (".tif", ".tiff"):
-            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)
-
-        # 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,
-        }
+            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)