♻️ Refactor / Split wsireader into Multiple Modules

tests/test_tiffreader.py

@@ -18,6 +18,7 @@
 from unittest.mock import MagicMock
 
 from tiatoolbox.wsicore import wsireader
+from tiatoolbox.wsicore.wsireader import tiff
 
 
 def test_ome_missing_instrument_ref(
@@ -154,7 +155,7 @@ def __init__(
     assert isinstance(reader, wsireader.VirtualWSIReader)
 
 
-def test_try_tiff_raises_other_valueerror(
+def test_try_tiff_raises_other_value_error(
     monkeypatch: pytest.MonkeyPatch, track_tmp_path: Path
 ) -> None:
     """Test try_tiff raises ValueError if not an unsupported TIFF format."""
@@ -174,7 +175,7 @@ def raise_other_valueerror(*args: object, **kwargs: object) -> None:
         msg = "Some other TIFF error"
         raise ValueError(msg)
 
-    monkeypatch.setattr(wsireader, "TIFFWSIReader", raise_other_valueerror)
+    monkeypatch.setattr(tiff, "TIFFWSIReader", raise_other_valueerror)
 
     with pytest.raises(ValueError, match="Some other TIFF error"):
         wsireader.WSIReader.try_tiff(
@@ -619,11 +620,11 @@ def test_handle_tiff_wsi_returns_tiff_reader(
     image.save(tiff_path)
 
     # Patch is_tiled_tiff to return True
-    monkeypatch.setattr(wsireader, "is_tiled_tiff", lambda _: True)
+    monkeypatch.setattr(wsireader.base, "is_tiled_tiff", lambda _: True)
 
     # Patch TIFFWSIReader.__init__ to bypass internal checks
     with patch(
-        "tiatoolbox.wsicore.wsireader.TIFFWSIReader.__init__", return_value=None
+        "tiatoolbox.wsicore.wsireader.tiff.TIFFWSIReader.__init__", return_value=None
     ):
         reader = wsireader._handle_tiff_wsi(
             input_path=tiff_path,
@@ -639,7 +640,7 @@ def raise_openslide_error(*args: object, **kwargs: object) -> None:
     _ = args
     _ = kwargs
     msg = "mock error"
-    raise wsireader.openslide.OpenSlideError(msg)
+    raise wsireader.openslide.openslide.OpenSlideError(msg)
 
 
 def test_handle_tiff_wsi_openslide_error(
@@ -651,19 +652,23 @@ def test_handle_tiff_wsi_openslide_error(
     Image.new("RGB", (10, 10), color="white").save(tiff_path)
 
     # Patch detect_format to return a non-None value
-    monkeypatch.setattr(wsireader.openslide.OpenSlide, "detect_format", lambda _: "SVS")
+    monkeypatch.setattr(
+        wsireader.openslide.openslide.OpenSlide, "detect_format", lambda _: "SVS"
+    )
 
     # Patch OpenSlideWSIReader to raise OpenSlideError
-    monkeypatch.setattr(wsireader, "OpenSlideWSIReader", raise_openslide_error)
+    monkeypatch.setattr(
+        wsireader.openslide, "OpenSlideWSIReader", raise_openslide_error
+    )
 
     # Patch is_tiled_tiff to return True so fallback to TIFFWSIReader is triggered
-    monkeypatch.setattr(wsireader, "is_tiled_tiff", lambda _: True)
+    monkeypatch.setattr(wsireader.base, "is_tiled_tiff", lambda _: True)
 
     # Patch TIFFWSIReader.__init__ to bypass internal checks
     with patch(
-        "tiatoolbox.wsicore.wsireader.TIFFWSIReader.__init__", return_value=None
+        "tiatoolbox.wsicore.wsireader.tiff.TIFFWSIReader.__init__", return_value=None
     ):
-        result = wsireader._handle_tiff_wsi(
+        result = wsireader.base._handle_tiff_wsi(
             input_path=tiff_path,
             mpp=(0.5, 0.5),
             power=20.0,
@@ -681,7 +686,9 @@ def test_handle_tiff_wsi_openslide_success(
     Image.new("RGB", (10, 10), color="white").save(tiff_path)
 
     # Patch detect_format to return a valid format
-    monkeypatch.setattr(wsireader.openslide.OpenSlide, "detect_format", lambda _: "SVS")
+    monkeypatch.setattr(
+        wsireader.openslide.openslide.OpenSlide, "detect_format", lambda _: "SVS"
+    )
 
     # Patch OpenSlideWSIReader.__init__ to bypass actual init logic
     with patch.object(wsireader.OpenSlideWSIReader, "__init__", return_value=None):

tests/test_wsireader.py

@@ -3125,7 +3125,9 @@ def test_fsspec_json_wsi_reader_instantiation() -> None:
             "tiatoolbox.wsicore.wsireader.FsspecJsonWSIReader.is_valid_zarr_fsspec",
             return_value=True,
         ),
-        patch("tiatoolbox.wsicore.wsireader.FsspecJsonWSIReader") as mock_reader,
+        patch(
+            "tiatoolbox.wsicore.wsireader.fsspec_json.FsspecJsonWSIReader"
+        ) as mock_reader,
     ):
         WSIReader.open(input_path, mpp, power)
         mock_reader.assert_called_once_with(input_path, mpp=mpp, power=power)
@@ -3785,14 +3787,14 @@ def test_virtualwsireader_mode_detection_edge_cases() -> None:
     """Test VirtualWSIReader mode detection with various image types."""
     # Test with 2D image (should set mode to 'feature')
     img_2d = np.ones((100, 100), dtype=np.uint8)
-    with patch("tiatoolbox.wsicore.wsireader.logger") as mock_logger:
+    with patch("tiatoolbox.wsicore.wsireader.base.logger") as mock_logger:
         wsi = VirtualWSIReader(img_2d, mode="rgb")
         mock_logger.warning.assert_called()
         assert wsi.mode == "feature"
 
     # Test with 5-channel image (should set mode to 'feature')
     img_5ch = np.ones((100, 100, 5), dtype=np.uint8)
-    with patch("tiatoolbox.wsicore.wsireader.logger") as mock_logger:
+    with patch("tiatoolbox.wsicore.wsireader.base.logger") as mock_logger:
         wsi = VirtualWSIReader(img_5ch, mode="rgb")
         mock_logger.warning.assert_called()
         assert wsi.mode == "feature"
@@ -3811,7 +3813,7 @@ def test_openslide_estimate_mpp_edge_cases() -> None:
         "tiff.ResolutionUnit": "inch",
         # Missing YResolution
     }
-    with patch("tiatoolbox.wsicore.wsireader.logger") as mock_logger:
+    with patch("tiatoolbox.wsicore.wsireader.openslide.logger") as mock_logger:
         result = OpenSlideWSIReader._estimate_mpp(props)
         mock_logger.warning.assert_called()
         assert result is None
@@ -4263,7 +4265,7 @@ def test_virtual_read_rect_resolution_coord_space_roundtrip() -> None:
 class TestTryOpenSlide:
     """Unit tests for the WSIReader.try_openslide static method."""
 
-    @patch("tiatoolbox.wsicore.wsireader.OpenSlideWSIReader")
+    @patch("tiatoolbox.wsicore.wsireader.openslide.OpenSlideWSIReader")
     def test_tiff_suffix_success(self, mock_reader: MagicMock) -> None:
         """Test that a valid TIFF file results in an OpenSlideWSIReader instance."""
         mock_instance = MagicMock()
@@ -4283,7 +4285,7 @@ def test_tiff_suffix_success(self, mock_reader: MagicMock) -> None:
         )
         assert result is mock_instance
 
-    @patch("tiatoolbox.wsicore.wsireader.OpenSlideWSIReader")
+    @patch("tiatoolbox.wsicore.wsireader.openslide.OpenSlideWSIReader")
     def test_tiff_suffix_raises_openslide_error(self, mock_reader: MagicMock) -> None:
         """Test that OpenSlide errors are caught and the function returns None."""
         mock_reader.side_effect = openslide.OpenSlideError("bad file")

tiatoolbox/wsicore/__init__.py

@@ -1,11 +1,12 @@
 """Package to read whole slide images."""
 
-from typing import TypedDict
+from numbers import Number
+from typing import TYPE_CHECKING, TypedDict
 
 from tiatoolbox.wsicore import metadata, wsimeta, wsireader
 
 from .wsimeta import WSIMeta
-from .wsireader import Number, WSIReader
+from .wsireader import WSIReader
 
 # Top level imports
 __all__ = [