🚸 Handle Multidimensional Features in WSIReader

tests/test_wsireader.py

@@ -78,6 +78,7 @@
 }
 RNG = np.random.default_rng()  # Numpy Random Generator
 
+
 # -------------------------------------------------------------------------------------
 # Utility Test Functions
 # -------------------------------------------------------------------------------------
@@ -2755,3 +2756,20 @@ def test_file_path_does_not_exist() -> None:
 def test_read_mpp(wsi: WSIReader) -> None:
     """Test that the mpp is read correctly."""
     assert wsi.info.mpp == pytest.approx(0.25, 1)
+
+
+def test_read_multi_channel() -> None:
+    """Test reading an image with more than three channels."""
+    # Create a simple array:
+    input_img = np.ones((1000, 1000, 6))
+    wsi = wsireader.VirtualWSIReader(input_img)
+
+    # Test read_bound function:
+    img = wsi.read_bounds(bounds=(0, 0, 50, 100))
+    assert img.shape == (100, 50, 6)
+
+    # Test read_rect function:
+    location = (0, 0)
+    size = (256, 256)
+    img = wsi.read_rect(location, size)
+    assert img.shape == (256, 256, 6)

tiatoolbox/wsicore/wsireader.py

@@ -2781,8 +2781,14 @@ class VirtualWSIReader(WSIReader):
     :func:`~tiatoolbox.utils.image.sub_pixel_read`.
 
     Attributes:
-        img (:class:`numpy.ndarray`)
-        mode (str)
+        img (:class:`numpy.ndarray`):
+            Input image as :class:`numpy.ndarray`.
+        mode (str):
+            Mode of the input image. Default is 'rgb'. Allowed values
+            are: rgb, bool, feature. "rgb" mode supports bright-field color images.
+            "bool" mode supports binary masks,
+            interpolation in this case will be "nearest" instead of "bicubic".
+            "feature" mode allows multichannel features.
 
     Args:
         input_img (str, :obj:`Path`, :class:`numpy.ndarray`):
@@ -2791,7 +2797,10 @@ class VirtualWSIReader(WSIReader):
             Metadata for the virtual wsi.
         mode (str):
             Mode of the input image. Default is 'rgb'. Allowed values
-            are: rgb, bool.
+            are: rgb, bool, feature. "rgb" mode supports bright-field color images.
+            "bool" mode supports binary masks,
+            interpolation in this case will be "nearest" instead of "bicubic".
+            "feature" mode allows multichannel features.
 
     """
 
@@ -2809,15 +2818,22 @@ def __init__(
             mpp=mpp,
             power=power,
         )
-        if mode.lower() not in ["rgb", "bool"]:
+        if mode.lower() not in ["rgb", "bool", "feature"]:
             msg = "Invalid mode."
             raise ValueError(msg)
-        self.mode = mode.lower()
+
         if isinstance(input_img, np.ndarray):
             self.img = input_img
         else:
             self.img = utils.imread(self.input_path)
 
+        if mode != "bool" and (
+            self.img.ndim == 2 or self.img.shape[2] not in [3, 4]  # noqa: PLR2004
+        ):
+            mode = "feature"
+
+        self.mode = mode.lower()
+
         if info is not None:
             self._m_info = info
 
@@ -3267,6 +3283,9 @@ class docstrings for more information.
         if interpolation in [None, "none"]:
             interpolation = None
 
+        if interpolation == "optimise" and self.mode == "bool":
+            interpolation = "nearest"
+
         im_region = utils.image.sub_pixel_read(
             self.img,
             bounds_at_read,