🩹 Support for np.ndarray and WSIReader in PatchPredictor

requirements.txt

@@ -14,7 +14,7 @@ opencv-python>=4.6.0
 openslide-python>=1.2.0
 pandas>=2.0.0
 pillow>=9.3.0
-pydicom>=2.3.1 # Used by wsidicom
+pydicom>=2.3.1 # Used by wsidef test_store_reader_no_types(tmp_path, remote_sample):dicom
 pyyaml>=6.0
 requests>=2.28.1
 scikit-image>=0.20

tests/conftest.py

@@ -3,6 +3,7 @@
 import pathlib
 import shutil
 from pathlib import Path
+from tempfile import NamedTemporaryFile
 from typing import Callable
 
 import pytest
@@ -59,6 +60,28 @@ def __remote_sample(key: str) -> pathlib.Path:
     return __remote_sample
 
 
+@pytest.fixture(scope="session")
+def blank_sample(tmp_path_factory: TempPathFactory):
+    """Factory fixture for creating blank sample files."""
+
+    class BlankSample:
+        """Sample file. Automatically deleted after use."""
+
+        def __init__(self, suffix: str):
+            self.suffix = suffix
+            self.file = None  # will be set in __enter__
+
+        def __enter__(self) -> pathlib.Path:
+            folder = tmp_path_factory.mktemp("data")
+            self.file = NamedTemporaryFile(suffix=self.suffix, dir=folder, delete=True)
+            return pathlib.Path(self.file.name)
+
+        def __exit__(self, exc_type, exc_value, traceback):
+            self.file.close()
+
+    return BlankSample
+
+
 @pytest.fixture(scope="session")
 def sample_ndpi(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for ndpi images.

tests/models/test_patch_predictor.py

@@ -25,7 +25,7 @@
 )
 from tiatoolbox.utils import env_detection as toolbox_env
 from tiatoolbox.utils.misc import download_data, imread, imwrite
-from tiatoolbox.wsicore.wsireader import WSIReader
+from tiatoolbox.wsicore.wsireader import VirtualWSIReader, WSIReader
 
 ON_GPU = toolbox_env.has_gpu()
 
@@ -222,9 +222,9 @@ def test_wsi_patch_dataset(sample_wsi_dict, tmp_path):
     mini_wsi_jpg = pathlib.Path(sample_wsi_dict["wsi2_4k_4k_jpg"])
     mini_wsi_msk = pathlib.Path(sample_wsi_dict["wsi2_4k_4k_msk"])
 
-    def reuse_init(img_path=mini_wsi_svs, **kwargs):
+    def reuse_init(input_img=mini_wsi_svs, **kwargs):
         """Testing function."""
-        return WSIPatchDataset(img_path=img_path, **kwargs)
+        return WSIPatchDataset(input_img=input_img, **kwargs)
 
     def reuse_init_wsi(**kwargs):
         """Testing function."""
@@ -249,20 +249,33 @@ def __getitem__(self, idx):
         Proto()  # skipcq
 
     # invalid path input
-    with pytest.raises(ValueError, match=r".*`img_path` must be a valid file path.*"):
+    with pytest.raises(ValueError, match=r".*`input_img` path must exist.*"):
         WSIPatchDataset(
-            img_path="aaaa",
+            input_img="aaaa",
             mode="wsi",
             patch_input_shape=[512, 512],
             stride_shape=[256, 256],
             auto_get_mask=False,
         )
 
     # invalid mask path input
-    with pytest.raises(ValueError, match=r".*`mask_path` must be a valid file path.*"):
+    with pytest.raises(ValueError, match=r".*`mask` must be a valid file path.*"):
         WSIPatchDataset(
-            img_path=mini_wsi_svs,
-            mask_path="aaaa",
+            input_img=mini_wsi_svs,
+            mask="aaaa",
+            mode="wsi",
+            patch_input_shape=[512, 512],
+            stride_shape=[256, 256],
+            resolution=1.0,
+            units="mpp",
+            auto_get_mask=False,
+        )
+
+    # mask as not VirtualWSIReader
+    with pytest.raises(ValueError, match=r".*`mask` must be .* VirtualWSIReader.*"):
+        WSIPatchDataset(
+            input_img=mini_wsi_svs,
+            mask=WSIReader.open(mini_wsi_svs),
             mode="wsi",
             patch_input_shape=[512, 512],
             stride_shape=[256, 256],
@@ -275,6 +288,10 @@ def __getitem__(self, idx):
     with pytest.raises(ValueError, match="`X` is not supported."):
         reuse_init(mode="X")
 
+    # invalid units
+    with pytest.raises(ValueError, match="`X` is not supported."):
+        reuse_init(units="X")
+
     # invalid patch
     with pytest.raises(ValueError, match="Invalid `patch_input_shape` value None."):
         reuse_init()
@@ -346,8 +363,8 @@ def __getitem__(self, idx):
     )
     assert len(ds) > 0
     ds = WSIPatchDataset(
-        img_path=mini_wsi_svs,
-        mask_path=mini_wsi_msk,
+        input_img=mini_wsi_svs,
+        mask=mini_wsi_msk,
         mode="wsi",
         patch_input_shape=[512, 512],
         stride_shape=[256, 256],
@@ -361,8 +378,8 @@ def __getitem__(self, idx):
     imwrite(negative_mask_path, negative_mask)
     with pytest.raises(ValueError, match="No patch coordinates remain after filtering"):
         ds = WSIPatchDataset(
-            img_path=mini_wsi_svs,
-            mask_path=negative_mask_path,
+            input_img=mini_wsi_svs,
+            mask=negative_mask_path,
             mode="wsi",
             patch_input_shape=[512, 512],
             stride_shape=[256, 256],
@@ -374,7 +391,7 @@ def __getitem__(self, idx):
     # * for tile
     reader = WSIReader.open(mini_wsi_jpg)
     tile_ds = WSIPatchDataset(
-        img_path=mini_wsi_jpg,
+        input_img=mini_wsi_jpg,
         mode="tile",
         patch_input_shape=patch_size,
         stride_shape=stride_size,
@@ -395,6 +412,72 @@ def __getitem__(self, idx):
     assert roi1.shape[1] == roi2.shape[1]
     assert np.min(correlation) > 0.9, correlation
 
+    positive_mask = (negative_mask + 1).astype(bool)
+    # check mask as np array
+    with pytest.raises(ValueError, match=r".*`mask` must be binary.*"):
+        WSIPatchDataset(
+            input_img=mini_wsi_svs,
+            mask=np.array([[0, 0, 1]]),
+            mode="wsi",
+            patch_input_shape=[512, 512],
+            stride_shape=[256, 256],
+            auto_get_mask=False,
+            resolution=1.0,
+            units="mpp",
+        )
+    ds = WSIPatchDataset(
+        input_img=mini_wsi_svs,
+        mask=positive_mask,
+        mode="wsi",
+        patch_input_shape=[512, 512],
+        stride_shape=[256, 256],
+        auto_get_mask=False,
+        resolution=1.0,
+        units="mpp",
+    )
+
+    assert len(ds) > 0
+
+    # check mask VirtualWSIReader
+    with pytest.raises(ValueError, match=r".*`mask` must be binary.*"):
+        WSIPatchDataset(
+            input_img=mini_wsi_svs,
+            mask=VirtualWSIReader(np.array([[0, 0, 5]])),
+            mode="wsi",
+            patch_input_shape=[512, 512],
+            stride_shape=[256, 256],
+            auto_get_mask=False,
+            resolution=1.0,
+            units="mpp",
+        )
+
+    ds_from_fp = WSIPatchDataset(
+        input_img=mini_wsi_svs,
+        mask=VirtualWSIReader(positive_mask, mode="bool"),
+        mode="wsi",
+        patch_input_shape=[512, 512],
+        stride_shape=[256, 256],
+        auto_get_mask=False,
+        resolution=1.0,
+        units="mpp",
+    )
+
+    assert len(ds_from_fp) > 0
+
+    mini_wsi_svs_np = imread(mini_wsi_svs)
+    ds_from_np = WSIPatchDataset(
+        input_img=mini_wsi_svs_np,
+        mask=VirtualWSIReader(positive_mask, mode="bool"),
+        mode="wsi",
+        patch_input_shape=[512, 512],
+        stride_shape=[256, 256],
+        auto_get_mask=False,
+        resolution=1.0,
+        units="baseline",
+    )
+
+    assert len(ds_from_np) > 0
+
 
 def test_patch_dataset_abc():
     """Test for ABC methods."""
@@ -489,6 +572,12 @@ def test_predictor_crash():
         predictor.predict([1, 2, 3], masks=[1, 2], mode="wsi")
     with pytest.raises(ValueError, match=r".*labels.*!=.*imgs.*"):
         predictor.predict([1, 2, 3], labels=[1, 2], mode="patch")
+    # mask on patch are not supported
+    with pytest.raises(ValueError, match=r".*masks are not supported .* `patch`.*"):
+        predictor.predict(
+            [np.array([1, 2, 3])], masks=[np.array([1, 2, 3])], mode="patch"
+        )
+
     # remove previously generated data
     _rm_dir("output")
 
@@ -673,7 +762,7 @@ def test_patch_predictor_api(sample_patch1, sample_patch2, tmp_path):
     # test prediction
     predictor = PatchPredictor(model=model, batch_size=1, verbose=False)
     output = predictor.predict(
-        inputs,
+        input_imgs=inputs,
         return_probabilities=True,
         labels=[1, "a"],
         return_labels=True,
@@ -799,6 +888,58 @@ def test_wsi_predictor_api(sample_wsi_dict, tmp_path):
     # remove previously generated data
     _rm_dir("output")
 
+    # check that predictor can take in WSIReader object
+    svs_objects = [WSIReader.open(i) for i in [mini_wsi_svs, mini_wsi_svs]]
+    output = predictor.predict(
+        svs_objects,
+        masks=[mini_wsi_msk, mini_wsi_msk],
+        mode="wsi",
+        **kwargs,
+    )
+    assert str(mini_wsi_svs) in output
+    # remove previously generated data
+    _rm_dir(kwargs["save_dir"])
+
+    # check that predictor can take in ndarray object
+    img_objects = [
+        WSIReader.open(i).slide_thumbnail(1, "baseline")
+        for i in [mini_wsi_svs, mini_wsi_svs]
+    ]
+
+    with pytest.raises(ValueError, match=".*Cannot determine scale.*"):
+        predictor.predict(
+            img_objects,
+            masks=[mini_wsi_msk, mini_wsi_msk],
+            mode="wsi",
+            **kwargs,
+        )
+    _rm_dir(kwargs["save_dir"])
+
+    _ = predictor.predict(
+        img_objects,
+        masks=[mini_wsi_msk, mini_wsi_msk],
+        mode="tile",
+        ignore_resolutions=True,
+        **kwargs,
+    )
+    _rm_dir(kwargs["save_dir"])
+
+    _kwargs = copy.deepcopy(kwargs)
+    _kwargs["units"] = "baseline"
+    _kwargs["resolution"] = 1.0
+
+    output = predictor.predict(
+        img_objects,
+        masks=[mini_wsi_msk, mini_wsi_msk],
+        mode="wsi",
+        **_kwargs,
+    )
+
+    assert len(output) == 2
+    assert 0 in output
+    assert 1 in output
+    _rm_dir(_kwargs["save_dir"])
+
 
 def test_wsi_predictor_merge_predictions(sample_wsi_dict):
     """Test normal run of wsi predictor with merge predictions option."""

tests/test_patch_extraction.py

@@ -98,10 +98,9 @@ def test_get_patch_extractor(source_image, patch_extr_csv):
 
 
 def test_points_patch_extractor_image_format(
-    sample_svs, sample_jp2, source_image, patch_extr_csv
+    sample_svs, sample_jp2, source_image, patch_extr_csv, blank_sample
 ):
     """Test PointsPatchExtractor returns the right object."""
-    file_parent_dir = pathlib.Path(__file__).parent
     locations_list = pathlib.Path(patch_extr_csv)
 
     points = patchextraction.get_patch_extractor(
@@ -131,10 +130,9 @@ def test_points_patch_extractor_image_format(
 
     assert isinstance(points.wsi, OmnyxJP2WSIReader)
 
-    false_image = pathlib.Path(file_parent_dir.joinpath("data/source_image.test"))
-    with pytest.raises(FileNotSupported):
+    with blank_sample(".test") as false_image_path, pytest.raises(FileNotSupported):
         _ = patchextraction.get_patch_extractor(
-            input_img=false_image,
+            input_img=false_image_path,
             locations_list=locations_list,
             method_name="point",
             patch_size=(200, 200),