Create and test mock slides dataset

Tests/ML/histopathology/datasets/test_slides_dataset.py

@@ -0,0 +1,40 @@
+import os
+
+import pandas as pd
+
+from InnerEye.Common.fixed_paths_for_tests import tests_root_directory
+from InnerEye.ML.Histopathology.datasets.base_dataset import SlidesDataset
+from InnerEye.ML.Histopathology.utils.naming import SlideKey
+
+HISTO_TEST_DATA_DIR = str(tests_root_directory("ML/histopathology/test_data"))
+
+
+class MockSlidesDataset(SlidesDataset):
+ DEFAULT_CSV_FILENAME = "test_slides_dataset.csv"
+ METADATA_COLUMNS = ('meta1', 'meta2')
+
+ def __init__(self) -> None:
+ super().__init__(root=HISTO_TEST_DATA_DIR)
+
+
+def test_slides_dataset() -> None:
+ dataset = MockSlidesDataset()
+ assert isinstance(dataset.dataset_df, pd.DataFrame)
+ assert dataset.dataset_df.index.name == dataset.SLIDE_ID_COLUMN
+ assert len(dataset) == len(dataset.dataset_df)
+
+ sample = dataset[0]
+ assert isinstance(sample, dict)
+ assert all(isinstance(key, SlideKey) for key in sample)
+
+ expected_keys = [SlideKey.SLIDE_ID, SlideKey.IMAGE, SlideKey.IMAGE_PATH, SlideKey.LABEL,
+ SlideKey.METADATA]
+ assert all(key in sample for key in expected_keys)
+
+ image_path = sample[SlideKey.IMAGE_PATH]
+ assert isinstance(image_path, str)
+ assert os.path.isfile(image_path)
+
+ metadata = sample[SlideKey.METADATA]
+ assert isinstance(metadata, dict)
+ assert all(meta_col in metadata for meta_col in type(dataset).METADATA_COLUMNS)

Tests/ML/histopathology/preprocessing/test_slide_loading.py

@@ -1,26 +1,19 @@
-import os
-from typing import Any, Dict, Optional
+from typing import Optional
 
 import numpy as np
 import pytest
 from cucim import CuImage
 from monai.data.image_reader import WSIReader
 
 from InnerEye.Common.fixed_paths_for_tests import tests_root_directory
-from InnerEye.ML.Histopathology.datasets.default_paths import PANDA_DATASET_DIR
-from InnerEye.ML.Histopathology.datasets.panda_dataset import PandaDataset
 from InnerEye.ML.Histopathology.preprocessing.tiling import tile_array_2d
 from InnerEye.ML.Histopathology.preprocessing.loading import LoadROId, get_luminance, load_slide_at_level, segment_foreground
 from InnerEye.ML.Histopathology.utils.naming import SlideKey
+from Tests.ML.histopathology.datasets.test_slides_dataset import MockSlidesDataset
 
 TEST_IMAGE_PATH = str(tests_root_directory("ML/histopathology/test_data/panda_wsi_example.tiff"))
 
 
-def _get_sample() -> Dict[SlideKey, Any]:
- dataset = PandaDataset(PANDA_DATASET_DIR)
- return dataset[0]
-
-
 def test_load_slide() -> None:
  level = 2
  reader = WSIReader('cuCIM')
@@ -134,13 +127,12 @@ def test_get_bounding_box(level: int, foreground_threshold: Optional[float]) ->
  assert level0_bbox_margin.h == level0_bbox.h + 2 * level0_margin
 
 
-@pytest.mark.skipif(not os.path.isdir(PANDA_DATASET_DIR),
- reason="PANDA dataset is unavailable")
 @pytest.mark.parametrize('level', [1, 2])
 @pytest.mark.parametrize('margin', [0, 42])
 @pytest.mark.parametrize('foreground_threshold', [None, 215])
 def test_load_roi(level: int, margin: int, foreground_threshold: Optional[float]) -> None:
- sample = _get_sample()
+ dataset = MockSlidesDataset()
+ sample = dataset[0]
  reader = WSIReader('cuCIM')
  loader = LoadROId(reader, image_key=SlideKey.IMAGE, level=level, margin=margin,
  foreground_threshold=foreground_threshold)

Tests/ML/histopathology/test_data/test_slides_dataset.csv

@@ -0,0 +1,2 @@
+slide_id,image,label,meta1,meta2
+foo,panda_wsi_example.tiff,0,bar,baz