Use PANDA instead of TCGA-PRAD in test

InnerEye/ML/Histopathology/datasets/default_paths.py

@@ -3,11 +3,13 @@
 # Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
 # ------------------------------------------------------------------------------------------
 
+PANDA_DATASET_ID = "PANDA"
 PANDA_TILES_DATASET_ID = "PANDA_tiles"
 TCGA_CRCK_DATASET_ID = "TCGA-CRCk"
 TCGA_PRAD_DATASET_ID = "TCGA-PRAD"
 
 DEFAULT_DATASET_LOCATION = "/tmp/datasets/"
+PANDA_DATASET_DIR = DEFAULT_DATASET_LOCATION + PANDA_DATASET_ID
 PANDA_TILES_DATASET_DIR = DEFAULT_DATASET_LOCATION + PANDA_TILES_DATASET_ID
 TCGA_CRCK_DATASET_DIR = DEFAULT_DATASET_LOCATION + TCGA_CRCK_DATASET_ID
 TCGA_PRAD_DATASET_DIR = DEFAULT_DATASET_LOCATION + TCGA_PRAD_DATASET_ID

InnerEye/ML/Histopathology/datasets/panda_dataset.py

@@ -39,7 +39,7 @@ def __init__(self,
  dataset_df: Optional[pd.DataFrame] = None) -> None:
  super().__init__(root, dataset_csv, dataset_df, validate_columns=False)
  # PANDA CSV does not come with paths for image and mask files
- slide_ids = self.dataset_df[self.SLIDE_ID_COLUMN]
+ slide_ids = self.dataset_df.index
  self.dataset_df[self.IMAGE_COLUMN] = "train_images/" + slide_ids + ".tiff"
  self.dataset_df[self.MASK_COLUMN] = "train_label_masks/" + slide_ids + "_mask.tiff"
  self.validate_columns()

Tests/ML/histopathology/preprocessing/test_slide_loading.py

@@ -7,8 +7,8 @@
 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 TCGA_PRAD_DATASET_DIR
-from InnerEye.ML.Histopathology.datasets.tcga_prad_dataset import TcgaPradDataset
+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
@@ -17,15 +17,13 @@
 
 
 def _get_sample() -> Dict[SlideKey, Any]:
- dataset = TcgaPradDataset(TCGA_PRAD_DATASET_DIR)
+ dataset = PandaDataset(PANDA_DATASET_DIR)
  return dataset[0]
 
 
 def test_load_slide() -> None:
  level = 2
  reader = WSIReader('cuCIM')
- # image_path = _get_sample()[SlideKey.IMAGE]
- # print(image_path)
  slide_obj: CuImage = reader.read(TEST_IMAGE_PATH)
  dims = slide_obj.resolutions['level_dimensions'][level][::-1]
 
@@ -136,9 +134,9 @@ 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(TCGA_PRAD_DATASET_DIR),
- reason="TCGA-PRAD dataset is unavailable")
-@pytest.mark.parametrize('level', [2, 3])
+@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: