def test_innereyecontainer_setup_passes_on_allow_incomplete_labels(
test_output_dirs: OutputFolderForTests,
allow_partial_ground_truth: bool) -> None:
"""
Test that InnerEyeContainer.setup passes on the correct value of allow_incomplete_labels to
full_image_dataset.convert_channels_to_file_paths
:param test_output_dirs: Test fixture.
:param allow_partial_ground_truth: The value to set allow_incomplete_labels to and check it is
passed through.
"""
config = DummyModel()
config.set_output_to(test_output_dirs.root_dir)
config.allow_incomplete_labels = allow_partial_ground_truth
container = InnerEyeContainer(config)
def mocked_convert_channels_to_file_paths(
_: List[str], __: pd.DataFrame, ___: Path, ____: str,
allow_incomplete_labels: bool) -> Tuple[List[Optional[Path]], str]:
paths: List[Optional[Path]] = []
failed_channel_info = ''
assert allow_incomplete_labels == allow_partial_ground_truth
return paths, failed_channel_info
with mock.patch("InnerEye.ML.lightning_base.convert_channels_to_file_paths"
) as convert_channels_to_file_paths_mock:
convert_channels_to_file_paths_mock.side_effect = mocked_convert_channels_to_file_paths
container.setup()
convert_channels_to_file_paths_mock.assert_called()
def test_convert_channels_to_file_paths(
default_config: ModelConfigBase) -> None:
"""
Test unit for missing channels and missing files.
"""
# Sets DummyModel config and container
container = InnerEyeContainer(default_config)
# 1 Should not return any errors given that no channels or files are missing
container.setup()
# 2 Creates InnerEyeContainer object with: missing channels: "channel1", "channel2", 'mask'
# for patients 1 and 4. Wrong file name for channel "mask", patient 2. Error report is generated
# for patients 1,2,4. Patient 3 should not generate any error as no channel, file is missing.
# Commented lines show missing and expected error reporting.
data_frame = [
# ["1", "train_and_test_data/id1_channel1.nii.gz", "channel1", "1"],
# ["1", "train_and_test_data/id1_channel1.nii.gz", "channel2", "1"],
# ["1", "train_and_test_data/id1_mask.nii.gz", "mask", "1"],
["1", "train_and_test_data/id1_region.nii.gz", "region", "1"],
["1", "train_and_test_data/id1_region.nii.gz", "region_1", "1"],
["2", "train_and_test_data/id2_channel1.nii.gz", "channel1", "2"],
["2", "train_and_test_data/id2_channel1.nii.gz", "channel2", "2"],
["2", "FILE_A", "mask", "2"],
["2", "train_and_test_data/id2_region.nii.gz", "region", "2"],
["2", "train_and_test_data/id2_region.nii.gz", "region_1", "2"],
["3", "train_and_test_data/id2_channel1.nii.gz", "channel1", "3"],
["3", "train_and_test_data/id2_channel1.nii.gz", "channel2", "3"],
["3", "train_and_test_data/id2_mask.nii.gz", "mask", "3"],
["3", "train_and_test_data/id2_region.nii.gz", "region", "3"],
["3", "train_and_test_data/id2_region.nii.gz", "region_1", "3"],
# ["4", "train_and_test_data/id2_channel1.nii.gz", "channel1", "4"],
# ["4", "train_and_test_data/id2_channel1.nii.gz", "channel2", "4"],
# ["4", "train_and_test_data/id2_mask.nii.gz", "mask", "4"],
["4", "train_and_test_data/id2_region.nii.gz", "region", "4"],
["4", "train_and_test_data/id2_region.nii.gz", "region_1", "4"]
]
# 3 Overwrite get_model_train_test_dataset_splits method for subjects 1,2,3,4
class MyDummyModel(DummyModel):
def get_model_train_test_dataset_splits(
self, dataset_df: pd.DataFrame) -> DatasetSplits:
return DatasetSplits(
train=dataset_df[dataset_df.subject.isin(['1'])],
test=dataset_df[dataset_df.subject.isin(['2', '3'])],
val=dataset_df[dataset_df.subject.isin(['4'])])
config_missing_channels_and_files = MyDummyModel()
data_frame_with_missing_channels_and_files = pd.DataFrame(
data_frame,
columns=['subject', 'filePath', 'channel', 'institutionId'])
config_missing_channels_and_files._dataset_data_frame = data_frame_with_missing_channels_and_files
container_missing_files_channels = InnerEyeContainer(
config_missing_channels_and_files)
with pytest.raises(ValueError) as e:
container_missing_files_channels.setup()
assert "Patient 1 does not have channel 'channel1'" in str(e.value)
assert "Patient 1 does not have channel 'channel2'" in str(e.value)
assert "Patient 1 does not have channel 'mask'" in str(e.value)
assert "Patient 2" in str(e.value) and "FILE_A does not exist" in str(
e.value)
assert "Patient 3" not in str(e.value)
assert "Patient 4 does not have channel 'channel1'" in str(e.value)
assert "Patient 4 does not have channel 'channel2'" in str(e.value)
assert "Patient 4 does not have channel 'mask'" in str(e.value)