def test_head_and_neck_paper_with_no_ground_truth_ids() -> None:
"""
Check that passing num_structures = default generates all default structures.
"""
ground_truth_ids = DEFAULT_HEAD_AND_NECK_GROUND_TRUTH_IDS
config = HeadAndNeckPaper(local_dataset=Path("foo"), )
assert config.ground_truth_ids == ground_truth_ids
def test_head_and_neck_paper_with_optional_params(
ground_truth_count: int) -> None:
"""
Check that optional parameters can be passed in.
"""
ground_truth_ids = DEFAULT_HEAD_AND_NECK_GROUND_TRUTH_IDS[:
ground_truth_count]
ground_truth_ids_display_names = generate_random_display_ids(
ground_truth_count)
colours = generate_random_colours_list(RANDOM_COLOUR_GENERATOR,
ground_truth_count)
fill_holes = generate_random_fill_holes(ground_truth_count)
class_weights = generate_random_class_weights(ground_truth_count + 1)
num_feature_channels = random.randint(1, ground_truth_count)
slice_exclusion_rules = generate_random_slice_exclusion_rules(
ground_truth_ids)
summed_probability_rules = generate_random_summed_probability_rules(
ground_truth_ids)
config = HeadAndNeckPaper(
num_structures=ground_truth_count,
ground_truth_ids_display_names=ground_truth_ids_display_names,
colours=colours,
fill_holes=fill_holes,
class_weights=class_weights,
num_feature_channels=num_feature_channels,
slice_exclusion_rules=slice_exclusion_rules,
summed_probability_rules=summed_probability_rules)
assert config.ground_truth_ids == ground_truth_ids
assert config.ground_truth_ids_display_names == ground_truth_ids_display_names
assert config.colours == colours
assert config.fill_holes == fill_holes
assert config.class_weights == class_weights
assert config.feature_channels == [num_feature_channels]
assert config.slice_exclusion_rules == slice_exclusion_rules
assert config.summed_probability_rules == summed_probability_rules
def test_head_and_neck_paper_with_0_ground_truth_ids() -> None:
"""
Check that passing num_structures = 0 raises ValueError exception.
"""
with pytest.raises(ValueError) as e:
assert HeadAndNeckPaper(local_dataset=Path("foo"), num_structures=0)
assert str(
e.value
) == f"num structures must be between 0 and {len(DEFAULT_HEAD_AND_NECK_GROUND_TRUTH_IDS)}"
def test_head_and_neck_paper_with_some_ground_truth_ids(
ground_truth_count: int) -> None:
"""
Check that passing a num_structures between 1 and len(defaults) generates the correct subset.
"""
ground_truth_ids = DEFAULT_HEAD_AND_NECK_GROUND_TRUTH_IDS[:
ground_truth_count]
config = HeadAndNeckPaper(num_structures=ground_truth_count)
assert config.ground_truth_ids == ground_truth_ids
def test_head_and_neck_paper_with_too_many_ground_truth_ids() -> None:
"""
Check that passing num_structures larger than len(defaults) raises ValueError exception.
"""
ground_truth_count = len(DEFAULT_HEAD_AND_NECK_GROUND_TRUTH_IDS) + 2
with pytest.raises(ValueError) as e:
assert HeadAndNeckPaper(num_structures=ground_truth_count)
assert str(
e.value
) == f"num structures must be between 0 and {len(DEFAULT_HEAD_AND_NECK_GROUND_TRUTH_IDS)}"
def test_head_and_neck_paper_with_mismatched_fill_holes_raises() -> None:
"""
Check that passing too many colours raises ValueError exception.
"""
ground_truth_count = len(DEFAULT_HEAD_AND_NECK_GROUND_TRUTH_IDS) - 2
fill_holes = generate_random_fill_holes(ground_truth_count - 1)
with pytest.raises(ValueError) as e:
assert HeadAndNeckPaper(num_structures=ground_truth_count,
fill_holes=fill_holes)
assert str(
e.value) == "len(ground_truth_ids_display_names)!=len(fill_holes)"
def test_head_and_neck_paper_with_mismatched_colours_raises() -> None:
"""
Check that passing too many colours raises ValueError exception.
"""
ground_truth_count = len(DEFAULT_HEAD_AND_NECK_GROUND_TRUTH_IDS) - 2
colours = generate_random_colours_list(RANDOM_COLOUR_GENERATOR,
ground_truth_count - 1)
with pytest.raises(ValueError) as e:
assert HeadAndNeckPaper(local_dataset=Path("foo"),
num_structures=ground_truth_count,
colours=colours)
assert str(e.value) == "len(ground_truth_ids_display_names)!=len(colours)"
def test_head_and_neck_paper_with_mismatched_class_weights_raises() -> None:
"""
Check that passing too many colours raises ValueError exception.
"""
ground_truth_count = len(DEFAULT_HEAD_AND_NECK_GROUND_TRUTH_IDS) - 2
class_weights = generate_random_class_weights(ground_truth_count - 1)
with pytest.raises(ValueError) as e:
assert HeadAndNeckPaper(num_structures=ground_truth_count,
class_weights=class_weights)
assert str(
e.value
) == "class_weights needs to be equal to number of ground_truth_ids + 1"