def test_BroadNucleusDataBinarized(cache_path):
spec_path = Path(
__file__
).parent / "../../../specs/readers/BroadNucleusDataBinarized.reader.yaml"
pybio_reader = load_spec_and_kwargs(str(spec_path),
kwargs={},
cache_path=cache_path)
reader = utils.get_instance(pybio_reader)
assert isinstance(reader, BroadNucleusDataBinarized)
roi = ((slice(2), slice(4), slice(6)), (slice(3), slice(5), slice(7)))
x, y = reader[roi]
assert numpy.equal(
x,
[
[
[138.0, 130.0, 140.0, 141.0, 138.0, 139.0],
[134.0, 134.0, 135.0, 137.0, 139.0, 136.0],
[127.0, 132.0, 140.0, 137.0, 130.0, 140.0],
[131.0, 134.0, 136.0, 135.0, 141.0, 141.0],
],
[
[133.0, 136.0, 134.0, 134.0, 130.0, 135.0],
[125.0, 132.0, 136.0, 133.0, 132.0, 127.0],
[135.0, 132.0, 137.0, 127.0, 138.0, 131.0],
[135.0, 129.0, 133.0, 138.0, 139.0, 133.0],
],
],
).all()
assert numpy.equal(y, numpy.zeros((3, 5, 7), dtype=bool)).all()
def test_load_specs_from_manifest(cache_path, category, spec_path, required_spec_kwargs):
kwargs = required_spec_kwargs.get(spec_path, {})
spec_path = MANIFEST_PATH.parent / spec_path
assert spec_path.exists()
loaded_spec = load_spec_and_kwargs(str(spec_path), **kwargs, cache_path=cache_path)
instance = utils.get_instance(loaded_spec)
assert instance
def test_exemplum(data_path, cache_path):
spec_path = data_path / "unet2d/UNet2DNucleiBroad.model.yaml"
assert spec_path.exists(), spec_path.absolute()
pybio_model = load_spec_and_kwargs(str(spec_path), cache_path=cache_path)
exemplum = Exemplum(pybio_model=pybio_model, _devices=[torch.device("cpu")])
test_ipt = numpy.load(pybio_model.spec.test_input) # test input with batch dim
out = exemplum.forward(test_ipt[0]) # todo: exemplum.forward should get batch with batch dim
# assert isinstance(out_seq, (list, tuple)) # todo: forward should return a list
# assert len(out_seq) == 1
# out = out_seq
expected_out = numpy.load(pybio_model.spec.test_output)[
0
] # todo: remove [0], exemplum.forward should return batch with batch dim
assert numpy.isclose(out, expected_out).all()
def test_load_non_existing_spec(cache_path):
spec_path = "some/none/existing/path/to/spec.model.yaml"
with pytest.raises(FileNotFoundError):
load_spec_and_kwargs(spec_path, cache_path=cache_path)
def test_load_non_valid_spec_name(cache_path):
spec_path = "some/none/existing/path/to/spec.not_valid.yaml"
with pytest.raises(ValueError):
load_spec_and_kwargs(spec_path, cache_path=cache_path)