def test_czi_reader(
resources_dir,
filename,
expected_shape,
expected_dims,
expected_dtype,
select_scene,
chunk_dims,
):
# Get file
f = resources_dir / filename
# Read file
img = CziReader(f, chunk_by_dims=chunk_dims, S=select_scene)
# Check that there are no open file pointers after init
proc = Process()
assert str(f) not in [f.path for f in proc.open_files()]
# Check basics
assert img.dims == expected_dims
assert img.metadata is not None
assert img.dask_data.shape == expected_shape
assert img.dtype() == expected_dtype
# Check that there are no open file pointers after basics
assert str(f) not in [f.path for f in proc.open_files()]
# Check array
assert isinstance(img.data, np.ndarray)
assert img.data.shape == expected_shape
# Check that there are no open file pointers after retrieval
assert str(f) not in [f.path for f in proc.open_files()]
def test_size_functions(resources_dir, filename, s, t, c, z, y, x):
# Get file
f = resources_dir / filename
# Init reader
img = CziReader(f)
# Check sizes
assert img.size_s() == s
assert img.size_t() == t
assert img.size_c() == c
assert img.size_z() == z
assert img.size_y() == y
assert img.size_x() == x
def test_czi_reader(
resources_dir,
filename,
expected_shape,
expected_dims,
expected_dtype,
select_scene,
chunk_dims,
):
# Get file
f = resources_dir / filename
# Read file
img = CziReader(f, chunk_by_dims=chunk_dims, S=select_scene)
# Check that there are no open file pointers after init
proc = Process()
assert str(f) not in [f.path for f in proc.open_files()]
# Check basics
assert img.dims == expected_dims
assert img.metadata is not None
assert img.shape == expected_shape
assert img.dask_data.shape == expected_shape
assert img.size(expected_dims) == expected_shape
assert img.dtype() == expected_dtype
# Will error because those dimensions don't exist in the file
with pytest.raises(exceptions.InvalidDimensionOrderingError):
assert img.size("ABCDEFG") == expected_shape
# Check that there are no open file pointers after basics
assert str(f) not in [f.path for f in proc.open_files()]
# Check array
assert isinstance(img.data, np.ndarray)
assert img.data.shape == expected_shape
# Check that there are no open file pointers after retrieval
assert str(f) not in [f.path for f in proc.open_files()]
def test_get_physical_pixel_size(resources_dir, filename, expected):
assert CziReader(resources_dir /
filename).get_physical_pixel_size() == expected
def test_get_channel_names(resources_dir, filename, scene, expected):
assert CziReader(resources_dir /
filename).get_channel_names(scene) == expected
def test_is_this_type(raw_bytes, expected):
res = CziReader._is_this_type(raw_bytes)
assert res == expected