def test_ome_save(tmp_path, bundle_test_dir, ome_xml, z_size):
data = np.zeros((z_size, 20, 20, 2), dtype=np.uint8)
image = Image(
data,
image_spacing=(27 * 10 ** -6, 6 * 10 ** -6, 6 * 10 ** -6),
axes_order="ZYXC",
channel_names=["a", "b"],
shift=(10, 9, 8),
name="Test",
)
ImageWriter.save(image, tmp_path / "test.tif")
with tifffile.TiffFile(tmp_path / "test.tif") as tiff:
assert tiff.is_ome
assert isinstance(tiff.ome_metadata, str)
meta_data = tifffile.xml2dict(tiff.ome_metadata)["OME"]["Image"]
assert "PhysicalSizeX" in meta_data["Pixels"]
assert meta_data["Pixels"]["PhysicalSizeX"] == 6
assert "PhysicalSizeXUnit" in meta_data["Pixels"]
assert meta_data["Pixels"]["PhysicalSizeXUnit"] == "µm"
assert len(meta_data["Pixels"]["Channel"]) == 2
assert meta_data["Pixels"]["Channel"][0]["Name"] == "a"
assert meta_data["Pixels"]["Channel"][1]["Name"] == "b"
assert meta_data["Name"] == "Test"
xml_file = etree.fromstring(tiff.ome_metadata.encode("utf8")) # nosec
ome_xml.assert_(xml_file)
read_image = TiffImageReader.read_image(tmp_path / "test.tif")
assert np.allclose(read_image.spacing, image.spacing)
assert np.allclose(read_image.shift, image.shift)
assert read_image.channel_names == ["a", "b"]
assert read_image.name == "Test"
def test_save_mask(tmp_path):
data = np.zeros((10, 40, 40), dtype=np.uint8)
data[1:-1, 1:-1, 1:-1] = 1
data[2:-3, 4:-4, 4:-4] = 2
mask = np.array(data > 0).astype(np.uint8)
image = Image(data, (0.4, 0.1, 0.1), mask=mask, axes_order="ZYX")
ImageWriter.save_mask(image, tmp_path / "mask.tif")
read_mask = TiffImageReader.read_image(tmp_path / "mask.tif")
assert np.all(np.isclose(read_mask.spacing, image.spacing))
def test_scaling(tmp_path):
image = Image(np.zeros((10, 50, 50), dtype=np.uint8), (30, 0.1, 0.1),
axes_order="ZYX")
ImageWriter.save(image, tmp_path / "image.tif")
read_image = TiffImageReader.read_image(tmp_path / "image.tif")
assert np.all(np.isclose(image.spacing, read_image.spacing))