def test_roundtrip(xml, benchmark):
"""Ensure we can losslessly round-trip XML through the model and back."""
xml = str(xml)
schema = get_schema(xml)
def canonicalize(xml, strip_empty):
d = schema.decode(xml, use_defaults=True)
# Strip extra whitespace in the schemaLocation value.
d["@xsi:schemaLocation"] = re.sub(r"\s+", " ",
d["@xsi:schemaLocation"])
root = schema.encode(d, path=NS_OME + "OME", use_defaults=True)
# These are the tags that appear in the example files with empty
# content. Since our round-trip will drop empty elements, we'll need to
# strip them from the "original" documents before comparison.
if strip_empty:
for tag in ("Description", "LightPath", "Map"):
for e in root.findall(f".//{NS_OME}{tag}[.='']..."):
e.remove(e.find(f"{NS_OME}{tag}"))
# ET.canonicalize can't handle an empty namespace so we need to
# re-register the OME namespace with an actual name before calling
# tostring.
ElementTree.register_namespace("ome", URI_OME)
xml_out = ElementTree.tostring(root, "unicode")
xml_out = util.canonicalize(xml_out, strip_text=True)
xml_out = minidom.parseString(xml_out).toprettyxml(indent=" ")
return xml_out
original = canonicalize(xml, True)
ome = from_xml(xml)
rexml = benchmark(to_xml, ome)
assert canonicalize(rexml, False) == original
def _get_dim_info(self) -> None:
if self._shape:
if self.tf.ome_metadata:
self.ome_metadata = from_xml(self.tf.ome_metadata)
spp = (self.ome_metadata.images[
self.largest_series].pixels.channels[0].samples_per_pixel)
interleaved = self.ome_metadata.images[
self.largest_series].pixels.interleaved
if spp and spp > 1:
self._is_rgb = True
else:
self._is_rgb = False
if guess_rgb(self._shape) is False:
self._channel_axis = 0
self._is_interleaved = False
elif interleaved and guess_rgb(self._shape):
self._is_interleaved = True
self._channel_axis = len(self._shape) - 1
else:
self._is_rgb = guess_rgb(self._shape)
self._is_interleaved = self._is_rgb
if self._is_rgb:
self._channel_axis = len(self._shape) - 1
else:
self._channel_axis = 0
self._n_ch = self._shape[self._channel_axis]
def test_serialization(xml):
"""Test pickle serialization and reserialization."""
if true_stem(xml) in SHOULD_RAISE_READ:
pytest.skip("Can't pickle unreadable xml")
ome = from_xml(xml)
serialized = pickle.dumps(ome)
deserialized = pickle.loads(serialized)
assert ome == deserialized
def test_to_xml_with_kwargs():
"""Ensure kwargs are passed to ElementTree"""
ome = from_xml(Path(__file__).parent / "data" / "example.ome.xml")
with mock.patch("xml.etree.ElementTree.tostring") as mocked_et_tostring:
element = to_xml_element(ome)
# Use an ElementTree.tostring kwarg and assert that it was passed through
to_xml(element, xml_declaration=True)
assert mocked_et_tostring.call_args.xml_declaration
def test_wsireg_run_reg_downsampling_m1m2_merge_ds_attach(
data_out_dir, disk_im_gry):
wsi_reg = WsiReg2D(gen_project_name_str(), str(data_out_dir))
img_fp1 = str(disk_im_gry)
wsi_reg.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg.add_attachment_images(
"mod2",
"mod3",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_reg_path("mod1", "mod2", reg_params=["rigid_test"])
wsi_reg.add_merge_modalities("mod12-merge", ["mod1", "mod2", "mod3"])
wsi_reg.register_images()
im_fps = wsi_reg.transform_images(transform_non_reg=False,
remove_merged=True)
regim = reg_image_loader(im_fps[0], 0.65)
ome_data = from_xml(TiffFile(im_fps[0]).ome_metadata)
assert regim.shape == (3, 2048, 2048)
assert ome_data.images[0].pixels.physical_size_x == 0.65
assert ome_data.images[0].pixels.physical_size_y == 0.65
assert ome_data.images[0].pixels.size_x == 2048
assert ome_data.images[0].pixels.size_y == 2048
assert ome_data.images[0].pixels.size_c == 3
def getMetadata(path):
with tifffile.TiffFile(path) as tif:
metadata = ome_types.from_xml(tif.ome_metadata)
return metadata.images[0].pixels
def test_with_ome_ns():
xml = Path(__file__).parent / "data" / "ome_ns.ome.xml"
ome = from_xml(xml)
assert ome.experimenters
def test_refs():
xml = Path(
__file__).parent / "data" / "two-screens-two-plates-four-wells.ome.xml"
ome = from_xml(xml)
assert ome.screens[0].plate_ref[0].ref is ome.plates[0]