def test_xml_read_function_gets_image_metadata_from_example_quicknii_file():
output = read_quicknii_xml(filename='data/deepslice_output/results.xml')
assert output.first == 1
assert output.last == 1
assert output.name == Path("richards_7.18-1-Nissl_2015.png")
assert output.filename == Path("richards_7.18-1-Nissl_2015.png")
assert output.height == 700
assert output.width == 700
assert output.nr == 0
def test_xml_read_function_gets_transformation_properties_from_example_quicknii_file(
):
output = read_quicknii_xml(filename='data/deepslice_output/results.xml')
assert output.ox == approx(475.8982543945312)
assert output.oy == approx(260.47747802734375)
assert output.oz == approx(346.73419189453125)
assert output.ux == approx(-481.19720458984375)
assert output.uy == approx(5.9310126304626465)
assert output.uz == approx(8.603763580322266)
assert output.vx == approx(-21.585269927978516)
assert output.vy == approx(-4.721147060394287)
assert output.vz == approx(-389.2110595703125)
def __call__(self, filename: str, resolution: Optional[float] = None) -> Result[LoadImageData, str]:
image_filename = read_quicknii_xml(filename).image_path if Path(filename).suffix == '.xml' else filename
image_data = self._image_reader.read(filename=image_filename)
if image_data is None:
return Err("Image failed to load.")
resolution = resolution if isinstance((resolution := image_data.resolution_um), float) else 1.
image = Image(channels=image_data.channels, resolution_um=resolution)
image = image.resample(resolution_um=10)
section = Section.create(
image=image,
image_transform=ImageTransformer(i_shift=-0.5, j_shift=-0.5)
)
self._repo.save_section(section=section)
return Ok(LoadImageData(
section_id=section.id,
section_image=section.image.channels[0],
resolution_um=image.resolution_um,
num_channels=image.num_channels,
))
def test_error_if_image_name_and_filename_are_different_in_xml_file():
with pytest.raises(ValueError):
read_quicknii_xml(
filename='data/deepslice_output/results_diffname.xml')
def test_xml_read_function_gets_full_image_path_from_example_xml_file():
output = read_quicknii_xml(filename='data/deepslice_output/results.xml')
assert output.image_path == Path(
'data/deepslice_output/richards_7.18-1-Nissl_2015.png')
def test_xml_read_function_gets_parent_path_from_example_xml_file():
output = read_quicknii_xml(filename='data/deepslice_output/results.xml')
assert output.path == Path('data/deepslice_output')