def test_image_builder_tiff(tmpdir_factory,):
# Copy resource files to writable temp folder
temp_dir = Path(tmpdir_factory.mktemp("temp") / "resources")
output_dir = Path(tmpdir_factory.mktemp("output"))
shutil.copytree(
RESOURCE_PATH,
temp_dir,
ignore=shutil.ignore_patterns("dicom*", "complex_tiff", "dzi_tiff"),
)
files = [Path(d[0]).joinpath(f) for d in os.walk(temp_dir) for f in d[2]]
image_builder_result = _build_files(
builder=image_builder_tiff, files=files, output_directory=output_dir
)
expected_files = [
temp_dir / "valid_tiff.tif",
temp_dir / "no_dzi.tif",
]
assert sorted(image_builder_result.consumed_files) == sorted(
expected_files
)
file_to_pk = {i.name: i.pk for i in image_builder_result.new_images}
for file in expected_files:
pk = file_to_pk[file.name]
assert os.path.isfile(output_dir / file.name / f"{pk}.tif")
# Assert that both tiff images are imported
assert len(image_builder_result.new_image_files) == 2
def test_image_builder_with_other_file_extension(tmpdir):
dest = Path(tmpdir) / "image10x10x10.mha"
shutil.copy(RESOURCE_PATH / dest.name, dest)
files = {Path(d[0]).joinpath(f) for d in os.walk(tmpdir) for f in d[2]}
with TemporaryDirectory() as output:
result = _build_files(builder=image_builder_nifti,
files=files,
output_directory=output)
assert result.consumed_files == set()
assert len(result.new_images) == 0
def test_error_handling(tmpdir_factory):
# Copy resource files to writable temp folder
# The content files are dummy files and won't compile to tiff.
# The point is to test the loading of gc_files and make sure all
# related files are associated with the gc_file
temp_dir = Path(tmpdir_factory.mktemp("temp") / "resources")
shutil.copytree(RESOURCE_PATH / "complex_tiff", temp_dir)
files = {Path(d[0]).joinpath(f) for d in os.walk(temp_dir) for f in d[2]}
with TemporaryDirectory() as output:
image_builder_result = _build_files(
builder=image_builder_tiff, files=files, output_directory=output
)
assert len(image_builder_result.file_errors) == 14
def test_image_builder_fallback_corrupt_file(tmpdir):
src = RESOURCE_PATH / "corrupt.png"
dest = Path(tmpdir) / src.name
shutil.copy(str(src), str(dest))
files = {Path(d[0]).joinpath(f) for d in os.walk(tmpdir) for f in d[2]}
with TemporaryDirectory() as output:
result = _build_files(
builder=image_builder_fallback,
files=files,
output_directory=output,
)
assert result.file_errors == {
dest: [format_error("Not a valid image file")],
}
assert result.consumed_files == set()
def test_image_builder_fallback(tmpdir, src, colorspace):
dest = Path(tmpdir) / src.name
shutil.copy(str(src), str(dest))
files = {Path(d[0]).joinpath(f) for d in os.walk(tmpdir) for f in d[2]}
with TemporaryDirectory() as output:
result = _build_files(
builder=image_builder_fallback,
files=files,
output_directory=output,
)
assert result.consumed_files == {dest}
assert len(result.new_images) == 1
image = result.new_images.pop()
assert image.color_space == colorspace
assert image.voxel_width_mm is None
assert image.voxel_height_mm is None
assert image.voxel_depth_mm is None
def test_image_builder_dicom_4dct(tmpdir):
files = {Path(d[0]).joinpath(f) for d in os.walk(DICOM_DIR) for f in d[2]}
result = _build_files(builder=image_builder_dicom,
files=files,
output_directory=tmpdir)
assert result.consumed_files == {
Path(DICOM_DIR).joinpath(f"{x}.dcm")
for x in range(1, 77)
}
assert len(result.new_images) == 1
image = Image(**asdict(result.new_images.pop()))
assert image.shape == [19, 4, 2, 3]
assert len(result.new_image_files) == 1
mha_file_obj = [
x for x in result.new_image_files if x.file.suffix == ".mha"
][0]
headers = parse_mh_header(mha_file_obj.file)
direction = headers["TransformMatrix"].split()
origin = headers["Offset"].split()
spacing = headers["ElementSpacing"].split()
exposures = headers["Exposures"].split()
content_times = headers["ContentTimes"].split()
assert len(exposures) == 19
assert exposures == [str(x) for x in range(100, 2000, 100)]
assert len(content_times) == 19
assert content_times == [str(x) for x in range(214501, 214520)]
dcm_ref = pydicom.dcmread(str(DICOM_DIR / "1.dcm"))
assert np.array_equal(
np.array(list(map(float, direction))).reshape((4, 4)), np.eye(4))
assert np.allclose(
list(map(float, spacing))[:2],
list(map(
float,
list(dcm_ref.PixelSpacing),
)),
)
assert np.allclose(
list(map(float, origin)),
list(map(float, dcm_ref.ImagePositionPatient)) + [0.0],
)
def test_dicom_rescaling(folder, element_type, tmpdir):
"""
2.dcm in dicom_intercept and dicom_slope has been modified to add a
small intercept (0.01) or slope (1.001) respectively.
"""
files = [
Path(d[0]).joinpath(f) for d in os.walk(RESOURCE_PATH / folder)
for f in d[2]
]
result = _build_files(builder=image_builder_dicom,
files=files,
output_directory=tmpdir)
assert len(result.new_image_files) == 1
mha_file_obj = [
x for x in result.new_image_files if x.file.suffix == ".mha"
][0]
headers = parse_mh_header(mha_file_obj.file)
assert headers["ElementType"] == element_type
def test_dicom_window_level(tmpdir):
files = {
Path(d[0]).joinpath(f)
for d in os.walk(RESOURCE_PATH / "dicom") for f in d[2]
}
result = _build_files(builder=image_builder_dicom,
files=files,
output_directory=tmpdir)
assert len(result.new_image_files) == 1
mha_file_obj = [
x for x in result.new_image_files if x.file.suffix == ".mha"
][0]
headers = parse_mh_header(mha_file_obj.file)
assert headers["WindowCenter"] == "30"
assert headers["WindowWidth"] == "200"
assert len(result.new_images) == 1
image_obj = result.new_images.pop()
assert image_obj.window_center == 30.0
assert image_obj.window_width == 200.0
def test_image_builder_nifti(tmpdir_factory, src: Path):
dest = Path(tmpdir_factory.mktemp("input"))
shutil.copy(src, dest / src.name)
files = {*dest.glob("*")}
result = _build_files(
builder=image_builder_nifti,
files=files,
output_directory=tmpdir_factory.mktemp("output"),
)
assert result.consumed_files == files
assert len(result.new_images) == 1
image = result.new_images.pop()
assert image.color_space == ColorSpace.GRAY.value
assert image.width == 10
assert image.height == 11
assert image.depth == 12
assert image.voxel_width_mm == pytest.approx(1.0)
assert image.voxel_height_mm == pytest.approx(2.0)
assert image.voxel_depth_mm == pytest.approx(3.0)