def test_too_many_headers_file(tmpdir):
# Generate test file...
test_file_path = Path(tmpdir) / "test.mhd"
with open(test_file_path, "w", encoding="utf-8") as f:
for i in range(1000000):
f.write(f"key{i} = {i}\n")
with pytest.raises(ValidationError):
parse_mh_header(test_file_path)
def test_line_too_long(tmpdir):
# Generate test file...
test_file_path = Path(tmpdir) / "test.mhd"
with open(test_file_path, "w", encoding="utf-8") as f:
f.write("key = ")
for i in range(1000000):
f.write(f"{i}")
with pytest.raises(ValidationError):
parse_mh_header(test_file_path)
def get_mh_header(self) -> Mapping[str, Union[str, None]]:
"""
Return header from mhd/mha file as key value pairs
Returns
-------
MetaIO headers as key value pairs.
Raises
------
FileNotFoundError
Raised when Image has no related mhd/mha ImageFile or actual file
cannot be found on storage
"""
mh_file = None
try:
mh_file = self.files.get(image_type=ImageFile.IMAGE_TYPE_MHD,
file__endswith=".mha")
except ObjectDoesNotExist:
# Fallback to files that are still stored as mhd/(z)raw
mh_file = self.files.get(image_type=ImageFile.IMAGE_TYPE_MHD,
file__endswith=".mhd")
if mh_file is None or not mh_file.file.storage.exists(
name=mh_file.file.name):
raise FileNotFoundError(f"No file found for {mh_file.file}")
return parse_mh_header(mh_file.file)
def test_does_not_choke_on_empty_file(tmpdir):
# Generate test file...
test_file_path = Path(tmpdir) / "test.mhd"
with open(test_file_path, "w", encoding="utf-8") as f:
f.write("\n")
assert parse_mh_header(test_file_path) == {}
def get_mh_header(self) -> Mapping[str, Union[str, None]]:
"""
Return header from mhd/mha file as key value pairs
Returns
-------
MetaIO headers as key value pairs.
Raises
------
FileNotFoundError
Raised when Image has no related mhd/mha ImageFile or actual file
cannot be found on storage
"""
mh_file, _ = self.get_metaimage_files()
return parse_mh_header(mh_file.file)
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_parse_header_valid_mhd():
headers = parse_mh_header(RESOURCE_PATH / "image10x10x10.mhd")
assert headers == {
"ObjectType": "Image",
"NDims": "3",
"BinaryData": "True",
"BinaryDataByteOrderMSB": "False",
"CompressedData": "True",
"CompressedDataSize": "7551",
"TransformMatrix": "1 0 0 0 1 0 0 0 1",
"Offset": "0 0 0",
"CenterOfRotation": "0 0 0",
"AnatomicalOrientation": "RAI",
"ElementSpacing": "1 1 1",
"DimSize": "10 10 10",
"ElementType": "MET_DOUBLE",
"ElementDataFile": "image10x10x10.zraw",
}
def test_parse_header_valid_4d_mhd():
headers = parse_mh_header(RESOURCE_PATH / "image10x11x12x13.mhd")
assert headers == {
"ObjectType": "Image",
"NDims": "4",
"BinaryData": "True",
"BinaryDataByteOrderMSB": "False",
"CompressedData": "True",
"CompressedDataSize": "39",
"TransformMatrix": "1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1",
"Offset": "-131 -99 -917 0",
"CenterOfRotation": "0 0 0 0",
"AnatomicalOrientation": "RAI",
"ElementSpacing": "0.429 0.429 0.5 1",
"DimSize": "10 11 12 13",
"ElementType": "MET_UCHAR",
"ElementDataFile": "image10x11x12x13.zraw",
}
def test_staged_mhd_upload_with_additional_headers(
settings, tmp_path, images: List[str]
):
# Override the celery settings
settings.task_eager_propagates = (True,)
settings.task_always_eager = (True,)
session, uploaded_images = create_raw_upload_image_session(images=images)
session.refresh_from_db()
assert session.status == session.SUCCESS
assert session.error_message is None
images = Image.objects.filter(origin=session).all()
assert len(images) == 1
raw_image_file: RawImageFile = list(uploaded_images.values())[0]
raw_image_file.refresh_from_db()
assert raw_image_file.staged_file_id is None
image: Image = images[0]
tmp_header_filename = tmp_path / "tmp_header.mhd"
with image.files.get(file__endswith=".mha").file.open(
"rb"
) as in_file, open(tmp_header_filename, "wb") as out_file:
out_file.write(in_file.read())
headers = parse_mh_header(tmp_header_filename)
for key in headers.keys():
assert (key in ADDITIONAL_HEADERS) or (key in EXPECTED_HEADERS)
sitk_image: SimpleITK.Image = image.get_sitk_image()
for key in ADDITIONAL_HEADERS:
assert key in sitk_image.GetMetaDataKeys()
if key in HEADERS_MATCHING_NUM_TIMEPOINTS:
if sitk_image.GetDimension() >= 4:
assert (
len(sitk_image.GetMetaData(key).split(" "))
== sitk_image.GetSize()[3]
)
else:
assert len(sitk_image.GetMetaData(key).split(" ")) == 1
assert "Bogus" not in sitk_image.GetMetaDataKeys()
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_fail_on_invalid_utf8():
with pytest.raises(ValidationError):
parse_mh_header(RESOURCE_PATH / "invalid_utf8.mhd")
