def test_4d_mh_loader_with_more_than_4_dimensions_fails(tmpdir):
src = RESOURCE_PATH / "image10x11x12x13.mhd"
dest = Path(tmpdir) / src.name
shutil.copy(str(src), str(dest))
with open(str(dest)) as f:
modified_header = f.read().replace("NDims = 4", "NDims = 5")
with open(str(dest), "w") as f:
f.write(modified_header)
with pytest.raises(NotImplementedError):
load_sitk_image(dest)
def test_load_sitk_image_with_corrupt_additional_meta_data_fails(
tmpdir, test_img: str, key: str, value: str):
src = RESOURCE_PATH / "image10x11x12x13.mhd"
dest = Path(tmpdir) / src.name
shutil.copy(str(src), str(dest))
with open(str(dest)) as f:
lines = f.readlines()
lines.insert(-1, f"{key} = {value}\n")
with open(str(dest), "w") as f:
f.writelines(lines)
with pytest.raises(ValidationError):
load_sitk_image(dest)
def test_writing_4d_mhd_produces_same_results(tmpdir, image: Path):
def assert_img_properties(img: SimpleITK.Image):
assert img.GetDimension() == 4
assert img.GetWidth() == 10
assert img.GetHeight() == 11
assert img.GetDepth() == 12
assert img.GetSize()[-1] == 13
img_ref = load_sitk_image(image)
assert_img_properties(img_ref)
copypath = Path(tmpdir / "temp4d.mhd")
SimpleITK.WriteImage(img_ref, str(copypath), True)
img = load_sitk_image(copypath)
assert_img_properties(img)
assert_sitk_img_equivalence(img, img_ref)
def test_load_sitk_image_with_additional_meta_data(tmpdir, test_img: str):
src = RESOURCE_PATH / test_img
sitk_image = load_sitk_image(src)
for key in sitk_image.GetMetaDataKeys():
assert key in ADDITIONAL_HEADERS
assert ADDITIONAL_HEADERS[key].match(sitk_image.GetMetaData(key))
assert "Bogus" not in sitk_image.GetMetaDataKeys()
def test_convert_itk_to_internal(image: Path):
def assert_img_properties(img: SimpleITK.Image,
internal_image: SimpleITKImage):
color_space = {
1: ColorSpace.GRAY,
3: ColorSpace.RGB,
4: ColorSpace.RGBA,
}
assert internal_image.color_space == color_space.get(
img.GetNumberOfComponentsPerPixel())
if img.GetDimension() == 4:
assert internal_image.timepoints == img.GetSize()[-1]
else:
assert internal_image.timepoints is None
if img.GetDepth():
assert internal_image.depth == img.GetDepth()
assert internal_image.voxel_depth_mm == img.GetSpacing()[2]
else:
assert internal_image.depth is None
assert internal_image.voxel_depth_mm is None
assert internal_image.width == img.GetWidth()
assert internal_image.height == img.GetHeight()
assert internal_image.voxel_width_mm == approx(img.GetSpacing()[0])
assert internal_image.voxel_height_mm == approx(img.GetSpacing()[1])
img_ref = load_sitk_image(image)
internal_image = SimpleITKImage(
name=image.name,
image=img_ref,
consumed_files=set(),
spacing_valid=True,
)
assert_img_properties(img_ref, internal_image)
def get_sitk_image(self):
"""
Return the image that belongs to this model as an SimpleITK image.
Requires that exactly one MHD/RAW file pair is associated with the model.
Otherwise it wil raise a MultipleObjectsReturned or ObjectDoesNotExist
exception.
Returns
-------
A SimpleITK image
"""
# self.files should contain 1 .mhd file
try:
mhd_file = self.files.get(image_type=ImageFile.IMAGE_TYPE_MHD,
file__endswith=".mha")
files = [mhd_file]
except ObjectDoesNotExist:
# Fallback to files that are still stored as mhd/(z)raw
mhd_file = self.files.get(image_type=ImageFile.IMAGE_TYPE_MHD,
file__endswith=".mhd")
raw_file = self.files.get(image_type=ImageFile.IMAGE_TYPE_MHD,
file__endswith="raw")
files = [mhd_file, raw_file]
file_size = 0
for file in files:
if not file.file.storage.exists(name=file.file.name):
raise FileNotFoundError(f"No file found for {file.file}")
# Add up file sizes of mhd and raw file to get total file size
file_size += file.file.size
# Check file size to guard for out of memory error
if file_size > settings.MAX_SITK_FILE_SIZE:
raise OSError(
f"File exceeds maximum file size. (Size: {file_size}, Max: {settings.MAX_SITK_FILE_SIZE})"
)
with TemporaryDirectory() as tempdirname:
for file in files:
with file.file.open("rb") as infile, open(
Path(tempdirname) / Path(file.file.name).name,
"wb") as outfile:
buffer = True
while buffer:
buffer = infile.read(1024)
outfile.write(buffer)
try:
hdr_path = Path(tempdirname) / Path(mhd_file.file.name).name
sitk_image = load_sitk_image(mhd_file=hdr_path)
except RuntimeError as e:
logging.error(
f"Failed to load SimpleITK image with error: {e}")
raise
return sitk_image
def test_4d_mh_loader_with_invalid_data_type_fails(tmpdir):
sources = [
RESOURCE_PATH / "image10x11x12x13.mhd",
RESOURCE_PATH / "image10x11x12x13.zraw",
]
targets = []
for src in sources:
dest = Path(tmpdir) / src.name
targets.append(dest)
shutil.copy(str(src), str(dest))
tmp_header_file = targets[0]
with open(str(tmp_header_file)) as f:
modified_header = f.read().replace("MET_UCHAR", "MET_OTHER")
with open(str(tmp_header_file), "w") as f:
f.write(modified_header)
with pytest.raises(RuntimeError, match="Unknown PixelType"):
load_sitk_image(tmp_header_file)
def test_load_sitk_image_with_various_window_formats(
test_img: str,
center: Union[float, List[float]],
width: Union[float, List[float]],
):
src = MHD_WINDOW_DIR / test_img
sitk_image = load_sitk_image(src)
assert center == sitk_image.GetMetaData("WindowCenter")
assert width == sitk_image.GetMetaData("WindowWidth")
def test_4d_mh_loader_with_uncompressed_data(tmpdir):
sources = [
RESOURCE_PATH / "image10x11x12x13.mhd",
RESOURCE_PATH / "image10x11x12x13.zraw",
]
targets = []
for src in sources:
dest = Path(tmpdir) / src.name
targets.append(dest)
shutil.copy(str(src), str(dest))
tmp_header_file, tmp_data_file = targets
with open(str(tmp_header_file)) as f:
modified_header = f.read().replace("CompressedData = True",
"CompressedData = False")
with open(str(tmp_header_file), "w") as f:
f.write(modified_header)
with open(str(tmp_data_file), "rb") as f:
data = zlib.decompress(f.read())
with open(str(tmp_data_file), "wb") as f:
f.write(data)
load_sitk_image(tmp_header_file)
def get_sitk_image(self):
"""
Return the image that belongs to this model as an SimpleITK image.
Requires that exactly one MHD/RAW file pair is associated with the model.
Otherwise it wil raise a MultipleObjectsReturned or ObjectDoesNotExist
exception.
Returns
-------
A SimpleITK image
"""
files = [i for i in self.get_metaimage_files() if i is not None]
file_size = 0
for file in files:
if not file.file.storage.exists(name=file.file.name):
raise FileNotFoundError(f"No file found for {file.file}")
# Add up file sizes of mhd and raw file to get total file size
file_size += file.file.size
# Check file size to guard for out of memory error
if file_size > settings.MAX_SITK_FILE_SIZE:
raise OSError(
f"File exceeds maximum file size. (Size: {file_size}, Max: {settings.MAX_SITK_FILE_SIZE})"
)
with TemporaryDirectory() as tempdirname:
for file in files:
with file.file.open("rb") as infile, open(
Path(tempdirname) / Path(file.file.name).name, "wb"
) as outfile:
buffer = True
while buffer:
buffer = infile.read(1024)
outfile.write(buffer)
try:
hdr_path = Path(tempdirname) / Path(files[0].file.name).name
sitk_image = load_sitk_image(mhd_file=hdr_path)
except RuntimeError as e:
logging.error(
f"Failed to load SimpleITK image with error: {e}"
)
raise
return sitk_image
def test_load_sitk_image_with_faulty_window_formats(test_img: str,
error_msg: str):
src = MHD_WINDOW_DIR / "errors" / test_img
with pytest.raises(ValidationError, match=error_msg):
load_sitk_image(src)
def test_4d_mh_loader_without_datafile_fails(tmpdir):
src = RESOURCE_PATH / "image10x11x12x13.mhd"
dest = Path(tmpdir) / src.name
shutil.copy(str(src), str(dest))
with pytest.raises(RuntimeError, match="File cannot be read"):
load_sitk_image(dest)
