def test_convert_itk_to_internal(image: Path):
def assert_img_properties(img: SimpleITK.Image, internal_image: Image):
color_space = {
1: Image.COLOR_SPACE_GRAY,
3: Image.COLOR_SPACE_RGB,
4: Image.COLOR_SPACE_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])
assert internal_image.resolution_levels is None
img_ref = load_sitk_image(image)
internal_image = convert_itk_to_internal(img_ref)
assert_img_properties(img_ref, internal_image[0])
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 IOError(
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 convert_itk_file(headers: Mapping[str, Union[str, None]],
filename: Path) -> Tuple[Image, Sequence[ImageFile]]:
try:
simple_itk_image = load_sitk_image(filename.absolute())
simple_itk_image: SimpleITK.Image
except RuntimeError:
raise ValueError("SimpleITK cannot open file")
return convert_itk_to_internal(simple_itk_image, name=filename.name)