def save_mha_files(request, img):
# Save MHA files to Image.files model
img_file_model = ImageFile(image=img)
# Save image fieldfile into ImageFile, also triggers ImageFile model save method
image_file = File(request.data["image_mha"])
image_name = "out.mha"
img_file_model.file.save(image_name, image_file, save=True)
def _create_image_file(*, path: str, image: Image) -> ImageFile:
temp_file = TemporaryFile()
with open(path, "rb") as open_file:
buffer = True
while buffer:
buffer = open_file.read(1024)
temp_file.write(buffer)
if path.lower().endswith("dzi"):
return ImageFile(
image=image,
image_type=ImageFile.IMAGE_TYPE_DZI,
file=File(temp_file, name=f"{image.pk}.dzi"),
)
else:
return ImageFile(
image=image,
image_type=ImageFile.IMAGE_TYPE_TIFF,
file=File(temp_file, name=f"{image.pk}.tif"),
)
def save_mhd_and_raw_files(self, request, img):
# Save MHD and ZRAW files to Image.files model
file_name = "out"
# Set ElementDataFile in mhd file to correct zraw filename
raw_file_name = file_name + ".zraw"
request.data["image_hd"] = self.set_element_data_file_header(
request.data["image_hd"], raw_file_name)
# Save mhd and zraw files
for image_key in ("image_hd", "image_raw"):
img_file_model = ImageFile(image=img)
# Save image fieldfile into ImageFile, also triggers ImageFile model save method
image_file = File(request.data[image_key])
extension = "zraw" if image_key == "image_raw" else "mhd"
image_name = f"{file_name}.{extension}"
img_file_model.file.save(image_name, image_file, save=True)
def convert_itk_file(headers: Mapping[str, Union[str, None]],
filename: Path) -> Tuple[Image, Sequence[ImageFile]]:
try:
simple_itk_image = sitk.ReadImage(str(filename.absolute()))
simple_itk_image: sitk.Image
except RuntimeError:
raise ValueError("SimpleITK cannot open file")
color_space = simple_itk_image.GetNumberOfComponentsPerPixel()
color_space = {
1: Image.COLOR_SPACE_GRAY,
3: Image.COLOR_SPACE_RGB,
4: Image.COLOR_SPACE_RGBA,
}.get(color_space, None)
if color_space is None:
raise ValueError("Unknown color space for MetaIO image.")
with TemporaryDirectory() as work_dir:
work_dir = Path(work_dir)
sitk.WriteImage(simple_itk_image, str(work_dir / "out.mhd"), True)
depth = simple_itk_image.GetDepth()
db_image = Image(
name=filename.name,
width=simple_itk_image.GetWidth(),
height=simple_itk_image.GetHeight(),
depth=depth if depth else None,
resolution_levels=None,
color_space=color_space,
)
db_image_files = []
for _file in work_dir.iterdir():
temp_file = TemporaryFile()
with open(_file, "rb") as open_file:
buffer = True
while buffer:
buffer = open_file.read(1024)
temp_file.write(buffer)
db_image_file = ImageFile(
image=db_image,
image_type=ImageFile.IMAGE_TYPE_MHD,
file=File(temp_file, name=_file.name),
)
db_image_files.append(db_image_file)
return db_image, db_image_files
def _convert_panimg_to_django(*,
panimg_result: PanImgResult) -> ConversionResult:
new_images = {Image(**asdict(im)) for im in panimg_result.new_images}
new_image_files = {
ImageFile(
image_id=f.image_id,
image_type=f.image_type,
file=File(open(f.file, "rb"), f.file.name),
)
for f in panimg_result.new_image_files
}
new_folders = {
FolderUpload(**asdict(f))
for f in panimg_result.new_folders
}
return ConversionResult(
new_images=new_images,
new_image_files=new_image_files,
new_folders=new_folders,
)
def image_builder_tiff(path: Path) -> ImageBuilderResult:
new_images = []
new_image_files = []
consumed_files = set()
invalid_file_errors = {}
for file_path in path.iterdir():
try:
tiff_file = load_tiff_file(path=file_path)
except ValidationError as e:
invalid_file_errors[file_path.name] = e.message
continue
image = create_tiff_image_entry(tiff_file=tiff_file)
temp_file = TemporaryFile()
with open(tiff_file.path.absolute(), "rb") as open_file:
buffer = True
while buffer:
buffer = open_file.read(1024)
temp_file.write(buffer)
new_image_files.append(
ImageFile(
image=image,
image_type=ImageFile.IMAGE_TYPE_TIFF,
file=File(temp_file, name="out.tif"),
)
)
new_images.append(image)
consumed_files.add(tiff_file.path.name)
return ImageBuilderResult(
consumed_files=consumed_files,
file_errors_map=invalid_file_errors,
new_images=new_images,
new_image_files=new_image_files,
)