def test_file_too_large_throws_error(self, tmpdir):
image = ImageFactoryWithImageFile()
# Remove zraw file
old_raw = image.files.get(file__endswith=".zraw")
raw_file_name = Path(old_raw.file.name).name
old_raw.delete()
# Create fake too large zraw file
too_large_file_raw = tmpdir.join(raw_file_name)
f = too_large_file_raw.open(mode="wb")
f.seek(settings.MAX_SITK_FILE_SIZE)
f.write(b"\0")
f.close()
# Add too large file as ImageFile model to image.files
too_large_file_field = factory.django.FileField(
from_path=str(too_large_file_raw))
too_large_imagefile = ImageFileFactory(file=too_large_file_field)
image.files.add(too_large_imagefile)
# Try to open and catch expected exception
with pytest.raises(IOError) as exec_info:
get_sitk_image(image=image)
assert "File exceeds maximum file size." in str(
exec_info.value.args[0])
def test_multiple_mhds(self):
extra_mhd = ImageFileFactoryWithMHDFile()
extra_mhd_file = ImageFileFactoryWithMHDFile()
extra_raw = ImageFileFactoryWithRAWFile()
extra_raw_file = ImageFileFactoryWithRAWFile()
image = ImageFactoryWithImageFile(files=(extra_mhd, extra_raw,
extra_mhd_file,
extra_raw_file))
with pytest.raises(MultipleObjectsReturned):
get_sitk_image(image=image)
def test_correct_dimensions(self):
image = ImageFactoryWithImageFile()
sitk_image = get_sitk_image(image=image)
assert sitk_image.GetDimension() == 2
assert sitk_image.GetSize() == (3, 4)
assert sitk_image.GetOrigin() == (0.0, 0.0)
assert sitk_image.GetSpacing() == (1.0, 1.0)
assert sitk_image.GetNumberOfComponentsPerPixel() == 3
assert sitk_image.GetPixelIDValue() == 13
assert (sitk_image.GetPixelIDTypeAsString() ==
"vector of 8-bit unsigned integer")
def test_staged_4d_mha_and_4d_mhd_upload(settings, images: List):
# 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
image = images[0]
assert image.shape == [13, 12, 11, 10]
assert image.shape_without_color == [13, 12, 11, 10]
assert image.color_space == Image.COLOR_SPACE_GRAY
sitk_image = get_sitk_image(image=image)
assert [e for e in reversed(sitk_image.GetSize())] == image.shape
def test_mhd_file_annotation_creation(settings):
# Override the celery settings
settings.task_eager_propagates = (True, )
settings.task_always_eager = (True, )
images = ["image5x6x7.mhd", "image5x6x7.zraw"]
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
image = images[0]
assert image.shape == [7, 6, 5]
assert image.shape_without_color == [7, 6, 5]
assert image.color_space == Image.COLOR_SPACE_GRAY
sitk_image = get_sitk_image(image=image)
assert [e for e in reversed(sitk_image.GetSize())] == image.shape
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
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 = get_sitk_image(image=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_file_not_found_raw(self):
image = ImageFactoryWithImageFile()
imagefile = image.files.get(file__endswith=".zraw")
imagefile.file.storage.delete(imagefile.file.name)
with pytest.raises(FileNotFoundError):
get_sitk_image(image=image)
def test_no_raw_object(self):
image = ImageFactoryWithImageFile()
image.files.get(file__endswith=".zraw").delete()
with pytest.raises(FileNotFoundError):
get_sitk_image(image=image)
def test_4d_mhd_object(self):
image = ImageFactoryWithImageFile4D()
img = get_sitk_image(image=image)
assert img.GetDimension() == 4
