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 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)
def image_builder_nifti(*, files: Set[Path], **_) -> ImageBuilderResult:
"""
Constructs image objects from files in NifTI format (nii/nii.gz)
Parameters
----------
files
Path to images that were uploaded during an upload session.
Returns
-------
An `ImageBuilder` object consisting of:
- a list of filenames for all files consumed by the image builder
- a list of detected images
- a list files associated with the detected images
- path->error message map describing what is wrong with a given file
"""
errors = {}
new_images = set()
new_image_files = set()
consumed_files = set()
for file in files:
if not (file.name.endswith(".nii") or file.name.endswith(".nii.gz")):
continue
try:
reader = SimpleITK.ImageFileReader()
reader.SetImageIO("NiftiImageIO")
reader.SetFileName(str(file.absolute()))
img: SimpleITK.Image = reader.Execute()
except RuntimeError:
errors[file] = format_error("Not a valid NifTI image file")
continue
try:
n_image, n_image_files = convert_itk_to_internal(
img, name=file.name
)
new_images.add(n_image)
new_image_files |= set(n_image_files)
consumed_files.add(file)
except ValueError as e:
errors[file] = format_error(e)
return ImageBuilderResult(
consumed_files=consumed_files,
file_errors=errors,
new_images=new_images,
new_image_files=new_image_files,
new_folders=set(),
)
def image_builder_fallback(*, files: Set[Path], **_) -> ImageBuilderResult:
"""
Constructs image objects by inspecting files in a directory.
Parameters
----------
path
Path to a directory that contains all images that were uploaded during
an upload session.
Returns
-------
An `ImageBuilder` object consisting of:
- a list of filenames for all files consumed by the image builder
- a list of detected images
- a list files associated with the detected images
- path->error message map describing what is wrong with a given file
"""
errors = {}
new_images = set()
new_image_files = set()
consumed_files = set()
for file in files:
try:
img = Image.open(file)
if img.format.lower() not in ["jpeg", "png"]:
raise ValidationError(
f"Unsupported image format: {img.format}"
)
img_array = np.array(img)
is_vector = img.mode != "L"
img = SimpleITK.GetImageFromArray(img_array, isVector=is_vector)
n_image, n_image_files = convert_itk_to_internal(
img, name=file.name, use_spacing=False
)
new_images.add(n_image)
new_image_files |= set(n_image_files)
consumed_files.add(file)
except (IOError, ValidationError, DecompressionBombError):
errors[file] = format_error("Not a valid image file")
return ImageBuilderResult(
consumed_files=consumed_files,
file_errors=errors,
new_images=new_images,
new_image_files=new_image_files,
new_folders=set(),
)
def _process_dicom_file(*, dicom_ds, created_image_prefix): # noqa: C901
ref_file = pydicom.dcmread(str(dicom_ds.headers[0]["file"]))
ref_origin = tuple(
float(i) for i in getattr(ref_file, "ImagePositionPatient", (0, 0, 0))
)
dimensions = 4 if dicom_ds.n_time and dicom_ds.n_time > 1 else 3
direction = np.eye(dimensions, dtype=np.float)
direction = _extract_direction(dicom_ds, direction)
pixel_dims = (
dicom_ds.n_slices,
int(ref_file.Rows),
int(ref_file.Columns),
)
if dimensions == 4:
pixel_dims = (dicom_ds.n_time,) + pixel_dims
# Additional Meta data Contenttimes and Exposures
content_times = []
exposures = []
origin = None
origin_diff = np.array((0, 0, 0), dtype=float)
n_diffs = 0
for partial in dicom_ds.headers:
ds = partial["data"]
if "ImagePositionPatient" in ds:
file_origin = np.array(ds.ImagePositionPatient, dtype=float)
if origin is not None:
diff = file_origin - origin
origin_diff = origin_diff + diff
n_diffs += 1
origin = file_origin
avg_origin_diff = tuple(origin_diff / n_diffs)
try:
z_i = avg_origin_diff[2]
except IndexError:
z_i = 1.0
img = _create_itk_from_dcm(
content_times=content_times,
dicom_ds=dicom_ds,
dimensions=dimensions,
exposures=exposures,
pixel_dims=pixel_dims,
z_i=z_i,
)
if origin is None:
origin = (0.0, 0.0, 0.0)
sitk_origin = ref_origin if z_i >= 0.0 else tuple(origin)
z_i = np.abs(z_i) if not np.isnan(z_i) else 1.0
if "PixelSpacing" in ref_file:
x_i, y_i = (float(x) for x in ref_file.PixelSpacing)
else:
x_i = y_i = 1.0
sitk_spacing = (x_i, y_i, z_i)
if dimensions == 4:
sitk_spacing += (1.0,)
sitk_origin += (0.0,)
sitk_direction = tuple(direction.flatten())
img.SetDirection(sitk_direction)
img.SetSpacing(sitk_spacing)
img.SetOrigin(sitk_origin)
if dimensions == 4:
# Set Additional Meta Data
img.SetMetaData("ContentTimes", " ".join(content_times))
img.SetMetaData("Exposures", " ".join(exposures))
for f in OPTIONAL_METADATA_FIELDS:
if getattr(ref_file, f, False):
img.SetMetaData(f, str(getattr(ref_file, f)))
# Convert the SimpleITK image to our internal representation
return convert_itk_to_internal(
img,
name=f"{created_image_prefix}-{dicom_ds.headers[0]['data'].StudyInstanceUID}-{dicom_ds.index}",
)