def read_multiple(self, path: str) -> List[Image]:
"""
Allows to read in multiple images at once in case they are mixed within a single directory.
"""
self._logger.info("Reading dicom images/series from: " + path)
file_paths_by_series_uid = self._build_file_paths_by_series_uid_map(
path)
self._logger.info("Reading in {} images with series UIDs: {}".format(
len(file_paths_by_series_uid),
", ".join([uid for uid in file_paths_by_series_uid.keys()])))
images: List[Image] = list()
for uid, file_path_list in file_paths_by_series_uid.items():
self._logger.debug("Reading in series {}".format(uid))
# read in all slices
slices = [
pydicom.dcmread(file_path) for file_path in file_path_list
]
# filter non-image slices
# todo: validate criterion
slices = [
slice for slice in slices if "ImagePositionPatient" in slice
]
if len(slices) == 0:
continue
# load image volume and meta-data
volume = self._build_volume(slices)
image_meta_data, slice_meta_data_by_index = self._get_meta_data(
slices)
image = Image(image_data=volume)
image.get_meta_data().update(
{DICOM_META_DATA_KEY: image_meta_data})
# attach slice-specific meta-data
for index, slice_meta_data in slice_meta_data_by_index.items():
image.get_or_add_slice(index).get_meta_data().update(
{DICOM_META_DATA_KEY: slice_meta_data})
# deduce image information from dicom meta-data
image.set_voxel_size(self._get_voxel_size(image))
image.set_voxel_spacing(self._get_voxel_spacing(image))
images.append(image)
return images
def _build_manifest(self, image: Image, segment_slugs: dict) -> dict:
manifest = {
"image": {
"precision_bytes":
image.get_image_data().dtype.itemsize,
"size":
list(image.get_image_data().shape
), # the image volume byte sequence does not contain this
"voxel_size":
list(image.get_voxel_size())
if image.get_voxel_size() else None,
"voxel_spacing":
list(image.get_voxel_spacing())
if image.get_voxel_spacing() else None,
},
"meta_data":
image.get_meta_data(),
"slices": [
self._build_image_slice_manifest(image_slice)
for image_slice in image.get_slices()
],
"segments": [
self._build_image_segment_manifest(
image_segment,
segment_slugs[image_segment.get_identifier()])
for image_segment in image.get_segments()
],
}
# make sure the result will actually be readable
self._validate_manifest(manifest)
return manifest
def _get_pixel_spacing(self,
image: Image) -> Optional[Tuple[float, float]]:
try:
# "Pixel Spacing" (0028,0030)
pixel_spacing = image.get_meta_data()[DICOM_META_DATA_KEY][str(
0x00280030)]
except KeyError:
return None
assert isinstance(pixel_spacing, list)
assert len(pixel_spacing) == 2
assert all(isinstance(value, float) for value in pixel_spacing)
return (pixel_spacing[0], pixel_spacing[1])
def _get_voxel_size(self, image: Image) -> Optional[Vector3]:
"""Deduces the voxel size based on slice thickness and pixel spacing.
Relies on the assumption of non-overlap and non-sparseness in the xy-plane.
"""
pixel_spacing = self._get_pixel_spacing(image)
if pixel_spacing is None:
return None
try:
slice_thickness = image.get_meta_data()["Slice Thickness"]
assert isinstance(slice_thickness, float)
assert slice_thickness > 0
except KeyError:
return None
return (
slice_thickness,
pixel_spacing[1],
pixel_spacing[0],
)
def _get_voxel_spacing(self, image: Image) -> Optional[Vector3]:
"""Deduces the voxel spacing based on slice increment and pixel spacing."""
pixel_spacing = self._get_pixel_spacing(image)
if pixel_spacing is None:
return None
explicit_slice_increment: Optional[float] = None
# Read explicit value from "Spacing Between Slices" (0018,0088)
try:
explicit_slice_increment = image.get_meta_data(
)[DICOM_META_DATA_KEY][str(0x00180088)]
assert isinstance(explicit_slice_increment, float)
explicit_slice_increment = abs(explicit_slice_increment)
except KeyError:
pass
implicit_slice_increment = self._calculate_z_spacing(image)
if explicit_slice_increment is None and implicit_slice_increment is None:
# Cannot do anything
return None
elif explicit_slice_increment is not None and implicit_slice_increment is not None:
# Assert consistency
assert explicit_slice_increment == implicit_slice_increment,\
"Derived slice increment differs from defined value"
slice_increment = explicit_slice_increment if explicit_slice_increment is not None else implicit_slice_increment
return (
slice_increment,
pixel_spacing[1],
pixel_spacing[0],
)