data

Load DICOM datasets as numpy arrays with voxel dimensions

CT scans in DiffDRR are stored using the torchio.Subject dataclass. torchio provides a convenient and consistent mechanism for reading volumes from a variety of formats and orientations. We canonicalize all volumes to the RAS+ coordinate space. In addition to reading an input volume, you can also pass the following to diffdrr.data.read when loading a subject: - labelmap : a 3D segmentation of the input volume - labels : a subset of structures from the labelmap that you want to render - orientation : a frame-of-reference change for the C-arm (currently, “AP” and “PA” are supported) - bone_attenuation_multiplier : a constant multiplier to the estimated density of bone voxels - fiducials : a tensor of 3D fiducial marks in world coordinates - **kwargs : any additional kwargs can be passed to the torchio.Subject and accessed as a dictionary


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load_example_ct

 load_example_ct (labels=None, orientation='AP',
                  bone_attenuation_multiplier=1.0, **kwargs)

Load an example chest CT for demonstration purposes.


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read

 read (volume:str|pathlib.Path|torchio.data.image.ScalarImage,
       labelmap:str|pathlib.Path|torchio.data.image.LabelMap=None,
       labels:int|list=None, orientation:str='AP',
       bone_attenuation_multiplier:float=1.0, fiducials:torch.Tensor=None,
       **kwargs)

Read an image volume from a variety of formats, and optionally, any given labelmap for the volume. Converts volume to a RAS+ coordinate system and moves the volume isocenter to the world origin.

Type Default Details
volume str | Path | ScalarImage CT volume
labelmap str | Path | LabelMap None Labelmap for the CT volume
labels int | list None Labels from the mask of structures to render
orientation str AP Frame-of-reference change
bone_attenuation_multiplier float 1.0 Scalar multiplier on density of high attenuation voxels
fiducials torch.Tensor None 3D fiducials in world coordinates
kwargs
Returns Subject Any additional information to be stored in the torchio.Subject