Details: Attenuation image

An attenuation map image can be generated from a voxelized volume and its associated materials using the AttenuationImageActor. The example below illustrates how to insert an image as a Geant4 volume and establish a correspondence between pixels and materials. Using this image, the actor creates an attenuation image that matches the dimensions of the ImageVolume, where each pixel is replaced by the linear attenuation coefficient of the respective material. This coefficient, referred to as mu, is derived from the NIST or EPDL database for a specified energy.

# image
patient = sim.add_volume("Image", "patient")
patient.image = paths.data / "patient-4mm.mhd"
patient.material = "G4_AIR"  # material used by default
patient.voxel_materials = [
    [-2000, -900, "G4_AIR"],
    [-900, -100, "Lung"],
    [-100, 0, "G4_ADIPOSE_TISSUE_ICRP"],
    [0, 300, "G4_TISSUE_SOFT_ICRP"],
    [300, 800, "G4_B-100_BONE"],
    [800, 6000, "G4_BONE_COMPACT_ICRU"],
]

# mu map actor (process at the first begin of run only)
mumap = sim.add_actor("AttenuationImageActor", "mumap")
mumap.image_volume = patient  # FIXME volume for the moment, not the name
mumap.output_filename = "mumap.mhd"
mumap.energy = 140.511 * keV
mumap.database = "NIST"  # EPDL
mumap.attenuation_image.write_to_disk = True
mumap.attenuation_image.active = True

Upon running the simulation, the “mumap.mhd” file is generated and written to disk.

There is a corresponding command line tools:

opengate_photon_attenuation_image -i my_image.mhd -l labels.json --mdb materials.db -o mumap.mhd

The inputs of the command line are: 1) the image, 2) the label to material correspondance, 3) a database of material.