# Demonstrates scoring in an XCAT file.

s:Ge/Patient/Type		= "TsImageCube"
s:Ge/Patient/InputDirectory	= "./"
s:Ge/Patient/InputFile		= "XCAT_FullMouse_86x86x161_atn_1.bin"
s:Ge/Patient/MetaDataFile	= "XCAT_FullMouse_86x86x161_atn_1.log"
s:Ge/Patient/ImagingToMaterialConverter = "XCAT_Attenuation" # "XCAT_Activity"
includeFile = XCAT_Materials.txt

# These parameters are only used if no MetaDataFile is provided.
i:Ge/Patient/NumberOfVoxelsX	= 86
i:Ge/Patient/NumberOfVoxelsY	= 86
i:Ge/Patient/NumberOfVoxelsZ	= 161
d:Ge/Patient/VoxelSizeX	= .5 mm
d:Ge/Patient/VoxelSizeY	= .5 mm
dv:Ge/Patient/VoxelSizeZ = 1 .5 mm

s:Ge/Patient/DataType = "FLOAT"
u:Ge/Patient/AttenuationForMaterial_XCAT_Air = 0.
u:Ge/Patient/AttenuationForMaterial_XCAT_Body_(water)   =     203.8293
u:Ge/Patient/AttenuationForMaterial_XCAT_Muscle         =     195.2515
u:Ge/Patient/AttenuationForMaterial_XCAT_Adipose_(fat)  =     114.9825
u:Ge/Patient/AttenuationForMaterial_XCAT_Lung           =      57.5347
u:Ge/Patient/AttenuationForMaterial_XCAT_Spine_Bone     =     225.7159
u:Ge/Patient/AttenuationForMaterial_XCAT_Rib_Bone       =     283.3633
u:Ge/Patient/AttenuationForMaterial_XCAT_Blood          =     201.7046
u:Ge/Patient/AttenuationForMaterial_XCAT_Heart          =     195.6546
u:Ge/Patient/AttenuationForMaterial_XCAT_Kidney         =     196.5382
u:Ge/Patient/AttenuationForMaterial_XCAT_Liver          =     197.4710
u:Ge/Patient/AttenuationForMaterial_XCAT_Lymph          =     204.0590
u:Ge/Patient/AttenuationForMaterial_XCAT_Pancreas       =     190.0039
u:Ge/Patient/AttenuationForMaterial_XCAT_Spleen         =     200.6941
u:Ge/Patient/AttenuationForMaterial_XCAT_Intestine      =     195.1612
u:Ge/Patient/AttenuationForMaterial_XCAT_Skull          =     247.5866
u:Ge/Patient/AttenuationForMaterial_XCAT_Cartilage      =     208.0629
u:Ge/Patient/AttenuationForMaterial_XCAT_Brain          =     192.2248

s:Ge/Patient/Parent   = "World"
d:Ge/Patient/TransX   = 0. m
d:Ge/Patient/TransY   = 0. m
d:Ge/Patient/TransZ   = 0. m
d:Ge/Patient/RotX     = 0. deg
d:Ge/Patient/RotY     = 0. deg
d:Ge/Patient/RotZ     = 0. deg

# Specify which slices to show.
# Comment this out or set to zero to show all slices.
# Set to -1 to show only center slice.
# Set to -2 to show first, center and last slice.
#iv:Ge/Patient/ShowSpecificSlicesX = 1 -2
#iv:Ge/Patient/ShowSpecificSlicesY = 1 -2
iv:Ge/Patient/ShowSpecificSlicesZ = 9 1 21 41 61 81 101 121 141 161

s:Ge/World/Material    = "G4_AIR"
d:Ge/World/HLX         = .5 m
d:Ge/World/HLY         = .5 m
d:Ge/World/HLZ         = .5 m
b:Ge/World/Invisible   = "TRUE"

s:So/Example/Type                     = "Beam"
s:So/Example/Component                = "BeamPosition"
s:So/Example/BeamParticle             = "proton"
d:So/Example/BeamEnergy               = 70. MeV
u:So/Example/BeamEnergySpread         = 0.757504
s:So/Example/BeamPositionDistribution = "Flat"
s:So/Example/BeamPositionCutoffShape  = "Ellipse"
d:So/Example/BeamPositionCutoffX      = 5. mm
d:So/Example/BeamPositionCutoffY      = 5. mm
s:So/Example/BeamAngularDistribution  = "None"
i:So/Example/NumberOfHistoriesInRun   = 10

s:Gr/ViewA/Type           = "OpenGL"
i:Gr/ViewA/WindowSizeX    = 900
i:Gr/ViewA/WindowSizeY    = 900
d:Gr/ViewA/Theta          = 60 deg
d:Gr/ViewA/Phi            = 10 deg

# Extra graphics options to handle complex voxel geometries
i:Gr/ShowOnlyOutlineIfVoxelCountExceeds = 210000000

i:Ts/ShowHistoryCountAtInterval = 100

b:Ts/PauseBeforeQuit = "True"
