AttenuationConv data should be in units of cm-1

[robbietuk]

In

STIR-GATE-Connection/VoxelisedSimulation/GATESubMacros/AttenuationConv.dat

Lines 1 to 11 in 9f5ddc0

	10
	0 0 Air
	114 114 Lung
	115 383 Body
	384 384 Adipose
	385 394 Body
	395 395 Muscle
	396 402 Body
	403 403 Body
	404 420 Body
	421 1000 SpineBone

the attenuation coefficient ranges are not intuitive. STIR uses attenuation coefficient units of cm^-1.
The input attenuation voxelised phantom for this project should use this attenuation coefficient unit for future STIR processing.

Body tissue has an approximate attenuation coefficient of 0.096cm^-1 (i.e. water).
In

STIR-GATE-Connection/VoxelisedSimulation/SubScripts/GenerateSTIRGATEImages.sh

Line 45 in 9f5ddc0

stir_math --including-first --times-scalar 10000 $AttenuationFilenameGATE".hv" $AttenuationFilename

the interfile attenuation image is multipled by 10,000 to create a GATE interfile image, which would corespond to a AttenuationConv of 960 for body tissue/water. This would corresponds to SpineBone in GATE.

Two options:

1. change the multiplier in In

   STIR-GATE-Connection/VoxelisedSimulation/SubScripts/GenerateSTIRGATEImages.sh

   Line 45 in 9f5ddc0

   stir_math --including-first --times-scalar 10000 $AttenuationFilenameGATE".hv" $AttenuationFilename

   to not be 10,000 but some scaling value that maps between the values in an XCAT and the expected GATE materials.

2. Change the values in

   STIR-GATE-Connection/VoxelisedSimulation/GATESubMacros/AttenuationConv.dat

   Lines 1 to 11 in 9f5ddc0

   	10
   	0 0 Air
   	114 114 Lung
   	115 383 Body
   	384 384 Adipose
   	385 394 Body
   	395 395 Muscle
   	396 402 Body
   	403 403 Body
   	404 420 Body
   	421 1000 SpineBone

   
   to better align the multiplied coefficients.

In my opinion, 2. is the better method.
To do this, we need to use something like XCAT to assertain the attenuation coefficients ranges of different body materials, multiply by 10,000, and update the AttenuationConv.dat file. Should be done for #37

[KrisThielemans]

I agree. conversion from XCAT to STIR is one thing. Conversion from STIR to GATE is another. They should be separate. This table should work for attenuation images generated by STIR really.

I think handling XCAT specifics belongs in https://github.com/UCL/STIR-GATE-Connection/tree/master/VoxelisedSimulation/SubScripts/CreateXCATImages (although that directory is in a bit a funny place as it doesn't contain just scripts., it might be better to move it one level up or so)