Problems with photon detection

[RecurvedBow]

Hello everyone,

I am currently facing some troubles with photon detection: My goal is to define a planar illumination at z = 0 and detect the photons escaping from the top volume face. Therefore, all optical parameters of the volume were padded by 0 at the beginning of the z-Axis and I called MCX with the following flags for photon detection: --bc ______000001 --savedetflag XV --saveref. However, for some optical parameters, MCX does not detect any photons (0 photons detected) when using 10^7 photons and my program fails for not being able to find the output file *.jdat. For some reason, I never face this issue if I use -bc ______000010 instead, for which MCX does indeed detect returning photons. While I could keep using this alternate command, problems occur if I want to mirror the sides of the tissue on the x and y axis. mm_mm_000010 obviously does not work, while mm_mm_000001 has similar problems as ______000001.

Is there something I have forgotten to check for photon detection or am I not using the flags correctly?

Thank you in advance for your answer.

[fangq]

@RecurvedBow, you don't have to pad zeros, or use --saveref if you want to capture detected photon using --bc, these are two different mechanisms to get diffuse transmittance - --saveref accumulates the dref for you, and --bc captures detected photons you post-process to get dref.

if the detected photon count via --bc is not what you have expected, please provide a sample code and describe the condition when the discrepancies happen

[RecurvedBow]

Thank you for your answer! I have investigated further and found out that "--savedetflag XV" was the actual problem as sometimes the photon position and direction on exit was not saved. If I can still replicate this issue even after your suggestion, I will provide a sample case then.

I have one more question: It seems like using only --bc without padding results in different reflectance/fluence values which I am used to. How do I accumulate the values such that I get the accumulated dref, like if using --saveref?

Thank you again in advance!

[fangq]

I have one more question: It seems like using only --bc without padding results in different reflectance/fluence values which I am used to. How do I accumulate the values such that I get the accumulated dref, like if using --saveref?

--bc only captures individual photon packets on the bounding box, you will have to use mcxdetweight() to get their exiting weights, and bin their exit positions to accumulate - but if you want an accumulated results, --saveref is the more efficient way. there is no need to use --bc in such case.

[RecurvedBow]

Thank you again for your answer! However, since I want the sides of the volume to reflect like a mirror, I will use -bc mm_mm_000000 --saveref for now. Is that the only option or is another intended way to capture the total photon count leaving a voxel while setting the behavior of the sides of the volumes to reflect the photons?