Summed Fluence/total transmittance
Matthias R
Dear Dr. Fang,
I’m investigating the light transport through a layered geometry. So far, the geometry consists of a 2.5 mm and 20 mm thick layer and a circular light source at z=22.5 pointing downwards, as shown in the attached photo. In future simulations I will replace the 20 mm thick layer with a stack of layers of other optical properties and I want to investigate the effect on photon distribution/penetration. I have 2 questions regarding these simulations:
1) I want to create a plot of fluence vs penetration depth (z axis). My approach to this is the summation of fluence for multiple z-layers/crosssections. So far, I’m able to plot selected z-layers with the qmeshplot command. Is their a way to export the data (x,y coordinates+Fluence) for a defined z height that was used to plot the cross-sections?
2) I would like to calculate the total transmittance through the sample (at z=0). Is their a function which outputs this information? Otherwise, I somehow need to define the light intensity at z=22.5 and z=0, respectively. Are the planar detectors which could do that?
Thank you so much,
Matthias 
Qianqian Fang
Dear Dr. Fang,
I’m investigating the light transport through a layered geometry. So far, the geometry consists of a 2.5 mm and 20 mm thick layer and a circular light source at z=22.5 pointing downwards, as shown in the attached photo. In future simulations I will replace the 20 mm thick layer with a stack of layers of other optical properties and I want to investigate the effect on photon distribution/penetration. I have 2 questions regarding these simulations:
1) I want to create a plot of fluence vs penetration depth (z axis). My approach to this is the summation of fluence for multiple z-layers/crosssections. So far, I’m able to plot selected z-layers with the qmeshplot command. Is their a way to export the data (x,y coordinates+Fluence) for a defined z height that was used to plot the cross-sections?
hi Matthias
if your source is a pencil beam (or one with a small aperture), I
often just plot the fluence along the 1-D line along z-axis right
under the source (do a 1D griddata in matlab if you use mmc). I am
not sure why you want to average/sum given that the horizontal
distribution varies w.r.t. radial distance from the source.
by the way, is this a mesh-based simulation or voxel-based?
2) I would like to calculate the total transmittance through the sample (at z=0). Is their a function which outputs this information? Otherwise, I somehow need to define the light intensity at z=22.5 and z=0, respectively. Are the planar detectors which could do that?
again, it depends on whether you use mcx or mmc.
for mcx, you want to output the diffuse reflectance (or transmittance) at z=0 by padding a layer of zeros at the bottom layer and add -X 1, then sum the voxel values in that layer.
https://github.com/fangq/mcx/blob/v2020/src/mcx_utils.c#L3345-L3347
please see this example my student Shijie wrote
https://github.com/fangq/mcx/blob/master/mcxlab/examples/demo_diffuse_reflectance_validation.m
for mmc, -X 1 returns the transmittance on all exterior triangles. You will have to extract the triangles on the z=0 plane, and integrate those using their relative areas.
https://github.com/fangq/mmc/blob/v2020/src/mcx_utils.c#L2406-L2415
if you provide more details, I'd be happy to give more specific
suggestions.
Qianqian
Thank you so much,
Matthias
--
You received this message because you are subscribed to the Google Groups "mcx-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to mcx-users+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/mcx-users/8852ac59-ed76-4f1f-90ce-cc2df86d6f62n%40googlegroups.com.