Inquiry Regarding MCXLAB Usage for Layered Media Simulation

[于赛薇]

Dear Professor Fang,

I hope this email finds you well. First and foremost, I would like to express my sincere gratitude for developing such an outstanding toolkit. Your contributions have been invaluable to our research community.

I am currently working with MCXLAB and have encountered several issues that have been quite perplexing. Therefore, I am reaching out to seek your guidance. Specifically, I aim to simulate a three-layer flat medium and wish to obtain the total diffuse reflectance, total transmittance, as well as the energy absorption distribution within each layer. However, I have run into difficulties when calculating the diffuse reflectance. By summing up the values in the fluence.data of the topmost layer, I obtained a reflectance value exceeding one, which is clearly incorrect. Upon reviewing some of your previous responses to similar inquiries, I understand that it might be necessary to add detectors and utilize the replay feature to track photons and accumulate relevant data packets to accurately compute the diffuse reflectance. Could you please confirm if this is indeed the correct approach?

Additionally, I would greatly appreciate any advice on how to calculate the absorption rate for each individual layer. Understanding this aspect is crucial for my ongoing research.

Your insights would be immensely helpful, and I look forward to your response.

With kind regards,

saiwei

[Qianqian Fang]

the code in your following post can not be executed in MATLAB - it contains multi-byte characters and full-width Chinese punctuation, which is not supported in my versions of matlab.

when you post codes, please make sure those are valid so others can reproduce the reported issue.

please reformat,

PS: please only post your question once. Everyone's first post will be moderated, sometimes I may not be able to approve your question immediately, so please be patient. do not double post.

PPS: my last name is "房"， not "方"

On 3/7/25 01:58, 'saiei yu' via mcx-users wrote:

此外，我将提供我的代码，以便您可以清楚地看到我遇到的问题。谢谢。中图分类病毒 （CLC）;

% 初始化配置
cfg.nphoton = 1e7;%

cfg.prop = [0.00， 0.01， 1.0， 1.0; %
0.00, 0.01, 1.0, 1.0;%
0.2179, 9.796820513, 0.7, 1.342;
0.110769643, 2.271119048, 0.7, 1.34];


cfg.vol = 个（50， 50， 60）;

cfg.vol（：，：，1） = 0;% 填充零层


cfg.vol（：，：，2） = 2;
cfg.vol（：，：，3：58） = 3;
cfg.vol（：，：，59） = 2;

% 将体积转换为uint8类型
cfg.vol = uint8（cfg.vol）;

% 光源位置和方向
cfg.srcpos = [25， 25， 2];
cfg.srcdir = [0， 0， 1];
% 定义参数
r = 1;
detector_diameter = 2 * r;
detector_positions = [];
src_x = 25;
src_y = 25;

% 在空气层（即z=1）上方布置探测器
对于 x = src_x + r + 1：detector_diameter：49 
detector_positions = [detector_positions; x， src_y， 1， r];
结束
对于 x = src_x - detector_diameter：-detector_diameter：2 
detector_positions = [detector_positions; x， src_y， 1， r];
结束
% 光速在真空中的值
c = 3e8; % 单位：米/秒

% 介质A的参数
d_A = 0.001; % 厚度，单位：米
n_A = 1.342; % 折射率
v_A = c / n_A; % 介质A中的光速

% 介质B的参数
d_B = 0.056; % 厚度，单位：米
n_B = 1.34; % 折射率
v_B = c / n_B;% 介质B中的光速

% 计算在两种介质中的最大飞行时间
t_A = (2 * d_A) / v_A; % 介质A中的最大飞行时间
t_B = (2 * d_B) / v_B; % 介质B中的最大飞行时间

% 设置 cfg.tend 为所有介质最大飞行时间之和，并增加一定余量
cfg.tend = (t_A + t_B) * 1.2; % 乘以1.2作为额外的余量

% 输出 cfg.tend 的值以便确认
fprintf（'cfg.tend 设置为： %.8e 秒\n'， cfg.tend）;

% 执行 mcxlab 模拟
[detp， fluence， cfg] = mcxlab（cfg）;% 请确保mcxlab函数已经定义并正确配置


total_energy_emitted = 1e7;

% 初始化接收总能量
energy_received_by_detectors = 0;

对于 i = 1：size（detp.data， 1）
detector_energy = sum（detp.data（i， :)）;
energy_received_by_detectors = energy_received_by_detectors + detector_energy;

fprintf（'探测器 %d 接收的能量： %.8e\n'， i， detector_energy）;
结束

% 计算漫反射率
反射率 = energy_received_by_detectors / total_energy_emitted;

% 显示结果
fprintf（'整体漫反射率： %.8e\n'， reflectance）;

在2025年3月6日星期四 UTC+8 21:51:22<saiei yu> 写道：

尊敬的方教授：

我希望这封电子邮件能找到你。首先，我想对开发如此出色的工具包表示衷心的感谢。您的贡献对我们的研究社区来说是无价的。

我目前正在使用 MCXLAB，并遇到了几个非常令人困惑的问题。因此，我正在寻求您的指导。具体来说，我的目标是模拟三层平面介质，并希望获得每层内的总漫反射率、总透射率以及能量吸收分布。但是，在计算漫反射率时，我遇到了困难。通过对最顶层的 fluence.data 中的值求和，我得到了一个超过 1 的反射率值，这显然是不正确的。在查看了您之前对类似询问的一些回复后，我了解到可能需要添加检测器并利用重放功能来跟踪光子并积累相关数据包，以准确计算漫反射率。您能否确认一下这是否确实是正确的方法？

此外，我非常感谢有关如何计算每个单独层的吸收率的任何建议。了解这方面对于我正在进行的研究至关重要。

您的见解将非常有帮助，我期待着您的回复。

致以诚挚的问候，

赛维

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[saiei yu]

Dear Professor Fang,

First of all, thank you very much for your reply to my question. Reading your reply has been greatly enlightening for me. After reviewing the Jupyter Notebook tutorial, I found that flux.dref(:, :, 1) can be used to calculate diffuse reflection. However, I still do not thoroughly understand how to calculate the diffuse reflectance. My understanding is that we can obtain the diffuse reflectance by summing up all diffuse reflection flux and dividing it by the total emitted energy. Using this formula, the calculated diffuse reflectance appears to be particularly small, and I am not sure whether my understanding is correct or if there is an issue with how I placed the detectors. Below is my MATLAB code. Could you please take a look? I am really confused and have tried many times.

[Here, you would normally include your MATLAB code for review.]

Thank you very much for your help!

Best regards,
saiwei

clear; clc;
cfg.nphoton = 1e6; 
cfg.maxdetphoton = 3e6;  
cfg.prop = [0.00, 0.0, 1.0, 1.0;   
            0.00, 0.0, 1.0, 1.0;   

            0.2179, 9.796820513, 0.7, 1.342; 
            0.110769643, 2.271119048, 0.7, 1.34]; 

cfg.vol = ones(50, 50, 60); 
cfg.vol(:,:,1) = 0; 
cfg.vol(:,:,2) = 2;  
cfg.vol(:,:,3:58) = 3;  
cfg.vol(:,:,59) = 2;  
cfg.vol(:,:,60) = 0;  
cfg.vol = uint8(cfg.vol); 
cfg.srcpos = [25, 25, 0]; 
cfg.srcdir = [0, 0, 1]; 
cfg.issrcfrom0 = 1;    
cfg.gpuid = 1;
cfg.autopilot = 1;
cfg.tstart = 0;
cfg.tstep = 1e-8;
cfg.tend = 100e-9;
cfg.issaveexit = 1;
detpy1 = 1:2:25;  
detpy2 = 25:2:50; 
r = 0.5; 
detpy = [detpy1, detpy2];
for i = 1:length(detpy)
    cfg.detpos(i, :) = [25, detpy(i), 1, r]; 
end
cfg.issaveref = 1;
[flux, detp,fluence] = mcxlab(cfg);
max_dref = max(flux.dref(:));
fprintf('Max flux.dref value: %.4f\n', max_dref);
fprintf('Sum of flux.dref: %.4f\n', sum(flux.dref(:)));
disp(fieldnames(flux));
mcxpreview(cfg);
detector_area = sum(pi * cfg.detpos(:,4).^2);  
fprintf('Total Detector Area: %.4f mm^2\n', detector_area);
total_reflectance = sum(flux.dref(:)) * cfg.tstep * detector_area / cfg.nphoton;
fprintf('Corrected Total Diffuse Reflectance: %.6f\n', total_reflectance);