This code was created for simulating Diffuse Reflectance Spectroscopy(DRS) of human skin tissue via Monte Carlo for Multi-Layered media(MCML)
You may need to refer to this paper to understand the principle.
MCML: https://omlc.org/software/mc/mcml/index.html and https://omlc.org/software/mc/mcml/MCman.pdf
The technical details of the Monte-Carlo multilayer (MCML) simulation have been described in the literature [Meglinski and Matcher (2002)]. We followed the algorithm but rewrote the code in Python to significantly accelerate the simulation speed (via CPU multicore processing).
In all simulations, 104 photon packets at each wavelength were used to enter the model from above (z<0) at the air at stratum corneum boundary. At this point a set of probabilities determine if the photon packets are reflected or enter the tissue. When a packet has entered the tissue, it can be partially or fully absorbed by event bins uniformly distributed throughout the tissue.With a starting photon weight W of 1, every time a photon packet interacts with a bin it loses part of its weight and then gets scattered in a direction determined by the anisotropy factor and scattering coefficient. At the end of the simulation, all diffusely scattered photons locating at the incident side (z<0) were added up to give a diffuse reflectance spectrum.
One of the simulation results is presented in below figure with filled circles enclosed in error bars estimated from 10 simulations.
For comparison, a diffuse reflectance spectrum measured on the inside ofthe right forearm of an adult with our DRS apparatus is also presented (red solid curve). A good agreement with the simulation profile was obtained, suggesting that the model used captured the essential elements of human skin tissue.
These file must be in same path with run.py
- wavelength.csv: all wavelength data for this program
- model_input.txt: some parameters of the simulated tissue model
- mua_water.csv: the optical absorption properties (μa cm-1) of water
- mua_oxy.csv: the optical absorption properties (μa cm-1) of oxygenated whole blood
- mua_deoxy.csv: the optical absorption properties (μa cm-1) of deoxygenated whole blood
- mua_melanin.csv: the optical absorption properties (μa cm-1) ofinterior of typical cutaneous melanosome
And these optical absorption properties referred to https://omlc.org/software/mc/mcxyz/index.html
This code is a preset 8-multicore processing. If you have enough CPU cores, you must increase/revise the code.
You must revise line731 the 8 to number of your CPU cores
if cpu_number>=1 and cpu_number<=8 and cpu_number<=cpu_count(): You must increase the following code below line791 (if you want to use 9 cores for mutiprocessing)
if c.get(8):
boundary = c[8]
q9 = Queue()
m9 = mp.Process(target=job, args=(q9,model,N,boundary))
m9.start() and increase the following code below line824
if c.get(8):
m9.join()
R.append(q9.get()) Run the run.py
Enter your requirements as prompted
save the Reflection Spectrum?(y/n):You can typeyornto choose whether to store the simulated spectrum on your hard drive.
the filename?(do NOT add extension):If you typey, you need to type the file name (you do not need to enter the filename extension)
How many photons for simulation?(1000 photons spend about 4 mins)more photons will result in better spectrum (but you will spend more time)
How many multicore operations to use?Please consider the number of your CPU cores