jinhuaxu97 / mcml-py

MCML Python

Port of MCML (Monte Carlo Multi-Layered) to Python.

Requires Python 3.10 or above, numba, and tqdm.

Getting started

1. Clone the repo (or download the zip file and extract).

2. Create a virtual environment. Use Miniconda if you don't know what that means. After installing miniconda, open "Anaconda Powershell Prompt" and run

   conda create -y -n mcml python=3.10 numba tqdm
   

   This command creates a new virtual environment named mcml, and installs Python 3.10 along with numba and tqdm.

3. Activate the mcml virtual environment:

   conda activate mcml
   

4. cd into the working directory. Replace <path> with the directory containing the file main.py.

   cd <path>
   

5. Run the MCML main program with a sample input file. The output will be written to text files specified in the input file. For the example input file, this will be sample.mco and sample2.mco.

   python main.py sample.mci
   

Accuracy

The program is checked against the original MCML program. Errors should be <1%.

Speed

Most of this program is JIT compiled with numba, hence the speed is reasonable. Simulating 1,000,000 photons in a 3 layer medium takes <20s on my laptop.