xopto/pyxopto

PyXOpto is a collection of python tools for performing Monte Carlo simulations of light propagation in turbid media.

PyXOpto

PyXOpto is a collection of Python tools for performing Monte Carlo simulations of light propagation in turbid media using massively parallel processing on a wide range of OpenCL-enabled devices. The tools allow steady-state and time-resolved simulations of light propagation, deposition and fluence simulations, tracing and filtering of photon packet paths, computation of sampling volumes for a number of source-detector configurations, support arbitrary scattering phase functions and are easy to customize or extend.

Energy deposit simulations for a voxelized volume with a laterally moving Gaussian beam.

Transmittance trajectories of photon packets on the way from the source to the laterally displaced detector optical fiber.

Sampling volume in transmittance configuration as a function of the lateral displacement between the source and detector optical fiber.

Sampling volume in reflectance configuration as a function of the distance between the source and detector optical fiber.

Sampling volume in reflectance configuration as a function of the incidence angle of the source optical fiber.

A sequence of voxelized simulations of energy deposition in a 2-layer skin model with an embedded blood vessel.

Time-resolved energy deposition simulation for a voxelized medium with an absorbing cylindrical inclusion that has a lower refractive index than the surrounding medium.

Documentation

Full documentation of PyXOpto is available here.

Installation

Detailed instructions are available here.

Python

PyXOpto requires a Python 3 installation. Most of the Linux OS distributions will come with a preinstalled Python 3. On Windows OS, the easiest way to install the Python 3 programming language is to use the WinPython or Anaconda distributions. There are numerous integrated development environments that work with Python, among these Visual Studio Code and PyCharm are two popular cross-platform options. The WinPython distributions can be downloaded with an embedded and preconfigured Visual Studio Code (e.g. Winpython64-3.9.4.0cod.exe).

PyXOpto

First, download or clone the PyXOpto source repository to a local directory. The source code can be installed as a Python package or used independently from the downloaded source.

As a Python package

PyXOpto can be installed as a package using the setup.py file. Run the following command from the root directory of PyXOpto (the one with the setup.py file).

python setup.py install

This will also install the dependencies that include several popular Python packages (SciPy, Matplotlib, NumPy, PyOpenCL, Shapely, Numba, and Jinja2).

Using from source

To use the PyXOpto package from source, you will have to manually install all the Python dependencies listed in the setup.py file (SciPy, Matplotlib, NumPy, PyOpenCL, Shapely, Numba, and Jinja2, ...). The easiest way to install the dependencies is to use the Python package installer pip. Note that the WinPython distribution will likely come with many if not all the dependencies already installed. Also note that on some Linux distributions, the Python 3 executable is named python3 and python is used for the deprecated Python 2. You will also have to manually include the root directory of the PyXOpto package into the Python search path. This can be conveniently accomplished through setting the PYTHONPATH environment variable. On Linux operating system use:

export PTYTHONPATH=path/to/pyxopto:$PYTHONPATH

On Windows operating systems use:

set PTYTHONPATH=path\to\pyxopto;%PYTHONPATH%

After installing the dependencies and setting the environment variable PYTHONPATH, you should be able to import PyXOpto.

Docker image

Docker images for NVIDIA CUDA 11 and Intel OpenCL with preinstalled PyXOpto and Jupyter Notebook environment are available from public repositories on the Docker Hub:

• xopto/pyxopto-intel-jupyter

  These images include all the required Python dependencies and Intel OpenCL.

• xopto/pyxopto-nvidia-jupyter

  These images include all the required Python dependencies and NVIDIA CUDA 11 and related OpenCL.

• xopto/pyxopto-nvidia-jupyter-dl

  In addition to to the previous xopto/pyxopto-nvidia-jupyter image, this image also includes the Tensorflow and PyTorch deep learning libraries.

All the images include many of the popular Python libraries for scientific computing, data management and visualization (SciPy, NumPy, Matplotlib, Pandas, etc.).

Summary of the latest PyXOpto Docker images.

Image	Tag	PyXOpto	OS	CUDA	CUDNN
xopto/pyxopto-intel-jupyter	v0.2.2	0.2.2	Ubuntu 20.04	-	-
xopto/pyxopto-nvidia-jupyter	v0.2.2	0.2.2	Ubuntu 20.04	11.03	8
xopto/pyxopto-nvidia-jupyter-dl	v0.2.2	0.2.2	Ubuntu 20.04	11.03	8

The xopto/pyxopto-nvidia-jupyter, and xopto/pyxopto-nvidia-jupyter-dl Docker images can be run by executing the following command:

sudo docker run --rm --runtime nvidia -p 8888:8888 -it xopto/pyxopto-nvidia-jupyter:v0.2.2

or

sudo docker run --rm --runtime nvidia -p 8888:8888 -it xopto/pyxopto-nvidia-jupyter-dl:v0.2.2

The Intel OpenCL images xopto/pyxopto-intel-jupyter can be run as:

sudo docker run --rm --device /dev/dri:/dev/dri -u 0 -p 8888:8888 -it xopto/pyxopto-intel-jupyter:v0.2.2

This will produce output in the terminal that should be similar to:

[I 2021-11-18 22:53:55.782 LabApp] JupyterLab extension loaded from /usr/local/lib/python3.8/dist-packages/jupyterlab
[I 2021-11-18 22:53:55.782 LabApp] JupyterLab application directory is /usr/local/share/jupyter/lab
[I 22:53:55.788 NotebookApp] Serving notebooks from local directory: /home/jovyan
[I 22:53:55.788 NotebookApp] Jupyter Notebook 6.4.6 is running at:
[I 22:53:55.788 NotebookApp] http://5a29ef955782:8888/?token=7e1168ae3711761bad536257a28745a02020c1fc9db6fe7a
[I 22:53:55.788 NotebookApp] or http://127.0.0.1:8888/?token=7e1168ae3711761bad536257a28745a02020c1fc9db6fe7a
[I 22:53:55.788 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

The Jupyter Notebook can be accessed in the host browser through the displayed link, which is in this example http://127.0.0.1:8888/?token=7e1168ae3711761bad536257a28745a02020c1fc9db6fe7a.

Persisting data

PyXopto and user data can be persisted by mounting a Docker Volume or a local directory to /home/jovyan/work. In the following example the /home/someuser/data directory of the host machine will be used to persist the container data. All the Python scripts, Jupyter Notebooks and other user files inside the container should be placed into the /home/jovyan/work directory.

sudo docker run --rm --runtime nvidia -p 8888:8888  -v /home/someuser/data:/home/jovyan/work -it xopto/pyxopto-nvidia-jupyter:v0.2.2

Building the Docker images from source

The PyXOpto Docker images can be build from source by running the docker/build_intel_jupyter.sh, docker/build_nvidia_jupyter.sh or docker/build_nvidia_jupyter-dl.sh scripts. This step might require super user rights.

sudo bash ./build_intel_jupyter.sh
sudo bash ./build_nvidia_jupyter.sh
sudo bash ./build_nvidia_jupyter-dl.sh

Note that the build scripts must be run from the docker directory of the PyXOpto source tree. The built images will be tagged with the version of the PyXOpto source distribution.

Basic Monte Carlo simulations of a layered medium

This basic example is available in the examples/mcml/basic_example.py file.

The functionality of layered Monte Carlo (MC) is accessible through the xopto.mcml.mc module. First, create an empty file, e.g. basic_example.py and import the xopto.mcml.mc module.

from xopto.mcml import mc

The layer stack

The layers of the medium can be defined through the mclayer submodule. The layers are stacked along the positive direction of the z coordinate axis.

The topmost and bottommost layers of the stack are used to describe the medium that surrounds the sample at the top and at the bottom surfaces, respectively. Therefore, at least three layers must be always defined, namely the two layers of the surrounding medium and one sample layer!

The bottom surface of the topmost layer (the surrounding medium) is located at coordinate z=0. The positive direction of the z axis points in the direction of the sample layer stack.

The thicknesses of the topmost and bottommost layers will be automatically set to infinity regardless of the specified layer thickness.

Note that all the layers in the stack must use the same scattering phase function model. A variety of scattering phase function models is available through the mcpf submodule.

An example of a basic turbid sample of thickness d=10.0 mm, with an absorption coefficient mua=1.0 1/cm, scattering coefficient mus=50.0 1/cm, a Henyey-Greenstein scattering phase function (mc.mcph.Hg) with an anisotropy g=0.8 and refractive index 1.33 is as follows.

layers = mc.mclayer.Layers(
    [
        mc.mclayer.Layer(n=1.00, d=np.inf,  mua=1.0e2, mus=50.0e2, pf=mc.mcpf.Hg(0.0)),
        mc.mclayer.Layer(n=1.33, d=10.0e-3, mua=1.0e2, mus=50.0e2, pf=mc.mcpf.Hg(0.8)),
        mc.mclayer.Layer(n=1.00, d=np.inf,  mua=1.0e2, mus=50.0e2, pf=mc.mcpf.Hg(0.0))
    ]
)

Note that the absorption coefficient mua, scattering coefficient mus and the scattering phase function pf of the topmost and bottommost layers are not used in the MC simulations, since the photon packets are not propagated through the surrounding medium. However, the refractive index n of the two outermost layers is used to properly refract/reflect the photon packet at the layer boundaries when launched by the source or when escaping the sample. The value of the layer thickness d should be given in m and the values of the scattering mus and absorption mua coefficient in 1/m.

The photon packet source

Different sources of photon packets are available through the mcsource submodule. The following example creates a basic line source (infinitely thin) at the top sample surface (x, y, z)=(0, 0, 0) with a perpendicular incidence (0, 0, 1).

source = mc.mcsource.Line()

The detectors

The photon packets can be collected by a surface detector after exiting the top or bottom sample surface. Different types of surface detectors are available through the mcdetector submodule. Note that the top and bottom sample surface can use different configurations and/or types of detectors.

detectors = mc.mcdetector.Detectors(
    top = mc.mcdetector.Radial(
        mc.mcdetector.Axis(0.0, 10.0e-3, 1000, cosmin=np.deg2rad(20))
    ),
    bottom = mc.mcdetector.Radial(
        mc.mcdetector.Axis(0.0, 10.0e-3, 100)
    )
)

In the above example, we create two radial detectors one at the top and one at the bottom sample surface. The spacing between the concentric accumulators of the radial detector at the top sample surface is set to 10 μm, while the spacing of the concentric accumulators at the bottom sample surface is set to 100 μm. Both detectors are accumulating photon packets from 0.0 mm to 10.0 mm. The detector at the top sample surface only collects photon packets that exit the sample within 20° of the surface normal, while the detector at the bottom sample surface collects all the photon packets that exit the sample.

The OpenCL device

The OpenCL device that will run the MC simulations can be selected through the xopto.cl.clinfo module. In the following example we pick the first available GPU device.

gpu = clinfo.gpu()

The Monte Carlo simulator

Next, we create a Monte Carlo simulator instance from the defined layers, photon packet source and detectors.

mc_obj = mc.Mc(layers, source, detectors, cl_devices=gpu)

Optionally, we can limit the maximum simulation radius that is measured from the position of the photon packet source. In this example, we limit the simulation radius to 25 mm.

mc_obj.rmax = 25.0e-3

Finally, we can run the simulator instance with a given number of photon packets (10,000,000 in this example) and collect the results. The simulator returns three objects/results, namely the trace, fluence and detectors. Since in this basic example we only use the surface detectors, the remaining two results (fluence and trace) will be set to None.

trace_res, fluence_res, detectors_res = mc_obj.run(10e6)

Note that the photon packets that exit the sample within the acceptance cone but at a distance/radius that exceeds the maximum radius of the detector will be accumulated in the last concentric ring.

Visualizing the results

We can plot the simulation results using the mtplotlib.pyplot module. For a better visualization of the reflectance/transmittance a logarithmic scale is used in the y axis of the plots.

fig, (ax1, ax2) = pp.subplots(2, 1)

ax1.semilogy(detectors_res.top.r*1e3, detectors_res.top.reflectance)
ax1.set_xlabel('Distance from source (mm)')
ax1.set_ylabel('Reflectance')

ax2.semilogy(detectors_res.bottom.r*1e3, detectors_res.bottom.reflectance)
ax2.set_xlabel('Distance from source (mm)')
ax2.set_ylabel('Reflectance')

pp.show()

Reflectance and transmittance collected by the surface detectors.

The complete example

basic.py

You can run this example from the root directory of the PyXopto package as:

python examples/mcml/basic.py

MC Dataset

Precomputed datasets of reflectance, transmittance, energy deposition and sampling volume for a number of different source, detector and sample configurations are available through a separate repository MC Dataset.

Citing PyXOpto

We, the authors of PyXOpto, expect that the package is used in accordance with the GPL3+ license and that any work using the PyXOpto package also cites the project and at least one of the following references:

• M. Bürmen, F. Pernuš, and P. Naglič, MCDataset: a public reference dataset of Monte Carlo simulated quantities for multilayered and voxelated tissues computed by massively parallel PyXOpto Python package, J. Biomed. Opt., 27 (8), 083012 (2022), https://doi.org/10.1117/1.JBO.27.8.083012.

• P. Naglič, F. Pernuš, B. Likar, and M. Bürmen, Limitations of the commonly used simplified laterally uniform optical fiber probe-tissue interface in Monte Carlo simulations of diffuse reflectance, Biomed. Opt. Expres, 6 (10), 3973-3988 (2015), https://doi.org/10.1364/BOE.6.003973.

• P. Naglič, F. Pernuš, B. Likar, and M. Bürmen, Lookup table-based sampling of the phase function for Monte Carlo simulations of light propagation in turbid media, Biomed. Opt. Expres, 8 (3), 1895-1910 (2017), https://doi.org/10.1364/BOE.8.001895.

For alternative licensing options of PyXOpto please contact us at [email protected].