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PyTissueOptics

Monte Carlo simulations of light transport made easy.

This python package is an object-oriented implementation of Monte Carlo modeling for light transport in diffuse media. The package is very easy to set up and use, and its mesh-based approach makes it a polyvalent tool to simulate light transport in arbitrarily complex scenes. The package offers both a native Python implementation and a hardware-accelerated version using OpenCL.

As discussed in the why use this package section, computation time isn't the only variable at play. This code is easy to understand, easily scalable and very simple to modify for your need. It was designed with research and education in mind.

Notable features

  • Arbitrarily complex 3D environments.
  • Import external 3D models (.OBJ).
  • Great data visualization with Mayavi.
  • Multi-layered tissues.
  • Hardware acceleration with OpenCL.
  • Accurate Fresnel reflection and refraction with surface smoothing.
  • Discard 3D data (auto-binning to 2D views).
  • Independent 3D graphics framework under scene.

Table of Contents

Installation

Requires Python 3.6+ installed on the device.

Installing the development version

  1. Clone the repository.
  2. Create a virtual environment inside the repository with python -m venv venv.
  3. Activate the virtual environment.
    • On MacOS/Linux: source venv/bin/activate.
    • On Windows: venv\Scripts\activate.bat.
  4. Upgrade pip with pip install --upgrade pip.
  5. Install the package requirements with pip install -r requirements.txt.

Installing the previous release

Currently, this pip version is outdated. We recommend installing the development version.

pip install --upgrade pip
pip install --upgrade pytissueoptics

Getting started

A command-line interface is available to help you run examples and tests.

python -m pytissueoptics --help
python -m pytissueoptics --list
python -m pytissueoptics --examples 1,2,3
python -m pytissueoptics --tests

To launch a simple simulation on your own, follow these steps.

  1. Import the pytissueoptics module
  2. Define the following objects:
    • scene: a ScatteringScene object, which defines the scene and the optical properties of the media, or use a pre-defined scene from the samples module. The scene takes in a list of Solid as its argument. These Solid will have a ScatteringMaterial and a position. This is clear in the examples below.
    • source: a Source object, which defines the source of photons.
    • logger: an EnergyLogger object, which logs the simulation progress ('keep3D=False' can be set to auto-bin to 2D views).
  3. Propagate the photons in your scene with source.propagate.
  4. Define a Viewer object and display the results by calling the desired methods. It offers various visualizations of the experiment as well as a statistics report.

Here's what it might look like:

from pytissueoptics import *

material = ScatteringMaterial(mu_s=3.0, mu_a=1.0, g=0.8, n=1.5)

tissue = Cuboid(a=1, b=3, c=1, position=Vector(2, 0, 0), material=material)
scene = ScatteringScene([tissue])

logger = EnergyLogger(scene)
source = PencilPointSource(position=Vector(-3, 0, 0), direction=Vector(1, 0, 0), N=1000)
source.propagate(scene, logger)

viewer = Viewer(scene, source, logger)
viewer.reportStats()
viewer.show3D()

Check out the pytissueoptics/examples folder for more examples on how to use the package.

Hardware acceleration

source = DivergentSource(useHardwareAcceleration=True, ...)

Hardware acceleration can offer a speed increase factor around 1000x depending on the scene. By default, the program will try to use hardware acceleration if possible, which will require OpenCL drivers for your hardware of choice. NVIDIA and AMD GPU drivers should contain their corresponding OpenCL driver by default. To force the use of the native Python implementation, set useHardwareAcceleration=False when creating a light Source.

Follow the instructions on screen to get setup properly for the first hardware accelerated execution which will offer to run a benchmark test to determine the ideal number of work units for your hardware.

Why use this package

It is known, as April 2022, Python is the most used language (Tiobe index). This is due to the ease of use, the gentle learning curve, and growing community and tools. There was a need for such a package in Python, so that not only long hardened C/C++ programmers could use the power of Monte Carlo simulations. It is fairly reasonable to imagine you could start a calculation in Python in a few minutes, run it overnight and get an answer the next day after a few hours of calculations. It is also reasonable to think you could modify the code yourself to suit your exact needs! (Do not attempt this in C). This is the solution that the CPU-based portion of this package offers you. With the new OpenCL implementation, speed is not an issue anymore, so using pytissueoptics should not even be a question.

Known limitations

  1. It uses Henyey-Greenstein approximation for scattering direction because it is sufficient most of the time.
  2. Reflections are specular, which does not accounts for the roughness of materials. It is planned to implement Bling-Phong reflection model in a future release.

Examples

Multi-layered phantom tissue

Located at pytissueoptics/examples/rayscattering/ex01.py. Using a pre-defined tissue from the samples module.

N = 500000
scene = samples.PhantomTissue()
source = DivergentSource(position=Vector(0, 0, -0.1), direction=Vector(0, 0, 1), N=N, diameter=0.2, divergence=np.pi / 4)
logger = EnergyLogger(scene)
source.propagate(scene, logger=logger)

viewer = Viewer(scene, source, logger)
viewer.reportStats()

viewer.show2D(View2DProjectionX())
viewer.show2D(View2DProjectionX(solidLabel="middleLayer"))
viewer.show2D(View2DSurfaceZ(solidLabel="middleLayer", surfaceLabel="interface0"))
viewer.show1D(Direction.Z_POS)
viewer.show3D()

Default figures generated

stack_visuals

Discarding the 3D data

When the raw simulation data gets too large, the 3D data can be automatically binned to pre-defined 2D views.

logger = EnergyLogger(scene, keep3D=False)

All 2D views are unchanged, because they are included in the default 2D views tracked by the EnergyLogger. The 1D profile and stats report are also properly computed from the stored 2D data. The 3D display will auto-switch to Visibility.DEFAULT_2D which includes Visibility.VIEWS with ViewGroup.SCENE (XYZ projections of the whole scene) visible by default. image

Display some 2D views with the 3D point cloud

The argument viewsVisibility can accept a ViewGroup tag like SCENE, SURFACES, etc., but also a list of indices for fine control. You can list all stored views with logger.listViews() or viewer.listViews(). Here we toggle the visibility of 2D views along the default 3D visibility (which includes the point cloud).

logger = EnergyLogger(scene)
[...]
viewer.show3D(visibility=Visibility.DEFAULT_3D | Visibility.VIEWS,  viewsVisibility=[0, 1])

image

Display custom 2D views

If keep3D=False, the custom views (like slices, which are not included in the default views) have to be added to the logger before propagation like so:

logger = EnergyLogger(scene, keep3D=False)
logger.addView(View2DSliceZ(position=0.5, thickness=0.1, limits=((-1, 1), (-1, 1))))
logger.addView(View2DSliceZ(position=1, thickness=0.1, limits=((-1, 1), (-1, 1))))
logger.addView(View2DSliceZ(position=1.5, thickness=0.1, limits=((-1, 1), (-1, 1))))

If the logger keeps track of 3D data, then it's not a problem and the views can be added later with logger.addView(customView) or implicitly when asking for a 2D display from viewer.show2D(customView). image

Display interactive 3D volume slicer

Requires 3D data.

viewer.show3DVolumeSlicer()

image

Save and append simulation results

The EnergyLogger data can be saved to file. This can also be used along with keep3D=False to only save 2D data. Every time the code is run, the previous data is loaded and extended. This is particularly useful to propagate a very large amount of photons (possibly infinite) in smaller batches so the hardware doesn't run out of memory.

[...]
logger = EnergyLogger(scene, "myExperiment.log", keep3D=False)
source.propagate(scene, logger)
logger.save()

Acknowledgment

This package was first inspired by the standard, tested, and loved MCML from Wang, Jacques and Zheng , itself based on Prahl and completely documented, explained, dissected by Jacques and Prahl. The original idea of using Monte Carlo for tissue optics calculations was first proposed by Wilson and Adam in 1983. This would not be possible without the work of these pioneers.