Getting Started with Jupyter Notebooks

Using VTS in a Jupyter Notebook

This information will likely change as more support for python and .NET is introduced.

Installation details

Step 1: Install .NET 8

You will need version 8 of .NET which is available from Microsoft below

https://dotnet.microsoft.com/en-us/download/dotnet/8.0

On MacOS: Save everything to $HOME/Documents/Code/dotnet8

Do not forget to update your ~/.bash_profile or whatever you use so that this directory is in your path. Also define DOTNET_ROOT

PATH=$PATH:$HOME/Documents/Code/dotnet8

export DOTNET_ROOT=$HOME/Documents/Code/dotnet8

Step 2: Clone the scripting repository

git clone https://github.com/VirtualPhotonics/vts.git

Step 3: Download the VTS libraries

Get the latest VTS libraries for the specific platform from releases and extract them into the libraries folder under scripting.

Step 4: Install pythonnet

pip install pythonnet

Note for MacOS and Linux: Because pythonnet under macOS (or linux) defaults to mono, two more things need to added to ~/.bash_profile

export PYTHONNET_RUNTIME=coreclr
export PYTHONNET_PYDLL=/usr/local/bin/python3   

Obviously use the path for python on your system (which python3 will tell you)

Next start a JupyterLab notebook to verify that things are installed correctly

import clr
clr.AddReference("System")
from System import Console
Console.WriteLine("Hello from .NET 8!")

The final test is importing from Vts.dll

from pythonnet import set_runtime
set_runtime("coreclr")

import clr
clr.AddReference("/path/to/libraries/Vts.dll")    

from Vts import *

where, of course, "/path/to" above has been adapted to your system

Step 5: Run programs

To run VTS programs in python include the following the header

    from pythonnet import set_runtime
    set_runtime("coreclr")

    import clr
    clr.AddReference("/path/to/libraries/Vts.dll")    
    
    from Vts import *
    from Vts.Common import *
    from Vts.Extensions import *
    from Vts.Modeling.Optimizers import *
    from Vts.Modeling.ForwardSolvers import *
    from Vts.Factories import *
    from Vts.MonteCarlo import *
    from Vts.MonteCarlo.Sources import *
    from Vts.MonteCarlo.Tissues import *
    from Vts.MonteCarlo.Detectors import *
    from Vts.MonteCarlo.Factories import *
    from Vts.MonteCarlo.PhotonData import *
    from Vts.MonteCarlo.PostProcessing import *
    from System import Array, Double

Start PowerShell and to bring up Jupyter Notebook run

python -m notebook

This will create a tab in your local browser with Files from PowerShell current directory folder. Click on any file ending in *.ipynb. Click on any "Code" segment "[]:" to execute.

Step 6: Submit new code or code changes to GitHub repository

Before submitting any code to GitHub that has been executed in Jupyter Notebooks, run "Kernel->Restart Kernel and Clear Outputs of All Cells...". This will clear code of any output and/or binary content. This is critical so that large files are not pushed to the repository.