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# Using VTS in a Jupyter notebook
# VTS Python Scripts

This information will likely change as more support for `python` and `.NET` is introduced.
This repository contains Python scripts that work within Jupyter Notebooks or Jupyter Labs as well as scripts that can be run from the command line. These scripts use PythonNet to access the VTS libraries.

## Installation details
For detailed instructions on using these scripts, view our [Wiki documentation](https://github.com/VirtualPhotonics/Vts.Scripting.Python/wiki).

### 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](https://github.com/VirtualPhotonics/Vts.Scripting.Python/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 4: 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
```
### Getting Started
* [Jupyter Notebooks/Labs](https://github.com/VirtualPhotonics/Vts.Scripting.Python/wiki/Getting-Started-with-Jupyter-Notebooks)
* [Command-Line Scripts](https://github.com/VirtualPhotonics/Vts.Scripting.Python/wiki/Getting-Started-with-Command‐Line)