Merge branch 'main' into feature/3-create-additional-plot-examples-for-monte-carlo

Author: Lisa Malenfant

README.md

@@ -1 +1,90 @@
-Jupyter notebooks to call the VTS using Python
+# Using VTS in a Jupyter notebook
+
+This is likely to change once `python` scripting is formally supported by `VTS`.  
+
+## macOS installation details
+
+This is a record of how I got `vts` working in `JupyterLab`.
+
+### Step 1: Install .NET 6
+
+You will need version 6 of .NET which is available from Microsoft below
+
+https://dotnet.microsoft.com/en-us/download/dotnet/6.0
+
+I saved everything to `$HOME/Documents/Code/dotnet6`
+
+Do not forget to update your `~/.bash_profile` or whatever you use so that this directory is in your path.  Also define `DOTNET_ROOT` 
+
+    PATH=$PATH:$HOME/Documents/Code/dotnet6
+  
+    export DOTNET_ROOT=$HOME/Documents/Code/dotnet6
+
+### Step 2: Install VTS
+
+Follow the guidelines at https://github.com/VirtualPhotonics/VTS/wiki/Getting-Started-on-Mac  Briefly, clone the `.git` repo 
+
+    git clone https://github.com/VirtualPhotonics/vts.git
+
+This will create the directory `vts` that is needed for the next step
+
+Install both `powershell` and `nuget` using [Homebrew](https://brew.sh)
+
+    brew install powershell
+    brew install nuget
+
+Now build VTS.  If you don't have `matlab` don't worry, it seemed to work fine without completing the `matlab` tests
+
+    pwsh
+    cd vts
+    ./BuildTestRelease.ps1 
+    exit
+
+### Step 3: Install pythonnet
+
+    pip install pythonnet
+
+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 6!")
+
+The final test is importing from `Vts.dll`
+
+    import clr
+    clr.AddReference("/path/to/vts/src/Vts/publish/local/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
+
+    import clr
+    clr.AddReference("/path/to/vts/src/Vts/publish/local/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