Windows Environment

Installing system Libraries and Tools

Update Windows

1. Latest Windows updates
2. Latest NVIDIA graphics driver (current version 446.16)

Development Tools

Install the following development tools by downloading the latest installer for each from their respective websites:

Visual Studio 2019
Typora
CMake 3.16 or higher (3.16 needed to support Visual Studio 2019)
Doxygen
SmartSVN
TortoiseSVN
7-Zip

NVIDIA Libraries

CUDA

1. Download the CUDA 10.2 Windows installer: cuda_10.2.89_411.22_win10.exe (x86_64)
2. Install CUDA 10.2 using the installer (use custom install and don't install the NVIDIA drivers, assume latest are installed). The default install location should be set to C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA

CuDNN

1. Download the cuDNN libraries for Windows, CUDA version 10.2, cuDNN v7.6.5 Library for Windows 10
2. Install the cuDNN package. Extract cudnn-10.2-windows10-x64-v7.6.5.32.zip to cuda and move the contents of the cuda directory to to C:/tools/NVIDIA/cudnn-7.6.5
3. Add the location of the dynamic libraries, C:\tools\NVIDIA\cudnn-7.6.5\bin to the Windows system Path variable

Install Third Party Libraries

1. Download the following third party libraries for Windows 10 - Visual Studio 2019 from the BAP development website at Third party libraries downloads (Will need your username and password to access the site)

   boost 1.73.0
   dcmtk 3.6.5
   glfw 3.3.2
   itk 5.1.0
   libjpeg-turbo 2.0.4
   libpng 1.6.37
   openms 2.5.0
   openms-contrib 2.5.0
   pdp 2.7.0
   rnifti 1.1.0
   sqlite 3.32.1
   zlib 1.2.11
   

2. Move the downloaded files to C:\tools\Projects directory and and extract with the 7-Zip Extract Here command from the file browser.

3. Add the environment variable QT_PLUGIN_PATH and assign the openms value C:\tools\Projects\openms-2.5.0\bin\plugins

Qt 5.15.0

1. Download the latest Qt unified windows installer from https://www.qt.io/download-qt-installer
2. Run the unified installer using open source user login. You will need to register as a QT Open Source user at the Qt website.
3. Select C:/tools/Projects/QT as the install directory
4. Select Qt 5.15.0 packages MSVC 2019 64-bit and QtCharts and run install
5. Add the environment variable QT_PLUGIN_PATH and assign the openms value C:\tools\Projects\openms-2.5.0\bin\plugins.

Assign Environment Variables

1. Add the following entries to the System Path environment variable

   C:\tools\NVIDIA\cudnn-7.6.5\bin
   C:\tools\Projects\QT\5.15.0\msvc2019_64\bin
   C:\tools\Projects\dcmtk-3.6.5\bin
   C:\tools\Projects\openms-2.5.0\bin
   C:\tools\Projects\libjpeg-turbo-2.0.4\bin
   

Install Datasets

1. Download the following Datasets for the BAP development website at Data sets (Will need your username and password to access the site)

   BRATS PBT voxel classification
   Radiogenomics Lung Cancer
   MNIST hand written numbers
   

2. Move the downloaded BRATS and MNIST datasets to "user home directory"\Projects\data\ImageData directory and and extract with the 7-Zip Extract Here command from the file browser.

3. Move the downloaded Radiogenomics dataset to "user home directory"\Projects\data\VolumeData directory and and extract with the 7-Zip Extract Here command from the file browser.

Install Neural Network models

1. Download the following models for the BAP development website at Models (Will need your username and password to access the site)

   BRATS PBT voxel classification
   MNIST hand written numbers
   

2. Move the downloaded files to "user home directory"\Projects\networks directory and and extract with the 7-Zip Extract Here command from the file browser.

BAP Visual Studio build

Checkout the source

Use either the SmartSVN or TortoiseSVN svn clients to checkout the BAP source code from svn://3.14.90.147/bap/trunk to "user home directory"\Projects\bap (Will need your username and password to access this repository).

Create the Visual Studio 2019 solutions file

1. Create directory `"user home directory"\Projects\bap-vstudio
2. Open up the CMake GUI and select "user home directory"\Projects\bap as the source directory and "user home directory"\Projects\bap-vstudio as the build directory.
3. Hit Configure. Once configuration is complete, hit Generate to create the build files.
4. Once initial configure has completed, if they are not checked yet, select Grouped and Advanced.
5. The solutions file "user home directory"\Projects\bap-vstudio\bap.sln is now ready to use in Visual Studio 2019.