How to compile and install gVirtualXRay Suite

Requirements

Make sure you have:

CMake 3.12 or newer (see http://www.cmake.org/);
A C++ compiler; and
A GPU that supports OpenGL (integrated GPUs are fine).

For GNU/Linux

The examples below are for openSUSE Leap but you can adapt them for your own distro.

You need cmake and a compiler:

    $ sudo zypper in cmake-full gcc-c++

You need some system libraires:

    $ sudo zypper in libX11-devel \
                     libXi-devel \
                     libXcursor-devel \
                     libXinerama-devel \
                     libXrandr-devel \
                     libXxf86vm-devel \
                     glu-devel

For unit testing, SimpleGVXR and wrappers (optional):

    $ sudo zypper in Mesa-libEGL1 Mesa-libEGL-devel libgbm1 libgbm-devel

For unit wrappers (optional):

    $ sudo zypper in swig \
        ruby-devel \
        tcl-devel \
        python3 python3-devel \
        java-11-openjdk \
        octave-devel \
        R-core R-base  R-core-devel R-base-devel

Mac OS X:

Install XCode from the Mac App Store.
Install the Command Line Tools package via the Terminal application using

    $ xcode-select --install command.

Install CMake from https://cmake.org/download/
For Wrappers, you may want to install SWIG and Python 3. I use homebrew for that purpose, see https://brew.sh/

Microsoft Windows

Install Visual Studio from https://visualstudio.microsoft.com/vs/
- Make sure to select the C++ language
Install CMake from https://cmake.org/download/
You may want to install a git client, e.g. https://git-scm.com/download/win
You may want to install a SVN client, e.g. TortoiseSVN from https://tortoisesvn.net/downloads.html
For Wrappers, you may want to install Python 3 from https://www.python.org/downloads/ Make sure to install the development libraries.

Download the latest version of the source code

The latest release (gVirtualXRay-1.1.3-Source.zip) available at https://sourceforge.net/projects/gvirtualxray/files/1.1/gVirtualXRay-1.1.3-Source.zip/download or
The latest version from SVN at https://svn.code.sf.net/p/gvirtualxray/code/trunk

Installation from the source code

GNU/Linux and Mac OS X

Assuming the system is ready.

Open a terminal and choose where the binaries should be installed. It must be a directory where you can write. If you can’t, make sure you use sudo make rather than make in Steps 5 and 6. In the example below, I install it in my home directory in gvxr-install.

    $ export GVXR_INSTALL_DIR=$HOME/gvirtualxray-install

go in the directory where you want to build the gVirtualXRay, e.g.

    $ mkdir ~/gvxr
    $ cd ~/gvxr

Download the latest release:

    $ wget https://sourceforge.net/projects/gvirtualxray/files/1.1/gVirtualXRay-1.1.3-Source.zip/download
    $ mv download gVirtualXRay-1.1.3-Source.zip
    $ unzip gVirtualXRay-1.1.3-Source.zip

Create a directory where the binaries will be created and go in this directory.

    $ mkdir gvxr-bin
    $ cd gvxr-bin

Configure the project using CMake. Use cmake, ccmake or cmake-gui depending on you preferences. ccmake and cmake-gui are interactive.

cmake:

     $ cmake \
         -DCMAKE_BUILD_TYPE:STRING=Release \
         -DCMAKE_INSTALL_PREFIX:STRING=$GVXR_INSTALL_DIR \
         -DBUILD_TESTING:BOOL=ON \
         -DBUILD_WRAPPER_CSHARP:BOOL=ON \
         -DBUILD_WRAPPER_JAVA:BOOL=ON \
         -DBUILD_WRAPPER_OCTAVE:BOOL=ON \
         -DBUILD_WRAPPER_PERL:BOOL=ON \
         -DBUILD_WRAPPER_PYTHON3:BOOL=ON \
         -DBUILD_WRAPPER_R:BOOL=ON \
         -DBUILD_WRAPPER_RUBY:BOOL=ON \
         -DBUILD_WRAPPER_TCL:BOOL=ON \
         -S .. \
         -B $PWD

ccmake:

     $ ccmake \
         -DCMAKE_BUILD_TYPE:STRING=Release \
         -DCMAKE_INSTALL_PREFIX:STRING=$GVXR_INSTALL_DIR \
         -S .. \
         -B $PWD

cmake-gui:

     $ ccmake \
         -DCMAKE_BUILD_TYPE:STRING=Release \
         -DCMAKE_INSTALL_PREFIX:STRING=$GVXR_INSTALL_DIR \
         -S .. \
         -B $PWD

Compile the project.

    $ make -j16

I used a parallel build with 16 jobs as I got 16 cores in my CPU. Adjust -j depending on your computer. Once the project is made, it is also installed. 7. Run the unit tests (optional)

    $ make test

Install

    $ make install

or at your own risk as root using:

    $ sudo make install

If you built the python wrapper, add its path to PYTHONPATH:

    $ PYTHONPATH=$GVXR_INSTALL_DIR/gvxrWrapper-1.0.1/python3:$PYTHONPATH

And to make it permanent:

    $ echo "" >> $HOME/.bashrc
    $ echo "################################################################################" >> $HOME/.bashrc
    $ echo "# Install gvxrPython3 in PYTHONPATH" >> $HOME/.bashrc
    $ echo export PYTHONPATH=$GVXR_INSTALL_DIR/gvxrWrapper-1.0.1/python3:\$PYTHONPATH >> $HOME/.bashrc
    $ echo "################################################################################" >> $HOME/.bashrc

Summary of all the commands:

export GVXR_INSTALL_DIR=$HOME/gvirtualxray-install

mkdir ~/gvxr
cd ~/gvxr

wget https://sourceforge.net/projects/gvirtualxray/files/1.1/gVirtualXRay-1.1.3-Source.zip/download
mv download gVirtualXRay-1.1.3-Source.zip
unzip gVirtualXRay-1.1.3-Source.zip

mkdir gvxr-bin
cd gvxr-bin

cmake \
    -DCMAKE_BUILD_TYPE:STRING=Release \
    -DCMAKE_INSTALL_PREFIX:STRING=$GVXR_INSTALL_DIR \
    -DBUILD_TESTING:BOOL=ON \
    -DBUILD_WRAPPER_CSHARP:BOOL=OFF \
    -DBUILD_WRAPPER_JAVA:BOOL=OFF \
    -DBUILD_WRAPPER_OCTAVE:BOOL=OFF \
    -DBUILD_WRAPPER_PERL:BOOL=OFF \
    -DBUILD_WRAPPER_PYTHON3:BOOL=ON \
    -DBUILD_WRAPPER_R:BOOL=OFF \
    -DBUILD_WRAPPER_RUBY:BOOL=OFF \
    -DBUILD_WRAPPER_TCL:BOOL=OFF \
    -S .. \
    -B $PWD

make -j16

make test

make install

export PYTHONPATH=$GVXR_INSTALL_DIR/gvxrWrapper-1.0.1/python3:PYTHONPATH

echo "" >> $HOME/.bashrc
echo "################################################################################" >> $HOME/.bashrc
echo "# Install gvxrPython3 in PYTHONPATH" >> $HOME/.bashrc
echo "PYTHONPATH=$GVXR_INSTALL_DIR/gvxrWrapper-1.0.1/python3:\$PYTHONPATH" >> $HOME/.bashrc
echo "################################################################################" >> $HOME/.bashrc

For Windows

I recommand to use 64 bits for all the components, including for Python 3.

Download and extract gVirtualXRay’s code from https://sourceforge.net/projects/gvirtualxray/files/1.1/gVirtualXRay-1.1.3-Source.zip/download.
Open CMake’s gui.

Illustration

Select where the source code is. This is the top directory of the repository that contains CMakeLists.txt.

Illustration

Select where the binaries are going to be compiled. It CANNOT be a sub-directory of the source directory chosen in the previous step.

Illustration

Press configure, then choose which compiler you want to use and which architecture. I used Visual Studio 15 2017’s native compilers, and x64 (for 64 bits).

Illustration

Click on Configure. There’ll be an error, but don’t worry about it.

Illustration

Search for install.

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Change the variable CMAKE_INSTALL_PREFIX into a path where you are allowed to write. Click on configure. If it does not work, change the path and make sure you have write privilege for that path.

Illustration

If you want to build a wrapper, e.g. for Python 3, go to BUILD and tick the right option(s) (in my case BUILD_PYTHON£_WRAPPER). Now you can click on Configure, then Generate, then Open Project.

Illustration

It will open Visual Studio. Change Debug into Release.

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Do a right click on BUILD_ALL or press the F7 key to build the project.

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Go and make some coffee, it’s gonna take a bit of time… At the end, in the output, you should see something like

========== Build: 4 succeeded, ...

Installation directory content in Windows

On Windows, you Should see 4 or 5 directories in the installation directory depending on wrappers:

bin
third_party
- include
- lib (Windows) or lib64 (GNU/Linux and Mac OS X???)
gVirtualXRay-1.1.3
- Bin2C.cmake
- CreateHeaderFiles.cmake
- gVirtualXRayConfig.cmake
- include
- lib
- LICENSE.txt
- test
- third_party
- UsegVirtualXRay.cmake
SimpleGVXR-1.0.1
- include
- lib
- SimpleGVXR-doc.i
- SimpleGVXRConfig.cmake
- test
- UseSimpleGVXR.cmake
gvxrWrapper-1.0.1
- data
- python3

Installation directory content in GNU/Linux and Mac OS X

On Unixes, you Should see 3 or 4 directories in the installation directory depending on wrappers:

third_party
- include
- lib (Windows and Mac OS X) or lib64 (GNU/Linux)
gVirtualXRay-1.1.3
- Bin2C.cmake
- CreateHeaderFiles.cmake
- gVirtualXRayConfig.cmake
- include
- lib
- LICENSE.txt
- test
- third_party
- UsegVirtualXRay.cmake
SimpleGVXR-1.0.1
- include
- lib
- SimpleGVXR-doc.i
- SimpleGVXRConfig.cmake
- test
- UseSimpleGVXR.cmake
gvxrWrapper-1.0.1
- data
- python3

Test the Python wrapper

Go to gvxrWrapper-1.0.1/python3,
Execute the test script. You should see something like:

The X-ray image is displayed using linear, log and power law colour scales using Matplotlib.

Press <Q> to close this window and the real-time viewer will open:

Illustration

Use the mouse wheel to zoom-out:

Illustration

Use the mouse left button and move the mouse around to adjust the view:

Illustration

Press <B> to hide/show the X-ray beam:

Illustration

Press <W> to view the 3-D object in solid/wireframe mode:

You can also press <N> to display the X-ray image in negative or positive and <H> to hide/show the X-ray detector.
Press <Q> or <ESC> to exit. When the script ends, there’ll be two new files:

xray_image-0.mha: contains the X-ray image. MHA fies can be viewed with the popular scientific image viewer tool ImageJ/Fiji.
lbuffer-0.mha: contains the length of X-rays crossed in the 3-D object.

If you want to create your own simulations, have a look at the script. You can find it at https://sourceforge.net/p/gvirtualxray/code/HEAD/tree/trunk/Wrappers/python3/test.py.

Topic 5 – Installing gVirtualXRay

How to compile and install gVirtualXRay Suite

Requirements

For GNU/Linux

Mac OS X:

Microsoft Windows

Download the latest version of the source code

Installation from the source code

GNU/Linux and Mac OS X

Summary of all the commands:

For Windows

Installation directory content in Windows

Installation directory content in GNU/Linux and Mac OS X

Test the Python wrapper

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