FourierConvolutionCUDALib

Implementation of 3d non-separable convolution using CUDA & FFT Convolution, originally implemented by Fernando Amat for our Nature Methods paper (http://www.nature.com/nmeth/journal/v11/n6/full/nmeth.2929.html).

Windows Build Instructions with NSight (Legacy)

To compile it under Windows, NSight available from the CUDA SDK is suggested. Clone this repository into your cuda-workspace directory. Then make a new shared library project with the same name as the directory.

Under Project > Properties > Build > Settings > Tool Settings > NVCC Linker add -lcufft and -lcuda to the command line pattern so that it looks like this:

${COMMAND} ${FLAGS} -lcufft -lcuda ${OUTPUT_FLAG} ${OUTPUT_PREFIX} ${OUTPUT} ${INPUTS}

Now build the .so/.dll library and put it into the Fiji directory.

Windows Build Instructions with CMake

The cmake build system is also supported under Windows 7 64bit now!

$ cd X:\path\to\repo
$ mkdir build
$ cd build
$ cmake.exe -G "Visual Studio 14 2015 Win64" -DCMAKE_INSTALL_PREFIX=C:/msys64/home/steinbac/ftmp -DBOOST_LIBRARYDIR=C:/boost_1_58_0/msvc-14-x86_64/lib64-msvc-14.0 -DBOOST_ROOT=C:/boost_1_58_0/msvc-12-x86_64 ..
$ cmake.exe --build .. --target ALL_BUILD --config Release
$ ctest.exe -C Release #(optional) the above builds in Release mode
$ cmake.exe --build .. --target install --config Release

OSX/Linux Build Instructions

First, make sure that CUDA must be available through PATH, LD_LIBRARY_PATH or equivalent. The build system is based on cmake, so please install this at any version higher or equal than 2.8.

$ cd /path/to/repo
$ mkdir build
$ cd build
$ cmake -DCMAKE_INSTALL_PREFIX=/directory/of/your/choice .. #default is /usr/lib/ or /usr/lib64 depending on your OS
$ make
$ ctest #(optional) in case you'd like to make sure the library does what it should on your system
$ make install

Dependencies

As the package supports a cmake based build system, having cmake (version >=2.8) installed is recommended.

The unit tests that come with the library require boost (version 1.42 or higher) to be available to the cmake build system. If cmake is unable to detect them, try:

$ cmake -DCMAKE_INSTALL_PREFIX=/directory/of/your/choice -DBOOST_ROOT=/path/to/boost/root .. #default is /usr/lib/ or /usr/lib64 depending on your OS

Here, /path/to/boost/root should contain the boost libraries and the boost headers.

How to get Help

In case something does not work, do not hesitate to open a ticket on our github page: https://github.com/StephanPreibisch/FourierConvolutionCUDALib