Shrink-Wrap Imaginar Coefficient Reconstruction Algorithm
To compile this library you need
-
C++ Compiler (with
c++11
support, e.g. GCC 4.7+) -
CUDA (
7.0+
) -
CMake (
3.3.1+
) -
OpenMP
-
FFTW3 (single precision build)
-
libSplash (for reading and writing HDF5)
-
PNGwriter (for storing reconstructed images as PNGs)
-
-DCMAKE_INSTALL_PREFIX
The prefix to install the library and additional files (such as headers) into.
-
-DRUN_TESTS
(default off)If true tests will be run.
-
-DBUILD_EXAMPLES
(default off)If true the examples from the examples directory will be built.
-
-DIMRESH_DEBUG
(default off)Adds at least debugging symbols to the code.
-
-DBUILD_DOC
(default on)Build the Doxygen documentation.
-
-DUSE_PNG
(default off)Enable PNG output.
-
-DUSE_SPLASH
(default off)Enable HDF5 in- and output.
-
Create a build directory
mkdir build cd build
-
Invoking CMake
cmake ..
For a clean build with debugging information, try
cmake .. -DIMRESH_DEBUG=on -DBUILD_DOC=off
To build and run everything, try
cmake .. -DRUN_TESTS=on -DBUILD_EXAMPLES=on -DUSE_PNG=on -DUSE_SPLASH=on
-
Invoking make
make
-
Installing
make install
The usage of imresh is mainly divided into five parts:
-
Library initialization
-
Image loading
-
Image processing
-
Image writing
-
Library deinitialization
where image loading and writing can also be handled outside the library.
-
The library initialization is (from the user's perspective) just a single call to
imresh::io::taskQueueInit( )
. Internally this createscudaStream_t
s for each multiprocessor on each CUDA capable device found and stores them for later access. -
Image loading can be done through imresh's own loading functions (found in
imresh::io::readInFuncs
) or with self-written functions.Note:
Your self-written functions have to provide you both the image dimensions and the host memory containing the image. This memory has to be allocated via
new
if you're using the built-in write-out functions. -
Image processing is just a call to
imresh::io::addTask( )
(for explanation of the parameters please have a look at the Doxygen). This will start a thread (a C++std::thread
thread to be precise) handling your data transfers and image processing on the least recently used stream available. The given data write out function will be called inside of this thread, too. -
Image writing can, just as the loading, be done via imresh's own write out functions (found in
imresh::io::writeOutFuncs
) or with self-written functions. These have to match the following signature:void writeOutFunc( float* memory, std::pair<unsigned int,unsigned int> size, std::string filename);
where
memory
is the raw image data,size
the image dimension (size.first
is horizontal,size.second
is vertical) andfilename
the name of the file to store the image in.Note:
If you're using imresh's own loading functions in combination with your own write-out functions be sure you're freeing the image memory with
delete
.Note:
imresh's workflow is designed in a way that you'd free your memory inside of your write out function. It's never called before the algorithm finishs and therefore the ideal place for freeing the image data. imresh's built-in functions handle it that way.
-
Library deinitialization is again just a call to
imresh::io::taskQueueDeinit( )
. This will handle stream destroying, memory freeing and so on for you.Note:
When you're using your own data reading and/or writing functions, you'll have to handle the memory inside of this functions yourself.
There's a set of in-action examples in the examples
directory. These can be
compiled by appending the -DBUILD_EXAMPLES=on
to your CMake call, e.g.
cmake .. -DBUILD_EXAMPLES=on
-
For a simple but complete example of how to use this library try
miniExample
and have a look atminiExample.cpp
. -
For a more complex example with batch processing please have a look at
threadedExample
andthreadedExamples.cpp
resp. -
If you need more example data for your tests, please run
outputExampleCreation
.
+-- benchmark: Contains older deprecated less optimized versions for comparison. Files in here should only be used by files in the tests folder
+-- cmake: CMake find package scripts
+-- examples: Executable examples showing how to use the library
| +-- createTestData: Functions for generating example objects and diffraction intensity to test the algorithm on
| +-- testData: Static examples with a fixed size to test e.g. `readInFuncs`
+-- src: The sources for the actual library. Only this folder is needed with the standard CMake options
| +-- imresh
| +-- algorithms
| +-- io: File input/output and batch processing
| +-- libs
+-- tests: Unit tests and benchmarks.
-
Maximilian Knespel (m.knespel at hzdr dot de)
-
Philipp Trommler (philipp.trommler at tu-dresden dot de)
-
/usr/include/fftw3.h(373): error: identifier "__float128" is undefined
Update your fftw library to something higher than
3.3.4
(not yet released as of this writing) or manually apply the patch shown here, i.e. add|| defined(__CUDACC__)
to the faulty line in the header. -
stddef.h(432): error: identifier "nullptr" is undefined
Your CMake version is too old.
-
/usr/include/host_config.h:105:2: error: #error -- unsupported GNU version! gcc 4.10 and up are not supported! #error -- unsupported GNU version! gcc 4.10 and up are not supported!
This is a common problem with debian and maybe its derivatives, because debian sid and stretch have by default GCC 5.x, but
nvidia-cuda-toolkit
7.0.x. The latter wants GCC 4.10 or lower versions, though.On Debian:
apt-get install gcc-4.9
cmake .. -DIMRESH_DEBUG=ON -DCMAKE_C_COMPILER=$(which gcc-4.9) -DCMAKE_CXX_COMPILER=$(which g++-4.9)