listed as name, version currently in use on my development machine, website, and a short description. I tend to update the installed libraries semi-consistently.
- Used to store particle locations
- set HDF5_ROOT in CMakeLists.txt to point to location if in non-standard location
- own license, but very permissive
- (CVS version)
- Used to get image data out of *.tif
- set FREEIMAGE_ROOT in iden/CMakeLists.txt if in non-standard location.
- GPL or commercial, used with commercial license to play nice with IPP
- Used to process images
- set IPP_ROOT in iden/CMakeLists.txt if in non-standard location.
- Closed license, I can not distribute the header,
- can’t link against non-exempted GPL code
- ok against apache, hdf, and free image commercial
- Used for parsing xml paramter files
- set XERCESC_ROOT in CMakeLists.txt if in non-standard location.
- Apache 2.0, kosher to pull into GPL project, kosher to link against IPP
Boost::date_time (from debian stable)
- Used to parse dates
- if not in standard location, set BOOST_ROOT
- super permissive license
- used to talk to the database of data sets and computations
- public domain
- h5py (svn version) http://code.google.com/p/h5py/
- Numpy
- scipy
- PIL
- build system
- more recent the version, the better
- need to patch and build from source if you want to compile mex file (see Matlab below)
- I do not think I use any GNU extension.
- if you want to compile the
mex
functions, the version needs to match what your version of matlab was compiled with.
- Version control software
- any version should do
- generates python wrappers
- used to generate documentation
Assumes that the source is in SOURCE_PATH
and is being built in
BUILD_PATH
which is a different directory.
The -DCMAKE_BUILD_TYPE
option controls the compiler flags. Useful options are
Release
and Debug
(doc).
This will build a collection of analysis programs, two libraries
In BUILD_DIR
:
cmake SOURCE_PATH -DCMAKE_BUILD_TYPE=Release
This builds two programs, Iden
and Iden_avg
, for finding features.
Iden_avg
averages frames together before finding particles.
In BUILD_PATH
:
cmake SOURCE_PATH -DCOMPILE_IDEN=1 -DCMAKE_BUILD_TYPE=Release
This compiles a collection of badly documented test programs that may or may not test anything useful. This might get cleaned up some day, but it is not high on the to-do list.
This will build a collection of matlab mex files. I do not use these regularly and they may not compile, and if they do may be broken.
In BUILD_DIR:
CC=mex CXX=mex cmake MATLAB_MEX_FILE=1 SOURCE_PATH
Note that this sets environment variables before calling cmake. This requires a patch to cmake (http://public.kitware.com/Bug/view.php?id=9240) to work properly. Also see http://www.vtk.org/Wiki/CMake:MatlabMex
I don’t do anything fancy to install at this point. Either run the binaries out of the build directory or manually copy them into your path.
For the python wrappers to work properly
:_rel_path,_dbg_path
in SOURCE_PATH/script_src/python/trackpy/cpp_wrapper.py need to point to BUILD_PATH/apps.