Required C++ Libraries:

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.

hdf5 (1.8.5)

• 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

freeimage

• (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

IPP (5.3.4.080)

• 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

xerces (3.0.1)

• 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

sqlite (3.7.3)

• used to talk to the database of data sets and computations
• public domain

Required python modules:

• h5py (svn version) http://code.google.com/p/h5py/
• Numpy
• scipy
• PIL

Required External Programs

Cmake

• 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)

GNU compiler

• 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.

git

• Version control software
• any version should do

optional External Programs

SWIG

• generates python wrappers

doxygen

• used to generate documentation

Compile

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).

basic

This will build a collection of analysis programs, two libraries

In BUILD_DIR:

   cmake SOURCE_PATH -DCMAKE_BUILD_TYPE=Release

Iden

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 

testing

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.

Matlab

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

Install

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.