gtsam/cython

Python Wrapper

This is the Python wrapper around the GTSAM C++ library. We use Cython to generate the bindings to the underlying C++ code.

Requirements

• If you want to build the GTSAM python library for a specific python version (eg 3.6), use the -DGTSAM_PYTHON_VERSION=3.6 option when running cmake otherwise the default interpreter will be used.

• If the interpreter is inside an environment (such as an anaconda environment or virtualenv environment), then the environment should be active while building GTSAM.

• This wrapper needs Cython(>=0.25.2), backports_abc(>=0.5), and numpy(>=1.11.0). These can be installed as follows:

  pip install -r <gtsam_folder>/cython/requirements.txt
  

• For compatibility with GTSAM's Eigen version, it contains its own cloned version of Eigency, named gtsam_eigency, to interface between C++'s Eigen and Python's numpy.

Install

• Run cmake with the GTSAM_INSTALL_CYTHON_TOOLBOX cmake flag enabled to configure building the wrapper. The wrapped module will be built and copied to the directory defined by GTSAM_CYTHON_INSTALL_PATH, which is by default <PROJECT_BINARY_DIR>/cython in Release mode and <PROJECT_BINARY_DIR>/cython<CMAKE_BUILD_TYPE> for other modes.

• Build GTSAM and the wrapper with make.

• To install, simply run make python-install.

  • The same command can be used to install into a virtual environment if it is active.
  • NOTE: if you don't want GTSAM to install to a system directory such as /usr/local, pass -DCMAKE_INSTALL_PREFIX="./install" to cmake to install GTSAM to a subdirectory of the build directory.

• You can also directly run make python-install without running make, and it will compile all the dependencies accordingly.

Unit Tests

The Cython toolbox also has a small set of unit tests located in the test directory. To run them:

cd <GTSAM_CYTHON_INSTALL_PATH>
python -m unittest discover

Utils

TODO

Examples

TODO

Writing Your Own Scripts

See the tests for examples.

Some Important Notes:

• Vector/Matrix:

  • GTSAM expects double-precision floating point vectors and matrices. Hence, you should pass numpy matrices with dtype=float, or float64.
  • Also, GTSAM expects column-major matrices, unlike the default storage scheme in numpy. Hence, you should pass column-major matrices to GTSAM using the flag order='F'. And you always get column-major matrices back. For more details, see this link.
  • Passing row-major matrices of different dtype, e.g. int, will also work as the wrapper converts them to column-major and dtype float for you, using numpy.array.astype(float, order='F', copy=False). However, this will result a copy if your matrix is not in the expected type and storage order.

• Inner namespace: Classes in inner namespace will be prefixed by _ in Python.

  Examples: noiseModel_Gaussian, noiseModel_mEstimator_Tukey

• Casting from a base class to a derive class must be done explicitly.

  Examples:

  noiseBase = factor.noiseModel()
  noiseGaussian = dynamic_cast_noiseModel_Gaussian_noiseModel_Base(noiseBase)
  

Wrapping Custom GTSAM-based Project

Please refer to the template project and the corresponding tutorial available here.

KNOWN ISSUES

• Doesn't work with python3 installed from homebrew
  • size-related issue: can only wrap up to a certain number of classes: up to mEstimator!
  • Guess: 64 vs 32b? disutils Compiler flags?
• Bug with Cython 0.24: instantiated factor classes return FastVector<size_t> for keys(), which can't be casted to FastVector
  • Upgrading to 0.25 solves the problem
• Need default constructor and default copy constructor for almost every classes... :(
  • support these constructors by default and declare "delete" for special classes?

TODO

• allow duplication of parent' functions in child classes. Not allowed for now due to conflicts in Cython.
• a common header for boost shared_ptr? (Or wait until everything is switched to std::shared_ptr in GTSAM?)
• inner namespaces ==> inner packages?
• Wrap fixed-size Matrices/Vectors?

Completed/Cancelled:

• Fix Python tests: don't use " import * ": Bad style!!! (18-03-17 19:50)

• Unit tests for cython wrappers @done (18-03-17 18:45) -- simply compare generated files

• Wrap unstable @done (18-03-17 15:30)

• Unify cython/GTSAM.h and the original GTSAM.h @done (18-03-17 15:30)

• 18-03-17: manage to unify the two versions by removing std container stubs from the matlab version,and keeping KeyList/KeyVector/KeySet as in the matlab version. Probably Cython 0.25 fixes the casting problem.

• 06-03-17: manage to remove the requirements for default and copy constructors

• 25-11-16: Try to unify but failed. Main reasons are: Key/size_t, std containers, KeyVector/KeyList/KeySet. Matlab doesn't need to know about Key, but I can't make Cython to ignore Key as it couldn't cast KeyVector, i.e. FastVector, to FastVector<size_t>.

• Marginal and JointMarginal: revert changes @failed (17-03-17 11:00) -- Cython does need a default constructor! It produces cpp code like this: GTSAM::JointMarginal __pyx_t_1; Users don't have to wrap this constructor, however.

• Convert input numpy Matrix/Vector to float dtype and storage order 'F' automatically, cannot crash! @done (15-03-17 13:00)

• Remove requirements.txt - Frank: don't bother with only 2 packages and a special case for eigency! @done (08-03-17 10:30)

• CMake install script @done (25-11-16 02:30)

• [REFACTOR] better name for uninstantiateClass: very vague!! @cancelled (25-11-16 02:30) -- lazy

• forward declaration? @cancelled (23-11-16 13:00) - nothing to do, seem to work?

• wrap VariableIndex: why is it in inference? If need to, shouldn't have constructors to specific FactorGraphs @done (23-11-16 13:00)

• Global functions @done (22-11-16 21:00)

• [REFACTOR] typesEqual --> isSameSignature @done (22-11-16 21:00)

• Proper overloads (constructors, static methods, methods) @done (20-11-16 21:00)

• Allow overloading methods. The current solution is annoying!!! @done (20-11-16 21:00)

• Casting from parent and grandparents @done (16-11-16 17:00)

• Allow overloading constructors. The current solution is annoying!!! @done (16-11-16 17:00)

• Support "print obj" @done (16-11-16 17:00)

• methods for FastVector: at, [], ... @done (16-11-16 17:00)

• Cython: Key and size_t: traits<size_t> doesn't exist @done (16-09-12 18:34)

• KeyVector, KeyList, KeySet... @done (16-09-13 17:19)

• [Nice to have] parse typedef @done (16-09-13 17:19)

• ctypedef at correct places @done (16-09-12 18:34)

• expand template variable type in constructor/static methods? @done (16-09-12 18:34)

• NonlinearOptimizer: copy constructor deleted!!! @done (16-09-13 17:20)

• Value: no default constructor @done (16-09-13 17:20)

• ctypedef PriorFactor[Vector] PriorFactorVector @done (16-09-19 12:25)

• Delete duplicate methods in derived class @done (16-09-12 13:38)

• Fix return properly @done (16-09-11 17:14)

• handle pair @done (16-09-11 17:14)

• Eigency: ambiguous call: A(const T&) A(const Vector& v) and Eigency A(Map[Vector]& v) @done (16-09-11 07:59)

• Eigency: Constructor: ambiguous construct from Vector/Matrix @done (16-09-11 07:59)

• Eigency: Fix method template of Vector/Matrix: template argument is [Vector] while arugment is Map[Vector] @done (16-09-11 08:22)

• Robust noise: copy assignment operator is deleted because of shared_ptr of the abstract Base class @done (16-09-10 09:05)

• Cython: Constructor: generate default constructor? (hack: if it's serializable?) @cancelled (16-09-13 17:20)

• Eigency: Map[] to Block @created(16-09-10 07:59) @cancelled (16-09-11 08:28)

• inference before symbolic/linear

• what's the purpose of "virtual" ??