183 lines
8.2 KiB
Markdown
183 lines
8.2 KiB
Markdown
This is the Cython/Python wrapper around the GTSAM C++ library.
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INSTALL
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=======
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- This wrapper needs Cython(>=0.25), numpy and eigency, which can be installed
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as follows:
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```bash
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cd <gtsam_folder>/cython
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pip install numpy>=1.11.1
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pip install Cython>=0.25.1
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pip install eigency
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```
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Note: If your eigency fails to install via pip, try to install it from source as below:
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```bash
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git clone https://github.com/wouterboomsma/eigency.git
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cd eigency
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python setup.py -v build
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python setup.py install
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```
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- Build and install gtsam using cmake with GTSAM_INSTALL_CYTHON_TOOLBOX enabled
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Note: The wrapped module will be installed to GTSAM_CYTHON_INSTALL_PATH, which is
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by default: <your CMAKE_INSTALL_PREFIX>/cython
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UNIT TESTS
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==========
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The Cython toolbox also has a small set of unit tests located in the
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test directory. To run them:
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```bash
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cd <your GTSAM_CYTHON_INSTALL_PATH>
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python -m unittest discover
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```
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WRITING YOUR OWN SCRIPTS
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========================
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See the tests for examples.
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## Some important notes:
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- Vector/Matrix:
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+ GTSAM expects double-precision floating point vectors and matrices.
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Hence, you should pass numpy matrices with dtype=float, or 'float64'.
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+ Also, GTSAM expects *column-major* matrices, unlike the default storage
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scheme in numpy. Hence, you should pass column-major matrices to gtsam using
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the flag order='F'. And you always get column-major matrices back.
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For more details, see: https://github.com/wouterboomsma/eigency#storage-layout---why-arrays-are-sometimes-transposed
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+ Passing row-major matrices of different dtype, e.g. 'int', will also work
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as the wrapper converts them to column-major and dtype float for you,
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using numpy.array.astype(float, order='F', copy=False).
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However, this will result a copy if your matrix is not in the expected type
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and storage order.
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- Inner namespace: Classes in inner namespace will be prefixed by <innerNamespace>_ in Python.
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Examples: noiseModel_Gaussian, noiseModel_mEstimator_Tukey
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- Casting from a base class to a derive class must be done explicitly.
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Examples:
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```Python
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noiseBase = factor.get_noiseModel()
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noiseGaussian = dynamic_cast_noiseModel_Gaussian_noiseModel_Base(noiseBase)
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```
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WRAPPING YOUR OWN PROJECT THAT USES GTSAM
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=========================================
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- Set PYTHONPATH to include ${GTSAM_CYTHON_INSTALL_PATH}
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+ so that it can find gtsam Cython header: gtsam/gtsam.pxd
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- Create your setup.py.in as follows:
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```python
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from distutils.core import setup
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from distutils.extension import Extension
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from Cython.Build import cythonize
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import eigency
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include_dirs = ["${CMAKE_SOURCE_DIR}/cpp", "${CMAKE_BINARY_DIR}"]
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include_dirs += "${GTSAM_INCLUDE_DIR}".split(";")
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include_dirs += eigency.get_includes(include_eigen=False)
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setup(
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ext_modules=cythonize(Extension(
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"your_module_name",
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sources=["your_module_name.pyx"],
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include_dirs= include_dirs,
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libraries=['gtsam'],
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library_dirs=["${GTSAM_DIR}/../../"],
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language="c++",
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extra_compile_args=["-std=c++11"])),
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)
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```
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- In your CMakeList.txt
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```cmake
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find_package(GTSAM REQUIRED) # Make sure gtsam's install folder is in your PATH
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set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH}" "${GTSAM_DIR}/../GTSAMCMakeTools")
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# Wrap
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include(GtsamCythonWrap)
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wrap_and_install_library_cython("your_project_interface.h"
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"from gtsam.gtsam cimport *" # extra import of gtsam/gtsam.pxd Cython header
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"path_to_your_setup.py.in"
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"your_install_path"
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```
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KNOWN ISSUES
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============
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- Doesn't work with python3 installed from homebrew
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- size-related issue: can only wrap up to a certain number of classes: up to mEstimator!
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- Guess: 64 vs 32b? disutils Compiler flags?
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- Bug with Cython 0.24: instantiated factor classes return FastVector<size_t> for keys(), which can't be casted to FastVector<Key>
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- Upgrading to 0.25 solves the problem
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- Need default constructor and default copy constructor for almost every classes... :(
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- support these constructors by default and declare "delete" for special classes?
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TODO
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=====
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☐ allow duplication of parent' functions in child classes. Not allowed for now due to conflicts in Cython.
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☐ a common header for boost shared_ptr? (Or wait until everything is switched to std::shared_ptr in gtsam?)
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☐ inner namespaces ==> inner packages?
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☐ Wrap fixed-size Matrices/Vectors?
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Completed/Cancelled:
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=====
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✔ Fix Python tests: don't use " import <package> * ": Bad style!!! @done (18-03-17 19:50)
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✔ Unit tests for cython wrappers @done (18-03-17 18:45) -- simply compare generated files
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✔ Wrap unstable @done (18-03-17 15:30)
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✔ Unify cython/gtsam.h and the original gtsam.h @done (18-03-17 15:30)
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✔ 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.
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✔ 06-03-17: manage to remove the requirements for default and copy constructors
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✘ 25-11-16:
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Try to unify but failed. Main reasons are: Key/size_t, std containers, KeyVector/KeyList/KeySet.
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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<Key>, to FastVector<size_t>.
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✘ 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.
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✔ Convert input numpy Matrix/Vector to float dtype and storage order 'F' automatically, cannot crash! @done (15-03-17 13:00)
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✔ Remove requirements.txt - Frank: don't bother with only 2 packages and a special case for eigency! @done (08-03-17 10:30)
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✔ CMake install script @done (25-11-16 02:30)
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✘ [REFACTOR] better name for uninstantiateClass: very vague!! @cancelled (25-11-16 02:30) -- lazy
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✘ forward declaration? @cancelled (23-11-16 13:00) - nothing to do, seem to work?
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✔ wrap VariableIndex: why is it in inference? If need to, shouldn't have constructors to specific FactorGraphs @done (23-11-16 13:00)
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✔ Global functions @done (22-11-16 21:00)
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✔ [REFACTOR] typesEqual --> isSameSignature @done (22-11-16 21:00)
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✔ Proper overloads (constructors, static methods, methods) @done (20-11-16 21:00)
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✔ Allow overloading methods. The current solution is annoying!!! @done (20-11-16 21:00)
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✔ Casting from parent and grandparents @done (16-11-16 17:00)
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✔ Allow overloading constructors. The current solution is annoying!!! @done (16-11-16 17:00)
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✔ Support "print obj" @done (16-11-16 17:00)
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✔ methods for FastVector: at, [], ... @done (16-11-16 17:00)
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✔ Cython: Key and size_t: traits<size_t> doesn't exist @done (16-09-12 18:34)
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✔ KeyVector, KeyList, KeySet... @done (16-09-13 17:19)
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✔ [Nice to have] parse typedef @done (16-09-13 17:19)
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✔ ctypedef at correct places @done (16-09-12 18:34)
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✔ expand template variable type in constructor/static methods? @done (16-09-12 18:34)
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✔ NonlinearOptimizer: copy constructor deleted!!! @done (16-09-13 17:20)
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✔ Value: no default constructor @done (16-09-13 17:20)
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✔ ctypedef PriorFactor[Vector] PriorFactorVector @done (16-09-19 12:25)
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✔ Delete duplicate methods in derived class @done (16-09-12 13:38)
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✔ Fix return properly @done (16-09-11 17:14)
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✔ handle pair @done (16-09-11 17:14)
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✔ Eigency: ambiguous call: A(const T&) A(const Vector& v) and Eigency A(Map[Vector]& v) @done (16-09-11 07:59)
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✔ Eigency: Constructor: ambiguous construct from Vector/Matrix @done (16-09-11 07:59)
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✔ Eigency: Fix method template of Vector/Matrix: template argument is [Vector] while arugment is Map[Vector] @done (16-09-11 08:22)
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✔ Robust noise: copy assignment operator is deleted because of shared_ptr of the abstract Base class @done (16-09-10 09:05)
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✘ Cython: Constructor: generate default constructor? (hack: if it's serializable?) @cancelled (16-09-13 17:20)
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✘ Eigency: Map[] to Block @created(16-09-10 07:59) @cancelled (16-09-11 08:28)
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- inference before symbolic/linear
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- what's the purpose of "virtual" ??
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Installation:
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☐ Prerequisite:
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- Users create venv and pip install requirements before compiling
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- Wrap cython script in gtsam/cython folder
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☐ Install built module into venv?
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