Add supplimentary files used by the new pybind11 wrapper
Fan Jiang
parent
03306cba9c
commit
d790f235a7
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@ -1,57 +1,104 @@
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# Install cython components
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include(GtsamCythonWrap)
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set(GTSAM_PYTHON_BUILD_DIRECTORY ${PROJECT_BINARY_DIR}/python)
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# Create the cython toolbox for the gtsam library
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if (GTSAM_INSTALL_CYTHON_TOOLBOX)
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# Add the new make target command
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set(python_install_target python-install)
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add_custom_target(${python_install_target}
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COMMAND ${PYTHON_EXECUTABLE} ${GTSAM_CYTHON_INSTALL_PATH}/setup.py install
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WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_PATH})
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if(GTSAM_BUILD_PYTHON)
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# Generate setup.py.
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file(READ "${PROJECT_SOURCE_DIR}/README.md" README_CONTENTS)
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configure_file(${PROJECT_SOURCE_DIR}/python/setup.py.in
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${GTSAM_PYTHON_BUILD_DIRECTORY}/setup.py)
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# build and include the eigency version of eigency
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add_subdirectory(gtsam_eigency)
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include_directories(${GTSAM_EIGENCY_INSTALL_PATH})
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set(WRAP_USE_CUSTOM_PYTHON_LIBRARY ${GTSAM_USE_CUSTOM_PYTHON_LIBRARY})
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set(WRAP_PYTHON_VERSION ${GTSAM_PYTHON_VERSION})
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# Fix for error "C1128: number of sections exceeded object file format limit"
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if(MSVC)
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add_compile_options(/bigobj)
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include(PybindWrap)
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add_custom_target(gtsam_header DEPENDS "${PROJECT_SOURCE_DIR}/gtsam/gtsam.i")
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add_custom_target(gtsam_unstable_header DEPENDS "${PROJECT_SOURCE_DIR}/gtsam_unstable/gtsam_unstable.i")
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# ignoring the non-concrete types (type aliases)
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set(ignore
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gtsam::Point2
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gtsam::Point3
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gtsam::LieVector
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gtsam::LieMatrix
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gtsam::ISAM2ThresholdMapValue
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gtsam::FactorIndices
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gtsam::FactorIndexSet
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gtsam::BetweenFactorPose3s
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gtsam::Point2Vector
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gtsam::Pose3Vector
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gtsam::KeyVector)
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pybind_wrap(gtsam_py # target
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${PROJECT_SOURCE_DIR}/gtsam/gtsam.i # interface_header
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"gtsam.cpp" # generated_cpp
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"gtsam" # module_name
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"gtsam" # top_namespace
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"${ignore}" # ignore_classes
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${PROJECT_SOURCE_DIR}/python/gtsam/gtsam.tpl
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gtsam # libs
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"gtsam;gtsam_header" # dependencies
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ON # use_boost
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)
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set_target_properties(gtsam_py PROPERTIES
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INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib"
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INSTALL_RPATH_USE_LINK_PATH TRUE
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OUTPUT_NAME "gtsam"
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LIBRARY_OUTPUT_DIRECTORY "${GTSAM_PYTHON_BUILD_DIRECTORY}/gtsam"
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DEBUG_POSTFIX "" # Otherwise you will have a wrong name
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RELWITHDEBINFO_POSTFIX "" # Otherwise you will have a wrong name
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)
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set(GTSAM_MODULE_PATH ${GTSAM_PYTHON_BUILD_DIRECTORY}/gtsam)
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# Symlink all tests .py files to build folder.
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create_symlinks("${CMAKE_CURRENT_SOURCE_DIR}/gtsam"
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"${GTSAM_MODULE_PATH}")
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if(GTSAM_UNSTABLE_BUILD_PYTHON)
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set(ignore
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gtsam::Point2
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gtsam::Point3
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gtsam::LieVector
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gtsam::LieMatrix
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gtsam::ISAM2ThresholdMapValue
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gtsam::FactorIndices
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gtsam::FactorIndexSet
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gtsam::BetweenFactorPose3s
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gtsam::Point2Vector
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gtsam::Pose3Vector
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gtsam::KeyVector
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gtsam::FixedLagSmootherKeyTimestampMapValue)
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pybind_wrap(gtsam_unstable_py # target
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${PROJECT_SOURCE_DIR}/gtsam_unstable/gtsam_unstable.i # interface_header
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"gtsam_unstable.cpp" # generated_cpp
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"gtsam_unstable" # module_name
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"gtsam" # top_namespace
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"${ignore}" # ignore_classes
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${PROJECT_SOURCE_DIR}/python/gtsam_unstable/gtsam_unstable.tpl
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gtsam_unstable # libs
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"gtsam_unstable;gtsam_unstable_header" # dependencies
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ON # use_boost
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)
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set_target_properties(gtsam_unstable_py PROPERTIES
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INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib"
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INSTALL_RPATH_USE_LINK_PATH TRUE
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OUTPUT_NAME "gtsam_unstable"
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LIBRARY_OUTPUT_DIRECTORY "${GTSAM_PYTHON_BUILD_DIRECTORY}/gtsam_unstable"
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DEBUG_POSTFIX "" # Otherwise you will have a wrong name
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RELWITHDEBINFO_POSTFIX "" # Otherwise you will have a wrong name
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)
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set(GTSAM_UNSTABLE_MODULE_PATH ${GTSAM_PYTHON_BUILD_DIRECTORY}/gtsam_unstable)
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# Symlink all tests .py files to build folder.
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create_symlinks("${CMAKE_CURRENT_SOURCE_DIR}/gtsam_unstable"
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"${GTSAM_UNSTABLE_MODULE_PATH}")
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endif()
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# First set up all the package related files.
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# This also ensures the below wrap operations work correctly.
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set(CYTHON_INSTALL_REQUIREMENTS_FILE "${PROJECT_SOURCE_DIR}/cython/requirements.txt")
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# Install the custom-generated __init__.py
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# This makes the cython (sub-)directories into python packages, so gtsam can be found while wrapping gtsam_unstable
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configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam/__init__.py ${GTSAM_CYTHON_INSTALL_PATH}/gtsam/__init__.py COPYONLY)
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configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam_unstable/__init__.py ${GTSAM_CYTHON_INSTALL_PATH}/gtsam_unstable/__init__.py COPYONLY)
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configure_file(${PROJECT_SOURCE_DIR}/cython/setup.py.in ${GTSAM_CYTHON_INSTALL_PATH}/setup.py)
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# Wrap gtsam
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add_custom_target(gtsam_header DEPENDS "../gtsam.h")
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wrap_and_install_library_cython("../gtsam.h" # interface_header
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"" # extra imports
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"${GTSAM_CYTHON_INSTALL_PATH}/gtsam" # install path
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gtsam # library to link with
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"wrap;cythonize_eigency;gtsam;gtsam_header" # dependencies which need to be built before wrapping
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)
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add_dependencies(${python_install_target} gtsam gtsam_header)
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# Wrap gtsam_unstable
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if(GTSAM_BUILD_UNSTABLE)
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add_custom_target(gtsam_unstable_header DEPENDS "../gtsam_unstable/gtsam_unstable.h")
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wrap_and_install_library_cython("../gtsam_unstable/gtsam_unstable.h" # interface_header
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"from gtsam.gtsam cimport *" # extra imports
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"${GTSAM_CYTHON_INSTALL_PATH}/gtsam_unstable" # install path
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gtsam_unstable # library to link with
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"gtsam_unstable;gtsam_unstable_header;cythonize_gtsam" # dependencies to be built before wrapping
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)
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add_dependencies(${python_install_target} gtsam_unstable gtsam_unstable_header)
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endif()
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# install scripts and tests
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install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
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install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
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endif ()
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set(GTSAM_PYTHON_INSTALL_TARGET python-install)
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add_custom_target(${GTSAM_PYTHON_INSTALL_TARGET}
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COMMAND ${PYTHON_EXECUTABLE} ${GTSAM_PYTHON_BUILD_DIRECTORY}/setup.py install
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WORKING_DIRECTORY ${GTSAM_PYTHON_BUILD_DIRECTORY})
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endif()
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@ -1,3 +1,5 @@
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# README
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# Python Wrapper
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This is the Python wrapper around the GTSAM C++ library. We use Cython to generate the bindings to the underlying C++ code.
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@ -83,65 +85,3 @@ See the tests for examples.
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## Wrapping Custom GTSAM-based Project
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Please refer to the template project and the corresponding tutorial available [here](https://github.com/borglab/GTSAM-project-python).
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## KNOWN ISSUES
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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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- [ ] 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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- [x] Fix Python tests: don't use " import <package> \* ": Bad style!!! (18-03-17 19:50)
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- [x] Unit tests for cython wrappers @done (18-03-17 18:45) -- simply compare generated files
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- [x] Wrap unstable @done (18-03-17 15:30)
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- [x] Unify cython/GTSAM.h and the original GTSAM.h @done (18-03-17 15:30)
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- [x] 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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- [x] 06-03-17: manage to remove the requirements for default and copy constructors
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- [ ] 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<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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- [x] 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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- [x] 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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- [x] 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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- [x] 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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- [x] Global functions @done (22-11-16 21:00)
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- [x] [REFACTOR] typesEqual --> isSameSignature @done (22-11-16 21:00)
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- [x] Proper overloads (constructors, static methods, methods) @done (20-11-16 21:00)
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- [x] Allow overloading methods. The current solution is annoying!!! @done (20-11-16 21:00)
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- [x] Casting from parent and grandparents @done (16-11-16 17:00)
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- [x] Allow overloading constructors. The current solution is annoying!!! @done (16-11-16 17:00)
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- [x] Support "print obj" @done (16-11-16 17:00)
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- [x] methods for FastVector: at, [], ... @done (16-11-16 17:00)
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- [x] Cython: Key and size_t: traits<size_t> doesn't exist @done (16-09-12 18:34)
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- [x] KeyVector, KeyList, KeySet... @done (16-09-13 17:19)
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- [x] [Nice to have] parse typedef @done (16-09-13 17:19)
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- [x] ctypedef at correct places @done (16-09-12 18:34)
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- [x] expand template variable type in constructor/static methods? @done (16-09-12 18:34)
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- [x] NonlinearOptimizer: copy constructor deleted!!! @done (16-09-13 17:20)
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- [x] Value: no default constructor @done (16-09-13 17:20)
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- [x] ctypedef PriorFactor[Vector] PriorFactorVector @done (16-09-19 12:25)
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- [x] Delete duplicate methods in derived class @done (16-09-12 13:38)
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- [x] Fix return properly @done (16-09-11 17:14)
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- [x] handle pair @done (16-09-11 17:14)
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- [x] 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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- [x] Eigency: Constructor: ambiguous construct from Vector/Matrix @done (16-09-11 07:59)
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- [x] 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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- [x] 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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@ -1,26 +1,27 @@
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from .gtsam import *
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try:
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import gtsam_unstable
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def _init():
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"""This function is to add shims for the long-gone Point2 and Point3 types"""
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import numpy as np
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global Point2 # export function
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def Point2(x=0, y=0):
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"""Shim for the deleted Point2 type."""
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return np.array([x, y], dtype=float)
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global Point3 # export function
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def Point3(x=0, y=0, z=0):
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"""Shim for the deleted Point3 type."""
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return np.array([x, y, z], dtype=float)
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# for interactive debugging
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if __name__ == "__main__":
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# we want all definitions accessible
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globals().update(locals())
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def _deprecated_wrapper(item, name):
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def wrapper(*args, **kwargs):
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from warnings import warn
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message = ('importing the unstable item "{}" directly from gtsam is deprecated. '.format(name) +
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'Please import it from gtsam_unstable.')
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warn(message)
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return item(*args, **kwargs)
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return wrapper
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for name in dir(gtsam_unstable):
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if not name.startswith('__'):
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item = getattr(gtsam_unstable, name)
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if callable(item):
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item = _deprecated_wrapper(item, name)
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globals()[name] = item
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except ImportError:
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pass
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_init()
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@ -0,0 +1,30 @@
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{include_boost}
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#include <pybind11/eigen.h>
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#include <pybind11/stl_bind.h>
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#include <pybind11/pybind11.h>
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#include "gtsam/base/serialization.h"
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#include "gtsam/nonlinear/utilities.h" // for RedirectCout.
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{includes}
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#include <boost/serialization/export.hpp>
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{boost_class_export}
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{hoder_type}
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#include "python/gtsam/preamble.h"
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using namespace std;
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namespace py = pybind11;
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PYBIND11_MODULE({module_name}, m_) {{
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m_.doc() = "pybind11 wrapper of {module_name}";
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{wrapped_namespace}
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#include "python/gtsam/specializations.h"
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}}
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from .gtsam.imuBias import *
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from .gtsam.noiseModel import *
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PYBIND11_MAKE_OPAQUE(std::vector<gtsam::Key>);
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PYBIND11_MAKE_OPAQUE(std::vector<gtsam::Point2, Eigen::aligned_allocator<gtsam::Point2> >);
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PYBIND11_MAKE_OPAQUE(std::vector<gtsam::Pose3>);
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PYBIND11_MAKE_OPAQUE(std::vector<gtsam::BetweenFactor<gtsam::Pose3>>);
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@ -0,0 +1,4 @@
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py::bind_vector<std::vector<gtsam::Key> >(m_, "KeyVector");
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py::bind_vector<std::vector<gtsam::Point2, Eigen::aligned_allocator<gtsam::Point2> > >(m_, "Point2Vector");
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py::bind_vector<std::vector<gtsam::Pose3> >(m_, "Pose3Vector");
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py::bind_vector<std::vector<boost::shared_ptr<gtsam::BetweenFactor<gtsam::Pose3> > > >(m_, "BetweenFactorPose3s");
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@ -0,0 +1 @@
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from .gtsam.symbol_shorthand import *
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{include_boost}
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#include <pybind11/eigen.h>
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#include <pybind11/stl_bind.h>
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#include <pybind11/pybind11.h>
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#include "gtsam/base/serialization.h"
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#include "gtsam/nonlinear/utilities.h" // for RedirectCout.
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{includes}
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#include <boost/serialization/export.hpp>
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{boost_class_export}
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{hoder_type}
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#include "python/gtsam_unstable/preamble.h"
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using namespace std;
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namespace py = pybind11;
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PYBIND11_MODULE({module_name}, m_) {{
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m_.doc() = "pybind11 wrapper of {module_name}";
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py::module::import("gtsam");
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{wrapped_namespace}
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#include "python/gtsam_unstable/specializations.h"
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}}
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@ -1,3 +1,2 @@
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Cython>=0.25.2
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backports_abc>=0.5
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numpy>=1.11.0
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pyparsing>=2.4.2
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@ -1,25 +1,20 @@
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import os
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import sys
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try:
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from setuptools import setup, find_packages
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except ImportError:
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from distutils.core import setup, find_packages
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packages = find_packages()
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packages = find_packages(where=".")
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print("PACKAGES: ", packages)
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package_data = {
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package:
|
||||
[f for f in os.listdir(package.replace('.', os.path.sep)) if os.path.splitext(f)[1] in ('.so', '.pyd')]
|
||||
for package in packages
|
||||
'': [
|
||||
'./*.so',
|
||||
'./*.dll',
|
||||
]
|
||||
}
|
||||
|
||||
cython_install_requirements = open("${CYTHON_INSTALL_REQUIREMENTS_FILE}").readlines()
|
||||
|
||||
install_requires = [line.strip() \
|
||||
for line in cython_install_requirements \
|
||||
if len(line.strip()) > 0 and not line.strip().startswith('#')
|
||||
]
|
||||
|
||||
# Cleaner to read in the contents rather than copy them over.
|
||||
readme_contents = open("${PROJECT_SOURCE_DIR}/README.md").read()
|
||||
|
||||
|
|
@ -33,8 +28,6 @@ setup(
|
|||
license='Simplified BSD license',
|
||||
keywords='slam sam robotics localization mapping optimization',
|
||||
long_description=readme_contents,
|
||||
long_description_content_type='text/markdown',
|
||||
python_requires='>=2.7',
|
||||
# https://pypi.org/pypi?%3Aaction=list_classifiers
|
||||
classifiers=[
|
||||
'Development Status :: 5 - Production/Stable',
|
||||
|
|
@ -48,8 +41,9 @@ setup(
|
|||
'Programming Language :: Python :: 2',
|
||||
'Programming Language :: Python :: 3',
|
||||
],
|
||||
|
||||
packages=packages,
|
||||
package_data=package_data,
|
||||
install_requires=install_requires
|
||||
test_suite="gtsam.tests",
|
||||
install_requires=["numpy"],
|
||||
zip_safe=False,
|
||||
)
|
||||
|
|
|
|||
Loading…
Reference in New Issue