Python supplementary files
Fan Jiang
parent
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set(GTSAM_PYTHON_BUILD_DIRECTORY ${PROJECT_BINARY_DIR}/python)
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if(GTSAM_BUILD_PYTHON)
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# Generate setup.py.
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file(READ "${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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set(WRAP_USE_CUSTOM_PYTHON_LIBRARY ${GTSAM_USE_CUSTOM_PYTHON_LIBRARY})
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set(WRAP_PYTHON_VERSION ${GTSAM_PYTHON_VERSION})
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include(PybindWrap)
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add_custom_target(gtsam_header DEPENDS "${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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"${GTSAM_UNSTABLE_MODULE_PATH}")
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endif()
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set(GTSAM_PYTHON_INSTALL_TARGET python-install)
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add_custom_target(${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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# 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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## Requirements
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- If you want to build the GTSAM python library for a specific python version (eg 3.6),
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use the `-DGTSAM_PYTHON_VERSION=3.6` option when running `cmake` otherwise the default interpreter will be used.
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- If the interpreter is inside an environment (such as an anaconda environment or virtualenv environment),
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then the environment should be active while building GTSAM.
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- This wrapper needs `Cython(>=0.25.2)`, `backports_abc(>=0.5)`, and `numpy(>=1.11.0)`. These can be installed as follows:
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```bash
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pip install -r <gtsam_folder>/cython/requirements.txt
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```
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- For compatibility with GTSAM's Eigen version, it contains its own cloned version of [Eigency](https://github.com/wouterboomsma/eigency.git),
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named `gtsam_eigency`, to interface between C++'s Eigen and Python's numpy.
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## Install
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- 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.
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- Build GTSAM and the wrapper with `make`.
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- To install, simply run `make python-install`.
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- The same command can be used to install into a virtual environment if it is active.
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- **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.
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- You can also directly run `make python-install` without running `make`, and it will compile all the dependencies accordingly.
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## Unit Tests
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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 <GTSAM_CYTHON_INSTALL_PATH>
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python -m unittest discover
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```
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## Utils
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TODO
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## Examples
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TODO
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## Writing Your Own Scripts
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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 [this link](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.noiseModel()
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noiseGaussian = dynamic_cast_noiseModel_Gaussian_noiseModel_Base(noiseBase)
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```
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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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{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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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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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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{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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numpy>=1.11.0
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pyparsing>=2.4.2
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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(where=".")
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print("PACKAGES: ", packages)
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package_data = {
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'': [
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'./*.so',
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'./*.dll',
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]
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}
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# Cleaner to read in the contents rather than copy them over.
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readme_contents = open("${PROJECT_SOURCE_DIR}/README.md").read()
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setup(
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name='gtsam',
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description='Georgia Tech Smoothing And Mapping library',
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url='https://gtsam.org/',
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version='${GTSAM_VERSION_STRING}', # https://www.python.org/dev/peps/pep-0440/
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author='Frank Dellaert et. al.',
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author_email='frank.dellaert@gtsam.org',
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license='Simplified BSD license',
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keywords='slam sam robotics localization mapping optimization',
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long_description=readme_contents,
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# https://pypi.org/pypi?%3Aaction=list_classifiers
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classifiers=[
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'Development Status :: 5 - Production/Stable',
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'Intended Audience :: Education',
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'Intended Audience :: Developers',
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'Intended Audience :: Science/Research',
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'Operating System :: MacOS',
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'Operating System :: Microsoft :: Windows',
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'Operating System :: POSIX',
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'License :: OSI Approved :: BSD License',
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'Programming Language :: Python :: 2',
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'Programming Language :: Python :: 3',
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],
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packages=packages,
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package_data=package_data,
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test_suite="gtsam.tests",
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install_requires=["numpy"],
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zip_safe=False,
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)
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