157 lines
8.3 KiB
Markdown
157 lines
8.3 KiB
Markdown
This is the Cython/Python wrapper around the GTSAM C++ library.
|
|
|
|
INSTALL
|
|
=======
|
|
- if you want to build the gtsam python library for a specific python version (eg 2.7), use the `-DGTSAM_PYTHON_VERSION=2.7` 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. These can be installed as follows:
|
|
|
|
```bash
|
|
pip install -r <gtsam_folder>/cython/requirements.txt
|
|
```
|
|
|
|
- For compatibility with gtsam's Eigen version, it contains its own cloned version of [Eigency](https://github.com/wouterboomsma/eigency.git),
|
|
named **gtsam_eigency**, to interface between C++'s Eigen and Python's numpy.
|
|
|
|
- Build and install gtsam using cmake with `GTSAM_INSTALL_CYTHON_TOOLBOX` enabled.
|
|
The wrapped module will be installed to `GTSAM_CYTHON_INSTALL_PATH`, which is
|
|
by default: `<your CMAKE_INSTALL_PREFIX>/cython`
|
|
|
|
- Modify your `PYTHONPATH` to include the `GTSAM_CYTHON_INSTALL_PATH`:
|
|
```bash
|
|
export PYTHONPATH=$PYTHONPATH:<GTSAM_CYTHON_INSTALL_PATH>
|
|
```
|
|
|
|
UNIT TESTS
|
|
==========
|
|
The Cython toolbox also has a small set of unit tests located in the
|
|
test directory. To run them:
|
|
|
|
```bash
|
|
cd <your GTSAM_CYTHON_INSTALL_PATH>
|
|
python -m unittest discover
|
|
```
|
|
|
|
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: https://github.com/wouterboomsma/eigency#storage-layout---why-arrays-are-sometimes-transposed
|
|
+ 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 <innerNamespace>_ in Python.
|
|
Examples: noiseModel_Gaussian, noiseModel_mEstimator_Tukey
|
|
|
|
- Casting from a base class to a derive class must be done explicitly.
|
|
Examples:
|
|
```Python
|
|
noiseBase = factor.get_noiseModel()
|
|
noiseGaussian = dynamic_cast_noiseModel_Gaussian_noiseModel_Base(noiseBase)
|
|
```
|
|
|
|
WRAPPING YOUR OWN PROJECT THAT USES GTSAM
|
|
=========================================
|
|
- Set PYTHONPATH to include ${GTSAM_CYTHON_INSTALL_PATH}
|
|
+ so that it can find gtsam Cython header: gtsam/gtsam.pxd
|
|
|
|
- In your CMakeList.txt
|
|
```cmake
|
|
find_package(GTSAM REQUIRED) # Make sure gtsam's install folder is in your PATH
|
|
set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH}" "${GTSAM_DIR}/../GTSAMCMakeTools")
|
|
|
|
# Wrap
|
|
include(GtsamCythonWrap)
|
|
include_directories(${GTSAM_EIGENCY_INSTALL_PATH})
|
|
wrap_and_install_library_cython("your_project_interface.h"
|
|
"from gtsam.gtsam cimport *" # extra import of gtsam/gtsam.pxd Cython header
|
|
"your_install_path"
|
|
"libraries_to_link_with_the_cython_module"
|
|
"dependencies_which_need_to_be_built_before_the_wrapper"
|
|
)
|
|
#Optional: install_cython_scripts and install_cython_files. See GtsamCythonWrap.cmake.
|
|
```
|
|
|
|
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<Key>
|
|
- 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 <package> * ": Bad style!!! @done (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<Key>, 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" ??
|
|
|
|
Installation:
|
|
☐ Prerequisite:
|
|
- Users create venv and pip install requirements before compiling
|
|
- Wrap cython script in gtsam/cython folder
|
|
☐ Install built module into venv?
|