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Merge pull request #709 from borglab/feature/pickle-support 

Adding pickle support by using serialization
release/4.3a0
Ayush Baid 2021-03-08 21:19:27 -05:00 committed by GitHub
parent 48232a3357 1670e68e2f
commit c58c00f1ac
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GPG Key ID: 4AEE18F83AFDEB23
7 changed files with 214 additions and 0 deletions
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100
gtsam/gtsam.i
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@ -105,6 +105,9 @@
* virtual class MyFactor : gtsam::NoiseModelFactor {...};
* - *DO NOT* re-define overriden function already declared in the external (forward-declared) base class
* - This will cause an ambiguity problem in Pybind header file
* Pickle support in Python:
* - Add "void pickle()" to a class to enable pickling via gtwrap. In the current implementation, "void serialize()"
* and a public constructor with no-arguments in needed for successful build.
*/
/**
@ -144,6 +147,9 @@ class KeyList {
void remove(size_t key);
void serialize() const;
// enable pickling in python
void pickle() const;
};
// Actually a FastSet<Key>
@ -169,6 +175,9 @@ class KeySet {
bool count(size_t key) const; // returns true if value exists
void serialize() const;
// enable pickling in python
void pickle() const;
};
// Actually a vector<Key>
@ -190,6 +199,9 @@ class KeyVector {
void push_back(size_t key) const;
void serialize() const;
// enable pickling in python
void pickle() const;
};
// Actually a FastMap<Key,int>
@ -361,6 +373,9 @@ class Point2 {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
// std::vector<gtsam::Point2>
@ -422,6 +437,9 @@ class StereoPoint2 {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/Point3.h>
@ -446,6 +464,9 @@ class Point3 {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/Rot2.h>
@ -491,6 +512,9 @@ class Rot2 {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/SO3.h>
@ -653,6 +677,9 @@ class Rot3 {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/Pose2.h>
@ -708,6 +735,9 @@ class Pose2 {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/Pose3.h>
@ -764,6 +794,9 @@ class Pose3 {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
// std::vector<gtsam::Pose3>
@ -797,6 +830,15 @@ class Unit3 {
size_t dim() const;
gtsam::Unit3 retract(Vector v) const;
Vector localCoordinates(const gtsam::Unit3& s) const;
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
// enabling function to compare objects
bool equals(const gtsam::Unit3& expected, double tol) const;
};
#include <gtsam/geometry/EssentialMatrix.h>
@ -856,6 +898,9 @@ class Cal3_S2 {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/Cal3DS2_Base.h>
@ -884,6 +929,9 @@ virtual class Cal3DS2_Base {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/Cal3DS2.h>
@ -905,6 +953,9 @@ virtual class Cal3DS2 : gtsam::Cal3DS2_Base {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/Cal3Unified.h>
@ -931,6 +982,9 @@ virtual class Cal3Unified : gtsam::Cal3DS2_Base {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/Cal3_S2Stereo.h>
@ -988,6 +1042,9 @@ class Cal3Bundler {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/CalibratedCamera.h>
@ -1018,6 +1075,9 @@ class CalibratedCamera {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/PinholeCamera.h>
@ -1056,6 +1116,9 @@ class PinholeCamera {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
// Forward declaration of PinholeCameraCalX is defined here.
@ -1103,6 +1166,9 @@ class StereoCamera {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/triangulation.h>
@ -1557,6 +1623,9 @@ class VectorValues {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/linear/GaussianFactor.h>
@ -1618,6 +1687,9 @@ virtual class JacobianFactor : gtsam::GaussianFactor {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/linear/HessianFactor.h>
@ -1649,6 +1721,9 @@ virtual class HessianFactor : gtsam::GaussianFactor {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/linear/GaussianFactorGraph.h>
@ -1728,6 +1803,9 @@ class GaussianFactorGraph {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/linear/GaussianConditional.h>
@ -2033,6 +2111,9 @@ class Ordering {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/nonlinear/NonlinearFactorGraph.h>
@ -2071,6 +2152,10 @@ class NonlinearFactorGraph {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
void saveGraph(const string& s) const;
};
@ -2128,6 +2213,9 @@ class Values {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
// New in 4.0, we have to specialize every insert/update/at to generate wrappers
// Instead of the old:
// void insert(size_t j, const gtsam::Value& value);
@ -2527,6 +2615,9 @@ virtual class PriorFactor : gtsam::NoiseModelFactor {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
@ -2538,6 +2629,9 @@ virtual class BetweenFactor : gtsam::NoiseModelFactor {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
};
#include <gtsam/nonlinear/NonlinearEquality.h>
@ -2774,6 +2868,9 @@ class SfmTrack {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
// enabling function to compare objects
bool equals(const gtsam::SfmTrack& expected, double tol) const;
};
@ -2790,6 +2887,9 @@ class SfmData {
// enabling serialization functionality
void serialize() const;
// enable pickling in python
void pickle() const;
// enabling function to compare objects
bool equals(const gtsam::SfmData& expected, double tol) const;
};

46
python/gtsam/tests/test_pickle.py Normal file
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@ -0,0 +1,46 @@
"""
GTSAM Copyright 2010-2020, Georgia Tech Research Corporation,
Atlanta, Georgia 30332-0415
All Rights Reserved
See LICENSE for the license information
Unit tests to check pickling.
Author: Ayush Baid
"""
from gtsam import Cal3Bundler, PinholeCameraCal3Bundler, Point2, Point3, Pose3, Rot3, SfmTrack, Unit3
from gtsam.utils.test_case import GtsamTestCase
class TestPickle(GtsamTestCase):
"""Tests pickling on some of the classes."""
def test_cal3Bundler_roundtrip(self):
obj = Cal3Bundler(fx=100, k1=0.1, k2=0.2, u0=100, v0=70)
self.assertEqualityOnPickleRoundtrip(obj)
def test_pinholeCameraCal3Bundler_roundtrip(self):
obj = PinholeCameraCal3Bundler(
Pose3(Rot3.RzRyRx(0, 0.1, -0.05), Point3(1, 1, 0)),
Cal3Bundler(fx=100, k1=0.1, k2=0.2, u0=100, v0=70),
)
self.assertEqualityOnPickleRoundtrip(obj)
def test_rot3_roundtrip(self):
obj = Rot3.RzRyRx(0, 0.05, 0.1)
self.assertEqualityOnPickleRoundtrip(obj)
def test_pose3_roundtrip(self):
obj = Pose3(Rot3.Ypr(0.0, 1.0, 0.0), Point3(1, 1, 0))
self.assertEqualityOnPickleRoundtrip(obj)
def test_sfmTrack_roundtrip(self):
obj = SfmTrack(Point3(1, 1, 0))
obj.add_measurement(0, Point2(-1, 5))
obj.add_measurement(1, Point2(6, 2))
self.assertEqualityOnPickleRoundtrip(obj)
def test_unit3_roundtrip(self):
obj = Unit3(Point3(1, 1, 0))
self.assertEqualityOnPickleRoundtrip(obj)

12
python/gtsam/utils/test_case.py
View File

@ -8,6 +8,7 @@ See LICENSE for the license information
TestCase class with GTSAM assert utils.
Author: Frank Dellaert
"""
import pickle
import unittest
@ -29,3 +30,14 @@ class GtsamTestCase(unittest.TestCase):
if not equal:
raise self.failureException(
"Values are not equal:\n{}!={}".format(actual, expected))
def assertEqualityOnPickleRoundtrip(self, obj: object, tol=1e-9) -> None:
""" Performs a round-trip using pickle and asserts equality.
Usage:
self.assertEqualityOnPickleRoundtrip(obj)
Keyword Arguments:
tol {float} -- tolerance passed to 'equals', default 1e-9
"""
roundTripObj = pickle.loads(pickle.dumps(obj))
self.gtsamAssertEquals(roundTripObj, obj)

12
wrap/gtwrap/matlab_wrapper.py
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@ -49,6 +49,8 @@ class MatlabWrapper(object):
}
"""Methods that should not be wrapped directly"""
whitelist = ['serializable', 'serialize']
"""Methods that should be ignored"""
ignore_methods = ['pickle']
"""Datatypes that do not need to be checked in methods"""
not_check_type = []
"""Data types that are primitive types"""
@ -563,6 +565,8 @@ class MatlabWrapper(object):
for method in methods:
if method.name in self.whitelist:
continue
if method.name in self.ignore_methods:
continue
comment += '%{name}({args})'.format(name=method.name, args=self._wrap_args(method.args))
@ -612,6 +616,9 @@ class MatlabWrapper(object):
methods = self._group_methods(methods)
for method in methods:
if method in self.ignore_methods:
continue
if globals:
self._debug("[wrap_methods] wrapping: {}..{}={}".format(method[0].parent.name, method[0].name,
type(method[0].parent.name)))
@ -861,6 +868,8 @@ class MatlabWrapper(object):
method_name = method[0].name
if method_name in self.whitelist and method_name != 'serialize':
continue
if method_name in self.ignore_methods:
continue
if method_name == 'serialize':
serialize[0] = True
@ -932,6 +941,9 @@ class MatlabWrapper(object):
format_name = list(static_method[0].name)
format_name[0] = format_name[0].upper()
if static_method[0].name in self.ignore_methods:
continue
method_text += textwrap.indent(textwrap.dedent('''\
function varargout = {name}(varargin)
'''.format(name=''.join(format_name))),

16
wrap/gtwrap/pybind_wrapper.py
View File

@ -76,6 +76,21 @@ class PybindWrapper(object):
gtsam::deserialize(serialized, *self);
}}, py::arg("serialized"))
'''.format(class_inst=cpp_class + '*'))
if cpp_method == "pickle":
if not cpp_class in self._serializing_classes:
raise ValueError("Cannot pickle a class which is not serializable")
return textwrap.dedent('''
.def(py::pickle(
[](const {cpp_class} &a){{ // __getstate__
/* Returns a string that encodes the state of the object */
return py::make_tuple(gtsam::serialize(a));
}},
[](py::tuple t){{ // __setstate__
{cpp_class} obj;
gtsam::deserialize(t[0].cast<std::string>(), obj);
return obj;
}}))
'''.format(cpp_class=cpp_class))
is_method = isinstance(method, instantiator.InstantiatedMethod)
is_static = isinstance(method, parser.StaticMethod)
@ -318,3 +333,4 @@ class PybindWrapper(object):
wrapped_namespace=wrapped_namespace,
boost_class_export=boost_class_export,
)

22
wrap/tests/expected-python/geometry_pybind.cpp
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@ -47,6 +47,17 @@ PYBIND11_MODULE(geometry_py, m_) {
[](gtsam::Point2* self, string serialized){
gtsam::deserialize(serialized, *self);
}, py::arg("serialized"))
.def(py::pickle(
[](const gtsam::Point2 &a){ // __getstate__
/* Returns a string that encodes the state of the object */
return py::make_tuple(gtsam::serialize(a));
},
[](py::tuple t){ // __setstate__
gtsam::Point2 obj;
gtsam::deserialize(t[0].cast<std::string>(), obj);
return obj;
}))
;
py::class_<gtsam::Point3, std::shared_ptr<gtsam::Point3>>(m_gtsam, "Point3")
@ -62,6 +73,17 @@ PYBIND11_MODULE(geometry_py, m_) {
gtsam::deserialize(serialized, *self);
}, py::arg("serialized"))
.def(py::pickle(
[](const gtsam::Point3 &a){ // __getstate__
/* Returns a string that encodes the state of the object */
return py::make_tuple(gtsam::serialize(a));
},
[](py::tuple t){ // __setstate__
gtsam::Point3 obj;
gtsam::deserialize(t[0].cast<std::string>(), obj);
return obj;
}))
.def_static("staticFunction",[](){return gtsam::Point3::staticFunction();})
.def_static("StaticFunctionRet",[]( double z){return gtsam::Point3::StaticFunctionRet(z);}, py::arg("z"));

6
wrap/tests/geometry.h
View File

@ -22,6 +22,9 @@ class Point2 {
VectorNotEigen vectorConfusion();
void serializable() const; // Sets flag and creates export, but does not make serialization functions
// enable pickling in python
void pickle() const;
};
#include <gtsam/geometry/Point3.h>
@ -35,6 +38,9 @@ class Point3 {
// enabling serialization functionality
void serialize() const; // Just triggers a flag internally and removes actual function
// enable pickling in python
void pickle() const;
};
}