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

Adding pickle support by using serialization

gtsam/gtsam.i

@@ -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;
 };

python/gtsam/tests/test_pickle.py

@@ -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)

python/gtsam/utils/test_case.py

@@ -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)

wrap/gtwrap/matlab_wrapper.py

@@ -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))),

wrap/gtwrap/pybind_wrapper.py

@@ -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,
         )
+

wrap/tests/expected-python/geometry_pybind.cpp

@@ -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"));
 

wrap/tests/geometry.h

@@ -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;
 };
 
 }