Merged gtborg/gtsam into develop

.gitignore

@@ -16,3 +16,4 @@ cython/gtsam.pyx
 cython/gtsam.so
 cython/gtsam_wrapper.pxd
 .vscode
+.env

bitbucket-pipelines.yml

@@ -1,9 +1,8 @@
-# This is a sample build configuration for C++ – Make.
+# Built from sample configuration for C++ – Make.
-# Check our guides at https://confluence.atlassian.com/x/5Q4SMw for more examples.
+# Check https://confluence.atlassian.com/x/5Q4SMw for more examples.
-# Only use spaces to indent your .yml configuration.
 # -----
-# You can specify a custom docker image from Docker Hub as your build environment.
+# Our custom docker image from Docker Hub as the build environment.
-image: ilssim/cmake-boost-qt5
+image: dellaert/ubuntu-boost-tbb-eigen3:bionic
 
 pipelines:
   default:
@@ -11,6 +10,6 @@ pipelines:
         script: # Modify the commands below to build your repository.
           - mkdir build
           - cd build
-          - cmake .. 
+          - cmake -DGTSAM_USE_SYSTEM_EIGEN=ON -DGTSAM_USE_EIGEN_MKL=OFF .. 
-          - make
+          - make -j2
-          - make check
+          - make -j2 check

docker/ubuntu-boost-tbb-eigen3/Dockerfile

@@ -0,0 +1,18 @@
+# Get the base Ubuntu image from Docker Hub
+FROM ubuntu:bionic
+
+# Update apps on the base image
+RUN apt-get -y update && apt-get install -y
+
+# Install C++
+RUN apt-get -y install build-essential 
+
+# Install boost and cmake
+RUN apt-get -y install libboost-all-dev cmake
+
+# Install TBB
+RUN apt-get -y install libtbb-dev
+
+# Install latest Eigen
+RUN apt-get install -y libeigen3-dev
+

examples/ISAM2Example_SmartFactor.cpp

@@ -0,0 +1,120 @@
+/**
+ * @file ISAM2Example_SmartFactor.cpp
+ * @brief test of iSAM with smart factors, led to bitbucket issue #367
+ * @author Alexander (pumaking on BitBucket)
+ */
+
+#include <gtsam/geometry/SimpleCamera.h>
+#include <gtsam/nonlinear/ISAM2.h>
+#include <gtsam/slam/BetweenFactor.h>
+#include <gtsam/slam/SmartProjectionPoseFactor.h>
+
+#include <iostream>
+#include <vector>
+
+using namespace std;
+using namespace gtsam;
+using symbol_shorthand::P;
+using symbol_shorthand::X;
+
+// Make the typename short so it looks much cleaner
+typedef SmartProjectionPoseFactor<Cal3_S2> SmartFactor;
+
+int main(int argc, char* argv[]) {
+  Cal3_S2::shared_ptr K(new Cal3_S2(50.0, 50.0, 0.0, 50.0, 50.0));
+
+  auto measurementNoise =
+      noiseModel::Isotropic::Sigma(2, 1.0);  // one pixel in u and v
+
+  Vector6 sigmas;
+  sigmas << Vector3::Constant(0.3), Vector3::Constant(0.1);
+  auto noise = noiseModel::Diagonal::Sigmas(sigmas);
+
+  ISAM2Params parameters;
+  parameters.relinearizeThreshold = 0.01;
+  parameters.relinearizeSkip = 1;
+  parameters.cacheLinearizedFactors = false;
+  parameters.enableDetailedResults = true;
+  parameters.print();
+  ISAM2 isam(parameters);
+
+  // Create a factor graph
+  NonlinearFactorGraph graph;
+  Values initialEstimate;
+
+  Point3 point(0.0, 0.0, 1.0);
+
+  // Intentionally initialize the variables off from the ground truth
+  Pose3 delta(Rot3::Rodrigues(0.0, 0.0, 0.0), Point3(0.05, -0.10, 0.20));
+
+  Pose3 pose1(Rot3(), Point3(0.0, 0.0, 0.0));
+  Pose3 pose2(Rot3(), Point3(0.0, 0.2, 0.0));
+  Pose3 pose3(Rot3(), Point3(0.0, 0.4, 0.0));
+  Pose3 pose4(Rot3(), Point3(0.0, 0.5, 0.0));
+  Pose3 pose5(Rot3(), Point3(0.0, 0.6, 0.0));
+
+  vector<Pose3> poses = {pose1, pose2, pose3, pose4, pose5};
+
+  // Add first pose
+  graph.emplace_shared<PriorFactor<Pose3>>(X(0), poses[0], noise);
+  initialEstimate.insert(X(0), poses[0].compose(delta));
+
+  // Create smart factor with measurement from first pose only
+  SmartFactor::shared_ptr smartFactor(new SmartFactor(measurementNoise, K));
+  smartFactor->add(PinholePose<Cal3_S2>(poses[0], K).project(point), X(0));
+  graph.push_back(smartFactor);
+
+  // loop over remaining poses
+  for (size_t i = 1; i < 5; i++) {
+    cout << "****************************************************" << endl;
+    cout << "i = " << i << endl;
+
+    // Add prior on new pose
+    graph.emplace_shared<PriorFactor<Pose3>>(X(i), poses[i], noise);
+    initialEstimate.insert(X(i), poses[i].compose(delta));
+
+    // "Simulate" measurement from this pose
+    PinholePose<Cal3_S2> camera(poses[i], K);
+    Point2 measurement = camera.project(point);
+    cout << "Measurement " << i << "" << measurement << endl;
+
+    // Add measurement to smart factor
+    smartFactor->add(measurement, X(i));
+
+    // Update iSAM2
+    ISAM2Result result = isam.update(graph, initialEstimate);
+    result.print();
+
+    cout << "Detailed results:" << endl;
+    for (auto keyedStatus : result.detail->variableStatus) {
+      const auto& status = keyedStatus.second;
+      PrintKey(keyedStatus.first);
+      cout << " {" << endl;
+      cout << "reeliminated: " << status.isReeliminated << endl;
+      cout << "relinearized above thresh: " << status.isAboveRelinThreshold
+           << endl;
+      cout << "relinearized involved: " << status.isRelinearizeInvolved << endl;
+      cout << "relinearized: " << status.isRelinearized << endl;
+      cout << "observed: " << status.isObserved << endl;
+      cout << "new: " << status.isNew << endl;
+      cout << "in the root clique: " << status.inRootClique << endl;
+      cout << "}" << endl;
+    }
+
+    Values currentEstimate = isam.calculateEstimate();
+    currentEstimate.print("Current estimate: ");
+
+    boost::optional<Point3> pointEstimate = smartFactor->point(currentEstimate);
+    if (pointEstimate) {
+      cout << *pointEstimate << endl;
+    } else {
+      cout << "Point degenerate." << endl;
+    }
+
+    // Reset graph and initial estimate for next iteration
+    graph.resize(0);
+    initialEstimate.clear();
+  }
+
+  return 0;
+}

examples/SolverComparer.cpp

@@ -206,7 +206,7 @@ int main(int argc, char *argv[]) {
   }
 
 #ifdef GTSAM_USE_TBB
-  std::auto_ptr<tbb::task_scheduler_init> init;
+  std::unique_ptr<tbb::task_scheduler_init> init;
   if(nThreads > 0) {
     cout << "Using " << nThreads << " threads" << endl;
     init.reset(new tbb::task_scheduler_init(nThreads));

examples/VisualISAM2Example.cpp

@@ -11,8 +11,8 @@
 
 /**
  * @file    VisualISAM2Example.cpp
- * @brief   A visualSLAM example for the structure-from-motion problem on a simulated dataset
+ * @brief   A visualSLAM example for the structure-from-motion problem on a
- * This version uses iSAM2 to solve the problem incrementally
+ * simulated dataset This version uses iSAM2 to solve the problem incrementally
  * @author  Duy-Nguyen Ta
  */
 
@@ -25,27 +25,28 @@
 // For loading the data
 #include "SFMdata.h"
 
-// Camera observations of landmarks (i.e. pixel coordinates) will be stored as Point2 (x, y).
+// Camera observations of landmarks will be stored as Point2 (x, y).
 #include <gtsam/geometry/Point2.h>
 
-// Each variable in the system (poses and landmarks) must be identified with a unique key.
+// Each variable in the system (poses and landmarks) must be identified with a
-// We can either use simple integer keys (1, 2, 3, ...) or symbols (X1, X2, L1).
+// unique key. We can either use simple integer keys (1, 2, 3, ...) or symbols
-// Here we will use Symbols
+// (X1, X2, L1). Here we will use Symbols
 #include <gtsam/inference/Symbol.h>
 
-// We want to use iSAM2 to solve the structure-from-motion problem incrementally, so
+// We want to use iSAM2 to solve the structure-from-motion problem
-// include iSAM2 here
+// incrementally, so include iSAM2 here
 #include <gtsam/nonlinear/ISAM2.h>
 
-// iSAM2 requires as input a set set of new factors to be added stored in a factor graph,
+// iSAM2 requires as input a set of new factors to be added stored in a factor
-// and initial guesses for any new variables used in the added factors
+// graph, and initial guesses for any new variables used in the added factors
 #include <gtsam/nonlinear/NonlinearFactorGraph.h>
 #include <gtsam/nonlinear/Values.h>
 
-// In GTSAM, measurement functions are represented as 'factors'. Several common factors
+// In GTSAM, measurement functions are represented as 'factors'. Several common
-// have been provided with the library for solving robotics/SLAM/Bundle Adjustment problems.
+// factors have been provided with the library for solving robotics/SLAM/Bundle
-// Here we will use Projection factors to model the camera's landmark observations.
+// Adjustment problems. Here we will use Projection factors to model the
-// Also, we will initialize the robot at some location using a Prior factor.
+// camera's landmark observations. Also, we will initialize the robot at some
+// location using a Prior factor.
 #include <gtsam/slam/PriorFactor.h>
 #include <gtsam/slam/ProjectionFactor.h>
 
@@ -56,12 +57,11 @@ using namespace gtsam;
 
 /* ************************************************************************* */
 int main(int argc, char* argv[]) {
-
   // Define the camera calibration parameters
   Cal3_S2::shared_ptr K(new Cal3_S2(50.0, 50.0, 0.0, 50.0, 50.0));
 
-  // Define the camera observation noise model
+  // Define the camera observation noise model, 1 pixel stddev
-  noiseModel::Isotropic::shared_ptr measurementNoise = noiseModel::Isotropic::Sigma(2, 1.0); // one pixel in u and v
+  auto measurementNoise = noiseModel::Isotropic::Sigma(2, 1.0);
 
   // Create the set of ground-truth landmarks
   vector<Point3> points = createPoints();
@@ -69,10 +69,12 @@ int main(int argc, char* argv[]) {
   // Create the set of ground-truth poses
   vector<Pose3> poses = createPoses();
 
-  // Create an iSAM2 object. Unlike iSAM1, which performs periodic batch steps to maintain proper linearization
+  // Create an iSAM2 object. Unlike iSAM1, which performs periodic batch steps
-  // and efficient variable ordering, iSAM2 performs partial relinearization/reordering at each step. A parameter
+  // to maintain proper linearization and efficient variable ordering, iSAM2
-  // structure is available that allows the user to set various properties, such as the relinearization threshold
+  // performs partial relinearization/reordering at each step. A parameter
-  // and type of linear solver. For this example, we we set the relinearization threshold small so the iSAM2 result
+  // structure is available that allows the user to set various properties, such
+  // as the relinearization threshold and type of linear solver. For this
+  // example, we we set the relinearization threshold small so the iSAM2 result
   // will approach the batch result.
   ISAM2Params parameters;
   parameters.relinearizeThreshold = 0.01;
@@ -83,44 +85,52 @@ int main(int argc, char* argv[]) {
   NonlinearFactorGraph graph;
   Values initialEstimate;
 
-  // Loop over the different poses, adding the observations to iSAM incrementally
+  // Loop over the poses, adding the observations to iSAM incrementally
   for (size_t i = 0; i < poses.size(); ++i) {
-
     // Add factors for each landmark observation
     for (size_t j = 0; j < points.size(); ++j) {
       SimpleCamera camera(poses[i], *K);
       Point2 measurement = camera.project(points[j]);
-      graph.emplace_shared<GenericProjectionFactor<Pose3, Point3, Cal3_S2> >(measurement, measurementNoise, Symbol('x', i), Symbol('l', j), K);
+      graph.emplace_shared<GenericProjectionFactor<Pose3, Point3, Cal3_S2> >(
+          measurement, measurementNoise, Symbol('x', i), Symbol('l', j), K);
     }
 
     // Add an initial guess for the current pose
     // Intentionally initialize the variables off from the ground truth
-    initialEstimate.insert(Symbol('x', i), poses[i].compose(Pose3(Rot3::Rodrigues(-0.1, 0.2, 0.25), Point3(0.05, -0.10, 0.20))));
+    static Pose3 kDeltaPose(Rot3::Rodrigues(-0.1, 0.2, 0.25),
+                            Point3(0.05, -0.10, 0.20));
+    initialEstimate.insert(Symbol('x', i), poses[i] * kDeltaPose);
 
-    // If this is the first iteration, add a prior on the first pose to set the coordinate frame
+    // If this is the first iteration, add a prior on the first pose to set the
-    // and a prior on the first landmark to set the scale
+    // coordinate frame and a prior on the first landmark to set the scale Also,
-    // Also, as iSAM solves incrementally, we must wait until each is observed at least twice before
+    // as iSAM solves incrementally, we must wait until each is observed at
-    // adding it to iSAM.
+    // least twice before adding it to iSAM.
-    if( i == 0) {
+    if (i == 0) {
-      // Add a prior on pose x0
+      // Add a prior on pose x0, 30cm std on x,y,z and 0.1 rad on roll,pitch,yaw
-      noiseModel::Diagonal::shared_ptr poseNoise = noiseModel::Diagonal::Sigmas((Vector(6) << Vector3::Constant(0.3),Vector3::Constant(0.1)).finished()); // 30cm std on x,y,z 0.1 rad on roll,pitch,yaw
+      static auto kPosePrior = noiseModel::Diagonal::Sigmas(
-      graph.emplace_shared<PriorFactor<Pose3> >(Symbol('x', 0), poses[0], poseNoise);
+          (Vector(6) << Vector3::Constant(0.3), Vector3::Constant(0.1))
+              .finished());
+      graph.emplace_shared<PriorFactor<Pose3> >(Symbol('x', 0), poses[0],
+                                                kPosePrior);
 
       // Add a prior on landmark l0
-      noiseModel::Isotropic::shared_ptr pointNoise = noiseModel::Isotropic::Sigma(3, 0.1);
+      static auto kPointPrior = noiseModel::Isotropic::Sigma(3, 0.1);
-      graph.emplace_shared<PriorFactor<Point3> >(Symbol('l', 0), points[0], pointNoise); // add directly to graph
+      graph.emplace_shared<PriorFactor<Point3> >(Symbol('l', 0), points[0],
+                                                 kPointPrior);
 
       // Add initial guesses to all observed landmarks
       // Intentionally initialize the variables off from the ground truth
+      static Point3 kDeltaPoint(-0.25, 0.20, 0.15);
       for (size_t j = 0; j < points.size(); ++j)
-        initialEstimate.insert<Point3>(Symbol('l', j), points[j] +Point3(-0.25, 0.20, 0.15));
+        initialEstimate.insert<Point3>(Symbol('l', j), points[j] + kDeltaPoint);
 
     } else {
       // Update iSAM with the new factors
       isam.update(graph, initialEstimate);
-      // Each call to iSAM2 update(*) performs one iteration of the iterative nonlinear solver.
+      // Each call to iSAM2 update(*) performs one iteration of the iterative
-      // If accuracy is desired at the expense of time, update(*) can be called additional times
+      // nonlinear solver. If accuracy is desired at the expense of time,
-      // to perform multiple optimizer iterations every step.
+      // update(*) can be called additional times to perform multiple optimizer
+      // iterations every step.
       isam.update();
       Values currentEstimate = isam.calculateEstimate();
       cout << "****************************************************" << endl;

gtsam/3rdparty/CCOLAMD/Source/ccolamd.c

@@ -1560,8 +1560,9 @@ PUBLIC Int CCOLAMD_2	    /* returns TRUE if successful, FALSE otherwise */
     Int *dead_cols ;
     Int set1 ;
     Int set2 ;
+#ifndef NDEBUG
     Int cs ;
-
+#endif
     int ok ;
 
 #ifndef NDEBUG
@@ -1909,8 +1910,10 @@ PUBLIC Int CCOLAMD_2	    /* returns TRUE if successful, FALSE otherwise */
             p [k] = col ;
             ASSERT (A [col] == EMPTY) ;
 
+#ifndef NDEBUG
 	    	cs = CMEMBER (col) ;
             ASSERT (k >= cset_start [cs] && k < cset_start [cs+1]) ;
+#endif
 
             A [col] = k ;
             k++ ;
@@ -1926,11 +1929,11 @@ PUBLIC Int CCOLAMD_2	    /* returns TRUE if successful, FALSE otherwise */
             if (A [col] == EMPTY)
             {
                 k = Col [col].shared2.order ;
-		cs = CMEMBER (col) ;
 #ifndef NDEBUG
+				cs = CMEMBER (col) ;
                 dead_cols [cs]-- ;
-#endif
                 ASSERT (k >= cset_start [cs] && k < cset_start [cs+1]) ;
+#endif
                 DEBUG1 (("ccolamd output ordering: k "ID" col "ID
                     " (dense or null col)\n", k, col)) ;
                 p [k] = col ;

gtsam/3rdparty/metis/GKlib/csr.c

@@ -1323,55 +1323,52 @@ void gk_csr_Normalize(gk_csr_t *mat, int what, int norm)
   ssize_t *ptr;
   float *val, sum;
 
-  if (what&GK_CSR_ROW && mat->rowval) {
+  if (what & GK_CSR_ROW && mat->rowval) {
     n = mat->nrows;
     ptr = mat->rowptr;
     val = mat->rowval;
 
-    #pragma omp parallel if (ptr[n] > OMPMINOPS) 
+#pragma omp parallel if (ptr[n] > OMPMINOPS)
     {
-      #pragma omp for private(j,sum) schedule(static)
+#pragma omp for private(j, sum) schedule(static)
-      for (i=0; i<n; i++) {
+      for (i = 0; i < n; i++) {
-        for (sum=0.0, j=ptr[i]; j<ptr[i+1]; j++){
+        for (sum = 0.0, j = ptr[i]; j < ptr[i + 1]; j++) {
           if (norm == 2)
-  	  sum += val[j]*val[j];
+            sum += val[j] * val[j];
           else if (norm == 1)
             sum += val[j]; /* assume val[j] > 0 */
         }
         if (sum > 0) {
           if (norm == 2)
-  	  sum=1.0/sqrt(sum); 
+            sum = 1.0 / sqrt(sum);
           else if (norm == 1)
-  	  sum=1.0/sum; 
+            sum = 1.0 / sum;
-          for (j=ptr[i]; j<ptr[i+1]; j++)
+          for (j = ptr[i]; j < ptr[i + 1]; j++) val[j] *= sum;
-            val[j] *= sum;
-  	
         }
       }
     }
   }
 
-  if (what&GK_CSR_COL && mat->colval) {
+  if (what & GK_CSR_COL && mat->colval) {
     n = mat->ncols;
     ptr = mat->colptr;
     val = mat->colval;
 
-    #pragma omp parallel if (ptr[n] > OMPMINOPS)
+#pragma omp parallel if (ptr[n] > OMPMINOPS)
     {
-    #pragma omp for private(j,sum) schedule(static)
+#pragma omp for private(j, sum) schedule(static)
-      for (i=0; i<n; i++) {
+      for (i = 0; i < n; i++) {
-        for (sum=0.0, j=ptr[i]; j<ptr[i+1]; j++)
+        for (sum = 0.0, j = ptr[i]; j < ptr[i + 1]; j++)
           if (norm == 2)
-  	  sum += val[j]*val[j];
+            sum += val[j] * val[j];
           else if (norm == 1)
             sum += val[j];
         if (sum > 0) {
           if (norm == 2)
-  	  sum=1.0/sqrt(sum); 
+            sum = 1.0 / sqrt(sum);
           else if (norm == 1)
-  	  sum=1.0/sum; 
+            sum = 1.0 / sum;
-          for (j=ptr[i]; j<ptr[i+1]; j++)
+          for (j = ptr[i]; j < ptr[i + 1]; j++) val[j] *= sum;
-            val[j] *= sum;
         }
       }
     }

gtsam/3rdparty/metis/GKlib/getopt.c

@@ -342,7 +342,7 @@ static int gk_getopt_internal(int argc, char **argv, char *optstring,
   if (gk_optind == 0 || !gk_getopt_initialized) {
     if (gk_optind == 0)
       gk_optind = 1; /* Don't scan ARGV[0], the program name.  */
-      optstring = gk_getopt_initialize (argc, argv, optstring);
+    optstring = gk_getopt_initialize(argc, argv, optstring);
     gk_getopt_initialized = 1;
   }
 
@@ -674,32 +674,33 @@ static int gk_getopt_internal(int argc, char **argv, char *optstring,
         if (*nextchar != '\0') {
           gk_optarg = nextchar;
           gk_optind++;
-	}
+        } else {
-	else
           gk_optarg = NULL;
-	nextchar = NULL;
         }
-      else {
+        nextchar = NULL;
+      } else {
         /* This is an option that requires an argument.  */
         if (*nextchar != '\0') {
           gk_optarg = nextchar;
-	  /* If we end this ARGV-element by taking the rest as an arg, we must advance to the next element now.  */
+          /* If we end this ARGV-element by taking the rest as an arg, we must
+           * advance to the next element now.  */
           gk_optind++;
-	}
+        } else if (gk_optind == argc) {
-	else if (gk_optind == argc) {
           if (print_errors) {
             /* 1003.2 specifies the format of this message.  */
-	    fprintf(stderr, "%s: option requires an argument -- %c\n", argv[0], c);
+            fprintf(stderr, "%s: option requires an argument -- %c\n", argv[0],
+                    c);
           }
           gk_optopt = c;
           if (optstring[0] == ':')
             c = ':';
           else
             c = '?';
-	}
+        } else {
-	else
+          /* We already incremented `gk_optind' once; increment it again when
-	  /* We already incremented `gk_optind' once; increment it again when taking next ARGV-elt as argument.  */
+           * taking next ARGV-elt as argument.  */
           gk_optarg = argv[gk_optind++];
+        }
         nextchar = NULL;
       }
     }

gtsam/3rdparty/metis/libmetis/balance.c

@@ -20,7 +20,7 @@ void Balance2Way(ctrl_t *ctrl, graph_t *graph, real_t *ntpwgts)
 
   if (graph->ncon == 1) {
     /* return right away if the balance is OK */
-    if (iabs(ntpwgts[0]*graph->tvwgt[0]-graph->pwgts[0]) < 3*graph->tvwgt[0]/graph->nvtxs)
+    if (fabs(ntpwgts[0]*graph->tvwgt[0]-graph->pwgts[0]) < 3*graph->tvwgt[0]/graph->nvtxs)
       return;
 
     if (graph->nbnd > 0)

gtsam/base/cholesky.cpp

@@ -111,8 +111,9 @@ bool choleskyPartial(Matrix& ABC, size_t nFrontal, size_t topleft) {
     return true;
 
   assert(ABC.cols() == ABC.rows());
-  const Eigen::DenseIndex n = ABC.rows() - topleft;
+  assert(ABC.rows() >= topleft);
-  assert(n >= 0 && nFrontal <= size_t(n));
+  const size_t n = static_cast<size_t>(ABC.rows() - topleft);
+  assert(nFrontal <= size_t(n));
 
   // Create views on blocks
   auto A = ABC.block(topleft, topleft, nFrontal, nFrontal);

gtsam/geometry/Unit3.cpp

@@ -36,13 +36,14 @@
 #include <iostream>
 #include <limits>
 #include <cmath>
+#include <vector>
 
 using namespace std;
 
 namespace gtsam {
 
 /* ************************************************************************* */
-Unit3 Unit3::FromPoint3(const Point3& point, OptionalJacobian<2,3> H) {
+Unit3 Unit3::FromPoint3(const Point3& point, OptionalJacobian<2, 3> H) {
   // 3*3 Derivative of representation with respect to point is 3*3:
   Matrix3 D_p_point;
   Unit3 direction;
@@ -54,7 +55,7 @@ Unit3 Unit3::FromPoint3(const Point3& point, OptionalJacobian<2,3> H) {
 
 /* ************************************************************************* */
 Unit3 Unit3::Random(boost::mt19937 & rng) {
-  // TODO allow any engine without including all of boost :-(
+  // TODO(dellaert): allow any engine without including all of boost :-(
   boost::uniform_on_sphere<double> randomDirection(3);
   // This variate_generator object is required for versions of boost somewhere
   // around 1.46, instead of drawing directly using boost::uniform_on_sphere(rng).
@@ -161,7 +162,8 @@ Matrix3 Unit3::skew() const {
 }
 
 /* ************************************************************************* */
-double Unit3::dot(const Unit3& q, OptionalJacobian<1,2> H_p, OptionalJacobian<1,2> H_q) const {
+double Unit3::dot(const Unit3& q, OptionalJacobian<1, 2> H_p,
+                  OptionalJacobian<1, 2> H_q) const {
   // Get the unit vectors of each, and the derivative.
   Matrix32 H_pn_p;
   Point3 pn = point3(H_p ? &H_pn_p : nullptr);
@@ -185,7 +187,7 @@ double Unit3::dot(const Unit3& q, OptionalJacobian<1,2> H_p, OptionalJacobian<1,
 }
 
 /* ************************************************************************* */
-Vector2 Unit3::error(const Unit3& q, OptionalJacobian<2,2> H_q) const {
+Vector2 Unit3::error(const Unit3& q, OptionalJacobian<2, 2> H_q) const {
   // 2D error is equal to B'*q, as B is 3x2 matrix and q is 3x1
   const Vector2 xi = basis().transpose() * q.p_;
   if (H_q) {
@@ -195,7 +197,8 @@ Vector2 Unit3::error(const Unit3& q, OptionalJacobian<2,2> H_q) const {
 }
 
 /* ************************************************************************* */
-Vector2 Unit3::errorVector(const Unit3& q, OptionalJacobian<2, 2> H_p, OptionalJacobian<2, 2> H_q) const {
+Vector2 Unit3::errorVector(const Unit3& q, OptionalJacobian<2, 2> H_p,
+                           OptionalJacobian<2, 2> H_q) const {
   // Get the point3 of this, and the derivative.
   Matrix32 H_qn_q;
   const Point3 qn = q.point3(H_q ? &H_qn_q : nullptr);
@@ -230,7 +233,7 @@ Vector2 Unit3::errorVector(const Unit3& q, OptionalJacobian<2, 2> H_p, OptionalJ
 }
 
 /* ************************************************************************* */
-double Unit3::distance(const Unit3& q, OptionalJacobian<1,2> H) const {
+double Unit3::distance(const Unit3& q, OptionalJacobian<1, 2> H) const {
   Matrix2 H_xi_q;
   const Vector2 xi = error(q, H ? &H_xi_q : nullptr);
   const double theta = xi.norm();
@@ -277,4 +280,4 @@ Vector2 Unit3::localCoordinates(const Unit3& other) const {
 }
 /* ************************************************************************* */
 
-}
+}  // namespace gtsam

gtsam/geometry/tests/testPoint2.cpp

@@ -100,12 +100,12 @@ TEST( Point2, expmap) {
 
 /* ************************************************************************* */
 TEST( Point2, arithmetic) {
-  EXPECT(assert_equal<Point2>( Point2(-5,-6), -Point2(5,6) ));
+  EXPECT(assert_equal<Point2>(Point2(-5, -6), -Point2(5, 6)));
-  EXPECT(assert_equal<Point2>( Point2(5,6), Point2(4,5)+Point2(1,1)));
+  EXPECT(assert_equal<Point2>(Point2(5, 6), Point2(4, 5) + Point2(1, 1)));
-  EXPECT(assert_equal<Point2>( Point2(3,4), Point2(4,5)-Point2(1,1) ));
+  EXPECT(assert_equal<Point2>(Point2(3, 4), Point2(4, 5) - Point2(1, 1)));
-  EXPECT(assert_equal<Point2>( Point2(8,6), Point2(4,3)*2));
+  EXPECT(assert_equal<Point2>(Point2(8, 6), Point2(4, 3) * 2));
-  EXPECT(assert_equal<Point2>( Point2(4,6), 2*Point2(2,3)));
+  EXPECT(assert_equal<Point2>(Point2(4, 6), 2.0 * Point2(2, 3)));
-  EXPECT(assert_equal<Point2>( Point2(2,3), Point2(4,6)/2));
+  EXPECT(assert_equal<Point2>(Point2(2, 3), Point2(4, 6) / 2));
 }
 
 /* ************************************************************************* */

gtsam/inference/BayesTree-inst.h

@@ -83,26 +83,28 @@ namespace gtsam {
     std::string parent = out.str();
     parent += "[label=\"";
 
-    for(Key index: clique->conditional_->frontals()) {
+    for (Key index : clique->conditional_->frontals()) {
-      if(!first) parent += ","; first = false;
+      if (!first) parent += ",";
+      first = false;
       parent += indexFormatter(index);
     }
 
-    if(clique->parent()){
+    if (clique->parent()) {
       parent += " : ";
       s << parentnum << "->" << num << "\n";
     }
 
     first = true;
-    for(Key sep: clique->conditional_->parents()) {
+    for (Key sep : clique->conditional_->parents()) {
-      if(!first) parent += ","; first = false;
+      if (!first) parent += ",";
+      first = false;
       parent += indexFormatter(sep);
     }
     parent += "\"];\n";
     s << parent;
     parentnum = num;
 
-    for(sharedClique c: clique->children) {
+    for (sharedClique c : clique->children) {
       num++;
       saveGraph(s, c, indexFormatter, parentnum);
     }

gtsam/inference/BayesTreeCliqueBase.h

@@ -17,9 +17,13 @@
 
 #pragma once
 
-#include <boost/optional.hpp>
+#include <gtsam/inference/Key.h>
+#include <gtsam/inference/Ordering.h>
 #include <gtsam/base/types.h>
 #include <gtsam/base/FastVector.h>
+#include <boost/optional.hpp>
+
+#include <string>
 
 namespace gtsam {
 

gtsam/linear/GaussianConditional.cpp

@@ -12,11 +12,13 @@
 /**
  * @file   GaussianConditional.cpp
  * @brief  Conditional Gaussian Base class
- * @author Christian Potthast
+ * @author Christian Potthast, Frank Dellaert
  */
 
-#include <string.h>
+#include <gtsam/linear/linearExceptions.h>
-#include <functional>
+#include <gtsam/linear/GaussianConditional.h>
+#include <gtsam/linear/VectorValues.h>
+
 #include <boost/format.hpp>
 #ifdef __GNUC__
 #pragma GCC diagnostic push
@@ -28,9 +30,9 @@
 #pragma GCC diagnostic pop
 #endif
 
-#include <gtsam/linear/linearExceptions.h>
+#include <functional>
-#include <gtsam/linear/GaussianConditional.h>
+#include <list>
-#include <gtsam/linear/VectorValues.h>
+#include <string>
 
 using namespace std;
 
@@ -54,38 +56,36 @@ namespace gtsam {
   BaseFactor(key, R, name1, S, name2, T, d, sigmas), BaseConditional(1) {}
 
   /* ************************************************************************* */
-  void GaussianConditional::print(const string &s, const KeyFormatter& formatter) const
+  void GaussianConditional::print(const string &s, const KeyFormatter& formatter) const {
-  {
     cout << s << "  Conditional density ";
-    for(const_iterator it = beginFrontals(); it != endFrontals(); ++it) {
+    for (const_iterator it = beginFrontals(); it != endFrontals(); ++it) {
       cout << (boost::format("[%1%]")%(formatter(*it))).str() << " ";
     }
     cout << endl;
     cout << formatMatrixIndented("  R = ", get_R()) << endl;
-    for(const_iterator it = beginParents() ; it != endParents() ; ++it ) {
+    for (const_iterator it = beginParents() ; it != endParents() ; ++it) {
       cout << formatMatrixIndented((boost::format("  S[%1%] = ")%(formatter(*it))).str(), getA(it))
         << endl;
     }
     cout << formatMatrixIndented("  d = ", getb(), true) << "\n";
-    if(model_)
+    if (model_)
       model_->print("  Noise model: ");
     else
       cout << "  No noise model" << endl;
   }
 
   /* ************************************************************************* */
-  bool GaussianConditional::equals(const GaussianFactor& f, double tol) const
+  bool GaussianConditional::equals(const GaussianFactor& f, double tol) const {
-  {
+    if (const GaussianConditional* c = dynamic_cast<const GaussianConditional*>(&f)) {
-    if (const GaussianConditional* c = dynamic_cast<const GaussianConditional*>(&f))
-    {
       // check if the size of the parents_ map is the same
       if (parents().size() != c->parents().size())
         return false;
 
       // check if R_ and d_ are linear independent
       for (DenseIndex i = 0; i < Ab_.rows(); i++) {
-        list<Vector> rows1; rows1.push_back(Vector(get_R().row(i)));
+        list<Vector> rows1, rows2;
-        list<Vector> rows2; rows2.push_back(Vector(c->get_R().row(i)));
+        rows1.push_back(Vector(get_R().row(i)));
+        rows2.push_back(Vector(c->get_R().row(i)));
 
         // check if the matrices are the same
         // iterate over the parents_ map
@@ -109,16 +109,13 @@ namespace gtsam {
         return false;
 
       return true;
-    }
+    } else {
-    else
-    {
       return false;
     }
   }
 
   /* ************************************************************************* */
-  VectorValues GaussianConditional::solve(const VectorValues& x) const
+  VectorValues GaussianConditional::solve(const VectorValues& x) const {
-  {
     // Concatenate all vector values that correspond to parent variables
     const Vector xS = x.vector(FastVector<Key>(beginParents(), endParents()));
 
@@ -146,8 +143,7 @@ namespace gtsam {
 
   /* ************************************************************************* */
   VectorValues GaussianConditional::solveOtherRHS(
-    const VectorValues& parents, const VectorValues& rhs) const
+    const VectorValues& parents, const VectorValues& rhs) const {
-  {
     // Concatenate all vector values that correspond to parent variables
     Vector xS = parents.vector(FastVector<Key>(beginParents(), endParents()));
 
@@ -159,13 +155,13 @@ namespace gtsam {
     Vector soln = get_R().triangularView<Eigen::Upper>().solve(xS);
 
     // Scale by sigmas
-    if(model_)
+    if (model_)
       soln.array() *= model_->sigmas().array();
 
     // Insert solution into a VectorValues
     VectorValues result;
     DenseIndex vectorPosition = 0;
-    for(const_iterator frontal = beginFrontals(); frontal != endFrontals(); ++frontal) {
+    for (const_iterator frontal = beginFrontals(); frontal != endFrontals(); ++frontal) {
       result.insert(*frontal, soln.segment(vectorPosition, getDim(frontal)));
       vectorPosition += getDim(frontal);
     }
@@ -174,8 +170,7 @@ namespace gtsam {
   }
 
   /* ************************************************************************* */
-  void GaussianConditional::solveTransposeInPlace(VectorValues& gy) const
+  void GaussianConditional::solveTransposeInPlace(VectorValues& gy) const {
-  {
     Vector frontalVec = gy.vector(FastVector<Key>(beginFrontals(), endFrontals()));
     frontalVec = gtsam::backSubstituteUpper(frontalVec, Matrix(get_R()));
 
@@ -186,25 +181,24 @@ namespace gtsam {
       gy[*it] += -1.0 * Matrix(getA(it)).transpose() * frontalVec;
 
     // Scale by sigmas
-    if(model_)
+    if (model_)
       frontalVec.array() *= model_->sigmas().array();
 
     // Write frontal solution into a VectorValues
     DenseIndex vectorPosition = 0;
-    for(const_iterator frontal = beginFrontals(); frontal != endFrontals(); ++frontal) {
+    for (const_iterator frontal = beginFrontals(); frontal != endFrontals(); ++frontal) {
       gy[*frontal] = frontalVec.segment(vectorPosition, getDim(frontal));
       vectorPosition += getDim(frontal);
     }
   }
 
   /* ************************************************************************* */
-  void GaussianConditional::scaleFrontalsBySigma(VectorValues& gy) const
+  void GaussianConditional::scaleFrontalsBySigma(VectorValues& gy) const {
-  {
     DenseIndex vectorPosition = 0;
-    for(const_iterator frontal = beginFrontals(); frontal != endFrontals(); ++frontal) {
+    for (const_iterator frontal = beginFrontals(); frontal != endFrontals(); ++frontal) {
       gy[*frontal].array() *= model_->sigmas().segment(vectorPosition, getDim(frontal)).array();
       vectorPosition += getDim(frontal);
     }
   }
 
-}
+}  // namespace gtsam

gtsam/linear/JacobianFactor.cpp

@@ -188,7 +188,7 @@ boost::tuple<FastVector<DenseIndex>, DenseIndex, DenseIndex> _countDims(
     m += factor->rows();
   }
 
-#ifdef GTSAM_EXTRA_CONSISTENCY_CHECKS
+#if !defined(NDEBUG) && defined(GTSAM_EXTRA_CONSISTENCY_CHECKS)
   for(DenseIndex d: varDims) {
     assert(d != numeric_limits<DenseIndex>::max());
   }

gtsam/linear/VectorValues.cpp

@@ -160,28 +160,6 @@ namespace gtsam {
     return result;
   }
 
-  /* ************************************************************************* */
-  Vector VectorValues::vector(const FastVector<Key>& keys) const
-  {
-    // Count dimensions and collect pointers to avoid double lookups
-    DenseIndex totalDim = 0;
-    FastVector<const Vector*> items(keys.size());
-    for(size_t i = 0; i < keys.size(); ++i) {
-      items[i] = &at(keys[i]);
-      totalDim += items[i]->size();
-    }
-
-    // Copy vectors
-    Vector result(totalDim);
-    DenseIndex pos = 0;
-    for(const Vector *v: items) {
-      result.segment(pos, v->size()) = *v;
-      pos += v->size();
-    }
-
-    return result;
-  }
-
   /* ************************************************************************* */
   Vector VectorValues::vector(const Dims& keys) const
   {

gtsam/linear/VectorValues.h

@@ -26,6 +26,9 @@
 
 #include <boost/shared_ptr.hpp>
 
+#include <map>
+#include <string>
+
 namespace gtsam {
 
   /**
@@ -43,10 +46,6 @@ namespace gtsam {
    *  - \ref exists (Key) to check if a variable is present
    *  - Other facilities like iterators, size(), dim(), etc.
    *
-   * Indices can be non-consecutive and inserted out-of-order, but you should not
-   * use indices that are larger than a reasonable array size because the indices
-   * correspond to positions in an internal array.
-   *
    * Example:
    * \code
      VectorValues values;
@@ -64,12 +63,6 @@ namespace gtsam {
    *
    * <h2>Advanced Interface and Performance Information</h2>
    *
-   * Internally, all vector values are stored as part of one large vector.  In
-   * gtsam this vector is always pre-allocated for efficiency, using the
-   * advanced interface described below.  Accessing and modifying already-allocated
-   * values is \f$ O(1) \f$.  Using the insert() function of the standard interface
-   * is slow because it requires re-allocating the internal vector.
-   *
    * For advanced usage, or where speed is important:
    *  - Allocate space ahead of time using a pre-allocating constructor
    *    (\ref AdvancedConstructors "Advanced Constructors"), Zero(),
@@ -90,18 +83,16 @@ namespace gtsam {
   class GTSAM_EXPORT VectorValues {
    protected:
     typedef VectorValues This;
-    typedef ConcurrentMap<Key, Vector> Values; ///< Typedef for the collection of Vectors making up a VectorValues
+    typedef ConcurrentMap<Key, Vector> Values;  ///< Collection of Vectors making up a VectorValues
-    Values values_; ///< Collection of Vectors making up this VectorValues
+    Values values_;                             ///< Vectors making up this VectorValues
 
    public:
     typedef Values::iterator iterator;              ///< Iterator over vector values
     typedef Values::const_iterator const_iterator;  ///< Const iterator over vector values
-    //typedef Values::reverse_iterator reverse_iterator; ///< Reverse iterator over vector values
-    //typedef Values::const_reverse_iterator const_reverse_iterator; ///< Const reverse iterator over vector values
     typedef boost::shared_ptr<This> shared_ptr;     ///< shared_ptr to this class
-    typedef Values::value_type value_type; ///< Typedef to pair<Key, Vector>, a key-value pair
+    typedef Values::value_type value_type;          ///< Typedef to pair<Key, Vector>
-    typedef value_type KeyValuePair; ///< Typedef to pair<Key, Vector>, a key-value pair
+    typedef value_type KeyValuePair;                ///< Typedef to pair<Key, Vector>
-    typedef std::map<Key,size_t> Dims;
+    typedef std::map<Key, size_t> Dims;             ///< Keyed vector dimensions
 
     /// @name Standard Constructors
     /// @{
@@ -111,7 +102,8 @@ namespace gtsam {
      */
     VectorValues() {}
 
-    /** Merge two VectorValues into one, this is more efficient than inserting elements one by one. */
+    /** Merge two VectorValues into one, this is more efficient than inserting
+     * elements one by one. */
     VectorValues(const VectorValues& first, const VectorValues& second);
 
     /** Create from another container holding pair<Key,Vector>. */
@@ -147,20 +139,26 @@ namespace gtsam {
     /** Check whether a variable with key \c j exists. */
     bool exists(Key j) const { return find(j) != end(); }
 
-    /** Read/write access to the vector value with key \c j, throws std::out_of_range if \c j does not exist, identical to operator[](Key). */
+    /** 
+     * Read/write access to the vector value with key \c j, throws
+     * std::out_of_range if \c j does not exist, identical to operator[](Key).
+     */
     Vector& at(Key j) {
       iterator item = find(j);
-      if(item == end())
+      if (item == end())
         throw std::out_of_range(
         "Requested variable '" + DefaultKeyFormatter(j) + "' is not in this VectorValues.");
       else
         return item->second;
     }
 
-    /** Access the vector value with key \c j (const version), throws std::out_of_range if \c j does not exist, identical to operator[](Key). */
+    /** 
+     * Access the vector value with key \c j (const version), throws
+     * std::out_of_range if \c j does not exist, identical to operator[](Key).
+     */
     const Vector& at(Key j) const {
       const_iterator item = find(j);
-      if(item == end())
+      if (item == end())
         throw std::out_of_range(
         "Requested variable '" + DefaultKeyFormatter(j) + "' is not in this VectorValues.");
       else
@@ -207,8 +205,10 @@ namespace gtsam {
 
     /** Erase the vector with the given key, or throw std::out_of_range if it does not exist */
     void erase(Key var) {
-      if(values_.unsafe_erase(var) == 0)
+      if (values_.unsafe_erase(var) == 0)
-        throw std::invalid_argument("Requested variable '" + DefaultKeyFormatter(var) + "', is not in this VectorValues.");
+        throw std::invalid_argument("Requested variable '" +
+                                    DefaultKeyFormatter(var) +
+                                    "', is not in this VectorValues.");
     }
 
     /** Set all values to zero vectors. */
@@ -218,15 +218,17 @@ namespace gtsam {
     const_iterator begin() const { return values_.begin(); }  ///< Iterator over variables
     iterator end()               { return values_.end(); }    ///< Iterator over variables
     const_iterator end() const   { return values_.end(); }    ///< Iterator over variables
-    //reverse_iterator rbegin()             { return values_.rbegin(); } ///< Reverse iterator over variables
-    //const_reverse_iterator rbegin() const { return values_.rbegin(); } ///< Reverse iterator over variables
-    //reverse_iterator rend()               { return values_.rend(); }   ///< Reverse iterator over variables
-    //const_reverse_iterator rend() const   { return values_.rend(); }   ///< Reverse iterator over variables
 
-    /** Return the iterator corresponding to the requested key, or end() if no variable is present with this key. */
+    /** 
+     * Return the iterator corresponding to the requested key, or end() if no
+     * variable is present with this key. 
+     */
     iterator find(Key j) { return values_.find(j); }
 
-    /** Return the iterator corresponding to the requested key, or end() if no variable is present with this key. */
+    /** 
+     * Return the iterator corresponding to the requested key, or end() if no
+     * variable is present with this key. 
+     */
     const_iterator find(Key j) const { return values_.find(j); }
 
     /** print required by Testable for unit testing */
@@ -244,7 +246,26 @@ namespace gtsam {
     Vector vector() const;
 
     /** Access a vector that is a subset of relevant keys. */
-    Vector vector(const FastVector<Key>& keys) const;
+    template <typename CONTAINER>
+    Vector vector(const CONTAINER& keys) const {
+      DenseIndex totalDim = 0;
+      FastVector<const Vector*> items;
+      items.reserve(keys.end() - keys.begin());
+      for (Key key : keys) {
+        const Vector* v = &at(key);
+        totalDim += v->size();
+        items.push_back(v);
+      }
+
+      Vector result(totalDim);
+      DenseIndex pos = 0;
+      for (const Vector* v : items) {
+        result.segment(pos, v->size()) = *v;
+        pos += v->size();
+      }
+
+      return result;
+    }
 
     /** Access a vector that is a subset of relevant keys, dims version. */
     Vector vector(const Dims& dims) const;
@@ -319,54 +340,6 @@ namespace gtsam {
 
     /// @}
 
-    /**
-     * scale a vector by a scalar
-     */
-    //friend VectorValues operator*(const double a, const VectorValues &v) {
-    //  VectorValues result = VectorValues::SameStructure(v);
-    //  for(Key j = 0; j < v.size(); ++j)
-    //    result.values_[j] = a * v.values_[j];
-    //  return result;
-    //}
-
-    //// TODO: linear algebra interface seems to have been added for SPCG.
-    //friend void axpy(double alpha, const VectorValues& x, VectorValues& y) {
-    //  if(x.size() != y.size())
-    //    throw std::invalid_argument("axpy(VectorValues) called with different vector sizes");
-    //  for(Key j = 0; j < x.size(); ++j)
-    //    if(x.values_[j].size() == y.values_[j].size())
-    //      y.values_[j] += alpha * x.values_[j];
-    //    else
-    //      throw std::invalid_argument("axpy(VectorValues) called with different vector sizes");
-    //}
-    //// TODO: linear algebra interface seems to have been added for SPCG.
-    //friend void sqrt(VectorValues &x) {
-    //  for(Key j = 0; j < x.size(); ++j)
-    //    x.values_[j] = x.values_[j].cwiseSqrt();
-    //}
-
-    //// TODO: linear algebra interface seems to have been added for SPCG.
-    //friend void ediv(const VectorValues& numerator, const VectorValues& denominator, VectorValues &result) {
-    //  if(numerator.size() != denominator.size() || numerator.size() != result.size())
-    //    throw std::invalid_argument("ediv(VectorValues) called with different vector sizes");
-    //  for(Key j = 0; j < numerator.size(); ++j)
-    //    if(numerator.values_[j].size() == denominator.values_[j].size() && numerator.values_[j].size() == result.values_[j].size())
-    //      result.values_[j] = numerator.values_[j].cwiseQuotient(denominator.values_[j]);
-    //    else
-    //      throw std::invalid_argument("ediv(VectorValues) called with different vector sizes");
-    //}
-
-    //// TODO: linear algebra interface seems to have been added for SPCG.
-    //friend void edivInPlace(VectorValues& x, const VectorValues& y) {
-    //  if(x.size() != y.size())
-    //    throw std::invalid_argument("edivInPlace(VectorValues) called with different vector sizes");
-    //  for(Key j = 0; j < x.size(); ++j)
-    //    if(x.values_[j].size() == y.values_[j].size())
-    //      x.values_[j].array() /= y.values_[j].array();
-    //    else
-    //      throw std::invalid_argument("edivInPlace(VectorValues) called with different vector sizes");
-    //}
-
   private:
     /** Serialization function */
     friend class boost::serialization::access;

gtsam/navigation/ImuFactor.h

@@ -106,6 +106,10 @@ public:
        preintMeasCov_(preintMeasCov) {
   }
 
+  /// Virtual destructor
+  virtual ~PreintegratedImuMeasurements() {
+  }
+
   /// print
   void print(const std::string& s = "Preintegrated Measurements:") const override;
 

gtsam/navigation/TangentPreintegration.h

@@ -42,7 +42,7 @@ class TangentPreintegration : public PreintegrationBase {
   }
 
 public:
-  /// @name Constructors
+  /// @name Constructors/destructors
   /// @{
 
   /**
@@ -53,6 +53,10 @@ public:
   TangentPreintegration(const boost::shared_ptr<Params>& p,
       const imuBias::ConstantBias& biasHat = imuBias::ConstantBias());
 
+  /// Virtual destructor
+  virtual ~TangentPreintegration() {
+  }
+
   /// @}
 
   /// @name Basic utilities

gtsam/nonlinear/ISAM2-impl.cpp

@@ -11,120 +11,89 @@
 
 /**
  * @file    ISAM2-impl.cpp
- * @brief   Incremental update functionality (ISAM2) for BayesTree, with fluid relinearization.
+ * @brief   Incremental update functionality (ISAM2) for BayesTree, with fluid
+ * relinearization.
  * @author  Michael Kaess
  * @author  Richard Roberts
  */
 
-#include <gtsam/nonlinear/ISAM2-impl.h>
-#include <gtsam/inference/Symbol.h> // for selective linearization thresholds
 #include <gtsam/base/debug.h>
 #include <gtsam/config.h>            // for GTSAM_USE_TBB
+#include <gtsam/inference/Symbol.h>  // for selective linearization thresholds
+#include <gtsam/nonlinear/ISAM2-impl.h>
 
-#include <functional>
 #include <boost/range/adaptors.hpp>
+#include <functional>
+#include <limits>
+#include <string>
 
 using namespace std;
 
 namespace gtsam {
 
 /* ************************************************************************* */
-void ISAM2::Impl::AddVariables(
+void ISAM2::Impl::AddFactorsStep1(const NonlinearFactorGraph& newFactors,
-    const Values& newTheta, Values& theta, VectorValues& delta,
+                                  bool useUnusedSlots,
-    VectorValues& deltaNewton, VectorValues& RgProd,
+                                  NonlinearFactorGraph* nonlinearFactors,
-    const KeyFormatter& keyFormatter)
+                                  FactorIndices* newFactorIndices) {
-{
+  newFactorIndices->resize(newFactors.size());
-  const bool debug = ISDEBUG("ISAM2 AddVariables");
 
-  theta.insert(newTheta);
+  if (useUnusedSlots) {
-  if(debug) newTheta.print("The new variables are: ");
-  // Add zeros into the VectorValues
-  delta.insert(newTheta.zeroVectors());
-  deltaNewton.insert(newTheta.zeroVectors());
-  RgProd.insert(newTheta.zeroVectors());
-}
-
-/* ************************************************************************* */
-void ISAM2::Impl::AddFactorsStep1(const NonlinearFactorGraph& newFactors, bool useUnusedSlots,
-  NonlinearFactorGraph& nonlinearFactors, FactorIndices& newFactorIndices)
-{
-  newFactorIndices.resize(newFactors.size());
-
-  if(useUnusedSlots)
-  {
     size_t globalFactorIndex = 0;
-    for(size_t newFactorIndex = 0; newFactorIndex < newFactors.size(); ++newFactorIndex)
+    for (size_t newFactorIndex = 0; newFactorIndex < newFactors.size();
-    {
+         ++newFactorIndex) {
       // Loop to find the next available factor slot
-      do 
+      do {
-      {
+        // If we need to add more factors than we have room for, resize
-        // If we need to add more factors than we have room for, resize nonlinearFactors,
+        // nonlinearFactors, filling the new slots with NULL factors. Otherwise,
-        // filling the new slots with NULL factors.  Otherwise, check if the current
+        // check if the current factor in nonlinearFactors is already used, and
-        // factor in nonlinearFactors is already used, and if so, increase
+        // if so, increase globalFactorIndex.  If the current factor in
-        // globalFactorIndex.  If the current factor in nonlinearFactors is unused, break
+        // nonlinearFactors is unused, break out of the loop and use the current
-        // out of the loop and use the current slot.
+        // slot.
-        if(globalFactorIndex >= nonlinearFactors.size())
+        if (globalFactorIndex >= nonlinearFactors->size())
-          nonlinearFactors.resize(nonlinearFactors.size() + newFactors.size() - newFactorIndex);
+          nonlinearFactors->resize(nonlinearFactors->size() +
-        else if(nonlinearFactors[globalFactorIndex])
+                                   newFactors.size() - newFactorIndex);
-          ++ globalFactorIndex;
+        else if ((*nonlinearFactors)[globalFactorIndex])
+          ++globalFactorIndex;
         else
           break;
-      } while(true);
+      } while (true);
 
       // Use the current slot, updating nonlinearFactors and newFactorSlots.
-      nonlinearFactors[globalFactorIndex] = newFactors[newFactorIndex];
+      (*nonlinearFactors)[globalFactorIndex] = newFactors[newFactorIndex];
-      newFactorIndices[newFactorIndex] = globalFactorIndex;
+      (*newFactorIndices)[newFactorIndex] = globalFactorIndex;
     }
-  }
+  } else {
-  else
-  {
     // We're not looking for unused slots, so just add the factors at the end.
-    for(size_t i = 0; i < newFactors.size(); ++i)
+    for (size_t i = 0; i < newFactors.size(); ++i)
-      newFactorIndices[i] = i + nonlinearFactors.size();
+      (*newFactorIndices)[i] = i + nonlinearFactors->size();
-    nonlinearFactors.push_back(newFactors);
+    nonlinearFactors->push_back(newFactors);
   }
 }
 
 /* ************************************************************************* */
-void ISAM2::Impl::RemoveVariables(const KeySet& unusedKeys, const FastVector<ISAM2::sharedClique>& roots,
+KeySet ISAM2::Impl::CheckRelinearizationFull(
-                                  Values& theta, VariableIndex& variableIndex,
+    const VectorValues& delta,
-                                  VectorValues& delta, VectorValues& deltaNewton, VectorValues& RgProd,
+    const ISAM2Params::RelinearizationThreshold& relinearizeThreshold) {
-                                  KeySet& replacedKeys, Base::Nodes& nodes,
-                                  KeySet& fixedVariables)
-{
-  variableIndex.removeUnusedVariables(unusedKeys.begin(), unusedKeys.end());
-  for(Key key: unusedKeys) {
-    delta.erase(key);
-    deltaNewton.erase(key);
-    RgProd.erase(key);
-    replacedKeys.erase(key);
-    nodes.unsafe_erase(key);
-    theta.erase(key);
-    fixedVariables.erase(key);
-  }
-}
-
-/* ************************************************************************* */
-KeySet ISAM2::Impl::CheckRelinearizationFull(const VectorValues& delta,
-    const ISAM2Params::RelinearizationThreshold& relinearizeThreshold)
-{
   KeySet relinKeys;
 
-  if(const double* threshold = boost::get<double>(&relinearizeThreshold))
+  if (const double* threshold = boost::get<double>(&relinearizeThreshold)) {
-  {
+    for (const VectorValues::KeyValuePair& key_delta : delta) {
-    for(const VectorValues::KeyValuePair& key_delta: delta) {
       double maxDelta = key_delta.second.lpNorm<Eigen::Infinity>();
-      if(maxDelta >= *threshold)
+      if (maxDelta >= *threshold) relinKeys.insert(key_delta.first);
-        relinKeys.insert(key_delta.first);
     }
-  }
+  } else if (const FastMap<char, Vector>* thresholds =
-  else if(const FastMap<char,Vector>* thresholds = boost::get<FastMap<char,Vector> >(&relinearizeThreshold))
+                 boost::get<FastMap<char, Vector> >(&relinearizeThreshold)) {
-  {
+    for (const VectorValues::KeyValuePair& key_delta : delta) {
-    for(const VectorValues::KeyValuePair& key_delta: delta) {
+      const Vector& threshold =
-      const Vector& threshold = thresholds->find(Symbol(key_delta.first).chr())->second;
+          thresholds->find(Symbol(key_delta.first).chr())->second;
-      if(threshold.rows() != key_delta.second.rows())
+      if (threshold.rows() != key_delta.second.rows())
-        throw std::invalid_argument("Relinearization threshold vector dimensionality for '" + std::string(1, Symbol(key_delta.first).chr()) + "' passed into iSAM2 parameters does not match actual variable dimensionality.");
+        throw std::invalid_argument(
-      if((key_delta.second.array().abs() > threshold.array()).any())
+            "Relinearization threshold vector dimensionality for '" +
+            std::string(1, Symbol(key_delta.first).chr()) +
+            "' passed into iSAM2 parameters does not match actual variable "
+            "dimensionality.");
+      if ((key_delta.second.array().abs() > threshold.array()).any())
         relinKeys.insert(key_delta.first);
     }
   }
@@ -133,167 +102,117 @@ KeySet ISAM2::Impl::CheckRelinearizationFull(const VectorValues& delta,
 }
 
 /* ************************************************************************* */
-void CheckRelinearizationRecursiveDouble(KeySet& relinKeys, double threshold,
+static void CheckRelinearizationRecursiveDouble(
-                                         const VectorValues& delta, const ISAM2Clique::shared_ptr& clique)
+    double threshold, const VectorValues& delta,
-{
+    const ISAM2::sharedClique& clique, KeySet* relinKeys) {
   // Check the current clique for relinearization
   bool relinearize = false;
-  for(Key var: *clique->conditional()) {
+  for (Key var : *clique->conditional()) {
     double maxDelta = delta[var].lpNorm<Eigen::Infinity>();
-    if(maxDelta >= threshold) {
+    if (maxDelta >= threshold) {
-      relinKeys.insert(var);
+      relinKeys->insert(var);
       relinearize = true;
     }
   }
 
   // If this node was relinearized, also check its children
-  if(relinearize) {
+  if (relinearize) {
-    for(const ISAM2Clique::shared_ptr& child: clique->children) {
+    for (const ISAM2::sharedClique& child : clique->children) {
-      CheckRelinearizationRecursiveDouble(relinKeys, threshold, delta, child);
+      CheckRelinearizationRecursiveDouble(threshold, delta, child, relinKeys);
     }
   }
 }
 
 /* ************************************************************************* */
-void CheckRelinearizationRecursiveMap(KeySet& relinKeys, const FastMap<char,Vector>& thresholds,
+static void CheckRelinearizationRecursiveMap(
-                                      const VectorValues& delta,
+    const FastMap<char, Vector>& thresholds, const VectorValues& delta,
-                                      const ISAM2Clique::shared_ptr& clique)
+    const ISAM2::sharedClique& clique, KeySet* relinKeys) {
-{
   // Check the current clique for relinearization
   bool relinearize = false;
-  for(Key var: *clique->conditional()) {
+  for (Key var : *clique->conditional()) {
     // Find the threshold for this variable type
     const Vector& threshold = thresholds.find(Symbol(var).chr())->second;
 
     const Vector& deltaVar = delta[var];
 
     // Verify the threshold vector matches the actual variable size
-    if(threshold.rows() != deltaVar.rows())
+    if (threshold.rows() != deltaVar.rows())
-      throw std::invalid_argument("Relinearization threshold vector dimensionality for '" + std::string(1, Symbol(var).chr()) + "' passed into iSAM2 parameters does not match actual variable dimensionality.");
+      throw std::invalid_argument(
+          "Relinearization threshold vector dimensionality for '" +
+          std::string(1, Symbol(var).chr()) +
+          "' passed into iSAM2 parameters does not match actual variable "
+          "dimensionality.");
 
     // Check for relinearization
-    if((deltaVar.array().abs() > threshold.array()).any()) {
+    if ((deltaVar.array().abs() > threshold.array()).any()) {
-      relinKeys.insert(var);
+      relinKeys->insert(var);
       relinearize = true;
     }
   }
 
   // If this node was relinearized, also check its children
-  if(relinearize) {
+  if (relinearize) {
-    for(const ISAM2Clique::shared_ptr& child: clique->children) {
+    for (const ISAM2::sharedClique& child : clique->children) {
-      CheckRelinearizationRecursiveMap(relinKeys, thresholds, delta, child);
+      CheckRelinearizationRecursiveMap(thresholds, delta, child, relinKeys);
     }
   }
 }
 
 /* ************************************************************************* */
-KeySet ISAM2::Impl::CheckRelinearizationPartial(const FastVector<ISAM2::sharedClique>& roots,
+KeySet ISAM2::Impl::CheckRelinearizationPartial(
-                                                        const VectorValues& delta,
+    const ISAM2::Roots& roots, const VectorValues& delta,
-                                                        const ISAM2Params::RelinearizationThreshold& relinearizeThreshold)
+    const ISAM2Params::RelinearizationThreshold& relinearizeThreshold) {
-{
   KeySet relinKeys;
-  for(const ISAM2::sharedClique& root: roots) {
+  for (const ISAM2::sharedClique& root : roots) {
-    if(relinearizeThreshold.type() == typeid(double))
+    if (relinearizeThreshold.type() == typeid(double))
-      CheckRelinearizationRecursiveDouble(relinKeys, boost::get<double>(relinearizeThreshold), delta, root);
+      CheckRelinearizationRecursiveDouble(
-    else if(relinearizeThreshold.type() == typeid(FastMap<char,Vector>))
+          boost::get<double>(relinearizeThreshold), delta, root, &relinKeys);
-      CheckRelinearizationRecursiveMap(relinKeys, boost::get<FastMap<char,Vector> >(relinearizeThreshold), delta, root);
+    else if (relinearizeThreshold.type() == typeid(FastMap<char, Vector>))
+      CheckRelinearizationRecursiveMap(
+          boost::get<FastMap<char, Vector> >(relinearizeThreshold), delta, root,
+          &relinKeys);
   }
   return relinKeys;
 }
 
-/* ************************************************************************* */
-void ISAM2::Impl::FindAll(ISAM2Clique::shared_ptr clique, KeySet& keys, const KeySet& markedMask)
-{
-  static const bool debug = false;
-  // does the separator contain any of the variables?
-  bool found = false;
-  for(Key key: clique->conditional()->parents()) {
-    if (markedMask.exists(key)) {
-      found = true;
-      break;
-    }
-  }
-  if (found) {
-    // then add this clique
-    keys.insert(clique->conditional()->beginFrontals(), clique->conditional()->endFrontals());
-    if(debug) clique->print("Key(s) marked in clique ");
-    if(debug) cout << "so marking key " << clique->conditional()->front() << endl;
-  }
-  for(const ISAM2Clique::shared_ptr& child: clique->children) {
-    FindAll(child, keys, markedMask);
-  }
-}
-
-/* ************************************************************************* */
-void ISAM2::Impl::ExpmapMasked(Values& values, const VectorValues& delta,
-    const KeySet& mask, boost::optional<VectorValues&> invalidateIfDebug, const KeyFormatter& keyFormatter)
-{
-  // If debugging, invalidate if requested, otherwise do not invalidate.
-  // Invalidating means setting expmapped entries to Inf, to trigger assertions
-  // if we try to re-use them.
-#ifdef NDEBUG
-  invalidateIfDebug = boost::none;
-#endif
-
-  assert(values.size() == delta.size());
-  Values::iterator key_value;
-  VectorValues::const_iterator key_delta;
-#ifdef GTSAM_USE_TBB
-  for(key_value = values.begin(); key_value != values.end(); ++key_value)
-  {
-    key_delta = delta.find(key_value->key);
-#else
-  for(key_value = values.begin(), key_delta = delta.begin(); key_value != values.end(); ++key_value, ++key_delta)
-  {
-    assert(key_value->key == key_delta->first);
-#endif
-    Key var = key_value->key;
-    assert(delta[var].size() == (int)key_value->value.dim());
-    assert(delta[var].allFinite());
-    if(mask.exists(var)) {
-      Value* retracted = key_value->value.retract_(delta[var]);
-      key_value->value = *retracted;
-      retracted->deallocate_();
-      if(invalidateIfDebug)
-        (*invalidateIfDebug)[var].operator=(Vector::Constant(delta[var].rows(), numeric_limits<double>::infinity())); // Strange syntax to work with clang++ (bug in clang?)
-    }
-  }
-}
-
 /* ************************************************************************* */
 namespace internal {
-inline static void optimizeInPlace(const boost::shared_ptr<ISAM2Clique>& clique, VectorValues& result) {
+inline static void optimizeInPlace(const ISAM2::sharedClique& clique,
+                                   VectorValues* result) {
   // parents are assumed to already be solved and available in result
-  result.update(clique->conditional()->solve(result));
+  result->update(clique->conditional()->solve(*result));
 
   // starting from the root, call optimize on each conditional
-  for(const boost::shared_ptr<ISAM2Clique>& child: clique->children)
+  for (const ISAM2::sharedClique& child : clique->children)
     optimizeInPlace(child, result);
 }
-}
+}  // namespace internal
 
 /* ************************************************************************* */
-size_t ISAM2::Impl::UpdateGaussNewtonDelta(const FastVector<ISAM2::sharedClique>& roots,
+size_t ISAM2::Impl::UpdateGaussNewtonDelta(const ISAM2::Roots& roots,
-    const KeySet& replacedKeys, VectorValues& delta, double wildfireThreshold) {
+                                           const KeySet& replacedKeys,
-
+                                           double wildfireThreshold,
+                                           VectorValues* delta) {
   size_t lastBacksubVariableCount;
 
   if (wildfireThreshold <= 0.0) {
     // Threshold is zero or less, so do a full recalculation
-    for(const ISAM2::sharedClique& root: roots)
+    for (const ISAM2::sharedClique& root : roots)
       internal::optimizeInPlace(root, delta);
-    lastBacksubVariableCount = delta.size();
+    lastBacksubVariableCount = delta->size();
 
   } else {
     // Optimize with wildfire
     lastBacksubVariableCount = 0;
-    for(const ISAM2::sharedClique& root: roots)
+    for (const ISAM2::sharedClique& root : roots)
       lastBacksubVariableCount += optimizeWildfireNonRecursive(
           root, wildfireThreshold, replacedKeys, delta);  // modifies delta
 
-#ifdef GTSAM_EXTRA_CONSISTENCY_CHECKS
+#if !defined(NDEBUG) && defined(GTSAM_EXTRA_CONSISTENCY_CHECKS)
-    for(size_t j=0; j<delta.size(); ++j)
+    for (VectorValues::const_iterator key_delta = delta->begin();
-      assert(delta[j].unaryExpr(ptr_fun(isfinite<double>)).all());
+         key_delta != delta->end(); ++key_delta) {
+      assert((*delta)[key_delta->first].allFinite());
+    }
 #endif
   }
 
@@ -302,57 +221,66 @@ size_t ISAM2::Impl::UpdateGaussNewtonDelta(const FastVector<ISAM2::sharedClique>
 
 /* ************************************************************************* */
 namespace internal {
-void updateRgProd(const boost::shared_ptr<ISAM2Clique>& clique, const KeySet& replacedKeys,
+void updateRgProd(const ISAM2::sharedClique& clique, const KeySet& replacedKeys,
-    const VectorValues& grad, VectorValues& RgProd, size_t& varsUpdated) {
+                  const VectorValues& grad, VectorValues* RgProd,
-
+                  size_t* varsUpdated) {
   // Check if any frontal or separator keys were recalculated, if so, we need
   // update deltas and recurse to children, but if not, we do not need to
   // recurse further because of the running separator property.
   bool anyReplaced = false;
-  for(Key j: *clique->conditional()) {
+  for (Key j : *clique->conditional()) {
-    if(replacedKeys.exists(j)) {
+    if (replacedKeys.exists(j)) {
       anyReplaced = true;
       break;
     }
   }
 
-  if(anyReplaced) {
+  if (anyReplaced) {
     // Update the current variable
     // Get VectorValues slice corresponding to current variables
-    Vector gR = grad.vector(FastVector<Key>(clique->conditional()->beginFrontals(), clique->conditional()->endFrontals()));
+    Vector gR =
-    Vector gS = grad.vector(FastVector<Key>(clique->conditional()->beginParents(), clique->conditional()->endParents()));
+        grad.vector(FastVector<Key>(clique->conditional()->beginFrontals(),
+                                    clique->conditional()->endFrontals()));
+    Vector gS =
+        grad.vector(FastVector<Key>(clique->conditional()->beginParents(),
+                                    clique->conditional()->endParents()));
 
     // Compute R*g and S*g for this clique
-    Vector RSgProd = clique->conditional()->get_R() * gR + clique->conditional()->get_S() * gS;
+    Vector RSgProd = clique->conditional()->get_R() * gR +
+                     clique->conditional()->get_S() * gS;
 
     // Write into RgProd vector
     DenseIndex vectorPosition = 0;
-    for(Key frontal: clique->conditional()->frontals()) {
+    for (Key frontal : clique->conditional()->frontals()) {
-      Vector& RgProdValue = RgProd[frontal];
+      Vector& RgProdValue = (*RgProd)[frontal];
       RgProdValue = RSgProd.segment(vectorPosition, RgProdValue.size());
       vectorPosition += RgProdValue.size();
     }
 
-    // Now solve the part of the Newton's method point for this clique (back-substitution)
+    // Now solve the part of the Newton's method point for this clique
-    //(*clique)->solveInPlace(deltaNewton);
+    // (back-substitution)
+    // (*clique)->solveInPlace(deltaNewton);
 
-    varsUpdated += clique->conditional()->nrFrontals();
+    *varsUpdated += clique->conditional()->nrFrontals();
 
     // Recurse to children
-    for(const ISAM2Clique::shared_ptr& child: clique->children) {
+    for (const ISAM2::sharedClique& child : clique->children) {
-      updateRgProd(child, replacedKeys, grad, RgProd, varsUpdated); }
+      updateRgProd(child, replacedKeys, grad, RgProd, varsUpdated);
+    }
   }
 }
-}
+}  // namespace internal
 
 /* ************************************************************************* */
-size_t ISAM2::Impl::UpdateRgProd(const ISAM2::Roots& roots, const KeySet& replacedKeys,
+size_t ISAM2::Impl::UpdateRgProd(const ISAM2::Roots& roots,
-    const VectorValues& gradAtZero, VectorValues& RgProd) {
+                                 const KeySet& replacedKeys,
-
+                                 const VectorValues& gradAtZero,
+                                 VectorValues* RgProd) {
   // Update variables
   size_t varsUpdated = 0;
-  for(const ISAM2::sharedClique& root: roots) {
+  for (const ISAM2::sharedClique& root : roots) {
-    internal::updateRgProd(root, replacedKeys, gradAtZero, RgProd, varsUpdated);
+    internal::updateRgProd(root, replacedKeys, gradAtZero, RgProd,
+                           &varsUpdated);
   }
 
   return varsUpdated;
@@ -360,8 +288,7 @@ size_t ISAM2::Impl::UpdateRgProd(const ISAM2::Roots& roots, const KeySet& replac
 
 /* ************************************************************************* */
 VectorValues ISAM2::Impl::ComputeGradientSearch(const VectorValues& gradAtZero,
-                                     const VectorValues& RgProd)
+                                                const VectorValues& RgProd) {
-{
   // Compute gradient squared-magnitude
   const double gradientSqNorm = gradAtZero.dot(gradAtZero);
 
@@ -373,4 +300,4 @@ VectorValues ISAM2::Impl::ComputeGradientSearch(const VectorValues& gradAtZero,
   return step * gradAtZero;
 }
 
-}
+}  // namespace gtsam

gtsam/nonlinear/ISAM2-impl.h

@@ -23,7 +23,6 @@
 namespace gtsam {
 
 struct GTSAM_EXPORT ISAM2::Impl {
-
   struct GTSAM_EXPORT PartialSolveResult {
     ISAM2::sharedClique bayesTree;
   };
@@ -32,35 +31,14 @@ struct GTSAM_EXPORT ISAM2::Impl {
     size_t nFullSystemVars;
     enum { /*AS_ADDED,*/ COLAMD } algorithm;
     enum { NO_CONSTRAINT, CONSTRAIN_LAST } constrain;
-    boost::optional<FastMap<Key,int> > constrainedKeys;
+    boost::optional<FastMap<Key, int> > constrainedKeys;
   };
 
-  /**
-   * Add new variables to the ISAM2 system.
-   * @param newTheta Initial values for new variables
-   * @param theta Current solution to be augmented with new initialization
-   * @param delta Current linear delta to be augmented with zeros
-   * @param ordering Current ordering to be augmented with new variables
-   * @param nodes Current BayesTree::Nodes index to be augmented with slots for new variables
-   * @param keyFormatter Formatter for printing nonlinear keys during debugging
-   */
-  static void AddVariables(const Values& newTheta, Values& theta, VectorValues& delta,
-      VectorValues& deltaNewton, VectorValues& RgProd,
-      const KeyFormatter& keyFormatter = DefaultKeyFormatter);
-
   /// Perform the first part of the bookkeeping updates for adding new factors.  Adds them to the
   /// complete list of nonlinear factors, and populates the list of new factor indices, both
   /// optionally finding and reusing empty factor slots.
   static void AddFactorsStep1(const NonlinearFactorGraph& newFactors, bool useUnusedSlots,
-    NonlinearFactorGraph& nonlinearFactors, FactorIndices& newFactorIndices);
+    NonlinearFactorGraph* nonlinearFactors, FactorIndices* newFactorIndices);
-    
-  /**
-   * Remove variables from the ISAM2 system.
-   */
-  static void RemoveVariables(const KeySet& unusedKeys, const FastVector<ISAM2::sharedClique>& roots,
-    Values& theta, VariableIndex& variableIndex, VectorValues& delta, VectorValues& deltaNewton,
-    VectorValues& RgProd, KeySet& replacedKeys, Base::Nodes& nodes,
-    KeySet& fixedVariables);
 
   /**
    * Find the set of variables to be relinearized according to relinearizeThreshold.
@@ -85,56 +63,21 @@ struct GTSAM_EXPORT ISAM2::Impl {
    * @return The set of variable indices in delta whose magnitude is greater than or
    * equal to relinearizeThreshold
    */
-  static KeySet CheckRelinearizationPartial(const FastVector<ISAM2::sharedClique>& roots,
+  static KeySet CheckRelinearizationPartial(const ISAM2::Roots& roots,
     const VectorValues& delta, const ISAM2Params::RelinearizationThreshold& relinearizeThreshold);
 
-  /**
-   * Recursively search this clique and its children for marked keys appearing
-   * in the separator, and add the *frontal* keys of any cliques whose
-   * separator contains any marked keys to the set \c keys.  The purpose of
-   * this is to discover the cliques that need to be redone due to information
-   * propagating to them from cliques that directly contain factors being
-   * relinearized.
-   *
-   * The original comment says this finds all variables directly connected to
-   * the marked ones by measurements.  Is this true, because it seems like this
-   * would also pull in variables indirectly connected through other frontal or
-   * separator variables?
-   *
-   * Alternatively could we trace up towards the root for each variable here?
-   */
-  static void FindAll(ISAM2Clique::shared_ptr clique, KeySet& keys, const KeySet& markedMask);
-
-  /**
-   * Apply expmap to the given values, but only for indices appearing in
-   * \c markedRelinMask.  Values are expmapped in-place.
-   * \param [in, out] values The value to expmap in-place
-   * \param delta The linear delta with which to expmap
-   * \param ordering The ordering
-   * \param mask Mask on linear indices, only \c true entries are expmapped
-   * \param invalidateIfDebug If this is true, *and* NDEBUG is not defined,
-   * expmapped deltas will be set to an invalid value (infinity) to catch bugs
-   * where we might expmap something twice, or expmap it but then not
-   * recalculate its delta.
-   * @param keyFormatter Formatter for printing nonlinear keys during debugging
-   */
-  static void ExpmapMasked(Values& values, const VectorValues& delta,
-      const KeySet& mask,
-      boost::optional<VectorValues&> invalidateIfDebug = boost::none,
-      const KeyFormatter& keyFormatter = DefaultKeyFormatter);
-
   /**
    * Update the Newton's method step point, using wildfire
    */
-  static size_t UpdateGaussNewtonDelta(const FastVector<ISAM2::sharedClique>& roots,
+  static size_t UpdateGaussNewtonDelta(const ISAM2::Roots& roots,
-      const KeySet& replacedKeys, VectorValues& delta, double wildfireThreshold);
+      const KeySet& replacedKeys, double wildfireThreshold, VectorValues* delta);
 
   /**
    * Update the RgProd (R*g) incrementally taking into account which variables
    * have been recalculated in \c replacedKeys.  Only used in Dogleg.
    */
   static size_t UpdateRgProd(const ISAM2::Roots& roots, const KeySet& replacedKeys,
-      const VectorValues& gradAtZero, VectorValues& RgProd);
+      const VectorValues& gradAtZero, VectorValues* RgProd);
 
   /**
    * Compute the gradient-search point.  Only used in Dogleg.

gtsam/nonlinear/ISAM2-inl.h

@@ -1,311 +0,0 @@
-/* ----------------------------------------------------------------------------
-
- * GTSAM Copyright 2010, Georgia Tech Research Corporation, 
- * Atlanta, Georgia 30332-0415
- * All Rights Reserved
- * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
-
- * See LICENSE for the license information
-
- * -------------------------------------------------------------------------- */
-
-/**
- * @file ISAM2-inl.h
- * @brief 
- * @author Richard Roberts
- * @date Mar 16, 2012
- */
-
-
-#pragma once
-
-#include <stack>
-#include <gtsam/inference/FactorGraph.h>
-#include <gtsam/linear/JacobianFactor.h>
-
-namespace gtsam {
-
-/* ************************************************************************* */
-template<class VALUE>
-VALUE ISAM2::calculateEstimate(Key key) const {
-  const Vector& delta = getDelta()[key];
-  return traits<VALUE>::Retract(theta_.at<VALUE>(key), delta);
-}
-
-/* ************************************************************************* */
-namespace internal {
-template<class CLIQUE>
-void optimizeWildfire(const boost::shared_ptr<CLIQUE>& clique, double threshold,
-    KeySet& changed, const KeySet& replaced, VectorValues& delta, size_t& count)
-{
-  // if none of the variables in this clique (frontal and separator!) changed
-  // significantly, then by the running intersection property, none of the
-  // cliques in the children need to be processed
-
-  // Are any clique variables part of the tree that has been redone?
-  bool cliqueReplaced = replaced.exists((*clique)->frontals().front());
-#ifdef GTSAM_EXTRA_CONSISTENCY_CHECKS
-  for(Key frontal: clique->conditional()->frontals()) {
-    assert(cliqueReplaced == replaced.exists(frontal));
-  }
-#endif
-
-  // If not redone, then has one of the separator variables changed significantly?
-  bool recalculate = cliqueReplaced;
-  if(!recalculate) {
-    for(Key parent: clique->conditional()->parents()) {
-      if(changed.exists(parent)) {
-        recalculate = true;
-        break;
-      }
-    }
-  }
-
-  // Solve clique if it was replaced, or if any parents were changed above the
-  // threshold or themselves replaced.
-  if(recalculate) {
-
-    // Temporary copy of the original values, to check how much they change
-    FastVector<Vector> originalValues(clique->conditional()->nrFrontals());
-    GaussianConditional::const_iterator it;
-    for(it = clique->conditional()->beginFrontals(); it!=clique->conditional()->endFrontals(); it++) {
-      originalValues[it - clique->conditional()->beginFrontals()] = delta[*it];
-    }
-
-    // Back-substitute
-    delta.update(clique->conditional()->solve(delta));
-    count += clique->conditional()->nrFrontals();
-
-    // Whether the values changed above a threshold, or always true if the
-    // clique was replaced.
-    bool valuesChanged = cliqueReplaced;
-    for(it = clique->conditional()->beginFrontals(); it != clique->conditional()->endFrontals(); it++) {
-      if(!valuesChanged) {
-        const Vector& oldValue(originalValues[it - clique->conditional()->beginFrontals()]);
-        const Vector& newValue(delta[*it]);
-        if((oldValue - newValue).lpNorm<Eigen::Infinity>() >= threshold) {
-          valuesChanged = true;
-          break;
-        }
-      } else
-        break;
-    }
-
-    // If the values were above the threshold or this clique was replaced
-    if(valuesChanged) {
-      // Set changed flag for each frontal variable and leave the new values
-      for(Key frontal: clique->conditional()->frontals()) {
-        changed.insert(frontal);
-      }
-    } else {
-      // Replace with the old values
-      for(it = clique->conditional()->beginFrontals(); it != clique->conditional()->endFrontals(); it++) {
-        delta[*it] = originalValues[it - clique->conditional()->beginFrontals()];
-      }
-    }
-
-    // Recurse to children
-    for(const typename CLIQUE::shared_ptr& child: clique->children) {
-      optimizeWildfire(child, threshold, changed, replaced, delta, count);
-    }
-  }
-}
-
-template<class CLIQUE>
-bool optimizeWildfireNode(const boost::shared_ptr<CLIQUE>& clique, double threshold,
-    KeySet& changed, const KeySet& replaced, VectorValues& delta, size_t& count)
-{
-  // if none of the variables in this clique (frontal and separator!) changed
-  // significantly, then by the running intersection property, none of the
-  // cliques in the children need to be processed
-
-  // Are any clique variables part of the tree that has been redone?
-  bool cliqueReplaced = replaced.exists(clique->conditional()->frontals().front());
-#ifdef GTSAM_EXTRA_CONSISTENCY_CHECKS
-  for(Key frontal: clique->conditional()->frontals()) {
-    assert(cliqueReplaced == replaced.exists(frontal));
-  }
-#endif
-
-  // If not redone, then has one of the separator variables changed significantly?
-  bool recalculate = cliqueReplaced;
-  if(!recalculate) {
-    for(Key parent: clique->conditional()->parents()) {
-      if(changed.exists(parent)) {
-        recalculate = true;
-        break;
-      }
-    }
-  }
-
-  // Solve clique if it was replaced, or if any parents were changed above the
-  // threshold or themselves replaced.
-  // TODO(gareth): This code shares a lot of logic w/ linearAlgorithms-inst, potentially refactor
-  if(recalculate)
-  {
-    // Temporary copy of the original values, to check how much they change
-    FastVector<Vector> originalValues(clique->conditional()->nrFrontals());
-    GaussianConditional::const_iterator it;
-    for(it = clique->conditional()->beginFrontals(); it != clique->conditional()->endFrontals(); it++) {
-      originalValues[it - clique->conditional()->beginFrontals()] = delta[*it];
-    }
-
-    // Back-substitute - special version stores solution pointers in cliques for fast access.
-    {
-      // Create solution part pointers if necessary and possible - necessary if solnPointers_ is
-      // empty, and possible if either we're a root, or we have a parent with valid solnPointers_.
-      boost::shared_ptr<CLIQUE> parent = clique->parent_.lock();
-      if(clique->solnPointers_.empty() && (clique->isRoot() || !parent->solnPointers_.empty()))
-      {
-        for(Key key: clique->conditional()->frontals())
-          clique->solnPointers_.insert(std::make_pair(key, delta.find(key)));
-        for(Key key: clique->conditional()->parents())
-          clique->solnPointers_.insert(std::make_pair(key, parent->solnPointers_.at(key)));
-      }
-
-      // See if we can use solution part pointers - we can if they either already existed or were
-      // created above.
-      if(!clique->solnPointers_.empty())
-      {
-        GaussianConditional& c = *clique->conditional();
-        // Solve matrix
-        Vector xS;
-        {
-          // Count dimensions of vector
-          DenseIndex dim = 0;
-          FastVector<VectorValues::const_iterator> parentPointers;
-          parentPointers.reserve(clique->conditional()->nrParents());
-          for(Key parent: clique->conditional()->parents()) {
-            parentPointers.push_back(clique->solnPointers_.at(parent));
-            dim += parentPointers.back()->second.size();
-          }
-
-          // Fill parent vector
-          xS.resize(dim);
-          DenseIndex vectorPos = 0;
-          for(const VectorValues::const_iterator& parentPointer: parentPointers) {
-            const Vector& parentVector = parentPointer->second;
-            xS.block(vectorPos,0,parentVector.size(),1) = parentVector.block(0,0,parentVector.size(),1);
-            vectorPos += parentVector.size();
-          }
-        }
-
-        // NOTE(gareth): We can no longer write: xS = b - S * xS
-        // This is because Eigen (as of 3.3) no longer evaluates S * xS into
-        // a temporary, and the operation trashes valus in xS.
-        // See: http://eigen.tuxfamily.org/index.php?title=3.3
-        const Vector rhs = c.getb() - c.get_S() * xS;
-        const Vector solution = c.get_R().triangularView<Eigen::Upper>().solve(rhs);
-
-        // Check for indeterminant solution
-        if(solution.hasNaN()) throw IndeterminantLinearSystemException(c.keys().front());
-
-        // Insert solution into a VectorValues
-        DenseIndex vectorPosition = 0;
-        for(GaussianConditional::const_iterator frontal = c.beginFrontals(); frontal != c.endFrontals(); ++frontal) {
-          clique->solnPointers_.at(*frontal)->second = solution.segment(vectorPosition, c.getDim(frontal));
-          vectorPosition += c.getDim(frontal);
-        }
-      }
-      else
-      {
-        // Just call plain solve because we couldn't use solution pointers.
-        delta.update(clique->conditional()->solve(delta));
-      }
-    }
-    count += clique->conditional()->nrFrontals();
-
-    // Whether the values changed above a threshold, or always true if the
-    // clique was replaced.
-    bool valuesChanged = cliqueReplaced;
-    for(it = clique->conditional()->beginFrontals(); it != clique->conditional()->endFrontals(); it++) {
-      if(!valuesChanged) {
-        const Vector& oldValue(originalValues[it - clique->conditional()->beginFrontals()]);
-        const Vector& newValue(delta[*it]);
-        if((oldValue - newValue).lpNorm<Eigen::Infinity>() >= threshold) {
-          valuesChanged = true;
-          break;
-        }
-      } else
-        break;
-    }
-
-    // If the values were above the threshold or this clique was replaced
-    if(valuesChanged) {
-      // Set changed flag for each frontal variable and leave the new values
-      for(Key frontal: clique->conditional()->frontals()) {
-        changed.insert(frontal);
-      }
-    } else {
-      // Replace with the old values
-      for(it = clique->conditional()->beginFrontals(); it != clique->conditional()->endFrontals(); it++) {
-        delta[*it] = originalValues[it - clique->conditional()->beginFrontals()];
-      }
-    }
-  }
-
-  return recalculate;
-}
-
-} // namespace internal
-
-/* ************************************************************************* */
-template<class CLIQUE>
-size_t optimizeWildfire(const boost::shared_ptr<CLIQUE>& root, double threshold, const KeySet& keys, VectorValues& delta) {
-  KeySet changed;
-  int count = 0;
-  // starting from the root, call optimize on each conditional
-  if(root)
-    internal::optimizeWildfire(root, threshold, changed, keys, delta, count);
-  return count;
-}
-
-/* ************************************************************************* */
-template<class CLIQUE>
-size_t optimizeWildfireNonRecursive(const boost::shared_ptr<CLIQUE>& root, double threshold, const KeySet& keys, VectorValues& delta)
-{
-  KeySet changed;
-  size_t count = 0;
-
-  if (root) {
-    std::stack<boost::shared_ptr<CLIQUE> > travStack;
-    travStack.push(root);
-    boost::shared_ptr<CLIQUE> currentNode = root;
-    while (!travStack.empty()) {
-      currentNode = travStack.top();
-      travStack.pop();
-      bool recalculate = internal::optimizeWildfireNode(currentNode, threshold, changed, keys, delta, count);
-      if (recalculate) {
-        for(const typename CLIQUE::shared_ptr& child: currentNode->children) {
-          travStack.push(child);
-        }
-      }
-    }
-  }
-
-  return count;
-}
-
-/* ************************************************************************* */
-template<class CLIQUE>
-void nnz_internal(const boost::shared_ptr<CLIQUE>& clique, int& result) {
-  int dimR = (int)clique->conditional()->rows();
-  int dimSep = (int)clique->conditional()->get_S().cols();
-  result += ((dimR+1)*dimR)/2 + dimSep*dimR;
-  // traverse the children
-  for(const typename CLIQUE::shared_ptr& child: clique->children) {
-    nnz_internal(child, result);
-  }
-}
-
-/* ************************************************************************* */
-template<class CLIQUE>
-int calculate_nnz(const boost::shared_ptr<CLIQUE>& clique) {
-  int result = 0;
-  // starting from the root, add up entries of frontal and conditional matrices of each conditional
-  nnz_internal(clique, result);
-  return result;
-}
-
-}
-

gtsam/nonlinear/ISAM2.h

@@ -11,438 +11,47 @@
 
 /**
  * @file    ISAM2.h
- * @brief   Incremental update functionality (ISAM2) for BayesTree, with fluid relinearization.
+ * @brief   Incremental update functionality (ISAM2) for BayesTree, with fluid
- * @author  Michael Kaess, Richard Roberts
+ * relinearization.
+ * @author  Michael Kaess, Richard Roberts, Frank Dellaert
  */
 
 // \callgraph
 
 #pragma once
 
+#include <gtsam/nonlinear/ISAM2Params.h>
+#include <gtsam/nonlinear/ISAM2Result.h>
+#include <gtsam/nonlinear/ISAM2Clique.h>
 #include <gtsam/nonlinear/NonlinearFactorGraph.h>
-#include <gtsam/nonlinear/DoglegOptimizerImpl.h>
 #include <gtsam/linear/GaussianBayesTree.h>
 
-#include <boost/variant.hpp>
+#include <vector>
 
 namespace gtsam {
 
 /**
  * @addtogroup ISAM2
- * Parameters for ISAM2 using Gauss-Newton optimization.  Either this class or
+ * Implementation of the full ISAM2 algorithm for incremental nonlinear
- * ISAM2DoglegParams should be specified as the optimizationParams in
+ * optimization.
- * ISAM2Params, which should in turn be passed to ISAM2(const ISAM2Params&).
- */
-struct GTSAM_EXPORT ISAM2GaussNewtonParams {
-  double wildfireThreshold; ///< Continue updating the linear delta only when changes are above this threshold (default: 0.001)
-
-  /** Specify parameters as constructor arguments */
-  ISAM2GaussNewtonParams(
-      double _wildfireThreshold = 0.001 ///< see ISAM2GaussNewtonParams public variables, ISAM2GaussNewtonParams::wildfireThreshold
-  ) : wildfireThreshold(_wildfireThreshold) {}
-
-  void print(const std::string str = "") const {
-    std::cout << str << "type:              ISAM2GaussNewtonParams\n";
-    std::cout << str << "wildfireThreshold: " << wildfireThreshold << "\n";
-    std::cout.flush();
-  }
-
-  double getWildfireThreshold() const { return wildfireThreshold; }
-  void setWildfireThreshold(double wildfireThreshold) { this->wildfireThreshold = wildfireThreshold; }
-};
-
-/**
- * @addtogroup ISAM2
- * Parameters for ISAM2 using Dogleg optimization.  Either this class or
- * ISAM2GaussNewtonParams should be specified as the optimizationParams in
- * ISAM2Params, which should in turn be passed to ISAM2(const ISAM2Params&).
- */
-struct GTSAM_EXPORT ISAM2DoglegParams {
-  double initialDelta; ///< The initial trust region radius for Dogleg
-  double wildfireThreshold; ///< Continue updating the linear delta only when changes are above this threshold (default: 1e-5)
-  DoglegOptimizerImpl::TrustRegionAdaptationMode adaptationMode; ///< See description in DoglegOptimizerImpl::TrustRegionAdaptationMode
-  bool verbose; ///< Whether Dogleg prints iteration and convergence information
-
-  /** Specify parameters as constructor arguments */
-  ISAM2DoglegParams(
-      double _initialDelta = 1.0, ///< see ISAM2DoglegParams::initialDelta
-      double _wildfireThreshold = 1e-5, ///< see ISAM2DoglegParams::wildfireThreshold
-      DoglegOptimizerImpl::TrustRegionAdaptationMode _adaptationMode = DoglegOptimizerImpl::SEARCH_EACH_ITERATION, ///< see ISAM2DoglegParams::adaptationMode
-      bool _verbose = false ///< see ISAM2DoglegParams::verbose
-  ) : initialDelta(_initialDelta), wildfireThreshold(_wildfireThreshold),
-  adaptationMode(_adaptationMode), verbose(_verbose) {}
-
-  void print(const std::string str = "") const {
-    std::cout << str << "type:              ISAM2DoglegParams\n";
-    std::cout << str << "initialDelta:      " << initialDelta << "\n";
-    std::cout << str << "wildfireThreshold: " << wildfireThreshold << "\n";
-    std::cout << str << "adaptationMode:    " << adaptationModeTranslator(adaptationMode) << "\n";
-    std::cout.flush();
-  }
-
-  double getInitialDelta() const { return initialDelta; }
-  double getWildfireThreshold() const { return wildfireThreshold; }
-  std::string getAdaptationMode() const { return adaptationModeTranslator(adaptationMode); };
-  bool isVerbose() const { return verbose; };
-
-  void setInitialDelta(double initialDelta) { this->initialDelta = initialDelta; }
-  void setWildfireThreshold(double wildfireThreshold) { this->wildfireThreshold = wildfireThreshold; }
-  void setAdaptationMode(const std::string& adaptationMode) { this->adaptationMode = adaptationModeTranslator(adaptationMode); }
-  void setVerbose(bool verbose) { this->verbose = verbose; };
-
-  std::string adaptationModeTranslator(const DoglegOptimizerImpl::TrustRegionAdaptationMode& adaptationMode) const;
-  DoglegOptimizerImpl::TrustRegionAdaptationMode adaptationModeTranslator(const std::string& adaptationMode) const;
-};
-
-/**
- * @addtogroup ISAM2
- * Parameters for the ISAM2 algorithm.  Default parameter values are listed below.
- */
-typedef FastMap<char,Vector> ISAM2ThresholdMap;
-typedef ISAM2ThresholdMap::value_type ISAM2ThresholdMapValue;
-struct GTSAM_EXPORT ISAM2Params {
-  typedef boost::variant<ISAM2GaussNewtonParams, ISAM2DoglegParams> OptimizationParams; ///< Either ISAM2GaussNewtonParams or ISAM2DoglegParams
-  typedef boost::variant<double, FastMap<char,Vector> > RelinearizationThreshold; ///< Either a constant relinearization threshold or a per-variable-type set of thresholds
-
-  /** Optimization parameters, this both selects the nonlinear optimization
-   * method and specifies its parameters, either ISAM2GaussNewtonParams or
-   * ISAM2DoglegParams.  In the former, Gauss-Newton optimization will be used
-   * with the specified parameters, and in the latter Powell's dog-leg
-   * algorithm will be used with the specified parameters.
-   */
-  OptimizationParams optimizationParams;
-
-  /** Only relinearize variables whose linear delta magnitude is greater than
-   * this threshold (default: 0.1).  If this is a FastMap<char,Vector> instead
-   * of a double, then the threshold is specified for each dimension of each
-   * variable type.  This parameter then maps from a character indicating the
-   * variable type to a Vector of thresholds for each dimension of that
-   * variable.  For example, if Pose keys are of type TypedSymbol<'x',Pose3>,
-   * and landmark keys are of type TypedSymbol<'l',Point3>, then appropriate
-   * entries would be added with:
-   * \code
-     FastMap<char,Vector> thresholds;
-     thresholds['x'] = (Vector(6) << 0.1, 0.1, 0.1, 0.5, 0.5, 0.5).finished(); // 0.1 rad rotation threshold, 0.5 m translation threshold
-     thresholds['l'] = Vector3(1.0, 1.0, 1.0);                // 1.0 m landmark position threshold
-     params.relinearizeThreshold = thresholds;
-     \endcode
-   */
-  RelinearizationThreshold relinearizeThreshold;
-
-  int relinearizeSkip; ///< Only relinearize any variables every relinearizeSkip calls to ISAM2::update (default: 10)
-
-  bool enableRelinearization; ///< Controls whether ISAM2 will ever relinearize any variables (default: true)
-
-  bool evaluateNonlinearError; ///< Whether to evaluate the nonlinear error before and after the update, to return in ISAM2Result from update()
-
-  enum Factorization { CHOLESKY, QR };
-  /** Specifies whether to use QR or CHOESKY numerical factorization (default: CHOLESKY).
-   * Cholesky is faster but potentially numerically unstable for poorly-conditioned problems, which can occur when
-   * uncertainty is very low in some variables (or dimensions of variables) and very high in others.  QR is
-   * slower but more numerically stable in poorly-conditioned problems.  We suggest using the default of Cholesky
-   * unless gtsam sometimes throws IndefiniteLinearSystemException when your problem's Hessian is actually positive
-   * definite.  For positive definite problems, numerical error accumulation can cause the problem to become
-   * numerically negative or indefinite as solving proceeds, especially when using Cholesky.
-   */
-  Factorization factorization;
-
-  /** Whether to cache linear factors (default: true).
-   * This can improve performance if linearization is expensive, but can hurt
-   * performance if linearization is very cleap due to computation to look up
-   * additional keys.
-   */
-  bool cacheLinearizedFactors;
-
-  KeyFormatter keyFormatter; ///< A KeyFormatter for when keys are printed during debugging (default: DefaultKeyFormatter)
-
-  bool enableDetailedResults; ///< Whether to compute and return ISAM2Result::detailedResults, this can increase running time (default: false)
-
-  /** Check variables for relinearization in tree-order, stopping the check once a variable does not need to be relinearized (default: false).
-   * This can improve speed by only checking a small part of the top of the tree. However, variables below the check cut-off can accumulate
-   * significant deltas without triggering relinearization. This is particularly useful in exploration scenarios where real-time performance
-   * is desired over correctness. Use with caution.
-   */
-  bool enablePartialRelinearizationCheck;
-
-  /// When you will be removing many factors, e.g. when using ISAM2 as a fixed-lag smoother, enable this option to
-  /// add factors in the first available factor slots, to avoid accumulating NULL factor slots, at the cost of
-  /// having to search for slots every time a factor is added.
-  bool findUnusedFactorSlots;
-
-  /** Specify parameters as constructor arguments */
-  ISAM2Params(
-      OptimizationParams _optimizationParams = ISAM2GaussNewtonParams(), ///< see ISAM2Params::optimizationParams
-      RelinearizationThreshold _relinearizeThreshold = 0.1, ///< see ISAM2Params::relinearizeThreshold
-      int _relinearizeSkip = 10, ///< see ISAM2Params::relinearizeSkip
-      bool _enableRelinearization = true, ///< see ISAM2Params::enableRelinearization
-      bool _evaluateNonlinearError = false, ///< see ISAM2Params::evaluateNonlinearError
-      Factorization _factorization = ISAM2Params::CHOLESKY, ///< see ISAM2Params::factorization
-      bool _cacheLinearizedFactors = true, ///< see ISAM2Params::cacheLinearizedFactors
-      const KeyFormatter& _keyFormatter = DefaultKeyFormatter ///< see ISAM2::Params::keyFormatter
-  ) : optimizationParams(_optimizationParams), relinearizeThreshold(_relinearizeThreshold),
-      relinearizeSkip(_relinearizeSkip), enableRelinearization(_enableRelinearization),
-      evaluateNonlinearError(_evaluateNonlinearError), factorization(_factorization),
-      cacheLinearizedFactors(_cacheLinearizedFactors), keyFormatter(_keyFormatter),
-      enableDetailedResults(false), enablePartialRelinearizationCheck(false),
-      findUnusedFactorSlots(false) {}
-
-  /// print iSAM2 parameters
-  void print(const std::string& str = "") const {
-    std::cout << str << "\n";
-    if(optimizationParams.type() == typeid(ISAM2GaussNewtonParams))
-      boost::get<ISAM2GaussNewtonParams>(optimizationParams).print("optimizationParams:                ");
-    else if(optimizationParams.type() == typeid(ISAM2DoglegParams))
-      boost::get<ISAM2DoglegParams>(optimizationParams).print("optimizationParams:                ");
-    else
-      std::cout << "optimizationParams:                " << "{unknown type}" << "\n";
-    if(relinearizeThreshold.type() == typeid(double))
-      std::cout << "relinearizeThreshold:              " << boost::get<double>(relinearizeThreshold) << "\n";
-    else
-    {
-      std::cout << "relinearizeThreshold:              " << "{mapped}" << "\n";
-      for(const ISAM2ThresholdMapValue& value: boost::get<ISAM2ThresholdMap>(relinearizeThreshold)) {
-        std::cout << "                                   '" << value.first << "' -> [" << value.second.transpose() << " ]\n";
-      }
-    }
-    std::cout << "relinearizeSkip:                   " << relinearizeSkip << "\n";
-    std::cout << "enableRelinearization:             " << enableRelinearization << "\n";
-    std::cout << "evaluateNonlinearError:            " << evaluateNonlinearError << "\n";
-    std::cout << "factorization:                     " << factorizationTranslator(factorization) << "\n";
-    std::cout << "cacheLinearizedFactors:            " << cacheLinearizedFactors << "\n";
-    std::cout << "enableDetailedResults:             " << enableDetailedResults << "\n";
-    std::cout << "enablePartialRelinearizationCheck: " << enablePartialRelinearizationCheck << "\n";
-    std::cout << "findUnusedFactorSlots:             " << findUnusedFactorSlots << "\n";
-    std::cout.flush();
-  }
-
-  /// @name Getters and Setters for all properties
-  /// @{
-
-  OptimizationParams getOptimizationParams() const { return this->optimizationParams; }
-  RelinearizationThreshold getRelinearizeThreshold() const { return relinearizeThreshold; }
-  int getRelinearizeSkip() const { return relinearizeSkip; }
-  bool isEnableRelinearization() const { return enableRelinearization; }
-  bool isEvaluateNonlinearError() const { return evaluateNonlinearError; }
-  std::string getFactorization() const { return factorizationTranslator(factorization); }
-  bool isCacheLinearizedFactors() const { return cacheLinearizedFactors; }
-  KeyFormatter getKeyFormatter() const { return keyFormatter; }
-  bool isEnableDetailedResults() const { return enableDetailedResults; }
-  bool isEnablePartialRelinearizationCheck() const { return enablePartialRelinearizationCheck; }
-
-  void setOptimizationParams(OptimizationParams optimizationParams) { this->optimizationParams = optimizationParams; }
-  void setRelinearizeThreshold(RelinearizationThreshold relinearizeThreshold) { this->relinearizeThreshold = relinearizeThreshold; }
-  void setRelinearizeSkip(int relinearizeSkip) { this->relinearizeSkip = relinearizeSkip; }
-  void setEnableRelinearization(bool enableRelinearization) { this->enableRelinearization = enableRelinearization; }
-  void setEvaluateNonlinearError(bool evaluateNonlinearError) { this->evaluateNonlinearError = evaluateNonlinearError; }
-  void setFactorization(const std::string& factorization) { this->factorization = factorizationTranslator(factorization); }
-  void setCacheLinearizedFactors(bool cacheLinearizedFactors) { this->cacheLinearizedFactors = cacheLinearizedFactors; }
-  void setKeyFormatter(KeyFormatter keyFormatter) { this->keyFormatter = keyFormatter; }
-  void setEnableDetailedResults(bool enableDetailedResults) { this->enableDetailedResults = enableDetailedResults; }
-  void setEnablePartialRelinearizationCheck(bool enablePartialRelinearizationCheck) { this->enablePartialRelinearizationCheck = enablePartialRelinearizationCheck; }
-
-  GaussianFactorGraph::Eliminate getEliminationFunction() const {
-    return factorization == CHOLESKY
-      ? (GaussianFactorGraph::Eliminate)EliminatePreferCholesky
-      : (GaussianFactorGraph::Eliminate)EliminateQR;
-  }
-
-  /// @}
-
-  /// @name Some utilities
-  /// @{
-
-  static Factorization factorizationTranslator(const std::string& str);
-  static std::string factorizationTranslator(const Factorization& value);
-
-  /// @}
-};
-
-typedef FastVector<size_t> FactorIndices;
-
-/**
- * @addtogroup ISAM2
- * This struct is returned from ISAM2::update() and contains information about
- * the update that is useful for determining whether the solution is
- * converging, and about how much work was required for the update.  See member
- * variables for details and information about each entry.
- */
-struct GTSAM_EXPORT ISAM2Result {
-  /** The nonlinear error of all of the factors, \a including new factors and
-   * variables added during the current call to ISAM2::update().  This error is
-   * calculated using the following variable values:
-   * \li Pre-existing variables will be evaluated by combining their
-   * linearization point before this call to update, with their partial linear
-   * delta, as computed by ISAM2::calculateEstimate().
-   * \li New variables will be evaluated at their initialization points passed
-   * into the current call to update.
-   * \par Note: This will only be computed if ISAM2Params::evaluateNonlinearError
-   * is set to \c true, because there is some cost to this computation.
-   */
-  boost::optional<double> errorBefore;
-
-  /** The nonlinear error of all of the factors computed after the current
-   * update, meaning that variables above the relinearization threshold
-   * (ISAM2Params::relinearizeThreshold) have been relinearized and new
-   * variables have undergone one linear update.  Variable values are
-   * again computed by combining their linearization points with their
-   * partial linear deltas, by ISAM2::calculateEstimate().
-   * \par Note: This will only be computed if ISAM2Params::evaluateNonlinearError
-   * is set to \c true, because there is some cost to this computation.
-   */
-  boost::optional<double> errorAfter;
-
-  /** The number of variables that were relinearized because their linear
-   * deltas exceeded the reslinearization threshold
-   * (ISAM2Params::relinearizeThreshold), combined with any additional
-   * variables that had to be relinearized because they were involved in
-   * the same factor as a variable above the relinearization threshold.
-   * On steps where no relinearization is considered
-   * (see ISAM2Params::relinearizeSkip), this count will be zero.
-   */
-  size_t variablesRelinearized;
-
-  /** The number of variables that were reeliminated as parts of the Bayes'
-   * Tree were recalculated, due to new factors.  When loop closures occur,
-   * this count will be large as the new loop-closing factors will tend to
-   * involve variables far away from the root, and everything up to the root
-   * will be reeliminated.
-   */
-  size_t variablesReeliminated;
-
-  /** The number of factors that were included in reelimination of the Bayes' tree. */
-  size_t factorsRecalculated;
-
-  /** The number of cliques in the Bayes' Tree */
-  size_t cliques;
-
-  /** The indices of the newly-added factors, in 1-to-1 correspondence with the
-   * factors passed as \c newFactors to ISAM2::update().  These indices may be
-   * used later to refer to the factors in order to remove them.
-   */
-  FactorIndices newFactorsIndices;
-
-  /** A struct holding detailed results, which must be enabled with
-   * ISAM2Params::enableDetailedResults.
-   */
-  struct DetailedResults {
-    /** The status of a single variable, this struct is stored in
-     * DetailedResults::variableStatus */
-    struct VariableStatus {
-      /** Whether the variable was just reeliminated, due to being relinearized,
-       * observed, new, or on the path up to the root clique from another
-       * reeliminated variable. */
-      bool isReeliminated;
-      bool isAboveRelinThreshold; ///< Whether the variable was just relinearized due to being above the relinearization threshold
-      bool isRelinearizeInvolved; ///< Whether the variable was below the relinearization threshold but was relinearized by being involved in a factor with a variable above the relinearization threshold
-      bool isRelinearized; /// Whether the variable was relinearized, either by being above the relinearization threshold or by involvement.
-      bool isObserved; ///< Whether the variable was just involved in new factors
-      bool isNew; ///< Whether the variable itself was just added
-      bool inRootClique; ///< Whether the variable is in the root clique
-      VariableStatus(): isReeliminated(false), isAboveRelinThreshold(false), isRelinearizeInvolved(false),
-          isRelinearized(false), isObserved(false), isNew(false), inRootClique(false) {}
-    };
-
-    /** The status of each variable during this update, see VariableStatus.
-     */
-    FastMap<Key, VariableStatus> variableStatus;
-  };
-
-  /** Detailed results, if enabled by ISAM2Params::enableDetailedResults.  See
-   * Detail for information about the results data stored here. */
-  boost::optional<DetailedResults> detail;
-
-
-  void print(const std::string str = "") const {
-    std::cout << str << "  Reelimintated: " << variablesReeliminated << "  Relinearized: " << variablesRelinearized << "  Cliques: " << cliques << std::endl;
-  }
-
-  /** Getters and Setters */
-  size_t getVariablesRelinearized() const { return variablesRelinearized; };
-  size_t getVariablesReeliminated() const { return variablesReeliminated; };
-  size_t getCliques() const { return cliques; };
-};
-
-/**
- * Specialized Clique structure for ISAM2, incorporating caching and gradient contribution
- * TODO: more documentation
- */
-class GTSAM_EXPORT ISAM2Clique : public BayesTreeCliqueBase<ISAM2Clique, GaussianFactorGraph>
-{
-public:
-  typedef ISAM2Clique This;
-  typedef BayesTreeCliqueBase<This, GaussianFactorGraph> Base;
-  typedef boost::shared_ptr<This> shared_ptr;
-  typedef boost::weak_ptr<This> weak_ptr;
-  typedef GaussianConditional ConditionalType;
-  typedef ConditionalType::shared_ptr sharedConditional;
-
-  Base::FactorType::shared_ptr cachedFactor_;
-  Vector gradientContribution_;
-  FastMap<Key, VectorValues::iterator> solnPointers_;
-
-  /// Default constructor
-  ISAM2Clique() : Base() {}
-
-  /// Copy constructor, does *not* copy solution pointers as these are invalid in different trees.
-  ISAM2Clique(const ISAM2Clique& other) :
-    Base(other), cachedFactor_(other.cachedFactor_), gradientContribution_(other.gradientContribution_) {}
-
-  /// Assignment operator, does *not* copy solution pointers as these are invalid in different trees.
-  ISAM2Clique& operator=(const ISAM2Clique& other)
-  {
-    Base::operator=(other);
-    cachedFactor_ = other.cachedFactor_;
-    gradientContribution_ = other.gradientContribution_;
-    return *this;
-  }
-
-  /// Overridden to also store the remaining factor and gradient contribution
-  void setEliminationResult(const FactorGraphType::EliminationResult& eliminationResult);
-
-  /** Access the cached factor */
-  Base::FactorType::shared_ptr& cachedFactor() { return cachedFactor_; }
-
-  /** Access the gradient contribution */
-  const Vector& gradientContribution() const { return gradientContribution_; }
-
-  bool equals(const This& other, double tol=1e-9) const;
-
-  /** print this node */
-  void print(const std::string& s = "", const KeyFormatter& formatter = DefaultKeyFormatter) const;
-
-private:
-
-  /** Serialization function */
-  friend class boost::serialization::access;
-  template<class ARCHIVE>
-  void serialize(ARCHIVE & ar, const unsigned int /*version*/) {
-    ar & BOOST_SERIALIZATION_BASE_OBJECT_NVP(Base);
-    ar & BOOST_SERIALIZATION_NVP(cachedFactor_);
-    ar & BOOST_SERIALIZATION_NVP(gradientContribution_);
-  }
-}; // \struct ISAM2Clique
-
-/**
- * @addtogroup ISAM2
- * Implementation of the full ISAM2 algorithm for incremental nonlinear optimization.
  *
- * The typical cycle of using this class to create an instance by providing ISAM2Params
+ * The typical cycle of using this class to create an instance by providing
- * to the constructor, then add measurements and variables as they arrive using the update()
+ * ISAM2Params to the constructor, then add measurements and variables as they
- * method.  At any time, calculateEstimate() may be called to obtain the current
+ * arrive using the update() method.  At any time, calculateEstimate() may be
- * estimate of all variables.
+ * called to obtain the current estimate of all variables.
  *
  */
-class GTSAM_EXPORT ISAM2: public BayesTree<ISAM2Clique> {
+class GTSAM_EXPORT ISAM2 : public BayesTree<ISAM2Clique> {
-
+ protected:
-protected:
-
   /** The current linearization point */
   Values theta_;
 
-  /** VariableIndex lets us look up factors by involved variable and keeps track of dimensions */
+  /** VariableIndex lets us look up factors by involved variable and keeps track
+   * of dimensions */
   VariableIndex variableIndex_;
 
-  /** The linear delta from the last linear solution, an update to the estimate in theta
+  /** The linear delta from the last linear solution, an update to the estimate
+   * in theta
    *
    * This is \c mutable because it is a "cached" variable - it is not updated
    * until either requested with getDelta() or calculateEstimate(), or needed
@@ -450,8 +59,10 @@ protected:
    */
   mutable VectorValues delta_;
 
-  mutable VectorValues deltaNewton_; // Only used when using Dogleg - stores the Gauss-Newton update
+  mutable VectorValues deltaNewton_;  // Only used when using Dogleg - stores
-  mutable VectorValues RgProd_; // Only used when using Dogleg - stores R*g and is updated incrementally
+                                      // the Gauss-Newton update
+  mutable VectorValues RgProd_;  // Only used when using Dogleg - stores R*g and
+                                 // is updated incrementally
 
   /** A cumulative mask for the variables that were replaced and have not yet
    * been updated in the linear solution delta_, this is only used internally,
@@ -461,9 +72,11 @@ protected:
    * This is \c mutable because it is used internally to not update delta_
    * until it is needed.
    */
-  mutable KeySet deltaReplacedMask_; // TODO: Make sure accessed in the right way
+  mutable KeySet
+      deltaReplacedMask_;  // TODO(dellaert): Make sure accessed in the right way
 
-  /** All original nonlinear factors are stored here to use during relinearization */
+  /** All original nonlinear factors are stored here to use during
+   * relinearization */
   NonlinearFactorGraph nonlinearFactors_;
 
   /** The current linear factors, which are only updated as needed */
@@ -479,10 +92,10 @@ protected:
    * variables and thus cannot have their linearization points changed. */
   KeySet fixedVariables_;
 
-  int update_count_; ///< Counter incremented every update(), used to determine periodic relinearization
+  int update_count_;  ///< Counter incremented every update(), used to determine
-
+                      ///< periodic relinearization
-public:
 
+ public:
   typedef ISAM2 This;                       ///< This class
   typedef BayesTree<ISAM2Clique> Base;      ///< The BayesTree base class
   typedef Base::Clique Clique;              ///< A clique
@@ -490,9 +103,10 @@ public:
   typedef Base::Cliques Cliques;  ///< List of Clique typedef from base class
 
   /** Create an empty ISAM2 instance */
-  ISAM2(const ISAM2Params& params);
+  explicit ISAM2(const ISAM2Params& params);
 
-  /** Create an empty ISAM2 instance using the default set of parameters (see ISAM2Params) */
+  /** Create an empty ISAM2 instance using the default set of parameters (see
+   * ISAM2Params) */
   ISAM2();
 
   /** default virtual destructor */
@@ -513,26 +127,31 @@ public:
    * thresholds.
    *
    * @param newFactors The new factors to be added to the system
-   * @param newTheta Initialization points for new variables to be added to the system.
+   * @param newTheta Initialization points for new variables to be added to the
-   * You must include here all new variables occuring in newFactors (which were not already
+   * system. You must include here all new variables occuring in newFactors
-   * in the system).  There must not be any variables here that do not occur in newFactors,
+   * (which were not already in the system).  There must not be any variables
-   * and additionally, variables that were already in the system must not be included here.
+   * here that do not occur in newFactors, and additionally, variables that were
+   * already in the system must not be included here.
    * @param removeFactorIndices Indices of factors to remove from system
-   * @param force_relinearize Relinearize any variables whose delta magnitude is sufficiently
+   * @param force_relinearize Relinearize any variables whose delta magnitude is
-   * large (Params::relinearizeThreshold), regardless of the relinearization interval
+   * sufficiently large (Params::relinearizeThreshold), regardless of the
-   * (Params::relinearizeSkip).
+   * relinearization interval (Params::relinearizeSkip).
-   * @param constrainedKeys is an optional map of keys to group labels, such that a variable can
+   * @param constrainedKeys is an optional map of keys to group labels, such
-   * be constrained to a particular grouping in the BayesTree
+   * that a variable can be constrained to a particular grouping in the
-   * @param noRelinKeys is an optional set of nonlinear keys that iSAM2 will hold at a constant linearization
+   * BayesTree
-   * point, regardless of the size of the linear delta
+   * @param noRelinKeys is an optional set of nonlinear keys that iSAM2 will
-   * @param extraReelimKeys is an optional set of nonlinear keys that iSAM2 will re-eliminate, regardless
+   * hold at a constant linearization point, regardless of the size of the
-   * of the size of the linear delta. This allows the provided keys to be reordered.
+   * linear delta
+   * @param extraReelimKeys is an optional set of nonlinear keys that iSAM2 will
+   * re-eliminate, regardless of the size of the linear delta. This allows the
+   * provided keys to be reordered.
    * @return An ISAM2Result struct containing information about the update
    */
-  virtual ISAM2Result update(const NonlinearFactorGraph& newFactors = NonlinearFactorGraph(),
+  virtual ISAM2Result update(
+      const NonlinearFactorGraph& newFactors = NonlinearFactorGraph(),
       const Values& newTheta = Values(),
       const FactorIndices& removeFactorIndices = FactorIndices(),
-      const boost::optional<FastMap<Key,int> >& constrainedKeys = boost::none,
+      const boost::optional<FastMap<Key, int> >& constrainedKeys = boost::none,
       const boost::optional<FastList<Key> >& noRelinKeys = boost::none,
       const boost::optional<FastList<Key> >& extraReelimKeys = boost::none,
       bool force_relinearize = false);
@@ -542,48 +161,54 @@ public:
    * requested to be marginalized.  Marginalization leaves a linear
    * approximation of the marginal in the system, and the linearization points
    * of any variables involved in this linear marginal become fixed.  The set
-   * fixed variables will include any key involved with the marginalized variables
+   * fixed variables will include any key involved with the marginalized
-   * in the original factors, and possibly additional ones due to fill-in.
+   * variables in the original factors, and possibly additional ones due to
+   * fill-in.
    *
-   * If provided, 'marginalFactorsIndices' will be augmented with the factor graph
+   * If provided, 'marginalFactorsIndices' will be augmented with the factor
-   * indices of the marginal factors added during the 'marginalizeLeaves' call
+   * graph indices of the marginal factors added during the 'marginalizeLeaves'
+   * call
    *
-   * If provided, 'deletedFactorsIndices' will be augmented with the factor graph
+   * If provided, 'deletedFactorsIndices' will be augmented with the factor
-   * indices of any factor that was removed during the 'marginalizeLeaves' call
+   * graph indices of any factor that was removed during the 'marginalizeLeaves'
+   * call
    */
-  void marginalizeLeaves(const FastList<Key>& leafKeys,
+  void marginalizeLeaves(
+      const FastList<Key>& leafKeys,
       boost::optional<FactorIndices&> marginalFactorsIndices = boost::none,
       boost::optional<FactorIndices&> deletedFactorsIndices = boost::none);
 
   /// Access the current linearization point
-  const Values& getLinearizationPoint() const {
+  const Values& getLinearizationPoint() const { return theta_; }
-    return theta_;
-  }
 
   /// Check whether variable with given key exists in linearization point
-  bool valueExists(Key key) const {
+  bool valueExists(Key key) const { return theta_.exists(key); }
-    return theta_.exists(key);
-  }
 
-  /** Compute an estimate from the incomplete linear delta computed during the last update.
+  /** Compute an estimate from the incomplete linear delta computed during the
-   * This delta is incomplete because it was not updated below wildfire_threshold.  If only
+   * last update. This delta is incomplete because it was not updated below
-   * a single variable is needed, it is faster to call calculateEstimate(const KEY&).
+   * wildfire_threshold.  If only a single variable is needed, it is faster to
+   * call calculateEstimate(const KEY&).
    */
   Values calculateEstimate() const;
 
-  /** Compute an estimate for a single variable using its incomplete linear delta computed
+  /** Compute an estimate for a single variable using its incomplete linear
-   * during the last update.  This is faster than calling the no-argument version of
+   * delta computed during the last update.  This is faster than calling the
-   * calculateEstimate, which operates on all variables.
+   * no-argument version of calculateEstimate, which operates on all variables.
    * @param key
    * @return
    */
-  template<class VALUE>
+  template <class VALUE>
-  VALUE calculateEstimate(Key key) const;
+  VALUE calculateEstimate(Key key) const {
+    const Vector& delta = getDelta()[key];
+    return traits<VALUE>::Retract(theta_.at<VALUE>(key), delta);
+  }
 
-  /** Compute an estimate for a single variable using its incomplete linear delta computed
+
-   * during the last update.  This is faster than calling the no-argument version of
+  /** Compute an estimate for a single variable using its incomplete linear
-   * calculateEstimate, which operates on all variables.  This is a non-templated version
+   * delta computed during the last update.  This is faster than calling the
-   * that returns a Value base class for use with the MATLAB wrapper.
+   * no-argument version of calculateEstimate, which operates on all variables.
+   * This is a non-templated version that returns a Value base class for use
+   * with the MATLAB wrapper.
    * @param key
    * @return
    */
@@ -598,7 +223,8 @@ public:
   /** Internal implementation functions */
   struct Impl;
 
-  /** Compute an estimate using a complete delta computed by a full back-substitution.
+  /** Compute an estimate using a complete delta computed by a full
+   * back-substitution.
    */
   Values calculateBestEstimate() const;
 
@@ -609,7 +235,9 @@ public:
   double error(const VectorValues& x) const;
 
   /** Access the set of nonlinear factors */
-  const NonlinearFactorGraph& getFactorsUnsafe() const { return nonlinearFactors_; }
+  const NonlinearFactorGraph& getFactorsUnsafe() const {
+    return nonlinearFactors_;
+  }
 
   /** Access the nonlinear variable index */
   const VariableIndex& getVariableIndex() const { return variableIndex_; }
@@ -629,9 +257,10 @@ public:
   /** prints out clique statistics */
   void printStats() const { getCliqueData().getStats().print(); }
 
-  /** Compute the gradient of the energy function, \f$ \nabla_{x=0} \left\Vert \Sigma^{-1} R x - d
+  /** Compute the gradient of the energy function, \f$ \nabla_{x=0} \left\Vert
-   * \right\Vert^2 \f$, centered around zero. The gradient about zero is \f$ -R^T d \f$.  See also
+   * \Sigma^{-1} R x - d \right\Vert^2 \f$, centered around zero. The gradient
-   * gradient(const GaussianBayesNet&, const VectorValues&).
+   * about zero is \f$ -R^T d \f$.  See also gradient(const GaussianBayesNet&,
+   * const VectorValues&).
    *
    * @return A VectorValues storing the gradient.
    */
@@ -639,45 +268,48 @@ public:
 
   /// @}
 
-protected:
+ protected:
+  /**
+   * Add new variables to the ISAM2 system.
+   * @param newTheta Initial values for new variables
+   * @param theta Current solution to be augmented with new initialization
+   * @param delta Current linear delta to be augmented with zeros
+   * @param deltaNewton 
+   * @param RgProd
+   * @param keyFormatter Formatter for printing nonlinear keys during debugging
+   */
+  void addVariables(const Values& newTheta);
+
+  /**
+   * Remove variables from the ISAM2 system.
+   */
+  void removeVariables(const KeySet& unusedKeys);
+
+  /**
+   * Apply expmap to the given values, but only for indices appearing in
+   * \c mask.  Values are expmapped in-place.
+   * \param mask Mask on linear indices, only \c true entries are expmapped
+   */
+  void expmapMasked(const KeySet& mask);
 
   FastSet<Key> getAffectedFactors(const FastList<Key>& keys) const;
-  GaussianFactorGraph::shared_ptr relinearizeAffectedFactors(const FastList<Key>& affectedKeys, const KeySet& relinKeys) const;
+  GaussianFactorGraph::shared_ptr relinearizeAffectedFactors(
-  GaussianFactorGraph getCachedBoundaryFactors(Cliques& orphans);
+      const FastList<Key>& affectedKeys, const KeySet& relinKeys) const;
+  GaussianFactorGraph getCachedBoundaryFactors(const Cliques& orphans);
+
+  virtual boost::shared_ptr<KeySet> recalculate(
+      const KeySet& markedKeys, const KeySet& relinKeys,
+      const std::vector<Key>& observedKeys, const KeySet& unusedIndices,
+      const boost::optional<FastMap<Key, int> >& constrainKeys,
+      ISAM2Result* result);
 
-  virtual boost::shared_ptr<KeySet > recalculate(const KeySet& markedKeys, const KeySet& relinKeys,
-      const std::vector<Key>& observedKeys, const KeySet& unusedIndices, const boost::optional<FastMap<Key,int> >& constrainKeys, ISAM2Result& result);
   void updateDelta(bool forceFullSolve = false) const;
-
 };  // ISAM2
 
 /// traits
-template<> struct traits<ISAM2> : public Testable<ISAM2> {};
+template <>
+struct traits<ISAM2> : public Testable<ISAM2> {};
 
-/// Optimize the BayesTree, starting from the root.
+}  // namespace gtsam
-/// @param replaced Needs to contain
-/// all variables that are contained in the top of the Bayes tree that has been
-/// redone.
-/// @param delta The current solution, an offset from the linearization
-/// point.
-/// @param threshold The maximum change against the PREVIOUS delta for
-/// non-replaced variables that can be ignored, ie. the old delta entry is kept
-/// and recursive backsubstitution might eventually stop if none of the changed
-/// variables are contained in the subtree.
-/// @return The number of variables that were solved for
-template<class CLIQUE>
-size_t optimizeWildfire(const boost::shared_ptr<CLIQUE>& root,
-    double threshold, const KeySet& replaced, VectorValues& delta);
 
-template<class CLIQUE>
-size_t optimizeWildfireNonRecursive(const boost::shared_ptr<CLIQUE>& root,
-    double threshold, const KeySet& replaced, VectorValues& delta);
-
-/// calculate the number of non-zero entries for the tree starting at clique (use root for complete matrix)
-template<class CLIQUE>
-int calculate_nnz(const boost::shared_ptr<CLIQUE>& clique);
-
-} /// namespace gtsam
-
-#include <gtsam/nonlinear/ISAM2-inl.h>
 #include <gtsam/nonlinear/ISAM2-impl.h>

gtsam/nonlinear/ISAM2Clique.cpp

@@ -0,0 +1,325 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file    ISAM2Clique.cpp
+ * @brief   Specialized iSAM2 Clique
+ * @author  Michael Kaess, Richard Roberts, Frank Dellaert
+ */
+
+#include <gtsam/inference/BayesTreeCliqueBase-inst.h>
+#include <gtsam/linear/VectorValues.h>
+#include <gtsam/linear/linearAlgorithms-inst.h>
+#include <gtsam/nonlinear/ISAM2Clique.h>
+#include <stack>
+
+using namespace std;
+
+namespace gtsam {
+
+// Instantiate base class
+template class BayesTreeCliqueBase<ISAM2Clique, GaussianFactorGraph>;
+
+/* ************************************************************************* */
+void ISAM2Clique::setEliminationResult(
+    const FactorGraphType::EliminationResult& eliminationResult) {
+  conditional_ = eliminationResult.first;
+  cachedFactor_ = eliminationResult.second;
+  // Compute gradient contribution
+  gradientContribution_.resize(conditional_->cols() - 1);
+  // Rewrite -(R * P')'*d   as   -(d' * R * P')'   for computational speed
+  // reasons
+  gradientContribution_ << -conditional_->get_R().transpose() *
+                               conditional_->get_d(),
+      -conditional_->get_S().transpose() * conditional_->get_d();
+}
+
+/* ************************************************************************* */
+bool ISAM2Clique::equals(const This& other, double tol) const {
+  return Base::equals(other) &&
+         ((!cachedFactor_ && !other.cachedFactor_) ||
+          (cachedFactor_ && other.cachedFactor_ &&
+           cachedFactor_->equals(*other.cachedFactor_, tol)));
+}
+
+/* ************************************************************************* */
+void ISAM2Clique::print(const string& s, const KeyFormatter& formatter) const {
+  Base::print(s, formatter);
+  if (cachedFactor_)
+    cachedFactor_->print(s + "Cached: ", formatter);
+  else
+    cout << s << "Cached empty" << endl;
+  if (gradientContribution_.rows() != 0)
+    gtsam::print(gradientContribution_, "Gradient contribution: ");
+}
+
+/* ************************************************************************* */
+bool ISAM2Clique::isDirty(const KeySet& replaced, const KeySet& changed) const {
+  // if none of the variables in this clique (frontal and separator!) changed
+  // significantly, then by the running intersection property, none of the
+  // cliques in the children need to be processed
+
+  // Are any clique variables part of the tree that has been redone?
+  bool dirty = replaced.exists(conditional_->frontals().front());
+#if !defined(NDEBUG) && defined(GTSAM_EXTRA_CONSISTENCY_CHECKS)
+  for (Key frontal : conditional_->frontals()) {
+    assert(dirty == replaced.exists(frontal));
+  }
+#endif
+
+  // If not, then has one of the separator variables changed significantly?
+  if (!dirty) {
+    for (Key parent : conditional_->parents()) {
+      if (changed.exists(parent)) {
+        dirty = true;
+        break;
+      }
+    }
+  }
+  return dirty;
+}
+
+/* ************************************************************************* */
+/**
+ * Back-substitute - special version stores solution pointers in cliques for
+ * fast access.
+ */
+void ISAM2Clique::fastBackSubstitute(VectorValues* delta) const {
+#ifdef USE_BROKEN_FAST_BACKSUBSTITUTE
+  // TODO(gareth): This code shares a lot of logic w/ linearAlgorithms-inst,
+  // potentially refactor
+
+  // Create solution part pointers if necessary and possible - necessary if
+  // solnPointers_ is empty, and possible if either we're a root, or we have
+  // a parent with valid solnPointers_.
+  ISAM2Clique::shared_ptr parent = parent_.lock();
+  if (solnPointers_.empty() && (isRoot() || !parent->solnPointers_.empty())) {
+    for (Key frontal : conditional_->frontals())
+      solnPointers_.emplace(frontal, delta->find(frontal));
+    for (Key parentKey : conditional_->parents()) {
+      assert(parent->solnPointers_.exists(parentKey));
+      solnPointers_.emplace(parentKey, parent->solnPointers_.at(parentKey));
+    }
+  }
+
+  // See if we can use solution part pointers - we can if they either
+  // already existed or were created above.
+  if (!solnPointers_.empty()) {
+    GaussianConditional& c = *conditional_;
+    // Solve matrix
+    Vector xS;
+    {
+      // Count dimensions of vector
+      DenseIndex dim = 0;
+      FastVector<VectorValues::const_iterator> parentPointers;
+      parentPointers.reserve(conditional_->nrParents());
+      for (Key parent : conditional_->parents()) {
+        parentPointers.push_back(solnPointers_.at(parent));
+        dim += parentPointers.back()->second.size();
+      }
+
+      // Fill parent vector
+      xS.resize(dim);
+      DenseIndex vectorPos = 0;
+      for (const VectorValues::const_iterator& parentPointer : parentPointers) {
+        const Vector& parentVector = parentPointer->second;
+        xS.block(vectorPos, 0, parentVector.size(), 1) =
+            parentVector.block(0, 0, parentVector.size(), 1);
+        vectorPos += parentVector.size();
+      }
+    }
+
+    // NOTE(gareth): We can no longer write: xS = b - S * xS
+    // This is because Eigen (as of 3.3) no longer evaluates S * xS into
+    // a temporary, and the operation trashes valus in xS.
+    // See: http://eigen.tuxfamily.org/index.php?title=3.3
+    const Vector rhs = c.getb() - c.get_S() * xS;
+    const Vector solution = c.get_R().triangularView<Eigen::Upper>().solve(rhs);
+
+    // Check for indeterminant solution
+    if (solution.hasNaN())
+      throw IndeterminantLinearSystemException(c.keys().front());
+
+    // Insert solution into a VectorValues
+    DenseIndex vectorPosition = 0;
+    for (GaussianConditional::const_iterator frontal = c.beginFrontals();
+         frontal != c.endFrontals(); ++frontal) {
+      solnPointers_.at(*frontal)->second =
+          solution.segment(vectorPosition, c.getDim(frontal));
+      vectorPosition += c.getDim(frontal);
+    }
+  } else {
+    // Just call plain solve because we couldn't use solution pointers.
+    delta->update(conditional_->solve(*delta));
+  }
+#else
+  delta->update(conditional_->solve(*delta));
+#endif
+}
+
+/* ************************************************************************* */
+bool ISAM2Clique::valuesChanged(const KeySet& replaced,
+                                const Vector& originalValues,
+                                const VectorValues& delta,
+                                double threshold) const {
+  auto frontals = conditional_->frontals();
+  if (replaced.exists(frontals.front())) return true;
+  auto diff = originalValues - delta.vector(frontals);
+  return diff.lpNorm<Eigen::Infinity>() >= threshold;
+}
+
+/* ************************************************************************* */
+/// Set changed flag for each frontal variable
+void ISAM2Clique::markFrontalsAsChanged(KeySet* changed) const {
+  for (Key frontal : conditional_->frontals()) {
+    changed->insert(frontal);
+  }
+}
+
+/* ************************************************************************* */
+void ISAM2Clique::restoreFromOriginals(const Vector& originalValues,
+                                       VectorValues* delta) const {
+  size_t pos = 0;
+  for (Key frontal : conditional_->frontals()) {
+    auto v = delta->at(frontal);
+    v = originalValues.segment(pos, v.size());
+    pos += v.size();
+  }
+}
+
+/* ************************************************************************* */
+// Note: not being used right now in favor of non-recursive version below.
+void ISAM2Clique::optimizeWildfire(const KeySet& replaced, double threshold,
+                                   KeySet* changed, VectorValues* delta,
+                                   size_t* count) const {
+  if (isDirty(replaced, *changed)) {
+    // Temporary copy of the original values, to check how much they change
+    auto originalValues = delta->vector(conditional_->frontals());
+
+    // Back-substitute
+    fastBackSubstitute(delta);
+    count += conditional_->nrFrontals();
+
+    if (valuesChanged(replaced, originalValues, *delta, threshold)) {
+      markFrontalsAsChanged(changed);
+    } else {
+      restoreFromOriginals(originalValues, delta);
+    }
+
+    // Recurse to children
+    for (const auto& child : children) {
+      child->optimizeWildfire(replaced, threshold, changed, delta, count);
+    }
+  }
+}
+
+size_t optimizeWildfire(const ISAM2Clique::shared_ptr& root, double threshold,
+                        const KeySet& keys, VectorValues* delta) {
+  KeySet changed;
+  size_t count = 0;
+  // starting from the root, call optimize on each conditional
+  if (root) root->optimizeWildfire(keys, threshold, &changed, delta, &count);
+  return count;
+}
+
+/* ************************************************************************* */
+bool ISAM2Clique::optimizeWildfireNode(const KeySet& replaced, double threshold,
+                                       KeySet* changed, VectorValues* delta,
+                                       size_t* count) const {
+  // TODO(gareth): This code shares a lot of logic w/ linearAlgorithms-inst,
+  // potentially refactor
+  bool dirty = isDirty(replaced, *changed);
+  if (dirty) {
+    // Temporary copy of the original values, to check how much they change
+    auto originalValues = delta->vector(conditional_->frontals());
+
+    // Back-substitute
+    fastBackSubstitute(delta);
+    count += conditional_->nrFrontals();
+
+    if (valuesChanged(replaced, originalValues, *delta, threshold)) {
+      markFrontalsAsChanged(changed);
+    } else {
+      restoreFromOriginals(originalValues, delta);
+    }
+  }
+
+  return dirty;
+}
+
+size_t optimizeWildfireNonRecursive(const ISAM2Clique::shared_ptr& root,
+                                    double threshold, const KeySet& keys,
+                                    VectorValues* delta) {
+  KeySet changed;
+  size_t count = 0;
+
+  if (root) {
+    std::stack<ISAM2Clique::shared_ptr> travStack;
+    travStack.push(root);
+    ISAM2Clique::shared_ptr currentNode = root;
+    while (!travStack.empty()) {
+      currentNode = travStack.top();
+      travStack.pop();
+      bool dirty = currentNode->optimizeWildfireNode(keys, threshold, &changed,
+                                                     delta, &count);
+      if (dirty) {
+        for (const auto& child : currentNode->children) {
+          travStack.push(child);
+        }
+      }
+    }
+  }
+
+  return count;
+}
+
+/* ************************************************************************* */
+void ISAM2Clique::nnz_internal(size_t* result) const {
+  size_t dimR = conditional_->rows();
+  size_t dimSep = conditional_->get_S().cols();
+  *result += ((dimR + 1) * dimR) / 2 + dimSep * dimR;
+  // traverse the children
+  for (const auto& child : children) {
+    child->nnz_internal(result);
+  }
+}
+
+/* ************************************************************************* */
+size_t ISAM2Clique::calculate_nnz() const {
+  size_t result = 0;
+  nnz_internal(&result);
+  return result;
+}
+
+/* ************************************************************************* */
+void ISAM2Clique::findAll(const KeySet& markedMask, KeySet* keys) const {
+  static const bool debug = false;
+  // does the separator contain any of the variables?
+  bool found = false;
+  for (Key key : conditional()->parents()) {
+    if (markedMask.exists(key)) {
+      found = true;
+      break;
+    }
+  }
+  if (found) {
+    // then add this clique
+    keys->insert(conditional()->beginFrontals(), conditional()->endFrontals());
+    if (debug) print("Key(s) marked in clique ");
+    if (debug) cout << "so marking key " << conditional()->front() << endl;
+  }
+  for (const auto& child : children) {
+    child->findAll(markedMask, keys);
+  }
+}
+
+/* ************************************************************************* */
+}  // namespace gtsam

gtsam/nonlinear/ISAM2Clique.h

@@ -0,0 +1,174 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file    ISAM2Clique.h
+ * @brief   Specialized iSAM2 Clique
+ * @author  Michael Kaess, Richard Roberts
+ */
+
+// \callgraph
+
+#pragma once
+
+#include <gtsam/inference/BayesTreeCliqueBase.h>
+#include <gtsam/inference/Key.h>
+#include <gtsam/linear/GaussianBayesNet.h>
+#include <gtsam/linear/GaussianConditional.h>
+#include <gtsam/linear/GaussianFactorGraph.h>
+#include <string>
+
+namespace gtsam {
+
+/**
+ * Specialized Clique structure for ISAM2, incorporating caching and gradient
+ * contribution
+ * TODO: more documentation
+ */
+class GTSAM_EXPORT ISAM2Clique
+    : public BayesTreeCliqueBase<ISAM2Clique, GaussianFactorGraph> {
+ public:
+  typedef ISAM2Clique This;
+  typedef BayesTreeCliqueBase<This, GaussianFactorGraph> Base;
+  typedef boost::shared_ptr<This> shared_ptr;
+  typedef boost::weak_ptr<This> weak_ptr;
+  typedef GaussianConditional ConditionalType;
+  typedef ConditionalType::shared_ptr sharedConditional;
+
+  Base::FactorType::shared_ptr cachedFactor_;
+  Vector gradientContribution_;
+#ifdef USE_BROKEN_FAST_BACKSUBSTITUTE
+  mutable FastMap<Key, VectorValues::iterator> solnPointers_;
+#endif
+
+  /// Default constructor
+  ISAM2Clique() : Base() {}
+
+  /// Copy constructor, does *not* copy solution pointers as these are invalid
+  /// in different trees.
+  ISAM2Clique(const ISAM2Clique& other)
+      : Base(other),
+        cachedFactor_(other.cachedFactor_),
+        gradientContribution_(other.gradientContribution_) {}
+
+  /// Assignment operator, does *not* copy solution pointers as these are
+  /// invalid in different trees.
+  ISAM2Clique& operator=(const ISAM2Clique& other) {
+    Base::operator=(other);
+    cachedFactor_ = other.cachedFactor_;
+    gradientContribution_ = other.gradientContribution_;
+    return *this;
+  }
+
+  /// Overridden to also store the remaining factor and gradient contribution
+  void setEliminationResult(
+      const FactorGraphType::EliminationResult& eliminationResult);
+
+  /** Access the cached factor */
+  Base::FactorType::shared_ptr& cachedFactor() { return cachedFactor_; }
+
+  /** Access the gradient contribution */
+  const Vector& gradientContribution() const { return gradientContribution_; }
+
+  bool equals(const This& other, double tol = 1e-9) const;
+
+  /** print this node */
+  void print(const std::string& s = "",
+             const KeyFormatter& formatter = DefaultKeyFormatter) const;
+
+  void optimizeWildfire(const KeySet& replaced, double threshold,
+                        KeySet* changed, VectorValues* delta,
+                        size_t* count) const;
+
+  bool optimizeWildfireNode(const KeySet& replaced, double threshold,
+                            KeySet* changed, VectorValues* delta,
+                            size_t* count) const;
+
+  /**
+   * Starting from the root, add up entries of frontal and conditional matrices
+   * of each conditional
+   */
+  void nnz_internal(size_t* result) const;
+  size_t calculate_nnz() const;
+
+  /**
+   * Recursively search this clique and its children for marked keys appearing
+   * in the separator, and add the *frontal* keys of any cliques whose
+   * separator contains any marked keys to the set \c keys.  The purpose of
+   * this is to discover the cliques that need to be redone due to information
+   * propagating to them from cliques that directly contain factors being
+   * relinearized.
+   *
+   * The original comment says this finds all variables directly connected to
+   * the marked ones by measurements.  Is this true, because it seems like this
+   * would also pull in variables indirectly connected through other frontal or
+   * separator variables?
+   *
+   * Alternatively could we trace up towards the root for each variable here?
+   */
+  void findAll(const KeySet& markedMask, KeySet* keys) const;
+
+ private:
+  /**
+   * Check if clique was replaced, or if any parents were changed above the
+   * threshold or themselves replaced.
+   */
+  bool isDirty(const KeySet& replaced, const KeySet& changed) const;
+
+  /**
+   * Back-substitute - special version stores solution pointers in cliques for
+   * fast access.
+   */
+  void fastBackSubstitute(VectorValues* delta) const;
+
+  /*
+   * Check whether the values changed above a threshold, or always true if the
+   * clique was replaced.
+   */
+  bool valuesChanged(const KeySet& replaced, const Vector& originalValues,
+                     const VectorValues& delta, double threshold) const;
+
+  /// Set changed flag for each frontal variable
+  void markFrontalsAsChanged(KeySet* changed) const;
+
+  /// Restore delta to original values, guided by frontal keys.
+  void restoreFromOriginals(const Vector& originalValues,
+                            VectorValues* delta) const;
+
+  /** Serialization function */
+  friend class boost::serialization::access;
+  template <class ARCHIVE>
+  void serialize(ARCHIVE& ar, const unsigned int /*version*/) {
+    ar& BOOST_SERIALIZATION_BASE_OBJECT_NVP(Base);
+    ar& BOOST_SERIALIZATION_NVP(cachedFactor_);
+    ar& BOOST_SERIALIZATION_NVP(gradientContribution_);
+  }
+};  // \struct ISAM2Clique
+
+/**
+ * Optimize the BayesTree, starting from the root.
+ * @param threshold The maximum change against the PREVIOUS delta for
+ * non-replaced variables that can be ignored, ie. the old delta entry is kept
+ * and recursive backsubstitution might eventually stop if none of the changed
+ * variables are contained in the subtree.
+ * @param replaced Needs to contain all variables that are contained in the top
+ * of the Bayes tree that has been redone.
+ * @return The number of variables that were solved for.
+ * @param delta The current solution, an offset from the linearization point.
+ */
+size_t optimizeWildfire(const ISAM2Clique::shared_ptr& root, double threshold,
+                        const KeySet& replaced, VectorValues* delta);
+
+size_t optimizeWildfireNonRecursive(const ISAM2Clique::shared_ptr& root,
+                                    double threshold, const KeySet& replaced,
+                                    VectorValues* delta);
+
+}  // namespace gtsam

gtsam/nonlinear/ISAM2Params.cpp

@@ -0,0 +1,89 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file    ISAM2Params.cpp
+ * @brief   Parameters for iSAM 2.
+ * @author  Michael Kaess, Richard Roberts, Frank Dellaert
+ */
+
+#include <gtsam/nonlinear/ISAM2Params.h>
+#include <boost/algorithm/string.hpp>
+
+using namespace std;
+
+namespace gtsam {
+
+/* ************************************************************************* */
+string ISAM2DoglegParams::adaptationModeTranslator(
+    const DoglegOptimizerImpl::TrustRegionAdaptationMode& adaptationMode)
+    const {
+  string s;
+  switch (adaptationMode) {
+    case DoglegOptimizerImpl::SEARCH_EACH_ITERATION:
+      s = "SEARCH_EACH_ITERATION";
+      break;
+    case DoglegOptimizerImpl::ONE_STEP_PER_ITERATION:
+      s = "ONE_STEP_PER_ITERATION";
+      break;
+    default:
+      s = "UNDEFINED";
+      break;
+  }
+  return s;
+}
+
+/* ************************************************************************* */
+DoglegOptimizerImpl::TrustRegionAdaptationMode
+ISAM2DoglegParams::adaptationModeTranslator(
+    const string& adaptationMode) const {
+  string s = adaptationMode;
+  boost::algorithm::to_upper(s);
+  if (s == "SEARCH_EACH_ITERATION")
+    return DoglegOptimizerImpl::SEARCH_EACH_ITERATION;
+  if (s == "ONE_STEP_PER_ITERATION")
+    return DoglegOptimizerImpl::ONE_STEP_PER_ITERATION;
+
+  /* default is SEARCH_EACH_ITERATION */
+  return DoglegOptimizerImpl::SEARCH_EACH_ITERATION;
+}
+
+/* ************************************************************************* */
+ISAM2Params::Factorization ISAM2Params::factorizationTranslator(
+    const string& str) {
+  string s = str;
+  boost::algorithm::to_upper(s);
+  if (s == "QR") return ISAM2Params::QR;
+  if (s == "CHOLESKY") return ISAM2Params::CHOLESKY;
+
+  /* default is CHOLESKY */
+  return ISAM2Params::CHOLESKY;
+}
+
+/* ************************************************************************* */
+string ISAM2Params::factorizationTranslator(
+    const ISAM2Params::Factorization& value) {
+  string s;
+  switch (value) {
+    case ISAM2Params::QR:
+      s = "QR";
+      break;
+    case ISAM2Params::CHOLESKY:
+      s = "CHOLESKY";
+      break;
+    default:
+      s = "UNDEFINED";
+      break;
+  }
+  return s;
+}
+
+}  // namespace gtsam

gtsam/nonlinear/ISAM2Params.h

@@ -0,0 +1,365 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file    ISAM2Params.h
+ * @brief   Parameters for iSAM 2.
+ * @author  Michael Kaess, Richard Roberts, Frank Dellaert
+ */
+
+// \callgraph
+
+#pragma once
+
+#include <gtsam/linear/GaussianFactorGraph.h>
+#include <gtsam/nonlinear/DoglegOptimizerImpl.h>
+#include <boost/variant.hpp>
+#include <string>
+
+namespace gtsam {
+
+/**
+ * @addtogroup ISAM2
+ * Parameters for ISAM2 using Gauss-Newton optimization.  Either this class or
+ * ISAM2DoglegParams should be specified as the optimizationParams in
+ * ISAM2Params, which should in turn be passed to ISAM2(const ISAM2Params&).
+ */
+struct GTSAM_EXPORT ISAM2GaussNewtonParams {
+  double
+      wildfireThreshold;  ///< Continue updating the linear delta only when
+                          ///< changes are above this threshold (default: 0.001)
+
+  /** Specify parameters as constructor arguments */
+  ISAM2GaussNewtonParams(
+      double _wildfireThreshold =
+          0.001  ///< see ISAM2GaussNewtonParams public variables,
+                 ///< ISAM2GaussNewtonParams::wildfireThreshold
+      )
+      : wildfireThreshold(_wildfireThreshold) {}
+
+  void print(const std::string str = "") const {
+    using std::cout;
+    cout << str << "type:              ISAM2GaussNewtonParams\n";
+    cout << str << "wildfireThreshold: " << wildfireThreshold << "\n";
+    cout.flush();
+  }
+
+  double getWildfireThreshold() const { return wildfireThreshold; }
+  void setWildfireThreshold(double wildfireThreshold) {
+    this->wildfireThreshold = wildfireThreshold;
+  }
+};
+
+/**
+ * @addtogroup ISAM2
+ * Parameters for ISAM2 using Dogleg optimization.  Either this class or
+ * ISAM2GaussNewtonParams should be specified as the optimizationParams in
+ * ISAM2Params, which should in turn be passed to ISAM2(const ISAM2Params&).
+ */
+struct GTSAM_EXPORT ISAM2DoglegParams {
+  double initialDelta;  ///< The initial trust region radius for Dogleg
+  double
+      wildfireThreshold;  ///< Continue updating the linear delta only when
+                          ///< changes are above this threshold (default: 1e-5)
+  DoglegOptimizerImpl::TrustRegionAdaptationMode
+      adaptationMode;  ///< See description in
+                       ///< DoglegOptimizerImpl::TrustRegionAdaptationMode
+  bool
+      verbose;  ///< Whether Dogleg prints iteration and convergence information
+
+  /** Specify parameters as constructor arguments */
+  ISAM2DoglegParams(
+      double _initialDelta = 1.0,  ///< see ISAM2DoglegParams::initialDelta
+      double _wildfireThreshold =
+          1e-5,  ///< see ISAM2DoglegParams::wildfireThreshold
+      DoglegOptimizerImpl::TrustRegionAdaptationMode _adaptationMode =
+          DoglegOptimizerImpl::
+              SEARCH_EACH_ITERATION,  ///< see ISAM2DoglegParams::adaptationMode
+      bool _verbose = false           ///< see ISAM2DoglegParams::verbose
+      )
+      : initialDelta(_initialDelta),
+        wildfireThreshold(_wildfireThreshold),
+        adaptationMode(_adaptationMode),
+        verbose(_verbose) {}
+
+  void print(const std::string str = "") const {
+    using std::cout;
+    cout << str << "type:              ISAM2DoglegParams\n";
+    cout << str << "initialDelta:      " << initialDelta << "\n";
+    cout << str << "wildfireThreshold: " << wildfireThreshold << "\n";
+    cout << str
+         << "adaptationMode:    " << adaptationModeTranslator(adaptationMode)
+         << "\n";
+    cout.flush();
+  }
+
+  double getInitialDelta() const { return initialDelta; }
+  double getWildfireThreshold() const { return wildfireThreshold; }
+  std::string getAdaptationMode() const {
+    return adaptationModeTranslator(adaptationMode);
+  }
+  bool isVerbose() const { return verbose; }
+  void setInitialDelta(double initialDelta) {
+    this->initialDelta = initialDelta;
+  }
+  void setWildfireThreshold(double wildfireThreshold) {
+    this->wildfireThreshold = wildfireThreshold;
+  }
+  void setAdaptationMode(const std::string& adaptationMode) {
+    this->adaptationMode = adaptationModeTranslator(adaptationMode);
+  }
+  void setVerbose(bool verbose) { this->verbose = verbose; }
+
+  std::string adaptationModeTranslator(
+      const DoglegOptimizerImpl::TrustRegionAdaptationMode& adaptationMode)
+      const;
+  DoglegOptimizerImpl::TrustRegionAdaptationMode adaptationModeTranslator(
+      const std::string& adaptationMode) const;
+};
+
+/**
+ * @addtogroup ISAM2
+ * Parameters for the ISAM2 algorithm.  Default parameter values are listed
+ * below.
+ */
+typedef FastMap<char, Vector> ISAM2ThresholdMap;
+typedef ISAM2ThresholdMap::value_type ISAM2ThresholdMapValue;
+struct GTSAM_EXPORT ISAM2Params {
+  typedef boost::variant<ISAM2GaussNewtonParams, ISAM2DoglegParams>
+      OptimizationParams;  ///< Either ISAM2GaussNewtonParams or
+                           ///< ISAM2DoglegParams
+  typedef boost::variant<double, FastMap<char, Vector> >
+      RelinearizationThreshold;  ///< Either a constant relinearization
+                                 ///< threshold or a per-variable-type set of
+                                 ///< thresholds
+
+  /** Optimization parameters, this both selects the nonlinear optimization
+   * method and specifies its parameters, either ISAM2GaussNewtonParams or
+   * ISAM2DoglegParams.  In the former, Gauss-Newton optimization will be used
+   * with the specified parameters, and in the latter Powell's dog-leg
+   * algorithm will be used with the specified parameters.
+   */
+  OptimizationParams optimizationParams;
+
+  /** Only relinearize variables whose linear delta magnitude is greater than
+   * this threshold (default: 0.1).  If this is a FastMap<char,Vector> instead
+   * of a double, then the threshold is specified for each dimension of each
+   * variable type.  This parameter then maps from a character indicating the
+   * variable type to a Vector of thresholds for each dimension of that
+   * variable.  For example, if Pose keys are of type TypedSymbol<'x',Pose3>,
+   * and landmark keys are of type TypedSymbol<'l',Point3>, then appropriate
+   * entries would be added with:
+   * \code
+     FastMap<char,Vector> thresholds;
+     thresholds['x'] = (Vector(6) << 0.1, 0.1, 0.1, 0.5, 0.5, 0.5).finished();
+   // 0.1 rad rotation threshold, 0.5 m translation threshold thresholds['l'] =
+   Vector3(1.0, 1.0, 1.0);                // 1.0 m landmark position threshold
+     params.relinearizeThreshold = thresholds;
+     \endcode
+   */
+  RelinearizationThreshold relinearizeThreshold;
+
+  int relinearizeSkip;  ///< Only relinearize any variables every
+                        ///< relinearizeSkip calls to ISAM2::update (default:
+                        ///< 10)
+
+  bool enableRelinearization;  ///< Controls whether ISAM2 will ever relinearize
+                               ///< any variables (default: true)
+
+  bool evaluateNonlinearError;  ///< Whether to evaluate the nonlinear error
+                                ///< before and after the update, to return in
+                                ///< ISAM2Result from update()
+
+  enum Factorization { CHOLESKY, QR };
+  /** Specifies whether to use QR or CHOESKY numerical factorization (default:
+   * CHOLESKY). Cholesky is faster but potentially numerically unstable for
+   * poorly-conditioned problems, which can occur when uncertainty is very low
+   * in some variables (or dimensions of variables) and very high in others.  QR
+   * is slower but more numerically stable in poorly-conditioned problems.  We
+   * suggest using the default of Cholesky unless gtsam sometimes throws
+   * IndefiniteLinearSystemException when your problem's Hessian is actually
+   * positive definite.  For positive definite problems, numerical error
+   * accumulation can cause the problem to become numerically negative or
+   * indefinite as solving proceeds, especially when using Cholesky.
+   */
+  Factorization factorization;
+
+  /** Whether to cache linear factors (default: true).
+   * This can improve performance if linearization is expensive, but can hurt
+   * performance if linearization is very cleap due to computation to look up
+   * additional keys.
+   */
+  bool cacheLinearizedFactors;
+
+  KeyFormatter
+      keyFormatter;  ///< A KeyFormatter for when keys are printed during
+                     ///< debugging (default: DefaultKeyFormatter)
+
+  bool enableDetailedResults;  ///< Whether to compute and return
+                               ///< ISAM2Result::detailedResults, this can
+                               ///< increase running time (default: false)
+
+  /** Check variables for relinearization in tree-order, stopping the check once
+   * a variable does not need to be relinearized (default: false). This can
+   * improve speed by only checking a small part of the top of the tree.
+   * However, variables below the check cut-off can accumulate significant
+   * deltas without triggering relinearization. This is particularly useful in
+   * exploration scenarios where real-time performance is desired over
+   * correctness. Use with caution.
+   */
+  bool enablePartialRelinearizationCheck;
+
+  /// When you will be removing many factors, e.g. when using ISAM2 as a
+  /// fixed-lag smoother, enable this option to add factors in the first
+  /// available factor slots, to avoid accumulating NULL factor slots, at the
+  /// cost of having to search for slots every time a factor is added.
+  bool findUnusedFactorSlots;
+
+  /**
+   * Specify parameters as constructor arguments
+   * See the documentation of member variables above.
+   */
+  ISAM2Params(OptimizationParams _optimizationParams = ISAM2GaussNewtonParams(),
+              RelinearizationThreshold _relinearizeThreshold = 0.1,
+              int _relinearizeSkip = 10, bool _enableRelinearization = true,
+              bool _evaluateNonlinearError = false,
+              Factorization _factorization = ISAM2Params::CHOLESKY,
+              bool _cacheLinearizedFactors = true,
+              const KeyFormatter& _keyFormatter =
+                  DefaultKeyFormatter  ///< see ISAM2::Params::keyFormatter
+              )
+      : optimizationParams(_optimizationParams),
+        relinearizeThreshold(_relinearizeThreshold),
+        relinearizeSkip(_relinearizeSkip),
+        enableRelinearization(_enableRelinearization),
+        evaluateNonlinearError(_evaluateNonlinearError),
+        factorization(_factorization),
+        cacheLinearizedFactors(_cacheLinearizedFactors),
+        keyFormatter(_keyFormatter),
+        enableDetailedResults(false),
+        enablePartialRelinearizationCheck(false),
+        findUnusedFactorSlots(false) {}
+
+  /// print iSAM2 parameters
+  void print(const std::string& str = "") const {
+    using std::cout;
+    cout << str << "\n";
+
+    static const std::string kStr("optimizationParams:                ");
+    if (optimizationParams.type() == typeid(ISAM2GaussNewtonParams))
+      boost::get<ISAM2GaussNewtonParams>(optimizationParams).print();
+    else if (optimizationParams.type() == typeid(ISAM2DoglegParams))
+      boost::get<ISAM2DoglegParams>(optimizationParams).print(kStr);
+    else
+      cout << kStr << "{unknown type}\n";
+
+    cout << "relinearizeThreshold:              ";
+    if (relinearizeThreshold.type() == typeid(double)) {
+      cout << boost::get<double>(relinearizeThreshold) << "\n";
+    } else {
+      cout << "{mapped}\n";
+      for (const ISAM2ThresholdMapValue& value :
+           boost::get<ISAM2ThresholdMap>(relinearizeThreshold)) {
+        cout << "                                   '" << value.first
+             << "' -> [" << value.second.transpose() << " ]\n";
+      }
+    }
+
+    cout << "relinearizeSkip:                   " << relinearizeSkip << "\n";
+    cout << "enableRelinearization:             " << enableRelinearization
+         << "\n";
+    cout << "evaluateNonlinearError:            " << evaluateNonlinearError
+         << "\n";
+    cout << "factorization:                     "
+         << factorizationTranslator(factorization) << "\n";
+    cout << "cacheLinearizedFactors:            " << cacheLinearizedFactors
+         << "\n";
+    cout << "enableDetailedResults:             " << enableDetailedResults
+         << "\n";
+    cout << "enablePartialRelinearizationCheck: "
+         << enablePartialRelinearizationCheck << "\n";
+    cout << "findUnusedFactorSlots:             " << findUnusedFactorSlots
+         << "\n";
+    cout.flush();
+  }
+
+  /// @name Getters and Setters for all properties
+  /// @{
+
+  OptimizationParams getOptimizationParams() const {
+    return this->optimizationParams;
+  }
+  RelinearizationThreshold getRelinearizeThreshold() const {
+    return relinearizeThreshold;
+  }
+  int getRelinearizeSkip() const { return relinearizeSkip; }
+  bool isEnableRelinearization() const { return enableRelinearization; }
+  bool isEvaluateNonlinearError() const { return evaluateNonlinearError; }
+  std::string getFactorization() const {
+    return factorizationTranslator(factorization);
+  }
+  bool isCacheLinearizedFactors() const { return cacheLinearizedFactors; }
+  KeyFormatter getKeyFormatter() const { return keyFormatter; }
+  bool isEnableDetailedResults() const { return enableDetailedResults; }
+  bool isEnablePartialRelinearizationCheck() const {
+    return enablePartialRelinearizationCheck;
+  }
+
+  void setOptimizationParams(OptimizationParams optimizationParams) {
+    this->optimizationParams = optimizationParams;
+  }
+  void setRelinearizeThreshold(RelinearizationThreshold relinearizeThreshold) {
+    this->relinearizeThreshold = relinearizeThreshold;
+  }
+  void setRelinearizeSkip(int relinearizeSkip) {
+    this->relinearizeSkip = relinearizeSkip;
+  }
+  void setEnableRelinearization(bool enableRelinearization) {
+    this->enableRelinearization = enableRelinearization;
+  }
+  void setEvaluateNonlinearError(bool evaluateNonlinearError) {
+    this->evaluateNonlinearError = evaluateNonlinearError;
+  }
+  void setFactorization(const std::string& factorization) {
+    this->factorization = factorizationTranslator(factorization);
+  }
+  void setCacheLinearizedFactors(bool cacheLinearizedFactors) {
+    this->cacheLinearizedFactors = cacheLinearizedFactors;
+  }
+  void setKeyFormatter(KeyFormatter keyFormatter) {
+    this->keyFormatter = keyFormatter;
+  }
+  void setEnableDetailedResults(bool enableDetailedResults) {
+    this->enableDetailedResults = enableDetailedResults;
+  }
+  void setEnablePartialRelinearizationCheck(
+      bool enablePartialRelinearizationCheck) {
+    this->enablePartialRelinearizationCheck = enablePartialRelinearizationCheck;
+  }
+
+  GaussianFactorGraph::Eliminate getEliminationFunction() const {
+    return factorization == CHOLESKY
+               ? (GaussianFactorGraph::Eliminate)EliminatePreferCholesky
+               : (GaussianFactorGraph::Eliminate)EliminateQR;
+  }
+
+  /// @}
+
+  /// @name Some utilities
+  /// @{
+
+  static Factorization factorizationTranslator(const std::string& str);
+  static std::string factorizationTranslator(const Factorization& value);
+
+  /// @}
+};
+
+}  // namespace gtsam

gtsam/nonlinear/ISAM2Result.h

@@ -0,0 +1,159 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file    ISAM2Result.h
+ * @brief   Class that stores detailed iSAM2 result.
+ * @author  Michael Kaess, Richard Roberts, Frank Dellaert
+ */
+
+// \callgraph
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+#include <gtsam/linear/GaussianBayesTree.h>
+#include <gtsam/nonlinear/DoglegOptimizerImpl.h>
+#include <gtsam/nonlinear/NonlinearFactorGraph.h>
+#include <gtsam/nonlinear/ISAM2Params.h>
+
+#include <boost/variant.hpp>
+
+namespace gtsam {
+
+typedef FastVector<size_t> FactorIndices;
+
+/**
+ * @addtogroup ISAM2
+ * This struct is returned from ISAM2::update() and contains information about
+ * the update that is useful for determining whether the solution is
+ * converging, and about how much work was required for the update.  See member
+ * variables for details and information about each entry.
+ */
+struct GTSAM_EXPORT ISAM2Result {
+  /** The nonlinear error of all of the factors, \a including new factors and
+   * variables added during the current call to ISAM2::update().  This error is
+   * calculated using the following variable values:
+   * \li Pre-existing variables will be evaluated by combining their
+   * linearization point before this call to update, with their partial linear
+   * delta, as computed by ISAM2::calculateEstimate().
+   * \li New variables will be evaluated at their initialization points passed
+   * into the current call to update.
+   * \par Note: This will only be computed if
+   * ISAM2Params::evaluateNonlinearError is set to \c true, because there is
+   * some cost to this computation.
+   */
+  boost::optional<double> errorBefore;
+
+  /** The nonlinear error of all of the factors computed after the current
+   * update, meaning that variables above the relinearization threshold
+   * (ISAM2Params::relinearizeThreshold) have been relinearized and new
+   * variables have undergone one linear update.  Variable values are
+   * again computed by combining their linearization points with their
+   * partial linear deltas, by ISAM2::calculateEstimate().
+   * \par Note: This will only be computed if
+   * ISAM2Params::evaluateNonlinearError is set to \c true, because there is
+   * some cost to this computation.
+   */
+  boost::optional<double> errorAfter;
+
+  /** The number of variables that were relinearized because their linear
+   * deltas exceeded the reslinearization threshold
+   * (ISAM2Params::relinearizeThreshold), combined with any additional
+   * variables that had to be relinearized because they were involved in
+   * the same factor as a variable above the relinearization threshold.
+   * On steps where no relinearization is considered
+   * (see ISAM2Params::relinearizeSkip), this count will be zero.
+   */
+  size_t variablesRelinearized;
+
+  /** The number of variables that were reeliminated as parts of the Bayes'
+   * Tree were recalculated, due to new factors.  When loop closures occur,
+   * this count will be large as the new loop-closing factors will tend to
+   * involve variables far away from the root, and everything up to the root
+   * will be reeliminated.
+   */
+  size_t variablesReeliminated;
+
+  /** The number of factors that were included in reelimination of the Bayes'
+   * tree. */
+  size_t factorsRecalculated;
+
+  /** The number of cliques in the Bayes' Tree */
+  size_t cliques;
+
+  /** The indices of the newly-added factors, in 1-to-1 correspondence with the
+   * factors passed as \c newFactors to ISAM2::update().  These indices may be
+   * used later to refer to the factors in order to remove them.
+   */
+  FactorIndices newFactorsIndices;
+
+  /** A struct holding detailed results, which must be enabled with
+   * ISAM2Params::enableDetailedResults.
+   */
+  struct DetailedResults {
+    /** The status of a single variable, this struct is stored in
+     * DetailedResults::variableStatus */
+    struct VariableStatus {
+      /** Whether the variable was just reeliminated, due to being relinearized,
+       * observed, new, or on the path up to the root clique from another
+       * reeliminated variable. */
+      bool isReeliminated;
+      bool isAboveRelinThreshold;  ///< Whether the variable was just
+                                   ///< relinearized due to being above the
+                                   ///< relinearization threshold
+      bool isRelinearizeInvolved;  ///< Whether the variable was below the
+                                   ///< relinearization threshold but was
+                                   ///< relinearized by being involved in a
+                                   ///< factor with a variable above the
+                                   ///< relinearization threshold
+      bool isRelinearized;  /// Whether the variable was relinearized, either by
+                            /// being above the relinearization threshold or by
+                            /// involvement.
+      bool isObserved;      ///< Whether the variable was just involved in new
+                            ///< factors
+      bool isNew;           ///< Whether the variable itself was just added
+      bool inRootClique;    ///< Whether the variable is in the root clique
+      VariableStatus()
+          : isReeliminated(false),
+            isAboveRelinThreshold(false),
+            isRelinearizeInvolved(false),
+            isRelinearized(false),
+            isObserved(false),
+            isNew(false),
+            inRootClique(false) {}
+    };
+
+    /** The status of each variable during this update, see VariableStatus.
+     */
+    FastMap<Key, VariableStatus> variableStatus;
+  };
+
+  /** Detailed results, if enabled by ISAM2Params::enableDetailedResults.  See
+   * Detail for information about the results data stored here. */
+  boost::optional<DetailedResults> detail;
+
+  void print(const std::string str = "") const {
+    using std::cout;
+    cout << str << "  Reelimintated: " << variablesReeliminated
+         << "  Relinearized: " << variablesRelinearized
+         << "  Cliques: " << cliques << std::endl;
+  }
+
+  /** Getters and Setters */
+  size_t getVariablesRelinearized() const { return variablesRelinearized; }
+  size_t getVariablesReeliminated() const { return variablesReeliminated; }
+  size_t getCliques() const { return cliques; }
+};
+
+}  // namespace gtsam

gtsam_unstable/slam/SmartRangeFactor.h

@@ -14,7 +14,12 @@
 #include <gtsam/inference/Key.h>
 #include <gtsam/geometry/Pose2.h>
 #include <gtsam/base/timing.h>
+
+#include <list>
 #include <map>
+#include <stdexcept>
+#include <string>
+#include <vector>
 
 namespace gtsam {
 
@@ -23,8 +28,7 @@ namespace gtsam {
  * @addtogroup SLAM
  */
 class SmartRangeFactor: public NoiseModelFactor {
-protected:
+ protected:
-
   struct Circle2 {
     Circle2(const Point2& p, double r) :
         center(p), radius(r) {
@@ -38,8 +42,7 @@ protected:
   std::vector<double> measurements_;  ///< Range measurements
   double variance_;  ///< variance on noise
 
-public:
+ public:
-
   /** Default constructor: don't use directly */
   SmartRangeFactor() {
   }
@@ -48,7 +51,7 @@ public:
    * Constructor
    * @param s standard deviation of range measurement noise
    */
-  SmartRangeFactor(double s) :
+  explicit SmartRangeFactor(double s) :
       NoiseModelFactor(noiseModel::Isotropic::Sigma(1, s)), variance_(s * s) {
   }
 
@@ -83,9 +86,10 @@ public:
   /**
    * Triangulate a point from at least three pose-range pairs
    * Checks for best pair that includes first point
+   * Raise runtime_error if not well defined.
    */
   Point2 triangulate(const Values& x) const {
-    //gttic_(triangulate);
+    // gttic_(triangulate);
     // create n circles corresponding to measured range around each pose
     std::list<Circle2> circles;
     size_t n = size();
@@ -96,10 +100,10 @@ public:
 
     Circle2 circle1 = circles.front();
     boost::optional<Point2> best_fh;
-    boost::optional<Circle2> best_circle;
+    boost::optional<Circle2> bestCircle2;
 
     // loop over all circles
-    for(const Circle2& it: circles) {
+    for (const Circle2& it : circles) {
       // distance between circle centers.
       double d = distance2(circle1.center, it.center);
       if (d < 1e-9)
@@ -111,23 +115,27 @@ public:
       // if h is large, the intersections are well defined.
       if (fh && (!best_fh || fh->y() > best_fh->y())) {
         best_fh = fh;
-        best_circle = it;
+        bestCircle2 = it;
       }
     }
 
     // use best fh to find actual intersection points
+    if (bestCircle2 && best_fh) {
     std::list<Point2> intersections = circleCircleIntersection(
-        circle1.center, best_circle->center, best_fh);
+        circle1.center, bestCircle2->center, best_fh);
 
     // pick winner based on other measurements
     double error1 = 0, error2 = 0;
     Point2 p1 = intersections.front(), p2 = intersections.back();
-    for(const Circle2& it: circles) {
+    for (const Circle2& it : circles) {
       error1 += distance2(it.center, p1);
       error2 += distance2(it.center, p2);
     }
     return (error1 < error2) ? p1 : p2;
-    //gttoc_(triangulate);
+    } else {
+      throw std::runtime_error("triangulate failed");
+    }
+    // gttoc_(triangulate);
   }
 
   /**
@@ -137,19 +145,20 @@ public:
       boost::optional<std::vector<Matrix>&> H = boost::none) const {
     size_t n = size();
     if (n < 3) {
-      if (H)
+      if (H) {
         // set Jacobians to zero for n<3
         for (size_t j = 0; j < n; j++)
           (*H)[j] = Matrix::Zero(3, 1);
+      }
       return Z_1x1;
     } else {
       Vector error = Z_1x1;
 
       // triangulate to get the optimized point
-      // TODO: Should we have a (better?) variant that does this in relative coordinates ?
+      // TODO(dellaert): Should we have a (better?) variant that does this in relative coordinates ?
       Point2 optimizedPoint = triangulate(x);
 
-      // TODO: triangulation should be followed by an optimization given poses
+      // TODO(dellaert): triangulation should be followed by an optimization given poses
       // now evaluate the errors between predicted and measured range
       for (size_t j = 0; j < n; j++) {
         const Pose2& pose = x.at<Pose2>(keys_[j]);
@@ -168,8 +177,6 @@ public:
     return boost::static_pointer_cast<gtsam::NonlinearFactor>(
         gtsam::NonlinearFactor::shared_ptr(new This(*this)));
   }
-
 };
-
 }  // \namespace gtsam
 

tests/testGaussianISAM2.cpp

@@ -304,7 +304,7 @@ TEST(ISAM2, AddFactorsStep1)
 
   FactorIndices actualNewFactorIndices;
 
-  ISAM2::Impl::AddFactorsStep1(newFactors, true, nonlinearFactors, actualNewFactorIndices);
+  ISAM2::Impl::AddFactorsStep1(newFactors, true, &nonlinearFactors, &actualNewFactorIndices);
 
   EXPECT(assert_equal(expectedNonlinearFactors, nonlinearFactors));
   EXPECT(assert_container_equality(expectedNewFactorIndices, actualNewFactorIndices));
@@ -843,7 +843,7 @@ TEST(ISAM2, calculate_nnz)
 {
   ISAM2 isam = createSlamlikeISAM2();
   int expected = 241;
-  int actual = calculate_nnz(isam.roots().front());
+  int actual = isam.roots().front()->calculate_nnz();
 
   EXPECT_LONGS_EQUAL(expected, actual);
 }

tests/testNonlinearOptimizer.cpp

@@ -20,13 +20,12 @@
 #include <gtsam/slam/BetweenFactor.h>
 #include <gtsam/nonlinear/NonlinearFactorGraph.h>
 #include <gtsam/nonlinear/Values.h>
-#include <gtsam/inference/Symbol.h>
-#include <gtsam/nonlinear/NonlinearFactorGraph.h>
 #include <gtsam/nonlinear/GaussNewtonOptimizer.h>
 #include <gtsam/nonlinear/DoglegOptimizer.h>
 #include <gtsam/nonlinear/LevenbergMarquardtOptimizer.h>
 #include <gtsam/linear/GaussianFactorGraph.h>
 #include <gtsam/linear/NoiseModel.h>
+#include <gtsam/inference/Symbol.h>
 #include <gtsam/geometry/Pose2.h>
 #include <gtsam/base/Matrix.h>
 
@@ -394,19 +393,20 @@ class IterativeLM: public LevenbergMarquardtOptimizer {
 
   /// Solver specific parameters
   ConjugateGradientParameters cgParams_;
+  Values initial_;
 
 public:
   /// Constructor
   IterativeLM(const NonlinearFactorGraph& graph, const Values& initialValues,
       const ConjugateGradientParameters &p,
       const LevenbergMarquardtParams& params = LevenbergMarquardtParams::LegacyDefaults()) :
-      LevenbergMarquardtOptimizer(graph, initialValues, params), cgParams_(p) {
+      LevenbergMarquardtOptimizer(graph, initialValues, params), cgParams_(p), initial_(initialValues) {
   }
 
   /// Solve that uses conjugate gradient
   virtual VectorValues solve(const GaussianFactorGraph &gfg,
-      const Values& initial, const NonlinearOptimizerParams& params) const {
+      const NonlinearOptimizerParams& params) const {
-    VectorValues zeros = initial.zeroVectors();
+    VectorValues zeros = initial_.zeroVectors();
     return conjugateGradientDescent(gfg, zeros, cgParams_);
   }
 };

wrap/FileWriter.cpp

@@ -29,7 +29,7 @@ void FileWriter::emit(bool add_header, bool force_overwrite) const {
   bool file_exists = true;
   try {
     existing_contents = file_contents(filename_.c_str(), add_header);
-  } catch (CantOpenFile) {
+  } catch (const CantOpenFile& e) {
     file_exists = false;
   }