Merge pull request #920 from borglab/fix/minor-stuff

gtsam/inference/EliminateableFactorGraph-inst.h

@@ -36,17 +36,17 @@ namespace gtsam {
       // no Ordering is provided.  When removing optional from VariableIndex, create VariableIndex
       // before creating ordering.
       VariableIndex computedVariableIndex(asDerived());
-      return eliminateSequential(function, computedVariableIndex, orderingType);
+      return eliminateSequential(orderingType, function, computedVariableIndex);
     }
     else {
       // Compute an ordering and call this function again.  We are guaranteed to have a 
       // VariableIndex already here because we computed one if needed in the previous 'if' block.
       if (orderingType == Ordering::METIS) {
         Ordering computedOrdering = Ordering::Metis(asDerived());
-        return eliminateSequential(computedOrdering, function, variableIndex, orderingType);
+        return eliminateSequential(computedOrdering, function, variableIndex);
       } else {
         Ordering computedOrdering = Ordering::Colamd(*variableIndex);
-        return eliminateSequential(computedOrdering, function, variableIndex, orderingType);
+        return eliminateSequential(computedOrdering, function, variableIndex);
       }
     }
   }

gtsam/nonlinear/GncOptimizer.h

@@ -142,8 +142,9 @@ class GTSAM_EXPORT GncOptimizer {
    * provides an extra interface for the user to initialize the weightst
    * */
   void setWeights(const Vector w) {
-    if(w.size() != nfg_.size()){
+    if (size_t(w.size()) != nfg_.size()) {
-      throw std::runtime_error("GncOptimizer::setWeights: the number of specified weights"
+      throw std::runtime_error(
+          "GncOptimizer::setWeights: the number of specified weights"
           " does not match the size of the factor graph.");
     }
     weights_ = w;

gtsam/nonlinear/factorTesting.h

@@ -35,8 +35,7 @@ namespace gtsam {
  * zero errors anyway. However, it means that below will only be exact for the correct measurement.
  */
 JacobianFactor linearizeNumerically(const NoiseModelFactor& factor,
-    const Values& values, double delta = 1e-5) {
+                                    const Values& values, double delta = 1e-5) {
-
   // We will fill a vector of key/Jacobians pairs (a map would sort)
   std::vector<std::pair<Key, Matrix> > jacobians;
 
@@ -46,24 +45,24 @@ JacobianFactor linearizeNumerically(const NoiseModelFactor& factor,
 
   // Loop over all variables
   const double one_over_2delta = 1.0 / (2.0 * delta);
-  for(Key key: factor) {
+  for (Key key : factor) {
     // Compute central differences using the values struct.
     VectorValues dX = values.zeroVectors();
     const size_t cols = dX.dim(key);
     Matrix J = Matrix::Zero(rows, cols);
     for (size_t col = 0; col < cols; ++col) {
       Eigen::VectorXd dx = Eigen::VectorXd::Zero(cols);
-      dx[col] = delta;
+      dx(col) = delta;
       dX[key] = dx;
       Values eval_values = values.retract(dX);
       const Eigen::VectorXd left = factor.whitenedError(eval_values);
-      dx[col] = -delta;
+      dx(col) = -delta;
       dX[key] = dx;
       eval_values = values.retract(dX);
       const Eigen::VectorXd right = factor.whitenedError(eval_values);
       J.col(col) = (left - right) * one_over_2delta;
     }
-    jacobians.push_back(std::make_pair(key,J));
+    jacobians.push_back(std::make_pair(key, J));
   }
 
   // Next step...return JacobianFactor

gtsam/nonlinear/nonlinear.i

@@ -115,6 +115,10 @@ class Ordering {
   Ordering();
   Ordering(const gtsam::Ordering& other);
 
+  template <FACTOR_GRAPH = {gtsam::NonlinearFactorGraph,
+                            gtsam::GaussianFactorGraph}>
+  static gtsam::Ordering Colamd(const FACTOR_GRAPH& graph);
+
   // Testable
   void print(string s = "", const gtsam::KeyFormatter& keyFormatter =
                                 gtsam::DefaultKeyFormatter) const;

python/gtsam/examples/SFMExample_bal.py

@@ -7,73 +7,79 @@
   See LICENSE for the license information
 
   Solve a structure-from-motion problem from a "Bundle Adjustment in the Large" file
-  Author: Frank Dellaert (Python: Akshay Krishnan, John Lambert)
+  Author: Frank Dellaert (Python: Akshay Krishnan, John Lambert, Varun Agrawal)
 """
 
 import argparse
 import logging
 import sys
 
-import matplotlib.pyplot as plt
-import numpy as np
-
 import gtsam
-from gtsam import (
+from gtsam import (GeneralSFMFactorCal3Bundler,
-    GeneralSFMFactorCal3Bundler,
+                   PriorFactorPinholeCameraCal3Bundler, PriorFactorPoint3)
-    PinholeCameraCal3Bundler,
+from gtsam.symbol_shorthand import C, P  # type: ignore
-    PriorFactorPinholeCameraCal3Bundler,
+from gtsam.utils import plot  # type: ignore
-    readBal,
+from matplotlib import pyplot as plt
-    symbol_shorthand
-)
 
-C = symbol_shorthand.C
+logging.basicConfig(stream=sys.stdout, level=logging.INFO)
-P = symbol_shorthand.P
+
+DEFAULT_BAL_DATASET = "dubrovnik-3-7-pre"
 
 
-logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
+def plot_scene(scene_data: gtsam.SfmData, result: gtsam.Values) -> None:
+    """Plot the SFM results."""
+    plot_vals = gtsam.Values()
+    for cam_idx in range(scene_data.number_cameras()):
+        plot_vals.insert(C(cam_idx),
+                         result.atPinholeCameraCal3Bundler(C(cam_idx)).pose())
+    for j in range(scene_data.number_tracks()):
+        plot_vals.insert(P(j), result.atPoint3(P(j)))
 
-def run(args):
+    plot.plot_3d_points(0, plot_vals, linespec="g.")
+    plot.plot_trajectory(0, plot_vals, title="SFM results")
+
+    plt.show()
+
+
+def run(args: argparse.Namespace) -> None:
     """ Run LM optimization with BAL input data and report resulting error """
-    input_file = gtsam.findExampleDataFile(args.input_file)
+    input_file = args.input_file
 
     # Load the SfM data from file
-    scene_data = readBal(input_file)
+    scene_data = gtsam.readBal(input_file)
-    logging.info(f"read {scene_data.number_tracks()} tracks on {scene_data.number_cameras()} cameras\n")
+    logging.info("read %d tracks on %d cameras\n", scene_data.number_tracks(),
+                 scene_data.number_cameras())
 
     # Create a factor graph
     graph = gtsam.NonlinearFactorGraph()
 
     # We share *one* noiseModel between all projection factors
-    noise = gtsam.noiseModel.Isotropic.Sigma(2, 1.0) # one pixel in u and v
+    noise = gtsam.noiseModel.Isotropic.Sigma(2, 1.0)  # one pixel in u and v
 
     # Add measurements to the factor graph
-    j = 0
+    for j in range(scene_data.number_tracks()):
-    for t_idx in range(scene_data.number_tracks()):
+        track = scene_data.track(j)  # SfmTrack
-        track = scene_data.track(t_idx) # SfmTrack
         # retrieve the SfmMeasurement objects
         for m_idx in range(track.number_measurements()):
             # i represents the camera index, and uv is the 2d measurement
             i, uv = track.measurement(m_idx)
             # note use of shorthand symbols C and P
             graph.add(GeneralSFMFactorCal3Bundler(uv, noise, C(i), P(j)))
-        j += 1
 
     # Add a prior on pose x1. This indirectly specifies where the origin is.
     graph.push_back(
-        gtsam.PriorFactorPinholeCameraCal3Bundler(
+        PriorFactorPinholeCameraCal3Bundler(
-            C(0), scene_data.camera(0), gtsam.noiseModel.Isotropic.Sigma(9, 0.1)
+            C(0), scene_data.camera(0),
-        )
+            gtsam.noiseModel.Isotropic.Sigma(9, 0.1)))
-    )
     # Also add a prior on the position of the first landmark to fix the scale
     graph.push_back(
-        gtsam.PriorFactorPoint3(
+        PriorFactorPoint3(P(0),
-            P(0), scene_data.track(0).point3(), gtsam.noiseModel.Isotropic.Sigma(3, 0.1)
+                          scene_data.track(0).point3(),
-        )
+                          gtsam.noiseModel.Isotropic.Sigma(3, 0.1)))
-    )
 
     # Create initial estimate
     initial = gtsam.Values()
-    
+
     i = 0
     # add each PinholeCameraCal3Bundler
     for cam_idx in range(scene_data.number_cameras()):
@@ -81,12 +87,10 @@ def run(args):
         initial.insert(C(i), camera)
         i += 1
 
-    j = 0
     # add each SfmTrack
-    for t_idx in range(scene_data.number_tracks()):
+    for j in range(scene_data.number_tracks()):
-        track = scene_data.track(t_idx)  
+        track = scene_data.track(j)
         initial.insert(P(j), track.point3())
-        j += 1
 
     # Optimize the graph and print results
     try:
@@ -94,25 +98,31 @@ def run(args):
         params.setVerbosityLM("ERROR")
         lm = gtsam.LevenbergMarquardtOptimizer(graph, initial, params)
         result = lm.optimize()
-    except Exception as e:
+    except RuntimeError:
         logging.exception("LM Optimization failed")
         return
+
     # Error drops from ~2764.22 to ~0.046
-    logging.info(f"final error: {graph.error(result)}")
+    logging.info("initial error: %f", graph.error(initial))
+    logging.info("final error: %f", graph.error(result))
+
+    plot_scene(scene_data, result)
+
+
+def main() -> None:
+    """Main runner."""
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i',
+                        '--input_file',
+                        type=str,
+                        default=gtsam.findExampleDataFile(DEFAULT_BAL_DATASET),
+                        help="""Read SFM data from the specified BAL file.
+        The data format is described here: https://grail.cs.washington.edu/projects/bal/.
+        BAL files contain (nrPoses, nrPoints, nrObservations), followed by (i,j,u,v) tuples,
+        then (wx,wy,wz,tx,ty,tz,f,k1,k1) as Bundler camera calibrations w/ Rodrigues vector
+        and (x,y,z) 3d point initializations.""")
+    run(parser.parse_args())
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
+    main()
-    parser.add_argument(
-        '-i',
-        '--input_file',
-        type=str,
-        default="dubrovnik-3-7-pre",
-        help='Read SFM data from the specified BAL file'
-        'The data format is described here: https://grail.cs.washington.edu/projects/bal/.'
-        'BAL files contain (nrPoses, nrPoints, nrObservations), followed by (i,j,u,v) tuples, '
-        'then (wx,wy,wz,tx,ty,tz,f,k1,k1) as Bundler camera calibrations w/ Rodrigues vector'
-        'and (x,y,z) 3d point initializations.'
-    )
-    run(parser.parse_args())
-