Initial import of ceres-solver 1.4.0

Added a NOTICE and a MODULE_LICENSE_BSD file.
Added Android.mk for master build and unbundled build.
Added CleanSpec.mk to optimize Android build.

Change-Id: I6cd82bcabc1a94b10239f9fca017de0afd20e769
diff --git a/internal/ceres/system_test.cc b/internal/ceres/system_test.cc
new file mode 100644
index 0000000..4548bd0
--- /dev/null
+++ b/internal/ceres/system_test.cc
@@ -0,0 +1,537 @@
+// Ceres Solver - A fast non-linear least squares minimizer
+// Copyright 2010, 2011, 2012 Google Inc. All rights reserved.
+// http://code.google.com/p/ceres-solver/
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// * Redistributions of source code must retain the above copyright notice,
+//   this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above copyright notice,
+//   this list of conditions and the following disclaimer in the documentation
+//   and/or other materials provided with the distribution.
+// * Neither the name of Google Inc. nor the names of its contributors may be
+//   used to endorse or promote products derived from this software without
+//   specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+// LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+// POSSIBILITY OF SUCH DAMAGE.
+//
+// Author: keir@google.com (Keir Mierle)
+//         sameeragarwal@google.com (Sameer Agarwal)
+//
+// System level tests for Ceres. The current suite of two tests. The
+// first test is a small test based on Powell's Function. It is a
+// scalar problem with 4 variables. The second problem is a bundle
+// adjustment problem with 16 cameras and two thousand cameras. The
+// first problem is to test the sanity test the factorization based
+// solvers. The second problem is used to test the various
+// combinations of solvers, orderings, preconditioners and
+// multithreading.
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <string>
+
+#include "ceres/autodiff_cost_function.h"
+#include "ceres/ordered_groups.h"
+#include "ceres/problem.h"
+#include "ceres/rotation.h"
+#include "ceres/solver.h"
+#include "ceres/stringprintf.h"
+#include "ceres/test_util.h"
+#include "ceres/types.h"
+#include "gflags/gflags.h"
+#include "glog/logging.h"
+#include "gtest/gtest.h"
+
+namespace ceres {
+namespace internal {
+
+const bool kAutomaticOrdering = true;
+const bool kUserOrdering = false;
+
+// Struct used for configuring the solver.
+struct SolverConfig {
+  SolverConfig(LinearSolverType linear_solver_type,
+               SparseLinearAlgebraLibraryType sparse_linear_algebra_library,
+               bool use_automatic_ordering)
+      : linear_solver_type(linear_solver_type),
+        sparse_linear_algebra_library(sparse_linear_algebra_library),
+        use_automatic_ordering(use_automatic_ordering),
+        preconditioner_type(IDENTITY),
+        num_threads(1) {
+  }
+
+  SolverConfig(LinearSolverType linear_solver_type,
+               SparseLinearAlgebraLibraryType sparse_linear_algebra_library,
+               bool use_automatic_ordering,
+               PreconditionerType preconditioner_type)
+      : linear_solver_type(linear_solver_type),
+        sparse_linear_algebra_library(sparse_linear_algebra_library),
+        use_automatic_ordering(use_automatic_ordering),
+        preconditioner_type(preconditioner_type),
+        num_threads(1) {
+  }
+
+  string ToString() const {
+    return StringPrintf(
+        "(%s, %s, %s, %s, %d)",
+        LinearSolverTypeToString(linear_solver_type),
+        SparseLinearAlgebraLibraryTypeToString(sparse_linear_algebra_library),
+        use_automatic_ordering ? "AUTOMATIC" : "USER",
+        PreconditionerTypeToString(preconditioner_type),
+        num_threads);
+  }
+
+  LinearSolverType linear_solver_type;
+  SparseLinearAlgebraLibraryType sparse_linear_algebra_library;
+  bool use_automatic_ordering;
+  PreconditionerType preconditioner_type;
+  int num_threads;
+};
+
+// Templated function that given a set of solver configurations,
+// instantiates a new copy of SystemTestProblem for each configuration
+// and solves it. The solutions are expected to have residuals with
+// coordinate-wise maximum absolute difference less than or equal to
+// max_abs_difference.
+//
+// The template parameter SystemTestProblem is expected to implement
+// the following interface.
+//
+//   class SystemTestProblem {
+//     public:
+//       SystemTestProblem();
+//       Problem* mutable_problem();
+//       Solver::Options* mutable_solver_options();
+//   };
+template <typename SystemTestProblem>
+void RunSolversAndCheckTheyMatch(const vector<SolverConfig>& configurations,
+                                 const double max_abs_difference) {
+  int num_configurations = configurations.size();
+  vector<SystemTestProblem*> problems;
+  vector<Solver::Summary> summaries(num_configurations);
+
+  for (int i = 0; i < num_configurations; ++i) {
+    SystemTestProblem* system_test_problem = new SystemTestProblem();
+
+    const SolverConfig& config = configurations[i];
+
+    Solver::Options& options = *(system_test_problem->mutable_solver_options());
+    options.linear_solver_type = config.linear_solver_type;
+    options.sparse_linear_algebra_library =
+        config.sparse_linear_algebra_library;
+    options.preconditioner_type = config.preconditioner_type;
+    options.num_threads = config.num_threads;
+    options.num_linear_solver_threads = config.num_threads;
+    options.return_final_residuals = true;
+
+    if (config.use_automatic_ordering) {
+      delete options.linear_solver_ordering;
+      options.linear_solver_ordering = NULL;
+    }
+
+    LOG(INFO) << "Running solver configuration: "
+              << config.ToString();
+
+    Solve(options,
+          system_test_problem->mutable_problem(),
+          &summaries[i]);
+
+    CHECK_NE(summaries[i].termination_type, ceres::NUMERICAL_FAILURE)
+        << "Solver configuration " << i << " failed.";
+    problems.push_back(system_test_problem);
+
+    // Compare the resulting solutions to each other. Arbitrarily take
+    // SPARSE_NORMAL_CHOLESKY as the golden solve. We compare
+    // solutions by comparing their residual vectors. We do not
+    // compare parameter vectors because it is much more brittle and
+    // error prone to do so, since the same problem can have nearly
+    // the same residuals at two completely different positions in
+    // parameter space.
+    if (i > 0) {
+      const vector<double>& reference_residuals = summaries[0].final_residuals;
+      const vector<double>& current_residuals = summaries[i].final_residuals;
+
+      for (int j = 0; j < reference_residuals.size(); ++j) {
+        EXPECT_NEAR(current_residuals[j],
+                    reference_residuals[j],
+                    max_abs_difference)
+            << "Not close enough residual:" << j
+            << " reference " << reference_residuals[j]
+            << " current " << current_residuals[j];
+      }
+    }
+  }
+
+  for (int i = 0; i < num_configurations; ++i) {
+    delete problems[i];
+  }
+}
+
+// This class implements the SystemTestProblem interface and provides
+// access to an implementation of Powell's singular function.
+//
+//   F = 1/2 (f1^2 + f2^2 + f3^2 + f4^2)
+//
+//   f1 = x1 + 10*x2;
+//   f2 = sqrt(5) * (x3 - x4)
+//   f3 = (x2 - 2*x3)^2
+//   f4 = sqrt(10) * (x1 - x4)^2
+//
+// The starting values are x1 = 3, x2 = -1, x3 = 0, x4 = 1.
+// The minimum is 0 at (x1, x2, x3, x4) = 0.
+//
+// From: Testing Unconstrained Optimization Software by Jorge J. More, Burton S.
+// Garbow and Kenneth E. Hillstrom in ACM Transactions on Mathematical Software,
+// Vol 7(1), March 1981.
+class PowellsFunction {
+ public:
+  PowellsFunction() {
+    x_[0] =  3.0;
+    x_[1] = -1.0;
+    x_[2] =  0.0;
+    x_[3] =  1.0;
+
+    problem_.AddResidualBlock(
+        new AutoDiffCostFunction<F1, 1, 1, 1>(new F1), NULL, &x_[0], &x_[1]);
+    problem_.AddResidualBlock(
+        new AutoDiffCostFunction<F2, 1, 1, 1>(new F2), NULL, &x_[2], &x_[3]);
+    problem_.AddResidualBlock(
+        new AutoDiffCostFunction<F3, 1, 1, 1>(new F3), NULL, &x_[1], &x_[2]);
+    problem_.AddResidualBlock(
+        new AutoDiffCostFunction<F4, 1, 1, 1>(new F4), NULL, &x_[0], &x_[3]);
+
+    options_.max_num_iterations = 10;
+  }
+
+  Problem* mutable_problem() { return &problem_; }
+  Solver::Options* mutable_solver_options() { return &options_; }
+
+ private:
+  // Templated functions used for automatically differentiated cost
+  // functions.
+  class F1 {
+   public:
+    template <typename T> bool operator()(const T* const x1,
+                                          const T* const x2,
+                                          T* residual) const {
+      // f1 = x1 + 10 * x2;
+      *residual = *x1 + T(10.0) * *x2;
+      return true;
+    }
+  };
+
+  class F2 {
+   public:
+    template <typename T> bool operator()(const T* const x3,
+                                          const T* const x4,
+                                          T* residual) const {
+      // f2 = sqrt(5) (x3 - x4)
+      *residual = T(sqrt(5.0)) * (*x3 - *x4);
+      return true;
+    }
+  };
+
+  class F3 {
+   public:
+    template <typename T> bool operator()(const T* const x2,
+                                          const T* const x4,
+                                          T* residual) const {
+      // f3 = (x2 - 2 x3)^2
+      residual[0] = (x2[0] - T(2.0) * x4[0]) * (x2[0] - T(2.0) * x4[0]);
+      return true;
+    }
+  };
+
+  class F4 {
+   public:
+    template <typename T> bool operator()(const T* const x1,
+                                          const T* const x4,
+                                          T* residual) const {
+      // f4 = sqrt(10) (x1 - x4)^2
+      residual[0] = T(sqrt(10.0)) * (x1[0] - x4[0]) * (x1[0] - x4[0]);
+      return true;
+    }
+  };
+
+  double x_[4];
+  Problem problem_;
+  Solver::Options options_;
+};
+
+TEST(SystemTest, PowellsFunction) {
+  vector<SolverConfig> configs;
+#define CONFIGURE(linear_solver, sparse_linear_algebra_library, ordering) \
+  configs.push_back(SolverConfig(linear_solver,                           \
+                                 sparse_linear_algebra_library,           \
+                                 ordering))
+
+  CONFIGURE(DENSE_QR,               SUITE_SPARSE, kAutomaticOrdering);
+  CONFIGURE(DENSE_NORMAL_CHOLESKY,  SUITE_SPARSE, kAutomaticOrdering);
+  CONFIGURE(DENSE_SCHUR,            SUITE_SPARSE, kAutomaticOrdering);
+
+#ifndef CERES_NO_SUITESPARSE
+  CONFIGURE(SPARSE_NORMAL_CHOLESKY, SUITE_SPARSE, kAutomaticOrdering);
+#endif  // CERES_NO_SUITESPARSE
+
+#ifndef CERES_NO_CXSPARSE
+  CONFIGURE(SPARSE_NORMAL_CHOLESKY, CX_SPARSE,    kAutomaticOrdering);
+#endif  // CERES_NO_CXSPARSE
+
+  CONFIGURE(ITERATIVE_SCHUR,        SUITE_SPARSE, kAutomaticOrdering);
+
+#undef CONFIGURE
+
+  const double kMaxAbsoluteDifference = 1e-8;
+  RunSolversAndCheckTheyMatch<PowellsFunction>(configs, kMaxAbsoluteDifference);
+}
+
+// This class implements the SystemTestProblem interface and provides
+// access to a bundle adjustment problem. It is based on
+// examples/bundle_adjustment_example.cc. Currently a small 16 camera
+// problem is hard coded in the constructor. Going forward we may
+// extend this to a larger number of problems.
+class BundleAdjustmentProblem {
+ public:
+  BundleAdjustmentProblem() {
+    const string input_file = TestFileAbsolutePath("problem-16-22106-pre.txt");
+    ReadData(input_file);
+    BuildProblem();
+  }
+
+  ~BundleAdjustmentProblem() {
+    delete []point_index_;
+    delete []camera_index_;
+    delete []observations_;
+    delete []parameters_;
+  }
+
+  Problem* mutable_problem() { return &problem_; }
+  Solver::Options* mutable_solver_options() { return &options_; }
+
+  int num_cameras()            const { return num_cameras_;        }
+  int num_points()             const { return num_points_;         }
+  int num_observations()       const { return num_observations_;   }
+  const int* point_index()     const { return point_index_;  }
+  const int* camera_index()    const { return camera_index_; }
+  const double* observations() const { return observations_; }
+  double* mutable_cameras() { return parameters_; }
+  double* mutable_points() { return parameters_  + 9 * num_cameras_; }
+
+ private:
+  void ReadData(const string& filename) {
+    FILE * fptr = fopen(filename.c_str(), "r");
+
+    if (!fptr) {
+      LOG(FATAL) << "File Error: unable to open file " << filename;
+    };
+
+    // This will die horribly on invalid files. Them's the breaks.
+    FscanfOrDie(fptr, "%d", &num_cameras_);
+    FscanfOrDie(fptr, "%d", &num_points_);
+    FscanfOrDie(fptr, "%d", &num_observations_);
+
+    VLOG(1) << "Header: " << num_cameras_
+            << " " << num_points_
+            << " " << num_observations_;
+
+    point_index_ = new int[num_observations_];
+    camera_index_ = new int[num_observations_];
+    observations_ = new double[2 * num_observations_];
+
+    num_parameters_ = 9 * num_cameras_ + 3 * num_points_;
+    parameters_ = new double[num_parameters_];
+
+    for (int i = 0; i < num_observations_; ++i) {
+      FscanfOrDie(fptr, "%d", camera_index_ + i);
+      FscanfOrDie(fptr, "%d", point_index_ + i);
+      for (int j = 0; j < 2; ++j) {
+        FscanfOrDie(fptr, "%lf", observations_ + 2*i + j);
+      }
+    }
+
+    for (int i = 0; i < num_parameters_; ++i) {
+      FscanfOrDie(fptr, "%lf", parameters_ + i);
+    }
+  }
+
+  void BuildProblem() {
+    double* points = mutable_points();
+    double* cameras = mutable_cameras();
+
+    for (int i = 0; i < num_observations(); ++i) {
+      // Each Residual block takes a point and a camera as input and
+      // outputs a 2 dimensional residual.
+      CostFunction* cost_function =
+          new AutoDiffCostFunction<BundlerResidual, 2, 9, 3>(
+              new BundlerResidual(observations_[2*i + 0],
+                                  observations_[2*i + 1]));
+
+      // Each observation correponds to a pair of a camera and a point
+      // which are identified by camera_index()[i] and
+      // point_index()[i] respectively.
+      double* camera = cameras + 9 * camera_index_[i];
+      double* point = points + 3 * point_index()[i];
+      problem_.AddResidualBlock(cost_function, NULL, camera, point);
+    }
+
+    options_.linear_solver_ordering = new ParameterBlockOrdering;
+
+    // The points come before the cameras.
+    for (int i = 0; i < num_points_; ++i) {
+      options_.linear_solver_ordering->AddElementToGroup(points + 3 * i, 0);
+    }
+
+    for (int i = 0; i < num_cameras_; ++i) {
+      options_.linear_solver_ordering->AddElementToGroup(cameras + 9 * i, 1);
+    }
+
+    options_.max_num_iterations = 25;
+    options_.function_tolerance = 1e-10;
+    options_.gradient_tolerance = 1e-10;
+    options_.parameter_tolerance = 1e-10;
+  }
+
+  template<typename T>
+  void FscanfOrDie(FILE *fptr, const char *format, T *value) {
+    int num_scanned = fscanf(fptr, format, value);
+    if (num_scanned != 1) {
+      LOG(FATAL) << "Invalid UW data file.";
+    }
+  }
+
+  // Templated pinhole camera model.  The camera is parameterized
+  // using 9 parameters. 3 for rotation, 3 for translation, 1 for
+  // focal length and 2 for radial distortion. The principal point is
+  // not modeled (i.e. it is assumed be located at the image center).
+  struct BundlerResidual {
+    // (u, v): the position of the observation with respect to the image
+    // center point.
+    BundlerResidual(double u, double v): u(u), v(v) {}
+
+    template <typename T>
+    bool operator()(const T* const camera,
+                    const T* const point,
+                    T* residuals) const {
+      T p[3];
+      AngleAxisRotatePoint(camera, point, p);
+
+      // Add the translation vector
+      p[0] += camera[3];
+      p[1] += camera[4];
+      p[2] += camera[5];
+
+      const T& focal = camera[6];
+      const T& l1 = camera[7];
+      const T& l2 = camera[8];
+
+      // Compute the center of distortion.  The sign change comes from
+      // the camera model that Noah Snavely's Bundler assumes, whereby
+      // the camera coordinate system has a negative z axis.
+      T xp = - focal * p[0] / p[2];
+      T yp = - focal * p[1] / p[2];
+
+      // Apply second and fourth order radial distortion.
+      T r2 = xp*xp + yp*yp;
+      T distortion = T(1.0) + r2  * (l1 + l2  * r2);
+
+      residuals[0] = distortion * xp - T(u);
+      residuals[1] = distortion * yp - T(v);
+
+      return true;
+    }
+
+    double u;
+    double v;
+  };
+
+
+  Problem problem_;
+  Solver::Options options_;
+
+  int num_cameras_;
+  int num_points_;
+  int num_observations_;
+  int num_parameters_;
+
+  int* point_index_;
+  int* camera_index_;
+  double* observations_;
+  // The parameter vector is laid out as follows
+  // [camera_1, ..., camera_n, point_1, ..., point_m]
+  double* parameters_;
+};
+
+TEST(SystemTest, BundleAdjustmentProblem) {
+  vector<SolverConfig> configs;
+
+#define CONFIGURE(linear_solver, sparse_linear_algebra_library, ordering, preconditioner) \
+  configs.push_back(SolverConfig(linear_solver,                         \
+                                 sparse_linear_algebra_library,         \
+                                 ordering,                              \
+                                 preconditioner))
+
+#ifndef CERES_NO_SUITESPARSE
+  CONFIGURE(SPARSE_NORMAL_CHOLESKY, SUITE_SPARSE, kAutomaticOrdering, IDENTITY);
+  CONFIGURE(SPARSE_NORMAL_CHOLESKY, SUITE_SPARSE, kUserOrdering,      IDENTITY);
+
+  CONFIGURE(SPARSE_SCHUR,           SUITE_SPARSE, kAutomaticOrdering, IDENTITY);
+  CONFIGURE(SPARSE_SCHUR,           SUITE_SPARSE, kUserOrdering,      IDENTITY);
+#endif  // CERES_NO_SUITESPARSE
+
+#ifndef CERES_NO_CXSPARSE
+  CONFIGURE(SPARSE_SCHUR,           CX_SPARSE,    kAutomaticOrdering, IDENTITY);
+  CONFIGURE(SPARSE_SCHUR,           CX_SPARSE,    kUserOrdering,      IDENTITY);
+#endif  // CERES_NO_CXSPARSE
+
+  CONFIGURE(DENSE_SCHUR,            SUITE_SPARSE, kAutomaticOrdering, IDENTITY);
+  CONFIGURE(DENSE_SCHUR,            SUITE_SPARSE, kUserOrdering,      IDENTITY);
+
+  CONFIGURE(CGNR,                   SUITE_SPARSE, kAutomaticOrdering, JACOBI);
+  CONFIGURE(ITERATIVE_SCHUR,        SUITE_SPARSE, kUserOrdering,      JACOBI);
+
+#ifndef CERES_NO_SUITESPARSE
+  CONFIGURE(ITERATIVE_SCHUR,        SUITE_SPARSE, kUserOrdering,      SCHUR_JACOBI);
+  CONFIGURE(ITERATIVE_SCHUR,        SUITE_SPARSE, kUserOrdering,      CLUSTER_JACOBI);
+  CONFIGURE(ITERATIVE_SCHUR,        SUITE_SPARSE, kUserOrdering,      CLUSTER_TRIDIAGONAL);
+#endif  // CERES_NO_SUITESPARSE
+
+  CONFIGURE(ITERATIVE_SCHUR,        SUITE_SPARSE, kAutomaticOrdering, JACOBI);
+
+#ifndef CERES_NO_SUITESPARSE
+  CONFIGURE(ITERATIVE_SCHUR,        SUITE_SPARSE, kAutomaticOrdering, SCHUR_JACOBI);
+  CONFIGURE(ITERATIVE_SCHUR,        SUITE_SPARSE, kAutomaticOrdering, CLUSTER_JACOBI);
+  CONFIGURE(ITERATIVE_SCHUR,        SUITE_SPARSE, kAutomaticOrdering, CLUSTER_TRIDIAGONAL);
+#endif  // CERES_NO_SUITESPARSE
+
+#undef CONFIGURE
+
+  // Single threaded evaluators and linear solvers.
+  const double kMaxAbsoluteDifference = 1e-4;
+  RunSolversAndCheckTheyMatch<BundleAdjustmentProblem>(configs,
+                                                       kMaxAbsoluteDifference);
+
+#ifdef CERES_USE_OPENMP
+  // Multithreaded evaluators and linear solvers.
+  for (int i = 0; i < configs.size(); ++i) {
+    configs[i].num_threads = 2;
+  }
+  RunSolversAndCheckTheyMatch<BundleAdjustmentProblem>(configs,
+                                                       kMaxAbsoluteDifference);
+#endif  // CERES_USE_OPENMP
+}
+
+}  // namespace internal
+}  // namespace ceres