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189 | /*
* Copyright (c) 2014-2021 National Technology and Engineering
* Solutions of Sandia, LLC. Under the terms of Contract DE-NA0003525
* with National Technology and Engineering Solutions of Sandia, LLC,
* the U.S. Government retains certain rights in this software.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
*
* 2. 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.
*
* 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
* HOLDER 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.
*/
#include "Correlation.h"
#include <tracktable/Analysis/ComputeDBSCANClustering.h>
#include <tracktable/Analysis/DistanceGeometry.h>
#include <tracktable/CommandLineFactories/AssemblerFromCommandLine.h>
#include <tracktable/CommandLineFactories/PointReaderFromCommandLine.h>
#include <tracktable/Domain/FeatureVectors.h>
#include <tracktable/Domain/Terrestrial.h>
#include <boost/timer/timer.hpp>
using FeatureVectorT = tracktable::domain::feature_vectors::FeatureVector<10>;
using TrajectoryT = tracktable::domain::terrestrial::trajectory_type;
using PointT = typename TrajectoryT::point_type;
using PointReaderT = tracktable::PointReader<PointT>;
using PointReaderIteratorT = typename PointReaderT::iterator;
using AssemblerT = tracktable::AssembleTrajectories<TrajectoryT, PointReaderIteratorT>;
static constexpr auto helpmsg = R"(
--------------------------------------------------------------------------------
The cluster example demonstrates:
- Using command line factories to read points and assemble trajectories
- Create features using distance geometries
- Cluster and and assign membership using dbscan
Typical use:
./cluster --input=/data/flights.tsv
Defaults assume a tab separated points file formatted as :
OBJECTID TIMESTAMP LON LAT
--------------------------------------------------------------------------------)";
int main(int _argc, char* _argv[]) {
constexpr auto timerFormat = "\u001b[30;1m %w seconds\u001b[0m\n";
// Set log level to reduce unecessary output
tracktable::set_log_level(tracktable::log::info);
// Create a basic command line option with boost
boost::program_options::options_description commandLineOptions;
commandLineOptions.add_options()("help", "Print help");
// Create command line factories
tracktable::PointReaderFromCommandLine<PointT> readerFactory;
tracktable::AssemblerFromCommandLine<TrajectoryT> assemblerFactory;
// Add options from the factories
readerFactory.addOptions(commandLineOptions);
assemblerFactory.addOptions(commandLineOptions);
// And a command line option for output
commandLineOptions.add_options()("output", bpo::value<std::string>()->default_value("-"),
"file to write to (use '-' for stdout), overridden by 'separate-kmls'");
/** Boost program options using a variable map to tie everything together.
* one parse will have a single variable map. We need to let the factories know
* about this variable map so they can pull information out of it */
auto vm = std::make_shared<boost::program_options::variables_map>();
readerFactory.setVariables(vm);
assemblerFactory.setVariables(vm);
// Parse the command lines, don't forget the 'notify' after
try {
// We use this try/catch to automatically display help when an unknown option is used
boost::program_options::store(
boost::program_options::command_line_parser(_argc, _argv).options(commandLineOptions).run(), *vm);
boost::program_options::notify(*vm);
} catch (boost::program_options::error e) {
std::cerr << e.what();
std::cerr << helpmsg << "\n\n";
std::cerr << commandLineOptions << std::endl;
return 1;
}
/** Parsing will give an error of an incorrect option is used, but it won't
* display the help unless we tell it too */
if (vm->count("help") != 0) {
std::cerr << helpmsg << "\n\n";
std::cerr << commandLineOptions << std::endl;
return 1;
}
// Create Point Reader and assembler
auto pointReader = readerFactory.createPointReader();
auto assembler = assemblerFactory.createAssembler(pointReader);
std::vector<std::shared_ptr<TrajectoryT>> trajectories = {};
{
std::cerr << "Assemble Trajectories" << std::endl;
boost::timer::auto_cpu_timer assembleTimer(std::cerr, timerFormat);
auto count = 0u;
std::cerr << std::right;
for (auto tIter = assembler->begin(); tIter != assembler->end(); ++tIter) {
if (tracktable::length(*tIter) < 100) { // filter out standing still
continue;
}
std::cerr << "\b\b\b\b\b\b\b\b\b\b" << std::setw(10) // Using backspaces for in place counter
<< count++;
trajectories.push_back(std::make_shared<TrajectoryT>(*tIter));
}
std::cerr << std::left << "\nStarting with " << trajectories.size() << " trajectories" << std::endl;
}
/* Create a set of features. distance geometry produces a vector of doubles
* and must be transferred to feature vectors to be consumed by certain functions */
std::vector<FeatureVectorT> features;
{
std::cerr << "Build features" << std::endl;
boost::timer::auto_cpu_timer featuretTimer(std::cerr, timerFormat);
for (auto& t : trajectories) {
auto v = tracktable::distance_geometry_by_distance(*t, 4);
FeatureVectorT f;
for (auto i = 0u; i < features.size() && i < v.size(); ++i) {
f[i] = v[i];
}
features.push_back(f);
}
}
using ClusterLabelT = std::pair<int, int>;
using ClusterLabelVectorT = std::vector<ClusterLabelT>;
using IdVectorT = std::vector<int>;
FeatureVectorT search_box;
for (auto i = 0u; i < search_box.size(); ++i) {
search_box[i] = 0.1;
}
ClusterLabelVectorT vertex_cluster_labels;
{
std::cerr << "Cluster with dbscan" << std::endl;
boost::timer::auto_cpu_timer clusterTimer(std::cerr, timerFormat);
tracktable::cluster_with_dbscan(features.begin(), features.end(), search_box, 3,
std::back_inserter(vertex_cluster_labels));
}
std::vector<IdVectorT> membership;
{
std::cerr << "Build Cluster membership List" << std::endl;
boost::timer::auto_cpu_timer membershiptTimer(std::cerr, timerFormat);
tracktable::build_cluster_membership_lists(vertex_cluster_labels.begin(), vertex_cluster_labels.end(),
std::back_inserter(membership));
}
for (unsigned int i = 0; i < membership.size(); ++i) {
std::cerr << i << "(" << std::setw(3) << membership[i].size() << "):";
FeatureVectorT avg;
avg = tracktable::arithmetic::zero<FeatureVectorT>();
for (unsigned int j = 0; j < membership[i].size(); ++j) {
// std::cout << trajectories[membership[i][j]].object_id() << " ";
tracktable::arithmetic::add_in_place(avg, features[membership[i][j]]);
}
tracktable::arithmetic::divide_scalar_in_place(avg, static_cast<double>(membership[i].size()));
std::cerr << avg;
std::cerr << std::endl;
}
std::cerr << "------------------------- Correlation --------------------------\n";
std::cerr << Correlation(features) << std::endl;
return 0;
}
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