structs.cpp

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/*
 * structs.cpp
 *
 *  Created on: Jul 25, 2010
 *      Author: sturm
 */

#include "structs.h"
#include "hogman_wrapper.h"
#include "boost/tuple/tuple.hpp"

using namespace std;
using namespace articulation_models;
using namespace geometry_msgs;
using namespace articulation_msgs;
using namespace std_msgs;
using namespace sensor_msgs;
using namespace articulation_structure;
using namespace Eigen;

USING_PART_OF_NAMESPACE_EIGEN

KinematicParams::KinematicParams() {
        sigma_position = 0.005;
        sigma_orientation = 0.001;
        eval_every = 1;
        eval_every_power = 1.0;
        supress_similar = false;
        reuse_model = true;
        restricted_graphs = "";
        restrict_graphs = false;
        reduce_dofs = false;
        search_all_models = false;
        full_eval="tree";
}

void KinematicParams::LoadParams(ros::NodeHandle &nh_local,bool show) {
        string filter_models("rigid rotational prismatic");
        nh_local.getParam("filter_models", filter_models);
        nh_local.getParam("sigma_position", sigma_position);
        nh_local.getParam("sigma_orientation", sigma_orientation);
        nh_local.getParam("sigmax_position", sigmax_position);
        nh_local.getParam("sigmax_orientation", sigmax_orientation);
        nh_local.getParam("full_eval", full_eval);
        nh_local.getParam("eval_every", eval_every);
        nh_local.getParam("eval_every_power", eval_every_power);
        nh_local.getParam("restricted_graphs", restricted_graphs);
        restricted_graphs = " "+restricted_graphs+" ";
        nh_local.getParam("restrict_graphs", restrict_graphs);

        nh_local.getParam("reuse_model", reuse_model);
        nh_local.getParam("supress_similar", supress_similar);
        nh_local.getParam("reduce_dofs", reduce_dofs);
        nh_local.getParam("search_all_models", search_all_models);

        factory.setFilter(filter_models);

}

void KinematicData::addPose(PoseStamped pose1, PoseStamped pose2, size_t id1, size_t id2,KinematicParams &params) {
        TrackMsgPtr& track = trajectories[id1][id2];
        if (!track) {
                track = boost::make_shared<TrackMsg>();
                ChannelFloat32 ch;
                ch.name = "stamp";
                track->channels.push_back(ch);
        }

        btTransform transf1 = poseToTransform(pose1.pose);
        btTransform transf2 = poseToTransform(pose2.pose);
        btTransform diff = transf1.inverseTimes(transf2);

        for(size_t i=0;i<trajectories[id1][id2]->pose.size();i++) {
                btTransform diff_to_known;
                Pose p;
                p = trajectories[id1][id2]->pose[i];
                btTransform t;
                t = poseToTransform( p );
                diff_to_known = t.inverseTimes( diff );
                double diff_position = diff_to_known.getOrigin().length();
                double diff_orientation = fabs(diff_to_known.getRotation().getAngle());
                if(params.supress_similar && diff_position < params.sigma_position/2 && diff_orientation < params.sigma_orientation/2) {
//                      cout <<"skipping relative pose information, too close to known sample"<<endl;
                        return;
                }
        }

        poseIndex[id1][id2][ pose1.header.stamp.toSec() ] = track->pose.size();

        track->pose.push_back(transformToPose( diff));
        track->channels[0].values.push_back( pose1.header.stamp.toSec() );
        track->header = pose1.header;

//      updateModel(id1, id2);
}

void KinematicData::updateModel(size_t id1, size_t id2,KinematicParams &params) {
        TrackMsgPtr& track = trajectories[id1][id2];
        GenericModelPtr& model = models[id1][id2];

        articulation_msgs::ModelMsg model_track;
        model_track.track = *track;
        model_track.header = track->header;
        setParamIfNotDefined(model_track.params, "sigma_position",
                        params.sigma_position, ParamMsg::PRIOR);
        setParamIfNotDefined(model_track.params, "sigma_orientation",
                        params.sigma_orientation, ParamMsg::PRIOR);

        GenericModelVector models_new = params.factory.createModels(model_track);
    map<double,GenericModelPtr> models_sorted;
    models_all[id1][id2].clear();
        for (size_t i = 0; i < models_new.size(); i++) {
                if (!models_new[i]->fitModel()) continue;
                if (!models_new[i]->fitMinMaxConfigurations()) continue;
                if (!models_new[i]->evaluateModel()) continue;
                if(isnan( models_new[i]->getBIC() )) continue;

                if(params.reuse_model && model && model->getModelName()==models_new[i]->getModelName()) {
                        model->setTrack(*track);
                        model->optimizeParameters();
                        model->evaluateModel();
                        if(!isnan( model->getBIC() ) &&
                                        (models_new[i]->getBIC() > model->getBIC())) {
                                models_new[i] = model;
                        }
                }

                models_sorted[models_new[i]->getBIC()] = models_new[i];
                models_all[id1][id2].push_back( models_new[i] );
        }

        if(models_sorted.size()==0) {
                ROS_INFO_STREAM("no models!! model["<<id1<<","<<id2<<"]: poses="<<track->pose.size());
                model.reset();
                return;
        }
        map<double,GenericModelPtr>::iterator it = models_sorted.begin();
        model = it->second;

//      model->evaluateModel();
//      while(it!=models_sorted.end()) {
//              ROS_INFO_STREAM(
//                      "model["<<id1<<","<<id2<<"]: poses="<<it->second->getSamples()<<
//                      ", type='"<<it->second->getModelName()<<
//                      ", BIC="<<it->first<<", logDL="<<it->second->loglikelihood<<", k="<<it->second->complexity<<
//                      " pos="<<it->second->getParam("avg_error_position")<<
//                      " orient="<<it->second->getParam("avg_error_orientation")
//              );
//              it++;
//      }
}

std::vector<double> KinematicData::intersectionOfStamps() {
        // timestamps where all markers were detected
        std::vector<double> intersection;

        size_t num_markers = markerStamped.size();
        for(map<double, map<int, PoseStampedIdMsgConstPtr> >::iterator it = stampedMarker.begin();
                        it != stampedMarker.end();
                        it++) {
                if(it->second.size() == num_markers) {
                        intersection.push_back( it->first );
                }

//              cout <<"timestamp "<<(it->first - stampedMarker.begin()->first )<<" markers "<<it->second.size()<<" total "<<num_markers<<" ";
//              for(map<int, PoseStampedIdMsgConstPtr>::iterator j = it->second.begin();j!=it->second.end();j++) {
//                      cout << " "<<j->first;
//              }
//              cout << endl;
        }

//      ROS_INFO_STREAM("full visibility rate: "<< intersection.size() / (double) stampedMarker.size() );
        return(intersection);
}

PoseMap KinematicData::getObservation(double timestamp) {
        PoseMap observedMarkers;
        for(std::map<int, articulation_structure::PoseStampedIdMsgConstPtr>::iterator it = stampedMarker[timestamp].begin();
                        it != stampedMarker[timestamp].end();it++) {
                observedMarkers[it->first] = it->second->pose.pose;
        }
        return observedMarkers;
}

KinematicGraph::KinematicGraph() {
        BIC = DBL_MAX;
        DOF = -1;
        avg_pos_err = -1;
        avg_orient_err = -1;
        loglh = DBL_MAX;
}

KinematicGraph::KinematicGraph(const KinematicGraph &other):
        KinematicGraphType( other ), BIC(other.BIC),DOF(other.DOF),avg_pos_err(other.avg_pos_err),avg_orient_err(other.avg_orient_err),loglh(other.loglh)
{
}

KinematicGraph::KinematicGraph(const KinematicGraph &other,bool deepcopy):
                        KinematicGraphType( other ), BIC(other.BIC),DOF(other.DOF),avg_pos_err(other.avg_pos_err),avg_orient_err(other.avg_orient_err),loglh(other.loglh)
{
        if(deepcopy) {
                CopyFrom(other);
        }
}

void KinematicGraph::CopyFrom(const KinematicGraph &other) {
        *this = other;
        static MultiModelFactory factory;
        for(KinematicGraph::iterator it=begin();it!=end();it++) {
                it->second = factory.restoreModel(it->second->getModel());
        }
}


size_t KinematicGraph::getNumberOfParameters() {
        size_t k = 0;
        for(KinematicGraph::iterator it=begin(); it != end();it++) {
                k += (size_t) it->second->complexity;
        }
        return k;
}



int KinematicGraph::getNominalDOFs() {
        int DOFs = 0;
        for(KinematicGraph::iterator it=begin(); it != end();it++) {
                DOFs += it->second->getDOFs();
        }
        return(DOFs);
}

PoseMap KinematicGraph::getPrediction(double timestamp, PoseMap &observedMarkers, PoseMap &predictedMarkersEmpty, KinematicParams &params,KinematicData &data) {
        return hogman_solver(*this, data.poseIndex, observedMarkers, predictedMarkersEmpty, params.sigma_position,params.sigma_orientation, timestamp);
}

string KinematicGraph::getTreeName(bool show_name,bool show_samples,bool show_dof) {
        stringstream s;
        if(show_dof) {
                s << DOF<<"-DOF ";
        }
        for(KinematicGraph::iterator it=begin(); it != end();it++) {
                if(it != begin()) s<<",";
                s << "(";
                if(show_name) {
                        s <<it->second->getModelName().substr(0,2)<<":";
                }
                s <<it->first.first<<","<<it->first.second;
                if(show_samples)
                        s << "/"<<it->second->getSamples();
                s<<")";
        }
        return s.str();
}

void KinematicGraph::evaluateSingleStamp(double timestamp,
                                double &avgPositionError,
                                double &avgOrientationError,
                                double &loglikelihood,KinematicParams &params,KinematicData &data) {

        if (size()==0) return;
        // compare observation versus prediction
        PoseMap observationMarkers = data.getObservation(timestamp);
        PoseMap predictedMarkers = getPrediction(timestamp,observationMarkers,observationMarkers,params,data);

        // store predicted poses
        for(PoseMap::iterator i=predictedMarkers.begin();i!=predictedMarkers.end();i++) {
                PoseStampedIdMsg p = *data.stampedMarker[timestamp][i->first];
                p.pose.pose = i->second;
                PoseStampedIdMsgConstPtr pptr = boost::make_shared<PoseStampedIdMsg>(p);
                data.stampedMarkerProjected[timestamp][i->first] = pptr;
        }

        // output data loglikelihood
        double sum_loglh = 0;
        double sum_pos2_err = 0;
        double sum_orient2_err = 0;

        double sigma2_position = SQR(params.sigmax_position);
        double sigma2_orientation = SQR(params.sigmax_orientation);

        for(PoseMap::iterator it = observationMarkers.begin();
                        it != observationMarkers.end(); it++ ) {
                btTransform p1 = poseToTransform(observationMarkers[it->first]);
                btTransform p2 = poseToTransform(predictedMarkers[it->first]);

                btTransform diff = p1.inverseTimes(p2);
                double err_position2 = diff.getOrigin().length2();
                if(isnan(err_position2 )) err_position2 =0;
                double err_orientation2 = SQR(diff.getRotation().getAngle());
                if(isnan(err_orientation2 )) err_orientation2 =0;

                sum_pos2_err += err_position2;
                sum_orient2_err += err_orientation2;

                double loglikelihood =
                                - log(2*M_PI * params.sigma_position*params.sigma_orientation)
                                - 0.5*(
                                                ( err_position2 / (sigma2_position) ) +
                                                ( err_orientation2 / (sigma2_orientation) ) );  // 2-dim multivariate normal distribution
                sum_loglh += loglikelihood;
        }

        size_t n = observationMarkers.size();
        avgPositionError = sqrt(sum_pos2_err/n);
        avgOrientationError = sqrt(sum_orient2_err/n);
        loglikelihood = sum_loglh;
}

void KinematicGraph::evaluate(
                std::vector<double> stamps,
                KinematicParams &params,KinematicData &data) {
        // first, copy our data
        static MultiModelFactory factory;
        for(KinematicGraph::iterator it=begin();it!=end();it++) {
                it->second = factory.restoreModel(it->second->getModel());
        }

        BIC = DBL_MAX;
        avg_pos_err = DBL_MAX;
        avg_orient_err = DBL_MAX;
        loglh = DBL_MIN;

        if (size()==0) return;

        if(DOF != getNominalDOFs())
                projectConfigurationSpace(DOF,stamps,params,data);

//      cout << getTreeName(true,true,true);

        double sum_pos2_err = 0;
        double sum_orient2_err = 0;
        double sum_loglh = 0;

        double pos_err,orient_err;

        data.stampedMarkerProjected.clear();
        for(size_t i=0;i<stamps.size();i++) {
                evaluateSingleStamp(stamps[i],pos_err, orient_err, loglh,params,data );
                sum_loglh += loglh;
                sum_pos2_err += SQR(pos_err);
                sum_orient2_err += SQR(orient_err);
        }

        avg_pos_err = sqrt(sum_pos2_err/stamps.size());
        avg_orient_err = sqrt(orient_err/stamps.size());
        loglh = sum_loglh;

        k = getNumberOfParameters();
        int k_pca = 0;
        double loglh_pca;
        if(DOF != getNominalDOFs()) {
                k_pca = getNominalDOFs() * DOF; // extra parameters needed to store projection matrix
                loglh_pca = stamps.size() * (getNominalDOFs() - DOF) * log(stamps.size());      // correct likelihood for reduced dimensionality of configuration space
        }
        BIC = getBIC( loglh + loglh_pca, k + k_pca,stamps.size() );     // BIC with penalty for size of configuratino space
//      cout << ": loglh="<<loglh<<" pos="<<avg_pos_err<<" orient="<<avg_orient_err<<" k="<<k<<" BIC="<<BIC << endl;
        return;
}

void KinematicGraph::projectConfigurationSpace(int reducedDOFs,std::vector<double> stamps, KinematicParams &params,KinematicData &data) {
        if(reducedDOFs == 0) return;
        if(stamps.size() == 0) return;

        map< GenericModelPtr, int> DOFoffsets;
        int DOFs = 0;
        for(KinematicGraph::iterator it=begin(); it != end();it++) {
                DOFoffsets[it->second] = DOFs;
                DOFs += it->second->getDOFs();
        }
        if(DOFs==0) return;

        MatrixXf X_trans(stamps.size(), DOFs);

        for(KinematicGraph::iterator it=begin(); it != end();it++) {
                GenericModelPtr model = it->second;
                int DOFoffset = DOFoffsets[model];

                if(model->getDOFs()==0) continue;

                for(size_t timestamp_idx = 0;timestamp_idx < stamps.size();timestamp_idx++) {
                        int idx = data.poseIndex[ it->first.first ][it->first.second][ stamps[timestamp_idx]];

                        VectorXd c = model->getConfiguration(idx);
                        for(size_t d=0;d< model->getDOFs();d++) {
                                X_trans( timestamp_idx,DOFoffset + d ) = c(d);
                        }
                }
        }

        VectorXf X_mean = VectorXf::Zero(DOFs,1);
        for( size_t i=0;i< stamps.size();i++) {
                for( int j=0;j< DOFs;j++) {
                        X_mean(j) += X_trans(i,j);
                }
        }
        X_mean /= stamps.size();


        // check for nans or large numbers (crash eigen while svd'ing)
        for( int j=0;j< DOFs;j++) {
                if(isnan(X_mean(j))) {
                        cout << X_trans << endl<<endl;
                        cout << X_mean << endl;
                        cout <<"reducing DOFs failed, NaN value"<<endl;
                        return;
                }
                if(fabs(X_mean(j))>100) {
                        cout << X_trans << endl<<endl;
                        cout << X_mean << endl;
                        cout <<"reducing DOFs failed, large value"<<endl;
                        return;
                }
        }

        MatrixXf X_center(stamps.size(), DOFs);
        for( size_t i=0;i< stamps.size();i++) {
                for( int j=0;j< DOFs;j++) {
                        X_center(i,j) = X_trans(i,j) - X_mean(j);
                }
        }

        if(stamps.size() < (size_t)DOFs) return;
        SVD<MatrixXf> svdOfA(X_center);
        const Eigen::MatrixXf U = svdOfA.matrixU();
        const Eigen::MatrixXf V = svdOfA.matrixV();
        const Eigen::VectorXf S = svdOfA.singularValues();

        //DiagonalMatrix<Eigen::VectorXf> S2(S);
        Eigen::MatrixXf V_projection = V.block(0,0,DOFs,reducedDOFs);
        MatrixXf X_reduced(stamps.size(),reducedDOFs);

        for( size_t i=0;i< stamps.size();i++) {
                for( int k=0;k< reducedDOFs;k++) {
                        X_reduced(i,k) = 0.0;
                        for( int j=0;j< DOFs;j++) {
                                X_reduced(i,k) += V(j,k) * X_center(i,j);
                        }
                }
        }

        MatrixXf X_projected(stamps.size(),DOFs);
        for( size_t i=0;i< stamps.size();i++) {
                for( int j=0;j< DOFs;j++) {
                        X_projected(i,j) = X_mean(j);
                        for( int k=0;k< reducedDOFs;k++) {
                                X_projected(i,j) += V(j,k) * X_reduced(i,k);
                        }
                }
        }

        for(KinematicGraph::iterator it=begin(); it != end();it++) {
                GenericModelPtr model = it->second;
                if(model->getDOFs()==0) continue;
                int DOFoffset = DOFoffsets[model];

                for(size_t timestamp_idx = 0;timestamp_idx < stamps.size();timestamp_idx++) {
                        int idx = data.poseIndex[ it->first.first ][it->first.second][ stamps[timestamp_idx]];

                        VectorXd c(model->getDOFs());
                        for(size_t d=0;d< model->getDOFs();d++) {
                                c(d) =X_projected( timestamp_idx,DOFoffset + d );
                        }

                        model->setConfiguration(idx,c);
                        model->model.track.pose_projected[idx] = model->predictPose( c );
                }
        }
        DOF = reducedDOFs;
}

#include "boost/tuple/tuple.hpp"

int KinematicGraph::distanceTo(KinematicGraph &other) {
        int distance = 0;
        distance +=fabs((getNominalDOFs()-DOF) - (other.getNominalDOFs()-other.DOF));

        // first only consider edge differences
        set< pair<int,int> > my_edges,other_edges,diff_edges;
        for(KinematicGraph::iterator it=begin();it!=end();it++) my_edges.insert( pair<int,int>(it->first.first,it->first.second) );
        for(KinematicGraph::iterator it = other.begin();it!=other.end();it++) other_edges.insert(pair<int,int>(it->first.first,it->first.second) );
        set_symmetric_difference(my_edges.begin(),my_edges.end(),other_edges.begin(),other_edges.end(),insert_iterator<set< pair<int,int> > >(diff_edges,diff_edges.begin()) );
        distance += diff_edges.size();  // new/deleted edges

        // now only consider common edges and count model changes
        set< pair<pair<int,int>,string> > my_models,other_models,intersec_models,diff_models;
        for(KinematicGraph::iterator it=begin();it!=end();it++)
                if(diff_edges.find(it->first)==diff_edges.end())
                        my_models.insert( pair<pair<int,int>,string>(pair<int,int>(it->first.first,it->first.second),it->second->getModelName()) );
        for(KinematicGraph::iterator it = other.begin();it!=other.end();it++)
                if(diff_edges.find(it->first)==diff_edges.end())
                        other_models.insert(pair<pair<int,int>,string>(pair<int,int>(it->first.first,it->first.second),it->second->getModelName()) );
        set_symmetric_difference(my_models.begin(),my_models.end(),other_models.begin(),other_models.end(),insert_iterator<set< pair<pair<int,int>,string> > >(diff_models,diff_models.begin()) );
        distance += diff_models.size()/2;       // changed models

        return distance;
}

---

articulation_structure
Author(s): sturm
autogenerated on Fri Jan 11 09:53:11 2013