pca_gp_model.cpp

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/*
 * pca_gp_model.cpp
 *
 *  Created on: Feb 10, 2010
 *      Author: sturm
 */

#include "articulation_models/models/pca_gp_model.h"
#include "articulation_models/utils.h"

using namespace std;
using namespace articulation_msgs;

#include "Eigen/Core"
#include <Eigen/SVD>

using namespace Eigen;

USING_PART_OF_NAMESPACE_EIGEN

#include <iomanip>
#define VEC(a) setprecision(5)<<fixed<<a.x()<<" "<<a.y()<<" "<<a.z()<<" "<<a.w()<<" l="<<a.length()
#define VEC2(a) "t=["<<VEC(a.getOrigin())<<"] r=[]"<<VEC(a.getRotation())<<"]"
#define PRINT(a) cout << #a <<"=" << VEC(a)<<endl;
#define PRINT2(a) cout << #a <<"=" << VEC2(a)<<endl;

#include <boost/format.hpp>
using namespace boost;

namespace articulation_models {

PCAGPModel::PCAGPModel() {
        complexity = 0;

        downsample = 20;

        //todo:add parameters here
        CovFuncND initialCovFunc;
        double initialSigmaNoise;
        vector<double> params = vector<double>(2);      // DOF + 1
        params[0] = -0.5;       // length scale, dof 1
        params[1] = 0.0;        // sigma
        initialCovFunc.setHyperparameter(params);
        initialSigmaNoise = -5;

        for(size_t i=0;i<7;i++) {
                gp.push_back( new gaussian_process::SingleGP(initialCovFunc,initialSigmaNoise) );
        }

        initialized = false;
        outlier_ratio = 0.0;

}

PCAGPModel::~PCAGPModel() {
        for(size_t i=0;i<gp.size();i++) {
                delete gp[i];
        }
        gp.clear();
}


void PCAGPModel::readParamsFromModel() {
        GenericModel::readParamsFromModel();
        getParam("downsample",downsample);
        getParam("rigid_position",rigid_position);
        getParam("prismatic_dir",prismatic_dir);
        double training_samples_float=0.00;
        getParam("training_samples",training_samples_float);
        training_samples = (int)training_samples_float;
        complexity = 3 + 6*training_samples;

        checkInitialized();//gp needs to build covariance matrix
}

void PCAGPModel::writeParamsToModel() {
        GenericModel::writeParamsToModel();
        setParam("downsample",downsample,ParamMsg::PARAM);
        setParam("rigid_position",rigid_position,ParamMsg::PARAM);
        setParam("prismatic_dir",prismatic_dir,ParamMsg::PARAM);
        setParam("training_samples",training_samples,ParamMsg::PARAM);
}

btTransform PCAGPModel::pose(size_t index) {
        btTransform pose;
        getParam(str(format("pose[%d]")%index),pose);
        return pose;
}

void PCAGPModel::storeData(bool inliersOnly) {
        // copy data into params
        bool resample = false;
        size_t n = model.track.pose.size();

        vector<double> inliers_cum(n,0);
        double sum = 0;
        for(size_t i=0;i<n;i++) {
                if(inliersOnly)
                        sum += 1 - model.track.channels[channelOutlier].values[i];
                else
                        sum += 1;
                inliers_cum[i] = sum;
        }
//      cout <<"inlier sum is "<<sum<<endl;

        training_samples = (int)sum;
        if(downsample>0 && n>downsample) {
                training_samples  = downsample;
                resample = true;
        }
        complexity = 1 + getDOFs() + 6*training_samples;

        for(size_t i=0;i<training_samples;i++) {
                double choice = i / (double)training_samples;
                size_t j=0;
                for(j=0;j<n;j++) {
                        if(inliers_cum[j]/sum>choice) break;
                }
//              cout <<"choosing j="<<j<<endl;
                setParam(str(format("pose[%d]")%i),poseToTransform(model.track.pose[j]),ParamMsg::PARAM);
        }

}

bool PCAGPModel::fitModel() {
        if(getSamples()<3) return true;




        // outlier experimental
        storeData(false);       // use all points
        outlier_ratio = 0.0;
        buildGPs();
        getLogLikelihood(true);
//
//      cout << "outlier ratio="<<this->outlier_ratio<<endl;

        return true;
}

void PCAGPModel::buildGPs() {
        if(training_samples<3) return;
        // fit PCA
        // compute center
        btVector3 sum_p(0,0,0);
        for (size_t j = 0; j < training_samples; j++) {
                sum_p = sum_p + pose(j).getOrigin();
        }
        rigid_position = sum_p / training_samples;

        // find line direction
        MatrixXf X_trans(training_samples, 3);
        for (size_t j = 0; j < training_samples; j++) {
                btVector3 diff = pose(j).getOrigin() - rigid_position;
                X_trans(j, 0) = diff.x();
                X_trans(j, 1) = diff.y();
                X_trans(j, 2) = diff.z();
        }

        VectorXf b(training_samples);
        VectorXf x(3);
        b = VectorXf::Zero(training_samples);
        SVD<MatrixXf> svdOfA(X_trans);
        svdOfA.solve(b, &x);

        const Eigen::MatrixXf U = svdOfA.matrixU();
        const Eigen::MatrixXf V = svdOfA.matrixV();
        const Eigen::VectorXf S = svdOfA.singularValues();

        Eigen::MatrixXf Y_trans = U * S.asDiagonal();
//      cout << endl;
//      cout <<"X=["<<endl;
//      for(int i=0;i<X_trans.rows();i++) {
//              for(int j=0;j<X_trans.cols();j++) {
//                      if(j!=0)
//                              cout <<", ";
//                      cout <<X_trans(i,j);
//              }
//              cout <<";"<<endl;
//      }
//      cout << "]"<<endl;
//      cout << X_trans<<endl;
//      cout << endl;
//      cout << Y_trans<<endl;
//      cout << endl;
//      cout << V;
//      cout << endl;
        prismatic_dir= btVector3(V(0, 0), V(1, 0), V(2, 0));
//      PRINT(prismatic_dir);

        if(!check_values(rigid_position)) {
                cerr <<"rigid_position has NaNs"<<endl;
                return ;
        }
        if(!check_values(prismatic_dir))  {
                cerr <<"prismatic_dir has NaNs"<<endl;
                return ;
        }
//      cout << X_trans << endl;
//      PRINT(rigid_position);
//      PRINT(prismatic_dir);
//      writeParamsToModel();
//      prismatic_dir = btVector3(1,-1,0);
//      prismatic_dir = btVector3(0.48308,-0.87558,0.00000);
//      prismatic_dir = btVector3(0.88215,0.46638,-0.06560);
//      prismatic_dir = btVector3(prismatic_dir.x(),prismatic_dir.y(),prismatic_dir.z());
//      prismatic_dir.normalize();
//      cout <<"fitting:";
//      PRINT(prismatic_dir);


        TVector<TDoubleVector> input(training_samples);
        TVector<double> output[7];
        for(size_t j=0;j<7;j++) {
                output[j] = TDoubleVector(training_samples);
        }

        for(size_t i=0;i<training_samples;i++) {
                input[i] = TDoubleVector(1);

                geometry_msgs::Pose p = transformToPose(pose(i));
                input[i][0] = predictConfiguration( p )[0];
                output[0][i] = p.position.x;
                output[1][i] = p.position.y;
                output[2][i] = p.position.z;
                output[3][i] = p.orientation.w;
                output[4][i] = p.orientation.x;
                output[5][i] = p.orientation.y;
                output[6][i] = p.orientation.z;
        }

        for(size_t j=0;j<7;j++) {
//              cout << "setting data, j="<<j<<" n="<<input.size()<<endl;
                gp[j]->SetData(input,output[j]);
//              gp[j]->OptimizeGP();
        }


 //     cout << "fitting model, end.."<<endl;
}

V_Configuration PCAGPModel::predictConfiguration(geometry_msgs::Pose pose) {
        btVector3 diff = (positionToVector(pose.position) - rigid_position);
//      PRINT(diff);
//      PRINT(prismatic_dir);

        V_Configuration q( 1 );
        q(0) = diff.dot(prismatic_dir);

        return q;
}

geometry_msgs::Pose PCAGPModel::predictPose(V_Configuration q) {
        geometry_msgs::Pose result;
        double mean_x=0,var_x=0;
        double mean_y=0,var_y=0;
        double mean_z=0,var_z=0;
        double mean_rw=0,var_rw=0;
        double mean_rx=0,var_rx=0;
        double mean_ry=0,var_ry=0;
        double mean_rz=0,var_rz=0;
        TDoubleVector inp(1);
        inp(0) = q[0];
        gp[0]->Evaluate( inp, mean_x, var_x );
        gp[1]->Evaluate( inp, mean_y, var_y );
        gp[2]->Evaluate( inp, mean_z, var_z );
        gp[3]->Evaluate( inp, mean_rw, var_rw );
        gp[4]->Evaluate( inp, mean_rx, var_rx );
        gp[5]->Evaluate( inp, mean_ry, var_ry );
        gp[6]->Evaluate( inp, mean_rz, var_rz );

        btQuaternion pred_rot(mean_rx,mean_ry,mean_rz,mean_rw);
        btVector3 pred_pos(mean_x,mean_y,mean_z);
        pred_rot.normalize();
        btTransform pred_pose(pred_rot,pred_pos);
        result = transformToPose(pred_pose);

//      btTransform t( rigid_orientation, rigid_position + prismatic_dir*q[0]);
//      result = transformToPose(t);

        return result;
}

void PCAGPModel::checkInitialized() {
        if(!initialized) {
                buildGPs();
                initialized = true;
        }
}

void PCAGPModel::projectPoseToConfiguration() {
        checkInitialized();
        GenericModel::projectPoseToConfiguration();
}

void PCAGPModel::projectConfigurationToPose() {
        checkInitialized();
        GenericModel::projectConfigurationToPose();
}

void PCAGPModel::projectConfigurationToJacobian() {
        checkInitialized();
        GenericModel::projectConfigurationToJacobian();
}

bool PCAGPModel::evaluateModel() {
        checkInitialized();
        return GenericModel::evaluateModel();
}

bool PCAGPModel::normalizeParameters() {
        if(model.track.pose.size()>2) {
                rigid_position = rigid_position + predictConfiguration(model.track.pose.front())[0] * prismatic_dir;
                if(predictConfiguration(model.track.pose.back())[0]<0)
                        prismatic_dir *= -1;
        }
        return true;
}
}

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articulation_models
Author(s): Juergen Sturm
autogenerated on Fri Jan 11 10:06:58 2013