minor changes to visualization, jakobi tests
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		@@ -56,6 +56,7 @@ MsckfVio::MsckfVio(ros::NodeHandle& pnh):
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  is_first_img(true),
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  image_sub(10),
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  nan_flag(false),
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  last_time_bound(0),
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  nh(pnh) {
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  return;
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}
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@@ -64,6 +65,7 @@ bool MsckfVio::loadParameters() {
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  //Photometry Flag
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  nh.param<bool>("PHOTOMETRIC", PHOTOMETRIC, false);
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  nh.param<bool>("PrintImages", PRINTIMAGES, false);
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  nh.param<bool>("GroundTruth", GROUNDTRUTH, false);
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  // Frame id
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  nh.param<string>("fixed_frame_id", fixed_frame_id, "world");
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@@ -255,6 +257,8 @@ bool MsckfVio::createRosIO() {
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  imu_sub = nh.subscribe("imu", 100,
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      &MsckfVio::imuCallback, this);
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  truth_sub = nh.subscribe("ground_truth", 100,
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      &MsckfVio::truthCallback, this);
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  cam0_img_sub.subscribe(nh, "cam0_image", 10);
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  cam1_img_sub.subscribe(nh, "cam1_image", 10);
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@@ -263,7 +267,6 @@ bool MsckfVio::createRosIO() {
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  image_sub.connectInput(cam0_img_sub, cam1_img_sub, feature_sub);
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  image_sub.registerCallback(&MsckfVio::imageCallback, this);
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  mocap_odom_sub = nh.subscribe("mocap_odom", 10,
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      &MsckfVio::mocapOdomCallback, this);
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  mocap_odom_pub = nh.advertise<nav_msgs::Odometry>("gt_odom", 1);
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@@ -292,7 +295,7 @@ bool MsckfVio::initialize() {
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  for (int i = 1; i < 100; ++i) {
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    boost::math::chi_squared chi_squared_dist(i);
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    chi_squared_test_table[i] =
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      boost::math::quantile(chi_squared_dist, 0.05);
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      boost::math::quantile(chi_squared_dist, 0.2);
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  }
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  if (!createRosIO()) return false;
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@@ -319,6 +322,10 @@ void MsckfVio::imuCallback(const sensor_msgs::ImuConstPtr& msg){
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  return;
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}
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void MsckfVio::truthCallback(const geometry_msgs::TransformStampedPtr& msg){
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  truth_msg_buffer.push_back(*msg);
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}
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void MsckfVio::imageCallback(
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    const sensor_msgs::ImageConstPtr& cam0_img,
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    const sensor_msgs::ImageConstPtr& cam1_img,
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@@ -342,7 +349,10 @@ void MsckfVio::imageCallback(
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  // Propogate the IMU state.
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  // that are received before the image feature_msg.
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  ros::Time start_time = ros::Time::now();
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  batchImuProcessing(feature_msg->header.stamp.toSec());
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  if(!GROUNDTRUTH)
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    batchImuProcessing(feature_msg->header.stamp.toSec());
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  else
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    batchTruthProcessing(feature_msg->header.stamp.toSec());
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  double imu_processing_time = (
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      ros::Time::now()-start_time).toSec();
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@@ -558,6 +568,9 @@ bool MsckfVio::resetCallback(
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  imu_sub = nh.subscribe("imu", 100,
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      &MsckfVio::imuCallback, this);
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  truth_sub = nh.subscribe("ground_truth", 100,
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      &MsckfVio::truthCallback, this);
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  //  feature_sub = nh.subscribe("features", 40,
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  //      &MsckfVio::featureCallback, this);
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@@ -632,6 +645,71 @@ void MsckfVio::mocapOdomCallback(const nav_msgs::OdometryConstPtr& msg) {
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  return;
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}
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void MsckfVio::batchTruthProcessing(const double& time_bound) {
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  // Counter how many IMU msgs in the buffer are used.
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  int used_truth_msg_cntr = 0;
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  for (const auto& truth_msg : truth_msg_buffer) {
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    double truth_time = truth_msg.header.stamp.toSec();
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    if (truth_time < state_server.imu_state.time) {
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      ++used_truth_msg_cntr;
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      continue;
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    }
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    if (truth_time > time_bound) break;
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    // Convert the msgs.
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    Eigen::Vector3d m_translation; 
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    Eigen::Vector4d m_rotation;
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    tf::vectorMsgToEigen(truth_msg.transform.translation, m_translation);
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    m_rotation[0] = truth_msg.transform.rotation.x;
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    m_rotation[1] = truth_msg.transform.rotation.y;
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    m_rotation[2] = truth_msg.transform.rotation.z;
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    m_rotation[3] = truth_msg.transform.rotation.w;
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    // Execute process model.
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    processTruthtoIMU(truth_time, m_rotation, m_translation);
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    ++used_truth_msg_cntr;
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  }
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  last_time_bound = time_bound;
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  // Set the state ID for the new IMU state.
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  state_server.imu_state.id = IMUState::next_id++;
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  // Remove all used Truth msgs.
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  truth_msg_buffer.erase(truth_msg_buffer.begin(),
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      truth_msg_buffer.begin()+used_truth_msg_cntr);
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}
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void MsckfVio::processTruthtoIMU(const double& time,
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    const Vector4d& m_rot,
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    const Vector3d& m_trans){
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  IMUState& imu_state = state_server.imu_state;
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  double dtime = time - imu_state.time;
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  Vector4d& q = imu_state.orientation;
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  Vector3d& v = imu_state.velocity;
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  Vector3d& p = imu_state.position;
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  double dt = time - imu_state.time;
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  v = (m_trans-v)/dt;
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  p = m_trans;
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  q = m_rot;
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  // Update the state correspondes to null space.
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  imu_state.orientation_null = imu_state.orientation;
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  imu_state.position_null = imu_state.position;
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  imu_state.velocity_null = imu_state.velocity;
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  // Update the state info
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  state_server.imu_state.time = time;
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}
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void MsckfVio::batchImuProcessing(const double& time_bound) {
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  // Counter how many IMU msgs in the buffer are used.
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  int used_imu_msg_cntr = 0;
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@@ -1039,17 +1117,22 @@ void MsckfVio::PhotometricMeasurementJacobian(
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    dh_dCpij.block<2, 2>(0, 0) = Eigen::Matrix<double, 2, 2>::Identity();
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    dh_dCpij(0, 2) = -(p_c0(0))/(p_c0(2)*p_c0(2));
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    dh_dCpij(1, 2) = -(p_c0(1))/(p_c0(2)*p_c0(2));
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    //orientation takes camera frame to world frame, we wa
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    dh_dGpij = dh_dCpij * quaternionToRotation(cam_state.orientation).transpose();
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    //dh / d X_{pl}
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    dh_dXplj.block<2, 3>(0, 0) = dh_dCpij * skewSymmetric(point);
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    dh_dXplj.block<2, 3>(0, 3) = dh_dCpij * -quaternionToRotation(cam_state.orientation);//.transpose();
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    dh_dXplj.block<2, 3>(0, 3) = dh_dCpij * -quaternionToRotation(cam_state.orientation).transpose();
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    //d{}^Gp_P{ij} / \rho_i
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    double rho = feature.anchor_rho;
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    dGpi_drhoj = feature.T_anchor_w.linear() * Eigen::Vector3d(-feature.anchorPatch_ideal[count].x/(rho*rho), -feature.anchorPatch_ideal[count].y/(rho*rho), -1/(rho*rho));
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    dGpi_XpAj.block<3, 3>(0, 0) = skewSymmetric(Eigen::Vector3d(feature.anchorPatch_ideal[count].x/(rho), feature.anchorPatch_ideal[count].y/(rho), 1/(rho)));
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    dGpi_XpAj.block<3, 3>(0, 0) = - skewSymmetric(feature.T_anchor_w.linear()
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                                 * Eigen::Vector3d(feature.anchorPatch_ideal[count].x/(rho), 
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                                                   feature.anchorPatch_ideal[count].y/(rho), 
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                                                   1/(rho)));
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    dGpi_XpAj.block<3, 3>(0, 3) = Matrix<double, 3, 3>::Identity();
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    // Intermediate Jakobians
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@@ -1091,6 +1174,7 @@ void MsckfVio::PhotometricMeasurementJacobian(
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  // set anchor Jakobi
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    // get position of anchor in cam states
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  auto cam_state_anchor = state_server.cam_states.find(feature.observations.begin()->first);
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  int cam_state_cntr_anchor = std::distance(state_server.cam_states.begin(), cam_state_anchor);
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  H_xl.block(0, 21+cam_state_cntr_anchor*7, N*N, 6) = -H_pA; 
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@@ -1122,8 +1206,10 @@ void MsckfVio::PhotometricMeasurementJacobian(
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  for(auto data : photo_r)
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    r[count++] = data;
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  std::stringstream ss;
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  ss << "INFO:" << " anchor: " << cam_state_cntr_anchor << "  frame: " << cam_state_cntr;
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  if(PRINTIMAGES)
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    feature.VisualizePatch(cam_state, cam_state_id, cam0, photo_r);
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    feature.VisualizePatch(cam_state, cam_state_id, cam0, photo_r, ss);
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  return;
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}
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@@ -1238,7 +1324,12 @@ void MsckfVio::measurementJacobian(
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  dz_dpc1(3, 2) = -p_c1(1) / (p_c1(2)*p_c1(2));
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  Matrix<double, 3, 6> dpc0_dxc = Matrix<double, 3, 6>::Zero();
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  dpc0_dxc.leftCols(3) = skewSymmetric(p_c0);
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  // original jacobi
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  //dpc0_dxc.leftCols(3) = skewSymmetric(p_c0);
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  // my version of calculation
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  dpc0_dxc.leftCols(3) = skewSymmetric(R_w_c0 * p_w) -  skewSymmetric(R_w_c0 * t_c0_w);
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  //dpc0_dxc.leftCols(3) = - skewSymmetric(R_w_c0.transpose() * (t_c0_w - p_w)) * R_w_c0;
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  dpc0_dxc.rightCols(3) = -R_w_c0;
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  Matrix<double, 3, 6> dpc1_dxc = Matrix<double, 3, 6>::Zero();
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