CRandomFieldGridMap3D.cpp

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/* +------------------------------------------------------------------------+
   |                     Mobile Robot Programming Toolkit (MRPT)            |
   |                          http://www.mrpt.org/                          |
   |                                                                        |
   | Copyright (c) 2005-2018, Individual contributors, see AUTHORS file     |
   | See: http://www.mrpt.org/Authors - All rights reserved.                |
   | Released under BSD License. See details in http://www.mrpt.org/License |
   +------------------------------------------------------------------------+ */
 
#include "maps-precomp.h"  // Precomp header
 
#include <mrpt/maps/CRandomFieldGridMap3D.h>
#include <mrpt/config/CConfigFileBase.h>
#include <mrpt/system/CTicTac.h>
#include <fstream>
#include <mrpt/config.h>
 
#if MRPT_HAS_VTK
#include <vtkStructuredGrid.h>
#include <vtkDoubleArray.h>
#include <vtkPointData.h>
#include <vtkVersion.h>
#include <vtkCellArray.h>
#include <vtkPoints.h>
#include <vtkXMLStructuredGridWriter.h>
#include <vtkSmartPointer.h>
#endif
 
using namespace mrpt;
using namespace mrpt::maps;
using namespace mrpt::system;
using namespace std;
 
IMPLEMENTS_SERIALIZABLE(CRandomFieldGridMap3D, CSerializable, mrpt::maps)
 
/*---------------------------------------------------------------
                                                Constructor
  ---------------------------------------------------------------*/
CRandomFieldGridMap3D::CRandomFieldGridMap3D(
        double x_min, double x_max, double y_min, double y_max, double z_min,
        double z_max, double voxel_size, bool call_initialize_now)
        : CDynamicGrid3D<TRandomFieldVoxel>(
                  x_min, x_max, y_min, y_max, z_min, z_max, voxel_size /*xy*/,
                  voxel_size /*z*/),
          COutputLogger("CRandomFieldGridMap3D")
{
        if (call_initialize_now) this->internal_initialize();
}
 
/** Changes the size of the grid, erasing previous contents */
void CRandomFieldGridMap3D::setSize(
        const double x_min, const double x_max, const double y_min,
        const double y_max, const double z_min, const double z_max,
        const double resolution_xy, const double resolution_z,
        const TRandomFieldVoxel* fill_value)
{
        MRPT_START;
 
        CDynamicGrid3D<TRandomFieldVoxel>::setSize(
                x_min, x_max, y_min, y_max, z_min, z_max, resolution_xy, resolution_z,
                fill_value);
        this->internal_initialize();
 
        MRPT_END;
}
 
void CRandomFieldGridMap3D::resize(
        double new_x_min, double new_x_max, double new_y_min, double new_y_max,
        double new_z_min, double new_z_max,
        const TRandomFieldVoxel& defaultValueNewCells,
        double additionalMarginMeters)
{
        MRPT_START;
 
        CDynamicGrid3D<TRandomFieldVoxel>::resize(
                new_x_min, new_x_max, new_y_min, new_y_max, new_z_min, new_z_max,
                defaultValueNewCells, additionalMarginMeters);
        this->internal_initialize(false);
 
        MRPT_END;
}
 
void CRandomFieldGridMap3D::clear()
{
        mrpt::containers::CDynamicGrid3D<TRandomFieldVoxel>::clear();
        internal_initialize();
}
 
void CRandomFieldGridMap3D::internal_initialize(bool erase_prev_contents)
{
        if (erase_prev_contents)
        {
                // Set the gridmap (m_map) to initial values:
                TRandomFieldVoxel def(0, 0);  // mean, std
                fill(def);
        }
 
        // Reset gmrf:
        m_gmrf.setVerbosityLevel(this->getMinLoggingLevel());
        if (erase_prev_contents)
        {
                m_gmrf.clear();
                m_mrf_factors_activeObs.clear();
        }
        else
        {
                // Only remove priors, leave observations:
                m_gmrf.clearAllConstraintsByType_Binary();
        }
        m_mrf_factors_priors.clear();
 
        // Initiating prior:
        const size_t nodeCount = m_map.size();
        ASSERT_EQUAL_(nodeCount, m_size_x * m_size_y * m_size_z);
        ASSERT_EQUAL_(m_size_x_times_y, m_size_x * m_size_y);
 
        MRPT_LOG_DEBUG_STREAM(
                "[internal_initialize] Creating priors for GMRF with "
                << nodeCount << " nodes." << std::endl);
        CTicTac tictac;
        tictac.Tic();
 
        m_mrf_factors_activeObs.resize(nodeCount);  // Alloc space for obs
        m_gmrf.initialize(nodeCount);
 
        ConnectivityDescriptor* custom_connectivity =
                m_gmrf_connectivity
                        .get();  // Use a raw ptr to avoid the cost in the inner loops
 
        size_t cx = 0, cy = 0, cz = 0;
        for (size_t j = 0; j < nodeCount; j++)
        {
                // add factors between this node and:
                // 1) the right node: j +1
                // 2) the back node:  j+m_size_x
                // 3) the top node: j+m_size_x*m_size*y
                //-------------------------------------------------
                const size_t c_idx_to_check[3] = {cx, cy, cz};
                const size_t c_idx_to_check_limits[3] = {m_size_x - 1, m_size_y - 1,
                                                                                                 m_size_z - 1};
                const size_t c_neighbor_idx_incr[3] = {1, m_size_x, m_size_x_times_y};
 
                for (int dir = 0; dir < 3; dir++)
                {
                        if (c_idx_to_check[dir] >= c_idx_to_check_limits[dir]) continue;
 
                        const size_t i = j + c_neighbor_idx_incr[dir];
                        ASSERT_(i < nodeCount);
 
                        double edge_lamdba = .0;
                        if (custom_connectivity != nullptr)
                        {
                                const bool is_connected =
                                        custom_connectivity->getEdgeInformation(
                                                this, cx, cy, cz, cx + (dir == 0 ? 1 : 0),
                                                cy + (dir == 1 ? 1 : 0), cz + (dir == 2 ? 1 : 0),
                                                edge_lamdba);
                                if (!is_connected) continue;
                        }
                        else
                        {
                                edge_lamdba = insertionOptions.GMRF_lambdaPrior;
                        }
 
                        TPriorFactorGMRF new_prior(*this);
                        new_prior.node_id_i = i;
                        new_prior.node_id_j = j;
                        new_prior.Lambda = edge_lamdba;
 
                        m_mrf_factors_priors.push_back(new_prior);
                        m_gmrf.addConstraint(
                                *m_mrf_factors_priors.rbegin());  // add to graph
                }
 
                // Increment coordinates:
                if (++cx >= m_size_x)
                {
                        cx = 0;
                        if (++cy >= m_size_y)
                        {
                                cy = 0;
                                cz++;
                        }
                }
        }  // end for "j"
 
        MRPT_LOG_DEBUG_STREAM(
                "[internal_initialize] Prior built in " << tictac.Tac() << " s\n"
                                                                                                << std::endl);
}
 
/*---------------------------------------------------------------
                                        TInsertionOptions
 ---------------------------------------------------------------*/
CRandomFieldGridMap3D::TInsertionOptions::TInsertionOptions()
        : GMRF_lambdaPrior(0.01f),  // [GMRF model] The information (Lambda) of
          // fixed map constraints
          GMRF_skip_variance(false)
{
}
 
void CRandomFieldGridMap3D::TInsertionOptions::dumpToTextStream(
        std::ostream& out) const
{
        out << mrpt::format(
                "GMRF_lambdaPrior                     = %f\n", GMRF_lambdaPrior);
        out << mrpt::format(
                "GMRF_skip_variance                   = %s\n",
                GMRF_skip_variance ? "true" : "false");
}
 
void CRandomFieldGridMap3D::TInsertionOptions::loadFromConfigFile(
        const mrpt::config::CConfigFileBase& iniFile, const std::string& section)
{
        GMRF_lambdaPrior = iniFile.read_double(
                section.c_str(), "GMRF_lambdaPrior", GMRF_lambdaPrior);
        GMRF_skip_variance = iniFile.read_bool(
                section.c_str(), "GMRF_skip_variance", GMRF_skip_variance);
}
 
/** Save the current estimated grid to a VTK file (.vts) as a "structured grid".
 * \sa saveAsCSV */
bool CRandomFieldGridMap3D::saveAsVtkStructuredGrid(
        const std::string& fil) const
{
        MRPT_START;
#if MRPT_HAS_VTK
 
        vtkStructuredGrid* vtkGrid = vtkStructuredGrid::New();
        this->getAsVtkStructuredGrid(vtkGrid);
 
        // Write file
        vtkSmartPointer<vtkXMLStructuredGridWriter> writer =
                vtkSmartPointer<vtkXMLStructuredGridWriter>::New();
        writer->SetFileName(fil.c_str());
 
#if VTK_MAJOR_VERSION <= 5
        writer->SetInput(vtkGrid);
#else
        writer->SetInputData(vtkGrid);
#endif
 
        int ret = writer->Write();
 
        vtkGrid->Delete();
 
        return ret == 0;
#else
        THROW_EXCEPTION("This method requires building MRPT against VTK!");
#endif
        MRPT_END
}
 
bool mrpt::maps::CRandomFieldGridMap3D::saveAsCSV(
        const std::string& filName_mean, const std::string& filName_stddev) const
{
        std::ofstream f_mean, f_stddev;
 
        f_mean.open(filName_mean);
        if (!f_mean.is_open())
        {
                return false;
        }
        else
        {
                f_mean << "x coord, y coord, z coord, scalar\n";
        }
 
        if (!filName_stddev.empty())
        {
                f_stddev.open(filName_stddev);
                if (!f_stddev.is_open())
                {
                        return false;
                }
                else
                {
                        f_mean << "x coord, y coord, z coord, scalar\n";
                }
        }
 
        const size_t nodeCount = m_map.size();
        size_t cx = 0, cy = 0, cz = 0;
        for (size_t j = 0; j < nodeCount; j++)
        {
                const double x = idx2x(cx), y = idx2y(cy), z = idx2z(cz);
                const double mean_val = m_map[j].mean_value;
                const double stddev_val = m_map[j].stddev_value;
 
                f_mean << mrpt::format("%f, %f, %f, %e\n", x, y, z, mean_val);
 
                if (f_stddev.is_open())
                        f_stddev << mrpt::format("%f, %f, %f, %e\n", x, y, z, stddev_val);
 
                // Increment coordinates:
                if (++cx >= m_size_x)
                {
                        cx = 0;
                        if (++cy >= m_size_y)
                        {
                                cy = 0;
                                cz++;
                        }
                }
        }  // end for "j"
 
        return true;
}
 
void CRandomFieldGridMap3D::updateMapEstimation()
{
        ASSERTMSG_(
                !m_mrf_factors_activeObs.empty(),
                "Cannot update a map with no observations!");
 
        Eigen::VectorXd x_incr, x_var;
        m_gmrf.updateEstimation(
                x_incr, insertionOptions.GMRF_skip_variance ? NULL : &x_var);
 
        ASSERT_(size_t(m_map.size()) == size_t(x_incr.size()));
        ASSERT_(
                insertionOptions.GMRF_skip_variance ||
                size_t(m_map.size()) == size_t(x_var.size()));
 
        // Update Mean-Variance in the base grid class
        for (size_t j = 0; j < m_map.size(); j++)
        {
                m_map[j].mean_value += x_incr[j];
                m_map[j].stddev_value =
                        insertionOptions.GMRF_skip_variance ? .0 : std::sqrt(x_var[j]);
        }
}
 
void mrpt::maps::CRandomFieldGridMap3D::setVoxelsConnectivity(
        const ConnectivityDescriptor::Ptr& new_connectivity_descriptor)
{
        m_gmrf_connectivity = new_connectivity_descriptor;
}
 
bool CRandomFieldGridMap3D::insertIndividualReading(
        /** [in] The value observed in the (x,y,z) position */
        const double sensorReading,
        /** [in] The variance of the sensor observation */
        const double sensorVariance,
        /** [in] The (x,y,z) location */
        const mrpt::math::TPoint3D& point,
        /** [in] Voxel interpolation method: how many voxels will be affected by the
           reading */
        const TVoxelInterpolationMethod method,
        /** [in] Run a global map update after inserting this observatin
           (algorithm-dependant) */
        const bool update_map)
{
        MRPT_START;
 
        ASSERT_ABOVE_(sensorVariance, .0);
        ASSERTMSG_(
                m_mrf_factors_activeObs.size() == m_map.size(),
                "Trying to insert observation in uninitialized map (!)");
 
        const size_t cell_idx =
                cellAbsIndexFromCXCYCZ(x2idx(point.x), y2idx(point.y), z2idx(point.z));
        if (cell_idx == INVALID_VOXEL_IDX) return false;
 
        TObservationGMRF new_obs(*this);
        new_obs.node_id = cell_idx;
        new_obs.obsValue = sensorReading;
        new_obs.Lambda = 1.0 / sensorVariance;
 
        m_mrf_factors_activeObs[cell_idx].push_back(new_obs);
        m_gmrf.addConstraint(
                *m_mrf_factors_activeObs[cell_idx].rbegin());  // add to graph
 
        if (update_map) this->updateMapEstimation();
 
        return true;
 
        MRPT_END;
}
 
uint8_t CRandomFieldGridMap3D::serializeGetVersion() const { return 0; }
void CRandomFieldGridMap3D::serializeTo(
        mrpt::serialization::CArchive& out) const
{
        dyngridcommon_writeToStream(out);
 
        // To assure compatibility: The size of each cell:
        uint32_t n = static_cast<uint32_t>(sizeof(TRandomFieldVoxel));
        out << n;
 
        // Save the map contents:
        n = static_cast<uint32_t>(m_map.size());
        out << n;
 
// Save the "m_map": This requires special handling for big endian systems:
#if MRPT_IS_BIG_ENDIAN
        for (uint32_t i = 0; i < n; i++)
                out << m_map[i].mean_value << m_map[i].stddev_value;
#else
        // Little endian: just write all at once:
        out.WriteBuffer(&m_map[0], sizeof(m_map[0]) * m_map.size());
#endif
 
        out << insertionOptions.GMRF_lambdaPrior
                << insertionOptions.GMRF_skip_variance;
}
 
void CRandomFieldGridMap3D::serializeFrom(
        mrpt::serialization::CArchive& in, uint8_t version)
{
        switch (version)
        {
                case 0:
                {
                        dyngridcommon_readFromStream(in);
 
                        // To assure compatibility: The size of each cell:
                        uint32_t n;
                        in >> n;
 
                        ASSERT_EQUAL_(n, static_cast<uint32_t>(sizeof(TRandomFieldVoxel)));
                        // Load the map contents:
                        in >> n;
                        m_map.resize(n);
 
// Read the note in writeToStream()
#if MRPT_IS_BIG_ENDIAN
                        for (uint32_t i = 0; i < n; i++)
                                in >> m_map[i].mean_value >> m_map[i].stddev_value;
#else
                        // Little endian: just read all at once:
                        in.ReadBuffer(&m_map[0], sizeof(m_map[0]) * m_map.size());
#endif
                        in >> insertionOptions.GMRF_lambdaPrior >>
                                insertionOptions.GMRF_skip_variance;
                }
                break;
                default:
                        MRPT_THROW_UNKNOWN_SERIALIZATION_VERSION(version);
        };
}
 
void CRandomFieldGridMap3D::getAsVtkStructuredGrid(
        vtkStructuredGrid* output, const std::string& label_mean,
        const std::string& label_stddev) const
{
        MRPT_START;
#if MRPT_HAS_VTK
 
        const size_t nx = this->getSizeX(), ny = this->getSizeY(),
                                 nz = this->getSizeZ();
 
        const int num_values = nx * ny * nz;
 
        vtkPoints* newPoints = vtkPoints::New();
 
        vtkDoubleArray* newData = vtkDoubleArray::New();
        newData->SetNumberOfComponents(3);
        newData->SetNumberOfTuples(num_values);
 
        vtkDoubleArray* mean_arr = vtkDoubleArray::New();
        mean_arr->SetNumberOfComponents(1);
        mean_arr->SetNumberOfTuples(num_values);
 
        vtkDoubleArray* std_arr = vtkDoubleArray::New();
        std_arr->SetNumberOfComponents(1);
        std_arr->SetNumberOfTuples(num_values);
 
        vtkIdType numtuples = newData->GetNumberOfTuples();
 
        {
                size_t cx = 0, cy = 0, cz = 0;
                for (vtkIdType cc = 0; cc < numtuples; cc++)
                {
                        const double x = idx2x(cx), y = idx2y(cy), z = idx2z(cz);
 
                        newData->SetComponent(cc, 0, x);
                        newData->SetComponent(cc, 1, y);
                        newData->SetComponent(cc, 2, z);
 
                        mean_arr->SetComponent(cc, 0, m_map[cc].mean_value);
                        std_arr->SetComponent(cc, 0, m_map[cc].stddev_value);
 
                        // Increment coordinates:
                        if (++cx >= m_size_x)
                        {
                                cx = 0;
                                if (++cy >= m_size_y)
                                {
                                        cy = 0;
                                        cz++;
                                }
                        }
                }
                ASSERT_(size_t(m_map.size()) == size_t(numtuples));
        }
 
        newPoints->SetData(newData);
        newData->Delete();
 
        output->SetExtent(0, nx - 1, 0, ny - 1, 0, nz - 1);
        output->SetPoints(newPoints);
        newPoints->Delete();
 
        mean_arr->SetName(label_mean.c_str());
        std_arr->SetName(label_stddev.c_str());
        output->GetPointData()->AddArray(mean_arr);
        output->GetPointData()->AddArray(std_arr);
 
        mean_arr->Delete();
        std_arr->Delete();
 
#else
        THROW_EXCEPTION("This method requires building MRPT against VTK!");
#endif  // VTK
        MRPT_END;
}
 
// ============ TObservationGMRF ===========
double CRandomFieldGridMap3D::TObservationGMRF::evaluateResidual() const
{
        return m_parent->m_map[this->node_id].mean_value - this->obsValue;
}
double CRandomFieldGridMap3D::TObservationGMRF::getInformation() const
{
        return this->Lambda;
}
void CRandomFieldGridMap3D::TObservationGMRF::evalJacobian(double& dr_dx) const
{
        dr_dx = 1.0;
}
// ============ TPriorFactorGMRF ===========
double CRandomFieldGridMap3D::TPriorFactorGMRF::evaluateResidual() const
{
        return m_parent->m_map[this->node_id_i].mean_value -
                   m_parent->m_map[this->node_id_j].mean_value;
}
double CRandomFieldGridMap3D::TPriorFactorGMRF::getInformation() const
{
        return this->Lambda;
}
void CRandomFieldGridMap3D::TPriorFactorGMRF::evalJacobian(
        double& dr_dx_i, double& dr_dx_j) const
{
        dr_dx_i = +1.0;
        dr_dx_j = -1.0;
}