PsfexPsf.cc

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// -*- LSST-C++ -*-
 
/*
 * LSST Data Management System
 * Copyright 2008, 2009, 2010 LSST Corporation.
 *
 * This product includes software developed by the
 * LSST Project (http://www.lsst.org/).
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the LSST License Statement and
 * the GNU General Public License along with this program.  If not,
 * see <http://www.lsstcorp.org/LegalNotices/>.
 */
 
#include <cmath>
#include <cassert>
#include <numeric>
#include <memory>
 
#include "lsst/base.h"
#include "lsst/pex/exceptions.h"
#include "lsst/afw/image/ImageUtils.h"
#include "lsst/afw/math/Statistics.h"
#include "lsst/afw/table/io/Persistable.cc"
extern "C" {
#include "vignet.h"
}
#include "lsst/meas/extensions/psfex/PsfexPsf.h"
#include "lsst/meas/algorithms/KernelPsfFactory.h"
#include "lsst/afw/table/aggregates.h"
 
namespace lsst {
namespace afw {
namespace table {
namespace io {
 
template std::shared_ptr<meas::extensions::psfex::PsfexPsf>
PersistableFacade<meas::extensions::psfex::PsfexPsf>::dynamicCast(std::shared_ptr<Persistable> const&);
 
}  // namespace io
}  // namespace table
}  // namespace afw
namespace meas {
namespace extensions {
namespace psfex {
 
namespace afw = lsst::afw;
 
PsfexPsf::PsfexPsf(
    lsst::meas::extensions::psfex::Psf const& psf,
    geom::Point2D const & averagePosition
                  ) : ImagePsf(), _averagePosition(averagePosition),
                      _size(psf.impl->dim),
                      _comp(psf.impl->npix),
                      _context(psf.impl->poly->ndim)
 
{
    _poly = poly_copy(psf.impl->poly);
 
    _pixstep = psf.impl->pixstep;
 
    std::copy(psf.impl->size, psf.impl->size + psf.impl->dim, _size.begin());
 
    std::copy(psf.impl->comp, psf.impl->comp + psf.impl->npix, _comp.begin());
 
    for (int i = 0; i != psf.impl->poly->ndim; ++i) {
        _context[i].first = psf.impl->contextoffset[i];
        _context[i].second = psf.impl->contextscale[i];
    }
}
 
    PsfexPsf::PsfexPsf() : ImagePsf(),
                           _averagePosition(geom::Point2I(0, 0)),
                           _poly(0),
                           _pixstep(0.0),
                           _size(),
                           _comp(),
                           _context()
{
    ;
}
 
PsfexPsf::~PsfexPsf()
{
    poly_end(_poly);
}
 
std::shared_ptr<afw::detection::Psf>
PsfexPsf::clone() const {
    return std::make_shared<PsfexPsf>(*this);
}
 
std::shared_ptr<afw::detection::Psf>
PsfexPsf::resized(int width, int height) const {
    throw LSST_EXCEPT(pex::exceptions::LogicError, "Not Implemented");
}
 
std::shared_ptr<afw::math::LinearCombinationKernel const>
PsfexPsf::getKernel(geom::Point2D position) const
{
    double pos[MAXCONTEXT];
    int const ndim = _context.size();
    if (ndim != 2) {                    // we're only handling spatial variation for now
        throw LSST_EXCEPT(lsst::pex::exceptions::InvalidParameterError,
                          str(boost::format("Only spatial variation (ndim == 2) is supported; saw %d")
                              % ndim));
 
    }
    // where we want to evaluate the basis function's weights
    if (!std::isfinite(position[0])) {
        position = _averagePosition;
    }
 
    for (int i = 0; i < ndim; ++i) {
        pos[i] = (position[i] - _context[i].first)/_context[i].second;
    }
 
    poly_func(_poly, pos);              // evaluate polynomial
 
    int const w = _size[0], h = _size[1];
    std::vector<float> fullresIm(w*h);       // accumulate full-resolution image into this buffer
    /*
     * Create a fixed Kernel out of each component, and then create a LinearCombinationKernel from them
     */
    const int nbasis = _size.size() > 2 ? _size[2] : 1; // number of basis functions
    afw::math::KernelList kernels; kernels.reserve(nbasis); // the insides of the LinearCombinationKernel
    std::vector<double>   weights; weights.reserve(nbasis);
 
    float const vigstep = 1/_pixstep;
    float const dx = 0.0, dy = 0.0;
 
    geom::Box2I bbox = _doComputeBBox(position, geom::Point2D(0, 0));
    afw::detection::Psf::Image kim(bbox); // a basis function image, to be copied into a FixedKernel
 
    int sampleW = bbox.getWidth();
    int sampleH = bbox.getHeight();
 
    std::vector<float> sampledBasis(sampleW*sampleH);
 
    for (int i = 0; i != nbasis; ++i) {
        /*
         * Resample the basis function onto the output resolution (and potentially subpixel offset)
         */
        vignet_resample(const_cast<float *>(&_comp[i*w*h]), w, h,
                        &sampledBasis[0],  sampleW, sampleH,
                        -dx*vigstep, -dy*vigstep, vigstep, 1.0);
        //
        // And copy it into place
        //
        {
            float *pl = &sampledBasis[0];
            for (int y = 0; y != sampleH; ++y) {
                for (int x = 0; x != sampleW; ++x) {
                    kim(x, y) = *pl++;
                }
            }
        }
 
        kernels.push_back(std::make_shared<afw::math::FixedKernel>(kim));
        weights.push_back(_poly->basis[i]);
    }
 
    _kernel = std::make_shared<afw::math::LinearCombinationKernel>(kernels, weights);
 
    return _kernel;
}
 
std::shared_ptr<afw::detection::Psf::Image>
PsfexPsf::doComputeImage(geom::Point2D const & position,
                         afw::image::Color const & color) const {
    return _doComputeImage(position, color, position);
}
 
std::shared_ptr<afw::detection::Psf::Image>
PsfexPsf::doComputeKernelImage(geom::Point2D const& position,
                               afw::image::Color const& color) const
{
    return _doComputeImage(position, color, geom::Point2D(0, 0));
}
 
geom::Box2I PsfexPsf::doComputeBBox(geom::Point2D const & position,
                               afw::image::Color const & color) const {
    return _doComputeBBox(position, geom::Point2D(0, 0));
}
 
geom::Box2I PsfexPsf::_doComputeBBox(geom::Point2D const & position,
                               geom::Point2D const & center) const {
    int const w = _size[0], h = _size[1];
    int sampleW = static_cast<int>(w*_pixstep);
    int sampleH = static_cast<int>(h*_pixstep);
 
    // Ensure that sizes are odd
    if (sampleW % 2 == 0) sampleW += 1;
    if (sampleH % 2 == 0) sampleH += 1;
 
    float dx = center[0] - static_cast<int>(center[0]);
    float dy = center[1] - static_cast<int>(center[1]);
 
    if (dx > 0.5) dx -= 1.0;
    if (dy > 0.5) dy -= 1.0;
    // N.b. center[0] - dx == (int)center[x] until we reduced dx to (-0.5, 0.5].
    // The + 0.5 is to handle floating point imprecision in this calculation
    geom::Box2I bbox(geom::Point2I(static_cast<int>(center[0] - dx + 0.5) - sampleW/2,
                                             static_cast<int>(center[1] - dy + 0.5) - sampleH/2),
                          geom::Extent2I(sampleW, sampleH));
    return bbox;
}
 
std::shared_ptr<afw::detection::Psf::Image>
PsfexPsf::_doComputeImage(geom::Point2D const& position,
                          afw::image::Color const& color,
                          geom::Point2D const& center
        ) const
{
    double pos[MAXCONTEXT];
    int const ndim = _context.size();
    if (ndim != 2) {                    // we're only handling spatial variation for now
        throw LSST_EXCEPT(lsst::pex::exceptions::InvalidParameterError,
                          str(boost::format("Only spatial variation (ndim == 2) is supported; saw %d")
                              % ndim));
 
    }
 
    for (int i = 0; i < ndim; ++i) {
        pos[i] = (position[i] - _context[i].first)/_context[i].second;
    }
 
    poly_func(_poly, pos);              // evaluate polynomial
 
    int const w = _size[0], h = _size[1];
    std::vector<float> fullresIm(w*h);       // accumulate full-resolution image into this buffer
    const int nbasis = _size.size() > 2 ? _size[2] : 1; // number of basis functions
 
    /* Sum each component */
    int const npix = w*h;
    for (int i = 0; i != nbasis; ++i) {
        float *pl = &fullresIm[0];
        float const fac = _poly->basis[i];
        float const *ppc = &_comp[i*w*h];
 
        for (int j = 0; j != npix; ++j) {
            pl[j] +=  fac*ppc[j];
        }
    }
    /*
     * We now have the image reconstructed at internal resolution; resample it onto the output resolution
     * and subpixel offset
     */
    float const vigstep = 1/_pixstep;
    float dx = center[0] - static_cast<int>(center[0]);
    float dy = center[1] - static_cast<int>(center[1]);
    if (dx > 0.5) dx -= 1.0;
    if (dy > 0.5) dy -= 1.0;
    //
    // And copy it into place
    //
    geom::Box2I bbox = _doComputeBBox(position, center);
    std::shared_ptr<afw::detection::Psf::Image> im = std::make_shared<afw::detection::Psf::Image>(bbox);
 
    int sampleW = bbox.getWidth();
    int sampleH = bbox.getHeight();
 
    std::vector<float> sampledIm(sampleW*sampleH);
 
    vignet_resample(&fullresIm[0], w, h,
                    &sampledIm[0], sampleW, sampleH,
                    -dx*vigstep, -dy*vigstep, vigstep, 1.0);
    {
        float *pl = &sampledIm[0];
        float const sum = std::accumulate(pl, pl + sampleW*sampleH, static_cast<float>(0));
        for (int y = 0; y != sampleH; ++y) {
            for (int x = 0; x != sampleW; ++x) {
                (*im)(x, y) = *pl++/sum;
            }
        }
    }
 
    return im;
}
 
/************************************************************************************************************/
/*
 * All the rest of this file handles persistence to FITS files
 */
namespace table = afw::table;
 
namespace {
 
class PsfexPsfSchema1 {
public:
    PsfexPsfSchema1() :
        schema(),
        ndim(schema.addField<int>("ndim", "Number of elements in group")),
        ngroup(schema.addField<int>("ngroup", "Number of elements in degree")),
        ncoeff(schema.addField<int>("ncoeff", "Number of coefficients")),
 
        _size_size(schema.addField<int>("_size_size", "Size of _size array")),
        _comp_size(schema.addField<int>("_comp_size", "Size of _comp array")),
        _context_size(schema.addField<int>("_context_size", "Size of _context array")),
    // Other scalars
        averagePosition(afw::table::PointKey<double>::addFields(schema,"averagePosition","average position of stars used to make the PSF","pixel")),
        _pixstep(schema.addField<float>("_pixstep", "oversampling", "pixel"))
    {
        ;
    }
 
    table::Schema schema;
 
    // Sizes in _poly
    table::Key<int> ndim;
    table::Key<int> ngroup;
    table::Key<int> ncoeff;
    // Sizes of vectors
    table::Key<int> _size_size;
    table::Key<int> _comp_size;
    table::Key<int> _context_size;
    // Other scalars
    table::PointKey<double> averagePosition;
    table::Key<float> _pixstep;
};
 
class PsfexPsfSchema2 {
public:
    PsfexPsfSchema2(int const ndim, int const ngroup, int const ncoeff,
                    int size_size, int comp_size, int context_size) :
 
        schema(),
        group(schema.addField<table::Array<int> >("group", "Groups (of coefficients?)", ndim)),
        degree(schema.addField<table::Array<int> >("degree", "Degree in each group", ngroup)),
        basis(schema.addField<table::Array<double> >("basis", "Values of the basis functions", ncoeff)),
        coeff(schema.addField<table::Array<double> >("coeff", "Polynomial coefficients", ncoeff)),
        _size(schema.addField<table::Array<int> >("_size", "PSF dimensions", size_size)),
        _comp(schema.addField<table::Array<float> >("_comp", "Complete pixel data", comp_size)),
        _context_first( schema.addField<table::Array<double> >("_context_first",
                                                   "Offset to apply to context data", context_size)),
        _context_second(schema.addField<table::Array<double> >("_context_second",
                                                   "Scale to apply to context data", context_size))
    {
        ;
    }
 
    table::Schema schema;
    // _poly
    table::Key<table::Array<int> > group;              // len(group) == ndim
    table::Key<table::Array<int> > degree;             // len(degree) == ngroup
    table::Key<table::Array<double> > basis;           // len(basis) == ncoeff
    table::Key<table::Array<double> > coeff;           // len(coeff) == ncoeff
    // vectors
    table::Key<table::Array<int> > _size;
    table::Key<table::Array<float> > _comp;
    table::Key<table::Array<double> > _context_first;
    table::Key<table::Array<double> > _context_second;
};
 
std::string getPsfexPsfPersistenceName() { return "PsfexPsf"; }
 
} // anonymous
 
/************************************************************************************************************/
 
namespace detail {                      // PsfexPsfFactory needs to be a friend of PsfexPsf
class PsfexPsfFactory : public table::io::PersistableFactory {
public:
 
virtual std::shared_ptr<table::io::Persistable>
read(InputArchive const & archive, CatalogVector const & catalogs) const {
    LSST_ARCHIVE_ASSERT(catalogs.size() == 2u);
 
    std::shared_ptr<PsfexPsf> result(new PsfexPsf());
 
    int ndim, ngroup, ncoeff;
    int size_size, comp_size, context_size;
    {
        PsfexPsfSchema1 const & keys = PsfexPsfSchema1();
        LSST_ARCHIVE_ASSERT(catalogs[0].size() == 1u);
        LSST_ARCHIVE_ASSERT(catalogs[0].getSchema() == keys.schema);
        table::BaseRecord const & record = catalogs[0].front();
 
        // fields in _poly
        ndim = record.get(keys.ndim);
        ngroup = record.get(keys.ngroup);
        ncoeff = record.get(keys.ncoeff);
        // Other scalars
        result->_averagePosition = record.get(keys.averagePosition);
        result->_pixstep = record.get(keys._pixstep);
        // sizes of vectors
        size_size = record.get(keys._size_size);
        comp_size = record.get(keys._comp_size);
        context_size = record.get(keys._context_size);
    }
    // Now we can read the data
    {
        PsfexPsfSchema2 const keys(ndim, ngroup, ncoeff,
                                   size_size, comp_size, context_size);
 
        LSST_ARCHIVE_ASSERT(catalogs[1].size() == 1u);
        LSST_ARCHIVE_ASSERT(catalogs[1].getSchema() == keys.schema);
        table::BaseRecord const & record = catalogs[1].front();
 
        // _poly
        std::vector<int> group;
        {
            int const *begin = record.getElement(keys.group);
            group.assign(begin, begin + ndim);
 
            for (int i = 0; i != ndim; ++i) {
                ++group[i];             // poly_init subtracts 1 from each element.  Sigh.
            }
        }
        std::vector<int> degree;
        {
            int const *begin = record.getElement(keys.degree);
            degree.assign(begin, begin + ngroup);
        }
        result->_poly = poly_init(&group[0], group.size(), &degree[0], degree.size());
        LSST_ARCHIVE_ASSERT(result->_poly->ncoeff == ncoeff);
 
        {
            double const *begin = record.getElement(keys.basis);
            std::copy(begin, begin + ncoeff, result->_poly->basis);
        }
        {
            double const *begin = record.getElement(keys.coeff);
            std::copy(begin, begin + ncoeff, result->_poly->coeff);
        }
        // vectors
        {
            int const *begin = record.getElement(keys._size);
            result->_size.assign(begin, begin + size_size);
        }
        {
            float const *begin = record.getElement(keys._comp);
            result->_comp.assign(begin, begin + comp_size);
        }
        {
            double const *begin1 = record.getElement(keys._context_first);
            double const *begin2 = record.getElement(keys._context_second);
            result->_context.resize(context_size);
            for (int i = 0; i != context_size; ++i) {
                result->_context[i].first  = begin1[i];
                result->_context[i].second = begin2[i];
            }
        }
    }
 
    return result;
}
 
explicit PsfexPsfFactory(std::string const & name) : table::io::PersistableFactory(name) {}
 
};
}
 
namespace {
    detail::PsfexPsfFactory registration(getPsfexPsfPersistenceName());
}
 
/************************************************************************************************************/
 
std::string PsfexPsf::getPythonModule() const { return "lsst.meas.extensions.psfex"; }
 
std::string PsfexPsf::getPersistenceName() const { return getPsfexPsfPersistenceName(); }
 
void PsfexPsf::write(afw::table::io::OutputArchiveHandle & handle) const {
    // First write the dimensions of the various arrays to an HDU, so we can construct the second
    // HDU using them when we read the Psf back
    {
        PsfexPsfSchema1 const keys;
        afw::table::BaseCatalog cat = handle.makeCatalog(keys.schema);
        std::shared_ptr<afw::table::BaseRecord> record = cat.addNew();
 
        // Sizes in _poly
        record->set(keys.ndim, _poly->ndim);
        record->set(keys.ngroup, _poly->ngroup);
        record->set(keys.ncoeff, _poly->ncoeff);
        // Other scalars
        record->set(keys.averagePosition, _averagePosition);
        record->set(keys._pixstep, _pixstep);
        record->set(keys._size_size, _size.size());
        record->set(keys._comp_size, _comp.size());
        record->set(keys._context_size, _context.size());
 
        handle.saveCatalog(cat);
    }
    // Now we can write the data
    {
        PsfexPsfSchema2 const keys(_poly->ndim, _poly->ngroup, _poly->ncoeff,
                                   _size.size(), _comp.size(), _context.size());
        afw::table::BaseCatalog cat = handle.makeCatalog(keys.schema);
        // _poly
        std::shared_ptr<afw::table::BaseRecord> record = cat.addNew();
        {
            int *begin = record->getElement(keys.group);
            std::copy(_poly->group, _poly->group + _poly->ndim, begin);
        }
        {
            int *begin = record->getElement(keys.degree);
            std::copy(_poly->degree, _poly->degree + _poly->ngroup, begin);
        }
        {
            double *begin = record->getElement(keys.basis);
            std::copy(_poly->basis, _poly->basis + _poly->ncoeff, begin);
        }
        {
            double *begin = record->getElement(keys.coeff);
            std::copy(_poly->coeff, _poly->coeff + _poly->ncoeff, begin);
        }
        // vectors
        {
            int *begin = record->getElement(keys._size);
            std::copy(_size.begin(), _size.end(), begin);
        }
        {
            float *begin = record->getElement(keys._comp);
            std::copy(_comp.begin(), _comp.end(), begin);
        }
        {
            double *begin1 = record->getElement(keys._context_first);
            double *begin2 = record->getElement(keys._context_second);
            for (unsigned int i = 0; i != _context.size(); ++i) {
                begin1[i] = _context[i].first;
                begin2[i] = _context[i].second;
            }
        }
 
        handle.saveCatalog(cat);
    }
}
 
}}}}