FootprintSet.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 <algorithm>
#include <cassert>
#include <set>
#include <string>
#include <typeinfo>
#include "boost/format.hpp"
#include "lsst/pex/exceptions.h"
#include "lsst/pex/logging/Trace.h"
#include "lsst/afw/image/MaskedImage.h"
#include "lsst/afw/math/Statistics.h"
#include "lsst/afw/detection/Peak.h"
#include "lsst/afw/detection/FootprintFunctor.h"
#include "lsst/afw/detection/FootprintSet.h"
#include "lsst/afw/detection/FootprintCtrl.h"
#include "lsst/afw/detection/HeavyFootprint.h"

namespace detection = lsst::afw::detection;
namespace image = lsst::afw::image;
namespace math = lsst::afw::math;
namespace pexLogging = lsst::pex::logging;
namespace geom = lsst::afw::geom;

/************************************************************************************************************/
namespace {

    typedef boost::uint64_t IdPixelT;    // Type of temporary Images used in merging Footprints

    struct Threshold_traits {
    };
    struct ThresholdLevel_traits : public Threshold_traits { // Threshold is a single number
    };
    struct ThresholdPixelLevel_traits : public Threshold_traits { // Threshold varies from pixel to pixel
    };
    struct ThresholdBitmask_traits : public Threshold_traits { // Threshold ORs with a bitmask
    };

    //
    // Define our own functions to handle NaN tests;  this gives us the
    // option to define a value for e.g. image::MaskPixel or int
    //
    template<typename T>
    inline bool isBadPixel(T) {
        return false;
    }

    template<>
    inline bool isBadPixel(float val) {
        return std::isnan(val);
    }

    template<>
    inline bool isBadPixel(double val) {
        return std::isnan(val);
    }

    /*
     * Return the number of bits required to represent a unsigned long
     */
    int nbit(unsigned long i) {
        int n = 0;
        while (i > 0) {
            ++n;
            i >>= 1;
        }

        return n;
    }
    /*
     * Find the list of pixel values that lie in a Footprint
     *
     * Used when the Footprints are constructed from an Image containing Footprint indices
     */
    template <typename ImageT>
    class FindIdsInFootprint: public detection::FootprintFunctor<ImageT> {
    public:
        explicit FindIdsInFootprint(ImageT const& image 
                                   ) : detection::FootprintFunctor<ImageT>(image), _ids(), _old(0) {}
        void reset() {
            _ids.clear();
            _old = 0;
        }
        
        void operator()(typename ImageT::xy_locator loc, 
                        int x,                           
                        int y                            
                       ) {
            typename ImageT::Pixel val = loc(0, 0);

            if (val != _old) {
                _ids.insert(val);
                _old = val;
            }
        }

        std::set<typename ImageT::Pixel> const& getIds() const {
            return _ids;
        }

    private:
        std::set<typename ImageT::Pixel> _ids;
        typename ImageT::Pixel _old;
    };

    /********************************************************************************************************/
    /*
     * Sort peaks by decreasing pixel value.  N.b. -ve peaks are sorted the same way as +ve ones
     */
    struct SortPeaks {
        bool operator()(CONST_PTR(detection::PeakRecord) a, CONST_PTR(detection::PeakRecord) b) {
            if (a->getPeakValue() != b->getPeakValue()) {
                return (a->getPeakValue() > b->getPeakValue());
            }

            if (a->getIx() != b->getIx()) {
                return (a->getIx() < b->getIx());
            }

            return (a->getIy() < b->getIy());
        }
    };
    /********************************************************************************************************/
    /*
     * Worker routine for merging two FootprintSets, possibly growing them as we proceed
     */
    detection::FootprintSet
    mergeFootprintSets(
        detection::FootprintSet const &lhs, // the FootprintSet to be merged to
        int rLhs,                                         // Grow lhs Footprints by this many pixels
        detection::FootprintSet const &rhs, // the FootprintSet to be merged into lhs
        int rRhs,                                         // Grow rhs Footprints by this many pixels
        detection::FootprintControl const& ctrl           // Control how the grow is done
                      )
    {
        typedef detection::Footprint Footprint;
        typedef detection::FootprintSet::FootprintList FootprintList;
        // The isXXX routines return <isset, value>
        bool const circular = ctrl.isCircular().first && ctrl.isCircular().second;
        bool const isotropic = ctrl.isIsotropic().second; // isotropic grow as opposed to a Manhattan metric
                                        // n.b. Isotropic grows are significantly slower
        bool const left =  ctrl.isLeft().first  && ctrl.isLeft().second;
        bool const right = ctrl.isRight().first && ctrl.isRight().second;
        bool const up =    ctrl.isUp().first    && ctrl.isUp().second;
        bool const down =  ctrl.isDown().first  && ctrl.isDown().second;

        geom::Box2I const region = lhs.getRegion();
        if (region != rhs.getRegion()) {
            throw LSST_EXCEPT(lsst::pex::exceptions::InvalidParameterError,
                              boost::format("The two FootprintSets must have the same region").str());
        }
        
        image::Image<IdPixelT>::Ptr idImage(new image::Image<IdPixelT>(region));
        idImage->setXY0(region.getMinX(), region.getMinY());
        *idImage = 0;

        FootprintList const& lhsFootprints = *lhs.getFootprints();
        FootprintList const& rhsFootprints = *rhs.getFootprints();
        int const nLhs = lhsFootprints.size();
        int const nRhs = rhsFootprints.size();
        /*
         * In general the lists of Footprints overlap, so we need to make sure that the IDs can be
         * uniquely recovered from the idImage.  We do this by allocating a range of bits to the lhs IDs
         */
        int const lhsIdNbit = nbit(nLhs);
        int const lhsIdMask = (lhsIdNbit == 0) ? 0x0 : (1 << lhsIdNbit) - 1;

        if (std::size_t(nRhs << lhsIdNbit) > std::numeric_limits<IdPixelT>::max() - 1) {
            throw LSST_EXCEPT(lsst::pex::exceptions::OverflowError,
                              (boost::format("%d + %d footprints need too many bits; change IdPixelT typedef")
                               % nLhs % nRhs).str());
        }
        /*
         * When we insert grown Footprints into the idImage we can potentially overwrite an entire Footprint,
         * losing any peaks that it might contain.  We'll preserve the overwritten Ids in case we need to
         * get them back (n.b. Footprints that overlap, but both if which survive, will appear in this list)
         */
        typedef std::map<int, std::set<boost::uint64_t> > OldIdMap;
        OldIdMap overwrittenIds;        // here's a map from id -> overwritten IDs

        IdPixelT id = 1;                     // the ID inserted into the image
        for (FootprintList::const_iterator ptr = lhsFootprints.begin(), end = lhsFootprints.end();
             ptr != end; ++ptr, ++id) {
            CONST_PTR(Footprint) foot = *ptr;

            if (rLhs > 0) {
                foot = circular ?
                    growFootprint(*foot, rLhs, isotropic) : growFootprint(*foot, rLhs, left, right, up, down);
            }

            std::set<boost::uint64_t> overwritten;
            foot->insertIntoImage(*idImage, id, true, 0x0, &overwritten);

            if (!overwritten.empty()) {
                overwrittenIds.insert(overwrittenIds.end(), std::make_pair(id, overwritten));
            }
        }

        assert (id <= std::size_t(1 << lhsIdNbit));
        id = (1 << lhsIdNbit);
        for (FootprintList::const_iterator ptr = rhsFootprints.begin(), end = rhsFootprints.end();
             ptr != end; ++ptr, id += (1 << lhsIdNbit)) {
            CONST_PTR(Footprint) foot = *ptr;

            if (rRhs > 0) {
                foot = circular ?
                    growFootprint(*foot, rRhs, isotropic) : growFootprint(*foot, rRhs, left, right, up, down);
            }

            std::set<boost::uint64_t> overwritten;
            foot->insertIntoImage(*idImage, id, true, lhsIdMask, &overwritten);

            if (!overwritten.empty()) {
                overwrittenIds.insert(overwrittenIds.end(), std::make_pair(id, overwritten));
            }
        }

        detection::FootprintSet fs(*idImage, detection::Threshold(1),
                                   1, false); // detect all pixels in rhs + lhs
        /*
         * Now go through the new Footprints looking up and remembering their progenitor's IDs; we'll use
         * these IDs to merge the peaks in a moment
         *
         * We can't do this as we go through the idFinder as the IDs it returns are
         *   (lhsId + 1) | ((rhsId + 1) << nbit)
         * and, depending on the geometry, values of lhsId and/or rhsId can appear multiple times
         * (e.g. if nbit is 2, idFinder IDs 0x5 and 0x6 both contain lhsId = 0) so we get duplicates
         * of peaks.  This is not too bad, but it's a bit of a pain to make the lists unique again,
         * and we avoid this by this two-step process.
         */
        FindIdsInFootprint<image::Image<IdPixelT> > idFinder(*idImage);
        for (FootprintList::iterator ptr = fs.getFootprints()->begin(),
                 end = fs.getFootprints()->end(); ptr != end; ++ptr) {
            PTR(Footprint) foot = *ptr;

            idFinder.apply(*foot);      // find the (mangled) [lr]hsFootprint IDs that contribute to foot

            std::set<boost::uint64_t> lhsFootprintIndxs, rhsFootprintIndxs; // indexes into [lr]hsFootprints

            for (std::set<IdPixelT>::iterator idptr = idFinder.getIds().begin(),
                     idend = idFinder.getIds().end(); idptr != idend; ++idptr) {
                unsigned int indx = *idptr;
                if ((indx & lhsIdMask) > 0) {
                    boost::uint64_t i = (indx & lhsIdMask) - 1;
                    lhsFootprintIndxs.insert(i);
                    /*
                     * Now allow for Footprints that vanished beneath this one
                     */
                    OldIdMap::iterator mapPtr = overwrittenIds.find(indx);
                    if (mapPtr != overwrittenIds.end()) {
                        std::set<boost::uint64_t> &overwritten = mapPtr->second;

                        for (std::set<boost::uint64_t>::iterator ptr = overwritten.begin(),
                                 end = overwritten.end(); ptr != end; ++ptr){
                            lhsFootprintIndxs.insert((*ptr & lhsIdMask) - 1);
                        }
                    }
                }
                indx >>= lhsIdNbit;

                if (indx > 0) {
                    boost::uint64_t i = indx - 1;
                    rhsFootprintIndxs.insert(i);
                    /*
                     * Now allow for Footprints that vanished beneath this one
                     */
                    OldIdMap::iterator mapPtr = overwrittenIds.find(indx);
                    if (mapPtr != overwrittenIds.end()) {
                        std::set<boost::uint64_t> &overwritten = mapPtr->second;

                        for (std::set<boost::uint64_t>::iterator ptr = overwritten.begin(),
                                 end = overwritten.end(); ptr != end; ++ptr) {
                            rhsFootprintIndxs.insert(*ptr - 1);
                        }
                    }
                }
            }
            /*
             * We now have a complete set of Footprints that contributed to this one, so merge
             * all their Peaks into the new one
             */
            detection::PeakCatalog &peaks = foot->getPeaks();

            for (std::set<boost::uint64_t>::iterator ptr = lhsFootprintIndxs.begin(),
                     end = lhsFootprintIndxs.end(); ptr != end; ++ptr) {
                boost::uint64_t i = *ptr;
                assert (i < lhsFootprints.size());
                detection::PeakCatalog const& oldPeaks = lhsFootprints[i]->getPeaks();

                int const nold = peaks.size();
                peaks.insert(peaks.end(), oldPeaks.begin(), oldPeaks.end());
                // We use getInternal() here to get the vector of shared_ptr that Catalog uses internally,
                // which causes the STL algorithm to copy pointers instead of PeakRecords (which is what
                // it'd try to do if we passed Catalog's own iterators).
                std::inplace_merge(peaks.getInternal().begin(), peaks.getInternal().begin() + nold,
                                   peaks.getInternal().end(), SortPeaks());
            }

            for (std::set<boost::uint64_t>::iterator ptr = rhsFootprintIndxs.begin(),
                     end = rhsFootprintIndxs.end(); ptr != end; ++ptr) {
                boost::uint64_t i = *ptr;
                assert (i < rhsFootprints.size());
                detection::PeakCatalog const& oldPeaks = rhsFootprints[i]->getPeaks();

                int const nold = peaks.size();
                peaks.insert(peaks.end(), oldPeaks.begin(), oldPeaks.end());
                // See note above on why we're using getInternal() here.
                std::inplace_merge(peaks.getInternal().begin(), peaks.getInternal().begin() + nold,
                                   peaks.getInternal().end(), SortPeaks());
            }
        }

        return fs;
    }
/*
 * run-length code for part of object
 */
    class IdSpan {
    public:
        typedef boost::shared_ptr<IdSpan> Ptr;
        
        explicit IdSpan(int id, int y, int x0, int x1, double good) : 
            id(id), y(y), x0(x0), x1(x1), good(good) {}
        int id;                         /* ID for object */
        int y;                          /* Row wherein IdSpan dwells */
        int x0, x1;                     /* inclusive range of columns */
        bool good;                      /* includes a value over the desired threshold? */
    };
/*
 * comparison functor; sort by ID then row
 */
    struct IdSpanCompar : public std::binary_function<const IdSpan::Ptr, const IdSpan::Ptr, bool> {
        bool operator()(IdSpan::Ptr const a, IdSpan::Ptr const b) {
            if (a->id < b->id) {
                return true;
            } else if (a->id > b->id) {
                return false;
            } else {
                return (a->y < b->y) ? true : false;
            }
        }
    };
/*
 * Follow a chain of aliases, returning the final resolved value.
 */
    int resolve_alias(std::vector<int> const &aliases, /* list of aliases */
                      int id) {         /* alias to look up */
        int resolved = id;              /* resolved alias */
        
        while (id != aliases[id]) {
            resolved = id = aliases[id];
        }
        
        return(resolved);
    }
}

/************************************************************************************************************/

namespace {
    /*
     * Find all the Peaks within a Footprint
     */
    template <typename ImageT>
    class FindPeaksInFootprint: public detection::FootprintFunctor<ImageT> {
    public:
        explicit FindPeaksInFootprint(ImageT const& image, 
                                      bool polarity,       
                                      detection::PeakCatalog &peaks
                                     ) : detection::FootprintFunctor<ImageT>(image),
                                         _polarity(polarity), _peaks(peaks) {}
        
        void operator()(typename ImageT::xy_locator loc, 
                        int x,                           
                        int y                            
                       ) {
            typename ImageT::Pixel val = loc(0, 0);

            if (_polarity) {            // look for +ve peaks
                if (loc(-1,  1) > val || loc( 0,  1) > val || loc( 1,  1) > val || 
                    loc(-1,  0) > val ||                      loc( 1,  0) > val || 
                    loc(-1, -1) > val || loc( 0, -1) > val || loc( 1, -1) > val) {
                    return;
                }
            } else {                    // look for -ve "peaks" (pits)
                if (loc(-1,  1) < val || loc( 0,  1) < val || loc( 1,  1) < val || 
                    loc(-1,  0) < val ||                      loc( 1,  0) < val || 
                    loc(-1, -1) < val || loc( 0, -1) < val || loc( 1, -1) < val) {
                    return;
                }
            }

            PTR(detection::PeakRecord) newPeak = _peaks.addNew();
            newPeak->setIx(x);
            newPeak->setIy(y);
            newPeak->setFx(x);
            newPeak->setFy(y);
            newPeak->setPeakValue(val);
        }
    private:
        bool _polarity;
        detection::PeakCatalog &_peaks;
    };

    /*
     * Find the maximum (or minimum, if polarity is false) pixel in a Footprint
     */
    template <typename ImageT>
    class FindMaxInFootprint : public detection::FootprintFunctor<ImageT> {
    public:
        explicit FindMaxInFootprint(ImageT const& image, 
                                    bool polarity        
                                   ) : detection::FootprintFunctor<ImageT>(image),
                                       _polarity(polarity), _x(0), _y(0),
                                       _min( std::numeric_limits<double>::max()),
                                       _max(-std::numeric_limits<double>::max()) {}

        void reset() {
            _x = _y = 0;
            _min =  std::numeric_limits<double>::max();
            _max = -std::numeric_limits<double>::max();
        }
        virtual void reset(detection::Footprint const&) {}

        void operator()(typename ImageT::xy_locator loc, 
                        int x,                           
                        int y                            
                       ) {
            typename ImageT::Pixel val = loc(0, 0);

            if (_polarity) {
                if (val > _max) {
                    _max = val;
                    _x = x;
                    _y = y;
                }
            } else {
                if (val < _min) {
                    _min = val;
                    _x = x;
                    _y = y;
                }
            }
        }

        // Add the Footprint's peak to the given PeakCatalog
        void addPeak(detection::PeakCatalog & peakCat) const {
            PTR(detection::PeakRecord) newPeak = peakCat.addNew();
            newPeak->setIx(_x);
            newPeak->setIy(_y);
            newPeak->setFx(_x);
            newPeak->setFy(_y);
            newPeak->setPeakValue(_polarity ? _max : _min);
        }
    private:
        bool _polarity;
        int _x, _y;
        double _min, _max;
    };
    
    template<typename ImageT, typename ThresholdT>
    void findPeaks(PTR(detection::Footprint) foot, ImageT const& img, bool polarity, ThresholdT)
    {
        FindPeaksInFootprint<ImageT> peakFinder(img, polarity, foot->getPeaks());
        peakFinder.apply(*foot, 1);

        // We use getInternal() here to get the vector of shared_ptr that Catalog uses internally,
        // which causes the STL algorithm to copy pointers instead of PeakRecords (which is what
        // it'd try to do if we passed Catalog's own iterators).
        std::stable_sort(foot->getPeaks().getInternal().begin(), foot->getPeaks().getInternal().end(),
                         SortPeaks());

        if (foot->getPeaks().empty()) {
            FindMaxInFootprint<ImageT> maxFinder(img, polarity);
            maxFinder.apply(*foot);
            maxFinder.addPeak(foot->getPeaks());
        }
    }

    // No need to search for peaks when processing a Mask
    template<typename ImageT>
    void findPeaks(PTR(detection::Footprint), ImageT const&, bool, ThresholdBitmask_traits)
    {
        ;
    }
}

/************************************************************************************************************/
/*
 * Functions to determine if a pixel's in a Footprint
 */
template<typename ImagePixelT, typename IterT>
static inline bool inFootprint(ImagePixelT pixVal, IterT,
                               bool polarity, double thresholdVal, ThresholdLevel_traits) {
    return (polarity ? pixVal : -pixVal) >= thresholdVal;
}

template<typename ImagePixelT, typename IterT>
static inline bool inFootprint(ImagePixelT pixVal, IterT var,
                               bool polarity, double thresholdVal, ThresholdPixelLevel_traits) {
    return (polarity ? pixVal : -pixVal) >= thresholdVal*::sqrt(*var);
}

template<typename ImagePixelT, typename IterT>
static inline bool inFootprint(ImagePixelT pixVal, IterT,
                               bool, double thresholdVal, ThresholdBitmask_traits) {
    return (pixVal & static_cast<long>(thresholdVal));
}

/*
 * Advance the x_iterator to the variance image, when relevant (it may be NULL otherwise)
 */
template<typename IterT>
static inline IterT
advancePtr(IterT varPtr, Threshold_traits) {
    return varPtr;
}

template<typename IterT>
static inline IterT
advancePtr(IterT varPtr, ThresholdPixelLevel_traits) {
    return varPtr + 1;
}

/*
 * Here's the working routine for the FootprintSet constructors; see documentation
 * of the constructors themselves
 */
template<typename ImagePixelT, typename MaskPixelT, typename VariancePixelT, typename ThresholdTraitT>
static void findFootprints(
        typename detection::FootprintSet::FootprintList *_footprints, // Footprints
        geom::Box2I const& _region,               // BBox of pixels that are being searched
        image::ImageBase<ImagePixelT> const &img, // Image to search for objects
        image::Image<VariancePixelT> const *var,  // img's variance
        double const footprintThreshold,  // threshold value for footprint
        double const includeThresholdMultiplier,  // threshold (relative to footprintThreshold) for inclusion
        bool const polarity,                      // if false, search _below_ thresholdVal
        int const npixMin,                        // minimum number of pixels in an object
        bool const setPeaks                       // should I set the Peaks list?
)
{
    int id;                             /* object ID */
    int in_span;                        /* object ID of current IdSpan */
    int nobj = 0;                       /* number of objects found */
    int x0 = 0;                         /* unpacked from a IdSpan */

    typedef typename image::Image<ImagePixelT> ImageT;
    double includeThreshold = footprintThreshold * includeThresholdMultiplier; // Threshold for inclusion
    
    int const row0 = img.getY0();
    int const col0 = img.getX0();
    int const height = img.getHeight();
    int const width = img.getWidth();
/*
 * Storage for arrays that identify objects by ID. We want to be able to
 * refer to idp[-1] and idp[width], hence the (width + 2)
 */
    std::vector<int> id1(width + 2);
    std::fill(id1.begin(), id1.end(), 0);
    std::vector<int> id2(width + 2);
    std::fill(id2.begin(), id2.end(), 0);
    std::vector<int>::iterator idc = id1.begin() + 1; // object IDs in current/
    std::vector<int>::iterator idp = id2.begin() + 1; //                       previous row

    std::vector<int> aliases;           // aliases for initially disjoint parts of Footprints
    aliases.reserve(1 + height/20);     // initial size of aliases

    std::vector<IdSpan::Ptr> spans;     // y:x0,x1 for objects
    spans.reserve(aliases.capacity());  // initial size of spans

    aliases.push_back(0);               // 0 --> 0
/*
 * Go through image identifying objects
 */
    typedef typename image::Image<ImagePixelT>::x_iterator x_iterator;
    typedef typename image::Image<VariancePixelT>::x_iterator x_var_iterator;

    in_span = 0;                        // not in a span
    for (int y = 0; y != height; ++y) {
        if (idc == id1.begin() + 1) {
            idc = id2.begin() + 1;
            idp = id1.begin() + 1;
        } else {
            idc = id1.begin() + 1;
            idp = id2.begin() + 1;
        }
        std::fill_n(idc - 1, width + 2, 0);
        
        in_span = 0;                    /* not in a span */
        bool good = (includeThresholdMultiplier == 1.0); /* Span exceeds the threshold? */

        x_iterator pixPtr = img.row_begin(y);
        x_var_iterator varPtr = (var == NULL) ? NULL : var->row_begin(y);
        for (int x = 0; x < width; ++x, ++pixPtr, varPtr = advancePtr(varPtr, ThresholdTraitT())) {
            ImagePixelT const pixVal = *pixPtr;

            if (isBadPixel(pixVal) ||
                !inFootprint(pixVal, varPtr, polarity, footprintThreshold, ThresholdTraitT())) {
                if (in_span) {
                    IdSpan::Ptr sp(new IdSpan(in_span, y, x0, x - 1, good));
                    spans.push_back(sp);

                    in_span = 0;
                    good = false;
                }
            } else {                    /* a pixel to fix */
                if (idc[x - 1] != 0) {
                    id = idc[x - 1];
                } else if (idp[x - 1] != 0) {
                    id = idp[x - 1];
                } else if (idp[x] != 0) {
                    id = idp[x];
                } else if (idp[x + 1] != 0) {
                    id = idp[x + 1];
                } else {
                    id = ++nobj;
                    aliases.push_back(id);
                }

                idc[x] = id;
                if (!in_span) {
                    x0 = x;
                    in_span = id;
                }
/*
 * Do we need to merge ID numbers? If so, make suitable entries in aliases[]
 */
                if (idp[x + 1] != 0 && idp[x + 1] != id) {
                    aliases[resolve_alias(aliases, idp[x + 1])] = resolve_alias(aliases, id);
               
                    idc[x] = id = idp[x + 1];
                }

                if (!good && inFootprint(pixVal, varPtr, polarity, includeThreshold, ThresholdTraitT())) {
                    good = true;
                }
            }
        }

        if (in_span) {
            IdSpan::Ptr sp(new IdSpan(in_span, y, x0, width - 1, good));
            spans.push_back(sp);
        }
    }
/*
 * Resolve aliases; first alias chains, then the IDs in the spans
 */
    for (unsigned int i = 0; i < spans.size(); i++) {
        spans[i]->id = resolve_alias(aliases, spans[i]->id);
    }
/*
 * Sort spans by ID, so we can sweep through them once
 */
    if (spans.size() > 0) {
        std::sort(spans.begin(), spans.end(), IdSpanCompar());
    }
/*
 * Build Footprints from spans
 */
    unsigned int i0;                    // initial value of i
    if (spans.size() > 0) {
        id = spans[0]->id;
        i0 = 0;
        for (unsigned int i = 0; i <= spans.size(); i++) { // <= size to catch the last object
            if (i == spans.size() || spans[i]->id != id) {
                PTR(detection::Footprint) fp(new detection::Footprint(i - i0, _region));
            
                bool good = false;      // Span includes pixel sufficient to include footprint in set?
                for (; i0 < i; i0++) {
                    good |= spans[i0]->good;
                    fp->addSpan(spans[i0]->y + row0, spans[i0]->x0 + col0, spans[i0]->x1 + col0);
                }

                if (good && !(fp->getNpix() < npixMin)) {
                    _footprints->push_back(fp);
                }
            }

            if (i < spans.size()) {
                id = spans[i]->id;
            }
        }
    }
/*
 * Find all peaks within those Footprints
 */
    if (setPeaks) {
        typedef detection::FootprintSet::FootprintList::iterator fiterator;
        for (fiterator ptr = _footprints->begin(), end = _footprints->end(); ptr != end; ++ptr) {
            findPeaks(*ptr, img, polarity, ThresholdTraitT());
        }
    }
}

/************************************************************************************************************/
/*
 * \brief Find a FootprintSet given an Image and a threshold
 */
template<typename ImagePixelT>
detection::FootprintSet::FootprintSet(
    image::Image<ImagePixelT> const &img, 
    Threshold const &threshold,     
    int const npixMin,              
    bool const setPeaks            
) : lsst::daf::base::Citizen(typeid(this)),
    _footprints(new FootprintList()),
    _region(img.getBBox())
{
    typedef float VariancePixelT;
     
    findFootprints<ImagePixelT, afw::image::MaskPixel, VariancePixelT, ThresholdLevel_traits>(
        _footprints.get(), 
        _region, 
        img,
        NULL,
        threshold.getValue(img), threshold.getIncludeMultiplier(), threshold.getPolarity(),
        npixMin,
        setPeaks
    );
}

// NOTE: not a template to appease swig (see note by instantiations at bottom)

/*
 * \brief Find a FootprintSet given a Mask and a threshold
 */
template <typename MaskPixelT>
detection::FootprintSet::FootprintSet(
    image::Mask<MaskPixelT> const &msk, 
    Threshold const &threshold,     
    int const npixMin               
) : lsst::daf::base::Citizen(typeid(this)),
    _footprints(new FootprintList()),
    _region(msk.getBBox())
{
    switch (threshold.getType()) {
      case Threshold::BITMASK:
          findFootprints<MaskPixelT, MaskPixelT, float, ThresholdBitmask_traits>(
            _footprints.get(), _region, msk, NULL, threshold.getValue(), threshold.getIncludeMultiplier(),
            threshold.getPolarity(), npixMin, false);
        break;

      case Threshold::VALUE:
        findFootprints<MaskPixelT, MaskPixelT, float, ThresholdLevel_traits>(
            _footprints.get(), _region, msk, NULL, threshold.getValue(), threshold.getIncludeMultiplier(),
            threshold.getPolarity(), npixMin, false);
        break;

      default:
        throw LSST_EXCEPT(lsst::pex::exceptions::InvalidParameterError,
                          "You must specify a numerical threshold value with a Mask");
    }
}


template<typename ImagePixelT, typename MaskPixelT>
detection::FootprintSet::FootprintSet(
    const image::MaskedImage<ImagePixelT, MaskPixelT> &maskedImg, 
    Threshold const &threshold,     
    std::string const &planeName,   
    int const npixMin,              
    bool const setPeaks            
) : lsst::daf::base::Citizen(typeid(this)),
    _footprints(new FootprintList()),
    _region(
        geom::Point2I(maskedImg.getX0(), maskedImg.getY0()),
        geom::Extent2I(maskedImg.getWidth(), maskedImg.getHeight())
    )
{
    typedef typename image::MaskedImage<ImagePixelT, MaskPixelT>::Variance::Pixel VariancePixelT;
    // Find the Footprints    
    switch (threshold.getType()) {
      case Threshold::PIXEL_STDEV:
        findFootprints<ImagePixelT, MaskPixelT, VariancePixelT, ThresholdPixelLevel_traits>(
            _footprints.get(), 
            _region,
            *maskedImg.getImage(), 
            maskedImg.getVariance().get(), 
            threshold.getValue(maskedImg),
            threshold.getIncludeMultiplier(),
            threshold.getPolarity(),
            npixMin,
            setPeaks
                                                                                  );
        break;
      default:
        findFootprints<ImagePixelT, MaskPixelT, VariancePixelT, ThresholdLevel_traits>(
            _footprints.get(), 
            _region,
            *maskedImg.getImage(), 
            maskedImg.getVariance().get(), 
            threshold.getValue(maskedImg),
            threshold.getIncludeMultiplier(),
            threshold.getPolarity(),
            npixMin,
            setPeaks
                                                                                  );
        break;
    }
    // Set Mask if requested    
    if (planeName == "") {
        return;
    }
    //
    // Define the maskPlane
    //
    const typename image::Mask<MaskPixelT>::Ptr mask = maskedImg.getMask();
    mask->addMaskPlane(planeName);

    MaskPixelT const bitPlane = mask->getPlaneBitMask(planeName);
    //
    // Set the bits where objects are detected
    //
    typedef image::Mask<MaskPixelT> MaskT;

    class MaskFootprint : public detection::FootprintFunctor<MaskT> {
    public:
        MaskFootprint(MaskT const& mimage,
                      MaskPixelT bit) : detection::FootprintFunctor<MaskT>(mimage), _bit(bit) {}

        void operator()(typename MaskT::xy_locator loc, int, int) {
            *loc |= _bit;
        }
    private:
        MaskPixelT _bit;
    };

    MaskFootprint maskit(*maskedImg.getMask(), bitPlane);
    for (FootprintList::const_iterator fiter = _footprints->begin();         
         fiter != _footprints->end(); ++fiter
    ) {
        Footprint::Ptr const foot = *fiter;

        maskit.apply(*foot);
    }
}


/************************************************************************************************************/
namespace {
    /*
     * A data structure to hold the starting point for a search for pixels above threshold,
     * used by pmFindFootprintAtPoint
     *
     * We don't want to find this span again --- it's already part of the footprint ---
     * so we set appropriate mask bits
     */
    //
    // An enum for what we should do with a Startspan
    //
    enum DIRECTION {DOWN = 0,   // scan down from this span
                    UP,         // scan up from this span
                    RESTART,     // restart scanning from this span
                    DONE                // this span is processed
    };
    //
    // A Class that remembers how to [re-]start scanning the image for pixels
    //
    template<typename MaskPixelT>
    class Startspan {
    public:
        typedef std::vector<boost::shared_ptr<Startspan> > Ptr;
        
        Startspan(detection::Span const *span, image::Mask<MaskPixelT> *mask, DIRECTION const dir);
        ~Startspan() { delete _span; }

        bool getSpan() { return _span; }
        bool Stop() { return _stop; }
        DIRECTION getDirection() { return _direction; }

        static int detectedPlane;       // The MaskPlane to use for detected pixels
        static int stopPlane;           // The MaskPlane to use for pixels that signal us to stop searching
    private:
        detection::Span::Ptr const _span; // The initial Span
        DIRECTION _direction;           // How to continue searching for further pixels
        bool _stop;                     // should we stop searching?
    };

    template<typename MaskPixelT>
    Startspan<MaskPixelT>::Startspan(detection::Span const *span, // The span in question
                         image::Mask<MaskPixelT> *mask, // Pixels that we've already detected
                         DIRECTION const dir // Should we continue searching towards the top of the image?
                        ) :
        _span(span),
        _direction(dir),
        _stop(false) {

        if (mask != NULL) {                     // remember that we've detected these pixels
            mask->setMaskPlaneValues(detectedPlane, span->getX0(), span->getX1(), span->getY());

            int const y = span->getY() - mask->getY0();
            for (int x = span->getX0() - mask->getX0(); x <= span->getX1() - mask->getX0(); x++) {
                if (mask(x, y, stopPlane)) {
                    _stop = true;
                    break;
                }
            }
        }
    }

    template<typename ImagePixelT, typename MaskPixelT>
    class StartspanSet {
    public:
        StartspanSet(image::MaskedImage<ImagePixelT, MaskPixelT>& image) :
            _image(image->getImage()),
            _mask(image->getMask()) {}
        ~StartspanSet() {}

        bool add(detection::Span *span, DIRECTION const dir, bool addToMask = true);
        bool process(detection::Footprint *fp,          // the footprint that we're building
                     detection::Threshold const &threshold, // Threshold
                     double const param = -1);           // parameter that Threshold may need
    private:
        image::Image<ImagePixelT> const *_image; // the Image we're searching
        image::Mask<MaskPixelT> *_mask;          // the mask that tells us where we've got to
        std::vector<typename Startspan<MaskPixelT>::Ptr> _spans; // list of Startspans
    };

    //
    // Add a new Startspan to a StartspansSet.  Iff we see a stop bit, return true
    //
    template<typename ImagePixelT, typename MaskPixelT>
    bool StartspanSet<ImagePixelT, MaskPixelT>::add(detection::Span *span, // the span in question
                                                    DIRECTION const dir, // the desired direction to search
                                                    bool addToMask) { // should I add the Span to the mask?
        if (dir == RESTART) {
            if (add(span,  UP) || add(span, DOWN, false)) {
                return true;
            }
        } else {
            typename Startspan<MaskPixelT>::Ptr sspan(new Startspan<MaskPixelT>(span, dir));
            if (sspan->stop()) {        // we detected a stop bit
                return true;
            } else {
                _spans.push_back(sspan);
            }
        }

        return false;
    }
    
    /************************************************************************************************/
    /*
     * Search the image for pixels above threshold, starting at a single Startspan.
     * We search the array looking for one to process; it'd be better to move the
     * ones that we're done with to the end, but it probably isn't worth it for
     * the anticipated uses of this routine.
     *
     * This is the guts of pmFindFootprintAtPoint
     */
    template<typename ImagePixelT, typename MaskPixelT>
    bool StartspanSet<ImagePixelT, MaskPixelT>::process(
                detection::Footprint *fp,              // the footprint that we're building
                detection::Threshold const &threshold, // Threshold
                double const param                     // parameter that Threshold may need
                                                             ) {
        int const row0 = _image->getY0();
        int const col0 = _image->getOffsetCols();
        int const height = _image->getHeight();
        
        /**********************************************************************************************/
        
        Startspan<MaskPixelT> *sspan = NULL;
        for (auto iter = _spans.begin(); iter != _spans.end(); iter++) {
            *sspan = *iter;
            if (sspan->getDirection() != DONE) {
                break;
            }
            if (sspan->Stop()) {
                break;
            }
        }
        if (sspan == NULL || sspan->getDirection() == DONE) { // no more Startspans to process
            return false;
        }
        if (sspan->Stop()) {                    // they don't want any more spans processed
            return false;
        }
        /*
         * Work
         */
        DIRECTION const dir = sspan->getDirection();
        /*
         * Set initial span to the startspan
         */
        int x0 = sspan->getSpan()->getX0() - col0;
        /*
         * Go through image identifying objects
         */
        int nx0 = -1;                        // new value of x0
        int const di = (dir == UP) ? 1 : -1; // how much i changes to get to the next row
        bool stop = false;                   // should I stop searching for spans?

        typedef typename image::Image<ImagePixelT>::pixel_accessor pixAccessT;
        double const thresholdVal = threshold.getValue(param);
        bool const polarity = threshold.getPolarity();
        
        for (int i = sspan->span->y -row0 + di; i < height && i >= 0; i += di) {
            pixAccessT imgRow = _image->origin().advance(0, i); // row pointer
            //maskPixAccessT maskRow = _mask->origin.advance(0, i);  //  masks's row pointer
            //
            // Search left from the pixel diagonally to the left of (i - di, x0). If there's
            // a connected span there it may need to grow up and/or down, so push it onto
            // the stack for later consideration
            //
            nx0 = -1;
            for (int j = x0 - 1; j >= -1; j--) {
                ImagePixelT pixVal = (j < 0) ? thresholdVal - 100 : (polarity ? imgRow[j] : -imgRow[j]);
                if (_mask(j, i, Startspan<MaskPixelT>::detectedPlane) || pixVal < threshold) {
                    if (j < x0 - 1) {   // we found some pixels above threshold
                        nx0 = j + 1;
                    }
                    break;
                }
            }
#if 0
            if (nx0 < 0) {                      // no span to the left
                nx1 = x0 - 1;           // we're going to resume searching at nx1 + 1
            } else {
                //
                // Search right in leftmost span
                //
                //nx1 = 0;                      // make gcc happy
                for (int j = nx0 + 1; j <= width; j++) {
                    ImagePixelT pixVal = (j >= width) ? threshold - 100 : 
                        (polarity ? (F32 ? imgRowF32[j] : imgRowS32[j]) :
                         (F32 ? -imgRowF32[j] : -imgRowS32[j]));
                    if ((maskRow[j] & DETECTED) || pixVal < threshold) {
                        nx1 = j - 1;
                        break;
                    }
                }
            
                pmSpan const *sp = pmFootprintAddSpan(fp, i + row0, nx0 + col0, nx1 + col0);
            
                if (add_startspan(startspans, sp, mask, RESTART)) {
                    stop = true;
                    break;
                }
            }
            //
            // Now look for spans connected to the old span.  The first of these we'll
            // simply process, but others will have to be deferred for later consideration.
            //
            // In fact, if the span overhangs to the right we'll have to defer the overhang
            // until later too, as it too can grow in both directions
            //
            // Note that column width exists virtually, and always ends the last span; this
            // is why we claim below that sx1 is always set
            //
            bool first = false;         // is this the first new span detected?
            for (int j = nx1 + 1; j <= x1 + 1; j++) {
                ImagePixelT pixVal = (j >= width) ? threshold - 100 : 
                    (polarity ? (F32 ? imgRowF32[j] : imgRowS32[j]) : (F32 ? -imgRowF32[j] : -imgRowS32[j]));
                if (!(maskRow[j] & DETECTED) && pixVal >= threshold) {
                    int sx0 = j++;              // span that we're working on is sx0:sx1
                    int sx1 = -1;               // We know that if we got here, we'll also set sx1
                    for (; j <= width; j++) {
                        ImagePixelT pixVal = (j >= width) ? threshold - 100 : 
                            (polarity ? (F32 ? imgRowF32[j] : imgRowS32[j]) :
                             (F32 ? -imgRowF32[j] : -imgRowS32[j]));
                        if ((maskRow[j] & DETECTED) || pixVal < threshold) { // end of span
                            sx1 = j;
                            break;
                        }
                    }
                    assert (sx1 >= 0);
                    
                    pmSpan const *sp;
                    if (first) {
                        if (sx1 <= x1) {
                            sp = pmFootprintAddSpan(fp, i + row0, sx0 + col0, sx1 + col0 - 1);
                            if (add_startspan(startspans, sp, mask, DONE)) {
                                stop = true;
                                break;
                            }
                        } else {                // overhangs to right
                            sp = pmFootprintAddSpan(fp, i + row0, sx0 + col0, x1 + col0);
                            if (add_startspan(startspans, sp, mask, DONE)) {
                                stop = true;
                                break;
                            }
                            sp = pmFootprintAddSpan(fp, i + row0, x1 + 1 + col0, sx1 + col0 - 1);
                            if (add_startspan(startspans, sp, mask, RESTART)) {
                                stop = true;
                                break;
                            }
                        }
                        first = false;
                    } else {
                        sp = pmFootprintAddSpan(fp, i + row0, sx0 + col0, sx1 + col0 - 1);
                        if (add_startspan(startspans, sp, mask, RESTART)) {
                            stop = true;
                            break;
                        }
                    }
                }
            }

            if (stop || first == false) {       // we're done
                break;
            }
            
            x0 = nx0;
            x1 = nx1;
#endif
        }
        /*
         * Cleanup
         */

        sspan->_direction = DONE;
        return stop ? false : true;
    }
} 
#if 0
    

/*
 * Go through an image, starting at (row, col) and assembling all the pixels
 * that are connected to that point (in a chess kings-move sort of way) into
 * a pmFootprint.
 *
 * This is much slower than pmFindFootprints if you want to find lots of
 * footprints, but if you only want a small region about a given point it
 * can be much faster
 *
 * N.b. The returned pmFootprint is not in "normal form"; that is the pmSpans
 * are not sorted by increasing y, x0, x1.  If this matters to you, call
 * pmFootprintNormalize()
 */
pmFootprint *
pmFindFootprintAtPoint(psImage const *img,      // image to search
                       Threshold const &threshold, // Threshold
                       psArray const *peaks, // array of peaks; finding one terminates search for footprint
                       int row, int col) { // starting position (in img's parent's coordinate system)
    assert(img != NULL);
    
    bool F32 = false;                    // is this an F32 image?
    if (img->type.type == PS_TYPE_F32) {
        F32 = true;
    } else if (img->type.type == PS_TYPE_S32) {
        F32 = false;
    } else {                             // N.b. You can't trivially add more cases here; F32 is just a bool
        psError(PS_ERR_UNKNOWN, true, "Unsupported psImage type: %d", img->type.type);
        return NULL;
    }
    psF32 *imgRowF32 = NULL;             // row pointer if F32
    psS32 *imgRowS32 = NULL;             //  "   "   "  "  !F32
    
    int const row0 = img->row0;
    int const col0 = img->col0;
    int const height = img->getHeight();
    int const width = img->getWidth();
/*
 * Is point in image, and above threshold?
 */
    row -= row0;
    col -= col0;
    if (row < 0 || row >= height ||
        col < 0 || col >= width) {
        psError(PS_ERR_BAD_PARAMETER_VALUE, true,
                "row/col == (%d, %d) are out of bounds [%d--%d, %d--%d]",
                row + row0, col + col0, row0, row0 + height - 1, col0, col0 + width - 1);
        return NULL;
    }
    
    ImagePixelT pixVal = F32 ? img->data.F32[row][col] : img->data.S32[row][col];
    if (pixVal < threshold) {
        return pmFootprintAlloc(0, img);
    }
    
    pmFootprint *fp = pmFootprintAlloc(1 + img->getHeight()/10, img);
/*
 * We need a mask for two purposes; to indicate which pixels are already detected,
 * and to store the "stop" pixels --- those that, once reached, should stop us
 * looking for the rest of the pmFootprint.  These are generally set from peaks.
 */
    psImage *mask = psImageAlloc(width, height, PS_TYPE_MASK);
    P_PSIMAGE_SET_ROW0(mask, row0);
    P_PSIMAGE_SET_COL0(mask, col0);
    psImageInit(mask, INITIAL);
    //
    // Set stop bits from peaks list
    //
    assert (peaks == NULL || peaks->n == 0 || pmIsPeak(peaks->data[0]));
    if (peaks != NULL) {
        for (int i = 0; i < peaks->n; i++) {
            pmPeak *peak = peaks->data[i];
            mask->data.PS_TYPE_MASK_DATA[peak->y - mask->row0][peak->x - mask->col0] |= STOP;
        }
    }
/*
 * Find starting span passing through (row, col)
 */
    psArray *startspans = psArrayAllocEmpty(1); // spans where we have to restart the search
    
    imgRowF32 = img->data.F32[row];      // only one of
    imgRowS32 = img->data.S32[row];      //      these is valid!
    psMaskType *maskRow = mask->data.PS_TYPE_MASK_DATA[row];
    {
        int i;
        for (i = col; i >= 0; i--) {
            pixVal = F32 ? imgRowF32[i] : imgRowS32[i];
            if ((maskRow[i] & DETECTED) || pixVal < threshold) {
                break;
            }
        }
        int i0 = i;
        for (i = col; i < width; i++) {
            pixVal = F32 ? imgRowF32[i] : imgRowS32[i];
            if ((maskRow[i] & DETECTED) || pixVal < threshold) {
                break;
            }
        }
        int i1 = i;
        pmSpan const *sp = pmFootprintAddSpan(fp, row + row0, i0 + col0 + 1, i1 + col0 - 1);
        
        (void)add_startspan(startspans, sp, mask, RESTART);
    }
    /*
     * Now workout from those Startspans, searching for pixels above threshold
     */
    while (do_startspan(fp, img, mask, threshold, startspans)) continue;
    /*
     * Cleanup
     */
    psFree(mask);
    psFree(startspans);                  // restores the image pixel
    
    return fp;                           // pmFootprint really
}
#endif

/************************************************************************************************************/
detection::FootprintSet::FootprintSet(geom::Box2I region 
) :
    lsst::daf::base::Citizen(typeid(this)),
    _footprints(PTR(FootprintList)(new FootprintList)), _region(region) {
}

detection::FootprintSet::FootprintSet(
    FootprintSet const &rhs         
) :
    lsst::daf::base::Citizen(typeid(this)),
    _footprints(new FootprintList), _region(rhs._region)
{
    _footprints->reserve(rhs._footprints->size());
    for (FootprintSet::FootprintList::const_iterator ptr = rhs._footprints->begin(),
             end = rhs._footprints->end(); ptr != end; ++ptr) {
        _footprints->push_back(PTR(Footprint)(new Footprint(**ptr)));
    }
}

detection::FootprintSet &
detection::FootprintSet::operator=(FootprintSet const& rhs) {
    FootprintSet tmp(rhs);
    swap(tmp);                          // See Meyers, Effective C++, Item 11    
    return *this;
}

/************************************************************************************************************/
void detection::FootprintSet::merge(
        detection::FootprintSet const& rhs, 
        int tGrow,                          
        int rGrow,                          
        bool isotropic                      
)
{
    detection::FootprintControl const ctrl(true, isotropic);
    detection::FootprintSet fs = mergeFootprintSets(*this, tGrow, rhs, rGrow, ctrl);
    swap(fs);                           // Swap the new FootprintSet into place
}

//
void detection::FootprintSet::setRegion(
    geom::Box2I const& region 
) {
    _region = region;

    for (FootprintSet::FootprintList::iterator ptr = _footprints->begin(),
             end = _footprints->end(); ptr != end; ++ptr
    ) {
        (*ptr)->setRegion(region);
    }
}

/************************************************************************************************************/
detection::FootprintSet::FootprintSet(
    FootprintSet const &rhs,        
    int r,                          
    bool isotropic                  
)
    : lsst::daf::base::Citizen(typeid(this)), _footprints(new FootprintList), _region(rhs._region)
{
    if (r == 0) {
        FootprintSet fs = rhs;
        swap(fs);                       // Swap the new FootprintSet into place
        return;
    } else if (r < 0) {
        throw LSST_EXCEPT(lsst::pex::exceptions::InvalidParameterError,
                          (boost::format("I cannot grow by negative numbers: %d") % r).str());
    }

    detection::FootprintControl const ctrl(true, isotropic);
    detection::FootprintSet fs = mergeFootprintSets(FootprintSet(rhs.getRegion()), 0, rhs, r, ctrl);
    swap(fs);                           // Swap the new FootprintSet into place
}

/************************************************************************************************************/

detection::FootprintSet::FootprintSet(detection::FootprintSet const& rhs,
                                      int ngrow,
                                      detection::FootprintControl const& ctrl)
    : lsst::daf::base::Citizen(typeid(this)), _footprints(new FootprintList), _region(rhs._region)
{
    if (ngrow == 0) {
        FootprintSet fs = rhs;
        swap(fs);                       // Swap the new FootprintSet into place
        return;
    } else if (ngrow < 0) {
        throw LSST_EXCEPT(lsst::pex::exceptions::InvalidParameterError,
                          str(boost::format("I cannot grow by negative numbers: %d") % ngrow));
    }

    detection::FootprintSet fs = mergeFootprintSets(FootprintSet(rhs.getRegion()), 0, rhs, ngrow, ctrl);
    swap(fs);                           // Swap the new FootprintSet into place
}

/************************************************************************************************************/
detection::FootprintSet::FootprintSet(
        FootprintSet const& fs1,
        FootprintSet const& fs2,
        bool const 
                                                              )
    : lsst::daf::base::Citizen(typeid(this)),
      _footprints(new FootprintList()),
      _region(fs1._region)
{
    _region.include(fs2._region);
    throw LSST_EXCEPT(lsst::pex::exceptions::LogicError, "NOT IMPLEMENTED");
}

/************************************************************************************************************/
PTR(image::Image<detection::FootprintIdPixel>)
detection::FootprintSet::insertIntoImage(
    bool const relativeIDs          
) const {
    PTR(image::Image<detection::FootprintIdPixel>) im(
        new image::Image<detection::FootprintIdPixel>(_region)
    );
    *im = 0;

    detection::FootprintIdPixel id = 0;
    for (FootprintList::const_iterator fiter = _footprints->begin(); 
         fiter != _footprints->end(); fiter++
    ) {
        Footprint::Ptr const foot = *fiter;
        
        if (relativeIDs) {
            id++;
        } else {
            id = foot->getId();
        }
        
        foot->insertIntoImage(*im.get(), id);
    }
    
    return im;
}

/************************************************************************************************************/
template<typename ImagePixelT, typename MaskPixelT>
void
detection::FootprintSet::makeHeavy(
    image::MaskedImage<ImagePixelT, MaskPixelT> const& mimg, 
    HeavyFootprintCtrl const *ctrl     
)
{
    HeavyFootprintCtrl ctrl_s = HeavyFootprintCtrl();

    if (!ctrl) {
        ctrl = &ctrl_s;
    }

    for (FootprintList::iterator ptr = _footprints->begin(),
                                          end = _footprints->end(); ptr != end; ++ptr) {
        ptr->reset(new detection::HeavyFootprint<ImagePixelT, MaskPixelT>(**ptr, mimg, ctrl));
    }
}

void detection::FootprintSet::makeSources(
    lsst::afw::table::SourceCatalog & cat
) const {
    for (FootprintList::const_iterator i = _footprints->begin(); i != _footprints->end(); ++i) {
        PTR(afw::table::SourceRecord) r = cat.addNew();
        r->setFootprint(*i);
    }
}


/************************************************************************************************************/
//
// Explicit instantiations
//

#ifndef DOXYGEN

#define INSTANTIATE(PIXEL)                      \
    template detection::FootprintSet::FootprintSet(                     \
        image::Image<PIXEL> const &, Threshold const &, int const, bool const); \
    template detection::FootprintSet::FootprintSet(                     \
        image::MaskedImage<PIXEL,image::MaskPixel> const &, Threshold const &, \
        std::string const &, int const, bool const);\
    template void detection::FootprintSet::makeHeavy(image::MaskedImage<PIXEL,image::MaskPixel> const &, \
                                                     HeavyFootprintCtrl const *)

template detection::FootprintSet::FootprintSet(image::Mask<image::MaskPixel> const &,
                                               Threshold const &, int const);

template void detection::FootprintSet::setMask(image::Mask<image::MaskPixel> *, std::string const &);
template void detection::FootprintSet::setMask(PTR(image::Mask<image::MaskPixel>), std::string const &);

INSTANTIATE(boost::uint16_t);
INSTANTIATE(int);
INSTANTIATE(float);
INSTANTIATE(double);

#endif // !DOXYGEN