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

**    iLand - an individual based forest landscape and disturbance model

**    http://iland.boku.ac.at

**    Copyright (C) 2009-  Werner Rammer, Rupert Seidl

**

**    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 GNU General Public License

**    along with this program.  If not, see <http://www.gnu.org/licenses/>.

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

#include "seeddispersal.h"

#include "globalsettings.h"

#include "model.h"

#include "debugtimer.h"

#include "helper.h"

#include "species.h"

#ifdef ILAND_GUI

#include <QtGui/QImage>

#endif

/** @class SeedDispersal

    @ingroup core

    The class encapsulates the dispersal of seeds of one species over the whole landscape.

    The dispersal algortihm operate on grids with a 20m resolution.

    See http://iland.boku.ac.at/dispersal

  */

Grid<float> *SeedDispersal::mExternalSeedBaseMap = 0;

QHash<QString, QVector<double> > SeedDispersal::mExtSeedData;

int SeedDispersal::mExtSeedSizeX = 0;

int SeedDispersal::mExtSeedSizeY = 0;

SeedDispersal::~SeedDispersal()

{

    if (isSetup()) {

    }

}

// ************ Setup **************

/** setup of the seedmaps.

  This sets the size of the seed map and creates the seed kernel (species specific)

  */

void SeedDispersal::setup()

{

    if (!GlobalSettings::instance()->model()

        || !GlobalSettings::instance()->model()->heightGrid()

        || !mSpecies)

        return;

    const float seedmap_size = 20.f;

    // setup of seed map

    mSeedMap.clear();

    mSeedMap.setup(GlobalSettings::instance()->model()->heightGrid()->metricRect(), seedmap_size );

    mSeedMap.initialize(0.);

    mExternalSeedMap.clear();

    mIndexFactor = int(seedmap_size) / cPxSize; // ratio seed grid / lip-grid:

    if (logLevelInfo()) qDebug() << "Seed map setup. Species:"<< mSpecies->id() << "kernel-size: " << mSeedMap.sizeX() << "x" << mSeedMap.sizeY() << "pixels.";

    if (mSpecies==0)

        throw IException("Setup of SeedDispersal: Species not defined.");

    if (fmod(GlobalSettings::instance()->settings().valueDouble("model.world.buffer",0),seedmap_size) != 0.)

        throw IException("SeedDispersal:setup(): The buffer (model.world.buffer) must be a integer multiple of the seed pixel size (currently 20m, e.g. 20,40,60,...)).");

    // settings

    mTM_occupancy = 1.; // is currently constant

    // copy values for the species parameters:

    mSpecies->treeMigKernel(mTM_as1, mTM_as2, mTM_ks);

    mTM_fecundity_cell = mSpecies->fecundity_m2() * seedmap_size*seedmap_size * mTM_occupancy; // scale to production for the whole cell

    mNonSeedYearFraction = mSpecies->nonSeedYearFraction();

    XmlHelper xml(GlobalSettings::instance()->settings().node("model.settings.seedDispersal"));

    mKernelThresholdArea = xml.valueDouble(".longDistanceDispersal.thresholdArea", 0.0001);

    mKernelThresholdLDD = xml.valueDouble(".longDistanceDispersal.thresholdLDD", 0.0001);

    mLDDProbability = xml.valueDouble(".longDistanceDispersal.minProbability", 0.0001);

    mLDDRings = xml.valueInt(".longDistanceDispersal.rings", 4);

    mLDDProbability = qMax(mLDDProbability, static_cast<float>(mKernelThresholdArea));

    mFecundityFactor = createKernel(mKernelSeedYear, mTM_fecundity_cell);

    // the kernel for non seed years looks similar, but is simply linearly scaled down

    // using the species parameter NonSeedYearFraction.

    // the central pixel still gets the value of 1 (i.e. 100% probability)

    createKernel(mKernelNonSeedYear, mTM_fecundity_cell*mNonSeedYearFraction);

    if (mSpecies->fecunditySerotiny()>0.) {

        // an extra seed map is used for storing information related to post-fire seed rain

        mSeedMapSerotiny.clear();

        mSeedMapSerotiny.setup(GlobalSettings::instance()->model()->heightGrid()->metricRect(), seedmap_size );

        mSeedMapSerotiny.initialize(0.);

        // set up the special seed kernel for post fire seed rain

        createKernel(mKernelSerotiny, mTM_fecundity_cell * mSpecies->fecunditySerotiny());

        qDebug() << "created extra seed map and serotiny seed kernel for species" << mSpecies->name() << "with fecundity factor" << mSpecies->fecunditySerotiny();

    }

    mHasPendingSerotiny = false;

    // debug info

    mDumpSeedMaps = GlobalSettings::instance()->settings().valueBool("model.settings.seedDispersal.dumpSeedMapsEnabled",false);

    if (mDumpSeedMaps) {

        QString path = GlobalSettings::instance()->path( GlobalSettings::instance()->settings().value("model.settings.seedDispersal.dumpSeedMapsPath") );

        Helper::saveToTextFile(QString("%1/seedkernelYes_%2.csv").arg(path).arg(mSpecies->id()),gridToString(mKernelSeedYear));

        Helper::saveToTextFile(QString("%1/seedkernelNo_%2.csv").arg(path).arg(mSpecies->id()),gridToString(mKernelNonSeedYear));

        if (!mKernelSerotiny.isEmpty())

            Helper::saveToTextFile(QString("%1/seedkernelSerotiny_%2.csv").arg(path).arg(mSpecies->id()),gridToString(mKernelSerotiny));

    }

    // long distance dispersal

    setupLDD();

    // external seeds

    mHasExternalSeedInput = false;

    mExternalSeedBuffer = 0;

    mExternalSeedDirection = 0;

    mExternalSeedBackgroundInput = 0.;

    if (GlobalSettings::instance()->settings().valueBool("model.settings.seedDispersal.externalSeedEnabled",false)) {

        if (GlobalSettings::instance()->settings().valueBool("model.settings.seedDispersal.seedBelt.enabled",false)) {

            // external seed input specified by sectors and around the project area (seedbelt)

            setupExternalSeedsForSpecies(mSpecies);

        } else {

            // external seeds specified fixedly per cardinal direction

            // current species in list??

            mHasExternalSeedInput = GlobalSettings::instance()->settings().value("model.settings.seedDispersal.externalSeedSpecies").contains(mSpecies->id());

            QString dir = GlobalSettings::instance()->settings().value("model.settings.seedDispersal.externalSeedSource").toLower();

            // encode cardinal positions as bits: e.g: "e,w" -> 6

            mExternalSeedDirection += dir.contains("n")?1:0;

            mExternalSeedDirection += dir.contains("e")?2:0;

            mExternalSeedDirection += dir.contains("s")?4:0;

            mExternalSeedDirection += dir.contains("w")?8:0;

            QStringList buffer_list = GlobalSettings::instance()->settings().value("model.settings.seedDispersal.externalSeedBuffer").split(QRegExp("([^\\.\\w]+)"));

            int index = buffer_list.indexOf(mSpecies->id());

            if (index>=0) {

                mExternalSeedBuffer = buffer_list[index+1].toInt();

                qDebug() << "enabled special buffer for species" <<mSpecies->id() << ": distance of" << mExternalSeedBuffer << "pixels = " << mExternalSeedBuffer*20. << "m";

            }

            // background seed rain (i.e. for the full landscape), use regexp

            QStringList background_input_list = GlobalSettings::instance()->settings().value("model.settings.seedDispersal.externalSeedBackgroundInput").split(QRegExp("([^\\.\\w]+)"));

            index = background_input_list.indexOf(mSpecies->id());

            if (index>=0) {

                mExternalSeedBackgroundInput = background_input_list[index+1].toDouble();

                qDebug() << "enabled background seed input (for full area) for species" <<mSpecies->id() << ": p=" << mExternalSeedBackgroundInput;

            }

            if (mHasExternalSeedInput)

                qDebug() << "External seed input enabled for" << mSpecies->id();

        }

    }

    // setup of seed kernel

//    const int max_radius = 15; // pixels

//

//    mSeedKernel.clear();

//    mSeedKernel.setup(mSeedMap.cellsize(), 2*max_radius + 1 , 2*max_radius + 1);

//    mKernelOffset = max_radius;

//    // filling of the kernel.... for simplicity: a linear kernel

//    QPoint center = QPoint(mKernelOffset, mKernelOffset);

//    const double max_dist = max_radius * seedmap_size;

//    for (float *p=mSeedKernel.begin(); p!=mSeedKernel.end();++p) {

//        double d = mSeedKernel.distance(center, mSeedKernel.indexOf(p));

//        *p = qMax( 1. - d / max_dist, 0.);

//    }

    // randomize seed map.... set 1/3 to "filled"

    //for (int i=0;i<mSeedMap.count(); i++)

    //    mSeedMap.valueAtIndex(mSeedMap.randomPosition()) = 1.;

//    QImage img = gridToImage(mSeedMap, true, -1., 1.);

//    img.save("seedmap.png");

//    img = gridToImage(mSeedMap, true, -1., 1.);

    //    img.save("seedmap_e.png");

}

void SeedDispersal::setupExternalSeeds()

{

    mExternalSeedBaseMap = 0;

    if (!GlobalSettings::instance()->settings().valueBool("model.settings.seedDispersal.seedBelt.enabled",false))

        return;

    DebugTimer t("setup of external seed maps.");

    XmlHelper xml(GlobalSettings::instance()->settings().node("model.settings.seedDispersal.seedBelt"));

    int seedbelt_width =xml.valueInt(".width",10);

    // setup of sectors

    // setup of base map

    const float seedmap_size = 20.f;

    mExternalSeedBaseMap = new Grid<float>;

    mExternalSeedBaseMap->setup(GlobalSettings::instance()->model()->heightGrid()->metricRect(), seedmap_size );

    mExternalSeedBaseMap->initialize(0.);

    if (mExternalSeedBaseMap->count()*4 != GlobalSettings::instance()->model()->heightGrid()->count())

        throw IException("error in setting up external seeds: the width and height of the project area need to be a multiple of 20m when external seeds are enabled.");

    // make a copy of the 10m height grid in lower resolution and mark pixels that are forested and outside of

    // the project area.

    for (int y=0;y<mExternalSeedBaseMap->sizeY();y++)

        for (int x=0;x<mExternalSeedBaseMap->sizeX();x++) {

            bool val = GlobalSettings::instance()->model()->heightGrid()->valueAtIndex(x*2,y*2).isForestOutside();

            mExternalSeedBaseMap->valueAtIndex(x,y) = val?1.f:0.f;

            if(GlobalSettings::instance()->model()->heightGrid()->valueAtIndex(x*2,y*2).isValid())

                mExternalSeedBaseMap->valueAtIndex(x,y) = -1.f;

        }

    QString path = GlobalSettings::instance()->path(GlobalSettings::instance()->settings().value("model.settings.seedDispersal.dumpSeedMapsPath"));

    if (GlobalSettings::instance()->settings().valueBool("model.settings.seedDispersal.dumpSeedMapsEnabled",false)) {

#ifdef ILAND_GUI

        QImage img = gridToImage(*mExternalSeedBaseMap, true, -1., 2.);

        img.save(path + "/seedbeltmap_before.png");

#endif

    }

    //    img.save("seedmap.png");

    // now scan the pixels of the belt: paint all pixels that are close to the project area

    // we do this 4 times (for all cardinal direcitons)

    for (int y=0;y<mExternalSeedBaseMap->sizeY();y++) {

        for (int x=0;x<mExternalSeedBaseMap->sizeX();x++) {

            if (mExternalSeedBaseMap->valueAtIndex(x, y)!=1.)

                continue;

            int look_forward = std::min(x + seedbelt_width, mExternalSeedBaseMap->sizeX()-1);

            if (mExternalSeedBaseMap->valueAtIndex(look_forward, y)==-1.f) {

                // fill pixels

                for(; x<look_forward;++x) {

                    float &v = mExternalSeedBaseMap->valueAtIndex(x, y);

                    if (v==1.f) v=2.f;

                }

            }

        }

    }

    // right to left

    for (int y=0;y<mExternalSeedBaseMap->sizeY();y++) {

        for (int x=mExternalSeedBaseMap->sizeX();x>=0;--x) {

            if (mExternalSeedBaseMap->valueAtIndex(x, y)!=1.)

                continue;

            int look_forward = std::max(x - seedbelt_width, 0);

            if (mExternalSeedBaseMap->valueAtIndex(look_forward, y)==-1.f) {

                // fill pixels

                for(; x>look_forward;--x) {

                    float &v = mExternalSeedBaseMap->valueAtIndex(x, y);

                    if (v==1.f) v=2.f;

                }

            }

        }

    }

    // up and down ***

    // from top to bottom

    for (int x=0;x<mExternalSeedBaseMap->sizeX();x++) {

        for (int y=0;y<mExternalSeedBaseMap->sizeY();y++) {

            if (mExternalSeedBaseMap->valueAtIndex(x, y)!=1.)

                continue;

            int look_forward = std::min(y + seedbelt_width, mExternalSeedBaseMap->sizeY()-1);

            if (mExternalSeedBaseMap->valueAtIndex(x, look_forward)==-1.) {

                // fill pixels

                for(; y<look_forward;++y) {

                    float &v = mExternalSeedBaseMap->valueAtIndex(x, y);

                    if (v==1.f) v=2.f;

                }

            }

        }

    }

    // bottom to top ***

    for (int y=0;y<mExternalSeedBaseMap->sizeY();y++) {

        for (int x=mExternalSeedBaseMap->sizeX();x>=0;--x) {

            if (mExternalSeedBaseMap->valueAtIndex(x, y)!=1.)

                continue;

            int look_forward = std::max(y - seedbelt_width, 0);

            if (mExternalSeedBaseMap->valueAtIndex(x, look_forward)==-1.) {

                // fill pixels

                for(; y>look_forward;--y) {

                    float &v = mExternalSeedBaseMap->valueAtIndex(x, y);

                    if (v==1.f) v=2.f;

                }

            }

        }

    }

    if (GlobalSettings::instance()->settings().valueBool("model.settings.seedDispersal.dumpSeedMapsEnabled",false)) {

#ifdef ILAND_GUI

        QImage img = gridToImage(*mExternalSeedBaseMap, true, -1., 2.);

        img.save(path + "/seedbeltmap_after.png");

#endif

    }

    mExtSeedData.clear();

    int sectors_x = xml.valueInt("sizeX",0);

    int sectors_y = xml.valueInt("sizeY",0);

    if(sectors_x<1 || sectors_y<1)

        throw IException(QString("setup of external seed dispersal: invalid number of sectors x=%1 y=%3").arg(sectors_x).arg(sectors_y));

    QDomElement elem = xml.node(".");

    for(QDomNode n = elem.firstChild(); !n.isNull(); n = n.nextSibling()) {

        if (n.nodeName().startsWith("species")) {

            QStringList coords = n.nodeName().split("_");

            if (coords.count()!=3)

                throw IException("external seed species definition is not valid: " + n.nodeName());

            int x = coords[1].toInt();

            int y = coords[2].toInt();

            if (x<0 || x>=sectors_x || y<0 || y>=sectors_y)

                throw IException(QString("invalid sector for specifiing external seed input (x y): %1 %2 ").arg(x).arg(y) );

            int index = y*sectors_x + x;

            QString text = xml.value("." + n.nodeName());

            qDebug() << "processing element " << n.nodeName() << "x,y:" << x << y << text;

            // we assume pairs of name and fraction

            QStringList species_list = text.split(" ");

            for (int i=0;i<species_list.count();++i) {

                QVector<double> &space = mExtSeedData[species_list[i]];

                if (space.isEmpty())

                    space.resize(sectors_x*sectors_y); // are initialized to 0s

                double fraction = species_list[++i].toDouble();

                space[index] = fraction;

            }

        }

    }

    mExtSeedSizeX = sectors_x;

    mExtSeedSizeY = sectors_y;

    qDebug() << "setting up of external seed maps finished";

}

void SeedDispersal::finalizeExternalSeeds()

{

    if (mExternalSeedBaseMap)

        delete mExternalSeedBaseMap;

    mExternalSeedBaseMap = 0;

}

void SeedDispersal::seedProductionSerotiny(const QPoint &position_index)

{

    if (mSeedMapSerotiny.isEmpty())

        throw IException("Invalid use seedProductionSerotiny(): tried to set a seed source for a non-serotinous species!");

    mSeedMapSerotiny.valueAtIndex(position_index.x()/mIndexFactor, position_index.y()/mIndexFactor)=1.f;

    mHasPendingSerotiny = true;

}

// ************ Kernel **************

float SeedDispersal::createKernel(Grid<float> &kernel, const double max_seed)

{

    double max_dist = treemig_distanceTo(mKernelThresholdArea);

    double cell_size = mSeedMap.cellsize();

    int max_radius = int(max_dist / cell_size);

    // e.g.: cell_size: regeneration grid (e.g. 400qm), px-size: light-grid (4qm)

    double occupation = cell_size*cell_size / (cPxSize*cPxSize * mTM_occupancy);

    kernel.clear();

    kernel.setup(mSeedMap.cellsize(), 2*max_radius + 1 , 2*max_radius + 1);

    int kernel_offset = max_radius;

    // filling of the kernel.... use the treemig

    double dist_center_cell = sqrt(cell_size*cell_size/M_PI);

    QPoint center = QPoint(kernel_offset, kernel_offset);

    const float *sk_end = kernel.end();

    for (float *p=kernel.begin(); p!=sk_end;++p) {

        double d = kernel.distance(center, kernel.indexOf(p));

        if (d==0.)

            *p = treemig_centercell(dist_center_cell); // r is the radius of a circle with the same area as a cell

        else

            *p = d<=max_dist?static_cast<float>(( treemig(d+dist_center_cell) + treemig(d+dist_center_cell))/2. ):0.f;

    }

    // normalize

    float sum = kernel.sum();

    if (sum==0. || occupation==0.)

        throw IException("create seed kernel: sum of probabilities = 0!");

    // the sum of all kernel cells has to equal 1

    // kernel.multiply(1.f/sum);

    float fecundity_factor = static_cast<float>( max_seed / occupation);

    // probabilities are derived in multiplying by seed number, and dividing by occupancy criterion

    kernel.multiply( fecundity_factor );

    // all cells that get more seeds than the occupancy criterion are considered to have no seed limitation for regeneration

    for (float *p=kernel.begin(); p!=sk_end;++p) {

        *p = qMin(*p, 1.f);

    }

    // set the parent cell to 1

    //kernel.valueAtIndex(kernel_offset, kernel_offset)=1.f;

    // some final statistics....

    if (logLevelInfo()) qDebug() << "kernel setup.Species:"<< mSpecies->id() << "kernel-size: " << kernel.sizeX() << "x" << kernel.sizeY() << "pixels, sum: " << kernel.sum();

    return fecundity_factor;

}

void SeedDispersal::setupLDD()

{

    mLDDDensity.clear(); mLDDDistance.clear();

    if (mKernelThresholdLDD >= mKernelThresholdArea) {

        // no long distance dispersal

        return;

    }

    double r_min = treemig_distanceTo(mKernelThresholdArea);

    double r_max = treemig_distanceTo(mKernelThresholdLDD);

    mLDDDistance.push_back(r_min);

    for (int i=0;i<mLDDRings;++i) {

        double r_in = mLDDDistance.last();

        mLDDDistance.push_back(mLDDDistance.last() + (r_max-r_min)/static_cast<float>(mLDDRings));

        double r_out = mLDDDistance.last();

        // calculate the value of the kernel for the middle of the ring

        double ring_in = treemig(r_in); // kernel value at the inner border of the ring

        double ring_out = treemig(r_out); // kernel value at the outer border of the ring

        double ring_val = (ring_in + ring_out)/2.; // this is the average p

        ring_val *= mFecundityFactor; // include fecundity (along the lines of the kernel calculations)

        // calculate the area of the ring

        double ring_area = (r_out*r_out - r_in*r_in)*M_PI; // in square meters

        double ring_px = ring_area / (mSeedMap.cellsize()*mSeedMap.cellsize()); // # of seed pixels on the ring

        double n_px = ring_val * ring_px / mLDDProbability;

        mLDDDensity.push_back(n_px);

    }

    qDebug() << "Setup LDD for" << species()->name() << ", using probability: "<< mLDDProbability<< ": Distances:" << mLDDDistance << ", seed pixels:" << mLDDDensity;

}

/* R-Code:

treemig=function(as1,as2,ks,d) # two-part exponential function, cf. Lischke & Loeffler (2006), Annex

        {

        p1=(1-ks)*exp(-d/as1)/as1

        if(as2>0){p2=ks*exp(-d/as2)/as2}else{p2=0}

        p1+p2

        }

*/

/// the used kernel function

/// see also Appendix B of iland paper II (note the different variable names)

/// the function returns the seed density at a point with distance 'distance'.

double SeedDispersal::treemig(const double &distance)

{

    double p1 = (1.-mTM_ks)*exp(-distance/mTM_as1)/mTM_as1;

    double p2 = 0.;

    if (mTM_as2>0.)

       p2 = mTM_ks*exp(-distance/mTM_as2)/mTM_as2;

    double s = p1 + p2;

    // 's' is the density for radius 'distance' - not for specific point with that distance.

    // (i.e. the integral over the one-dimensional treemig function is 1, but if applied for 2d cells, the

    // sum would be much larger as all seeds arriving at 'distance' would be arriving somewhere at the circle with radius 'distance')

    // convert that to a density at a point, by dividing with the circumference at the circle with radius 'distance'

    s = s / (2.*std::max(distance, 0.01)*M_PI);

    return s;

}

double SeedDispersal::treemig_centercell(const double &max_distance)

{

    // use 100 steps and calculate dispersal kernel for consecutive rings

    double sum = 0.;

    for (int i=0;i<100;i++) {

        double r_in = i*max_distance/100.;

        double r_out = (i+1)*max_distance/100.;

        double ring_area = (r_out*r_out-r_in*r_in)*M_PI;

        // the value of each ring is: treemig(r) * area of the ring

        sum += treemig((r_out+r_in)/2.)*ring_area;

    }

    return sum;

}

/// calculate the distance where the probability falls below 'value'

double SeedDispersal::treemig_distanceTo(const double value)

{

    double dist = 0.;

    while (treemig(dist)>value && dist<10000.)

        dist+=10;

    return dist;

}

void SeedDispersal::setupExternalSeedsForSpecies(Species *species)

{

    if (!mExtSeedData.contains(species->id()))

        return; // nothing to do

    qDebug() << "setting up external seed map for" << species->id();

    QVector<double> &pcts = mExtSeedData[species->id()];

    mExternalSeedMap.setup(mSeedMap);

    mExternalSeedMap.initialize(0.f);

    for (int sector_x=0; sector_x<mExtSeedSizeX; ++sector_x)

        for (int sector_y=0; sector_y<mExtSeedSizeY; ++sector_y) {

            int xmin,xmax,ymin,ymax;

            int fx = mExternalSeedMap.sizeX() / mExtSeedSizeX; // number of cells per sector

            xmin = sector_x*fx;

            xmax = (sector_x+1)*fx;

            fx = mExternalSeedMap.sizeY() / mExtSeedSizeY; // number of cells per sector

            ymin = sector_y*fx;

            ymax = (sector_y+1)*fx;

            // now loop over the whole sector

            int index = sector_y*mExtSeedSizeX  + sector_x;

            double p = pcts[index];

            for (int y=ymin;y<ymax;++y)

                for (int x=xmin;x<xmax;++x) {

                    // check

                    if (mExternalSeedBaseMap->valueAtIndex(x,y)==2.f)

                        if (drandom()<p)

                            mExternalSeedMap.valueAtIndex(x,y) = 1.f; // flag

                }

        }

}

// ************ Dispersal **************

/// debug function: loads a image of arbirtrary size...

void SeedDispersal::loadFromImage(const QString &fileName)

{

    mSeedMap.clear();

    loadGridFromImage(fileName, mSeedMap);

    for (float* p=mSeedMap.begin();p!=mSeedMap.end();++p)

        *p = *p>0.8?1.f:0.f;

}

void SeedDispersal::clear()

{

    if (!mExternalSeedMap.isEmpty()) {

        // we have a preprocessed initial value for the external seed map (see setupExternalSeeds() et al)

        mSeedMap.copy(mExternalSeedMap);

        return;

    }

    // clear the map

    float background_value = static_cast<float>(mExternalSeedBackgroundInput); // there is potentitally a background probability <>0 for all pixels.

    mSeedMap.initialize(background_value);

    if (mHasExternalSeedInput) {

        // if external seed input is enabled, the buffer area of the seed maps is

        // "turned on", i.e. set to 1.

        int buf_size = GlobalSettings::instance()->settings().valueInt("model.world.buffer",0.) / static_cast<int>(mSeedMap.cellsize());

        // if a special buffer is defined, reduce the size of the input

        if (mExternalSeedBuffer>0)

            buf_size -= mExternalSeedBuffer;

        if (buf_size>0) {

            int ix,iy;

            for (iy=0;iy<mSeedMap.sizeY();++iy)

                for (ix=0;ix<mSeedMap.sizeX(); ++ix)

                    if (iy<buf_size || iy>=mSeedMap.sizeY()-buf_size || ix<buf_size || ix>=mSeedMap.sizeX()-buf_size) {

                        if (mExternalSeedDirection==0) {

                            // seeds from all directions

                            mSeedMap.valueAtIndex(ix,iy)=1.f;

                        } else {

                            // seeds only from specific directions

                            float value = 0.f;

                            if (isBitSet(mExternalSeedDirection,1) && ix>=mSeedMap.sizeX()-buf_size) value = 1; // north

                            if (isBitSet(mExternalSeedDirection,2) && iy<buf_size) value = 1; // east

                            if (isBitSet(mExternalSeedDirection,3) && ix<buf_size) value = 1; // south

                            if (isBitSet(mExternalSeedDirection,4) && iy>=mSeedMap.sizeY()-buf_size) value = 1; // west

                            mSeedMap.valueAtIndex(ix,iy)=value;

                        }

                    }

        } else {

            qDebug() << "external seed input: Error: invalid buffer size???";

        }

    }

}

static int _debug_ldd=0;

void SeedDispersal::execute()

{

#ifdef ILAND_GUI

    int year = GlobalSettings::instance()->currentYear();

    QString path;

    if (mDumpSeedMaps) {

        path = GlobalSettings::instance()->path( GlobalSettings::instance()->settings().value("model.settings.seedDispersal.dumpSeedMapsPath") );

        gridToImage(seedMap(), true, 0., 1.).save(QString("%1/seed_before_%2_%3.png").arg(path).arg(mSpecies->id()).arg(year));

        qDebug() << "saved seed map image to" << path;

    }

#else

    if (mDumpSeedMaps)

        qDebug() << "saving of seedmaps only supported in the iLand GUI.";

#endif

    DebugTimer t("seed dispersal", true);

    {

    // (1) detect edges

    if (edgeDetection()) {

#ifdef ILAND_GUI

        if (mDumpSeedMaps) {

            gridToImage(seedMap(), true, -1., 1.).save(QString("%1/seed_edge_%2_%3.png").arg(path).arg(mSpecies->id()).arg(year));

        }

#endif

        // (2) distribute seed probabilites from edges

        distribute();

    }

    // special case serotiny

    if (mHasPendingSerotiny) {

        qDebug() << "calculating extra seed rain (serotiny)....";

#ifdef ILAND_GUI

        if (mDumpSeedMaps) {

            gridToImage(mSeedMapSerotiny, true, 0., 1.).save(QString("%1/seed_serotiny_before_%2_%3.png").arg(path).arg(mSpecies->id()).arg(year));

        }

#endif

        if (edgeDetection(&mSeedMapSerotiny))

            distribute(&mSeedMapSerotiny);

        // copy back data

        float *sero=mSeedMapSerotiny.begin();

        for (float* p=mSeedMap.begin();p!=mSeedMap.end();++p, ++sero)

            *p = std::max(*p, *sero);

        float total = mSeedMapSerotiny.sum();

#ifdef ILAND_GUI

        if (mDumpSeedMaps) {

            gridToImage(mSeedMapSerotiny, true, 0., 1.).save(QString("%1/seed_serotiny_after_%2_%3.png").arg(path).arg(mSpecies->id()).arg(year));

        }

#endif

        mSeedMapSerotiny.initialize(0.f); // clear

        mHasPendingSerotiny = false;

        qDebug() << "serotiny event: extra seed input" << total << "(total sum of seed probability over all pixels of the serotiny seed map) of species" << mSpecies->name();

    }

    } // debugtimer

#ifdef ILAND_GUI

    if (mDumpSeedMaps) {

        qDebug() << "finished seed dispersal for species. time: " << mSpecies->id() << t.elapsed();

        gridToImage(seedMap(), true, 0., 1.).save(QString("%1/seed_after_%2_%3.png").arg(path).arg(mSpecies->id()).arg(year));

    }

    if (!mDumpNextYearFileName.isEmpty()) {

        Helper::saveToTextFile(GlobalSettings::instance()->path(mDumpNextYearFileName), gridToESRIRaster(seedMap()));

        qDebug() << "saved seed map for " << species()->id() << "to" << GlobalSettings::instance()->path(mDumpNextYearFileName);

        mDumpNextYearFileName = QString();

    }