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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 "global.h"

#include "tree.h"

#include "grid.h"

#include "stamp.h"

#include "species.h"

#include "resourceunit.h"

#include "model.h"

#include "snag.h"

#include "forestmanagementengine.h"

#include "modules.h"

// static varaibles

FloatGrid *Tree::mGrid = 0;

HeightGrid *Tree::mHeightGrid = 0;

int Tree::m_statPrint=0;

int Tree::m_statAboveZ=0;

int Tree::m_statCreated=0;

int Tree::m_nextId=0;

#ifdef ALT_TREE_MORTALITY

double _stress_threshold = 0.05;

int _stress_years = 5;

double _stress_death_prob = 0.33;

#endif

/** @class Tree

    @ingroup core

    A tree is the basic simulation entity of iLand and represents a single tree.

    Trees in iLand are designed to be lightweight, thus the list of stored properties is limited. Basic properties

    are dimensions (dbh, height), biomass pools (stem, leaves, roots), the reserve NPP pool. Additionally, the location and species are stored.

    A Tree has a height of at least 4m; trees below this threshold are covered by the regeneration layer (see Sapling).

    Trees are stored in lists managed at the resource unit level.

  */

/** get distance and direction between two points.

  returns the distance (m), and the angle between PStart and PEnd (radians) in referenced param rAngle. */

float dist_and_direction(const QPointF &PStart, const QPointF &PEnd, float &rAngle)

{

    float dx = PEnd.x() - PStart.x();

    float dy = PEnd.y() - PStart.y();

    float d = sqrt(dx*dx + dy*dy);

    // direction:

    rAngle = atan2(dx, dy);

    return d;

}

// lifecycle

Tree::Tree()

{

    mDbh = mHeight = 0;

    mRU = 0; mSpecies = 0;

    mFlags = mAge = 0;

    mOpacity=mFoliageMass=mWoodyMass=mCoarseRootMass=mFineRootMass=mLeafArea=0.;

    mDbhDelta=mNPPReserve=mLRI=mStressIndex=0.;

    mLightResponse = 0.;

    mStamp=0;

    mId = m_nextId++;

    m_statCreated++;

}

float Tree::crownRadius() const

{

    Q_ASSERT(mStamp!=0);

    return mStamp->crownRadius();

}

float Tree::biomassBranch() const

{

    return mSpecies->biomassBranch(mDbh);

}

void Tree::setGrid(FloatGrid* gridToStamp, Grid<HeightGridValue> *dominanceGrid)

{

    mGrid = gridToStamp; mHeightGrid = dominanceGrid;

}

// calculate the thickness of the bark of the tree

double Tree::barkThickness() const

{

    return mSpecies->barkThickness(mDbh);

}

/// dumps some core variables of a tree to a string.

QString Tree::dump()

{

    QString result = QString("id %1 species %2 dbh %3 h %4 x/y %5/%6 ru# %7 LRI %8")

                            .arg(mId).arg(species()->id()).arg(mDbh).arg(mHeight)

                            .arg(position().x()).arg(position().y())

                            .arg(mRU->index()).arg(mLRI);

    return result;

}

void Tree::dumpList(DebugList &rTargetList)

{

    rTargetList << mId << species()->id() << mDbh << mHeight  << position().x() << position().y()   << mRU->index() << mLRI

                << mWoodyMass << mCoarseRootMass << mFoliageMass << mLeafArea;

}

void Tree::setup()

{

    if (mDbh<=0 || mHeight<=0) {

        throw IException(QString("Error: trying to set up a tree with invalid dimensions: dbh: %1 height: %2 id: %3 RU-index: %4").arg(mDbh).arg(mHeight).arg(mId).arg(mRU->index()));

    }

    // check stamp

    Q_ASSERT_X(species()!=0, "Tree::setup()", "species is NULL");

    mStamp = species()->stamp(mDbh, mHeight);

    if (!mStamp) {

        throw IException("Tree::setup() with invalid stamp!");

    }

    mFoliageMass = species()->biomassFoliage(mDbh);

    mCoarseRootMass = species()->biomassRoot(mDbh); // coarse root (allometry)

    mFineRootMass = mFoliageMass * species()->finerootFoliageRatio(); //  fine root (size defined  by finerootFoliageRatio)

    mWoodyMass = species()->biomassWoody(mDbh);

    // LeafArea[m2] = LeafMass[kg] * specificLeafArea[m2/kg]

    mLeafArea = mFoliageMass * species()->specificLeafArea();

    mOpacity = 1. - exp(- Model::settings().lightExtinctionCoefficientOpacity * mLeafArea / mStamp->crownArea());

    mNPPReserve = (1+species()->finerootFoliageRatio())*mFoliageMass; // initial value

    mDbhDelta = 0.1f; // initial value: used in growth() to estimate diameter increment

}

void Tree::setAge(const int age, const float treeheight)

{

    mAge = age;

    if (age==0) {

        // estimate age using the tree height

        mAge = mSpecies->estimateAge(treeheight);

    }

}

//////////////////////////////////////////////////

////  Light functions (Pattern-stuff)

//////////////////////////////////////////////////

#define NOFULLDBG

//#define NOFULLOPT

void Tree::applyLIP()

{

    if (!mStamp)

        return;

    Q_ASSERT(mGrid!=0 && mStamp!=0 && mRU!=0);

    QPoint pos = mPositionIndex;

    int offset = mStamp->offset();

    pos-=QPoint(offset, offset);

    float local_dom; // height of Z* on the current position

    int x,y;

    float value, z, z_zstar;

    int gr_stamp = mStamp->size();

    if (!mGrid->isIndexValid(pos) || !mGrid->isIndexValid(pos+QPoint(gr_stamp, gr_stamp))) {

        // this should not happen because of the buffer

        return;

    }

    int grid_y = pos.y();

    for (y=0;y<gr_stamp; ++y) {

        float *grid_value_ptr = mGrid->ptr(pos.x(), grid_y);

        int grid_x = pos.x();

        for (x=0;x<gr_stamp;++x, ++grid_x, ++grid_value_ptr) {

            // suppose there is no stamping outside

            value = (*mStamp)(x,y); // stampvalue

            //if (value>0.f) {

                local_dom = (*mHeightGrid)(grid_x/cPxPerHeight, grid_y/cPxPerHeight).height;

                z = std::max(mHeight - (*mStamp).distanceToCenter(x,y), 0.f); // distance to center = height (45 degree line)

                z_zstar = (z>=local_dom)?1.f:z/local_dom;

                value = 1. - value*mOpacity * z_zstar; // calculated value

                value = std::max(value, 0.02f); // limit value

                *grid_value_ptr *= value;

            //}

        }

        grid_y++;

    }

    m_statPrint++; // count # of stamp applications...

}

/// helper function for gluing the edges together

/// index: index at grid

/// count: number of pixels that are the simulation area (e.g. 100m and 2m pixel -> 50)

/// buffer: size of buffer around simulation area (in pixels)

inline int torusIndex(int index, int count, int buffer, int ru_index)

{

    return buffer + ru_index + (index-buffer+count)%count;

}

/** Apply LIPs. This "Torus" functions wraps the influence at the edges of a 1ha simulation area.

  */

void Tree::applyLIP_torus()

{

    if (!mStamp)

        return;

    Q_ASSERT(mGrid!=0 && mStamp!=0 && mRU!=0);

    int bufferOffset = mGrid->indexAt(QPointF(0.,0.)).x(); // offset of buffer

    QPoint pos = QPoint((mPositionIndex.x()-bufferOffset)%cPxPerRU  + bufferOffset,

                        (mPositionIndex.y()-bufferOffset)%cPxPerRU + bufferOffset); // offset within the ha

    QPoint ru_offset = QPoint(mPositionIndex.x() - pos.x(), mPositionIndex.y() - pos.y()); // offset of the corner of the resource index

    int offset = mStamp->offset();

    pos-=QPoint(offset, offset);

    float local_dom; // height of Z* on the current position

    int x,y;

    float value;

    int gr_stamp = mStamp->size();

    int grid_x, grid_y;

    float *grid_value;

    if (!mGrid->isIndexValid(pos) || !mGrid->isIndexValid(pos+QPoint(gr_stamp, gr_stamp))) {

        // todo: in this case we should use another algorithm!!! necessary????

        return;

    }

    float z, z_zstar;

    int xt, yt; // wraparound coordinates

    for (y=0;y<gr_stamp; ++y) {

        grid_y = pos.y() + y;

        yt = torusIndex(grid_y, cPxPerRU,bufferOffset, ru_offset.y()); // 50 cells per 100m

        for (x=0;x<gr_stamp;++x) {

            // suppose there is no stamping outside

            grid_x = pos.x() + x;

            xt = torusIndex(grid_x,cPxPerRU,bufferOffset, ru_offset.x());

            local_dom = mHeightGrid->valueAtIndex(xt/cPxPerHeight,yt/cPxPerHeight).height;

            z = std::max(mHeight - (*mStamp).distanceToCenter(x,y), 0.f); // distance to center = height (45 degree line)

            z_zstar = (z>=local_dom)?1.f:z/local_dom;

            value = (*mStamp)(x,y); // stampvalue

            value = 1. - value*mOpacity * z_zstar; // calculated value

            // old: value = 1. - value*mOpacity / local_dom; // calculated value

            value = qMax(value, 0.02f); // limit value

            grid_value = mGrid->ptr(xt, yt); // use wraparound coordinates

            *grid_value *= value;

        }

    }

    m_statPrint++; // count # of stamp applications...

}

/** heightGrid()

  This function calculates the "dominant height field". This grid is coarser as the fine-scaled light-grid.

*/

void Tree::heightGrid()

{

    QPoint p = QPoint(mPositionIndex.x()/cPxPerHeight, mPositionIndex.y()/cPxPerHeight); // pos of tree on height grid

    // count trees that are on height-grid cells (used for stockable area)

    mHeightGrid->valueAtIndex(p).increaseCount();

    if (mHeight > mHeightGrid->valueAtIndex(p).height)

        mHeightGrid->valueAtIndex(p).height=mHeight;

    int r = mStamp->reader()->offset(); // distance between edge and the center pixel. e.g.: if r = 2 -> stamp=5x5

    int index_eastwest = mPositionIndex.x() % cPxPerHeight; // 4: very west, 0 east edge

    int index_northsouth = mPositionIndex.y() % cPxPerHeight; // 4: northern edge, 0: southern edge

    if (index_eastwest - r < 0) { // east

        mHeightGrid->valueAtIndex(p.x()-1, p.y()).height=qMax(mHeightGrid->valueAtIndex(p.x()-1, p.y()).height,mHeight);

    }

    if (index_eastwest + r >= cPxPerHeight) {  // west

        mHeightGrid->valueAtIndex(p.x()+1, p.y()).height=qMax(mHeightGrid->valueAtIndex(p.x()+1, p.y()).height,mHeight);

    }

    if (index_northsouth - r < 0) {  // south

        mHeightGrid->valueAtIndex(p.x(), p.y()-1).height=qMax(mHeightGrid->valueAtIndex(p.x(), p.y()-1).height,mHeight);

    }

    if (index_northsouth + r >= cPxPerHeight) {  // north

        mHeightGrid->valueAtIndex(p.x(), p.y()+1).height=qMax(mHeightGrid->valueAtIndex(p.x(), p.y()+1).height,mHeight);

    }

    // without spread of the height grid

//    // height of Z*

//    const float cellsize = mHeightGrid->cellsize();

//

//    int index_eastwest = mPositionIndex.x() % cPxPerHeight; // 4: very west, 0 east edge

//    int index_northsouth = mPositionIndex.y() % cPxPerHeight; // 4: northern edge, 0: southern edge

//    int dist[9];

//    dist[3] = index_northsouth * 2 + 1; // south

//    dist[1] = index_eastwest * 2 + 1; // west

//    dist[5] = 10 - dist[3]; // north

//    dist[7] = 10 - dist[1]; // east

//    dist[8] = qMax(dist[5], dist[7]); // north-east

//    dist[6] = qMax(dist[3], dist[7]); // south-east

//    dist[0] = qMax(dist[3], dist[1]); // south-west

//    dist[2] = qMax(dist[5], dist[1]); // north-west

//    dist[4] = 0; // center cell

//    /* the scheme of indices is as follows:  if sign(ix)= -1, if ix<0, 0 for ix=0, 1 for ix>0 (detto iy), then:

//       index = 4 + 3*sign(ix) + sign(iy) transforms combinations of directions to unique ids (0..8), which are used above.

//        e.g.: sign(ix) = -1, sign(iy) = 1 (=north-west) -> index = 4 + -3 + 1 = 2

//    */

//

//

//    int ringcount = int(floor(mHeight / cellsize)) + 1;

//    int ix, iy;

//    int ring;

//    float hdom;

//

//    for (ix=-ringcount;ix<=ringcount;ix++)

//        for (iy=-ringcount; iy<=+ringcount; iy++) {

//        ring = qMax(abs(ix), abs(iy));

//        QPoint pos(ix+p.x(), iy+p.y());

//        if (mHeightGrid->isIndexValid(pos)) {

//            float &rHGrid = mHeightGrid->valueAtIndex(pos).height;

//            if (rHGrid > mHeight) // skip calculation if grid is higher than tree

//                continue;

//            int direction = 4 + (ix?(ix<0?-3:3):0) + (iy?(iy<0?-1:1):0); // 4 + 3*sgn(x) + sgn(y)

//            hdom = mHeight - dist[direction];

//            if (ring>1)

//                hdom -= (ring-1)*10;

//

//            rHGrid = qMax(rHGrid, hdom); // write value

//        } // is valid

//    } // for (y)

}

void Tree::heightGrid_torus()

{

    // height of Z*

    QPoint p = QPoint(mPositionIndex.x()/cPxPerHeight, mPositionIndex.y()/cPxPerHeight); // pos of tree on height grid

    int bufferOffset = mHeightGrid->indexAt(QPointF(0.,0.)).x(); // offset of buffer (i.e.: size of buffer in height-pixels)

    p.setX((p.x()-bufferOffset)%10 + bufferOffset); // 10: 10 x 10m pixeln in 100m

    p.setY((p.y()-bufferOffset)%10 + bufferOffset);

    // torus coordinates: ru_offset = coords of lower left corner of 1ha patch

    QPoint ru_offset =QPoint(mPositionIndex.x()/cPxPerHeight - p.x(), mPositionIndex.y()/cPxPerHeight - p.y());

    // count trees that are on height-grid cells (used for stockable area)

    HeightGridValue &v = mHeightGrid->valueAtIndex(torusIndex(p.x(),10,bufferOffset,ru_offset.x()),

                                                   torusIndex(p.y(),10,bufferOffset,ru_offset.y()));

    v.increaseCount();

    v.height = qMax(v.height, mHeight);

    int r = mStamp->reader()->offset(); // distance between edge and the center pixel. e.g.: if r = 2 -> stamp=5x5

    int index_eastwest = mPositionIndex.x() % cPxPerHeight; // 4: very west, 0 east edge

    int index_northsouth = mPositionIndex.y() % cPxPerHeight; // 4: northern edge, 0: southern edge

    if (index_eastwest - r < 0) { // east

        HeightGridValue &v = mHeightGrid->valueAtIndex(torusIndex(p.x()-1,10,bufferOffset,ru_offset.x()),

                                                       torusIndex(p.y(),10,bufferOffset,ru_offset.y()));

        v.height = qMax(v.height, mHeight);

    }

    if (index_eastwest + r >= cPxPerHeight) {  // west

        HeightGridValue &v = mHeightGrid->valueAtIndex(torusIndex(p.x()+1,10,bufferOffset,ru_offset.x()),

                                                       torusIndex(p.y(),10,bufferOffset,ru_offset.y()));

        v.height = qMax(v.height, mHeight);

    }

    if (index_northsouth - r < 0) {  // south

        HeightGridValue &v = mHeightGrid->valueAtIndex(torusIndex(p.x(),10,bufferOffset,ru_offset.x()),

                                                       torusIndex(p.y()-1,10,bufferOffset,ru_offset.y()));

        v.height = qMax(v.height, mHeight);

    }

    if (index_northsouth + r >= cPxPerHeight) {  // north

        HeightGridValue &v = mHeightGrid->valueAtIndex(torusIndex(p.x(),10,bufferOffset,ru_offset.x()),

                                                       torusIndex(p.y()+1,10,bufferOffset,ru_offset.y()));

        v.height = qMax(v.height, mHeight);

    }

//    int index_eastwest = mPositionIndex.x() % cPxPerHeight; // 4: very west, 0 east edge

//    int index_northsouth = mPositionIndex.y() % cPxPerHeight; // 4: northern edge, 0: southern edge

//    int dist[9];

//    dist[3] = index_northsouth * 2 + 1; // south

//    dist[1] = index_eastwest * 2 + 1; // west

//    dist[5] = 10 - dist[3]; // north

//    dist[7] = 10 - dist[1]; // east

//    dist[8] = qMax(dist[5], dist[7]); // north-east

//    dist[6] = qMax(dist[3], dist[7]); // south-east

//    dist[0] = qMax(dist[3], dist[1]); // south-west

//    dist[2] = qMax(dist[5], dist[1]); // north-west

//    dist[4] = 0; // center cell

//    /* the scheme of indices is as follows:  if sign(ix)= -1, if ix<0, 0 for ix=0, 1 for ix>0 (detto iy), then:

//       index = 4 + 3*sign(ix) + sign(iy) transforms combinations of directions to unique ids (0..8), which are used above.

//        e.g.: sign(ix) = -1, sign(iy) = 1 (=north-west) -> index = 4 + -3 + 1 = 2

//    */

//

//

//    int ringcount = int(floor(mHeight / cellsize)) + 1;

//    int ix, iy;

//    int ring;

//    float hdom;

//    for (ix=-ringcount;ix<=ringcount;ix++)

//        for (iy=-ringcount; iy<=+ringcount; iy++) {

//        ring = qMax(abs(ix), abs(iy));

//        QPoint pos(ix+p.x(), iy+p.y());

//        QPoint p_torus(torusIndex(pos.x(),10,bufferOffset,ru_offset.x()),

//                       torusIndex(pos.y(),10,bufferOffset,ru_offset.y()));

//        if (mHeightGrid->isIndexValid(p_torus)) {

//            float &rHGrid = mHeightGrid->valueAtIndex(p_torus.x(),p_torus.y()).height;

//            if (rHGrid > mHeight) // skip calculation if grid is higher than tree

//                continue;

//            int direction = 4 + (ix?(ix<0?-3:3):0) + (iy?(iy<0?-1:1):0); // 4 + 3*sgn(x) + sgn(y)

//            hdom = mHeight - dist[direction];

//            if (ring>1)

//                hdom -= (ring-1)*10;

//

//            rHGrid = qMax(rHGrid, hdom); // write value

//        } // is valid

//    } // for (y)

}

/** reads the light influence field value for a tree.

    The LIF field is scanned within the crown area of the focal tree, and the influence of

    the focal tree is "subtracted" from the LIF values.

    Finally, the "LRI correction" is applied.

    see http://iland.boku.ac.at/competition+for+light for details.

  */

void Tree::readLIF()

{

    if (!mStamp)

        return;

    const Stamp *reader = mStamp->reader();

    if (!reader)

        return;

    QPoint pos_reader = mPositionIndex;

    const float outside_area_factor = 0.1f; //

    int offset_reader = reader->offset();

    int offset_writer = mStamp->offset();

    int d_offset = offset_writer - offset_reader; // offset on the *stamp* to the crown-cells

    pos_reader-=QPoint(offset_reader, offset_reader);

    float local_dom;

    int x,y;

    double sum=0.;

    double value, own_value;

    float *grid_value;

    float z, z_zstar;

    int reader_size = reader->size();

    int rx = pos_reader.x();

    int ry = pos_reader.y();

    for (y=0;y<reader_size; ++y, ++ry) {

        grid_value = mGrid->ptr(rx, ry);

        for (x=0;x<reader_size;++x) {

            const HeightGridValue &hgv = mHeightGrid->constValueAtIndex((rx+x)/cPxPerHeight, ry/cPxPerHeight); // the height grid value, ry: gets ++ed in outer loop, rx not

            local_dom = hgv.height;

            z = std::max(mHeight - reader->distanceToCenter(x,y), 0.f); // distance to center = height (45 degree line)

            z_zstar = (z>=local_dom)?1.f:z/local_dom;

            own_value = 1. - mStamp->offsetValue(x,y,d_offset)*mOpacity * z_zstar;

            own_value = qMax(own_value, 0.02);

            value =  *grid_value++ / own_value; // remove impact of focal tree

            // additional punishment if pixel is outside:

            if (hgv.isForestOutside())

               value *= outside_area_factor;

            //qDebug() << x << y << local_dom << z << z_zstar << own_value << value << *(grid_value-1) << (*reader)(x,y) << mStamp->offsetValue(x,y,d_offset);

            //if (value>0.)

            sum += value * (*reader)(x,y);

        }

    }

    mLRI = sum;

    // LRI correction...

    double hrel = mHeight / mHeightGrid->valueAtIndex(mPositionIndex.x()/cPxPerHeight, mPositionIndex.y()/cPxPerHeight).height;

    if (hrel<1.)

        mLRI = species()->speciesSet()->LRIcorrection(mLRI, hrel);

    if (mLRI > 1.)

        mLRI = 1.;

    // Finally, add LRI of this Tree to the ResourceUnit!

    mRU->addWLA(mLeafArea, mLRI);

    //qDebug() << "Tree #"<< id() << "value" << sum << "Impact" << mImpact;

}

/// Torus version of read stamp (glued edges)

void Tree::readLIF_torus()

{

    if (!mStamp)

        return;

    const Stamp *reader = mStamp->reader();

    if (!reader)

        return;

    int bufferOffset = mGrid->indexAt(QPointF(0.,0.)).x(); // offset of buffer

    QPoint pos_reader = QPoint((mPositionIndex.x()-bufferOffset)%cPxPerRU + bufferOffset,

                               (mPositionIndex.y()-bufferOffset)%cPxPerRU + bufferOffset); // offset within the ha

    QPoint ru_offset = QPoint(mPositionIndex.x() - pos_reader.x(), mPositionIndex.y() - pos_reader.y()); // offset of the corner of the resource index

    int offset_reader = reader->offset();

    int offset_writer = mStamp->offset();

    int d_offset = offset_writer - offset_reader; // offset on the *stamp* to the crown-cells

    pos_reader-=QPoint(offset_reader, offset_reader);

    float local_dom;

    int x,y;

    double sum=0.;

    double value, own_value;

    float *grid_value;

    float z, z_zstar;

    int reader_size = reader->size();

    int rx = pos_reader.x();

    int ry = pos_reader.y();

    int xt, yt; // wrapped coords

    for (y=0;y<reader_size; ++y) {

        yt = torusIndex(ry+y,cPxPerRU, bufferOffset, ru_offset.y());

        for (x=0;x<reader_size;++x) {

            xt = torusIndex(rx+x,cPxPerRU, bufferOffset, ru_offset.x());

            grid_value = mGrid->ptr(xt,yt);

            local_dom = mHeightGrid->valueAtIndex(xt/cPxPerHeight, yt/cPxPerHeight).height; // ry: gets ++ed in outer loop, rx not

            z = std::max(mHeight - reader->distanceToCenter(x,y), 0.f); // distance to center = height (45 degree line)

            z_zstar = (z>=local_dom)?1.f:z/local_dom;

            own_value = 1. - mStamp->offsetValue(x,y,d_offset)*mOpacity * z_zstar;

            // old: own_value = 1. - mStamp->offsetValue(x,y,d_offset)*mOpacity / local_dom; // old: dom_height;

            own_value = qMax(own_value, 0.02);

            value =  *grid_value++ / own_value; // remove impact of focal tree

            // debug for one tree in HJA

            //if (id()==178020)

            //    qDebug() << x << y << xt << yt << *grid_value << local_dom << own_value << value << (*reader)(x,y);

            //if (_isnan(value))

            //    qDebug() << "isnan" << id();

            if (value * (*reader)(x,y)>1.)

                qDebug() << "LIFTorus: value>1.";

            sum += value * (*reader)(x,y);

            //} // isIndexValid

        }

    }

    mLRI = sum;

    // LRI correction...

    double hrel = mHeight / mHeightGrid->valueAtIndex(mPositionIndex.x()/cPxPerHeight, mPositionIndex.y()/cPxPerHeight).height;

    if (hrel<1.)

        mLRI = species()->speciesSet()->LRIcorrection(mLRI, hrel);

    if (isnan(mLRI)) {

        qDebug() << "LRI invalid (nan)!" << id();

        mLRI=0.;

        //qDebug() << reader->dump();

    }

    if (mLRI > 1.)

        mLRI = 1.;

    //qDebug() << "Tree #"<< id() << "value" << sum << "Impact" << mImpact;

    // Finally, add LRI of this Tree to the ResourceUnit!

    mRU->addWLA(mLeafArea, mLRI);

}

void Tree::resetStatistics()

{

    m_statPrint=0;

    m_statCreated=0;

    m_statAboveZ=0;

    m_nextId=1;

}

#ifdef ALT_TREE_MORTALITY

void Tree::mortalityParams(double dbh_inc_threshold, int stress_years, double stress_mort_prob)

{

    _stress_threshold = dbh_inc_threshold;

    _stress_years = stress_years;

    _stress_death_prob = stress_mort_prob;

    qDebug() << "Alternative Mortality enabled: threshold" << dbh_inc_threshold << ", years:" << _stress_years << ", level:" << _stress_death_prob;

}

#endif

void Tree::calcLightResponse()

{

    // calculate a light response from lri:

    // http://iland.boku.ac.at/individual+tree+light+availability

    double lri = limit(mLRI * mRU->LRImodifier(), 0., 1.); // Eq. (3)

    mLightResponse = mSpecies->lightResponse(lri); // Eq. (4)

    mRU->addLR(mLeafArea, mLightResponse);

}

//////////////////////////////////////////////////

////  Growth Functions

//////////////////////////////////////////////////

/** grow() is the main function of the yearly tree growth.

  The main steps are:

  - Production of GPP/NPP   @sa http://iland.boku.ac.at/primary+production http://iland.boku.ac.at/individual+tree+light+availability

  - Partitioning of NPP to biomass compartments of the tree @sa http://iland.boku.ac.at/allocation

  - Growth of the stem http://iland.boku.ac.at/stem+growth (???)

  Further activties: * the age of the tree is increased

                     * the mortality sub routine is executed

                     * seeds are produced */

void Tree::grow()

{

    TreeGrowthData d;

    mAge++; // increase age

    // step 1: get "interception area" of the tree individual [m2]

    // the sum of all area of all trees of a unit equal the total stocked area * interception_factor(Beer-Lambert)

    double effective_area = mRU->interceptedArea(mLeafArea, mLightResponse);

    // step 2: calculate GPP of the tree based

    // (1) get the amount of GPP for a "unit area" of the tree species

    double raw_gpp_per_area = mRU->resourceUnitSpecies(species()).prod3PG().GPPperArea();

    // (2) GPP (without aging-effect) in kg Biomass / year

    double raw_gpp = raw_gpp_per_area * effective_area;

    // apply aging according to the state of the individuum

    const double aging_factor = mSpecies->aging(mHeight, mAge);

    mRU->addTreeAging(mLeafArea, aging_factor);

    double gpp = raw_gpp * aging_factor; //

    d.NPP = gpp * cAutotrophicRespiration; // respiration loss (0.47), cf. Waring et al 1998.

    //DBGMODE(

        if (GlobalSettings::instance()->isDebugEnabled(GlobalSettings::dTreeNPP) && isDebugging()) {

            DebugList &out = GlobalSettings::instance()->debugList(mId, GlobalSettings::dTreeNPP);

            dumpList(out); // add tree headers

            out << mLRI * mRU->LRImodifier() << mLightResponse << effective_area << raw_gpp << gpp << d.NPP << aging_factor;

        }

    //); // DBGMODE()

    if (d.NPP>0.)

        partitioning(d); // split npp to compartments and grow (diameter, height)

    // mortality

#ifdef ALT_TREE_MORTALITY

    // alternative variant of tree mortality (note: mStrssIndex used otherwise)

    altMortality(d);

#else

    if (Model::settings().mortalityEnabled)

        mortality(d);

    mStressIndex = d.stress_index;

#endif

    if (!isDead())

        mRU->resourceUnitSpecies(species()).statistics().add(this, &d);

    // regeneration

    mSpecies->seedProduction(mAge, mHeight, mPositionIndex);

}

/** partitioning of this years assimilates (NPP) to biomass compartments.

  Conceptionally, the algorithm is based on Duursma, 2007.

  @sa http://iland.boku.ac.at/allocation */

inline void Tree::partitioning(TreeGrowthData &d)

{

    double npp = d.NPP;

    // add content of reserve pool

    npp += mNPPReserve;

    const double foliage_mass_allo = species()->biomassFoliage(mDbh);

    const double reserve_size = foliage_mass_allo * (1. + mSpecies->finerootFoliageRatio());

    double refill_reserve = qMin(reserve_size, (1. + mSpecies->finerootFoliageRatio())*mFoliageMass); // not always try to refill reserve 100%

    double apct_wood, apct_root, apct_foliage; // allocation percentages (sum=1) (eta)

    ResourceUnitSpecies &rus = mRU->resourceUnitSpecies(species());

    // turnover rates

    const double &to_fol = species()->turnoverLeaf();

    const double &to_root = species()->turnoverRoot();

    // the turnover rate of wood depends on the size of the reserve pool:

    double to_wood = refill_reserve / (mWoodyMass + refill_reserve);

    apct_root = rus.prod3PG().rootFraction();

    d.NPP_above = d.NPP * (1. - apct_root); // aboveground: total NPP - fraction to roots

    double b_wf = species()->allometricRatio_wf(); // ratio of allometric exponents (b_woody / b_foliage)

    // Duursma 2007, Eq. (20)