source: cpp/frams/genetics/fF/conv_fF.cpp @ 174

// This file is a part of the Framsticks GDK.
// Copyright (C) 2002-2014  Maciej Komosinski and Szymon Ulatowski.  See LICENSE.txt for details.
// Refer to http://www.framsticks.com/ for further information.

#include "conv_fF.h"
#include "fF_genotype.h"
#include <frams/model/model.h>
#include <common/nonstd_stl.h>

GenoConv_fF0::GenoConv_fF0() {
    name = "7-value Foraminifera encoding";
    in_format = 'F';
    out_format = '0';
    mapsupport = 0;
    cosines = new double[LATITUDE_NUM];
    sines = new double[LATITUDE_NUM];  
    fill_cos_and_sin();
}

GenoConv_fF0::~GenoConv_fF0() {
    delete []cosines;
    delete []sines;
}

SString GenoConv_fF0::convert(SString &in, MultiMap *map) {
    fF_growth_params gp;
    if (!gp.load(in)) //invalid input genotype?
        return ""; //so we return an invalid f0 genotype

    double div_radius_length = 1;//div_radius_lenght=1 or kx=ky=kz=1
    double radius = 1;

    Model m;
    m.open();
    // subsequent parts (chambers) are placed relative to the previous part's orientation and location
    Part *p1, *p2;

    fF_chamber3d **chambers = new fF_chamber3d*[gp.number_of_chambers];

    for (int i = 0; i < gp.number_of_chambers; i++) {
        createSphere(i, chambers, radius, div_radius_length, gp.translation, gp.angle1, gp.angle2, gp.scalex, gp.scaley, gp.scalez);
    }

    p1 = m.addNewPart(Part::SHAPE_ELLIPSOID);
    p1->p = Pt3D(chambers[0]->centerX, chambers[0]->centerY, chambers[0]->centerZ);


    for (int i = 1; i < gp.number_of_chambers; i++, p1 = p2) {
        p2 = m.addNewPart(Part::SHAPE_ELLIPSOID);
        p2->scale = p1->scale.entrywiseProduct(Pt3D(gp.scalex, gp.scaley, gp.scalez)); //each part's scale is its predecessor's scale * scaling

        p2->p = Pt3D(chambers[i]->centerX, chambers[i]->centerY, chambers[i]->centerZ);

        m.addNewJoint(p1, p2, Joint::SHAPE_SOLID); //all parts must be connected
    }

    for (int i = 0; i < gp.number_of_chambers; i++)
        delete chambers[i];
    delete []chambers;

    m.close();
    return m.getF0Geno().getGene();
}

void GenoConv_fF0::createSphere(int which, fF_chamber3d **chambers, double radius_, double div_radius_length_, double div_vector_length_,
        double alpha_, double gamma_, double kx_, double ky_, double kz_) 
{    
    chambers[which]=new fF_chamber3d(0.0f, 0.0f, 0.0f, 
            (float) radius_, (float) radius_ * (float) kx_, 0.0f, 0.0f, 
            (float) (radius_ * div_vector_length_), 0.0f, 0.0f, 0.0f, 0.0f); 
    if (which == 0)
        chambers[which]->points = generate_points(chambers[which], which, kx_, ky_, kz_);
    if (which > 0) {
        /* old radius */
        double radiusOld, radius;
        radiusOld = chambers[which - 1]->radius;
        radius = div_radius_length_ * radiusOld;
        /* new growth vector length */
        double len = radius * div_vector_length_;
        if (radius < TOO_LITTLE) {
            radius = TOO_LITTLE;
            if (fabs(len) > (TOO_MUCH * radius)) {
                len = ((len < 0) ? (-1) : 1) * TOO_MUCH * radius;
            }
        }
        if (len == 0) {
            len = -0.0000001;
        }

        /* aperture of the previous chamber */
        double pzx = chambers[which - 1]->holeX;
        double pzy = chambers[which - 1]->holeY;
        double pzz = chambers[which - 1]->holeZ;

        //center of the previous chamber
        double pcx = chambers[which - 1]->centerX;
        double pcy = chambers[which - 1]->centerY;
        double pcz = chambers[which - 1]->centerZ;

        /* aperture of the next to last chamber */
        double ppx;
        double ppy;
        double ppz;

        if (which == 1) {
            ppx = pcx;
            ppy = pcy;
            ppz = pcz;
        } else {
            ppx = chambers[which - 2]->holeX;
            ppy = chambers[which - 2]->holeY;
            ppz = chambers[which - 2]->holeZ;
        }

        double pzxprim = pzx - ppx;
        double pzyprim = pzy - ppy;
        double angle;

        angle = atan2(pzyprim, pzxprim);
        double alpha = angle - alpha_;


        double gamma = chambers[which - 1]->phi + gamma_;

        /* x */
        double wx = len * cos(alpha);
        /* y */
        double wy = len * sin(alpha);
        /* y */
        double wz = len * sin(alpha) * sin(gamma);

        /*center of the new sphere*/
        double x = pzx + wx;
        double y = pzy + wy;
        double z = pzz + wz;

        chambers[which]->centerX = (float) x;
        chambers[which]->centerY = (float) y;
        chambers[which]->centerZ = (float) z;
        chambers[which]->radius= (float) radius;
        chambers[which]->vectorTfX = (float) wx;
        chambers[which]->vectorTfY = (float) wy;
        chambers[which]->vectorTfZ = (float) wz;
        chambers[which]->beta = (float) alpha;
        chambers[which]->phi = (float) gamma;

        chambers[which]->points = generate_points(chambers[which], which, kx_,  ky_,  kz_);
        search_hid(which, chambers, kx_,  ky_,  kz_);
        int pun;
        pun = find_hole(which, pzx, pzy, pzz, chambers, kx_,  ky_,  kz_);

        chambers[which]->holeX = (float) chambers[which]->points[pun][0];
        chambers[which]->holeY = (float) chambers[which]->points[pun][1];
        chambers[which]->holeZ = (float) chambers[which]->points[pun][2];
    }
}

void GenoConv_fF0::fill_cos_and_sin() {
    int i;
    double pi = acos(-1.0);
    double angle = pi / (((double) LATITUDE_NUM)*0.5);
    for (i = 0; i < LATITUDE_NUM; i++) {
        cosines[i] = cos((double) i * angle);
        sines[i] = sin((double) i * angle);
    }
}

double** GenoConv_fF0::generate_points(fF_chamber3d *chamber, int which, double kx_, double ky_, double kz_) {
    float radius = chamber->radius;
    float cenx = chamber->centerX;
    float ceny = chamber->centerY;
    float cenz = chamber->centerZ;

    double maxX = 0;
    double maxY = 0;
    double minX = 0;
    double minY = 0;
    double minZ = 0;

    double kx = 1;
    double ky = 1;
    double kz = 1;

    if (which > 0) {
        for (int kt = 1; kt < (which + 1); kt++) {
            kx = kx * kx_;
            ky = ky * ky_;
            kz = kz * kz_;
        }
    }

    int i, j;
    double x, y, z;
    
    double **points = new double*[SIZE];
    for (int i = 0; i < SIZE; i++) {
        points[i] = new double[4];
    }
    
    for (i = 0; i < LONGITUDE_NUM; i++) {
        if (kx_ == 1 && ky_ == 1 && kz_ == 1) {
            y = ceny + radius * cosines[i];
        }
        else {
            y = ceny + ky * cosines[i];
        }
        for (j = 0; j < LATITUDE_NUM; j++) {
            if (kx_ == 1 && ky_ == 1 && kz_ == 1) {
                points[(i * LATITUDE_NUM) + j][0] = x = cenx + radius * cosines[j] * sines[i];
                points[(i * LATITUDE_NUM) + j][1] = y;
                points[(i * LATITUDE_NUM) + j][2] = z = cenz + radius * sines[j] * sines[i];
            } else {
                points[(i * LATITUDE_NUM) + j][0] = x = cenx + kx * cosines[j] * sines[i];
                points[(i * LATITUDE_NUM) + j][1] = y;
                points[(i * LATITUDE_NUM) + j][2] = z = cenz + kz * sines[j] * sines[i];
            }

            points[(i * LATITUDE_NUM) + j][3] = 1.0;
            if (x < minX) minX = x;
            if (x > maxX) maxX = x;
            if (y < minY) minY = y;
            if (y > maxY) maxY = y;

            if (z < minZ) minZ = z;
        };
    };
    return points;

}

double GenoConv_fF0::dist(double x1, double y1, double z1, double x2, double y2, double z2) {
    return sqrt((x2 - x1)*(x2 - x1) + (y2 - y1)*(y2 - y1) + (z2 - z1)*(z2 - z1));
}

void GenoConv_fF0::search_hid(int nr, fF_chamber3d **spheres, double kx_, double ky_, double kz_) {

    int i, j;
    if (nr != 0) {
        for (i = 0; i < nr; i++) {
            for (j = 0; j < AMOUNT; j++) {
                double X = spheres[nr]->points[j][0];
                double Y = spheres[nr]->points[j][1];
                double Z = spheres[nr]->points[j][2];

                double srX0 = spheres[i]->centerX;
                double srY0 = spheres[i]->centerY;
                double srZ0 = spheres[i]->centerZ;

                double a2;
                double b2;
                double c2;

                if (kx_ != 1) {
                    a2 = (kx_ * kx_);
                } else {
                    a2 = (spheres[i]->radius * spheres[i]->radius);
                }

                if (ky_ != 1) {
                    b2 = (ky_ * ky_);

                } else {
                    b2 = (spheres[i]->radius * spheres[i]->radius);
                }

                c2 = (kz_ * spheres[i]->radius) * (kz_ * spheres[i]->radius);

                double up1 = (X - srX0) * (X - srX0);
                double up2 = (Y - srY0) * (Y - srY0);
                double up3 = (Z - srZ0) * (Z - srZ0);

                double exp = up1 / a2;
                double exp2 = up2 / b2;
                double exp3 = up3 / c2;

                double result = exp + exp2 + exp3;

                if (result < (THICK_RATIO)
                        ) {
                    spheres[nr]->points[j][3] = 0;
                }
            }
        }
    }
}

int GenoConv_fF0::find_hole(int which, double x, double y, double z, fF_chamber3d **chambers, double kx_, double ky_, double kz_) {
    int i;
    double distance;
    int found = 0;
    double dist_found = 0;
    int first = 1;

    for (i = 0; i < AMOUNT; i++) {
        if (chambers[which]->points[i][3] != 0) //nie jest wewnatrz inne komory
        {
            distance = sqrt((chambers[which]->points[i][0] - x)*(chambers[which]->points[i][0] - x) +
                    (chambers[which]->points[i][1] - y)*(chambers[which]->points[i][1] - y)+
                    (chambers[which]->points[i][2] - z)*(chambers[which]->points[i][2] - z));
            if (first != 0) {
                found = i;
                dist_found = distance;
                first = 0;
            };
            if (distance < dist_found) {
                if (which != 0) {
                    bool good = true;
                    for (int j = 0; j < which; j++) {
                        {
                            double X = chambers[which]->points[i][0];
                            double Y = chambers[which]->points[i][1];
                            double Z = chambers[which]->points[i][2];

                            double srX0 = chambers[j]->centerX;
                            double srY0 = chambers[j]->centerY;
                            double srZ0 = chambers[j]->centerZ;

                            double a2 = (kx_ * chambers[j]->radius) * (kx_ * chambers[j]->radius);
                            double b2 = (ky_ * chambers[j]->radius) * (ky_ * chambers[j]->radius);
                            double c2 = (kz_ * chambers[j]->radius) * (kz_ * chambers[j]->radius);

                            double up1 = (X - srX0) * (X - srX0);
                            double up2 = (Y - srY0) * (Y - srY0);
                            double up3 = (Z - srZ0) * (Z - srZ0);

                            double exp1 = up1 / a2;
                            double exp2 = up2 / b2;
                            double exp3 = up3 / c2;

                            double result = exp1 + exp2 + exp3;
                            if (result < 1.0) 
                            {
                                good = false;
                            }
                        }
                    }
                    if (good) {
                        found = i;
                        dist_found = distance;
                    }
                }
            };
        };
    };

    return (found); 
}