source: cpp/frams/genetics/fF/conv_fF.cpp @ 531

// This file is a part of Framsticks SDK.  http://www.framsticks.com/
// Copyright (C) 1999-2015  Maciej Komosinski and Szymon Ulatowski.
// See LICENSE.txt for details.

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

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

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

Part *GenoConv_fF0::addNewPart(Model *m, const fF_chamber3d* c)
{
        Part *part = m->addNewPart(Part::SHAPE_ELLIPSOID);
        part->p = Pt3D(c->centerX, c->centerY, c->centerZ);
        Pt3D hole = Pt3D(c->holeX, c->holeY, c->holeZ);
        Orient o;
        o.lookAt(part->p - hole);
        part->setOrient(o);
        return part;
}

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

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

        Model m;
        m.open();

        m.vis_style = "foram"; //dedicated visual look for Foraminifera

        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);

        Part *p1 = addNewPart(&m, chambers[0]);
        for (int i = 1; i < gp.number_of_chambers; i++)
        {
                Part *p2 = addNewPart(&m, chambers[i]);
                p2->scale = p1->scale.entrywiseProduct(Pt3D(gp.scalex, gp.scaley, gp.scalez)); //each part's scale is its predecessor's scale * scaling
                m.addNewJoint(p1, p2, Joint::SHAPE_SOLID); //all parts must be connected
                p1 = p2;
        }

        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 < fF_TOO_LITTLE) {
                        radius = fF_TOO_LITTLE;
                        if (fabs(len) > (fF_TOO_MUCH * radius)) {
                                len = ((len < 0) ? (-1) : 1) * fF_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; //not used

                /* aperture of the next to last chamber */
                double ppx;
                double ppy;
                //double ppz; //not used

                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 = Convert::atan_2(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].x;
                chambers[which]->holeY = (float)chambers[which]->points[pun].y;
                chambers[which]->holeZ = (float)chambers[which]->points[pun].z;
        }
}

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

fF_point* 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_;
                }
        }

        bool all_k_ones = kx_ == 1 && ky_ == 1 && kz_ == 1;

        double rx = all_k_ones ? radius : kx;
        double ry = all_k_ones ? radius : ky;
        double rz = all_k_ones ? radius : kz;

        fF_point *points = new fF_point[fF_SIZE];

        for (int i = 0; i < fF_LONGITUDE_NUM; i++)
        {
                double y = ceny + ry * cosines[i];

                for (int j = 0; j < fF_LATITUDE_NUM; j++)
                {
                        double x = cenx + rx * cosines[j] * sines[i];
                        double z = cenz + rz * sines[j] * sines[i];
                        fF_point &p = points[(i * fF_LATITUDE_NUM) + j];
                        p.x = x;
                        p.y = y;
                        p.z = z;
                        p.inside = false;

                        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_)
{
        double kxsq = kx_*kx_;
        double kysq = ky_*ky_;
        double kzsq = kz_*kz_;

        for (int i = 0; i < nr; i++)
        {
                double srX0 = spheres[i]->centerX;
                double srY0 = spheres[i]->centerY;
                double srZ0 = spheres[i]->centerZ;

                double radsq = spheres[i]->radius * spheres[i]->radius;

                double a2 = kx_ != 1 ? kxsq : radsq;
                double b2 = ky_ != 1 ? kysq : radsq;
                double c2 = kzsq * radsq;

                for (int j = 0; j < fF_AMOUNT; j++)
                {
                        fF_point &p = spheres[nr]->points[j];

                        double up1 = (p.x - srX0) * (p.x - srX0);
                        double up2 = (p.y - srY0) * (p.y - srY0);
                        double up3 = (p.z - srZ0) * (p.z - srZ0);

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

                        double result = exp1 + exp2 + exp3;

                        if (result < fF_THICK_RATIO)
                        {
                                p.inside = true;
                        }
                }
        }
}

int GenoConv_fF0::find_hole(int which, double x, double y, double z, fF_chamber3d **chambers, double kx_, double ky_, double kz_)
{
        int found = -1;
        double distsq_found;

        double kxsq = kx_*kx_;
        double kysq = ky_*ky_;
        double kzsq = kz_*kz_;

        for (int i = 0; i < fF_AMOUNT; i++)
        {
                fF_point &p = chambers[which]->points[i];
                if (!p.inside) //it is not inside another chamber
                {
                        double distancesq = (p.x - x)*(p.x - x) + (p.y - y)*(p.y - y) + (p.z - z)*(p.z - z);
                        if (found < 0)
                        {
                                found = i;
                                distsq_found = distancesq;
                        }
                        if (distancesq < distsq_found)
                        {
                                if (which != 0)
                                {
                                        bool good = true;
                                        for (int j = 0; j < which && good; j++)
                                        {
                                                double srX0 = chambers[j]->centerX;
                                                double srY0 = chambers[j]->centerY;
                                                double srZ0 = chambers[j]->centerZ;

                                                double radsq = chambers[j]->radius * chambers[j]->radius;

                                                double a2 = kxsq * radsq;
                                                double b2 = kysq * radsq;
                                                double c2 = kzsq * radsq;

                                                double up1 = (p.x - srX0) * (p.x - srX0);
                                                double up2 = (p.y - srY0) * (p.y - srY0);
                                                double up3 = (p.z - srZ0) * (p.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;
                                                distsq_found = distancesq;
                                        }
                                }
                        }
                }
        }

        return found;
}