source: cpp/frams/genetics/fF/fF_conv.cpp @ 1228

// This file is a part of Framsticks SDK.  http://www.framsticks.com/
// Copyright (C) 1999-2021  Maciej Komosinski and Szymon Ulatowski.
// See LICENSE.txt for details.

#include "fF_conv.h"
#include "fF_genotype.h"
#include <common/Convert.h>

GenoConv_fF0::GenoConv_fF0()
{
        name = "10-parameter Foraminifera encoding";
        in_format = "F";
        out_format = "0s";
        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, bool using_checkpoints)
{
        fF_growth_params gp;
        if (!gp.load(in.c_str())) //invalid input genotype?
                return ""; //so we return an invalid f0 genotype

        Model m;
        m.open(using_checkpoints);

        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, gp.radius0x, gp.radius0y, gp.radius0z, gp.translation, gp.angle1, gp.angle2, gp.scalex, gp.scaley, gp.scalez);

        Part *p1 = addNewPart(&m, chambers[0]);
        p1->scale = Pt3D(gp.radius0x, gp.radius0y, gp.radius0z); //size of the initial chamber
        m.checkpoint();
        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_FIXED); //all parts must be connected
                m.checkpoint();
                p1 = p2;
        }

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

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

void GenoConv_fF0::createSphere(int which, fF_chamber3d **chambers, double radius0x, double radius0y, double radius0z, double translation, double alpha_, double gamma_, double kx_, double ky_, double kz_)
{
        chambers[which] = new fF_chamber3d(0.0, 0.0, 0.0,
                radius0x, radius0y, radius0z, radius0x * kx_, 0.0, 0.0,
                radius0x * translation, 0.0, 0.0, 0.0, 0.0);
        if (which == 0)
                chambers[which]->points = generate_points(chambers[which]);
        if (which > 0)
        {
                chambers[which]->radius_x = get_radius(chambers[which - 1]->radius_x, kx_, chambers[0]->radius_x);
                chambers[which]->radius_y = get_radius(chambers[which - 1]->radius_y, ky_, chambers[0]->radius_y);
                chambers[which]->radius_z = get_radius(chambers[which - 1]->radius_z, kz_, chambers[0]->radius_z);

                /* new growth vector length */
                double len = chambers[which]->radius_y * translation;
                double max_radius = fF_TOO_MUCH * chambers[which]->radius_y;
                if (fabs(len) > (max_radius))
                        len = ((len < 0) ? (-1) : 1) * max_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_;

                double wx = len * cos(alpha);
                double wy = len * sin(alpha);
                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 = x;
                chambers[which]->centerY = y;
                chambers[which]->centerZ = z;
                chambers[which]->vectorTfX = wx;
                chambers[which]->vectorTfY = wy;
                chambers[which]->vectorTfZ = wz;
                chambers[which]->beta = alpha;
                chambers[which]->phi = gamma;

                chambers[which]->points = generate_points(chambers[which]);
                search_hid(which, chambers);
                int pun;
                pun = find_hole(which, pzx, pzy, pzz, chambers);
                if (pun < 0) //should never happen
                {
                        logPrintf("GenoConv_fF0", "createSphere", LOG_ERROR, "find_hole(%d) returned %d", which, pun);
                        pun = 0;
                }
                chambers[which]->holeX = chambers[which]->points[pun].x;
                chambers[which]->holeY = chambers[which]->points[pun].y;
                chambers[which]->holeZ = chambers[which]->points[pun].z;
        }
}

double GenoConv_fF0::get_radius(double prev_radius, double scale, double start_radius)
{
        double radius = prev_radius * scale;
        double min_radius = fF_TOO_LITTLE*start_radius;
        if (radius < min_radius) {
                radius = min_radius;
        }

        return radius;
}

void GenoConv_fF0::precompute_cos_and_sin()
{
        double angle = M_PI * 2 / fF_LATITUDE_NUM;
        for (int i = 0; i < fF_LATITUDE_NUM; i++)
        {
                cosines[i] = cos(i * angle);
                sines[i] = sin(i * angle);
        }
}

fF_point* GenoConv_fF0::generate_points(fF_chamber3d *chamber)
{
        double cenx = chamber->centerX;
        double ceny = chamber->centerY;
        double cenz = chamber->centerZ;

        double rx = chamber->radius_x;
        double ry = chamber->radius_y;
        double rz = chamber->radius_z;

        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;
                }
        }
        return points;

}

template<typename T> T Square(T x) { return x * x; }

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

void GenoConv_fF0::search_hid(int nr, fF_chamber3d **chambers)
{
        for (int i = 0; i < nr; i++)
        {
                fF_chamber3d *chamber = chambers[i];

                double rx_sq = Square(chamber->radius_x);
                double ry_sq = Square(chamber->radius_y);
                double rz_sq = Square(chamber->radius_z);

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

                        double upx = Square(p.x - chamber->centerX);
                        double upy = Square(p.y - chamber->centerY);
                        double upz = Square(p.z - chamber->centerZ);

                        double expx = upx / rx_sq;
                        double expy = upy / ry_sq;
                        double expz = upz / rz_sq;

                        double result = expx + expy + expz;

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

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

        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 = Square(p.x - x) + Square(p.y - y) + Square(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++)
                                        {
                                                fF_chamber3d *chamber = chambers[j];

                                                double rx_sq = Square(chamber->radius_x);
                                                double ry_sq = Square(chamber->radius_y);
                                                double rz_sq = Square(chamber->radius_z);

                                                double upx = Square(p.x - chamber->centerX);
                                                double upy = Square(p.y - chamber->centerY);
                                                double upz = Square(p.z - chamber->centerZ);

                                                double expx = upx / rx_sq;
                                                double expy = upy / ry_sq;
                                                double expz = upz / rz_sq;

                                                double result = expx + expy + expz;
                                                if (result < 1.0)
                                                {
                                                        good = false;
                                                }
                                        }
                                        if (good)
                                        {
                                                found = i;
                                                distsq_found = distancesq;
                                        }
                                }
                        }
                }
        }

        return found;
}