Changeset 177 for cpp/frams/genetics

Timestamp:

03/15/14 22:59:10 (11 years ago)

Author:

Maciej Komosinski

Message:

Optimizations and simplifications

Location:

cpp/frams/genetics/fF

Files:

• conv_fF.cpp (modified) (12 diffs)
• fF_genotype.cpp (modified) (1 diff)

cpp/frams/genetics/fF/conv_fF.cpp

@@ -8 +8 @@
 #include <common/nonstd_stl.h>
 
-GenoConv_fF0::GenoConv_fF0() 
+GenoConv_fF0::GenoConv_fF0()
 {
         name = "7-value Foraminifera encoding";
@@ -19 +19 @@
 }
 
-GenoConv_fF0::~GenoConv_fF0() 
+GenoConv_fF0::~GenoConv_fF0()
 {
         delete[] cosines;
@@ -31 +31 @@
                 return ""; //so we return an invalid f0 genotype
 
-        double div_radius_length = 1;//div_radius_length=1 or kx=ky=kz=1
+        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
+
         // subsequent parts (chambers) are placed relative to the previous part's orientation and location
         Part *p1, *p2;
@@ -41 +44 @@
         fF_chamber3d **chambers = new fF_chamber3d*[gp.number_of_chambers];
 
-        for (int i = 0; i < gp.number_of_chambers; i++) {
+        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);
@@ -49 +51 @@
 
 
-        for (int i = 1; i < gp.number_of_chambers; i++, p1 = p2) {
+        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
@@ -106 +109 @@
                 double ppz;
 
-                if (which == 1) {
+                if (which == 1)
+                {
                         ppx = pcx;
                         ppy = pcy;
                         ppz = pcz;
                 }
-                else {
+                else
+                {
                         ppx = chambers[which - 2]->holeX;
                         ppy = chambers[which - 2]->holeY;
@@ -189 +194 @@
         double kz = 1;
 
-        if (which > 0) {
-                for (int kt = 1; kt < (which + 1); kt++) {
+        if (which > 0)
+        {
+                for (int kt = 1; kt < (which + 1); kt++)
+                {
                         kx = kx * kx_;
                         ky = ky * ky_;
@@ -197 +204 @@
         }
 
-        int i, j;
-        double x, y, z;
+        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;
 
         double **points = new double*[fF_SIZE];
-        for (int i = 0; i < fF_SIZE; i++) {
+        for (int i = 0; i < fF_SIZE; i++)
+        {
                 points[i] = new double[4];
         }
 
-        for (i = 0; i < fF_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 < fF_LATITUDE_NUM; j++) {
-                        if (kx_ == 1 && ky_ == 1 && kz_ == 1) {
-                                points[(i * fF_LATITUDE_NUM) + j][0] = x = cenx + radius * cosines[j] * sines[i];
-                                points[(i * fF_LATITUDE_NUM) + j][1] = y;
-                                points[(i * fF_LATITUDE_NUM) + j][2] = z = cenz + radius * sines[j] * sines[i];
-                        }
-                        else {
-                                points[(i * fF_LATITUDE_NUM) + j][0] = x = cenx + kx * cosines[j] * sines[i];
-                                points[(i * fF_LATITUDE_NUM) + j][1] = y;
-                                points[(i * fF_LATITUDE_NUM) + j][2] = z = cenz + kz * sines[j] * sines[i];
-                        }
-
-                        points[(i * fF_LATITUDE_NUM) + j][3] = 1.0;
+        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];
+                        double *p = points[(i * fF_LATITUDE_NUM) + j];
+                        p[0] = x;
+                        p[1] = y;
+                        p[2] = z;
+                        p[3] = 1.0;
+
                         if (x < minX) minX = x;
                         if (x > maxX) maxX = x;
@@ -231 +236 @@
 
                         if (z < minZ) minZ = z;
-                };
-        };
+                }
+        }
         return points;
 
@@ -244 +249 @@
 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 < fF_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 < (fF_THICK_RATIO)
-                                        ) {
-                                        spheres[nr]->points[j][3] = 0;
-                                }
+        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++)
+                {
+                        double *p = spheres[nr]->points[j];
+                        double X = p[0];
+                        double Y = p[1];
+                        double Z = p[2];
+
+                        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 < fF_THICK_RATIO)
+                        {
+                                p[3] = 0.0;
                         }
                 }
@@ -298 +292 @@
 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 < fF_AMOUNT; i++) {
-                if (chambers[which]->points[i][3] != 0) //it is not inside another chamber
-                {
-                        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) {
+        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++)
+        {
+                double *p = chambers[which]->points[i];
+                if (p[3] != 0) //it is not inside another chamber
+                {
+                        double distancesq = (p[0] - x)*(p[0] - x) + (p[1] - y)*(p[1] - y) + (p[2] - z)*(p[2] - z);
+                        if (found < 0)
+                        {
                                 found = i;
-                                dist_found = distance;
-                                first = 0;
+                                distsq_found = distancesq;
                         }
-                        if (distance < dist_found) {
-                                if (which != 0) {
+                        if (distancesq < distsq_found)
+                        {
+                                if (which != 0)
+                                {
+                                        double X = p[0];
+                                        double Y = p[1];
+                                        double Z = p[2];
                                         bool good = true;
-                                        for (int j = 0; j < which; j++) {
+                                        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 = (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)
                                                 {
-                                                        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;
-                                                        }
+                                                        good = false;
                                                 }
                                         }
-                                        if (good) {
+                                        if (good)
+                                        {
                                                 found = i;
-                                                dist_found = distance;
+                                                distsq_found = distancesq;
                                         }
                                 }
@@ -356 +354 @@
         }
 
-        return (found);
-}
+        return found;
+}

cpp/frams/genetics/fF/fF_genotype.cpp

@@ -9 +9 @@
 {
         { "fF", 1, 7, "fF" },
-        { "n", 0, PARAM_CANOMITNAME, "number of chambers", "d 1 15 1", FIELD(number_of_chambers), },
+        { "n", 0, PARAM_CANOMITNAME, "number of chambers", "d 1 15 6", FIELD(number_of_chambers), },
         { "sx", 0, PARAM_CANOMITNAME, "scale x", "f 1.0 1.1 1.05", FIELD(scalex), },
         { "sy", 0, PARAM_CANOMITNAME, "scale y", "f 1.0 1.1 1.05", FIELD(scaley), },