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 03/14/14 00:45:03 (10 years ago)
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 cpp
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cpp

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cpp/frams/MakefileGDKfiles
r145 r174 4 4 ALL_DIRS={common,frams,frams/canvas,frams/config,frams/errmgr,frams/genetics,frams/genetics/f0,frams/genetics/f1,frams/genetics/f2,frams/genetics/f3,frams/genetics/f4,frams/genetics/f5,frams/genetics/f6,frams/genetics/f7,frams/genetics/f8,frams/genetics/f9,frams/genetics/fF,frams/model,frams/neuro,frams/neuro/impl,frams/param,frams/test,frams/util,frams/vm/classes,frams/virtfile,frams/_demos} 5 5 6 GENOCONV_GDK_OBJS=frams/genetics/defgenoconv.o frams/genetics/f1/conv_f1.o frams/genetics/f9/conv_f9.o frams/genetics/fF/conv_fF.o frams/genetics/fF/fF_genotype.o 6 GENOCONV_GDK_OBJS=frams/genetics/defgenoconv.o frams/genetics/f1/conv_f1.o frams/genetics/f9/conv_f9.o frams/genetics/fF/conv_fF.o frams/genetics/fF/fF_genotype.o frams/genetics/fF/fF_chamber3d.o 7 7 8 8 GENMAN_COMMON_OBJS=frams/genetics/genman.o frams/param/mutableparam.o frams/param/mutparamlist.o frams/neuro/geneticneuroparam.o frams/neuro/neurolibparam.o frams/vm/classes/genoobj.o frams/model/autoname.o 
cpp/frams/genetics/fF/conv_fF.cpp
r157 r174 8 8 #include <common/nonstd_stl.h> 9 9 10 GenoConv_fF0::GenoConv_fF0() 11 { 12 name = "7value Foraminifera encoding"; 13 in_format = 'F'; 14 out_format = '0'; 15 mapsupport = 0; 16 } 17 18 SString GenoConv_fF0::convert(SString &in, MultiMap *map) 19 { 20 fF_growth_params gp; 21 if (!gp.load(in)) //invalid input genotype? 22 return ""; //so we return an invalid f0 genotype 23 Model m; 24 m.open(); 25 // subsequent parts (chambers) are placed relative to the previous part's orientation and location 26 Part *p1, *p2; 27 p1 = m.addNewPart(Part::SHAPE_ELLIPSOID); //initial part 28 Pt3D scaling(gp.scalex, gp.scaley, gp.scalez); 29 p1>scale = scaling; 30 31 Orient rotation = Orient_1; //must be initialized explicitly because the default Orient constructor does not initialize anything 32 rotation.rotate(Pt3D(0, gp.angle1, gp.angle2)); //assumed rotation around x is 0, which is limiting if we use assymetrical shapes (i.e., not spheres). But the original model had only two angles... 33 34 for (int i = 1; i < gp.number_of_chambers; i++, p1 = p2) 35 { 36 p2 = m.addNewPart(Part::SHAPE_ELLIPSOID); 37 p2>scale = p1>scale.entrywiseProduct(scaling); //each part's scale is its predecessor's scale * scaling 38 39 p2>setOrient(p1>o.transform(rotation)); //rotation transformed by p1 orientation 40 41 // Part's tip (offset from the center) is the point at (scale.x,0,0) in part's local coordinates. 42 // Get the offset in global coordinates by transforming it by the part's orientation. 43 p2>p = p1>p 44 + p1>o.transform(Pt3D(p1>scale.x*gp.translation,0,0)) // p1's tip transformed 45 + p2>o.transform(Pt3D(p2>scale.x*gp.translation,0,0)); // p2's tip transformed 46 47 m.addNewJoint(p1, p2, Joint::SHAPE_SOLID); //all parts must be connected 48 } 49 m.close(); 50 return m.getF0Geno().getGene(); 51 } 10 GenoConv_fF0::GenoConv_fF0() { 11 name = "7value Foraminifera encoding"; 12 in_format = 'F'; 13 out_format = '0'; 14 mapsupport = 0; 15 cosines = new double[LATITUDE_NUM]; 16 sines = new double[LATITUDE_NUM]; 17 fill_cos_and_sin(); 18 } 19 20 GenoConv_fF0::~GenoConv_fF0() { 21 delete []cosines; 22 delete []sines; 23 } 24 25 SString GenoConv_fF0::convert(SString &in, MultiMap *map) { 26 fF_growth_params gp; 27 if (!gp.load(in)) //invalid input genotype? 28 return ""; //so we return an invalid f0 genotype 29 30 double div_radius_length = 1;//div_radius_lenght=1 or kx=ky=kz=1 31 double radius = 1; 32 33 Model m; 34 m.open(); 35 // subsequent parts (chambers) are placed relative to the previous part's orientation and location 36 Part *p1, *p2; 37 38 fF_chamber3d **chambers = new fF_chamber3d*[gp.number_of_chambers]; 39 40 for (int i = 0; i < gp.number_of_chambers; i++) { 41 createSphere(i, chambers, radius, div_radius_length, gp.translation, gp.angle1, gp.angle2, gp.scalex, gp.scaley, gp.scalez); 42 } 43 44 p1 = m.addNewPart(Part::SHAPE_ELLIPSOID); 45 p1>p = Pt3D(chambers[0]>centerX, chambers[0]>centerY, chambers[0]>centerZ); 46 47 48 for (int i = 1; i < gp.number_of_chambers; i++, p1 = p2) { 49 p2 = m.addNewPart(Part::SHAPE_ELLIPSOID); 50 p2>scale = p1>scale.entrywiseProduct(Pt3D(gp.scalex, gp.scaley, gp.scalez)); //each part's scale is its predecessor's scale * scaling 51 52 p2>p = Pt3D(chambers[i]>centerX, chambers[i]>centerY, chambers[i]>centerZ); 53 54 m.addNewJoint(p1, p2, Joint::SHAPE_SOLID); //all parts must be connected 55 } 56 57 for (int i = 0; i < gp.number_of_chambers; i++) 58 delete chambers[i]; 59 delete []chambers; 60 61 m.close(); 62 return m.getF0Geno().getGene(); 63 } 64 65 void GenoConv_fF0::createSphere(int which, fF_chamber3d **chambers, double radius_, double div_radius_length_, double div_vector_length_, 66 double alpha_, double gamma_, double kx_, double ky_, double kz_) 67 { 68 chambers[which]=new fF_chamber3d(0.0f, 0.0f, 0.0f, 69 (float) radius_, (float) radius_ * (float) kx_, 0.0f, 0.0f, 70 (float) (radius_ * div_vector_length_), 0.0f, 0.0f, 0.0f, 0.0f); 71 if (which == 0) 72 chambers[which]>points = generate_points(chambers[which], which, kx_, ky_, kz_); 73 if (which > 0) { 74 /* old radius */ 75 double radiusOld, radius; 76 radiusOld = chambers[which  1]>radius; 77 radius = div_radius_length_ * radiusOld; 78 /* new growth vector length */ 79 double len = radius * div_vector_length_; 80 if (radius < TOO_LITTLE) { 81 radius = TOO_LITTLE; 82 if (fabs(len) > (TOO_MUCH * radius)) { 83 len = ((len < 0) ? (1) : 1) * TOO_MUCH * radius; 84 } 85 } 86 if (len == 0) { 87 len = 0.0000001; 88 } 89 90 /* aperture of the previous chamber */ 91 double pzx = chambers[which  1]>holeX; 92 double pzy = chambers[which  1]>holeY; 93 double pzz = chambers[which  1]>holeZ; 94 95 //center of the previous chamber 96 double pcx = chambers[which  1]>centerX; 97 double pcy = chambers[which  1]>centerY; 98 double pcz = chambers[which  1]>centerZ; 99 100 /* aperture of the next to last chamber */ 101 double ppx; 102 double ppy; 103 double ppz; 104 105 if (which == 1) { 106 ppx = pcx; 107 ppy = pcy; 108 ppz = pcz; 109 } else { 110 ppx = chambers[which  2]>holeX; 111 ppy = chambers[which  2]>holeY; 112 ppz = chambers[which  2]>holeZ; 113 } 114 115 double pzxprim = pzx  ppx; 116 double pzyprim = pzy  ppy; 117 double angle; 118 119 angle = atan2(pzyprim, pzxprim); 120 double alpha = angle  alpha_; 121 122 123 double gamma = chambers[which  1]>phi + gamma_; 124 125 /* x */ 126 double wx = len * cos(alpha); 127 /* y */ 128 double wy = len * sin(alpha); 129 /* y */ 130 double wz = len * sin(alpha) * sin(gamma); 131 132 /*center of the new sphere*/ 133 double x = pzx + wx; 134 double y = pzy + wy; 135 double z = pzz + wz; 136 137 chambers[which]>centerX = (float) x; 138 chambers[which]>centerY = (float) y; 139 chambers[which]>centerZ = (float) z; 140 chambers[which]>radius= (float) radius; 141 chambers[which]>vectorTfX = (float) wx; 142 chambers[which]>vectorTfY = (float) wy; 143 chambers[which]>vectorTfZ = (float) wz; 144 chambers[which]>beta = (float) alpha; 145 chambers[which]>phi = (float) gamma; 146 147 chambers[which]>points = generate_points(chambers[which], which, kx_, ky_, kz_); 148 search_hid(which, chambers, kx_, ky_, kz_); 149 int pun; 150 pun = find_hole(which, pzx, pzy, pzz, chambers, kx_, ky_, kz_); 151 152 chambers[which]>holeX = (float) chambers[which]>points[pun][0]; 153 chambers[which]>holeY = (float) chambers[which]>points[pun][1]; 154 chambers[which]>holeZ = (float) chambers[which]>points[pun][2]; 155 } 156 } 157 158 void GenoConv_fF0::fill_cos_and_sin() { 159 int i; 160 double pi = acos(1.0); 161 double angle = pi / (((double) LATITUDE_NUM)*0.5); 162 for (i = 0; i < LATITUDE_NUM; i++) { 163 cosines[i] = cos((double) i * angle); 164 sines[i] = sin((double) i * angle); 165 } 166 } 167 168 double** GenoConv_fF0::generate_points(fF_chamber3d *chamber, int which, double kx_, double ky_, double kz_) { 169 float radius = chamber>radius; 170 float cenx = chamber>centerX; 171 float ceny = chamber>centerY; 172 float cenz = chamber>centerZ; 173 174 double maxX = 0; 175 double maxY = 0; 176 double minX = 0; 177 double minY = 0; 178 double minZ = 0; 179 180 double kx = 1; 181 double ky = 1; 182 double kz = 1; 183 184 if (which > 0) { 185 for (int kt = 1; kt < (which + 1); kt++) { 186 kx = kx * kx_; 187 ky = ky * ky_; 188 kz = kz * kz_; 189 } 190 } 191 192 int i, j; 193 double x, y, z; 194 195 double **points = new double*[SIZE]; 196 for (int i = 0; i < SIZE; i++) { 197 points[i] = new double[4]; 198 } 199 200 for (i = 0; i < LONGITUDE_NUM; i++) { 201 if (kx_ == 1 && ky_ == 1 && kz_ == 1) { 202 y = ceny + radius * cosines[i]; 203 } 204 else { 205 y = ceny + ky * cosines[i]; 206 } 207 for (j = 0; j < LATITUDE_NUM; j++) { 208 if (kx_ == 1 && ky_ == 1 && kz_ == 1) { 209 points[(i * LATITUDE_NUM) + j][0] = x = cenx + radius * cosines[j] * sines[i]; 210 points[(i * LATITUDE_NUM) + j][1] = y; 211 points[(i * LATITUDE_NUM) + j][2] = z = cenz + radius * sines[j] * sines[i]; 212 } else { 213 points[(i * LATITUDE_NUM) + j][0] = x = cenx + kx * cosines[j] * sines[i]; 214 points[(i * LATITUDE_NUM) + j][1] = y; 215 points[(i * LATITUDE_NUM) + j][2] = z = cenz + kz * sines[j] * sines[i]; 216 } 217 218 points[(i * LATITUDE_NUM) + j][3] = 1.0; 219 if (x < minX) minX = x; 220 if (x > maxX) maxX = x; 221 if (y < minY) minY = y; 222 if (y > maxY) maxY = y; 223 224 if (z < minZ) minZ = z; 225 }; 226 }; 227 return points; 228 229 } 230 231 double GenoConv_fF0::dist(double x1, double y1, double z1, double x2, double y2, double z2) { 232 return sqrt((x2  x1)*(x2  x1) + (y2  y1)*(y2  y1) + (z2  z1)*(z2  z1)); 233 } 234 235 void GenoConv_fF0::search_hid(int nr, fF_chamber3d **spheres, double kx_, double ky_, double kz_) { 236 237 int i, j; 238 if (nr != 0) { 239 for (i = 0; i < nr; i++) { 240 for (j = 0; j < AMOUNT; j++) { 241 double X = spheres[nr]>points[j][0]; 242 double Y = spheres[nr]>points[j][1]; 243 double Z = spheres[nr]>points[j][2]; 244 245 double srX0 = spheres[i]>centerX; 246 double srY0 = spheres[i]>centerY; 247 double srZ0 = spheres[i]>centerZ; 248 249 double a2; 250 double b2; 251 double c2; 252 253 if (kx_ != 1) { 254 a2 = (kx_ * kx_); 255 } else { 256 a2 = (spheres[i]>radius * spheres[i]>radius); 257 } 258 259 if (ky_ != 1) { 260 b2 = (ky_ * ky_); 261 262 } else { 263 b2 = (spheres[i]>radius * spheres[i]>radius); 264 } 265 266 c2 = (kz_ * spheres[i]>radius) * (kz_ * spheres[i]>radius); 267 268 double up1 = (X  srX0) * (X  srX0); 269 double up2 = (Y  srY0) * (Y  srY0); 270 double up3 = (Z  srZ0) * (Z  srZ0); 271 272 double exp = up1 / a2; 273 double exp2 = up2 / b2; 274 double exp3 = up3 / c2; 275 276 double result = exp + exp2 + exp3; 277 278 if (result < (THICK_RATIO) 279 ) { 280 spheres[nr]>points[j][3] = 0; 281 } 282 } 283 } 284 } 285 } 286 287 int GenoConv_fF0::find_hole(int which, double x, double y, double z, fF_chamber3d **chambers, double kx_, double ky_, double kz_) { 288 int i; 289 double distance; 290 int found = 0; 291 double dist_found = 0; 292 int first = 1; 293 294 for (i = 0; i < AMOUNT; i++) { 295 if (chambers[which]>points[i][3] != 0) //nie jest wewnatrz inne komory 296 { 297 distance = sqrt((chambers[which]>points[i][0]  x)*(chambers[which]>points[i][0]  x) + 298 (chambers[which]>points[i][1]  y)*(chambers[which]>points[i][1]  y)+ 299 (chambers[which]>points[i][2]  z)*(chambers[which]>points[i][2]  z)); 300 if (first != 0) { 301 found = i; 302 dist_found = distance; 303 first = 0; 304 }; 305 if (distance < dist_found) { 306 if (which != 0) { 307 bool good = true; 308 for (int j = 0; j < which; j++) { 309 { 310 double X = chambers[which]>points[i][0]; 311 double Y = chambers[which]>points[i][1]; 312 double Z = chambers[which]>points[i][2]; 313 314 double srX0 = chambers[j]>centerX; 315 double srY0 = chambers[j]>centerY; 316 double srZ0 = chambers[j]>centerZ; 317 318 double a2 = (kx_ * chambers[j]>radius) * (kx_ * chambers[j]>radius); 319 double b2 = (ky_ * chambers[j]>radius) * (ky_ * chambers[j]>radius); 320 double c2 = (kz_ * chambers[j]>radius) * (kz_ * chambers[j]>radius); 321 322 double up1 = (X  srX0) * (X  srX0); 323 double up2 = (Y  srY0) * (Y  srY0); 324 double up3 = (Z  srZ0) * (Z  srZ0); 325 326 double exp1 = up1 / a2; 327 double exp2 = up2 / b2; 328 double exp3 = up3 / c2; 329 330 double result = exp1 + exp2 + exp3; 331 if (result < 1.0) 332 { 333 good = false; 334 } 335 } 336 } 337 if (good) { 338 found = i; 339 dist_found = distance; 340 } 341 } 342 }; 343 }; 344 }; 345 346 return (found); 347 } 
cpp/frams/genetics/fF/conv_fF.h
r140 r174 6 6 #define _CONV_FF_H_ 7 7 8 #define TOO_MUCH 0.75 9 #define TOO_LITTLE 0.10 10 11 #define HOLE_RADIUS 0.05f 12 #define LONGITUDE_NUM 69 13 14 #define LATITUDE_NUM ((LONGITUDE_NUM  1)*2) 15 #define AMOUNT ((LATITUDE_NUM)*(LONGITUDE_NUM)) 16 17 #define THICK_RATIO 0.95 18 19 #define SIZE LONGITUDE_NUM * LATITUDE_NUM + LATITUDE_NUM 20 8 21 #include <frams/util/multimap.h> 9 22 #include <frams/util/sstring.h> 10 23 #include <frams/genetics/genoconv.h> 11 12 24 #include "fF_chamber3d.h" 13 25 14 26 // The f9>f0 converter 15 class GenoConv_fF0: public GenoConverter 16 {27 28 class GenoConv_fF0 : public GenoConverter { 17 29 public: 18 19 20 21 30 GenoConv_fF0(); 31 ~GenoConv_fF0(); 32 //implementation of the GenoConverter method 33 SString convert(SString &in, MultiMap *map); 22 34 23 35 protected: 24 //auxiliary methods 25 //... 36 double* cosines; 37 double* sines; 38 void createSphere(int ktora, fF_chamber3d **chambers, double radius, double div_radius_length, double div_vector_length, 39 double alpha, double gamma, double kx, double ky, double kz); 40 double** generate_points(fF_chamber3d *chamber, int which, double kx, double ky, double kz); 41 void fill_cos_and_sin(); 42 double dist(double x1, double y1, double z1, double x2, double y2, double z2); 43 void search_hid(int nr, fF_chamber3d **spheres, double kx_, double ky_, double kz_); 44 int find_hole(int which, double x, double y, double z, fF_chamber3d **chambers, double kx_, double ky_, double kz_); 26 45 }; 27 46 28 47 #endif 48 49 
cpp/frams/genetics/fF/fF_genotype.cpp
r145 r174 10 10 { "fF", 1, 7, "fF" }, 11 11 { "n", 0, PARAM_CANOMITNAME, "number of chambers", "d 1 15 1", FIELD(number_of_chambers), }, 12 { "sx", 0, PARAM_CANOMITNAME, "scale x", "f 0.5 1.0 0.9", FIELD(scalex), },13 { "sy", 0, PARAM_CANOMITNAME, "scale y", "f 0.5 1.0 0.9", FIELD(scaley), },14 { "sz", 0, PARAM_CANOMITNAME, "scale z", "f 0.5 1.0 0.9", FIELD(scalez), },15 { "tr", 0, PARAM_CANOMITNAME, "translation factor", "f 0 1 0.5", FIELD(translation), }, //formally 1..1, but let's avoid redundancy and elliminate symmetrical constructs12 { "sx", 0, PARAM_CANOMITNAME, "scale x", "f 1.0 1.1 1.01", FIELD(scalex), }, 13 { "sy", 0, PARAM_CANOMITNAME, "scale y", "f 1.0 1.1 1.01", FIELD(scaley), }, 14 { "sz", 0, PARAM_CANOMITNAME, "scale z", "f 1.0 1.1 1.01", FIELD(scalez), }, 15 { "tr", 0, PARAM_CANOMITNAME, "translation factor", "f 1 1 0.5", FIELD(translation), }, 16 16 { "a1", 0, PARAM_CANOMITNAME, "angle 1", "f 3.1415926 3.1415926 0", FIELD(angle1), }, 17 17 { "a2", 0, PARAM_CANOMITNAME, "angle 2", "f 3.1415926 3.1415926 0", FIELD(angle2), },
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