codebase / stimlib

Commit 7d3162a2521c1ecb18443d24ce3e46d482dfb441

Authored by Pavel Govyadinov
1 parent 03c403fa

fixed majority of the merge conflicts, edited vector.h and vec3.h and spider.h i… 

…n order to accomplish this. added copy constructors and additional necessary methods.
Showing 4 changed files with 133 additions and 121 deletions   Show diff stats
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stim/gl/gl_spider.h
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... ... @@ -7,13 +7,14 @@
7 7 #include <cuda_gl_interop.h>
8 8 #include <cudaGL.h>
9 9 #include <math.h>
10   -#include "stim/gl/gl_texture.h"
11   -#include "stim/visualization/camera.h"
12   -#include "stim/gl/error.h"
13   -#include "stim/math/vector.h"
14   -#include "stim/math/rect.h"
15   -#include "stim/math/matrix.h"
16   -#include "stim/cuda/spider_cost.cuh"
  10 +#include <stim/gl/gl_texture.h>
  11 +#include <stim/visualization/camera.h>
  12 +#include <stim/gl/error.h>
  13 +#include <stim/math/vector.h>
  14 +#include <stim/math/vec3.h>
  15 +#include <stim/math/rect.h>
  16 +#include <stim/math/matrix.h>
  17 +#include <stim/cuda/spider_cost.cuh>
17 18 #include <stim/cuda/cudatools/glbind.h>
18 19 #include <stim/cuda/arraymath.cuh>
19 20 #include <stim/cuda/cudatools.h>
... ... @@ -48,15 +49,15 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
48 49 private:
49 50  
50 51 //
51   - stim::vec<float> p; //vector designating the position of the spider.
52   - stim::vec<float> d; //vector designating the orientation of the spider
  52 + stim::vec3<float> p; //vector designating the position of the spider.
  53 + stim::vec3<float> d; //vector designating the orientation of the spider
53 54 //always a unit vector.
54   - stim::vec<float> m; //magnitude of the spider vector.
  55 + stim::vec3<float> m; //magnitude of the spider vector.
55 56 //mag[0] = length.
56 57 //mag[1] = width.
57   - std::vector<stim::vec<float> > dV; //A list of all the direction vectors.
58   - std::vector<stim::vec<float> > pV; //A list of all the position vectors.
59   - std::vector<stim::vec<float> > mV; //A list of all the size vectors.
  58 + std::vector<stim::vec3<float> > dV; //A list of all the direction vectors.
  59 + std::vector<stim::vec3<float> > pV; //A list of all the position vectors.
  60 + std::vector<stim::vec3<float> > mV; //A list of all the size vectors.
60 61  
61 62 stim::matrix<float, 4> cT; //current Transformation matrix
62 63 //From tissue space to texture space.
... ... @@ -88,21 +89,21 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
88 89  
89 90  
90 91 //Tracing variables.
91   - std::stack< stim::vec<float> > seeds; //seed positions.
92   - std::stack< stim::vec<float> > seedsvecs; //seed directions.
  92 + std::stack< stim::vec3<float> > seeds; //seed positions.
  93 + std::stack< stim::vec3<float> > seedsvecs; //seed directions.
93 94 std::stack< float > seedsmags; //seed magnitudes.
94 95  
95   - std::vector< stim::vec<float> > cL; //Positions of line currently being traced.
96   - std::vector< stim::vec<float> > cD; //Direction of line currently being traced.
  96 + std::vector< stim::vec3<float> > cL; //Positions of line currently being traced.
  97 + std::vector< stim::vec3<float> > cD; //Direction of line currently being traced.
97 98 std::vector< stim::vec<float> > cM; //Magnitude of line currently being traced.
98 99  
99 100 stim::glnetwork<float> nt; //object for storing the network.
100 101  
101 102 stim::vec<float> rev; //reverse vector;
102 103 stim::camera camSel;
103   - stim::vec<float> ps;
104   - stim::vec<float> ups;
105   - stim::vec<float> ds;
  104 + stim::vec3<float> ps;
  105 + stim::vec3<float> ups;
  106 + stim::vec3<float> ds;
106 107  
107 108 static const float t_length = 16.0;
108 109  
... ... @@ -188,7 +189,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
188 189 glCallList(dList+3);
189 190 std::vector< stim::vec<float> > result = find_branch(
190 191 btexbufferID, GL_TEXTURE_2D, 16, 216);
191   - stim::vec<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
  192 + stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
192 193 if(!result.empty())
193 194 {
194 195 for(int i = 1; i < result.size(); i++)
... ... @@ -200,11 +201,11 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
200 201 1.0);
201 202 cylp = cT*cylp;
202 203  
203   - stim::vec<float> vec(
  204 + stim::vec3<float> vec(
204 205 cylp[0]*S[0]*R[0],
205 206 cylp[1]*S[1]*R[1],
206 207 cylp[2]*S[2]*R[2]);
207   - stim::vec<float> seeddir(-p[0] + cylp[0]*S[0]*R[0],
  208 + stim::vec3<float> seeddir(-p[0] + cylp[0]*S[0]*R[0],
208 209 -p[1] + cylp[1]*S[1]*R[1],
209 210 -p[2] + cylp[2]*S[2]*R[2]);
210 211 seeddir = seeddir.norm();
... ... @@ -236,7 +237,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
236 237 DrawLongCylinder(n, l_template, l_square);
237 238 stim::cylinder<float> cyl(cL, cM);
238 239 std::vector< stim::vec<float> > result = find_branch(btexbufferID, GL_TEXTURE_2D, n*l_square, (cL.size()-1)*l_template);
239   - stim::vec<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
  240 + stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
240 241 float pval;
241 242 if(!result.empty())
242 243 {
... ... @@ -257,8 +258,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
257 258 {
258 259 pval = (cyl.getl(id)/cyl.getl(cL.size()-1));
259 260 }
260   - stim::vec<float> v = cyl.surf(pval, result[i][0]);
261   - stim::vec<float> di = cyl.p(pval);
  261 + stim::vec3<float> v = cyl.surf(pval, result[i][0]);
  262 + stim::vec3<float> di = cyl.p(pval);
262 263 float rad = cyl.r(pval);
263 264 if(
264 265 !(v[0] > size[0] || v[1] > size[1]
... ... @@ -287,15 +288,15 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
287 288 return cos(2.0*atan(1.0)*u2)*sqrt(-1.0*log(u1));
288 289 }
289 290  
290   - stim::vec<float> uniformRandVector()
  291 + stim::vec3<float> uniformRandVector()
291 292 {
292   - stim::vec<float> r(uniformRandom(), uniformRandom(), 1.0);
  293 + stim::vec3<float> r(uniformRandom(), uniformRandom(), 1.0);
293 294 return r;
294 295 }
295 296  
296   - stim::vec<float> normalRandVector()
  297 + stim::vec3<float> normalRandVector()
297 298 {
298   - stim::vec<float> r(normalRandom(), normalRandom(), 1.0);
  299 + stim::vec3<float> r(normalRandom(), normalRandom(), 1.0);
299 300 return r;
300 301 }
301 302  
... ... @@ -339,10 +340,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
339 340  
340 341 float z, theta, phi;
341 342  
342   - std::vector<stim::vec<float> > vecsUni;
  343 + std::vector<stim::vec3<float> > vecsUni;
343 344 for(int i = 0; i < numSamplesPos; i++)
344 345 {
345   - stim::vec<float> a(uniformRandom()*0.8, uniformRandom()*0.8, 0.0);
  346 + stim::vec3<float> a(uniformRandom()*0.8, uniformRandom()*0.8, 0.0);
346 347 a[0] = a[0]-0.4;
347 348 a[1] = a[1]-0.4;
348 349 vecsUni.push_back(a);
... ... @@ -369,10 +370,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
369 370 {
370 371  
371 372 //Set up the vectors necessary for Rectangle creation.
372   - vec<float> Y(1.0,0.0,0.0); //orthogonal vec.
373   - vec<float> pos(0.0,0.0,0.0);
374   - vec<float> mag(1.0, 1.0, 1.0);
375   - vec<float> dir(0.0, 0.0, 1.0);
  373 + stim::vec3<float> Y(1.0,0.0,0.0); //orthogonal vec.
  374 + stim::vec3<float> pos(0.0,0.0,0.0);
  375 + stim::vec3<float> mag(1.0, 1.0, 1.0);
  376 + stim::vec3<float> dir(0.0, 0.0, 1.0);
376 377  
377 378 float PHI[2], Z[2], range;
378 379 PHI[0] = solidAngle/2;
... ... @@ -390,8 +391,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
390 391 z = uniformRandom()*range + Z[1];
391 392 theta = uniformRandom()*2*M_PI;
392 393 phi = acos(z);
393   - stim::vec<float> sph(1, theta, phi);
394   - stim::vec<float> cart = sph.sph2cart();
  394 + stim::vec3<float> sph(1, theta, phi);
  395 + stim::vec3<float> cart = sph.sph2cart();
395 396 dV.push_back(cart);
396 397 if(cos(Y.dot(cart)) < 0.087)
397 398 {
... ... @@ -420,16 +421,16 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
420 421 genPositionVectors(float delta = 0.4)
421 422 {
422 423 //Set up the vectors necessary for Rectangle creation.
423   - vec<float> Y(1.0,0.0,0.0); //orthogonal vec.
424   - vec<float> pos(0.0,0.0,0.0);
425   - vec<float> mag(1.0, 1.0, 1.0);
426   - vec<float> dir(0.0, 0.0, 1.0);
  424 + stim::vec3<float> Y(1.0,0.0,0.0); //orthogonal vec.
  425 + stim::vec3<float> pos(0.0,0.0,0.0);
  426 + stim::vec3<float> mag(1.0, 1.0, 1.0);
  427 + stim::vec3<float> dir(0.0, 0.0, 1.0);
427 428  
428 429 //Set up the variable necessary for vector creation.
429 430 glNewList(dList+1, GL_COMPILE);
430 431 for(int i = 0; i < numSamplesPos; i++)
431 432 {
432   - stim::vec<float> temp = uniformRandVector();
  433 + stim::vec3<float> temp = uniformRandVector();
433 434 temp = temp*delta*2.0 - delta/2.0;
434 435 temp[2] = 0.0;
435 436 pV.push_back(temp);
... ... @@ -456,10 +457,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
456 457 {
457 458  
458 459 //Set up the vectors necessary for Rectangle creation.
459   - vec<float> Y(1.0, 0.0, 0.0); //orthogonal vec.
460   - vec<float> pos(0.0, 0.0, 0.0);
461   - vec<float> mag(1.0, 1.0, 1.0);
462   - vec<float> dir(0.0, 0.0, 1.0);
  460 + stim::vec3<float> Y(1.0, 0.0, 0.0); //orthogonal vec.
  461 + stim::vec3<float> pos(0.0, 0.0, 0.0);
  462 + stim::vec3<float> mag(1.0, 1.0, 1.0);
  463 + stim::vec3<float> dir(0.0, 0.0, 1.0);
463 464  
464 465 //Set up the variable necessary for vector creation.
465 466 int dim = (sqrt(numSamplesMag)-1)/2;
... ... @@ -467,7 +468,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
467 468 float max = 1.0+delta;
468 469 float step = (max-min)/(numSamplesMag-1);
469 470 float factor;
470   - vec<float> temp(0.0,0.0,0.0);
  471 + stim::vec3<float> temp(0.0,0.0,0.0);
471 472  
472 473 glNewList(dList+2, GL_COMPILE);
473 474 for(int i = 0; i < numSamplesMag; i++){
... ... @@ -495,10 +496,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
495 496 void
496 497 UpdateBuffer(float v_x, float v_y)
497 498 {
498   - stim::vec<float>p1;
499   - stim::vec<float>p2;
500   - stim::vec<float>p3;
501   - stim::vec<float>p4;
  499 + stim::vec3<float>p1;
  500 + stim::vec3<float>p2;
  501 + stim::vec3<float>p3;
  502 + stim::vec3<float>p4;
502 503 p1 = hor.p(1,1);
503 504 p2 = hor.p(1,0);
504 505 p3 = hor.p(0,0);
... ... @@ -712,10 +713,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
712 713 Bind(GLuint &textureID, GLuint &framebufferID, int nSamples, float len = 8.0)
713 714 {
714 715  
715   -// std::cout << glGetIntegerv(GL_MAX_TEXTURE_SIZE) << std::endl;
716   - GLint max;
717   - glGetIntegerv(GL_MAX_TEXTURE_SIZE, &max);
718   -// std::cout << max << std::endl;
719 716 glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);//set up GL buffer
720 717 glFramebufferTexture2D(
721 718 GL_FRAMEBUFFER,
... ... @@ -727,8 +724,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
727 724 GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0};
728 725 glDrawBuffers(1, DrawBuffers);
729 726 glBindTexture(GL_TEXTURE_2D, textureID);
730   -// glClearColor(1,1,1,1);
731   -// glClear(GL_COLOR_BUFFER_BIT);
732 727 glMatrixMode(GL_PROJECTION);
733 728 glLoadIdentity();
734 729 glMatrixMode(GL_MODELVIEW);
... ... @@ -837,10 +832,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
837 832 initCuda()
838 833 {
839 834 stim::cudaSetDevice();
840   - MonteCarloDirectionVectors(500);
841   - //GLint max;
842   - //glGetIntegerv(GL_MAX_TEXTURE_SIZE, &max);
843   - //std::cout << max << std::endl;
844 835 }
845 836  
846 837 //horizonal rectangle forming the spider.
... ... @@ -869,11 +860,11 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
869 860 (int samples = 1089, int samplespos = 441,int samplesmag = 144)
870 861 {
871 862 // std::cout << "I ran this constructor" << std::endl;
872   - p = vec<float>(0.0, 0.0, 0.0);
873   - d = vec<float>(0.0, 0.0, 1.0);
874   - m = vec<float>(1.0, 1.0);
875   - S = vec<float>(1.0, 1.0, 1.0);
876   - R = vec<float>(1.0, 1.0, 1.0);
  863 + p = stim::vec3<float>(0.0, 0.0, 0.0);
  864 + d = stim::vec3<float>(0.0, 0.0, 1.0);
  865 + m = stim::vec<float>(1.0, 1.0);
  866 + S = stim::vec3<float>(1.0, 1.0, 1.0);
  867 + R = stim::vec3<float>(1.0, 1.0, 1.0);
877 868 // std::cout << samples << std::endl;
878 869 numSamples = samples;
879 870 // std::cout << numSamples << std::endl;
... ... @@ -894,11 +885,11 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
894 885 (float pos_x, float pos_y, float pos_z, float dir_x, float dir_y, float dir_z,
895 886 float mag_x, int numsamples = 1089, int numsamplespos = 441, int numsamplesmag =144)
896 887 {
897   - p = vec<float>(pos_x, pos_y, pos_z);
898   - d = vec<float>(dir_x, dir_y, dir_z);
899   - m = vec<float>(mag_x, mag_x, mag_x);
900   - S = vec<float>(1.0,1.0,1.0);
901   - R = vec<float>(1.0,1.0,1.0);
  888 + p = stim::vec3<float>(pos_x, pos_y, pos_z);
  889 + d = stim::vec3<float>(dir_x, dir_y, dir_z);
  890 + m = stim::vec<float>(mag_x, mag_x, mag_x);
  891 + S = stim::vec3<float>(1.0,1.0,1.0);
  892 + R = stim::vec3<float>(1.0,1.0,1.0);
902 893 numSamples = numsamples;
903 894 numSamplesPos = numsamplespos;
904 895 numSamplesMag = numsamplesmag;
... ... @@ -910,13 +901,13 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
910 901 ///@param float mag, size of the vector.
911 902 ///@param int samples, number of templates this spider is going to use.
912 903 gl_spider
913   - (stim::vec<float> pos, stim::vec<float> dir, float mag, int samples = 1089, int samplesPos = 441, int samplesMag = 144)
  904 + (stim::vec3<float> pos, stim::vec3<float> dir, float mag, int samples = 1089, int samplesPos = 441, int samplesMag = 144)
914 905 {
915 906 p = pos;
916 907 d = dir;
917 908 m = vec<float>(mag, mag, mag);
918   - S = vec<float>(1.0,1.0,1.0);
919   - R = vec<float>(1.0,1.0,1.0);
  909 + S = vec3<float>(1.0,1.0,1.0);
  910 + R = vec3<float>(1.0,1.0,1.0);
920 911 numSamples = samples;
921 912 numSamplesPos = samplesPos;
922 913 numSamplesMag = samplesMag;
... ... @@ -978,14 +969,14 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
978 969 //-----------------------------ACCESS METHODS-------------------------------//
979 970 //--------------------------------------------------------------------------//
980 971 ///Returns the p vector.
981   - vec<float>
  972 + vec3<float>
982 973 getPosition()
983 974 {
984 975 return p;
985 976 }
986 977  
987 978 ///Returns the d vector.
988   - vec<float>
  979 + vec3<float>
989 980 getDirection()
990 981 {
991 982 return d;
... ... @@ -1001,7 +992,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1001 992 ///@param stim::vec<float> pos, the new p.
1002 993 ///Sets the p vector to input vector pos.
1003 994 void
1004   - setPosition(vec<float> pos)
  995 + setPosition(stim::vec3<float> pos)
1005 996 {
1006 997 p = pos;
1007 998 }
... ... @@ -1021,7 +1012,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1021 1012 ///@param stim::vec<float> dir, the new d.
1022 1013 ///Sets the d vector to input vector dir.
1023 1014 void
1024   - setDirection(vec<float> dir)
  1015 + setDirection(stim::vec3<float> dir)
1025 1016 {
1026 1017 d = dir;
1027 1018 }
... ... @@ -1041,7 +1032,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1041 1032 ///@param stim::vec<float> dir, the new d.
1042 1033 ///Sets the m vector to the input vector mag.
1043 1034 void
1044   - setMagnitude(vec<float> mag)
  1035 + setMagnitude(stim::vec<float> mag)
1045 1036 {
1046 1037 m[0] = mag[0];
1047 1038 m[1] = mag[0];
... ... @@ -1071,7 +1062,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1071 1062 ///@param stim::vec<float> Dims, voxel size.
1072 1063 ///Sets the voxel sizes in each direction. necessary for non-standard data.
1073 1064 void
1074   - setDims(stim::vec<float> Dims)
  1065 + setDims(stim::vec3<float> Dims)
1075 1066 {
1076 1067 S = Dims;
1077 1068 }
... ... @@ -1091,7 +1082,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1091 1082 ///@param stim::vec<float> Dims, size of the volume.
1092 1083 ///Sets the data volume sizes in each direction.
1093 1084 void
1094   - setSize(stim::vec<float> Siz)
  1085 + setSize(stim::vec3<float> Siz)
1095 1086 {
1096 1087 S = Siz;
1097 1088 }
... ... @@ -1125,7 +1116,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1125 1116 ///Adds a seed to the seed list.
1126 1117 ///Assumes that the coordinates passes are in tissue space.
1127 1118 void
1128   - setSeed(stim::vec<float> pos)
  1119 + setSeed(stim::vec3<float> pos)
1129 1120 {
1130 1121 seeds.push(pos);
1131 1122 }
... ... @@ -1133,7 +1124,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1133 1124 ///@param stim::vec<float> dir, the direction of the seed to be added.
1134 1125 ///Adds a seed to the seed directions list.
1135 1126 void
1136   - setSeedVec(stim::vec<float> dir)
  1127 + setSeedVec(stim::vec3<float> dir)
1137 1128 {
1138 1129 seedsvecs.push(dir);
1139 1130 }
... ... @@ -1173,18 +1164,18 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1173 1164 }
1174 1165  
1175 1166 ///Method to get the top of the seed positions stack.
1176   - stim::vec<float>
  1167 + stim::vec3<float>
1177 1168 getLastSeed()
1178 1169 {
1179   - stim::vec<float> tp = seeds.top();
  1170 + stim::vec3<float> tp = seeds.top();
1180 1171 return tp;
1181 1172 }
1182 1173  
1183 1174 ///Method to get the top of the seed direction stack.
1184   - stim::vec<float>
  1175 + stim::vec3<float>
1185 1176 getLastSeedVec()
1186 1177 {
1187   - stim::vec<float> tp = seedsvecs.top();
  1178 + stim::vec3<float> tp = seedsvecs.top();
1188 1179 return tp;
1189 1180 }
1190 1181  
... ... @@ -1206,7 +1197,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1206 1197 }
1207 1198  
1208 1199 ///returns the seeds position stack.
1209   - std::stack<stim::vec<float> >
  1200 + std::stack<stim::vec3<float> >
1210 1201 getSeeds()
1211 1202 {
1212 1203 return seeds;
... ... @@ -1252,7 +1243,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1252 1243 for(int i = 0; i < nt.sizeE(); i++)
1253 1244 {
1254 1245 std::vector<stim::vec< float > > cm = nt.getEdgeCenterLineMag(i);
1255   - std::vector<stim::vec< float > > ce = nt.getEdgeCenterLine(i);
  1246 + std::vector<stim::vec3< float > > ce = nt.getEdgeCenterLine(i);
1256 1247 sk.Begin(stim::OBJ_LINE);
1257 1248 for(int j = 0; j < ce.size(); j++)
1258 1249 {
... ... @@ -1269,7 +1260,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1269 1260 stim::glObj<float>
1270 1261 getNetwork()
1271 1262 {
1272   -// return sk;
  1263 +
1273 1264 }
1274 1265  
1275 1266 ///returns a COPY of the entire stim::glnetwork object.
... ... @@ -1295,7 +1286,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1295 1286 void
1296 1287 Update()
1297 1288 {
1298   - vec<float> Y(1.0,0.0,0.0);
  1289 + vec3<float> Y(1.0,0.0,0.0);
1299 1290 if(cos(Y.dot(d))< 0.087){
1300 1291 Y[0] = 0.0; Y[1] = 1.0;}
1301 1292 hor = stim::rect<float>(m, p, d.norm(),
... ... @@ -1389,7 +1380,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1389 1380 GenerateFBO(n*l_square, cylLen*l_template, btexbufferID, bfboID);
1390 1381 Bind(btexbufferID, bfboID, cylLen, l_template*l_square/2.0);
1391 1382 stim::cylinder<float> cyl(cL, cM);
1392   - std::vector<std::vector<stim::vec<float> > > p = cyl.getPoints(n);
  1383 + std::vector<std::vector<stim::vec3<float> > > p = cyl.getPoints(n);
1393 1384 for(int i = 0; i < p.size()-1; i++) ///number of circles
1394 1385 {
1395 1386 for(int j = 0; j < p[0].size()-1; j++) ///points in the circle
... ... @@ -1418,11 +1409,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1418 1409 void
1419 1410 trace(int min_cost)
1420 1411 {
1421   -// rev = stim::vec<float>(0.0,0.0,1.0);
1422 1412 bool sEmpty = true;
1423 1413 float lastmag = 16.0;;
1424   - stim::vec<float> curSeed;
1425   - stim::vec<float> curSeedVec;
  1414 + stim::vec3<float> curSeed;
  1415 + stim::vec3<float> curSeedVec;
1426 1416 float curSeedMag;
1427 1417 while(!Empty())
1428 1418 {
... ... @@ -1448,7 +1438,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1448 1438 }
1449 1439  
1450 1440 int
1451   - selectObject(stim::vec<float> loc, stim::vec<float> dir, float mag)
  1441 + selectObject(stim::vec3<float> loc, stim::vec3<float> dir, float mag)
1452 1442 {
1453 1443 //Define the varibles and turn on Selection Mode
1454 1444  
... ... @@ -1554,10 +1544,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1554 1544 }
1555 1545  
1556 1546 void
1557   - addToNetwork(pair<stim::fiber<float>, int> in, stim::vec<float> spos,
1558   - stim::vec<float> smag, stim::vec<float> sdir)
  1547 + addToNetwork(pair<stim::fiber<float>, int> in, stim::vec3<float> spos,
  1548 + stim::vec<float> smag, stim::vec3<float> sdir)
1559 1549 {
1560   - std::vector<stim::vec<float> > ce = in.first.centerline();
  1550 + std::vector<stim::vec3<float> > ce = in.first.centerline();
1561 1551 std::vector<stim::vec<float> > cm = in.first.centerlinemag();
1562 1552 //if the fiber is longer than 2 steps (the number it takes to diverge)
1563 1553 if(ce.size() > 3)
... ... @@ -1602,12 +1592,12 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1602 1592 }
1603 1593  
1604 1594 std::pair<stim::fiber<float>, int >
1605   - traceLine(stim::vec<float> pos, stim::vec<float> mag, int min_cost)
  1595 + traceLine(stim::vec3<float> pos, stim::vec<float> mag, int min_cost)
1606 1596 {
1607 1597 //starting (seed) position and magnitude.
1608   - stim::vec<float> spos = getPosition();
  1598 + stim::vec3<float> spos = getPosition();
1609 1599 stim::vec<float> smag = getMagnitude();
1610   - stim::vec<float> sdir = getDirection();
  1600 + stim::vec3<float> sdir = getDirection();
1611 1601  
1612 1602 Bind();
1613 1603 // sk.Begin(stim::OBJ_LINE);
... ... @@ -1624,7 +1614,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1624 1614 int h;
1625 1615 bool started = false;
1626 1616 bool running = true;
1627   - stim::vec<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
  1617 + stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
1628 1618 while(running)
1629 1619 {
1630 1620 int cost = Step();
... ... @@ -1684,7 +1674,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1684 1674 break;
1685 1675 }
1686 1676 else {
1687   - cL.push_back(stim::vec<float>(p[0], p[1],p[2]));
  1677 + cL.push_back(stim::vec3<float>(p[0], p[1],p[2]));
1688 1678 cM.push_back(stim::vec<float>(m[0], m[0]));
1689 1679 // Bind(btexbufferID, bfboID, 27);
1690 1680 Unbind();
... ...
stim/math/vec3.h
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... ... @@ -37,10 +37,14 @@ public:
37 37 }
38 38  
39 39 //access an element using an index
40   - CUDA_CALLABLE T& operator[](int idx){
  40 + CUDA_CALLABLE T& operator[](size_t idx){
41 41 return ptr[idx];
42 42 }
43 43  
  44 + CUDA_CALLABLE T* data(){
  45 + return ptr;
  46 + }
  47 +
44 48 /// Casting operator. Creates a new vector with a new type U.
45 49 template< typename U >
46 50 CUDA_CALLABLE operator vec3<U>(){
... ... @@ -249,4 +253,4 @@ std::ostream&amp; operator&lt;&lt;(std::ostream&amp; os, stim::vec3&lt;T&gt; const&amp; rhs){
249 253 return os;
250 254 }
251 255  
252   -#endif
253 256 \ No newline at end of file
  257 +#endif
... ...
stim/math/vector.h
  Show/Hide comments   View file @7d3162a
... ... @@ -74,6 +74,13 @@ struct vec : public std::vector&lt;T&gt;
74 74 at(i) = other[i];
75 75 }
76 76 }
  77 +
  78 + vec( vec3<T>& other){
  79 + resize(3); //resize the current vector to match the copy
  80 + for(size_t i=0; i<3; i++){ //copy each element
  81 + at(i) = other[i];
  82 + }
  83 + }
77 84  
78 85 //I'm not sure what these were doing here.
79 86 //Keep them now, we'll worry about it later.
... ... @@ -328,15 +335,16 @@ struct vec : public std::vector&lt;T&gt;
328 335 return *this;
329 336 }
330 337  
331   - /// Cast to a vec3
332   - operator stim::vec3<T>(){
333   - stim::vec3<T> r;
334   - size_t N = std::min<size_t>(size(), 3);
335   - for(size_t i = 0; i < N; i++)
336   - r[i] = at(i);
337   - return r;
338   - }
339   -
  338 + /// Cast to a vec3
  339 + operator stim::vec3<T>(){
  340 + stim::vec3<T> r;
  341 + size_t N = std::min<size_t>(size(), 3);
  342 + for(size_t i = 0; i < N; i++)
  343 + r[i] = at(i);
  344 + return r;
  345 + }
  346 +
  347 +
340 348 /// Casting and assignment
341 349 template<typename Y>
342 350 vec<T> & operator=(vec<Y> rhs){
... ... @@ -347,6 +355,16 @@ struct vec : public std::vector&lt;T&gt;
347 355 at(i) = rhs[i];
348 356 return *this;
349 357 }
  358 +
  359 + /// Assign a vec = vec3
  360 + template<typename Y>
  361 + vec<T> & operator=(vec3<Y> rhs)
  362 + {
  363 + resize(3);
  364 + for(size_t i=0; i<3; i++)
  365 + at(i) = rhs[i];
  366 + return *this;
  367 + }
350 368  
351 369 /// Unary minus (returns the negative of the vector)
352 370 vec<T> operator-() const{
... ...
stim/visualization/cylinder.h
  Show/Hide comments   View file @7d3162a
... ... @@ -23,7 +23,7 @@ class cylinder
23 23  
24 24 }
25 25  
26   - ///inits the cylinder from a list of points (inP) and radii (inM)
  26 + ///inits the cylinder from a list of points (std::vector of stim::vec3 --inP) and radii (inM)
27 27 void
28 28 init(std::vector<stim::vec3<T> > inP, std::vector<stim::vec<T> > inM)
29 29 {
... ... @@ -142,14 +142,15 @@ class cylinder
142 142 }
143 143  
144 144 ///constructor to create a cylinder from a set of points, radii, and the number of sides for the cylinder.
145   - ///@param inP: Vector of stim vecs composing the points of the centerline.
  145 + ///@param inP: Vector of stim vec3 composing the points of the centerline.
146 146 ///@param inM: Vector of stim vecs composing the radii of the centerline.
147   - cylinder(std::vector<stim::vec3<T> > inP, std::vector<stim::vec3<T> > inM){
  147 + cylinder(std::vector<stim::vec3<T> > inP, std::vector<stim::vec<T> > inM){
148 148 init(inP, inM);
149 149 }
150 150  
  151 +
151 152 ///Constructor defines a cylinder with centerline inP and magnitudes of zero
152   - ///@param inP: Vector of stim vecs composing the points of the centerline
  153 + ///@param inP: Vector of stim vec3 composing the points of the centerline
153 154 cylinder(std::vector< stim::vec3<T> > inP){
154 155 std::vector< stim::vec<T> > inM; //create an array of arbitrary magnitudes
155 156  
... ... @@ -160,7 +161,6 @@ class cylinder
160 161 init(inP, inM);
161 162 }
162 163  
163   -
164 164 ///Returns the number of points on the cylinder centerline
165 165  
166 166 unsigned int size(){
... ...