codebase / stimlib

Commit 385d2447fe1df96d07a60a6856c8189019445d32

Authored by Pavel Govyadinov
1 parent 5f81932b

Checkpoint: Converted the previous version of the code to a more seperable versi… 

…on with each function doing a seperate job. Renamed the series of 'sample' methods and changed what they do. The vector arrays are now owned by the spider class, and the previously-named 'sample' functions fill in the arrays with vectors. Update() has been renamed into genTemplate and now maps from the TissueSpace to bufferSpace. Some new comments for the documentation
Showing 5 changed files with 220 additions and 201 deletions   Show diff stats
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stim/cuda/cost.h
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... ... @@ -2,8 +2,6 @@
2 2 #include <cuda.h>
3 3 #include <cuda_runtime.h>
4 4 #include <cublas_v2.h>
5   -//#include "cuPrintf.cu"
6   -//#include "cuPrintf.cuh"
7 5 #include <stdio.h>
8 6 #include "../visualization/colormap.h"
9 7 #include <sstream>
... ... @@ -11,9 +9,6 @@
11 9 #define DIM_Y 10890
12 10 #define DIM_X 20
13 11 typedef unsigned char uchar;
14   -//surface<void, 2> texOut; ///// maybe just do a normal array instead of a surface.
15   - //we may not need a surface at all.
16   -//texture<float, cudaTextureType2D, cudaReadModeElementType> texTemplate
17 12 texture<uchar, cudaTextureType2D, cudaReadModeElementType> texIn;
18 13 float *result;
19 14 float* v_dif;
... ... @@ -66,11 +61,9 @@ void get_diff (float *result)
66 61 float valIn = tex2D(texIn, x, y)/255.0;
67 62 float valTemp = Template(x);
68 63 result[idx] = abs(valIn-valTemp);
69   - //result[idx] = abs(valTemp);
70 64 // #if __CUDA_ARCH__>=200
71 65 // printf("Value is : %f\n and the result is : %f\n", valIn, result[idx]);
72 66 // #endif
73   - //cuPrintf("Value is : %f\n and the result is : %f\n", valIn, result[idx]);
74 67 }
75 68  
76 69  
... ... @@ -128,7 +121,6 @@ int get_cost(cudaGraphicsResource_t src, int inter)
128 121 initArray(src);
129 122 dim3 grid(20, 10890);
130 123 dim3 block(1, 1);
131   - //texIn.normalized = 1;
132 124 get_diff <<< grid, block >>> (result);
133 125 stim::gpu2image<float>(result, "test.bmp", 20,10890,0,1);
134 126 for (int i = 0; i < 1089; i++){
... ... @@ -136,19 +128,11 @@ int get_cost(cudaGraphicsResource_t src, int inter)
136 128 if(output[i] <= mini){
137 129 mini = output[i];
138 130 idx = i;
139   -// if(!testing)
140   -
141   -// testing = true;
142   - } //float* out = (float*) malloc(sizeof(float));
  131 + }
143 132 }
144 133 name << "sample_" << inter << "_" << idx << ".bmp";
145 134 output[idx] = get_sum(result+(20*10*idx));
146 135 stim::gpu2image<float>(v_dif, name.str(), 20,10,0,1);
147   - std::cout << output[0] << std::endl;
148   - std::cout << output[100] << std::endl;
149   - std::cout << output[500] << std::endl;
150   - std::cout << output[1000] << std::endl;
151   - std::cout << idx << std::endl;
152 136 cleanUP(src);
153 137 return idx;
154 138 }
... ...
stim/gl/gl_spider.h
  Show/Hide comments   View file @385d244
... ... @@ -14,6 +14,7 @@
14 14 #include "../math/rect.h"
15 15 #include "../cuda/cost.h"
16 16 #include "../cuda/glbind.h"
  17 +#include <vector>
17 18  
18 19 #include <iostream>
19 20 #include <fstream>
... ... @@ -33,8 +34,11 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
33 34 stim::vec<float> magnitude; //magnitude of the direction vector.
34 35 //mag[0] = length.
35 36 //mag[1] = width.
  37 + std::vector<stim::vec<float> > dirVectors;
  38 + std::vector<stim::vec<float> > posVectors;
  39 + std::vector<stim::vec<float> > magVectors;
36 40 using gl_texture<T>::texID;
37   - //using image_stack<T>::S;
  41 + using gl_texture<T>::S;
38 42 cudaArray* c_Array;
39 43 //void** devPtr;
40 44 //size_t size;
... ... @@ -49,6 +53,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
49 53 /* Method for finding the best direction for the spider.
50 54 Not sure if necessary since the next position for the spider
51 55 will be at direction * magnitude. */
  56 + genTemplate(posVectors, 1);
  57 + int best = getCost();
52 58 }
53 59  
54 60 void
... ... @@ -57,20 +63,20 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
57 63 /* Method for finding the best scale for the spider.
58 64 changes the x, y, z size of the spider to minimize the cost
59 65 function. */
  66 + genTemplate(magVectors, 1);
  67 + int best = getCost();
60 68 }
61 69  
62 70 void
63   - Evaluate()
64   - {
65   - /* Uses uniform sampler2D in order to take a difference between
66   - the colors of two textures. 1st texture is the spider template,
67   - the 2nd is the location of the spider's overlap with the
68   - gl_template
69   -
70   - does the spider need to track it's location? Prob not since
71   - position can be set with gl_texture coordinates */
72   -
  71 + findOptimalDirection()
  72 + {
  73 + /* Method for finding the best scale for the spider.
  74 + changes the x, y, z size of the spider to minimize the cost
  75 + function. */
  76 + genTemplate(dirVectors, 1);
  77 + int best = getCost();
73 78 }
  79 +
74 80  
75 81 void
76 82 Optimize()
... ... @@ -120,6 +126,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
120 126 p4 = hor.p(0,1);
121 127 glBegin(GL_QUADS);
122 128 glTexCoord3f(
  129 + // p1[0]/S[1],
  130 + // p1[1]/S[2],
  131 + // p1[2]/S[3]
  132 + // );
123 133 p1[0],
124 134 p1[1],
125 135 p1[2]
... ... @@ -127,6 +137,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
127 137 //glVertex2f(0.0,0.0);
128 138 glVertex2f(v_x,v_y);
129 139 glTexCoord3f(
  140 + // p2[0]/S[1],
  141 + // p2[1]/S[2],
  142 + // p2[2]/S[3]
130 143 p2[0],
131 144 p2[1],
132 145 p2[2]
... ... @@ -134,6 +147,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
134 147 //glVertex2f(1.0, 0.0);
135 148 glVertex2f(v_x+len, v_y);
136 149 glTexCoord3f(
  150 + // p2[0]/S[1],
  151 + // p2[1]/S[2],
  152 + // p2[2]/S[3]
137 153 p3[0],
138 154 p3[1],
139 155 p3[2]
... ... @@ -141,6 +157,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
141 157 //glVertex2f(1.0, 2.0);
142 158 glVertex2f(v_x+len, v_y+len);
143 159 glTexCoord3f(
  160 + // p4[0]/S[1],
  161 + // p4[1]/S[2],
  162 + // p4[2]/S[3]
144 163 p4[0],
145 164 p4[1],
146 165 p4[2]
... ... @@ -154,6 +173,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
154 173 p4 = ver.p(0,1);
155 174 glBegin(GL_QUADS);
156 175 glTexCoord3f(
  176 + // p1[0]/S[1],
  177 + // p1[1]/S[2],
  178 + // p1[2]/S[3]
157 179 p1[0],
158 180 p1[1],
159 181 p1[2]
... ... @@ -161,6 +183,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
161 183 //glVertex2f(1.0, 0.0);
162 184 glVertex2f(v_x+len, v_y);
163 185 glTexCoord3f(
  186 + // p2[0]/S[1],
  187 + // p2[1]/S[2],
  188 + // p2[2]/S[3]
164 189 p2[0],
165 190 p2[1],
166 191 p2[2]
... ... @@ -168,6 +193,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
168 193 //glVertex2f(2.0, 0.0);
169 194 glVertex2f(v_x+2*len, v_y);
170 195 glTexCoord3f(
  196 + // p3[0]/S[1],
  197 + // p3[1]/S[2],
  198 + // p3[2]/S[3]
171 199 p3[0],
172 200 p3[1],
173 201 p3[2]
... ... @@ -175,6 +203,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
175 203 //glVertex2f(2.0, 2.0);
176 204 glVertex2f(v_x+2*len, v_y+len);
177 205 glTexCoord3f(
  206 + // p4[0]/S[1],
  207 + // p4[1]/S[2],
  208 + // p4[2]/S[3]
178 209 p4[0],
179 210 p4[1],
180 211 p4[2]
... ... @@ -185,35 +216,60 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
185 216 }
186 217  
187 218 void
188   - UpdatePlanes(float v_x, float v_y, vec<float> vctr, int type = 0)
  219 + genTemplate(std::vector<stim::vec<float> > in, int type = 0)
189 220 {
  221 + float x = 0.0;
190 222 vec<float> Y(1.0,0.0,0.0);
191   - if(cos(Y.dot(vctr))< 0.087){ Y[0] = 0.0; Y[1] = 1.0;}
  223 + Bind();
192 224 switch(type) {
193   - case 0:
194   - hor = stim::rect<float>(magnitude, position, vctr.norm(),
195   - ((Y.cross(vctr)).cross(vctr)).norm());
196   - ver = stim::rect<float>(magnitude, position, vctr.norm(),
197   - hor.n());
  225 + case 0: //Direction
  226 + for(int i = 0; i < in.size(); i++)
  227 + {
  228 + if(cos(Y.dot(in[i]))< 0.087){ Y[0] = 0.0; Y[1] = 1.0;}
  229 + else{Y[0] = 1.0; Y[1] = 0.0;}
  230 +
  231 + hor = stim::rect<float>(magnitude,
  232 + position, in[i],
  233 + ((Y.cross(in[i])).cross(in[i])).norm());
  234 + ver = stim::rect<float>(magnitude,
  235 + position, in[i],
  236 + hor.n());
  237 + UpdateBuffer(x, x+i*10.0);
  238 + }
198 239 break;
199   - case 1:
200   - hor = stim::rect<float>(magnitude, vctr, direction,
201   - ((Y.cross(direction)).cross(direction)).norm());
202   - ver = stim::rect<float>(magnitude, vctr, direction,
203   - hor.n());
  240 + case 1: //Position
  241 + if(cos(Y.dot(direction))< 0.087){ Y[0] = 0.0; Y[1] = 1.0;}
  242 + else{Y[0] = 1.0; Y[1] = 0.0;}
  243 +
  244 + for(int i = 0; i < in.size(); i++)
  245 + {
  246 + hor = stim::rect<float>(magnitude, in[i], direction,
  247 + ((Y.cross(direction)).cross(direction))
  248 + .norm());
  249 + ver = stim::rect<float>(magnitude, in[i], direction,
  250 + hor.n());
  251 + UpdateBuffer(x, x+i*10.0);
  252 + }
204 253 break;
205   - case 2:
206   - hor = stim::rect<float>(vctr, position, direction,
207   - ((Y.cross(direction)).cross(direction)).norm());
208   - ver = stim::rect<float>(vctr, position, direction,
209   - hor.n());
210   - break;
  254 + case 2: //Scale
  255 + if(cos(Y.dot(direction))< 0.087){ Y[0] = 0.0; Y[1] = 1.0;}
  256 + else{Y[0] = 1.0; Y[1] = 0.0;}
  257 +
  258 + for(int i = 0; i < in.size(); i++)
  259 + {
  260 + hor = stim::rect<float>(in[i], position, direction,
  261 + ((Y.cross(direction)).cross(direction))
  262 + .norm());
  263 + ver = stim::rect<float>(in[i], position, direction,
  264 + hor.n());
  265 + }
  266 + break;
211 267 default:
212 268 std::cout << "unknown case have been passed"
213 269 << std::endl;
214 270 break;
215 271 }
216   - UpdateBuffer(v_x, v_y);
  272 + Unbind();
217 273 }
218 274  
219 275 /*
... ... @@ -247,6 +303,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
247 303 glBindTexture(GL_TEXTURE_3D, texID);
248 304 }
249 305  
  306 + /*
  307 + Method for Unbinding all of the texture resources
  308 + */
250 309 void
251 310 Unbind()
252 311 {
... ... @@ -256,83 +315,46 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
256 315 glBindFramebuffer(GL_FRAMEBUFFER,0);
257 316 glBindTexture(GL_TEXTURE_2D, 0);
258 317 }
  318 +
259 319 /*
260 320 Method for populating the buffer with the sampled texture.
261 321 usually uses the default direction vector and then
262 322 */
263 323 void
264   - sampleDirection(int numSamples = 1089, float solidAngle = M_PI)
  324 + genDirectionVectors(int numSamples = 1089, float solidAngle = M_PI/1.5)
265 325 {
266 326  
267   - //ofstream file;
268   - //file.open("samples.txt", std::ios_base::app);
269   - float samples[numSamples][3]; //Set up the variables
270   - //necessary for sample generation
271 327 vec<float> d_s = direction.cart2sph();
  328 + dirVectors.resize(1089);
272 329 vec<float> temp;
273 330 int dim = (sqrt(numSamples)-1)/2;
274   - //std::cout << dim << std::endl;
275   - float y_0 = 0.0;
276 331 float p0 = M_PI/3;
277 332 float dt = solidAngle/(1.0 * dim);
278 333 float dp = p0/(1.0*dim);
279 334  
280   - Bind();
281   - //file << "Step: Direction" << "\n";
282   - //file << "iteration: " << iter << "\n";
283   - //file << "starting pos and dir:" << "[" << position[0] << "," <<position[1] << "," << position[2] << "]" << ":" << "[" << direction[0] << "," << direction[1] << "," << direction[2] << "]\n";
284   - //Loop over the samples such that the original orientation is in the
285   - //center of the resulting texture index (544)
286   - //file << position[0] << "," <<position[1] << "," << position[2] << "\n";
287   - int idx;
288 335 for(int i = -dim; i <= dim; i++){
289 336 for(int j = -dim; j <= dim; j++){
290 337 //Create linear index
291   - idx = (i+dim)*(dim*2+1) + (j+dim);
292   -
  338 +
293 339 temp[0] = d_s[0]; //rotate vector
294 340 temp[1] = d_s[1]+dt*i;
295 341 temp[2] = d_s[2]+dp*j;
296 342  
297 343 temp = (temp.sph2cart()).norm(); //back to cart
298   - samples[idx][0] = temp[0]; //save sample vector
299   - samples[idx][1] = temp[1];
300   - samples[idx][2] = temp[2];
301   -
302   - // file << idx << ":" <<"[" << samples[idx][0] << "," << samples[idx][1] << "," << samples[idx][2] << "]" << "\n";
303   -
304   - UpdatePlanes(0.0, y_0+(idx)*10, temp);
  344 + dirVectors.push_back(temp);
305 345 }
306 346 }
307   - Unbind();
308   - int nxt = getCost();
309   - stim::vec<float> next(samples[nxt][0], samples[nxt][1], samples[nxt][2]);
310   - //next[0] = samples[nxt][0];
311   - //next[1] = samples[nxt][1];
312   - //next[2] = samples[nxt][2];
313   - next.norm();
314   - //file << "next direction" << "[" << next[0] << "," << next[1] << "," << next[2] << "]\n\n";
315   - setPosition(position[0] + next[0]*magnitude[0]/2,
316   - position[1]+next[1]*magnitude[0]/2,
317   - position[2]+next[2]*magnitude[0]/2);
318   - setDirection(next[0], next[1], next[2]);
319   - //file.close();
320   - setDirection(next);
321   - //file << "ending pos and dir:" << "[" << position[0] << "," <<position[1] << "," << position[2] << "]" << ":" << "[" << direction[0] << "," << direction[1] << "," << direction[2] << "]\n";
322 347 }
323 348  
324 349 void
325   - samplePosition(int numSamples = 1089, float delta = 0.2)
  350 + genPositionVectors(int numSamples = 1089, float delta = 0.2)
326 351 {
327 352  
328   - float samples[numSamples][3]; //Set up the variables
329 353 vec<float> temp;
330 354 int dim = (sqrt(numSamples)-1)/2;
331   - float y_0 = 0.0; //location of the first sample in the buffer
332 355 stim::rect<float> samplingPlane =
333 356 stim::rect<float>(magnitude[0]*delta, position, direction);
334 357 float step = 1.0/(dim);
335   - Bind();
336 358 //Loop over the samples, keeping the original position sample
337 359 //in the center of the resulting texture.
338 360  
... ... @@ -340,52 +362,34 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
340 362 for(int i = -dim; i <= dim; i++){
341 363 for(int j = -dim; j <= dim; j++){
342 364 //Create linear index
343   - idx = (i+dim)*(dim*2+1) + (j+dim);
344 365  
345 366 temp = samplingPlane.p(
346 367 0.5+step*i,
347 368 0.5+step*j
348 369 );
349   -
350   - samples[idx][0] = temp[0]; //save sample vector
351   - samples[idx][1] = temp[1];
352   - samples[idx][2] = temp[2];
353   -
354   - UpdatePlanes(0.0, y_0+(idx)*10, temp, 1);
  370 + dirVectors.push_back(temp);
355 371 }
356 372 }
357   - Unbind();
358   - int nxt = getCost();
359   - setPosition(samples[nxt][0], samples[nxt][1], samples[nxt][2]);
360 373 }
361 374  
362 375 void
363   - sampleMagnitude(int numSamples = 1089, float delta = 0.5)
  376 + genMagnitudeVectors(int numSamples = 1089, float delta = 0.5)
364 377 {
365 378  
366   - ofstream file;
367   - file.open("samples.txt", std::ios_base::app);
368   - float samples[numSamples]; //Set up the variables
369 379 int dim = (sqrt(numSamples)-1)/2;
370   - float y_0 = 0.0; //location of the first sample in the buffer
371 380 float min = 1.0-delta;
372 381 float max = 1.0+delta;
373 382 float step = (max-min)/(numSamples-1);
374 383 float factor;
375 384 vec<float> temp;
376   - Bind();
377 385  
378 386 for(int i = 0; i < numSamples; i++){
379   - //Create linear index
380   - factor = (min+step*i)*magnitude[0];
381   - samples[i] = factor; //save sample vector
382   - stim::vec<float> temp(factor);
383   - UpdatePlanes(0.0, y_0+(i)*10, temp, 2);
  387 + //Create linear index
  388 + factor = (min+step*i)*magnitude[0];
  389 + temp[0] = factor;
  390 + temp[1] = factor;
  391 + magVectors.push_back(temp);
384 392 }
385   - Unbind();
386   - int nxt = getCost();
387   - setMagnitude(samples[nxt]);
388   - file << position[0] << "," <<position[1] << "," << position[2] << "\n";
389 393 }
390 394  
391 395 //--------------------------------------------------------------------------//
... ... @@ -433,36 +437,40 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
433 437 stim::rect<float> hor;
434 438 stim::rect<float> ver;
435 439  
436   - //Default Constructor
  440 + ///Default Constructor
437 441 gl_spider
438 442 ()
439 443 {
440 444 setPosition(0.0,0.0,0.0);
441 445 setDirection(0.0,0.0,1.0);
442   - setMagnitude(0.03);
  446 + setMagnitude(1.0);
443 447 }
444 448  
445   - //temporary constructor for convenience, will be removed in further updates.
  449 + ///temporary constructor for convenience, will be removed in further updates.
446 450 gl_spider
447 451 (float pos_x, float pos_y, float pos_z, float dir_x, float dir_y, float dir_z,
448 452 float mag_x)
449 453 {
450   - setPosition(pos_x, pos_y, pos_z);
451   - setDirection(dir_x, dir_y, dir_z);
452   - setMagnitude(mag_x);
453   - }
454   -
455   - //Attached the spider to the texture with the given GLuint ID.
456   - //Samples in the default direction acting as the init method.
  454 + //setPosition(pos_x, pos_y, pos_z);
  455 + //setDirection(dir_x, dir_y, dir_z);
  456 + //setMagnitude(mag_x);
  457 + }
  458 + ///@param GLuint id texture that is going to be sampled.
  459 + ///@param numSamples number of samples per operation.
  460 + ///Attached the spider to the texture with the given GLuint ID.
  461 + ///Samples in the default direction acting as the init method.
457 462 void
458 463 attachSpider(GLuint id, int numSamples = 1089)
459 464 {
460 465 texID = id;
461 466 GenerateFBO(20, numSamples*10);
462   - sampleDirection();
  467 + //sampleDirection();
  468 + genDirectionVectors();
  469 + gl_texture<T>::setDims(0.6, 0.6, 1.0);
  470 + //gl_texture<T>::setDims(1.0, 1.0,1.0);
463 471 }
464 472  
465   - //temporary Method necessary for visualization and testing.
  473 + ///temporary Method necessary for visualization and testing.
466 474 void
467 475 Update()
468 476 {
... ... @@ -475,35 +483,39 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
475 483 hor.n());
476 484 }
477 485  
478   - //Returns the position vector.
  486 + ///Returns the position vector.
479 487 vec<float>
480 488 getPosition()
481 489 {
482 490 return position;
483 491 }
484 492  
485   - //Returns the direction vector.
  493 + ///Returns the direction vector.
486 494 vec<float>
487 495 getDirection()
488 496 {
489 497 return direction;
490 498 }
491 499  
492   - //Returns the magnitude vector.
  500 + ///Returns the magnitude vector.
493 501 vec<float>
494 502 getMagnitude()
495 503 {
496 504 return magnitude;
497 505 }
498 506  
499   - //Sets the position vector to input vector pos
  507 + ///@param vector pos, the new position.
  508 + ///Sets the position vector to input vector pos.
500 509 void
501 510 setPosition(vec<float> pos)
502 511 {
503 512 position = pos;
504 513 }
505   -
506   - //Sets the position vector to the input float coordinates x,y,z
  514 +
  515 + ///@param x x-coordinate.
  516 + ///@param y y-coordinate.
  517 + ///@param z z-coordinate.
  518 + ///Sets the position vector to the input float coordinates x,y,z.
507 519 void
508 520 setPosition(float x, float y, float z)
509 521 {
... ... @@ -513,14 +525,18 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
513 525 }
514 526  
515 527  
516   - //Sets the direction vector to input vector dir
  528 + ///@param vector dir, the new direction.
  529 + ///Sets the direction vector to input vector dir.
517 530 void
518 531 setDirection(vec<float> dir)
519 532 {
520 533 direction = dir;
521 534 }
522 535  
523   - //Sets the direction vector to the input float coordinates x,y,z
  536 + ///@param x x-coordinate.
  537 + ///@param y y-coordinate.
  538 + ///@param z z-coordinate.
  539 + ///Sets the direction vector to the input float coordinates x,y,z.
524 540 void
525 541 setDirection(float x, float y, float z)
526 542 {
... ... @@ -528,8 +544,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
528 544 direction[1] = y;
529 545 direction[2] = z;
530 546 }
531   -
532   - //Sets the magnitude vector to the input vector mag.
  547 +
  548 + ///@param vector dir, the new direction.
  549 + ///Sets the magnitude vector to the input vector mag.
533 550 void
534 551 setMagnitude(vec<float> mag)
535 552 {
... ... @@ -537,6 +554,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
537 554 magnitude[1] = mag[0];
538 555 }
539 556  
  557 + ///@param mag size of the sampled region.
  558 + ///Sets the magnitude vector to the input mag for both templates.
540 559 void
541 560 setMagnitude(float mag)
542 561 {
... ... @@ -544,7 +563,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
544 563 magnitude[1] = mag;
545 564 }
546 565  
547   - //temporary method for visualization.
  566 + ///temporary method for visualization.
548 567 GLuint
549 568 getFB()
550 569 {
... ... @@ -564,9 +583,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
564 583 /* Method for finding the best direction for the spider.
565 584 Uses the camera to rotate. Then Calls Evaluate to find new cost.
566 585 */
567   - sampleDirection();
568   - samplePosition();
569   - sampleMagnitude();
  586 + //sampleDirection();
  587 + //samplePosition();
  588 + //sampleMagnitude();
570 589 }
571 590  
572 591 /* Method for initializing the cuda devices, necessary only
... ...
stim/gl/gl_texture.h
  Show/Hide comments   View file @385d244
... ... @@ -31,13 +31,10 @@ template&lt;typename T&gt;
31 31 class gl_texture : public virtual image_stack<T>
32 32 {
33 33 private:
34   - /*
35   - Method: setTextureType
36   - Inputs:
37   - Outputs:
38   - Sets the internal texture_type, based on the data
39   - size. Either 3D, 2D, 1D textures.
40   - */
  34 +
  35 + ///Method: setTextureType
  36 + /// Sets the internal texture_type, based on the data
  37 + /// size. Either 3D, 2D, 1D textures.
41 38  
42 39 void
43 40 setTextureType()
... ... @@ -54,28 +51,22 @@ class gl_texture : public virtual image_stack&lt;T&gt;
54 51 GLuint texID; //OpenGL object
55 52 GLenum texture_type; //1D, 2D, 3D
56 53 using image_stack<T>::R;
  54 + using image_stack<T>::S;
57 55 using image_stack<T>::ptr;
58 56 using image_stack<T>::samples;
59 57  
60 58 public:
61 59  
62   - /*
63   - Method: Basic Constructor
64   - Inputs:
65   - Outputs:
66   - Creates an instance of the gl_texture object.
67   - */
  60 + ///Method: Basic Constructor
  61 + /// Creates an instance of the gl_texture object.
68 62 gl_texture()
69 63 {
70 64  
71 65 }
72 66  
73   - /*
74   - Method: Path Constructor
75   - Inputs: string file_path
76   - Outputs:
77   - Creates an instance of the gl_texture object with a path to the data.
78   - */
  67 + ///Method: Path Constructor
  68 + ///@param string file_path path to the directory with the files.
  69 + /// Creates an instance of the gl_texture object with a path to the data.
79 70  
80 71 gl_texture(std::string file_path)
81 72 {
... ... @@ -84,13 +75,34 @@ class gl_texture : public virtual image_stack&lt;T&gt;
84 75 setTextureType();
85 76 }
86 77  
87   - /*
88   - Method: setPath
89   - Inputs:string file_Path
90   - Outputs:
91   - sets the protected path variable of an instance of the gl_texture class
92   - to the method input.
93   - */
  78 +
  79 + ///Method:setDims
  80 + ///@param x size of the voxel in x direction
  81 + ///@param y size of the voxel in y direction
  82 + ///@param z size of the voxel in z direction
  83 + /// Sets the dimenstions of the voxels.
  84 + void
  85 + setDims(float x, float y, float z)
  86 + {
  87 + S[1] = x;
  88 + S[2] = y;
  89 + S[3] = z;
  90 + }
  91 +
  92 + ///Method:getDims
  93 + /// get the dimenstions of the voxels.
  94 +
  95 + vec<float>
  96 + getDims()
  97 + {
  98 + vec<float> dims(S[1], S[2], S[3]);
  99 + return dims;
  100 + }
  101 +
  102 + ///Method:setPath
  103 + ///@param file_Path location of the directory with the files
  104 + /// Sets the path and calls the loader on that path.
  105 +
94 106  
95 107 void
96 108 setPath(std::string file_path)
... ... @@ -100,12 +112,9 @@ class gl_texture : public virtual image_stack&lt;T&gt;
100 112 setTextureType();
101 113 }
102 114  
103   - /*
104   - Method: getPath
105   - Inputs:
106   - Outputs: string path
107   - Returns the path associated with an instance of the gl_texture class.
108   - */
  115 + ///Method: getPath
  116 + ///Outputs: string path
  117 + /// Returns the path associated with an instance of the gl_texture class.
109 118  
110 119 std::string
111 120 getPath()
... ... @@ -113,27 +122,20 @@ class gl_texture : public virtual image_stack&lt;T&gt;
113 122 return path;
114 123 }
115 124  
116   - /*
117   - Method: getTexture
118   - Inputs:
119   - Outputs: GLuint texID
120   - Returns the id of the texture create by/associated with the
121   - instance of the gl_texture class.
122   - */
  125 + ///Method: getTexture
  126 + ///Outputs: GLuint texID
  127 + /// Returns the id of the texture create by/associated with the
  128 + /// instance of the gl_texture class.
123 129  
124 130 GLuint
125 131 getTexture()
126 132 {
127 133 return texID;
128 134 }
129   -
130   - /*
131   - Method: createTexture
132   - Inputs:
133   - Outputs:
134   - Creates a texture and from the data located at <path> and
135   - assigns that texture to texID
136   - */
  135 +
  136 + ///Method: createTexture
  137 + /// Creates a texture and from the loaded data and
  138 + /// assigns that texture to texID
137 139 //TO DO :::: 1D textures
138 140 //TO DO:::add methods for handling the cases of T
139 141 // and convert them to GL equivalent.
... ... @@ -154,11 +156,11 @@ class gl_texture : public virtual image_stack&lt;T&gt;
154 156 {
155 157 case GL_TEXTURE_3D:
156 158 glTexParameteri(texture_type,
157   - GL_TEXTURE_WRAP_S, GL_REPEAT);
  159 + GL_TEXTURE_WRAP_S, GL_CLAMP_TO_EDGE);
158 160 glTexParameteri(texture_type,
159   - GL_TEXTURE_WRAP_T, GL_REPEAT);
  161 + GL_TEXTURE_WRAP_T, GL_CLAMP_TO_EDGE);
160 162 glTexParameteri(texture_type,
161   - GL_TEXTURE_WRAP_R, GL_REPEAT);
  163 + GL_TEXTURE_WRAP_R, GL_CLAMP_TO_EDGE);
162 164 glTexImage3D(texture_type,
163 165 0,
164 166 // GL_RGB16,
... ... @@ -190,15 +192,8 @@ class gl_texture : public virtual image_stack&lt;T&gt;
190 192 break;
191 193 }
192 194 }
193   - /*
194   - Temporary methods for debugging and testing are below.
195   - Self-explanatory.
196   - */
197   - stim::vec<unsigned long,4>
198   - getDims()
199   - {
200   - return R;
201   - }
  195 + ///Temporary methods for debugging and testing are below.
  196 + ///Self-explanatory.
202 197  
203 198 T*
204 199 getData()
... ...
stim/grids/grid.h
  Show/Hide comments   View file @385d244
... ... @@ -21,6 +21,7 @@ class grid{
21 21 protected:
22 22  
23 23 stim::vec<unsigned long, D> R; //elements in each dimension
  24 + stim::vec<float, D> S;
24 25 T* ptr; //pointer to the data (on the GPU or CPU)
25 26  
26 27 ///Return the total number of values in the binary file
... ... @@ -63,6 +64,12 @@ public:
63 64 init();
64 65 }
65 66  
  67 + void
  68 + setDim(stim::vec<float, D> s)
  69 + {
  70 + S = s;
  71 + }
  72 +
66 73 ///Constructor used to specify the grid size as a set of parameters
67 74  
68 75 /// @param X0... is a list of values describing the grid size along each dimension
... ... @@ -156,6 +163,7 @@ public:
156 163 ptr[p] = value;
157 164 }
158 165  
  166 +
159 167 ///Outputs grid data as a string
160 168 std::string str(){
161 169  
... ...
stim/grids/image_stack.h
  Show/Hide comments   View file @385d244
... ... @@ -17,6 +17,7 @@ class image_stack : public virtual stim::grid&lt;T, 4&gt;{
17 17 enum image_type {stimAuto, stimMono, stimRGB, stimRGBA};
18 18  
19 19 protected:
  20 + using stim::grid<T, 4>::S;
20 21 using stim::grid<T, 4>::R;
21 22 using stim::grid<T, 4>::ptr;
22 23 using stim::grid<T, 4>::samples;
... ... @@ -83,7 +84,19 @@ public:
83 84  
84 85 I.save(file_name);
85 86 }
86   -
  87 + ///Sets the dimensions of the image in each direction
  88 + ///Voxel-size.
  89 + /// @param x size in the x direction
  90 + /// @param y size in the y direction
  91 + /// @param z size in the z direction
  92 + void
  93 + set_dim(float x, float y, float z)
  94 + {
  95 + S[0] = 1;
  96 + S[1] = x;
  97 + S[2] = y;
  98 + S[3] = z;
  99 + }
87 100 ///Saves the entire stack to a set of images
88 101  
89 102 /// @param file_mask is the mask describing how the file names will be saved (ex. image????.bmp)
... ...