codebase / stimlib

Commit e45b97ced627871662615e182099a0dfba38cd7f

Authored by Pavel Govyadinov
1 parent d06d3dbd

safety commit, I broke something and couldn't go back because I didn't commit

Showing 3 changed files with 129 additions and 45 deletions   Show diff stats
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stim/cuda/branch_detection.cuh
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... ... @@ -111,6 +111,7 @@ find_branch(GLint texbufferID, GLenum texType, unsigned int x, unsigned int y)
111 111  
112 112  
113 113  
  114 + test(texbufferID, texType, x, y);
114 115 std::vector<stim::vec<float> > output;
115 116 initCuda(bytes_table, bytes_ds);
116 117  
... ... @@ -123,6 +124,8 @@ find_branch(GLint texbufferID, GLenum texType, unsigned int x, unsigned int y)
123 124 stim::cuda::tex_gaussian_blur2<float>(
124 125 gpuI, sigma, x, y, t.getTexture(), t.getArray()
125 126 );
  127 + stim::gpu2image<float>(gpuI, "Blur.jpg", x,y , 0, 255);
  128 +// stim::gpu2image<float>(t.getArray(), "ORIGINAL.jpg", x,y , 0, 255);
126 129 cudaDeviceSynchronize();
127 130  
128 131  
... ... @@ -146,12 +149,14 @@ find_branch(GLint texbufferID, GLenum texType, unsigned int x, unsigned int y)
146 149  
147 150 cudaDeviceSynchronize();
148 151 stim::cuda::gpu_local_max<float>(gpuCenters, gpuVote, final_t, conn, x, y);
  152 + stim::gpu2image<float>(gpuCenters, "Centers.jpg", x, y, 0, 1);
149 153 cudaMemcpy(cpuCenters, gpuCenters, bytes_ds, cudaMemcpyDeviceToHost);
  154 + stim::cpu2image<float>(cpuCenters, "CentersXPU.jpg", x, y, 0, 1);
150 155 for(int i = 0; i < pixels; i++)
151 156 {
152 157 int ix = (i % x);
153 158 int iy = (i / x);
154   - if((cpuCenters[i] == 1) && (ix > 4) && (ix < x-4))
  159 + if((cpuCenters[i] != 0))
155 160 {
156 161  
157 162 float x_v = (float) ix;
... ...
stim/cuda/testKernel.cuh
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... ... @@ -14,9 +14,9 @@
14 14 ///Initialization function, allocates the memory and passes the necessary
15 15 ///handles from OpenGL and Cuda.
16 16 ///@param DIM_Y --integer controlling how much memory to allocate.
17   - void initArray()
  17 + void initArray(int x, int y)
18 18 {
19   - cudaMalloc( (void**) &print, 216*16*sizeof(float)); ///temporary
  19 + cudaMalloc( (void**) &print, x*y*sizeof(float)); ///temporary
20 20 }
21 21  
22 22 ///Deinit function that frees the memery used and releases the texture resource
... ... @@ -48,12 +48,14 @@
48 48 {
49 49 int x = threadIdx.x + blockIdx.x * blockDim.x;
50 50 int y = threadIdx.y + blockIdx.y * blockDim.y;
51   - int idx = y*16+x;
  51 + int idx = y*64+x;
  52 +// int idx = y*32+x;
  53 +// int idx = y*16+x;
52 54  
53 55 float valIn = tex2D<unsigned char>(texIn, x, y);
54 56 float templa = templ(x);
55   - //print[idx] = abs(valIn); ///temporary
56   - print[idx] = abs(templa); ///temporary
  57 + print[idx] = valIn; ///temporary
  58 + //print[idx] = abs(templa); ///temporary
57 59  
58 60 }
59 61  
... ... @@ -64,7 +66,7 @@
64 66 ///@param GLenum texType --either GL_TEXTURE_1D, GL_TEXTURE_2D or GL_TEXTURE_3D
65 67 /// may work with other gl texture types, but untested.
66 68 ///@param DIM_Y, the number of samples in the template.
67   - void test(GLint texbufferID, GLenum texType)
  69 + void test(GLint texbufferID, GLenum texType, int x, int y)
68 70 {
69 71  
70 72 //Bind the Texture in GL and allow access to cuda.
... ... @@ -72,16 +74,12 @@
72 74  
73 75 //initialize the return arrays.
74 76  
75   - initArray();
76   -
77   - int x = 16;
78   - int y = 27*8;
79   - y = 8* 1089;
  77 + initArray(x,y);
  78 + dim3 numBlocks(1, y);
  79 + dim3 threadsPerBlock(x, 1);
80 80 int max_threads = stim::maxThreadsPerBlock();
81 81 //dim3 threads(max_threads, 1);
82 82 //dim3 blocks(x / threads.x + 1, y);
83   - dim3 numBlocks(1, 1089);
84   - dim3 threadsPerBlock(16, 8);
85 83 //dim3 numBlocks(2, 2);
86 84 //dim3 threadsPerBlock(8, 108);
87 85  
... ... @@ -92,7 +90,7 @@
92 90 cudaDeviceSynchronize();
93 91 stringstream name; //for debugging
94 92 name << "FromTex.bmp";
95   - stim::gpu2image<float>(print, name.str(),16,1089*8,0,1.0);
  93 + stim::gpu2image<float>(print, name.str(),x,y,0,255);
96 94  
97 95 tx.UnmapCudaTexture();
98 96 cleanUP();
... ...
stim/gl/gl_spider.h
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... ... @@ -23,6 +23,7 @@
23 23 #include <stim/cuda/branch_detection.cuh>
24 24 #include "../../../volume-spider/fiber.h"
25 25 #include "../../../volume-spider/glnetwork.h"
  26 +#include <stim/visualization/cylinder.h>
26 27 //#include <stim/cuda/testKernel.cuh>
27 28  
28 29 //#include <stim/cuda/testKernel.cuh>
... ... @@ -218,6 +219,37 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
218 219  
219 220 }
220 221  
  222 +
  223 + void
  224 + branchDetection2(int n = 8, int l_template = 8, int l_square = 8)
  225 + {
  226 + if(cL.size() < 4){}
  227 + else{
  228 + setMatrix(1);
  229 + DrawLongCylinder(n, l_template, l_square);
  230 + stim::cylinder<float> cyl(cL, cM);
  231 + std::vector< stim::vec<float> > result = find_branch(btexbufferID, GL_TEXTURE_2D, n*l_square, (cL.size()-1)*l_template);
  232 + std::cerr << "the number of points is " << result.size() << std::endl;
  233 + if(!result.empty())
  234 + {
  235 + for(int i = 0; i < result.size(); i++)
  236 + {
  237 + std::cout << "Testing "<< i << ": " << result[i][0] << ", " << result[i][1] << std::endl;
  238 + stim::vec<float> v = cyl.surf(result[i][0], result[i][1]*360);
  239 + std::cout << v[0] << " ," << v[1] << " ," << v[2] << std::endl;
  240 + stim::vec<float> di = cyl.p(result[i][0]);
  241 + std::cout << di[0] << " ," << di[1] << " ," << di[2] << std::endl;
  242 + float rad = cyl.r(result[i][0]);
  243 + std::cout << rad << std::endl;
  244 + setSeed(v);
  245 + setSeedVec(stim::vec<float>(-di[0]+v[0], -di[1]+v[1], -di[2]+v[2]).norm());
  246 + setSeedMag(cyl.r(result[i][0]));
  247 + }
  248 + }
  249 + std::cout << "I ran the new branch detection" << std::endl;
  250 + }
  251 + }
  252 +
221 253  
222 254 //--------------------------------------------------------------------------//
223 255 //---------------------TEMPLATE CREATION METHODS----------------------------//
... ... @@ -459,6 +491,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
459 491 void
460 492 GenerateFBO(unsigned int width, unsigned int height, GLuint &textureID, GLuint &framebufferID)
461 493 {
  494 + glDeleteFramebuffers(1, &framebufferID);
462 495 glGenFramebuffers(1, &framebufferID);
463 496 glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);
464 497 int numChannels = 1;
... ... @@ -506,45 +539,60 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
506 539 }
507 540  
508 541  
  542 + ///IF type == 0
509 543 ///Method for using the gl manipulation to align templates from
510 544 ///Template space (-0.5 0.5) to Texture space (0.0, 1.0),
511 545 ///Based on the p of the spider in real space (arbitrary).
  546 +
  547 + ///IF type == 1
  548 + ///Method for using the gl manipulation to set up a matrix
  549 + ///To transform from tissue space into texture space.
  550 + ///All transformation happen in glMatrixMode(GL_TEXTURE).
512 551 ///All transformation happen in glMatrixMode(GL_TEXTURE).
513   - void setMatrix()
  552 + void setMatrix(int type = 0)
514 553 {
515   - float curTrans[16]; //array to store the matrix values.
516   - stim::vec<float> rot = getRotation(d); //get the rotation parameters for the current direction vector.
517   - glMatrixMode(GL_TEXTURE);
518   - glLoadIdentity();
  554 + if(type == 0)
  555 + {
  556 + float curTrans[16]; //array to store the matrix values.
  557 + stim::vec<float> rot = getRotation(d); //get the rotation parameters for the current direction vector.
  558 + glMatrixMode(GL_TEXTURE);
  559 + glLoadIdentity();
519 560  
520   - //Scale by the voxel size and number of slices.
521   - glScalef(1.0/S[0]/R[0], 1.0/S[1]/R[1], 1.0/S[2]/R[2]);
522   - //translate to the current position of the spider in the texture.
523   - glTranslatef(p[0],
524   - p[1],
525   - p[2]);
526   - //rotate to the current direction of the spider.
527   - glRotatef(rot[0], rot[1], rot[2], rot[3]);
528   - //scale to the magnitude of the spider.
529   - glScalef(m[0],
530   - m[0],
531   - m[0]);
532   - //get and store the current transformation matrix for later use.
533   - glGetFloatv(GL_TEXTURE_MATRIX, curTrans);
534   - cT.set(curTrans);
535   - // printTransform();
536   -
537   - CHECK_OPENGL_ERROR
538   - //revert back to default gl mode.
539   - glMatrixMode(GL_MODELVIEW);
  561 + //Scale by the voxel size and number of slices.
  562 + glScalef(1.0/S[0]/R[0], 1.0/S[1]/R[1], 1.0/S[2]/R[2]);
  563 + //translate to the current position of the spider in the texture.
  564 + glTranslatef(p[0],
  565 + p[1],
  566 + p[2]);
  567 + //rotate to the current direction of the spider.
  568 + glRotatef(rot[0], rot[1], rot[2], rot[3]);
  569 + //scale to the magnitude of the spider.
  570 + glScalef(m[0],
  571 + m[0],
  572 + m[0]);
  573 + //get and store the current transformation matrix for later use.
  574 + glGetFloatv(GL_TEXTURE_MATRIX, curTrans);
  575 + cT.set(curTrans);
  576 + // printTransform();
  577 +
  578 + CHECK_OPENGL_ERROR
  579 + //revert back to default gl mode.
  580 + glMatrixMode(GL_MODELVIEW);
  581 + }
  582 + else if(type == 1)
  583 + {
  584 + glMatrixMode(GL_TEXTURE);
  585 + glLoadIdentity();
  586 + glScalef(1.0/S[0]/R[0], 1.0/S[1]/R[1], 1.0/S[2]/R[2]);
  587 + glMatrixMode(GL_MODELVIEW);
  588 + }
540 589 }
541 590  
542 591 ///Method for controling the buffer and texture binding.
543 592 ///Clears the buffer upon binding.
544 593 void
545   - Bind()
  594 + Bind(float len = 8.0)
546 595 {
547   - float len = 8.0;
548 596 glBindFramebuffer(GL_FRAMEBUFFER, fboID);//set up GL buffer
549 597 glFramebufferTexture2D(
550 598 GL_FRAMEBUFFER,
... ... @@ -576,9 +624,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
576 624 ///@param GLuint &framebufferID, framebuffer used for storage.
577 625 ///@param int nSamples, number of rectanges to create.
578 626 void
579   - Bind(GLuint &textureID, GLuint &framebufferID, int nSamples)
  627 + Bind(GLuint &textureID, GLuint &framebufferID, int nSamples, float len = 8.0)
580 628 {
581   - float len = 8.0;
582 629 glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);//set up GL buffer
583 630 glFramebufferTexture2D(
584 631 GL_FRAMEBUFFER,
... ... @@ -1216,6 +1263,36 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1216 1263 glEnd();
1217 1264 glEndList();
1218 1265 }
  1266 +
  1267 + void
  1268 + DrawLongCylinder(int n = 8, int l_template = 8,int l_square = 8)
  1269 + {
  1270 + int cylLen = cL.size()-1;
  1271 + GenerateFBO(n*l_square, cylLen*l_template, btexbufferID, bfboID);
  1272 + Bind(btexbufferID, bfboID, cylLen, l_template*l_square/2.0);
  1273 + stim::cylinder<float> cyl(cL, cM);
  1274 + std::vector<std::vector<stim::vec<float> > > p = cyl.getPoints(n);
  1275 + for(int i = 0; i < p.size()-1; i++) ///number of circles
  1276 + {
  1277 + for(int j = 0; j < p[0].size()-1; j++) ///points in the circle
  1278 + {
  1279 + glBegin(GL_QUADS);
  1280 + glTexCoord3f(p[i][j][0], p[i][j][1], p[i][j][2]);
  1281 + glVertex2f(j*l_square, i*(float)l_template);
  1282 +
  1283 + glTexCoord3f(p[i][j+1][0], p[i][j+1][1], p[i][j+1][2]);
  1284 + glVertex2f(j*l_square+l_square, i*(float)l_template);
  1285 +
  1286 + glTexCoord3f(p[i+1][j+1][0], p[i+1][j+1][1], p[i+1][j+1][2]);
  1287 + glVertex2f(j*l_square+l_square, i*(float)l_template+(float)l_template);
  1288 +
  1289 + glTexCoord3f(p[i+1][j][0], p[i+1][j][1], p[i+1][j][2]);
  1290 + glVertex2f(j*l_square,i*(float)l_template+(float)l_template);
  1291 + glEnd();
  1292 + }
  1293 + }
  1294 + Unbind();
  1295 + }
1219 1296  
1220 1297  
1221 1298 ///@param min_cost the cost value used for tracing
... ... @@ -1515,6 +1592,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1515 1592 if (cost > min_cost){
1516 1593 running = false;
1517 1594 sk.End();
  1595 + branchDetection2();
1518 1596 pair<stim::fiber<float>, int> a(stim::fiber<float> (cL, cM), -1);
1519 1597 addToNetwork(a, spos, smag, sdir);
1520 1598 return a;
... ... @@ -1529,6 +1607,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1529 1607 // std::cout << "Found Edge" << std::endl;
1530 1608 running = false;
1531 1609 sk.End();
  1610 + branchDetection2();
1532 1611 pair<stim::fiber<float>, int> a(stim::fiber<float> (cL, cM), -1);
1533 1612 addToNetwork(a, spos, smag, sdir);
1534 1613 return a;
... ... @@ -1548,6 +1627,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1548 1627 // std::cout << "Magnitude Limit" << std::endl;
1549 1628 running = false;
1550 1629 sk.End();
  1630 + branchDetection2();
1551 1631 pair<stim::fiber<float>, int> a(stim::fiber<float> (cL, cM), -1);
1552 1632 addToNetwork(a, spos, smag, sdir);
1553 1633 return a;
... ... @@ -1560,6 +1640,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1560 1640 if(h != -1){
1561 1641 running = false;
1562 1642 sk.End();
  1643 + branchDetection2();
1563 1644 pair<stim::fiber<float>, int> a(stim::fiber<float> (cL, cM), h);
1564 1645 addToNetwork(a, spos, smag, sdir);
1565 1646 return a;
... ... @@ -1574,7 +1655,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1574 1655 sk.Vertex(p[0], p[1], p[2]);
1575 1656 Bind(btexbufferID, bfboID, 27);
1576 1657 CHECK_OPENGL_ERROR
1577   - branchDetection();
  1658 +// branchDetection();
1578 1659 CHECK_OPENGL_ERROR
1579 1660 Unbind();
1580 1661 CHECK_OPENGL_ERROR
... ...