codebase / stimlib

Commit ad9345728682e41b55856cb4f4572bba8738096a

Authored by David Mayerich
2 parents d11e2fb6 fac43319

Merge branch 'master' of git.stim.ee.uh.edu:codebase/stimlib

Showing 9 changed files with 685 additions and 748 deletions   Show diff stats
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stim/biomodels/fiber.h renamed to stim/biomodels/centerline.h
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1 -#ifndef STIM_FIBER_H  
2 -#define STIM_FIBER_H 1 +#ifndef STIM_CENTERLINE_H
  2 +#define STIM_CENTERLINE_H
3 3
4 #include <vector> 4 #include <vector>
5 -#include <ANN/ANN.h> 5 +#include <stim/math/vec3.h>
  6 +//#include <ANN/ANN.h>
6 7
7 namespace stim{ 8 namespace stim{
8 9
@@ -11,22 +12,19 @@ namespace stim{ @@ -11,22 +12,19 @@ namespace stim{
11 * class to describe an interconnected (often biological) network. 12 * class to describe an interconnected (often biological) network.
12 */ 13 */
13 template<typename T> 14 template<typename T>
14 -class fiber{ 15 +class centerline{
15 16
16 protected: 17 protected:
17 unsigned int N; //number of points in the fiber 18 unsigned int N; //number of points in the fiber
18 double **c; //centerline (array of double pointers) 19 double **c; //centerline (array of double pointers)
19 -  
20 - T* r; // array of fiber radii  
21 - ANNkd_tree* kdt; //kd-tree stores all points in the fiber for fast searching 20 +// ANNkd_tree* kdt; //kd-tree stores all points in the fiber for fast searching
22 21
23 /// Initialize an empty fiber 22 /// Initialize an empty fiber
24 void init() 23 void init()
25 { 24 {
26 - kdt = NULL;  
27 - c=NULL;  
28 - r=NULL;  
29 N=0; 25 N=0;
  26 + c=NULL;
  27 +// kdt = NULL;
30 } 28 }
31 29
32 /// Initialize a fiber with N centerline points (all located at [0, 0, 0] with radius 0) 30 /// Initialize a fiber with N centerline points (all located at [0, 0, 0] with radius 0)
@@ -34,19 +32,17 @@ protected: @@ -34,19 +32,17 @@ protected:
34 { 32 {
35 33
36 N = n; //set the number of points 34 N = n; //set the number of points
37 - kdt = NULL; 35 +// kdt = NULL;
38 c = (double**) malloc(sizeof(double*) * N); //allocate the array pointer 36 c = (double**) malloc(sizeof(double*) * N); //allocate the array pointer
39 37
40 for(unsigned int i = 0; i < N; i++) //allocate space for each point 38 for(unsigned int i = 0; i < N; i++) //allocate space for each point
41 c[i] = (double*) malloc(sizeof(double) * 3); 39 c[i] = (double*) malloc(sizeof(double) * 3);
42 -  
43 - r = (T*) malloc(sizeof(T) * N); //allocate space for the radii  
44 } 40 }
45 41
46 /// Copies an existing fiber to the current fiber 42 /// Copies an existing fiber to the current fiber
47 43
48 /// @param cpy stores the new copy of the fiber 44 /// @param cpy stores the new copy of the fiber
49 - void copy( const stim::fiber<T>& cpy ){ 45 + void copy( const stim::centerline<T>& cpy, bool kd = 0){
50 46
51 ///allocate space for the new fiber 47 ///allocate space for the new fiber
52 init(cpy.N); 48 init(cpy.N);
@@ -55,20 +51,18 @@ protected: @@ -55,20 +51,18 @@ protected:
55 for(unsigned int i = 0; i < N; i++){ 51 for(unsigned int i = 0; i < N; i++){
56 for(unsigned int d = 0; d < 3; d++) //for each dimension 52 for(unsigned int d = 0; d < 3; d++) //for each dimension
57 c[i][d] = cpy.c[i][d]; //copy the coordinate 53 c[i][d] = cpy.c[i][d]; //copy the coordinate
58 -  
59 - r[i] = cpy.r[i]; //copy the radius  
60 } 54 }
61 -  
62 - gen_kdtree(); //generate the kd tree for the new fiber 55 +// if(kd)
  56 +// gen_kdtree(); //generate the kd tree for the new fiber
63 } 57 }
64 58
65 /// generate a KD tree for points on fiber 59 /// generate a KD tree for points on fiber
66 - void gen_kdtree()  
67 - {  
68 - int n_data = N; //create an array of data points  
69 - ANNpointArray pts = (ANNpointArray)c; //cast the centerline list to an ANNpointArray  
70 - kdt = new ANNkd_tree(pts, n_data, 3); //build a KD tree  
71 - } 60 +// void gen_kdtree()
  61 +// {
  62 +// int n_data = N; //create an array of data points
  63 +// ANNpointArray pts = (ANNpointArray)c; //cast the centerline list to an ANNpointArray
  64 +// kdt = new ANNkd_tree(pts, n_data, 3); //build a KD tree
  65 +// }
72 66
73 /// find distance between two points 67 /// find distance between two points
74 double dist(double* p0, double* p1){ 68 double dist(double* p0, double* p1){
@@ -79,7 +73,6 @@ protected: @@ -79,7 +73,6 @@ protected:
79 { 73 {
80 v = p1[d] - p0[d]; 74 v = p1[d] - p0[d];
81 sum +=v * v; 75 sum +=v * v;
82 -  
83 } 76 }
84 return sqrt(sum); 77 return sqrt(sum);
85 } 78 }
@@ -87,21 +80,18 @@ protected: @@ -87,21 +80,18 @@ protected:
87 /// This function retreives the index for the fiber point closest to q 80 /// This function retreives the index for the fiber point closest to q
88 81
89 /// @param q is a reference point used to find the closest point on the fiber center line 82 /// @param q is a reference point used to find the closest point on the fiber center line
90 - unsigned int ann( stim::vec<double> q ){  
91 -  
92 - ANNidxArray idx = new ANNidx[1]; //variable used to hold the nearest point  
93 - ANNdistArray sq_dist = new ANNdist[1]; //variable used to hold the squared distance to the nearest point  
94 -  
95 - kdt->annkSearch(q.data(), 1, idx, sq_dist); //search the KD tree for the nearest neighbor  
96 -  
97 - return *idx;  
98 - } 83 +// unsigned int ann( stim::vec<double> q ){
  84 +// ANNidxArray idx = new ANNidx[1]; //variable used to hold the nearest point
  85 +// ANNdistArray sq_dist = new ANNdist[1]; //variable used to hold the squared distance to the nearest point
  86 +// kdt->annkSearch(q.data(), 1, idx, sq_dist); //search the KD tree for the nearest neighbor
  87 +// return *idx;
  88 +// }
99 89
100 /// Returns a stim::vec representing the point at index i 90 /// Returns a stim::vec representing the point at index i
101 91
102 /// @param i is an index of the desired centerline point 92 /// @param i is an index of the desired centerline point
103 stim::vec<T> get_vec(unsigned i){ 93 stim::vec<T> get_vec(unsigned i){
104 - stim::vec<T> r; 94 + stim::vec3<T> r;
105 r.resize(3); 95 r.resize(3);
106 r[0] = c[i][0]; 96 r[0] = c[i][0];
107 r[1] = c[i][1]; 97 r[1] = c[i][1];
@@ -113,25 +103,23 @@ protected: @@ -113,25 +103,23 @@ protected:
113 103
114 public: 104 public:
115 105
116 - fiber(){ 106 + centerline(){
117 init(); 107 init();
118 } 108 }
119 109
120 /// Copy constructor 110 /// Copy constructor
121 - fiber(const stim::fiber<T> &obj){  
122 - 111 + centerline(const stim::centerline<T> &obj){
123 copy(obj); 112 copy(obj);
124 -  
125 } 113 }
126 114
127 //temp constructor for graph visualization 115 //temp constructor for graph visualization
128 - fiber(int n) 116 + centerline(int n)
129 { 117 {
130 init(n); 118 init(n);
131 } 119 }
132 120
133 /// Constructor takes a list of stim::vec points, the radius at each point is set to zero 121 /// Constructor takes a list of stim::vec points, the radius at each point is set to zero
134 - fiber(std::vector< stim::vec<T> > p){ 122 + centerline(std::vector< stim::vec<T> > p, bool kd = 0){
135 init(p.size()); //initialize the fiber 123 init(p.size()); //initialize the fiber
136 124
137 //for each point, set the centerline position and radius 125 //for each point, set the centerline position and radius
@@ -142,200 +130,77 @@ public: @@ -142,200 +130,77 @@ public:
142 c[i][d] = (double) p[i][d]; 130 c[i][d] = (double) p[i][d];
143 131
144 //set the radius 132 //set the radius
145 - r[i] = 0;  
146 } 133 }
147 -  
148 //generate a kd tree 134 //generate a kd tree
149 - gen_kdtree(); 135 +// if(kd)
  136 +// gen_kdtree();
150 } 137 }
151 138
152 - /// constructor takes a list of points and radii  
153 - fiber(std::vector< stim::vec< T > > pos, std::vector< T > radii){ 139 + /// constructor takes a list of points
  140 + centerline(std::vector< stim::vec3< T > > pos, bool kd = 0){
154 init(pos.size()); //initialize the fiber 141 init(pos.size()); //initialize the fiber
155 142
156 //for each point, set the centerline position and radius 143 //for each point, set the centerline position and radius
157 for(unsigned int i = 0; i < N; i++){ 144 for(unsigned int i = 0; i < N; i++){
158 -  
159 //set the centerline position 145 //set the centerline position
160 for(unsigned int d = 0; d < 3; d++) 146 for(unsigned int d = 0; d < 3; d++)
161 c[i][d] = (double) pos[i][d]; 147 c[i][d] = (double) pos[i][d];
162 -  
163 //set the radius 148 //set the radius
164 - r[i] = radii[i];  
165 } 149 }
166 150
167 //generate a kd tree 151 //generate a kd tree
168 - gen_kdtree();  
169 - }  
170 -  
171 - /// constructor takes an array of points and radii  
172 - // this function is used when the radii are represented as a stim::vec,  
173 - // since this may be easier when importing OBJs  
174 - fiber(std::vector< stim::vec<T> > pos, std::vector< stim::vec<T> > radii){  
175 -  
176 - init(pos.size());  
177 -  
178 - //for each point, set the position and radius  
179 - for(unsigned int i = 0; i < N; i++){  
180 - //at(i) = (double*)malloc(sizeof(double) * 3);  
181 - for(unsigned int d = 0; d < 3; d++)  
182 - c[i][d] = (double) pos[i][d];  
183 -  
184 - r[i] = radii[i][(unsigned int)0];  
185 - }  
186 -  
187 - gen_kdtree(); 152 + //if(kd)
  153 + // gen_kdtree();
188 } 154 }
189 155
190 /// Assignment operation 156 /// Assignment operation
191 - fiber& operator=(const fiber &rhs){  
192 - 157 + centerline& operator=(const centerline &rhs){
193 if(this == &rhs) return *this; //test for and handle self-assignment 158 if(this == &rhs) return *this; //test for and handle self-assignment
194 -  
195 copy(rhs); 159 copy(rhs);
  160 + return *this;
196 } 161 }
197 162
198 - /// Calculate the length of the fiber and return it.  
199 - double length(){  
200 -  
201 - double* p0;  
202 - double *p1;  
203 - double l = 0; //initialize the length to zero  
204 -  
205 - //for each point  
206 - //typename std::list< point<T> >::iterator i; //create a point iterator  
207 - for(unsigned int i = 0; i < N; i++){ //for each point in the fiber  
208 -  
209 - if(i == 0) //if this is the first point, just store it  
210 - p1 = c[0];  
211 - else{ //if this is any other point  
212 - p0 = p1; //shift p1->p0  
213 - p1 = c[i]; //set p1 to the new point  
214 - l += dist(p0, p1); //add the length of p1 - p0 to the running sum  
215 - }  
216 - }  
217 -  
218 - return l; //return the length  
219 - }  
220 -  
221 - /// Calculates the length and average radius of the fiber  
222 -  
223 - /// @param length is filled with the fiber length  
224 - T radius(T& length){  
225 -  
226 - double* p0; //temporary variables to store point positions  
227 - double* p1;  
228 - T r0, r1; //temporary variables to store radii at points  
229 - double l;  
230 - T r_mean; //temporary variable to store the length and average radius of a fiber segment  
231 - double length_sum = 0; //initialize the length to zero  
232 - T radius_sum = 0; //initialize the radius sum to zero  
233 -  
234 - //for each point  
235 - //typename std::list< point<T> >::iterator i; //create a point iterator  
236 - for(unsigned int i = 0; i < N; i++){ //for each point in the fiber  
237 -  
238 - if(i == 0){ //if this is the first point, just store it  
239 - p1 = c[0];  
240 - r1 = r[0];  
241 - }  
242 - else{ //if this is any other point  
243 - p0 = p1; //shift p1->p0 and r1->r0  
244 - r0 = r1;  
245 - p1 = c[i]; //set p1 to the new point  
246 - r1 = r[i];  
247 -  
248 - l = dist(p0, p1); //calculate the length of the p0-p1 segment  
249 - r_mean = (r0 + r1) / 2; //calculate the average radius of the segment  
250 -  
251 - radius_sum += r_mean * (T) l; //add the radius scaled by the length to a running sum  
252 - length_sum += l; //add the length of p1 - p0 to the running sum  
253 - }  
254 - }  
255 -  
256 - length = length_sum; //store the total length  
257 -  
258 - //if the total length is zero, store a radius of zero  
259 - if(length == 0)  
260 - return 0;  
261 - else  
262 - return (T)(radius_sum / length); //return the average radius of the fiber  
263 - }  
264 - T average_radius()  
265 - {  
266 - T r_sum = 0.;  
267 - for(unsigned int i = 0; i < N; i++)  
268 - {  
269 - r_sum = r_sum + r[i];  
270 - }  
271 - return r_sum/((T) N);  
272 - }  
273 -  
274 - /// Calculates the average radius of the fiber  
275 - T radius(){  
276 - T length;  
277 - return radius(length);  
278 - }  
279 -  
280 - /// Returns the radius at index idx.  
281 - T radius(int idx){  
282 - return r[idx];  
283 - }  
284 163
285 /// Return the point on the fiber closest to q 164 /// Return the point on the fiber closest to q
286 /// @param q is the query point used to locate the nearest point on the fiber centerline 165 /// @param q is the query point used to locate the nearest point on the fiber centerline
287 - stim::vec<T> nearest(stim::vec<T> q){  
288 -  
289 - stim::vec<double> temp( (double) q[0], (double) q[1], (double) q[2]);  
290 -  
291 - unsigned int idx = ann(temp); //determine the index of the nearest neighbor  
292 -  
293 - return stim::vec<T>((T) c[idx][0], (T) c[idx][1], (T) c[idx][2]); //return the nearest centerline point  
294 - } 166 +// stim::vec<T> nearest(stim::vec<T> q){
  167 +//
  168 +// stim::vec<double> temp( (double) q[0], (double) q[1], (double) q[2]);
  169 +//
  170 +// unsigned int idx = ann(temp); //determine the index of the nearest neighbor
  171 +//
  172 +// return stim::vec<T>((T) c[idx][0], (T) c[idx][1], (T) c[idx][2]); //return the nearest centerline point
  173 +// }
295 174
296 /// Return the point index on the fiber closest to q 175 /// Return the point index on the fiber closest to q
297 /// @param q is the query point used to locate the nearest point on the fiber centerline 176 /// @param q is the query point used to locate the nearest point on the fiber centerline
298 - unsigned int nearest_idx(stim::vec<T> q){  
299 -  
300 - stim::vec<double> temp((double) q[0], (double) q[1], (double) q[2]);  
301 -  
302 - unsigned int idx = ann(temp); //determine the index of the nearest neighbor  
303 -  
304 - return idx; //return the nearest centerline point index  
305 - } 177 +// unsigned int nearest_idx(stim::vec<T> q){
  178 +//
  179 +// stim::vec<double> temp((double) q[0], (double) q[1], (double) q[2]);
  180 +//
  181 +// unsigned int idx = ann(temp); //determine the index of the nearest neighbor
  182 +//
  183 +// return idx; //return the nearest centerline point index
  184 +// }
306 185
307 /// Returns the fiber centerline as an array of stim::vec points 186 /// Returns the fiber centerline as an array of stim::vec points
308 - std::vector< stim::vec<T> > centerline(){ 187 + std::vector< stim::vec<T> > get_centerline(){
309 188
310 //create an array of stim vectors 189 //create an array of stim vectors
311 - std::vector< stim::vec<T> > pts(N); 190 + std::vector< stim::vec3<T> > pts(N);
312 191
313 //cast each point to a stim::vec, keeping only the position information 192 //cast each point to a stim::vec, keeping only the position information
314 for(unsigned int i = 0; i < N; i++) 193 for(unsigned int i = 0; i < N; i++)
315 - pts[i] = stim::vec<T>((T) c[i][0], (T) c[i][1], (T) c[i][2]);  
316 -  
317 - //return the centerline array  
318 - return pts;  
319 - }  
320 -  
321 - /// Returns the fiber centerline magnitudes as an array of stim::vec points  
322 - std::vector< stim::vec<T> > centerlinemag(){  
323 -  
324 - //create an array of stim vectors  
325 - std::vector< stim::vec<T> > pts(N);  
326 -  
327 - //cast each point to a stim::vec, keeping only the position information  
328 - for(unsigned int i = 0; i < N; i++)  
329 - pts[i] = stim::vec<T>(r[i], r[i]);; 194 + pts[i] = stim::vec3<T>((T) c[i][0], (T) c[i][1], (T) c[i][2]);
330 195
331 //return the centerline array 196 //return the centerline array
332 return pts; 197 return pts;
333 } 198 }
334 199
335 /// Split the fiber at the specified index. If the index is an end point, only one fiber is returned 200 /// Split the fiber at the specified index. If the index is an end point, only one fiber is returned
336 - std::vector< stim::fiber<T> > split(unsigned int idx){ 201 + std::vector< stim::centerline<T> > split(unsigned int idx){
337 202
338 - std::vector< stim::fiber<T> > fl; //create an array to store up to two fibers 203 + std::vector< stim::centerline<T> > fl; //create an array to store up to two fibers
339 204
340 //if the index is an end point, only the existing fiber is returned 205 //if the index is an end point, only the existing fiber is returned
341 if(idx == 0 || idx == N-1){ 206 if(idx == 0 || idx == N-1){
@@ -361,14 +226,13 @@ public: @@ -361,14 +226,13 @@ public:
361 for(i = 0; i < N1; i++){ //for each centerline point 226 for(i = 0; i < N1; i++){ //for each centerline point
362 for(d = 0; d < 3; d++) 227 for(d = 0; d < 3; d++)
363 fl[0].c[i][d] = c[i][d]; //copy each coordinate 228 fl[0].c[i][d] = c[i][d]; //copy each coordinate
364 - fl[0].r[i] = r[i]; //copy the corresponding radius  
365 } 229 }
366 230
367 //second half 231 //second half
368 for(i = 0; i < N2; i++){ 232 for(i = 0; i < N2; i++){
369 for(d = 0; d < 3; d++) 233 for(d = 0; d < 3; d++)
370 fl[1].c[i][d] = c[idx + i][d]; 234 fl[1].c[i][d] = c[idx + i][d];
371 - fl[1].r[i] = r[idx + i]; 235 +
372 } 236 }
373 } 237 }
374 238
@@ -379,7 +243,7 @@ public: @@ -379,7 +243,7 @@ public:
379 /// Calculates the set of fibers resulting from a connection between the current fiber and a fiber f 243 /// Calculates the set of fibers resulting from a connection between the current fiber and a fiber f
380 244
381 /// @param f is the fiber that will be connected to the current fiber 245 /// @param f is the fiber that will be connected to the current fiber
382 - std::vector< stim::fiber<T> > connect( stim::fiber<T> &f, double dist){ 246 +/* std::vector< stim::centerline<T> > connect( stim::centerline<T> &f, double dist){
383 247
384 double min_dist; 248 double min_dist;
385 unsigned int idx0, idx1; 249 unsigned int idx0, idx1;
@@ -393,7 +257,7 @@ public: @@ -393,7 +257,7 @@ public:
393 257
394 258
395 } 259 }
396 - 260 +*/
397 /// Outputs the fiber as a string 261 /// Outputs the fiber as a string
398 std::string str(){ 262 std::string str(){
399 std::stringstream ss; 263 std::stringstream ss;
@@ -405,7 +269,6 @@ public: @@ -405,7 +269,6 @@ public:
405 for(unsigned int d = 0; d < 3; d++){ 269 for(unsigned int d = 0; d < 3; d++){
406 ss<<c[i][d]<<" "; 270 ss<<c[i][d]<<" ";
407 } 271 }
408 - ss<<"] r = "<<r[i]<<std::endl;  
409 } 272 }
410 273
411 return ss.str(); 274 return ss.str();
@@ -428,7 +291,7 @@ public: @@ -428,7 +291,7 @@ public:
428 return get_vec(N-1); 291 return get_vec(N-1);
429 } 292 }
430 ////resample a fiber in the network 293 ////resample a fiber in the network
431 - stim::fiber<T> resample(T spacing) 294 + stim::centerline<T> resample(T spacing)
432 { 295 {
433 std::cout<<"fiber::resample()"<<std::endl; 296 std::cout<<"fiber::resample()"<<std::endl;
434 297
@@ -468,7 +331,7 @@ public: @@ -468,7 +331,7 @@ public:
468 newPointList.push_back(fiberPositions[f+1]); 331 newPointList.push_back(fiberPositions[f+1]);
469 } 332 }
470 newPointList.push_back(fiberPositions[N-1]); //add the last point on the fiber to the new fiber list 333 newPointList.push_back(fiberPositions[N-1]); //add the last point on the fiber to the new fiber list
471 - fiber newFiber(newPointList); 334 + centerline newFiber(newPointList);
472 return newFiber; 335 return newFiber;
473 } 336 }
474 337
stim/cuda/testKernel.cuh
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@@ -8,7 +8,7 @@ @@ -8,7 +8,7 @@
8 #include <stim/cuda/cudatools/devices.h> 8 #include <stim/cuda/cudatools/devices.h>
9 #include <stim/cuda/cudatools/threads.h> 9 #include <stim/cuda/cudatools/threads.h>
10 #include <stim/cuda/cuda_texture.cuh> 10 #include <stim/cuda/cuda_texture.cuh>
11 - stim::cuda::cuda_texture tx; //texture object. 11 +
12 float* print; 12 float* print;
13 13
14 ///Initialization function, allocates the memory and passes the necessary 14 ///Initialization function, allocates the memory and passes the necessary
@@ -26,16 +26,16 @@ @@ -26,16 +26,16 @@
26 cudaFree(print); ///temporary 26 cudaFree(print); ///temporary
27 } 27 }
28 28
29 - __device__  
30 - float templ(int x)  
31 - {  
32 - if(x < 32/6 || x > 32*5/6 || (x > 32*2/6 && x < 32*4/6)){  
33 - return 1.0;  
34 - }else{  
35 - return 0.0;  
36 - }  
37 -  
38 - } 29 + __device__
  30 + float templ(int x, int max_x)
  31 + {
  32 + if(x < max_x/6 || x > max_x*5/6 || (x > max_x*2/6 && x < max_x*4/6))
  33 + {
  34 + return 1.0;
  35 + }else{
  36 + return 0.0;
  37 + }
  38 + }
39 39
40 ///Find the difference of the given set of samples and the template 40 ///Find the difference of the given set of samples and the template
41 ///using cuda acceleration. 41 ///using cuda acceleration.
@@ -44,33 +44,24 @@ @@ -44,33 +44,24 @@
44 ///@param float* result --a pointer to the memory that stores the result. 44 ///@param float* result --a pointer to the memory that stores the result.
45 __global__ 45 __global__
46 //void get_diff (float *result) 46 //void get_diff (float *result)
47 - void get_diff (cudaTextureObject_t texIn, float *print) 47 + void get_diff (cudaTextureObject_t texIn, float *print, int dx)
48 { 48 {
49 int x = threadIdx.x + blockIdx.x * blockDim.x; 49 int x = threadIdx.x + blockIdx.x * blockDim.x;
50 int y = threadIdx.y + blockIdx.y * blockDim.y; 50 int y = threadIdx.y + blockIdx.y * blockDim.y;
51 -// int idx = y*64+x;  
52 - int idx = y*32+x; 51 + int idx = y*dx+x;
53 // int idx = y*16+x; 52 // int idx = y*16+x;
54 53
55 float valIn = tex2D<unsigned char>(texIn, x, y); 54 float valIn = tex2D<unsigned char>(texIn, x, y);
56 - float templa = templ(x);  
57 - print[idx] = valIn; ///temporary 55 + float templa = templ(x, 32)*255.0;
  56 + print[idx] = abs(valIn-templa); ///temporary
58 //print[idx] = abs(templa); ///temporary 57 //print[idx] = abs(templa); ///temporary
59 58
60 } 59 }
61 60
62 -  
63 - ///External access-point to the cuda function  
64 - ///@param GLuint texbufferID --GLtexture (most be contained in a framebuffer object)  
65 - /// that holds the data that will be handed to cuda.  
66 - ///@param GLenum texType --either GL_TEXTURE_1D, GL_TEXTURE_2D or GL_TEXTURE_3D  
67 - /// may work with other gl texture types, but untested.  
68 - ///@param DIM_Y, the number of samples in the template.  
69 - void test(GLint texbufferID, GLenum texType, int x, int y) 61 + void test(cudaTextureObject_t tObj, int x, int y, std::string nam)
70 { 62 {
71 63
72 //Bind the Texture in GL and allow access to cuda. 64 //Bind the Texture in GL and allow access to cuda.
73 - tx.MapCudaTexture(texbufferID, texType);  
74 65
75 //initialize the return arrays. 66 //initialize the return arrays.
76 67
@@ -85,44 +76,13 @@ @@ -85,44 +76,13 @@
85 76
86 77
87 // get_diff <<< blocks, threads >>> (tx.getTexture(), print); 78 // get_diff <<< blocks, threads >>> (tx.getTexture(), print);
88 - get_diff <<< numBlocks, threadsPerBlock >>> (tx.getTexture(), print);  
89 -  
90 - cudaDeviceSynchronize();  
91 - stringstream name; //for debugging  
92 - name << "FromTex.bmp";  
93 - stim::gpu2image<float>(print, name.str(),x,y,0,255);  
94 -  
95 - tx.UnmapCudaTexture();  
96 - cleanUP();  
97 - }  
98 -  
99 - void test(GLint texbufferID, GLenum texType, int x, int y, std::string nam)  
100 - {  
101 -  
102 - //Bind the Texture in GL and allow access to cuda.  
103 - tx.MapCudaTexture(texbufferID, texType);  
104 -  
105 - //initialize the return arrays.  
106 -  
107 - initArray(x,y);  
108 - dim3 numBlocks(1, y);  
109 - dim3 threadsPerBlock(x, 1);  
110 - int max_threads = stim::maxThreadsPerBlock();  
111 - //dim3 threads(max_threads, 1);  
112 - //dim3 blocks(x / threads.x + 1, y);  
113 - //dim3 numBlocks(2, 2);  
114 - //dim3 threadsPerBlock(8, 108);  
115 -  
116 -  
117 -// get_diff <<< blocks, threads >>> (tx.getTexture(), print);  
118 - get_diff <<< numBlocks, threadsPerBlock >>> (tx.getTexture(), print); 79 + get_diff <<< numBlocks, threadsPerBlock >>> (tObj, print, x);
119 80
120 cudaDeviceSynchronize(); 81 cudaDeviceSynchronize();
121 stringstream name; //for debugging 82 stringstream name; //for debugging
122 name << nam.c_str(); 83 name << nam.c_str();
123 - //stim::gpu2image<float>(print, name.str(),x,y,0,255); 84 + stim::gpu2image<float>(print, name.str(),x,y,0,255);
124 85
125 - tx.UnmapCudaTexture();  
126 cleanUP(); 86 cleanUP();
127 } 87 }
128 88
stim/gl/gl_spider.h
  Show/Hide comments   View file @ad93457
@@ -23,14 +23,11 @@ @@ -23,14 +23,11 @@
23 #include <stim/cuda/ivote.cuh> 23 #include <stim/cuda/ivote.cuh>
24 #include <stim/visualization/glObj.h> 24 #include <stim/visualization/glObj.h>
25 #include <vector> 25 #include <vector>
  26 +#include <stack>
26 #include <stim/cuda/branch_detection.cuh> 27 #include <stim/cuda/branch_detection.cuh>
27 -#include "../../../volume-spider/fiber.h"  
28 #include "../../../volume-spider/glnetwork.h" 28 #include "../../../volume-spider/glnetwork.h"
29 #include <stim/visualization/cylinder.h> 29 #include <stim/visualization/cylinder.h>
30 #include <stim/cuda/testKernel.cuh> 30 #include <stim/cuda/testKernel.cuh>
31 -  
32 -//#include <stim/cuda/testKernel.cuh>  
33 -  
34 #include <iostream> 31 #include <iostream>
35 #include <fstream> 32 #include <fstream>
36 #ifdef TIMING 33 #ifdef TIMING
@@ -39,7 +36,6 @@ @@ -39,7 +36,6 @@
39 #endif 36 #endif
40 37
41 #ifdef TESTING 38 #ifdef TESTING
42 - #include <iostream>  
43 #include <cstdio> 39 #include <cstdio>
44 #include <ctime> 40 #include <ctime>
45 #endif 41 #endif
@@ -49,7 +45,7 @@ namespace stim @@ -49,7 +45,7 @@ namespace stim
49 { 45 {
50 46
51 template<typename T> 47 template<typename T>
52 -class gl_spider : public virtual gl_texture<T> 48 +class gl_spider // : public virtual gl_texture<T>
53 { 49 {
54 //doen't use gl_texture really, just needs the GLuint id. 50 //doen't use gl_texture really, just needs the GLuint id.
55 //doesn't even need the texture iD really. 51 //doesn't even need the texture iD really.
@@ -65,72 +61,87 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -65,72 +61,87 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
65 double hit_time;// = 0; 61 double hit_time;// = 0;
66 #endif 62 #endif
67 63
68 - //  
69 stim::vec3<float> p; //vector designating the position of the spider. 64 stim::vec3<float> p; //vector designating the position of the spider.
70 - stim::vec3<float> d; //vector designating the orientation of the spider  
71 - //always a unit vector.  
72 - stim::vec<float> m; //magnitude of the spider vector.  
73 - //mag[0] = length.  
74 - //mag[1] = width. 65 + stim::vec3<float> d; //normalized direction of travel
  66 + float m; //size of the spider in tissue space.
  67 +
75 std::vector<stim::vec3<float> > dV; //A list of all the direction vectors. 68 std::vector<stim::vec3<float> > dV; //A list of all the direction vectors.
76 - std::vector<stim::vec3<float> > pV; //A list of all the position vectors.  
77 - std::vector<stim::vec3<float> > mV; //A list of all the size vectors. 69 + std::vector<stim::vec3<float> > pV; //A list of all test positions (relative to p)
  70 + std::vector<float> mV; //A list of all the size vectors.
78 71
79 - stim::matrix<float, 4> cT; //current Transformation matrix  
80 - //From tissue space to texture space.  
81 - GLuint texID;  
82 - stim::vec<float> S; //Size of a voxel in the volume.  
83 - stim::vec<float> R; //Dimensions of the volume. 72 + stim::matrix<float, 4> cT; //current Transformation matrix (tissue)->(texture)
  73 + GLuint texID; //OpenGL ID for the texture to be traced
  74 + stim::vec3<float> S; //Size of a voxel in the volume.
  75 + stim::vec3<float> R; //Dimensions of the volume.
84 76
85 77
86 //GL and Cuda variables 78 //GL and Cuda variables
87 - GLuint dList; //displaylist ID  
88 - GLuint fboID; //framebuffer ID  
89 - GLuint texbufferID; //texbuffer ID, only necessary for  
90 - //cuda aspect of the calculation.  
91 - GLuint pfboID; //buffer object for position tracking.  
92 - GLuint ptexbufferID; //texture object for position tracking.  
93 -  
94 - GLuint mfboID; //buffer object for magnitude adjustment.  
95 - GLuint mtexbufferID; //texture object for magnitude adjustment.  
96 - GLuint bfboID; //buffer object for position adjustment.  
97 - GLuint btexbufferID; //buffer object for position adjustment. 79 + GLuint dList; //ID of the starting display lists (series of 4)
  80 + //dList + 0 = direction template rectangles
  81 + //dList + 1 = position template rectangles
  82 + //dList + 2 = size template rectangles
  83 + //dList + 3 = branch detection cylinder around the fiber
  84 +
  85 + GLuint fboID; //framebuffer ID for direction templates
  86 + GLuint texbufferID; //texture ID for direction templates
  87 + GLuint direction_buffID; //framebuffer ID, position templates
  88 + GLuint direction_texID; //texture ID, position templates
  89 +
  90 + GLuint position_buffID; //framebuffer ID, position templates
  91 + GLuint position_texID; //texture ID, position templates
  92 +
  93 + GLuint radius_buffID; //framebuffer ID, radius templates
  94 + GLuint radius_texID; //texture ID, radius templates
  95 +
  96 + GLuint cylinder_buffID; //framebuffer ID, cylinder (surrounding fiber)
  97 + GLuint cylinder_texID; //texture ID, cylinder
98 98
99 int numSamples; //The number of templates in the buffer. 99 int numSamples; //The number of templates in the buffer.
100 int numSamplesPos; 100 int numSamplesPos;
101 int numSamplesMag; 101 int numSamplesMag;
102 102
103 - float stepsize;// = 5.0; //Step size.  
104 -// float stepsize = 3.0; //Step size.  
105 - int current_cost; //variable to store the cost of the current step.  
106 - 103 + float length; //this will be a function of the radius
  104 + float stepsize; //this will be a function of the length
  105 +
  106 + int current_cost; //variable to store the cost of the current step
107 107
108 //Tracing variables. 108 //Tracing variables.
109 - std::stack< stim::vec3<float> > seeds; //seed positions.  
110 - std::stack< stim::vec3<float> > seedsvecs; //seed directions.  
111 - std::stack< float > seedsmags; //seed magnitudes. 109 + std::stack< stim::vec3<float> > seeds; //seed positions
  110 + std::stack< stim::vec3<float> > seedsvecs; //seed directions
  111 + std::stack< float > seedsmags; //seed magnitudes
  112 +
  113 + std::vector< stim::vec3<float> > cL; //centerline up to the current point
  114 + std::vector< stim::vec3<float> > cD; //directions up to the current point (debugging)
  115 + std::vector< float > cM; //radius up to the current point
112 116
113 - std::vector< stim::vec3<float> > cL; //Positions of line currently being traced.  
114 - std::vector< stim::vec3<float> > cD; //Direction of line currently being traced.  
115 - std::vector< stim::vec<float> > cM; //Magnitude of line currently being traced. 117 + stim::glnetwork<float> nt; //network object holding the currently traced centerlines
  118 + stim::glObj<float> sk; //OBJ file storing the network (identical to above)
116 119
117 - stim::glnetwork<float> nt; //object for storing the network. 120 + //consider replacing with two seed points facing opposite directions
  121 + stim::vec<float> rev; //reverse vector
118 122
119 - stim::vec<float> rev; //reverse vector;  
120 - stim::camera camSel;  
121 - stim::vec3<float> ps;  
122 - stim::vec3<float> ups;  
123 - stim::vec3<float> ds; 123 + //selection mode - detecting fiber intersections
  124 + stim::camera camSel; //camera for selection mode (detecting collisions)
  125 + stim::vec3<float> ps; //position for the selection camera
  126 + stim::vec3<float> ups; //up direction for the selection camera
  127 + stim::vec3<float> ds; //direction for the selection camera
124 128
125 - //static const float t_length = 16.0;  
126 - float t_length; 129 + float n_pixels; //length of the template (in pixels)
127 130
128 //cuda texture variables that keep track of the binding. 131 //cuda texture variables that keep track of the binding.
129 - stim::cuda::cuda_texture t_dir;  
130 - stim::cuda::cuda_texture t_pos;  
131 - stim::cuda::cuda_texture t_mag; 132 + stim::cuda::cuda_texture t_dir; //cuda_texture object used as an interface between OpenGL and cuda for direction vectors.
  133 + stim::cuda::cuda_texture t_pos; //cuda_texture object used as an interface between OpenGL and cuda for position vectors.
  134 + stim::cuda::cuda_texture t_mag; //cuda_texture object used as an interface between OpenGL and cuda for size vectors.
132 135
133 136
  137 + #ifdef DEBUG
  138 + stringstream name;
  139 + int iter;
  140 + int iter_pos;
  141 + int iter_dir;
  142 + int iter_siz;
  143 + #endif
  144 +
134 //--------------------------------------------------------------------------// 145 //--------------------------------------------------------------------------//
135 //-------------------------------PRIVATE METHODS----------------------------// 146 //-------------------------------PRIVATE METHODS----------------------------//
136 //--------------------------------------------------------------------------// 147 //--------------------------------------------------------------------------//
@@ -142,31 +153,32 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -142,31 +153,32 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
142 findOptimalDirection() 153 findOptimalDirection()
143 { 154 {
144 #ifdef TIMING 155 #ifdef TIMING
145 - gpuStartTimer(); 156 + gpuStartTimer(); //Timer for profiling
146 #endif 157 #endif
147 setMatrix(); //create the transformation matrix. 158 setMatrix(); //create the transformation matrix.
148 glCallList(dList); //move the templates to p, d, m. 159 glCallList(dList); //move the templates to p, d, m.
149 - glFinish();  
150 -// glFlush(); 160 + glFinish(); //flush the pipeline
151 #ifdef TIMING 161 #ifdef TIMING
152 - direction_time += gpuStopTimer();  
153 - #endif  
154 - #ifdef TESTING  
155 -// test(texbufferID, GL_TEXTURE_2D,2*t_length,numSamples*t_length, "Final_Cost_Direction.bmp"); 162 + direction_time += gpuStopTimer(); //profiling
156 #endif 163 #endif
157 164
158 int best = getCost(t_dir.getTexture(), t_dir.getAuxArray() ,numSamples); //find min cost. 165 int best = getCost(t_dir.getTexture(), t_dir.getAuxArray() ,numSamples); //find min cost.
159 - stim::vec<float> next( //find next vector. 166 + #ifdef DEBUG
  167 + name.str("");
  168 + name << "Final_Cost_Direction_fiber_"<< iter << "_" << iter_dir << ".bmp";
  169 + test(t_dir.getTexture(), n_pixels*2.0, numSamples*n_pixels, name.str());
  170 + iter_dir++;
  171 + #endif
  172 + stim::vec<float> next( ///calculate the next vector.
160 dV[best][0]*S[0]*R[0], 173 dV[best][0]*S[0]*R[0],
161 dV[best][1]*S[1]*R[1], 174 dV[best][1]*S[1]*R[1],
162 dV[best][2]*S[2]*R[2], 175 dV[best][2]*S[2]*R[2],
163 0); 176 0);
164 - next = (cT*next).norm(); //find next vector.  
165 - setPosition( p[0]+next[0]*m[0]/stepsize,  
166 - p[1]+next[1]*m[0]/stepsize,  
167 - p[2]+next[2]*m[0]/stepsize);  
168 - setDirection(next[0], next[1], next[2]);  
169 - //move forward and change direction. 177 + next = (cT*next).norm(); ///transform the next vector into Tissue space.
  178 + setPosition( p[0]+next[0]*m/stepsize,
  179 + p[1]+next[1]*m/stepsize,
  180 + p[2]+next[2]*m/stepsize);
  181 + setDirection(next[0], next[1], next[2]); //move forward and change direction.
170 } 182 }
171 183
172 /// Method for finding the best d (direction) for the spider. 184 /// Method for finding the best d (direction) for the spider.
@@ -176,27 +188,29 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -176,27 +188,29 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
176 findOptimalPosition() 188 findOptimalPosition()
177 { 189 {
178 #ifdef TIMING 190 #ifdef TIMING
179 - gpuStartTimer(); 191 + gpuStartTimer(); //timer for profiling
180 #endif 192 #endif
181 setMatrix(); //create the transformation matrix. 193 setMatrix(); //create the transformation matrix.
182 glCallList(dList+1); //move the templates to p, d, m. 194 glCallList(dList+1); //move the templates to p, d, m.
183 - glFinish(); 195 + glFinish(); //flush the pipeline
184 // glFlush(); 196 // glFlush();
185 #ifdef TIMING 197 #ifdef TIMING
186 - position_time += gpuStopTimer(); 198 + position_time += gpuStopTimer(); ///timer for profiling
187 #endif 199 #endif
188 200
189 - #ifdef TESTING  
190 -// test(ptexbufferID, GL_TEXTURE_2D,2*t_length, numSamplesPos*t_length, "Final_Cost_Position.bmp");  
191 - #endif  
192 int best = getCost(t_pos.getTexture(), t_pos.getAuxArray(), numSamplesPos); //find min cost. 201 int best = getCost(t_pos.getTexture(), t_pos.getAuxArray(), numSamplesPos); //find min cost.
193 -// std::cerr << best << std::endl; 202 + #ifdef DEBUG
  203 + name.str("");
  204 + name << "Final_Cost_Position_" << iter << "_" << iter_pos << ".bmp";
  205 + test(t_pos.getTexture(), n_pixels*2.0, numSamplesPos*n_pixels, name.str());
  206 + iter_pos++;
  207 + #endif
194 stim::vec<float> next( //find next position. 208 stim::vec<float> next( //find next position.
195 pV[best][0], 209 pV[best][0],
196 pV[best][1], 210 pV[best][1],
197 pV[best][2], 211 pV[best][2],
198 1); 212 1);
199 - next = cT*next; //find next position. 213 + next = cT*next; //transform the next position vector into tissue space.
200 setPosition( 214 setPosition(
201 next[0]*S[0]*R[0], 215 next[0]*S[0]*R[0],
202 next[1]*S[1]*R[1], 216 next[1]*S[1]*R[1],
@@ -206,7 +220,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -206,7 +220,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
206 220
207 /// Method for finding the best scale for the spider. 221 /// Method for finding the best scale for the spider.
208 /// changes the x, y, z size of the spider to minimize the cost 222 /// changes the x, y, z size of the spider to minimize the cost
209 - /// function. */ 223 + /// function.
210 void 224 void
211 findOptimalScale() 225 findOptimalScale()
212 { 226 {
@@ -215,64 +229,21 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -215,64 +229,21 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
215 #endif 229 #endif
216 setMatrix(); //create the transformation. 230 setMatrix(); //create the transformation.
217 glCallList(dList+2); //move the templates to p, d, m. 231 glCallList(dList+2); //move the templates to p, d, m.
218 - glFinish();  
219 -// glFlush(); 232 + glFinish(); //flush the drawing pipeline.
220 #ifdef TIMING 233 #ifdef TIMING
221 size_time += gpuStopTimer(); 234 size_time += gpuStopTimer();
222 #endif 235 #endif
223 - #ifdef TESTING  
224 -// test(mtexbufferID, GL_TEXTURE_2D, 2*t_length, numSamplesMag*t_length, "Final_Cost_Position.bmp");  
225 - #endif  
226 int best = getCost(t_mag.getTexture(), t_mag.getAuxArray(), numSamplesMag); //get best cost. 236 int best = getCost(t_mag.getTexture(), t_mag.getAuxArray(), numSamplesMag); //get best cost.
227 - setMagnitude(m[0]*mV[best][0]); //adjust the magnitude. 237 + #ifdef DEBUG
  238 + name.str("");
  239 + name << "Final_Cost_Size_" << iter << "_" << iter_siz << ".bmp";
  240 + test(t_mag.getTexture(), n_pixels*2.0, numSamplesMag*n_pixels, name.str());
  241 + iter_siz++;
  242 + #endif
  243 + setMagnitude(m*mV[best]); //adjust the magnitude.
228 } 244 }
229 245
230 246
231 - ///subject to change.  
232 - ///finds branches.  
233 - ///depreciated  
234 - void  
235 - branchDetection()  
236 - {  
237 - setMatrix();  
238 - glCallList(dList+3);  
239 - std::vector< stim::vec<float> > result = find_branch(  
240 - btexbufferID, GL_TEXTURE_2D, 16, 216);  
241 - stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);  
242 - if(!result.empty())  
243 - {  
244 - for(int i = 1; i < result.size(); i++)  
245 - {  
246 - stim::vec<float> cylp(  
247 - 0.5 * cos(2*M_PI*(result[i][1])),  
248 - 0.5 * sin(2*M_PI*(result[i][1])),  
249 - result[i][0]-0.5,  
250 - 1.0);  
251 - cylp = cT*cylp;  
252 -  
253 - stim::vec3<float> vec(  
254 - cylp[0]*S[0]*R[0],  
255 - cylp[1]*S[1]*R[1],  
256 - cylp[2]*S[2]*R[2]);  
257 - stim::vec3<float> seeddir(-p[0] + cylp[0]*S[0]*R[0],  
258 - -p[1] + cylp[1]*S[1]*R[1],  
259 - -p[2] + cylp[2]*S[2]*R[2]);  
260 - seeddir = seeddir.norm();  
261 - float seedm = m[0];  
262 -// Uncomment for global run  
263 - if(  
264 - !(vec[0] > size[0] || vec[1] > size[1]  
265 - || vec[2] > size[2] || vec[0] < 0  
266 - || vec[1] < 0 || vec[2] < 0))  
267 - {  
268 - setSeed(vec);  
269 - setSeedVec(seeddir);  
270 - setSeedMag(seedm);  
271 - }  
272 - }  
273 - }  
274 -  
275 - }  
276 247
277 248
278 ///finds all the branches in the a given fiber. 249 ///finds all the branches in the a given fiber.
@@ -281,78 +252,78 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -281,78 +252,78 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
281 branchDetection2(int n = 8, int l_template = 8, int l_square = 8) 252 branchDetection2(int n = 8, int l_template = 8, int l_square = 8)
282 { 253 {
283 #ifdef TIMING 254 #ifdef TIMING
284 - gpuStartTimer(); 255 + gpuStartTimer(); ///timer for performance analysis
285 #endif 256 #endif
286 257
287 - if(cL.size() < 4){} 258 + if(cL.size() < 4){} ///if the size of the fiber is less then 4 we do nothing.
288 else{ 259 else{
289 - setMatrix(1);  
290 - DrawLongCylinder(n, l_template, l_square); 260 + setMatrix(1); ///finds the current transformation matrix
  261 + DrawLongCylinder(n, l_template, l_square); ///Draw the cylinder.
291 stim::cylinder<float> cyl(cL, cM); 262 stim::cylinder<float> cyl(cL, cM);
292 - std::vector< stim::vec<float> > result = find_branch(btexbufferID, GL_TEXTURE_2D, n*l_square, (cL.size()-1)*l_template);  
293 - stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);  
294 - float pval;  
295 - if(!result.empty()) 263 + std::vector< stim::vec<float> > result = find_branch(cylinder_texID, GL_TEXTURE_2D, n*l_square, (cL.size()-1)*l_template); ///find all the centers in cuda
  264 + stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]); ///the borders of the texture.
  265 + float pval; //pvalue associated with the points on the cylinder.
  266 + if(!result.empty()) ///if we have any points
296 { 267 {
297 - for(int i = 0; i < result.size(); i++) 268 + for(int i = 0; i < result.size(); i++) ///for each point
298 { 269 {
299 int id = result[i][2]; 270 int id = result[i][2];
300 - if(fmod(result[i][2], id) != 0 && id != 0) 271 + if(fmod(result[i][2], id) != 0 && id != 0) ///if the remainer is odd
301 { 272 {
302 273
303 pval = ((cyl.getl(id+1)-cyl.getl(id))* 274 pval = ((cyl.getl(id+1)-cyl.getl(id))*
304 - (fmod(result[i][2], id))+cyl.getl(id))/cyl.getl(cL.size()-1); 275 + (fmod(result[i][2], id))+cyl.getl(id))/cyl.getl(cL.size()-1); ///calculate pvalue
305 } 276 }
306 - else if(id == 0) 277 + else if(id == 0) ///if the point is on the edge
307 { 278 {
308 - pval = (cyl.getl(id+1)*result[i][2])/cyl.getl(cL.size()-1); 279 + pval = (cyl.getl(id+1)*result[i][2])/cyl.getl(cL.size()-1);
309 } 280 }
310 else 281 else
311 { 282 {
312 - pval = (cyl.getl(id)/cyl.getl(cL.size()-1)); 283 + pval = (cyl.getl(id)/cyl.getl(cL.size()-1)); ///if the point is somewhere on the surface of the cylinder other than the edge
313 } 284 }
314 - stim::vec3<float> v = cyl.surf(pval, result[i][0]);  
315 - stim::vec3<float> di = cyl.p(pval);  
316 - float rad = cyl.r(pval); 285 + stim::vec3<float> v = cyl.surf(pval, result[i][0]); ///find the coordinates of the point at pval on the surface in tissue space.
  286 + stim::vec3<float> di = cyl.p(pval); ///find the coord of v in tissue space projected on the centerline.
  287 + float rad = cyl.r(pval)/2; ///find the radius at the pvalue's location
317 if( 288 if(
318 !(v[0] > size[0] || v[1] > size[1] 289 !(v[0] > size[0] || v[1] > size[1]
319 || v[2] > size[2] || v[0] < 0 290 || v[2] > size[2] || v[0] < 0
320 - || v[1] < 0 || v[2] < 0)) 291 + || v[1] < 0 || v[2] < 0)) ///if the v point is INSIDE the volume
321 { 292 {
322 - setSeed(v);  
323 - setSeedVec((v-di).norm());  
324 - setSeedMag(rad); 293 + setSeed(v); ///add a seedpoint's position.
  294 + setSeedVec((v-di).norm()); ///add a seedpoints direction
  295 + setSeedMag(rad); ///add the starting radius.
325 } 296 }
326 } 297 }
327 } 298 }
328 } 299 }
329 #ifdef TIMING 300 #ifdef TIMING
330 - branch_time += gpuStopTimer(); 301 + branch_time += gpuStopTimer(); ///timer for performance.
331 #endif 302 #endif
332 } 303 }
333 304
334 305
335 float uniformRandom() 306 float uniformRandom()
336 { 307 {
337 - return ( (float)(rand()))/( (float)(RAND_MAX)); 308 + return ( (float)(rand()))/( (float)(RAND_MAX)); ///generates a random number between 0 and 1 using the uniform distribution.
338 } 309 }
339 310
340 float normalRandom() 311 float normalRandom()
341 { 312 {
342 float u1 = uniformRandom(); 313 float u1 = uniformRandom();
343 float u2 = uniformRandom(); 314 float u2 = uniformRandom();
344 - return cos(2.0*atan(1.0)*u2)*sqrt(-1.0*log(u1)); 315 + return cos(2.0*atan(1.0)*u2)*sqrt(-1.0*log(u1)); ///generate a random number using the normal distribution between 0 and 1.
345 } 316 }
346 317
347 stim::vec3<float> uniformRandVector() 318 stim::vec3<float> uniformRandVector()
348 { 319 {
349 - stim::vec3<float> r(uniformRandom(), uniformRandom(), 1.0); 320 + stim::vec3<float> r(uniformRandom(), uniformRandom(), 1.0); ///generate a random vector using the uniform distribution between 0 and 1.
350 return r; 321 return r;
351 } 322 }
352 323
353 stim::vec3<float> normalRandVector() 324 stim::vec3<float> normalRandVector()
354 { 325 {
355 - stim::vec3<float> r(normalRandom(), normalRandom(), 1.0); 326 + stim::vec3<float> r(normalRandom(), normalRandom(), 1.0); ///generate a random vector using the normal distribution between 0 and 1.
356 return r; 327 return r;
357 } 328 }
358 329
@@ -370,49 +341,57 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -370,49 +341,57 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
370 ///Stored in a display list. 341 ///Stored in a display list.
371 ///uses the default d vector <0,0,1> 342 ///uses the default d vector <0,0,1>
372 void 343 void
373 - genDirectionVectors(float solidAngle = M_PI/2) 344 + genDirectionVectors(float solidAngle = stim::PI/2)
374 { 345 {
375 346
376 //Set up the vectors necessary for Rectangle creation. 347 //Set up the vectors necessary for Rectangle creation.
377 stim::vec3<float> Y(1.0,0.0,0.0); //orthogonal vec. 348 stim::vec3<float> Y(1.0,0.0,0.0); //orthogonal vec.
378 - stim::vec3<float> pos(0.0,0.0,0.0);  
379 - stim::vec3<float> mag(1.0, 1.0, 1.0);  
380 - stim::vec3<float> dir(0.0, 0.0, 1.0); 349 + stim::vec3<float> pos(0.0,0.0,0.0); //center point of a rectangle
  350 + float mag = 1.0; //size of the generated rectangle.
  351 + stim::vec3<float> dir(0.0, 0.0, 1.0); //normal of the rectangle
381 352
382 - float PHI[2], Z[2], range;  
383 - PHI[0] = solidAngle/2; 353 + float PHI[2], Z[2], range;
  354 + PHI[0] = solidAngle/2; ///Project the solid angle into spherical coordinates
384 PHI[1] = asin(0); 355 PHI[1] = asin(0);
385 356
386 - Z[0] = cos(PHI[0]); 357 + Z[0] = cos(PHI[0]); ///Project the z into spherical coordinates
387 Z[1] = cos(PHI[1]); 358 Z[1] = cos(PHI[1]);
388 359
389 - range = Z[0] - Z[1]; 360 + range = Z[0] - Z[1]; ///The range the possible values can be.
390 361
391 float z, theta, phi; 362 float z, theta, phi;
392 - glNewList(dList, GL_COMPILE);  
393 - for(int i = 0; i < numSamples; i++) 363 + glNewList(dList, GL_COMPILE); ///create a display list of all the direction templates.
  364 + for(int i = 0; i < numSamples; i++) ///for each sample
394 { 365 {
395 - z = uniformRandom()*range + Z[1];  
396 - theta = uniformRandom()*2*M_PI;  
397 - phi = acos(z);  
398 - stim::vec3<float> sph(1, theta, phi);  
399 - stim::vec3<float> cart = sph.sph2cart();  
400 - dV.push_back(cart);  
401 - if(cos(Y.dot(cart)) < 0.087) 366 + z = uniformRandom()*range + Z[1]; ///generate a z coordinate
  367 + theta = uniformRandom()*stim::TAU; ///generate a theta coordinate
  368 + phi = acos(z); ///generate a phi from the z.
  369 + stim::vec3<float> sph(1, theta, phi); ///combine into a vector in spherical coordinates.
  370 + stim::vec3<float> cart = sph.sph2cart();///convert to cartesian.
  371 + dV.push_back(cart); ///save the generated vector for further use.
  372 + #ifdef DEBUG
  373 +// std::cout << cart << std::endl;
  374 + #endif
  375 + if(cos(Y.dot(cart)) < 0.087) ///make sure that the Y is not parallel to the new vector.
402 { 376 {
403 Y[0] = 0.0; Y[1] = 1.0; 377 Y[0] = 0.0; Y[1] = 1.0;
404 }else{ 378 }else{
405 Y[0] = 1.0; Y[1] = 0.0; 379 Y[0] = 1.0; Y[1] = 0.0;
406 } 380 }
407 - hor = stim::rect<float>(mag, 381 +
  382 + hor = stim::rect<float>(mag, ///generate a rectangle with the new vectro as a normal.
408 pos, cart, 383 pos, cart,
409 ((Y.cross(cart)).cross(cart)).norm()); 384 ((Y.cross(cart)).cross(cart)).norm());
410 - ver = stim::rect<float>(mag, 385 +
  386 + #ifdef DEBUG
  387 + // std::cout << hor.n() << std::endl;
  388 + #endif
  389 + ver = stim::rect<float>(mag, ///generate another rectangle that's perpendicular the first but parallel to the cart vector.
411 pos, cart, 390 pos, cart,
412 hor.n()); 391 hor.n());
413 - UpdateBuffer(0.0, 0.0+i*t_length); 392 + UpdateBuffer(0.0, 0.0+i*n_pixels); ///Put the necessary points into the diplaylist.
414 } 393 }
415 - glEndList(); 394 + glEndList(); ///finilize the display list.
416 } 395 }
417 396
418 ///@param float delta, How much the rectangles vary in position. 397 ///@param float delta, How much the rectangles vary in position.
@@ -426,28 +405,45 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -426,28 +405,45 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
426 { 405 {
427 //Set up the vectors necessary for Rectangle creation. 406 //Set up the vectors necessary for Rectangle creation.
428 stim::vec3<float> Y(1.0,0.0,0.0); //orthogonal vec. 407 stim::vec3<float> Y(1.0,0.0,0.0); //orthogonal vec.
429 - stim::vec3<float> pos(0.0,0.0,0.0);  
430 - stim::vec3<float> mag(1.0, 1.0, 1.0);  
431 - stim::vec3<float> dir(0.0, 0.0, 1.0); 408 + stim::vec3<float> pos(0.0,0.0,0.0); //center point of a rectangle
  409 + float mag = 1.0; ///size of each rectangle
  410 + stim::vec3<float> dir(0.0, 0.0, 1.0); ///normal of the rectangle plane.
432 411
433 //Set up the variable necessary for vector creation. 412 //Set up the variable necessary for vector creation.
434 - glNewList(dList+1, GL_COMPILE);  
435 - for(int i = 0; i < numSamplesPos; i++) 413 + glNewList(dList+1, GL_COMPILE); ///generate a new display list.
  414 + pV.push_back(pos);
  415 + hor = stim::rect<float>(mag, ///generate a rec tangle with the new vector as a normal.
  416 + pos, dir,
  417 + ((Y.cross(d)).cross(d))
  418 + .norm());
  419 + ver = stim::rect<float>(mag, ///generate anoth er rectangle that's perpendicular the first but parallel to the cart vector.
  420 + pos, dir,
  421 + hor.n());
  422 + ///The first vector is always in the center.
  423 + UpdateBuffer(0.0, 0.0+0*n_pixels);
  424 + for(int i = 1; i < numSamplesPos; i++) ///for the number of position samples
436 { 425 {
437 - stim::vec3<float> temp = uniformRandVector();  
438 - temp = temp*delta*2.0 - delta/2.0; 426 + stim::vec3<float> temp = uniformRandVector(); ///generate a random point on a plane.
  427 + temp[0] = temp[0]*delta;
  428 + temp[1] = temp[1]*2*stim::PI;
  429 +
439 temp[2] = 0.0; 430 temp[2] = 0.0;
440 - pV.push_back(temp);  
441 - hor = stim::rect<float>(mag, 431 + temp = temp.cyl2cart();
  432 + pV.push_back(temp); ///save the point for further use.
  433 + hor = stim::rect<float>(mag, ///generate a rectangle with the new vector as a normal.
442 temp, dir, 434 temp, dir,
443 ((Y.cross(d)).cross(d)) 435 ((Y.cross(d)).cross(d))
444 .norm()); 436 .norm());
445 - ver = stim::rect<float>(mag, 437 + ver = stim::rect<float>(mag, ///generate another rectangle that's perpendicular the first but parallel to the cart vector.
446 temp, dir, 438 temp, dir,
447 hor.n()); 439 hor.n());
448 - UpdateBuffer(0.0, 0.0+i*t_length); 440 + UpdateBuffer(0.0, 0.0+i*n_pixels); ///sample the necessary points and put them into a display list.
449 } 441 }
450 - glEndList(); 442 + glEndList(); ///finilize the display list.
  443 + #ifdef DEBUG
  444 + for(int i = 0; i < numSamplesPos; i++)
  445 + std::cout << pV[i] << std::endl;
  446 + #endif
451 } 447 }
452 448
453 ///@param float delta, How much the rectangles are allowed to expand. 449 ///@param float delta, How much the rectangles are allowed to expand.
@@ -462,35 +458,31 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -462,35 +458,31 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
462 458
463 //Set up the vectors necessary for Rectangle creation. 459 //Set up the vectors necessary for Rectangle creation.
464 stim::vec3<float> Y(1.0, 0.0, 0.0); //orthogonal vec. 460 stim::vec3<float> Y(1.0, 0.0, 0.0); //orthogonal vec.
465 - stim::vec3<float> pos(0.0, 0.0, 0.0);  
466 - stim::vec3<float> mag(1.0, 1.0, 1.0);  
467 - stim::vec3<float> dir(0.0, 0.0, 1.0); 461 + stim::vec3<float> pos(0.0, 0.0, 0.0); //center of the future rect.
  462 + float mag = 1.0; ///size of the rectangle
  463 + stim::vec3<float> dir(0.0, 0.0, 1.0); ///normal of the rectangle plane.
468 464
469 //Set up the variable necessary for vector creation. 465 //Set up the variable necessary for vector creation.
470 - int dim = (sqrt(numSamplesMag)-1)/2;  
471 - float min = 1.0-delta;  
472 - float max = 1.0+delta;  
473 - float step = (max-min)/(numSamplesMag-1); 466 + float min = 1.0-delta; ///smallest size
  467 + float max = 1.0+delta; ///largers size.
  468 + float step = (max-min)/(numSamplesMag-1); ///the size variation from one rect to the next.
474 float factor; 469 float factor;
475 - stim::vec3<float> temp(0.0,0.0,0.0);  
476 -  
477 glNewList(dList+2, GL_COMPILE); 470 glNewList(dList+2, GL_COMPILE);
478 - for(int i = 0; i < numSamplesMag; i++){ 471 + for(int i = 0; i < numSamplesMag; i++){ ///for the number of position samples
479 //Create linear index 472 //Create linear index
480 - factor = (min+step*i)*mag[0];  
481 - temp = factor;  
482 - mV.push_back(temp);  
483 - hor = stim::rect<float>(temp, 473 + factor = (min+step*i)*mag; ///scaling factor
  474 + mV.push_back(factor); ///save the size factor for further use.
  475 + hor = stim::rect<float>(factor, ///generate a rectangle with the new vector as a normal.
484 pos, dir, 476 pos, dir,
485 ((Y.cross(d)).cross(d)) 477 ((Y.cross(d)).cross(d))
486 .norm()); 478 .norm());
487 - ver = stim::rect<float>(temp, 479 + ver = stim::rect<float>(factor, ///generate another rectangle that's perpendicular the first but parallel to the cart vector.
488 pos, dir, 480 pos, dir,
489 hor.n()); 481 hor.n());
490 - UpdateBuffer(0.0, 0.0+i*t_length); 482 + UpdateBuffer(0.0, 0.0+i*n_pixels); ///sample the necessary points and put them into a display list.
491 CHECK_OPENGL_ERROR 483 CHECK_OPENGL_ERROR
492 } 484 }
493 - glEndList(); 485 + glEndList(); ///finilize the displaylist.
494 } 486 }
495 487
496 ///@param float v_x x-coordinate in buffer-space, 488 ///@param float v_x x-coordinate in buffer-space,
@@ -500,15 +492,15 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -500,15 +492,15 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
500 void 492 void
501 UpdateBuffer(float v_x, float v_y) 493 UpdateBuffer(float v_x, float v_y)
502 { 494 {
503 - stim::vec3<float>p1;  
504 - stim::vec3<float>p2;  
505 - stim::vec3<float>p3;  
506 - stim::vec3<float>p4;  
507 - p1 = hor.p(1,1);  
508 - p2 = hor.p(1,0);  
509 - p3 = hor.p(0,0);  
510 - p4 = hor.p(0,1);  
511 - glBegin(GL_QUADS); 495 + stim::vec3<float>p1; ///first point.
  496 + stim::vec3<float>p2; ///second point.
  497 + stim::vec3<float>p3; ///third point.
  498 + stim::vec3<float>p4; ///fourth point.
  499 + p1 = hor.p(1,1); ///generate the top right point from the horizontal template.
  500 + p2 = hor.p(1,0); ///generate the bottom right point from the horizonatal template.
  501 + p3 = hor.p(0,0); ///generate the bottom left point from the horizontal template.
  502 + p4 = hor.p(0,1); ///generate the top left point from the horizonatal template.
  503 + glBegin(GL_QUADS); ///generate the Quad from the 4 points.
512 glTexCoord3f( 504 glTexCoord3f(
513 p1[0], 505 p1[0],
514 p1[1], 506 p1[1],
@@ -520,51 +512,51 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -520,51 +512,51 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
520 p2[1], 512 p2[1],
521 p2[2] 513 p2[2]
522 ); 514 );
523 - glVertex2f(v_x+t_length, v_y); 515 + glVertex2f(v_x+n_pixels, v_y);
524 glTexCoord3f( 516 glTexCoord3f(
525 p3[0], 517 p3[0],
526 p3[1], 518 p3[1],
527 p3[2] 519 p3[2]
528 ); 520 );
529 - glVertex2f(v_x+t_length, v_y+t_length); 521 + glVertex2f(v_x+n_pixels, v_y+n_pixels);
530 glTexCoord3f( 522 glTexCoord3f(
531 p4[0], 523 p4[0],
532 p4[1], 524 p4[1],
533 p4[2] 525 p4[2]
534 ); 526 );
535 - glVertex2f(v_x, v_y+t_length);  
536 - glEnd();  
537 -  
538 - p1 = ver.p(1,1);  
539 - p2 = ver.p(1,0);  
540 - p3 = ver.p(0,0);  
541 - p4 = ver.p(0,1);  
542 - glBegin(GL_QUADS); 527 + glVertex2f(v_x, v_y+n_pixels);
  528 + glEnd(); ///finish the quad.
  529 +
  530 + p1 = ver.p(1,1); ///generate the top right point from the vertical template.
  531 + p2 = ver.p(1,0); ///generate the bottom right point from the vertical template.
  532 + p3 = ver.p(0,0); ///generate the bottom left point from the vertical template.
  533 + p4 = ver.p(0,1); ///generate the top left point from the vertical template.
  534 + glBegin(GL_QUADS); ///generate the Quad from the 4 points.
543 glTexCoord3f( 535 glTexCoord3f(
544 p1[0], 536 p1[0],
545 p1[1], 537 p1[1],
546 p1[2] 538 p1[2]
547 ); 539 );
548 - glVertex2f(v_x+t_length, v_y); 540 + glVertex2f(v_x+n_pixels, v_y);
549 glTexCoord3f( 541 glTexCoord3f(
550 p2[0], 542 p2[0],
551 p2[1], 543 p2[1],
552 p2[2] 544 p2[2]
553 ); 545 );
554 - glVertex2f(v_x+2.0*t_length, v_y); 546 + glVertex2f(v_x+2.0*n_pixels, v_y);
555 glTexCoord3f( 547 glTexCoord3f(
556 p3[0], 548 p3[0],
557 p3[1], 549 p3[1],
558 p3[2] 550 p3[2]
559 ); 551 );
560 - glVertex2f(v_x+2.0*t_length, v_y+t_length); 552 + glVertex2f(v_x+2.0*n_pixels, v_y+n_pixels);
561 glTexCoord3f( 553 glTexCoord3f(
562 p4[0], 554 p4[0],
563 p4[1], 555 p4[1],
564 p4[2] 556 p4[2]
565 ); 557 );
566 - glVertex2f(v_x+t_length, v_y+t_length);  
567 - glEnd(); 558 + glVertex2f(v_x+n_pixels, v_y+n_pixels);
  559 + glEnd(); ///finish the quad.
568 } 560 }
569 561
570 562
@@ -582,50 +574,24 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -582,50 +574,24 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
582 void 574 void
583 GenerateFBO(unsigned int width, unsigned int height, GLuint &textureID, GLuint &framebufferID) 575 GenerateFBO(unsigned int width, unsigned int height, GLuint &textureID, GLuint &framebufferID)
584 { 576 {
585 - glDeleteFramebuffers(1, &framebufferID);  
586 - glGenFramebuffers(1, &framebufferID);  
587 - glBindFramebuffer(GL_FRAMEBUFFER, framebufferID); 577 + glDeleteFramebuffers(1, &framebufferID); ///clear the framebuffer.
  578 + glGenFramebuffers(1, &framebufferID); ///generate a clean buffer.
  579 + glBindFramebuffer(GL_FRAMEBUFFER, framebufferID); ///bind the new buffer.
588 // int numChannels = 1; 580 // int numChannels = 1;
589 // unsigned char* texels = new unsigned char[width * height * numChannels]; 581 // unsigned char* texels = new unsigned char[width * height * numChannels];
590 - glGenTextures(1, &textureID); 582 + glGenTextures(1, &textureID); ///generate a texture that will attach to the buffer.
591 glBindTexture(GL_TEXTURE_2D, textureID); 583 glBindTexture(GL_TEXTURE_2D, textureID);
592 584
593 //Textures repeat and use linear interpolation, luminance format. 585 //Textures repeat and use linear interpolation, luminance format.
594 - glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_REPEAT);  
595 - glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_REPEAT);  
596 - glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR); 586 + glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_BORDER); ///Set up the texture to repeat at edges.
  587 + glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_BORDER);
  588 + glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR); ///Set up the texture to use Linear interpolation
597 glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR); 589 glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
598 - glTexImage2D(GL_TEXTURE_2D, 0, GL_LUMINANCE, 590 + glTexImage2D(GL_TEXTURE_2D, 0, GL_LUMINANCE, ///Create the texture with no data.
599 width, height, 0, GL_LUMINANCE, GL_UNSIGNED_BYTE, NULL); 591 width, height, 0, GL_LUMINANCE, GL_UNSIGNED_BYTE, NULL);
600 // delete[] texels; 592 // delete[] texels;
601 - glBindFramebuffer(GL_FRAMEBUFFER, 0);  
602 - glBindTexture(GL_TEXTURE_2D, 0);  
603 - }  
604 -  
605 - ///@param uint width sets the width of the buffer.  
606 - ///@param uint height sets the height of the buffer.  
607 - ///Function for setting up the 2D buffer that stores the samples.  
608 - void  
609 - GenerateFBO(unsigned int width, unsigned int height)  
610 - {  
611 - glGenFramebuffers(1, &fboID);  
612 - glBindFramebuffer(GL_FRAMEBUFFER, fboID);  
613 -// int numChannels = 1;  
614 -// unsigned char* texels = new unsigned char[width * height * numChannels];  
615 - glGenTextures(1, &texbufferID);  
616 - glBindTexture(GL_TEXTURE_2D, texbufferID);  
617 -  
618 - //Textures repeat and use linear interpolation, luminance format.  
619 - glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_REPEAT);  
620 - glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_REPEAT);  
621 - glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);  
622 - glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);  
623 - glTexImage2D(GL_TEXTURE_2D, 0, GL_LUMINANCE,  
624 - width, height, 0, GL_LUMINANCE, GL_UNSIGNED_BYTE, NULL);  
625 -// delete[] texels;  
626 - glBindFramebuffer(GL_FRAMEBUFFER, 0);  
627 - glBindTexture(GL_TEXTURE_2D, 0);  
628 - CHECK_OPENGL_ERROR 593 + glBindFramebuffer(GL_FRAMEBUFFER, 0); ///Bind the frontbuffer
  594 + glBindTexture(GL_TEXTURE_2D, 0); ///Unbind the texture.
629 } 595 }
630 596
631 597
@@ -657,13 +623,12 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -657,13 +623,12 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
657 //rotate to the current direction of the spider. 623 //rotate to the current direction of the spider.
658 glRotatef(rot[0], rot[1], rot[2], rot[3]); 624 glRotatef(rot[0], rot[1], rot[2], rot[3]);
659 //scale to the magnitude of the spider. 625 //scale to the magnitude of the spider.
660 - glScalef(m[0],  
661 - m[0],  
662 - m[0]); 626 + glScalef(m,
  627 + m,
  628 + m);
663 //get and store the current transformation matrix for later use. 629 //get and store the current transformation matrix for later use.
664 glGetFloatv(GL_TEXTURE_MATRIX, curTrans); 630 glGetFloatv(GL_TEXTURE_MATRIX, curTrans);
665 cT.set(curTrans); 631 cT.set(curTrans);
666 - // printTransform();  
667 632
668 CHECK_OPENGL_ERROR 633 CHECK_OPENGL_ERROR
669 //revert back to default gl mode. 634 //revert back to default gl mode.
@@ -683,31 +648,31 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -683,31 +648,31 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
683 void 648 void
684 Bind() 649 Bind()
685 { 650 {
686 - glBindFramebuffer(GL_FRAMEBUFFER, fboID);//set up GL buffer 651 + glBindFramebuffer(GL_FRAMEBUFFER, direction_buffID);//set up GL buffer
687 glFramebufferTexture2D( 652 glFramebufferTexture2D(
688 GL_FRAMEBUFFER, 653 GL_FRAMEBUFFER,
689 GL_COLOR_ATTACHMENT0, 654 GL_COLOR_ATTACHMENT0,
690 GL_TEXTURE_2D, 655 GL_TEXTURE_2D,
691 - texbufferID, 656 + direction_texID,
692 0); 657 0);
693 - glBindFramebuffer(GL_FRAMEBUFFER, fboID); 658 + glBindFramebuffer(GL_FRAMEBUFFER, direction_buffID);
694 GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0}; 659 GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0};
695 glDrawBuffers(1, DrawBuffers); 660 glDrawBuffers(1, DrawBuffers);
696 - glBindTexture(GL_TEXTURE_2D, texbufferID); 661 + glBindTexture(GL_TEXTURE_2D, direction_texID);
697 glClearColor(1,1,1,1); 662 glClearColor(1,1,1,1);
698 glClear(GL_COLOR_BUFFER_BIT); 663 glClear(GL_COLOR_BUFFER_BIT);
699 glMatrixMode(GL_PROJECTION); 664 glMatrixMode(GL_PROJECTION);
700 glLoadIdentity(); 665 glLoadIdentity();
701 glMatrixMode(GL_MODELVIEW); 666 glMatrixMode(GL_MODELVIEW);
702 glLoadIdentity(); 667 glLoadIdentity();
703 - glViewport(0,0,2.0*t_length, numSamples*t_length);  
704 - gluOrtho2D(0.0,2.0*t_length,0.0,numSamples*t_length); 668 + glViewport(0,0,2.0*n_pixels, numSamples*n_pixels);
  669 + gluOrtho2D(0.0,2.0*n_pixels,0.0,numSamples*n_pixels);
705 glEnable(GL_TEXTURE_3D); 670 glEnable(GL_TEXTURE_3D);
706 glBindTexture(GL_TEXTURE_3D, texID); 671 glBindTexture(GL_TEXTURE_3D, texID);
707 672
708 CHECK_OPENGL_ERROR 673 CHECK_OPENGL_ERROR
709 } 674 }
710 - 675 +
711 ///Method for controling the buffer and texture binding. 676 ///Method for controling the buffer and texture binding.
712 ///Clears the buffer upon binding. 677 ///Clears the buffer upon binding.
713 ///@param GLuint &textureID, texture to be bound. 678 ///@param GLuint &textureID, texture to be bound.
@@ -717,25 +682,25 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -717,25 +682,25 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
717 Bind(GLuint &textureID, GLuint &framebufferID, int nSamples, float len = 8.0) 682 Bind(GLuint &textureID, GLuint &framebufferID, int nSamples, float len = 8.0)
718 { 683 {
719 684
720 - glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);//set up GL buffer  
721 - glFramebufferTexture2D( 685 + glBindFramebuffer(GL_FRAMEBUFFER, framebufferID); ///Bind the framebuffer.
  686 + glFramebufferTexture2D( ///associate it with the texture
722 GL_FRAMEBUFFER, 687 GL_FRAMEBUFFER,
723 GL_COLOR_ATTACHMENT0, 688 GL_COLOR_ATTACHMENT0,
724 GL_TEXTURE_2D, 689 GL_TEXTURE_2D,
725 textureID, 690 textureID,
726 0); 691 0);
727 - glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);  
728 - GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0};  
729 - glDrawBuffers(1, DrawBuffers);  
730 - glBindTexture(GL_TEXTURE_2D, textureID);  
731 - glMatrixMode(GL_PROJECTION); 692 + glBindFramebuffer(GL_FRAMEBUFFER, framebufferID); ///Bind the framebuffer.
  693 + GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0}; ///generate the drawbuffer.
  694 + glDrawBuffers(1, DrawBuffers); ///set the drawbuffer.
  695 + glBindTexture(GL_TEXTURE_2D, textureID); ///Bind the texture passed.
  696 + glMatrixMode(GL_PROJECTION); ///clear out the draw matrices
732 glLoadIdentity(); 697 glLoadIdentity();
733 glMatrixMode(GL_MODELVIEW); 698 glMatrixMode(GL_MODELVIEW);
734 glLoadIdentity(); 699 glLoadIdentity();
735 - glViewport(0,0,2.0*len, nSamples*len);  
736 - gluOrtho2D(0.0,2.0*len,0.0,nSamples*len);  
737 - glEnable(GL_TEXTURE_3D);  
738 - glBindTexture(GL_TEXTURE_3D, texID); 700 + glViewport(0,0,2.0*len, nSamples*len); ///set up viewport
  701 + gluOrtho2D(0.0,2.0*len,0.0,nSamples*len); ///Set up ortho
  702 + glEnable(GL_TEXTURE_3D);
  703 + glBindTexture(GL_TEXTURE_3D, texID); ///bind the main texture (return to original state).
739 704
740 CHECK_OPENGL_ERROR 705 CHECK_OPENGL_ERROR
741 } 706 }
@@ -745,34 +710,16 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -745,34 +710,16 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
745 Unbind() 710 Unbind()
746 { 711 {
747 //Finalize GL_buffer 712 //Finalize GL_buffer
748 - glBindTexture(GL_TEXTURE_3D, 0); 713 + glBindTexture(GL_TEXTURE_3D, 0); ///Bind the front buffer.
749 CHECK_OPENGL_ERROR 714 CHECK_OPENGL_ERROR
750 - glBindTexture(GL_TEXTURE_2D, 0); 715 + glBindTexture(GL_TEXTURE_2D, 0); ///Bind the default GL texture.
751 CHECK_OPENGL_ERROR 716 CHECK_OPENGL_ERROR
752 - glBindFramebuffer(GL_FRAMEBUFFER, 0); 717 + glBindFramebuffer(GL_FRAMEBUFFER, 0); ///Bind the defautl framebuffer.
753 CHECK_OPENGL_ERROR 718 CHECK_OPENGL_ERROR
754 - glDisable(GL_TEXTURE_3D); 719 + glDisable(GL_TEXTURE_3D); ///Turn off texturing.
755 CHECK_OPENGL_ERROR 720 CHECK_OPENGL_ERROR
756 } 721 }
757 722
758 - ///Makes the spider take a step.  
759 - ///starting with the current p, d, m, find the next optimal p, d, m.  
760 - ///Performs the branch detection on each step.  
761 - int  
762 - StepP()  
763 - {  
764 - Bind();  
765 - CHECK_OPENGL_ERROR  
766 - findOptimalDirection();  
767 - findOptimalPosition();  
768 - findOptimalScale();  
769 - Unbind();  
770 - Bind(btexbufferID, bfboID, 27);  
771 - branchDetection();  
772 - Unbind();  
773 - return current_cost;  
774 - }  
775 -  
776 723
777 724
778 725
@@ -785,42 +732,17 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -785,42 +732,17 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
785 ///finds the minimum cost and sets the current_cost to that value. 732 ///finds the minimum cost and sets the current_cost to that value.
786 /// and returns the index of the template with the minimal cost. 733 /// and returns the index of the template with the minimal cost.
787 int 734 int
788 - getCost()  
789 - {  
790 - stim::vec<int> cost =  
791 -// stim::cuda::get_cost(texbufferID, GL_TEXTURE_2D, numSamples);  
792 - cudaDeviceSynchronize();  
793 - current_cost = cost[1];  
794 - return cost[0];  
795 - }  
796 -  
797 -// int  
798 -// getCost(GLuint tID, int n)  
799 -// {  
800 -// #ifdef TIMING  
801 -// gpuStartTimer();  
802 -// #endif  
803 -// stim::vec<int> cost =  
804 -// stim::cuda::get_cost(tID, GL_TEXTURE_2D, n, 2*t_length, t_length);  
805 -// #ifdef TIMING  
806 -// cost_time += gpuStopTimer();  
807 -// #endif  
808 -// current_cost = cost[1];  
809 -// return cost[0];  
810 -// }  
811 -  
812 - int  
813 getCost(cudaTextureObject_t tObj, float* result, int n) 735 getCost(cudaTextureObject_t tObj, float* result, int n)
814 { 736 {
815 #ifdef TIMING 737 #ifdef TIMING
816 gpuStartTimer(); 738 gpuStartTimer();
817 #endif 739 #endif
818 stim::vec<int> cost = 740 stim::vec<int> cost =
819 - stim::cuda::get_cost(tObj, result, n, 2*t_length, t_length); 741 + stim::cuda::get_cost(tObj, result, n, 2*n_pixels, n_pixels); ///call the cuda function with the appropriate texture buffer.
820 #ifdef TIMING 742 #ifdef TIMING
821 cost_time += gpuStopTimer(); 743 cost_time += gpuStopTimer();
822 #endif 744 #endif
823 - current_cost = cost[1]; 745 + current_cost = cost[1]; ///current cost.
824 return cost[0]; 746 return cost[0];
825 } 747 }
826 748
@@ -854,17 +776,20 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -854,17 +776,20 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
854 gl_spider 776 gl_spider
855 (int samples = 1089, int samplespos = 441,int samplesmag = 144) 777 (int samples = 1089, int samplespos = 441,int samplesmag = 144)
856 { 778 {
857 -// std::cout << "I ran this constructor" << std::endl;  
858 p = stim::vec3<float>(0.0, 0.0, 0.0); 779 p = stim::vec3<float>(0.0, 0.0, 0.0);
859 d = stim::vec3<float>(0.0, 0.0, 1.0); 780 d = stim::vec3<float>(0.0, 0.0, 1.0);
860 - m = stim::vec<float>(1.0, 1.0); 781 + m = 1.0;
861 S = stim::vec3<float>(1.0, 1.0, 1.0); 782 S = stim::vec3<float>(1.0, 1.0, 1.0);
862 R = stim::vec3<float>(1.0, 1.0, 1.0); 783 R = stim::vec3<float>(1.0, 1.0, 1.0);
863 -// std::cout << samples << std::endl;  
864 numSamples = samples; 784 numSamples = samples;
865 -// std::cout << numSamples << std::endl;  
866 numSamplesPos = samplespos; 785 numSamplesPos = samplespos;
867 numSamplesMag = samplesmag; 786 numSamplesMag = samplesmag;
  787 + #ifdef DEBUG
  788 + iter = 0;
  789 + iter_pos = 0;
  790 + iter_dir = 0;
  791 + iter_siz = 0;
  792 + #endif
868 } 793 }
869 794
870 ///Position constructor: floats. 795 ///Position constructor: floats.
@@ -882,12 +807,18 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -882,12 +807,18 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
882 { 807 {
883 p = stim::vec3<float>(pos_x, pos_y, pos_z); 808 p = stim::vec3<float>(pos_x, pos_y, pos_z);
884 d = stim::vec3<float>(dir_x, dir_y, dir_z); 809 d = stim::vec3<float>(dir_x, dir_y, dir_z);
885 - m = stim::vec<float>(mag_x, mag_x, mag_x); 810 + m = mag_x;
886 S = stim::vec3<float>(1.0,1.0,1.0); 811 S = stim::vec3<float>(1.0,1.0,1.0);
887 R = stim::vec3<float>(1.0,1.0,1.0); 812 R = stim::vec3<float>(1.0,1.0,1.0);
888 numSamples = numsamples; 813 numSamples = numsamples;
889 numSamplesPos = numsamplespos; 814 numSamplesPos = numsamplespos;
890 numSamplesMag = numsamplesmag; 815 numSamplesMag = numsamplesmag;
  816 + #ifdef DEBUG
  817 + iter = 0;
  818 + iter_pos = 0;
  819 + iter_dir = 0;
  820 + iter_siz = 0;
  821 + #endif
891 } 822 }
892 823
893 ///Position constructor: vecs of floats. 824 ///Position constructor: vecs of floats.
@@ -900,12 +831,18 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -900,12 +831,18 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
900 { 831 {
901 p = pos; 832 p = pos;
902 d = dir; 833 d = dir;
903 - m = vec<float>(mag, mag, mag); 834 + m = mag;
904 S = vec3<float>(1.0,1.0,1.0); 835 S = vec3<float>(1.0,1.0,1.0);
905 R = vec3<float>(1.0,1.0,1.0); 836 R = vec3<float>(1.0,1.0,1.0);
906 numSamples = samples; 837 numSamples = samples;
907 numSamplesPos = samplesPos; 838 numSamplesPos = samplesPos;
908 numSamplesMag = samplesMag; 839 numSamplesMag = samplesMag;
  840 + #ifdef DEBUG
  841 + iter = 0;
  842 + iter_pos = 0;
  843 + iter_dir = 0;
  844 + iter_siz = 0;
  845 + #endif
909 } 846 }
910 847
911 ///destructor 848 ///destructor
@@ -913,14 +850,14 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -913,14 +850,14 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
913 (void) 850 (void)
914 { 851 {
915 Unbind(); 852 Unbind();
916 - glDeleteTextures(1, &texbufferID);  
917 - glDeleteBuffers(1, &fboID);  
918 - glDeleteTextures(1, &ptexbufferID);  
919 - glDeleteBuffers(1, &pfboID);  
920 - glDeleteTextures(1, &mtexbufferID);  
921 - glDeleteBuffers(1, &mfboID);  
922 - glDeleteTextures(1, &btexbufferID);  
923 - glDeleteBuffers(1, &bfboID); 853 + glDeleteTextures(1, &direction_texID);
  854 + glDeleteBuffers(1, &direction_buffID);
  855 + glDeleteTextures(1, &position_texID);
  856 + glDeleteBuffers(1, &position_buffID);
  857 + glDeleteTextures(1, &radius_texID);
  858 + glDeleteBuffers(1, &radius_buffID);
  859 + glDeleteTextures(1, &cylinder_texID);
  860 + glDeleteBuffers(1, &cylinder_buffID);
924 } 861 }
925 862
926 ///@param GLuint id, texture that is going to be sampled. 863 ///@param GLuint id, texture that is going to be sampled.
@@ -939,45 +876,45 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -939,45 +876,45 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
939 network_time = 0; 876 network_time = 0;
940 hit_time = 0; 877 hit_time = 0;
941 #endif 878 #endif
942 - stepsize = 2.5;  
943 - t_length = 16.0; 879 +#ifdef DEBUG
  880 + iter = 0;
  881 + iter_pos = 0;
  882 + iter_dir = 0;
  883 + iter_siz = 0;
  884 +#endif
  885 + stepsize = 10.0;
  886 + n_pixels = 16.0;
944 887
945 srand(100); 888 srand(100);
946 texID = id; 889 texID = id;
947 - //GenerateFBO(16, numSamples*8);  
948 - GenerateFBO(t_length*2, numSamples*t_length, texbufferID, fboID);  
949 - std::cout << numSamples << std::endl; 890 + GenerateFBO(n_pixels*2, numSamples*n_pixels, direction_texID, direction_buffID);
950 CHECK_OPENGL_ERROR 891 CHECK_OPENGL_ERROR
951 - GenerateFBO(t_length*2, numSamplesPos*t_length, ptexbufferID, pfboID);  
952 - std::cout << numSamplesPos << std::endl; 892 + GenerateFBO(n_pixels*2, numSamplesPos*n_pixels, position_texID, position_buffID);
953 CHECK_OPENGL_ERROR 893 CHECK_OPENGL_ERROR
954 - GenerateFBO(t_length*2, numSamplesMag*t_length, mtexbufferID, mfboID);  
955 - std::cout << numSamplesMag << std::endl; 894 + GenerateFBO(n_pixels*2, numSamplesMag*n_pixels, radius_texID, radius_buffID);
956 CHECK_OPENGL_ERROR 895 CHECK_OPENGL_ERROR
957 - GenerateFBO(16, 216, btexbufferID, bfboID); 896 + GenerateFBO(16, 216, cylinder_texID, cylinder_buffID);
958 CHECK_OPENGL_ERROR 897 CHECK_OPENGL_ERROR
959 - t_dir.MapCudaTexture(texbufferID, GL_TEXTURE_2D); 898 + t_dir.MapCudaTexture(direction_texID, GL_TEXTURE_2D);
960 t_dir.Alloc(numSamples); 899 t_dir.Alloc(numSamples);
961 - t_pos.MapCudaTexture(ptexbufferID, GL_TEXTURE_2D); 900 + t_pos.MapCudaTexture(position_texID, GL_TEXTURE_2D);
962 t_pos.Alloc(numSamplesPos); 901 t_pos.Alloc(numSamplesPos);
963 - t_mag.MapCudaTexture(mtexbufferID, GL_TEXTURE_2D); 902 + t_mag.MapCudaTexture(radius_texID, GL_TEXTURE_2D);
964 t_mag.Alloc(numSamplesMag); 903 t_mag.Alloc(numSamplesMag);
965 -// setDims(0.6, 0.6, 1.0);  
966 -// setSize(1024.0, 1024.0, 1024.0);  
967 setMatrix(); 904 setMatrix();
968 dList = glGenLists(3); 905 dList = glGenLists(3);
969 glListBase(dList); 906 glListBase(dList);
970 - Bind(texbufferID, fboID, numSamples, t_length);  
971 - genDirectionVectors(5*M_PI/4); 907 + Bind(direction_texID, direction_buffID, numSamples, n_pixels);
  908 + genDirectionVectors(5*stim::PI/4);
972 Unbind(); 909 Unbind();
973 - Bind(ptexbufferID, pfboID, numSamplesPos, t_length);  
974 - genPositionVectors(); 910 + Bind(position_texID, position_buffID, numSamplesPos, n_pixels);
  911 + genPositionVectors(0.2);
975 Unbind(); 912 Unbind();
976 - Bind(mtexbufferID, mfboID, numSamplesMag, t_length); 913 + Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
977 genMagnitudeVectors(); 914 genMagnitudeVectors();
978 Unbind(); 915 Unbind();
979 - Bind(btexbufferID, bfboID, 27);  
980 - DrawCylinder(); 916 + Bind(cylinder_texID, cylinder_buffID, 27);
  917 +// DrawCylinder();
981 Unbind(); 918 Unbind();
982 } 919 }
983 920
@@ -999,7 +936,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -999,7 +936,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
999 } 936 }
1000 937
1001 ///Returns the m vector. 938 ///Returns the m vector.
1002 - stim::vec<float> 939 + float
1003 getMagnitude() 940 getMagnitude()
1004 { 941 {
1005 return m; 942 return m;
@@ -1045,22 +982,13 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1045,22 +982,13 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1045 d[2] = z; 982 d[2] = z;
1046 } 983 }
1047 984
1048 - ///@param stim::vec<float> dir, the new d.  
1049 - ///Sets the m vector to the input vector mag.  
1050 - void  
1051 - setMagnitude(stim::vec<float> mag)  
1052 - {  
1053 - m[0] = mag[0];  
1054 - m[1] = mag[0];  
1055 - }  
1056 985
1057 ///@param float mag, size of the sampled region. 986 ///@param float mag, size of the sampled region.
1058 ///Sets the m vector to the input mag for both templates. 987 ///Sets the m vector to the input mag for both templates.
1059 void 988 void
1060 setMagnitude(float mag) 989 setMagnitude(float mag)
1061 { 990 {
1062 - m[0] = mag;  
1063 - m[1] = mag; 991 + m = mag;
1064 } 992 }
1065 993
1066 ///@param float x, voxel size in the x direction. 994 ///@param float x, voxel size in the x direction.
@@ -1111,17 +1039,27 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1111,17 +1039,27 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1111 getRotation(stim::vec3<float> dir) 1039 getRotation(stim::vec3<float> dir)
1112 { 1040 {
1113 stim::vec<float> out(0.0,0.0,0.0,0.0); 1041 stim::vec<float> out(0.0,0.0,0.0,0.0);
1114 - stim::vec<float> from(0.0,0.0,1.0);  
1115 - out[0] = acos(dir.dot(from))*180/M_PI;  
1116 - if(out[0] < 1.0){ 1042 + stim::vec3<float> from(0.0,0.0,1.0);
  1043 + out[0] = acos(dir.dot(from))*180/stim::PI;
  1044 + #ifdef DEBUG
  1045 + std::cout << "out is " << out << std::endl;
  1046 + std::cout << "when rotating from " << from << " to " << dir << std::endl;
  1047 + #endif
  1048 + if(out[0] < 0.01){
1117 out[0] = 0.0; 1049 out[0] = 0.0;
1118 out[1] = 0.0; 1050 out[1] = 0.0;
1119 out[2] = 0.0; 1051 out[2] = 0.0;
1120 out[3] = 1.0; 1052 out[3] = 1.0;
  1053 + }
  1054 + else if(out[0] < -180.0+0.01)
  1055 + {
  1056 + out[0] = 180.0;
  1057 + out[1] = 1.0;
  1058 + out[2] = 0.0;
  1059 + out[3] = 0.0;
1121 } else { 1060 } else {
1122 - stim::vec<float> temp(0.0, 0.0, 0.0);;  
1123 - stim::vec<float> dir1(dir[0], dir[1], dir[2]);  
1124 - temp = (from.cross(dir1)).norm(); 1061 + stim::vec3<float> temp(0.0, 0.0, 0.0);;
  1062 + temp = (from.cross(dir)).norm();
1125 out[1] = temp[0]; 1063 out[1] = temp[0];
1126 out[2] = temp[1]; 1064 out[2] = temp[1];
1127 out[3] = temp[2]; 1065 out[3] = temp[2];
@@ -1152,7 +1090,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1152,7 +1090,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1152 void 1090 void
1153 setSeedMag(float mag) 1091 setSeedMag(float mag)
1154 { 1092 {
1155 -// std::cout << "sMag: " << mag << std::endl;  
1156 seedsmags.push(mag); 1093 seedsmags.push(mag);
1157 } 1094 }
1158 1095
@@ -1165,7 +1102,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1165,7 +1102,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1165 void 1102 void
1166 setSeed(float x, float y, float z) 1103 setSeed(float x, float y, float z)
1167 { 1104 {
1168 -// std::cout << "sPos: " << x << " " << y << " " << z << std::endl;  
1169 seeds.push(stim::vec<float>(x, y, z)); 1105 seeds.push(stim::vec<float>(x, y, z));
1170 } 1106 }
1171 1107
@@ -1176,7 +1112,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1176,7 +1112,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1176 void 1112 void
1177 setSeedVec(float x, float y, float z) 1113 setSeedVec(float x, float y, float z)
1178 { 1114 {
1179 -// std::cout << "sDir: " << x << " " << y << " " << z << std::endl;  
1180 seedsvecs.push(stim::vec<float>(x, y, z)); 1115 seedsvecs.push(stim::vec<float>(x, y, z));
1181 } 1116 }
1182 1117
@@ -1297,7 +1232,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1297,7 +1232,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1297 void 1232 void
1298 saveNetwork(std::string name) 1233 saveNetwork(std::string name)
1299 { 1234 {
1300 - stim::glObj<float> sk; 1235 +/* stim::glObj<float> sk;
1301 for(int i = 0; i < nt.sizeE(); i++) 1236 for(int i = 0; i < nt.sizeE(); i++)
1302 { 1237 {
1303 std::vector<stim::vec< float > > cm = nt.getEdgeCenterLineMag(i); 1238 std::vector<stim::vec< float > > cm = nt.getEdgeCenterLineMag(i);
@@ -1310,7 +1245,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1310,7 +1245,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1310 } 1245 }
1311 sk.End(); 1246 sk.End();
1312 } 1247 }
1313 - sk.save(name); 1248 +*/ sk.save(name);
1314 } 1249 }
1315 1250
1316 ///Depreciated, but might be reused later() 1251 ///Depreciated, but might be reused later()
@@ -1318,7 +1253,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1318,7 +1253,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1318 stim::glObj<float> 1253 stim::glObj<float>
1319 getNetwork() 1254 getNetwork()
1320 { 1255 {
1321 - 1256 + return sk;
1322 } 1257 }
1323 1258
1324 ///returns a COPY of the entire stim::glnetwork object. 1259 ///returns a COPY of the entire stim::glnetwork object.
@@ -1333,7 +1268,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1333,7 +1268,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1333 GLuint 1268 GLuint
1334 getFB() 1269 getFB()
1335 { 1270 {
1336 - return bfboID; 1271 + return cylinder_buffID;
1337 } 1272 }
1338 1273
1339 //--------------------------------------------------------------------------// 1274 //--------------------------------------------------------------------------//
@@ -1357,14 +1292,17 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1357,14 +1292,17 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1357 int 1292 int
1358 Step() 1293 Step()
1359 { 1294 {
1360 - Bind(texbufferID, fboID, numSamples, t_length); 1295 + #ifdef DEBUG
  1296 + std::cerr << "Took a step" << std::endl;
  1297 + #endif
  1298 + Bind(direction_texID, direction_buffID, numSamples, n_pixels);
1361 CHECK_OPENGL_ERROR 1299 CHECK_OPENGL_ERROR
1362 findOptimalDirection(); 1300 findOptimalDirection();
1363 Unbind(); 1301 Unbind();
1364 - Bind(ptexbufferID, pfboID, numSamplesPos, t_length); 1302 + Bind(position_texID, position_buffID, numSamplesPos, n_pixels);
1365 findOptimalPosition(); 1303 findOptimalPosition();
1366 Unbind(); 1304 Unbind();
1367 - Bind(mtexbufferID, mfboID, numSamplesMag, t_length); 1305 + Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
1368 findOptimalScale(); 1306 findOptimalScale();
1369 Unbind(); 1307 Unbind();
1370 CHECK_OPENGL_ERROR 1308 CHECK_OPENGL_ERROR
@@ -1385,16 +1323,16 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1385,16 +1323,16 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1385 //--------------------------------------------------------------------------// 1323 //--------------------------------------------------------------------------//
1386 1324
1387 void 1325 void
1388 - MonteCarloDirectionVectors(int nSamples, float solidAngle = 2*M_PI) 1326 + MonteCarloDirectionVectors(int nSamples, float solidAngle = stim::TAU)
1389 { 1327 {
1390 - float PHI[2], Z[2], range;  
1391 - PHI[0] = asin(solidAngle/2);  
1392 - PHI[1] = asin(0); 1328 +// float PHI[2];//, Z[2];//, range;
  1329 +// PHI[0] = asin(solidAngle/2);
  1330 +// PHI[1] = asin(0);
1393 1331
1394 - Z[0] = cos(PHI[0]);  
1395 - Z[1] = cos(PHI[1]); 1332 +// Z[0] = cos(PHI[0]);
  1333 +// Z[1] = cos(PHI[1]);
1396 1334
1397 - range = Z[0] - Z[1]; 1335 +// range = Z[0] - Z[1];
1398 1336
1399 std::vector<stim::vec3<float> > vecsUni; 1337 std::vector<stim::vec3<float> > vecsUni;
1400 for(int i = 0; i < numSamplesPos; i++) 1338 for(int i = 0; i < numSamplesPos; i++)
@@ -1428,8 +1366,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1428,8 +1366,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1428 int j = 0; 1366 int j = 0;
1429 for(float i = step; i <= 360.0; i += step) 1367 for(float i = step; i <= 360.0; i += step)
1430 { 1368 {
1431 - x=r0*cos(i*2.0*M_PI/360.0);  
1432 - y=r0*sin(i*2.0*M_PI/360.0); 1369 + x=r0*cos(i*stim::TAU/360.0);
  1370 + y=r0*sin(i*stim::TAU/360.0);
1433 glTexCoord3f(x,y,z0); 1371 glTexCoord3f(x,y,z0);
1434 glVertex2f(0.0, j*6.4+6.4); 1372 glVertex2f(0.0, j*6.4+6.4);
1435 // glVertex2f(0.0, j*27.0+27.0); 1373 // glVertex2f(0.0, j*27.0+27.0);
@@ -1451,12 +1389,13 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1451,12 +1389,13 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1451 } 1389 }
1452 1390
1453 ///need to return the cylinder. 1391 ///need to return the cylinder.
  1392 +///SOMETHING MIGHT BE GOING ON HERE IN GENERATE BUFFER.
1454 void 1393 void
1455 DrawLongCylinder(int n = 8, int l_template = 8,int l_square = 8) 1394 DrawLongCylinder(int n = 8, int l_template = 8,int l_square = 8)
1456 { 1395 {
1457 int cylLen = cL.size()-1; 1396 int cylLen = cL.size()-1;
1458 - GenerateFBO(n*l_square, cylLen*l_template, btexbufferID, bfboID);  
1459 - Bind(btexbufferID, bfboID, cylLen, l_template*l_square/2.0); 1397 + GenerateFBO(n*l_square, cylLen*l_template, cylinder_texID, cylinder_buffID);
  1398 + Bind(cylinder_texID, cylinder_buffID, cylLen, l_template*l_square/2.0);
1460 stim::cylinder<float> cyl(cL, cM); 1399 stim::cylinder<float> cyl(cL, cM);
1461 std::vector<std::vector<stim::vec3<float> > > p = cyl.getPoints(n); 1400 std::vector<std::vector<stim::vec3<float> > > p = cyl.getPoints(n);
1462 for(int i = 0; i < p.size()-1; i++) ///number of circles 1401 for(int i = 0; i < p.size()-1; i++) ///number of circles
@@ -1502,14 +1441,28 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1502,14 +1441,28 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1502 seeds.pop(); 1441 seeds.pop();
1503 seedsvecs.pop(); 1442 seedsvecs.pop();
1504 seedsmags.pop(); 1443 seedsmags.pop();
1505 -// std::cout << "The current seed Vector is " << curSeedVec << std::endl;  
1506 setPosition(curSeed); 1444 setPosition(curSeed);
1507 setDirection(curSeedVec); 1445 setDirection(curSeedVec);
1508 setMagnitude(curSeedMag); 1446 setMagnitude(curSeedMag);
  1447 +
  1448 + #ifdef DEBUG
  1449 + std::cout << "The new seed " << curSeed << curSeedVec << curSeedMag << std::endl;
  1450 + #endif
  1451 +
  1452 +// Bind(direction_texID, direction_buffID, numSamples, n_pixels);
  1453 +// CHECK_OPENGL_ERROR
  1454 +// findOptimalDirection();
  1455 +// Unbind();
  1456 +//THIS IS EXPERIMENTAL
  1457 + Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
  1458 + findOptimalScale();
  1459 + Unbind();
  1460 +//THIS IS EXPERIMENTAL
  1461 +
1509 // cL.push_back(curSeed); 1462 // cL.push_back(curSeed);
1510 // cM.push_back(curSeedMag); 1463 // cM.push_back(curSeedMag);
1511 // cD.push_back(curSeedMag); 1464 // cD.push_back(curSeedMag);
1512 - pair<stim::fiber<float>, int> a = traceLine(p, m, min_cost); 1465 + traceLine(p, m, min_cost);
1513 } 1466 }
1514 } 1467 }
1515 1468
@@ -1556,17 +1509,17 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1556,17 +1509,17 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1556 ds[0], ds[1], ds[2], 1509 ds[0], ds[1], ds[2],
1557 ups[0], ups[1], ups[2]); 1510 ups[0], ups[1], ups[2]);
1558 1511
1559 -// sk.Render();  
1560 - nt.Render(); 1512 + sk.Render();
  1513 +// nt.Render();
1561 1514
1562 CHECK_OPENGL_ERROR 1515 CHECK_OPENGL_ERROR
1563 1516
1564 1517
1565 -// glLoadName((int) sk.numL());  
1566 - glLoadName(nt.sizeE()); 1518 + glLoadName((int) sk.numL());
  1519 +// glLoadName(nt.sizeE());
1567 1520
1568 -// sk.RenderLine(cL);  
1569 - nt.RenderLine(cL); 1521 + sk.RenderLine(cL);
  1522 +// nt.RenderLine(cL);
1570 1523
1571 // glPopName(); 1524 // glPopName();
1572 glFlush(); 1525 glFlush();
@@ -1615,8 +1568,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1615,8 +1568,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1615 { 1568 {
1616 cL.clear(); 1569 cL.clear();
1617 cM.clear(); 1570 cM.clear();
1618 - } 1571 + }
1619 1572
  1573 +/*
1620 void 1574 void
1621 addToNetwork(pair<stim::fiber<float>, int> in, stim::vec3<float> spos, 1575 addToNetwork(pair<stim::fiber<float>, int> in, stim::vec3<float> spos,
1622 stim::vec<float> smag, stim::vec3<float> sdir) 1576 stim::vec<float> smag, stim::vec3<float> sdir)
@@ -1664,13 +1618,26 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1664,13 +1618,26 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1664 network_time += nt * 1000.0; 1618 network_time += nt * 1000.0;
1665 #endif 1619 #endif
1666 } 1620 }
  1621 +*/
  1622 + void
  1623 + addToNetwork(std::vector<stim::vec3<float> > L, std::vector<float > M)
  1624 + {
  1625 + if(L.size() > 3)
  1626 + {
  1627 + sk.Begin(stim::OBJ_LINE);
  1628 + for(int i = 0; i < L.size(); i++)
  1629 + {
  1630 + sk.TexCoord(M[i]);
  1631 + sk.Vertex(L[i][0], L[i][1], L[i][2]);
  1632 + }
  1633 + sk.End();
1667 1634
1668 -// void  
1669 -// addToNetwork(pair<stim::fiber<float>, int> in, stim::vec3<float> spos,  
1670 -// stim::vec<float> smag, stim::vec3<float> sdir)  
1671 -// {  
1672 -//  
1673 -// } 1635 + nt.addEdge(L,M);
  1636 + #ifdef DEBUG
  1637 + iter++;
  1638 + #endif
  1639 + }
  1640 + }
1674 1641
1675 1642
1676 void 1643 void
@@ -1678,23 +1645,22 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1678,23 +1645,22 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1678 { 1645 {
1679 std::cout << nt.sizeE() << " edges " << std::endl; 1646 std::cout << nt.sizeE() << " edges " << std::endl;
1680 std::cout << nt.sizeV() << " nodes " << std::endl; 1647 std::cout << nt.sizeV() << " nodes " << std::endl;
1681 -  
1682 } 1648 }
1683 1649
1684 - std::pair<stim::fiber<float>, int >  
1685 - traceLine(stim::vec3<float> pos, stim::vec<float> mag, int min_cost) 1650 + void
  1651 + traceLine(stim::vec3<float> pos, float mag, int min_cost)
1686 { 1652 {
1687 //starting (seed) position and magnitude. 1653 //starting (seed) position and magnitude.
1688 stim::vec3<float> spos = getPosition(); 1654 stim::vec3<float> spos = getPosition();
1689 - stim::vec<float> smag = getMagnitude(); 1655 + float smag = getMagnitude();
1690 stim::vec3<float> sdir = getDirection(); 1656 stim::vec3<float> sdir = getDirection();
1691 1657
1692 - Bind(); 1658 +// Bind();
1693 // sk.Begin(stim::OBJ_LINE); 1659 // sk.Begin(stim::OBJ_LINE);
1694 1660
1695 1661
1696 -// sk.createFromSelf(GL_SELECT);  
1697 - nt.createFromSelf(GL_SELECT); 1662 + sk.createFromSelf(GL_SELECT);
  1663 +// nt.createFromSelf(GL_SELECT);
1698 1664
1699 cL.push_back(pos); 1665 cL.push_back(pos);
1700 cM.push_back(mag); 1666 cM.push_back(mag);
@@ -1710,12 +1676,11 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1710,12 +1676,11 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1710 int cost = Step(); 1676 int cost = Step();
1711 if (cost > min_cost){ 1677 if (cost > min_cost){
1712 running = false; 1678 running = false;
1713 -// sk.End();  
1714 branchDetection2(); 1679 branchDetection2();
1715 - pair<stim::fiber<float>, int> a(stim::fiber<float> (cL, cM), -1);  
1716 - addToNetwork(a, spos, smag, sdir);  
1717 -// std::cout << "the cost of " << cost << " > " << min_cost << std::endl;  
1718 - return a; 1680 + addToNetwork(cL, cM);
  1681 + #ifdef DEBUG
  1682 + std::cerr << "the cost of " << cost << " > " << min_cost << std::endl;
  1683 + #endif
1719 break; 1684 break;
1720 } else { 1685 } else {
1721 //Have we found the edge of the map? 1686 //Have we found the edge of the map?
@@ -1726,10 +1691,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1726,10 +1691,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1726 { 1691 {
1727 running = false; 1692 running = false;
1728 branchDetection2(); 1693 branchDetection2();
1729 - pair<stim::fiber<float>, int> a(stim::fiber<float> (cL, cM), -1);  
1730 - addToNetwork(a, spos, smag, sdir);  
1731 -// std::cout << "I hit and edge" << std::endl;  
1732 - return a; 1694 + addToNetwork(cL, cM);
  1695 + #ifdef DEBUG
  1696 + std::cerr << "I hit and edge" << std::endl;
  1697 + #endif
1733 break; 1698 break;
1734 } 1699 }
1735 //If this is the first step in the trace, 1700 //If this is the first step in the trace,
@@ -1741,39 +1706,40 @@ class gl_spider : public virtual gl_texture&lt;T&gt; @@ -1741,39 +1706,40 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1741 } 1706 }
1742 //Has the template size gotten unreasonable? 1707 //Has the template size gotten unreasonable?
1743 mag = getMagnitude(); 1708 mag = getMagnitude();
1744 - if(mag[0] > 75 || mag[0] < 1){ 1709 + if(mag > 75 || mag < 1){
1745 running = false; 1710 running = false;
1746 branchDetection2(); 1711 branchDetection2();
1747 - pair<stim::fiber<float>, int> a(stim::fiber<float> (cL, cM), -1);  
1748 - addToNetwork(a, spos, smag, sdir);  
1749 -// std::cout << "The templates are too big" << std::endl;  
1750 - return a; 1712 + addToNetwork(cL, cM);
  1713 + #ifdef DEBUG
  1714 + std::cerr << "The templates are too big" << std::endl;
  1715 + #endif
1751 break; 1716 break;
1752 } 1717 }
1753 else 1718 else
1754 { 1719 {
1755 - h = selectObject(p, getDirection(), m[0]); 1720 + h = selectObject(p, getDirection(), m);
1756 //Have we hit something previously traced? 1721 //Have we hit something previously traced?
1757 if(h != -1){ 1722 if(h != -1){
1758 -// std::cout << "I hit the fiber " << h << std::endl; 1723 + #ifdef DEBUG
  1724 + std::cerr << "I hit the fiber " << h << std::endl;
  1725 + #endif
1759 running = false; 1726 running = false;
1760 branchDetection2(); 1727 branchDetection2();
1761 - pair<stim::fiber<float>, int> a(stim::fiber<float> (cL, cM), h);  
1762 - addToNetwork(a, spos, smag, sdir);  
1763 - return a; 1728 + addToNetwork(cL, cM);
1764 break; 1729 break;
1765 } 1730 }
1766 else { 1731 else {
1767 cL.push_back(stim::vec3<float>(p[0], p[1],p[2])); 1732 cL.push_back(stim::vec3<float>(p[0], p[1],p[2]));
1768 - cM.push_back(stim::vec<float>(m[0], m[0]));  
1769 -// Bind(btexbufferID, bfboID, 27);  
1770 - Unbind(); 1733 + cM.push_back(m);
  1734 +// Unbind();
1771 CHECK_OPENGL_ERROR 1735 CHECK_OPENGL_ERROR
1772 -  
1773 } 1736 }
1774 } 1737 }
1775 } 1738 }
1776 } 1739 }
  1740 + #ifdef DEBUG
  1741 + std::cout << "I broke out!" << std::endl;
  1742 + #endif
1777 } 1743 }
1778 }; 1744 };
1779 } 1745 }
stim/gl/gl_texture.h
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@@ -64,7 +64,7 @@ class gl_texture : public virtual image_stack&lt;T, F&gt; @@ -64,7 +64,7 @@ class gl_texture : public virtual image_stack&lt;T, F&gt;
64 case 4: 64 case 4:
65 return GL_RGBA; 65 return GL_RGBA;
66 default: 66 default:
67 - std::cout<<"Error in stim::gl_texture - unable to guess texture format based on number of channels ("<<R[4]<<")"<<std::endl; 67 + std::cout<<"Error in stim::gl_texture - unable to guess texture format based on number of channels" << std::endl;
68 exit(1); 68 exit(1);
69 } 69 }
70 } 70 }
@@ -236,7 +236,7 @@ class gl_texture : public virtual image_stack&lt;T, F&gt; @@ -236,7 +236,7 @@ class gl_texture : public virtual image_stack&lt;T, F&gt;
236 if(texID == 0) generate_texture(); //generate the texture if it doesn't already exist 236 if(texID == 0) generate_texture(); //generate the texture if it doesn't already exist
237 else{ 237 else{
238 std::cout<<"Texture has already been attached to a context."<<std::endl; 238 std::cout<<"Texture has already been attached to a context."<<std::endl;
239 - exit(1); 239 + //exit(1); Why do we need to quit if it's attached. print the message and continue.
240 } 240 }
241 } 241 }
242 242
stim/math/circle.h
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@@ -48,9 +48,9 @@ public: @@ -48,9 +48,9 @@ public:
48 CUDA_CALLABLE 48 CUDA_CALLABLE
49 circle(T size, T z_pos = (T)0) : plane<T>() 49 circle(T size, T z_pos = (T)0) : plane<T>()
50 { 50 {
51 - init();  
52 center(stim::vec3<T>(0,0,z_pos)); 51 center(stim::vec3<T>(0,0,z_pos));
53 scale(size); 52 scale(size);
  53 + init();
54 } 54 }
55 55
56 ///create a rectangle from a center point, normal 56 ///create a rectangle from a center point, normal
@@ -88,6 +88,7 @@ public: @@ -88,6 +88,7 @@ public:
88 { 88 {
89 init(); 89 init();
90 setU(u); 90 setU(u);
  91 +// U = u;
91 center(c); 92 center(c);
92 normal(n); 93 normal(n);
93 scale(s); 94 scale(s);
@@ -174,6 +175,13 @@ public: @@ -174,6 +175,13 @@ public:
174 return p(x,y); 175 return p(x,y);
175 } 176 }
176 177
  178 + std::string str() const
  179 + {
  180 + std::stringstream ss;
  181 + ss << "(P=" << P.str() << ", N=" << N.str() << ", U=" << U.str() << ", Y=" << Y.str();
  182 + return ss.str();
  183 + }
  184 +
177 }; 185 };
178 } 186 }
179 #endif 187 #endif
@@ -80,6 +80,15 @@ public: @@ -80,6 +80,15 @@ public:
80 return sph; 80 return sph;
81 } 81 }
82 82
  83 + CUDA_CALLABLE vec3<T> cart2cyl() const{
  84 + vec3<T> cyl;
  85 + cyl.ptr[0] = sqrt(pow(ptr[0],2) + pow(ptr[1],2));
  86 + cyl.ptr[1] = atan(ptr[1]/ptr[0]);
  87 + cyl.ptr[2] = ptr[2];
  88 +
  89 + return cyl;
  90 + }
  91 +
83 /// Convert the vector from cartesian to spherical coordinates (r, theta, phi -> x, y, z where theta = [0, 2*pi]) 92 /// Convert the vector from cartesian to spherical coordinates (r, theta, phi -> x, y, z where theta = [0, 2*pi])
84 CUDA_CALLABLE vec3<T> sph2cart() const{ 93 CUDA_CALLABLE vec3<T> sph2cart() const{
85 vec3<T> cart; 94 vec3<T> cart;
@@ -90,6 +99,16 @@ public: @@ -90,6 +99,16 @@ public:
90 return cart; 99 return cart;
91 } 100 }
92 101
  102 + /// Convert the vector from cylindrical to cart coordinates (r, theta, z -> x, y, z where theta = [0, 2*pi])
  103 + CUDA_CALLABLE vec3<T> cyl2cart() const{
  104 + vec3<T> cart;
  105 + cart.ptr[0] = ptr[0] * std::cos(ptr[1]);
  106 + cart.ptr[1] = ptr[0] * std::sin(ptr[1]);
  107 + cart.ptr[2] = ptr[2];
  108 +
  109 + return cart;
  110 + }
  111 +
93 /// Computes the normalized vector (where each coordinate is divided by the L2 norm) 112 /// Computes the normalized vector (where each coordinate is divided by the L2 norm)
94 CUDA_CALLABLE vec3<T> norm() const{ 113 CUDA_CALLABLE vec3<T> norm() const{
95 vec3<T> result; 114 vec3<T> result;
stim/visualization/cylinder.h
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@@ -2,19 +2,27 @@ @@ -2,19 +2,27 @@
2 #define STIM_CYLINDER_H 2 #define STIM_CYLINDER_H
3 #include <iostream> 3 #include <iostream>
4 #include <stim/math/circle.h> 4 #include <stim/math/circle.h>
5 -#include <stim/math/vec3.h> 5 +#include <stim/biomodels/centerline.h>
6 6
7 7
8 namespace stim 8 namespace stim
9 { 9 {
10 template<typename T> 10 template<typename T>
11 class cylinder 11 class cylinder
  12 + : public centerline<T>
12 { 13 {
13 private: 14 private:
14 stim::circle<T> s; //an arbitrary circle 15 stim::circle<T> s; //an arbitrary circle
15 - std::vector<stim::circle<T> > e; 16 + std::vector<stim::circle<T> > e; //an array of circles that store the centerline
  17 +
  18 + std::vector<stim::vec3<T> > norms;
  19 + std::vector<stim::vec<T> > Us;
16 std::vector<stim::vec<T> > mags; 20 std::vector<stim::vec<T> > mags;
17 std::vector< T > L; //length of the cylinder at each position. 21 std::vector< T > L; //length of the cylinder at each position.
  22 +
  23 +
  24 + using stim::centerline<T>::c;
  25 + using stim::centerline<T>::N;
18 26
19 ///default init 27 ///default init
20 void 28 void
@@ -23,6 +31,20 @@ class cylinder @@ -23,6 +31,20 @@ class cylinder
23 31
24 } 32 }
25 33
  34 + ///Calculate the physical length of the fiber at each point in the fiber.
  35 + void
  36 + calculateL()
  37 + {
  38 +/* L.resize(inP.size());
  39 + T temp = (T)0;
  40 + L[0] = 0;
  41 + for(size_t i = 1; i < L.size(); i++)
  42 + {
  43 + temp += (inP[i-1] - inP[i]).len();
  44 + L[i] = temp;
  45 + }
  46 +*/ }
  47 +
26 ///inits the cylinder from a list of points (std::vector of stim::vec3 --inP) and radii (inM) 48 ///inits the cylinder from a list of points (std::vector of stim::vec3 --inP) and radii (inM)
27 void 49 void
28 init(std::vector<stim::vec3<T> > inP, std::vector<stim::vec<T> > inM) 50 init(std::vector<stim::vec3<T> > inP, std::vector<stim::vec<T> > inM)
@@ -31,6 +53,10 @@ class cylinder @@ -31,6 +53,10 @@ class cylinder
31 stim::vec3<float> v1; 53 stim::vec3<float> v1;
32 stim::vec3<float> v2; 54 stim::vec3<float> v2;
33 e.resize(inP.size()); 55 e.resize(inP.size());
  56 +
  57 + norms.resize(inP.size());
  58 + Us.resize(inP.size());
  59 +
34 if(inP.size() < 2) 60 if(inP.size() < 2)
35 return; 61 return;
36 62
@@ -46,7 +72,9 @@ class cylinder @@ -46,7 +72,9 @@ class cylinder
46 72
47 stim::vec3<T> dr = (inP[1] - inP[0]).norm(); 73 stim::vec3<T> dr = (inP[1] - inP[0]).norm();
48 s = stim::circle<T>(inP[0], inM[0][0], dr, stim::vec3<T>(1,0,0)); 74 s = stim::circle<T>(inP[0], inM[0][0], dr, stim::vec3<T>(1,0,0));
  75 + norms[0] = s.N;
49 e[0] = s; 76 e[0] = s;
  77 + Us[0] = e[0].U;
50 for(size_t i = 1; i < inP.size()-1; i++) 78 for(size_t i = 1; i < inP.size()-1; i++)
51 { 79 {
52 s.center(inP[i]); 80 s.center(inP[i]);
@@ -54,16 +82,24 @@ class cylinder @@ -54,16 +82,24 @@ class cylinder
54 v2 = (inP[i+1] - inP[i]).norm(); 82 v2 = (inP[i+1] - inP[i]).norm();
55 dr = (v1+v2).norm(); 83 dr = (v1+v2).norm();
56 s.normal(dr); 84 s.normal(dr);
  85 +
  86 + norms[i] = s.N;
  87 +
57 s.scale(inM[i][0]/inM[i-1][0]); 88 s.scale(inM[i][0]/inM[i-1][0]);
58 e[i] = s; 89 e[i] = s;
  90 + Us[i] = e[i].U;
59 } 91 }
60 92
61 int j = inP.size()-1; 93 int j = inP.size()-1;
62 s.center(inP[j]); 94 s.center(inP[j]);
63 dr = (inP[j] - inP[j-1]).norm(); 95 dr = (inP[j] - inP[j-1]).norm();
64 s.normal(dr); 96 s.normal(dr);
  97 +
  98 + norms[j] = s.N;
  99 +
65 s.scale(inM[j][0]/inM[j-1][0]); 100 s.scale(inM[j][0]/inM[j-1][0]);
66 e[j] = s; 101 e[j] = s;
  102 + Us[j] = e[j].U;
67 } 103 }
68 104
69 ///returns the direction vector at point idx. 105 ///returns the direction vector at point idx.
@@ -72,18 +108,42 @@ class cylinder @@ -72,18 +108,42 @@ class cylinder
72 { 108 {
73 if(idx == 0) 109 if(idx == 0)
74 { 110 {
75 - return (e[idx+1].P - e[idx].P).norm(); 111 + stim::vec3<T> temp(
  112 + c[idx+1][0]-c[idx][0],
  113 + c[idx+1][1]-c[idx][1],
  114 + c[idx+1][2]-c[idx][2]
  115 + );
  116 +// return (e[idx+1].P - e[idx].P).norm();
  117 + return (temp.norm());
76 } 118 }
77 - else if(idx == e.size()-1) 119 + else if(idx == N-1)
78 { 120 {
79 - return (e[idx].P - e[idx-1].P).norm(); 121 + stim::vec3<T> temp(
  122 + c[idx][0]-c[idx+1][0],
  123 + c[idx][1]-c[idx+1][1],
  124 + c[idx][2]-c[idx+1][2]
  125 + );
  126 + // return (e[idx].P - e[idx-1].P).norm();
  127 + return (temp.norm());
80 } 128 }
81 else 129 else
82 { 130 {
83 // return (e[idx+1].P - e[idx].P).norm(); 131 // return (e[idx+1].P - e[idx].P).norm();
84 - stim::vec3<float> v1 = (e[idx].P-e[idx-1].P).norm();  
85 - stim::vec3<float> v2 = (e[idx+1].P-e[idx].P).norm();  
86 - return (v1+v2).norm(); 132 +// stim::vec3<float> v1 = (e[idx].P-e[idx-1].P).norm();
  133 + stim::vec3<T> v1(
  134 + c[idx][0]-c[idx-1][0],
  135 + c[idx][1]-c[idx-1][1],
  136 + c[idx][2]-c[idx-1][2]
  137 + );
  138 +
  139 +// stim::vec3<float> v2 = (e[idx+1].P-e[idx].P).norm();
  140 + stim::vec3<T> v2(
  141 + c[idx+1][0]-c[idx][0],
  142 + c[idx+1][1]-c[idx][1],
  143 + c[idx+1][2]-c[idx][2]
  144 + );
  145 +
  146 + return (v1.norm()+v2.norm()).norm();
87 } 147 }
88 // return e[idx].N; 148 // return e[idx].N;
89 149
@@ -92,14 +152,17 @@ class cylinder @@ -92,14 +152,17 @@ class cylinder
92 stim::vec3<T> 152 stim::vec3<T>
93 d(T l, int idx) 153 d(T l, int idx)
94 { 154 {
95 - if(idx == 0 || idx == e.size()-1) 155 + if(idx == 0 || idx == N-1)
96 { 156 {
97 - return e[idx].N; 157 + return norms[idx];
  158 +// return e[idx].N;
98 } 159 }
99 else 160 else
100 { 161 {
  162 +
101 T rat = (l-L[idx])/(L[idx+1]-L[idx]); 163 T rat = (l-L[idx])/(L[idx+1]-L[idx]);
102 - return( e[idx].N + (e[idx+1].N - e[idx].N)*rat); 164 + return( norms[idx] + (norms[idx+1] - norms[idx])*rat);
  165 +// return( e[idx].N + (e[idx+1].N - e[idx].N)*rat);
103 } 166 }
104 } 167 }
105 168
@@ -137,6 +200,7 @@ class cylinder @@ -137,6 +200,7 @@ class cylinder
137 public: 200 public:
138 ///default constructor 201 ///default constructor
139 cylinder() 202 cylinder()
  203 + // : centerline<T>()
140 { 204 {
141 205
142 } 206 }
@@ -144,15 +208,33 @@ class cylinder @@ -144,15 +208,33 @@ class cylinder
144 ///constructor to create a cylinder from a set of points, radii, and the number of sides for the cylinder. 208 ///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 vec3 composing the points of the centerline. 209 ///@param inP: Vector of stim vec3 composing the points of the centerline.
146 ///@param inM: Vector of stim vecs composing the radii of the centerline. 210 ///@param inM: Vector of stim vecs composing the radii of the centerline.
147 - cylinder(std::vector<stim::vec3<T> > inP, std::vector<stim::vec<T> > inM){ 211 + cylinder(std::vector<stim::vec3<T> > inP, std::vector<stim::vec<T> > inM)
  212 + : centerline<T>(inP)
  213 + {
148 init(inP, inM); 214 init(inP, inM);
149 } 215 }
150 216
  217 + ///constructor to create a cylinder from a set of points, radii, and the number of sides for the cylinder.
  218 + ///@param inP: Vector of stim vec3 composing the points of the centerline.
  219 + ///@param inM: Vector of stim vecs composing the radii of the centerline.
  220 + cylinder(std::vector<stim::vec3<T> > inP, std::vector< T > inM)
  221 + : centerline<T>(inP)
  222 + {
  223 + std::vector<stim::vec<T> > temp;
  224 + stim::vec<T> zero(0.0,0.0);
  225 + temp.resize(inM.size(), zero);
  226 + for(int i = 0; i < inM.size(); i++)
  227 + temp[i][0] = inM[i];
  228 + init(inP, temp);
  229 + }
  230 +
151 231
152 ///Constructor defines a cylinder with centerline inP and magnitudes of zero 232 ///Constructor defines a cylinder with centerline inP and magnitudes of zero
153 ///@param inP: Vector of stim vec3 composing the points of the centerline 233 ///@param inP: Vector of stim vec3 composing the points of the centerline
154 - cylinder(std::vector< stim::vec3<T> > inP){  
155 - std::vector< stim::vec<T> > inM; //create an array of arbitrary magnitudes 234 + cylinder(std::vector< stim::vec3<T> > inP)
  235 + : centerline<T>(inP)
  236 + {
  237 + std::vector< T > inM; //create an array of arbitrary magnitudes
156 238
157 stim::vec<T> zero; 239 stim::vec<T> zero;
158 zero.push_back(0); 240 zero.push_back(0);
@@ -164,7 +246,7 @@ class cylinder @@ -164,7 +246,7 @@ class cylinder
164 ///Returns the number of points on the cylinder centerline 246 ///Returns the number of points on the cylinder centerline
165 247
166 unsigned int size(){ 248 unsigned int size(){
167 - return e.size(); 249 + return N;
168 } 250 }
169 251
170 252
@@ -180,9 +262,23 @@ class cylinder @@ -180,9 +262,23 @@ class cylinder
180 } 262 }
181 T l = pvalue*L[L.size()-1]; 263 T l = pvalue*L[L.size()-1];
182 int idx = findIdx(l); 264 int idx = findIdx(l);
183 - T rat = (l-L[idx])/(L[idx+1]-L[idx]);  
184 - return( e[idx].P + (e[idx+1].P-e[idx].P)*rat);  
185 - } 265 + return (p(l,idx));
  266 +/* T rat = (l-L[idx])/(L[idx+1]-L[idx]);
  267 + stim::vec3<T> v1(
  268 + c[idx][0],
  269 + c[idx][1],
  270 + c[idx][2]
  271 + );
  272 +
  273 + stim::vec3<T> v2(
  274 + c[idx+1][0],
  275 + c[idx+1][1],
  276 + c[idx+1][2]
  277 + );
  278 +
  279 +// return( e[idx].P + (e[idx+1].P-e[idx].P)*rat);
  280 + return( v1 + (v2 - v1)*rat);
  281 +*/ }
186 282
187 ///Returns a position vector at the given length into the fiber (based on the pvalue). 283 ///Returns a position vector at the given length into the fiber (based on the pvalue).
188 ///Interpolates the radius along the line. 284 ///Interpolates the radius along the line.
@@ -192,7 +288,19 @@ class cylinder @@ -192,7 +288,19 @@ class cylinder
192 p(T l, int idx) 288 p(T l, int idx)
193 { 289 {
194 T rat = (l-L[idx])/(L[idx+1]-L[idx]); 290 T rat = (l-L[idx])/(L[idx+1]-L[idx]);
195 - return( e[idx].P + (e[idx+1].P-e[idx].P)*rat); 291 + stim::vec3<T> v1(
  292 + c[idx][0],
  293 + c[idx][1],
  294 + c[idx][2]
  295 + );
  296 +
  297 + stim::vec3<T> v2(
  298 + c[idx+1][0],
  299 + c[idx+1][1],
  300 + c[idx+1][2]
  301 + );
  302 +// return( e[idx].P + (e[idx+1].P-e[idx].P)*rat);
  303 + return( v1 + (v2-v1)*rat);
196 // return( 304 // return(
197 // return (pos[idx] + (pos[idx+1]-pos[idx])*((l-L[idx])/(L[idx+1]- L[idx]))); 305 // return (pos[idx] + (pos[idx+1]-pos[idx])*((l-L[idx])/(L[idx+1]- L[idx])));
198 } 306 }
@@ -209,8 +317,11 @@ class cylinder @@ -209,8 +317,11 @@ class cylinder
209 } 317 }
210 T l = pvalue*L[L.size()-1]; 318 T l = pvalue*L[L.size()-1];
211 int idx = findIdx(l); 319 int idx = findIdx(l);
212 - return (e[idx].U.len() + (e[idx+1].U.len() - e[idx].U.len())*((l-L[idx])/(L[idx+1]- L[idx])));  
213 - } 320 + return (r(l,idx));
  321 +/* T rat = (l-L[idx])/(L[idx+1]-L[idx]);
  322 +// return (mags[idx][0] + (mags[idx+1][0]-mags[idx][0])*rat);
  323 + return (e[idx].U.len() + (e[idx+1].U.len() - e[idx].U.len())*rat);
  324 +*/ }
214 325
215 ///Returns a radius at the given length into the fiber (based on the pvalue). 326 ///Returns a radius at the given length into the fiber (based on the pvalue).
216 ///Interpolates the position along the line. 327 ///Interpolates the position along the line.
@@ -220,7 +331,23 @@ class cylinder @@ -220,7 +331,23 @@ class cylinder
220 r(T l, int idx) 331 r(T l, int idx)
221 { 332 {
222 T rat = (l-L[idx])/(L[idx+1]-L[idx]); 333 T rat = (l-L[idx])/(L[idx+1]-L[idx]);
223 - return( e[idx].U.len() + (e[idx+1].U.len() - e[idx].U.len())*rat); 334 + T v1 = (e[idx].U.len() + (e[idx+1].U.len() - e[idx].U.len())*rat);
  335 + T v3 = (Us[idx].len() + (Us[idx+1].len() - Us[idx].len())*rat);
  336 + T v2 = (mags[idx][0] + (mags[idx+1][0]-mags[idx][0])*rat);
  337 +// std::cout << (float)v1 = (float) v2 << std::endl;
  338 + if(abs(v3 - v1) >= 10e-6)
  339 + {
  340 + std::cout << "-------------------------" << std::endl;
  341 + std::cout << e[idx].str() << std::endl << std::endl;
  342 + std::cout << Us[idx].str() << std::endl;
  343 + std::cout << (float)v1 - (float) v2 << std::endl;
  344 + std::cout << "failed" << std::endl;
  345 + }
  346 +// std::cout << e[idx].U.len() << " " << mags[idx][0] << std::endl;
  347 +// std::cout << v2 << std::endl;
  348 + return(v2);
  349 +// return (mags[idx][0] + (mags[idx+1][0]-mags[idx][0])*rat);
  350 + // (
224 } 351 }
225 352
226 /// Returns the magnitude at the given index 353 /// Returns the magnitude at the given index
@@ -233,7 +360,7 @@ class cylinder @@ -233,7 +360,7 @@ class cylinder
233 /// Adds a new magnitude value to all points 360 /// Adds a new magnitude value to all points
234 /// @param m is the starting value for the new magnitude 361 /// @param m is the starting value for the new magnitude
235 void add_mag(T m = 0){ 362 void add_mag(T m = 0){
236 - for(unsigned int p = 0; p < e.size(); p++) 363 + for(unsigned int p = 0; p < N; p++)
237 mags[p].push_back(m); 364 mags[p].push_back(m);
238 } 365 }
239 366
@@ -279,8 +406,8 @@ class cylinder @@ -279,8 +406,8 @@ class cylinder
279 getPoints(int sides) 406 getPoints(int sides)
280 { 407 {
281 std::vector<std::vector <vec3<T> > > points; 408 std::vector<std::vector <vec3<T> > > points;
282 - points.resize(e.size());  
283 - for(int i = 0; i < e.size(); i++) 409 + points.resize(N);
  410 + for(int i = 0; i < N; i++)
284 { 411 {
285 points[i] = e[i].getPoints(sides); 412 points[i] = e[i].getPoints(sides);
286 } 413 }
@@ -319,7 +446,7 @@ class cylinder @@ -319,7 +446,7 @@ class cylinder
319 T len = L[0]; //allocate space for the segment length 446 T len = L[0]; //allocate space for the segment length
320 447
321 //for every consecutive point in the cylinder 448 //for every consecutive point in the cylinder
322 - for(unsigned p = 1; p < e.size(); p++){ 449 + for(unsigned p = 1; p < N; p++){
323 450
324 //p1 = pos[p]; //get the position and magnitude for the next point 451 //p1 = pos[p]; //get the position and magnitude for the next point
325 m1 = mags[p][m]; 452 m1 = mags[p][m];
stim/visualization/glObj.h
  Show/Hide comments   View file @ad93457
@@ -5,6 +5,7 @@ @@ -5,6 +5,7 @@
5 #include <GL/glut.h> 5 #include <GL/glut.h>
6 #include <stim/math/vector.h> 6 #include <stim/math/vector.h>
7 #include <stim/visualization/obj.h> 7 #include <stim/visualization/obj.h>
  8 +#include <stim/gl/error.h>
8 9
9 10
10 namespace stim 11 namespace stim
@@ -35,9 +36,9 @@ private: @@ -35,9 +36,9 @@ private:
35 glListBase(dList); 36 glListBase(dList);
36 37
37 glMatrixMode(GL_PROJECTION); 38 glMatrixMode(GL_PROJECTION);
38 - glLoadIdentity; 39 + glLoadIdentity();
39 glMatrixMode(GL_MODELVIEW); 40 glMatrixMode(GL_MODELVIEW);
40 - glLoadIdentity; 41 + glLoadIdentity();
41 42
42 } 43 }
43 44
@@ -129,7 +130,7 @@ public: @@ -129,7 +130,7 @@ public:
129 } 130 }
130 131
131 void 132 void
132 - RenderLine(std::vector< stim::vec<T> > l) 133 + RenderLine(std::vector< stim::vec3<T> > l)
133 { 134 {
134 glColor3f(0.5, 1.0, 0.5); 135 glColor3f(0.5, 1.0, 0.5);
135 glLineWidth(3.0); 136 glLineWidth(3.0);
stim/visualization/obj.h
  Show/Hide comments   View file @ad93457
@@ -322,13 +322,6 @@ protected: @@ -322,13 +322,6 @@ protected:
322 return OBJ_INVALID; 322 return OBJ_INVALID;
323 } 323 }
324 324
325 - //private method returns the vertex indices for a line  
326 - std::vector<unsigned> get_l_v(unsigned l){  
327 -  
328 -  
329 -  
330 - }  
331 -  
332 public: 325 public:
333 /// Constructor loads a Wavefront OBJ file 326 /// Constructor loads a Wavefront OBJ file
334 obj(std::string filename){ 327 obj(std::string filename){