codebase / stimlib

Commit 46a9cc269055e91eff7777a51fb55a83f4b3b57c

Authored by Jiaming Guo
1 parent 30b20d4f

fix minor errors in getting circle at specific point

Showing 2 changed files with 168 additions and 118 deletions   Show diff stats
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stim/biomodels/centerline.h
  Show/Hide comments   View file @46a9cc2
... ... @@ -22,7 +22,7 @@ protected:
22 22 if (size() <= 1) return vec3<T>(0, 0, 0); //if there is insufficient information to calculate the direction, return a null vector
23 23 if (size() == 2) return (at(1) - at(0)).norm(); //if there are only two points, the direction vector at both is the direction of the line segment
24 24 if (i == 0) return (at(1) - at(0)).norm(); //the first direction vector is oriented towards the first line segment
25   - if (i == size() - 1) return at(size() - 1) - at(size() - 2); //the last direction vector is oriented towards the last line segment
  25 + if (i == size() - 1) return (at(size() - 1) - at(size() - 2)).norm(); //the last direction vector is oriented towards the last line segment
26 26  
27 27 //all other direction vectors are the average direction of the two joined line segments
28 28 vec3<T> a = at(i) - at(i - 1);
... ...
stim/visualization/gl_network.h
  Show/Hide comments   View file @46a9cc2
... ... @@ -85,86 +85,6 @@ public:
85 85 glCallList(dlist); // render the display list
86 86 }
87 87  
88   - /// render the network centerline from swc file as a series of strips in different colors based on the neuronal type
89   - /// glCenterline0_swc is for only one input
90   - /*void glCenterline0_swc() {
91   - if (!glIsList(dlist)) { // if dlist isn't a display list, create it
92   - dlist = glGenLists(1); // generate a display list
93   - glNewList(dlist, GL_COMPILE); // start a new display list
94   - for (unsigned e = 0; e < E.size(); e++) {
95   - int type = NT[e]; // get the neuronal type
96   - switch (type) {
97   - case 0:
98   - glColor3f(1.0f, 1.0f, 1.0f); // white for undefined
99   - glBegin(GL_LINE_STRIP);
100   - for (unsigned p = 0; p < E[e].size(); p++) {
101   - glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
102   - }
103   - glEnd();
104   - break;
105   - case 1:
106   - glColor3f(1.0f, 0.0f, 0.0f); // red for soma
107   - glBegin(GL_LINE_STRIP);
108   - for (unsigned p = 0; p < E[e].size(); p++) {
109   - glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
110   - }
111   - glEnd();
112   - break;
113   - case 2:
114   - glColor3f(1.0f, 0.5f, 0.0f); // orange for axon
115   - glBegin(GL_LINE_STRIP);
116   - for (unsigned p = 0; p < E[e].size(); p++) {
117   - glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
118   - }
119   - glEnd();
120   - break;
121   - case 3:
122   - glColor3f(1.0f, 1.0f, 0.0f); // yellow for undefined
123   - glBegin(GL_LINE_STRIP);
124   - for (unsigned p = 0; p < E[e].size(); p++) {
125   - glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
126   - }
127   - glEnd();
128   - break;
129   - case 4:
130   - glColor3f(0.0f, 1.0f, 0.0f); // green for undefined
131   - glBegin(GL_LINE_STRIP);
132   - for (unsigned p = 0; p < E[e].size(); p++) {
133   - glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
134   - }
135   - glEnd();
136   - break;
137   - case 5:
138   - glColor3f(0.0f, 1.0f, 1.0f); // verdant for undefined
139   - glBegin(GL_LINE_STRIP);
140   - for (unsigned p = 0; p < E[e].size(); p++) {
141   - glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
142   - }
143   - glEnd();
144   - break;
145   - case 6:
146   - glColor3f(0.0f, 0.0f, 1.0f); // blue for undefined
147   - glBegin(GL_LINE_STRIP);
148   - for (unsigned p = 0; p < E[e].size(); p++) {
149   - glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
150   - }
151   - glEnd();
152   - break;
153   - case 7:
154   - glColor3f(0.5f, 0.0f, 1.0f); // purple for undefined
155   - glBegin(GL_LINE_STRIP);
156   - for (unsigned p = 0; p < E[e].size(); p++) {
157   - glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
158   - }
159   - glEnd();
160   - break;
161   - }
162   - }
163   - glEndList(); //end the display list
164   - }
165   - glCallList(dlist); // render the display list
166   - }*/
167   -
168 88 ///render the network centerline as a series of line strips(when loading at least two networks, otherwise using glCenterline0())
169 89 ///colors are based on metric values
170 90 void glCenterline(){
... ... @@ -188,16 +108,19 @@ public:
188 108  
189 109 ///render the network cylinder as a series of tubes
190 110 ///colors are based on metric values
191   - void glCylinder(float sigma) {
192   - if (!glIsList(dlist)) { //if dlist isn't a display list, create it
193   - dlist = glGenLists(1); //generate a display list
194   - glNewList(dlist, GL_COMPILE); //start a new display list
195   - for (unsigned e = 0; e < E.size(); e++) { //for each edge in the network
  111 + void glCylinder(float sigma, float radius) {
  112 +
  113 + if (radius != sigma) // if render radius was changed by user, create a new display list
  114 + glDeleteLists(dlist, 1);
  115 + if (!glIsList(dlist)) { // if dlist isn't a display list, create it
  116 + dlist = glGenLists(1); // generate a display list
  117 + glNewList(dlist, GL_COMPILE); // start a new display list
  118 + for (unsigned e = 0; e < E.size(); e++) { // for each edge in the network
196 119 for (unsigned p = 1; p < E[e].size(); p++) { // for each point on that edge
197 120 stim::circle<T> C1 = E[e].circ(p - 1);
198 121 stim::circle<T> C2 = E[e].circ(p);
199   - C1.set_R(3*sigma); // scale the circle to the same
200   - C2.set_R(3*sigma);
  122 + C1.set_R(2*radius); // scale the circle to the same
  123 + C2.set_R(2*radius);
201 124 std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
202 125 std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
203 126 glBegin(GL_QUAD_STRIP);
... ... @@ -207,30 +130,33 @@ public:
207 130 glTexCoord1f(E[e].r(p));
208 131 }
209 132 glEnd();
210   - } //set the texture coordinate based on the specified magnitude index
  133 + } // set the texture coordinate based on the specified magnitude index
211 134 }
212 135 for (unsigned n = 0; n < V.size(); n++) {
213   - size_t num = V[n].e[0].size(); //store the number of outgoing edge of that vertex
214   - if (num != 0) { //if it has outgoing edge
215   - unsigned idx = V[n].e[0][0]; //find the index of first outgoing edge of that vertex
216   - glTexCoord1f(E[idx].r(0)); //bind the texture as metric of first point on that edge
  136 + size_t num = V[n].e[0].size(); // store the number of outgoing edge of that vertex
  137 + if (num != 0) { // if it has outgoing edge
  138 + unsigned idx = V[n].e[0][0]; // find the index of first outgoing edge of that vertex
  139 + glTexCoord1f(E[idx].r(0)); // bind the texture as metric of first point on that edge
217 140 }
218 141 else {
219   - unsigned idx = V[n].e[1][0]; //find the index of first incoming edge of that vertex
220   - glTexCoord1f(E[idx].r(E[idx].size() - 1)); //bind the texture as metric of last point on that edge
  142 + unsigned idx = V[n].e[1][0]; // find the index of first incoming edge of that vertex
  143 + glTexCoord1f(E[idx].r(E[idx].size() - 1)); // bind the texture as metric of last point on that edge
221 144 }
222   - renderBall(V[n][0], V[n][1], V[n][2], 3*sigma, 20);
  145 + renderBall(V[n][0], V[n][1], V[n][2], 2*radius, 20);
223 146 }
224   - glEndList(); //end the display list
  147 + glEndList(); // end the display list
225 148 }
226   - glCallList(dlist); //render the display list
  149 + glCallList(dlist); // render the display list
227 150 }
228 151  
229 152 ///render the GT network cylinder as series of tubes
230 153 ///@param dlist1 is the display list
231 154 ///@param map is the mapping relationship between two networks
232 155 ///@param colormap is the random generated color set for render
233   - void glRandColorCylinder1(GLuint &dlist1, std::vector<unsigned> map, std::vector<T> colormap, float sigma) {
  156 + void glRandColorCylinder1(GLuint &dlist1, std::vector<unsigned> map, std::vector<T> colormap, float sigma, float radius) {
  157 +
  158 + if (radius != sigma) // if render radius was changed by user, create a new display list
  159 + glDeleteLists(dlist1, 1);
234 160 if (!glIsList(dlist1)) { // if dlist1 isn't a display list, create it
235 161 dlist1 = glGenLists(1); // generate a display list
236 162 glNewList(dlist1, GL_COMPILE); // start a new display list
... ... @@ -240,8 +166,8 @@ public:
240 166 for (unsigned p = 1; p < E[e].size(); p++) {// for each point on that edge
241 167 stim::circle<T> C1 = E[e].circ(p - 1);
242 168 stim::circle<T> C2 = E[e].circ(p);
243   - C1.set_R(3*sigma); // scale the circle to the same
244   - C2.set_R(3*sigma);
  169 + C1.set_R(2*radius); // scale the circle to the same
  170 + C2.set_R(2*radius);
245 171 std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
246 172 std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
247 173 renderCylinder(Cp1, Cp2);
... ... @@ -252,8 +178,8 @@ public:
252 178 for (unsigned p = 1; p < E[e].size(); p++) { // for each point on that edge
253 179 stim::circle<T> C1 = E[e].circ(p - 1);
254 180 stim::circle<T> C2 = E[e].circ(p);
255   - C1.set_R(3*sigma); // scale the circle to the same
256   - C2.set_R(3*sigma);
  181 + C1.set_R(2*radius); // scale the circle to the same
  182 + C2.set_R(2*radius);
257 183 std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
258 184 std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
259 185 renderCylinder(Cp1, Cp2);
... ... @@ -264,11 +190,11 @@ public:
264 190 size_t num_edge = V[v].e[0].size() + V[v].e[1].size();
265 191 if (num_edge > 1) { // if it is the joint vertex
266 192 glColor3f(0.3, 0.3, 0.3); // gray color
267   - renderBall(V[v][0], V[v][1], V[v][2], 6*sigma, 20);
  193 + renderBall(V[v][0], V[v][1], V[v][2], 3*radius, 20);
268 194 }
269 195 else { // if it is the terminal vertex
270 196 glColor3f(0.6, 0.6, 0.6); // more white gray
271   - renderBall(V[v][0], V[v][1], V[v][2], 6*sigma, 20);
  197 + renderBall(V[v][0], V[v][1], V[v][2], 3*radius, 20);
272 198 }
273 199 }
274 200 glEndList();
... ... @@ -280,18 +206,21 @@ public:
280 206 ///@param dlist2 is the display list
281 207 ///@param map is the mapping relationship between two networks
282 208 ///@param colormap is the random generated color set for render
283   - void glRandColorCylinder2(GLuint &dlist2, std::vector<unsigned> map, std::vector<T> colormap, float sigma) {
  209 + void glRandColorCylinder2(GLuint &dlist2, std::vector<unsigned> map, std::vector<T> colormap, float sigma, float radius) {
  210 +
  211 + if (radius != sigma) // if render radius was changed by user, create a new display list
  212 + glDeleteLists(dlist2, 1);
284 213 if (!glIsList(dlist2)) {
285 214 dlist2 = glGenLists(1);
286 215 glNewList(dlist2, GL_COMPILE);
287 216 for (unsigned e = 0; e < E.size(); e++) { // for each edge in the network
288 217 if (map[e] != unsigned(-1)) {
289 218 glColor3f(colormap[map[e] * 3 + 0], colormap[map[e] * 3 + 1], colormap[map[e] * 3 + 2]);
290   - for (unsigned p = 0; p < E[e].size() - 1; p++) {// for each point on that edge
291   - stim::circle<T> C1 = E[e].circ(p);
292   - stim::circle<T> C2 = E[e].circ(p + 1);
293   - C1.set_R(3*sigma); // scale the circle to the same
294   - C2.set_R(3*sigma);
  219 + for (unsigned p = 1; p < E[e].size(); p++) { // for each point on that edge(except last one)
  220 + stim::circle<T> C1 = E[e].circ(p - 1);
  221 + stim::circle<T> C2 = E[e].circ(p);
  222 + C1.set_R(2*radius); // scale the circle to the same
  223 + C2.set_R(2*radius);
295 224 std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
296 225 std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
297 226 renderCylinder(Cp1, Cp2);
... ... @@ -299,11 +228,11 @@ public:
299 228 }
300 229 else {
301 230 glColor3f(1.0f, 1.0f, 1.0f); // white color for the un-mapping edges
302   - for (unsigned p = 0; p < E[e].size() - 1; p++) {// for each point on that edge
303   - stim::circle<T> C1 = E[e].circ(p);
304   - stim::circle<T> C2 = E[e].circ(p + 1);
305   - C1.set_R(3*sigma); // scale the circle to the same
306   - C2.set_R(3*sigma);
  231 + for (unsigned p = 1; p < E[e].size(); p++) { // for each point on that edge
  232 + stim::circle<T> C1 = E[e].circ(p - 1);
  233 + stim::circle<T> C2 = E[e].circ(p);
  234 + C1.set_R(2*radius); // scale the circle to the same
  235 + C2.set_R(2*radius);
307 236 std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
308 237 std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
309 238 renderCylinder(Cp1, Cp2);
... ... @@ -314,11 +243,11 @@ public:
314 243 size_t num_edge = V[v].e[0].size() + V[v].e[1].size();
315 244 if (num_edge > 1) { // if it is the joint vertex
316 245 glColor3f(0.3, 0.3, 0.3); // gray color
317   - renderBall(V[v][0], V[v][1], V[v][2], 6*sigma, 20);
  246 + renderBall(V[v][0], V[v][1], V[v][2], 3*radius, 20);
318 247 }
319 248 else { // if it is the terminal vertex
320 249 glColor3f(0.6, 0.6, 0.6); // more white gray
321   - renderBall(V[v][0], V[v][1], V[v][2], 6*sigma, 20);
  250 + renderBall(V[v][0], V[v][1], V[v][2], 3*radius, 20);
322 251 }
323 252 }
324 253 glEndList();
... ... @@ -485,6 +414,127 @@ public:
485 414 // glPopMatrix();
486 415 //}
487 416  
  417 +
  418 + /// render the network centerline from swc file as a series of strips in different colors based on the neuronal type
  419 + /// glCenterline0_swc is for only one input
  420 + /*void glCenterline0_swc() {
  421 + if (!glIsList(dlist)) { // if dlist isn't a display list, create it
  422 + dlist = glGenLists(1); // generate a display list
  423 + glNewList(dlist, GL_COMPILE); // start a new display list
  424 + for (unsigned e = 0; e < E.size(); e++) {
  425 + int type = NT[e]; // get the neuronal type
  426 + switch (type) {
  427 + case 0:
  428 + glColor3f(1.0f, 1.0f, 1.0f); // white for undefined
  429 + glBegin(GL_LINE_STRIP);
  430 + for (unsigned p = 0; p < E[e].size(); p++) {
  431 + glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
  432 + }
  433 + glEnd();
  434 + break;
  435 + case 1:
  436 + glColor3f(1.0f, 0.0f, 0.0f); // red for soma
  437 + glBegin(GL_LINE_STRIP);
  438 + for (unsigned p = 0; p < E[e].size(); p++) {
  439 + glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
  440 + }
  441 + glEnd();
  442 + break;
  443 + case 2:
  444 + glColor3f(1.0f, 0.5f, 0.0f); // orange for axon
  445 + glBegin(GL_LINE_STRIP);
  446 + for (unsigned p = 0; p < E[e].size(); p++) {
  447 + glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
  448 + }
  449 + glEnd();
  450 + break;
  451 + case 3:
  452 + glColor3f(1.0f, 1.0f, 0.0f); // yellow for undefined
  453 + glBegin(GL_LINE_STRIP);
  454 + for (unsigned p = 0; p < E[e].size(); p++) {
  455 + glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
  456 + }
  457 + glEnd();
  458 + break;
  459 + case 4:
  460 + glColor3f(0.0f, 1.0f, 0.0f); // green for undefined
  461 + glBegin(GL_LINE_STRIP);
  462 + for (unsigned p = 0; p < E[e].size(); p++) {
  463 + glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
  464 + }
  465 + glEnd();
  466 + break;
  467 + case 5:
  468 + glColor3f(0.0f, 1.0f, 1.0f); // verdant for undefined
  469 + glBegin(GL_LINE_STRIP);
  470 + for (unsigned p = 0; p < E[e].size(); p++) {
  471 + glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
  472 + }
  473 + glEnd();
  474 + break;
  475 + case 6:
  476 + glColor3f(0.0f, 0.0f, 1.0f); // blue for undefined
  477 + glBegin(GL_LINE_STRIP);
  478 + for (unsigned p = 0; p < E[e].size(); p++) {
  479 + glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
  480 + }
  481 + glEnd();
  482 + break;
  483 + case 7:
  484 + glColor3f(0.5f, 0.0f, 1.0f); // purple for undefined
  485 + glBegin(GL_LINE_STRIP);
  486 + for (unsigned p = 0; p < E[e].size(); p++) {
  487 + glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
  488 + }
  489 + glEnd();
  490 + break;
  491 + }
  492 + }
  493 + glEndList(); //end the display list
  494 + }
  495 + glCallList(dlist); // render the display list
  496 + }*/
  497 +
  498 + ///render the network cylinder as a series of tubes
  499 + ///colors are based on metric values
  500 + //void glCylinder(float sigma) {
  501 + // if (!glIsList(dlist)) { //if dlist isn't a display list, create it
  502 + // dlist = glGenLists(1); //generate a display list
  503 + // glNewList(dlist, GL_COMPILE); //start a new display list
  504 + // for (unsigned e = 0; e < E.size(); e++) { //for each edge in the network
  505 + // for (unsigned p = 1; p < E[e].size() - 1; p++) { // for each point on that edge
  506 + // stim::circle<T> C1 = E[e].circ(p - 1);
  507 + // stim::circle<T> C2 = E[e].circ(p);
  508 + // C1.set_R(2.5*sigma); // scale the circle to the same
  509 + // C2.set_R(2.5*sigma);
  510 + // std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
  511 + // std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
  512 + // glBegin(GL_QUAD_STRIP);
  513 + // for (unsigned i = 0; i < Cp1.size(); i++) { // for every point on the circle(+1 means closing the circle)
  514 + // glVertex3f(Cp1[i][0], Cp1[i][1], Cp1[i][2]);
  515 + // glVertex3f(Cp2[i][0], Cp2[i][1], Cp2[i][2]);
  516 + // glTexCoord1f(E[e].r(p));
  517 + // }
  518 + // glEnd();
  519 + // } //set the texture coordinate based on the specified magnitude index
  520 + // }
  521 + // for (unsigned n = 0; n < V.size(); n++) {
  522 + // size_t num = V[n].e[0].size(); //store the number of outgoing edge of that vertex
  523 + // if (num != 0) { //if it has outgoing edge
  524 + // unsigned idx = V[n].e[0][0]; //find the index of first outgoing edge of that vertex
  525 + // glTexCoord1f(E[idx].r(0)); //bind the texture as metric of first point on that edge
  526 + // }
  527 + // else {
  528 + // unsigned idx = V[n].e[1][0]; //find the index of first incoming edge of that vertex
  529 + // glTexCoord1f(E[idx].r(E[idx].size() - 1)); //bind the texture as metric of last point on that edge
  530 + // }
  531 + // renderBall(V[n][0], V[n][1], V[n][2], 2.5*sigma, 20);
  532 + // }
  533 + // glEndList(); //end the display list
  534 + // }
  535 + // glCallList(dlist); //render the display list
  536 + //}
  537 +
488 538 }; //end stim::gl_network class
489 539 }; //end stim namespace
490 540  
... ...