codebase / stimlib

Commit 0311ab81ccc840968f323354738811bd1a1ee33e

Authored by Pavel Govyadinov
1 parent eb119a4f

fixed some issues with std98 in filename, fixes to glObj, debugging code added, … 

…Cylinder now uses centerline
Showing 6 changed files with 206 additions and 127 deletions   Show diff stats
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stim/gl/gl_spider.h
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... ... @@ -24,7 +24,6 @@
24 24 #include <stim/visualization/glObj.h>
25 25 #include <vector>
26 26 #include <stim/cuda/branch_detection.cuh>
27   -#include "../../../volume-spider/fiber.h"
28 27 #include "../../../volume-spider/glnetwork.h"
29 28 #include <stim/visualization/cylinder.h>
30 29 #include <stim/cuda/testKernel.cuh>
... ... @@ -115,6 +114,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
115 114 std::vector< stim::vec<float> > cM; //Magnitude of line currently being traced.
116 115  
117 116 stim::glnetwork<float> nt; //object for storing the network.
  117 + stim::glObj<float> sk;
118 118  
119 119 stim::vec<float> rev; //reverse vector;
120 120 stim::camera camSel;
... ... @@ -228,51 +228,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
228 228 }
229 229  
230 230  
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   - }
276 231  
277 232  
278 233 ///finds all the branches in the a given fiber.
... ... @@ -314,6 +269,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
314 269 stim::vec3<float> v = cyl.surf(pval, result[i][0]);
315 270 stim::vec3<float> di = cyl.p(pval);
316 271 float rad = cyl.r(pval);
  272 +
  273 + std::cout << v << " " << di << " " << rad << std::endl;
317 274 if(
318 275 !(v[0] > size[0] || v[1] > size[1]
319 276 || v[2] > size[2] || v[0] < 0
... ... @@ -768,7 +725,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
768 725 findOptimalScale();
769 726 Unbind();
770 727 Bind(btexbufferID, bfboID, 27);
771   - branchDetection();
  728 + branchDetection2();
772 729 Unbind();
773 730 return current_cost;
774 731 }
... ... @@ -1297,7 +1254,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1297 1254 void
1298 1255 saveNetwork(std::string name)
1299 1256 {
1300   - stim::glObj<float> sk;
  1257 +/* stim::glObj<float> sk;
1301 1258 for(int i = 0; i < nt.sizeE(); i++)
1302 1259 {
1303 1260 std::vector<stim::vec< float > > cm = nt.getEdgeCenterLineMag(i);
... ... @@ -1310,7 +1267,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1310 1267 }
1311 1268 sk.End();
1312 1269 }
1313   - sk.save(name);
  1270 +*/ sk.save(name);
1314 1271 }
1315 1272  
1316 1273 ///Depreciated, but might be reused later()
... ... @@ -1318,7 +1275,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1318 1275 stim::glObj<float>
1319 1276 getNetwork()
1320 1277 {
1321   -
  1278 + return sk;
1322 1279 }
1323 1280  
1324 1281 ///returns a COPY of the entire stim::glnetwork object.
... ... @@ -1387,14 +1344,14 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1387 1344 void
1388 1345 MonteCarloDirectionVectors(int nSamples, float solidAngle = 2*M_PI)
1389 1346 {
1390   - float PHI[2], Z[2], range;
1391   - PHI[0] = asin(solidAngle/2);
1392   - PHI[1] = asin(0);
  1347 +// float PHI[2];//, Z[2];//, range;
  1348 +// PHI[0] = asin(solidAngle/2);
  1349 +// PHI[1] = asin(0);
1393 1350  
1394   - Z[0] = cos(PHI[0]);
1395   - Z[1] = cos(PHI[1]);
  1351 +// Z[0] = cos(PHI[0]);
  1352 +// Z[1] = cos(PHI[1]);
1396 1353  
1397   - range = Z[0] - Z[1];
  1354 +// range = Z[0] - Z[1];
1398 1355  
1399 1356 std::vector<stim::vec3<float> > vecsUni;
1400 1357 for(int i = 0; i < numSamplesPos; i++)
... ... @@ -1506,10 +1463,13 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1506 1463 setPosition(curSeed);
1507 1464 setDirection(curSeedVec);
1508 1465 setMagnitude(curSeedMag);
  1466 + std::cout << "This was done" << std::endl;
  1467 + findOptimalScale();
  1468 +
1509 1469 // cL.push_back(curSeed);
1510 1470 // cM.push_back(curSeedMag);
1511 1471 // cD.push_back(curSeedMag);
1512   - pair<stim::fiber<float>, int> a = traceLine(p, m, min_cost);
  1472 + traceLine(p, m, min_cost);
1513 1473 }
1514 1474 }
1515 1475  
... ... @@ -1556,17 +1516,17 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1556 1516 ds[0], ds[1], ds[2],
1557 1517 ups[0], ups[1], ups[2]);
1558 1518  
1559   -// sk.Render();
1560   - nt.Render();
  1519 + sk.Render();
  1520 +// nt.Render();
1561 1521  
1562 1522 CHECK_OPENGL_ERROR
1563 1523  
1564 1524  
1565   -// glLoadName((int) sk.numL());
1566   - glLoadName(nt.sizeE());
  1525 + glLoadName((int) sk.numL());
  1526 +// glLoadName(nt.sizeE());
1567 1527  
1568   -// sk.RenderLine(cL);
1569   - nt.RenderLine(cL);
  1528 + sk.RenderLine(cL);
  1529 +// nt.RenderLine(cL);
1570 1530  
1571 1531 // glPopName();
1572 1532 glFlush();
... ... @@ -1615,8 +1575,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1615 1575 {
1616 1576 cL.clear();
1617 1577 cM.clear();
1618   - }
  1578 + }
1619 1579  
  1580 +/*
1620 1581 void
1621 1582 addToNetwork(pair<stim::fiber<float>, int> in, stim::vec3<float> spos,
1622 1583 stim::vec<float> smag, stim::vec3<float> sdir)
... ... @@ -1664,13 +1625,23 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1664 1625 network_time += nt * 1000.0;
1665 1626 #endif
1666 1627 }
  1628 +*/
  1629 + void
  1630 + addToNetwork(std::vector<stim::vec3<float> > L, std::vector<stim::vec<float> > M)
  1631 + {
  1632 + if(L.size() > 3)
  1633 + {
  1634 + sk.Begin(stim::OBJ_LINE);
  1635 + for(int i = 0; i < L.size(); i++)
  1636 + {
  1637 + sk.TexCoord(M[i][0]);
  1638 + sk.Vertex(L[i][0], L[i][1], L[i][2]);
  1639 + }
  1640 + sk.End();
1667 1641  
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   -// }
  1642 + nt.addEdge(L,M);
  1643 + }
  1644 + }
1674 1645  
1675 1646  
1676 1647 void
... ... @@ -1681,11 +1652,13 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1681 1652  
1682 1653 }
1683 1654  
1684   - std::pair<stim::fiber<float>, int >
  1655 + void
1685 1656 traceLine(stim::vec3<float> pos, stim::vec<float> mag, int min_cost)
1686 1657 {
1687 1658 //starting (seed) position and magnitude.
1688 1659 stim::vec3<float> spos = getPosition();
  1660 +// std::cout << "I did this" << std::endl;
  1661 +// findOptimalScale();
1689 1662 stim::vec<float> smag = getMagnitude();
1690 1663 stim::vec3<float> sdir = getDirection();
1691 1664  
... ... @@ -1693,8 +1666,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1693 1666 // sk.Begin(stim::OBJ_LINE);
1694 1667  
1695 1668  
1696   -// sk.createFromSelf(GL_SELECT);
1697   - nt.createFromSelf(GL_SELECT);
  1669 + sk.createFromSelf(GL_SELECT);
  1670 +// nt.createFromSelf(GL_SELECT);
1698 1671  
1699 1672 cL.push_back(pos);
1700 1673 cM.push_back(mag);
... ... @@ -1712,10 +1685,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1712 1685 running = false;
1713 1686 // sk.End();
1714 1687 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;
  1688 + addToNetwork(cL, cM);
  1689 + std::cout << "the cost of " << cost << " > " << min_cost << std::endl;
1719 1690 break;
1720 1691 } else {
1721 1692 //Have we found the edge of the map?
... ... @@ -1726,10 +1697,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1726 1697 {
1727 1698 running = false;
1728 1699 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;
  1700 + addToNetwork(cL, cM);
  1701 + std::cout << "I hit and edge" << std::endl;
1733 1702 break;
1734 1703 }
1735 1704 //If this is the first step in the trace,
... ... @@ -1744,10 +1713,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1744 1713 if(mag[0] > 75 || mag[0] < 1){
1745 1714 running = false;
1746 1715 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;
  1716 + addToNetwork(cL, cM);
  1717 + std::cout << "The templates are too big" << std::endl;
1751 1718 break;
1752 1719 }
1753 1720 else
... ... @@ -1755,12 +1722,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
1755 1722 h = selectObject(p, getDirection(), m[0]);
1756 1723 //Have we hit something previously traced?
1757 1724 if(h != -1){
1758   -// std::cout << "I hit the fiber " << h << std::endl;
  1725 + std::cout << "I hit the fiber " << h << std::endl;
1759 1726 running = false;
1760 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 1729 break;
1765 1730 }
1766 1731 else {
... ...
stim/math/circle.h
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... ... @@ -48,9 +48,9 @@ public:
48 48 CUDA_CALLABLE
49 49 circle(T size, T z_pos = (T)0) : plane<T>()
50 50 {
51   - init();
52 51 center(stim::vec3<T>(0,0,z_pos));
53 52 scale(size);
  53 + init();
54 54 }
55 55  
56 56 ///create a rectangle from a center point, normal
... ... @@ -88,6 +88,7 @@ public:
88 88 {
89 89 init();
90 90 setU(u);
  91 +// U = u;
91 92 center(c);
92 93 normal(n);
93 94 scale(s);
... ... @@ -174,6 +175,13 @@ public:
174 175 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 }
179 187 #endif
... ...
stim/parser/filename.h
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... ... @@ -110,11 +110,11 @@ protected:
110 110 unix_dir = unix_dir.substr(2, unix_dir.length()-2); //extract the directory structure
111 111 }
112 112  
113   - if(unix_dir.front() == '/'){ //if there is a leading slash
  113 + if(unix_dir.at(0) == '/'){ //if there is a leading slash
114 114 relative = false; //the path is not relative
115 115 unix_dir = unix_dir.substr(1, unix_dir.length() - 1); //remove the slash
116 116 }
117   - if(unix_dir.back() == '/')
  117 + if(unix_dir.at(unix_dir.size()-1) == '/')
118 118 unix_dir = unix_dir.substr(0, unix_dir.length() - 1);
119 119  
120 120 path = stim::parser::split(unix_dir, '/'); //split up the directory structure
... ...
stim/visualization/cylinder.h
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... ... @@ -2,19 +2,27 @@
2 2 #define STIM_CYLINDER_H
3 3 #include <iostream>
4 4 #include <stim/math/circle.h>
5   -#include <stim/math/vec3.h>
  5 +#include <stim/biomodels/centerline.h>
6 6  
7 7  
8 8 namespace stim
9 9 {
10 10 template<typename T>
11 11 class cylinder
  12 + : public centerline<T>
12 13 {
13 14 private:
14 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 20 std::vector<stim::vec<T> > mags;
17 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 27 ///default init
20 28 void
... ... @@ -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 48 ///inits the cylinder from a list of points (std::vector of stim::vec3 --inP) and radii (inM)
27 49 void
28 50 init(std::vector<stim::vec3<T> > inP, std::vector<stim::vec<T> > inM)
... ... @@ -31,6 +53,10 @@ class cylinder
31 53 stim::vec3<float> v1;
32 54 stim::vec3<float> v2;
33 55 e.resize(inP.size());
  56 +
  57 + norms.resize(inP.size());
  58 + Us.resize(inP.size());
  59 +
34 60 if(inP.size() < 2)
35 61 return;
36 62  
... ... @@ -46,7 +72,9 @@ class cylinder
46 72  
47 73 stim::vec3<T> dr = (inP[1] - inP[0]).norm();
48 74 s = stim::circle<T>(inP[0], inM[0][0], dr, stim::vec3<T>(1,0,0));
  75 + norms[0] = s.N;
49 76 e[0] = s;
  77 + Us[0] = e[0].U;
50 78 for(size_t i = 1; i < inP.size()-1; i++)
51 79 {
52 80 s.center(inP[i]);
... ... @@ -54,16 +82,24 @@ class cylinder
54 82 v2 = (inP[i+1] - inP[i]).norm();
55 83 dr = (v1+v2).norm();
56 84 s.normal(dr);
  85 +
  86 + norms[i] = s.N;
  87 +
57 88 s.scale(inM[i][0]/inM[i-1][0]);
58 89 e[i] = s;
  90 + Us[i] = e[i].U;
59 91 }
60 92  
61 93 int j = inP.size()-1;
62 94 s.center(inP[j]);
63 95 dr = (inP[j] - inP[j-1]).norm();
64 96 s.normal(dr);
  97 +
  98 + norms[j] = s.N;
  99 +
65 100 s.scale(inM[j][0]/inM[j-1][0]);
66 101 e[j] = s;
  102 + Us[j] = e[j].U;
67 103 }
68 104  
69 105 ///returns the direction vector at point idx.
... ... @@ -72,18 +108,42 @@ class cylinder
72 108 {
73 109 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 }
81 129 else
82 130 {
83 131 // 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 }
88 148 // return e[idx].N;
89 149  
... ... @@ -92,14 +152,17 @@ class cylinder
92 152 stim::vec3<T>
93 153 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 }
99 160 else
100 161 {
  162 +
101 163 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
137 200 public:
138 201 ///default constructor
139 202 cylinder()
  203 + // : centerline<T>()
140 204 {
141 205  
142 206 }
... ... @@ -144,14 +208,18 @@ class cylinder
144 208 ///constructor to create a cylinder from a set of points, radii, and the number of sides for the cylinder.
145 209 ///@param inP: Vector of stim vec3 composing the points of the centerline.
146 210 ///@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 + {
148 214 init(inP, inM);
149 215 }
150 216  
151 217  
152 218 ///Constructor defines a cylinder with centerline inP and magnitudes of zero
153 219 ///@param inP: Vector of stim vec3 composing the points of the centerline
154   - cylinder(std::vector< stim::vec3<T> > inP){
  220 + cylinder(std::vector< stim::vec3<T> > inP)
  221 + : centerline<T>(inP)
  222 + {
155 223 std::vector< stim::vec<T> > inM; //create an array of arbitrary magnitudes
156 224  
157 225 stim::vec<T> zero;
... ... @@ -164,7 +232,7 @@ class cylinder
164 232 ///Returns the number of points on the cylinder centerline
165 233  
166 234 unsigned int size(){
167   - return e.size();
  235 + return N;
168 236 }
169 237  
170 238  
... ... @@ -180,9 +248,23 @@ class cylinder
180 248 }
181 249 T l = pvalue*L[L.size()-1];
182 250 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   - }
  251 + return (p(l,idx));
  252 +/* T rat = (l-L[idx])/(L[idx+1]-L[idx]);
  253 + stim::vec3<T> v1(
  254 + c[idx][0],
  255 + c[idx][1],
  256 + c[idx][2]
  257 + );
  258 +
  259 + stim::vec3<T> v2(
  260 + c[idx+1][0],
  261 + c[idx+1][1],
  262 + c[idx+1][2]
  263 + );
  264 +
  265 +// return( e[idx].P + (e[idx+1].P-e[idx].P)*rat);
  266 + return( v1 + (v2 - v1)*rat);
  267 +*/ }
186 268  
187 269 ///Returns a position vector at the given length into the fiber (based on the pvalue).
188 270 ///Interpolates the radius along the line.
... ... @@ -192,7 +274,19 @@ class cylinder
192 274 p(T l, int idx)
193 275 {
194 276 T rat = (l-L[idx])/(L[idx+1]-L[idx]);
195   - return( e[idx].P + (e[idx+1].P-e[idx].P)*rat);
  277 + stim::vec3<T> v1(
  278 + c[idx][0],
  279 + c[idx][1],
  280 + c[idx][2]
  281 + );
  282 +
  283 + stim::vec3<T> v2(
  284 + c[idx+1][0],
  285 + c[idx+1][1],
  286 + c[idx+1][2]
  287 + );
  288 +// return( e[idx].P + (e[idx+1].P-e[idx].P)*rat);
  289 + return( v1 + (v2-v1)*rat);
196 290 // return(
197 291 // return (pos[idx] + (pos[idx+1]-pos[idx])*((l-L[idx])/(L[idx+1]- L[idx])));
198 292 }
... ... @@ -209,8 +303,11 @@ class cylinder
209 303 }
210 304 T l = pvalue*L[L.size()-1];
211 305 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   - }
  306 + return (r(l,idx));
  307 +/* T rat = (l-L[idx])/(L[idx+1]-L[idx]);
  308 +// return (mags[idx][0] + (mags[idx+1][0]-mags[idx][0])*rat);
  309 + return (e[idx].U.len() + (e[idx+1].U.len() - e[idx].U.len())*rat);
  310 +*/ }
214 311  
215 312 ///Returns a radius at the given length into the fiber (based on the pvalue).
216 313 ///Interpolates the position along the line.
... ... @@ -220,7 +317,23 @@ class cylinder
220 317 r(T l, int idx)
221 318 {
222 319 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);
  320 + T v1 = (e[idx].U.len() + (e[idx+1].U.len() - e[idx].U.len())*rat);
  321 + T v3 = (Us[idx].len() + (Us[idx+1].len() - Us[idx].len())*rat);
  322 + T v2 = (mags[idx][0] + (mags[idx+1][0]-mags[idx][0])*rat);
  323 +// std::cout << (float)v1 = (float) v2 << std::endl;
  324 + if(abs(v3 - v1) >= 10e-6)
  325 + {
  326 + std::cout << "-------------------------" << std::endl;
  327 + std::cout << e[idx].str() << std::endl << std::endl;
  328 + std::cout << Us[idx] << std::endl;
  329 + std::cout << (float)v1 - (float) v2 << std::endl;
  330 + std::cout << "failed" << std::endl;
  331 + }
  332 +// std::cout << e[idx].U.len() << " " << mags[idx][0] << std::endl;
  333 +// std::cout << v2 << std::endl;
  334 + return(v1);
  335 +// return (mags[idx][0] + (mags[idx+1][0]-mags[idx][0])*rat);
  336 + // (
224 337 }
225 338  
226 339 /// Returns the magnitude at the given index
... ... @@ -233,7 +346,7 @@ class cylinder
233 346 /// Adds a new magnitude value to all points
234 347 /// @param m is the starting value for the new magnitude
235 348 void add_mag(T m = 0){
236   - for(unsigned int p = 0; p < e.size(); p++)
  349 + for(unsigned int p = 0; p < N; p++)
237 350 mags[p].push_back(m);
238 351 }
239 352  
... ... @@ -279,8 +392,8 @@ class cylinder
279 392 getPoints(int sides)
280 393 {
281 394 std::vector<std::vector <vec3<T> > > points;
282   - points.resize(e.size());
283   - for(int i = 0; i < e.size(); i++)
  395 + points.resize(N);
  396 + for(int i = 0; i < N; i++)
284 397 {
285 398 points[i] = e[i].getPoints(sides);
286 399 }
... ... @@ -319,7 +432,7 @@ class cylinder
319 432 T len = L[0]; //allocate space for the segment length
320 433  
321 434 //for every consecutive point in the cylinder
322   - for(unsigned p = 1; p < e.size(); p++){
  435 + for(unsigned p = 1; p < N; p++){
323 436  
324 437 //p1 = pos[p]; //get the position and magnitude for the next point
325 438 m1 = mags[p][m];
... ...
stim/visualization/glObj.h
  Show/Hide comments   View file @0311ab8
... ... @@ -35,9 +35,9 @@ private:
35 35 glListBase(dList);
36 36  
37 37 glMatrixMode(GL_PROJECTION);
38   - glLoadIdentity;
  38 + glLoadIdentity();
39 39 glMatrixMode(GL_MODELVIEW);
40   - glLoadIdentity;
  40 + glLoadIdentity();
41 41  
42 42 }
43 43  
... ... @@ -129,7 +129,7 @@ public:
129 129 }
130 130  
131 131 void
132   - RenderLine(std::vector< stim::vec<T> > l)
  132 + RenderLine(std::vector< stim::vec3<T> > l)
133 133 {
134 134 glColor3f(0.5, 1.0, 0.5);
135 135 glLineWidth(3.0);
... ...
stim/visualization/obj.h
  Show/Hide comments   View file @0311ab8
... ... @@ -322,13 +322,6 @@ protected:
322 322 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   -
332 325 public:
333 326 /// Constructor loads a Wavefront OBJ file
334 327 obj(std::string filename){
... ...