codebase / stimlib

Commit 0d0ef1a95d99ca400df0ccbad7c68b0f373e806e

Authored by David Mayerich
1 parent 32ba91f2

Adapted classes to work with the new stim::cylinder class.

Showing 5 changed files with 66 additions and 28 deletions   Show diff stats
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stim/biomodels/centerline.h
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... ... @@ -57,10 +57,14 @@ protected:
57 57 ///finds the index of the point closest to the length l on the lower bound.
58 58 ///binary search.
59 59 size_t findIdx(T l) {
60   - size_t i = L.size() / 2;
  60 + for (size_t i = 1; i < L.size(); i++) { //for each point in the centerline
  61 + if (L[i] > l) return i - 1; //if we have passed the desired length value, return i-1
  62 + }
  63 + return L.size() - 1;
  64 + /*size_t i = L.size() / 2;
61 65 size_t max = L.size() - 1;
62 66 size_t min = 0;
63   - while (i > 0 && i < L.size() - 1){
  67 + while (i < L.size() - 1){
64 68 if (l < L[i]) {
65 69 max = i;
66 70 i = min + (max - min) / 2;
... ... @@ -73,7 +77,7 @@ protected:
73 77 i = min + (max - min) / 2;
74 78 }
75 79 }
76   - return i;
  80 + return i;*/
77 81 }
78 82  
79 83 ///Returns a position vector at the given length into the fiber (based on the pvalue).
... ... @@ -118,6 +122,10 @@ public:
118 122 return p(l, idx);
119 123 }
120 124  
  125 + ///Update centerline internal parameters (currently the L vector)
  126 + void update() {
  127 + init();
  128 + }
121 129 ///Return the length of the entire centerline
122 130 T length() {
123 131 return L.back();
... ...
stim/biomodels/network.h
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... ... @@ -338,6 +338,7 @@ public:
338 338 stim::centerline<T> c3(c.size());
339 339 for(size_t j = 0; j < c.size(); j++)
340 340 c3[j] = c[j];
  341 + c3.update();
341 342  
342 343 // edge new_edge = c3; ///This is dangerous.
343 344 edge new_edge(c3);
... ... @@ -512,8 +513,8 @@ public:
512 513 kdt.create(c, n_data, MaxTreeLevels); // build a KD tree
513 514  
514 515 for(unsigned e = 0; e < R.E.size(); e++){ //for each edge in A
515   - R.E[e].add_mag(0); //add a new magnitude for the metric
516   - size_t errormag_id = R.E[e].nmags() - 1; //get the id for the new magnitude
  516 + //R.E[e].add_mag(0); //add a new magnitude for the metric
  517 + //size_t errormag_id = R.E[e].nmags() - 1; //get the id for the new magnitude
517 518  
518 519 size_t n = R.E[e].size(); // the number of points in current edge
519 520 T* queryPt = new T[3 * n];
... ... @@ -540,7 +541,7 @@ public:
540 541 cudaMemcpy(m1, d_m1, n * sizeof(T), cudaMemcpyDeviceToHost);
541 542  
542 543 for(unsigned p = 0; p < n; p++){
543   - R.E[e].set_mag(errormag_id, p, m1[p]);
  544 + R.E[e].set_r(p, m1[p]);
544 545 }
545 546  
546 547 //d_set_mag<<<blocks, threads>>>(R.E[e].M, errormag_id, n, m1);
... ... @@ -608,8 +609,8 @@ public:
608 609 relation.resize(A.E.size());
609 610  
610 611 for(unsigned e = 0; e < A.E.size(); e++){ //for each edge in A
611   - A.E[e].add_mag(0); //add a new magnitude for the metric
612   - size_t errormag_id = A.E[e].nmags() - 1;
  612 + //A.E[e].add_mag(0); //add a new magnitude for the metric
  613 + //size_t errormag_id = A.E[e].nmags() - 1;
613 614  
614 615 size_t n = A.E[e].size(); // the number of edges in A
615 616  
... ... @@ -643,7 +644,7 @@ public:
643 644 cudaMemcpy(m1, d_m1, n * sizeof(T), cudaMemcpyDeviceToHost);
644 645  
645 646 for(unsigned p = 0; p < n; p++){
646   - A.E[e].set_mag(errormag_id, p, m1[p]); // set the error(radius) value to every point in current edge
  647 + A.E[e].set_r(p, m1[p]); // set the error(radius) value to every point in current edge
647 648 }
648 649  
649 650 relation[e].resize(n); // resize every edge relation size
... ... @@ -723,10 +724,10 @@ public:
723 724 if(p == E[e].size() - 2) // if there is no splitting index, set the id to the last point index of current edge
724 725 id = p + 1;
725 726 }
726   - unsigned errormag_id = E[e].nmags() - 1;
  727 + //unsigned errormag_id = E[e].nmags() - 1;
727 728 T G = 0; // test to see whether it has its nearest neighbor
728 729 for(unsigned i = 0; i < E[e].size(); i++)
729   - G += E[e].m(i, errormag_id); // won't split special edges
  730 + G += E[e].r(i); // won't split special edges
730 731 if(G / E[e].size() > metric_fac) // should based on the color map
731 732 id = E[e].size() - 1; // set split idx to outgoing direction vertex
732 733  
... ... @@ -795,12 +796,12 @@ public:
795 796 kdt.create(c, n_data, MaxTreeLevels); // build a KD tree
796 797  
797 798 for(unsigned e = 0; e < n; e++){ //for each edge in A
798   - size_t errormag_id = A.E[e].nmags() - 1; //get the id for the new magnitude
  799 + //size_t errormag_id = A.E[e].nmags() - 1; //get the id for the new magnitude
799 800  
800 801 //pre-judge to get rid of impossibly mapping edges
801 802 T M = 0;
802 803 for(unsigned p = 0; p < A.E[e].size(); p++)
803   - M += A.E[e].m(p, errormag_id);
  804 + M += A.E[e].r(p);
804 805 M = M / A.E[e].size();
805 806 if(M > metric_fac)
806 807 C[e] = (unsigned)-1; //set the nearest edge of impossibly mapping edges to maximum of unsigned
... ... @@ -862,9 +863,9 @@ public:
862 863 }
863 864  
864 865 /// Returns the number of magnitude values stored in each edge. This should be uniform across the network.
865   - unsigned nmags(){
866   - return E[0].nmags();
867   - }
  866 + //unsigned nmags(){
  867 + // return E[0].nmags();
  868 + //}
868 869 // split a string in text by the character sep
869 870 stim::vec<T> split(std::string &text, char sep)
870 871 {
... ...
stim/visualization/camera.h
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1 1 #include <stim/math/vector.h>
2 2 #include <stim/math/quaternion.h>
3   -#include <stim/math/matrix.h>
  3 +#include <stim/math/matrix_sq.h>
4 4  
5 5 #include <ostream>
6 6  
... ... @@ -92,7 +92,7 @@ public:
92 92 quaternion<float> final = qz*qy*qx;
93 93  
94 94 //get the rotation matrix
95   - matrix<float, 3> rot_matrix = final.toMatrix3();
  95 + matrix_sq<float, 3> rot_matrix = final.toMatrix3();
96 96  
97 97 //apply the rotation
98 98 d = rot_matrix*d;
... ...
stim/visualization/cylinder.h
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... ... @@ -21,6 +21,7 @@ protected:
21 21 // this function assumes that the centerline has already been set
22 22 void init() {
23 23 U.resize(size()); //allocate space for the frenet frame vectors
  24 + R.resize(size());
24 25  
25 26 stim::circle<T> c; //create a circle
26 27 stim::vec3<T> d0, d1;
... ... @@ -44,13 +45,13 @@ public:
44 45  
45 46 cylinder(centerline& c, T r) : centerline(c) {
46 47 init();
47   - add_mag(r);
  48 + //add_mag(r);
48 49 }
49 50  
50 51 //initialize a cylinder with a list of points and magnitude values
51 52 cylinder(centerline& c, std::vector<T> r) : centerline(c){
52 53 init();
53   - add_mag(r);
  54 + //add_mag(r);
54 55 }
55 56  
56 57 ///Returns magnitude i at the given length into the fiber (based on the pvalue).
... ... @@ -73,15 +74,15 @@ public:
73 74  
74 75 T l = pvalue*L[L.size() - 1];
75 76 int idx = findIdx(l);
76   - return r(l, idx, i);
  77 + return r(l, idx);
77 78 }
78 79  
79 80 /// Returns the magnitude at the given index
80 81 /// @param i is the index of the desired point
81 82 /// @param r is the index of the magnitude value
82   - T r(unsigned i) {
83   - return R[i];
84   - }
  83 + //T r(unsigned i) {
  84 + // return R[i];
  85 + //}
85 86  
86 87 ///adds a magnitude to each point in the cylinder
87 88 /*void add_mag(V val = 0) {
... ... @@ -210,9 +211,37 @@ public:
210 211 c.R[i] = r(t); //retrieve the interpolated magnitude from the current cylinder and store it in the new one
211 212 //}
212 213 }
  214 + return c;
  215 + }
213 216  
  217 + std::vector< stim::cylinder<T> > split(unsigned int idx) {
  218 +
  219 + unsigned N = size();
  220 + std::vector< stim::centerline<T> > LL;
  221 + LL.resize(2);
  222 + LL = (*this).centerline<T>::split(idx);
  223 + std::vector< stim::cylinder<T> > C(LL.size());
  224 + unsigned i = 0;
  225 + C[0] = LL[0];
  226 + //C[0].R.resize(idx);
  227 + for (; i < idx; i++) {
  228 + //for(unsigned d = 0; d < 3; d++)
  229 + //C[0][i][d] = LL[0].c[i][d];
  230 + C[0].R[i] = R[i];
  231 + //C[0].R[i].resize(1);
  232 + }
  233 + if (C.size() == 2) {
  234 + C[1] = LL[1];
  235 + //C[1].M.resize(N - idx);
  236 + for (; i < N; i++) {
  237 + //for(unsigned d = 0; d < 3; d++)
  238 + //C[1][i - idx][d] = LL[1].c[i - idx][d];
  239 + C[1].R[i - idx] = R[i];
  240 + //C[1].M[i - idx].resize(1);
  241 + }
  242 + }
214 243  
215   - return c;
  244 + return C;
216 245 }
217 246  
218 247  
... ...
stim/visualization/gl_network.h
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... ... @@ -63,17 +63,17 @@ public:
63 63 }
64 64  
65 65 /// @param m specifies the magnitude value used as the vertex weight (radius, error, etc.)
66   - void glCenterline(unsigned m = 0){
  66 + void glCenterline(){
67 67  
68 68 if(!glIsList(dlist)){ //if dlist isn't a display list, create it
69 69 dlist = glGenLists(3); //generate a display list
70 70 glNewList(dlist, GL_COMPILE); //start a new display list
71 71 for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
72   - unsigned errormag_id = E[e].nmags() - 1;
  72 + //unsigned errormag_id = E[e].nmags() - 1;
73 73 glBegin(GL_LINE_STRIP);
74 74 for(unsigned p = 0; p < E[e].size(); p++){ //for each point on that edge
75 75 glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]); //set the vertex position based on the current point
76   - glTexCoord1f(E[e].m(p, errormag_id)); //set the texture coordinate based on the specified magnitude index
  76 + glTexCoord1f(E[e].r(p)); //set the texture coordinate based on the specified magnitude index
77 77 }
78 78 glEnd();
79 79 }
... ...