codebase / stimlib

Commit 0e0feff0b1769026d8583cd76be3e2553d15e6e9

Authored by Jiaming Guo
1 parent 4ea8daa8

fixed bugs in merging new network format, temporary version

Showing 3 changed files with 107 additions and 48 deletions   Show diff stats
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stim/biomodels/centerline.h
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... ... @@ -31,20 +31,6 @@ protected:
31 31 vec3<T> ab = a.norm() + b.norm();
32 32 return ab.norm();
33 33 }
34   - //initializes the integrated length vector to make parameterization easier, starting with index idx (all previous indices are assumed to be correct)
35   - void update_L(size_t start = 0) {
36   - L.resize(size()); //allocate space for the L array
37   - if (start == 0) {
38   - L[0] = 0; //initialize the length value for the first point to zero (0)
39   - start++;
40   - }
41   -
42   - stim::vec3<T> d;
43   - for (size_t i = start; i < size(); i++) { //for each line segment in the centerline
44   - d = at(i) - at(i - 1);
45   - L[i] = L[i - 1] + d.len(); //calculate the running length total
46   - }
47   - }
48 34  
49 35 void init() {
50 36 if (size() == 0) return; //return if there aren't any points
... ... @@ -135,6 +121,21 @@ public:
135 121 return L.back();
136 122 }
137 123  
  124 + //initializes the integrated length vector to make parameterization easier, starting with index idx (all previous indices are assumed to be correct)
  125 + void update_L(size_t start = 0) {
  126 + L.resize(size()); //allocate space for the L array
  127 + if (start == 0) {
  128 + L[0] = 0; //initialize the length value for the first point to zero (0)
  129 + start++;
  130 + }
  131 +
  132 + stim::vec3<T> d;
  133 + for (size_t i = start; i < size(); i++) { //for each line segment in the centerline
  134 + d = at(i) - at(i - 1);
  135 + L[i] = L[i - 1] + d.len(); //calculate the running length total
  136 + }
  137 + }
  138 +
138 139 /// stitch two centerlines
139 140 ///@param c1, c2: two centerlines
140 141 ///@param sigma: sample rate
... ...
stim/biomodels/network.h
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... ... @@ -63,6 +63,7 @@ class network{
63 63 class edge : public cylinder<T>
64 64 {
65 65 public:
  66 +
66 67 unsigned int v[2]; //unique id's designating the starting and ending
67 68 // default constructor
68 69 edge() : cylinder<T>() {
... ... @@ -127,7 +128,7 @@ class network{
127 128 // for(int j = 0; j < nmags(); j++) //future code for multiple mags
128 129 // {
129 130 out.write(reinterpret_cast<const char*>(&e.R[i]), sizeof(T)); ///write the radius
130   - std::cout << point.str() << " " << e.R[i] << std::endl;
  131 + //std::cout << point.str() << " " << e.R[i] << std::endl;
131 132 // }
132 133 }
133 134 return out; //return stream
... ... @@ -141,7 +142,7 @@ class network{
141 142 in.read(reinterpret_cast<char*>(&v1), sizeof(unsigned int)); //read the ending point
142 143 in.read(reinterpret_cast<char*>(&sz), sizeof(unsigned int)); //read the number of points in the edge
143 144 stim::centerline<T> temp = stim::centerline<T>(sz); //allocate the new edge
144   - e = edge(temp);
  145 + e = edge(temp);
145 146 e.v[0] = v0; e.v[1] = v1;
146 147 for(int i = 0; i < sz; i++) //set the points and radii to the newly read values
147 148 {
... ... @@ -152,10 +153,12 @@ class network{
152 153 // for(int j = 0; j < nmags(); j++) ///future code for mags
153 154 // {
154 155 in.read(reinterpret_cast<char*>(&mag), sizeof(T));
155   - e.set_r(0, mag);
156   - std::cout << point.str() << " " << mag << std::endl;
  156 + e.set_r(i, mag);
  157 + //std::cout << point.str() << " " << mag << std::endl;
157 158 // }
158 159 }
  160 + e.init();
  161 + e.update();
159 162 return in;
160 163 }
161 164 };
... ... @@ -193,21 +196,23 @@ class network{
193 196  
194 197 return ss.str();
195 198 }
196   - ///operator for writing the edge into the stream;
  199 + ///operator for writing the vector into the stream;
197 200 friend std::ofstream& operator<<(std::ofstream& out, const vertex& v)
198 201 {
199 202 unsigned int s0, s1;
200 203 s0 = v.e[0].size();
201 204 s1 = v.e[1].size();
202 205 out.write(reinterpret_cast<const char*>(&v.ptr[0]), 3*sizeof(T)); ///write physical vertex location
203   - out.write(reinterpret_cast<const char*>(&s0), sizeof(unsigned int)); ///write the number of "incoming edges"
204   - out.write(reinterpret_cast<const char*>(&s1), sizeof(unsigned int)); ///write the number of "outgoing edges"
205   - out.write(reinterpret_cast<const char*>(&v.e[0][0]), sizeof(unsigned int)*v.e[0].size()); ///write the "incoming edges"
206   - out.write(reinterpret_cast<const char*>(&v.e[1][0]), sizeof(unsigned int)*v.e[1].size()); ///write the "outgoing edges"
  206 + out.write(reinterpret_cast<const char*>(&s0), sizeof(unsigned int)); ///write the number of "outgoing edges"
  207 + out.write(reinterpret_cast<const char*>(&s1), sizeof(unsigned int)); ///write the number of "incoming edges"
  208 + if (s0 != 0)
  209 + out.write(reinterpret_cast<const char*>(&v.e[0][0]), sizeof(unsigned int)*v.e[0].size()); ///write the "outgoing edges"
  210 + if (s1 != 0)
  211 + out.write(reinterpret_cast<const char*>(&v.e[1][0]), sizeof(unsigned int)*v.e[1].size()); ///write the "incoming edges"
207 212 return out;
208 213 }
209 214  
210   - ///operator for reading the edge out of the stream;
  215 + ///operator for reading the vector out of the stream;
211 216 friend std::ifstream& operator>>(std::ifstream& in, vertex& v)
212 217 {
213 218 in.read(reinterpret_cast<char*>(&v[0]), 3*sizeof(T)); ///read the physical position
... ... @@ -218,8 +223,10 @@ class network{
218 223 std::vector<unsigned int> two(s[1]);
219 224 v.e[0] = one;
220 225 v.e[1] = two;
221   - in.read(reinterpret_cast<char*>(&v.e[0][0]),s[0]*sizeof(unsigned int)); ///read the arrays of "incoming edges"
222   - in.read(reinterpret_cast<char*>(&v.e[1][0]),s[1]*sizeof(unsigned int)); ///read the arrays of "outgoing edges"
  226 + if (one.size() != 0)
  227 + in.read(reinterpret_cast<char*>(&v.e[0][0]), s[0] * sizeof(unsigned int)); ///read the arrays of "outgoing edges"
  228 + if (two.size() != 0)
  229 + in.read(reinterpret_cast<char*>(&v.e[1][0]), s[1] * sizeof(unsigned int)); ///read the arrays of "incoming edges"
223 230 return in;
224 231 }
225 232  
... ... @@ -501,10 +508,24 @@ public:
501 508 it = find(id2vert.begin(), id2vert.end(), i[0]); //look for the first node
502 509 if(it == id2vert.end()){ //if i[0] hasn't already been used
503 510 vertex new_vertex = new_edge[0]; //create a new vertex, assign it a position
504   - new_vertex.e[0].push_back(E.size()); //add the current edge as outgoing
505   - new_edge.v[0] = V.size(); //add the new edge to the edge
506   - V.push_back(new_vertex); //add the new vertex to the vertex list
507   - id2vert.push_back(i[0]); //add the ID to the ID->vertex conversion list
  511 + bool flag = false;
  512 + unsigned j = 0;
  513 + for (; j < V.size(); j++) { // check whether current vertex is already exist
  514 + if (new_vertex == V[j]) {
  515 + flag = true;
  516 + break;
  517 + }
  518 + }
  519 + if (!flag) { // unique one
  520 + new_vertex.e[0].push_back(E.size()); //add the current edge as outgoing
  521 + new_edge.v[0] = V.size(); //add the new edge to the edge
  522 + V.push_back(new_vertex); //add the new vertex to the vertex list
  523 + id2vert.push_back(i[0]); //add the ID to the ID->vertex conversion list
  524 + }
  525 + else {
  526 + V[j].e[0].push_back(E.size());
  527 + new_edge.v[0] = j;
  528 + }
508 529 }
509 530 else{ //if the vertex already exists
510 531 it_idx = std::distance(id2vert.begin(), it);
... ... @@ -515,10 +536,24 @@ public:
515 536 it = find(id2vert.begin(), id2vert.end(), i[1]); //look for the second ID
516 537 if(it == id2vert.end()){ //if i[1] hasn't already been used
517 538 vertex new_vertex = new_edge[I-1]; //create a new vertex, assign it a position
518   - new_vertex.e[1].push_back(E.size()); //add the current edge as incoming
519   - new_edge.v[1] = V.size(); //add the new vertex to the edge
520   - V.push_back(new_vertex); //add the new vertex to the vertex list
521   - id2vert.push_back(i[1]); //add the ID to the ID->vertex conversion list
  539 + bool flag = false;
  540 + unsigned j = 0;
  541 + for (; j < V.size(); j++) { // check whether current vertex is already exist
  542 + if (new_vertex == V[j]) {
  543 + flag = true;
  544 + break;
  545 + }
  546 + }
  547 + if (!flag) {
  548 + new_vertex.e[1].push_back(E.size()); //add the current edge as incoming
  549 + new_edge.v[1] = V.size(); //add the new vertex to the edge
  550 + V.push_back(new_vertex); //add the new vertex to the vertex list
  551 + id2vert.push_back(i[1]); //add the ID to the ID->vertex conversion list
  552 + }
  553 + else {
  554 + V[j].e[1].push_back(E.size());
  555 + new_edge.v[1] = j;
  556 + }
522 557 }
523 558 else{ //if the vertex already exists
524 559 it_idx = std::distance(id2vert.begin(), it);
... ... @@ -529,6 +564,27 @@ public:
529 564 E.push_back(new_edge); //push the edge to the list
530 565  
531 566 }
  567 +
  568 + // copy the radii information from OBJ
  569 + /*if (O.numVT()) {
  570 + unsigned k = 0;
  571 + for (unsigned i = 0; i < E.size(); i++) {
  572 + for (unsigned j = 0; j < E[i].size(); j++) {
  573 + E[i].cylinder<T>::set_r(j, O.getVT(k)[0] / 2);
  574 + k++;
  575 + }
  576 + }
  577 + }*/
  578 + // OBJ class assumes that in L the two values are equal
  579 + if (O.numVT()) {
  580 + std::vector< unsigned > id; //create an array to store the centerline point IDs
  581 + for (unsigned i = 0; i < O.numL(); i++) {
  582 + id.clear();
  583 + O.getLinei(i + 1, id); //get the list of point IDs for the line
  584 + for (unsigned j = 0; j < id.size(); j++)
  585 + E[i].cylinder<T>::set_r(j, O.getVT(id[j] - 1)[0] / 2);
  586 + }
  587 + }
532 588 }
533 589  
534 590 ///loads a .nwt file. Reads the header and loads the data into the network according to the header.
... ... @@ -554,7 +610,7 @@ public:
554 610 edge e;
555 611 file >> e;
556 612 E.push_back(e);
557   - std::cout << i << " " << E[i].str() << std::endl;
  613 + //std::cout << i << " " << E[i].str() << std::endl; // not necessary?
558 614 }
559 615 file.close();
560 616 }
... ... @@ -573,7 +629,7 @@ public:
573 629 }
574 630 for(int i = 0; i < E.size(); i++) ///loop through the Edges and write each one.
575 631 {
576   - std::cout << i << " " << E[i].str() << std::endl;
  632 + //std::cout << i << " " << E[i].str() << std::endl; // not necesarry?
577 633 file << E[i];
578 634 }
579 635 file.close();
... ...
stim/visualization/cylinder.h
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... ... @@ -21,18 +21,6 @@ protected:
21 21  
22 22 //calculates the U values for each point to initialize the frenet frame
23 23 // this function assumes that the centerline has already been set
24   - void init() {
25   - U.resize(size()); //allocate space for the frenet frame vectors
26   - R.resize(size());
27   -
28   - stim::circle<T> c; //create a circle
29   - stim::vec3<T> d0, d1;
30   - for (size_t i = 0; i < size() - 1; i++) { //for each line segment in the centerline
31   - c.rotate(d(i)); //rotate the circle to match that normal
32   - U[i] = c.U; //save the U vector from the circle
33   - }
34   - U[size() - 1] = c.U; //for the last point, duplicate the final frenet frame vector
35   - }
36 24  
37 25 public:
38 26  
... ... @@ -94,6 +82,20 @@ public:
94 82 return R[i];
95 83 }
96 84  
  85 + void init() {
  86 + U.resize(size()); //allocate space for the frenet frame vectors
  87 +// if (R.size() != 0)
  88 + R.resize(size());
  89 +
  90 + stim::circle<T> c; //create a circle
  91 + stim::vec3<T> d0, d1;
  92 + for (size_t i = 0; i < size() - 1; i++) { //for each line segment in the centerline
  93 + c.rotate(d(i)); //rotate the circle to match that normal
  94 + U[i] = c.U; //save the U vector from the circle
  95 + }
  96 + U[size() - 1] = c.U; //for the last point, duplicate the final frenet frame vector
  97 + }
  98 +
97 99 ///adds a magnitude to each point in the cylinder
98 100 /*void add_mag(V val = 0) {
99 101 if (M.size() == 0) M.resize(size()); //if the magnitude vector isn't initialized, resize it to match the centerline
... ...