df036f4c
David Mayerich
added the network...
|
1
2
3
|
#ifndef STIM_NETWORK_H
#define STIM_NETWORK_H
|
7f27eafa
David Mayerich
simplified the st...
|
4
|
#include <stdlib.h>
|
9c97e126
David Mayerich
added an axis-ali...
|
5
|
#include <assert.h>
|
7f27eafa
David Mayerich
simplified the st...
|
6
7
8
9
10
|
#include <sstream>
#include <fstream>
#include <algorithm>
#include <string.h>
#include <math.h>
|
c61fd046
David Mayerich
fixed vessel mode...
|
11
|
#include <stim/math/vector.h>
|
5687cf1b
Cherub P. Harder
Added #include <s...
|
12
|
#include <stim/visualization/obj.h>
|
58ee2b21
David Mayerich
incorporated stim...
|
13
|
#include <stim/visualization/cylinder.h>
|
df036f4c
David Mayerich
added the network...
|
14
|
#include <ANN/ANN.h>
|
7f27eafa
David Mayerich
simplified the st...
|
15
16
|
#include <boost/tuple/tuple.hpp>
|
df036f4c
David Mayerich
added the network...
|
17
18
|
namespace stim{
|
7f27eafa
David Mayerich
simplified the st...
|
19
20
21
22
23
|
/** This is the a class that interfaces with gl_spider in order to store the currently
* segmented network. The following data is stored and can be extracted:
* 1)Network geometry and centerline.
* 2)Network connectivity (a graph of nodes and edges), reconstructed using ANN library.
*/
|
df036f4c
David Mayerich
added the network...
|
24
|
|
df036f4c
David Mayerich
added the network...
|
25
26
27
28
|
template<typename T>
class network{
|
7f27eafa
David Mayerich
simplified the st...
|
29
30
|
///Each edge is a fiber with two nodes.
///Each node is an in index to the endpoint of the fiber in the nodes array.
|
58ee2b21
David Mayerich
incorporated stim...
|
31
|
class edge : public cylinder<T>
|
7f27eafa
David Mayerich
simplified the st...
|
32
33
34
|
{
public:
unsigned v[2]; //unique id's designating the starting and ending
|
7c43b7f9
pranathivemuri
return resampled ...
|
35
|
// default constructor
|
58ee2b21
David Mayerich
incorporated stim...
|
36
|
edge() : cylinder<T>(){v[1] = -1; v[0] = -1;}
|
7f27eafa
David Mayerich
simplified the st...
|
37
|
/// Constructor - creates an edge from a list of points by calling the stim::fiber constructor
|
e376212f
David Mayerich
added support for...
|
38
|
|
3800c27f
David Mayerich
added code to sub...
|
39
|
///@param p is an array of positions in space
|
58ee2b21
David Mayerich
incorporated stim...
|
40
|
edge(std::vector< stim::vec<T> > p) : cylinder<T>(p){}
|
3800c27f
David Mayerich
added code to sub...
|
41
42
|
/// Copy constructor creates an edge from a fiber
|
58ee2b21
David Mayerich
incorporated stim...
|
43
|
edge(stim::cylinder<T> f) : cylinder<T>(f) {}
|
3800c27f
David Mayerich
added code to sub...
|
44
45
46
|
/// Resamples an edge by calling the fiber resampling function
edge resample(T spacing){
|
58ee2b21
David Mayerich
incorporated stim...
|
47
|
edge e(cylinder<T>::resample(spacing)); //call the fiber->edge constructor
|
3800c27f
David Mayerich
added code to sub...
|
48
49
50
51
52
|
e.v[0] = v[0]; //copy the vertex data
e.v[1] = v[1];
return e; //return the new edge
}
|
9c97e126
David Mayerich
added an axis-ali...
|
53
|
|
7f27eafa
David Mayerich
simplified the st...
|
54
|
/// Output the edge information as a string
|
df036f4c
David Mayerich
added the network...
|
55
56
|
std::string str(){
std::stringstream ss;
|
58ee2b21
David Mayerich
incorporated stim...
|
57
|
ss<<"("<<cylinder<T>::size()<<")\tl = "<<length()<<"\t"<<v[0]<<"----"<<v[1];
|
df036f4c
David Mayerich
added the network...
|
58
59
|
return ss.str();
}
|
df036f4c
David Mayerich
added the network...
|
60
|
|
9c97e126
David Mayerich
added an axis-ali...
|
61
62
|
};
|
7f27eafa
David Mayerich
simplified the st...
|
63
64
65
66
67
68
|
///Node class that stores the physical position of the node as well as the edges it is connected to (edges that connect to it), As well as any additional data necessary.
class vertex : public stim::vec<T>
{
public:
//std::vector<unsigned int> edges; //indices of edges connected to this node.
std::vector<unsigned int> e[2]; //indices of edges going out (e[0]) and coming in (e[1])
|
df480014
pranathivemuri
added in comments...
|
69
|
//stim::vec<T> p; //position of this node in physical space.
|
7f27eafa
David Mayerich
simplified the st...
|
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
|
//constructor takes a stim::vec
vertex(stim::vec<T> p) : stim::vec<T>(p){}
/// Output the vertex information as a string
std::string str(){
std::stringstream ss;
ss<<"\t(x, y, z) = "<<stim::vec<T>::str();
if(e[0].size() > 0){
ss<<"\t> ";
for(unsigned int o = 0; o < e[0].size(); o++)
ss<<e[0][o]<<" ";
}
if(e[1].size() > 0){
ss<<"\t< ";
for(unsigned int i = 0; i < e[1].size(); i++)
ss<<e[1][i]<<" ";
}
|
df036f4c
David Mayerich
added the network...
|
89
|
|
7f27eafa
David Mayerich
simplified the st...
|
90
|
return ss.str();
|
df036f4c
David Mayerich
added the network...
|
91
|
}
|
9c97e126
David Mayerich
added an axis-ali...
|
92
|
|
df036f4c
David Mayerich
added the network...
|
93
94
|
};
|
9c97e126
David Mayerich
added an axis-ali...
|
95
|
protected:
|
df036f4c
David Mayerich
added the network...
|
96
|
|
7f27eafa
David Mayerich
simplified the st...
|
97
98
|
std::vector<edge> E; //list of edges
std::vector<vertex> V; //list of vertices.
|
9c97e126
David Mayerich
added an axis-ali...
|
99
100
|
public:
|
df036f4c
David Mayerich
added the network...
|
101
|
|
7f27eafa
David Mayerich
simplified the st...
|
102
103
104
|
///Returns the number of edges in the network.
unsigned int edges(){
return E.size();
|
df036f4c
David Mayerich
added the network...
|
105
106
|
}
|
7f27eafa
David Mayerich
simplified the st...
|
107
108
109
|
///Returns the number of nodes in the network.
unsigned int vertices(){
return V.size();
|
df036f4c
David Mayerich
added the network...
|
110
111
|
}
|
58ee2b21
David Mayerich
incorporated stim...
|
112
|
stim::cylinder<T> get_cylinder(unsigned f){
|
3800c27f
David Mayerich
added code to sub...
|
113
114
115
|
return E[f]; //return the specified edge (casting it to a fiber)
}
|
7f27eafa
David Mayerich
simplified the st...
|
116
117
|
//load a network from an OBJ file
void load_obj(std::string filename){
|
e376212f
David Mayerich
added support for...
|
118
|
|
7f27eafa
David Mayerich
simplified the st...
|
119
120
|
stim::obj<T> O; //create an OBJ object
O.load(filename); //load the OBJ file as an object
|
df036f4c
David Mayerich
added the network...
|
121
|
|
7f27eafa
David Mayerich
simplified the st...
|
122
|
std::vector<unsigned> id2vert; //this list stores the OBJ vertex ID associated with each network vertex
|
df036f4c
David Mayerich
added the network...
|
123
|
|
4df9ec0e
pranathivemuri
compare networks ...
|
124
|
unsigned i[2]; //temporary, IDs associated with the first and last points in an OBJ line
|
df036f4c
David Mayerich
added the network...
|
125
|
|
7f27eafa
David Mayerich
simplified the st...
|
126
127
|
//for each line in the OBJ object
for(unsigned int l = 1; l <= O.numL(); l++){
|
df036f4c
David Mayerich
added the network...
|
128
|
|
7f27eafa
David Mayerich
simplified the st...
|
129
130
|
std::vector< stim::vec<T> > c; //allocate an array of points for the vessel centerline
O.getLine(l, c); //get the fiber centerline
|
df036f4c
David Mayerich
added the network...
|
131
|
|
3800c27f
David Mayerich
added code to sub...
|
132
|
edge new_edge = c; //create an edge from the given centerline
|
58ee2b21
David Mayerich
incorporated stim...
|
133
|
unsigned int I = new_edge.size(); //calculate the number of points on the centerline
|
df036f4c
David Mayerich
added the network...
|
134
|
|
7f27eafa
David Mayerich
simplified the st...
|
135
136
|
//get the first and last vertex IDs for the line
std::vector< unsigned > id; //create an array to store the centerline point IDs
|
9c97e126
David Mayerich
added an axis-ali...
|
137
|
O.getLinei(l, id); //get the list of point IDs for the line
|
7f27eafa
David Mayerich
simplified the st...
|
138
139
|
i[0] = id.front(); //get the OBJ ID for the first element of the line
i[1] = id.back(); //get the OBJ ID for the last element of the line
|
df036f4c
David Mayerich
added the network...
|
140
|
|
7f27eafa
David Mayerich
simplified the st...
|
141
142
|
std::vector<unsigned>::iterator it; //create an iterator for searching the id2vert array
unsigned it_idx; //create an integer for the id2vert entry index
|
df036f4c
David Mayerich
added the network...
|
143
|
|
7f27eafa
David Mayerich
simplified the st...
|
144
145
146
147
|
//find out if the nodes for this fiber have already been created
it = find(id2vert.begin(), id2vert.end(), i[0]); //look for the first node
it_idx = std::distance(id2vert.begin(), it);
if(it == id2vert.end()){ //if i[0] hasn't already been used
|
4df9ec0e
pranathivemuri
compare networks ...
|
148
149
150
151
|
vertex new_vertex = new_edge[0]; //create a new vertex, assign it a position
new_vertex.e[0].push_back(E.size()); //add the current edge as outgoing
new_edge.v[0] = V.size(); //add the new vertex to the edge
V.push_back(new_vertex); //add the new vertex to the vertex list
|
7f27eafa
David Mayerich
simplified the st...
|
152
|
id2vert.push_back(i[0]); //add the ID to the ID->vertex conversion list
|
df036f4c
David Mayerich
added the network...
|
153
|
}
|
7f27eafa
David Mayerich
simplified the st...
|
154
|
else{ //if the vertex already exists
|
df480014
pranathivemuri
added in comments...
|
155
|
V[it_idx].e[0].push_back(E.size()); //add the current edge as outgoing
|
3800c27f
David Mayerich
added code to sub...
|
156
|
new_edge.v[0] = it_idx;
|
df036f4c
David Mayerich
added the network...
|
157
158
|
}
|
7f27eafa
David Mayerich
simplified the st...
|
159
160
161
|
it = find(id2vert.begin(), id2vert.end(), i[1]); //look for the second ID
it_idx = std::distance(id2vert.begin(), it);
if(it == id2vert.end()){ //if i[1] hasn't already been used
|
58ee2b21
David Mayerich
incorporated stim...
|
162
|
vertex new_vertex = new_edge[I-1]; //create a new vertex, assign it a position
|
3800c27f
David Mayerich
added code to sub...
|
163
164
165
|
new_vertex.e[1].push_back(E.size()); //add the current edge as incoming
new_edge.v[1] = V.size();
V.push_back(new_vertex); //add the new vertex to the vertex list
|
7f27eafa
David Mayerich
simplified the st...
|
166
|
id2vert.push_back(i[1]); //add the ID to the ID->vertex conversion list
|
df036f4c
David Mayerich
added the network...
|
167
|
}
|
7f27eafa
David Mayerich
simplified the st...
|
168
|
else{ //if the vertex already exists
|
df480014
pranathivemuri
added in comments...
|
169
|
V[it_idx].e[1].push_back(E.size()); //add the current edge as incoming
|
3800c27f
David Mayerich
added code to sub...
|
170
|
new_edge.v[1] = it_idx;
|
df036f4c
David Mayerich
added the network...
|
171
|
}
|
9c97e126
David Mayerich
added an axis-ali...
|
172
|
|
4df9ec0e
pranathivemuri
compare networks ...
|
173
|
E.push_back(new_edge); //push the edge to the list
|
df036f4c
David Mayerich
added the network...
|
174
|
|
df036f4c
David Mayerich
added the network...
|
175
|
}
|
e376212f
David Mayerich
added support for...
|
176
177
|
}
|
7f27eafa
David Mayerich
simplified the st...
|
178
179
|
/// Output the network as a string
std::string str(){
|
e376212f
David Mayerich
added support for...
|
180
|
|
7f27eafa
David Mayerich
simplified the st...
|
181
182
183
184
|
std::stringstream ss;
ss<<"Nodes ("<<V.size()<<")--------"<<std::endl;
for(unsigned int v = 0; v < V.size(); v++){
ss<<"\t"<<v<<V[v].str()<<std::endl;
|
e376212f
David Mayerich
added support for...
|
185
186
|
}
|
7f27eafa
David Mayerich
simplified the st...
|
187
188
189
|
ss<<"Edges ("<<E.size()<<")--------"<<std::endl;
for(unsigned e = 0; e < E.size(); e++){
ss<<"\t"<<e<<E[e].str()<<std::endl;
|
df036f4c
David Mayerich
added the network...
|
190
191
|
}
|
7f27eafa
David Mayerich
simplified the st...
|
192
|
return ss.str();
|
df036f4c
David Mayerich
added the network...
|
193
|
}
|
3800c27f
David Mayerich
added code to sub...
|
194
195
|
/// This function resamples all fibers in a network given a desired minimum spacing
|
9c97e126
David Mayerich
added an axis-ali...
|
196
|
/// @param spacing is the minimum distance between two points on the network
|
3800c27f
David Mayerich
added code to sub...
|
197
|
stim::network<T> resample(T spacing){
|
3800c27f
David Mayerich
added code to sub...
|
198
199
200
|
stim::network<T> n; //create a new network that will be an exact copy, with resampled fibers
n.V = V; //copy all vertices
|
4df9ec0e
pranathivemuri
compare networks ...
|
201
|
n.E.resize(edges()); //allocate space for the edge list
|
3800c27f
David Mayerich
added code to sub...
|
202
203
|
//copy all fibers, resampling them in the process
|
4df9ec0e
pranathivemuri
compare networks ...
|
204
|
for(unsigned e = 0; e < edges(); e++){ //for each edge in the edge list
|
3800c27f
David Mayerich
added code to sub...
|
205
|
n.E[e] = E[e].resample(spacing); //resample the edge and copy it to the new network
|
3800c27f
David Mayerich
added code to sub...
|
206
207
|
}
|
4df9ec0e
pranathivemuri
compare networks ...
|
208
209
210
211
|
return n; //return the resampled network
}
|
4df9ec0e
pranathivemuri
compare networks ...
|
212
|
|
9c97e126
David Mayerich
added an axis-ali...
|
213
|
/// Calculate the total number of points on all edges.
|
797f8ab0
David Mayerich
cleaned up the st...
|
214
215
216
217
|
unsigned total_points(){
unsigned n = 0;
for(unsigned e = 0; e < E.size(); e++)
n += E[e].size();
|
4df9ec0e
pranathivemuri
compare networks ...
|
218
|
return n;
|
797f8ab0
David Mayerich
cleaned up the st...
|
219
|
}
|
4df9ec0e
pranathivemuri
compare networks ...
|
220
221
222
223
|
// gaussian function
float gaussianFunction(float x, float std=25){ return exp(-x/(2*std*std));} // by default std = 25
|
e06b2e0b
pranathivemuri
removed functions...
|
224
|
// stim 3d vector to annpoint of 3 dimensions
|
797f8ab0
David Mayerich
cleaned up the st...
|
225
226
227
228
229
230
|
void stim2ann(ANNpoint &a, stim::vec<T> b){
a[0] = b[0];
a[1] = b[1];
a[2] = b[2];
}
|
9c97e126
David Mayerich
added an axis-ali...
|
231
232
233
234
235
236
237
238
239
240
|
/// Calculate the average magnitude across the entire network.
/// @param m is the magnitude value to use. The default is 0 (usually radius).
T average(unsigned m = 0){
T M, L; //allocate space for the total magnitude and length
M = L = 0; //initialize both the initial magnitude and length to zero
for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
M += E[e].integrate(m); //get the integrated magnitude
L += E[e].length(); //get the edge length
}
|
4df9ec0e
pranathivemuri
compare networks ...
|
241
|
|
9c97e126
David Mayerich
added an axis-ali...
|
242
243
244
245
246
247
248
249
250
251
252
253
254
|
return M / L; //return the average magnitude
}
/// This function compares two networks and returns the percentage of the current network that is missing from A.
/// @param A is the network to compare to - the field is generated for A
/// @param sigma is the user-defined tolerance value - smaller values provide a stricter comparison
stim::network<T> compare(stim::network<T> A, float sigma){
stim::network<T> R; //generate a network storing the result of the comparison
R = (*this); //initialize the result with the current network
//generate a KD-tree for network A
|
4df9ec0e
pranathivemuri
compare networks ...
|
255
256
257
|
float metric = 0.0; // initialize metric to be returned after comparing the networks
ANNkd_tree* kdt; // initialize a pointer to a kd tree
double **c; // centerline (array of double pointers) - points on kdtree must be double
|
9c97e126
David Mayerich
added an axis-ali...
|
258
|
unsigned int n_data = A.total_points(); // set the number of points
|
4df9ec0e
pranathivemuri
compare networks ...
|
259
260
|
c = (double**) malloc(sizeof(double*) * n_data); // allocate the array pointer
for(unsigned int i = 0; i < n_data; i++) // allocate space for each point of 3 dimensions
|
797f8ab0
David Mayerich
cleaned up the st...
|
261
|
c[i] = (double*) malloc(sizeof(double) * 3);
|
9c97e126
David Mayerich
added an axis-ali...
|
262
|
|
797f8ab0
David Mayerich
cleaned up the st...
|
263
|
unsigned t = 0;
|
9c97e126
David Mayerich
added an axis-ali...
|
264
265
|
for(unsigned e = 0; e < A.E.size(); e++){ //for each edge in the network
for(unsigned p = 0; p < A.E[e].size(); p++){ //for each point in the edge
|
797f8ab0
David Mayerich
cleaned up the st...
|
266
267
|
for(unsigned d = 0; d < 3; d++){ //for each coordinate
|
9c97e126
David Mayerich
added an axis-ali...
|
268
|
c[t][d] = A.E[e][p][d];
|
4df9ec0e
pranathivemuri
compare networks ...
|
269
|
}
|
797f8ab0
David Mayerich
cleaned up the st...
|
270
|
t++;
|
4df9ec0e
pranathivemuri
compare networks ...
|
271
|
}
|
797f8ab0
David Mayerich
cleaned up the st...
|
272
273
|
}
|
9c97e126
David Mayerich
added an axis-ali...
|
274
|
//compare each point in the current network to the field produced by A
|
4df9ec0e
pranathivemuri
compare networks ...
|
275
276
277
|
ANNpointArray pts = (ANNpointArray)c; // create an array of data points of type double
kdt = new ANNkd_tree(pts, n_data, 3); // build a KD tree using the annpointarray
double eps = 0; // error bound
|
797f8ab0
David Mayerich
cleaned up the st...
|
278
279
280
281
282
283
284
285
286
|
ANNdistArray dists = new ANNdist[1]; // near neighbor distances
ANNidxArray nnIdx = new ANNidx[1]; // near neighbor indices // allocate near neigh indices
stim::vec<T> p0, p1;
float m0, m1;
float M = 0; //stores the total metric value
float l; //stores the segment length
float L = 0; //stores the total network length
ANNpoint queryPt = annAllocPt(3);
|
9c97e126
David Mayerich
added an axis-ali...
|
287
288
|
for(unsigned e = 0; e < R.E.size(); e++){ //for each edge in A
R.E[e].add_mag(0); //add a new magnitude for the metric
|
797f8ab0
David Mayerich
cleaned up the st...
|
289
|
|
9c97e126
David Mayerich
added an axis-ali...
|
290
|
for(unsigned p = 0; p < R.E[e].size(); p++){ //for each point in the edge
|
797f8ab0
David Mayerich
cleaned up the st...
|
291
|
|
9c97e126
David Mayerich
added an axis-ali...
|
292
|
p1 = R.E[e][p]; //get the next point in the edge
|
797f8ab0
David Mayerich
cleaned up the st...
|
293
294
295
|
stim2ann(queryPt, p1);
kdt->annkSearch( queryPt, 1, nnIdx, dists, eps); //find the distance between A and the current network
m1 = 1.0f - gaussianFunction(dists[0], sigma); //calculate the metric value based on the distance
|
9c97e126
David Mayerich
added an axis-ali...
|
296
|
R.E[e].set_mag(m1, p, 1); //set the error for the second point in the segment
|
797f8ab0
David Mayerich
cleaned up the st...
|
297
|
|
797f8ab0
David Mayerich
cleaned up the st...
|
298
299
300
|
}
}
|
9c97e126
David Mayerich
added an axis-ali...
|
301
|
return R; //return the resulting network
|
3800c27f
David Mayerich
added code to sub...
|
302
|
}
|
9c97e126
David Mayerich
added an axis-ali...
|
303
|
|
b3a38641
David Mayerich
added the ability...
|
304
305
306
307
308
|
/// Returns the number of magnitude values stored in each edge. This should be uniform across the network.
unsigned nmags(){
return E[0].nmags();
}
|
9c97e126
David Mayerich
added an axis-ali...
|
309
|
|
7f27eafa
David Mayerich
simplified the st...
|
310
311
|
}; //end stim::network class
}; //end stim namespace
|
df036f4c
David Mayerich
added the network...
|
312
|
#endif
|