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/*
Copyright <2017> <David Mayerich>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
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#ifndef STIM_NETWORK_H
#define STIM_NETWORK_H
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#include <stdlib.h>
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#include <assert.h>
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#include <sstream>
#include <fstream>
#include <algorithm>
#include <string.h>
#include <math.h>
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#include <stim/math/vec3.h>
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#include <stim/visualization/obj.h>
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#include <stim/visualization/swc.h>
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#include <stim/visualization/cylinder.h>
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#include <stim/cuda/cudatools/timer.h>
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#include <stim/cuda/cudatools/callable.h>
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#include <stim/structures/kdtree.cuh>
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//********************help function********************
// gaussian_function
CUDA_CALLABLE float gaussianFunction(float x, float std = 25) { return exp(-x / (2 * std*std)); } // std default sigma value is 25
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// compute metric in parallel
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#ifdef __CUDACC__
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template <typename T>
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__global__ void find_metric_parallel(T* M, size_t n, T* D, float sigma){
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size_t x = blockDim.x * blockIdx.x + threadIdx.x;
if(x >= n) return;
M[x] = 1.0f - gaussianFunction(D[x], sigma);
}
//find the corresponding edge index from array index
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__global__ void find_edge_index_parallel(size_t* I, size_t n, unsigned* R, size_t* E, size_t ne){
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size_t x = blockDim.x * blockIdx.x + threadIdx.x;
if(x >= n) return;
unsigned i = 0;
size_t N = 0;
for(unsigned e = 0; e < ne; e++){
N += E[e];
if(I[x] < N){
R[x] = i;
break;
}
i++;
}
}
#endif
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int threshold_fac;
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namespace stim{
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/** 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.
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* 2)Network connectivity (a graph of nodes and edges), reconstructed using kdtree.
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*/
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template<typename T>
class network{
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///Each edge is a fiber with two nodes.
///Each node is an in index to the endpoint of the fiber in the nodes array.
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class edge : public cylinder<T>
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{
public:
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unsigned int v[2]; //unique id's designating the starting and ending
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// default constructor
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edge() : cylinder<T>() {
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v[1] = (unsigned)(-1); v[0] = (unsigned)(-1);
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}
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/// Constructor - creates an edge from a list of points by calling the stim::fiber constructor
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/*
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///@param v0, the starting index.
///@param v1, the ending index.
///@param sz, the number of point in the fiber.
edge(unsigned int v0, unsigned int v1, unsigned int sz) : cylinder<T>(
{
}
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*/
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edge(std::vector<stim::vec3<T> > p, std::vector<T> s)
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: cylinder<T>(p,s)
{
}
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///@param p is an array of positions in space
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edge(stim::centerline<T> p) : cylinder<T>(p){}
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/// Copy constructor creates an edge from a cylinder
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edge(stim::cylinder<T> f) : cylinder<T>(f) {}
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/// Resamples an edge by calling the fiber resampling function
edge resample(T spacing){
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edge e(cylinder<T>::resample(spacing)); //call the fiber->edge constructor
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e.v[0] = v[0]; //copy the vertex data
e.v[1] = v[1];
return e; //return the new edge
}
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/// Output the edge information as a string
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std::string str(){
std::stringstream ss;
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ss<<"("<<cylinder<T>::size()<<")\tl = "<<this->length()<<"\t"<<v[0]<<"----"<<v[1];
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return ss.str();
}
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std::vector<edge> split(unsigned int idx){
std::vector< stim::cylinder<T> > C;
C.resize(2);
C = (*this).cylinder<T>::split(idx);
std::vector<edge> E(C.size());
for(unsigned e = 0; e < E.size(); e++){
E[e] = C[e];
}
return E;
}
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/// operator for writing the edge information into a binary .nwt file.
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friend std::ofstream& operator<<(std::ofstream& out, const edge& e)
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{
out.write(reinterpret_cast<const char*>(&e.v[0]), sizeof(unsigned int)); ///write the starting point.
out.write(reinterpret_cast<const char*>(&e.v[1]), sizeof(unsigned int)); ///write the ending point.
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unsigned int sz = e.size(); ///write the number of point in the edge.
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out.write(reinterpret_cast<const char*>(&sz), sizeof(unsigned int));
for(int i = 0; i < sz; i++) ///write each point
{
stim::vec3<T> point = e[i];
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out.write(reinterpret_cast<const char*>(&point[0]), 3*sizeof(T));
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// for(int j = 0; j < nmags(); j++) //future code for multiple mags
// {
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out.write(reinterpret_cast<const char*>(&e.R[i]), sizeof(T)); ///write the radius
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//std::cout << point.str() << " " << e.R[i] << std::endl;
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// }
}
return out; //return stream
}
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/// operator for reading an edge from a binary .nwt file.
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friend std::ifstream& operator>>(std::ifstream& in, edge& e)
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{
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unsigned int v0, v1, sz;
in.read(reinterpret_cast<char*>(&v0), sizeof(unsigned int)); //read the staring point.
in.read(reinterpret_cast<char*>(&v1), sizeof(unsigned int)); //read the ending point
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in.read(reinterpret_cast<char*>(&sz), sizeof(unsigned int)); //read the number of points in the edge
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// stim::centerline<T> temp = stim::centerline<T>(sz); //allocate the new edge
// e = edge(temp);
std::vector<stim::vec3<T> > p(sz);
std::vector<T> r(sz);
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for(int i = 0; i < sz; i++) //set the points and radii to the newly read values
{
stim::vec3<T> point;
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in.read(reinterpret_cast<char*>(&point[0]), 3*sizeof(T));
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p[i] = point;
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T mag;
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// for(int j = 0; j < nmags(); j++) ///future code for mags
// {
in.read(reinterpret_cast<char*>(&mag), sizeof(T));
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r[i] = mag;
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//std::cout << point.str() << " " << mag << std::endl;
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// }
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}
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e = edge(p,r);
e.v[0] = v0; e.v[1] = v1;
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return in;
}
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};
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///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.
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class vertex : public stim::vec3<T>
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{
public:
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//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])
//stim::vec3<T> p; //position of this node in physical space.
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//default constructor
vertex() : stim::vec3<T>()
{
}
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//constructor takes a stim::vec
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vertex(stim::vec3<T> p) : stim::vec3<T>(p){}
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/// Output the vertex information as a string
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std::string
str(){
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std::stringstream ss;
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ss<<"\t(x, y, z) = "<<stim::vec3<T>::str();
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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]<<" ";
}
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return ss.str();
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}
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///operator for writing the vector into the stream;
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friend std::ofstream& operator<<(std::ofstream& out, const vertex& v)
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{
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unsigned int s0, s1;
s0 = v.e[0].size();
s1 = v.e[1].size();
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out.write(reinterpret_cast<const char*>(&v.ptr[0]), 3*sizeof(T)); ///write physical vertex location
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out.write(reinterpret_cast<const char*>(&s0), sizeof(unsigned int)); ///write the number of "outgoing edges"
out.write(reinterpret_cast<const char*>(&s1), sizeof(unsigned int)); ///write the number of "incoming edges"
if (s0 != 0)
out.write(reinterpret_cast<const char*>(&v.e[0][0]), sizeof(unsigned int)*v.e[0].size()); ///write the "outgoing edges"
if (s1 != 0)
out.write(reinterpret_cast<const char*>(&v.e[1][0]), sizeof(unsigned int)*v.e[1].size()); ///write the "incoming edges"
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return out;
}
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///operator for reading the vector out of the stream;
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friend std::ifstream& operator>>(std::ifstream& in, vertex& v)
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{
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in.read(reinterpret_cast<char*>(&v[0]), 3*sizeof(T)); ///read the physical position
unsigned int s[2];
in.read(reinterpret_cast<char*>(&s[0]), 2*sizeof(unsigned int)); ///read the sizes of incoming and outgoing edge arrays
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std::vector<unsigned int> one(s[0]);
std::vector<unsigned int> two(s[1]);
v.e[0] = one;
v.e[1] = two;
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if (one.size() != 0)
in.read(reinterpret_cast<char*>(&v.e[0][0]), s[0] * sizeof(unsigned int)); ///read the arrays of "outgoing edges"
if (two.size() != 0)
in.read(reinterpret_cast<char*>(&v.e[1][0]), s[1] * sizeof(unsigned int)); ///read the arrays of "incoming edges"
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return in;
}
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};
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protected:
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std::vector<edge> E; //list of edges
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std::vector<vertex> V; //list of vertices.
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public:
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///default constructor
network()
{
}
///constructor with a file to load.
network(std::string fileLocation)
{
load_obj(fileLocation);
}
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///Returns the number of edges in the network.
unsigned int edges(){
return E.size();
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}
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///Returns the number of nodes in the network.
unsigned int vertices(){
return V.size();
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}
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///Returns the radius at specific point in the edge
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T get_r(unsigned e, unsigned i) {
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return E[e].r(i);
}
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///Returns the average radius of specific edge
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T get_average_r(unsigned e) {
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T result = 0.0;
unsigned n = E[e].size();
for (unsigned p = 0; p < n; p++)
result += E[e].r(p);
return (T)result / n;
}
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///Returns the length of current edge
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T get_l(unsigned e) {
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return E[e].length();
}
///Returns the start vertex of current edge
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size_t get_start_vertex(unsigned e) {
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return E[e].v[0];
}
///Returns the end vertex of current edge
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size_t get_end_vertex(unsigned e) {
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return E[e].v[1];
}
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///Returns one vertex
stim::vec3<T> get_vertex(unsigned i) {
return V[i];
}
///Returns the boundary vertices' indices
std::vector<unsigned> get_boundary_vertex() {
std::vector<unsigned> result;
for (unsigned v = 0; v < V.size(); v++) {
if (V[v].e[0].size() + V[v].e[1].size() == 1) { // boundary vertex
result.push_back(v);
}
}
return result;
}
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///Set radius
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void set_r(unsigned e, std::vector<T> radius) {
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E[e].cylinder<T>::copy_r(radius);
}
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void set_r(unsigned e, T radius) {
for (size_t i = 0; i < E[e].size(); i++)
E[e].cylinder<T>::set_r(i, radius);
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}
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//scale the network by some constant value
// I don't think these work??????
/*std::vector<vertex> operator*(T s){
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for (unsigned i=0; i< vertices; i ++ ){
V[i] = V[i] * s;
}
return V;
}
std::vector<vertex> operator*(vec<T> s){
for (unsigned i=0; i< vertices; i ++ ){
for (unsigned dim = 0 ; dim< 3; dim ++){
V[i][dim] = V[i][dim] * s[dim];
}
}
return V;
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}*/
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// Returns an average of branching index in the network
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double BranchingIndex(){
double B=0;
for(unsigned v=0; v < V.size(); v ++){
B += ((V[v].e[0].size()) + (V[v].e[1].size()));
}
B = B / V.size();
return B;
}
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// Returns number of branch points in thenetwork
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unsigned int BranchP(){
unsigned int B=0;
unsigned int c;
for(unsigned v=0; v < V.size(); v ++){
c = ((V[v].e[0].size()) + (V[v].e[1].size()));
if (c > 2){
B += 1;}
}
return B;
}
// Returns number of end points (tips) in thenetwork
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unsigned int EndP(){
unsigned int B=0;
unsigned int c;
for(unsigned v=0; v < V.size(); v ++){
c = ((V[v].e[0].size()) + (V[v].e[1].size()));
if (c == 1){
B += 1;}
}
return B;
}
//// Returns a dictionary with the key as the vertex
//std::map<std::vector<vertex>,unsigned int> DegreeDict(){
// std::map<std::vector<vertex>,unsigned int> dd;
// unsigned int c = 0;
// for(unsigned v=0; v < V.size(); v ++){
// c = ((V[v].e[0].size()) + (V[v].e[1].size()));
// dd[V[v]] = c;
// }
// return dd;
//}
//// Return number of branching stems
//unsigned int Stems(){
// unsigned int s = 0;
// std::map<std::vector<vertex>,unsigned int> dd;
// dd = DegreeDict();
// //for(unsigned v=0; v < V.size(); v ++){
// // V[v].e[0].
// return s;
//}
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//Calculate Metrics---------------------------------------------------
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// Returns an average of fiber/edge lengths in the network
double Lengths(){
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stim::vec<T> L;
double sumLength = 0;
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for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
L.push_back(E[e].length()); //append the edge length
sumLength = sumLength + E[e].length();
}
double avg = sumLength / E.size();
return avg;
}
// Returns an average of tortuosities in the network
double Tortuosities(){
stim::vec<T> t;
stim::vec<T> id1, id2; // starting and ending vertices of the edge
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double distance;double tortuosity;double sumTortuosity = 0;
for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
id1 = E[e][0]; //get the edge starting point
id2 = E[e][E[e].size() - 1]; //get the edge ending point
distance = (id1 - id2).len(); //displacement between the starting and ending points
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if(distance > 0){
tortuosity = E[e].length()/ distance ; // tortuoisty = edge length / edge displacement
}
else{
tortuosity = 0;}
t.push_back(tortuosity);
sumTortuosity += tortuosity;
}
double avg = sumTortuosity / E.size();
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return avg;
}
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// Returns average contraction of the network
double Contractions(){
stim::vec<T> t;
stim::vec<T> id1, id2; // starting and ending vertices of the edge
double distance;double contraction;double sumContraction = 0;
for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
id1 = E[e][0]; //get the edge starting point
id2 = E[e][E[e].size() - 1]; //get the edge ending point
distance = (id1 - id2).len(); //displacement between the starting and ending points
contraction = distance / E[e].length(); // tortuoisty = edge length / edge displacement
t.push_back(contraction);
sumContraction += contraction;
}
double avg = sumContraction / E.size();
return avg;
}
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|
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// returns average fractal dimension of the branches of the network
double FractalDimensions(){
stim::vec<T> t;
stim::vec<T> id1, id2; // starting and ending vertices of the edge
double distance;double fract;double sumFractDim = 0;
for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
id1 = E[e][0]; //get the edge starting point
id2 = E[e][E[e].size() - 1]; //get the edge ending point
distance = (id1 - id2).len(); //displacement between the starting and ending points
fract = std::log(distance) / std::log(E[e].length()); // tortuoisty = edge length / edge displacement
t.push_back(sumFractDim);
sumFractDim += fract;
}
double avg = sumFractDim / E.size();
return avg;
}
|
87d0a1d2
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//returns a cylinder represented a given fiber (based on edge index)
stim::cylinder<T> get_cylinder(unsigned e){
return E[e]; //return the specified edge (casting it to a fiber)
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}
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//load a network from an OBJ file
void load_obj(std::string filename){
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2e0f052a
Pavel Govyadinov
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stim::obj<T> O; //create an OBJ object
O.load(filename); //load the OBJ file as an object
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Pavel Govyadinov
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std::vector<unsigned> id2vert; //this list stores the OBJ vertex ID associated with each network vertex
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|
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2e0f052a
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unsigned i[2]; //temporary, IDs associated with the first and last points in an OBJ line
|
df036f4c
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496
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//for each line in the OBJ object
for(unsigned int l = 1; l <= O.numL(); l++){
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497
|
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std::vector< stim::vec<T> > c; //allocate an array of points for the vessel centerline
|
7f27eafa
David Mayerich
simplified the st...
|
499
|
O.getLine(l, c); //get the fiber centerline
|
df036f4c
David Mayerich
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|
500
|
|
eb554b48
David Mayerich
bug fixes for Net...
|
501
|
stim::centerline<T> c3(c.size());
|
308a743c
David Mayerich
fixed class compa...
|
502
503
|
for(size_t j = 0; j < c.size(); j++)
c3[j] = c[j];
|
0d0ef1a9
David Mayerich
Adapted classes t...
|
504
|
c3.update();
|
308a743c
David Mayerich
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|
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|
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Pavel Govyadinov
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|
506
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|
// edge new_edge = c3; ///This is dangerous.
edge new_edge(c3);
//create an edge from the given centerline
unsigned int I = new_edge.size(); //calculate the number of points on the centerline
|
df036f4c
David Mayerich
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|
511
|
|
7f27eafa
David Mayerich
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|
512
|
//get the first and last vertex IDs for the line
|
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|
513
|
std::vector< unsigned > id; //create an array to store the centerline point IDs
|
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David Mayerich
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|
514
|
O.getLinei(l, id); //get the list of point IDs for the line
|
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|
515
516
|
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
|
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David Mayerich
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|
517
|
|
2e0f052a
Pavel Govyadinov
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|
518
|
std::vector<unsigned>::iterator it; //create an iterator for searching the id2vert array
|
7f27eafa
David Mayerich
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|
519
|
unsigned it_idx; //create an integer for the id2vert entry index
|
df036f4c
David Mayerich
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|
520
|
|
7f27eafa
David Mayerich
simplified the st...
|
521
|
//find out if the nodes for this fiber have already been created
|
7f27eafa
David Mayerich
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|
522
|
it = find(id2vert.begin(), id2vert.end(), i[0]); //look for the first node
|
7f27eafa
David Mayerich
simplified the st...
|
523
|
if(it == id2vert.end()){ //if i[0] hasn't already been used
|
4df9ec0e
pranathivemuri
compare networks ...
|
524
|
vertex new_vertex = new_edge[0]; //create a new vertex, assign it a position
|
0e0feff0
Jiaming Guo
fixed bugs in mer...
|
525
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bool flag = false;
unsigned j = 0;
for (; j < V.size(); j++) { // check whether current vertex is already exist
if (new_vertex == V[j]) {
flag = true;
break;
}
}
if (!flag) { // unique one
new_vertex.e[0].push_back(E.size()); //add the current edge as outgoing
new_edge.v[0] = V.size(); //add the new edge to the edge
V.push_back(new_vertex); //add the new vertex to the vertex list
id2vert.push_back(i[0]); //add the ID to the ID->vertex conversion list
}
else {
V[j].e[0].push_back(E.size());
new_edge.v[0] = j;
}
|
df036f4c
David Mayerich
added the network...
|
543
|
}
|
2e0f052a
Pavel Govyadinov
minor changes to ...
|
544
|
else{ //if the vertex already exists
|
15a53122
pranathivemuri
Added other simpl...
|
545
|
it_idx = std::distance(id2vert.begin(), it);
|
df480014
pranathivemuri
added in comments...
|
546
|
V[it_idx].e[0].push_back(E.size()); //add the current edge as outgoing
|
3800c27f
David Mayerich
added code to sub...
|
547
|
new_edge.v[0] = it_idx;
|
df036f4c
David Mayerich
added the network...
|
548
549
|
}
|
2e0f052a
Pavel Govyadinov
minor changes to ...
|
550
|
it = find(id2vert.begin(), id2vert.end(), i[1]); //look for the second ID
|
2e0f052a
Pavel Govyadinov
minor changes to ...
|
551
552
|
if(it == id2vert.end()){ //if i[1] hasn't already been used
vertex new_vertex = new_edge[I-1]; //create a new vertex, assign it a position
|
0e0feff0
Jiaming Guo
fixed bugs in mer...
|
553
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|
bool flag = false;
unsigned j = 0;
for (; j < V.size(); j++) { // check whether current vertex is already exist
if (new_vertex == V[j]) {
flag = true;
break;
}
}
if (!flag) {
new_vertex.e[1].push_back(E.size()); //add the current edge as incoming
new_edge.v[1] = V.size(); //add the new vertex to the edge
V.push_back(new_vertex); //add the new vertex to the vertex list
id2vert.push_back(i[1]); //add the ID to the ID->vertex conversion list
}
else {
V[j].e[1].push_back(E.size());
new_edge.v[1] = j;
}
|
df036f4c
David Mayerich
added the network...
|
571
|
}
|
2e0f052a
Pavel Govyadinov
minor changes to ...
|
572
|
else{ //if the vertex already exists
|
15a53122
pranathivemuri
Added other simpl...
|
573
|
it_idx = std::distance(id2vert.begin(), it);
|
df480014
pranathivemuri
added in comments...
|
574
|
V[it_idx].e[1].push_back(E.size()); //add the current edge as incoming
|
3800c27f
David Mayerich
added code to sub...
|
575
|
new_edge.v[1] = it_idx;
|
df036f4c
David Mayerich
added the network...
|
576
|
}
|
9c97e126
David Mayerich
added an axis-ali...
|
577
|
|
2e0f052a
Pavel Govyadinov
minor changes to ...
|
578
|
E.push_back(new_edge); //push the edge to the list
|
df036f4c
David Mayerich
added the network...
|
579
|
|
df036f4c
David Mayerich
added the network...
|
580
|
}
|
0e0feff0
Jiaming Guo
fixed bugs in mer...
|
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// copy the radii information from OBJ
/*if (O.numVT()) {
unsigned k = 0;
for (unsigned i = 0; i < E.size(); i++) {
for (unsigned j = 0; j < E[i].size(); j++) {
E[i].cylinder<T>::set_r(j, O.getVT(k)[0] / 2);
k++;
}
}
}*/
// OBJ class assumes that in L the two values are equal
if (O.numVT()) {
std::vector< unsigned > id; //create an array to store the centerline point IDs
for (unsigned i = 0; i < O.numL(); i++) {
id.clear();
O.getLinei(i + 1, id); //get the list of point IDs for the line
for (unsigned j = 0; j < id.size(); j++)
E[i].cylinder<T>::set_r(j, O.getVT(id[j] - 1)[0] / 2);
}
}
|
e376212f
David Mayerich
added support for...
|
602
|
}
|
66d1c0ff
Pavel Govyadinov
fixed some cuda c...
|
603
|
|
3b14b0f5
Pavel Govyadinov
added operators f...
|
604
|
///loads a .nwt file. Reads the header and loads the data into the network according to the header.
|
66d1c0ff
Pavel Govyadinov
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|
605
|
void
|
3b14b0f5
Pavel Govyadinov
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|
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|
loadNwt(std::string filename)
{
|
029c021a
Pavel Govyadinov
filled in the res...
|
608
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610
|
int dims[2]; ///number of vertex, number of edges
readHeader(filename, &dims[0]); //read header
std::ifstream file;
|
296aa37d
Pavel Govyadinov
fixed parsing errors
|
611
|
file.open(filename.c_str(), std::ios::in | std::ios::binary); ///skip header information.
|
029c021a
Pavel Govyadinov
filled in the res...
|
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613
614
615
616
617
618
619
|
file.seekg(14+58+4+4, file.beg);
vertex v;
for(int i = 0; i < dims[0]; i++) ///for every vertex, read vertex, add to network.
{
file >> v;
V.push_back(v);
// std::cout << i << " " << v.str() << std::endl;
}
|
e376212f
David Mayerich
added support for...
|
620
|
|
029c021a
Pavel Govyadinov
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|
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623
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|
std::cout << std::endl;
for(int i = 0; i < dims[1]; i++) ///for every edge, read edge, add to network.
{
edge e;
file >> e;
E.push_back(e);
|
0e0feff0
Jiaming Guo
fixed bugs in mer...
|
627
|
//std::cout << i << " " << E[i].str() << std::endl; // not necessary?
|
029c021a
Pavel Govyadinov
filled in the res...
|
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629
|
}
file.close();
|
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Pavel Govyadinov
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|
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|
}
///saves a .nwt file. Writes the header in raw text format, then saves the network as a binary file.
|
3b14b0f5
Pavel Govyadinov
added operators f...
|
633
634
635
|
void
saveNwt(std::string filename)
{
|
029c021a
Pavel Govyadinov
filled in the res...
|
636
|
writeHeader(filename);
|
66d1c0ff
Pavel Govyadinov
fixed some cuda c...
|
637
|
std::ofstream file;
|
296aa37d
Pavel Govyadinov
fixed parsing errors
|
638
|
file.open(filename.c_str(), std::ios::out | std::ios::binary | std::ios::app); ///since we have written the header we are not appending.
|
029c021a
Pavel Govyadinov
filled in the res...
|
639
|
for(int i = 0; i < V.size(); i++) ///look through the Vertices and write each one.
|
66d1c0ff
Pavel Govyadinov
fixed some cuda c...
|
640
|
{
|
029c021a
Pavel Govyadinov
filled in the res...
|
641
|
// std::cout << i << " " << V[i].str() << std::endl;
|
66d1c0ff
Pavel Govyadinov
fixed some cuda c...
|
642
643
|
file << V[i];
}
|
029c021a
Pavel Govyadinov
filled in the res...
|
644
|
for(int i = 0; i < E.size(); i++) ///loop through the Edges and write each one.
|
66d1c0ff
Pavel Govyadinov
fixed some cuda c...
|
645
|
{
|
0e0feff0
Jiaming Guo
fixed bugs in mer...
|
646
|
//std::cout << i << " " << E[i].str() << std::endl; // not necesarry?
|
66d1c0ff
Pavel Govyadinov
fixed some cuda c...
|
647
648
|
file << E[i];
}
|
029c021a
Pavel Govyadinov
filled in the res...
|
649
|
file.close();
|
3b14b0f5
Pavel Govyadinov
added operators f...
|
650
651
|
}
|
66d1c0ff
Pavel Govyadinov
fixed some cuda c...
|
652
653
|
///Writes the header information to a .nwt file.
|
3b14b0f5
Pavel Govyadinov
added operators f...
|
654
655
656
|
void
writeHeader(std::string filename)
{
|
029c021a
Pavel Govyadinov
filled in the res...
|
657
658
659
660
661
|
std::string magicString = "nwtFileFormat "; ///identifier for the file.
std::string desc = "fileid(14B), desc(58B), #vertices(4B), #edges(4B): bindata";
int hNumVertices = V.size(); ///int byte header storing the number of vertices in the file
int hNumEdges = E.size(); ///int byte header storing the number of edges.
std::ofstream file;
|
296aa37d
Pavel Govyadinov
fixed parsing errors
|
662
|
file.open(filename.c_str(), std::ios::out | std::ios::binary);
|
029c021a
Pavel Govyadinov
filled in the res...
|
663
664
665
666
667
668
669
|
std::cout << hNumVertices << " " << hNumEdges << std::endl;
file.write(reinterpret_cast<const char*>(&magicString.c_str()[0]), 14); //write the file id
file.write(reinterpret_cast<const char*>(&desc.c_str()[0]), 58); //write the description
file.write(reinterpret_cast<const char*>(&hNumVertices), sizeof(int)); //write #vert.
file.write(reinterpret_cast<const char*>(&hNumEdges), sizeof(int)); //write #edges
// file << magicString.c_str() << desc.c_str() << hNumVertices << hNumEdges;
file.close();
|
3b14b0f5
Pavel Govyadinov
added operators f...
|
670
671
|
}
|
66d1c0ff
Pavel Govyadinov
fixed some cuda c...
|
672
673
674
|
///Reads the header information from a .nwt file.
void
|
029c021a
Pavel Govyadinov
filled in the res...
|
675
|
readHeader(std::string filename, int *dims)
|
66d1c0ff
Pavel Govyadinov
fixed some cuda c...
|
676
|
{
|
029c021a
Pavel Govyadinov
filled in the res...
|
677
678
679
680
681
|
char magicString[14]; ///id
char desc[58]; ///description
int hNumVertices; ///#vert
int hNumEdges; ///#edges
std::ifstream file; ////create stream
|
296aa37d
Pavel Govyadinov
fixed parsing errors
|
682
|
file.open(filename.c_str(), std::ios::in | std::ios::binary);
|
029c021a
Pavel Govyadinov
filled in the res...
|
683
684
685
686
687
688
689
690
|
file.read(reinterpret_cast<char*>(&magicString[0]), 14); ///read the file id.
file.read(reinterpret_cast<char*>(&desc[0]), 58); ///read the description
file.read(reinterpret_cast<char*>(&hNumVertices), sizeof(int)); ///read the number of vertices
file.read(reinterpret_cast<char*>(&hNumEdges), sizeof(int)); ///read the number of edges
// std::cout << magicString << desc << hNumVertices << " " << hNumEdges << std::endl;
file.close(); ///close the file.
dims[0] = hNumVertices; ///fill the returned reference.
dims[1] = hNumEdges;
|
66d1c0ff
Pavel Govyadinov
fixed some cuda c...
|
691
692
|
}
|
58674036
Jiaming Guo
fix minor error f...
|
693
|
//load a network from an SWC file
|
1599ae65
Jiaming Guo
add swc.h and fun...
|
694
695
696
697
|
void load_swc(std::string filename) {
stim::swc<T> S; // create swc variable
S.load(filename); // load the node information
S.create_tree(); // link those node according to their linking relationships as a tree
|
2b28db3e
Jiaming Guo
better render
|
698
|
S.resample();
|
1599ae65
Jiaming Guo
add swc.h and fun...
|
699
|
|
30b20d4f
Jiaming Guo
make it render be...
|
700
|
//NT.push_back(S.node[0].type); // set the neuronal_type value to the first vertex in the network
|
1599ae65
Jiaming Guo
add swc.h and fun...
|
701
702
|
std::vector<unsigned> id2vert; // this list stores the SWC vertex ID associated with each network vertex
unsigned i[2]; // temporary, IDs associated with the first and last points
|
2b28db3e
Jiaming Guo
better render
|
703
704
|
for (unsigned int l = 0; l < S.numE(); l++) { // for every edge
|
30b20d4f
Jiaming Guo
make it render be...
|
705
|
//NT.push_back(S.node[l].type);
|
2b28db3e
Jiaming Guo
better render
|
706
707
708
709
710
711
712
713
|
std::vector< stim::vec3<T> > c;
S.get_points(l, c);
stim::centerline<T> c3(c.size()); // new fiber
for (unsigned j = 0; j < c.size(); j++)
c3[j] = c[j]; // copy the points
|
1599ae65
Jiaming Guo
add swc.h and fun...
|
714
715
|
c3.update(); // update the L information
|
58674036
Jiaming Guo
fix minor error f...
|
716
717
718
719
|
stim::cylinder<T> C3(c3); // create a new cylinder in order to copy the origin radius information
// upadate the R information
std::vector<T> radius;
|
2b28db3e
Jiaming Guo
better render
|
720
721
|
S.get_radius(l, radius);
|
58674036
Jiaming Guo
fix minor error f...
|
722
723
|
C3.copy_r(radius);
|
2b28db3e
Jiaming Guo
better render
|
724
725
726
727
|
edge new_edge(C3); // new edge
//create an edge from the given centerline
unsigned int I = new_edge.size(); //calculate the number of points on the centerline
|
58674036
Jiaming Guo
fix minor error f...
|
728
|
|
1599ae65
Jiaming Guo
add swc.h and fun...
|
729
|
//get the first and last vertex IDs for the line
|
2b28db3e
Jiaming Guo
better render
|
730
731
|
i[0] = S.E[l].front();
i[1] = S.E[l].back();
|
1599ae65
Jiaming Guo
add swc.h and fun...
|
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
|
std::vector<unsigned>::iterator it; //create an iterator for searching the id2vert array
unsigned it_idx; //create an integer for the id2vert entry index
//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
if (it == id2vert.end()) { //if i[0] hasn't already been used
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 edge to the edge
V.push_back(new_vertex); //add the new vertex to the vertex list
id2vert.push_back(i[0]); //add the ID to the ID->vertex conversion list
}
else { //if the vertex already exists
it_idx = std::distance(id2vert.begin(), it);
V[it_idx].e[0].push_back(E.size()); //add the current edge as outgoing
new_edge.v[0] = it_idx;
}
it = find(id2vert.begin(), id2vert.end(), i[1]); //look for the second ID
if (it == id2vert.end()) { //if i[1] hasn't already been used
|
2b28db3e
Jiaming Guo
better render
|
753
|
vertex new_vertex = new_edge[I - 1]; //create a new vertex, assign it a position
|
1599ae65
Jiaming Guo
add swc.h and fun...
|
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
|
new_vertex.e[1].push_back(E.size()); //add the current edge as incoming
new_edge.v[1] = V.size(); //add the new vertex to the edge
V.push_back(new_vertex); //add the new vertex to the vertex list
id2vert.push_back(i[1]); //add the ID to the ID->vertex conversion list
}
else { //if the vertex already exists
it_idx = std::distance(id2vert.begin(), it);
V[it_idx].e[1].push_back(E.size()); //add the current edge as incoming
new_edge.v[1] = it_idx;
}
E.push_back(new_edge); //push the edge to the list
}
}
|
26e84a59
Jiaming Guo
add adjacency_mat...
|
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
|
/// Get adjacency matrix of the network
std::vector< typename std::vector<int> > get_adj_mat() {
unsigned n = V.size(); // get the number of vertices in the networks
std::vector< typename std::vector<int> > result(n, std::vector<int>(n, 0)); // initialize every entry in the matrix to be 0
result.resize(n); // resize rows
for (unsigned i = 0; i < n; i++)
result[i].resize(n); // resize columns
for (unsigned i = 0; i < n; i++) { // for every vertex
unsigned num_out = V[i].e[0].size(); // number of outgoing edges of current vertex
if (num_out != 0) {
for (unsigned j = 0; j < num_out; j++) {
int edge_idx = V[i].e[0][j]; // get the jth out-going edge index of current vertex
int vertex_idx = E[edge_idx].v[1]; // get the ending vertex of specific out-going edge
result[i][vertex_idx] = 1; // can simply set to 1 if it is simple-graph
result[vertex_idx][i] = 1; // symmetric
}
}
}
return result;
}
|
7f27eafa
David Mayerich
simplified the st...
|
794
795
|
/// Output the network as a string
std::string str(){
|
e376212f
David Mayerich
added support for...
|
796
|
|
7f27eafa
David Mayerich
simplified the st...
|
797
798
799
800
|
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...
|
801
802
|
}
|
7f27eafa
David Mayerich
simplified the st...
|
803
804
805
|
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...
|
806
807
|
}
|
7f27eafa
David Mayerich
simplified the st...
|
808
|
return ss.str();
|
df036f4c
David Mayerich
added the network...
|
809
|
}
|
3800c27f
David Mayerich
added code to sub...
|
810
811
|
/// This function resamples all fibers in a network given a desired minimum spacing
|
9c97e126
David Mayerich
added an axis-ali...
|
812
|
/// @param spacing is the minimum distance between two points on the network
|
3800c27f
David Mayerich
added code to sub...
|
813
|
stim::network<T> resample(T spacing){
|
2e0f052a
Pavel Govyadinov
minor changes to ...
|
814
815
|
stim::network<T> n; //create a new network that will be an exact copy, with resampled fibers
n.V = V; //copy all vertices
|
30b20d4f
Jiaming Guo
make it render be...
|
816
|
//n.NT = NT; //copy all the neuronal type information
|
2e0f052a
Pavel Govyadinov
minor changes to ...
|
817
|
n.E.resize(edges()); //allocate space for the edge list
|
3800c27f
David Mayerich
added code to sub...
|
818
819
|
//copy all fibers, resampling them in the process
|
2e0f052a
Pavel Govyadinov
minor changes to ...
|
820
821
|
for(unsigned e = 0; e < edges(); e++){ //for each edge in the edge list
n.E[e] = E[e].resample(spacing); //resample the edge and copy it to the new network
|
3800c27f
David Mayerich
added code to sub...
|
822
823
|
}
|
2e0f052a
Pavel Govyadinov
minor changes to ...
|
824
|
return n; //return the resampled network
|
4df9ec0e
pranathivemuri
compare networks ...
|
825
826
|
}
|
9c97e126
David Mayerich
added an axis-ali...
|
827
|
/// Calculate the total number of points on all edges.
|
797f8ab0
David Mayerich
cleaned up the st...
|
828
829
830
831
|
unsigned total_points(){
unsigned n = 0;
for(unsigned e = 0; e < E.size(); e++)
n += E[e].size();
|
4df9ec0e
pranathivemuri
compare networks ...
|
832
|
return n;
|
797f8ab0
David Mayerich
cleaned up the st...
|
833
|
}
|
4df9ec0e
pranathivemuri
compare networks ...
|
834
|
|
fcd2eb7c
David Mayerich
added support for...
|
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
|
//Copy the point cloud representing the centerline for the network into an array
void centerline_cloud(T* dst) {
size_t p; //stores the current edge point
size_t P; //stores the number of points in an edge
size_t i = 0; //index into the output array of points
for (size_t e = 0; e < E.size(); e++) { //for each edge in the network
P = E[e].size(); //get the number of points in this edge
for (p = 0; p < P; p++) {
dst[i * 3 + 0] = E[e][p][0];
dst[i * 3 + 1] = E[e][p][1];
dst[i * 3 + 2] = E[e][p][2];
i++;
}
}
}
|
fbbc07be
Jiaming Guo
replace ANN by kd...
|
851
852
|
// convert vec3 to array
void stim2array(float *a, stim::vec3<T> b){
|
797f8ab0
David Mayerich
cleaned up the st...
|
853
854
855
856
857
|
a[0] = b[0];
a[1] = b[1];
a[2] = b[2];
}
|
c72184d1
Jiaming Guo
add many function...
|
858
|
// convert vec3 to array in bunch
|
c9712fb4
Jiaming Guo
fix minor error w...
|
859
|
void edge2array(T* a, edge b){
|
c72184d1
Jiaming Guo
add many function...
|
860
861
862
863
864
865
866
867
|
size_t n = b.size();
for(size_t i = 0; i < n; i++){
a[i * 3 + 0] = b[i][0];
a[i * 3 + 1] = b[i][1];
a[i * 3 + 2] = b[i][2];
}
}
|
5068402b
Jiaming Guo
add function to a...
|
868
869
870
871
872
873
874
875
876
877
878
879
880
|
// get list of metric
std::vector<T> metric() {
std::vector<T> result;
T m;
for (size_t e = 0; e < E.size(); e++) {
for (size_t p = 0; p < E[e].size(); p++) {
m = E[e].r(p);
result.push_back(m);
}
}
return result;
}
|
9c97e126
David Mayerich
added an axis-ali...
|
881
882
883
884
|
/// 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){
|
2e0f052a
Pavel Govyadinov
minor changes to ...
|
885
886
887
|
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
|
c72184d1
Jiaming Guo
add many function...
|
888
|
M += E[e].integrate(); //get the integrated magnitude
|
2e0f052a
Pavel Govyadinov
minor changes to ...
|
889
|
L += E[e].length(); //get the edge length
|
9c97e126
David Mayerich
added an axis-ali...
|
890
|
}
|
4df9ec0e
pranathivemuri
compare networks ...
|
891
|
|
2e0f052a
Pavel Govyadinov
minor changes to ...
|
892
|
return M / L; //return the average magnitude
|
9c97e126
David Mayerich
added an axis-ali...
|
893
894
895
|
}
/// This function compares two networks and returns the percentage of the current network that is missing from A.
|
9c97e126
David Mayerich
added an axis-ali...
|
896
897
|
/// @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
|
eb554b48
David Mayerich
bug fixes for Net...
|
898
|
stim::network<T> compare(stim::network<T> A, float sigma, int device = -1){
|
9c97e126
David Mayerich
added an axis-ali...
|
899
|
|
fcd2eb7c
David Mayerich
added support for...
|
900
901
|
stim::network<T> R; //generate a network storing the result of the comparison
R = (*this); //initialize the result with the current network
|
9c97e126
David Mayerich
added an axis-ali...
|
902
|
|
fcd2eb7c
David Mayerich
added support for...
|
903
|
T *c; // centerline (array of double pointers) - points on kdtree must be double
|
41100e51
Jiaming Guo
add cpu kdtree ve...
|
904
|
size_t n_data = A.total_points(); // set the number of points
|
c9712fb4
Jiaming Guo
fix minor error w...
|
905
|
c = (T*) malloc(sizeof(T) * n_data * 3); // allocate an array to store all points in the data set
|
9c97e126
David Mayerich
added an axis-ali...
|
906
|
|
797f8ab0
David Mayerich
cleaned up the st...
|
907
|
unsigned t = 0;
|
fcd2eb7c
David Mayerich
added support for...
|
908
909
|
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...
|
910
911
|
for(unsigned d = 0; d < 3; d++){ //for each coordinate
|
fcd2eb7c
David Mayerich
added support for...
|
912
|
c[t * 3 + d] = A.E[e][p][d]; //copy the point into the array c
|
4df9ec0e
pranathivemuri
compare networks ...
|
913
|
}
|
797f8ab0
David Mayerich
cleaned up the st...
|
914
|
t++;
|
4df9ec0e
pranathivemuri
compare networks ...
|
915
|
}
|
797f8ab0
David Mayerich
cleaned up the st...
|
916
917
|
}
|
41100e51
Jiaming Guo
add cpu kdtree ve...
|
918
|
//generate a KD-tree for network A
|
fcd2eb7c
David Mayerich
added support for...
|
919
|
size_t MaxTreeLevels = 3; // max tree level
|
41100e51
Jiaming Guo
add cpu kdtree ve...
|
920
921
922
|
#ifdef __CUDACC__
cudaSetDevice(device);
|
c72184d1
Jiaming Guo
add many function...
|
923
924
|
stim::kdtree<T, 3> kdt; // initialize a pointer to a kd tree
|
41100e51
Jiaming Guo
add cpu kdtree ve...
|
925
|
kdt.create(c, n_data, MaxTreeLevels); // build a KD tree
|
797f8ab0
David Mayerich
cleaned up the st...
|
926
|
|
9c97e126
David Mayerich
added an axis-ali...
|
927
|
for(unsigned e = 0; e < R.E.size(); e++){ //for each edge in A
|
0d0ef1a9
David Mayerich
Adapted classes t...
|
928
929
|
//R.E[e].add_mag(0); //add a new magnitude for the metric
//size_t errormag_id = R.E[e].nmags() - 1; //get the id for the new magnitude
|
c72184d1
Jiaming Guo
add many function...
|
930
931
|
size_t n = R.E[e].size(); // the number of points in current edge
|
c9712fb4
Jiaming Guo
fix minor error w...
|
932
|
T* queryPt = new T[3 * n];
|
c72184d1
Jiaming Guo
add many function...
|
933
934
935
|
T* m1 = new T[n];
T* dists = new T[n];
size_t* nnIdx = new size_t[n];
|
797f8ab0
David Mayerich
cleaned up the st...
|
936
|
|
c72184d1
Jiaming Guo
add many function...
|
937
938
939
940
|
T* d_dists;
T* d_m1;
cudaMalloc((void**)&d_dists, n * sizeof(T));
cudaMalloc((void**)&d_m1, n * sizeof(T));
|
797f8ab0
David Mayerich
cleaned up the st...
|
941
|
|
c72184d1
Jiaming Guo
add many function...
|
942
943
944
945
946
947
948
949
950
|
edge2array(queryPt, R.E[e]);
kdt.search(queryPt, n, nnIdx, dists);
cudaMemcpy(d_dists, dists, n * sizeof(T), cudaMemcpyHostToDevice); // copy dists from host to device
// configuration parameters
size_t threads = (1024>n)?n:1024;
size_t blocks = n/threads + (n%threads)?1:0;
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Jiaming Guo
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find_metric_parallel<<<blocks, threads>>>(d_m1, n, d_dists, sigma); //calculate the metric value based on the distance
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cudaMemcpy(m1, d_m1, n * sizeof(T), cudaMemcpyDeviceToHost);
for(unsigned p = 0; p < n; p++){
|
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|
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R.E[e].set_r(p, m1[p]);
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}
//d_set_mag<<<blocks, threads>>>(R.E[e].M, errormag_id, n, m1);
}
#else
stim::kdtree<T, 3> kdt;
kdt.create(c, n_data, MaxTreeLevels);
for(unsigned e = 0; e < R.E.size(); e++){ //for each edge in A
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size_t n = R.E[e].size(); // the number of points in current edge
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T* query = new T[3 * n];
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T* m1 = new T[n];
T* dists = new T[n];
|
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fixed some cuda c...
|
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size_t* nnIdx = new size_t[n];
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edge2array(query, R.E[e]);
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kdt.cpu_search(query, n, nnIdx, dists); //find the distance between A and the current network
|
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for(unsigned p = 0; p < R.E[e].size(); p++){
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m1[p] = 1.0f - gaussianFunction((T)dists[p], sigma); //calculate the metric value based on the distance
R.E[e].set_r(p, m1[p]); //set the error for the second point in the segment
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}
}
#endif
return R; //return the resulting network
}
/// This function compares two networks and split the current one according to the nearest neighbor of each point in each edge
/// @param A is the network to split
/// @param B is the corresponding mapping network
/// @param sigma is the user-defined tolerance value - smaller values provide a stricter comparison
/// @param device is the device that user want to use
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void split(stim::network<T> A, stim::network<T> B, float sigma, int device, float threshold){
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T *c;
size_t n_data = B.total_points();
c = (T*) malloc(sizeof(T) * n_data * 3);
size_t NB = B.E.size(); // the number of edges in B
unsigned t = 0;
for(unsigned e = 0; e < NB; e++){ // for every edge in B
for(unsigned p = 0; p < B.E[e].size(); p++){ // for every points in B.E[e]
for(unsigned d = 0; d < 3; d++){
c[t * 3 + d] = B.E[e][p][d]; // convert to array
}
t++;
}
}
size_t MaxTreeLevels = 3; // max tree level
#ifdef __CUDACC__
cudaSetDevice(device);
stim::kdtree<T, 3> kdt; // initialize a pointer to a kd tree
|
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//compare each point in the current network to the field produced by A
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kdt.create(c, n_data, MaxTreeLevels); // build a KD tree
|
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Jiaming Guo
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std::vector<std::vector<unsigned> > relation; // the relationship between GT and T corresponding to NN
|
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relation.resize(A.E.size());
for(unsigned e = 0; e < A.E.size(); e++){ //for each edge in A
|
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|
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|
//A.E[e].add_mag(0); //add a new magnitude for the metric
//size_t errormag_id = A.E[e].nmags() - 1;
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size_t n = A.E[e].size(); // the number of edges in A
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T* queryPt = new T[3 * n]; // set of all the points in current edge
|
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T* m1 = new T[n]; // array of metrics for every point in current edge
T* dists = new T[n]; // store the distances for every point in current edge
size_t* nnIdx = new size_t[n]; // store the indices for every point in current edge
// define pointers in device
T* d_dists;
T* d_m1;
size_t* d_nnIdx;
// allocate memory for defined pointers
cudaMalloc((void**)&d_dists, n * sizeof(T));
cudaMalloc((void**)&d_m1, n * sizeof(T));
cudaMalloc((void**)&d_nnIdx, n * sizeof(size_t));
edge2array(queryPt, A.E[e]); // convert edge to array
kdt.search(queryPt, n, nnIdx, dists); // search the tree to find the NN for every point in current edge
cudaMemcpy(d_dists, dists, n * sizeof(T), cudaMemcpyHostToDevice); // copy dists from host to device
cudaMemcpy(d_nnIdx, nnIdx, n * sizeof(size_t), cudaMemcpyHostToDevice); // copy Idx from host to device
// configuration parameters
size_t threads = (1024>n)?n:1024; // test to see whether the number of point in current edge is more than 1024
size_t blocks = n/threads + (n%threads)?1:0;
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find_metric_parallel<<<blocks, threads>>>(d_m1, n, d_dists, sigma); // calculate the metrics in parallel
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cudaMemcpy(m1, d_m1, n * sizeof(T), cudaMemcpyDeviceToHost);
for(unsigned p = 0; p < n; p++){
|
0d0ef1a9
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A.E[e].set_r(p, m1[p]); // set the error(radius) value to every point in current edge
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}
relation[e].resize(n); // resize every edge relation size
unsigned* d_relation;
cudaMalloc((void**)&d_relation, n * sizeof(unsigned)); // allocate memory
std::vector<size_t> edge_point_num(NB); // %th element is the number of points that %th edge has
for(unsigned ee = 0; ee < NB; ee++)
edge_point_num[ee] = B.E[ee].size();
size_t* d_edge_point_num;
cudaMalloc((void**)&d_edge_point_num, NB * sizeof(size_t));
cudaMemcpy(d_edge_point_num, &edge_point_num[0], NB * sizeof(size_t), cudaMemcpyHostToDevice);
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find_edge_index_parallel<<<blocks, threads>>>(d_nnIdx, n, d_relation, d_edge_point_num, NB); // find the edge corresponding to the array index in parallel
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cudaMemcpy(&relation[e][0], d_relation, n * sizeof(unsigned), cudaMemcpyDeviceToHost); //copy relationship from device to host
}
#else
stim::kdtree<T, 3> kdt;
kdt.create(c, n_data, MaxTreeLevels);
std::vector<std::vector<unsigned>> relation; // the mapping relationship between two networks
relation.resize(A.E.size());
for(unsigned i = 0; i < A.E.size(); i++)
relation[i].resize(A.E[i].size());
std::vector<size_t> edge_point_num(NB); //%th element is the number of points that %th edge has
for(unsigned ee = 0; ee < NB; ee++)
edge_point_num[ee] = B.E[ee].size();
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for(unsigned e = 0; e < A.E.size(); e++){ //for each edge in A
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size_t n = A.E[e].size(); //the number of edges in A
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T* queryPt = new T[3 * n];
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T* m1 = new T[n];
T* dists = new T[n]; //store the distances
size_t* nnIdx = new size_t[n]; //store the indices
edge2array(queryPt, A.E[e]);
kdt.search(queryPt, n, nnIdx, dists);
for(unsigned p = 0; p < A.E[e].size(); p++){
m1[p] = 1.0f - gaussianFunction((T)dists[p], sigma); //calculate the metric value based on the distance
|
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Jiaming Guo
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|
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|
A.E[e].set_r(p, m1[p]); //set the error for the second point in the segment
|
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unsigned id = 0; //mapping edge's idx
size_t num = 0; //total number of points before #th edge
for(unsigned i = 0; i < NB; i++){
num += B.E[i].size();
if(nnIdx[p] < num){ //find the edge it belongs to
relation[e][p] = id;
break;
}
id++; //current edge won't be the one, move to next edge
}
}
}
#endif
E = A.E;
V = A.V;
unsigned int id = 0; // split value
for(unsigned e = 0; e < E.size(); e++){ // for every edge
for(unsigned p = 0; p < E[e].size() - 1; p++){ // for every point in each edge
|
470ab611
David Mayerich
started fixing wa...
|
1125
|
int t = (int)(E[e].length() / sigma * 2);
|
62d95dcd
Jiaming Guo
fixed resample bugs
|
1126
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1128
1129
|
if (t <= 20)
threshold_fac = E[e].size();
else
threshold_fac = (E[e].length() / sigma * 2)/10;
|
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1130
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if(relation[e][p] != relation[e][p + 1]){ // find the nearest edge changing point
id = p + 1; // if there is no change in NN
|
62d95dcd
Jiaming Guo
fixed resample bugs
|
1132
|
if(id < threshold_fac || (E[e].size() - id) < threshold_fac)
|
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id = E[e].size() - 1; // extreme situation is not acceptable
else
break;
}
if(p == E[e].size() - 2) // if there is no splitting index, set the id to the last point index of current edge
|
62d95dcd
Jiaming Guo
fixed resample bugs
|
1138
|
id = E[e].size() - 1;
|
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1139
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}
|
0d0ef1a9
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|
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|
//unsigned errormag_id = E[e].nmags() - 1;
|
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T G = 0; // test to see whether it has its nearest neighbor
for(unsigned i = 0; i < E[e].size(); i++)
|
0d0ef1a9
David Mayerich
Adapted classes t...
|
1143
|
G += E[e].r(i); // won't split special edges
|
6b317c71
Jiaming Guo
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if(G / E[e].size() > threshold) // should based on the color map
|
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|
id = E[e].size() - 1; // set split idx to outgoing direction vertex
std::vector<edge> tmpe;
tmpe.resize(2);
tmpe = E[e].split(id);
vertex tmpv = stim::vec3<T>(-1, -1, 0); // store the split point as vertex
if(tmpe.size() == 2){
relation.resize(relation.size() + 1);
for(unsigned d = id; d < E[e].size(); d++)
relation[relation.size() - 1].push_back(relation[e][d]);
tmpe[0].v[0] = E[e].v[0]; // begining vertex of first half edge -> original begining vertex
tmpe[1].v[1] = E[e].v[1]; // ending vertex of second half edge -> original ending vertex
tmpv = E[e][id];
V.push_back(tmpv);
tmpe[0].v[1] = (unsigned)V.size() - 1; // ending vertex of first half edge -> new vertex
tmpe[1].v[0] = (unsigned)V.size() - 1; // begining vertex of second half edge -> new vertex
edge tmp(E[e]);
E[e] = tmpe[0]; // replace original edge by first half edge
E.push_back(tmpe[1]); // push second half edge to the last
V[V.size() - 1].e[1].push_back(e); // push first half edge to the incoming of new vertex
V[V.size() - 1].e[0].push_back((unsigned)E.size() - 1); // push second half edge to the outgoing of new vertex
for(unsigned i = 0; i < V[tmp.v[1]].e[1].size(); i++) // find the incoming edge of original ending vertex
if(V[tmp.v[1]].e[1][i] == e)
|
30b20d4f
Jiaming Guo
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1168
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V[tmp.v[1]].e[1][i] = (unsigned)E.size() - 1; // set to new edge
|
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}
}
}
|
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|
1172
|
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/// This function compares two splitted networks and yields a mapping relationship between them according to NN
/// @param B is the network that the current network is going to map to
/// @param C is the mapping relationship: C[e1] = _e1 means e1 edge in current network is mapping the _e1 edge in B
/// @param device is the device that user want to use
|
6b317c71
Jiaming Guo
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1177
|
void mapping(stim::network<T> B, std::vector<unsigned> &C, int device, float threshold){
|
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stim::network<T> A; //generate a network storing the result of the comparison
A = (*this);
|
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|
1180
|
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size_t n = A.E.size(); // the number of edges in A
size_t NB = B.E.size(); // the number of edges in B
C.resize(A.E.size());
T *c; // centerline (array of double pointers) - points on kdtree must be double
size_t n_data = B.total_points(); // set the number of points
c = (T*) malloc(sizeof(T) * n_data * 3);
unsigned t = 0;
for(unsigned e = 0; e < NB; e++){ // for each edge in the network
for(unsigned p = 0; p < B.E[e].size(); p++){ // for each point in the edge
for(unsigned d = 0; d < 3; d++){ // for each coordinate
c[t * 3 + d] = B.E[e][p][d];
}
t++;
}
}
|
fbbc07be
Jiaming Guo
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1200
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//generate a KD-tree for network A
//float metric = 0.0; // initialize metric to be returned after comparing the network
size_t MaxTreeLevels = 3; // max tree level
#ifdef __CUDACC__
cudaSetDevice(device);
stim::kdtree<T, 3> kdt; // initialize a pointer to a kd tree
kdt.create(c, n_data, MaxTreeLevels); // build a KD tree
|
797f8ab0
David Mayerich
cleaned up the st...
|
1210
|
|
c72184d1
Jiaming Guo
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|
1211
|
for(unsigned e = 0; e < n; e++){ //for each edge in A
|
0d0ef1a9
David Mayerich
Adapted classes t...
|
1212
|
//size_t errormag_id = A.E[e].nmags() - 1; //get the id for the new magnitude
|
c72184d1
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|
1213
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//pre-judge to get rid of impossibly mapping edges
T M = 0;
for(unsigned p = 0; p < A.E[e].size(); p++)
|
0d0ef1a9
David Mayerich
Adapted classes t...
|
1217
|
M += A.E[e].r(p);
|
c72184d1
Jiaming Guo
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|
1218
|
M = M / A.E[e].size();
|
6b317c71
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|
1219
|
if(M > threshold)
|
c72184d1
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C[e] = (unsigned)-1; //set the nearest edge of impossibly mapping edges to maximum of unsigned
else{
|
c9712fb4
Jiaming Guo
fix minor error w...
|
1222
|
T* queryPt = new T[3];
|
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|
1223
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T* dists = new T[1];
size_t* nnIdx = new size_t[1];
stim2array(queryPt, A.E[e][A.E[e].size()/2]);
kdt.search(queryPt, 1, nnIdx, dists);
unsigned id = 0; //mapping edge's idx
size_t num = 0; //total number of points before #th edge
for(unsigned i = 0; i < NB; i++){
num += B.E[i].size();
if(nnIdx[0] < num){
C[e] = id;
break;
}
id++;
}
|
797f8ab0
David Mayerich
cleaned up the st...
|
1239
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}
}
|
41100e51
Jiaming Guo
add cpu kdtree ve...
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1241
|
#else
|
c72184d1
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|
stim::kdtree<T, 3> kdt;
|
41100e51
Jiaming Guo
add cpu kdtree ve...
|
1243
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|
kdt.create(c, n_data, MaxTreeLevels);
T *dists = new T[1]; // near neighbor distances
|
fcd2eb7c
David Mayerich
added support for...
|
1245
|
size_t *nnIdx = new size_t[1]; // near neighbor indices // allocate near neigh indices
|
797f8ab0
David Mayerich
cleaned up the st...
|
1246
|
|
41100e51
Jiaming Guo
add cpu kdtree ve...
|
1247
|
stim::vec3<T> p0, p1;
|
41100e51
Jiaming Guo
add cpu kdtree ve...
|
1248
|
T* queryPt = new T[3];
|
41100e51
Jiaming Guo
add cpu kdtree ve...
|
1249
|
|
66d1c0ff
Pavel Govyadinov
fixed some cuda c...
|
1250
|
for(unsigned int e = 0; e < R.E.size(); e++){ // for each edge in A
|
c72184d1
Jiaming Guo
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|
1251
|
T M; // the sum of metrics of current edge
|
c72184d1
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|
1252
|
for(unsigned p = 0; p < R.E[e].size(); p++)
|
2b28db3e
Jiaming Guo
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|
1253
|
M += A.E[e].r(p);
|
c72184d1
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|
1254
|
M = M / A.E[e].size();
|
6b317c71
Jiaming Guo
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|
1255
|
if(M > threshold)
|
c72184d1
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C[e] = (unsigned)-1;
else{ // if it should have corresponding edge in B, then...
p1 = R.E[e][R.E[e].size()/2];
|
41100e51
Jiaming Guo
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|
1259
|
stim2array(queryPt, p1);
|
c72184d1
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|
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kdt.cpu_search(queryPt, 1, nnIdx, dists); // search the tree
unsigned id = 0; //mapping edge's idx
size_t num = 0; //total number of points before #th edge
for(unsigned i = 0; i < NB; i++){
num += B.E[i].size();
if(nnIdx[0] < num){
C[e] = id;
break;
}
id++;
}
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41100e51
Jiaming Guo
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}
}
#endif
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3800c27f
David Mayerich
added code to sub...
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}
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9c97e126
David Mayerich
added an axis-ali...
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1276
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b3a38641
David Mayerich
added the ability...
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1277
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/// Returns the number of magnitude values stored in each edge. This should be uniform across the network.
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0d0ef1a9
David Mayerich
Adapted classes t...
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//unsigned nmags(){
// return E[0].nmags();
//}
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10b95d6e
pranathivemuri
load text file to...
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// split a string in text by the character sep
stim::vec<T> split(std::string &text, char sep)
{
stim::vec<T> tokens;
std::size_t start = 0, end = 0;
while ((end = text.find(sep, start)) != std::string::npos) {
tokens.push_back(atof(text.substr(start, end - start).c_str()));
start = end + 1;
}
tokens.push_back(atof(text.substr(start).c_str()));
return tokens;
}
// load a network in text file to a network class
void load_txt(std::string filename)
{
std::vector <std::string> file_contents;
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e8c9a82b
David Mayerich
fixed GCC errors ...
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1297
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std::ifstream file(filename.c_str());
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10b95d6e
pranathivemuri
load text file to...
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std::string line;
std::vector<unsigned> id2vert; //this list stores the vertex ID associated with each network vertex
//for each line in the text file, store them as strings in file_contents
while (std::getline(file, line))
{
std::stringstream ss(line);
file_contents.push_back(ss.str());
}
unsigned int numEdges = atoi(file_contents[0].c_str()); //number of edges in the network
unsigned int I = atoi(file_contents[1].c_str()) ; //calculate the number of points3d on the first edge
unsigned int count = 1; unsigned int k = 2; // count is global counter through the file contents, k is for the vertices on the edges
// for each edge in the network.
for (unsigned int i = 0; i < numEdges; i ++ )
{
// pre allocate a position vector p with number of points3d on the edge p
std::vector< stim::vec<T> > p(0, I);
// for each point on the nth edge
for (unsigned int j = k; j < I + k; j++)
{
// split the points3d of floats with separator space and form a float3 position vector out of them
p.push_back(split(file_contents[j], ' '));
}
count += p.size() + 1; // increment count to point at the next edge in the network
I = atoi(file_contents[count].c_str()); // read in the points3d at the next edge and convert it to an integer
k = count + 1;
edge new_edge = p; // create an edge with a vector of points3d on the edge
E.push_back(new_edge); // push the edge into the network
}
unsigned int numVertices = atoi(file_contents[count].c_str()); // this line in the text file gives the number of distinct vertices
count = count + 1; // this line of text file gives the first verrtex
// push each vertex into V
for (unsigned int i = 0; i < numVertices; i ++)
{
vertex new_vertex = split(file_contents[count], ' ');
V.push_back(new_vertex);
count += atoi(file_contents[count + 1].c_str()) + 2; // Skip number of edge ids + 2 to point to the next vertex
}
} // end load_txt function
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b3a38641
David Mayerich
added the ability...
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1336
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abce2443
pranathivemuri
average branching...
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// strTxt returns a string of edges
std::string
strTxt(std::vector< stim::vec<T> > p)
{
std::stringstream ss;
std::stringstream oss;
for(unsigned int i = 0; i < p.size(); i++){
ss.str(std::string());
for(unsigned int d = 0; d < 3; d++){
|
9f5c0d4a
Pavel Govyadinov
edits to make net...
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1346
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ss<<p[i][d];
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abce2443
pranathivemuri
average branching...
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}
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8b7d6f9a
David Mayerich
light modificatio...
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ss << "\n";
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abce2443
pranathivemuri
average branching...
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}
return ss.str();
}
// removes specified character from string
void removeCharsFromString(std::string &str, char* charsToRemove ) {
for ( unsigned int i = 0; i < strlen(charsToRemove); ++i ) {
str.erase( remove(str.begin(), str.end(), charsToRemove[i]), str.end() );
}
}
//exports network to txt file
void
to_txt(std::string filename)
{
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e8c9a82b
David Mayerich
fixed GCC errors ...
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1362
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std::ofstream ofs(filename.c_str(), std::ofstream::out | std::ofstream::app);
//int num;
|
abce2443
pranathivemuri
average branching...
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ofs << (E.size()).str() << "\n";
for(unsigned int i = 0; i < E.size(); i++)
{
std::string str;
ofs << (E[i].size()).str() << "\n";
str = E[i].strTxt();
ofs << str << "\n";
}
for(int i = 0; i < V.size(); i++)
{
std::string str;
str = V[i].str();
|
e8c9a82b
David Mayerich
fixed GCC errors ...
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1376
1377
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char temp[4] = "[],";
removeCharsFromString(str, temp);
|
abce2443
pranathivemuri
average branching...
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ofs << str << "\n";
}
ofs.close();
}
|
7f27eafa
David Mayerich
simplified the st...
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}; //end stim::network class
}; //end stim namespace
|
3b14b0f5
Pavel Govyadinov
added operators f...
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1384
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#endif
|