From 5bccf89d07af8ec102d3e351ccb7455841b1c1ad Mon Sep 17 00:00:00 2001
From: David <mayerich@uh.edu>
Date: Fri, 5 Feb 2016 15:36:39 -0600
Subject: [PATCH] fixed some errors with loading networks as OBJ files

---
 stim/biomodels/fiber.h   |  2 +-
 stim/biomodels/network.h |  3 +++
 stim/visualization/obj.h | 26 ++++++++++++++++++--------
 3 files changed, 22 insertions(+), 9 deletions(-)

diff --git a/stim/biomodels/fiber.h b/stim/biomodels/fiber.h
index 944e625..c901dd4 100644
--- a/stim/biomodels/fiber.h
+++ b/stim/biomodels/fiber.h
@@ -430,7 +430,7 @@ public:
 		////resample a fiber in the network
 	stim::fiber<T> resample(T spacing)
 	{
-
+		std::cout<<"fiber::resample()"<<std::endl;
 
 		std::vector<T> v(3);    //v-direction vector of the segment
 		stim::vec<T> p(3);      //- intermediate point to be added
diff --git a/stim/biomodels/network.h b/stim/biomodels/network.h
index 30116fd..eada0c4 100644
--- a/stim/biomodels/network.h
+++ b/stim/biomodels/network.h
@@ -193,6 +193,7 @@ class network{
 
 	/// This function resamples all fibers in a network given a desired minimum spacing
 	stim::network<T> resample(T spacing){
+		std::cout<<"network::resample()"<<std::endl;
 		stim::network<T> n;					//create a new network that will be an exact copy, with resampled fibers
 		n.V = V;							//copy all vertices
 
@@ -200,7 +201,9 @@ class network{
 
 		//copy all fibers, resampling them in the process
 		for(unsigned e = 0; e < edges(); e++){				//for each edge in the edge list
+			std::cout<<"edge: "<<e<<std::endl;
 			n.E[e] = E[e].resample(spacing);				//resample the edge and copy it to the new network
+			std::cout<<"resampled"<<std::endl;
 		}
 
 		return n;							              //return the resampled network
diff --git a/stim/visualization/obj.h b/stim/visualization/obj.h
index a9500bc..7c7a988 100644
--- a/stim/visualization/obj.h
+++ b/stim/visualization/obj.h
@@ -9,6 +9,8 @@
 #include <stim/math/vector.h>
 #include <algorithm>
 
+#include <time.h>
+
 namespace stim{
 
 /** This class provides an interface for loading, saving, and working with Wavefront OBJ files.
@@ -92,6 +94,9 @@ protected:
 
 	//triplet used to specify geometric vertices consisting of a position vertex, texture vertex, and normal
 	struct triplet : public std::vector<unsigned int>{
+
+		//default constructor, empty triplet
+		triplet(){}
 		
 		//create a triplet given a parameter list (OBJ indices start at 1, so 0 can be used to indicate no value)
 		triplet(unsigned int v, unsigned int vt = 0, unsigned int vn = 0){
@@ -162,10 +167,12 @@ protected:
 			//create a temporary vector used to store string tokens
 			std::vector<std::string> tokens = stim::parser::split(line, ' ');
 
+			resize(tokens.size() - 1);											//set the geometry size based on the number of tokens
 			//for each triplet in the line
 			for(unsigned int i = 1; i < tokens.size(); i++){
 				//construct the triplet and push it to the geometry
-				push_back( triplet(tokens[i]) );
+				//push_back( triplet(tokens[i]) );
+				at(i-1) = triplet(tokens[i]);
 			}
 
 		}
@@ -173,14 +180,15 @@ protected:
 		//returns a vector containing the vertex indices for the geometry
 		void get_v(std::vector<unsigned>& v){
 			v.resize(size());							//resize the vector to match the number of vertices
-			for(unsigned int i = 0; i<size(); i++)		//for each vertex
-				v[i] = at(i)[0];						//copy the vertex index
+			for(unsigned int i = 0; i<size(); i++){		//for each vertex
+				v[i] = at(i)[0];						//copy the vertex index (1st element of triplet)
+			}
 		}
 
 		void get_vt(std::vector<unsigned>& vt){
 			vt.resize(size());							//resize the vector to match the number of vertices
 			for(unsigned int i = 0; i<size(); i++)		//for each vertex
-				vt[i] = at(i)[1];						//copy the vertex index
+				vt[i] = at(i)[1];						//copy the vertex texture index (2nd element of triplet)
 		}
 
 		void get_vn(std::vector<unsigned>& vn){
@@ -492,9 +500,10 @@ public:
 
 		std::string line;
 		getline(infile, line);		//get the first line
+		unsigned int l = 0;
 		while(infile){
-
-
+			l++;
+			//unsigned int t = time(NULL);
 
 			//get the token representing the first parameter
 			token_type token = get_token(line);
@@ -521,16 +530,17 @@ public:
 				break;
 
 			case OBJ_L:
+				
 				L.push_back(geometry(line));
 				break;
 
 			};
 
+			
 			//get the next line
 			getline(infile, line);
-		}
-
 
+		}
 
 		//close the file
 		infile.close();
--
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