From 62d95dcd31d679da63b494a86df736fb9ee08d14 Mon Sep 17 00:00:00 2001
From: Jiaming Guo <jackguo523@gmail.com>
Date: Tue, 17 Jan 2017 14:45:11 -0600
Subject: [PATCH] fixed resample bugs

---
 stim/biomodels/centerline.h |  2 +-
 stim/biomodels/network.h    | 11 ++++++++---
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/stim/biomodels/centerline.h b/stim/biomodels/centerline.h
index 1aa7563..4b3b5bf 100644
--- a/stim/biomodels/centerline.h
+++ b/stim/biomodels/centerline.h
@@ -227,7 +227,7 @@ public:
 				}
 			}
 			else       // length of the segment is now less than standard deviation, push the ending point of the segment and proceed to the next point in the fiber
-				new_c.push_back(at(f+1));
+				new_c.push_back(at(f));
 		}
 		new_c.push_back(at(N-1));   //add the last point on the fiber to the new fiber list
 		//centerline newFiber(newPointList);
diff --git a/stim/biomodels/network.h b/stim/biomodels/network.h
index 97f34a1..4559390 100644
--- a/stim/biomodels/network.h
+++ b/stim/biomodels/network.h
@@ -46,7 +46,7 @@ __global__ void d_findedge(size_t* I, size_t n, unsigned* R, size_t* E, size_t n
 #endif
 
 //hard-coded factor
-int threshold_fac = 10;
+int threshold_fac = 0;
 
 namespace stim{
 /** This is the a class that interfaces with gl_spider in order to store the currently
@@ -782,15 +782,20 @@ public:
 		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
+				int t = E[e].length() / sigma * 2;
+				if (t <= 20)
+					threshold_fac = E[e].size();
+				else
+					threshold_fac = (E[e].length() / sigma * 2)/10;
 				if(relation[e][p] != relation[e][p + 1]){		// find the nearest edge changing point
 					id = p + 1;									// if there is no change in NN
-					if(id < E[e].size()/threshold_fac || (E[e].size() - id) < E[e].size()/threshold_fac)				// set tolerance to 10, tentatively--should find out the mathematical threshold!
+					if(id < threshold_fac || (E[e].size() - id) < threshold_fac)				
 						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
-					id = p + 1;
+					id = E[e].size() - 1;
 			}
 			//unsigned errormag_id = E[e].nmags() - 1;
 			T G = 0;																					// test to see whether it has its nearest neighbor
--
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