diff --git a/.gitignore b/.gitignore
old mode 100644
new mode 100755
index 2920afa..2920afa
--- a/.gitignore
+++ b/.gitignore
diff --git a/Doxyfile b/Doxyfile
old mode 100644
new mode 100755
index faa49d9..faa49d9
--- a/Doxyfile
+++ b/Doxyfile
diff --git a/LICENSE.txt b/LICENSE.txt
old mode 100644
new mode 100755
index de206bd..de206bd
--- a/LICENSE.txt
+++ b/LICENSE.txt
diff --git a/cmake/FindANN.cmake b/cmake/FindANN.cmake
old mode 100644
new mode 100755
index c4b5649..c4b5649
--- a/cmake/FindANN.cmake
+++ b/cmake/FindANN.cmake
diff --git a/cmake/FindSTIM.cmake b/cmake/FindSTIM.cmake
old mode 100644
new mode 100755
index 919f33c..919f33c
--- a/cmake/FindSTIM.cmake
+++ b/cmake/FindSTIM.cmake
diff --git a/stim/biology/fibernet.h b/stim/biology/fibernet.h
old mode 100644
new mode 100755
index e69de29..e69de29
--- a/stim/biology/fibernet.h
+++ b/stim/biology/fibernet.h
diff --git a/stim/biomodels/flow.h b/stim/biomodels/flow.h
old mode 100644
new mode 100755
index 7154ad6..7154ad6
--- a/stim/biomodels/flow.h
+++ b/stim/biomodels/flow.h
diff --git a/stim/biomodels/network.h b/stim/biomodels/network.h
old mode 100644
new mode 100755
index f604361..f604361
--- a/stim/biomodels/network.h
+++ b/stim/biomodels/network.h
diff --git a/stim/cuda/arraymath.cuh b/stim/cuda/arraymath.cuh
old mode 100644
new mode 100755
index adbf66a..adbf66a
--- a/stim/cuda/arraymath.cuh
+++ b/stim/cuda/arraymath.cuh
diff --git a/stim/cuda/arraymath/array_abs.cuh b/stim/cuda/arraymath/array_abs.cuh
old mode 100644
new mode 100755
index fc4d176..fc4d176
--- a/stim/cuda/arraymath/array_abs.cuh
+++ b/stim/cuda/arraymath/array_abs.cuh
diff --git a/stim/cuda/arraymath/array_add.cuh b/stim/cuda/arraymath/array_add.cuh
old mode 100644
new mode 100755
index 82be364..82be364
--- a/stim/cuda/arraymath/array_add.cuh
+++ b/stim/cuda/arraymath/array_add.cuh
diff --git a/stim/cuda/arraymath/array_atan.cuh b/stim/cuda/arraymath/array_atan.cuh
old mode 100644
new mode 100755
index 65fc458..65fc458
--- a/stim/cuda/arraymath/array_atan.cuh
+++ b/stim/cuda/arraymath/array_atan.cuh
diff --git a/stim/cuda/arraymath/array_cart2polar.cuh b/stim/cuda/arraymath/array_cart2polar.cuh
old mode 100644
new mode 100755
index d5fb85c..d5fb85c
--- a/stim/cuda/arraymath/array_cart2polar.cuh
+++ b/stim/cuda/arraymath/array_cart2polar.cuh
diff --git a/stim/cuda/arraymath/array_cos.cuh b/stim/cuda/arraymath/array_cos.cuh
old mode 100644
new mode 100755
index 6880c6b..6880c6b
--- a/stim/cuda/arraymath/array_cos.cuh
+++ b/stim/cuda/arraymath/array_cos.cuh
diff --git a/stim/cuda/arraymath/array_divide.cuh b/stim/cuda/arraymath/array_divide.cuh
old mode 100644
new mode 100755
index c92c9df..c92c9df
--- a/stim/cuda/arraymath/array_divide.cuh
+++ b/stim/cuda/arraymath/array_divide.cuh
diff --git a/stim/cuda/arraymath/array_multiply.cuh b/stim/cuda/arraymath/array_multiply.cuh
old mode 100644
new mode 100755
index 4385e77..4385e77
--- a/stim/cuda/arraymath/array_multiply.cuh
+++ b/stim/cuda/arraymath/array_multiply.cuh
diff --git a/stim/cuda/arraymath/array_multiply2.cuh b/stim/cuda/arraymath/array_multiply2.cuh
old mode 100644
new mode 100755
index 6296ed0..6296ed0
--- a/stim/cuda/arraymath/array_multiply2.cuh
+++ b/stim/cuda/arraymath/array_multiply2.cuh
diff --git a/stim/cuda/arraymath/array_sin.cuh b/stim/cuda/arraymath/array_sin.cuh
old mode 100644
new mode 100755
index 1c150d7..1c150d7
--- a/stim/cuda/arraymath/array_sin.cuh
+++ b/stim/cuda/arraymath/array_sin.cuh
diff --git a/stim/cuda/bsds500/cPb.cpp b/stim/cuda/bsds500/cPb.cpp
old mode 100644
new mode 100755
index 3d9f23c..3d9f23c
--- a/stim/cuda/bsds500/cPb.cpp
+++ b/stim/cuda/bsds500/cPb.cpp
diff --git a/stim/cuda/bsds500/dG1_conv2.cpp b/stim/cuda/bsds500/dG1_conv2.cpp
old mode 100644
new mode 100755
index ed50990..ed50990
--- a/stim/cuda/bsds500/dG1_conv2.cpp
+++ b/stim/cuda/bsds500/dG1_conv2.cpp
diff --git a/stim/cuda/bsds500/dG1_theta_conv2.cpp b/stim/cuda/bsds500/dG1_theta_conv2.cpp
old mode 100644
new mode 100755
index b1ea9aa..b1ea9aa
--- a/stim/cuda/bsds500/dG1_theta_conv2.cpp
+++ b/stim/cuda/bsds500/dG1_theta_conv2.cpp
diff --git a/stim/cuda/bsds500/dG2_conv2.cpp b/stim/cuda/bsds500/dG2_conv2.cpp
old mode 100644
new mode 100755
index 85414b1..85414b1
--- a/stim/cuda/bsds500/dG2_conv2.cpp
+++ b/stim/cuda/bsds500/dG2_conv2.cpp
diff --git a/stim/cuda/bsds500/dG_d2x_theta_conv2.cpp b/stim/cuda/bsds500/dG_d2x_theta_conv2.cpp
old mode 100644
new mode 100755
index a268d95..a268d95
--- a/stim/cuda/bsds500/dG_d2x_theta_conv2.cpp
+++ b/stim/cuda/bsds500/dG_d2x_theta_conv2.cpp
diff --git a/stim/cuda/bsds500/kmeans.cpp b/stim/cuda/bsds500/kmeans.cpp
old mode 100644
new mode 100755
index fee17b7..fee17b7
--- a/stim/cuda/bsds500/kmeans.cpp
+++ b/stim/cuda/bsds500/kmeans.cpp
diff --git a/stim/cuda/bsds500/laplacian_conv2.cpp b/stim/cuda/bsds500/laplacian_conv2.cpp
old mode 100644
new mode 100755
index 4b41d0d..4b41d0d
--- a/stim/cuda/bsds500/laplacian_conv2.cpp
+++ b/stim/cuda/bsds500/laplacian_conv2.cpp
diff --git a/stim/cuda/bsds500/tPb.cpp b/stim/cuda/bsds500/tPb.cpp
old mode 100644
new mode 100755
index e066dae..e066dae
--- a/stim/cuda/bsds500/tPb.cpp
+++ b/stim/cuda/bsds500/tPb.cpp
diff --git a/stim/cuda/bsds500/textons.cpp b/stim/cuda/bsds500/textons.cpp
old mode 100644
new mode 100755
index dbe66f1..dbe66f1
--- a/stim/cuda/bsds500/textons.cpp
+++ b/stim/cuda/bsds500/textons.cpp
diff --git a/stim/cuda/cost.h b/stim/cuda/cost.h
old mode 100644
new mode 100755
index aaed177..aaed177
--- a/stim/cuda/cost.h
+++ b/stim/cuda/cost.h
diff --git a/stim/cuda/cudatools.h b/stim/cuda/cudatools.h
old mode 100644
new mode 100755
index 1f1a9e6..1f1a9e6
--- a/stim/cuda/cudatools.h
+++ b/stim/cuda/cudatools.h
diff --git a/stim/cuda/cudatools/callable.h b/stim/cuda/cudatools/callable.h
old mode 100644
new mode 100755
index eefc437..eefc437
--- a/stim/cuda/cudatools/callable.h
+++ b/stim/cuda/cudatools/callable.h
diff --git a/stim/cuda/cudatools/devices.h b/stim/cuda/cudatools/devices.h
old mode 100644
new mode 100755
index 231a26b..231a26b
--- a/stim/cuda/cudatools/devices.h
+++ b/stim/cuda/cudatools/devices.h
diff --git a/stim/cuda/cudatools/error.h b/stim/cuda/cudatools/error.h
old mode 100644
new mode 100755
index b49cf4b..b49cf4b
--- a/stim/cuda/cudatools/error.h
+++ b/stim/cuda/cudatools/error.h
diff --git a/stim/cuda/cudatools/glbind.h b/stim/cuda/cudatools/glbind.h
old mode 100644
new mode 100755
index 85a8f31..85a8f31
--- a/stim/cuda/cudatools/glbind.h
+++ b/stim/cuda/cudatools/glbind.h
diff --git a/stim/cuda/cudatools/threads.h b/stim/cuda/cudatools/threads.h
old mode 100644
new mode 100755
index 0315082..0315082
--- a/stim/cuda/cudatools/threads.h
+++ b/stim/cuda/cudatools/threads.h
diff --git a/stim/cuda/cudatools/timer.h b/stim/cuda/cudatools/timer.h
old mode 100644
new mode 100755
index 27d6352..27d6352
--- a/stim/cuda/cudatools/timer.h
+++ b/stim/cuda/cudatools/timer.h
diff --git a/stim/cuda/filter.h b/stim/cuda/filter.h
old mode 100644
new mode 100755
index 8e91075..8e91075
--- a/stim/cuda/filter.h
+++ b/stim/cuda/filter.h
diff --git a/stim/cuda/ivote.cuh b/stim/cuda/ivote.cuh
old mode 100644
new mode 100755
index cc07d1d..cc07d1d
--- a/stim/cuda/ivote.cuh
+++ b/stim/cuda/ivote.cuh
diff --git a/stim/cuda/ivote/down_sample.cuh b/stim/cuda/ivote/down_sample.cuh
old mode 100644
new mode 100755
index 3e26b50..3e26b50
--- a/stim/cuda/ivote/down_sample.cuh
+++ b/stim/cuda/ivote/down_sample.cuh
diff --git a/stim/cuda/ivote/local_max.cuh b/stim/cuda/ivote/local_max.cuh
old mode 100644
new mode 100755
index a2bd2fe..a2bd2fe
--- a/stim/cuda/ivote/local_max.cuh
+++ b/stim/cuda/ivote/local_max.cuh
diff --git a/stim/cuda/ivote/update_dir.cuh b/stim/cuda/ivote/update_dir.cuh
old mode 100644
new mode 100755
index 5b3d37e..5b3d37e
--- a/stim/cuda/ivote/update_dir.cuh
+++ b/stim/cuda/ivote/update_dir.cuh
diff --git a/stim/cuda/ivote/vote.cuh b/stim/cuda/ivote/vote.cuh
old mode 100644
new mode 100755
index fdc3677..fdc3677
--- a/stim/cuda/ivote/vote.cuh
+++ b/stim/cuda/ivote/vote.cuh
diff --git a/stim/cuda/sharedmem.cuh b/stim/cuda/sharedmem.cuh
old mode 100644
new mode 100755
index 77de31f..77de31f
--- a/stim/cuda/sharedmem.cuh
+++ b/stim/cuda/sharedmem.cuh
diff --git a/stim/cuda/templates/chi_gradient.cuh b/stim/cuda/templates/chi_gradient.cuh
old mode 100644
new mode 100755
index cb4b225..cb4b225
--- a/stim/cuda/templates/chi_gradient.cuh
+++ b/stim/cuda/templates/chi_gradient.cuh
diff --git a/stim/cuda/templates/conv2.cuh b/stim/cuda/templates/conv2.cuh
old mode 100644
new mode 100755
index ca9918d..ca9918d
--- a/stim/cuda/templates/conv2.cuh
+++ b/stim/cuda/templates/conv2.cuh
diff --git a/stim/cuda/templates/conv2sep.cuh b/stim/cuda/templates/conv2sep.cuh
old mode 100644
new mode 100755
index b7156c1..b7156c1
--- a/stim/cuda/templates/conv2sep.cuh
+++ b/stim/cuda/templates/conv2sep.cuh
diff --git a/stim/cuda/templates/gaussian_blur.cuh b/stim/cuda/templates/gaussian_blur.cuh
old mode 100644
new mode 100755
index f4485ae..f4485ae
--- a/stim/cuda/templates/gaussian_blur.cuh
+++ b/stim/cuda/templates/gaussian_blur.cuh
diff --git a/stim/cuda/templates/gradient.cuh b/stim/cuda/templates/gradient.cuh
old mode 100644
new mode 100755
index d0718b2..d0718b2
--- a/stim/cuda/templates/gradient.cuh
+++ b/stim/cuda/templates/gradient.cuh
diff --git a/stim/envi/bil.h b/stim/envi/bil.h
old mode 100644
new mode 100755
index 5bef1e0..5bef1e0
--- a/stim/envi/bil.h
+++ b/stim/envi/bil.h
diff --git a/stim/envi/binary.h b/stim/envi/binary.h
old mode 100644
new mode 100755
index 7c431a0..7c431a0
--- a/stim/envi/binary.h
+++ b/stim/envi/binary.h
diff --git a/stim/envi/bip.h b/stim/envi/bip.h
old mode 100644
new mode 100755
index 82b7eeb..82b7eeb
--- a/stim/envi/bip.h
+++ b/stim/envi/bip.h
diff --git a/stim/envi/bsq.h b/stim/envi/bsq.h
old mode 100644
new mode 100755
index 6c2b240..6c2b240
--- a/stim/envi/bsq.h
+++ b/stim/envi/bsq.h
diff --git a/stim/envi/envi.h b/stim/envi/envi.h
old mode 100644
new mode 100755
index 240c49c..240c49c
--- a/stim/envi/envi.h
+++ b/stim/envi/envi.h
diff --git a/stim/envi/envi_header.h b/stim/envi/envi_header.h
old mode 100644
new mode 100755
index 6650557..6650557
--- a/stim/envi/envi_header.h
+++ b/stim/envi/envi_header.h
diff --git a/stim/gl/error.h b/stim/gl/error.h
old mode 100644
new mode 100755
index d9324ef..d9324ef
--- a/stim/gl/error.h
+++ b/stim/gl/error.h
diff --git a/stim/gl/gl_spider.h b/stim/gl/gl_spider.h
old mode 100644
new mode 100755
index ed5d99b..ed5d99b
--- a/stim/gl/gl_spider.h
+++ b/stim/gl/gl_spider.h
diff --git a/stim/gl/gl_texture.h b/stim/gl/gl_texture.h
old mode 100644
new mode 100755
index dbab17e..dbab17e
--- a/stim/gl/gl_texture.h
+++ b/stim/gl/gl_texture.h
diff --git a/stim/gl/rtsSourceCode.h b/stim/gl/rtsSourceCode.h
old mode 100644
new mode 100755
index 0ff6c25..0ff6c25
--- a/stim/gl/rtsSourceCode.h
+++ b/stim/gl/rtsSourceCode.h
diff --git a/stim/gl/rts_glShaderObject.h b/stim/gl/rts_glShaderObject.h
old mode 100644
new mode 100755
index 85a96c5..85a96c5
--- a/stim/gl/rts_glShaderObject.h
+++ b/stim/gl/rts_glShaderObject.h
diff --git a/stim/gl/rts_glShaderProgram.h b/stim/gl/rts_glShaderProgram.h
old mode 100644
new mode 100755
index a39f375..a39f375
--- a/stim/gl/rts_glShaderProgram.h
+++ b/stim/gl/rts_glShaderProgram.h
diff --git a/stim/gl/rts_glShaderUniform.h b/stim/gl/rts_glShaderUniform.h
old mode 100644
new mode 100755
index 804da30..804da30
--- a/stim/gl/rts_glShaderUniform.h
+++ b/stim/gl/rts_glShaderUniform.h
diff --git a/stim/gl/rts_glUtilities.h b/stim/gl/rts_glUtilities.h
old mode 100644
new mode 100755
index e25a412..e25a412
--- a/stim/gl/rts_glUtilities.h
+++ b/stim/gl/rts_glUtilities.h
diff --git a/stim/gl/texture.h b/stim/gl/texture.h
old mode 100644
new mode 100755
index 56f8fbd..56f8fbd
--- a/stim/gl/texture.h
+++ b/stim/gl/texture.h
diff --git a/stim/grids/grid.h b/stim/grids/grid.h
old mode 100644
new mode 100755
index 1ac2ab1..1ac2ab1
--- a/stim/grids/grid.h
+++ b/stim/grids/grid.h
diff --git a/stim/grids/image_stack.h b/stim/grids/image_stack.h
old mode 100644
new mode 100755
index 0f99409..0f99409
--- a/stim/grids/image_stack.h
+++ b/stim/grids/image_stack.h
diff --git a/stim/image/CImg.h b/stim/image/CImg.h
old mode 100644
new mode 100755
index 06cb44e..06cb44e
--- a/stim/image/CImg.h
+++ b/stim/image/CImg.h
diff --git a/stim/image/image.h b/stim/image/image.h
old mode 100644
new mode 100755
index 594095e..594095e
--- a/stim/image/image.h
+++ b/stim/image/image.h
diff --git a/stim/image/image_contour_detection.h b/stim/image/image_contour_detection.h
old mode 100644
new mode 100755
index 055d06a..055d06a
--- a/stim/image/image_contour_detection.h
+++ b/stim/image/image_contour_detection.h
diff --git a/stim/math/bessel.h b/stim/math/bessel.h
old mode 100644
new mode 100755
index d291deb..d291deb
--- a/stim/math/bessel.h
+++ b/stim/math/bessel.h
diff --git a/stim/math/complex.h b/stim/math/complex.h
old mode 100644
new mode 100755
index 84ba67e..e6a8ce3
--- a/stim/math/complex.h
+++ b/stim/math/complex.h
@@ -5,7 +5,7 @@ and can therefore be used in CUDA code and on CUDA devices.
 #ifndef RTS_COMPLEX
 #define RTS_COMPLEX
 
-#include "../cuda/callable.h"
+#include "stim/cuda/cudatools/callable.h"
 #include <cmath>
 #include <string>
 #include <sstream>
diff --git a/stim/math/complexfield.cuh b/stim/math/complexfield.cuh
old mode 100644
new mode 100755
index 81488cf..81488cf
--- a/stim/math/complexfield.cuh
+++ b/stim/math/complexfield.cuh
diff --git a/stim/math/constants.h b/stim/math/constants.h
old mode 100644
new mode 100755
index d333887..d333887
--- a/stim/math/constants.h
+++ b/stim/math/constants.h
diff --git a/stim/math/field.cuh b/stim/math/field.cuh
old mode 100644
new mode 100755
index 1a3a2ab..1a3a2ab
--- a/stim/math/field.cuh
+++ b/stim/math/field.cuh
diff --git a/stim/math/function.h b/stim/math/function.h
old mode 100644
new mode 100755
index 033337d..033337d
--- a/stim/math/function.h
+++ b/stim/math/function.h
diff --git a/stim/math/legendre.h b/stim/math/legendre.h
old mode 100644
new mode 100755
index 4859740..3dcd83a
--- a/stim/math/legendre.h
+++ b/stim/math/legendre.h
@@ -1,7 +1,7 @@
 #ifndef RTS_LEGENDRE_H
 #define RTS_LEGENDRE_H
 
-#include "rts/cuda/callable.h"
+#include "stim/cuda/cudatools/callable.h"
 
 namespace stim{
 
diff --git a/stim/math/matrix.h b/stim/math/matrix.h
old mode 100644
new mode 100755
index 777ba9e..777ba9e
--- a/stim/math/matrix.h
+++ b/stim/math/matrix.h
diff --git a/stim/math/plane.h b/stim/math/plane.h
old mode 100644
new mode 100755
index b009cad..b009cad
--- a/stim/math/plane.h
+++ b/stim/math/plane.h
diff --git a/stim/math/quad.h b/stim/math/quad.h
old mode 100644
new mode 100755
index c983008..a5f132b
--- a/stim/math/quad.h
+++ b/stim/math/quad.h
@@ -1,8 +1,8 @@
-#ifndef RTS_QUAD_H
-#define RTS_QUAD_H
+#ifndef STIM_QUAD_H
+#define STIM_QUAD_H
 
 //enable CUDA_CALLABLE macro
-#include <stim/cuda/callable.h>
+#include <stim/cuda/cudatools/callable.h>
 #include <stim/math/vector.h>
 #include <stim/math/triangle.h>
 #include <stim/math/quaternion.h>
@@ -13,7 +13,7 @@
 namespace stim{
 
 //template for a quadangle class in ND space
-template <class T, int N = 3>
+template <class T>
 struct quad
 {
 	/*
@@ -30,9 +30,9 @@ struct quad
 	T B[N];
 	T C[N];*/
 
-	rts::vec<T, N> A;
-	rts::vec<T, N> X;
-	rts::vec<T, N> Y;
+	stim::vec<T> A;
+	stim::vec<T> X;
+	stim::vec<T> Y;
 
 
 	CUDA_CALLABLE quad()
@@ -40,7 +40,7 @@ struct quad
 
 	}
 
-	CUDA_CALLABLE quad(vec<T, N> a, vec<T, N> b, vec<T, N> c)
+	CUDA_CALLABLE quad(vec<T> a, vec<T> b, vec<T> c)
 	{
 
 		A = a;		
@@ -52,20 +52,20 @@ struct quad
 	/*******************************************************************
 	Constructor - create a quad from a position, normal, and rotation
 	*******************************************************************/
-	CUDA_CALLABLE quad(rts::vec<T, N> c, rts::vec<T, N> normal, T width, T height, T theta)
+	CUDA_CALLABLE quad(stim::vec<T> c, stim::vec<T> normal, T width, T height, T theta)
 	{
 
         //compute the X direction - start along world-space X
-        Y = rts::vec<T, N>(0, 1, 0);
+        Y = stim::vec<T>(0, 1, 0);
         if(Y == normal)
-            Y = rts::vec<T, N>(0, 0, 1);
+            Y = stim::vec<T>(0, 0, 1);
 
         X = Y.cross(normal).norm();
 
         std::cout<<X<<std::endl;
 
         //rotate the X axis by theta radians
-        rts::quaternion<T> q;
+        stim::quaternion<T> q;
         q.CreateRotation(theta, normal);
         X = q.toMatrix3() * X;
         Y = normal.cross(X);
@@ -85,7 +85,7 @@ struct quad
 	}
 
 	//boolean comparison
-	bool operator==(const quad<T, N> & rhs)
+	bool operator==(const quad<T> & rhs)
 	{
 		if(A == rhs.A && X == rhs.X && Y == rhs.Y)
 			return true;
@@ -96,21 +96,21 @@ struct quad
 	/*******************************************
 	Return the normal for the quad
 	*******************************************/
-	CUDA_CALLABLE rts::vec<T, N> n()
+	CUDA_CALLABLE stim::vec<T> n()
 	{
         return (X.cross(Y)).norm();
 	}
 
-	CUDA_CALLABLE rts::vec<T, N> p(T a, T b)
+	CUDA_CALLABLE stim::vec<T> p(T a, T b)
 	{
-		rts::vec<T, N> result;
+		stim::vec<T> result;
 		//given the two parameters a, b = [0 1], returns the position in world space
 		result = A + X * a + Y * b;
 
 		return result;
 	}
 
-	CUDA_CALLABLE rts::vec<T, N> operator()(T a, T b)
+	CUDA_CALLABLE stim::vec<T> operator()(T a, T b)
 	{
 		return p(a, b);
 	}
@@ -127,15 +127,15 @@ struct quad
 
 	}
 
-	CUDA_CALLABLE quad<T, N> operator*(T rhs)
+	CUDA_CALLABLE quad<T> operator*(T rhs)
 	{
 		//scales the plane by a scalar value
 
 		//compute the center point
-		rts::vec<T, N> c = A + X*0.5f + Y*0.5f;
+		stim::vec<T> c = A + X*0.5f + Y*0.5f;
 
 		//create the new quadangle
-		quad<T, N> result;
+		quad<T> result;
 		result.X = X * rhs;
 		result.Y = Y * rhs;
 		result.A = c - result.X*0.5f - result.Y*0.5f;
@@ -144,7 +144,7 @@ struct quad
 
 	}
 
-	CUDA_CALLABLE T dist(vec<T, N> p)
+	CUDA_CALLABLE T dist(vec<T> p)
 	{
         //compute the distance between a point and this quad
 
@@ -162,7 +162,7 @@ struct quad
             return d1;
 	}
 
-	CUDA_CALLABLE T dist_max(vec<T, N> p)
+	CUDA_CALLABLE T dist_max(vec<T> p)
 	{
         T da = (A - p).len();
         T db = (A+X - p).len();
@@ -176,7 +176,7 @@ struct quad
 }	//end namespace rts
 
 template <typename T, int N>
-std::ostream& operator<<(std::ostream& os, rts::quad<T, N> R)
+std::ostream& operator<<(std::ostream& os, stim::quad<T> R)
 {
     os<<R.str();
     return os;
diff --git a/stim/math/quaternion.h b/stim/math/quaternion.h
old mode 100644
new mode 100755
index 57bfa45..57bfa45
--- a/stim/math/quaternion.h
+++ b/stim/math/quaternion.h
diff --git a/stim/math/realfield.cuh b/stim/math/realfield.cuh
old mode 100644
new mode 100755
index 7d6ce26..7d6ce26
--- a/stim/math/realfield.cuh
+++ b/stim/math/realfield.cuh
diff --git a/stim/math/rect.h b/stim/math/rect.h
old mode 100644
new mode 100755
index 9767f26..9767f26
--- a/stim/math/rect.h
+++ b/stim/math/rect.h
diff --git a/stim/math/spharmonics.h b/stim/math/spharmonics.h
old mode 100644
new mode 100755
index 3182faa..3182faa
--- a/stim/math/spharmonics.h
+++ b/stim/math/spharmonics.h
diff --git a/stim/math/stimlib-math.config b/stim/math/stimlib-math.config
new file mode 100755
index 0000000..e0284f4
--- /dev/null
+++ b/stim/math/stimlib-math.config
@@ -0,0 +1,2 @@
+// Add predefined macros for your project here. For example:
+// #define THE_ANSWER 42
diff --git a/stim/math/stimlib-math.creator b/stim/math/stimlib-math.creator
new file mode 100755
index 0000000..e94cbbd
--- /dev/null
+++ b/stim/math/stimlib-math.creator
@@ -0,0 +1 @@
+[General]
diff --git a/stim/math/stimlib-math.files b/stim/math/stimlib-math.files
new file mode 100755
index 0000000..d4c171e
--- /dev/null
+++ b/stim/math/stimlib-math.files
@@ -0,0 +1,16 @@
+bessel.h
+complex.h
+complexfield.cuh
+constants.h
+field.cuh
+function.h
+legendre.h
+matrix.h
+plane.h
+quad.h
+quaternion.h
+realfield.cuh
+rect.h
+spharmonics.h
+triangle.h
+vector.h
\ No newline at end of file
diff --git a/stim/math/stimlib-math.includes b/stim/math/stimlib-math.includes
new file mode 100755
index 0000000..945c9b4
--- /dev/null
+++ b/stim/math/stimlib-math.includes
@@ -0,0 +1 @@
+.
\ No newline at end of file
diff --git a/stim/math/triangle.h b/stim/math/triangle.h
old mode 100644
new mode 100755
index bf81fcc..bf81fcc
--- a/stim/math/triangle.h
+++ b/stim/math/triangle.h
diff --git a/stim/math/vector.h b/stim/math/vector.h
old mode 100644
new mode 100755
index 5034cc1..5034cc1
--- a/stim/math/vector.h
+++ b/stim/math/vector.h
diff --git a/stim/matlab/rtsApplyBrewer.m b/stim/matlab/rtsApplyBrewer.m
old mode 100644
new mode 100755
index bdc0693..bdc0693
--- a/stim/matlab/rtsApplyBrewer.m
+++ b/stim/matlab/rtsApplyBrewer.m
diff --git a/stim/matlab/rtsBaselineCorrect.m b/stim/matlab/rtsBaselineCorrect.m
old mode 100644
new mode 100755
index 673296d..673296d
--- a/stim/matlab/rtsBaselineCorrect.m
+++ b/stim/matlab/rtsBaselineCorrect.m
diff --git a/stim/matlab/rtsClass2Color.m b/stim/matlab/rtsClass2Color.m
old mode 100644
new mode 100755
index 5b8df59..5b8df59
--- a/stim/matlab/rtsClass2Color.m
+++ b/stim/matlab/rtsClass2Color.m
diff --git a/stim/matlab/rtsColorMapField.m b/stim/matlab/rtsColorMapField.m
old mode 100644
new mode 100755
index 3ada8c7..3ada8c7
--- a/stim/matlab/rtsColorMapField.m
+++ b/stim/matlab/rtsColorMapField.m
diff --git a/stim/matlab/rtsColorMapRainbow.m b/stim/matlab/rtsColorMapRainbow.m
old mode 100644
new mode 100755
index 0c79394..0c79394
--- a/stim/matlab/rtsColorMapRainbow.m
+++ b/stim/matlab/rtsColorMapRainbow.m
diff --git a/stim/matlab/rtsCropMask.m b/stim/matlab/rtsCropMask.m
old mode 100644
new mode 100755
index 5ac7fb3..5ac7fb3
--- a/stim/matlab/rtsCropMask.m
+++ b/stim/matlab/rtsCropMask.m
diff --git a/stim/matlab/rtsEnviClassify.m b/stim/matlab/rtsEnviClassify.m
old mode 100644
new mode 100755
index 8326995..8326995
--- a/stim/matlab/rtsEnviClassify.m
+++ b/stim/matlab/rtsEnviClassify.m
diff --git a/stim/matlab/rtsEnviClose.m b/stim/matlab/rtsEnviClose.m
old mode 100644
new mode 100755
index 3ee3283..3ee3283
--- a/stim/matlab/rtsEnviClose.m
+++ b/stim/matlab/rtsEnviClose.m
diff --git a/stim/matlab/rtsEnviID.m b/stim/matlab/rtsEnviID.m
old mode 100644
new mode 100755
index 10f559e..10f559e
--- a/stim/matlab/rtsEnviID.m
+++ b/stim/matlab/rtsEnviID.m
diff --git a/stim/matlab/rtsEnviLoadHeader.m b/stim/matlab/rtsEnviLoadHeader.m
old mode 100644
new mode 100755
index 2746cc2..2746cc2
--- a/stim/matlab/rtsEnviLoadHeader.m
+++ b/stim/matlab/rtsEnviLoadHeader.m
diff --git a/stim/matlab/rtsEnviLoadImage.m b/stim/matlab/rtsEnviLoadImage.m
old mode 100644
new mode 100755
index 6a7ab0f..6a7ab0f
--- a/stim/matlab/rtsEnviLoadImage.m
+++ b/stim/matlab/rtsEnviLoadImage.m
diff --git a/stim/matlab/rtsEnviLoadTraining.m b/stim/matlab/rtsEnviLoadTraining.m
old mode 100644
new mode 100755
index 1788a08..1788a08
--- a/stim/matlab/rtsEnviLoadTraining.m
+++ b/stim/matlab/rtsEnviLoadTraining.m
diff --git a/stim/matlab/rtsEnviOpen.m b/stim/matlab/rtsEnviOpen.m
old mode 100644
new mode 100755
index badc640..badc640
--- a/stim/matlab/rtsEnviOpen.m
+++ b/stim/matlab/rtsEnviOpen.m
diff --git a/stim/matlab/rtsEnviRandomForest2C_apply.m b/stim/matlab/rtsEnviRandomForest2C_apply.m
old mode 100644
new mode 100755
index e1d2a7c..e1d2a7c
--- a/stim/matlab/rtsEnviRandomForest2C_apply.m
+++ b/stim/matlab/rtsEnviRandomForest2C_apply.m
diff --git a/stim/matlab/rtsEnviRandomForest2C_train.m b/stim/matlab/rtsEnviRandomForest2C_train.m
old mode 100644
new mode 100755
index 8bf13d7..8bf13d7
--- a/stim/matlab/rtsEnviRandomForest2C_train.m
+++ b/stim/matlab/rtsEnviRandomForest2C_train.m
diff --git a/stim/matlab/rtsEnviRandomForest2C_validate.m b/stim/matlab/rtsEnviRandomForest2C_validate.m
old mode 100644
new mode 100755
index 626a03c..626a03c
--- a/stim/matlab/rtsEnviRandomForest2C_validate.m
+++ b/stim/matlab/rtsEnviRandomForest2C_validate.m
diff --git a/stim/matlab/rtsEnviRead.m b/stim/matlab/rtsEnviRead.m
old mode 100644
new mode 100755
index d46db6c..d46db6c
--- a/stim/matlab/rtsEnviRead.m
+++ b/stim/matlab/rtsEnviRead.m
diff --git a/stim/matlab/rtsEnviSaveImage.m b/stim/matlab/rtsEnviSaveImage.m
old mode 100644
new mode 100755
index a22402b..a22402b
--- a/stim/matlab/rtsEnviSaveImage.m
+++ b/stim/matlab/rtsEnviSaveImage.m
diff --git a/stim/matlab/rtsGaussianBlurND.m b/stim/matlab/rtsGaussianBlurND.m
old mode 100644
new mode 100755
index 3699850..3699850
--- a/stim/matlab/rtsGaussianBlurND.m
+++ b/stim/matlab/rtsGaussianBlurND.m
diff --git a/stim/matlab/rtsHSVtoRGB.m b/stim/matlab/rtsHSVtoRGB.m
old mode 100644
new mode 100755
index 9770aea..9770aea
--- a/stim/matlab/rtsHSVtoRGB.m
+++ b/stim/matlab/rtsHSVtoRGB.m
diff --git a/stim/matlab/rtsInt2Str.m b/stim/matlab/rtsInt2Str.m
old mode 100644
new mode 100755
index 06b9b8d..06b9b8d
--- a/stim/matlab/rtsInt2Str.m
+++ b/stim/matlab/rtsInt2Str.m
diff --git a/stim/matlab/rtsLoadImageStack.m b/stim/matlab/rtsLoadImageStack.m
old mode 100644
new mode 100755
index 15c921a..15c921a
--- a/stim/matlab/rtsLoadImageStack.m
+++ b/stim/matlab/rtsLoadImageStack.m
diff --git a/stim/matlab/rtsMaskReconstruct.m b/stim/matlab/rtsMaskReconstruct.m
old mode 100644
new mode 100755
index eed102e..eed102e
--- a/stim/matlab/rtsMaskReconstruct.m
+++ b/stim/matlab/rtsMaskReconstruct.m
diff --git a/stim/matlab/rtsMonteCarloSphere.m b/stim/matlab/rtsMonteCarloSphere.m
old mode 100644
new mode 100755
index 0d80b0b..0d80b0b
--- a/stim/matlab/rtsMonteCarloSphere.m
+++ b/stim/matlab/rtsMonteCarloSphere.m
diff --git a/stim/matlab/rtsOffsetPlots.m b/stim/matlab/rtsOffsetPlots.m
old mode 100644
new mode 100755
index f3e7e84..f3e7e84
--- a/stim/matlab/rtsOffsetPlots.m
+++ b/stim/matlab/rtsOffsetPlots.m
diff --git a/stim/matlab/rtsRAW2Images.m b/stim/matlab/rtsRAW2Images.m
old mode 100644
new mode 100755
index eea8065..eea8065
--- a/stim/matlab/rtsRAW2Images.m
+++ b/stim/matlab/rtsRAW2Images.m
diff --git a/stim/matlab/rtsROC.m b/stim/matlab/rtsROC.m
old mode 100644
new mode 100755
index 82721b1..82721b1
--- a/stim/matlab/rtsROC.m
+++ b/stim/matlab/rtsROC.m
diff --git a/stim/matlab/rtsRandomizeMask.m b/stim/matlab/rtsRandomizeMask.m
old mode 100644
new mode 100755
index 62866d3..62866d3
--- a/stim/matlab/rtsRandomizeMask.m
+++ b/stim/matlab/rtsRandomizeMask.m
diff --git a/stim/matlab/rtsSaveRAW.m b/stim/matlab/rtsSaveRAW.m
old mode 100644
new mode 100755
index 042b5e5..042b5e5
--- a/stim/matlab/rtsSaveRAW.m
+++ b/stim/matlab/rtsSaveRAW.m
diff --git a/stim/matlab/stimBrewerColormap.m b/stim/matlab/stimBrewerColormap.m
old mode 100644
new mode 100755
index 34568a0..34568a0
--- a/stim/matlab/stimBrewerColormap.m
+++ b/stim/matlab/stimBrewerColormap.m
diff --git a/stim/optics/beam.h b/stim/optics/beam.h
old mode 100644
new mode 100755
index 8587bb4..8587bb4
--- a/stim/optics/beam.h
+++ b/stim/optics/beam.h
diff --git a/stim/optics/efield.cuh b/stim/optics/efield.cuh
old mode 100644
new mode 100755
index 5002478..5002478
--- a/stim/optics/efield.cuh
+++ b/stim/optics/efield.cuh
diff --git a/stim/optics/esphere.cuh b/stim/optics/esphere.cuh
old mode 100644
new mode 100755
index 1b5a559..1b5a559
--- a/stim/optics/esphere.cuh
+++ b/stim/optics/esphere.cuh
diff --git a/stim/optics/halfspace.cuh b/stim/optics/halfspace.cuh
old mode 100644
new mode 100755
index 0905ce1..0905ce1
--- a/stim/optics/halfspace.cuh
+++ b/stim/optics/halfspace.cuh
diff --git a/stim/optics/material.h b/stim/optics/material.h
old mode 100644
new mode 100755
index fb97cd6..fb97cd6
--- a/stim/optics/material.h
+++ b/stim/optics/material.h
diff --git a/stim/optics/mirst-1d.cuh b/stim/optics/mirst-1d.cuh
old mode 100644
new mode 100755
index 9279087..9279087
--- a/stim/optics/mirst-1d.cuh
+++ b/stim/optics/mirst-1d.cuh
diff --git a/stim/optics/planewave.h b/stim/optics/planewave.h
old mode 100644
new mode 100755
index 6a295f9..6a295f9
--- a/stim/optics/planewave.h
+++ b/stim/optics/planewave.h
diff --git a/stim/parser/arguments.h b/stim/parser/arguments.h
old mode 100644
new mode 100755
index 5a758f8..5a758f8
--- a/stim/parser/arguments.h
+++ b/stim/parser/arguments.h
diff --git a/stim/parser/filename.h b/stim/parser/filename.h
old mode 100644
new mode 100755
index 2fa0db2..2fa0db2
--- a/stim/parser/filename.h
+++ b/stim/parser/filename.h
diff --git a/stim/parser/parser.h b/stim/parser/parser.h
old mode 100644
new mode 100755
index 2583fde..2583fde
--- a/stim/parser/parser.h
+++ b/stim/parser/parser.h
diff --git a/stim/parser/wildcards.h b/stim/parser/wildcards.h
old mode 100644
new mode 100755
index ac8c42d..ac8c42d
--- a/stim/parser/wildcards.h
+++ b/stim/parser/wildcards.h
diff --git a/stim/stimlib.config b/stim/stimlib.config
new file mode 100755
index 0000000..e0284f4
--- /dev/null
+++ b/stim/stimlib.config
@@ -0,0 +1,2 @@
+// Add predefined macros for your project here. For example:
+// #define THE_ANSWER 42
diff --git a/stim/stimlib.creator b/stim/stimlib.creator
new file mode 100755
index 0000000..e94cbbd
--- /dev/null
+++ b/stim/stimlib.creator
@@ -0,0 +1 @@
+[General]
diff --git a/stim/stimlib.files b/stim/stimlib.files
new file mode 100755
index 0000000..27d24b8
--- /dev/null
+++ b/stim/stimlib.files
@@ -0,0 +1,77 @@
+biology/fibernet.h
+biomodels/flow.h
+biomodels/network.h
+cuda/array_abs.cuh
+cuda/array_add.cuh
+cuda/array_cart2polar.cuh
+cuda/array_multiply.cuh
+cuda/arraymath.cuh
+cuda/callable.h
+cuda/conv2.cuh
+cuda/cost.h
+cuda/devices.h
+cuda/down_sample.cuh
+cuda/error.h
+cuda/filter.h
+cuda/gaussian_blur.cuh
+cuda/glbind.h
+cuda/gradient.cuh
+cuda/local_max.cuh
+cuda/sharedmem.cuh
+cuda/threads.h
+cuda/timer.h
+cuda/update_dir.cuh
+cuda/vote.cuh
+envi/bil.h
+envi/binary.h
+envi/bip.h
+envi/bsq.h
+envi/envi.h
+envi/envi_header.h
+gl/error.h
+gl/gl_spider.h
+gl/gl_texture.h
+gl/rts_glShaderObject.h
+gl/rts_glShaderProgram.h
+gl/rts_glShaderUniform.h
+gl/rts_glUtilities.h
+gl/rtsSourceCode.h
+gl/texture.h
+grids/grid.h
+grids/image_stack.h
+image/CImg.h
+image/image.h
+image/image_contour_detection.h
+math/bessel.h
+math/complex.h
+math/complexfield.cuh
+math/constants.h
+math/field.cuh
+math/function.h
+math/legendre.h
+math/matrix.h
+math/plane.h
+math/quad.h
+math/quaternion.h
+math/realfield.cuh
+math/rect.h
+math/spharmonics.h
+math/triangle.h
+math/vector.h
+optics/beam.h
+optics/efield.cuh
+optics/esphere.cuh
+optics/halfspace.cuh
+optics/material.h
+optics/mirst-1d.cuh
+optics/planewave.h
+parser/arguments.h
+parser/filename.h
+parser/parser.h
+parser/wildcards.h
+ui/progressbar.h
+visualization/camera.h
+visualization/colormap.h
+visualization/gl_spharmonics.h
+visualization/glObj.h
+visualization/obj.h
\ No newline at end of file
diff --git a/stim/stimlib.includes b/stim/stimlib.includes
new file mode 100755
index 0000000..c12cad1
--- /dev/null
+++ b/stim/stimlib.includes
@@ -0,0 +1,12 @@
+biology
+biomodels
+cuda
+envi
+gl
+grids
+image
+math
+optics
+parser
+ui
+visualization
\ No newline at end of file
diff --git a/stim/ui/progressbar.h b/stim/ui/progressbar.h
old mode 100644
new mode 100755
index aed05ef..aed05ef
--- a/stim/ui/progressbar.h
+++ b/stim/ui/progressbar.h
diff --git a/stim/visualization/camera.h b/stim/visualization/camera.h
old mode 100644
new mode 100755
index 6c615dc..6c615dc
--- a/stim/visualization/camera.h
+++ b/stim/visualization/camera.h
diff --git a/stim/visualization/colormap.h b/stim/visualization/colormap.h
old mode 100644
new mode 100755
index 8a43c33..8a43c33
--- a/stim/visualization/colormap.h
+++ b/stim/visualization/colormap.h
diff --git a/stim/visualization/glObj.h b/stim/visualization/glObj.h
old mode 100644
new mode 100755
index 6ae3315..6ae3315
--- a/stim/visualization/glObj.h
+++ b/stim/visualization/glObj.h
diff --git a/stim/visualization/gl_spharmonics.h b/stim/visualization/gl_spharmonics.h
old mode 100644
new mode 100755
index 1ff0395..1ff0395
--- a/stim/visualization/gl_spharmonics.h
+++ b/stim/visualization/gl_spharmonics.h
diff --git a/stim/visualization/obj.h b/stim/visualization/obj.h
old mode 100644
new mode 100755
index 854ffdc..854ffdc
--- a/stim/visualization/obj.h
+++ b/stim/visualization/obj.h
--
libgit2 0.21.4