changes needed to compile and run the bimsim code

Sebastian Berisha
1 parent 945ee13c
Showing 138 changed files with 137 additions and 25 deletions Show diff stats
.gitignore
Doxyfile
LICENSE.txt
cmake/FindANN.cmake
cmake/FindSTIM.cmake
stim/biology/fibernet.h
stim/biomodels/flow.h
stim/biomodels/network.h
stim/cuda/arraymath.cuh
stim/cuda/arraymath/array_abs.cuh
stim/cuda/arraymath/array_add.cuh
stim/cuda/arraymath/array_atan.cuh
stim/cuda/arraymath/array_cart2polar.cuh
stim/cuda/arraymath/array_cos.cuh
stim/cuda/arraymath/array_divide.cuh
stim/cuda/arraymath/array_multiply.cuh
stim/cuda/arraymath/array_multiply2.cuh
stim/cuda/arraymath/array_sin.cuh
stim/cuda/bsds500/cPb.cpp
stim/cuda/bsds500/dG1_conv2.cpp
@@ -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>
 #ifndef RTS_LEGENDRE_H
 #define RTS_LEGENDRE_H
  
-#include "rts/cuda/callable.h"
+#include "stim/cuda/cudatools/callable.h"
  
 namespace stim{
  
-#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;
+// Add predefined macros for your project here. For example:
+// #define THE_ANSWER 42
+[General]
+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
+// Add predefined macros for your project here. For example:
+// #define THE_ANSWER 42
+[General]
+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
+biology
+biomodels
+cuda
+envi
+gl
+grids
+image
+math
+optics
+parser
+ui
+visualization
 \ No newline at end of file