gl_spider.h
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#ifndef STIM_GL_SPIDER_H
#define STIM_GL_SPIDER_H
#include <GL/glew.h>
#include <GL/glut.h>
#include <cuda.h>
#include <cuda_gl_interop.h>
#include <cudaGL.h>
#include <math.h>
#include <stim/gl/gl_texture.h>
#include <stim/visualization/camera.h>
#include <stim/gl/error.h>
#include <stim/math/vector.h>
#include <stim/math/vec3.h>
#include <stim/math/rect.h>
#include <stim/math/matrix.h>
#include <stim/cuda/spider_cost.cuh>
#include <stim/cuda/cudatools/glbind.h>
#include <stim/cuda/arraymath.cuh>
#include <stim/cuda/cudatools.h>
#include <stim/cuda/ivote.cuh>
#include <stim/visualization/glObj.h>
#include <vector>
#include <stim/cuda/branch_detection.cuh>
#include "../../../volume-spider/fiber.h"
#include "../../../volume-spider/glnetwork.h"
#include <stim/visualization/cylinder.h>
#include <stim/cuda/testKernel.cuh>
//#include <stim/cuda/testKernel.cuh>
#include <iostream>
#include <fstream>
#ifdef TESTING
#include <iostream>
#include <cstdio>
#include <ctime>
#endif
namespace stim
{
template<typename T>
class gl_spider : public virtual gl_texture<T>
{
//doen't use gl_texture really, just needs the GLuint id.
//doesn't even need the texture iD really.
private:
//
stim::vec3<float> p; //vector designating the position of the spider.
stim::vec3<float> d; //vector designating the orientation of the spider
//always a unit vector.
stim::vec<float> m; //magnitude of the spider vector.
//mag[0] = length.
//mag[1] = width.
std::vector<stim::vec3<float> > dV; //A list of all the direction vectors.
std::vector<stim::vec3<float> > pV; //A list of all the position vectors.
std::vector<stim::vec3<float> > mV; //A list of all the size vectors.
stim::matrix<float, 4> cT; //current Transformation matrix
//From tissue space to texture space.
GLuint texID;
stim::vec<float> S; //Size of a voxel in the volume.
stim::vec<float> R; //Dimensions of the volume.
//GL and Cuda variables
GLuint dList; //displaylist ID
GLuint fboID; //framebuffer ID
GLuint texbufferID; //texbuffer ID, only necessary for
//cuda aspect of the calculation.
GLuint pfboID; //buffer object for position tracking.
GLuint ptexbufferID; //texture object for position tracking.
GLuint mfboID; //buffer object for magnitude adjustment.
GLuint mtexbufferID; //texture object for magnitude adjustment.
GLuint bfboID; //buffer object for position adjustment.
GLuint btexbufferID; //buffer object for position adjustment.
int numSamples; //The number of templates in the buffer.
int numSamplesPos;
int numSamplesMag;
float stepsize = 5.0; //Step size.
// float stepsize = 3.0; //Step size.
int current_cost; //variable to store the cost of the current step.
//Tracing variables.
std::stack< stim::vec3<float> > seeds; //seed positions.
std::stack< stim::vec3<float> > seedsvecs; //seed directions.
std::stack< float > seedsmags; //seed magnitudes.
std::vector< stim::vec3<float> > cL; //Positions of line currently being traced.
std::vector< stim::vec3<float> > cD; //Direction of line currently being traced.
std::vector< stim::vec<float> > cM; //Magnitude of line currently being traced.
stim::glnetwork<float> nt; //object for storing the network.
stim::vec<float> rev; //reverse vector;
stim::camera camSel;
stim::vec3<float> ps;
stim::vec3<float> ups;
stim::vec3<float> ds;
static const float t_length = 16.0;
//--------------------------------------------------------------------------//
//-------------------------------PRIVATE METHODS----------------------------//
//--------------------------------------------------------------------------//
/// Method for finding the best scale for the spider.
/// changes the x, y, z size of the spider to minimize the cost
/// function.
void
findOptimalDirection()
{
setMatrix(); //create the transformation matrix.
glCallList(dList); //move the templates to p, d, m.
#ifdef TESTING
test(texbufferID, GL_TEXTURE_2D,2*t_length,numSamples*t_length, "Final_Cost_Direction.bmp");
#endif
int best = getCost(texbufferID,numSamples); //find min cost.
stim::vec<float> next( //find next vector.
dV[best][0]*S[0]*R[0],
dV[best][1]*S[1]*R[1],
dV[best][2]*S[2]*R[2],
0);
next = (cT*next).norm(); //find next vector.
setPosition( p[0]+next[0]*m[0]/stepsize,
p[1]+next[1]*m[0]/stepsize,
p[2]+next[2]*m[0]/stepsize);
setDirection(next[0], next[1], next[2]);
//move forward and change direction.
}
/// Method for finding the best d (direction) for the spider.
/// Not sure if necessary since the next p (position) for the spider
/// will be at d * m.
void
findOptimalPosition()
{
setMatrix(); //create the transformation matrix.
glCallList(dList+1); //move the templates to p, d, m.
#ifdef TESTING
test(ptexbufferID, GL_TEXTURE_2D,2*t_length, numSamplesPos*t_length, "Final_Cost_Position.bmp");
#endif
int best = getCost(ptexbufferID, numSamplesPos); //find min cost.
// std::cerr << best << std::endl;
stim::vec<float> next( //find next position.
pV[best][0],
pV[best][1],
pV[best][2],
1);
next = cT*next; //find next position.
setPosition(
next[0]*S[0]*R[0],
next[1]*S[1]*R[1],
next[2]*S[2]*R[2]
); //adjust position.
}
/// Method for finding the best scale for the spider.
/// changes the x, y, z size of the spider to minimize the cost
/// function. */
void
findOptimalScale()
{
setMatrix(); //create the transformation.
glCallList(dList+2); //move the templates to p, d, m.
#ifdef TESTING
test(mtexbufferID, GL_TEXTURE_2D, 2*t_length, numSamplesMag*t_length, "Final_Cost_Position.bmp");
#endif
int best = getCost(mtexbufferID, numSamplesMag); //get best cost.
setMagnitude(m[0]*mV[best][0]); //adjust the magnitude.
}
///subject to change.
///finds branches.
///depreciated
void
branchDetection()
{
setMatrix();
glCallList(dList+3);
std::vector< stim::vec<float> > result = find_branch(
btexbufferID, GL_TEXTURE_2D, 16, 216);
stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
if(!result.empty())
{
for(int i = 1; i < result.size(); i++)
{
stim::vec<float> cylp(
0.5 * cos(2*M_PI*(result[i][1])),
0.5 * sin(2*M_PI*(result[i][1])),
result[i][0]-0.5,
1.0);
cylp = cT*cylp;
stim::vec3<float> vec(
cylp[0]*S[0]*R[0],
cylp[1]*S[1]*R[1],
cylp[2]*S[2]*R[2]);
stim::vec3<float> seeddir(-p[0] + cylp[0]*S[0]*R[0],
-p[1] + cylp[1]*S[1]*R[1],
-p[2] + cylp[2]*S[2]*R[2]);
seeddir = seeddir.norm();
float seedm = m[0];
// Uncomment for global run
if(
!(vec[0] > size[0] || vec[1] > size[1]
|| vec[2] > size[2] || vec[0] < 0
|| vec[1] < 0 || vec[2] < 0))
{
setSeed(vec);
setSeedVec(seeddir);
setSeedMag(seedm);
}
}
}
}
///finds all the branches in the a given fiber.
///using LoG method.
void
branchDetection2(int n = 8, int l_template = 8, int l_square = 8)
{
if(cL.size() < 4){}
else{
setMatrix(1);
DrawLongCylinder(n, l_template, l_square);
stim::cylinder<float> cyl(cL, cM);
std::vector< stim::vec<float> > result = find_branch(btexbufferID, GL_TEXTURE_2D, n*l_square, (cL.size()-1)*l_template);
stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
float pval;
if(!result.empty())
{
for(int i = 0; i < result.size(); i++)
{
int id = result[i][2];
if(fmod(result[i][2], id) != 0 && id != 0)
{
pval = ((cyl.getl(id+1)-cyl.getl(id))*
(fmod(result[i][2], id))+cyl.getl(id))/cyl.getl(cL.size()-1);
}
else if(id == 0)
{
pval = (cyl.getl(id+1)*result[i][2])/cyl.getl(cL.size()-1);
}
else
{
pval = (cyl.getl(id)/cyl.getl(cL.size()-1));
}
stim::vec3<float> v = cyl.surf(pval, result[i][0]);
stim::vec3<float> di = cyl.p(pval);
float rad = cyl.r(pval);
if(
!(v[0] > size[0] || v[1] > size[1]
|| v[2] > size[2] || v[0] < 0
|| v[1] < 0 || v[2] < 0))
{
setSeed(v);
setSeedVec((v-di).norm());
setSeedMag(rad);
}
}
}
}
}
float uniformRandom()
{
return ( (float)(rand()))/( (float)(RAND_MAX));
}
float normalRandom()
{
float u1 = uniformRandom();
float u2 = uniformRandom();
return cos(2.0*atan(1.0)*u2)*sqrt(-1.0*log(u1));
}
stim::vec3<float> uniformRandVector()
{
stim::vec3<float> r(uniformRandom(), uniformRandom(), 1.0);
return r;
}
stim::vec3<float> normalRandVector()
{
stim::vec3<float> r(normalRandom(), normalRandom(), 1.0);
return r;
}
//--------------------------------------------------------------------------//
//---------------------TEMPLATE CREATION METHODS----------------------------//
//--------------------------------------------------------------------------//
void
MonteCarloDirectionVectors(int nSamples, float solidAngle = 2*M_PI)
{
///equal area projection.
// std::vector<stim::vec<float> > vecsUni;
// for(int i = 0; i < nSamples; i++)
// {
// stim::vec<float> a = uniformRandVector();
// a[1] = a[1]*2*M_PI;
// a[0] = a[0]*(solidAngle);
// a = a.cyl2cart();
// stim::vec<float> b(
// sqrt(1.-(pow(a[0],2)+(pow(a[1],2)))/4)*a[0],
// sqrt(1.-(pow(a[0],2)+(pow(a[1],2)))/4)*a[1],
// 1.-(pow(a[0],2)+pow(a[1],2))/2);
// 2.*a[0]/(1.+pow(a[0],2)+pow(a[1],2)),
// 2.*a[1]/(1.+pow(a[0],2)+pow(a[1],2)),
// (-1.0+pow(a[0],2)+pow(a[1],2))/(1.0+pow(a[0],2)+pow(a[1],2)));
// b = b.norm();
// b[2] = -b[2]; //this doeswn't want to change
// vecsUni.push_back(b);
// }
float PHI[2], Z[2], range;
PHI[0] = asin(solidAngle/2);
PHI[1] = asin(0);
Z[0] = cos(PHI[0]);
Z[1] = cos(PHI[1]);
range = Z[0] - Z[1];
float z, theta, phi;
std::vector<stim::vec3<float> > vecsUni;
for(int i = 0; i < numSamplesPos; i++)
{
stim::vec3<float> a(uniformRandom()*0.8, uniformRandom()*0.8, 0.0);
a[0] = a[0]-0.4;
a[1] = a[1]-0.4;
vecsUni.push_back(a);
}
stringstream name;
for(int i = 0; i < numSamplesPos; i++)
name << vecsUni[i].str() << std::endl;
std::ofstream outFile;
outFile.open("New_Pos_Vectors.txt");
outFile << name.str().c_str();
}
///@param solidAngle, the size of the arc to sample.
///Method for populating the vector arrays with sampled vectors.
///Objects created are rectangles the with the created directions.
///All points are sampled from a texture.
///Stored in a display list.
///uses the default d vector <0,0,1>
void
genDirectionVectors(float solidAngle = 5/M_PI*4)
{
//Set up the vectors necessary for Rectangle creation.
stim::vec3<float> Y(1.0,0.0,0.0); //orthogonal vec.
stim::vec3<float> pos(0.0,0.0,0.0);
stim::vec3<float> mag(1.0, 1.0, 1.0);
stim::vec3<float> dir(0.0, 0.0, 1.0);
float PHI[2], Z[2], range;
PHI[0] = solidAngle/2;
PHI[1] = asin(0);
Z[0] = cos(PHI[0]);
Z[1] = cos(PHI[1]);
range = Z[0] - Z[1];
float z, theta, phi;
glNewList(dList, GL_COMPILE);
for(int i = 0; i < numSamples; i++)
{
z = uniformRandom()*range + Z[1];
theta = uniformRandom()*2*M_PI;
phi = acos(z);
stim::vec3<float> sph(1, theta, phi);
stim::vec3<float> cart = sph.sph2cart();
dV.push_back(cart);
if(cos(Y.dot(cart)) < 0.087)
{
Y[0] = 0.0; Y[1] = 1.0;
}else{
Y[0] = 1.0; Y[1] = 0.0;
}
hor = stim::rect<float>(mag,
pos, cart,
((Y.cross(cart)).cross(cart)).norm());
ver = stim::rect<float>(mag,
pos, cart,
hor.n());
UpdateBuffer(0.0, 0.0+i*t_length);
}
glEndList();
}
///@param float delta, How much the rectangles vary in position.
///Method for populating the buffer with the sampled texture.
///Objects created are rectangles the with the created positions.
///All points are sampled from a texture.
///Stored in a display list.
///uses the default vector <0,0,0>
void
genPositionVectors(float delta = 0.4)
{
//Set up the vectors necessary for Rectangle creation.
stim::vec3<float> Y(1.0,0.0,0.0); //orthogonal vec.
stim::vec3<float> pos(0.0,0.0,0.0);
stim::vec3<float> mag(1.0, 1.0, 1.0);
stim::vec3<float> dir(0.0, 0.0, 1.0);
//Set up the variable necessary for vector creation.
glNewList(dList+1, GL_COMPILE);
for(int i = 0; i < numSamplesPos; i++)
{
stim::vec3<float> temp = uniformRandVector();
temp = temp*delta*2.0 - delta/2.0;
temp[2] = 0.0;
pV.push_back(temp);
hor = stim::rect<float>(mag,
temp, dir,
((Y.cross(d)).cross(d))
.norm());
ver = stim::rect<float>(mag,
temp, dir,
hor.n());
UpdateBuffer(0.0, 0.0+i*t_length);
}
glEndList();
}
///@param float delta, How much the rectangles are allowed to expand.
///Method for populating the buffer with the sampled texture.
///Objects created are rectangles the with the created sizes.
///All points are sampled from a texture.
///Stored in a display list.
///uses the default m <1,1,0>
void
genMagnitudeVectors(float delta = 0.70)
{
//Set up the vectors necessary for Rectangle creation.
stim::vec3<float> Y(1.0, 0.0, 0.0); //orthogonal vec.
stim::vec3<float> pos(0.0, 0.0, 0.0);
stim::vec3<float> mag(1.0, 1.0, 1.0);
stim::vec3<float> dir(0.0, 0.0, 1.0);
//Set up the variable necessary for vector creation.
int dim = (sqrt(numSamplesMag)-1)/2;
float min = 1.0-delta;
float max = 1.0+delta;
float step = (max-min)/(numSamplesMag-1);
float factor;
stim::vec3<float> temp(0.0,0.0,0.0);
glNewList(dList+2, GL_COMPILE);
for(int i = 0; i < numSamplesMag; i++){
//Create linear index
factor = (min+step*i)*mag[0];
temp = factor;
mV.push_back(temp);
hor = stim::rect<float>(temp,
pos, dir,
((Y.cross(d)).cross(d))
.norm());
ver = stim::rect<float>(temp,
pos, dir,
hor.n());
UpdateBuffer(0.0, 0.0+i*t_length);
CHECK_OPENGL_ERROR
}
glEndList();
}
///@param float v_x x-coordinate in buffer-space,
///@param float v_y y-coordinate in buffer-space.
///Samples the texture space.
///places a sample in the provided coordinates of bufferspace.
void
UpdateBuffer(float v_x, float v_y)
{
stim::vec3<float>p1;
stim::vec3<float>p2;
stim::vec3<float>p3;
stim::vec3<float>p4;
p1 = hor.p(1,1);
p2 = hor.p(1,0);
p3 = hor.p(0,0);
p4 = hor.p(0,1);
glBegin(GL_QUADS);
glTexCoord3f(
p1[0],
p1[1],
p1[2]
);
glVertex2f(v_x,v_y);
glTexCoord3f(
p2[0],
p2[1],
p2[2]
);
glVertex2f(v_x+t_length, v_y);
glTexCoord3f(
p3[0],
p3[1],
p3[2]
);
glVertex2f(v_x+t_length, v_y+t_length);
glTexCoord3f(
p4[0],
p4[1],
p4[2]
);
glVertex2f(v_x, v_y+t_length);
glEnd();
p1 = ver.p(1,1);
p2 = ver.p(1,0);
p3 = ver.p(0,0);
p4 = ver.p(0,1);
glBegin(GL_QUADS);
glTexCoord3f(
p1[0],
p1[1],
p1[2]
);
glVertex2f(v_x+t_length, v_y);
glTexCoord3f(
p2[0],
p2[1],
p2[2]
);
glVertex2f(v_x+2.0*t_length, v_y);
glTexCoord3f(
p3[0],
p3[1],
p3[2]
);
glVertex2f(v_x+2.0*t_length, v_y+t_length);
glTexCoord3f(
p4[0],
p4[1],
p4[2]
);
glVertex2f(v_x+t_length, v_y+t_length);
glEnd();
}
//--------------------------------------------------------------------------//
//--------------------------------GL METHODS--------------------------------//
//--------------------------------------------------------------------------//
///@param uint width sets the width of the buffer.
///@param uint height sets the height of the buffer.
///@param GLuint &textureID gives the texture ID of the texture to be initialized.
///@param GLuint &framebufferID gives the buffer ID of the texture to be initialized.
///Function for setting up the 2D buffer that stores the samples.
///Initiates and sets parameters.
void
GenerateFBO(unsigned int width, unsigned int height, GLuint &textureID, GLuint &framebufferID)
{
glDeleteFramebuffers(1, &framebufferID);
glGenFramebuffers(1, &framebufferID);
glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);
int numChannels = 1;
unsigned char* texels = new unsigned char[width * height * numChannels];
glGenTextures(1, &textureID);
glBindTexture(GL_TEXTURE_2D, textureID);
//Textures repeat and use linear interpolation, luminance format.
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_REPEAT);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_REPEAT);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
glTexImage2D(GL_TEXTURE_2D, 0, GL_LUMINANCE,
width, height, 0, GL_LUMINANCE, GL_UNSIGNED_BYTE, texels);
delete[] texels;
glBindFramebuffer(GL_FRAMEBUFFER, 0);
glBindTexture(GL_TEXTURE_2D, 0);
}
///@param uint width sets the width of the buffer.
///@param uint height sets the height of the buffer.
///Function for setting up the 2D buffer that stores the samples.
void
GenerateFBO(unsigned int width, unsigned int height)
{
glGenFramebuffers(1, &fboID);
glBindFramebuffer(GL_FRAMEBUFFER, fboID);
int numChannels = 1;
unsigned char* texels = new unsigned char[width * height * numChannels];
glGenTextures(1, &texbufferID);
glBindTexture(GL_TEXTURE_2D, texbufferID);
//Textures repeat and use linear interpolation, luminance format.
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_REPEAT);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_REPEAT);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
glTexImage2D(GL_TEXTURE_2D, 0, GL_LUMINANCE,
width, height, 0, GL_LUMINANCE, GL_UNSIGNED_BYTE, texels);
delete[] texels;
glBindFramebuffer(GL_FRAMEBUFFER, 0);
glBindTexture(GL_TEXTURE_2D, 0);
CHECK_OPENGL_ERROR
}
///IF type == 0
///Method for using the gl manipulation to align templates from
///Template space (-0.5 0.5) to Texture space (0.0, 1.0),
///Based on the p of the spider in real space (arbitrary).
///IF type == 1
///Method for using the gl manipulation to set up a matrix
///To transform from tissue space into texture space.
///All transformation happen in glMatrixMode(GL_TEXTURE).
///All transformation happen in glMatrixMode(GL_TEXTURE).
void setMatrix(int type = 0)
{
if(type == 0)
{
float curTrans[16]; //array to store the matrix values.
stim::vec<float> rot = getRotation(d); //get the rotation parameters for the current direction vector.
glMatrixMode(GL_TEXTURE);
glLoadIdentity();
//Scale by the voxel size and number of slices.
glScalef(1.0/S[0]/R[0], 1.0/S[1]/R[1], 1.0/S[2]/R[2]);
//translate to the current position of the spider in the texture.
glTranslatef(p[0],
p[1],
p[2]);
//rotate to the current direction of the spider.
glRotatef(rot[0], rot[1], rot[2], rot[3]);
//scale to the magnitude of the spider.
glScalef(m[0],
m[0],
m[0]);
//get and store the current transformation matrix for later use.
glGetFloatv(GL_TEXTURE_MATRIX, curTrans);
cT.set(curTrans);
// printTransform();
CHECK_OPENGL_ERROR
//revert back to default gl mode.
glMatrixMode(GL_MODELVIEW);
}
else if(type == 1)
{
glMatrixMode(GL_TEXTURE);
glLoadIdentity();
glScalef(1.0/S[0]/R[0], 1.0/S[1]/R[1], 1.0/S[2]/R[2]);
glMatrixMode(GL_MODELVIEW);
}
}
///Method for controling the buffer and texture binding.
///Clears the buffer upon binding.
void
Bind()
{
glBindFramebuffer(GL_FRAMEBUFFER, fboID);//set up GL buffer
glFramebufferTexture2D(
GL_FRAMEBUFFER,
GL_COLOR_ATTACHMENT0,
GL_TEXTURE_2D,
texbufferID,
0);
glBindFramebuffer(GL_FRAMEBUFFER, fboID);
GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0};
glDrawBuffers(1, DrawBuffers);
glBindTexture(GL_TEXTURE_2D, texbufferID);
glClearColor(1,1,1,1);
glClear(GL_COLOR_BUFFER_BIT);
glMatrixMode(GL_PROJECTION);
glLoadIdentity();
glMatrixMode(GL_MODELVIEW);
glLoadIdentity();
glViewport(0,0,2.0*t_length, numSamples*t_length);
gluOrtho2D(0.0,2.0*t_length,0.0,numSamples*t_length);
glEnable(GL_TEXTURE_3D);
glBindTexture(GL_TEXTURE_3D, texID);
CHECK_OPENGL_ERROR
}
///Method for controling the buffer and texture binding.
///Clears the buffer upon binding.
///@param GLuint &textureID, texture to be bound.
///@param GLuint &framebufferID, framebuffer used for storage.
///@param int nSamples, number of rectanges to create.
void
Bind(GLuint &textureID, GLuint &framebufferID, int nSamples, float len = 8.0)
{
glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);//set up GL buffer
glFramebufferTexture2D(
GL_FRAMEBUFFER,
GL_COLOR_ATTACHMENT0,
GL_TEXTURE_2D,
textureID,
0);
glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);
GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0};
glDrawBuffers(1, DrawBuffers);
glBindTexture(GL_TEXTURE_2D, textureID);
glMatrixMode(GL_PROJECTION);
glLoadIdentity();
glMatrixMode(GL_MODELVIEW);
glLoadIdentity();
glViewport(0,0,2.0*len, nSamples*len);
gluOrtho2D(0.0,2.0*len,0.0,nSamples*len);
glEnable(GL_TEXTURE_3D);
glBindTexture(GL_TEXTURE_3D, texID);
CHECK_OPENGL_ERROR
}
///Unbinds all texture resources.
void
Unbind()
{
//Finalize GL_buffer
glBindTexture(GL_TEXTURE_3D, 0);
CHECK_OPENGL_ERROR
glBindTexture(GL_TEXTURE_2D, 0);
CHECK_OPENGL_ERROR
glBindFramebuffer(GL_FRAMEBUFFER, 0);
CHECK_OPENGL_ERROR
glDisable(GL_TEXTURE_3D);
CHECK_OPENGL_ERROR
}
///Makes the spider take a step.
///starting with the current p, d, m, find the next optimal p, d, m.
///Performs the branch detection on each step.
int
StepP()
{
Bind();
CHECK_OPENGL_ERROR
#ifdef TESTING
start = std::clock();
#endif
findOptimalDirection();
findOptimalPosition();
findOptimalScale();
Unbind();
Bind(btexbufferID, bfboID, 27);
branchDetection();
Unbind();
#ifdef TESTING
duration_sampling = duration_sampling +
(std::clock() - start) / (double) CLOCKS_PER_SEC;
num_sampling = num_sampling + 1.0;
#endif
return current_cost;
}
//--------------------------------------------------------------------------//
//--------------------------------CUDA METHODS------------------------------//
//--------------------------------------------------------------------------//
///Entry-point into the cuda code for calculating the cost of a given samples array (in texture form)
///finds the minimum cost and sets the current_cost to that value.
/// and returns the index of the template with the minimal cost.
int
getCost()
{
#ifdef TESTING
start = std::clock();
#endif
stim::vec<int> cost =
stim::cuda::get_cost(texbufferID, GL_TEXTURE_2D, numSamples);
cudaDeviceSynchronize();
#ifdef TESTING
duration_cuda = duration_cuda +
(std::clock() - start) / (double) CLOCKS_PER_SEC;
num_cuda = num_cuda + 1.0;
#endif
current_cost = cost[1];
return cost[0];
}
int
getCost(GLuint tID, int n)
{
#ifdef TESTING
start = std::clock();
#endif
stim::vec<int> cost =
stim::cuda::get_cost(tID, GL_TEXTURE_2D, n, 2*t_length, t_length);
cudaDeviceSynchronize();
#ifdef TESTING
duration_cuda = duration_cuda +
(std::clock() - start) / (double) CLOCKS_PER_SEC;
num_cuda = num_cuda + 1.0;
#endif
current_cost = cost[1];
return cost[0];
}
public:
///ininializes the cuda device and environment.
void
initCuda()
{
stim::cudaSetDevice();
}
//horizonal rectangle forming the spider.
stim::rect<float> hor;
//vectical rectangle forming the spider.
stim::rect<float> ver;
//Testing and Timing variables.
#ifdef TESTING
std::clock_t start;
double duration_sampling = 0.0;
double duration_cuda = 0.0;
double num_sampling = 0.0;
double num_cuda = 0.0;
#endif
//--------------------------------------------------------------------------//
//-----------------------------CONSTRUCTORS---------------------------------//
//--------------------------------------------------------------------------//
///@param int samples, the number of samples this spider is going to use.
///Best results if samples is can create a perfect root.
///Default Constructor
gl_spider
(int samples = 1089, int samplespos = 441,int samplesmag = 144)
{
// std::cout << "I ran this constructor" << std::endl;
p = stim::vec3<float>(0.0, 0.0, 0.0);
d = stim::vec3<float>(0.0, 0.0, 1.0);
m = stim::vec<float>(1.0, 1.0);
S = stim::vec3<float>(1.0, 1.0, 1.0);
R = stim::vec3<float>(1.0, 1.0, 1.0);
// std::cout << samples << std::endl;
numSamples = samples;
// std::cout << numSamples << std::endl;
numSamplesPos = samplespos;
numSamplesMag = samplesmag;
}
///Position constructor: floats.
///@param float pos_x, position x.
///@param float pos_y, position y.
///@param float pos_z, position z.
///@param float dir_x, direction x.
///@param float dir_y, direction y.
///@param float dir_z, direction z.
///@param float mag_x, size of the vector.
///@param int samples, number of templates this spider is going to use.
gl_spider
(float pos_x, float pos_y, float pos_z, float dir_x, float dir_y, float dir_z,
float mag_x, int numsamples = 1089, int numsamplespos = 441, int numsamplesmag =144)
{
p = stim::vec3<float>(pos_x, pos_y, pos_z);
d = stim::vec3<float>(dir_x, dir_y, dir_z);
m = stim::vec<float>(mag_x, mag_x, mag_x);
S = stim::vec3<float>(1.0,1.0,1.0);
R = stim::vec3<float>(1.0,1.0,1.0);
numSamples = numsamples;
numSamplesPos = numsamplespos;
numSamplesMag = numsamplesmag;
}
///Position constructor: vecs of floats.
///@param stim::vec<float> pos, position.
///@param stim::vec<float> dir, direction.
///@param float mag, size of the vector.
///@param int samples, number of templates this spider is going to use.
gl_spider
(stim::vec3<float> pos, stim::vec3<float> dir, float mag, int samples = 1089, int samplesPos = 441, int samplesMag = 144)
{
p = pos;
d = dir;
m = vec<float>(mag, mag, mag);
S = vec3<float>(1.0,1.0,1.0);
R = vec3<float>(1.0,1.0,1.0);
numSamples = samples;
numSamplesPos = samplesPos;
numSamplesMag = samplesMag;
}
///destructor
~gl_spider
(void)
{
Unbind();
glDeleteTextures(1, &texbufferID);
glDeleteBuffers(1, &fboID);
glDeleteTextures(1, &ptexbufferID);
glDeleteBuffers(1, &pfboID);
glDeleteTextures(1, &mtexbufferID);
glDeleteBuffers(1, &mfboID);
glDeleteTextures(1, &btexbufferID);
glDeleteBuffers(1, &bfboID);
}
///@param GLuint id, texture that is going to be sampled.
///Attached the spider to the texture with the given GLuint ID.
///Samples in the default d acting as the init method.
///Also acts an init.
void
attachSpider(GLuint id)
{
srand(100);
texID = id;
//GenerateFBO(16, numSamples*8);
GenerateFBO(t_length*2, numSamples*t_length, texbufferID, fboID);
CHECK_OPENGL_ERROR
GenerateFBO(t_length*2, numSamplesPos*t_length, ptexbufferID, pfboID);
CHECK_OPENGL_ERROR
GenerateFBO(t_length*2, numSamplesMag*t_length, mtexbufferID, mfboID);
CHECK_OPENGL_ERROR
GenerateFBO(16, 216, btexbufferID, bfboID);
CHECK_OPENGL_ERROR
// setDims(0.6, 0.6, 1.0);
// setSize(1024.0, 1024.0, 1024.0);
setMatrix();
dList = glGenLists(3);
glListBase(dList);
Bind(texbufferID, fboID, numSamples, t_length);
genDirectionVectors(5*M_PI/4);
Unbind();
Bind(ptexbufferID, pfboID, numSamplesPos, t_length);
genPositionVectors();
Unbind();
Bind(mtexbufferID, mfboID, numSamplesMag, t_length);
genMagnitudeVectors();
Unbind();
Bind(btexbufferID, bfboID, 27);
DrawCylinder();
Unbind();
}
//--------------------------------------------------------------------------//
//-----------------------------ACCESS METHODS-------------------------------//
//--------------------------------------------------------------------------//
///Returns the p vector.
vec3<float>
getPosition()
{
return p;
}
///Returns the d vector.
vec3<float>
getDirection()
{
return d;
}
///Returns the m vector.
stim::vec<float>
getMagnitude()
{
return m;
}
///@param stim::vec<float> pos, the new p.
///Sets the p vector to input vector pos.
void
setPosition(stim::vec3<float> pos)
{
p = pos;
}
///@param float x x-coordinate.
///@param float y y-coordinate.
///@param float z z-coordinate.
///Sets the p vector to the input float coordinates x,y,z.
void
setPosition(float x, float y, float z)
{
p[0] = x;
p[1] = y;
p[2] = z;
}
///@param stim::vec<float> dir, the new d.
///Sets the d vector to input vector dir.
void
setDirection(stim::vec3<float> dir)
{
d = dir;
}
///@param stim::vec<float> x x-coordinate.
///@param stim::vec<float> y y-coordinate.
///@param stim::vec<float> z z-coordinate.
///Sets the d vector to the input float coordinates x,y,z.
void
setDirection(float x, float y, float z)
{
d[0] = x;
d[1] = y;
d[2] = z;
}
///@param stim::vec<float> dir, the new d.
///Sets the m vector to the input vector mag.
void
setMagnitude(stim::vec<float> mag)
{
m[0] = mag[0];
m[1] = mag[0];
}
///@param float mag, size of the sampled region.
///Sets the m vector to the input mag for both templates.
void
setMagnitude(float mag)
{
m[0] = mag;
m[1] = mag;
}
///@param float x, voxel size in the x direction.
///@param float y, voxel size in the y direction.
///@param float z, voxel size in the z direction.
///Sets the voxel sizes in each direction. necessary for non-standard data.
void
setDims(float x, float y, float z)
{
S[0] = x;
S[1] = y;
S[2] = z;
}
///@param stim::vec<float> Dims, voxel size.
///Sets the voxel sizes in each direction. necessary for non-standard data.
void
setDims(stim::vec3<float> Dims)
{
S = Dims;
}
///@param float x, size of the data in the x direction.
///@param float y, size of the data in the y direction.
///@param float z, size of the data in the z direction.
///Sets the data volume sizes in each direction.
void
setSize(float x, float y, float z)
{
R[0] = x;
R[1] = y;
R[2] = z;
}
///@param stim::vec<float> Dims, size of the volume.
///Sets the data volume sizes in each direction.
void
setSize(stim::vec3<float> Siz)
{
S = Siz;
}
///@param stim::vec<float> dir, the vector to which we are rotating.
///given a vector to align to, finds the required axis and angle for glRotatef.
///rotates from 0.0, 0.0, 1.0 to dir.
///return is in degrees for use with glRotatef.
stim::vec<float>
getRotation(stim::vec3<float> dir)
{
stim::vec<float> out(0.0,0.0,0.0,0.0);
stim::vec<float> from(0.0,0.0,1.0);
out[0] = acos(dir.dot(from))*180/M_PI;
if(out[0] < 1.0){
out[0] = 0.0;
out[1] = 0.0;
out[2] = 0.0;
out[3] = 1.0;
} else {
stim::vec<float> temp(0.0, 0.0, 0.0);;
stim::vec<float> dir1(dir[0], dir[1], dir[2]);
temp = (from.cross(dir1)).norm();
out[1] = temp[0];
out[2] = temp[1];
out[3] = temp[2];
}
return out;
}
///@param stim::vec<float> pos, the position of the seed to be added.
///Adds a seed to the seed list.
///Assumes that the coordinates passes are in tissue space.
void
setSeed(stim::vec3<float> pos)
{
seeds.push(pos);
}
///@param stim::vec<float> dir, the direction of the seed to be added.
///Adds a seed to the seed directions list.
void
setSeedVec(stim::vec3<float> dir)
{
seedsvecs.push(dir);
}
///@param float mag, the size of the seed to be added.
///Adds a seed to the seed list.
///Assumes that the coordinates passes are in tissue space.
void
setSeedMag(float mag)
{
// std::cout << "sMag: " << mag << std::endl;
seedsmags.push(mag);
}
///@param float x, x-position of the seed to be added.
///@param float y, y-position of the seed to be added.
///@param float z, z-position of the seed to be added.
///Adds a seed to the seed list.
///Assumes that the coordinates passes are in tissue space.
void
setSeed(float x, float y, float z)
{
// std::cout << "sPos: " << x << " " << y << " " << z << std::endl;
seeds.push(stim::vec<float>(x, y, z));
}
///@param float x, x-direction of the seed to be added.
///@param float y, y-direction of the seed to be added.
///@param float z, z-direction of the seed to be added.
///Adds a seed to the seed directions list.
void
setSeedVec(float x, float y, float z)
{
// std::cout << "sDir: " << x << " " << y << " " << z << std::endl;
seedsvecs.push(stim::vec<float>(x, y, z));
}
///Method to get the top of the seed positions stack.
stim::vec3<float>
getLastSeed()
{
stim::vec3<float> tp = seeds.top();
return tp;
}
///Method to get the top of the seed direction stack.
stim::vec3<float>
getLastSeedVec()
{
stim::vec3<float> tp = seedsvecs.top();
return tp;
}
///Method to get the top of the seed magnitude stack.
float
getLastSeedMag()
{
float tp = seedsmags.top();
return tp;
}
///deletes all data associated with the last seed.
void
popSeed()
{
seeds.pop();
seedsvecs.pop();
seedsmags.pop();
}
///returns the seeds position stack.
std::stack<stim::vec3<float> >
getSeeds()
{
return seeds;
}
///returns true if all seed stacks are empty, else false.
bool
Empty()
{
//return (seeds.empty() && seedsvecs.empty() && seedsmags.empty());
return (seeds.empty() && seedsvecs.empty());
}
///@param std::string file:file with variables to populate the seed stacks.
///Adds a seed to the seed list, including the position, direction and magnitude.
///Assumes that the coordinates passes are in tissue space.
void
setSeeds(std::string file)
{
std::ifstream myfile(file.c_str());
string line;
if(myfile.is_open())
{
while (getline(myfile, line))
{
float x, y, z, u, v, w, m;
myfile >> x >> y >> z >> u >> v >> w >> m;
setSeed(x, y, z);
setSeedVec(u, v, w);
setSeedMag(m);
}
myfile.close();
} else {
std::cerr<<"failed" << std::endl;
}
}
///Saves the network to a file.
void
saveNetwork(std::string name)
{
stim::glObj<float> sk;
for(int i = 0; i < nt.sizeE(); i++)
{
std::vector<stim::vec< float > > cm = nt.getEdgeCenterLineMag(i);
std::vector<stim::vec3< float > > ce = nt.getEdgeCenterLine(i);
sk.Begin(stim::OBJ_LINE);
for(int j = 0; j < ce.size(); j++)
{
sk.TexCoord(cm[j][0]);
sk.Vertex(ce[j][0], ce[j][1], ce[j][2]);
}
sk.End();
}
sk.save(name);
}
///Depreciated, but might be reused later()
///returns a COPY of the entire stim::glObj object.
stim::glObj<float>
getNetwork()
{
}
///returns a COPY of the entire stim::glnetwork object.
stim::glnetwork<T>
getGLNetwork()
{
return nt;
}
///Function to get back the framebuffer Object attached to the spider.
///For external access.
GLuint
getFB()
{
return bfboID;
}
//--------------------------------------------------------------------------//
//-----------------------------TEMPORARY METHODS----------------------------//
//--------------------------------------------------------------------------//
///temporary Method necessary for visualization and testing.
void
Update()
{
vec3<float> Y(1.0,0.0,0.0);
if(cos(Y.dot(d))< 0.087){
Y[0] = 0.0; Y[1] = 1.0;}
hor = stim::rect<float>(m, p, d.norm(),
((Y.cross(d)).cross(d)).norm());
ver = stim::rect<float>(m, p, d.norm(),
hor.n());
}
int
Step()
{
Bind(texbufferID, fboID, numSamples, t_length);
CHECK_OPENGL_ERROR
#ifdef TESTING
start = std::clock();
#endif
findOptimalDirection();
Unbind();
Bind(ptexbufferID, pfboID, numSamplesPos, t_length);
findOptimalPosition();
Unbind();
Bind(mtexbufferID, mfboID, numSamplesMag, t_length);
findOptimalScale();
Unbind();
CHECK_OPENGL_ERROR
#ifdef TESTING
duration_sampling = duration_sampling +
(std::clock() - start) / (double) CLOCKS_PER_SEC;
num_sampling = num_sampling + 1.0;
#endif
std::cout << current_cost << std::endl;
return current_cost;
}
void
printTransform()
{
std::cout << cT << std::endl;
}
//--------------------------------------------------------------------------//
//-----------------------------EXPERIMENTAL METHODS-------------------------//
//--------------------------------------------------------------------------//
void
DrawCylinder()
{
glNewList(dList+3, GL_COMPILE);
float z0 = -0.5; float z1 = 0.5; float r0 = 0.5;
float x,y;
float xold = 0.5; float yold = 0.0;
float step = 360.0/numSamples*32;
//float step = 360.0/8.0;
glEnable(GL_TEXTURE_3D);
glBindTexture(GL_TEXTURE_3D, texID);
glBegin(GL_QUAD_STRIP);
int j = 0;
for(float i = step; i <= 360.0; i += step)
{
x=r0*cos(i*2.0*M_PI/360.0);
y=r0*sin(i*2.0*M_PI/360.0);
glTexCoord3f(x,y,z0);
glVertex2f(0.0, j*6.4+6.4);
// glVertex2f(0.0, j*27.0+27.0);
glTexCoord3f(x,y,z1);
glVertex2f(16.0, j*6.4+6.4);
// glVertex2f(16.0, j*27.0+27.0);
glTexCoord3f(xold,yold,z1);
glVertex2f(16.0, j*6.4);
// glVertex2f(16.0, j*27.0);
glTexCoord3f(xold,yold,z0);
glVertex2f(0.0, j*6.4);
// glVertex2f(0.0, j*27.0);
xold=x;
yold=y;
j++;
}
glEnd();
glEndList();
}
///need to return the cylinder.
void
DrawLongCylinder(int n = 8, int l_template = 8,int l_square = 8)
{
int cylLen = cL.size()-1;
GenerateFBO(n*l_square, cylLen*l_template, btexbufferID, bfboID);
Bind(btexbufferID, bfboID, cylLen, l_template*l_square/2.0);
stim::cylinder<float> cyl(cL, cM);
std::vector<std::vector<stim::vec3<float> > > p = cyl.getPoints(n);
for(int i = 0; i < p.size()-1; i++) ///number of circles
{
for(int j = 0; j < p[0].size()-1; j++) ///points in the circle
{
glBegin(GL_QUADS);
glTexCoord3f(p[i][j][0], p[i][j][1], p[i][j][2]);
glVertex2f(j*l_square, i*(float)l_template);
glTexCoord3f(p[i][j+1][0], p[i][j+1][1], p[i][j+1][2]);
glVertex2f(j*l_square+l_square, i*(float)l_template);
glTexCoord3f(p[i+1][j+1][0], p[i+1][j+1][1], p[i+1][j+1][2]);
glVertex2f(j*l_square+l_square, i*(float)l_template+(float)l_template);
glTexCoord3f(p[i+1][j][0], p[i+1][j][1], p[i+1][j][2]);
glVertex2f(j*l_square,i*(float)l_template+(float)l_template);
glEnd();
}
}
Unbind();
}
///@param min_cost the cost value used for tracing
///traces out each seedpoint in the seeds queue to completion in both directions.
void
trace(int min_cost)
{
bool sEmpty = true;
float lastmag = 16.0;;
stim::vec3<float> curSeed;
stim::vec3<float> curSeedVec;
float curSeedMag;
while(!Empty())
{
//clear the currently traced line and start a new one.
cL.clear();
cM.clear();
cD.clear();
curSeed = seeds.top();
curSeedVec = seedsvecs.top();
curSeedMag = seedsmags.top();
seeds.pop();
seedsvecs.pop();
seedsmags.pop();
// std::cout << "The current seed Vector is " << curSeedVec << std::endl;
setPosition(curSeed);
setDirection(curSeedVec);
setMagnitude(curSeedMag);
// cL.push_back(curSeed);
// cM.push_back(curSeedMag);
// cD.push_back(curSeedMag);
pair<stim::fiber<float>, int> a = traceLine(p, m, min_cost);
}
}
int
selectObject(stim::vec3<float> loc, stim::vec3<float> dir, float mag)
{
//Define the varibles and turn on Selection Mode
float s = 3.0;
GLuint selectBuf[2048];
GLint hits;
glSelectBuffer(2048, selectBuf);
glDisable(GL_CULL_FACE);
(void) glRenderMode(GL_SELECT);
//Init Names stack
glInitNames();
glPushName(1);
CHECK_OPENGL_ERROR
//What would that vessel see in front of it.
camSel.setPosition(loc);
camSel.setFocalDistance(mag/s);
camSel.LookAt((loc[0]+dir[0]*mag/s),
(loc[1]+dir[1]*mag/s),
(loc[2]+dir[2]*mag/s));
ps = camSel.getPosition();
ups = camSel.getUp();
ds = camSel.getLookAt();
glMatrixMode(GL_PROJECTION);
glPushMatrix();
glLoadIdentity();
glOrtho(-mag/s/2.0, mag/s/2.0, -mag/s/2.0, mag/s/2.0, 0.0, mag/s/2.0);
glMatrixMode(GL_MODELVIEW);
glPushMatrix();
glLoadIdentity();
CHECK_OPENGL_ERROR
gluLookAt(ps[0], ps[1], ps[2],
ds[0], ds[1], ds[2],
ups[0], ups[1], ups[2]);
// sk.Render();
nt.Render();
CHECK_OPENGL_ERROR
// glLoadName((int) sk.numL());
glLoadName(nt.sizeE());
// sk.RenderLine(cL);
nt.RenderLine(cL);
// glPopName();
glFlush();
glMatrixMode(GL_PROJECTION);
glPopMatrix();
glMatrixMode(GL_MODELVIEW);
CHECK_OPENGL_ERROR
glPopMatrix();
// glEnable(GL_CULL_FACE);
hits = glRenderMode(GL_RENDER);
int found_hits = processHits(hits, selectBuf);
return found_hits;
}
//Given a size of the array (hits) and the memory holding it (buffer)
//returns whether a hit tool place or not.
int
processHits(GLint hits, GLuint buffer[])
{
GLuint names, *ptr;
//printf("hits = %u\n", hits);
ptr = (GLuint *) buffer;
// for (int i = 0; i < hits; i++) { /* for each hit */
names = *ptr;
// printf (" number of names for hit = %u\n", names);
ptr++;
ptr++; //Skip the minimum depth value.
ptr++; //Skip the maximum depth value.
// printf (" the name is ");
// for (int j = 0; j < names; j++) { /* for each name */
// printf ("%u ", *ptr); ptr++;
// }
// printf ("\n");
// }
if(hits == 0)
{
return -1;
}
else
{
// printf ("%u ", *ptr);
return *ptr;
}
}
void
clearCurrent()
{
cL.clear();
cM.clear();
}
void
addToNetwork(pair<stim::fiber<float>, int> in, stim::vec3<float> spos,
stim::vec<float> smag, stim::vec3<float> sdir)
{
std::vector<stim::vec3<float> > ce = in.first.centerline();
std::vector<stim::vec<float> > cm = in.first.centerlinemag();
//if the fiber is longer than 2 steps (the number it takes to diverge)
if(ce.size() > 3)
{
//if we did not hit a fiber
if(in.second == -1)
{
spos[0] = spos[0]-sdir[0]*smag[0]/2.;
spos[1] = spos[1]-sdir[1]*smag[0]/2.;
spos[2] = spos[2]-sdir[2]*smag[0]/2.;
int h = selectObject(spos, -sdir, smag[0]);
//did we start with a fiber?
if(h != -1 && h < nt.sizeE())
nt.addEdge(ce, cm, h, -1);
else
nt.addEdge(ce, cm, -1, -1);
}
//if we hit a fiber?
else if(in.second != -1)
{
nt.addEdge(ce,cm,-1, in.second);
spos[0] = spos[0]-sdir[0]*smag[0]/2.;
spos[1] = spos[1]-sdir[1]*smag[0]/2.;
spos[2] = spos[2]-sdir[2]*smag[0]/2.;
int h = selectObject(spos, -sdir, smag[0]);
//did start with a fiber?
if(h != -1 && h < nt.sizeE()){
// std::cout << "got here double" << smag.str() << std::endl;
nt.addEdge(ce,cm, h, in.second);
} else { nt.addEdge(ce,cm, -1, -1);}
}
}
}
void
printSizes()
{
std::cout << nt.sizeE() << " edges " << std::endl;
std::cout << nt.sizeV() << " nodes " << std::endl;
}
std::pair<stim::fiber<float>, int >
traceLine(stim::vec3<float> pos, stim::vec<float> mag, int min_cost)
{
//starting (seed) position and magnitude.
stim::vec3<float> spos = getPosition();
stim::vec<float> smag = getMagnitude();
stim::vec3<float> sdir = getDirection();
Bind();
// sk.Begin(stim::OBJ_LINE);
// sk.createFromSelf(GL_SELECT);
nt.createFromSelf(GL_SELECT);
cL.push_back(pos);
cM.push_back(mag);
// setPosition(pos);
// setMagnitude(mag);
int h;
bool started = false;
bool running = true;
stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
while(running)
{
int cost = Step();
if (cost > min_cost){
running = false;
// sk.End();
branchDetection2();
pair<stim::fiber<float>, int> a(stim::fiber<float> (cL, cM), -1);
addToNetwork(a, spos, smag, sdir);
// std::cout << "the cost of " << cost << " > " << min_cost << std::endl;
return a;
break;
} else {
//Have we found the edge of the map?
pos = getPosition();
if(pos[0] > size[0] || pos[1] > size[1]
|| pos[2] > size[2] || pos[0] < 0
|| pos[1] < 0 || pos[2] < 0)
{
running = false;
branchDetection2();
pair<stim::fiber<float>, int> a(stim::fiber<float> (cL, cM), -1);
addToNetwork(a, spos, smag, sdir);
// std::cout << "I hit and edge" << std::endl;
return a;
break;
}
//If this is the first step in the trace,
// save the direction
//(to be used later to trace the fiber in the opposite direction)
if(started == false){
rev = -getDirection();
started = true;
}
//Has the template size gotten unreasonable?
mag = getMagnitude();
if(mag[0] > 75 || mag[0] < 1){
running = false;
branchDetection2();
pair<stim::fiber<float>, int> a(stim::fiber<float> (cL, cM), -1);
addToNetwork(a, spos, smag, sdir);
// std::cout << "The templates are too big" << std::endl;
return a;
break;
}
else
{
h = selectObject(p, getDirection(), m[0]);
//Have we hit something previously traced?
if(h != -1){
// std::cout << "I hit the fiber " << h << std::endl;
running = false;
branchDetection2();
pair<stim::fiber<float>, int> a(stim::fiber<float> (cL, cM), h);
addToNetwork(a, spos, smag, sdir);
return a;
break;
}
else {
cL.push_back(stim::vec3<float>(p[0], p[1],p[2]));
cM.push_back(stim::vec<float>(m[0], m[0]));
// Bind(btexbufferID, bfboID, 27);
Unbind();
CHECK_OPENGL_ERROR
}
}
}
}
}
};
}
#endif