gl_spider.h
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#ifndef STIM_GL_SPIDER_H
#define STIM_GL_SPIDER_H
//#include <GL/glew.h>
///basic GL and Cuda libs
#include <GL/glut.h>
#include <cuda.h>
#include <cuda_gl_interop.h>
#include <cudaGL.h>
///stim .*h for gl tracking and visualization
#include <stim/gl/gl_texture.h>
#include <stim/gl/error.h>
#include <stim/visualization/camera.h>
#include <stim/math/matrix_sq.h>
#include <stim/cuda/spider_cost.cuh>
#include <stim/visualization/glObj.h>
#include <stim/cuda/cudatools/glbind.h>
///stim *.h for CUDA
#include <stim/cuda/cuda_texture.cuh>
#include <stim/cuda/cudatools.h>
///stim *.h for branch detection
#include <stim/visualization/cylinder.h>
#include <stim/cuda/branch_detection.cuh>
#include <stim/visualization/gl_network.h>
/// *.h for math
#include <math.h>
#include <stim/math/vector.h>
#include <stim/math/vec3.h>
#include <stim/math/rect.h>
#include <stim/math/constants.h>
#include <stim/cuda/arraymath.cuh>
#include <stim/math/random.h>
///c++ libs for everything
#include <vector>
#include <stack>
#include <iostream>
#include <fstream>
#ifdef TIMING
#include <ctime>
#include <cstdio>
#endif
#ifdef TESTING
#include <cstdio>
#include <ctime>
#endif
#ifdef DEBUG
#include <stim/cuda/testKernel.cuh>
#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:
#ifdef TIMING
double branch_time;// = 0;
double direction_time;// = 0;
double position_time;// = 0;
double size_time;// = 0;
double cost_time;// = 0;
double network_time;// = 0;
double hit_time;// = 0;
#endif
stim::vec3<float> p; //vector designating the position of the spider.
stim::vec3<float> d; //normalized direction of travel
float m; //size of the spider in tissue space.
std::vector<stim::vec3<float> > dV; //A list of all the direction vectors.
std::vector<stim::vec3<float> > pV; //A list of all test positions (relative to p)
std::vector<float> mV; //A list of all the size vectors.
std::vector<float> lV; //A list of all the size vectors.
stim::matrix_sq<float, 4> cT; //current Transformation matrix (tissue)->(texture)
GLuint texID; //OpenGL ID for the texture to be traced
stim::vec3<float> S; //Size of a voxel in the volume.
stim::vec3<float> R; //Dimensions of the volume.
//GL and Cuda variables
GLuint dList; //ID of the starting display lists (series of 4)
//dList + 0 = direction template rectangles
//dList + 1 = position template rectangles
//dList + 2 = size template rectangles
//dList + 3 = branch detection cylinder around the fiber
GLuint fboID; //framebuffer ID for direction templates
GLuint texbufferID; //texture ID for direction templates
GLuint direction_buffID; //framebuffer ID, position templates
GLuint direction_texID; //texture ID, position templates
GLuint position_buffID; //framebuffer ID, position templates
GLuint position_texID; //texture ID, position templates
GLuint radius_buffID; //framebuffer ID, radius templates
GLuint radius_texID; //texture ID, radius templates
GLuint length_buffID; //framebuffer ID, radius templates
GLuint length_texID; //texture ID, radius templates
GLuint cylinder_buffID; //framebuffer ID, cylinder (surrounding fiber)
GLuint cylinder_texID; //texture ID, cylinder
int numSamples; //The number of templates in the buffer.
int numSamplesPos;
int numSamplesMag;
float length; //this will be a function of the radius
float stepsize; //this will be a function of the length
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; //centerline up to the current point
std::vector< stim::vec3<float> > cD; //directions up to the current point (debugging)
std::vector< float > cM; //radius up to the current point
std::vector< float > cLen; //radius up to the current point
stim::gl_network<float> nt; //network object holding the currently traced centerlines
stim::glObj<float> sk; //OBJ file storing the network (identical to above)
//consider replacing with two seed points facing opposite directions
stim::vec<float> rev; //reverse vector
//selection mode - detecting fiber intersections
stim::camera camSel; //camera for selection mode (detecting collisions)
stim::vec3<float> ps; //position for the selection camera
stim::vec3<float> ups; //up direction for the selection camera
stim::vec3<float> ds; //direction for the selection camera
float n_pixels; //length of the template (in pixels)
//cuda texture variables that keep track of the binding.
stim::cuda::cuda_texture t_dir; //cuda_texture object used as an interface between OpenGL and cuda for direction vectors.
stim::cuda::cuda_texture t_pos; //cuda_texture object used as an interface between OpenGL and cuda for position vectors.
stim::cuda::cuda_texture t_mag; //cuda_texture object used as an interface between OpenGL and cuda for size vectors.
stim::cuda::cuda_texture t_len; //cuda_texture object used as an interface between OpenGL and cuda for size vectors.
int last_fiber; //variable that tracks the last fiber hit during tracing. -1 if no fiber was hit.
#ifdef DEBUG
int iter;
stringstream name;
int iter_pos;
int iter_dir;
int iter_siz;
#endif
//--------------------------------------------------------------------------//
//-------------------------------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()
{
#ifdef TIMING
gpuStartTimer(); //Timer for profiling
#endif
setMatrix(); //create the transformation matrix.
glCallList(dList); //move the templates to p, d, m.
glFinish(); //flush the pipeline
#ifdef TIMING
direction_time += gpuStopTimer(); //profiling
#endif
int best = getCost(t_dir.getTexture(), t_dir.getAuxArray() ,numSamples); //find min cost.
#ifdef DEBUG
name.str("");
name << "Final_Cost_Direction_fiber_"<< iter << "_" << iter_dir << ".bmp";
test(t_dir.getTexture(), n_pixels*2.0, numSamples*n_pixels, name.str());
iter_dir++;
#endif
stim::vec<float> next( ///calculate the 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(); ///transform the next vector into Tissue space.
setPosition( p[0]+next[0]*m/stepsize,
p[1]+next[1]*m/stepsize,
p[2]+next[2]*m/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()
{
#ifdef TIMING
gpuStartTimer(); //timer for profiling
#endif
setMatrix(); //create the transformation matrix.
glCallList(dList+1); //move the templates to p, d, m.
glFinish(); //flush the pipeline
// glFlush();
#ifdef TIMING
position_time += gpuStopTimer(); ///timer for profiling
#endif
int best = getCost(t_pos.getTexture(), t_pos.getAuxArray(), numSamplesPos); //find min cost.
#ifdef DEBUG
name.str("");
name << "Final_Cost_Position_" << iter << "_" << iter_pos << ".bmp";
test(t_pos.getTexture(), n_pixels*2.0, numSamplesPos*n_pixels, name.str());
iter_pos++;
#endif
stim::vec<float> next( //find next position.
pV[best][0],
pV[best][1],
pV[best][2],
1);
next = cT*next; //transform the next position vector into tissue space.
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
findOptimalRadius()
{
#ifdef TIMING
gpuStartTimer();
#endif
setMatrix(); //create the transformation.
glCallList(dList+2); //move the templates to p, d, m.
glFinish(); //flush the drawing pipeline.
#ifdef TIMING
size_time += gpuStopTimer();
#endif
int best = getCost(t_mag.getTexture(), t_mag.getAuxArray(), numSamplesMag); //get best cost.
#ifdef DEBUG
name.str("");
name << "Final_Cost_Size_" << iter << "_" << iter_siz << ".bmp";
test(t_mag.getTexture(), n_pixels*2.0, numSamplesMag*n_pixels, name.str());
iter_siz++;
#endif
setMagnitude(m*mV[best]); //adjust the magnitude.
}
/// Method for finding the best length for the spider.
/// changes the x, y, z size of the spider to minimize the cost
/// function.
void
findOptimalLength()
{
#ifdef TIMING
gpuStartTimer();
#endif
setMatrix(); //create the transformation.
glCallList(dList+3); //move the templates to p, d, m.
glFinish(); //flush the drawing pipeline.
#ifdef TIMING
size_time += gpuStopTimer();
#endif
int best = getCost(t_len.getTexture(), t_len.getAuxArray(), numSamplesMag); //get best cost.
#ifdef DEBUG
// name.str("");
// name << "Final_Cost_Size_" << iter << "_" << iter_siz << ".bmp";
// test(t_mag.getTexture(), n_pixels*2.0, numSamplesMag*n_pixels, name.str());
// iter_siz++;
#endif
setLength(mV[best]); //adjust the magnitude.
}
///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)
{
#ifdef TIMING
gpuStartTimer(); ///timer for performance analysis
#endif
if(cL.size() < 4){} ///if the size of the fiber is less then 4 we do nothing.
else{
setMatrix(1); ///finds the current transformation matrix
DrawLongCylinder(n, l_template, l_square); ///Draw the cylinder.
stim::cylinder<float> cyl(cL, cM);
std::vector< stim::vec<float> > result = find_branch(cylinder_texID, GL_TEXTURE_2D, n*l_square, (cL.size()-1)*l_template); ///find all the centers in cuda
stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]); ///the borders of the texture.
float pval; //pvalue associated with the points on the cylinder.
if(!result.empty()) ///if we have any points
{
for(int i = 0; i < result.size(); i++) ///for each point
{
int id = result[i][2];
if(fmod(result[i][2], id) != 0 && id != 0) ///if the remainer is odd
{
pval = ((cyl.getl(id+1)-cyl.getl(id))*
(fmod(result[i][2], id))+cyl.getl(id))/cyl.getl(cL.size()-1); ///calculate pvalue
}
else if(id == 0) ///if the point is on the edge
{
pval = (cyl.getl(id+1)*result[i][2])/cyl.getl(cL.size()-1);
}
else
{
pval = (cyl.getl(id)/cyl.getl(cL.size()-1)); ///if the point is somewhere on the surface of the cylinder other than the edge
}
stim::vec3<float> v = cyl.surf(pval, result[i][0]); ///find the coordinates of the point at pval on the surface in tissue space.
stim::vec3<float> di = cyl.p(pval); ///find the coord of v in tissue space projected on the centerline.
float rad = cyl.r(pval); ///find the radius at the pvalue's location
// float rad = cyl.r(pval)/2; ///find the radius at the pvalue's location
if(
!(v[0] > size[0] || v[1] > size[1]
|| v[2] > size[2] || v[0] < 0
|| v[1] < 0 || v[2] < 0)) ///if the v point is INSIDE the volume
{
setSeed(v); ///add a seedpoint's position.
setSeedVec((v-di).norm()); ///add a seedpoints direction
setSeedMag(rad); ///add the starting radius.
}
}
}
}
#ifdef TIMING
branch_time += gpuStopTimer(); ///timer for performance.
#endif
}
float uniformRandom()
{
return ( (float)(rand()))/( (float)(RAND_MAX)); ///generates a random number between 0 and 1 using the uniform distribution.
}
float normalRandom()
{
float u1 = uniformRandom();
float u2 = uniformRandom();
return cos(2.0*atan(1.0)*u2)*sqrt(-1.0*log(u1)); ///generate a random number using the normal distribution between 0 and 1.
}
stim::vec3<float> uniformRandVector()
{
stim::vec3<float> r(uniformRandom(), uniformRandom(), 1.0); ///generate a random vector using the uniform distribution between 0 and 1.
return r;
}
stim::vec3<float> normalRandVector()
{
stim::vec3<float> r(normalRandom(), normalRandom(), 1.0); ///generate a random vector using the normal distribution between 0 and 1.
return r;
}
//--------------------------------------------------------------------------//
//---------------------TEMPLATE CREATION METHODS----------------------------//
//--------------------------------------------------------------------------//
///@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 = 3*stim::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); //center point of a rectangle
float mag = 1.0; //size of the generated rectangle.
stim::vec3<float> dir(0.0, 0.0, 1.0); //normal of the rectangle
float PHI[2], Z[2], range;
PHI[0] = solidAngle/2; ///Project the solid angle into spherical coordinates
PHI[1] = asin(0);
Z[0] = cos(PHI[0]); ///Project the z into spherical coordinates
Z[1] = cos(PHI[1]);
range = Z[0] - Z[1]; ///The range the possible values can be.
float z, theta, phi;
glNewList(dList, GL_COMPILE); ///create a display list of all the direction templates.
for(int i = 0; i < numSamples; i++) ///for each sample
{
z = uniformRandom()*range + Z[1]; ///generate a z coordinate
theta = uniformRandom()*stim::TAU; ///generate a theta coordinate
phi = acos(z); ///generate a phi from the z.
stim::vec3<float> sph(1, theta, phi); ///combine into a vector in spherical coordinates.
stim::vec3<float> cart = sph.sph2cart();///convert to cartesian.
dV.push_back(cart); ///save the generated vector for further use.
#ifdef DEBUG
// std::cout << cart << std::endl;
#endif
if(cos(Y.dot(cart)) < 0.087) ///make sure that the Y is not parallel to the new vector.
{
Y[0] = 0.0; Y[1] = 1.0;
}else{
Y[0] = 1.0; Y[1] = 0.0;
}
hor = stim::rect<float>(mag, ///generate a rectangle with the new vectro as a normal.
pos, cart,
((Y.cross(cart)).cross(cart)).norm());
#ifdef DEBUG
// std::cout << hor.n() << std::endl;
#endif
ver = stim::rect<float>(mag, ///generate another rectangle that's perpendicular the first but parallel to the cart vector.
pos, cart,
hor.n());
UpdateBuffer(0.0, 0.0+i*n_pixels); ///Put the necessary points into the diplaylist.
}
glEndList(); ///finilize the display list.
}
///@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); //center point of a rectangle
float mag = 1.0; ///size of each rectangle
stim::vec3<float> dir(0.0, 0.0, 1.0); ///normal of the rectangle plane.
//Set up the variable necessary for vector creation.
glNewList(dList+1, GL_COMPILE); ///generate a new display list.
pV.push_back(pos);
hor = stim::rect<float>(mag, ///generate a rec tangle with the new vector as a normal.
pos, dir,
((Y.cross(d)).cross(d))
.norm());
ver = stim::rect<float>(mag, ///generate anoth er rectangle that's perpendicular the first but parallel to the cart vector.
pos, dir,
hor.n());
///The first vector is always in the center.
UpdateBuffer(0.0, 0.0+0*n_pixels);
for(int i = 1; i < numSamplesPos; i++) ///for the number of position samples
{
stim::vec3<float> temp = uniformRandVector(); ///generate a random point on a plane.
temp[0] = temp[0]*delta;
temp[1] = temp[1]*2*stim::PI;
temp[2] = 0.0;
temp = temp.cyl2cart();
pV.push_back(temp); ///save the point for further use.
hor = stim::rect<float>(mag, ///generate a rectangle with the new vector as a normal.
temp, dir,
((Y.cross(d)).cross(d))
.norm());
ver = stim::rect<float>(mag, ///generate another rectangle that's perpendicular the first but parallel to the cart vector.
temp, dir,
hor.n());
UpdateBuffer(0.0, 0.0+i*n_pixels); ///sample the necessary points and put them into a display list.
}
glEndList(); ///finilize the display list.
#ifdef DEBUG
for(int i = 0; i < numSamplesPos; i++)
std::cout << pV[i].str() << std::endl;
#endif
}
///@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); //center of the future rect.
float mag = 1.0; ///size of the rectangle
stim::vec3<float> dir(0.0, 0.0, 1.0); ///normal of the rectangle plane.
//Set up the variable necessary for vector creation.
float min = 1.0-delta; ///smallest size
float max = 1.0+delta; ///largers size.
float step = (max-min)/(numSamplesMag-1); ///the size variation from one rect to the next.
float factor;
glNewList(dList+2, GL_COMPILE);
for(int i = 0; i < numSamplesMag; i++){ ///for the number of position samples
//Create linear index
factor = (min+step*i)*mag; ///scaling factor
mV.push_back(factor); ///save the size factor for further use.
hor = stim::rect<float>(factor, ///generate a rectangle with the new vector as a normal.
pos, dir,
((Y.cross(d)).cross(d))
.norm());
ver = stim::rect<float>(factor, ///generate another rectangle that's perpendicular the first but parallel to the cart vector.
pos, dir,
hor.n());
UpdateBuffer(0.0, 0.0+i*n_pixels); ///sample the necessary points and put them into a display list.
CHECK_OPENGL_ERROR
}
glEndList(); ///finilize the displaylist.
}
///@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
genLengthVectors(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); //center of the future rect.
float mag = 1.0; ///size of the rectangle
stim::vec3<float> dir(0.0, 0.0, 1.0); ///normal of the rectangle plane.
stim::vec<float> temp(0.0,0.0,0.0);
//Set up the variable necessary for vector creation.
float min = 1.0-delta; ///smallest size
float max = 1.0+delta; ///largers size.
float step = (max-min)/(numSamplesMag-1); ///the size variation from one rect to the next.
float factor;
glNewList(dList+3, GL_COMPILE);
for(int i = 0; i < numSamplesMag; i++){ ///for the number of position samples
//Create linear index
factor = (min+step*i)*mag; ///scaling factor
lV.push_back(factor); ///save the size factor for further use.
temp[0] = factor;
temp[1] = mag;
hor = stim::rect<float>(temp, ///generate a rectangle with the new vector as a normal.
pos, dir,
((Y.cross(d)).cross(d))
.norm());
ver = stim::rect<float>(temp, ///generate another rectangle that's perpendicular the first but parallel to the cart vector.
pos, dir,
hor.n());
UpdateBuffer(0.0, 0.0+i*n_pixels); ///sample the necessary points and put them into a display list.
CHECK_OPENGL_ERROR
}
glEndList(); ///finilize the displaylist.
}
///@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; ///first point.
stim::vec3<float>p2; ///second point.
stim::vec3<float>p3; ///third point.
stim::vec3<float>p4; ///fourth point.
p1 = hor.p(1,1); ///generate the top right point from the horizontal template.
p2 = hor.p(1,0); ///generate the bottom right point from the horizonatal template.
p3 = hor.p(0,0); ///generate the bottom left point from the horizontal template.
p4 = hor.p(0,1); ///generate the top left point from the horizonatal template.
glBegin(GL_QUADS); ///generate the Quad from the 4 points.
glTexCoord3f(
p1[0],
p1[1],
p1[2]
);
glVertex2f(v_x,v_y);
glTexCoord3f(
p2[0],
p2[1],
p2[2]
);
glVertex2f(v_x+n_pixels, v_y);
glTexCoord3f(
p3[0],
p3[1],
p3[2]
);
glVertex2f(v_x+n_pixels, v_y+n_pixels);
glTexCoord3f(
p4[0],
p4[1],
p4[2]
);
glVertex2f(v_x, v_y+n_pixels);
glEnd(); ///finish the quad.
p1 = ver.p(1,1); ///generate the top right point from the vertical template.
p2 = ver.p(1,0); ///generate the bottom right point from the vertical template.
p3 = ver.p(0,0); ///generate the bottom left point from the vertical template.
p4 = ver.p(0,1); ///generate the top left point from the vertical template.
glBegin(GL_QUADS); ///generate the Quad from the 4 points.
glTexCoord3f(
p1[0],
p1[1],
p1[2]
);
glVertex2f(v_x+n_pixels, v_y);
glTexCoord3f(
p2[0],
p2[1],
p2[2]
);
glVertex2f(v_x+2.0*n_pixels, v_y);
glTexCoord3f(
p3[0],
p3[1],
p3[2]
);
glVertex2f(v_x+2.0*n_pixels, v_y+n_pixels);
glTexCoord3f(
p4[0],
p4[1],
p4[2]
);
glVertex2f(v_x+n_pixels, v_y+n_pixels);
glEnd(); ///finish the quad.
}
//--------------------------------------------------------------------------//
//--------------------------------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); ///clear the framebuffer.
glGenFramebuffers(1, &framebufferID); ///generate a clean buffer.
glBindFramebuffer(GL_FRAMEBUFFER, framebufferID); ///bind the new buffer.
// int numChannels = 1;
// unsigned char* texels = new unsigned char[width * height * numChannels];
glGenTextures(1, &textureID); ///generate a texture that will attach to the buffer.
glBindTexture(GL_TEXTURE_2D, textureID);
//Textures repeat and use linear interpolation, luminance format.
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_BORDER); ///Set up the texture to repeat at edges.
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_BORDER);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR); ///Set up the texture to use Linear interpolation
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
glTexImage2D(GL_TEXTURE_2D, 0, GL_LUMINANCE, ///Create the texture with no data.
width, height, 0, GL_LUMINANCE, GL_UNSIGNED_BYTE, NULL);
// delete[] texels;
glBindFramebuffer(GL_FRAMEBUFFER, 0); ///Bind the frontbuffer
glBindTexture(GL_TEXTURE_2D, 0); ///Unbind the texture.
}
///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,
m,
m);
//get and store the current transformation matrix for later use.
glGetFloatv(GL_TEXTURE_MATRIX, curTrans);
cT.set(curTrans);
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, direction_buffID);//set up GL buffer
glFramebufferTexture2D(
GL_FRAMEBUFFER,
GL_COLOR_ATTACHMENT0,
GL_TEXTURE_2D,
direction_texID,
0); ///Bind the texture to the 0th color attachement of the framebuffer
glBindFramebuffer(GL_FRAMEBUFFER, direction_buffID); ///Bind the buffer again (safety operation).
GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0}; ///Designate the texture to be the drawbuffer of the framebuffer
glDrawBuffers(1, DrawBuffers); ///Set the current drawbuffer to the texture.
glBindTexture(GL_TEXTURE_2D, direction_texID); ///Bind the Texture
glClearColor(1,1,1,1); ///Set clear color to white
glClear(GL_COLOR_BUFFER_BIT); ///Clear the texture
glMatrixMode(GL_PROJECTION);
glLoadIdentity();
glMatrixMode(GL_MODELVIEW);
glLoadIdentity(); ///Load identity matrix into the projection and modelview
glViewport(0,0,2.0*n_pixels, numSamples*n_pixels); ///Designate the viewport and orth
gluOrtho2D(0.0,2.0*n_pixels,0.0,numSamples*n_pixels);
glEnable(GL_TEXTURE_3D);
glBindTexture(GL_TEXTURE_3D, texID); ///Bind the larger 3D texture.
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); ///Bind the framebuffer.
glFramebufferTexture2D( ///associate it with the texture
GL_FRAMEBUFFER,
GL_COLOR_ATTACHMENT0,
GL_TEXTURE_2D,
textureID,
0);
glBindFramebuffer(GL_FRAMEBUFFER, framebufferID); ///Bind the framebuffer.
GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0}; ///generate the drawbuffer.
glDrawBuffers(1, DrawBuffers); ///set the drawbuffer.
glBindTexture(GL_TEXTURE_2D, textureID); ///Bind the texture passed.
glMatrixMode(GL_PROJECTION); ///clear out the draw matrices
glLoadIdentity();
glMatrixMode(GL_MODELVIEW);
glLoadIdentity();
glViewport(0,0,2.0*len, nSamples*len); ///set up viewport
gluOrtho2D(0.0,2.0*len,0.0,nSamples*len); ///Set up ortho
glEnable(GL_TEXTURE_3D);
glBindTexture(GL_TEXTURE_3D, texID); ///bind the main texture (return to original state).
CHECK_OPENGL_ERROR
}
///Unbinds all texture resources.
void
Unbind()
{
//Finalize GL_buffer
glBindTexture(GL_TEXTURE_3D, 0); ///Bind the front buffer.
CHECK_OPENGL_ERROR
glBindTexture(GL_TEXTURE_2D, 0); ///Bind the default GL texture.
CHECK_OPENGL_ERROR
glBindFramebuffer(GL_FRAMEBUFFER, 0); ///Bind the defautl framebuffer.
CHECK_OPENGL_ERROR
glDisable(GL_TEXTURE_3D); ///Turn off texturing.
CHECK_OPENGL_ERROR
}
//--------------------------------------------------------------------------//
//--------------------------------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(cudaTextureObject_t tObj, float* result, int n)
{
#ifdef TIMING
gpuStartTimer(); ///Add timing variables
#endif
stim::vec<int> cost =
stim::cuda::get_cost(tObj, result, n, 2*n_pixels, n_pixels); ///call the cuda function with the appropriate texture buffer.
#ifdef TIMING
cost_time += gpuStopTimer();
#endif
current_cost = cost[1]; ///current cost.
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;
//Timing variables.
//--------------------------------------------------------------------------//
//-----------------------------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)
{
p = stim::vec3<float>(0.0, 0.0, 0.0);
d = stim::vec3<float>(0.0, 0.0, 1.0);
m = 1.0;
S = stim::vec3<float>(1.0, 1.0, 1.0);
R = stim::vec3<float>(1.0, 1.0, 1.0);
numSamples = samples;
numSamplesPos = samplespos;
numSamplesMag = samplesmag;
#ifdef DEBUG
iter = 0;
iter_pos = 0;
iter_dir = 0;
iter_siz = 0;
#endif
}
///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 = 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;
#ifdef DEBUG
iter = 0;
iter_pos = 0;
iter_dir = 0;
iter_siz = 0;
#endif
}
///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 = 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;
#ifdef DEBUG
iter = 0;
iter_pos = 0;
iter_dir = 0;
iter_siz = 0;
#endif
}
///destructor deletes all the texture and buffer objects.
~gl_spider
(void)
{
Unbind();
glDeleteTextures(1, &direction_texID);
glDeleteBuffers(1, &direction_buffID);
glDeleteTextures(1, &position_texID);
glDeleteBuffers(1, &position_buffID);
glDeleteTextures(1, &radius_texID);
glDeleteBuffers(1, &radius_buffID);
glDeleteTextures(1, &length_texID);
glDeleteBuffers(1, &length_buffID);
glDeleteTextures(1, &cylinder_texID);
glDeleteBuffers(1, &cylinder_buffID);
}
///@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)
{
#ifdef TIMING
branch_time = 0;
direction_time = 0;
position_time = 0;
size_time = 0;
cost_time = 0;
network_time = 0;
hit_time = 0;
#endif
#ifdef DEBUG
iter = 0;
iter_pos = 0;
iter_dir = 0;
iter_siz = 0;
#endif
stepsize = 6.0;
n_pixels = 16.0;
srand(100);
texID = id;
GenerateFBO(n_pixels*2, numSamples*n_pixels, direction_texID, direction_buffID);
CHECK_OPENGL_ERROR
GenerateFBO(n_pixels*2, numSamplesPos*n_pixels, position_texID, position_buffID);
CHECK_OPENGL_ERROR
GenerateFBO(n_pixels*2, numSamplesMag*n_pixels, radius_texID, radius_buffID);
CHECK_OPENGL_ERROR
GenerateFBO(n_pixels*2, numSamplesMag*n_pixels, length_texID, length_buffID);
CHECK_OPENGL_ERROR
GenerateFBO(16, 216, cylinder_texID, cylinder_buffID);
CHECK_OPENGL_ERROR
t_dir.MapCudaTexture(direction_texID, GL_TEXTURE_2D);
t_dir.Alloc(numSamples);
t_pos.MapCudaTexture(position_texID, GL_TEXTURE_2D);
t_pos.Alloc(numSamplesPos);
t_mag.MapCudaTexture(radius_texID, GL_TEXTURE_2D);
t_mag.Alloc(numSamplesMag);
t_len.MapCudaTexture(length_texID, GL_TEXTURE_2D);
t_len.Alloc(numSamplesMag);
setMatrix();
dList = glGenLists(4);
glListBase(dList);
Bind(direction_texID, direction_buffID, numSamples, n_pixels);
genDirectionVectors(5*stim::PI/4);
Unbind();
Bind(position_texID, position_buffID, numSamplesPos, n_pixels);
genPositionVectors(0.2);
Unbind();
Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
genMagnitudeVectors();
Unbind();
Bind(length_texID, length_buffID, numSamplesMag, n_pixels);
genLengthVectors();
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.
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 float mag, size of the sampled region.
///Sets the m value to the input mag for both templates.
void
setMagnitude(float mag)
{
m = mag;
}
///@param float len, length of the sampled region.
///Sets the length value to the input len for both templates.
void
setLength(float len)
{
length = len;
}
///@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); ///The 4D rotation matrix for GL rotation
stim::vec3<float> from(0.0,0.0,1.0); ///Converting from template always involves 0,0,1 as a starting vector
out[0] = acos(dir.dot(from))*180/stim::PI; ///angle of rotation
if(out[0] < 1.0){
out[0] = 0.0;
out[1] = 0.0;
out[2] = 0.0;
out[3] = 1.0;
} ///if we rotate less what one degree don't rotate
else if(out[0] < -179.0) ///if we rotate more than -179 degrees rotate 180.
{
out[0] = 180.0;
out[1] = 1.0;
out[2] = 0.0;
out[3] = 0.0;
} else { ///the rotational axis is the cross fromxdir.
stim::vec3<float> temp(0.0, 0.0, 0.0);;
temp = (from.cross(dir)).norm();
out[1] = temp[0];
out[2] = temp[1];
out[3] = temp[2];
}
#ifdef DEBUG
std::cout << "out is " << out.str() << std::endl;
std::cout << "when rotating from " << from.str() << " to " << dir.str() << std::endl;
#endif
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)
{
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)
{
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)
{
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;
}
///sets the number of direction templates.
void
setNumberDirectionTemplates(int n)
{
numSamples = n;
}
///sets the number of position templates.
void
setNumberPositionTemplates(int n)
{
numSamplesPos = n;
}
///sets the number of position templates.
void
setNumberSizeTemplates(int n)
{
numSamplesMag = n;
}
#ifdef TIMING
///Returns the timings at the moment the method is called.
///In the following order: Branch, Direction, Position, Size, Cost, Network, Hit_detetion.
std::vector<double>
getTimings()
{
std::vector <double> ret;
ret.resize(7);
ret[0] = branch_time;
ret[1] = direction_time;
ret[2] = position_time;
ret[3] = size_time;
ret[4] = cost_time;
ret[5] = network_time;
ret[6] = hit_time;
return ret;
}
#endif
///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()); ///open a stream
string line;
if(myfile.is_open())
{
while (getline(myfile, line))
{
float x, y, z, u, v, w, m; ///read the xyz uvw and m coordinates.
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, int xoffset = 0, int yoffset = 0, int zoffset = 0)
{
stim::glObj<float> sk1;
for(int i = 0; i < nt.sizeE(); i++)
{
std::vector<float> cm = nt.getEdgeCenterLineMag(i);
std::vector<stim::vec3< float > > ce = nt.getEdgeCenterLine(i);
sk1.Begin(stim::OBJ_LINE);
for(int j = 0; j < ce.size(); j++)
{
sk1.TexCoord(cm[j]);
sk1.Vertex(ce[j][0]+xoffset, ce[j][1]+yoffset, ce[j][2]+zoffset);
}
sk1.End();
}
sk1.save(name);
}
///Depreciated, but might be reused later()
///returns a COPY of the entire stim::glObj object.
stim::glObj<float>
getNetwork()
{
return sk;
}
///returns a COPY of the entire stim::glnetwork object.
stim::gl_network<T>
getGLNetwork()
{
return nt;
}
///Function to get back the framebuffer Object attached to the spider.
///For external access.
GLuint
getFB()
{
return cylinder_buffID;
}
//--------------------------------------------------------------------------//
//-----------------------------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()
{
#ifdef DEBUG
std::cerr << "Took a step";
#endif
Bind(direction_texID, direction_buffID, numSamples, n_pixels);
CHECK_OPENGL_ERROR
findOptimalDirection();
Unbind();
#ifdef DEBUG
std::cerr << " " << current_cost;
#endif
Bind(position_texID, position_buffID, numSamplesPos, n_pixels);
findOptimalPosition();
Unbind();
#ifdef DEBUG
std::cerr << " " << current_cost;
#endif
Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
findOptimalRadius();
Unbind();
#ifdef DEBUG
std::cerr << " " << current_cost;
#endif
CHECK_OPENGL_ERROR
#ifdef DEBUG
std::cerr << std::endl;
#endif
return current_cost;
}
void
printTransform()
{
std::cout << cT << std::endl;
}
//--------------------------------------------------------------------------//
//-----------------------------EXPERIMENTAL METHODS-------------------------//
//--------------------------------------------------------------------------//
void
MonteCarloDirectionVectors(int nSamples, float solidAngle = stim::TAU)
{
// 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];
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();
}
/*
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*stim::TAU/360.0);
y=r0*sin(i*stim::TAU/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.
///SOMETHING MIGHT BE GOING ON HERE IN GENERATE BUFFER.
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, cylinder_texID, cylinder_buffID);
Bind(cylinder_texID, cylinder_buffID, 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)
{
stim::vec3<float> curSeed;
stim::vec3<float> curSeedVec;
float curSeedMag;
while(!Empty())
{
//clear the currently traced line and start a new one.
curSeed = seeds.top();
curSeedVec = seedsvecs.top();
curSeedMag = seedsmags.top();
seeds.pop();
seedsvecs.pop();
seedsmags.pop();
setPosition(curSeed);
setDirection(curSeedVec);
setMagnitude(curSeedMag);
#ifdef DEBUG
std::cout << "The new seed " << curSeed.str() << curSeedVec.str() << curSeedMag << std::endl;
#endif
// Bind(direction_texID, direction_buffID, numSamples, n_pixels);
// CHECK_OPENGL_ERROR
// findOptimalDirection();
// Unbind();
//THIS IS EXPERIMENTAL
// Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
// findOptimalRadius();
// Unbind();
//THIS IS EXPERIMENTAL
// cL.push_back(curSeed);
// cM.push_back(curSeedMag);
// cD.push_back(curSeedMag);
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
#ifdef TIMING
gpuStartTimer();
#endif
GLuint selectBuf[2048]; ///size of the selection buffer in bytes.
GLint hits; ///hit fibers
glSelectBuffer(2048, selectBuf); ///bind the selection mode to the selection buffer.
glDisable(GL_CULL_FACE); ///Disable cullFace
(void) glRenderMode(GL_SELECT); ///initialize GL select mode.
//Init Names stack
glInitNames(); ///Initialize the naming array.
glPushName(1); ///Push a single name to the stack.
CHECK_OPENGL_ERROR
//What would that vessel see in front of it.
camSel.setPosition(loc); ///Set the viewing camera
camSel.setFocalDistance(mag/stepsize); ///Set how far the fiber looks forward.
camSel.LookAt((loc[0]+dir[0]*mag/stepsize),
(loc[1]+dir[1]*mag/stepsize),
(loc[2]+dir[2]*mag/stepsize)); ///Set the look direction
ps = camSel.getPosition(); ///get all the necessary rotation variable for openGL
ups = camSel.getUp();
ds = camSel.getLookAt();
glMatrixMode(GL_PROJECTION); ///Push the projection matrix.
glPushMatrix(); ///Reset the current projection matrix
glLoadIdentity();
glOrtho(-mag/stepsize/2.0, mag/stepsize/2.0, -mag/stepsize/2.0, mag/stepsize/2.0, 0.0, mag/stepsize/2.0); ///Finalize the look paramenters
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]);
///Set the look at distance
// sk.Render(); ///Render the network
nt.Render();
CHECK_OPENGL_ERROR
// glLoadName((int) sk.numL()); ///Load all the names
glLoadName(nt.sizeE());
// sk.RenderLine(cL); ///Render the current line.
nt.RenderLine(cL);
// glPopName();
glFlush(); ///Flush the buffer
glMatrixMode(GL_PROJECTION);
glPopMatrix();
glMatrixMode(GL_MODELVIEW);
CHECK_OPENGL_ERROR
glPopMatrix(); ///clear the vis matrices and pop the matrix
// glEnable(GL_CULL_FACE);
hits = glRenderMode(GL_RENDER); ///Check for hits.
int found_hits = processHits(hits, selectBuf); ///Process the hits.
#ifdef TIMING
hit_time += gpuStopTimer();
#endif
return found_hits; ///return whether we hit something or not.
}
//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 *ptr; ///pointer to the detection buffer
ptr = (GLuint *) buffer;
ptr++;
ptr++; //Skip the minimum depth value.
ptr++; //Skip the maximum depth value.
if(hits == 0)
{
return -1;
}
else
{
// printf ("%u ", *ptr);
return *ptr;
}
}
void
clearCurrent()
{
cL.clear();
cM.clear();
}
void
addToNetwork(std::vector<stim::vec3<float> > L, std::vector<float > M, stim::vec3<float> spos, stim::vec3<float> sdir, float smag)
{
//if the fiber is longer than 2 steps (the number it takes to diverge)
if(L.size() > 3)
{
//if we did not hit a fiber
if(last_fiber == -1)
{
spos[0] = spos[0]-sdir[0]*smag;
spos[1] = spos[1]-sdir[1]*smag;
spos[2] = spos[2]-sdir[2]*smag;
int h = selectObject(spos, -sdir, smag);
//did we start with a fiber?
if(h != -1 && h < nt.sizeE())
nt.addEdge(L, M, h, -1);
else
nt.addEdge(L, M, -1, -1);
}
//if we hit a fiber?
else if(last_fiber != -1)
{
nt.addEdge(L, M, -1, last_fiber);
spos[0] = spos[0]-sdir[0]*smag;
spos[1] = spos[1]-sdir[1]*smag;
spos[2] = spos[2]-sdir[2]*smag;
int h = selectObject(spos, -sdir, smag);
//did start with a fiber?
if(h != -1 && h < nt.sizeE()){
// std::cout << "got here double" << smag.str() << std::endl;
nt.addEdge(L, M, h, last_fiber);
}
else
{
nt.addEdge(L, M, -1, -1);
}
}
}
#ifdef DEBUG
iter++;
#endif
}
/*
void
addToNetwork(std::vector<stim::vec3<float> > L, std::vector<float > M)
{
if(L.size() > 3)
{
sk.Begin(stim::OBJ_LINE);
for(int i = 0; i < L.size(); i++)
{
sk.TexCoord(M[i]);
sk.Vertex(L[i][0], L[i][1], L[i][2]);
}
sk.End();
nt.addEdge(L,M);
#ifdef DEBUG
iter++;
#endif
}
}
*/
void
printSizes()
{
std::cout << nt.sizeE() << " edges " << std::endl;
std::cout << nt.sizeV() << " nodes " << std::endl;
}
void
traceLine(stim::vec3<float> pos, float mag, int min_cost)
{
//starting (seed) position and magnitude.
last_fiber = -1;
cL.clear();
cM.clear();
cD.clear();
stim::vec3<float> spos = getPosition();
stim::vec3<float> sdir = getDirection();
float smag = getMagnitude();
setPosition(pos);
setMagnitude(mag);
cL.push_back(p);
cD.push_back(d);
cM.push_back(m);
// stim::vec3<float> spos = getPosition();
// float smag = getMagnitude();
// stim::vec3<float> sdir = getDirection();
// Bind();
// sk.Begin(stim::OBJ_LINE);
//sk.createFromSelf(GL_SELECT);
nt.createFromSelf(GL_SELECT);
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;
branchDetection2();
addToNetwork(cL, cM, spos, sdir, smag);
#ifdef DEBUG
std::cerr << "the cost of " << cost << " > " << min_cost << std::endl;
#endif
break;
} else {
//Have we found the edge of the map?
pos = getPosition();
if(p[0] > size[0] || p[1] > size[1]
|| p[2] > size[2] || p[0] < 0
|| p[1] < 0 || p[2] < 0)
{
running = false;
branchDetection2();
// addToNetwork(cL, cM);
addToNetwork(cL, cM, spos, sdir, smag);
#ifdef DEBUG
std::cerr << "I hit and edge" << std::endl;
#endif
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(m > 75 || m < 1){
running = false;
branchDetection2();
// addToNetwork(cL, cM);
addToNetwork(cL, cM, spos, sdir, smag);
#ifdef DEBUG
std::cerr << "The templates are too big" << std::endl;
#endif
break;
}
else
{
h = selectObject(p, getDirection(), m);
//Have we hit something previously traced?
if(h != -1){
#ifdef DEBUG
std::cerr << "I hit the fiber " << h << std::endl;
#endif
last_fiber = h;
running = false;
branchDetection2();
// addToNetwork(cL, cM);
addToNetwork(cL, cM, spos, sdir, smag);
break;
}
else {
cL.push_back(p);
cD.push_back(d);
cM.push_back(m);
// Unbind();
CHECK_OPENGL_ERROR
}
}
}
}
#ifdef DEBUG
std::cout << "I broke out!" << std::endl;
#endif
}
};
}
#endif