// Compute mean Gamma Rate (Yang)
std::vector<double> computeGammaRate(size_t N_GAMMA, double alpha) {
std::vector<double> gammaRates(N_GAMMA);
double beta = alpha;
boost::math::chi_squared_distribution<double> chi2Dist(2.*alpha);
// Compute cutting point (Eq. 9) (could use gamma QUANTILE instead)
std::vector<double> cPoints(1, 0.);
for(size_t iG=1; iG<N_GAMMA; ++iG) {
double cPoint = boost::math::quantile(chi2Dist, (double)iG/(double)N_GAMMA) / (2.*beta);
cPoints.push_back(cPoint);
}
// Compute all lower incomplete gamma functions required in Eq. 10
double alphaP1 = alpha + 1;
std::vector<double> lowerIncGamma(1, 0.);
for(size_t iL=1; iL<cPoints.size(); ++iL) {
double liGamma = boost::math::gamma_p(alphaP1, cPoints[iL]*beta);
lowerIncGamma.push_back(liGamma);
}
lowerIncGamma.push_back(1.);
// Equation 10.
for(size_t iG=0; iG<N_GAMMA; ++iG) {
// alpha = beta, thus alpha/beta = 1.0 || k=iG
gammaRates[iG] = ((double)N_GAMMA)*(lowerIncGamma[iG+1]-lowerIncGamma[iG]);
}
return gammaRates;
}
void SetupAxis(int nm, GLuint &vao, GLuint &vbo, GLuint &ibo)
{
std::vector<gmtl::Point3f>start;
std::vector<gmtl::Point3f> verts;
std::vector<unsigned int> indices;
std::vector<gmtl::Point3f> color;
std::vector<gmtl::Point2f> uvs;
std::vector<gmtl::Point3f> normals;
int np = 5;
gmtl::Point3f p0(.0f, .0f, .0f);
gmtl::Point3f p1(.025f, .0f, .0f);
gmtl::Point3f p2(.025f, .85f, .0f);
gmtl::Point3f p3(.055f, .85f, .0f);
gmtl::Point3f p4(.0f, 1.0f, .0f);
start.push_back(p0);
start.push_back(p1);
start.push_back(p2);
start.push_back(p3);
start.push_back(p4);
verts = rPoints(start, nm, np, 'y');
color = cPoints(verts, 'o');
normals = nPoints(verts, 'a');
uvs = uvPoints(nm, np);
GenerateIndices(nm, np, indices);
axisIndexSize = indices.size();
int vertOffset = verts.size() * sizeof(gmtl::Point3f);
int uvOffset = uvs.size() * sizeof(gmtl::Point2f);
int colorOffset = color.size() * sizeof(gmtl::Point3f);
int indexOffset = indices.size() * sizeof(GLuint);
int normalOffset = normals.size() * sizeof(gmtl::Point3f);
glGenVertexArrays(1, &vao);
glBindVertexArray(vao);
glGenBuffers(1, &ibo); //Setup 1 buffer name and store the generated buffer object name their
glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, ibo); //bind the buffer name to the target
glBufferData(GL_ELEMENT_ARRAY_BUFFER, //target buffer object
indexOffset, //size of buffer object
&indices[0], //pointer to the data
GL_STATIC_DRAW);
glGenBuffers(1, &vbo);
glBindBuffer(GL_ARRAY_BUFFER, vbo);
//Set the size and data of the Vertex Buffer Object and set it to STATIC_DRAW
glBufferData(GL_ARRAY_BUFFER, //this is the target we are buffering to
vertOffset + colorOffset + normalOffset + uvOffset, //this is the total size of the buffer
NULL, //address of the content to be updated nothing because we are setting it in the subData buffers
GL_STATIC_DRAW);//+ uvOffset + normalOffset
glBufferSubData(GL_ARRAY_BUFFER,
0, //offset where data replacement will begin
vertOffset, //size
&verts[0]);//address of the content to be updated
glBufferSubData(GL_ARRAY_BUFFER,
vertOffset, //offset where data replacement will begin
colorOffset, //size
&color[0]);//data
glBufferSubData(GL_ARRAY_BUFFER,
vertOffset + colorOffset,
normalOffset,
&normals[0]);
glBufferSubData(GL_ARRAY_BUFFER,
vertOffset + colorOffset + normalOffset,
uvOffset,
&uvs[0]);
//verts|uv|color|normals
//layout(location = 0) in vec4 VertexPosition;
//layout(location = 1) in vec4 VertexColor;
//layout(location = 2) in vec3 VertexNormal;
//layout(location = 3) in vec2 VertexUV;
//This is the layout in the shader for the attribute variables
//that will be binded to the different geometry buffers
glEnableVertexAttribArray(0);
glVertexAttribPointer(0,
3,
GL_FLOAT,
GL_FALSE,
0,
(void*)(0));
glEnableVertexAttribArray(1);
glVertexAttribPointer(1,
3,
GL_FLOAT,
GL_FALSE,
0,
(void*)(vertOffset)); // vertex buffer object
glEnableVertexAttribArray(2);
glVertexAttribPointer(2,
3,
GL_FLOAT,
GL_FALSE,
0,
(void*)(vertOffset + colorOffset)); // vertex buffer object
glEnableVertexAttribArray(3);
glVertexAttribPointer(3,
2,
GL_FLOAT,
GL_FALSE,
0,
(void*)(vertOffset + colorOffset + normalOffset));
glBindVertexArray(0);
//Bind the index buffer for the object
glBindBuffer(GL_ARRAY_BUFFER, 0);
// Bind the index buffer for the object
glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, 0);
}
