/**
* Generate indices that would sort this vector in ascending order
* @param indx :: STD vector to output the sorting indices.
*/
void GSLVector::indexSort(std::vector<size_t>& indx)
{
indx.resize( size() );
for(size_t i = 0; i < indx.size(); ++i)
{
indx[i] = i;
}
std::sort(indx.begin(),indx.end(),SortAscending(*this));
}
void Jacobi(const SymmetricMatrix& X, DiagonalMatrix& D, SymmetricMatrix& A,
Matrix& V, bool eivec)
{
Real epsilon = FloatingPointPrecision::Epsilon();
Tracer et("Jacobi");
REPORT
int n = X.Nrows(); DiagonalMatrix B(n), Z(n); D.resize(n); A = X;
if (eivec) { REPORT V.resize(n,n); D = 1.0; V = D; }
B << A; D = B; Z = 0.0; A.Inject(Z);
bool converged = false;
for (int i=1; i<=50; i++)
{
Real sm=0.0; Real* a = A.Store(); int p = A.Storage();
while (p--) sm += fabs(*a++); // have previously zeroed diags
if (sm==0.0) { REPORT converged = true; break; }
Real tresh = (i<4) ? 0.2 * sm / square(n) : 0.0; a = A.Store();
for (p = 0; p < n; p++)
{
Real* ap1 = a + (p*(p+1))/2;
Real& zp = Z.element(p); Real& dp = D.element(p);
for (int q = p+1; q < n; q++)
{
Real* ap = ap1; Real* aq = a + (q*(q+1))/2;
Real& zq = Z.element(q); Real& dq = D.element(q);
Real& apq = A.element(q,p);
Real g = 100 * fabs(apq); Real adp = fabs(dp); Real adq = fabs(dq);
if (i>4 && g < epsilon*adp && g < epsilon*adq) { REPORT apq = 0.0; }
else if (fabs(apq) > tresh)
{
REPORT
Real t; Real h = dq - dp; Real ah = fabs(h);
if (g < epsilon*ah) { REPORT t = apq / h; }
else
{
REPORT
Real theta = 0.5 * h / apq;
t = 1.0 / ( fabs(theta) + sqrt(1.0 + square(theta)) );
if (theta<0.0) { REPORT t = -t; }
}
Real c = 1.0 / sqrt(1.0 + square(t)); Real s = t * c;
Real tau = s / (1.0 + c); h = t * apq;
zp -= h; zq += h; dp -= h; dq += h; apq = 0.0;
int j = p;
while (j--)
{
g = *ap; h = *aq;
*ap++ = g-s*(h+g*tau); *aq++ = h+s*(g-h*tau);
}
int ip = p+1; j = q-ip; ap += ip++; aq++;
while (j--)
{
g = *ap; h = *aq;
*ap = g-s*(h+g*tau); *aq++ = h+s*(g-h*tau);
ap += ip++;
}
if (q < n-1) // last loop is non-empty
{
int iq = q+1; j = n-iq; ap += ip++; aq += iq++;
for (;;)
{
g = *ap; h = *aq;
*ap = g-s*(h+g*tau); *aq = h+s*(g-h*tau);
if (!(--j)) break;
ap += ip++; aq += iq++;
}
}
if (eivec)
{
REPORT
RectMatrixCol VP(V,p); RectMatrixCol VQ(V,q);
Rotate(VP, VQ, tau, s);
}
}
}
}
B = B + Z; D = B; Z = 0.0;
}
if (!converged) Throw(ConvergenceException(X));
if (eivec) SortSV(D, V, true);
else SortAscending(D);
}
void BaseCaller::MakeCall( Trace& Tr, SimpleMatrix<int>& Peak, int nPos, int nAmbiguityWindow )
{
assert(nPos>=0);
assert(nAmbiguityWindow>0);
call_t Signal[4];
// Initialisation
Init();
// m_nPosition[2] = nPos; jkb 25/06/2003. What should this be?
// Search for peaks and load them in
int peaks = LoadPeaks( Peak, nPos, nAmbiguityWindow, Signal );
// Find biggest peaks position
if( peaks > 0 )
{
int max_sig = 0;
int max_amp = -1;
for( int n=3; n>=0; n-- )
{
if( Signal[n].Position >= 0 )
{
if( Signal[n].Amplitude > max_amp )
{
max_sig = n;
max_amp = Signal[n].Amplitude;
}
}
}
nPos = Signal[max_sig].Position;
}
// Load trace amplitudes for peakless bases
for( int n=0; n<4; n++ )
{
if( Signal[n].Position < 0 )
Signal[n].Amplitude = Tr[n][nPos];
}
// Sort the entire lot by amplitude
SortAscending( Signal );
// Basecall single peak
DNATable Table;
if( peaks == 1 )
{
for( int n=3; n>=0; n-- )
{
if( Signal[n].Position >= 0 )
{
m_nCall[0] = Table.LookupBase( Signal[n].Index );
m_nCall[1] = m_nCall[0];
m_nPosition[0] = Signal[n].Position;
m_nAmplitude[0] = Signal[n].Amplitude;
}
}
}
// Basecall multiple peaks
else if( peaks >= 2 )
{
call_t highest_signal;
int highest_signal_n;
highest_signal.Index = -1;
for( int n=3; n>=0; n-- )
{
if( Signal[n].Position >= 0 )
{
if( highest_signal.Index < 0 )
{
highest_signal = Signal[n];
highest_signal_n = n;
}
else
{
m_nCall[0] = Table.LookupBase( highest_signal.Index, Signal[n].Index );
m_nCall[1] = Table.LookupBase( highest_signal.Index );
m_nCall[2] = Table.LookupBase( Signal[n].Index );
m_nPosition[0] = highest_signal.Position;
m_nAmplitude[0] = highest_signal.Amplitude;
m_nPosition[1] = Signal[n].Position;
m_nAmplitude[1] = Signal[n].Amplitude;
}
}
}
}
// Compute confidence value, just SNR(db) = 20*log(S/N)
double S = Signal[3].Amplitude;
double N = Signal[2].Amplitude;
if( N <= 0.0 )
N = 1.0;
m_nPeakRatio = S / N;
m_nConfidence = m_nPeakRatio
? 20.0 * std::log10( m_nPeakRatio )
: 0;
}
//-----------------------------------------------------------------------
void MeshInfo::getMeshInformation( Ogre::MeshPtr mesh,
const Vector3 &position,
const Quaternion &orient,
const Vector3 &scale)
{
size_t vertexCount = 0;
size_t indexCount = 0;
Vector3* vertices = 0;
Vector3* normals;
unsigned long* indices = 0;
bool added_shared = false;
size_t current_offset = 0;
size_t shared_offset = 0;
size_t next_offset = 0;
size_t index_offset = 0;
// Calculate how many vertices and indices we're going to need
for ( unsigned short i = 0; i < mesh->getNumSubMeshes(); ++i)
{
Ogre::SubMesh* submesh = mesh->getSubMesh( i );
// We only need to add the shared vertices once
if(submesh->useSharedVertices)
{
if( !added_shared )
{
vertexCount += mesh->sharedVertexData->vertexCount;
added_shared = true;
}
}
else
{
vertexCount += submesh->vertexData->vertexCount;
}
// Add the indices
indexCount += submesh->indexData->indexCount;
}
// Allocate space for the vertices and indices
vertices = new Vector3[vertexCount];
normals = new Vector3[vertexCount];
indices = new unsigned long[indexCount];
added_shared = false;
// Run through the submeshes again, adding the data into the arrays
for ( unsigned short i = 0; i < mesh->getNumSubMeshes(); ++i)
{
Ogre::SubMesh* submesh = mesh->getSubMesh(i);
Ogre::VertexData* vertex_data = submesh->useSharedVertices ? mesh->sharedVertexData : submesh->vertexData;
if((!submesh->useSharedVertices)||(submesh->useSharedVertices && !added_shared))
{
if(submesh->useSharedVertices)
{
added_shared = true;
shared_offset = current_offset;
}
const Ogre::VertexElement* posElem = vertex_data->vertexDeclaration->findElementBySemantic(Ogre::VES_POSITION);
const Ogre::VertexElement* normalElem = vertex_data->vertexDeclaration->findElementBySemantic(Ogre::VES_NORMAL);
Ogre::HardwareVertexBufferSharedPtr vbuf = vertex_data->vertexBufferBinding->getBuffer(posElem->getSource());
unsigned char* vertex = static_cast<unsigned char*>(vbuf->lock(Ogre::HardwareBuffer::HBL_READ_ONLY));
float* pReal;
for( size_t j = 0; j < vertex_data->vertexCount; ++j, vertex += vbuf->getVertexSize())
{
posElem->baseVertexPointerToElement(vertex, &pReal);
Vector3 pt(pReal[0], pReal[1], pReal[2]);
vertices[current_offset + j] = (orient * (pt * scale)) + position;
normalElem->baseVertexPointerToElement(vertex, &pReal);
Vector3 nt(pReal[0], pReal[1], pReal[2]);
normals[current_offset + j] = nt;
}
vbuf->unlock();
next_offset += vertex_data->vertexCount;
}
Ogre::IndexData* index_data = submesh->indexData;
size_t numTris = index_data->indexCount / 3;
Ogre::HardwareIndexBufferSharedPtr ibuf = index_data->indexBuffer;
bool use32bitindexes = (ibuf->getType() == Ogre::HardwareIndexBuffer::IT_32BIT);
unsigned long* pLong = static_cast<unsigned long*>(ibuf->lock(Ogre::HardwareBuffer::HBL_READ_ONLY));
unsigned short* pShort = reinterpret_cast<unsigned short*>(pLong);
size_t offset = (submesh->useSharedVertices)? shared_offset : current_offset;
size_t numTrisMultThree = numTris*3;
if ( use32bitindexes )
{
for ( size_t k = 0; k < numTrisMultThree; ++k)
{
indices[index_offset++] = pLong[k] + static_cast<unsigned long>(offset);
}
}
else
{
for ( size_t k = 0; k < numTrisMultThree; ++k)
{
indices[index_offset++] = static_cast<unsigned long>(pShort[k]) + static_cast<unsigned long>(offset);
}
}
ibuf->unlock();
current_offset = next_offset;
}
// Create triangles from the retrieved data
for (size_t k = 0; k < indexCount-1; k+=3)
{
Triangle t;
t.v1 = vertices [indices[k]];
t.vn1 = normals [indices[k]];
t.v2 = vertices [indices[k+1]];
t.vn2 = normals [indices[k+1]];
t.v3 = vertices [indices[k+2]];
t.vn3 = normals [indices[k+2]];
t.calculateSquareSurface();
t.calculateSurfaceNormal();
t.calculateEdgeNormals();
_triangles.push_back(t);
}
// Delete intermediate arrays
delete [] indices;
delete [] normals;
delete [] vertices;
// Sort the triangle on their size, if needed (only if a gaussian random number generator
// function is used to perform a random lookup of a triangle)
if (mDistribution == MSD_HOMOGENEOUS)
sort(_triangles.begin(), _triangles.end(), SortDescending());
else
if (mDistribution == MSD_HETEROGENEOUS_1)
sort(_triangles.begin(), _triangles.end(), SortAscending());
}
