//-------------------------------------
// compute number of element by cluster
//-------------------------------------
void XEMModel::computeNk() {
int64_t k;
int64_t i;
double ** p_tabCik = _tabCik ; // parcours le tableau _tabCik
double * w = _data->_weight;// parcours des poids
double wi; // poids courant
double * p_tabCik_i;
// initialisation
initToZero(_tabNk,_nbCluster);
for(i=0 ; i<_nbSample ; i++) {
wi = *w;
p_tabCik_i = *p_tabCik;
for(k=0 ; k<_nbCluster ; k++) {
_tabNk[k] += p_tabCik_i[k] * wi;
}
p_tabCik++;
w++;
}
// verification
for(k=0 ; k<_nbCluster ; k++) {
if (_tabNk[k]==0.0) {
throw nullNk;
}
}
}
void XEMGaussianParameter::computeMeanOne(double * Mean, double * weight, double** y_Store, int64_t nbSample, double totalWeight)const{
double ** p_yStore = y_Store;
double * p_weight = weight;
double * p_yStore_i;
int64_t p;
int64_t i;
double wi;
initToZero(Mean,_pbDimension);
for(i=0 ; i<nbSample ; i++){
p_yStore_i = *p_yStore;
wi = *p_weight;
for(p=0 ; p<_pbDimension ; p++){
Mean[p] += p_yStore_i[p] * wi;
}
p_weight++;
p_yStore++;
}
for(p=0 ; p<_pbDimension ; p++){
Mean[p] /= totalWeight;
}
}
void QSnpgwa::process(){
int sz = data->geno_size();
// This is the primary loop.
for(int i=0;i < sz;i++){
SnpInfo s;
ContPopStatsResults p;
ContGenoStatsResults g;
s.index = i+param_reader->get_begin();
data->get_map_info(i, s.chr, s.name, s.position);
data->get_allele_codes(i, s.majAllele, s.minAllele, s.refAllele);
if(s.majAllele == ' '){
s.majAllele = '.';
}
if(s.minAllele == ' '){
s.minAllele = '.';
}
if(s.refAllele == ' '){
s.refAllele = '.';
}
// calc difference in genetic position.
if(i < sz-1){
string t, chr;
int pos = 0;
data->get_map_info(i+1, chr, t, pos);
if(chr.compare(s.chr) == 0){
s.diff = pos-s.position;
}else{
s.diff = -999;
}
}else{
s.diff = -999;
}
if(data->getDataObject()->isUsable(i)){
ContPopStats pop_calc(data);
ContGenoStats gen_calc(data);
LinkageDisequilibrium ld(data);
ld.enslave(snp_param); // We have to do this or the ld engine will think
// that it owns the data and might erase it.
LinkageMeasures lr;
pop_calc.prepPopStatsForOutput(i,p);
gen_calc.prepGenoStatsForOutput(i,g);
if(i + 1 < data->geno_size()){
ld.dprimeOnPair(i, i+1, lr);
g.rsquare = lr.rsquare;
g.dprime = lr.dPrime;
}else{
g.rsquare = g.dprime = -1.0;
}
}else{
initToZero(p, g);
}
out.writeLine(i, s,p,g);
}
out.close();
}
///////////////////////////////////////////////////////////////////////
// Class : CStochastic
// Method : rasterBegin
// Description :
/// \brief Begin drawing an image
// Return Value : -
// Comments :
void CStochastic::rasterBegin(int w,int h,int l,int t,int nullBucket) {
int i,j,pxi,pxj;
float zoldStart;
CFragment *cFragment;
assert(numFragments == 0);
zoldStart = CRenderer::clipMax;
// Set the digits
width = w;
height = h;
left = l;
top = t;
sampleWidth = width*CRenderer::pixelXsamples + 2*CRenderer::xSampleOffset;
sampleHeight = height*CRenderer::pixelYsamples + 2*CRenderer::ySampleOffset;
right = left + sampleWidth;
bottom = top + sampleHeight;
// Early-out if we have no data
if (!(CRenderer::flags & OPTIONS_FLAGS_DEEP_SHADOW_RENDERING) && nullBucket) return;
assert(sampleWidth <= totalWidth);
assert(sampleHeight <= totalHeight);
// Init the occlusion culler to zero
initToZero();
for (i=0,pxi=CRenderer::pixelYsamples-CRenderer::ySampleOffset;i<sampleHeight;i++,pxi++) {
CPixel *pixel = fb[i];
if (pxi >= CRenderer::pixelYsamples) pxi = 0;
for (j=0,pxj=CRenderer::pixelXsamples-CRenderer::xSampleOffset;j<sampleWidth;j++,pxj++,pixel++) {
float aperture[2];
// The stratified sample
pixel->jx = (CRenderer::jitter*(urand()-0.5f) + 0.5001011f);
pixel->jy = (CRenderer::jitter*(urand()-0.5f) + 0.5001017f);
// Time of the sample for motion blur
if (pxj >= CRenderer::pixelXsamples) pxj = 0;
pixel->jt = ( pxi*CRenderer::pixelXsamples + pxj + CRenderer::jitter*(urand()-0.5f) + 0.5001011f)/(float)(CRenderer::pixelXsamples*CRenderer::pixelYsamples);
// Importance blend / jitter
pixel->jimp = 1.0f - ( pxj*CRenderer::pixelYsamples + pxi + CRenderer::jitter*(urand()-0.5f) + 0.5001011f)/(float)(CRenderer::pixelXsamples*CRenderer::pixelYsamples);
if (CRenderer::flags & OPTIONS_FLAGS_FOCALBLUR) {
// Aperture sample for depth of field
while (TRUE) {
apertureGenerator.get(aperture);
aperture[0] = 2.0f*aperture[0] - 1.0f;
aperture[1] = 2.0f*aperture[1] - 1.0f;
if ((aperture[0]*aperture[0] + aperture[1]*aperture[1]) < 1.0f) break;
}
pixel->jdx = aperture[0];
pixel->jdy = aperture[1];
} else {
pixel->jdx = 0;
pixel->jdy = 0;
}
// Center location of the sample
pixel->xcent = (j+pixel->jx) + left;
pixel->ycent = (i+pixel->jy) + top;
pixel->z = CRenderer::clipMax;
pixel->zold = zoldStart;
pixel->numSplats = 0;
pixel->node = getNode(j,i);
pixel->node->zmax = CRenderer::clipMax;
cFragment = &pixel->last;
cFragment->z = CRenderer::clipMax;
initv(cFragment->color,0);
initv(cFragment->opacity,0);
cFragment->next = NULL;
cFragment->prev = &pixel->first;
// The last sample's extra samples are genuine AOV data
if (CRenderer::numExtraSamples > 0)
memcpy(cFragment->extraSamples,CRenderer::sampleDefaults,sizeof(float)*CRenderer::numExtraSamples);
initv(cFragment->accumulatedOpacity,0);
cFragment = &pixel->first;
cFragment->z = -C_INFINITY;
initv(cFragment->color,0);
initv(cFragment->opacity,0);
cFragment->next = &pixel->last;
cFragment->prev = NULL;
// Note: The first fragment's extra samples are not used, and the pointer is NULL
assert(cFragment->extraSamples == NULL);
initv(cFragment->accumulatedOpacity,0);
pixel->update = &pixel->first;
}
}
resetHierarchy();
}
