int HrPwWindow::fit(QVector<double> &Xi,QVector<double> &Yi,int n)
{
QVector<double> r(5),lnXi(100),lnYi(100),logXi(100),logYi(100),invXi(100);
//Linear correlation
r[0]=val_abs(corr(Xi,Yi,n));
//Exponential correlation
lnarray(Yi,lnYi,n);
r[1]=val_abs(corr(Xi,lnYi,n));
//Power correlation
logarray(Xi,logXi,n);
logarray(Yi,logYi,n);
r[2]=val_abs(corr(logXi,logYi,n));
//Inverse correlation
invarray(Xi,invXi,n);
r[3]=val_abs(corr(invXi,Yi,n));
//Logarithmic correlation
lnarray(Xi,lnXi,n);
r[4]=val_abs(corr(lnXi,Yi,n));
//Best fit test
return rmax(r);
}
int
Statistic::ajustement(QVector<double> &Xi,QVector<double> &Yi,int n)
{
QVector<double> r(5),lnXi(100),lnYi(100),logXi(100),logYi(100),invXi(100);
//corrélation pour linéaire
r[0]=val_abs(corr(Xi,Yi,n));
//corrélation pour exponetielle
lntab(Yi,lnYi,n);
r[1]=val_abs(corr(Xi,lnYi,n));
//corrélation pour puissance
logtab(Xi,logXi,n);
logtab(Yi,logYi,n);
r[2]=val_abs(corr(logXi,logYi,n));
//corrélation pour inverse
invtab(Xi,invXi,n);
r[3]=val_abs(corr(invXi,Yi,n));
//corrélation pour logarithmique
lntab(Xi,lnXi,n);
r[4]=val_abs(corr(lnXi,Yi,n));
//Test du meilleur ajustement
return rmax(r);
}
double NCC(const Image<float>& I1,const Image<float>& meanI1,Point m1,const Image<float>& I2,const Image<float>& meanI2,Point m2,int n) {
if (m1.x<n || m1.x>=I1.width()-n || m1.y<n || m1.y>=I1.height()-n) return -1;
if (m2.x<n || m2.x>=I2.width()-n || m2.y<n || m2.y>=I2.height()-n) return -1;
double c1=corr(I1,meanI1,m1,I1,meanI1,m1,n);
if (c1==0) return -1;
double c2=corr(I2,meanI2,m2,I2,meanI2,m2,n);
if (c2==0) return -1;
return corr(I1,meanI1,m1,I2,meanI2,m2,n)/sqrt(c1*c2);
}
double NCC(const Image<float>& I1,const Image<float>& meanI1,const Image<float>& corrI1,Point m1,const Image<float>& I2,const Image<float>& meanI2,const Image<float>& corrI2,Point m2,int n) {
if (m1.x<n || m1.x>=I1.width()-n || m1.y<n || m1.y>=I1.height()-n) return -1;
if (m2.x<n || m2.x>=I2.width()-n || m2.y<n || m2.y>=I2.height()-n) return -1;
if (corrI1(m1)==0) return -1;
if (corrI2(m2)==0) return -1;
return corr(I1,m1,I2,m2,n)/sqrt(corrI1(m1)*corrI2(m2));
}
int
HrPwWindow::findDelay(QVector<double> &wattsArray, QVector<double> &hrArray, int rideTimeSecs)
{
int delay = 0;
double maxr = 0;
if (rideTimeSecs>= 60) {
for (int a = 10; a <=60; ++a) {
QVector<double> delayHr(rideTimeSecs);
for (int j = a; j<rideTimeSecs; ++j) {
delayHr[j-a] = hrArray[j];
}
for (int j = rideTimeSecs-a; j<rideTimeSecs; ++j) {
delayHr[j] = 0.0;
}
double r = corr(wattsArray, delayHr, rideTimeSecs-a);
//fprintf(stderr, "findDelay %d: %.2f \n", a, r);
if (r>maxr) {
maxr = r;
delay = a;
}
}
}
delayEdit->setText(QString("%1").arg(delay));
rDelayEdit->setText(QString("%1").arg(delay));
delaySlider->setValue(delay);
rDelaySlider->setValue(delay);
return delay;
}
void bmfm_fancy(float *disp, // output disparities image (dx, dy)
float *errc, // output error image
float *a, // input image A
float *b, // input image B
int w, // width
int h, // height
int pd, // pixel dimension
double fm[9], // fundamental matrix
float *disp_init, // initialization (optional)
float *search_radius // optional, w.r.t. initialization
)
{
int maxpoints = 2 * (w+h), (*p)[2] = xmalloc(maxpoints*sizeof*p);
for (int j = 0; j < h; j++)
for (int i = 0; i < w; i++) {
float rad = NAN, ini[2] = {0, 0};
if (search_radius) rad = search_radius[j*w+i];
if (disp_init) ini[0] = disp_init[2*(j*w+i)+0];
if (disp_init) ini[1] = disp_init[2*(j*w+i)+1];
int np = plot_epipolar_fancy(p, fm, w, h, i, j, ini, rad);
float mincorr = INFINITY;
int minidx = 0;
for (int k = 0; k < np; k++) {
float c = corr(a, b, w, h, pd, i, j, p[k][0], p[k][1]);
if (c < mincorr) {
mincorr = c;
minidx = k;
}
}
if (disp) disp[2*(j*w+i) + 0] = p[minidx][0] - i;
if (disp) disp[2*(j*w+i) + 1] = p[minidx][1] - j;
if (errc) errc[j*w+i] = mincorr;
}
free(p);
}
void shot_detector::compare(pcl::PointCloud<DescriptorType>::Ptr model_descriptions, pcl::PointCloud<DescriptorType>::Ptr scene_descriptions)
{
model_scene_corrs->clear();
pcl::KdTreeFLANN<DescriptorType> match_search;
match_search.setInputCloud (model_descriptions);
std::cerr << scene_descriptions->size() << " and " << model_descriptions->size() << std::endl;
model_good_keypoints_indices.clear();
scene_good_keypoints_indices.clear();
// For each scene keypoint descriptor, find nearest neighbor into the model keypoints descriptor cloud and add it to the correspondences vector.
for (size_t i = 0; i < scene_descriptions->size (); ++i) {
std::vector<int> neigh_indices (1);
std::vector<float> neigh_sqr_dists (1);
if (!pcl_isfinite (scene_descriptors->at (i).descriptor[0])) { //skipping NaNs
continue;
}
int found_neighs = match_search.nearestKSearch (scene_descriptors->at (i), 1, neigh_indices, neigh_sqr_dists);
if(found_neighs == 1 && neigh_sqr_dists[0] < corr_dist_) { // add match only if the squared descriptor distance is less than 0.25 (SHOT descriptor distances are between 0 and 1 by design)
pcl::Correspondence corr (neigh_indices[0], static_cast<int> (i), neigh_sqr_dists[0]);
model_scene_corrs->push_back (corr);
}
}
pcl::copyPointCloud (*model_keypoints, model_good_keypoints_indices, *model_good_kp);
pcl::copyPointCloud (*scene_keypoints, scene_good_keypoints_indices, *scene_good_kp);
std::cerr << "Correspondences found: " << model_scene_corrs->size () << std::endl;
}
double operator()(configuration const& c) const {
auto delta = (rhs - kern(c)) / error_bars;
int M = first_dim(delta);
double kappa = 0;
for(int i = 1; i < M; ++i) kappa += corr(delta(i), delta(i-1));
kappa /= M - 1;
return kappa;
}
// Renvoit la matrice avec toutes les auto-correlations
Image<float> corrImage(const Image<float>& I, const Image<float>& meanI, int n){
Image<float> corrI(I.width(), I.height(),CV_32F);
for(int i=n+1; i<I.height()-n-1; i++){
for(int j=n+1; j<I.width()-n-1; j++){
//cout<< i << " " << j << endl;
corrI.at<float>(i,j) = (float)(corr(I, meanI, Point(j,i), I, meanI, Point(j,i),n));
}
}
return corrI;
}
int InitialGuess (double *s, double *p, int nphase, int nchn, int *chn)
{
int index;
double frac_off = 0.05; // set to be 0.05
double ptemp[nphase];
double temp[nchn];
int i, h;
for (i = 0; i < nchn; i++)
{
for (h = 0; h < nphase; h++)
{
ptemp[h] = p[i*nphase+h];
}
int x;
x = def_off_pulse (nphase, ptemp, frac_off);
double ptemp_out[nphase];
pre_diff (ptemp, nphase, x, frac_off, ptemp_out);
temp[i] = find_peak_value(nphase,ptemp_out);
}
int peak;
find_peak (0, nchn, temp, &peak);
//printf ("%d\n",peak);
(*chn) = peak;
double p_use[nphase];
double s_use[nphase];
for (h = 0; h < nphase; h++)
{
p_use[h] = p[peak*nphase+h];
s_use[h] = s[peak*nphase+h];
}
// remove the baseline of template
index = def_off_pulse (nphase, s_use, frac_off);
double s_out[nphase];
pre_diff (s_use, nphase, index, frac_off, s_out);
// remove the baseline of profile
index = def_off_pulse (nphase, p_use, frac_off);
double p_out[nphase];
pre_diff (p_use, nphase, index, frac_off, p_out);
// Guess the phase shift
int d;
d = corr (s_out, p_out, nphase);
return d;
}
int main()
{
int a, i, j;
gets(string);
a = 1;
i = 0;
for(j = 0; string[j] != '\0'; j++);
j--;
while(j - i >= 1)
{
while(corr(string[i])) i++;
while(corr(string[j]) && (j >= 1)) j--;
if ((reg(string[i]) != reg(string[j])) && (j - i >= 1)) a = 0;
i++;
j--;
}
if (a) printf("Yes");
else printf("No");
return 0;
}
static void roguejoin(struct level *lev, int x1, int y1, int x2, int y2, int horiz)
{
int x,y,middle;
#ifndef MAX
#define MAX(a,b) (((a) > (b)) ? (a) : (b))
#endif
#ifndef MIN
#define MIN(a,b) (((a) < (b)) ? (a) : (b))
#endif
if (horiz) {
middle = x1 + rn2(x2-x1+1);
for (x=MIN(x1,middle); x<=MAX(x1,middle); x++)
corr(lev, x, y1);
for (y=MIN(y1,y2); y<=MAX(y1,y2); y++)
corr(lev, middle,y);
for (x=MIN(middle,x2); x<=MAX(middle,x2); x++)
corr(lev, x, y2);
} else {
middle = y1 + rn2(y2-y1+1);
for (y=MIN(y1,middle); y<=MAX(y1,middle); y++)
corr(lev, x1, y);
for (x=MIN(x1,x2); x<=MAX(x1,x2); x++)
corr(lev, x, middle);
for (y=MIN(middle,y2); y<=MAX(middle,y2); y++)
corr(lev, x2,y);
}
}
int fit() {
cout << "start of fit procedure" << endl;
readsource("run369/CRS/CRS_QDC_01!qdc01.dat",7214);
readbackgr("run371/CRS/CRS_QDC_01!qdc01.dat",56948);
corr();
TCanvas* c1 = new TCanvas("c1","c1",800,600);
int maxbin=-1;
Double_t maxvalue=-1;
Double_t tempbin=0;
TString text="";
hcorr->GetXaxis()->SetRange(200,4000);
maxbin=hcorr->GetMaximumBin();
maxvalue=hcorr->GetBinContent(maxbin);
hcorr->GetXaxis()->SetRange(0,4095);
TF1* f1 = new TF1("f1","[0]*exp(-((x-[1])^2)/[2])");
f1->SetParameter(0,maxvalue);
f1->SetParameter(1,maxbin);
f1->SetParameter(2,1);
f1->SetLineColor(2);
hcorr->SetMinimum(0);
hcorr->SetMaximum(1.2*maxvalue);
hcorr->Fit("f1","","",maxbin-maxbin/6,4095);
tempbin=sqrt(-log(maxvalue*2/3/(f1->GetParameter(0)))*(f1->GetParameter(2)))+f1->GetParameter(1);
cout << "2/3 of maximum height is in bin " << tempbin << "->" <<int(tempbin+0.5) << endl;
cout << endl << "max bin = " << maxbin << " with content = " << maxvalue << endl;
}
static void
spatial_mat(double *par, double *dist, longint *n, longint *nug,
double (*corr)(double ), double *mat)
{
longint i, j, np1 = *n + 1;
double aux, *sdist, ratio = 1.0;
sdist = dist;
if (*nug) ratio = par[1];
for(i = 0; i < *n; i++) {
mat[i * np1] = 1.0;
for(j = i + 1; j < *n; j++, sdist++) {
aux = *sdist / *par;
*(mat + i + j * (*n)) = *(mat + j + i * (*n)) = ratio * corr(aux);
}
}
}
std::vector<Joystick::CalibrationData>
Joystick::get_calibration()
{
std::vector<struct js_corr> corr(get_axis_count());
if (ioctl(fd, JSIOCGCORR, &*corr.begin()) < 0)
{
std::ostringstream str;
str << filename << ": " << strerror(errno);
throw std::runtime_error(str.str());
}
else
{
std::vector<CalibrationData> data;
std::transform(corr.begin(), corr.end(), std::back_inserter(data), corr2cal);
return data;
}
}
void AddEntryDlg::OnButtonEditInsertPressed()
{
//QString insert_cmd("UPDATE 'musicdb'.'main' SET 'titel' = '");
QString insert_cmd("UPDATE 'main' SET 'titel' = '");
insert_cmd.append(corr(le_title.text()));
insert_cmd.append("', 'kuenstler' = '");
insert_cmd.append(corr(le_artist.text()));
insert_cmd.append("', 'album' = '");
insert_cmd.append(corr(le_album.text()));
insert_cmd.append("', 'tag' = '");
insert_cmd.append(corr(le_tag.text()));
insert_cmd.append("', 'genre' = '");
insert_cmd.append(corr(le_genre.text()));
insert_cmd.append("', 'jahr' = '");
insert_cmd.append(le_year.text());
insert_cmd.append("', 'others' = '");
if(cb_interest_others.isChecked())
insert_cmd.append("1");
else
insert_cmd.append("0");
insert_cmd.append("', 'yours' = '");
if(cb_interest_yours.isChecked())
insert_cmd.append("1");
else
insert_cmd.append("0");
insert_cmd.append("', 'dateityp' = '");
insert_cmd.append(le_filetype.text());
insert_cmd.append("', 'qualitaet' = '");
insert_cmd.append(le_quality.text());
insert_cmd.append("', 'bew_yours' = '");
insert_cmd.append(QString::number(sb_vote_yours.value()));
insert_cmd.append("', 'bew_others' = '");
insert_cmd.append(QString::number(sb_vote_others.value()));
insert_cmd.append("', 'pfad' = '");
insert_cmd.append(le_path.text());
insert_cmd.append("', 'url' = '");
insert_cmd.append(corr(le_source.text()));
insert_cmd.append("' WHERE 'main'.'id' =");
insert_cmd.append(QString::number(editnum));
printf("Query command: %s\n", insert_cmd.toAscii().data());
sqlhelper.exec(insert_cmd);
accept();
}
int main(){
int i,j,st;
int sp = n();
double data[500000];
double theta[5] = {0.3,0.2,0.3,0,0};
double phi[5] = {1.,0.3,0.7,0,0};
double nofphot[5] = {1000.,1000.,1000,0,0};
st = corr(data,3,theta,phi,0.25,50,5,nofphot,0.,50);
FILE* f = fopen("T.txt","w+");
for(i=0;i<256;i++){
for(j=0;j<256;j++){
fprintf(f,"%f ",data[sp*256*256+j*256+i]);
}
fprintf(f,"\n");
}
fclose(f);
return 0;
}
void DSPEngine::dcOffset(SampleVector::iterator begin, SampleVector::iterator end)
{
double count;
int io = 0;
int qo = 0;
Sample corr((qint16)m_iOffset, (qint16)m_qOffset);
// sum and correct in one pass
for(SampleVector::iterator it = begin; it < end; it++) {
io += it->real();
qo += it->imag();
*it -= corr;
}
// moving average
count = end - begin;
m_iOffset = (15.0 * m_iOffset + (double)io / count) / 16.0;
m_qOffset = (15.0 * m_qOffset + (double)qo / count) / 16.0;
}
doublereal WaterPropsIAPWS::psat(doublereal temperature, int waterState) {
doublereal densLiq = -1.0, densGas = -1.0, delGRT = 0.0;
doublereal dp, pcorr;
if (temperature >= T_c) {
densGas = density(temperature, P_c, WATER_SUPERCRIT);
setState_TR(temperature, densGas);
return P_c;
}
doublereal p = psat_est(temperature);
bool conv = false;
for (int i = 0; i < 30; i++) {
if (method == 1) {
corr(temperature, p, densLiq, densGas, delGRT);
doublereal delV = M_water * (1.0/densLiq - 1.0/densGas);
dp = - delGRT * Rgas * temperature / delV;
} else {
corr1(temperature, p, densLiq, densGas, pcorr);
dp = pcorr - p;
}
p += dp;
if ((method == 1) && delGRT < 1.0E-8) {
conv = true;
break;
} else {
if (fabs(dp/p) < 1.0E-9) {
conv = true;
break;
}
}
}
// Put the fluid in the desired end condition
if (waterState == WATER_LIQUID) {
setState_TR(temperature, densLiq);
} else if (waterState == WATER_GAS) {
setState_TR(temperature, densGas);
} else {
throw Cantera::CanteraError("WaterPropsIAPWS::psat",
"unknown water state input: " + Cantera::int2str(waterState));
}
return p;
}
int go_appendix_backgr(){
readsource("run370/CRS/CRS_QDC_00!qdc00.dat",7215);
readbackgr("run371/CRS/CRS_QDC_00!qdc00.dat",56948);
corr();
TPaveText *pt = new TPaveText(0.65,0.7,0.85,0.85, "NDC");
pt->AddText("run371");
pt->AddText("background");
pt->AddText("box I (QDC ch00)");
hbackgr->GetXaxis()->SetTitle("QDC energy [bin]");
hbackgr->SetTitle("Background - box I");
TCanvas* c1=new TCanvas("c1","c1",800,300);
hbackgr->Draw();
pt->Draw("same");
c1->SaveAs("appendix/backgr_boxI.jpg");
}
/* MEX FUNCTION */
void mexFunction(int nargout, mxArray* argout[], int nargin, const mxArray* argin[])
{
if (nargin != 4)
mexErrMsgTxt("Four input arguments must be provided to this function. See documentation for syntax details.");
double* x = mxGetPr(argin[0]);
double* y = mxGetPr(argin[1]);
int window = (int)mxGetScalar(argin[2]);
int noverlap = (int)mxGetScalar(argin[3]);
int increment = window - noverlap;
int ncx, ncy, nrx, nry;
nrx = mxGetM(argin[0]);
ncx = mxGetN(argin[0]);
nry = mxGetM(argin[1]);
ncy = mxGetN(argin[1]);
if (nrx == 0 || nry == 0) { mexErrMsgTxt("Inputs cannot be empty arrays."); }
if (nrx != nry) { mexErrMsgTxt("X and Y must contain equivalent length signals."); }
// We need a higher precision calculation for the number of SWC points per signal. Otherwise, if this ends up being fractional,
// it could get rounded up and result in out-of-bounds indexing later on. We need to always force it downward.
float temp = (float)(nrx - window) / (float)increment;
int nswc = (int)floor(temp);
argout[0] = mxCreateDoubleMatrix(nswc, ncx * ncy, mxREAL);
double* swc = mxGetPr(argout[0]);
int nrxToUse = nswc * increment;
if (ncy == 1)
{
cilk_for (int a = 0; a < ncx; a++)
{
int idxSWC = a * nswc;
int idxColX = a * nrx;
for (int b = 0; b < nrxToUse; b += increment)
swc[idxSWC++] = corr(x + idxColX + b, y + b, window);
}
}
int go_appendix(){
readsource("run370/CRS/CRS_QDC_00!qdc00.dat",7215);
readbackgr("run371/CRS/CRS_QDC_00!qdc00.dat",56948);
corr();
TPaveText *pt = new TPaveText(0.65,0.7,0.85,0.85, "NDC");
pt->AddText("run371");
pt->AddText("Cs-137");
pt->AddText("box I (QDC ch00)");
pt->AddText("compton edge in bin 860 +- 20");
hcorr->GetXaxis()->SetTitle("QDC energy [bin]");
hcorr->SetTitle("Cs-137 - box I");
TCanvas* c1=new TCanvas("c1","c1",800,300);
hcorr->Draw();
pt->Draw("same");
c1->SaveAs("appendix/Cs-137_boxI.jpg");
}
tree
texmacs_invarianted (tree t, tree oldt, string src) {
tree orgbody= extract (t, "body");
tree oldbody= extract (oldt, "body");
hashmap<tree,tree> corr (UNINIT);
hashmap<tree,tree> pred (UNINIT);
hashmap<tree,tree> succ (UNINIT);
tree uoldbody= texmacs_correspondence (oldbody, corr);
texmacs_neighbours (oldbody, pred, succ);
tree body= orgbody;
body= texmacs_invarianted (body, UNINIT, -1, src, corr, pred, succ);
hashmap<tree,path> h (path (-1));
//cout << "body" << LF << HRULE << body << LF << HRULE;
//cout << "orgbody" << LF << HRULE << orgbody << LF << HRULE;
//cout << "uoldbody" << LF << HRULE << uoldbody << LF << HRULE;
get_subtree_paths (uoldbody, path (), h);
body= texmacs_invarianted_merge (body, src, orgbody, uoldbody, h);
//cout << "merged" << LF << HRULE << body << LF << HRULE;
body= texmacs_invarianted_replace (body, src);
return change_doc_attr (t, "body", body);
}
TEST (CorrespondenceEstimation, CorrespondenceEstimationNormalShooting)
{
pcl::PointCloud<pcl::PointXYZ>::Ptr cloud1 (new pcl::PointCloud<pcl::PointXYZ> ());
pcl::PointCloud<pcl::PointXYZ>::Ptr cloud2 (new pcl::PointCloud<pcl::PointXYZ> ());
// Defining two parallel planes differing only by the y co-ordinate
for (float i = 0; i < 10; i += 0.2)
{
for (float z = 0; z < 5; z += 0.2)
{
cloud1->points.push_back (pcl::PointXYZ (i, 0, z));
cloud2->points.push_back (pcl::PointXYZ (i, 2, z)); // Ideally this should be the corresponding point to the point defined in the previous line
}
}
pcl::NormalEstimation<pcl::PointXYZ, pcl::Normal> ne;
ne.setInputCloud (cloud1);
pcl::search::KdTree<pcl::PointXYZ>::Ptr tree (new pcl::search::KdTree<pcl::PointXYZ> ());
ne.setSearchMethod (tree);
pcl::PointCloud<pcl::Normal>::Ptr cloud1_normals (new pcl::PointCloud<pcl::Normal>);
ne.setKSearch (5);
ne.compute (*cloud1_normals); // All normals are perpendicular to the plane defined
pcl::CorrespondencesPtr corr (new pcl::Correspondences);
pcl::registration::CorrespondenceEstimationNormalShooting <pcl::PointXYZ, pcl::PointXYZ, pcl::Normal> ce;
ce.setInputCloud (cloud1);
ce.setKSearch (10);
ce.setSourceNormals (cloud1_normals);
ce.setInputTarget (cloud2);
ce.determineCorrespondences (*corr);
// Based on the data defined, the correspondence indices should be 1 <-> 1 , 2 <-> 2 , 3 <-> 3 etc.
for (unsigned int i = 0; i < corr->size (); i++)
{
EXPECT_EQ ((*corr)[i].index_query, (*corr)[i].index_match);
}
}
pcl::CorrespondencesPtr Recognizer::flann_matcher(pcl::PointCloud<DescriptorType>::Ptr input_descriptors, pcl::PointCloud<DescriptorType>::Ptr target_descriptors, float match_thresh) {
pcl::KdTreeFLANN<DescriptorType> match_search;
match_search.setInputCloud(input_descriptors);
for(size_t i = 0; i < target_descriptors->size (); ++i) {
std::vector<int> neigh_indices (1);
std::vector<float> neigh_sqr_dists (1);
for (int j = 0; j < 33; j++) { // for each bin
if(pcl_isnan(target_descriptors->at(i).histogram[j]) || !pcl_isfinite(target_descriptors->at(i).histogram[j]))
continue;
}
int found_neighs = match_search.nearestKSearch(target_descriptors->at(i), 1, neigh_indices, neigh_sqr_dists);
if(found_neighs == 1 && neigh_sqr_dists[0] < match_thresh) { // add match only if the squared descriptor distance is less than 0.25 (SHOT descriptor distances are between 0 and 1 by design)
pcl::Correspondence corr (neigh_indices[0], static_cast<int> (i), neigh_sqr_dists[0]);
(this->corrs)->push_back(corr);
}
}
return this->corrs;
}
// return the log-density for the prior on the correlations
double CorrPrior(std::vector<double> arctanh_corr) {
std::vector<double> corr(pchi);
for (int j = 0; j < pchi; ++j) {
corr[j] = tanh(arctanh_corr[j]);
//std::cout << "corr[" << j << "]: " << corr[j] << ", ";
}
//std::cout << std::endl;
// make sure correlation matrix is positive definite
double determ =
(1.0 - corr[2] * corr[2]) - corr[0] * (corr[0] - corr[2] * corr[3]) + corr[1] * (corr[0] * corr[2] - corr[1]);
double logprior;
if (determ > 0) {
// correlation matrix is positive definite, so calculate the log prior density
logprior = (0.5 * pchi * (pchi - 1.0) - 1.0) * log(determ);
logprior -= 0.5 * (pchi + 1.0) * log(1.0 - corr[2] * corr[2]);
logprior -= 0.5 * (pchi + 1.0) * log(1.0 - corr[1] * corr[1]);
logprior -= 0.5 * (pchi + 1.0) * log(1.0 - corr[0] * corr[0]);
} else {
// correlation matrix is not positive definite
logprior = -std::numeric_limits<double>::infinity();
}
return logprior;
}
// Generate a WWW-Authenticate header. This has the format:
// WWW-Authenticate: Digest realm="<home domain>",
// qop="auth",
// nonce="<nonce>",
// opaque="<opaque>",
// [stale=TRUE]
void HTTPDigestAuthenticate::generate_www_auth_header(std::string& www_auth_header, bool include_stale, AuthStore::Digest* digest)
{
www_auth_header = "Digest";
www_auth_header.append(" realm=\"").append(_home_domain).append("\"");
www_auth_header.append(",qop=\"").append("auth").append("\"");
www_auth_header.append(",nonce=\"").append(digest->_nonce).append("\"");
www_auth_header.append(",opaque=\"").append(digest->_opaque).append("\"");
if (include_stale)
{
www_auth_header.append(",stale=TRUE");
}
TRC_DEBUG("WWW-Authenticate header generated: %s", www_auth_header.c_str());
TRC_DEBUG("Raising correlating marker with opaque value = %s",
digest->_opaque.c_str());
SAS::Marker corr(_trail, MARKED_ID_GENERIC_CORRELATOR, 0);
corr.add_var_param(digest->_opaque);
// The marker should be trace-scoped, and should not reactivate any trail
// groups
SAS::report_marker(corr, SAS::Marker::Scope::Trace, false);
}
shared_ptr<MarketModel>
FlatVolFactory::create(const EvolutionDescription& evolution,
Size numberOfFactors) const {
const vector<Time>& rateTimes = evolution.rateTimes();
Size numberOfRates = rateTimes.size()-1;
vector<Rate> initialRates(numberOfRates);
for (Size i=0; i<numberOfRates; ++i)
initialRates[i] = yieldCurve_->forwardRate(rateTimes[i],
rateTimes[i+1],
Simple);
vector<Volatility> displacedVolatilities(numberOfRates);
for (Size i=0; i<numberOfRates; ++i) {
Volatility vol = // to be changes
volatility_(rateTimes[i]);
displacedVolatilities[i] =
initialRates[i]*vol/(initialRates[i]+displacement_);
}
vector<Spread> displacements(numberOfRates, displacement_);
Matrix correlations = exponentialCorrelations(evolution.rateTimes(),
longTermCorrelation_,
beta_);
shared_ptr<PiecewiseConstantCorrelation> corr(new
TimeHomogeneousForwardCorrelation(correlations,
rateTimes));
return shared_ptr<MarketModel>(new
FlatVol(displacedVolatilities,
corr,
evolution,
numberOfFactors,
initialRates,
displacements));
}
pcl::CorrespondencesPtr ORPointCloud::correspondences(const ORPointCloud* model, const ORPointCloud* scene)
{
pcl::CorrespondencesPtr model_scene_corrs (new pcl::Correspondences ());
pcl::KdTreeFLANN<DescriptorType> match_search;
match_search.setInputCloud (model->descriptors);
// For each scene keypoint descriptor, find nearest neighbor into the model keypoints descriptor cloud and add it to the correspondences vector.
for (size_t i = 0; i < scene->descriptors->size (); ++i)
{
std::vector<int> neigh_indices (1);
std::vector<float> neigh_sqr_dists (1);
if (!pcl_isfinite (scene->descriptors->at (i).descriptor[0])) //skipping NaNs
{
continue;
}
int found_neighs = match_search.nearestKSearch (scene->descriptors->at (i), 1, neigh_indices, neigh_sqr_dists);
if(found_neighs == 1 && neigh_sqr_dists[0] < 0.25f) // add match only if the squared descriptor distance is less than 0.25 (SHOT descriptor distances are between 0 and 1 by design)
{
pcl::Correspondence corr (neigh_indices[0], static_cast<int> (i), neigh_sqr_dists[0]);
model_scene_corrs->push_back(corr);
}
}
return model_scene_corrs;
}
int KinshipHolder::loadDecomposed() {
LineReader lr(this->eigenFileName);
int lineNo = 0;
int fieldLen = 0;
std::vector<std::string> fd;
std::vector<int> columnToExtract;
std::vector<std::string> header; // header line of the kinship eigen file
Eigen::MatrixXf& matK = this->matK->mat;
Eigen::MatrixXf& matS = this->matS->mat;
Eigen::MatrixXf& matU = this->matU->mat;
const std::vector<std::string>& names = *this->pSample;
const int NumSample = (int)names.size();
std::map<std::string, int> nameMap;
makeMap(names, &nameMap);
std::map<std::string, int> headerMap;
while (lr.readLineBySep(&fd, "\t ")) {
++lineNo;
if (lineNo == 1) { // check header
header = fd;
fieldLen = fd.size();
if (fieldLen < 3) { // at least three columns: IID, Lambda, U1
logger->error(
"Insufficient column number (<3) in the first line of kinsihp "
"file!");
return -1;
};
for (size_t i = 0; i != fd.size(); ++i) {
fd[i] = tolower(fd[i]);
}
makeMap(fd, &headerMap);
if (fd.size() != headerMap.size()) {
logger->error("Kinship file have duplicated headers!");
return -1;
}
// check IID, Lambda, U1, U2, ... U(N) where (N) is the sample size
if (headerMap.count("iid") == 0) {
logger->error("Missing 'IID' column!");
return -1;
}
columnToExtract.push_back(headerMap["iid"]);
if (headerMap.count("lambda") == 0) {
logger->error("Missing 'Lambda' column!");
return -1;
}
columnToExtract.push_back(headerMap["lambda"]);
std::string s;
for (int i = 0; i < NumSample; ++i) {
s = "u";
s += toString(i + 1);
if (headerMap.count(s) == 0) {
logger->error("Missing '%s' column!", s.c_str());
return -1;
}
columnToExtract.push_back(headerMap[s]);
}
s = "u";
s += toString(NumSample + 1);
if (headerMap.count(s) != 0) {
logger->error("Unexpected column '%s'!", s.c_str());
return -1;
}
matS.resize(NumSample, 1);
matU.resize(NumSample, NumSample);
continue;
}
// body lines
if ((int)fd.size() != fieldLen) {
logger->error(
"Inconsistent column number [ %zu ] (used to be [ %d ])in kinship "
"file line [ %d ] - skip this file!",
fd.size(), fieldLen, lineNo);
return -1;
}
const int iidColumn = columnToExtract[0];
const std::string& iid = fd[iidColumn];
if (nameMap.count(iid) == 0) {
logger->error("Unexpected sample [ %s ]!", iid.c_str());
return -1;
}
const int row = nameMap[iid];
const int lambdaColumn = columnToExtract[1];
double temp = 0.0;
if (!str2double(fd[lambdaColumn], &temp)) {
logger->warn("Invalid numeric value [ %s ] treated as zero!",
fd[lambdaColumn].c_str());
}
matS(lineNo - 2, 0) = temp;
for (int i = 0; i < NumSample; ++i) {
int uColumn = columnToExtract[i + 2];
if (!str2double(fd[uColumn], &temp)) {
logger->warn("Invalid numeric value [ %s ] treated as zero!",
fd[lambdaColumn].c_str());
}
matU(row, i) = temp;
}
}
// verify eigen decomposition results make senses
// check largest eigen vector and eigen value
Eigen::MatrixXf v1 = matK * matU.col(0);
Eigen::MatrixXf v2 = matS(0, 0) * matU.col(0);
if (matS(0, 0) > 0.5 && v1.col(0).norm() > .5 && v2.col(0).norm() > 0.5 &&
corr(v1, v2) < 0.8) {
logger->warn("Cannot verify spectral decompose results!");
return -1;
}
// check the min(10, NumSample) random eigen vector and eigen value
int randomCol = 10;
if (randomCol > NumSample - 1) {
randomCol = NumSample - 1;
}
v1 = matK * matU.col(randomCol);
v2 = matS(randomCol, 0) * matU.col(randomCol);
if (matS(randomCol, 0) > 0.5 && v1.col(0).norm() > 0.5 &&
v2.col(0).norm() > 0.5 && corr(v1, v2) < 0.8) {
logger->warn("Cannot verify spectral decompose results!");
return -1;
}
#ifdef DEBUG
std::string tmp = fn;
tmp += ".tmp";
std::ofstream ofs(tmp.c_str(), std::ofstream::out);
ofs << mat;
ofs.close();
#endif
// fprintf(stderr, "Kinship matrix [ %d x %d ] loaded", (int)mat.rows(),
// (int)mat.cols());
if (this->matK) {
delete this->matK;
this->matK = NULL;
}
return 0;
}