Vector_double stfnum::get_scale(Vector_double& data, double oldx) {
Vector_double xyscale(4);
if (data.size() == 0) {
xyscale[0] = 1.0/oldx;
xyscale[1] = 0.0;
xyscale[2] = 1.0;
xyscale[3] = 0.0;
return xyscale;
}
double ymin,ymax,amp,off;
ymin = *data.begin();
ymax = ymin;
for (Vector_double::iterator it = data.begin(); it != data.end(); ++it) {
double v = *it;
if (v < ymin) ymin = v;
else if (ymax < v) ymax = v;
}
amp = ymax - ymin;
off = ymin / amp;
data = stfio::vec_scal_mul(data, 1.0 / amp);
data = stfio::vec_scal_minus(data, off);
xyscale[0] = 1.0/(data.size()*oldx);
xyscale[1] = 0;
xyscale[2] = 1.0/amp;
xyscale[3] = off;
return xyscale;
}
std::map<double, int>
stf::histogram(const Vector_double& data, int nbins) {
if (nbins==-1) {
nbins = int(data.size()/100.0);
}
double fmax = *std::max_element(data.begin(), data.end());
double fmin = *std::min_element(data.begin(), data.end());
fmax += (fmax-fmin)*1e-9;
double bin = (fmax-fmin)/nbins;
std::map<double,int> histo;
for (int nbin=0; fmin + nbin*bin < fmax; ++nbin) {
histo[fmin + nbin*bin] = 0;
}
for (std::size_t npoint=0; npoint < data.size(); ++npoint) {
int nbin = int((data[npoint]-fmin) / bin);
histo[fmin + nbin*bin]++;
}
return histo;
}
Vector_double
stf::deconvolve(const Vector_double& data, const Vector_double& templ,
int SR, double hipass, double lopass, stfio::ProgressInfo& progDlg)
{
bool skipped = false;
progDlg.Update( 0, "Starting deconvolution...", &skipped );
if (data.size()<=0 || templ.size() <=0 || templ.size() > data.size()) {
std::out_of_range e("subscript out of range in stf::filter()");
throw e;
}
/* pad templ */
Vector_double templ_padded(data.size());
std::copy(templ.begin(), templ.end(), templ_padded.begin());
if (templ.size() < templ_padded.size()) {
std::fill(templ_padded.begin()+templ.size(), templ_padded.end(), 0);
}
Vector_double data_return(data.size());
if (skipped) {
data_return.resize(0);
return data_return;
}
double *in_data, *in_templ_padded;
//fftw_complex is a double[2]; hence, out is an array of
//double[2] with out[n][0] being the real and out[n][1] being
//the imaginary part.
fftw_complex *out_data, *out_templ_padded;
fftw_plan p_data, p_templ, p_inv;
//memory allocation as suggested by fftw:
in_data =(double *)fftw_malloc(sizeof(double) * data.size());
out_data = (fftw_complex *)fftw_malloc(sizeof(fftw_complex) * ((int)(data.size()/2)+1));
in_templ_padded =(double *)fftw_malloc(sizeof(double) * templ_padded.size());
out_templ_padded = (fftw_complex *)fftw_malloc(sizeof(fftw_complex) * ((int)(templ_padded.size()/2)+1));
std::copy(data.begin(), data.end(), &in_data[0]);
std::copy(templ_padded.begin(), templ_padded.end(), &in_templ_padded[0]);
//plan the ffts and execute them:
p_data =fftw_plan_dft_r2c_1d((int)data.size(), in_data, out_data,
FFTW_ESTIMATE);
fftw_execute(p_data);
p_templ =fftw_plan_dft_r2c_1d((int)templ_padded.size(),
in_templ_padded, out_templ_padded, FFTW_ESTIMATE);
fftw_execute(p_templ);
double SI=1.0/SR; //the sampling interval
progDlg.Update( 25, "Performing deconvolution...", &skipped );
if (skipped) {
data_return.resize(0);
return data_return;
}
Vector_double f_c(1);
for (std::size_t n_point=0; n_point < (unsigned int)(data.size()/2)+1; ++n_point) {
/* highpass filter */
double f = n_point / (data.size()*SI);
double rslt_hi = 1.0;
if (hipass > 0) {
f_c[0] = hipass;
rslt_hi = 1.0-fgaussColqu(f, f_c);
}
/* lowpass filter */
double rslt_lo = 1.0;
if (lopass > 0) {
f_c[0] = lopass;
rslt_lo= fgaussColqu(f, f_c);
}
/* do the division in place */
double a = out_data[n_point][0];
double b = out_data[n_point][1];
double c = out_templ_padded[n_point][0];
double d = out_templ_padded[n_point][1];
double mag2 = c*c + d*d;
out_data[n_point][0] = rslt_hi * rslt_lo * (a*c + b*d)/mag2;
out_data[n_point][1] = rslt_hi * rslt_lo * (b*c - a*d)/mag2;
}
//do the reverse fft:
p_inv = fftw_plan_dft_c2r_1d((int)data.size(),out_data, in_data, FFTW_ESTIMATE);
fftw_execute(p_inv);
//fill the return array, adding the offset, and scaling by data.size()
//(because fftw computes an unnormalized transform):
for (std::size_t n_point=0; n_point < data.size(); ++n_point) {
data_return[n_point]= in_data[n_point]/data.size();
}
fftw_destroy_plan(p_data);
fftw_destroy_plan(p_templ);
fftw_destroy_plan(p_inv);
fftw_free(in_data);
fftw_free(out_data);
fftw_free(in_templ_padded);
fftw_free(out_templ_padded);
progDlg.Update( 50, "Computing data histogram...", &skipped );
if (skipped) {
data_return.resize(0);
return data_return;
}
int nbins = int(data_return.size()/500.0);
std::map<double, int> histo = histogram(data_return, nbins);
double max_value = -1;
double max_time = 0;
double maxhalf_time = 0;
Vector_double histo_fit(0);
for (std::map<double,int>::const_iterator it=histo.begin();
it != histo.end(); ++it) {
if (it->second > max_value) {
max_value = it->second;
max_time = it->first;
}
histo_fit.push_back(it->second);
#ifdef _STFDEBUG
std::cout << it->first << "\t" << it->second << std::endl;
#endif
}
for (std::map<double,int>::const_iterator it=histo.begin();
it != histo.end(); ++it) {
if (it->second > 0.5*max_value) {
maxhalf_time = it->first;
break;
}
}
maxhalf_time = fabs(max_time-maxhalf_time);
progDlg.Update( 75, "Fitting Gaussian...", &skipped );
if (skipped) {
data_return.resize(0);
return data_return;
}
/* Fit Gaussian to histogram */
Vector_double opts = LM_default_opts();
std::string info;
int warning;
std::vector< stf::storedFunc > funcLib = stf::GetFuncLib();
double interval = (++histo.begin())->first-histo.begin()->first;
/* Initial parameter guesses */
Vector_double pars(3);
pars[0] = max_value;
pars[1] = (max_time - histo.begin()->first);
pars[2] = maxhalf_time *sqrt(2.0)/2.35482;
#ifdef _STFDEBUG
std::cout << "nbins: " << nbins << std::endl;
std::cout << "initial values:" << std::endl;
for (std::size_t np=0; np<pars.size(); ++np) {
std::cout << pars[np] << std::endl;
}
#endif
#ifdef _STFDEBUG
double chisqr =
#endif
lmFit(histo_fit, interval, funcLib[funcLib.size()-1], opts, true,
pars, info, warning );
#ifdef _STFDEBUG
std::cout << chisqr << "\t" << interval << std::endl;
std::cout << "final values:" << std::endl;
for (std::size_t np=0; np<pars.size(); ++np) {
std::cout << pars[np] << std::endl;
}
#endif
double sigma = pars[2]/sqrt(2.0);
/* return data in terms of sigma */
for (std::size_t n_point=0; n_point < data.size(); ++n_point) {
data_return[n_point] /= sigma;
}
progDlg.Update( 100, "Done.", &skipped );
return data_return;
}
Vector_double stfio::vec_vec_div(const Vector_double& vec1, const Vector_double& vec2) {
Vector_double ret_vec(vec1.size());
std::transform(vec1.begin(), vec1.end(), vec2.begin(), ret_vec.begin(), std::divides<double>());
return ret_vec;
}
Vector_double stfio::vec_scal_div(const Vector_double& vec, double scalar) {
Vector_double ret_vec(vec.size(), scalar);
std::transform(vec.begin(), vec.end(), ret_vec.begin(), ret_vec.begin(), std::divides<double>());
return ret_vec;
}