static double ssim(float *x, float *y, int n)
{
double mx, my, sx, sy, sxy = 0;
meanvar(&mx, &sx, x, n);
meanvar(&my, &sy, y, n);
for (int i = 0; i < n; i++)
sxy += (x[i] - mx)*(y[i] - my);
sxy /= n - 1;
double Lx = dynamic_range(x, n);
double Ly = dynamic_range(x, n);
double L = (Lx + Ly)/2;
double C1 = SSIM_K1 * L;
double C2 = SSIM_K2 * L;
C1 *= C1;
C2 *= C2;
double r = (2*mx*my + C1) * (2*sxy + C2);
r /= (mx*mx + my*my + C1) * (sx + sx + C2);
return r;
}
void print_parameter_settings ()
{
fprintf (stderr, "\tImage size = %i %i\n", cvts.xmax, cvts.ymax);
fprintf (stderr, "\tLowest scale = %i pixels\t\t(-low <integer>)\n", scale_low);
fprintf (stderr, "\tHighest scale = %i pixels\t\t(-high <integer>)\n", scale_high);
fprintf (stderr, "\tNumber of scales = %i\t\t\t(-num <integer>)\n", range);
fprintf (stderr, "\tScale spacing = %f\n", S_I(1) / S_I(0));
fprintf (stderr, "\tKey value = %f\t\t(-key <float>)\n", key);
fprintf (stderr, "\tWhite value = %f\t\t(-white <float>)\n", white);
fprintf (stderr, "\tPhi = %f\t\t(-phi <float>)\n", phi);
fprintf (stderr, "\tThreshold = %f\t\t(-threshold <float>)\n", threshold);
dynamic_range ();
}
static double psnr(float *x, float *y, int n)
{
return 20 * log10(dynamic_range(x, n)/root_mean_square_error(x, y, n));
}
bool mspectrumcondition::condition(mspectrum &_s)
{
/*
* bail out if conditioning has been turned off
*/
if(m_bUsePhosphoDetection) {
if(!find_loss(_s,98.0,3.0)) {
return false;
}
}
_s.m_vMINeutral.clear();
sort(_s.m_vMI.begin(),_s.m_vMI.end(),lessThanMImz);
if(_s.m_dMH < 1.0 && !_s.m_vMI.empty()) {
m_bCharge = true;
if(_s.m_fZ == 2.0) {
_s.m_dMH = _s.m_vMI[_s.m_vMI.size()-1].m_fM*1.2;
}
else if(_s.m_fZ == 3.0) {
_s.m_dMH = _s.m_vMI[_s.m_vMI.size()-1].m_fM*1.7;
}
}
if(_s.m_vdStats.size() == 0) {
vector<mi>::iterator itMI = _s.m_vMI.begin();
vector<mi>::iterator itEnd = _s.m_vMI.end();
double dSum = 0.0;
double dMax = 0.0;
while(itMI != itEnd) {
if(dMax < itMI->m_fI) {
dMax = itMI->m_fI;
}
dSum += itMI->m_fI;
itMI++;
}
_s.m_vdStats.push_back(dSum);
_s.m_vdStats.push_back(dMax);
_s.m_vdStats.push_back(m_fFactor);
}
if(_s.m_fZ > m_fMaxZ) {
return false;
}
if(!m_bCondition) {
return true;
}
/*
* check the parent ion charge and return false if it is too large
*/
if(m_bUseNoiseSuppression) {
/*
* check the parent ion mass against the minimum mass allowed (about 600.0 is usually safe)
*/
if(m_bUseMinMass) {
if(_s.m_dMH < m_fMinMass)
return false;
}
if(m_bUseChargeSuppression) {
if((long)(_s.m_fZ+0.5) > m_lMaxCharge) {
return false;
}
}
}
size_t tSize = _s.m_vMI.size();
size_t a = 0;
float fMaxI = 0;
/*
* this method doesn't really remove isotopes: it cleans up multiple intensities within one Dalton
* of each other.
*/
// sort(_s.m_vMI.begin(),_s.m_vMI.end(),lessThanMImz);
if(m_bUseIsotopes) {
remove_isotopes(_s);
}
/*
* remove ions near the parent ion m/z
*/
if(m_bUseParent) {
remove_parent(_s);
}
/*
* remove low mass immonium ions prior to normalization
*/
if(m_bUseLowestMass) {
remove_low_masses(_s);
}
/*
* normalize the spectrum
*/
vector<mi>::iterator itMI = _s.m_vMI.begin();
vector<mi>::iterator itEnd = _s.m_vMI.end();
double dSum = 0.0;
double dMax = 0.0;
while(itMI != itEnd) {
if(dMax < itMI->m_fI) {
dMax = itMI->m_fI;
}
dSum += itMI->m_fI;
itMI++;
}
_s.m_vdStats.clear();
_s.m_vdStats.push_back(dSum);
_s.m_vdStats.push_back(dMax);
_s.m_vdStats.push_back(m_fFactor);
if(m_bUseDynamicRange) {
dynamic_range(_s);
}
if(m_bUseNeutralLoss) {
remove_neutral(_s);
}
/*
* reject the spectrum if there aren't enough peaks
*/
if(m_bUseMinSize) {
if((long)_s.m_vMI.size() < m_lMinSize)
return false;
}
/*
* check to see if the spectrum has the characteristics of noise
*/
if(m_bUseNoiseSuppression) {
if(is_noise(_s)) {
return false;
}
}
/*
* retrieve the N most intense peaks
*/
if(m_bUseIsotopes) {
clean_isotopes(_s);
}
if(m_bUseMaxPeaks) {
sort(_s.m_vMI.begin(),_s.m_vMI.end(),lessThanMI);
remove_small(_s);
}
sort(_s.m_vMI.begin(),_s.m_vMI.end(),lessThanMImz);
itMI = _s.m_vMI.begin();
itEnd = _s.m_vMI.end();
dSum = 0.0;
dMax = 0.0;
while(itMI != itEnd) {
if(dMax < itMI->m_fI) {
dMax = itMI->m_fI;
}
dSum += itMI->m_fI;
itMI++;
}
_s.m_vdStats[0] = dSum*m_fFactor;
_s.m_vdStats[1] = dMax*m_fFactor;
_s.m_vdStats[2] = m_fFactor;
return true;
}
