integer
copy_font (integer f) {
int i;
charinfo *ci , *co;
integer k = new_font();
memcpy(font_tables[k],font_tables[f],sizeof(texfont));
set_font_cache_id(k,0);
set_font_used(k,0);
set_font_touched(k,0);
font_tables[k]->_font_name = NULL;
font_tables[k]->_font_filename = NULL;
font_tables[k]->_font_fullname = NULL;
font_tables[k]->_font_encodingname = NULL;
font_tables[k]->_font_area = NULL;
font_tables[k]->_font_cidregistry = NULL;
font_tables[k]->_font_cidordering = NULL;
font_tables[k]->_left_boundary = NULL;
font_tables[k]->_right_boundary = NULL;
set_font_name(k,xstrdup(font_name(f)));
if (font_filename(f)!= NULL)
set_font_filename(k,xstrdup(font_filename(f)));
if (font_fullname(f)!= NULL)
set_font_fullname(k,xstrdup(font_fullname(f)));
if (font_encodingname(f)!= NULL)
set_font_encodingname(k,xstrdup(font_encodingname(f)));
if (font_area(f)!= NULL)
set_font_area(k,xstrdup(font_area(f)));
if (font_cidregistry(f)!= NULL)
set_font_cidregistry(k,xstrdup(font_cidregistry(f)));
if (font_cidordering(f)!= NULL)
set_font_cidordering(k,xstrdup(font_cidordering(f)));
i = sizeof(*param_base(f))*font_params(f);
font_bytes += i;
param_base(k) = xmalloc (i);
memcpy(param_base(k),param_base(f), i);
i = sizeof(charinfo)*(Charinfo_size(f)+1);
font_bytes += i;
font_tables[k]->charinfo = xmalloc(i);
memset(font_tables[k]->charinfo,0,i);
for(i=0;i<=Charinfo_size(k);i++) {
ci = copy_charinfo(&font_tables[f]->charinfo[i]);
font_tables[k]->charinfo[i] = *ci;
}
if (left_boundary(f)!= NULL ) {
ci = copy_charinfo(left_boundary(f));
set_charinfo(k,left_boundarychar,ci);
}
if (right_boundary(f)!= NULL ) {
ci = copy_charinfo(right_boundary(f));
set_charinfo(k,right_boundarychar,ci);
}
return k;
}
charinfo *
get_charinfo (internal_font_number f, integer c) {
sa_tree_item glyph;
charinfo *ci;
if (proper_char_index(c)) {
glyph = get_sa_item(Characters(f), c);
if (!glyph) {
/* this could be optimized using controlled growth */
font_bytes += sizeof(charinfo);
glyph = ++font_tables[f]->charinfo_count;
do_realloc(font_tables[f]->charinfo, (glyph+1), charinfo);
memset (&(font_tables[f]->charinfo[glyph]),0,sizeof(charinfo));
font_tables[f]->charinfo[glyph].ef = 1000; /* init */
font_tables[f]->charinfo_size = glyph;
set_sa_item(font_tables[f]->characters, c, glyph, 1); /* 1= global */
}
return &(font_tables[f]->charinfo[glyph]);
} else if (c == left_boundarychar) {
if (left_boundary(f)==NULL) {
ci = xcalloc(1,sizeof(charinfo));
font_bytes += sizeof(charinfo);
set_left_boundary(f,ci);
}
return left_boundary(f);
} else if (c == right_boundarychar) {
if (right_boundary(f)==NULL) {
ci = xcalloc(1,sizeof(charinfo));
font_bytes += sizeof(charinfo);
set_right_boundary(f,ci);
}
return right_boundary(f);
}
return &(font_tables[f]->charinfo[0]);
}
charinfo *
char_info (internal_font_number f, integer c) {
if (f>font_id_maxval)
return 0;
if (proper_char_index(c)) {
register int glyph = find_charinfo_id(f,c);
return &(font_tables[f]->charinfo[glyph]);
} else if (c == left_boundarychar && left_boundary(f)!=NULL) {
return left_boundary(f);
} else if (c == right_boundarychar && right_boundary(f)!=NULL) {
return right_boundary(f);
}
return &(font_tables[f]->charinfo[0]);
}
int maximalRectangle(vector<vector<char>>& matrix) {
if (matrix.empty() || matrix[0].empty()) return 0;
int m = matrix.size(), n = matrix[0].size();
vector<int> height(n, 0), left_boundary(n, 0), right_boundary(n, n);
int result = 0;
for (int i = 0; i < m; ++i) {
int left = 0, right = n;
for (int j = 0; j < n; ++j) {
if (matrix[i][j] == '0') {
left = j + 1;
height[j] = 0;
left_boundary[j] = 0;
right_boundary[j] = n;
} else {
height[j]++;
left_boundary[j] = max(left_boundary[j], left);
}
}
for (int j = n - 1; j >= 0; --j) {
if (matrix[i][j] == '0') {
right = j;
} else {
right_boundary[j] = min(right_boundary[j], right);
result = max(result, height[j] * (right_boundary[j] - left_boundary[j]));
}
}
}
return result;
}
void PeakPickerHiRes::pick(const MSSpectrum& input, MSSpectrum& output, std::vector<PeakBoundary>& boundaries, bool check_spacings) const
{
// copy meta data of the input spectrum
output.clear(true);
output.SpectrumSettings::operator=(input);
output.MetaInfoInterface::operator=(input);
output.setRT(input.getRT());
output.setMSLevel(input.getMSLevel());
output.setName(input.getName());
output.setType(SpectrumSettings::CENTROID);
if (report_FWHM_)
{
output.getFloatDataArrays().resize(1);
output.getFloatDataArrays()[0].setName( report_FWHM_as_ppm_ ? "FWHM_ppm" : "FWHM");
}
// don't pick a spectrum with less than 5 data points
if (input.size() < 5) return;
// if both spacing constraints are disabled, don't check spacings at all:
if ((spacing_difference_ == std::numeric_limits<double>::infinity()) &&
(spacing_difference_gap_ == std::numeric_limits<double>::infinity()))
{
check_spacings = false;
}
// signal-to-noise estimation
SignalToNoiseEstimatorMedian<MSSpectrum > snt;
snt.setParameters(param_.copy("SignalToNoise:", true));
if (signal_to_noise_ > 0.0)
{
snt.init(input);
}
// find local maxima in profile data
for (Size i = 2; i < input.size() - 2; ++i)
{
double central_peak_mz = input[i].getMZ(), central_peak_int = input[i].getIntensity();
double left_neighbor_mz = input[i - 1].getMZ(), left_neighbor_int = input[i - 1].getIntensity();
double right_neighbor_mz = input[i + 1].getMZ(), right_neighbor_int = input[i + 1].getIntensity();
// do not interpolate when the left or right support is a zero-data-point
if (std::fabs(left_neighbor_int) < std::numeric_limits<double>::epsilon()) continue;
if (std::fabs(right_neighbor_int) < std::numeric_limits<double>::epsilon()) continue;
// MZ spacing sanity checks
double left_to_central = 0.0, central_to_right = 0.0, min_spacing = 0.0;
if (check_spacings)
{
left_to_central = central_peak_mz - left_neighbor_mz;
central_to_right = right_neighbor_mz - central_peak_mz;
min_spacing = (left_to_central < central_to_right) ? left_to_central : central_to_right;
}
double act_snt = 0.0, act_snt_l1 = 0.0, act_snt_r1 = 0.0;
if (signal_to_noise_ > 0.0)
{
act_snt = snt.getSignalToNoise(input[i]);
act_snt_l1 = snt.getSignalToNoise(input[i - 1]);
act_snt_r1 = snt.getSignalToNoise(input[i + 1]);
}
// look for peak cores meeting MZ and intensity/SNT criteria
if ((central_peak_int > left_neighbor_int) &&
(central_peak_int > right_neighbor_int) &&
(act_snt >= signal_to_noise_) &&
(act_snt_l1 >= signal_to_noise_) &&
(act_snt_r1 >= signal_to_noise_) &&
(!check_spacings ||
((left_to_central < spacing_difference_ * min_spacing) &&
(central_to_right < spacing_difference_ * min_spacing))))
{
// special case: if a peak core is surrounded by more intense
// satellite peaks (indicates oscillation rather than
// real peaks) -> remove
double act_snt_l2 = 0.0, act_snt_r2 = 0.0;
if (signal_to_noise_ > 0.0)
{
act_snt_l2 = snt.getSignalToNoise(input[i - 2]);
act_snt_r2 = snt.getSignalToNoise(input[i + 2]);
}
// checking signal-to-noise?
if ((i > 1) &&
(i + 2 < input.size()) &&
(left_neighbor_int < input[i - 2].getIntensity()) &&
(right_neighbor_int < input[i + 2].getIntensity()) &&
(act_snt_l2 >= signal_to_noise_) &&
(act_snt_r2 >= signal_to_noise_) &&
(!check_spacings ||
((left_neighbor_mz - input[i - 2].getMZ() < spacing_difference_ * min_spacing) &&
(input[i + 2].getMZ() - right_neighbor_mz < spacing_difference_ * min_spacing))))
{
++i;
continue;
}
std::map<double, double> peak_raw_data;
peak_raw_data[central_peak_mz] = central_peak_int;
peak_raw_data[left_neighbor_mz] = left_neighbor_int;
peak_raw_data[right_neighbor_mz] = right_neighbor_int;
// peak core found, now extend it
// to the left
Size k = 2;
bool previous_zero_left(false); // no need to extend peak if previous intensity was zero
Size missing_left(0);
Size left_boundary(i - 1); // index of the left boundary for the spline interpolation
while ((k <= i) && // prevent underflow
(i - k + 1 > 0) &&
!previous_zero_left &&
(missing_left <= missing_) &&
(input[i - k].getIntensity() <= peak_raw_data.begin()->second) &&
(!check_spacings ||
(peak_raw_data.begin()->first - input[i - k].getMZ() < spacing_difference_gap_ * min_spacing)))
{
double act_snt_lk = 0.0;
if (signal_to_noise_ > 0.0)
{
act_snt_lk = snt.getSignalToNoise(input[i - k]);
}
if ((act_snt_lk >= signal_to_noise_) &&
(!check_spacings ||
(peak_raw_data.begin()->first - input[i - k].getMZ() < spacing_difference_ * min_spacing)))
{
peak_raw_data[input[i - k].getMZ()] = input[i - k].getIntensity();
}
else
{
++missing_left;
if (missing_left <= missing_)
{
peak_raw_data[input[i - k].getMZ()] = input[i - k].getIntensity();
}
}
previous_zero_left = (input[i - k].getIntensity() == 0);
left_boundary = i - k;
++k;
}
// to the right
k = 2;
bool previous_zero_right(false); // no need to extend peak if previous intensity was zero
Size missing_right(0);
Size right_boundary(i+1); // index of the right boundary for the spline interpolation
while ((i + k < input.size()) &&
!previous_zero_right &&
(missing_right <= missing_) &&
(input[i + k].getIntensity() <= peak_raw_data.rbegin()->second) &&
(!check_spacings ||
(input[i + k].getMZ() - peak_raw_data.rbegin()->first < spacing_difference_gap_ * min_spacing)))
{
double act_snt_rk = 0.0;
if (signal_to_noise_ > 0.0)
{
act_snt_rk = snt.getSignalToNoise(input[i + k]);
}
if ((act_snt_rk >= signal_to_noise_) &&
(!check_spacings ||
(input[i + k].getMZ() - peak_raw_data.rbegin()->first < spacing_difference_ * min_spacing)))
{
peak_raw_data[input[i + k].getMZ()] = input[i + k].getIntensity();
}
else
{
++missing_right;
if (missing_right <= missing_)
{
peak_raw_data[input[i + k].getMZ()] = input[i + k].getIntensity();
}
}
previous_zero_right = (input[i + k].getIntensity() == 0);
right_boundary = i + k;
++k;
}
// skip if the minimal number of 3 points for fitting is not reached
if (peak_raw_data.size() < 3) continue;
CubicSpline2d peak_spline (peak_raw_data);
// calculate maximum by evaluating the spline's 1st derivative
// (bisection method)
double max_peak_mz = central_peak_mz;
double max_peak_int = central_peak_int;
double threshold = 1e-6;
OpenMS::Math::spline_bisection(peak_spline, left_neighbor_mz, right_neighbor_mz, max_peak_mz, max_peak_int, threshold);
//
// compute FWHM
//
if (report_FWHM_)
{
double fwhm_int = max_peak_int / 2.0;
threshold = 0.01 * fwhm_int;
double mz_mid, int_mid;
// left:
double mz_left = peak_raw_data.begin()->first;
double mz_center = max_peak_mz;
if (peak_spline.eval(mz_left) > fwhm_int)
{ // the spline ends before half max is reached -- take the leftmost point (probably an underestimation)
mz_mid = mz_left;
}
else
{
do
{
mz_mid = mz_left / 2 + mz_center / 2;
int_mid = peak_spline.eval(mz_mid);
if (int_mid < fwhm_int)
{
mz_left = mz_mid;
}
else
{
mz_center = mz_mid;
}
} while (fabs(int_mid - fwhm_int) > threshold);
}
const double fwhm_left_mz = mz_mid;
// right ...
double mz_right = peak_raw_data.rbegin()->first;
mz_center = max_peak_mz;
if (peak_spline.eval(mz_right) > fwhm_int)
{ // the spline ends before half max is reached -- take the rightmost point (probably an underestimation)
mz_mid = mz_right;
}
else
{
do
{
mz_mid = mz_right / 2 + mz_center / 2;
int_mid = peak_spline.eval(mz_mid);
if (int_mid < fwhm_int)
{
mz_right = mz_mid;
}
else
{
mz_center = mz_mid;
}
} while (fabs(int_mid - fwhm_int) > threshold);
}
const double fwhm_right_mz = mz_mid;
const double fwhm_absolute = fwhm_right_mz - fwhm_left_mz;
output.getFloatDataArrays()[0].push_back( report_FWHM_as_ppm_ ? fwhm_absolute / max_peak_mz * 1e6 : fwhm_absolute);
} // FWHM
// save picked peak into output spectrum
Peak1D peak;
PeakBoundary peak_boundary;
peak.setMZ(max_peak_mz);
peak.setIntensity(max_peak_int);
peak_boundary.mz_min = input[left_boundary].getMZ();
peak_boundary.mz_max = input[right_boundary].getMZ();
output.push_back(peak);
boundaries.push_back(peak_boundary);
// jump over profile data points that have been considered already
i = i + k - 1;
}
}
return;
}