Example #1
0
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;
}
Example #2
0
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]);
}
Example #3
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]);
}
Example #4
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;
    }
Example #5
0
  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;
  }