Example #1
0
bool CNoiseReduction::NewScanAverage(Spectrum& sp, char* file, int width, float cutoff, int scanNum){
  
  Spectrum ts;

  vector<int> vPos;
   
  int i;
  int j;
  int k;
  int m;
  int widthCount=0;
  int numScans=1;
  double dif;
  double prec;
  double dt;
  double c;

  bool bLeft=true;
  int posLeft;
  int posRight;
  int index;
  char cFilter1[256];
  //char cFilter2[256];

  //double slope;
  //double intercept;

  sp.clear();
  Spectrum* specs;
  specs = new Spectrum[width*2+1];

  //if file is not null, create new buffer
  if(file!=NULL){
    strcpy(lastFile,file);
    bs.clear();
    if(scanNum>0) r->readFile(file,ts,scanNum);
    else r->readFile(file,ts);
    if(ts.getScanNumber()==0) {
      delete [] specs;
      return false;
    }
    bs.push_back(ts);
    specs[0]=bs[0];
    c=CParam(specs[0],3);
    posA=0;
  } else {
    posA++;
    if(posA>=(int)bs.size()) { //end of buffer, no more data
      delete [] specs;
      return false; 
    }
    specs[0]=bs[posA];
    c=CParam(specs[0],3);
  }

  specs[0].getRawFilter(cFilter1,256);

  posLeft=posA;
  posRight=posA;
  while(widthCount<(width*2)){

    index=-1;

    //Alternate looking left and right
    if(bLeft){
      bLeft=false;
      widthCount++;
      
      while(true){
        posLeft--;
        if(posLeft<0) { //buffer is too short on left, add spectra
          i=bs[0].getScanNumber();
          while(true){
            i--;
            if(i==0) break;
            r->readFile(lastFile,ts,i);
            if(ts.getScanNumber()==0) continue;
            else break;
          }
          if(i==0) break;
          bs.push_front(ts);
          posA++;
          posRight++;
          posLeft=0;
          //ts.getRawFilter(cFilter2,256);
          if(ts.getMsLevel()==cs.msLevel) {
            index=posLeft;
            break;
          }
        } else {
          //bs[posLeft].getRawFilter(cFilter2,256);
          if(bs[posLeft].getMsLevel()==cs.msLevel) {
            index=posLeft;
            break;
          }
        }
      }

    } else {
      bLeft=true;
      widthCount++;

      while(true){
        posRight++;
        if(posRight>=(int)bs.size()) { //buffer is too short on right, add spectra
          r->readFile(lastFile,ts,bs[bs.size()-1].getScanNumber());
          r->readFile(NULL,ts);
          if(ts.getScanNumber()==0) {
            posRight--;
            break;
          }
          bs.push_back(ts);
          //ts.getRawFilter(cFilter2,256);
          if(ts.getMsLevel()==cs.msLevel) {
            index=posRight;
            break;
          }
        } else {
          //bs[posRight].getRawFilter(cFilter2,256);
          if(bs[posRight].getMsLevel()==cs.msLevel) {
            index=posRight;
            break;
          }
        }
      }
    }

    if(index==-1)  continue;
    specs[numScans++]=bs[index];

  }
  
  double tmz;
  int mzcount=0;

  /* Ledford equation correction
  double freq;
  double conA=0.0;
  double conB=0.0;

  for(m=0;m<numScans;m++){
    conA+=specs[m].getConversionA();
    conB+=specs[m].getConversionB();
  }
  conA/=numScans;
  conB/=numScans;

  printf("%.10lf, %.10lf\n",conA,conB);
  for(k=0;k<numScans;k++){
    for(j=0;j<specs[k].size();j++){
      freq = sqrt(specs[k].getConversionA()*specs[k].getConversionA() - (4*specs[k].at(j).mz*(-specs[k].getConversionB())));
      freq += specs[k].getConversionA();
      freq /= (2*specs[k].at(j).mz);

      specs[k].at(j).mz = conA/freq + conB/(freq*freq);
    }
  }
  */

  //Match peaks between pivot scan (0) and neighbors (the rest)
  for(m=0;m<numScans;m++){
    
    vPos.clear();
    for(i=0;i<numScans;i++) vPos.push_back(0);

    for(i=0;i<specs[m].size();i++){ //iterate all points
      if(specs[m].at(i).intensity<0.1) continue;
      tmz=specs[m].at(i).mz;
      mzcount=1;
      prec = c * tmz * tmz / 2;
      
      for(k=m+1;k<numScans;k++){ //iterate all neighbors
        dif=100000.0;

        for(j=vPos[k];j<specs[k].size();j++){ //check if point is a match
          if(specs[k].at(j).intensity<0.1) continue; //skip meaningless datapoints to speed along
          dt=fabs(tmz-specs[k].at(j).mz);

          if(dt<=dif) {
            if(dt<prec) {
              //linear interpolate
              //if(specs[k].at(j).mz<tmz && j<specs[k].size()-1){
              //  slope=(specs[k].at(j+1).intensity-specs[k].at(j).intensity)/(specs[k].at(j+1).mz-specs[k].at(j).mz);
              //  intercept=specs[k].at(j).intensity-specs[k].at(j).mz*slope;
              //  specs[m].at(i).intensity+=(tmz*slope+intercept);
              //} else if(specs[k].at(j).mz>tmz && j>0) {
              //  slope=(specs[k].at(j).intensity-specs[k].at(j-1).intensity)/(specs[k].at(j).mz-specs[k].at(j-1).mz);
              //  intercept=specs[k].at(j).intensity-specs[k].at(j).mz*slope;
              //  specs[m].at(i).intensity+=(tmz*slope+intercept);
              //} else {
              specs[m].at(i).intensity += specs[k].at(j).intensity;
              //}

              //Averaging the mz values appears equivalent to realigning all spectra against
              //an average Ledford correction.
              specs[m].at(i).mz += specs[k].at(j).mz;
              vPos[k]=j+1;
              specs[k].at(j).intensity=-1.0;
              mzcount++;
              break;
            }
            dif=dt;
          } else {
            vPos[k]=j-1;
            break;
          }
        }
      }//for k

      sp.add(specs[m].at(i).mz/mzcount,specs[m].at(i).intensity/numScans);

    } //next i
  } //next m

  if(sp.size()>0) sp.sortMZ();
  sp.setScanNumber(specs[0].getScanNumber());
  sp.setScanNumber(specs[0].getScanNumber(true),true);
  sp.setRTime(specs[0].getRTime());
  sp.setRawFilter(cFilter1);

  if(posLeft>0){
    while(posLeft>0){
      bs.pop_front();
      posLeft--;
      posA--;
    }
  }
  delete [] specs;
  return true;
}
Example #2
0
bool CNoiseReduction::ScanAveragePlusDeNoise(Spectrum& sp, char* file, int width, float cutoff, int scanNum){
  
  Spectrum ts;
  Spectrum ps;
  //MSReader r;

  vector<int> v;
  vector<int> vPos;
 
  int i;
  int j;
  int k;
  int widthCount=0;
  int numScans=1;
  int match;
  double dif;
  double prec;
  double dt;
  double c;

  bool bLeft=true;
  int posLeft=ps.getScanNumber()-1;
  int posRight=ps.getScanNumber()+1;
  int index;
  char cFilter1[256];
  //char cFilter2[256];

  sp.clear();

  //if file is not null, create new buffer
  if(file!=NULL){
    strcpy(lastFile,file);
    bs.clear();
    if(scanNum>0) r->readFile(file,ts,scanNum);
    else r->readFile(file,ts);
    if(ts.getScanNumber()==0) return false;
    bs.push_back(ts);
    ps=bs[0];
    c=CParam(ps,3);
    posA=0;
  } else {
    posA++;
    //cout << "ER: " << posA << " " << bs.size() << endl;
    if(posA>=(int)bs.size()) return false; //end of buffer, no more data
    ps=bs[posA];
    c=CParam(ps,3);
  }

  //set our pivot spectrum
  //ps=bs[posA];
  ps.getRawFilter(cFilter1,256);
  //cout << "Averaging: " << ps.getScanNumber() << endl;

  posLeft=posA;
  posRight=posA;
  while(widthCount<(width*2)){

    index=-1;

    //Alternate looking left and right
    if(bLeft){
      bLeft=false;
      widthCount++;
      
      while(true){
        posLeft--;
        //cout << posLeft << endl;
        if(posLeft<0) { //buffer is too short on left, add spectra
          i=bs[0].getScanNumber();
          while(true){
            i--;
            //cout << "I: " << i << endl;
            if(i==0) break;
            r->readFile(lastFile,ts,i);
            if(ts.getScanNumber()==0) continue;
            else break;
          }
          if(i==0) break;
          bs.push_front(ts);
          for(i=0;i<(int)v.size();i++)v[i]++;
          posA++;
          posRight++;
          posLeft=0;
          //ts.getRawFilter(cFilter2,256);
          if(ts.getMsLevel()==cs.msLevel) {
            index=posLeft;
            break;
          }
        } else {
          //bs[posLeft].getRawFilter(cFilter2,256);
          if(bs[posLeft].getMsLevel()==cs.msLevel) {
            index=posLeft;
            break;
          }
        }
      }

    } else {
      bLeft=true;
      widthCount++;

      while(true){
        posRight++;
        if(posRight>=(int)bs.size()) { //buffer is too short on right, add spectra
          r->readFile(lastFile,ts,bs[bs.size()-1].getScanNumber());
          r->readFile(NULL,ts);
          if(ts.getScanNumber()==0) {
            posRight--;
            break;
          }
          bs.push_back(ts);
          //ts.getRawFilter(cFilter2,256);
          if(ts.getMsLevel()==cs.msLevel) {
            index=posRight;
            break;
          }
        } else {
          //bs[posRight].getRawFilter(cFilter2,256);
          if(bs[posRight].getMsLevel()==cs.msLevel) {
            index=posRight;
            break;
          }
        }
      }
    }

    if(index==-1)  continue;
   
    //ts=bs[index];
    v.push_back(index);

    numScans++;
  }

  //cout << "Still Averaging: " << ps.getScanNumber() << endl;
  //cout << " with: ";
  //for(i=0;i<v.size();i++) cout << bs[v[i]].getScanNumber() << " ";
  //cout << endl;

  //cout << numScans << " " << v.size() << endl;

  //Match peaks between pivot scan and neighbors
  for(i=0;i<(int)v.size();i++) vPos.push_back(0);
  for(i=0;i<(int)ps.size();i++){ //iterate all points
    prec = c * ps.at(i).mz * ps.at(i).mz / 2;
    match=1;

    for(k=0;k<(int)v.size();k++){ //iterate all neighbors
      dif=100000.0;
      //cout << "Checking " << bs[v[k]].getScanNumber() << " pos " << vPos[k] << endl;

      for(j=vPos[k];j<bs[v[k]].size();j++){ //check if point is a match
        dt=fabs(ps.at(i).mz-bs[v[k]].at(j).mz);
        if(dt<=dif) {
          if(dt<prec) {
            ps.at(i).intensity+=bs[v[k]].at(j).intensity;
            vPos[k]=j+1;
            match++;
            break;
          }
          dif=dt;
        } else {
          vPos[k]=j-1;
          break;
        }
      }

    }

    //if data point was not visible across enough scans, set it to 0
		if(match<cs.boxcarFilter && match<(int)v.size()) ps.at(i).intensity=0.0;

  }


  //Average points and apply cutoff
  for(i=0;i<ps.size();i++) {
    ps.at(i).intensity/=numScans;
    sp.add(ps.at(i));
    //if(ps.at(i).intensity>=cutoff) sp.add(ps.at(i));
  }

  sp.setScanNumber(ps.getScanNumber());
  sp.setScanNumber(ps.getScanNumber(true),true);
  sp.setRTime(ps.getRTime());
  sp.setRawFilter(cFilter1);

  //clear unused buffer
  if(posLeft>0){
    while(posLeft>0){
      bs.pop_front();
      posLeft--;
      posA--;
    }
  }

  //cout << "Done averaging" << endl;

  return true;
}