C++ Spectrum::add方法代码示例

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;
//.........这里部分代码省略.........

bool CNoiseReduction::ScanAverage(Spectrum& sp, char* file, int width, float cutoff){
  
  Spectrum ts;
  Spectrum ps=sp;
  MSReader r;
 
  int i;
  int j;
  int k;
  int widthCount=0;
  int numScans=1;
  double dif;
  double prec;
  double dt;
  double c=CParam(ps,3);

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

  ps.getRawFilter(cFilter1,256);

  while(widthCount<(width*2)){

    //Alternate looking left and right
    if(bLeft){
      bLeft=false;
      widthCount++;
      while(posLeft>0){
        r.readFile(file,ts,posLeft);
        if(ts.getScanNumber()==0) break;
        ts.getRawFilter(cFilter2,256);
        if(strcmp(cFilter1,cFilter2)==0) break;
        posLeft--;
      }
    } else {
      bLeft=true;
      widthCount++;
      while(true){
        r.readFile(file,ts,posRight);
        if(ts.getScanNumber()==0) break;
        ts.getRawFilter(cFilter2,256);
        if(strcmp(cFilter1,cFilter2)==0) break;
        posRight++;
      }
    }
    if(ts.getScanNumber()==0) continue;

    numScans++;

    //Match peaks between pivot scan and temp scan
    k=0;
    for(i=0;i<ps.size();i++){
      dif=100000.0;
      prec = c * ps.at(i).mz * ps.at(i).mz / 2;

      for(j=k;j<ts.size();j++){
        dt=fabs(ps.at(i).mz-ts.at(j).mz);
        if(dt<=dif) {
          if(dt<prec) {
            ps.at(i).intensity+=ts.at(j).intensity;
            ts.at(j).mz=-1.0;
            k=j+1;
            break;
          }
          dif=dt;
        } else {
          k=j-1;
          break;
        }
      }
    }

    //Add unmatched peaks from temp scan
    for(i=0;i<ts.size();i++){
      if(ts.at(i).mz>-1.0) ps.add(ts.at(i));
    }

    //Sort pivot scan peaks for fast traversal against next temp scan
    ps.sortMZ();

  }

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

  return true;
}

//.........这里部分代码省略.........
      //Assume High resolution data at all times
      if(!cs.centroid) {
        FirstDerivativePeaks(tmpSpec,1);
        tmpSpec.setRawFilter(cFilter2);
      }

      s.push_back(tmpSpec);
      //cout << tmpSpec.getScanNumber() << " " << cFilter1 << " xx " << cFilter2 << endl;
      if(strcmp(cFilter1,cFilter2)==0){  
        j++;
				if(j==(int)(cs.boxcar/2)) break;
      }
      i++;
    }

  }

  //return false if we reached the end
  if(pos>=(int)s.size()) return false;

  //Because Deque may have mixed spectra, create list of Deque indexes to compare
  //Shrink Deque on the left if some spectra are not needed
  //Expand Deque to the right if needed and possible
  //cout << "Checking scan " << s[pos].getScanNumber() << endl;
  v.clear();
  s[pos].getRawFilter(cFilter1,256);

  //look left
  for(i=pos-1;i>=0;i--){
    s[i].getRawFilter(cFilter2,256);
    if(strcmp(cFilter1,cFilter2)==0) {
      v.push_back(i);
			if(v.size()==(int)(cs.boxcar/2)) break;
    }
  }

  //erase unneeded left items
  while(i>0){
    s.pop_front();
    i--;
    for(j=0;j<(int)v.size();j++) v[j]--;
    pos--;
  }

  //look right
  j=0;
  for(i=pos+1;i<(int)s.size();i++){
    s[i].getRawFilter(cFilter2,256);
    if(strcmp(cFilter1,cFilter2)==0) {
      v.push_back(i);
      j++;
      if(j==(int)(cs.boxcar/2)) break;
    }
  }

  //extend right side if needed
  while(j<(int)(cs.boxcar/2)){
    r->readFile(NULL,tmpSpec);
    if(tmpSpec.getScanNumber()==0) break;    
    tmpSpec.getRawFilter(cFilter2,256);

    //Assume High resolution data at all times
    if(!cs.centroid) {
      FirstDerivativePeaks(tmpSpec,1);
      tmpSpec.setRawFilter(cFilter2);
    }

    s.push_back(tmpSpec);
    if(strcmp(cFilter1,cFilter2)==0) {
      v.push_back(s.size()-1);
      j++;
    }
  }

  //if there is nothing to compare to, exit now
  if(v.size()==0) return false;

  //compare peaks
  //cout << "Checking " << s[pos].size() << " peaks." << endl;
  for(i=0;i<s[pos].size();i++){
    matchCount=1;
    for(j=0;j<(int)v.size();j++){
      if(s[v[j]].size()<1) continue;
      index = NearestPeak(s[v[j]],s[pos].at(i).mz);
      ppm=fabs( (s[v[j]].at(index).mz-s[pos].at(i).mz)/s[pos].at(i).mz * 1000000);
      if(ppm<cs.ppm) matchCount++;
    }
		if(matchCount>=cs.boxcarFilter || matchCount==v.size()) sp.add(s[pos].at(i));
  }
  sp.setScanNumber(s[pos].getScanNumber());
  sp.setScanNumber(s[pos].getScanNumber(true),true);
  sp.setRTime(s[pos].getRTime());
  pos++;

  //cout << sp.getScanNumber() << endl;

  //cout << "Done! " << sp.size() << " " << pos << endl;
  return true;

}

//First derivative method taken from CSpecAnalyze, returns base peak intensity of the set
void CNoiseReduction::FirstDerivativePeaks(Spectrum& sp, int winSize){
  int i,j;
  float maxIntensity;
  int bestPeak;
  bool bLastPos;
  Spectrum gp;

	int nextBest;
	double FWHM;
	Peak_T centroid;

  bLastPos=false;
  for(i=0;i<sp.size()-winSize;i++){

    if(sp.at(i).intensity<sp.at(i+winSize).intensity) {
      bLastPos=true;
      continue;
    } else {
      if(bLastPos){
				bLastPos=false;
	
				//find max and add peak
				maxIntensity=0;
				for(j=i;j<i+winSize;j++){
				  if (sp.at(j).intensity>maxIntensity){
				    maxIntensity=sp.at(j).intensity;
				    bestPeak = j;
				  }
				}

				//Best estimate of Gaussian centroid
				//Get 2nd highest point of peak
				if(bestPeak==sp.size()-1){
					nextBest=bestPeak-1;
				} else if(sp.at(bestPeak-1).intensity > sp.at(bestPeak+1).intensity){
					nextBest=bestPeak-1;
				} else {
					nextBest=bestPeak+1;
				}

				//Get FWHM
				FWHM = calcFWHM(sp.at(bestPeak).mz);

				//Calc centroid MZ (in three lines for easy reading)
				centroid.mz = pow(FWHM,2)*log(sp.at(bestPeak).intensity/sp.at(nextBest).intensity);
				centroid.mz /= GC*(sp.at(bestPeak).mz-sp.at(nextBest).mz);
				centroid.mz += (sp.at(bestPeak).mz+sp.at(nextBest).mz)/2;

				//Calc centroid intensity
				centroid.intensity=(float)(sp.at(bestPeak).intensity/exp(-pow((sp.at(bestPeak).mz-centroid.mz)/FWHM,2)*GC));

				//some peaks are funny shaped and have bad gaussian fit.
				//if error is more than 10%, keep existing intensity
				if( fabs((sp.at(bestPeak).intensity - centroid.intensity) / centroid.intensity * 100) > 10 ||
            //not a good check for infinity
            centroid.intensity>999999999999.9 ||
            centroid.intensity < 0 ) {
					centroid.intensity=sp.at(bestPeak).intensity;
				}

				//Hack until I put in mass ranges
				if(centroid.mz<0 || centroid.mz>2000) {
					//do nothing if invalid mz
				} else {
					gp.add(centroid);
				}
				i+=winSize-1;
      }

    }
  }
  
  int scanNumber=sp.getScanNumber();
  int scanNumber2=sp.getScanNumber(false);
  float rTime=sp.getRTime();
  sp = gp;
  sp.setRTime(rTime);
  sp.setScanNumber(scanNumber);
  sp.setScanNumber(scanNumber2,true);

}

bool CNoiseReduction::NewScanAveragePlusDeNoise(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;
  int match;
  double dif;
  double prec;
  double dt;
  double c;

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

  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);
  }

  //set our pivot spectrum
  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(strcmp(cFilter1,cFilter2)==0) {
            index=posLeft;
            break;
          }
        } else {
          bs[posLeft].getRawFilter(cFilter2,256);
          if(strcmp(cFilter1,cFilter2)==0) {
            index=posLeft;
            break;
          }
        }
      }

    } else {
      bLeft=true;
//.........这里部分代码省略.........

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++;
//.........这里部分代码省略.........