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; }
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; }
bool CNoiseReduction::DeNoise(Spectrum& sp){ double ppm; int i,j,k; int index; int matchCount; char cFilter1[256]; char cFilter2[256]; Spectrum tmpSpec; vector<int> v; sp.clear(); if(pos==0){ if((cs.scan.iLower>0)) { k=cs.scan.iLower; r->readFile(&cs.inFile[0],tmpSpec,cs.scan.iLower); } else { r->readFile(&cs.inFile[0],tmpSpec); k=tmpSpec.getScanNumber(); } if(tmpSpec.getScanNumber()==0) return false; tmpSpec.getRawFilter(cFilter1,256); //Gather left side of scan i=1; j=0; while( k-i > 0){ r->readFile(&cs.inFile[0],tmpSpec,cs.scan.iLower-i); if(tmpSpec.getScanNumber()==0) { i++; continue; } tmpSpec.getRawFilter(cFilter2,256); //Assume High resolution data at all times if(!cs.centroid) { FirstDerivativePeaks(tmpSpec,1); tmpSpec.setRawFilter(cFilter2); } s.push_front(tmpSpec); if(strcmp(cFilter1,cFilter2)==0){ j++; if(j==(int)(cs.boxcar/2)) break; } i++; } //cout << "Done left " << s.size() << " " << cs.rawAvgWidth << endl; //Get our position again r->readFile(&cs.inFile[0],tmpSpec,k); //Assume High resolution data at all times if(!cs.centroid) { FirstDerivativePeaks(tmpSpec,1); tmpSpec.setRawFilter(cFilter1); } //Add first target scan s.push_back(tmpSpec); pos=s.size()-1; //Add right side of scan i=1; j=0; while(true){ 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); //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; 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(strcmp(cFilter1,cFilter2)==0) { index=posRight; break; } } else { bs[posRight].getRawFilter(cFilter2,256); if(strcmp(cFilter1,cFilter2)==0) { index=posRight; break; } } } } if(index==-1) continue; //ts=bs[index]; specs[numScans++]=bs[index]; //cout << "NumScans: " << numScans << endl; } //Match peaks between pivot scan (0) and neighbors (the rest) //for(m=0;m<cs.ppMatch && m<numScans;m++){ for(m=0;m<1;m++){ //cout << "m " << m << " = " << specs[m].getScanNumber() << endl; vPos.clear(); for(i=0;i<numScans;i++) vPos.push_back(0); //cout << "Checking " << m << " of " << numScans << " points remaining: " << specs[m].size() << endl; for(i=0;i<specs[m].size();i++){ //iterate all points if(specs[m].at(i).intensity<0.1) continue; prec = c * specs[m].at(i).mz * specs[m].at(i).mz / 2; match=1; 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 //cout << "Checking " << j << " of " << specs[k].size() << endl; if(specs[k].at(j).intensity<0.1) continue; //skip meaningless datapoints to speed along dt=fabs(specs[m].at(i).mz-specs[k].at(j).mz); //dt=specs[m].at(i).mz-specs[k].at(j).mz; //if(dt<0.0)dt=-dt; if(dt<=dif) { if(dt<prec) { specs[m].at(i).intensity+=specs[k].at(j).intensity; vPos[k]=j+1; specs[k].at(j).intensity=-1.0; match++; break; } dif=dt; } else { vPos[k]=j-1; break; } } }//for k //if data point was not visible across enough scans, set it to 0 if(match<cs.boxcarFilter && match<numScans) { //ignore point //cout << "BAH! " << specs[m].at(i).mz << " has " << match << " matches." << endl; } else { //add to temp spectrum //cout << specs[m].at(i).mz << " has " << match << " matches." << endl; //sp.add(specs[m].at(i).mz,specs[m].at(i).intensity/numScans); sp.add(specs[m].at(i).mz,specs[m].at(i).intensity/match); } } //next i } //next m //sort //cout << "Done " << sp.size() << endl; 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); //clear unused buffer if(posLeft>0){ while(posLeft>0){ bs.pop_front(); posLeft--; posA--; } } delete [] specs; return true; }
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; }