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::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::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;
}
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;
}
