/**
* * Loads the pax file and does a nearest neighbor search to match the nearest geo record in time
*/
public void loadPax() {
// Open pax file
// for each line
// create a PeopleRecord
// match it to a Geo record
try {
CSVReader reader = new CSVReader(new FileReader(PAXFILE));
String[] nextLine;
int lineCounter = 0;
while ((nextLine = reader.readNext()) != null) {
// nextLine[] is an array of values from the line
if (lineCounter > 0) {
int secSinceMidnight = Integer.parseInt(nextLine[8]);
double[] key = new double[1];
key[0] = TIME_SHIFT + 1.0 * secSinceMidnight;
GeoRecord matchingGeo = (GeoRecord) geoRecords.nearest(key);
if (matchingGeo != null) {
PeopleRecord pr = new PeopleRecord(nextLine);
pr.setTimeShiftSeconds(TIME_SHIFT);
matchingGeo.addPeopleRecord(pr);
} else {
System.err.println("Null Geo Returned!!");
}
}
lineCounter++;
}
} catch (Exception e) {
System.err.println(e);
}
}
public void loadGeo() {
try {
CSVReader reader = new CSVReader(new FileReader(GEOFILE));
String[] nextLine;
int lineCounter = 0;
while ((nextLine = reader.readNext()) != null) {
// nextLine[] is an array of values from the line
if (lineCounter > 0) {
GeoRecord newRecord = new GeoRecord(nextLine);
double[] key = new double[1];
// Keep track of trps
int tripNumber = newRecord.getTripId();
if (tripNumber > tripCounter) tripCounter = tripNumber;
key[0] = newRecord.getSecondsSinceMidnight();
// Key the time range
if (key[0] < firstTime) firstTime = key[0];
if (key[0] > lastTime) lastTime = key[0];
System.err.println("trying sec " + newRecord.getSecondsSinceMidnight());
geoRecords.insert(key, newRecord);
}
lineCounter++;
}
} catch (Exception e) {
System.err.println(e);
}
}
@Override
public void run() {
float lowrt = peakA.ApexRT - parameter.ApexDelta;
float highrt = peakA.ApexRT + parameter.ApexDelta;
float lowmz = InstrumentParameter.GetMzByPPM(peakA.TargetMz, 1, parameter.MS1PPM);
float highmz =
InstrumentParameter.GetMzByPPM(
(peakA.TargetMz + ((float) this.MaxNoOfClusters / this.StartCharge)),
1,
-parameter.MS1PPM);
Object[] found = null;
try {
found = PeakCurveSearchTree.range(new double[] {lowrt, lowmz}, new double[] {highrt, highmz});
} catch (KeySizeException ex) {
Logger.getRootLogger().error(ExceptionUtil.printStackTrace(ex));
}
if (found == null || found.length == 0) {
return;
}
SortedCurveCollectionMZ PeakCurveListMZ = new SortedCurveCollectionMZ();
for (Object peakCurve : found) {
PeakCurveListMZ.add((PeakCurve) peakCurve);
}
float Arange = peakA.EndRT() - peakA.StartRT();
for (int charge = EndCharge; charge >= StartCharge; charge--) {
float mass = charge * (peakA.TargetMz - (float) ElementaryIon.proton.getTheoreticMass());
if (mass < parameter.MinPrecursorMass
|| mass > parameter.MaxPrecursorMass
|| (parameter.MassDefectFilter
&& !MD.InMassDefectRange(mass, parameter.MassDefectOffset))) {
continue;
}
PeakCluster peakCluster = new PeakCluster(MaxNoOfClusters, charge);
peakCluster.IsoPeaksCurves[0] = peakA;
peakCluster.MonoIsotopePeak = peakA;
XYData[] Ranges = new XYData[MaxNoOfClusters - 1];
for (int i = 0; i < MaxNoOfClusters - 1; i++) {
Entry range = IsotopePatternMap[i].ceilingEntry(peakCluster.NeutralMass());
if (range == null) {
range = IsotopePatternMap[i].lastEntry();
}
Ranges[i] = (XYData) range.getValue();
}
for (int pkidx = 1; pkidx < MaxNoOfClusters; pkidx++) {
float ppmthreshold = parameter.MS1PPM + (parameter.MS1PPM * pkidx * 0.5f);
float lowtheomz =
InstrumentParameter.GetMzByPPM(
peakA.TargetMz
+ (pkidx * ((float) ElementaryIon.proton.getTheoreticMass() / charge)),
charge,
ppmthreshold);
float uptheomz =
InstrumentParameter.GetMzByPPM(
peakA.TargetMz
+ (pkidx * ((float) ElementaryIon.proton.getTheoreticMass() / charge)),
charge,
-ppmthreshold);
int startmzidx = PeakCurveListMZ.BinarySearchLower(lowtheomz);
float theomz =
peakA.TargetMz + (pkidx * ((float) ElementaryIon.proton.getTheoreticMass() / charge));
float maxscore = 0f;
float maxcorr = 0f;
float maxoverlap = 0f;
PeakCurve closestPeak = null;
for (int mzidx = startmzidx; mzidx < PeakCurveListMZ.size(); mzidx++) {
PeakCurve peakB = PeakCurveListMZ.get(mzidx);
if (peakB.TargetMz <= peakA.TargetMz) {
continue;
}
if (peakB.TargetMz > uptheomz) {
break;
}
float Brange = peakB.EndRT() - peakB.StartRT();
float OverlapP = 0f;
if (peakA.StartRT() >= peakB.StartRT()
&& peakA.StartRT() <= peakB.EndRT()
&& peakA.EndRT() >= peakB.EndRT()) {
OverlapP = (peakB.EndRT() - peakA.StartRT()) / Brange;
} else if (peakA.EndRT() >= peakB.StartRT()
&& peakA.EndRT() <= peakB.EndRT()
&& peakA.StartRT() <= peakB.StartRT()) {
OverlapP = (peakA.EndRT() - peakB.StartRT()) / Brange;
} else if (peakA.StartRT() <= peakB.StartRT() && peakA.EndRT() >= peakB.EndRT()) {
OverlapP = 1;
} else if (peakA.StartRT() >= peakB.StartRT() && peakA.EndRT() <= peakB.EndRT()) {
OverlapP = Arange / Brange;
}
if (parameter.TargetIDOnly
|| (OverlapP > parameter.MiniOverlapP
&& (!parameter.CheckMonoIsotopicApex
|| (peakA.ApexRT >= peakB.StartRT()
&& peakA.ApexRT <= peakB.EndRT()
&& peakB.ApexRT >= peakA.StartRT()
&& peakB.ApexRT <= peakA.EndRT())))) {
float ppm = InstrumentParameter.CalcPPM(theomz, peakB.TargetMz);
if (ppm < ppmthreshold) {
float corr = 0f;
try {
corr = PeakCurveCorrCalc.CalPeakCorr(peakA, peakB, parameter.NoPeakPerMin);
} catch (IOException ex) {
Logger.getRootLogger().error(ExceptionUtil.printStackTrace(ex));
}
if (Float.isNaN(corr)) {
corr = 0f;
// System.out.print("Corr=NAN\n");
}
float PeakIntA = peakA.ApexInt;
float PeakIntB =
peakB.GetMaxIntensityByRegionRange(
Math.max(peakA.StartRT(), peakB.StartRT()),
Math.min(peakB.EndRT(), peakA.EndRT()));
if ((parameter.TargetIDOnly && corr > 0.2f) || corr > parameter.IsoCorrThreshold) {
// if (corr > parameter.IsoCorrThreshold || (PeakIntA > PeakIntB*1.5f &&
// PeakIntB>0.1f * PeakIntA && (peakA.EndScan-peakA.StartScan)>4 &&
// (peakB.EndScan-peakB.StartScan)>4)) {
float intscore = 0f;
float IntRatio = PeakIntB / PeakIntA;
if (IntRatio > Ranges[pkidx - 1].getY() && IntRatio <= Ranges[pkidx - 1].getX()) {
intscore = 1f;
} else {
if (Math.abs(IntRatio - Ranges[pkidx - 1].getY())
> Math.abs(IntRatio - Ranges[pkidx - 1].getX())) {
intscore = 1 - Math.abs(IntRatio - Ranges[pkidx - 1].getX());
} else {
intscore = 1 - Math.abs(IntRatio - Ranges[pkidx - 1].getY());
}
}
if (intscore < 0f) {
intscore = 0f;
}
float score = ((ppmthreshold - ppm) / ppmthreshold) + corr + intscore;
if (maxscore < score) {
maxscore = score;
closestPeak = peakB;
maxcorr = corr;
maxoverlap = OverlapP;
}
}
}
}
}
if (closestPeak != null) {
peakCluster.Corrs[pkidx - 1] = maxcorr;
peakCluster.IsoPeaksCurves[pkidx] = closestPeak;
peakCluster.OverlapRT[pkidx - 1] = maxoverlap;
peakCluster.GetSNR(pkidx - 1);
if (pkidx == 1) {
peakCluster.OverlapP = maxoverlap;
}
}
if (closestPeak == null) {
break;
}
}
if (peakCluster.IsotopeComplete(MinNoOfClusters)) {
peakCluster.CalcPeakArea_V2();
peakCluster.UpdateIsoMapProb(IsotopePatternMap);
peakCluster.AssignConfilictCorr();
peakCluster.LeftInt = peakA.GetSmoothedList().Data.get(0).getY();
peakCluster.RightInt =
peakA.GetSmoothedList().Data.get(peakA.GetSmoothedList().PointCount() - 1).getY();
if (parameter.TargetIDOnly || peakCluster.IsoMapProb > parameter.IsoPattern) {
ResultClusters.add(peakCluster);
if (!parameter.TargetIDOnly
|| (parameter.RemoveGroupedPeaks
&& peakCluster.Corrs[0] > parameter.RemoveGroupedPeaksCorr
&& peakCluster.OverlapP > parameter.RemoveGroupedPeaksRTOverlap)) {
for (int i = 1; i < peakCluster.IsoPeaksCurves.length; i++) {
PeakCurve peak = peakCluster.IsoPeaksCurves[i];
if (peak != null
&& peakCluster.Corrs[i - 1] > parameter.RemoveGroupedPeaksCorr
&& peakCluster.OverlapRT[i - 1] > parameter.RemoveGroupedPeaksRTOverlap) {
peak.ChargeGrouped.add(charge);
}
}
}
}
}
}
PeakCurveListMZ = null;
// System.out.print("....done\n");
}
/** Dumps the results as a series of KML's..one per trip */
public void writeKMLandCSV() {
String csv_header =
"INDEX,DATE,TIME,SECONDS_SINCE_MIDNIGHT,TRIP_ID,DIR,SPEED,LAT,LONG,ALT,EXITS,ENTRANCES";
try {
CSVWriter writer = new CSVWriter(new FileWriter("bus_data.csv"), ',');
// Write the header
String[] entries = csv_header.split(",");
writer.writeNext(entries);
// Setup some style
LineStyle lineStyle = new LineStyle();
lineStyle.setColor("ff005555");
lineStyle.setWidth(5.0);
IconStyle peopleIconStyle = new IconStyle();
// Icon peopleIcon = new Icon();
// peopleIcon.setHref("http://maps.google.com/mapfiles/kml/man.png");
peopleIconStyle.setIconHref("http://maps.google.com/mapfiles/kml/shapes/man.png");
peopleIconStyle.setScale(1.50);
IconStyle wpIconStyleNorth = new IconStyle();
// wpIcon.setHref("http://maps.google.com/mapfiles/kml/paddle/red-stars.png");
// wpIconStyleNorth.setIconHref("http://maps.google.com/mapfiles/kml/shapes/placemark_circle.png");
wpIconStyleNorth.setIconHref("http://maps.google.com/mapfiles/ms/micons/green-dot.png");
wpIconStyleNorth.setScale(0.50);
IconStyle wpIconStyleSouth = new IconStyle();
// wpIcon.setHref("http://maps.google.com/mapfiles/kml/paddle/red-stars.png");
wpIconStyleSouth.setIconHref("http://maps.google.com/mapfiles/ms/micons/yellow-dot.png");
wpIconStyleSouth.setScale(0.50);
Style style_lineStyle = new Style();
style_lineStyle.setLineStyle(lineStyle);
Style style_peopleIconStyle = new Style();
style_peopleIconStyle.setId("peopleIcon");
style_peopleIconStyle.setIconStyle(peopleIconStyle);
Style style_wpIconStyleNorth = new Style();
style_wpIconStyleNorth.setId("wpIconNorth");
style_wpIconStyleNorth.setIconStyle(wpIconStyleNorth);
Style style_wpIconStyleSouth = new Style();
style_wpIconStyleSouth.setId("wpIconSouth");
style_wpIconStyleSouth.setIconStyle(wpIconStyleSouth);
Kml[] kml = new Kml[tripCounter];
Document[] document = new Document[tripCounter];
Folder[] northFolders = new Folder[tripCounter];
Folder[] southFolders = new Folder[tripCounter];
Folder[] peopleFolders = new Folder[tripCounter];
// Folder[] tracksFolders = new Folder[tripCounter];
for (int i = 0; i < tripCounter; i++) {
kml[i] = new Kml();
kml[i].setXmlIndent(true);
document[i] = new Document();
document[i].addStyleSelector(style_lineStyle);
document[i].addStyleSelector(style_peopleIconStyle);
document[i].addStyleSelector(style_wpIconStyleNorth);
document[i].addStyleSelector(style_wpIconStyleSouth);
kml[i].setFeature(document[i]);
northFolders[i] = new Folder();
northFolders[i].setName("North Route");
southFolders[i] = new Folder();
southFolders[i].setName("South Route");
peopleFolders[i] = new Folder();
peopleFolders[i].setName("People");
// tracksFolders[i] = new Folder();
// tracksFolders[i].setName("Tracks");
document[i].addFeature(northFolders[i]);
document[i].addFeature(southFolders[i]);
document[i].addFeature(peopleFolders[i]);
// document[i].addFeature(tracksFolders[i]);
}
double[] lowerKey = new double[1];
double[] upperKey = new double[1];
lowerKey[0] = firstTime;
upperKey[0] = lastTime;
Object[] foo = geoRecords.range(lowerKey, upperKey);
for (int i = 0; i < foo.length; i++) {
GeoRecord nextRecord = (GeoRecord) foo[i];
int tripNumber = nextRecord.getTripId();
// System.out.println(foo[i]);
if (nextRecord.getDirection().equals("N")) {
northFolders[tripNumber - 1].addFeature(nextRecord.toKML());
} else {
southFolders[tripNumber - 1].addFeature(nextRecord.toKML());
}
if (nextRecord.getAssociatedPeople().size() > 0) {
peopleFolders[tripNumber - 1].addFeature(nextRecord.toKMLWithPeople());
}
// Write CSV entry
String csvLine = nextRecord.toCSV();
String[] entries2 = csvLine.split(",");
writer.writeNext(entries2);
}
// Write the KML files
for (int i = 0; i < tripCounter; i++) {
kml[i].createKml("bus_route" + i + ".kml");
}
// Close the csv writer
writer.close();
} catch (Exception e) {
System.err.println(e);
}
}