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Merge pull request #801 from Mailaender/wsd-1st-derivative-filter-wav…
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Added support to filter per wavelength in DAD 1st derivative peak detection
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@eselmeister
eselmeister authored Nov 13, 2021
2 parents bab8237 + 9f716bb commit a66ae19
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Showing 21 changed files with 754 additions and 242 deletions.
78 changes: 0 additions & 78 deletions ...clipse/chromatogram/xxd/peak/detector/supplier/firstderivative/core/BasePeakDetector.java
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Expand Up @@ -23,15 +23,7 @@
import org.eclipse.chemclipse.chromatogram.xxd.peak.detector.supplier.firstderivative.support.IFirstDerivativeDetectorSlopes;
import org.eclipse.chemclipse.model.core.IChromatogram;
import org.eclipse.chemclipse.model.core.IPeak;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.model.support.ScanRange;
import org.eclipse.chemclipse.msd.model.core.IPeakModelMSD;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;
import org.eclipse.chemclipse.msd.model.core.support.IMarkedIons;
import org.eclipse.chemclipse.numeric.core.IPoint;
import org.eclipse.chemclipse.numeric.core.Point;
import org.eclipse.chemclipse.numeric.equations.Equations;
import org.eclipse.chemclipse.numeric.equations.LinearEquation;
import org.eclipse.chemclipse.numeric.miscellaneous.Evaluation;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.SubMonitor;
Expand Down Expand Up @@ -111,76 +103,6 @@ public static List<IRawPeak> getRawPeaks(IFirstDerivativeDetectorSlopes slopes,
return rawPeaks;
}

protected ScanRange optimizeBaseline(IChromatogram<? extends IPeak> chromatogram, int startScan, int centerScan, int stopScan, IMarkedIons ions) {

/*
* Right and left baseline optimization
*/
int stopScanOptimized = optimizeRightBaseline(chromatogram, startScan, centerScan, stopScan, ions);
int startScanOptimized = optimizeLeftBaseline(chromatogram, startScan, centerScan, stopScanOptimized, ions);
//
return new ScanRange(startScanOptimized, stopScanOptimized);
}

protected float getScanSignal(IChromatogram<? extends IPeak> chromatogram, int scanNumber, IMarkedIons ions) {

float scanSignal = 0.0f;
IScan scan = chromatogram.getScan(scanNumber);
if(scan instanceof IScanMSD) {
IScanMSD scanMSD = (IScanMSD)scan;
scanSignal = scanMSD.getTotalSignal(ions);
} else {
scanSignal = scan.getTotalSignal();
}
return scanSignal;
}

private int optimizeRightBaseline(IChromatogram<? extends IPeak> chromatogram, int startScan, int centerScan, int stopScan, IMarkedIons ions) {

IPoint p1 = new Point(getRetentionTime(chromatogram, startScan), getScanSignal(chromatogram, startScan, ions));
IPoint p2 = new Point(getRetentionTime(chromatogram, stopScan), getScanSignal(chromatogram, stopScan, ions));
LinearEquation backgroundEquation = Equations.createLinearEquation(p1, p2);
/*
* Right border optimization
*/
int stopScanOptimized = stopScan;
for(int i = stopScan; i > centerScan; i--) {
float signal = getScanSignal(chromatogram, i, ions);
int retentionTime = chromatogram.getScan(i).getRetentionTime();
if(signal < backgroundEquation.calculateY(retentionTime)) {
stopScanOptimized = i;
}
}
//
return stopScanOptimized;
}

private int optimizeLeftBaseline(IChromatogram<? extends IPeak> chromatogram, int startScan, int centerScan, int stopScan, IMarkedIons ions) {

IPoint p1 = new Point(getRetentionTime(chromatogram, startScan), getScanSignal(chromatogram, startScan, ions));
IPoint p2 = new Point(getRetentionTime(chromatogram, stopScan), getScanSignal(chromatogram, stopScan, ions));
LinearEquation backgroundEquation = Equations.createLinearEquation(p1, p2);
/*
* Right border optimization
*/
int startScanOptimized = startScan;
for(int i = startScan; i < centerScan; i++) {
float signal = getScanSignal(chromatogram, i, ions);
int retentionTime = chromatogram.getScan(i).getRetentionTime();
if(signal < backgroundEquation.calculateY(retentionTime)) {
/*
* Create a new equation
*/
startScanOptimized = i;
p1 = new Point(getRetentionTime(chromatogram, startScanOptimized), getScanSignal(chromatogram, startScanOptimized, ions));
p2 = new Point(getRetentionTime(chromatogram, stopScan), getScanSignal(chromatogram, stopScan, ions));
backgroundEquation = Equations.createLinearEquation(p1, p2);
}
}
//
return startScanOptimized;
}

protected int getRetentionTime(IChromatogram<? extends IPeak> chromatogram, int scanNumber) {

return chromatogram.getScan(scanNumber).getRetentionTime();
Expand Down
3 changes: 2 additions & 1 deletion ...matogram/xxd/peak/detector/supplier/firstderivative/core/FirstDerivativePeakDetector.java
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Expand Up @@ -91,7 +91,8 @@ public <T extends IMeasurement> Map<T, PeakList> detectIMeasurementPeaks(Collect
} else {
configuration = globalConfiguration;
}
slopes = PeakDetectorWSD.getFirstDerivativeSlopes(new ChromatogramSelectionWSD((IChromatogramWSD)measurement), configuration.getMovingAverageWindowSize());
// TODO: filter wavelengths
slopes = PeakDetectorWSD.getFirstDerivativeSlopes(new ChromatogramSelectionWSD((IChromatogramWSD)measurement), configuration.getMovingAverageWindowSize(), null);
} else if(measurement instanceof SpectrumMeasurement) {
if(globalConfiguration == null) {
configuration = new FirstDerivativePeakDetectorSettings(DataType.NMR);
Expand Down
68 changes: 64 additions & 4 deletions ...mclipse/chromatogram/xxd/peak/detector/supplier/firstderivative/core/PeakDetectorCSD.java
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Expand Up @@ -35,6 +35,7 @@
import org.eclipse.chemclipse.logging.core.Logger;
import org.eclipse.chemclipse.model.core.IChromatogram;
import org.eclipse.chemclipse.model.core.IPeak;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.model.exceptions.PeakException;
import org.eclipse.chemclipse.model.signals.ITotalScanSignal;
import org.eclipse.chemclipse.model.signals.ITotalScanSignals;
Expand All @@ -45,6 +46,8 @@
import org.eclipse.chemclipse.msd.model.core.IChromatogramPeakMSD;
import org.eclipse.chemclipse.numeric.core.IPoint;
import org.eclipse.chemclipse.numeric.core.Point;
import org.eclipse.chemclipse.numeric.equations.Equations;
import org.eclipse.chemclipse.numeric.equations.LinearEquation;
import org.eclipse.chemclipse.processing.core.IProcessingInfo;
import org.eclipse.chemclipse.processing.core.MessageType;
import org.eclipse.chemclipse.processing.core.ProcessingMessage;
Expand Down Expand Up @@ -197,7 +200,7 @@ private List<IChromatogramPeakCSD> extractPeaks(List<IRawPeak> rawPeaks, IChroma
*/
ScanRange scanRange = new ScanRange(rawPeak.getStartScan(), rawPeak.getStopScan());
if(includeBackground && optimizeBaseline) {
scanRange = optimizeBaseline(chromatogram, scanRange.getStartScan(), rawPeak.getMaximumScan(), scanRange.getStopScan(), null);
scanRange = optimizeBaseline(chromatogram, scanRange.getStartScan(), rawPeak.getMaximumScan(), scanRange.getStopScan());
}
/*
* includeBackground
Expand Down Expand Up @@ -272,9 +275,66 @@ public static IFirstDerivativeDetectorSlopes getFirstDerivativeSlopes(IChromatog
*/
private boolean isValidPeak(IChromatogramPeakCSD peak, PeakDetectorSettingsCSD peakDetectorSettings) {

if(peak != null && peak.getSignalToNoiseRatio() >= peakDetectorSettings.getMinimumSignalToNoiseRatio()) {
return true;
return (peak != null && peak.getSignalToNoiseRatio() >= peakDetectorSettings.getMinimumSignalToNoiseRatio());
}

private ScanRange optimizeBaseline(IChromatogramCSD chromatogram, int startScan, int centerScan, int stopScan) {

int stopScanOptimized = optimizeRightBaseline(chromatogram, startScan, centerScan, stopScan);
int startScanOptimized = optimizeLeftBaseline(chromatogram, startScan, centerScan, stopScanOptimized);
//
return new ScanRange(startScanOptimized, stopScanOptimized);
}

private int optimizeRightBaseline(IChromatogramCSD chromatogram, int startScan, int centerScan, int stopScan) {

IPoint p1 = new Point(getRetentionTime(chromatogram, startScan), getScanSignal(chromatogram, startScan));
IPoint p2 = new Point(getRetentionTime(chromatogram, stopScan), getScanSignal(chromatogram, stopScan));
LinearEquation backgroundEquation = Equations.createLinearEquation(p1, p2);
/*
* Right border optimization
*/
int stopScanOptimized = stopScan;
for(int i = stopScan; i > centerScan; i--) {
float signal = getScanSignal(chromatogram, i);
int retentionTime = chromatogram.getScan(i).getRetentionTime();
if(signal < backgroundEquation.calculateY(retentionTime)) {
stopScanOptimized = i;
}
}
//
return stopScanOptimized;
}

private int optimizeLeftBaseline(IChromatogramCSD chromatogram, int startScan, int centerScan, int stopScan) {

IPoint p1 = new Point(getRetentionTime(chromatogram, startScan), getScanSignal(chromatogram, startScan));
IPoint p2 = new Point(getRetentionTime(chromatogram, stopScan), getScanSignal(chromatogram, stopScan));
LinearEquation backgroundEquation = Equations.createLinearEquation(p1, p2);
/*
* Right border optimization
*/
int startScanOptimized = startScan;
for(int i = startScan; i < centerScan; i++) {
float signal = getScanSignal(chromatogram, i);
int retentionTime = chromatogram.getScan(i).getRetentionTime();
if(signal < backgroundEquation.calculateY(retentionTime)) {
/*
* Create a new equation
*/
startScanOptimized = i;
p1 = new Point(getRetentionTime(chromatogram, startScanOptimized), getScanSignal(chromatogram, startScanOptimized));
p2 = new Point(getRetentionTime(chromatogram, stopScan), getScanSignal(chromatogram, stopScan));
backgroundEquation = Equations.createLinearEquation(p1, p2);
}
}
return false;
//
return startScanOptimized;
}

protected float getScanSignal(IChromatogramCSD chromatogram, int scanNumber) {

IScan scan = chromatogram.getScan(scanNumber);
return scan.getTotalSignal();
}
}
88 changes: 79 additions & 9 deletions ...mclipse/chromatogram/xxd/peak/detector/supplier/firstderivative/core/PeakDetectorMSD.java
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Expand Up @@ -36,6 +36,7 @@
import org.eclipse.chemclipse.logging.core.Logger;
import org.eclipse.chemclipse.model.core.IChromatogram;
import org.eclipse.chemclipse.model.core.IPeak;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.model.exceptions.ChromatogramIsNullException;
import org.eclipse.chemclipse.model.signals.ITotalScanSignal;
import org.eclipse.chemclipse.model.signals.ITotalScanSignals;
Expand All @@ -44,6 +45,7 @@
import org.eclipse.chemclipse.model.support.ScanRange;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.IChromatogramPeakMSD;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;
import org.eclipse.chemclipse.msd.model.core.selection.IChromatogramSelectionMSD;
import org.eclipse.chemclipse.msd.model.core.support.IMarkedIons;
import org.eclipse.chemclipse.msd.model.core.support.IMarkedIons.IonMarkMode;
Expand All @@ -53,6 +55,8 @@
import org.eclipse.chemclipse.msd.model.xic.TotalIonSignalExtractor;
import org.eclipse.chemclipse.numeric.core.IPoint;
import org.eclipse.chemclipse.numeric.core.Point;
import org.eclipse.chemclipse.numeric.equations.Equations;
import org.eclipse.chemclipse.numeric.equations.LinearEquation;
import org.eclipse.chemclipse.processing.core.IProcessingInfo;
import org.eclipse.chemclipse.processing.core.MessageType;
import org.eclipse.chemclipse.processing.core.ProcessingMessage;
Expand Down Expand Up @@ -131,12 +135,13 @@ public List<IChromatogramPeakMSD> detectPeaks(IChromatogramSelectionMSD chromato

List<IChromatogramPeakMSD> extractPeaks = new ArrayList<>();
Collection<IMarkedIons> filterIons = peakDetectorSettings.getFilterIons();
IChromatogramMSD chromatogram = chromatogramSelection.getChromatogram();
for(IMarkedIons ions : filterIons) {
Threshold threshold = peakDetectorSettings.getThreshold();
int windowSize = peakDetectorSettings.getMovingAverageWindowSize();
List<IRawPeak> rawPeaks = new ArrayList<>();
//
if(noiseSegments != null && noiseSegments.size() > 0) {
if(noiseSegments != null && !noiseSegments.isEmpty()) {
/*
* Initial retention time range before running the detection using
* noise segments.
Expand All @@ -159,11 +164,11 @@ public List<IChromatogramPeakMSD> detectPeaks(IChromatogramSelectionMSD chromato
* Ranges between the noise segments
* [S] --- [N] --- [E]
*/
while(iterator.hasNext()) {
int startRetentionTimeSegment = noiseSegment.getStopRetentionTime();
while(iterator.hasNext() && noiseSegment != null) {
int previousStopRetentionTimeSegment = noiseSegment.getStopRetentionTime();
noiseSegment = iterator.next();
int stopRetentionTimeSegment = noiseSegment.getStartRetentionTime();
chromatogramSelection.setRangeRetentionTime(startRetentionTimeSegment, stopRetentionTimeSegment);
int nextStartRetentionTimeSegment = noiseSegment.getStartRetentionTime();
chromatogramSelection.setRangeRetentionTime(previousStopRetentionTimeSegment, nextStartRetentionTimeSegment);
IFirstDerivativeDetectorSlopes slopes = getFirstDerivativeSlopes(chromatogramSelection, windowSize, ions);
rawPeaks.addAll(getRawPeaks(slopes, threshold, monitor));
}
Expand All @@ -187,7 +192,7 @@ public List<IChromatogramPeakMSD> detectPeaks(IChromatogramSelectionMSD chromato
IFirstDerivativeDetectorSlopes slopes = getFirstDerivativeSlopes(chromatogramSelection, windowSize, ions);
rawPeaks.addAll(getRawPeaks(slopes, threshold, monitor));
}
List<IChromatogramPeakMSD> peaks = extractPeaks(rawPeaks, chromatogramSelection.getChromatogram(), peakDetectorSettings, ions);
List<IChromatogramPeakMSD> peaks = extractPeaks(rawPeaks, chromatogram, peakDetectorSettings, ions);
if(peakDetectorSettings.isUseIndividualTraces()) {
String classifier = "Trace " + ions.getIonsNominal().iterator().next();
for(IChromatogramPeakMSD msd : peaks) {
Expand Down Expand Up @@ -326,9 +331,74 @@ private static IonMarkMode buildFilterMode(FilterMode mode) {
*/
private boolean isValidPeak(IChromatogramPeakMSD peak, PeakDetectorSettingsMSD peakDetectorSettings) {

if(peak != null && peak.getSignalToNoiseRatio() >= peakDetectorSettings.getMinimumSignalToNoiseRatio()) {
return true;
return (peak != null && peak.getSignalToNoiseRatio() >= peakDetectorSettings.getMinimumSignalToNoiseRatio());
}

protected ScanRange optimizeBaseline(IChromatogramMSD chromatogram, int startScan, int centerScan, int stopScan, IMarkedIons ions) {

/*
* Right and left baseline optimization
*/
int stopScanOptimized = optimizeRightBaseline(chromatogram, startScan, centerScan, stopScan, ions);
int startScanOptimized = optimizeLeftBaseline(chromatogram, startScan, centerScan, stopScanOptimized, ions);
//
return new ScanRange(startScanOptimized, stopScanOptimized);
}

protected float getScanSignal(IChromatogramMSD chromatogram, int scanNumber, IMarkedIons ions) {

IScan scan = chromatogram.getScan(scanNumber);
if(scan instanceof IScanMSD) {
IScanMSD scanMSD = (IScanMSD)scan;
return scanMSD.getTotalSignal(ions);
} else {
return scan.getTotalSignal();
}
}

private int optimizeRightBaseline(IChromatogramMSD chromatogram, int startScan, int centerScan, int stopScan, IMarkedIons ions) {

IPoint p1 = new Point(getRetentionTime(chromatogram, startScan), getScanSignal(chromatogram, startScan, ions));
IPoint p2 = new Point(getRetentionTime(chromatogram, stopScan), getScanSignal(chromatogram, stopScan, ions));
LinearEquation backgroundEquation = Equations.createLinearEquation(p1, p2);
/*
* Right border optimization
*/
int stopScanOptimized = stopScan;
for(int i = stopScan; i > centerScan; i--) {
float signal = getScanSignal(chromatogram, i, ions);
int retentionTime = chromatogram.getScan(i).getRetentionTime();
if(signal < backgroundEquation.calculateY(retentionTime)) {
stopScanOptimized = i;
}
}
return false;
//
return stopScanOptimized;
}

private int optimizeLeftBaseline(IChromatogramMSD chromatogram, int startScan, int centerScan, int stopScan, IMarkedIons ions) {

IPoint p1 = new Point(getRetentionTime(chromatogram, startScan), getScanSignal(chromatogram, startScan, ions));
IPoint p2 = new Point(getRetentionTime(chromatogram, stopScan), getScanSignal(chromatogram, stopScan, ions));
LinearEquation backgroundEquation = Equations.createLinearEquation(p1, p2);
/*
* Right border optimization
*/
int startScanOptimized = startScan;
for(int i = startScan; i < centerScan; i++) {
float signal = getScanSignal(chromatogram, i, ions);
int retentionTime = chromatogram.getScan(i).getRetentionTime();
if(signal < backgroundEquation.calculateY(retentionTime)) {
/*
* Create a new equation
*/
startScanOptimized = i;
p1 = new Point(getRetentionTime(chromatogram, startScanOptimized), getScanSignal(chromatogram, startScanOptimized, ions));
p2 = new Point(getRetentionTime(chromatogram, stopScan), getScanSignal(chromatogram, stopScan, ions));
backgroundEquation = Equations.createLinearEquation(p1, p2);
}
}
//
return startScanOptimized;
}
}
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