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fix #677 channel wise subtraction #678

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merged 2 commits into from
Jul 7, 2021
Merged

fix #677 channel wise subtraction #678

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54251b6
fix #677 channel wise subtraction
lorenzgerber Jul 6, 2021
45dfb25
fix #677 adjust year in header
lorenzgerber Jul 6, 2021
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72 changes: 70 additions & 2 deletions ...clipse/chromatogram/xxd/filter/supplier/baselinesubtract/core/ChromatogramSubtractor.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2019 Lablicate GmbH.
* Copyright (c) 2019, 2021 Lablicate GmbH.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
Expand All @@ -8,15 +8,26 @@
*
* Contributors:
* Dr. Philip Wenig - initial API and implementation
* Lorenz Gerber - channel wise subtraction for WSD / MSD
*******************************************************************************/
package org.eclipse.chemclipse.chromatogram.xxd.filter.supplier.baselinesubtract.core;

import java.util.ArrayList;
import java.util.List;

import org.eclipse.chemclipse.model.core.IChromatogram;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.model.exceptions.AbundanceLimitExceededException;
import org.eclipse.chemclipse.msd.model.core.IIon;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;
import org.eclipse.chemclipse.msd.model.exceptions.IonLimitExceededException;
import org.eclipse.chemclipse.wsd.model.core.IScanSignalWSD;
import org.eclipse.chemclipse.wsd.model.core.IScanWSD;

public class ChromatogramSubtractor {

private final static boolean CHANNEL_WISE_SUBTRACTION = true;

public void perform(IChromatogram<?> chromatogramMaster, IChromatogram<?> chromatogramSubtract) {

if(chromatogramMaster != null && chromatogramSubtract != null) {
Expand All @@ -34,7 +45,13 @@ public void perform(IChromatogram<?> chromatogramMaster, IChromatogram<?> chroma
//
for(int i = startScan; i <= stopScan; i++) {
IScan scanMaster = chromatogramMaster.getScan(i);
if(scanMaster != null) {
if(scanMaster instanceof IScanMSD && CHANNEL_WISE_SUBTRACTION) {
IScanMSD scanMasterMSD = (IScanMSD)scanMaster;
subtractMSD(scanMasterMSD, chromatogramSubtract);
} else if(scanMaster instanceof IScanWSD && CHANNEL_WISE_SUBTRACTION) {
IScanWSD scanMasterWSD = (IScanWSD)scanMaster;
subtractWSD(scanMasterWSD, chromatogramSubtract);
} else if(scanMaster != null) {
int scanNumberSubtract = chromatogramSubtract.getScanNumber(scanMaster.getRetentionTime());
IScan scanSubtract = chromatogramSubtract.getScan(scanNumberSubtract);
if(scanSubtract != null) {
Expand All @@ -60,4 +77,55 @@ public void perform(IChromatogram<?> chromatogramMaster, IChromatogram<?> chroma
}
}
}

private void subtractWSD(IScanWSD scanMasterWSD, IChromatogram<?> chromatogramSubtract) {

if(scanMasterWSD != null) {
int scanNumberSubtract = chromatogramSubtract.getScanNumber(scanMasterWSD.getRetentionTime());
IScanWSD scanSubtract = (IScanWSD)chromatogramSubtract.getScan(scanNumberSubtract);
if(scanSubtract != null) {
List<IScanSignalWSD> signals = scanMasterWSD.getScanSignals();
for(IScanSignalWSD signal : signals) {
double wavelength = signal.getWavelength();
IScanSignalWSD subtract = scanSubtract.getScanSignal(wavelength).orElse(null);
if(subtract != null) {
float abundance = signal.getAbundance() - subtract.getAbundance();
signal.setAbundance(abundance);
}
}
}
}
}

private void subtractMSD(IScanMSD scanMasterMSD, IChromatogram<?> chromatogramSubtract) {

if(scanMasterMSD != null) {
int scanNumberSubtract = chromatogramSubtract.getScanNumber(scanMasterMSD.getRetentionTime());
IScanMSD scanSubtract = (IScanMSD)chromatogramSubtract.getScan(scanNumberSubtract);
if(scanSubtract != null) {
List<IIon> ions = scanMasterMSD.getIons();
List<IIon> zeroAbundanceIons = new ArrayList<>();
for(IIon ion : ions) {
double mass = ion.getIon();
IIon subtract;
try {
subtract = scanSubtract.getIon(mass);
if(subtract != null) {
float abundance = ion.getAbundance() - subtract.getAbundance();
if(abundance <= 0.0) {
zeroAbundanceIons.add(ion);
} else {
ion.setAbundance(abundance);
}
}
} catch(AbundanceLimitExceededException e1) {
System.out.println(e1);
} catch(IonLimitExceededException e1) {
System.out.println(e1);
}
}
zeroAbundanceIons.stream().forEach(x -> scanMasterMSD.removeIon(x));
}
}
}
}