Translate the options available in MSD to WSD.

chemclipse/plugins/org.eclipse.chemclipse.chromatogram.xxd.peak.detector.supplier.firstderivative/src/org/eclipse/chemclipse/chromatogram/xxd/peak/detector/supplier/firstderivative/settings/PeakDetectorSettingsWSD.java

@@ -9,17 +9,34 @@
  * Contributors:
  * Dr. Philip Wenig - initial API and implementation
  * Matthias Mailänder - remove the window size enum
+ * Matthias Mailänder - add wavelength filters
  *******************************************************************************/
 package org.eclipse.chemclipse.chromatogram.xxd.peak.detector.supplier.firstderivative.settings;
 
+import java.math.BigDecimal;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import org.apache.commons.lang3.StringUtils;
+import org.eclipse.chemclipse.chromatogram.peak.detector.core.FilterMode;
 import org.eclipse.chemclipse.chromatogram.peak.detector.model.Threshold;
 import org.eclipse.chemclipse.chromatogram.wsd.peak.detector.settings.AbstractPeakDetectorWSDSettings;
 import org.eclipse.chemclipse.chromatogram.xxd.peak.detector.supplier.firstderivative.preferences.PreferenceSupplier;
 import org.eclipse.chemclipse.support.settings.FloatSettingsProperty;
 import org.eclipse.chemclipse.support.settings.IntSettingsProperty;
 import org.eclipse.chemclipse.support.settings.IntSettingsProperty.Validation;
 import org.eclipse.chemclipse.support.settings.serialization.WindowSizeDeserializer;
+import org.eclipse.chemclipse.wsd.model.core.support.IMarkedWavelength;
+import org.eclipse.chemclipse.wsd.model.core.support.IMarkedWavelength.WavelengthMarkMode;
+import org.eclipse.chemclipse.wsd.model.core.support.IMarkedWavelengths;
+import org.eclipse.chemclipse.wsd.model.core.support.MarkedWavelength;
+import org.eclipse.chemclipse.wsd.model.core.support.MarkedWavelengths;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.annotation.JsonPropertyDescription;
 import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
@@ -39,6 +56,18 @@ public class PeakDetectorSettingsWSD extends AbstractPeakDetectorWSDSettings {
 	@IntSettingsProperty(minValue = PreferenceSupplier.MIN_WINDOW_SIZE, maxValue = PreferenceSupplier.MAX_WINDOW_SIZE, validation = Validation.ODD_NUMBER_INCLUDING_ZERO)
 	@JsonDeserialize(using = WindowSizeDeserializer.class)
 	private int windowSize;
+	@JsonProperty(value = "Use Noise-Segments", defaultValue = "false")
+	@JsonPropertyDescription(value = "Whether to use noise segments to decide where peaks should be detected. This can improve the sensitivity of the algorithm.")
+	private boolean useNoiseSegments = false;
+	@JsonProperty(value = "Filter Mode", defaultValue = "EXCLUDE")
+	private FilterMode filterMode = FilterMode.EXCLUDE;
+	@JsonProperty(value = "Wavelengths to filter", defaultValue = "")
+	private String filterWavelengths;
+	@JsonProperty(value = "Use Individual Wavelengths", defaultValue = "false")
+	@JsonPropertyDescription("Uses each wavelength in the filter-list individualy to detect peaks")
+	private boolean useIndividualWavelengths = false;
+	@JsonProperty(value = "Optimize Baseline (VV)", defaultValue = "false")
+	private boolean optimizeBaseline = false;
 
 	public PeakDetectorSettingsWSD() {
 
@@ -86,4 +115,91 @@ public void setMovingAverageWindowSize(int windowSize) {
 
 		this.windowSize = windowSize;
 	}
+
+	public boolean isUseNoiseSegments() {
+
+		return useNoiseSegments;
+	}
+
+	public void setUseNoiseSegments(boolean useNoiseSegments) {
+
+		this.useNoiseSegments = useNoiseSegments;
+	}
+
+	public FilterMode getFilterMode() {
+
+		return filterMode == null ? FilterMode.EXCLUDE : filterMode;
+	}
+
+	public void setFilterMode(FilterMode filterMode) {
+
+		this.filterMode = filterMode;
+	}
+
+	static Collection<Number> parseWavelengths(String input) {
+
+		if(StringUtils.isBlank(input)) {
+			return Collections.emptyList();
+		}
+		List<Number> waveLengths = new ArrayList<>();
+		String[] split = input.trim().split("[\\s.,;]+");
+		for(String s : split) {
+			try {
+				waveLengths.add(new BigDecimal(s));
+			} catch(NumberFormatException e) {
+				// invalid or empty string
+			}
+		}
+		return waveLengths;
+	}
+
+	public boolean isIndividualWavelengths() {
+
+		return useIndividualWavelengths;
+	}
+
+	public void setUseIndividualTraces(boolean useIndividualWavelengths) {
+
+		this.useIndividualWavelengths = useIndividualWavelengths;
+	}
+
+	@JsonIgnore
+	public Collection<IMarkedWavelengths> getFilterWavelengths() {
+
+		WavelengthMarkMode wavelengthMarkMode;
+		switch(getFilterMode()) {
+			case EXCLUDE:
+				wavelengthMarkMode = WavelengthMarkMode.INCLUDE;
+				break;
+			case INCLUDE:
+				wavelengthMarkMode = WavelengthMarkMode.EXCLUDE;
+				break;
+			default:
+				throw new IllegalArgumentException("Unsupported filter mode " + getFilterMode());
+		}
+		Set<IMarkedWavelength> parsedWavelengths = parseWavelengths(filterWavelengths).stream().map(e -> new MarkedWavelength(e.doubleValue())).collect(Collectors.toSet());
+		if(isIndividualWavelengths()) {
+			List<IMarkedWavelengths> listedWavelengths = new ArrayList<>();
+			for(IMarkedWavelength wavelength : parsedWavelengths) {
+				IMarkedWavelengths markedWavelengths = new MarkedWavelengths(wavelengthMarkMode);
+				markedWavelengths.add(wavelength);
+				listedWavelengths.add(markedWavelengths);
+			}
+			return listedWavelengths;
+		} else {
+			IMarkedWavelengths markedWavelengths = new MarkedWavelengths(wavelengthMarkMode);
+			markedWavelengths.addAll(parsedWavelengths);
+			return Collections.singleton(markedWavelengths);
+		}
+	}
+
+	public boolean isOptimizeBaseline() {
+
+		return optimizeBaseline;
+	}
+
+	public void setOptimizeBaseline(boolean optimizeBaseline) {
+
+		this.optimizeBaseline = optimizeBaseline;
+	}
 }

chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/AbstractScanWSD.java

@@ -14,6 +14,7 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
@@ -22,6 +23,7 @@
 import org.eclipse.chemclipse.wsd.model.comparator.WavelengthCombinedComparator;
 import org.eclipse.chemclipse.wsd.model.comparator.WavelengthComparatorMode;
 import org.eclipse.chemclipse.wsd.model.core.implementation.ScanSignalWSD;
+import org.eclipse.chemclipse.wsd.model.core.support.IMarkedWavelengths;
 import org.eclipse.chemclipse.wsd.model.xwc.ExtractedSingleWavelengthSignal;
 import org.eclipse.chemclipse.wsd.model.xwc.ExtractedWavelengthSignal;
 import org.eclipse.chemclipse.wsd.model.xwc.IExtractedSingleWavelengthSignal;
@@ -135,6 +137,40 @@ public float getTotalSignal() {
 		return totalSignal;
 	}
 
+	@Override
+	public float getTotalSignal(IMarkedWavelengths markedWavelengths) {
+
+		float totalSignal = 0;
+		/*
+		 * If the excluded ions are null, return the total signal.
+		 */
+		if(markedWavelengths == null || markedWavelengths.isEmpty()) {
+			totalSignal = getTotalSignal();
+		} else {
+			Iterator<IScanSignalWSD> iterator = scanSignals.iterator();
+			while(iterator.hasNext()) {
+				IScanSignalWSD scan = iterator.next();
+				if(useWavelength(scan, markedWavelengths)) {
+					totalSignal += scan.getAbundance();
+				}
+			}
+		}
+		return totalSignal;
+	}
+
+	private static boolean useWavelength(IScanSignalWSD scan, IMarkedWavelengths filterWavelengths) {
+
+		Set<Double> wavelengths = filterWavelengths.getWavelengths();
+		switch(filterWavelengths.getMode()) {
+			case EXCLUDE:
+				return wavelengths.contains(scan.getWavelength());
+			case INCLUDE:
+				return !wavelengths.contains(scan.getWavelength());
+			default:
+				return true;
+		}
+	}
+
 	@Override
 	public void adjustTotalSignal(float totalSignal) {
 

chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/IScanWSD.java

@@ -8,6 +8,7 @@
  * 
  * Contributors:
  * Dr. Philip Wenig - initial API and implementation
+ * Matthias Mailänder - add total signal except excluded
  *******************************************************************************/
 package org.eclipse.chemclipse.wsd.model.core;
 
@@ -16,6 +17,7 @@
 import java.util.Set;
 
 import org.eclipse.chemclipse.model.core.IScan;
+import org.eclipse.chemclipse.wsd.model.core.support.IMarkedWavelengths;
 import org.eclipse.chemclipse.wsd.model.xwc.IExtractedSingleWavelengthSignal;
 import org.eclipse.chemclipse.wsd.model.xwc.IExtractedWavelengthSignal;
 
@@ -47,11 +49,17 @@ public interface IScanWSD extends IScan {
 
 	IExtractedWavelengthSignal getExtractedWavelengthSignal();
 
-	IExtractedWavelengthSignal getExtractedWavelengthSignal(double startIon, double stopIon);
+	IExtractedWavelengthSignal getExtractedWavelengthSignal(double startWavelength, double stopWavelength);
 
 	Optional<IExtractedSingleWavelengthSignal> getExtractedSingleWavelengthSignal(double wavelength);
 
 	boolean hasScanSignals();
 
 	IWavelengthBounds getWavelengthBounds();
+
+	/**
+	 * 
+	 * @return total intensity count (TIC) excepted excluded wavelengths
+	 */
+	float getTotalSignal(IMarkedWavelengths excludedWavelenths);
 }

chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/support/AbstractMarkedWavelengths.java

@@ -16,7 +16,7 @@
 import java.util.Iterator;
 import java.util.Set;
 
-public class AbstractMarkedWavelengths implements IMarkedWavelengths {
+public abstract class AbstractMarkedWavelengths implements IMarkedWavelengths {
 
 	private Set<IMarkedWavelength> markedWavelengths;
 
@@ -25,6 +25,16 @@ public AbstractMarkedWavelengths() {
 		markedWavelengths = new HashSet<>();
 	}
 
+	protected AbstractMarkedWavelengths(Collection<? extends Number> wavelengths) {
+
+		markedWavelengths = new HashSet<>();
+		if(wavelengths != null) {
+			for(Number wavelength : wavelengths) {
+				markedWavelengths.add(new MarkedWavelength(wavelength.intValue()));
+			}
+		}
+	}
+
 	@Override
 	public boolean add(IMarkedWavelength e) {
 

chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/support/IMarkedWavelength.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2016, 2018 Lablicate GmbH.
+ * Copyright (c) 2016, 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
@@ -12,9 +12,40 @@
 package org.eclipse.chemclipse.wsd.model.core.support;
 
 import org.eclipse.chemclipse.model.core.IMarkedSignal;
+import org.eclipse.chemclipse.support.text.ILabel;
 
 public interface IMarkedWavelength extends IMarkedSignal {
 
+	enum WavelengthMarkMode implements ILabel {
+
+		/**
+		 * In this mode, all wavelengths in the list are considered as an exclusion, that means apply the given function to all except the given wavelengths
+		 */
+		EXCLUDE("Exclude"),
+		/**
+		 * In this mode, all wavelengths in the list are considered as an inclusion, that means apply the given function to all wavelengths given
+		 */
+		INCLUDE("Include");
+
+		private String label = "";
+
+		private WavelengthMarkMode(String label) {
+
+			this.label = label;
+		}
+
+		@Override
+		public String label() {
+
+			return label;
+		}
+
+		public static String[][] getOptions() {
+
+			return ILabel.getOptions(values());
+		}
+	}
+
 	double getWavelength();
 
 	void setWavelength(double wavelength);

chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/support/IMarkedWavelengths.java

@@ -15,6 +15,7 @@
 import java.util.Set;
 
 import org.eclipse.chemclipse.model.core.IMarkedSignals;
+import org.eclipse.chemclipse.wsd.model.core.support.IMarkedWavelength.WavelengthMarkMode;
 
 public interface IMarkedWavelengths extends IMarkedSignals<IMarkedWavelength> {
 
@@ -43,4 +44,6 @@ public interface IMarkedWavelengths extends IMarkedSignals<IMarkedWavelength> {
 	 */
 	@Deprecated
 	void add(int wavelengthStart, int wavelengthStop);
+
+	WavelengthMarkMode getMode();
 }

chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/support/MarkedWavelengths.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2016, 2018 Lablicate GmbH.
+ * Copyright (c) 2016, 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
@@ -8,8 +8,36 @@
  * 
  * Contributors:
  * Dr. Philip Wenig - initial API and implementation
+ * Matthias Mailänder - add inclusive/exclusive mode
  *******************************************************************************/
 package org.eclipse.chemclipse.wsd.model.core.support;
 
+import java.util.Collection;
+
+import org.eclipse.chemclipse.wsd.model.core.support.IMarkedWavelength.WavelengthMarkMode;
+
 public class MarkedWavelengths extends AbstractMarkedWavelengths implements IMarkedWavelengths {
+
+	private WavelengthMarkMode mode;
+
+	public MarkedWavelengths() {
+
+	}
+
+	public MarkedWavelengths(WavelengthMarkMode mode) {
+
+		this.mode = mode;
+	}
+
+	public MarkedWavelengths(Collection<? extends Number> wavelengths, WavelengthMarkMode mode) {
+
+		super(wavelengths);
+		this.mode = mode;
+	}
+
+	@Override
+	public WavelengthMarkMode getMode() {
+
+		return mode;
+	}
 }