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Fix #34, #36, #37 #35

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merged 13 commits into from
Oct 4, 2019
Merged

Fix #34, #36, #37 #35

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b3d71f3
Fix #34
kerner1000 Sep 28, 2019
ed58c5a
Fix #36
kerner1000 Sep 28, 2019
c0b7f1a
Fix [37]
kerner1000 Sep 28, 2019
a31a1d3
Readability
kerner1000 Sep 30, 2019
26855ee
Update header
kerner1000 Sep 30, 2019
96ddd06
Reduce dependency tree for static methods
kerner1000 Sep 30, 2019
5111dbf
Do not unecessary StringSettingsProperty annotation
kerner1000 Sep 30, 2019
b8919e7
Do not unecessary StringSettingsProperty annotation
kerner1000 Sep 30, 2019
b9788db
Squashed commit of the following:
kerner1000 Sep 30, 2019
d44a1ca
Merge remote-tracking branch 'origin/develop' into develop-kerner1000
kerner1000 Oct 1, 2019
8299a78
Pass filter ions directly
kerner1000 Oct 1, 2019
2e8416c
Merge remote-tracking branch 'origin/develop' into develop-kerner1000
kerner1000 Oct 1, 2019
69ea649
Pass filter ions directly
kerner1000 Oct 1, 2019
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20 changes: 20 additions & 0 deletions .../org/eclipse/chemclipse/chromatogram/msd/peak/detector/settings/PeakDetectorSettings.java
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Expand Up @@ -11,10 +11,30 @@
*******************************************************************************/
package org.eclipse.chemclipse.chromatogram.msd.peak.detector.settings;

import java.util.Collection;
import java.util.Collections;

import org.eclipse.chemclipse.numeric.statistics.WindowSize;

/**
* THIS IS A TESTCLASS! ONLY USE IT FOR TEST CASES! IT'S NOT FOR PRODUCTIVE USE!
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*
* @author eselmeister
*/
public class PeakDetectorSettings extends AbstractPeakDetectorSettingsMSD {

@Override
public WindowSize getMovingAverageWindowSize() {
return WindowSize.WIDTH_15;
}

@Override
public Collection<Number> getFilterIon() {
return Collections.emptyList();
}

@Override
public FilterMode getFilterMode() {
return FilterMode.EXCLUDE;
}
}
1 change: 1 addition & 0 deletions ...clipse/plugins/org.eclipse.chemclipse.chromatogram.msd.peak.detector/META-INF/MANIFEST.MF
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Expand Up @@ -16,6 +16,7 @@ Export-Package: org.eclipse.chemclipse.chromatogram.msd.peak.detector.core,
org.eclipse.chemclipse.chromatogram.msd.peak.detector.settings
Bundle-Vendor: ChemClipse
Import-Package: org.eclipse.chemclipse.model.types,
org.eclipse.chemclipse.numeric.statistics,
org.eclipse.chemclipse.support.settings.parser,
org.osgi.service.component.annotations;version="1.2.0"
Service-Component: OSGI-INF/org.eclipse.chemclipse.chromatogram.msd.peak.detector.core.PeakDetectorMSDProcessTypeSupplier.xml
28 changes: 27 additions & 1 deletion ...e/chemclipse/chromatogram/msd/peak/detector/settings/AbstractPeakDetectorSettingsMSD.java
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Expand Up @@ -13,5 +13,31 @@

import org.eclipse.chemclipse.chromatogram.peak.detector.settings.AbstractPeakDetectorSettings;

public abstract class AbstractPeakDetectorSettingsMSD extends AbstractPeakDetectorSettings implements IPeakDetectorSettingsMSD {
public abstract class AbstractPeakDetectorSettingsMSD extends AbstractPeakDetectorSettings
implements IPeakDetectorSettingsMSD {

private boolean includeBackground = false;
private float minimumSignalToNoiseRatio = 0;

@Override
public boolean isIncludeBackground() {

return includeBackground;
}

public void setIncludeBackground(boolean includeBackground) {

this.includeBackground = includeBackground;
}

@Override
public float getMinimumSignalToNoiseRatio() {

return minimumSignalToNoiseRatio;
}

public void setMinimumSignalToNoiseRatio(float minimumSignalToNoiseRatio) {

this.minimumSignalToNoiseRatio = minimumSignalToNoiseRatio;
}
}
18 changes: 18 additions & 0 deletions .../eclipse/chemclipse/chromatogram/msd/peak/detector/settings/IPeakDetectorSettingsMSD.java
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Expand Up @@ -11,7 +11,25 @@
*******************************************************************************/
package org.eclipse.chemclipse.chromatogram.msd.peak.detector.settings;

import java.util.Collection;

import org.eclipse.chemclipse.chromatogram.peak.detector.settings.IPeakDetectorSettings;
import org.eclipse.chemclipse.numeric.statistics.WindowSize;

public interface IPeakDetectorSettingsMSD extends IPeakDetectorSettings {

enum FilterMode {
INCLUDE, EXCLUDE
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}

float getMinimumSignalToNoiseRatio();

boolean isIncludeBackground();

WindowSize getMovingAverageWindowSize();

Collection<Number> getFilterIon();

FilterMode getFilterMode();

}
2 changes: 1 addition & 1 deletion ...matogram/xxd/peak/detector/supplier/firstderivative/core/FirstDerivativePeakDetector.java
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Expand Up @@ -70,7 +70,7 @@ public <T extends IMeasurement> Map<T, PeakList> detectIMeasurementPeaks(Collect
} else {
configuration = globalConfiguration;
}
slopes = PeakDetectorMSD.getFirstDerivativeSlopes(new ChromatogramSelectionMSD((IChromatogramMSD)measurement), configuration.getMovingAverageWindowSize());
slopes = PeakDetectorMSD.getFirstDerivativeSlopes(new ChromatogramSelectionMSD((IChromatogramMSD)measurement), configuration);
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} else if(measurement instanceof IChromatogramCSD) {
if(globalConfiguration == null) {
configuration = new FirstDerivativePeakDetectorSettings(DataType.CSD);
Expand Down
51 changes: 43 additions & 8 deletions ...mclipse/chromatogram/xxd/peak/detector/supplier/firstderivative/core/PeakDetectorMSD.java
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Expand Up @@ -13,10 +13,13 @@
*******************************************************************************/
package org.eclipse.chemclipse.chromatogram.xxd.peak.detector.supplier.firstderivative.core;

import java.util.Collection;
import java.util.Iterator;
import java.util.List;

import org.eclipse.chemclipse.chromatogram.msd.peak.detector.core.IPeakDetectorMSD;
import org.eclipse.chemclipse.chromatogram.msd.peak.detector.settings.IPeakDetectorSettingsMSD;
import org.eclipse.chemclipse.chromatogram.msd.peak.detector.settings.IPeakDetectorSettingsMSD.FilterMode;
import org.eclipse.chemclipse.chromatogram.peak.detector.exceptions.ValueMustNotBeNullException;
import org.eclipse.chemclipse.chromatogram.peak.detector.support.IRawPeak;
import org.eclipse.chemclipse.chromatogram.xxd.peak.detector.supplier.firstderivative.preferences.PreferenceSupplier;
Expand All @@ -36,12 +39,14 @@
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.IChromatogramPeakMSD;
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;
import org.eclipse.chemclipse.msd.model.core.support.MarkedIons;
import org.eclipse.chemclipse.msd.model.core.support.PeakBuilderMSD;
import org.eclipse.chemclipse.msd.model.xic.ITotalIonSignalExtractor;
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.statistics.WindowSize;
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 @@ -99,7 +104,7 @@ public IProcessingInfo detect(IChromatogramSelectionMSD chromatogramSelection, I
*/
private void detectPeaks(IChromatogramSelectionMSD chromatogramSelection, PeakDetectorSettingsMSD peakDetectorSettings, IProgressMonitor monitor) {

IFirstDerivativeDetectorSlopes slopes = getFirstDerivativeSlopes(chromatogramSelection, peakDetectorSettings.getMovingAverageWindowSize());
IFirstDerivativeDetectorSlopes slopes = getFirstDerivativeSlopes(chromatogramSelection, peakDetectorSettings);
List<IRawPeak> rawPeaks = getRawPeaks(slopes, peakDetectorSettings.getThreshold(), monitor);
buildAndStorePeaks(rawPeaks, chromatogramSelection.getChromatogramMSD(), peakDetectorSettings);
}
Expand All @@ -111,7 +116,7 @@ private void detectPeaks(IChromatogramSelectionMSD chromatogramSelection, PeakDe
* @param rawPeaks
* @param chromatogram
*/
private void buildAndStorePeaks(List<IRawPeak> rawPeaks, IChromatogramMSD chromatogram, PeakDetectorSettingsMSD peakDetectorSettings) {
private void buildAndStorePeaks(List<IRawPeak> rawPeaks, IChromatogramMSD chromatogram, IPeakDetectorSettingsMSD peakDetectorSettings) {

IChromatogramPeakMSD peak = null;
IScanRange scanRange = null;
Expand Down Expand Up @@ -159,12 +164,12 @@ private void buildAndStorePeaks(List<IRawPeak> rawPeaks, IChromatogramMSD chroma
* @param windowSize
* @return {@link IFirstDerivativeDetectorSlopes}
*/
public static IFirstDerivativeDetectorSlopes getFirstDerivativeSlopes(IChromatogramSelectionMSD chromatogramSelection, WindowSize windowSize) {
public static IFirstDerivativeDetectorSlopes getFirstDerivativeSlopes(IChromatogramSelectionMSD chromatogramSelection, IPeakDetectorSettingsMSD peakDetectorSettings) {
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IChromatogramMSD chromatogram = chromatogramSelection.getChromatogramMSD();
try {
ITotalIonSignalExtractor totalIonSignalExtractor = new TotalIonSignalExtractor(chromatogram);
ITotalScanSignals signals = totalIonSignalExtractor.getTotalIonSignals(chromatogramSelection);
ITotalScanSignals signals = totalIonSignalExtractor.getTotalIonSignals(chromatogramSelection, getIonFilter(peakDetectorSettings));
TotalScanSignalsModifier.normalize(signals, NORMALIZATION_BASE);
/*
* Get the start and stop scan of the chromatogram selection.
Expand All @@ -185,22 +190,52 @@ public static IFirstDerivativeDetectorSlopes getFirstDerivativeSlopes(IChromatog
slopes.add(slope);
}
}
slopes.calculateMovingAverage(windowSize);
slopes.calculateMovingAverage(peakDetectorSettings.getMovingAverageWindowSize());
return slopes;
} catch(ChromatogramIsNullException e) {
logger.warn(e);
logger.warn(e.getLocalizedMessage(), e);
return null;
}
}

private static IMarkedIons getIonFilter(IPeakDetectorSettingsMSD peakDetectorSettings) {

Collection<Number> filterIons = peakDetectorSettings.getFilterIon();
FilterMode mode = peakDetectorSettings.getFilterMode();
MarkedIons result = new MarkedIons(buildIons(filterIons), buildFilterMode(mode));
return result;
}

private static int[] buildIons(Collection<Number> filterIons) {

int[] result = new int[filterIons.size()];
int cnt = 0;
Iterator<Number> it = filterIons.iterator();
while(it.hasNext()) {
result[cnt++] = it.next().intValue();
}
return result;
}

private static IonMarkMode buildFilterMode(FilterMode mode) {

switch(mode) {
case EXCLUDE:
return IonMarkMode.EXCLUDE;
case INCLUDE:
return IonMarkMode.INCLUDE;
}
throw new IllegalArgumentException("Unknown mode " + mode);
}

/**
* Checks that the peak is not null and that it matches
* the min S/N requirements.
*
* @param peak
* @return boolean
*/
private boolean isValidPeak(IChromatogramPeakMSD peak, PeakDetectorSettingsMSD peakDetectorSettings) {
private boolean isValidPeak(IChromatogramPeakMSD peak, IPeakDetectorSettingsMSD peakDetectorSettings) {

if(peak != null && peak.getSignalToNoiseRatio() >= peakDetectorSettings.getMinimumSignalToNoiseRatio()) {
return true;
Expand Down
53 changes: 11 additions & 42 deletions .../peak/detector/supplier/firstderivative/settings/FirstDerivativePeakDetectorSettings.java
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Expand Up @@ -11,18 +11,19 @@
*******************************************************************************/
package org.eclipse.chemclipse.chromatogram.xxd.peak.detector.supplier.firstderivative.settings;

import org.eclipse.chemclipse.chromatogram.msd.peak.detector.settings.AbstractPeakDetectorSettingsMSD;
import org.eclipse.chemclipse.chromatogram.xxd.peak.detector.supplier.firstderivative.preferences.PreferenceSupplier;
import org.eclipse.chemclipse.logging.core.Logger;
import org.eclipse.chemclipse.model.types.DataType;
import org.eclipse.chemclipse.numeric.statistics.WindowSize;
import org.eclipse.chemclipse.support.settings.EnumSelectionRadioButtonsSettingProperty;
import org.eclipse.chemclipse.support.settings.EnumSelectionSettingProperty;
import org.eclipse.chemclipse.support.settings.FloatSettingsProperty;
import org.eclipse.chemclipse.support.settings.StringSettingsProperty;

import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonPropertyDescription;

public class FirstDerivativePeakDetectorSettings extends AbstractPeakDetectorSettingsMSD {
public class FirstDerivativePeakDetectorSettings extends PeakDetectorSettingsMSD {

@JsonProperty(value = "Threshold", defaultValue = "MEDIUM")
@EnumSelectionRadioButtonsSettingProperty
Expand All @@ -36,52 +37,20 @@ public class FirstDerivativePeakDetectorSettings extends AbstractPeakDetectorSet
@JsonPropertyDescription(value = "Window Size: 3, 5, 7, ..., 45")
@EnumSelectionSettingProperty
private WindowSize windowSize = WindowSize.WIDTH_5;
@JsonProperty(value = "IonFilter", defaultValue = "EXCLUDE")
@EnumSelectionRadioButtonsSettingProperty
FilterMode filterMode = FilterMode.EXCLUDE;
@JsonPropertyDescription(value = "Ions to filter: 16, 18, ...")
@StringSettingsProperty
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String filterIonsString;

public FirstDerivativePeakDetectorSettings() {

this(DataType.MSD);
}

public FirstDerivativePeakDetectorSettings(DataType dataType) {
// we could load optimized settings depending on datatype here
}

public Threshold getThreshold() {

return threshold;
}

public void setThreshold(Threshold threshold) {

this.threshold = threshold;
}

public boolean isIncludeBackground() {

return includeBackground;
}

public void setIncludeBackground(boolean includeBackground) {

this.includeBackground = includeBackground;
}

public float getMinimumSignalToNoiseRatio() {

return minimumSignalToNoiseRatio;
}

public void setMinimumSignalToNoiseRatio(float minimumSignalToNoiseRatio) {

this.minimumSignalToNoiseRatio = minimumSignalToNoiseRatio;
}

public WindowSize getMovingAverageWindowSize() {

return windowSize;
}

public void setMovingAverageWindowSize(WindowSize windowSize) {

this.windowSize = windowSize;
// we could load optimized settings depending on datatype here
}
}
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