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eselmeistereselmeister
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Merge pull request #2320 from lorenzgerber/pca_statistics
PCA, descriptive statistics for features
2 parents 52f58da + 91c1ade commit 0da6598

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‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/META-INF/MANIFEST.MF‎

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@@ -47,7 +47,8 @@ Require-Bundle: org.eclipse.ui,
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org.eclipse.help
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Bundle-RequiredExecutionEnvironment: JavaSE-21
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Import-Package: jakarta.annotation;version="2.1.1",
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jakarta.inject;version="2.0.1"
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jakarta.inject;version="2.0.1",
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org.apache.commons.math3.stat.descriptive;version="[3.6.0,4.0.0)"
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Bundle-ActivationPolicy: lazy
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Service-Component: OSGI-INF/org.eclipse.chemclipse.xxd.process.supplier.pca.ui.quickstart.FileTileDefinition.xml,
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OSGI-INF/org.eclipse.chemclipse.xxd.process.supplier.pca.ui.quickstart.FilesLongFormatTileDefinition.xml,

‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/fragment.e4xmi‎

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@@ -7,6 +7,7 @@
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<elements xsi:type="basic:Part" xmi:id="_pUF1wPRuEeeapKw7g2Cagg" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.part.pca2dscoreplot" contributionURI="bundleclass://org.eclipse.chemclipse.xxd.process.supplier.pca.ui/org.eclipse.chemclipse.xxd.process.supplier.pca.ui.parts.ScorePlot2DPart" label="Score Plot 2D" iconURI="platform:/plugin/org.eclipse.chemclipse.rcp.ui.icons/icons/16x16/scoreplot2D.png"/>
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<elements xsi:type="basic:Part" xmi:id="_T6DG0D7wEeiZJpBc4U-l1A" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.part.explainedvariance" contributionURI="bundleclass://org.eclipse.chemclipse.xxd.process.supplier.pca.ui/org.eclipse.chemclipse.xxd.process.supplier.pca.ui.parts.VariancePart" label="Explained Variance" iconURI="platform:/plugin/org.eclipse.chemclipse.rcp.ui.icons/icons/16x16/barchart2.png"/>
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<elements xsi:type="basic:Part" xmi:id="_4x8EIDVNEfCIk78mmk2-TA" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.part.filterdistribution" contributionURI="bundleclass://org.eclipse.chemclipse.xxd.process.supplier.pca.ui/org.eclipse.chemclipse.xxd.process.supplier.pca.ui.parts.FilterDistributionPart" label="Filter Distribution" iconURI="platform:/plugin/org.eclipse.chemclipse.rcp.ui.icons/icons/16x16/filter.png"/>
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<elements xsi:type="basic:Part" xmi:id="_PixEIdPaDNEfCIPokk2-TA" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.part.featurestattable" contributionURI="bundleclass://org.eclipse.chemclipse.xxd.process.supplier.pca.ui/org.eclipse.chemclipse.xxd.process.supplier.pca.ui.parts.FeatureStatTablePart" label="Feature Statistics" iconURI="platform:/plugin/org.eclipse.chemclipse.rcp.ui.icons/icons/16x16/table.png"/>
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</fragments>
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<fragments xsi:type="fragment:StringModelFragment" xmi:id="_cgvnsN3IEee_Jr66fOQ3Hg" featurename="children" parentElementId="org.eclipse.chemclipse.rcp.app.ui.perspectivestack.main">
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<elements xsi:type="advanced:Perspective" xmi:id="_gMoqoN3IEee_Jr66fOQ3Hg" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.perspective" label="PCA (Principal Component Analysis)" iconURI="platform:/plugin/org.eclipse.chemclipse.rcp.ui.icons/icons/16x16/pca.gif">
@@ -19,6 +20,7 @@
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<children xsi:type="advanced:Placeholder" xmi:id="_jHao4D7wEeiZJpBc4U-l1A" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.part.explainedvariance" ref="_T6DG0D7wEeiZJpBc4U-l1A"/>
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<children xsi:type="advanced:Placeholder" xmi:id="_ZAXTIPRvEeeapKw7g2Cagg" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.part.pcadatatable" ref="_f3a8cPRtEeeapKw7g2Cagg"/>
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<children xsi:type="advanced:Placeholder" xmi:id="_roEjgDVQEfCIk78mmk2-TA" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.part.filterDistribution" ref="_4x8EIDVNEfCIk78mmk2-TA"/>
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<children xsi:type="advanced:Placeholder" xmi:id="_PioEgDVPaQEIkPo78mm-TA" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.part.featurestattable" ref="_PixEIdPaDNEfCIPokk2-TA"/>
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</children>
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</children>
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<children xsi:type="basic:PartSashContainer" xmi:id="_J7oIoPRvEeeapKw7g2Cagg" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.partsashcontainer.2" horizontal="true">

‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/internal/provider/FeatureStatComparator.java‎

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/*******************************************************************************
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* Copyright (c) 2025 Lablicate GmbH.
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*
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* This program and the accompanying materials are made
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* available under the terms of the Eclipse Public License 2.0
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* which is available at https://www.eclipse.org/legal/epl-2.0/
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*
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* SPDX-License-Identifier: EPL-2.0
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*
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* Contributors:
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* Lorenz Gerber - initial API and implementation
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*******************************************************************************/
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package org.eclipse.chemclipse.xxd.process.supplier.pca.ui.internal.provider;
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import java.util.List;
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import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
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import org.eclipse.chemclipse.model.statistics.ISampleData;
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import org.eclipse.chemclipse.model.statistics.IVariable;
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import org.eclipse.chemclipse.support.ui.swt.AbstractRecordTableComparator;
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import org.eclipse.chemclipse.support.ui.swt.IRecordTableComparator;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.Feature;
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import org.eclipse.jface.viewers.Viewer;
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public class FeatureStatComparator extends AbstractRecordTableComparator implements IRecordTableComparator {
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@Override
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public int compare(Viewer viewer, Object e1, Object e2) {
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int sortOrder = 0;
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if(e1 instanceof Feature feature1 && e2 instanceof Feature feature2) {
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IVariable variable1 = feature1.getVariable();
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IVariable variable2 = feature2.getVariable();
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DescriptiveStatistics stats = new DescriptiveStatistics();
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List<ISampleData<?>> sampleData1 = feature1.getSampleData();
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List<ISampleData<?>> sampleData2 = feature2.getSampleData();
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//
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int columnIndex = getPropertyIndex();
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switch(columnIndex) {
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case 0:
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try {
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double value1 = Double.parseDouble(variable1.getValue());
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double value2 = Double.parseDouble(variable2.getValue());
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sortOrder = Double.compare(value2, value1);
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} catch(Exception e) {
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sortOrder = variable2.getValue().compareTo(variable1.getValue());
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}
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break;
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case 1:
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sortOrder = variable2.getDescription().compareTo(variable1.getDescription());
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break;
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case 2:
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for(int i = 0; i < sampleData1.size(); i++) {
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stats.addValue(sampleData1.get(i).getData());
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}
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Double mean1 = stats.getMean();
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stats = new DescriptiveStatistics();
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for(int i = 0; i < sampleData2.size(); i++) {
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stats.addValue(sampleData2.get(i).getData());
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}
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Double mean2 = stats.getMean();
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sortOrder = Double.compare(mean2, mean1);
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break;
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case 3:
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for(int i = 0; i < sampleData1.size(); i++) {
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stats.addValue(sampleData1.get(i).getData());
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}
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Double min1 = stats.getMin();
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stats = new DescriptiveStatistics();
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for(int i = 0; i < sampleData2.size(); i++) {
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stats.addValue(sampleData2.get(i).getData());
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}
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Double min2 = stats.getMin();
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sortOrder = Double.compare(min2, min1);
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break;
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case 4:
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for(int i = 0; i < sampleData1.size(); i++) {
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stats.addValue(sampleData1.get(i).getData());
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}
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Double max1 = stats.getMax();
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stats = new DescriptiveStatistics();
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for(int i = 0; i < sampleData2.size(); i++) {
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stats.addValue(sampleData2.get(i).getData());
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}
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Double max2 = stats.getMax();
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sortOrder = Double.compare(max2, max1);
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break;
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case 5:
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for(int i = 0; i < sampleData1.size(); i++) {
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stats.addValue(sampleData1.get(i).getData());
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}
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Double rsd1 = stats.getStandardDeviation();
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rsd1 = 100.0 / stats.getSum() * rsd1;
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stats = new DescriptiveStatistics();
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for(int i = 0; i < sampleData2.size(); i++) {
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stats.addValue(sampleData2.get(i).getData());
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}
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Double rsd2 = stats.getStandardDeviation();
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rsd2 = 100.0 / stats.getSum() * rsd2;
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sortOrder = Double.compare(rsd2, rsd1);
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break;
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case 6:
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for(int i = 0; i < sampleData1.size(); i++) {
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stats.addValue(sampleData1.get(i).getData());
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}
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Double skew1 = stats.getSkewness();
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stats = new DescriptiveStatistics();
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for(int i = 0; i < sampleData2.size(); i++) {
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stats.addValue(sampleData2.get(i).getData());
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}
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Double skew2 = stats.getSkewness();
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sortOrder = Double.compare(skew2, skew1);
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break;
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case 7:
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for(int i = 0; i < sampleData1.size(); i++) {
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stats.addValue(sampleData1.get(i).getData());
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}
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Double kurt1 = stats.getKurtosis();
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stats = new DescriptiveStatistics();
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for(int i = 0; i < sampleData2.size(); i++) {
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stats.addValue(sampleData2.get(i).getData());
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}
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Double kurt2 = stats.getKurtosis();
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sortOrder = Double.compare(kurt2, kurt1);
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break;
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default:
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break;
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}
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}
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if(getDirection() == ASCENDING) {
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sortOrder = -sortOrder;
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}
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return sortOrder;
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}
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}

‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/internal/provider/FeatureStatLabelProvider.java‎

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/*******************************************************************************
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* Copyright (c) 2025 Lablicate GmbH.
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*
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* This program and the accompanying materials are made
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* available under the terms of the Eclipse Public License 2.0
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* which is available at https://www.eclipse.org/legal/epl-2.0/
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*
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* SPDX-License-Identifier: EPL-2.0
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*
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* Contributors:
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* Lorenz Gerber - initial API and implementation
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*******************************************************************************/
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package org.eclipse.chemclipse.xxd.process.supplier.pca.ui.internal.provider;
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import java.text.DecimalFormat;
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import java.util.List;
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import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
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import org.eclipse.chemclipse.model.statistics.ISampleData;
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import org.eclipse.chemclipse.model.statistics.IVariable;
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import org.eclipse.chemclipse.support.ui.provider.AbstractChemClipseLabelProvider;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.Feature;
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import org.eclipse.swt.graphics.Image;
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public class FeatureStatLabelProvider extends AbstractChemClipseLabelProvider {
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public static final String VARIABLE = "Variable";
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public static final String NAME = "Name";
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public static final String MEAN = "Mean";
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public static final String MIN = "Min";
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public static final String MAX = "Max";
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public static final String RELATIVESTDDEV = "RSD";
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public static final String SKEWNESS = "Skewness";
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public static final String KURTOSIS = "Excess Kurtosis";
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//
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private DecimalFormat decimalFormat = getDecimalFormat();
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//
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public static String[] TITLES = {//
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VARIABLE, //
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NAME, //
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MEAN, //
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MIN, //
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MAX, //
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RELATIVESTDDEV, //
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SKEWNESS, //
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KURTOSIS, //
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};
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public static int[] BOUNDS = {//
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50, //
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280, //
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140, //
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140, //
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140, //
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140, //
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140, //
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140 //
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};
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public FeatureStatLabelProvider(String pattern) {
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super(pattern);
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}
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@Override
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public String getColumnText(Object element, int columnIndex) {
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String text = "";
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if(element instanceof Feature feature) {
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IVariable variable = feature.getVariable();
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List<ISampleData<?>> sampleData = feature.getSampleData();
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DescriptiveStatistics stats = new DescriptiveStatistics();
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for(int i = 0; i < sampleData.size(); i++) {
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stats.addValue(sampleData.get(i).getData());
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}
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double value = 0.0;
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//
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switch(columnIndex) {
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case 0:
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text = variable.getValue();
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break;
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case 1:
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text = variable.getDescription();
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break;
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case 2:
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value = 0.0;
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value = stats.getMean();
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text = Double.isNaN(value) ? "NaN" : decimalFormat.format(value);
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break;
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case 3:
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value = 0.0;
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value = stats.getMin();
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text = Double.isNaN(value) ? "NaN" : decimalFormat.format(value);
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break;
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case 4:
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value = 0.0;
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value = stats.getMax();
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text = Double.isNaN(value) ? "NaN" : decimalFormat.format(value);
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break;
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case 5:
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value = 0.0;
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value = 100.0 / stats.getSum() * stats.getStandardDeviation();
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text = Double.isNaN(value) ? "NaN" : decimalFormat.format(value);
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break;
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case 6:
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value = 0.0;
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value = stats.getSkewness();
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text = Double.isNaN(value) ? "NaN" : decimalFormat.format(value);
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break;
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case 7:
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value = 0.0;
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value = stats.getKurtosis() - 3.0;
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text = Double.isNaN(value) ? "NaN" : decimalFormat.format(value);
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default:
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break;
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}
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}
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return text;
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}
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@Override
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public Image getColumnImage(Object element, int columnIndex) {
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return null;
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}
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}

‎chemclipse/plugins/org.eclipse.chemclipse.xxd.process.supplier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/parts/FeatureStatTablePart.java‎

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/*******************************************************************************
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* Copyright (c) 2025 Lablicate GmbH.
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*
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* This program and the accompanying materials are made
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* available under the terms of the Eclipse Public License 2.0
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* which is available at https://www.eclipse.org/legal/epl-2.0/
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*
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* SPDX-License-Identifier: EPL-2.0
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*
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* Contributors:
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* Lorenz Gerber - initial API and implementation
12+
*******************************************************************************/
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package org.eclipse.chemclipse.xxd.process.supplier.pca.ui.parts;
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import java.util.List;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IEvaluation;
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import org.eclipse.chemclipse.xxd.process.supplier.pca.ui.swt.ExtendedFeatureStatListUI;
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import org.eclipse.swt.SWT;
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import org.eclipse.swt.widgets.Composite;
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import jakarta.inject.Inject;
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public class FeatureStatTablePart extends AbstractPartPCA<ExtendedFeatureStatListUI> {
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@Inject
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public FeatureStatTablePart(Composite parent) {
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super(parent);
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}
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@Override
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protected ExtendedFeatureStatListUI createControl(Composite parent) {
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return new ExtendedFeatureStatListUI(parent, SWT.NONE);
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}
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@SuppressWarnings("unchecked")
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@Override
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protected boolean updateData(List<Object> objects, String topic) {
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if(objects.size() == 1) {
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if(isUnloadEvent(topic)) {
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getControl().setInput(null);
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unloadData();
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return false;
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} else if(isUpdateSelection(topic)) {
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Object object = objects.get(0);
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if(object instanceof IEvaluation evaluation) {
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getControl().setInput(evaluation);
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return true;
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}
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}
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}
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//
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return false;
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}
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}

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