PCA, descriptive statistics for features

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

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

@@ -7,6 +7,7 @@
     <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"/>
     <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"/>
     <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"/>
+    <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"/>
   </fragments>
   <fragments xsi:type="fragment:StringModelFragment" xmi:id="_cgvnsN3IEee_Jr66fOQ3Hg" featurename="children" parentElementId="org.eclipse.chemclipse.rcp.app.ui.perspectivestack.main">
     <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 @@
             <children xsi:type="advanced:Placeholder" xmi:id="_jHao4D7wEeiZJpBc4U-l1A" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.part.explainedvariance" ref="_T6DG0D7wEeiZJpBc4U-l1A"/>
             <children xsi:type="advanced:Placeholder" xmi:id="_ZAXTIPRvEeeapKw7g2Cagg" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.part.pcadatatable" ref="_f3a8cPRtEeeapKw7g2Cagg"/>
             <children xsi:type="advanced:Placeholder" xmi:id="_roEjgDVQEfCIk78mmk2-TA" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.part.filterDistribution" ref="_4x8EIDVNEfCIk78mmk2-TA"/>
+            <children xsi:type="advanced:Placeholder" xmi:id="_PioEgDVPaQEIkPo78mm-TA" elementId="org.eclipse.chemclipse.xxd.process.supplier.pca.ui.part.featurestattable" ref="_PixEIdPaDNEfCIPokk2-TA"/>
           </children>
         </children>
         <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

@@ -0,0 +1,135 @@
+/*******************************************************************************
+ * Copyright (c) 2025 Lablicate GmbH.
+ *
+ * This program and the accompanying materials are made
+ * available under the terms of the Eclipse Public License 2.0
+ * which is available at https://www.eclipse.org/legal/epl-2.0/
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ * 
+ * Contributors:
+ * Lorenz Gerber - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.xxd.process.supplier.pca.ui.internal.provider;
+
+import java.util.List;
+
+import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
+import org.eclipse.chemclipse.model.statistics.ISampleData;
+import org.eclipse.chemclipse.model.statistics.IVariable;
+import org.eclipse.chemclipse.support.ui.swt.AbstractRecordTableComparator;
+import org.eclipse.chemclipse.support.ui.swt.IRecordTableComparator;
+import org.eclipse.chemclipse.xxd.process.supplier.pca.model.Feature;
+import org.eclipse.jface.viewers.Viewer;
+
+public class FeatureStatComparator extends AbstractRecordTableComparator implements IRecordTableComparator {
+
+	@Override
+	public int compare(Viewer viewer, Object e1, Object e2) {
+
+		int sortOrder = 0;
+		if(e1 instanceof Feature feature1 && e2 instanceof Feature feature2) {
+			IVariable variable1 = feature1.getVariable();
+			IVariable variable2 = feature2.getVariable();
+			DescriptiveStatistics stats = new DescriptiveStatistics();
+			List<ISampleData<?>> sampleData1 = feature1.getSampleData();
+			List<ISampleData<?>> sampleData2 = feature2.getSampleData();
+			//
+			int columnIndex = getPropertyIndex();
+			switch(columnIndex) {
+				case 0:
+					try {
+						double value1 = Double.parseDouble(variable1.getValue());
+						double value2 = Double.parseDouble(variable2.getValue());
+						sortOrder = Double.compare(value2, value1);
+					} catch(Exception e) {
+						sortOrder = variable2.getValue().compareTo(variable1.getValue());
+					}
+					break;
+				case 1:
+					sortOrder = variable2.getDescription().compareTo(variable1.getDescription());
+					break;
+				case 2:
+					for(int i = 0; i < sampleData1.size(); i++) {
+						stats.addValue(sampleData1.get(i).getData());
+					}
+					Double mean1 = stats.getMean();
+					stats = new DescriptiveStatistics();
+					for(int i = 0; i < sampleData2.size(); i++) {
+						stats.addValue(sampleData2.get(i).getData());
+					}
+					Double mean2 = stats.getMean();
+					sortOrder = Double.compare(mean2, mean1);
+					break;
+				case 3:
+					for(int i = 0; i < sampleData1.size(); i++) {
+						stats.addValue(sampleData1.get(i).getData());
+					}
+					Double min1 = stats.getMin();
+					stats = new DescriptiveStatistics();
+					for(int i = 0; i < sampleData2.size(); i++) {
+						stats.addValue(sampleData2.get(i).getData());
+					}
+					Double min2 = stats.getMin();
+					sortOrder = Double.compare(min2, min1);
+					break;
+				case 4:
+					for(int i = 0; i < sampleData1.size(); i++) {
+						stats.addValue(sampleData1.get(i).getData());
+					}
+					Double max1 = stats.getMax();
+					stats = new DescriptiveStatistics();
+					for(int i = 0; i < sampleData2.size(); i++) {
+						stats.addValue(sampleData2.get(i).getData());
+					}
+					Double max2 = stats.getMax();
+					sortOrder = Double.compare(max2, max1);
+					break;
+				case 5:
+					for(int i = 0; i < sampleData1.size(); i++) {
+						stats.addValue(sampleData1.get(i).getData());
+					}
+					Double rsd1 = stats.getStandardDeviation();
+					rsd1 = 100.0 / stats.getSum() * rsd1;
+					stats = new DescriptiveStatistics();
+					for(int i = 0; i < sampleData2.size(); i++) {
+						stats.addValue(sampleData2.get(i).getData());
+					}
+					Double rsd2 = stats.getStandardDeviation();
+					rsd2 = 100.0 / stats.getSum() * rsd2;
+					sortOrder = Double.compare(rsd2, rsd1);
+					break;
+				case 6:
+					for(int i = 0; i < sampleData1.size(); i++) {
+						stats.addValue(sampleData1.get(i).getData());
+					}
+					Double skew1 = stats.getSkewness();
+					stats = new DescriptiveStatistics();
+					for(int i = 0; i < sampleData2.size(); i++) {
+						stats.addValue(sampleData2.get(i).getData());
+					}
+					Double skew2 = stats.getSkewness();
+					sortOrder = Double.compare(skew2, skew1);
+					break;
+				case 7:
+					for(int i = 0; i < sampleData1.size(); i++) {
+						stats.addValue(sampleData1.get(i).getData());
+					}
+					Double kurt1 = stats.getKurtosis();
+					stats = new DescriptiveStatistics();
+					for(int i = 0; i < sampleData2.size(); i++) {
+						stats.addValue(sampleData2.get(i).getData());
+					}
+					Double kurt2 = stats.getKurtosis();
+					sortOrder = Double.compare(kurt2, kurt1);
+					break;
+				default:
+					break;
+			}
+		}
+		if(getDirection() == ASCENDING) {
+			sortOrder = -sortOrder;
+		}
+		return sortOrder;
+	}
+}

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

@@ -0,0 +1,125 @@
+/*******************************************************************************
+ * Copyright (c) 2025 Lablicate GmbH.
+ *
+ * This program and the accompanying materials are made
+ * available under the terms of the Eclipse Public License 2.0
+ * which is available at https://www.eclipse.org/legal/epl-2.0/
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ * 
+ * Contributors:
+ * Lorenz Gerber - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.xxd.process.supplier.pca.ui.internal.provider;
+
+import java.text.DecimalFormat;
+import java.util.List;
+
+import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
+import org.eclipse.chemclipse.model.statistics.ISampleData;
+import org.eclipse.chemclipse.model.statistics.IVariable;
+import org.eclipse.chemclipse.support.ui.provider.AbstractChemClipseLabelProvider;
+import org.eclipse.chemclipse.xxd.process.supplier.pca.model.Feature;
+import org.eclipse.swt.graphics.Image;
+
+public class FeatureStatLabelProvider extends AbstractChemClipseLabelProvider {
+
+	public static final String VARIABLE = "Variable";
+	public static final String NAME = "Name";
+	public static final String MEAN = "Mean";
+	public static final String MIN = "Min";
+	public static final String MAX = "Max";
+	public static final String RELATIVESTDDEV = "RSD";
+	public static final String SKEWNESS = "Skewness";
+	public static final String KURTOSIS = "Excess Kurtosis";
+	//
+	private DecimalFormat decimalFormat = getDecimalFormat();
+	//
+	public static String[] TITLES = {//
+			VARIABLE, //
+			NAME, //
+			MEAN, //
+			MIN, //
+			MAX, //
+			RELATIVESTDDEV, //
+			SKEWNESS, //
+			KURTOSIS, //
+	};
+	public static int[] BOUNDS = {//
+			50, //
+			280, //
+			140, //
+			140, //
+			140, //
+			140, //
+			140, //
+			140 //
+	};
+
+	public FeatureStatLabelProvider(String pattern) {
+
+		super(pattern);
+	}
+
+	@Override
+	public String getColumnText(Object element, int columnIndex) {
+
+		String text = "";
+		if(element instanceof Feature feature) {
+			IVariable variable = feature.getVariable();
+			List<ISampleData<?>> sampleData = feature.getSampleData();
+			DescriptiveStatistics stats = new DescriptiveStatistics();
+			for(int i = 0; i < sampleData.size(); i++) {
+				stats.addValue(sampleData.get(i).getData());
+			}
+			double value = 0.0;
+			//
+			switch(columnIndex) {
+				case 0:
+					text = variable.getValue();
+					break;
+				case 1:
+					text = variable.getDescription();
+					break;
+				case 2:
+					value = 0.0;
+					value = stats.getMean();
+					text = Double.isNaN(value) ? "NaN" : decimalFormat.format(value);
+					break;
+				case 3:
+					value = 0.0;
+					value = stats.getMin();
+					text = Double.isNaN(value) ? "NaN" : decimalFormat.format(value);
+					break;
+				case 4:
+					value = 0.0;
+					value = stats.getMax();
+					text = Double.isNaN(value) ? "NaN" : decimalFormat.format(value);
+					break;
+				case 5:
+					value = 0.0;
+					value = 100.0 / stats.getSum() * stats.getStandardDeviation();
+					text = Double.isNaN(value) ? "NaN" : decimalFormat.format(value);
+					break;
+				case 6:
+					value = 0.0;
+					value = stats.getSkewness();
+					text = Double.isNaN(value) ? "NaN" : decimalFormat.format(value);
+					break;
+				case 7:
+					value = 0.0;
+					value = stats.getKurtosis() - 3.0;
+					text = Double.isNaN(value) ? "NaN" : decimalFormat.format(value);
+				default:
+					break;
+			}
+		}
+		return text;
+	}
+
+	@Override
+	public Image getColumnImage(Object element, int columnIndex) {
+
+		return null;
+	}
+}

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

@@ -0,0 +1,58 @@
+/*******************************************************************************
+ * Copyright (c) 2025 Lablicate GmbH.
+ *
+ * This program and the accompanying materials are made
+ * available under the terms of the Eclipse Public License 2.0
+ * which is available at https://www.eclipse.org/legal/epl-2.0/
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ * 
+ * Contributors:
+ * Lorenz Gerber - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.xxd.process.supplier.pca.ui.parts;
+
+import java.util.List;
+
+import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IEvaluation;
+import org.eclipse.chemclipse.xxd.process.supplier.pca.ui.swt.ExtendedFeatureStatListUI;
+import org.eclipse.swt.SWT;
+import org.eclipse.swt.widgets.Composite;
+
+import jakarta.inject.Inject;
+
+public class FeatureStatTablePart extends AbstractPartPCA<ExtendedFeatureStatListUI> {
+
+	@Inject
+	public FeatureStatTablePart(Composite parent) {
+
+		super(parent);
+	}
+
+	@Override
+	protected ExtendedFeatureStatListUI createControl(Composite parent) {
+
+		return new ExtendedFeatureStatListUI(parent, SWT.NONE);
+	}
+
+	@SuppressWarnings("unchecked")
+	@Override
+	protected boolean updateData(List<Object> objects, String topic) {
+
+		if(objects.size() == 1) {
+			if(isUnloadEvent(topic)) {
+				getControl().setInput(null);
+				unloadData();
+				return false;
+			} else if(isUpdateSelection(topic)) {
+				Object object = objects.get(0);
+				if(object instanceof IEvaluation evaluation) {
+					getControl().setInput(evaluation);
+					return true;
+				}
+			}
+		}
+		//
+		return false;
+	}
+}