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Merged
eselmeister merged 1 commit into from
Jul 17, 2025
Merged

PCA, Add Evaluation as generic base of EvaluationPCA #2318

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25 changes: 12 additions & 13 deletions ....ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/chart2d/ErrorResidueChart.java
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Expand Up @@ -9,21 +9,20 @@
*
* Contributors:
* Philip Wenig - initial API and implementation
* Lorenz Gerber - Specific result type for multivariate analysis (MVA)
*******************************************************************************/
package org.eclipse.chemclipse.xxd.process.supplier.pca.ui.chart2d;

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

import org.eclipse.chemclipse.model.statistics.ISample;
import org.eclipse.chemclipse.model.statistics.IVariable;
import org.eclipse.chemclipse.support.text.ValueFormat;
import org.eclipse.chemclipse.support.ui.workbench.DisplayUtils;
import org.eclipse.chemclipse.support.ui.workbench.PreferencesSupport;
import org.eclipse.chemclipse.swt.ui.support.Colors;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.EvaluationPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultsPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultMVA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultsMVA;
import org.eclipse.swt.SWT;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swtchart.IBarSeries.BarWidthStyle;
Expand Down Expand Up @@ -51,10 +50,10 @@ public ErrorResidueChart(Composite parent, int style) {
createControl();
}

public void setInput(EvaluationPCA<IVariable, ISample, IResultPCA> evaluationPCA) {
public void setInput(EvaluationPCA evaluationPCA) {

if(evaluationPCA != null) {
IResultsPCA<IResultPCA, ?> resultsPCA = evaluationPCA.getResults();
IResultsMVA resultsPCA = evaluationPCA.getResults();
updateChart(resultsPCA);
} else {
updateChart(null);
Expand Down Expand Up @@ -118,7 +117,7 @@ private void setPrimaryAxisSet(IChartSettings chartSettings) {
}
}

private void updateChart(IResultsPCA<IResultPCA, ?> pcaResults) {
private void updateChart(IResultsMVA pcaResults) {

deleteSeries();
if(pcaResults != null) {
Expand All @@ -142,29 +141,29 @@ private void updateChart(IResultsPCA<IResultPCA, ?> pcaResults) {
}
}

private String[] getCategories(IResultsPCA<IResultPCA, ?> pcaResults) {
private String[] getCategories(IResultsMVA pcaResults) {

List<IResultPCA> pcaResultList = pcaResults.getPcaResultList();
List<IResultMVA> pcaResultList = pcaResults.getPcaResultList();
int size = pcaResultList.size();
String[] categories = new String[size];
//
for(int i = 0; i < size; i++) {
IResultPCA pcaResult = pcaResultList.get(i);
IResultMVA pcaResult = pcaResultList.get(i);
categories[i] = pcaResult.getSample().getSampleName();
}
//
return categories;
}

private ISeriesData getSeries(IResultsPCA<IResultPCA, ?> pcaResults) {
private ISeriesData getSeries(IResultsMVA pcaResults) {

List<IResultPCA> pcaResultList = pcaResults.getPcaResultList();
List<IResultMVA> pcaResultList = pcaResults.getPcaResultList();
int size = pcaResultList.size();
double[] xSeries = new double[size];
double[] ySeries = new double[size];
//
for(int i = 0; i < size; i++) {
IResultPCA pcaResult = pcaResultList.get(i);
IResultMVA pcaResult = pcaResultList.get(i);
xSeries[i] = i;
ySeries[i] = pcaResult.getErrorMetric();
}
Expand Down
9 changes: 3 additions & 6 deletions ...r.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/chart2d/LoadingsPlot.java
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Expand Up @@ -16,11 +16,8 @@

import java.util.List;

import org.eclipse.chemclipse.model.statistics.ISample;
import org.eclipse.chemclipse.model.statistics.IVariable;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.EvaluationPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultsPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultsMVA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.ui.support.SeriesConverter;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swtchart.extensions.scattercharts.IScatterSeriesData;
Expand Down Expand Up @@ -49,11 +46,11 @@ public void setLabelsType(int labelsType) {
}
}

public void setInput(EvaluationPCA<IVariable, ISample, IResultPCA> evaluationPCA, int pcX, int pcY) {
public void setInput(EvaluationPCA evaluationPCA, int pcX, int pcY) {

deleteSeries();
if(evaluationPCA != null) {
IResultsPCA<IResultPCA, IVariable> resultsPCA = evaluationPCA.getResults();
IResultsMVA resultsPCA = evaluationPCA.getResults();
List<IScatterSeriesData> series;
if(labelType == LABEL_RETENTION_TIME_MINUTES) {
series = SeriesConverter.basisVectorsToSeries(resultsPCA, evaluationPCA.getHighlightedVariables(), pcX, pcY);
Expand Down
11 changes: 5 additions & 6 deletions ...lier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/chart2d/ScorePlot.java
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Expand Up @@ -19,27 +19,26 @@
import java.util.Map;

import org.eclipse.chemclipse.model.statistics.ISample;
import org.eclipse.chemclipse.model.statistics.IVariable;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.EvaluationPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultsPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultMVA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultsMVA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.ui.support.SeriesConverter;
import org.eclipse.swt.widgets.Composite;

public class ScorePlot extends AbtractPlotPCA {

private final Map<ISample, IResultPCA> extractedResults = new HashMap<>();
private final Map<ISample, IResultMVA> extractedResults = new HashMap<>();

public ScorePlot(Composite parent, int style) {

super(parent, style, "Score Plot");
}

public void setInput(EvaluationPCA<IVariable, ISample, IResultPCA> evaluationPCA, int pcX, int pcY) {
public void setInput(EvaluationPCA evaluationPCA, int pcX, int pcY) {

deleteSeries();
if(evaluationPCA != null) {
IResultsPCA<IResultPCA, ?> resultsPCA = evaluationPCA.getResults();
IResultsMVA resultsPCA = evaluationPCA.getResults();
List<ISample> highlightedSamples = evaluationPCA.getHighlightedSamples();
addSeriesData(SeriesConverter.sampleToSeries(resultsPCA, highlightedSamples, pcX, pcY, extractedResults));
}
Expand Down
18 changes: 8 additions & 10 deletions ....pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/chart2d/VarianceChart.java
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Expand Up @@ -9,21 +9,19 @@
*
* Contributors:
* Philip Wenig - initial API and implementation
* Lorenz Gerber - refactor
*******************************************************************************/
package org.eclipse.chemclipse.xxd.process.supplier.pca.ui.chart2d;

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

import org.eclipse.chemclipse.model.statistics.ISample;
import org.eclipse.chemclipse.model.statistics.IVariable;
import org.eclipse.chemclipse.support.text.ValueFormat;
import org.eclipse.chemclipse.support.ui.workbench.DisplayUtils;
import org.eclipse.chemclipse.support.ui.workbench.PreferencesSupport;
import org.eclipse.chemclipse.swt.ui.support.Colors;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.EvaluationPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultsPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultsMVA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.Variance;
import org.eclipse.swt.SWT;
import org.eclipse.swt.widgets.Composite;
Expand All @@ -44,7 +42,7 @@
public class VarianceChart extends BarChart {

private Variance variance = Variance.EXPLAINED;
private EvaluationPCA<IVariable, ISample, IResultPCA> evaluationPCA;
private EvaluationPCA evaluationPCA;

public VarianceChart() {

Expand All @@ -64,7 +62,7 @@ public void setVariance(Variance variance) {
updateChart();
}

public void setInput(EvaluationPCA<IVariable, ISample, IResultPCA> evaluationPCA) {
public void setInput(EvaluationPCA evaluationPCA) {

this.evaluationPCA = evaluationPCA;
updateChart();
Expand Down Expand Up @@ -126,7 +124,7 @@ private void updateChart() {
deleteSeries();
if(evaluationPCA != null) {
//
IResultsPCA<?, ?> resultsPCA = evaluationPCA.getResults();
IResultsMVA resultsPCA = evaluationPCA.getResults();
//
IChartSettings chartSettings = getChartSettings();
IPrimaryAxisSettings primaryAxisSettingsX = chartSettings.getPrimaryAxisSettingsX();
Expand Down Expand Up @@ -168,7 +166,7 @@ private void updateChart() {
}
}

private String[] getCategories(IResultsPCA<?, ?> pcaResults) {
private String[] getCategories(IResultsMVA pcaResults) {

int size = pcaResults.getCumulativeExplainedVariances().length;
String[] categories = new String[size];
Expand All @@ -180,7 +178,7 @@ private String[] getCategories(IResultsPCA<?, ?> pcaResults) {
return categories;
}

private ISeriesData getSeriesVariance(IResultsPCA<?, ?> pcaResults) {
private ISeriesData getSeriesVariance(IResultsMVA pcaResults) {

double[] ySeries;
String label;
Expand All @@ -202,7 +200,7 @@ private ISeriesData getSeriesVariance(IResultsPCA<?, ?> pcaResults) {
return new SeriesData(xSeries, ySeries, label);
}

private ISeriesData getSeriesQ2(IResultsPCA<?, ?> pcaResults) {
private ISeriesData getSeriesQ2(IResultsMVA pcaResults) {

double[] ySeries;
String label;
Expand Down
53 changes: 38 additions & 15 deletions ...eclipse/chemclipse/xxd/process/supplier/pca/ui/internal/runnable/CalculationExecutor.java
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Expand Up @@ -9,6 +9,7 @@
*
* Contributors:
* Philip Wenig - initial API and implementation
* Lorenz Gerber - Use IEvaluation
*******************************************************************************/
package org.eclipse.chemclipse.xxd.process.supplier.pca.ui.internal.runnable;

Expand All @@ -20,9 +21,11 @@
import org.eclipse.chemclipse.xxd.process.supplier.pca.core.CrossValidatorOPLS;
import org.eclipse.chemclipse.xxd.process.supplier.pca.core.ProcessorPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.Algorithm;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.EvaluationPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IAnalysisSettings;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.ICrossValidationProcessor;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IEvaluation;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IProcessor;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResult;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.ISamplesPCA;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.jface.operation.IRunnableWithProgress;
Expand All @@ -32,45 +35,65 @@ public class CalculationExecutor implements IRunnableWithProgress {
private static final Logger logger = Logger.getLogger(CalculationExecutor.class);
//
private ISamplesPCA<IVariable, ISample> samples = null;
private EvaluationPCA<IVariable, ISample, IResultPCA> masterEvaluationPCA = null;
private IEvaluation<IVariable, ISample, IResult> masterEvaluation = null;
//
private EvaluationPCA<IVariable, ISample, IResultPCA> evaluationPCA = null;
private IEvaluation<IVariable, ISample, IResult> evaluation = null;

public CalculationExecutor(ISamplesPCA<IVariable, ISample> samples, EvaluationPCA<IVariable, ISample, IResultPCA> masterEvaluationPCA) {
public CalculationExecutor(ISamplesPCA<IVariable, ISample> samples, IEvaluation<IVariable, ISample, IResult> masterEvaluation) {

this.samples = samples;
this.masterEvaluationPCA = masterEvaluationPCA;
this.masterEvaluation = masterEvaluation;
}

public EvaluationPCA<IVariable, ISample, IResultPCA> getEvaluationPCA() {
public IEvaluation<IVariable, ISample, IResult> getEvaluation() {

return evaluationPCA;
return evaluation;
}

@Override
public void run(IProgressMonitor monitor) throws InvocationTargetException, InterruptedException {

if(samples != null) {
try {
ProcessorPCA processorPCA = new ProcessorPCA();
evaluationPCA = processorPCA.process(samples, masterEvaluationPCA, monitor);
IAnalysisSettings settings = samples.getAnalysisSettings();
IProcessor processor = getProcessor(settings.getAlgorithm());
evaluation = processor.process(samples, masterEvaluation, monitor);
if(settings.getCrossValidation()) {
if(settings.getAlgorithm() == Algorithm.OPLS) {
CrossValidatorOPLS crossValidator = new CrossValidatorOPLS();
double[] q2 = crossValidator.crossValidate(samples, masterEvaluationPCA, monitor);
evaluationPCA.addCrossValidation(q2);
ICrossValidationProcessor crossValidator = getCrossValidationProcessor(settings.getAlgorithm());
if(crossValidator != null) {
double[] q2 = crossValidator.crossValidate(samples, masterEvaluation, monitor);
evaluation.addCrossValidation(q2);
double[] q2Cum = new double[q2.length];
q2Cum[0] = q2[0];
for(int i = 1; i < q2.length; i++) {
q2Cum[i] = q2Cum[i - 1] + q2[i];
}
evaluationPCA.addCumulativeCrossValidation(q2Cum);
evaluation.addCumulativeCrossValidation(q2Cum);
}
}
} catch(Exception e) {
logger.error(e);
}
}
}

private IProcessor getProcessor(Algorithm algorithm) {

if(Algorithm.NIPALS == algorithm) {
return new ProcessorPCA();
} else if(Algorithm.SVD == algorithm) {
return new ProcessorPCA();
} else if(Algorithm.OPLS == algorithm) {
return new ProcessorPCA();
}
return null;
}

private ICrossValidationProcessor getCrossValidationProcessor(Algorithm algorithm) {

if(Algorithm.OPLS == algorithm) {
return new CrossValidatorOPLS();
}
return null;
}
}
1 change: 0 additions & 1 deletion ...pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/parts/ErrorResiduePart.java
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Expand Up @@ -36,7 +36,6 @@ protected ErrorResidueChart createControl(Composite parent) {
return new ErrorResidueChart(parent, SWT.NONE);
}

@SuppressWarnings("unchecked")
@Override
protected boolean updateData(List<Object> objects, String topic) {

Expand Down
1 change: 0 additions & 1 deletion ...pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/parts/FeatureTablePart.java
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Expand Up @@ -37,7 +37,6 @@ protected ExtendedFeatureListUI createControl(Composite parent) {
return new ExtendedFeatureListUI(parent, SWT.NONE);
}

@SuppressWarnings("unchecked")
@Override
protected boolean updateData(List<Object> objects, String topic) {

Expand Down
1 change: 0 additions & 1 deletion ...pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/parts/LoadingsPlotPart.java
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Expand Up @@ -35,7 +35,6 @@ protected ExtendedLoadingsPlot createControl(Composite parent) {
return new ExtendedLoadingsPlot(parent, SWT.NONE);
}

@SuppressWarnings("unchecked")
@Override
protected boolean updateData(List<Object> objects, String topic) {

Expand Down
1 change: 0 additions & 1 deletion ....pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/parts/ScorePlot2DPart.java
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Expand Up @@ -35,7 +35,6 @@ protected ExtendedScorePlot2D createControl(Composite parent) {
return new ExtendedScorePlot2D(parent, SWT.NONE);
}

@SuppressWarnings("unchecked")
@Override
protected boolean updateData(List<Object> objects, String topic) {

Expand Down
1 change: 0 additions & 1 deletion ...ier.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/parts/VariancePart.java
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Expand Up @@ -36,7 +36,6 @@ protected ExtendedVarianceUI createControl(Composite parent) {
return new ExtendedVarianceUI(parent, SWT.NONE);
}

@SuppressWarnings("unchecked")
@Override
protected boolean updateData(List<Object> objects, String topic) {

Expand Down
7 changes: 4 additions & 3 deletions ...r.pca.ui/src/org/eclipse/chemclipse/xxd/process/supplier/pca/ui/support/ColorSupport.java
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Expand Up @@ -9,6 +9,7 @@
*
* Contributors:
* Philip Wenig - initial API and implementation
* Lorenz Gerber - Specific result type for multivariate analysis (MVA)
*******************************************************************************/
package org.eclipse.chemclipse.xxd.process.supplier.pca.ui.support;

Expand All @@ -23,7 +24,7 @@
import org.eclipse.chemclipse.model.statistics.ISample;
import org.eclipse.chemclipse.swt.ui.support.Colors;
import org.eclipse.chemclipse.swt.ui.support.IColorScheme;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultPCA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.IResultMVA;
import org.eclipse.chemclipse.xxd.process.supplier.pca.model.LabelOptionPCA;
import org.eclipse.swt.graphics.Color;

Expand All @@ -32,10 +33,10 @@ public class ColorSupport {
public static final String COLOR_GROUP_DEFAULT = "Unknown";
public static final Color COLOR_FALLBACK = Colors.DARK_RED;

public static Map<String, Color> getColorMapResults(List<IResultPCA> resultList, LabelOptionPCA labelOptionPCA, String colorScheme) {
public static Map<String, Color> getColorMapResults(List<IResultMVA> resultList, LabelOptionPCA labelOptionPCA, String colorScheme) {

Set<String> colorGroups = new HashSet<>();
for(IResultPCA pcaResult : resultList) {
for(IResultMVA pcaResult : resultList) {
String colorGroup = getColorGroup(pcaResult.getSample(), labelOptionPCA);
if(colorGroup != null) {
colorGroups.add(colorGroup);
Expand Down
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