Add literature references to baseline detectors.

eclipse · Nov 2, 2024 · 36d4e29 · 36d4e29
1 parent 12e0607
commit 36d4e29
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Showing 8 changed files with 72 additions and 6 deletions.
diff --git a/...se/plugins/org.eclipse.chemclipse.chromatogram.xxd.baseline.detector/META-INF/MANIFEST.MF b/...se/plugins/org.eclipse.chemclipse.chromatogram.xxd.baseline.detector/META-INF/MANIFEST.MF
@@ -12,7 +12,8 @@ Require-Bundle: org.eclipse.core.runtime,
  org.eclipse.chemclipse.model;bundle-version="0.8.0",
  org.eclipse.chemclipse.csd.model;bundle-version="0.8.0",
  org.eclipse.chemclipse.wsd.model;bundle-version="0.8.0",
- com.fasterxml.jackson.core.jackson-annotations;bundle-version="2.9.9"
+ com.fasterxml.jackson.core.jackson-annotations;bundle-version="2.9.9",
+ org.eclipse.chemclipse.support;bundle-version="0.9.0"
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-17
 Export-Package: org.eclipse.chemclipse.chromatogram.xxd.baseline.detector.core,

diff --git a/.../src/org/eclipse/chemclipse/chromatogram/xxd/baseline/detector/core/BaselineDetector.java b/.../src/org/eclipse/chemclipse/chromatogram/xxd/baseline/detector/core/BaselineDetector.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2008, 2023 Lablicate GmbH.
+ * Copyright (c) 2008, 2024 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -121,6 +121,7 @@ public static IBaselineDetectorSupport getBaselineDetectorSupport() {
 				try {
 					IBaselineDetectorSettings instance = (IBaselineDetectorSettings)element.createExecutableExtension(DETECTOR_SETTINGS);
 					supplier.setSettingsClass(instance.getClass());
+					supplier.getLiteratureReferences().addAll(instance.getLiteratureReferences());
 				} catch(CoreException e) {
 					logger.warn(e);
 					// settings class is optional, set null instead

diff --git a/...emclipse/chromatogram/xxd/baseline/detector/core/BaselineDetectorProcessTypeSupplier.java b/...emclipse/chromatogram/xxd/baseline/detector/core/BaselineDetectorProcessTypeSupplier.java
@@ -60,6 +60,7 @@ private static final class BaselineDetectorProcessorSupplier extends Chromatogra
 		public BaselineDetectorProcessorSupplier(IBaselineDetectorSupplier supplier, IProcessTypeSupplier parent) {
 
 			super(supplier.getId(), supplier.getDetectorName(), supplier.getDescription(), (Class<IBaselineDetectorSettings>)supplier.getSettingsClass(), parent, DataType.MSD, DataType.CSD, DataType.WSD, DataType.VSD);
+			getLiteratureReferences().addAll(supplier.getLiteratureReferences());
 		}
 
 		@Override

diff --git a/.../eclipse/chemclipse/chromatogram/xxd/baseline/detector/core/BaselineDetectorSupplier.java b/.../eclipse/chemclipse/chromatogram/xxd/baseline/detector/core/BaselineDetectorSupplier.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2008, 2018 Lablicate GmbH.
+ * Copyright (c) 2008, 2024 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -11,14 +11,19 @@
  *******************************************************************************/
 package org.eclipse.chemclipse.chromatogram.xxd.baseline.detector.core;
 
+import java.util.ArrayList;
+import java.util.List;
+
 import org.eclipse.chemclipse.chromatogram.xxd.baseline.detector.settings.IBaselineDetectorSettings;
+import org.eclipse.chemclipse.support.literature.LiteratureReference;
 
 public class BaselineDetectorSupplier implements IBaselineDetectorSupplier {
 
 	private String id = "";
 	private String description = "";
 	private String detectorName = "";
 	private Class<? extends IBaselineDetectorSettings> settingsClass;
+	private List<LiteratureReference> literatureReference = new ArrayList<>();
 
 	@Override
 	public String getId() {
@@ -86,6 +91,12 @@ protected void setSettingsClass(Class<? extends IBaselineDetectorSettings> setti
 		this.settingsClass = settingsClass;
 	}
 
+	@Override
+	public List<LiteratureReference> getLiteratureReferences() {
+
+		return literatureReference;
+	}
+
 	@Override
 	public boolean equals(Object other) {
 

diff --git a/...eclipse/chemclipse/chromatogram/xxd/baseline/detector/core/IBaselineDetectorSupplier.java b/...eclipse/chemclipse/chromatogram/xxd/baseline/detector/core/IBaselineDetectorSupplier.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2008, 2018 Lablicate GmbH.
+ * Copyright (c) 2008, 2024 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -11,7 +11,10 @@
  *******************************************************************************/
 package org.eclipse.chemclipse.chromatogram.xxd.baseline.detector.core;
 
+import java.util.List;
+
 import org.eclipse.chemclipse.chromatogram.xxd.baseline.detector.settings.IBaselineDetectorSettings;
+import org.eclipse.chemclipse.support.literature.LiteratureReference;
 
 public interface IBaselineDetectorSupplier {
 
@@ -43,4 +46,6 @@ public interface IBaselineDetectorSupplier {
 	 * @return
 	 */
 	Class<? extends IBaselineDetectorSettings> getSettingsClass();
+
+	List<LiteratureReference> getLiteratureReferences();
 }
diff --git a/...e/plugins/org.eclipse.chemclipse.chromatogram.xxd.edit.supplier.snip/META-INF/MANIFEST.MF b/...e/plugins/org.eclipse.chemclipse.chromatogram.xxd.edit.supplier.snip/META-INF/MANIFEST.MF
@@ -15,7 +15,8 @@ Require-Bundle: org.eclipse.core.runtime,
  org.eclipse.chemclipse.support;bundle-version="0.8.0",
  org.eclipse.chemclipse.numeric;bundle-version="0.8.0",
  org.eclipse.chemclipse.chromatogram.filter;bundle-version="0.8.0",
- com.fasterxml.jackson.core.jackson-annotations;bundle-version="2.7.1"
+ com.fasterxml.jackson.core.jackson-annotations;bundle-version="2.7.1",
+ org.eclipse.chemclipse.logging;bundle-version="0.9.0"
 Bundle-RequiredExecutionEnvironment: JavaSE-17
 Bundle-ActivationPolicy: lazy
 Export-Package: org.eclipse.chemclipse.chromatogram.xxd.edit.supplier.snip.calculator,

diff --git a/.../org/eclipse/chemclipse/chromatogram/xxd/edit/supplier/snip/settings/0168583X88900638.ris b/.../org/eclipse/chemclipse/chromatogram/xxd/edit/supplier/snip/settings/0168583X88900638.ris
@@ -0,0 +1,19 @@
+TY  - JOUR
+T1  - SNIP, a statistics-sensitive background treatment for the quantitative analysis of PIXE spectra in geoscience applications
+AU  - Ryan, C.G.
+AU  - Clayton, E.
+AU  - Griffin, W.L.
+AU  - Sie, S.H.
+AU  - Cousens, D.R.
+JO  - Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms
+VL  - 34
+IS  - 3
+SP  - 396
+EP  - 402
+PY  - 1988
+DA  - 1988/09/01/
+SN  - 0168-583X
+DO  - https://doi.org/10.1016/0168-583X(88)90063-8
+UR  - https://www.sciencedirect.com/science/article/pii/0168583X88900638
+AB  - Statistical fluctuations in X-ray spectra must be treated properly for reliable quantitative PIXE analysis. A background approximation that provides reliable treatment of fluctuations, the Statistics-sensitive Non-linear Iterative Peak-clipping (SNIP) algorithm, is described. Monte Carlo simulation demonstrates the stability of this background approximation, and hence the deduced trace element concentrations, over a wide range of counting statistics.
+ER  - 
diff --git a/...pse/chemclipse/chromatogram/xxd/edit/supplier/snip/settings/BaselineDetectorSettings.java b/...pse/chemclipse/chromatogram/xxd/edit/supplier/snip/settings/BaselineDetectorSettings.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2013, 2021 Lablicate GmbH.
+ * Copyright (c) 2013, 2024 Lablicate GmbH.
  * 
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -12,8 +12,13 @@
  *******************************************************************************/
 package org.eclipse.chemclipse.chromatogram.xxd.edit.supplier.snip.settings;
 
+import java.util.ArrayList;
+import java.util.List;
+
 import org.eclipse.chemclipse.chromatogram.xxd.baseline.detector.settings.AbstractBaselineDetectorSettings;
 import org.eclipse.chemclipse.chromatogram.xxd.edit.supplier.snip.preferences.PreferenceSupplier;
+import org.eclipse.chemclipse.logging.core.Logger;
+import org.eclipse.chemclipse.support.literature.LiteratureReference;
 import org.eclipse.chemclipse.support.settings.IntSettingsProperty;
 import org.eclipse.chemclipse.support.settings.IntSettingsProperty.Validation;
 import org.eclipse.chemclipse.support.settings.serialization.WindowSizeDeserializer;
@@ -24,6 +29,8 @@
 
 public class BaselineDetectorSettings extends AbstractBaselineDetectorSettings {
 
+	private static final Logger logger = Logger.getLogger(BaselineDetectorSettings.class);
+	//
 	@JsonProperty(value = "Number of Iterations", defaultValue = "100")
 	@JsonPropertyDescription(value = "The number of iterations to apply the SNIP filter.")
 	@IntSettingsProperty(minValue = PreferenceSupplier.MIN_ITERATIONS, maxValue = PreferenceSupplier.MAX_ITERATIONS)
@@ -53,4 +60,24 @@ public void setIterations(int iterations) {
 
 		this.iterations = iterations;
 	}
+
+	@Override
+	public List<LiteratureReference> getLiteratureReferences() {
+
+		List<LiteratureReference> literatureReferences = new ArrayList<>();
+		literatureReferences.add(createLiteratureReference("0168583X88900638.ris", "10.1016/0168-583X(88)90063-8"));
+		return literatureReferences;
+	}
+
+	private static LiteratureReference createLiteratureReference(String file, String doi) {
+
+		String content;
+		try {
+			content = new String(BaselineDetectorSettings.class.getResourceAsStream(file).readAllBytes());
+		} catch(Exception e) {
+			content = doi;
+			logger.warn(e);
+		}
+		return new LiteratureReference(content);
+	}
 }