Merge pull request #60 from bowring/shrimpdibbs

Tweaks to U-series and Shrimp
CIRDLES · Feb 29, 2016 · 159d48f · 159d48f
2 parents ddd9f76 + 31df03c
commit 159d48f
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Showing 9 changed files with 56 additions and 29 deletions.
diff --git a/src/main/java/org/earthtime/Tripoli/rawDataFiles/templates/AbstractRawDataFileTemplate.java b/src/main/java/org/earthtime/Tripoli/rawDataFiles/templates/AbstractRawDataFileTemplate.java
@@ -123,8 +123,7 @@ public AbstractRawDataFileTemplate() {
     @Override
     public int compareTo(AbstractRawDataFileTemplate abstractRawDataFileTemplate) {
         String abstractRawDataFileTemplateName
-                =//
-                ((AbstractRawDataFileTemplate) abstractRawDataFileTemplate).NAME.trim();
+                = abstractRawDataFileTemplate.NAME.trim();
         return (this.NAME.trim().compareToIgnoreCase(abstractRawDataFileTemplateName));
     }
 

diff --git a/...ava/org/earthtime/UPb_Redux/dialogs/projectManagers/AbstractProjectManagerForRawData.java b/...ava/org/earthtime/UPb_Redux/dialogs/projectManagers/AbstractProjectManagerForRawData.java
@@ -50,6 +50,7 @@
 import org.earthtime.Tripoli.massSpecSetups.AbstractMassSpecSetup;
 import org.earthtime.Tripoli.rawDataFiles.handlers.AbstractRawDataFileHandler;
 import org.earthtime.Tripoli.rawDataFiles.templates.AbstractRawDataFileTemplate;
+import org.earthtime.Tripoli.rawDataFiles.templates.shrimp.ShrimpPrawn_RawDataTemplate_GA;
 import org.earthtime.Tripoli.samples.AbstractTripoliSample;
 import org.earthtime.Tripoli.sessions.TripoliSession;
 import org.earthtime.Tripoli.sessions.TripoliSessionInterface;
@@ -310,15 +311,24 @@ private synchronized void loadRawDataWorkflow() {
 
         // may 2013 split task to allow for custom parameters ********************
         AbstractAcquisitionModel acquisitionModel = rawDataFileTemplate.makeNewAcquisitionModel();
-        try {
-            if (acquisitionModel.getPrimaryMineralStandardModel() == null) {
-                acquisitionModel.setPrimaryMineralStandardModel(ReduxLabData.getInstance().getDefaultLAICPMSPrimaryMineralStandardModel());
-            }
-            acquisitionModel.setLeftShadeCount(ReduxLabData.getInstance().getDefaultLeftShadeCountForLAICPMSAquisitions());
+        if (rawDataFileTemplate instanceof ShrimpPrawn_RawDataTemplate_GA) {
+//                if (acquisitionModel.getPrimaryMineralStandardModel() == null) {
+//                    acquisitionModel.setPrimaryMineralStandardModel(ReduxLabData.getInstance().getDefaultLAICPMSPrimaryMineralStandardModel());
+//                }
+                acquisitionModel.setLeftShadeCount(ReduxLabData.getInstance().getDefaultLeftShadeCountForSHRIMPAquisitions());
 
-        } catch (BadLabDataException ex) {
-            new ETWarningDialog(ex).setVisible(true);
+        } else {
+            try {
+                if (acquisitionModel.getPrimaryMineralStandardModel() == null) {
+                    acquisitionModel.setPrimaryMineralStandardModel(ReduxLabData.getInstance().getDefaultLAICPMSPrimaryMineralStandardModel());
+                }
+                acquisitionModel.setLeftShadeCount(ReduxLabData.getInstance().getDefaultLeftShadeCountForLAICPMSAquisitions());
+
+            } catch (BadLabDataException ex) {
+                new ETWarningDialog(ex).setVisible(true);
+            }
         }
+
         project.setAcquisitionModel(acquisitionModel);
 
         // user selects raw data file(s)
@@ -476,7 +486,7 @@ public void propertyChange(PropertyChangeEvent pce) {
                 loadDataTaskProgressBar.setValue(progress);
                 loadDataTaskProgressBar.validate();
             } else if ("projectName".equalsIgnoreCase(pce.getPropertyName())) {
-                project.setProjectName((String)pce.getNewValue());
+                project.setProjectName((String) pce.getNewValue());
                 projectName_text.setText(project.getProjectName());
             }
         }

diff --git a/src/main/java/org/earthtime/UPb_Redux/reports/ReportCategory.java b/src/main/java/org/earthtime/UPb_Redux/reports/ReportCategory.java
@@ -70,11 +70,12 @@ public ReportCategory(
         this.legacyData = false;
 
     }
+
     private ReportColumnInterface SetupReportColumn(int index, String[][] specs) {
         String displayName1 = specs[index][0];
         ReportColumnInterface retVal = new ReportColumn(//
                 displayName1, //specs[index][0], // displayname1
-                specs[index][1].equalsIgnoreCase("delta") ? " \u03B4" : specs[index][1], // displayname2
+                specs[index][1].contains("delta") ? specs[index][1].replace("delta", "\u03B4") : specs[index][1], // displayname2
                 specs[index][2], // displayname3
                 index, // positionIndex
                 specs[index][3], // units

diff --git a/src/main/java/org/earthtime/UPb_Redux/reports/ReportCategoryXMLConverter.java b/src/main/java/org/earthtime/UPb_Redux/reports/ReportCategoryXMLConverter.java
@@ -2,7 +2,7 @@
  * ReportCategoryXMLConverter.java
  *
  *
- * Copyright 2006-2015 James F. Bowring and www.Earth-Time.org
+ * Copyright 2006-2016 James F. Bowring and www.Earth-Time.org
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.

diff --git a/src/main/java/org/earthtime/UPb_Redux/reports/ReportColumnXMLConverter.java b/src/main/java/org/earthtime/UPb_Redux/reports/ReportColumnXMLConverter.java
@@ -2,7 +2,7 @@
  * ReportColumnXMLConverter.java
  *
  *
- * Copyright 2006-2015 James F. Bowring and www.Earth-Time.org
+ * Copyright 2006-2016 James F. Bowring and www.Earth-Time.org
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.
@@ -93,11 +93,7 @@ public void marshal(Object value, HierarchicalStreamWriter writer,
         writer.startNode("displayName2");
         String displayName2 = reportColumn.getDisplayName2();
         // test for delta
-        if (displayName2.contains("\u03B4")) {
-            writer.setValue("LOWERCASEDELTA");
-        } else {
-            writer.setValue(reportColumn.getDisplayName2());
-        }
+        writer.setValue(displayName2.replace("\u03B4", "LOWERCASEDELTA"));
         writer.endNode();
 
         writer.startNode("displayName3");
@@ -204,11 +200,7 @@ public Object unmarshal(HierarchicalStreamReader reader,
         reader.moveDown();
         String displayName2 = reader.getValue();
         // test for delta
-        if (displayName2.contains("LOWERCASEDELTA")) {
-            reportColumn.setDisplayName2(" \u03B4");
-        } else {
-            reportColumn.setDisplayName2(displayName2);
-        }
+        reportColumn.setDisplayName2(displayName2.replace("LOWERCASEDELTA", "\u03B4"));
         reader.moveUp();
 
         reader.moveDown();

diff --git a/src/main/java/org/earthtime/UPb_Redux/reports/ReportSettings.java b/src/main/java/org/earthtime/UPb_Redux/reports/ReportSettings.java
@@ -45,7 +45,7 @@ public class ReportSettings implements
      * version number is advanced so that any existing analysis will update its
      * report models upon opening in ET_Redux.
      */
-    private static transient int CURRENT_VERSION_REPORT_SETTINGS = 338;
+    private static transient int CURRENT_VERSION_REPORT_SETTINGS = 340;
 
     // Fields
     private String name;

diff --git a/src/main/java/org/earthtime/UTh_Redux/fractions/fractionReduction/UThFractionReducer.java b/src/main/java/org/earthtime/UTh_Redux/fractions/fractionReduction/UThFractionReducer.java
@@ -378,7 +378,8 @@ private static void calculateDatesFromLegacyData(UThLegacyFractionI fraction) {
 //        outvec(8)  = tcorr/1000; % detrital-corrected date, ka
 //        outvec(9)  = (tcorr - di.yearsSince1950)/1000; % detrital-corrected date, ka BP (1950)
 //        outvec(11) = nai(2)/nai(1) * lambda.U234/lambda.U238; % initial corrected 234/238 AR
-//
+        double initialCorrected234_238atomTatio = nai.get(1, 0) / nai.get(0, 0);//*lambda234D /lambda238D;
+
 //        outvec(2) = 2*sqrt(Cout(3,3))/outvec(1) * 100; % 2s% ar08t corrected
         double ar230_238correctedOneSigmaABS = Math.sqrt(Cout.get(2, 2) / ar230_238corrected);
 
@@ -390,6 +391,7 @@ private static void calculateDatesFromLegacyData(UThLegacyFractionI fraction) {
         double correctedDateOneSigmaAbs = Math.sqrt(Cout.get(0, 0));
 
 //        outvec(12) = 2*sqrt(Cout(4,4)); % 2s abs ar48i
+        double initialCorrected234_238atomTatioOneSigmaAbs = Math.sqrt(Cout.get(3, 3));
 //        outvec(13) = Cout(1,4)/sqrt(Cout(1,1)*Cout(4,4));
 
         ValueModel dateCorr = new ValueModel(//
@@ -410,15 +412,22 @@ private static void calculateDatesFromLegacyData(UThLegacyFractionI fraction) {
                 .setValue(ar234_238corrected);
         fraction.getAnalysisMeasure(UThAnalysisMeasures.ar234U_238Ufc.getName())//
                 .setOneSigma(ar234_238correctedOneSigmaABS);
+
+        BigDecimal secularEquilibrium = lambda238.getValue().divide(lambda234.getValue(), ReduxConstants.mathContext15);
+        BigDecimal delta234UInitialValue
+                = new BigDecimal(initialCorrected234_238atomTatio).subtract(secularEquilibrium)//
+                .divide(secularEquilibrium, ReduxConstants.mathContext15).movePointRight(3);
+        BigDecimal delta234UInitialValueOneSigmaAbs
+                = new BigDecimal(initialCorrected234_238atomTatioOneSigmaAbs).movePointRight(3);
 
         ValueModel delta234U = new ValueModel(//
                 UThFractionationCorrectedIsotopicRatios.delta234U.getName(), //
-                BigDecimal.ZERO, ///
+                delta234UInitialValue, ///
                 "ABS", //
-                BigDecimal.ZERO, //
+                delta234UInitialValueOneSigmaAbs, //
                 BigDecimal.ZERO);
         fraction.setRadiogenicIsotopeRatioByName(UThFractionationCorrectedIsotopicRatios.delta234U.getName(), delta234U);
-        
+
     }
 
     private static Matrix exponentialGUTh(Double t) {

diff --git a/src/main/java/org/earthtime/dataDictionaries/ReportSpecifications.java b/src/main/java/org/earthtime/dataDictionaries/ReportSpecifications.java
@@ -289,7 +289,7 @@ public class ReportSpecifications {
         {"", "Corr", "Date", "ka", "getRadiogenicIsotopeDateByName", RadDates.dateCorr.getName(), "ABS",
             "", "true", "false", "2", "true", "", "false", "false"
         },
-        {"", "delta", "234U", "", "getRadiogenicIsotopeRatioByName", UThFractionationCorrectedIsotopicRatios.delta234U.getName(), "ABS",
+        {"", "delta 234U", "initial", "", "getRadiogenicIsotopeRatioByName", UThFractionationCorrectedIsotopicRatios.delta234U.getName(), "ABS",
             "", "true", "false", "2", "true", "", "false", "false"
         }
     };

diff --git a/src/main/java/org/earthtime/reduxLabData/ReduxLabData.java b/src/main/java/org/earthtime/reduxLabData/ReduxLabData.java
@@ -111,6 +111,7 @@ public final class ReduxLabData implements Serializable {
     private AbstractRatiosDataModel defaultLAICPMSPrimaryMineralStandardModel;
     private AbstractRatiosDataModel defaultRareEarthElementModel;
     private int defaultLeftShadeCountForLAICPMSAquisitions;
+    private int defaultLeftShadeCountForSHRIMPAquisitions;
     // nov 2015
     private AbstractRatiosDataModel defaultDetritalUraniumAndThoriumModel;
     // feb 2016
@@ -218,6 +219,7 @@ private ReduxLabData() {
         }
 
         this.defaultLeftShadeCountForLAICPMSAquisitions = 0;
+        this.defaultLeftShadeCountForSHRIMPAquisitions = 0;
 
         initDefaultInterReferenceMaterialReproducibilityMap();
 
@@ -2026,4 +2028,18 @@ public void setDefaultInterReferenceMaterialReproducibilityMap(Map<RadRatios, Va
         this.defaultInterReferenceMaterialReproducibilityMap = defaultInterReferenceMaterialReproducibilityMap;
     }
 
+    /**
+     * @return the defaultLeftShadeCountForSHRIMPAquisitions
+     */
+    public int getDefaultLeftShadeCountForSHRIMPAquisitions() {
+        return defaultLeftShadeCountForSHRIMPAquisitions;
+    }
+
+    /**
+     * @param defaultLeftShadeCountForSHRIMPAquisitions the defaultLeftShadeCountForSHRIMPAquisitions to set
+     */
+    public void setDefaultLeftShadeCountForSHRIMPAquisitions(int defaultLeftShadeCountForSHRIMPAquisitions) {
+        this.defaultLeftShadeCountForSHRIMPAquisitions = defaultLeftShadeCountForSHRIMPAquisitions;
+    }
+
 }