Adds features for USeries date interpretations (#176)

* refactors * advances sea water in u-series * advances boundaries
CIRDLES · Apr 25, 2019 · b8c2c42 · b8c2c42
1 parent 273e5ef
commit b8c2c42
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Showing 33 changed files with 1,983 additions and 387 deletions.
diff --git a/nb-configuration.xml b/nb-configuration.xml
@@ -14,5 +14,6 @@ That way multiple projects can share the same settings (useful for formatting ru
 Any value defined here will override the pom.xml file value but is only applicable to the current project.
 -->
         <org-netbeans-modules-javascript2-requirejs.enabled>true</org-netbeans-modules-javascript2-requirejs.enabled>
+        <netbeans.hint.jdkPlatform>JDK_1.8</netbeans.hint.jdkPlatform>
     </properties>
 </project-shared-configuration>
diff --git a/pom.xml b/pom.xml
@@ -21,7 +21,7 @@
     <groupId>org.cirdles</groupId>
     <artifactId>ET_Redux</artifactId>
     <name>ET_Redux</name>
-    <version>3.6.74</version>
+    <version>3.6.80</version>
     <description>Successor to U-Pb_Redux</description>
     <url>https://cirdles.org</url>
     <inceptionYear>2006</inceptionYear>
@@ -257,6 +257,14 @@
             <artifactId>fop</artifactId>
             <version>2.2</version>
         </dependency>
+
+        <!-- https://mvnrepository.com/artifact/math.geom2d/javaGeom -->
+        <dependency>
+            <groupId>math.geom2d</groupId>
+            <artifactId>javaGeom</artifactId>
+            <version>0.11.1</version>
+        </dependency>
+
     </dependencies>
     <build>
         <plugins>

diff --git a/src/main/java/org/earthtime/ETRedux.java b/src/main/java/org/earthtime/ETRedux.java
@@ -123,6 +123,7 @@ public ETRedux(File reduxFile) //throws3 IOException, InvalidPreferencesFormatEx
         ToolTipManager.sharedInstance().setDismissDelay(10000);
 
         if (theUPbReduxFrame != null) {
+            theUPbReduxFrame.pack();
             theUPbReduxFrame.setVisible(true);
         }
 

diff --git a/src/main/java/org/earthtime/ETReduxFrame.form b/src/main/java/org/earthtime/ETReduxFrame.form
@@ -552,12 +552,12 @@
                 <Property name="text" type="java.lang.String" value="UTh"/>
               </Properties>
               <SubComponents>
-                <MenuItem class="javax.swing.JMenuItem" name="editDetrritalUraniumthoriumModels">
+                <MenuItem class="javax.swing.JMenuItem" name="editPhysicalConstantsModelsUTh">
                   <Properties>
                     <Property name="text" type="java.lang.String" value="Physical Constants Models"/>
                   </Properties>
                   <Events>
-                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="editDetrritalUraniumthoriumModelsActionPerformed"/>
+                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="editPhysicalConstantsModelsUThActionPerformed"/>
                   </Events>
                 </MenuItem>
                 <MenuItem class="javax.swing.JMenuItem" name="editDetritalUraniumThoriumModels">
@@ -568,6 +568,14 @@
                     <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="editDetritalUraniumThoriumModelsActionPerformed"/>
                   </Events>
                 </MenuItem>
+                <MenuItem class="javax.swing.JMenuItem" name="jMenuItem1">
+                  <Properties>
+                    <Property name="text" type="java.lang.String" value="Sea Water Models"/>
+                  </Properties>
+                  <Events>
+                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItem1ActionPerformed"/>
+                  </Events>
+                </MenuItem>
               </SubComponents>
             </Menu>
           </SubComponents>

diff --git a/src/main/java/org/earthtime/ETReduxFrame.java b/src/main/java/org/earthtime/ETReduxFrame.java
@@ -28,11 +28,12 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
-import java.io.FileWriter;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
+import java.nio.charset.StandardCharsets;
 import java.text.DecimalFormat;
 import java.util.ArrayList;
 import java.util.Vector;
@@ -675,7 +676,7 @@ private boolean checkSavedStatusTheProject() {
         try {
             if (theProject.isChanged()) {
                 // Modal dialog with OK/cancel and a text field
-                int response = JOptionPane.showConfirmDialog(null,
+                int response = JOptionPane.showConfirmDialog(this,
                         new String[]{"The current Project " + theProject.getProjectName() + " has been changed.",
                             "Do you want to Save it before proceeding ?"
                         },
@@ -1043,7 +1044,7 @@ private boolean checkSavedStatusTheSample() {
         try {
             if (theSample.isChanged()) {
                 // Modal dialog with OK/cancel and a text field
-                int response = JOptionPane.showConfirmDialog(null,
+                int response = JOptionPane.showConfirmDialog(this,
                         new String[]{"The current Sample " + theSample.getSampleName() + " has been changed.",
                             "Do you want to Save it before proceeding ?"
                         },
@@ -1931,7 +1932,7 @@ public void producePbcCorrectionReport() {
                 File pbcCorrReportFile = new File("LAICPMS_Pbc_Correction_Report_for_" + theProject.getProjectName() + ".txt");
                 PrintWriter outputWriter = null;
                 try {
-                    outputWriter = new PrintWriter(new FileWriter(pbcCorrReportFile));
+                    outputWriter = new PrintWriter(new OutputStreamWriter(new FileOutputStream(pbcCorrReportFile), StandardCharsets.UTF_8));//new FileWriter(pbcCorrReportFile));
                     for (AliquotInterface activeAliquot : theProject.getSuperSample().getActiveAliquots()) {
                         outputWriter.println("Fractions from " + activeAliquot.getAliquotName() + "\n");
                         outputWriter.println(PbcCorrectionDetails.headerString() + "\n");
@@ -2104,8 +2105,9 @@ private void initComponents() {
         manageTIMSLabDefaults = new javax.swing.JMenuItem();
         manageLAICPMSLabDefaults = new javax.swing.JMenuItem();
         labDataUTh = new javax.swing.JMenu();
-        editDetrritalUraniumthoriumModels = new javax.swing.JMenuItem();
+        editPhysicalConstantsModelsUTh = new javax.swing.JMenuItem();
         editDetritalUraniumThoriumModels = new javax.swing.JMenuItem();
+        jMenuItem1 = new javax.swing.JMenuItem();
         reportMenu = new javax.swing.JMenu();
         editCurrentReportSettingsModel_menuItem = new javax.swing.JMenuItem();
         showReportHeadings_menuItem = new javax.swing.JMenuItem();
@@ -2161,7 +2163,6 @@ private void initComponents() {
         setTitle("EARTHTIME Redux");
         setBackground(new java.awt.Color(237, 242, 250));
         setLocationByPlatform(true);
-        setPreferredSize(new java.awt.Dimension(1175, 750));
         addComponentListener(new java.awt.event.ComponentAdapter() {
             public void componentResized(java.awt.event.ComponentEvent evt) {
                 formComponentResized(evt);
@@ -2867,13 +2868,13 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
 
         labDataUTh.setText("UTh");
 
-        editDetrritalUraniumthoriumModels.setText("Physical Constants Models");
-        editDetrritalUraniumthoriumModels.addActionListener(new java.awt.event.ActionListener() {
+        editPhysicalConstantsModelsUTh.setText("Physical Constants Models");
+        editPhysicalConstantsModelsUTh.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
-                editDetrritalUraniumthoriumModelsActionPerformed(evt);
+                editPhysicalConstantsModelsUThActionPerformed(evt);
             }
         });
-        labDataUTh.add(editDetrritalUraniumthoriumModels);
+        labDataUTh.add(editPhysicalConstantsModelsUTh);
 
         editDetritalUraniumThoriumModels.setText("Detrital Uranium Thorium Models");
         editDetritalUraniumThoriumModels.addActionListener(new java.awt.event.ActionListener() {
@@ -2883,6 +2884,14 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
         });
         labDataUTh.add(editDetritalUraniumThoriumModels);
 
+        jMenuItem1.setText("Sea Water Models");
+        jMenuItem1.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                jMenuItem1ActionPerformed(evt);
+            }
+        });
+        labDataUTh.add(jMenuItem1);
+
         labDataMenu.add(labDataUTh);
 
         mainMenuBar.add(labDataMenu);
@@ -3705,6 +3714,10 @@ private void manageSampleDateInterpretation(SampleTreeI dateTreeByAliquot, Sampl
         }
 
     }
+
+    public void updateEvolutionPlot(){
+        ((EvolutionPlotPanel)myEvolutionPlotPanel).repaint();
+    }
 
     /**
      *
@@ -4424,13 +4437,13 @@ private void visitUseriesRocksActionPerformed(java.awt.event.ActionEvent evt) {/
         BrowserControl.displayURL("https://sites.google.com/site/useriesrocks/");
     }//GEN-LAST:event_visitUseriesRocksActionPerformed
 
-    private void editDetrritalUraniumthoriumModelsActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_editDetrritalUraniumthoriumModelsActionPerformed
+    private void editPhysicalConstantsModelsUThActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_editPhysicalConstantsModelsUThActionPerformed
         try {
             editLabDataUTh(0);
         } catch (BadLabDataException ex) {
             new ETWarningDialog(ex).setVisible(true);
         }
-    }//GEN-LAST:event_editDetrritalUraniumthoriumModelsActionPerformed
+    }//GEN-LAST:event_editPhysicalConstantsModelsUThActionPerformed
 
     private void editDetritalUraniumThoriumModelsActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_editDetritalUraniumThoriumModelsActionPerformed
         try {
@@ -4474,6 +4487,14 @@ private void genericUPbSquid3DataTableCSV_menuItemActionPerformed(java.awt.event
         setUpNewCompiledLegacyProject(GENERIC_SQUID3_UPB.getName(), GENERIC_SQUID3_UPB.getIsotypeSystem(), GENERIC_SQUID3_UPB.getDefaultReportSpecsType());
     }//GEN-LAST:event_genericUPbSquid3DataTableCSV_menuItemActionPerformed
 
+    private void jMenuItem1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItem1ActionPerformed
+        try {
+            editLabDataUTh(3);
+        } catch (BadLabDataException ex) {
+            new ETWarningDialog(ex).setVisible(true);
+        }
+    }//GEN-LAST:event_jMenuItem1ActionPerformed
+
     private void helpMenuItemActionPerformed(java.awt.event.ActionEvent evt) {
         BrowserControl.displayURL("http://cirdles.org/projects/et_redux/");
     }
@@ -4502,13 +4523,13 @@ private void helpMenuItemActionPerformed(java.awt.event.ActionEvent evt) {
     private javax.swing.JMenu earthTimeWebSiteMenu;
     private javax.swing.JMenuItem editCurrentReportSettingsModel_menuItem;
     private javax.swing.JMenuItem editDetritalUraniumThoriumModels;
-    private javax.swing.JMenuItem editDetrritalUraniumthoriumModels;
     private javax.swing.JMenuItem editInitialPbModels;
     private javax.swing.JMenuItem editLabFractionationModels;
     private javax.swing.JMenuItem editLabTracers;
     private javax.swing.JMenuItem editMineralStandardsModels;
     private javax.swing.JMenuItem editPbBlanks;
     private javax.swing.JMenuItem editPhysicalConstantsModels;
+    private javax.swing.JMenuItem editPhysicalConstantsModelsUTh;
     private javax.swing.JMenuItem exitRedux;
     private javax.swing.JSeparator exitSeparator;
     private javax.swing.JMenuItem exit_menuItem;
@@ -4525,6 +4546,7 @@ private void helpMenuItemActionPerformed(java.awt.event.ActionEvent evt) {
     private javax.swing.JMenu helpMenu;
     private javax.swing.JMenuItem helpMenuItem;
     private javax.swing.JButton interpretSampleDates_button;
+    private javax.swing.JMenuItem jMenuItem1;
     private javax.swing.JMenuItem jMenuItem2;
     private javax.swing.JMenuItem jMenuItem4;
     private javax.swing.JMenuItem jMenuItem5;

diff --git a/src/main/java/org/earthtime/UPb_Redux/dateInterpretation/DateProbabilityDensityPanel.java b/src/main/java/org/earthtime/UPb_Redux/dateInterpretation/DateProbabilityDensityPanel.java
@@ -251,7 +251,7 @@ public void paint(Graphics2D g2d) {
 
             // draw sample curve as backdrop
             Path2D sampleProbabilities = new Path2D.Double(Path2D.WIND_NON_ZERO);
-            Path2D sampleKDE = new Path2D.Double(Path2D.WIND_NON_ZERO);
+//            Path2D sampleKDE = new Path2D.Double(Path2D.WIND_NON_ZERO);
 
             // handle zoom
             int startX = 0;
@@ -275,7 +275,7 @@ public void paint(Graphics2D g2d) {
 
 //            sampleProbabilities.moveTo( mapX( getMinX_Display() ), mapY( 0.01 ) );
             sampleProbabilities.moveTo(Math.max(leftMargin, mapX(pdfPoints.get(startX))), mapY(0.01));
-            sampleKDE.moveTo(Math.max(leftMargin, mapX(timescale[startX])), mapY(0.01));
+//            sampleKDE.moveTo(Math.max(leftMargin, mapX(timescale[startX])), mapY(0.01));
 
             double scale = 0.96/*
                      * 8
@@ -289,12 +289,12 @@ public void paint(Graphics2D g2d) {
                         Math.max(leftMargin, mapX(pdfPoints.get(i))),//
                         mapY(stackedAliquotKernels[0][i] * scale + .01));
 
-                try {
-                    sampleKDE.lineTo(//
-                            Math.max(leftMargin, mapX(timescale[i])),//
-                            mapY(pdfOfKDE[i] * scaleKDE + .01));
-                } catch (Exception e) {
-                }
+//                try {
+//                    sampleKDE.lineTo(//
+//                            Math.max(leftMargin, mapX(timescale[i])),//
+//                            mapY(pdfOfKDE[i] * scaleKDE + .01));
+//                } catch (Exception e) {
+//                }
             }
 
             sampleProbabilities.lineTo(mapX(pdfPoints.get(endX)), mapY(0.01));
@@ -770,29 +770,29 @@ public void preparePanel(boolean doReScale, boolean inLiveMode) {
         //stackedAliquotKernels = new double[sample.getAliquots().size() + 1][pdfPoints.size() + 1];
         // aug 2016 hack to fix project problem
         stackedAliquotKernels = new double[Math.max(sample.getAliquots().size(), 9) + 1][pdfPoints.size() + 1];
-
-        // June 2013 experiment with Vermeesch KDE
-        ArrayList<Double> X = new ArrayList<>();
-        ArrayList<Double> Y = new ArrayList<>();
-        ArrayList<Double> Z = new ArrayList<>();
-
-        // 4096 = 2^12
-        timescale = new double[4096];
-        for (int i = 0; i < timescale.length; i++) {
-            timescale[i] = i;
-        }
-        // end June 2013 experiment with Vermeesch KDE
+//////
+//////        // June 2013 experiment with Vermeesch KDE
+//////        ArrayList<Double> X = new ArrayList<>();
+//////        ArrayList<Double> Y = new ArrayList<>();
+//////        ArrayList<Double> Z = new ArrayList<>();
+//////
+//////        // 4096 = 2^12
+//////        timescale = new double[4096];
+//////        for (int i = 0; i < timescale.length; i++) {
+//////            timescale[i] = i;
+//////        }
+//////        // end June 2013 experiment with Vermeesch KDE
 
         for (ETFractionInterface f : selectedFractions) {
             // April 2016 remove primary standard
             if (!f.isStandard() && !f.isSecondaryStandard()) {
                 ValueModel date = f.getRadiogenicIsotopeDateByName(chosenDateName);
 
-                // June 2013 experiment with Vermeesch KDE
-                X.add(date.getValue().movePointLeft(6).doubleValue());
-                Y.add(Math.pow(date.getOneSigmaAbs().movePointLeft(6).doubleValue(), 2));
-                Z.add(Double.NaN);
-                // end June 2013 experiment with Vermeesch KDE
+//////                // June 2013 experiment with Vermeesch KDE
+//////                X.add(date.getValue().movePointLeft(6).doubleValue());
+//////                Y.add(Math.pow(date.getOneSigmaAbs().movePointLeft(6).doubleValue(), 2));
+//////                Z.add(Double.NaN);
+//////                // end June 2013 experiment with Vermeesch KDE
 
                 int aliquotNumber = f.getAliquotNumber();
                 KernelF myKernel = new KernelF(date);
@@ -804,22 +804,22 @@ public void preparePanel(boolean doReScale, boolean inLiveMode) {
             }
         }
 
-        // more vermeesch ************************
-        try {
-            OtherData otherData = new OtherData(X, Y, Z, new Preferences(true));
-            double[][] ae = otherData.getDataErrArray(otherData.preferences.logarithmic());
-
-            KDE kde = new KDE();
-            pdfOfKDE = kde.pdf(ae[0], timescale, true);
-
-            maxKDE = 0.0;
-            for (int i = 0; i < pdfOfKDE.length; i++) {
-                maxKDE = Math.max(maxKDE, pdfOfKDE[i]);
-            }
-
-        } catch (Exception ex) {
-        }
-        // end vermeesch ************************
+//////        // more vermeesch ************************
+//////        try {
+//////            OtherData otherData = new OtherData(X, Y, Z, new Preferences(true));
+//////            double[][] ae = otherData.getDataErrArray(otherData.preferences.logarithmic());
+//////
+//////            KDE kde = new KDE();
+//////            pdfOfKDE = kde.pdf(ae[0], timescale, true);
+//////
+//////            maxKDE = 0.0;
+//////            for (int i = 0; i < pdfOfKDE.length; i++) {
+//////                maxKDE = Math.max(maxKDE, pdfOfKDE[i]);
+//////            }
+//////
+//////        } catch (Exception ex) {
+//////        }
+//////        // end vermeesch ************************
 
         double maxDateProb = 0.0;
         for (int i = 0; i < pdfPoints.size(); i++) {

diff --git a/src/main/java/org/earthtime/UPb_Redux/dateInterpretation/SampleTreeAnalysisMode.java b/src/main/java/org/earthtime/UPb_Redux/dateInterpretation/SampleTreeAnalysisMode.java
@@ -27,7 +27,7 @@
 import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
-import javax.swing.JDialog;
+import javax.swing.JFrame;
 import javax.swing.JMenuItem;
 import javax.swing.JPopupMenu;
 import javax.swing.JTree;
@@ -436,8 +436,8 @@ public void mousePressed(MouseEvent e) {
                                     ((AliquotInterface) nodeInfo).determineUnusedSampleDateModels());
 
                     myEditor.setSize(340, 395);
-//                    JDialog.setDefaultLookAndFeelDecorated(true);
-
+                    myEditor.setLocationRelativeTo(this);
+                    
                     myEditor.setVisible(true);
 
                     // get a master vector of active fraction names

diff --git a/src/main/java/org/earthtime/UPb_Redux/dateInterpretation/SampleTreeCompilationMode.java b/src/main/java/org/earthtime/UPb_Redux/dateInterpretation/SampleTreeCompilationMode.java
@@ -193,14 +193,12 @@ private void populateSampleDateModel(
             DefaultMutableTreeNode SAMnode) {
 
         DefaultMutableTreeNode sampleDateValue
-                = 
-                new DefaultMutableTreeNode(//
+                = new DefaultMutableTreeNode(//
                         ((SampleDateModel) SAM).ShowCustomDateNode());
         SAMnode.add(sampleDateValue);
 
         DefaultMutableTreeNode sampleDateMSWD
-                = 
-                new DefaultMutableTreeNode(//
+                = new DefaultMutableTreeNode(//
                         ((SampleDateModel) SAM).ShowCustomMSWDwithN());
         SAMnode.add(sampleDateMSWD);
 
@@ -366,7 +364,7 @@ public void mousePressed(MouseEvent e) {
                                     ((SampleInterface) nodeInfo).determineUnusedSampleDateModels(false));
 
                     myEditor.setSize(340, 395);
-//                    DialogEditor.setDefaultLookAndFeelDecorated(true);
+                    myEditor.setLocationRelativeTo(this);
 
                     myEditor.setVisible(true);