Merge pull request #47 from bowring/az

Maintenance and bug fixes
CIRDLES · Jan 24, 2016 · aba9943 · aba9943
2 parents 522c4d4 + 215bf08
commit aba9943
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Showing 19 changed files with 427 additions and 655 deletions.
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>3.4.0</version>
+    <version>3.4.1</version>
     <description>Successor to U-Pb_Redux</description>
     <url>https://cirdles.org</url>
     <inceptionYear>2006</inceptionYear>

diff --git a/src/main/java/org/earthtime/ETReduxFrame.form b/src/main/java/org/earthtime/ETReduxFrame.form
@@ -786,7 +786,7 @@
                 <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
                   <KeyStroke key="F1"/>
                 </Property>
-                <Property name="text" type="java.lang.String" value="Help-currently under construction"/>
+                <Property name="text" type="java.lang.String" value="Help from CIRDLES.org"/>
               </Properties>
               <Events>
                 <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="helpMenuItemActionPerformed"/>

diff --git a/src/main/java/org/earthtime/ETReduxFrame.java b/src/main/java/org/earthtime/ETReduxFrame.java
@@ -38,8 +38,6 @@
 import java.util.Vector;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-import javax.help.DefaultHelpBroker;
-import javax.help.HelpBroker;
 import javax.swing.AbstractButton;
 import javax.swing.ImageIcon;
 import javax.swing.JButton;
@@ -112,7 +110,6 @@
 import org.earthtime.UPb_Redux.utilities.BrowserControl;
 import org.earthtime.UPb_Redux.utilities.CustomIcon;
 import org.earthtime.UPb_Redux.utilities.ETSerializer;
-import org.earthtime.UPb_Redux.utilities.JHelpAction;
 import org.earthtime.UPb_Redux.utilities.MacOSAboutHandler;
 import org.earthtime.UTh_Redux.dateInterpretation.TopsoilEvolutionPlot;
 import org.earthtime.XMLExceptions.BadOrMissingXMLSchemaException;
@@ -205,6 +202,7 @@ public class ETReduxFrame extends javax.swing.JFrame implements ReportPainterI,
     //oct 2014
     private DialogEditor sampleDateInterpDialog;
     private DialogEditor myFractionEditor;
+    private DialogEditor geochronProjectExportManager;
 
     /**
      * Creates new form UPbReduxFrame
@@ -538,7 +536,7 @@ private void openProjectFile() {
 
     private void openTheProject(File projectReduxFile) {
 
-        forceCloseOfSampleDateInterpretations();
+        closeProjectAndOrSample();
 
         theProject = null;
         System.gc();
@@ -785,9 +783,9 @@ private void manageTheProject() {
 
         myProjectManager.initDialogContent();
         myProjectManager.setVisible(true);
-        
+
         updateReportTable();
-        
+
         saveProject();
     }
 
@@ -911,9 +909,8 @@ private void exportProjectSamplesToGeochron() {
         theProject.prepareSamplesForExport();
 
         // launch manager
-        DialogEditor geochronProjectExportManager
-                = //
-                new GeochronProjectExportManager(this, true, theProject, myState);
+        geochronProjectExportManager
+                = GeochronProjectExportManager.getInstance(null, false, theProject, myState);
 
         geochronProjectExportManager.setVisible(true);
     }
@@ -1412,12 +1409,12 @@ private void customizeReduxSkin() {
             // show the welcome page
             jSplitPane1.setDividerLocation(1.0);
         }
-        
+
         // jan 2016
-        if (theSample.isSampleTypeProject() && theSample.isAnalysisTypeCOMPILED()){
+        if (theSample.isSampleTypeProject() && theSample.isAnalysisTypeCOMPILED()) {
             manageProjectRawData_button.setText("Manage Project");
         } else {
-            manageProjectRawData_button.setText("Project Raw Data");            
+            manageProjectRawData_button.setText("Project Raw Data");
         }
     }
 
@@ -1490,7 +1487,8 @@ public void loadAndShowReportTableData() {
 
     private void openTheSample(File selFile, boolean checkSavedStatus) throws BadLabDataException {
 
-        forceCloseOfSampleDateInterpretations();
+//        forceCloseOfSampleDateInterpretations();
+        closeProjectAndOrSample();
 
         if (checkSavedStatus) {
             checkSavedStatusTheSample();
@@ -1499,8 +1497,7 @@ private void openTheSample(File selFile, boolean checkSavedStatus) throws BadLab
         setLiveUpdateTimerIsRunning(false);
 
         EarthTimeSerializedFileInterface deserializedFile
-                = //
-                (EarthTimeSerializedFileInterface) ETSerializer.GetSerializedObjectFromFile(selFile.getPath());
+                = (EarthTimeSerializedFileInterface) ETSerializer.GetSerializedObjectFromFile(selFile.getPath());
 
         // TODO: Oct 2011 check for Project file?? or is it automatically a project file
         // created here for a single sample??
@@ -1549,16 +1546,29 @@ private void openTheSample(File selFile, boolean checkSavedStatus) throws BadLab
 
     }
 
+    private void closeProjectAndOrSample() {
+
+        try {
+            closeTheSample();
+        } catch (BadLabDataException badLabDataException) {
+        }
+        try {
+            closeTheProject();
+        } catch (BadLabDataException badLabDataException) {
+        }
+
+    }
+
     private boolean closeTheSample() throws BadLabDataException {
 
         boolean retval = checkSavedStatusTheSample();
 
         setLiveUpdateTimerIsRunning(false);
 
-        forceCloseOfSampleDateInterpretations();
+        closeOpenDialogs();
 
         if (retval) {
-            setUpEmptySample();//theSample.getSampleType() );
+            setUpEmptySample();
         }
 
         return retval;
@@ -1567,12 +1577,19 @@ private boolean closeTheSample() throws BadLabDataException {
     private boolean closeTheProject() throws BadLabDataException {
 
         saveTheProject();
-        forceCloseOfSampleDateInterpretations();
+        closeOpenDialogs();
+
         setUpEmptySample();
 
         return true;
     }
 
+    private void closeOpenDialogs() {
+        GeochronProjectExportManager.removeInstance();
+
+        forceCloseOfSampleDateInterpretations();
+    }
+
     private void setUpEmptySample() //
             throws BadLabDataException {
         theSample
@@ -2933,7 +2950,7 @@ public void menuCanceled(javax.swing.event.MenuEvent evt) {
         });
 
         helpMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_F1, 0));
-        helpMenuItem.setText("Help-currently under construction");
+        helpMenuItem.setText("Help from CIRDLES.org");
         helpMenuItem.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
                 helpMenuItemActionPerformed(evt);
@@ -4139,13 +4156,8 @@ private void dibbs_USeriesActionPerformed(java.awt.event.ActionEvent evt) {//GEN
     }//GEN-LAST:event_dibbs_USeriesActionPerformed
 
     private void helpMenuItemActionPerformed(java.awt.event.ActionEvent evt) {
-        //Needed for having a nice look in windows... weird
-        ETReduxFrame.setDefaultLookAndFeelDecorated(false);
-        HelpBroker heb = JHelpAction.getHelpBroker();
-        //To Bypass the modal parent window issue.
-        ((DefaultHelpBroker) heb).setActivationWindow(this);
-        JHelpAction.setHelpBroker(heb);
-        JHelpAction.showHelp();
+        BrowserControl.displayURL("http://cirdles.org/projects/et_redux/");
+
     }
     // Variables declaration - do not modify//GEN-BEGIN:variables
     private javax.swing.JMenuItem ID_TIMSLegacyAnalysis_MIT_menuItem;

diff --git a/...a/org/earthtime/Tripoli/dataModels/sessionModels/AbstractSessionForStandardDataModel.java b/...a/org/earthtime/Tripoli/dataModels/sessionModels/AbstractSessionForStandardDataModel.java
@@ -170,7 +170,6 @@ public void generateSetOfFitFunctions(boolean propagateUncertainties, boolean do
 
         // dec 2014 ... needs refactoring to be property
         // ?always true for sessions USING_FULL_PROPAGATION =  tripoliSession.getRawDataFileHandler().getAcquisitionModel().isUsingFullPropagation();//  RawRatioDataModel.USING_FULL_PROPAGATION;       
-
         // for plotting - want to show all even those excluded
         int countOfAllStandards = standardFractions.size();
         allStandardsMeanLogRatios = new double[countOfAllStandards];
@@ -182,13 +181,15 @@ public void generateSetOfFitFunctions(boolean propagateUncertainties, boolean do
         while (fractionIterator.hasNext()) {
             TripoliFraction tf = fractionIterator.next();
 
-            RawRatioDataModel rawRatio = //
+            RawRatioDataModel rawRatio
+                    = //
                     ((RawRatioDataModel) tf.getRawRatioDataModelByName(rawRatioName));
 
-            allStandardsMeanLogRatios[index] = //
+            allStandardsMeanLogRatios[index]
+                    = //
                     rawRatio.getSessionValueBySessionTechnique(sessionTechnique);
-            allStandardsMeanLogRatioStdErrs[index] = //
-                    rawRatio.getSessionErrorBySessionTechnique(sessionTechnique);
+            allStandardsMeanLogRatioStdErrs[index]
+                    = rawRatio.getSessionErrorBySessionTechnique(sessionTechnique);
 
             index++;
 
@@ -217,11 +218,14 @@ public void generateSetOfFitFunctions(boolean propagateUncertainties, boolean do
             includedStandardsDataActiveMap[index] = true;
             includedStandardsAquireTimes[index] = tf.getZeroBasedNormalizedTimeStamp();
 
-            RawRatioDataModel rawRatio = //
+            RawRatioDataModel rawRatio
+                    = //
                     ((RawRatioDataModel) tf.getRawRatioDataModelByName(rawRatioName));
-            includedStandardsMeanLogRatios[index] = //
+            includedStandardsMeanLogRatios[index]
+                    = //
                     rawRatio.getSessionValueBySessionTechnique(sessionTechnique);
-            includedStandardsMeanLogRatioStdErrs[index] = //
+            includedStandardsMeanLogRatioStdErrs[index]
+                    = //
                     rawRatio.getSessionErrorBySessionTechnique(sessionTechnique);
             sessionIncludedStandardsCovariance.set( //
                     index, index, rawRatio.getSessionVarianceBySessionTechnique(sessionTechnique));
@@ -233,7 +237,8 @@ public void generateSetOfFitFunctions(boolean propagateUncertainties, boolean do
         if (countOfIncludedStandards > 0) {
             // begin section 8 of uncertainty propagation paper
 
-            RawRatioDataModel rawRatioFirst = //
+            RawRatioDataModel rawRatioFirst
+                    = //
                     ((RawRatioDataModel) getActiveStandardFractions().first().getRawRatioDataModelByName(rawRatioName));
             if (rawRatioFirst.hasTwoIdenticalIonCounters()) {
                 // calculate the covariance between each pair of standards
@@ -244,15 +249,17 @@ public void generateSetOfFitFunctions(boolean propagateUncertainties, boolean do
                 while (fractionIterator.hasNext()) {
                     TripoliFraction tf = fractionIterator.next();
 
-                    RawRatioDataModel rawRatio = //
+                    RawRatioDataModel rawRatio
+                            = //
                             ((RawRatioDataModel) tf.getRawRatioDataModelByName(rawRatioName));
 
                     dLrInt_dDt.set(index2, 0, rawRatio.getSelectedFitFunction().getdLrInt_dDt());
 
                     index2++;
                 }
 
-                double deadtimeUnctSqr = //
+                double deadtimeUnctSqr
+                        = //
                         ((IonCounterCollectorModel) rawRatioFirst.getBotIsotope().getCollectorModel())//
                         .getDeadTime().getOneSigmaAbs().movePointLeft(0).pow(2).doubleValue();
 
@@ -548,7 +555,7 @@ private void generateSPLINEfitFunction(Matrix mySessionIncludedStandardsCovarian
                     // oct 2014 use overdispersion from LINE function
                     double myOverDispersion = 0.0;//fOfXexist.getOverDispersion();
                     //if (myOverDispersion == 0.0) {
-                    if(sessionOfStandardsFitFunctionsWithOD.containsKey(FitFunctionTypeEnum.LINE.getName())){
+                    if (sessionOfStandardsFitFunctionsWithOD.containsKey(FitFunctionTypeEnum.LINE.getName())) {
                         myOverDispersion = sessionOfStandardsFitFunctionsWithOD.get(FitFunctionTypeEnum.LINE.getName()).getOverDispersion();
                     }
 //                        try {
@@ -582,7 +589,6 @@ private void calculateFitFunctions() {
                 + "  USING " + (USING_FULL_PROPAGATION ? "FULL PROPAGATION" : "FAST PROPAGATION"));
 
 //////        FitFunctionTypeEnum saveSelectedFitFunctionType = selectedFitFunctionType;
-
         if (generateMEANfitFunctionUsingLM()) {
             try {
                 generateLINEfitFunctionUsingLM();
@@ -601,7 +607,6 @@ private void calculateFitFunctions() {
 ////        if (saveSelectedFitFunctionType != null) {
 ////            selectedFitFunctionType = saveSelectedFitFunctionType;
 ////        }
-
         System.out.println("Session complete\n");
 
     }
@@ -619,7 +624,7 @@ public SortedMap<Double, AbstractFunctionOfX> generateSetOfSplineWithODfitFuncti
         sessionSplineRangeOD = new SessionSplineRangeOD();
 
         // safety valve
-        if (increment == 0){
+        if (increment == 0) {
             increment = (stopValue - startValue) / 10.0;
         }
         for (double i = startValue; i < stopValue; i += increment) {
@@ -645,8 +650,6 @@ public SortedMap<Double, AbstractFunctionOfX> generateSetOfSplineWithODfitFuncti
 //            } else {
 //                sessionOfStandardsSplinesWithOD.put(Math.sqrt(fOfX_SMOOTHING_SPLINE.getOverDispersion()), fOfX_SMOOTHING_SPLINE);
 //            }
-
-
             // oct 2014 new take
             // stop processing if roughness bad
             if (Double.isNaN(fOfX_SMOOTHING_SPLINE.getLogRoughness())) {//|| (fOfX_SMOOTHING_SPLINE.getLogRoughness() < -41.0)) {
@@ -662,7 +665,6 @@ public SortedMap<Double, AbstractFunctionOfX> generateSetOfSplineWithODfitFuncti
 //                    }
 //                } catch (Exception e) {
 //                }
-
                 break;
             } else {
                 //sessionOfStandardsSplinesWithOD.put(Math.sqrt(fOfX_SMOOTHING_SPLINE.getOverDispersion()), fOfX_SMOOTHING_SPLINE);
@@ -678,7 +680,8 @@ public SortedMap<Double, AbstractFunctionOfX> generateSetOfSplineWithODfitFuncti
     private AbstractFunctionOfX generateSplineWithSpecificOD(double overDispersion) {
         int rowColCount = sessionIncludedStandardsCovariance.getRowDimension();
 
-        Matrix sessionIncludedStandardsCovarianceCopyWithOD = //
+        Matrix sessionIncludedStandardsCovarianceCopyWithOD
+                = //
                 sessionIncludedStandardsCovariance.plus(Matrix.identity(rowColCount, rowColCount).times(overDispersion));
 
         AbstractFunctionOfX fOfX_SMOOTHING_SPLINE_WITH_OD = SmoothingSplineWithCov.getInstance().getFunctionOfX(//
@@ -718,7 +721,6 @@ public Map<String, AbstractFunctionOfX> getFitFunctions() {
 //    @Override
 //    public void calculateFittedFunctions(String fitFunctionTypeName) {
 //    }
-
     /**
      *
      * @param selectedFitFunctionType
@@ -757,7 +759,7 @@ public AbstractFunctionOfX getSelectedFitFunction() {
     public AbstractFunctionOfX getSelectedDownHoleFitFunction() {
         throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
     }
-    
+
     /**
      *
      * @param fitFunctionType
@@ -825,7 +827,6 @@ public double[] getIncludedStandardsAquireTimes() {
         return includedStandardsAquireTimes.clone();
     }
 
-
     /**
      * @return the includedStandardsMeanLogRatios
      */
@@ -870,7 +871,6 @@ public SortedSet<TripoliFraction> getActiveStandardFractions() {
 ////    public boolean[] getDataActiveMap() {
 ////        return includedStandardsDataActiveMap;
 ////    }
-
     /**
      * @return the sessionTechnique
      */