Merge pull request #777 from bowring/fixswap

Fixed #776

Author: bowring

common.gradle

@@ -7,7 +7,7 @@ apply plugin: 'maven-publish'
 
 
 String mavenGroupId = 'org.cirdles'
-String mavenVersion = '2.0.8'
+String mavenVersion = '2.0.9'
 
 [compileJava, compileTestJava]*.options*.encoding = 'UTF-8'
 

squidApp/src/main/java/org/cirdles/squid/gui/dateInterpretations/commonLeadAssignment/CommonLeadAssignmentController.java

@@ -125,6 +125,10 @@ public void initialize(URL url, ResourceBundle rb) {
     }
 
     private void init() throws SquidException {
+        if (squidProject.getTask().getOvercountCorrectionType().equals(Squid3Constants.OvercountCorrectionTypes.FR_Custom))
+        {
+            OvercountCorrection.correctionCustom(squidProject.getTask());
+        }
         // update
         try {
             squidProject.getTask().setupSquidSessionSpecsAndReduceAndReport(false);
@@ -161,10 +165,13 @@ private void init() throws SquidException {
             mapOfWeightedMeansBySampleNames.put(entry.getKey(), spotSummaryDetails);
         }
 
-//        showUnknownsWithOvercountCorrections();
+        ExpressionTreeInterface customExpression = squidProject.getTask().getNamedExpressionsMap().get(SWAP_CUSTOM_CORRECTION_204);
+        if ((customExpression == null) || !customExpression.isValueModel()){
+            customSWAPRB.setDisable(true);
+            squidProject.getTask().setOvercountCorrectionType(Squid3Constants.OvercountCorrectionTypes.NONE);
+            correctionNoneRB.setSelected(true);
+        }
 
-        ExpressionTreeInterface customExpression = squidProject.getTask().getNamedExpressionsMap().get("SWAPCustomCorrection204");
-        customSWAPRB.setDisable((customExpression == null) || !customExpression.isValueModel());
         switch (squidProject.getTask().getOvercountCorrectionType()) {
             case NONE:
                 correctionNoneRB.setSelected(true);
@@ -177,7 +184,6 @@ private void init() throws SquidException {
                 break;
             case FR_Custom:
                 customSWAPRB.setSelected(true);
-                OvercountCorrection.correctionCustom(squidProject.getTask());
         }
 
         showUnknownsWithOvercountCorrections();
@@ -228,7 +234,7 @@ public void setUpHeader() {
 
         biweight208Label.setText("biWgt 204 ovrCnts:  " + formatter);
 
-        customSWAPLabel.setText("SWAPCustomCorrection204");
+        customSWAPLabel.setText(SWAP_CUSTOM_CORRECTION_204);
 
         viewDetailsButton.setStyle("-fx-font-size: 12px;-fx-font-weight: bold; -fx-padding: 0 0 0 0;");
     }

squidApp/src/main/java/org/cirdles/squid/gui/dateInterpretations/countCorrections/CountCorrectionsController.java

@@ -44,8 +44,7 @@
 import static org.cirdles.squid.gui.SquidUI.PIXEL_OFFSET_FOR_MENU;
 import static org.cirdles.squid.gui.SquidUI.primaryStageWindow;
 import static org.cirdles.squid.gui.SquidUIController.squidProject;
-import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.BIWT_204_OVR_CTS_FROM_207;
-import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.BIWT_204_OVR_CTS_FROM_208;
+import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.*;
 
 /**
  * FXML Controller class
@@ -84,6 +83,13 @@ public class CountCorrectionsController implements Initializable {
      */
     @Override
     public void initialize(URL url, ResourceBundle rb) {
+        if (squidProject.getTask().getOvercountCorrectionType().equals(Squid3Constants.OvercountCorrectionTypes.FR_Custom)) {
+            try {
+                OvercountCorrection.correctionCustom(squidProject.getTask());
+            } catch (SquidException e) {
+//                    throw new RuntimeException(e);
+            }
+        }
         // update 
         try {
             squidProject.getTask().setupSquidSessionSpecsAndReduceAndReport(false);
@@ -95,8 +101,12 @@ public void initialize(URL url, ResourceBundle rb) {
         spotsTreeViewTextFlow.prefHeightProperty().bind(primaryStageWindow.getScene().heightProperty()
                 .subtract(PIXEL_OFFSET_FOR_MENU + headerHBox.getPrefHeight()));
 
-        ExpressionTreeInterface customExpression = squidProject.getTask().getNamedExpressionsMap().get("SWAPCustomCorrection204");
-        customSWAPRB.setDisable((customExpression == null) || !customExpression.isValueModel());
+        ExpressionTreeInterface customExpression = squidProject.getTask().getNamedExpressionsMap().get(SWAP_CUSTOM_CORRECTION_204);
+        if ((customExpression == null) || !customExpression.isValueModel()) {
+            customSWAPRB.setDisable(true);
+            squidProject.getTask().setOvercountCorrectionType(Squid3Constants.OvercountCorrectionTypes.NONE);
+        }
+
         switch (squidProject.getTask().getOvercountCorrectionType()) {
             case NONE:
                 correctionNoneRB.setSelected(true);
@@ -109,11 +119,6 @@ public void initialize(URL url, ResourceBundle rb) {
                 break;
             case FR_Custom:
                 customSWAPRB.setSelected(true);
-                try {
-                    OvercountCorrection.correctionCustom(squidProject.getTask());
-                } catch (SquidException e) {
-//                    throw new RuntimeException(e);
-                }
         }
 
         setUpHeader();
@@ -181,10 +186,10 @@ private void showUnknownsWithOvercountCorrections() {
                 double[][] r204_206_208 = spot.getTaskExpressionsEvaluationsPerSpot()
                         .get(squidProject.getTask().getNamedExpressionsMap().get("SWAPCountCorrectionExpression204From208"));
                 double[][] custom204 = new double[r204_206_208.length][r204_206_208[0].length];
-                ExpressionTreeInterface customExp = squidProject.getTask().getNamedExpressionsMap().get("SWAPCustomCorrection204");
+                ExpressionTreeInterface customExp = squidProject.getTask().getNamedExpressionsMap().get(SWAP_CUSTOM_CORRECTION_204);
                 if ((null != customExp) && customExp.isValueModel()) {
                     custom204 = spot.getTaskExpressionsEvaluationsPerSpot()
-                            .get(squidProject.getTask().getNamedExpressionsMap().get("SWAPCustomCorrection204"));
+                            .get(squidProject.getTask().getNamedExpressionsMap().get(SWAP_CUSTOM_CORRECTION_204));
                 }
 
                 TextFlow textFlowI = new TextFlow();

squidApp/src/main/resources/org/cirdles/squid/gui/parameters/SquidParametersManagerGUI.fxml

@@ -18,7 +18,8 @@
 
 <?import javafx.scene.control.*?>
 <?import javafx.scene.layout.*?>
-<AnchorPane xmlns:fx="http://javafx.com/fxml/1" maxHeight="-Infinity" maxWidth="-Infinity" minHeight="600.0" minWidth="900.0"
+<AnchorPane xmlns:fx="http://javafx.com/fxml/1" maxHeight="-Infinity" maxWidth="-Infinity" minHeight="600.0"
+            minWidth="900.0"
             prefHeight="600.0" prefWidth="900.0" stylesheets="@../css/squidLabData.css"
             xmlns="http://javafx.com/javafx/17"
             fx:controller="org.cirdles.squid.gui.parameters.ParametersManagerGUIController">

squidCore/src/main/java/org/cirdles/squid/shrimp/ShrimpFraction.java

@@ -28,6 +28,7 @@
 import java.math.RoundingMode;
 import java.util.*;
 
+import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.SWAP_CUSTOM_CORRECTION_204;
 import static org.cirdles.squid.utilities.conversionUtilities.CloningUtilities.clone2dArray;
 
 /**
@@ -1001,7 +1002,7 @@ public String getOverCtCorr() {
                 retVal.append("Corrected from 208");
                 break;
             case CUSTOM:
-                retVal.append("SWAPCustomCorrection204");
+                retVal.append(SWAP_CUSTOM_CORRECTION_204);
                 break;
         }
         return retVal.toString();

squidCore/src/main/java/org/cirdles/squid/tasks/Task.java

@@ -503,6 +503,9 @@ public void updateTaskFromTaskDesign(TaskDesign taskDesign, boolean taskSkeleton
                 String targetSampleName = customExp.getName().split("_WM_")[1].trim();
                 customExp.getExpressionTree().setUnknownsGroupSampleName(targetSampleName);
             }
+            if (taskExpressionsOrdered.contains(customExp)) {
+                taskExpressionsOrdered.remove(customExp);
+            }
             taskExpressionsOrdered.add(customExp);
         }
 
@@ -668,9 +671,10 @@ public void generateBuiltInExpressions() {
 
             SortedSet<Expression> overCountExpressionsOrdered = generateOverCountExpressions(isDirectAltPD());
             taskExpressionsOrdered.addAll(overCountExpressionsOrdered);
-            if (!namedExpressionsMap.containsKey("SWAPCustomCorrection204")) {
+            if (!namedExpressionsMap.containsKey(SWAP_CUSTOM_CORRECTION_204)) {
                 Expression customExp = buildCountCorrectionCustomExpression();
-                namedExpressionsMap.put("SWAPCustomCorrection204", customExp.getExpressionTree());
+                namedExpressionsMap.put(SWAP_CUSTOM_CORRECTION_204, customExp.getExpressionTree());
+                taskExpressionsOrdered.remove(customExp);
                 taskExpressionsOrdered.add(customExp);
             }
 
@@ -1080,7 +1084,7 @@ public void updateAllUnknownSpotsWithOverCountCorrectedBy204_206_208() {
     }
 
     public void updateAllUnknownSpotsWithCustomCorrection() {
-        ExpressionTreeInterface customExp = namedExpressionsMap.get("SWAPCustomCorrection204");
+        ExpressionTreeInterface customExp = namedExpressionsMap.get(SWAP_CUSTOM_CORRECTION_204);
         if ((null != customExp) && customExp.isValueModel()) {
             for (ShrimpFractionExpressionInterface spot : unknownSpots) {
                 SquidRatiosModel ratio204_206 = ((ShrimpFraction) spot).getRatioByName("204/206");

squidCore/src/main/java/org/cirdles/squid/tasks/TaskInterface.java

@@ -40,7 +40,7 @@
 
 import static org.cirdles.squid.constants.Squid3Constants.TaskTypeEnum.GEOCHRON;
 import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.*;
-import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltinExpressionsCountCorrection204.*;
+import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltinExpressionsCountCorrection204.buildCountCorrectionCustomExpression;
 
 /**
  * @author James F. Bowring
@@ -415,10 +415,6 @@ default void applyDirectives(boolean customizeTaskExpressions) throws SquidExcep
         }
 
         List<Expression> customExpressions = getCustomTaskExpressions();
-        // special temporary case Sep 2019
-        customExpressions.remove(buildCountCorrectionExpressionFrom207());
-        customExpressions.remove(buildCountCorrectionExpressionFrom208());
-        customExpressions.remove(buildCountCorrectionCustomExpression());
 
         getTaskExpressionsOrdered().clear();
 
@@ -497,6 +493,14 @@ default void applyDirectives(boolean customizeTaskExpressions) throws SquidExcep
             getTaskExpressionsOrdered().add(parentPPM);
         }
 
+
+        Expression defaultCustomExp = buildCountCorrectionCustomExpression();
+        if (customExpressions.contains(defaultCustomExp)) {
+            Expression customExp = customExpressions.get(customExpressions.indexOf(defaultCustomExp));
+            getNamedExpressionsMap().put(SWAP_CUSTOM_CORRECTION_204, customExp.getExpressionTree());
+            getTaskExpressionsOrdered().remove(defaultCustomExp);
+        }
+
         getTaskExpressionsOrdered().addAll(customExpressions);
 
         setChanged(true);

squidCore/src/main/java/org/cirdles/squid/tasks/expressions/Expression.java

@@ -45,6 +45,7 @@
 
 import static org.cirdles.squid.constants.Squid3Constants.*;
 import static org.cirdles.squid.constants.Squid3Constants.SpotTypes.UNKNOWN;
+import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.SWAP_CUSTOM_CORRECTION_204;
 import static org.cirdles.squid.tasks.expressions.functions.Function.replaceAliasedFunctionNamesInExpressionString;
 
 /**
@@ -350,6 +351,9 @@ public String getNotes() {
         if (this.expressionTree.isSquidSpecialUPbThExpression()) {
             notes = BuiltInExpressionsNotes.BUILTIN_EXPRESSION_NOTES.get(name);
         }
+        if (this.expressionTree.getName().compareToIgnoreCase(SWAP_CUSTOM_CORRECTION_204) == 0) {
+            notes = BuiltInExpressionsNotes.BUILTIN_EXPRESSION_NOTES.get(SWAP_CUSTOM_CORRECTION_204);
+        }
         if (this.isParameterValue()
                 || this.isReferenceMaterialValue()) {
             notes = "from Model: " + sourceModelNameAndVersion + "\n\n" + BuiltInExpressionsNotes.BUILTIN_EXPRESSION_NOTES.get(name);

squidCore/src/main/java/org/cirdles/squid/tasks/expressions/builtinExpressions/BuiltInExpressionsDataDictionary.java

@@ -193,6 +193,9 @@ public class BuiltInExpressionsDataDictionary {
     public static final String RAD_206PB204PB_FACTOR = "Rad_206Pb204Pb_Factor";
     public static final String RAD_208PB204PB_FACTOR = "Rad_208Pb204Pb_Factor";
     public static final List<String> COMPOSITION_EXPRESSION_NAMES = new ArrayList<>();
+    // ************************ CUSTOM SWAPPING *********************
+    public static final String SWAP_CUSTOM_CORRECTION_204 = "SWAPCustomCorrection204";
+    // ************************ MISC CONSTANTS *********************
     private static final String R206_238CALIB_CONST = CALIB_CONST_206_238_ROOT + "_CalibConst";
     public static final String PB4COR206_238CALIB_CONST = PB4CORR + R206_238CALIB_CONST;
     public static final String PB4COR206_238CALIB_CONST_WM = WTDAV_PREFIX + PB4COR206_238CALIB_CONST;

squidCore/src/main/java/org/cirdles/squid/tasks/expressions/builtinExpressions/BuiltInExpressionsNotes.java

@@ -546,5 +546,14 @@ public class BuiltInExpressionsNotes {
                         + " (i.e. the third element of the WtdAv vector output) calculated from "
                         + "any RM dataset of WtdAv_Xcor_208Pb232Th_CalibConst values. In this context, "
                         + "Xcor denotes the index isotope used for the common Pb correction in the RM (i.e. 204Pb or 207Pb).");
+
+        BUILTIN_EXPRESSION_NOTES.put(SWAP_CUSTOM_CORRECTION_204,
+                "Edit this expression to calculate a custom corrected value "
+                        + "for 204/206 as per Squid2.5 'column swapping' and invoke it from the Common Pb menu "
+                        + "window for overcounts of 204.  \n\n"
+                        + "REQUIRED: Use the expression name '" + SWAP_CUSTOM_CORRECTION_204 + "' and define a ValueModel.  \n"
+                        + "The default definition is: 'ValueModel(Orig([\"204/206\"]),Orig([±\"204/206\"]),true)'. \n\n"
+                        + " NOTE:  Use the 'Orig' function to retrieve the unmutable value of a ratio.  Otherwise, "
+                        + "a circular logic obtains.");
     }
 }

squidCore/src/main/java/org/cirdles/squid/tasks/expressions/builtinExpressions/BuiltinExpressionsCountCorrection204.java

@@ -17,8 +17,7 @@
 
 import org.cirdles.squid.tasks.expressions.Expression;
 
-import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.BIWT_204_OVR_CTS_FROM_207;
-import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.BIWT_204_OVR_CTS_FROM_208;
+import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.*;
 import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsFactory.buildExpression;
 
 /**
@@ -28,7 +27,7 @@ public class BuiltinExpressionsCountCorrection204 {
 
     /**
      * @return
-     * @see https://github.com/CIRDLES/ET_Redux/wiki/SQ2.50-Procedural-Framework:-Part-7a-(204-overcounts)
+     * @see <a href="https://github.com/CIRDLES/ET_Redux/wiki/SQ2.50-Procedural-Framework:-Part-7a-(204-overcounts)">...</a>
      */
     public static Expression buildCountCorrectionExpressionFrom207() {
 
@@ -67,7 +66,7 @@ public static Expression buildCountCorrectionExpressionFrom207() {
 
     /**
      * @return
-     * @see https://github.com/CIRDLES/ET_Redux/wiki/SQ2.50-Procedural-Framework:-Part-7a-(204-overcounts)
+     * @see <a href="https://github.com/CIRDLES/ET_Redux/wiki/SQ2.50-Procedural-Framework:-Part-7a-(204-overcounts)">...</a>
      */
     public static Expression buildCountCorrectionExpressionFrom208() {
 
@@ -107,18 +106,10 @@ public static Expression buildCountCorrectionExpressionFrom208() {
     public static Expression buildCountCorrectionCustomExpression() {
 
         Expression countCorrectionCustom = buildExpression(
-                "SWAPCustomCorrection204",
+                SWAP_CUSTOM_CORRECTION_204,
                 "ValueModel(Orig([\"204/206\"]),Orig([±\"204/206\"]),true)", false, true, false);
 
-        countCorrectionCustom.getExpressionTree().setSquidSpecialUPbThExpression(true);
-        countCorrectionCustom.setNotes(
-                "Edit this expression to calculate a custom corrected value "
-                        + "for 204/206 as per Squid2.5 'column swapping' and invoke it from the Common Pb menu "
-                        + "window for overcounts of 204.  \n\n"
-                        + "REQUIRED: Use the expression name 'SWAPCustomCorrection204' and define a ValueModel.  \n"
-                        + "The default definition is: 'ValueModel(Orig([\"204/206\"]),Orig([±\"204/206\"]),true)'. \n\n"
-                        + " NOTE:  Use the 'Orig' function to retrieve the unmutable value of a ratio.  Otherwise, "
-                        + "a circular logic obtains.");
+        countCorrectionCustom.getExpressionTree().setSquidSpecialUPbThExpression(false);
 
         return countCorrectionCustom;
     }