Performance tweaks and bug fixes. (#142)

* adds more expressions per Bodorkos and refactors * corrects bug with extperr calculation * refines reports for testing
CIRDLES · Aug 9, 2018 · e2c9a1e · e2c9a1e
1 parent aca0f62
commit e2c9a1e
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Showing 15 changed files with 668 additions and 517 deletions.
diff --git a/common.gradle b/common.gradle
@@ -6,7 +6,7 @@ apply plugin: 'java'
 apply plugin: 'maven'
 
 String mavenGroupId = 'org.cirdles'
-String mavenVersion = '0.4.0'
+String mavenVersion = '0.4.1'
 
 
 sourceCompatibility = '1.8'

diff --git a/squidApp/src/main/java/org/cirdles/squid/gui/MassesAuditController.java b/squidApp/src/main/java/org/cirdles/squid/gui/MassesAuditController.java
@@ -528,7 +528,9 @@ public void handle(ActionEvent e) {
     private void produceGraphOnScrolledPane(int massCounter, String title, List<Double> data, MassStationDetail entry, VBox scrolledBox) {
 
         int heightOfMassPlot = 150;
-        int widthOfView = squidProject.getPrawnFileRuns().size() * 25 + 350;
+        // aug 2018 to manage large spot counts and pixels used
+        int customSpotWidth = (1000 - squidProject.getPrawnFileRuns().size()) / 25;//was just 25, then 15
+        int widthOfView = squidProject.getPrawnFileRuns().size() * customSpotWidth + 350;
 
         AbstractDataView canvas
                 = new MassStationAuditViewForShrimp(new Rectangle(25, (massCounter * heightOfMassPlot) + 25, widthOfView, heightOfMassPlot),

diff --git a/squidApp/src/main/java/org/cirdles/squid/gui/plots/PlotsController.java b/squidApp/src/main/java/org/cirdles/squid/gui/plots/PlotsController.java
@@ -377,10 +377,9 @@ private void customizePlotChooserToolbarAndInvokePlotter() {
                 plotFlavorOneRadioButton.setText("Wetherill Concordia");
                 plotFlavorTwoRadioButton.setText("Tera-Wasserburg");
                 plotFlavorOneRadioButton.setDisable(false);
-                plotFlavorTwoRadioButton.setDisable(false);
+                plotFlavorTwoRadioButton.setDisable(true);
 
                 corr7_RadioButton.setVisible(false);
-                corr8_RadioButton.setDisable(true);
                 corr8_RadioButton.setVisible(true);
 
                 showConcordiaPlotsOfUnknownsOrRefMat();
@@ -399,7 +398,6 @@ private void customizePlotChooserToolbarAndInvokePlotter() {
                     plotFlavorOneRadioButton.setSelected(true);
                     plotFlavorTwoRadioButton.setDisable(true);
                     corr8_RadioButton.setVisible(true);
-                    corr8_RadioButton.setDisable(false);
                 } else if (!isDirectAltPD && has232) {// perm3
                     plotFlavorOneRadioButton.setDisable(true);
                     plotFlavorTwoRadioButton.setSelected(true);
@@ -493,13 +491,15 @@ public Map<String, Object> getDatum() {
         /**
          * @return the selectedProperty
          */
+        @Override
         public SimpleBooleanProperty getSelectedProperty() {
             return selectedProperty;
         }
 
         /**
          * @param selectedProperty the selectedProperty to set
          */
+        @Override
         public void setSelectedProperty(SimpleBooleanProperty selectedProperty) {
             this.selectedProperty = selectedProperty;
             this.shrimpFraction.setSelected(selectedProperty.getValue());

diff --git a/squidApp/src/main/java/org/cirdles/squid/gui/topsoil/TopsoilDataFactory.java b/squidApp/src/main/java/org/cirdles/squid/gui/topsoil/TopsoilDataFactory.java
@@ -74,12 +74,12 @@ public static Map<String, Object> prepareWetherillDatum(
 
         Map<String, Object> datum = new HashMap<>();
         // default is for reference materials
-        String ratioBase75 = " 207Pb/235U";
-        String ratioBase68 = " 206Pb/238U";
+        String ratioBase75 = " 207*/235";
+        String ratioBase68 = " 206*/238";
         String errCorr = "-errcorr";
         if (isUnknown) {
-            ratioBase75 = " 207*/235";
-            ratioBase68 = " 206*/238";
+            ratioBase75 = " 207*/235S";
+            ratioBase68 = " 206*/238S";
             errCorr = " err corr";
         }
 

diff --git a/squidApp/src/main/resources/org/cirdles/squid/gui/expressions/ExpressionBuilder.fxml b/squidApp/src/main/resources/org/cirdles/squid/gui/expressions/ExpressionBuilder.fxml
@@ -29,7 +29,7 @@
 <?import javafx.scene.text.TextFlow?>
 <?import javafx.scene.web.WebView?>
 
-<SplitPane fx:id="mainPane" dividerPositions="0.0" maxHeight="-Infinity" maxWidth="-Infinity" styleClass="backgroundCalamari" stylesheets="@../css/projectManager.css" xmlns="http://javafx.com/javafx/10.0.1" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.cirdles.squid.gui.expressions.ExpressionBuilderController">
+<SplitPane fx:id="mainPane" dividerPositions="0.0" maxHeight="-Infinity" maxWidth="-Infinity" styleClass="backgroundCalamari" stylesheets="@../css/projectManager.css" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.cirdles.squid.gui.expressions.ExpressionBuilderController">
    <items>
       <SplitPane fx:id="leftSplitPane" dividerPositions="0.75" maxWidth="500.0" minWidth="275.0" orientation="VERTICAL" styleClass="backgroundCalamari">
          <items>
@@ -126,7 +126,7 @@
             <VBox prefHeight="149.0" prefWidth="275.0">
                <children>
                   <Text strokeType="OUTSIDE" strokeWidth="0.0" text="Entities" />
-                  <Accordion fx:id="othersAccordion">
+                  <Accordion fx:id="othersAccordion" nodeOrientation="LEFT_TO_RIGHT">
                      <panes>
                         <TitledPane fx:id="constantsTitledPane" animated="false" text="Constants and Numbers">
                            <content>

diff --git a/squidCore/src/main/java/org/cirdles/squid/projects/SquidProject.java b/squidCore/src/main/java/org/cirdles/squid/projects/SquidProject.java
@@ -31,6 +31,7 @@
 import org.cirdles.squid.constants.Squid3Constants;
 import static org.cirdles.squid.constants.Squid3Constants.DUPLICATE_STRING;
 import org.cirdles.squid.core.PrawnFileHandler;
+import org.cirdles.squid.dialogs.SquidMessageDialog;
 import org.cirdles.squid.exceptions.SquidException;
 import org.cirdles.squid.prawn.PrawnFile;
 import org.cirdles.squid.prawn.PrawnFile.Run;
@@ -137,6 +138,21 @@ public void createTaskFromImportedSquid25Task(File squidTaskFile) {
 
         TaskSquid25 taskSquid25 = TaskSquid25.importSquidTaskFile(squidTaskFile);
 
+        // if Task is ashort of nominal masses, add them
+        int prawnSpeciesCount = Integer.parseInt(prawnFile.getRun().get(0).getPar().get(2).getValue());
+        if (prawnSpeciesCount != taskSquid25.getNominalMasses().size()) {
+            SquidMessageDialog.showWarningDialog(
+                    "The PrawnFile has "
+                    + prawnSpeciesCount
+                    + " mass stations and the Task has "
+                    + taskSquid25.getNominalMasses().size()
+                    + " masses - please confirm.",
+                    null);
+            for (int i = 0; i < (prawnSpeciesCount - taskSquid25.getNominalMasses().size()); i++) {
+                taskSquid25.getNominalMasses().add("DUMMY" + (i + 1));
+            }
+        }
+
         // need to remove stored expression results on fractions to clear the decks
         this.task.getShrimpFractions().forEach((spot) -> {
             spot.getTaskExpressionsForScansEvaluated().clear();
@@ -510,6 +526,7 @@ public void updateFilterForRefMatSpotNames(String filterForRefMatSpotNames) {
             task.setFilterForRefMatSpotNames(filterForRefMatSpotNames);
         }
     }
+
     public String getFilterForConcRefMatSpotNames() {
         return filterForConcRefMatSpotNames;
     }

diff --git a/...cirdles/squid/reports/reportSpecifications/ReportSpecificationsUPbReferenceMaterials.java b/...cirdles/squid/reports/reportSpecifications/ReportSpecificationsUPbReferenceMaterials.java
@@ -21,6 +21,8 @@
 import java.util.Map;
 import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.SQUID_PPM_PARENT_EQN_NAME_TH;
 import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.SQUID_PPM_PARENT_EQN_NAME_U;
+import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.SQUID_PRIMARY_UTH_EQN_NAME_TH;
+import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.SQUID_PRIMARY_UTH_EQN_NAME_U;
 import static org.cirdles.squid.tasks.expressions.builtinExpressions.BuiltInExpressionsDataDictionary.SQUID_TH_U_EQN_NAME;
 
 /**
@@ -30,7 +32,6 @@
  */
 public class ReportSpecificationsUPbReferenceMaterials extends ReportSpecificationsAbstract {
 
-
     // Report column order =
     //  displayName1, displayName2, displayName3, displayName4, units, retrieveMethodName, retrieveParameterName, uncertaintyType,
     //     footnoteSpec, visible, useArbitrary? for value, digitcount value, unct visible (if required), description where needed,
@@ -70,9 +71,6 @@ public class ReportSpecificationsUPbReferenceMaterials extends ReportSpecificati
         {"", "204", "/206", "(fr. 207)", "", "getTaskExpressionsEvaluationsPerSpotByField", "204/206 (fr. 207)", "PCT",
             "", "true", "true", "6", "true", "", "false", "false"
         },
-//        {"", "", "%", "err", "", "getTaskExpressionsEvaluationsPerSpotByField", "204/206 (fr. 207) %err", "",
-//            "", "true", "true", "0", "true", "", "false", "false"
-//        },
         {"", "204", "/206", "(fr. 208)", "", "getTaskExpressionsEvaluationsPerSpotByField", "204/206 (fr. 208)", "",
             "", "true", "true", "6", "true", "", "false", "false"
         },
@@ -82,11 +80,12 @@ public class ReportSpecificationsUPbReferenceMaterials extends ReportSpecificati
         {"8-corr", "206Pb", "/238U", "const delta%", "", "getTaskExpressionsEvaluationsPerSpotByField", "8-corrPrimary calib const. delta%", "",
             "", "true", "true", "3", "true", "", "false", "false"
         },
-        {"", "Uncorr", "Pb/U", "const", "", "getTaskExpressionsEvaluationsPerSpotByField", "UncorrPb/Uconst", "PCT",
-            "", "true", "false", "3", "true", "232/238 ratio", "false", "false"
-        }
-
-    };
+        {"", "", "UncorrPb", "/Uconst", "", "getTaskExpressionsEvaluationsPerSpotByField", SQUID_PRIMARY_UTH_EQN_NAME_U, "PCT",
+            "", "true", "false", "6", "true", "", "false", "false"
+        },
+        {"", "", "UncorrPb", "/Thconst", "", "getTaskExpressionsEvaluationsPerSpotByField", SQUID_PRIMARY_UTH_EQN_NAME_TH, "PCT",
+            "", "true", "false", "6", "true", "", "false", "false"
+        },};
     // Report column order =
     //  displayName1, displayName2, displayName3, displayName4, units, retrieveMethodName, retrieveParameterName, uncertaintyType,
     //     footnoteSpec, visible, useArbitrary? for value, digitcount value, unct visible (if required), description where needed,
@@ -98,46 +97,45 @@ public class ReportSpecificationsUPbReferenceMaterials extends ReportSpecificati
         {"4-corr", "206Pb", "/238U", "calCon", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr 206Pb/238Ucalibr.const", "PCT",
             "", "true", "false", "4", "true", "", "false", "false"
         },
+        {"4-corr", "206Pb", "/238U", "Age", "Ma", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr 206Pb/238U Age", "ABS",
+            "", "true", "false", "4", "true", "", "false", "false"
+        },
         {"4-corr", "208Pb", "/232Th", "calCon", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr 208Pb/232Thcalibr.const", "PCT",
             "", "true", "false", "4", "true", "", "false", "false"
         },
-        {"", "", "Age", "", "Ma", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr 206Pb/238U Age", "ABS",
-            "", "true", "true", "0", "true", "", "false", "false"
+        {"4-corr", "208Pb", "/232Th", "Age", "Ma", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr 208Pb/232Th Age", "ABS",
+            "", "true", "false", "4", "true", "", "false", "false"
+        },
+        {"4-corr", "Total", "206Pb", "/238U", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corrTotal 206Pb/238U", "PCT",
+            "", "true", "false", "4", "true", "", "false", "false"
+        },
+        {"4-corr", "Total", "208Pb", "/232Th", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corrTotal 208Pb/232Th", "PCT",
+            "", "true", "false", "4", "true", "", "false", "false"
         },
         {"", "4-corr", "%com", "206", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr %com206", "",
             "", "true", "false", "3", "", "", "false", "false"
         },
-        {"", "4-corr", "208Pb*", "/206Pb*", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr208Pb*/206Pb*", "",
-            "", "true", "false", "4", "", "", "false", "false"
-        },
-        {"", "", "%", "err", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr208Pb*/206Pb* %err", "",
+        {"", "4-corr", "%com", "208", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr %com208", "",
             "", "true", "false", "3", "", "", "false", "false"
-        },       
-        {"4-corr", "207Pb", "206Pb", "age","Ma",  "getTaskExpressionsEvaluationsPerSpotByField", "4-corr207Pb/206Pbage", "ABS",
+        },
+        {"", "4-corr", "208Pb*", "/206Pb*", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr208Pb*/206Pb*", "PCT",
+            "", "true", "false", "4", "true", "", "false", "false"
+        },
+        {"4-corr", "207Pb", "206Pb", "age", "Ma", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr207Pb/206Pbage", "ABS",
             "", "true", "false", "3", "true", "", "false", "false"
         },
         {"", "4-corr", "207Pb", "/206Pb", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr 207Pb/206Pb", "PCT",
             "", "true", "false", "4", "true", "", "false", "false"
         },
-//        {"", "", "%", "err", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr207Pb/206Pb%err", "",
-//            "", "true", "false", "3", "", "", "false", "false"
-//        },
-        {"", "4-corr", "207Pb", "/235U", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr 207Pb/235U", "PCT",
+        {"", "4-corr", "207Pb", "/235U", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr 207*/235", "PCT",
             "", "true", "false", "4", "true", "", "false", "false"
         },
-//        {"", "", "%", "err", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr207Pb/235U %err", "",
-//            "", "true", "false", "3", "", "", "false", "false"
-//        },
-        {"", "4-corr", "206Pb", "/238U", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr 206Pb/238U", "PCT",
+        {"", "4-corr", "206Pb", "/238U", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr 206*/238", "PCT",
             "", "true", "false", "4", "true", "", "false", "false"
         },
-//        {"", "", "%", "err", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr206Pb/238U %err", "",
-//            "", "true", "false", "3", "", "", "false", "false"
-//        },
         {"", "4-corr", "err", "corr", "", "getTaskExpressionsEvaluationsPerSpotByField", "4-corr-errcorr", "",
             "", "true", "false", "3", "", "", "false", "false"
         }
-
     };
     // Report column order =
     //  displayName1, displayName2, displayName3, displayName4, units, retrieveMethodName, retrieveParameterName, uncertaintyType,
@@ -150,24 +148,36 @@ public class ReportSpecificationsUPbReferenceMaterials extends ReportSpecificati
         {"7-corr", "206Pb", "/238U", "calCon", "", "getTaskExpressionsEvaluationsPerSpotByField", "7-corr 206Pb/238Ucalibr.const", "PCT",
             "", "true", "false", "4", "true", "", "false", "false"
         },
+        {"7-corr", "206Pb", "/238U", "Age", "Ma", "getTaskExpressionsEvaluationsPerSpotByField", "7-corr 206Pb/238U Age", "ABS",
+            "", "true", "false", "4", "true", "", "false", "false"
+        },
         {"7-corr", "208Pb", "/232Th", "calCon", "", "getTaskExpressionsEvaluationsPerSpotByField", "7-corr 208Pb/232Thcalibr.const", "PCT",
             "", "true", "false", "4", "true", "", "false", "false"
-        },        {"", "", "Age", "", "Ma", "getTaskExpressionsEvaluationsPerSpotByField", "7-corr 206Pb/238U Age", "ABS",
-            "", "true", "true", "0", "true", "", "false", "false"
         },
-//        {"", "", "\u00B11\u03C3", "", "Ma", "getTaskExpressionsEvaluationsPerSpotByField", "7-corr206Pb/238U Age 1sigma", "",
-//            "", "true", "true", "0", "", "", "false", "false"
-//        },
+        {"7-corr", "208Pb", "/232Th", "Age", "Ma", "getTaskExpressionsEvaluationsPerSpotByField", "7-corr 208Pb/232Th Age", "ABS",
+            "", "true", "false", "4", "true", "", "false", "false"
+        },
+        {"7-corr", "Total", "206Pb", "/238U", "", "getTaskExpressionsEvaluationsPerSpotByField", "7-corrTotal 206Pb/238U", "PCT",
+            "", "true", "false", "4", "true", "", "false", "false"
+        },
+        {"7-corr", "Total", "208Pb", "/232Th", "", "getTaskExpressionsEvaluationsPerSpotByField", "7-corrTotal 208Pb/232Th", "PCT",
+            "", "true", "false", "4", "true", "", "false", "false"
+        },
         {"", "7-corr", "%com", "206", "", "getTaskExpressionsEvaluationsPerSpotByField", "7-corr %com206", "",
             "", "true", "false", "3", "", "", "false", "false"
         },
+        {"", "7-corr", "%com", "208", "", "getTaskExpressionsEvaluationsPerSpotByField", "7-corr %com208", "",
+            "", "true", "false", "3", "", "", "false", "false"
+        },
         {"", "7-corr", "208Pb*", "/206Pb*", "", "getTaskExpressionsEvaluationsPerSpotByField", "7-corr208Pb*/206Pb*", "",
             "", "true", "false", "4", "", "", "false", "false"
         },
         {"", "", "%", "err", "", "getTaskExpressionsEvaluationsPerSpotByField", "7-corr208Pb*/206Pb* %err", "",
             "", "true", "false", "3", "", "", "false", "false"
+        },
+        {"", "7-corr", "206Pb", "/238U", "", "getTaskExpressionsEvaluationsPerSpotByField", "7-corr 206*/238", "PCT",
+            "", "true", "false", "4", "true", "", "false", "false"
         }
-
     };
 
     // Report column order =
@@ -181,19 +191,30 @@ public class ReportSpecificationsUPbReferenceMaterials extends ReportSpecificati
         {"8-corr", "206Pb", "/238U", "calCon", "", "getTaskExpressionsEvaluationsPerSpotByField", "8-corr 206Pb/238Ucalibr.const", "PCT",
             "", "true", "false", "4", "true", "", "false", "false"
         },
-//        {"", "", "%", "err", "", "getTaskExpressionsEvaluationsPerSpotByField", "8-corr 206Pb/238Ucalibr.const %err", "",
-//            "", "true", "false", "2", "", "", "false", "false"
-//        },
         {"", "", "Age", "", "Ma", "getTaskExpressionsEvaluationsPerSpotByField", "8-corr 206Pb/238U Age", "ABS",
             "", "true", "true", "0", "true", "", "false", "false"
         },
-        {"", "", "\u00B11\u03C3", "", "Ma", "getTaskExpressionsEvaluationsPerSpotByField", "8-corr206Pb/238U Age 1sigma", "",
-            "", "true", "true", "0", "", "", "false", "false"
+        {"8-corr", "Total", "206Pb", "/238U", "", "getTaskExpressionsEvaluationsPerSpotByField", "8-corrTotal 206Pb/238U", "PCT",
+            "", "true", "false", "4", "true", "", "false", "false"
         },
         {"", "8-corr", "%com", "206", "", "getTaskExpressionsEvaluationsPerSpotByField", "8-corr %com206", "",
             "", "true", "false", "3", "", "", "false", "false"
+        },
+        {"8-corr", "207Pb", "/206Pb", "Age", "Ma", "getTaskExpressionsEvaluationsPerSpotByField", "8-corr 207Pb/206Pb Age", "ABS",
+            "", "true", "false", "4", "true", "", "false", "false"
+        },
+        {"", "8-corr", "207Pb", "/206Pb", "", "getTaskExpressionsEvaluationsPerSpotByField", "8-corr 207*/206*", "PCT",
+            "", "true", "false", "4", "true", "", "false", "false"
+        },
+        {"", "8-corr", "207Pb", "/235U", "", "getTaskExpressionsEvaluationsPerSpotByField", "8-corr 207*/235", "PCT",
+            "", "true", "false", "4", "true", "", "false", "false"
+        },
+        {"", "8-corr", "206*", "/238", "", "getTaskExpressionsEvaluationsPerSpotByField", "8-corr 206*/238", "PCT",
+            "", "true", "false", "6", "true", "", "false", "false"
+        },
+        {"", "8-corr", "err", "corr", "", "getTaskExpressionsEvaluationsPerSpotByField", "8-corr-errcorr", "",
+            "", "true", "false", "3", "", "", "false", "false"
         }
-
     };
 
     /**