use of org.cirdles.squid.tasks.Task in project Squid by CIRDLES.
the class CommonLeadAssignmentController method init.
private void init() throws SquidException {
// update
try {
squidProject.getTask().setupSquidSessionSpecsAndReduceAndReport(false);
} catch (SquidException squidException) {
SquidMessageDialog.showWarningDialog(squidException.getMessage(), primaryStageWindow);
}
spotsTreeViewCommonLeadTools.prefWidthProperty().bind(primaryStageWindow.getScene().widthProperty());
spotsTreeViewCommonLeadTools.prefHeightProperty().bind(primaryStageWindow.getScene().heightProperty().subtract(PIXEL_OFFSET_FOR_MENU + headerHBox.getPrefHeight() + headerHBoxForCorrections.getPrefHeight() + footerHBox.getPrefHeight()));
// prime StaceyKramer
StaceyKramerCommonLeadModel.updatePhysicalConstants(squidProject.getTask().getPhysicalConstantsModel());
StaceyKramerCommonLeadModel.updateU_Ratio(squidProject.getTask().getReferenceMaterialModel().getDatumByName(REF_238U235U_RM_MODEL_NAME).getValue().doubleValue());
setupAgeTypes();
// set up groups and refresh calculations
mapOfSpotsBySampleNames = squidProject.getTask().getMapOfUnknownsBySampleNames();
// case of sample names chosen
if (mapOfSpotsBySampleNames.size() > 1) {
// task.getMapOfUnknownsBySampleNames restores this global set
mapOfSpotsBySampleNames.remove(Squid3Constants.SpotTypes.UNKNOWN.getSpotTypeName());
}
mapOfWeightedMeansBySampleNames = new TreeMap<>();
for (Map.Entry<String, List<ShrimpFractionExpressionInterface>> entry : mapOfSpotsBySampleNames.entrySet()) {
((Task) squidProject.getTask()).evaluateUnknownsWithChangedParameters(entry.getValue());
SpotSummaryDetails spotSummaryDetails = ((Task) squidProject.getTask()).evaluateSelectedAgeWeightedMeanForUnknownGroup(entry.getKey(), entry.getValue());
mapOfWeightedMeansBySampleNames.put(entry.getKey(), spotSummaryDetails);
}
showUnknownsWithOvercountCorrections();
switch(squidProject.getTask().getOvercountCorrectionType()) {
case NONE:
correctionNoneRB.setSelected(true);
break;
case FR_207:
correction207RB.setSelected(true);
break;
case FR_208:
correction208RB.setSelected(true);
}
setUpHeader();
setUpFooter();
}
use of org.cirdles.squid.tasks.Task in project Squid by CIRDLES.
the class PlotsController method showAnyTwoExpressions.
private void showAnyTwoExpressions() throws SquidException {
spotsTreeViewCheckBox = new CheckTreeView<>();
spotsTreeViewCheckBox.setStyle(SPOT_TREEVIEW_CSS_STYLE_SPECS);
final List<ShrimpFractionExpressionInterface> allRefMatShrimpFractions;
Map<String, List<ShrimpFractionExpressionInterface>> mapOfSpotsBySampleNames;
// ref mat
allRefMatShrimpFractions = squidProject.getTask().getReferenceMaterialSpots();
mapOfSpotsBySampleNames = new TreeMap<>();
mapOfSpotsBySampleNames.put("Ref Mat " + ((Task) squidProject.getTask()).getFilterForRefMatSpotNames(), squidProject.getTask().getReferenceMaterialSpots());
// need current physical constants for plotting of data
ParametersModel physicalConstantsModel = squidProject.getTask().getPhysicalConstantsModel();
// want plot choices sticky during execution
if (mapOfPlotsOfSpotSets == null) {
mapOfPlotsOfSpotSets = new TreeMap<>();
}
rootPlot = mapOfPlotsOfSpotSets.get("Ref Mat " + ((Task) squidProject.getTask()).getFilterForRefMatSpotNames() + xAxisExpressionName + yAxisExpressionName);
if (rootPlot == null) {
rootPlot = generateAnyTwoPlot(allRefMatShrimpFractions, physicalConstantsModel);
mapOfPlotsOfSpotSets.put("Ref Mat " + ((Task) squidProject.getTask()).getFilterForRefMatSpotNames() + xAxisExpressionName + yAxisExpressionName, rootPlot);
}
rootData = new ArrayList<>();
plot = rootPlot;
List<SampleTreeNodeInterface> fractionNodeDetails = new ArrayList<>();
// build out set of rootData for samples
CheckBoxTreeItem<SampleTreeNodeInterface> rootItem = new CheckBoxTreeItem<>(new SampleNode(fractionTypeSelected.getSpotTypeName()));
chosenSample = rootItem;
rootItem.setExpanded(true);
rootItem.setIndependent(true);
rootItem.setSelected(true);
rootItem.selectedProperty().addListener(new ChangeListener<Boolean>() {
@Override
public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
rootItem.getValue().setSelectedProperty(new SimpleBooleanProperty(newValue));
ObservableList<TreeItem<SampleTreeNodeInterface>> mySamples = rootItem.getChildren();
Iterator<TreeItem<SampleTreeNodeInterface>> mySamplesIterator = mySamples.iterator();
while (mySamplesIterator.hasNext()) {
CheckBoxTreeItem<SampleTreeNodeInterface> mySampleItem = (CheckBoxTreeItem<SampleTreeNodeInterface>) mySamplesIterator.next();
mySampleItem.setSelected(newValue);
}
try {
provisionAnyTwoToolbox(newValue);
} catch (SquidException squidException) {
}
}
});
rootItem.indeterminateProperty().addListener(new ChangeListener<Boolean>() {
@Override
public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
try {
provisionAnyTwoToolbox(newValue || rootItem.isSelected());
} catch (SquidException squidException) {
}
}
});
spotsTreeViewCheckBox.setRoot(rootItem);
spotsTreeViewCheckBox.setShowRoot((fractionTypeSelected.compareTo(SpotTypes.UNKNOWN) == 0));
for (Map.Entry<String, List<ShrimpFractionExpressionInterface>> entry : mapOfSpotsBySampleNames.entrySet()) {
CheckBoxTreeItem<SampleTreeNodeInterface> sampleItem = new CheckBoxTreeItem<>(new SampleNode(entry.getKey()));
sampleItem.setSelected(true);
rootItem.getChildren().add(sampleItem);
List<Map<String, Object>> myData = new ArrayList<>();
PlotDisplayInterface myPlotTry = mapOfPlotsOfSpotSets.get(sampleItem.getValue().getNodeName() + xAxisExpressionName + yAxisExpressionName);
if (myPlotTry == null) {
myPlotTry = generateAnyTwoPlot(entry.getValue(), physicalConstantsModel);
mapOfPlotsOfSpotSets.put(sampleItem.getValue().getNodeName() + xAxisExpressionName + yAxisExpressionName, myPlotTry);
}
// final for listener
final PlotDisplayInterface myPlot = myPlotTry;
for (ShrimpFractionExpressionInterface spot : entry.getValue()) {
SampleTreeNodeInterface fractionNode = new PlotAnyTwoFractionNode(spot, xAxisExpressionName, yAxisExpressionName);
if (((PlotAnyTwoFractionNode) fractionNode).isValid()) {
fractionNodeDetails.add(fractionNode);
// handles each spot
CheckBoxTreeItem<SampleTreeNodeInterface> checkBoxTreeSpotItem = new CheckBoxTreeItem<>(fractionNode);
sampleItem.getChildren().add(checkBoxTreeSpotItem);
checkBoxTreeSpotItem.setIndependent(false);
checkBoxTreeSpotItem.setSelected(fractionNode.getSelectedProperty().getValue());
myData.add(fractionNode.getDatum());
// this contains all samples at the tree top
rootData.add(fractionNode.getDatum());
checkBoxTreeSpotItem.selectedProperty().addListener(new ChangeListener<Boolean>() {
@Override
public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
checkBoxTreeSpotItem.getValue().setSelectedProperty(new SimpleBooleanProperty(newValue));
myPlot.setData(myData);
}
});
}
}
myPlot.setData(myData);
// this sample item contains all the spot item checkboxes
sampleItem.setIndependent(false);
sampleItem.setExpanded(fractionTypeSelected.compareTo(SpotTypes.REFERENCE_MATERIAL) == 0);
sampleItem.selectedProperty().addListener(new ChangeListener<Boolean>() {
@Override
public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
myPlot.setData(myData);
rootPlot.setData(rootData);
}
});
if (currentlyPlottedSampleTreeNode == null) {
currentlyPlottedSampleTreeNode = sampleItem;
}
}
rootPlot.setData(rootData);
fractionNodes = FXCollections.observableArrayList(fractionNodeDetails);
spotsTreeViewCheckBox.setCellFactory(cell -> new CheckBoxTreeCell<>((TreeItem<SampleTreeNodeInterface> item) -> item.getValue().getSelectedProperty(), new StringConverter<TreeItem<SampleTreeNodeInterface>>() {
@Override
public String toString(TreeItem<SampleTreeNodeInterface> object) {
SampleTreeNodeInterface item = object.getValue();
String nodeString = "";
try {
nodeString = item.getNodeName();
} catch (SquidException squidException) {
}
if ((object.getParent() != null) && !(item instanceof SampleNode)) {
double[][] expressionValues = item.getShrimpFraction().getTaskExpressionsEvaluationsPerSpotByField((fractionTypeSelected.compareTo(SpotTypes.REFERENCE_MATERIAL) == 0) ? PB4COR206_238AGE_RM : PB4COR206_238AGE);
double uncertainty = 0.0;
if (expressionValues[0].length > 1) {
uncertainty = expressionValues[0][1];
}
String ageOrValueSource = WeightedMeanPlot.makeAgeString(expressionValues[0][0], uncertainty);
try {
nodeString += " " + ageOrValueSource + " (" + squid3RoundedToSize(((Double) item.getDatum().get(X.getTitle())), 5) + ", " + squid3RoundedToSize(((Double) item.getDatum().get(Y.getTitle())), 5) + ")";
} catch (Exception e) {
}
}
return nodeString;
}
@Override
public TreeItem<SampleTreeNodeInterface> fromString(String string) {
throw new UnsupportedOperationException("Not supported yet.");
}
}));
spotListAnchorPane.getChildren().clear();
spotListAnchorPane.getChildren().add(spotsTreeViewCheckBox);
spotsTreeViewCheckBox.prefHeightProperty().bind(spotListAnchorPane.prefHeightProperty());
spotsTreeViewCheckBox.prefWidthProperty().bind(spotListAnchorPane.prefWidthProperty());
topsoilPlotsCheckBoxListener = (observable, oldValue, newValue) -> {
rootPlot.setData(rootData);
try {
if (newValue.getValue() instanceof SampleNode) {
if (newValue.getValue().getNodeName().equals(SpotTypes.UNKNOWN.getSpotTypeName())) {
plot = rootPlot;
} else if (chosenSample != newValue) {
plot = mapOfPlotsOfSpotSets.get(newValue.getValue().getNodeName() + xAxisExpressionName + yAxisExpressionName);
}
chosenSample = (CheckBoxTreeItem<SampleTreeNodeInterface>) newValue;
currentlyPlottedSampleTreeNode = chosenSample;
}
} catch (Exception e) {
}
refreshPlot();
};
spotsTreeViewCheckBox.getSelectionModel().selectedItemProperty().addListener(topsoilPlotsCheckBoxListener);
spotsTreeViewCheckBox.getSelectionModel().select(currentlyPlottedSampleTreeNode);
currentlyPlottedSampleTreeNode.setExpanded(true);
provisionAnyTwoToolbox(true);
}
use of org.cirdles.squid.tasks.Task in project Squid by CIRDLES.
the class PlotsController method showConcordiaPlotsOfUnknownsOrRefMat.
private void showConcordiaPlotsOfUnknownsOrRefMat() {
// may 2020 new approach per Nicole
if (vboxMaster.getChildren().get(0) instanceof ToolBoxNodeInterface) {
vboxMaster.getChildren().remove(0);
}
HBox toolBox = new ConcordiaControlNode(this);
vboxMaster.getChildren().add(0, toolBox);
spotsTreeViewCheckBox = new CheckTreeView<>();
spotsTreeViewCheckBox.setStyle(SPOT_TREEVIEW_CSS_STYLE_SPECS);
spotsTreeViewString.setStyle(SPOT_TREEVIEW_CSS_STYLE_SPECS);
final List<ShrimpFractionExpressionInterface> allUnknownOrRefMatShrimpFractions;
Map<String, List<ShrimpFractionExpressionInterface>> mapOfSpotsBySampleNames;
if (fractionTypeSelected.compareTo(SpotTypes.UNKNOWN) == 0) {
allUnknownOrRefMatShrimpFractions = squidProject.getTask().getUnknownSpots();
mapOfSpotsBySampleNames = squidProject.getTask().getMapOfUnknownsBySampleNames();
// case of sample names chosen
if (mapOfSpotsBySampleNames.size() > 1) {
mapOfSpotsBySampleNames.remove(SpotTypes.UNKNOWN.getSpotTypeName());
}
} else {
// ref mat
allUnknownOrRefMatShrimpFractions = squidProject.getTask().getReferenceMaterialSpots();
mapOfSpotsBySampleNames = new TreeMap<>();
mapOfSpotsBySampleNames.put("Ref Mat " + ((Task) squidProject.getTask()).getFilterForRefMatSpotNames(), squidProject.getTask().getReferenceMaterialSpots());
// mapOfSpotsBySampleNames.put("Concentration Ref Mat", squidProject.getTask().getConcentrationReferenceMaterialSpots());
// used to synchronize rejects between weighted mean and concordia
spotSummaryDetails = squidProject.getTask().getTaskExpressionsEvaluationsPerSpotSet().get(WTDAV_PREFIX + correction + calibrConstAgeBaseName + "_CalibConst");
}
// need current physical contants for plotting of concordia etc.
ParametersModel physicalConstantsModel = squidProject.getTask().getPhysicalConstantsModel();
rootPlot = generateConcordiaPlot(fractionTypeSelected.getSpotTypeName(), allUnknownOrRefMatShrimpFractions, physicalConstantsModel);
rootData = new ArrayList<>();
List<SampleTreeNodeInterface> fractionNodeDetails = new ArrayList<>();
// build out set of rootData for samples
CheckBoxTreeItem<SampleTreeNodeInterface> rootItem = new CheckBoxTreeItem<>(new SampleNode(fractionTypeSelected.getSpotTypeName()));
chosenSample = rootItem;
rootItem.setExpanded(true);
rootItem.setIndependent(true);
rootItem.setSelected(true);
rootItem.selectedProperty().addListener(new ChangeListener<Boolean>() {
@Override
public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
rootItem.getValue().setSelectedProperty(new SimpleBooleanProperty(newValue));
ObservableList<TreeItem<SampleTreeNodeInterface>> mySamples = rootItem.getChildren();
Iterator<TreeItem<SampleTreeNodeInterface>> mySamplesIterator = mySamples.iterator();
while (mySamplesIterator.hasNext()) {
CheckBoxTreeItem<SampleTreeNodeInterface> mySampleItem = (CheckBoxTreeItem<SampleTreeNodeInterface>) mySamplesIterator.next();
mySampleItem.setSelected(newValue);
}
plot = rootPlot;
plot.setData(rootData);
}
});
spotsTreeViewCheckBox.setRoot(rootItem);
spotsTreeViewCheckBox.setShowRoot((fractionTypeSelected.compareTo(SpotTypes.UNKNOWN) == 0));
// want plot choices sticky during execution
if (mapOfPlotsOfSpotSets == null) {
mapOfPlotsOfSpotSets = new TreeMap<>();
}
for (Map.Entry<String, List<ShrimpFractionExpressionInterface>> entry : mapOfSpotsBySampleNames.entrySet()) {
CheckBoxTreeItem<SampleTreeNodeInterface> sampleItem = new CheckBoxTreeItem<>(new SampleNode(entry.getKey()));
sampleItem.setSelected(true);
rootItem.getChildren().add(sampleItem);
if (currentlyPlottedSampleTreeNode == null) {
currentlyPlottedSampleTreeNode = sampleItem;
}
List<Map<String, Object>> myData = new ArrayList<>();
PlotDisplayInterface myPlotTry = mapOfPlotsOfSpotSets.get(entry.getKey() + topsoilPlotFlavor);
if (myPlotTry == null) {
myPlotTry = generateConcordiaPlot(entry.getKey(), entry.getValue(), physicalConstantsModel);
mapOfPlotsOfSpotSets.put(entry.getKey() + topsoilPlotFlavor, myPlotTry);
}
// final for listener
final PlotDisplayInterface myPlot = myPlotTry;
for (ShrimpFractionExpressionInterface spot : entry.getValue()) {
SampleTreeNodeInterface fractionNode = new ConcordiaFractionNode(topsoilPlotFlavor, spot, correction);
if (((ConcordiaFractionNode) fractionNode).isValid()) {
fractionNodeDetails.add(fractionNode);
// handles each spot
CheckBoxTreeItem<SampleTreeNodeInterface> checkBoxTreeSpotItem = new CheckBoxTreeItem<>(fractionNode);
sampleItem.getChildren().add(checkBoxTreeSpotItem);
// for ref material synchronize rejects
if (doSynchIncludedSpotsBetweenConcordiaAndWM && (fractionTypeSelected.compareTo(SpotTypes.REFERENCE_MATERIAL) == 0)) {
fractionNode.setSelectedProperty(new SimpleBooleanProperty(!spotSummaryDetails.getRejectedIndices()[entry.getValue().indexOf(spot)]));
}
checkBoxTreeSpotItem.setIndependent(false);
checkBoxTreeSpotItem.setSelected(fractionNode.getSelectedProperty().getValue());
myData.add(fractionNode.getDatum());
// this contains all samples at the tree top
rootData.add(fractionNode.getDatum());
checkBoxTreeSpotItem.selectedProperty().addListener(new ChangeListener<Boolean>() {
@Override
public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
checkBoxTreeSpotItem.getValue().setSelectedProperty(new SimpleBooleanProperty(newValue));
myPlot.setData(myData);
}
});
}
}
myPlot.setData(myData);
// this sample item contains all the spot item checkboxes
sampleItem.setIndependent(false);
sampleItem.setExpanded(fractionTypeSelected.compareTo(SpotTypes.REFERENCE_MATERIAL) == 0);
sampleItem.selectedProperty().addListener(new ChangeListener<Boolean>() {
@Override
public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
myPlot.setData(myData);
rootPlot.setData(rootData);
}
});
if (currentlyPlottedSampleTreeNode == null) {
currentlyPlottedSampleTreeNode = sampleItem;
}
}
rootPlot.setData(rootData);
fractionNodes = FXCollections.observableArrayList(fractionNodeDetails);
spotsTreeViewCheckBox.setCellFactory(cell -> new CheckBoxTreeCell<>((TreeItem<SampleTreeNodeInterface> item) -> item.getValue().getSelectedProperty(), new StringConverter<TreeItem<SampleTreeNodeInterface>>() {
@Override
public String toString(TreeItem<SampleTreeNodeInterface> object) {
SampleTreeNodeInterface item = object.getValue();
String nodeString = "";
try {
nodeString = item.getNodeName();
} catch (SquidException squidException) {
}
if ((object.getParent() != null) && !(item instanceof SampleNode)) {
double[][] expressionValues = item.getShrimpFraction().getTaskExpressionsEvaluationsPerSpotByField((fractionTypeSelected.compareTo(SpotTypes.REFERENCE_MATERIAL) == 0) ? PB4COR206_238AGE_RM : PB4COR206_238AGE);
double uncertainty = 0.0;
if (expressionValues[0].length > 1) {
uncertainty = expressionValues[0][1];
}
String ageOrValueSource = WeightedMeanPlot.makeAgeString(expressionValues[0][0], uncertainty);
nodeString += " " + ageOrValueSource;
}
return nodeString;
}
@Override
public TreeItem<SampleTreeNodeInterface> fromString(String string) {
throw new UnsupportedOperationException("Not supported yet.");
}
}));
spotListAnchorPane.getChildren().clear();
spotListAnchorPane.getChildren().add(spotsTreeViewCheckBox);
spotsTreeViewCheckBox.prefHeightProperty().bind(spotListAnchorPane.prefHeightProperty());
spotsTreeViewCheckBox.prefWidthProperty().bind(spotListAnchorPane.prefWidthProperty());
// dec 2018 improvement suggested by Nicole Rayner to use checkboxes to select members
// thus selecting tree item displays it and checkbox (see above) for a sample will
// allow toggling of all spots
topsoilPlotsCheckBoxListener = (observable, oldValue, newValue) -> {
rootPlot.setData(rootData);
try {
if (newValue.getValue() instanceof SampleNode) {
if (newValue.getValue().getNodeName().equals(SpotTypes.UNKNOWN.getSpotTypeName())) {
plot = rootPlot;
} else if (chosenSample != newValue) {
plot = mapOfPlotsOfSpotSets.get(newValue.getValue().getNodeName() + topsoilPlotFlavor);
}
chosenSample = (CheckBoxTreeItem<SampleTreeNodeInterface>) newValue;
currentlyPlottedSampleTreeNode = chosenSample;
}
} catch (Exception e) {
}
refreshPlot();
};
spotsTreeViewCheckBox.getSelectionModel().selectedItemProperty().addListener(topsoilPlotsCheckBoxListener);
refreshPlot();
spotsTreeViewCheckBox.getSelectionModel().select(currentlyPlottedSampleTreeNode);
currentlyPlottedSampleTreeNode.setExpanded(true);
}
use of org.cirdles.squid.tasks.Task in project Squid by CIRDLES.
the class ExpressionBuilderController method updateEditor.
public void updateEditor() {
if (selectedExpression.isNotNull().get()) {
Expression exp;
if (selectedExpressionIsEditable.get()) {
exp = makeExpression(expressionNameTextField.getText(), expressionString.get());
} else {
exp = selectedExpression.get();
}
((Task) task).evaluateTaskExpression(exp.getExpressionTree());
boolean localAmHealthy = exp.amHealthy() && (exp.getName().length() > 0);
auditTextArea.setText(customizeExpressionTreeAudit(exp));
auditPane.setTextFill(localAmHealthy ? Paint.valueOf("black") : Paint.valueOf("red"));
auditPane.setText(localAmHealthy ? "Audit" : "Audit - ALERT !!!" + ((exp.getName().length() == 0) ? " Expression needs name" : ""));
auditPane.setGraphic(localAmHealthy ? new ImageView(HEALTHY) : new ImageView(UNHEALTHY));
((ImageView) auditPane.getGraphic()).setFitHeight(16);
((ImageView) auditPane.getGraphic()).setFitWidth(16);
graphExpressionTree(exp.getExpressionTree());
populatePeeks(exp);
} else {
graphExpressionTree(null);
auditTextArea.setText("");
rmPeekTextArea.setText("");
unPeekTextArea.setText("");
}
}
use of org.cirdles.squid.tasks.Task in project Squid by CIRDLES.
the class RefMatWeightedMeanToolBoxNode method samplesVBox.
private VBox samplesVBox() {
VBox sampleNameToolBox = new VBox(0);
Label sampleInfoLabel = new Label("Reference Material:");
formatNode(sampleInfoLabel, 125);
mapOfSpotsBySampleNames = ((Task) squidProject.getTask()).produceMapOfRefMatSpotsNames();
formatNode(sampleComboBox, 100);
sampleComboBox.setItems(FXCollections.observableArrayList(((Task) squidProject.getTask()).getFilterForRefMatSpotNames()));
sampleComboBox.valueProperty().addListener((observable, oldValue, newValue) -> {
try {
displaySample(newValue);
} catch (SquidException squidException) {
}
});
sampleNameToolBox.getChildren().addAll(sampleInfoLabel, sampleComboBox);
return sampleNameToolBox;
}
Aggregations