Example usage for javafx.beans.property SimpleStringProperty SimpleStringProperty

Introduction

In this page you can find the example usage for javafx.beans.property SimpleStringProperty SimpleStringProperty.

Prototype

public SimpleStringProperty(String initialValue) 

Source Link

Document

The constructor of StringProperty

Usage

From source file:de.ks.idnadrev.information.chart.ChartDataEditor.java

public void reset() {
    dataContainer.getChildren().clear();
    dataContainer.getChildren().remove(xaxisTitle);//FXML loader doesn't set row and column in gridpane :(
    dataContainer.add(xaxisTitle, 0, 0);

    rows.clear();//from   w w  w .j a  va  2 s. c om
    columnHeaders.clear();
    categoryEditors.clear();
    valueEditors.clear();
    headers.clear();

    rows.add(new ChartRow());
    columnHeaders.add(new SimpleStringProperty(Localized.get("col", 1)));
    columnHeaders.add(new SimpleStringProperty(Localized.get("col", 2)));
    if (callback != null) {
        callback.accept(getData());
    }
}

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From source file:com.ggvaidya.scinames.model.Project.java

public Project(String projectName, File projectFile) {
    this.projectName = new SimpleStringProperty(projectName);
    this.projectFile = new SimpleObjectProperty<>(projectFile);
}

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From source file:UI.MainStageController.java

/**
 * shows the correlation table in the analysis view
 *///  www .j  a v  a 2 s  . co  m
@FXML
private void displayCorrelationTable() {
    //Delete whatever's been in the table before
    TableView<String[]> analysisTable = new TableView<>();

    //We want to display correlations and p-Values of every node combination
    double[][] correlationMatrix = AnalysisData.getCorrelationMatrix().getData();
    double[][] pValueMatrix = AnalysisData.getPValueMatrix().getData();
    LinkedList<TaxonNode> taxonList = SampleComparison.getUnifiedTaxonList(LoadedData.getSamplesToAnalyze(),
            AnalysisData.getLevelOfAnalysis());

    //Table will consist of strings
    String[][] tableValues = new String[correlationMatrix.length][correlationMatrix[0].length + 1];

    //Add the values as formatted strings
    for (int i = 0; i < tableValues.length; i++) {
        tableValues[i][0] = taxonList.get(i).getName();
        for (int j = 1; j < tableValues[0].length; j++) {
            tableValues[i][j] = String.format("%.3f", correlationMatrix[i][j - 1]).replace(",", ".") + "\n("
                    + String.format("%.2f", pValueMatrix[i][j - 1]).replace(",", ".") + ")";
        }
    }

    for (int i = 0; i < tableValues[0].length; i++) {
        String columnTitle;
        if (i > 0) {
            columnTitle = taxonList.get(i - 1).getName();
        } else {
            columnTitle = "";
        }
        TableColumn<String[], String> column = new TableColumn<>(columnTitle);
        final int columnIndex = i;
        column.setCellValueFactory(cellData -> {
            String[] row = cellData.getValue();
            return new SimpleStringProperty(row[columnIndex]);
        });
        analysisTable.getColumns().add(column);

        //First column contains taxon names and should be italic
        if (i == 0)
            column.setStyle("-fx-font-style:italic;");
    }

    for (int i = 0; i < tableValues.length; i++) {
        analysisTable.getItems().add(tableValues[i]);
    }

    //Display table on a new stage
    Stage tableStage = new Stage();
    tableStage.setTitle("Correlation Table");
    BorderPane tablePane = new BorderPane();
    Button exportCorrelationsButton = new Button("Save correlation table to CSV");
    Button exportPValuesButton = new Button("Save p-value table to CSV");
    exportCorrelationsButton.setOnAction(e -> exportTableToCSV(tableValues, false));
    exportPValuesButton.setOnAction(e -> exportTableToCSV(tableValues, true));
    HBox exportBox = new HBox(exportCorrelationsButton, exportPValuesButton);
    exportBox.setPadding(new Insets(10));
    exportBox.setSpacing(10);
    tablePane.setTop(exportBox);
    tablePane.setCenter(analysisTable);
    Scene tableScene = new Scene(tablePane);
    tableStage.setScene(tableScene);
    tableStage.show();
}

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From source file:gov.va.isaac.gui.refexViews.refexEdit.AddSememePopup.java

private void buildDataFields(boolean assemblageValid, DynamicSememeDataBI[] currentValues) {
    if (assemblageValid) {
        for (ReadOnlyStringProperty ssp : currentDataFieldWarnings_) {
            allValid_.removeBinding(ssp);
        }/*from   w  ww . ja  v a 2s .  c o  m*/
        currentDataFieldWarnings_.clear();
        for (SememeGUIDataTypeNodeDetails nd : currentDataFields_) {
            nd.cleanupListener();
        }
        currentDataFields_.clear();

        GridPane gp = new GridPane();
        gp.setHgap(10.0);
        gp.setVgap(10.0);
        gp.setStyle("-fx-padding: 5;");
        int row = 0;
        boolean extraInfoColumnIsRequired = false;
        for (DynamicSememeColumnInfo ci : assemblageInfo_.getColumnInfo()) {
            SimpleStringProperty valueIsRequired = (ci.isColumnRequired() ? new SimpleStringProperty("")
                    : null);
            SimpleStringProperty defaultValueTooltip = ((ci.getDefaultColumnValue() == null
                    && ci.getValidator() == null) ? null : new SimpleStringProperty());
            ComboBox<DynamicSememeDataType> polymorphicType = null;

            Label l = new Label(ci.getColumnName());
            l.getStyleClass().add("boldLabel");
            l.setMinWidth(FxUtils.calculateNecessaryWidthOfBoldLabel(l));
            Tooltip.install(l, new Tooltip(ci.getColumnDescription()));
            int col = 0;
            gp.add(l, col++, row);

            if (ci.getColumnDataType() == DynamicSememeDataType.POLYMORPHIC) {
                polymorphicType = new ComboBox<>();
                polymorphicType.setEditable(false);
                polymorphicType.setConverter(new StringConverter<DynamicSememeDataType>() {

                    @Override
                    public String toString(DynamicSememeDataType object) {
                        return object.getDisplayName();
                    }

                    @Override
                    public DynamicSememeDataType fromString(String string) {
                        throw new RuntimeException("unecessary");
                    }
                });
                for (DynamicSememeDataType type : DynamicSememeDataType.values()) {
                    if (type == DynamicSememeDataType.POLYMORPHIC || type == DynamicSememeDataType.UNKNOWN) {
                        continue;
                    } else {
                        polymorphicType.getItems().add(type);
                    }
                }
                polymorphicType.getSelectionModel()
                        .select((currentValues == null ? DynamicSememeDataType.STRING
                                : (currentValues[row] == null ? DynamicSememeDataType.STRING
                                        : currentValues[row].getDynamicSememeDataType())));
            }

            SememeGUIDataTypeNodeDetails nd = SememeGUIDataTypeFXNodeBuilder.buildNodeForType(
                    ci.getColumnDataType(), ci.getDefaultColumnValue(),
                    (currentValues == null ? null : currentValues[row]), valueIsRequired, defaultValueTooltip,
                    (polymorphicType == null ? null
                            : polymorphicType.getSelectionModel().selectedItemProperty()),
                    allValid_, ci.getValidator(), ci.getValidatorData());

            currentDataFieldWarnings_.addAll(nd.getBoundToAllValid());
            if (ci.getColumnDataType() == DynamicSememeDataType.POLYMORPHIC) {
                nd.addUpdateParentListListener(currentDataFieldWarnings_);
            }

            currentDataFields_.add(nd);

            gp.add(nd.getNodeForDisplay(), col++, row);

            Label colType = new Label(ci.getColumnDataType().getDisplayName());
            colType.setMinWidth(FxUtils.calculateNecessaryWidthOfLabel(colType));
            gp.add((polymorphicType == null ? colType : polymorphicType), col++, row);

            if (ci.isColumnRequired() || ci.getDefaultColumnValue() != null || ci.getValidator() != null) {
                extraInfoColumnIsRequired = true;

                StackPane stackPane = new StackPane();
                stackPane.setMaxWidth(Double.MAX_VALUE);

                if (ci.getDefaultColumnValue() != null || ci.getValidator() != null) {
                    ImageView information = Images.INFORMATION.createImageView();
                    Tooltip tooltip = new Tooltip();
                    tooltip.textProperty().bind(defaultValueTooltip);
                    Tooltip.install(information, tooltip);
                    tooltip.setAutoHide(true);
                    information.setOnMouseClicked(
                            event -> tooltip.show(information, event.getScreenX(), event.getScreenY()));
                    stackPane.getChildren().add(information);
                }

                if (ci.isColumnRequired()) {
                    ImageView exclamation = Images.EXCLAMATION.createImageView();

                    final BooleanProperty showExclamation = new SimpleBooleanProperty(
                            StringUtils.isNotBlank(valueIsRequired.get()));
                    valueIsRequired.addListener((ChangeListener<String>) (observable, oldValue,
                            newValue) -> showExclamation.set(StringUtils.isNotBlank(newValue)));

                    exclamation.visibleProperty().bind(showExclamation);
                    Tooltip tooltip = new Tooltip();
                    tooltip.textProperty().bind(valueIsRequired);
                    Tooltip.install(exclamation, tooltip);
                    tooltip.setAutoHide(true);

                    exclamation.setOnMouseClicked(
                            event -> tooltip.show(exclamation, event.getScreenX(), event.getScreenY()));
                    stackPane.getChildren().add(exclamation);
                }

                gp.add(stackPane, col++, row);
            }
            row++;
        }

        ColumnConstraints cc = new ColumnConstraints();
        cc.setHgrow(Priority.NEVER);
        gp.getColumnConstraints().add(cc);

        cc = new ColumnConstraints();
        cc.setHgrow(Priority.ALWAYS);
        gp.getColumnConstraints().add(cc);

        cc = new ColumnConstraints();
        cc.setHgrow(Priority.NEVER);
        gp.getColumnConstraints().add(cc);

        if (extraInfoColumnIsRequired) {
            cc = new ColumnConstraints();
            cc.setHgrow(Priority.NEVER);
            gp.getColumnConstraints().add(cc);
        }

        if (row == 0) {
            sp_.setContent(new Label("This assemblage does not allow data fields"));
        } else {
            sp_.setContent(gp);
        }
        allValid_.invalidate();
    } else {
        sp_.setContent(null);
    }
}

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From source file:gov.va.isaac.gui.refexViews.refexEdit.AddRefexPopup.java

private void buildDataFields(boolean assemblageValid, RefexDynamicDataBI[] currentValues) {
    if (assemblageValid) {
        for (ReadOnlyStringProperty ssp : currentDataFieldWarnings_) {
            allValid_.removeBinding(ssp);
        }//from  w w w. j  av a2s .  c  o  m
        currentDataFieldWarnings_.clear();
        for (RefexDataTypeNodeDetails nd : currentDataFields_) {
            nd.cleanupListener();
        }
        currentDataFields_.clear();

        GridPane gp = new GridPane();
        gp.setHgap(10.0);
        gp.setVgap(10.0);
        gp.setStyle("-fx-padding: 5;");
        int row = 0;
        boolean extraInfoColumnIsRequired = false;
        for (RefexDynamicColumnInfo ci : assemblageInfo_.getColumnInfo()) {
            SimpleStringProperty valueIsRequired = (ci.isColumnRequired() ? new SimpleStringProperty("")
                    : null);
            SimpleStringProperty defaultValueTooltip = ((ci.getDefaultColumnValue() == null
                    && ci.getValidator() == null) ? null : new SimpleStringProperty());
            ComboBox<RefexDynamicDataType> polymorphicType = null;

            Label l = new Label(ci.getColumnName());
            l.getStyleClass().add("boldLabel");
            l.setMinWidth(FxUtils.calculateNecessaryWidthOfBoldLabel(l));
            Tooltip.install(l, new Tooltip(ci.getColumnDescription()));
            int col = 0;
            gp.add(l, col++, row);

            if (ci.getColumnDataType() == RefexDynamicDataType.POLYMORPHIC) {
                polymorphicType = new ComboBox<>();
                polymorphicType.setEditable(false);
                polymorphicType.setConverter(new StringConverter<RefexDynamicDataType>() {

                    @Override
                    public String toString(RefexDynamicDataType object) {
                        return object.getDisplayName();
                    }

                    @Override
                    public RefexDynamicDataType fromString(String string) {
                        throw new RuntimeException("unecessary");
                    }
                });
                for (RefexDynamicDataType type : RefexDynamicDataType.values()) {
                    if (type == RefexDynamicDataType.POLYMORPHIC || type == RefexDynamicDataType.UNKNOWN) {
                        continue;
                    } else {
                        polymorphicType.getItems().add(type);
                    }
                }
                polymorphicType.getSelectionModel()
                        .select((currentValues == null ? RefexDynamicDataType.STRING
                                : (currentValues[row] == null ? RefexDynamicDataType.STRING
                                        : currentValues[row].getRefexDataType())));
            }

            RefexDataTypeNodeDetails nd = RefexDataTypeFXNodeBuilder.buildNodeForType(ci.getColumnDataType(),
                    ci.getDefaultColumnValue(), (currentValues == null ? null : currentValues[row]),
                    valueIsRequired, defaultValueTooltip,
                    (polymorphicType == null ? null
                            : polymorphicType.getSelectionModel().selectedItemProperty()),
                    allValid_, new SimpleObjectProperty<>(ci.getValidator()),
                    new SimpleObjectProperty<>(ci.getValidatorData()));

            currentDataFieldWarnings_.addAll(nd.getBoundToAllValid());
            if (ci.getColumnDataType() == RefexDynamicDataType.POLYMORPHIC) {
                nd.addUpdateParentListListener(currentDataFieldWarnings_);
            }

            currentDataFields_.add(nd);

            gp.add(nd.getNodeForDisplay(), col++, row);

            Label colType = new Label(ci.getColumnDataType().getDisplayName());
            colType.setMinWidth(FxUtils.calculateNecessaryWidthOfLabel(colType));
            gp.add((polymorphicType == null ? colType : polymorphicType), col++, row);

            if (ci.isColumnRequired() || ci.getDefaultColumnValue() != null || ci.getValidator() != null) {
                extraInfoColumnIsRequired = true;

                StackPane stackPane = new StackPane();
                stackPane.setMaxWidth(Double.MAX_VALUE);

                if (ci.getDefaultColumnValue() != null || ci.getValidator() != null) {
                    ImageView information = Images.INFORMATION.createImageView();
                    Tooltip tooltip = new Tooltip();
                    tooltip.textProperty().bind(defaultValueTooltip);
                    Tooltip.install(information, tooltip);
                    tooltip.setAutoHide(true);
                    information.setOnMouseClicked(
                            event -> tooltip.show(information, event.getScreenX(), event.getScreenY()));
                    stackPane.getChildren().add(information);
                }

                if (ci.isColumnRequired()) {
                    ImageView exclamation = Images.EXCLAMATION.createImageView();

                    final BooleanProperty showExclamation = new SimpleBooleanProperty(
                            StringUtils.isNotBlank(valueIsRequired.get()));
                    valueIsRequired.addListener((ChangeListener<String>) (observable, oldValue,
                            newValue) -> showExclamation.set(StringUtils.isNotBlank(newValue)));

                    exclamation.visibleProperty().bind(showExclamation);
                    Tooltip tooltip = new Tooltip();
                    tooltip.textProperty().bind(valueIsRequired);
                    Tooltip.install(exclamation, tooltip);
                    tooltip.setAutoHide(true);

                    exclamation.setOnMouseClicked(
                            event -> tooltip.show(exclamation, event.getScreenX(), event.getScreenY()));
                    stackPane.getChildren().add(exclamation);
                }

                gp.add(stackPane, col++, row);
            }
            row++;
        }

        ColumnConstraints cc = new ColumnConstraints();
        cc.setHgrow(Priority.NEVER);
        gp.getColumnConstraints().add(cc);

        cc = new ColumnConstraints();
        cc.setHgrow(Priority.ALWAYS);
        gp.getColumnConstraints().add(cc);

        cc = new ColumnConstraints();
        cc.setHgrow(Priority.NEVER);
        gp.getColumnConstraints().add(cc);

        if (extraInfoColumnIsRequired) {
            cc = new ColumnConstraints();
            cc.setHgrow(Priority.NEVER);
            gp.getColumnConstraints().add(cc);
        }

        if (row == 0) {
            sp_.setContent(new Label("This assemblage does not allow data fields"));
        } else {
            sp_.setContent(gp);
        }
        allValid_.invalidate();
    } else {
        sp_.setContent(null);
    }
}

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From source file:qupath.lib.gui.panels.survival.KaplanMeierDisplay.java

@SuppressWarnings("unchecked")
private void generatePlot() {

    KaplanMeierDisplay.ScoreData newScoreData = scoreData;

    // If we have a hierarchy, update the scores with the most recent data
    if (hierarchy != null) {
        List<TMACoreObject> cores = PathObjectTools.getTMACoreObjects(hierarchy, false);
        double[] survival = new double[cores.size()];
        boolean[] censored = new boolean[cores.size()];
        double[] scores = new double[cores.size()];

        //            // Optionally sort by scores... helps a bit when debugging e.g. p-values, Hazard ratios etc.
        //            cores.sort((c1, c2) -> Double.compare(c1.getMeasurementList().getMeasurementValue(scoreColumn), c2.getMeasurementList().getMeasurementValue(scoreColumn)));

        //            scoreColumn = "Positive %";
        //         scoreColumn = "RoughScore";
        for (int i = 0; i < cores.size(); i++) {
            TMACoreObject core = cores.get(i);
            MeasurementList ml = core.getMeasurementList();
            survival[i] = core.getMeasurementList().getMeasurementValue(survivalColumn);
            double censoredValue = core.getMeasurementList().getMeasurementValue(censoredColumn);
            boolean hasCensoredValue = !Double.isNaN(censoredValue)
                    && (censoredValue == 0 || censoredValue == 1);
            censored[i] = censoredValue != 0;
            if (!hasCensoredValue) {
                // If we don't have a censored value, ensure we mask out everything else
                scores[i] = Double.NaN;
                survival[i] = Double.NaN;
            } else if (ml.containsNamedMeasurement(scoreColumn))
                // Get the score if we can
                scores[i] = ml.getMeasurementValue(scoreColumn);
            else {
                //               // Try to compute score if we need to
                //               Map<String, Number> map = ROIMeaningfulMeasurements.getPathClassSummaryMeasurements(core.getChildObjects(), true);
                //               Number value = map.get(scoreColumn);
                //               if (value == null)
                scores[i] = Double.NaN;
                //               else
                //                  scores[i] = value.doubleValue();
            }/*from  w ww  . j a  v  a  2 s  .co m*/
        }
        // Mask out any scores that don't have associated survival data
        for (int i = 0; i < survival.length; i++) {
            if (Double.isNaN(survival[i]))
                scores[i] = Double.NaN;
        }

        newScoreData = new ScoreData(scores, survival, censored);

    }

    if (newScoreData == null || newScoreData.scores.length == 0)
        return;

    //         KaplanMeier kmHigh = new KaplanMeier("Above threshold");
    //         KaplanMeier kmLow = new KaplanMeier("Below threshold");

    double[] quartiles = StatisticsHelper.getQuartiles(newScoreData.scores);
    double q1 = quartiles[0];
    double median = quartiles[1];
    double q3 = quartiles[2];
    double[] thresholds;
    if (params != null) {
        Object thresholdMethod = params.getChoiceParameterValue("scoreThresholdMethod");
        if (thresholdMethod.equals("Median")) {
            //               panelParams.setNumericParameterValue("scoreThreshold", median);
            //               ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG!
            thresholds = new double[] { median };
        } else if (thresholdMethod.equals("Tertiles")) {
            //                  ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG!
            thresholds = StatisticsHelper.getTertiles(newScoreData.scores);
        } else if (thresholdMethod.equals("Quartiles")) {
            //               ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG!
            thresholds = new double[] { q1, median, q3 };
        } else if (thresholdMethod.equals("Manual (1)")) {
            thresholds = new double[] { params.getDoubleParameterValue("threshold1") };
        } else if (thresholdMethod.equals("Manual (2)")) {
            thresholds = new double[] { params.getDoubleParameterValue("threshold1"),
                    params.getDoubleParameterValue("threshold2") };
        } else //if (thresholdMethod.equals("Manual (3)")) {
            thresholds = new double[] { params.getDoubleParameterValue("threshold1"),
                    params.getDoubleParameterValue("threshold2"),
                    params.getDoubleParameterValue("threshold3") };
    } else
        thresholds = new double[] { median };

    double minVal = Double.POSITIVE_INFINITY;
    double maxVal = Double.NEGATIVE_INFINITY;
    int numNonNaN = 0;
    for (double d : newScoreData.scores) {
        if (Double.isNaN(d))
            continue;
        if (d < minVal)
            minVal = d;
        if (d > maxVal)
            maxVal = d;
        numNonNaN++;
    }
    boolean scoresValid = maxVal > minVal; // If not this, we don't have valid scores that we can work with

    double maxTimePoint = 0;
    for (double d : newScoreData.survival) {
        if (Double.isNaN(d))
            continue;
        if (d > maxTimePoint)
            maxTimePoint = d;
    }
    if (panelParams != null
            && maxTimePoint > ((IntParameter) params.getParameters().get("censorTimePoints")).getUpperBound()) {
        panelParams.setNumericParameterValueRange("censorTimePoints", 0, Math.ceil(maxTimePoint));
    }

    // Optionally censor at specified time
    double censorThreshold = params == null ? maxTimePoint : params.getIntParameterValue("censorTimePoints");

    // Compute log-rank p-values for *all* possible thresholds
    // Simultaneously determine the threshold that yields the lowest p-value, 
    // resolving ties in favour of a more even split between high/low numbers of events
    boolean pValuesChanged = false;
    if (calculateAllPValues) {
        if (!(pValues != null && pValueThresholds != null && newScoreData.equals(scoreData)
                && censorThreshold == lastPValueCensorThreshold)) {
            Map<Double, Double> mapLogRank = new TreeMap<>();
            Set<Double> setObserved = new HashSet<>();
            for (int i = 0; i < newScoreData.scores.length; i++) {
                Double d = newScoreData.scores[i];
                boolean observed = !newScoreData.censored[i] && newScoreData.survival[i] < censorThreshold;
                if (observed)
                    setObserved.add(d);
                if (mapLogRank.containsKey(d))
                    continue;
                List<KaplanMeierData> kmsTemp = splitByThresholds(newScoreData, new double[] { d },
                        censorThreshold, false);
                //               if (kmsTemp.get(1).nObserved() == 0 || kmsTemp.get(1).nObserved() == 0)
                //                  continue;
                LogRankResult test = LogRankTest.computeLogRankTest(kmsTemp.get(0), kmsTemp.get(1));
                double pValue = test.getPValue();
                //                  double pValue = test.hazardRatio < 1 ? test.hazardRatio : 1.0/test.hazardRatio; // Checking usefulness of Hazard ratios...
                if (!Double.isFinite(pValue))
                    continue;
                //               if (!Double.isFinite(test.getHazardRatio())) {
                ////                  continue;
                //                  pValue = Double.NaN;
                //               }
                mapLogRank.put(d, pValue);
            }
            pValueThresholds = new double[mapLogRank.size()];
            pValues = new double[mapLogRank.size()];
            pValueThresholdsObserved = new boolean[mapLogRank.size()];
            int count = 0;
            for (Entry<Double, Double> entry : mapLogRank.entrySet()) {
                pValueThresholds[count] = entry.getKey();
                pValues[count] = entry.getValue();
                if (setObserved.contains(entry.getKey()))
                    pValueThresholdsObserved[count] = true;
                count++;
            }

            // Find the longest 'significant' stretch
            int maxSigCount = 0;
            int maxSigInd = -1;
            int sigCurrent = 0;
            int[] sigCount = new int[pValues.length];
            for (int i = 0; i < pValues.length; i++) {
                if (pValues[i] < 0.05) {
                    sigCurrent++;
                    sigCount[i] = sigCurrent;
                    if (sigCurrent > maxSigCount) {
                        maxSigCount = sigCurrent;
                        maxSigInd = i;
                    }
                } else
                    sigCurrent = 0;
            }
            if (maxSigCount == 0) {
                logger.info("No p-values < 0.05");
            } else {
                double minThresh = maxSigInd - maxSigCount < 0 ? pValueThresholds[0] - 0.0000001
                        : pValueThresholds[maxSigInd - maxSigCount];
                double maxThresh = pValueThresholds[maxSigInd];
                int nBetween = 0;
                int nBetweenObserved = 0;
                for (int i = 0; i < newScoreData.scores.length; i++) {
                    if (newScoreData.scores[i] > minThresh && newScoreData.scores[i] <= maxThresh) {
                        nBetween++;
                        if (newScoreData.survival[i] < censorThreshold && !newScoreData.censored[i])
                            nBetweenObserved++;
                    }
                }
                logger.info("Longest stretch of p-values < 0.05: {} - {} ({} entries, {} observed)", minThresh,
                        maxThresh, nBetween, nBetweenObserved);
            }

            pValuesSmoothed = new double[pValues.length];
            Arrays.fill(pValuesSmoothed, Double.NaN);
            int n = (pValues.length / 20) * 2 + 1;
            logger.info("Smoothing log-rank test p-values by " + n);
            for (int i = n / 2; i < pValues.length - n / 2; i++) {
                double sum = 0;
                for (int k = i - n / 2; k < i - n / 2 + n; k++) {
                    sum += pValues[k];
                }
                pValuesSmoothed[i] = sum / n;
            }
            //               for (int i = 0; i < pValues.length; i++) {
            //                  double sum = 0;
            //                  for (int k = Math.max(0, i-n/2); k < Math.min(pValues.length, i-n/2+n); k++) {
            //                     sum += pValues[k];
            //                  }
            //                  pValuesSmoothed[i] = sum/n;
            //               }
            //               pValues = pValuesSmoothed;

            lastPValueCensorThreshold = censorThreshold;
            pValuesChanged = true;
        }
    } else {
        lastPValueCensorThreshold = Double.NaN;
        pValueThresholds = null;
        pValues = null;
    }

    //            if (params != null && !Double.isNaN(bestThreshold) && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value")))
    if (params != null && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value"))) {
        int bestIdx = -1;
        double bestPValue = Double.POSITIVE_INFINITY;
        for (int i = pValueThresholds.length / 10; i < pValueThresholds.length * 9 / 10; i++) {
            if (pValues[i] < bestPValue) {
                bestIdx = i;
                bestPValue = pValues[i];
            }
        }
        thresholds = bestIdx >= 0 ? new double[] { pValueThresholds[bestIdx] } : new double[0];
    } else if (params != null
            && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest smoothed p-value"))) {
        int bestIdx = -1;
        double bestPValue = Double.POSITIVE_INFINITY;
        for (int i = pValueThresholds.length / 10; i < pValueThresholds.length * 9 / 10; i++) {
            if (pValuesSmoothed[i] < bestPValue) {
                bestIdx = i;
                bestPValue = pValuesSmoothed[i];
            }
        }
        thresholds = bestIdx >= 0 ? new double[] { pValueThresholds[bestIdx] } : new double[0];
    }

    // Split into different curves using the provided thresholds
    List<KaplanMeierData> kms = splitByThresholds(newScoreData, thresholds, censorThreshold,
            params != null && "Quartiles".equals(params.getChoiceParameterValue("scoreThresholdMethod")));

    //         for (KaplanMeier km : kms)
    //            km.censorAtTime(censorThreshold);
    ////         kmHigh.censorAtTime(censorThreshold);
    ////         kmLow.censorAtTime(censorThreshold);

    //         logger.info("High: " + kmHigh.toString());
    //         logger.info("Low: " + kmLow.toString());
    //         logger.info("Log rank comparison: {}", LogRankTest.computeLogRankTest(kmLow, kmHigh));

    if (plotter == null) {
        plotter = new KaplanMeierChartWrapper(survivalColumn + " time");
        //            plotter.setBorder(BorderFactory.createTitledBorder("Survival plot"));
        //            plotter.getCanvas().setWidth(300);
        //            plotter.getCanvas().setHeight(300);
    }
    KaplanMeierData[] kmArray = new KaplanMeierData[kms.size()];
    plotter.setKaplanMeierCurves(survivalColumn + " time", kms.toArray(kmArray));
    tableModel.setSurvivalCurves(thresholds,
            params != null && params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value"),
            kmArray);

    // Bar width determined using 'Freedman and Diaconis' rule' (but overridden if this gives < 16 bins...)
    double barWidth = (2 * q3 - q1) * Math.pow(numNonNaN, -1.0 / 3.0);
    int nBins = 100;
    if (!Double.isNaN(barWidth))
        barWidth = (int) Math.max(16, Math.ceil((maxVal - minVal) / barWidth));
    Histogram histogram = scoresValid ? new Histogram(newScoreData.scores, nBins) : null;
    if (histogramPanel == null) {
        GridPane paneHistogram = new GridPane();
        histogramPanel = new HistogramPanelFX();
        histogramPanel.getChart().setAnimated(false);
        histogramWrapper = new ThresholdedChartWrapper(histogramPanel.getChart());
        for (ObservableNumberValue val : threshProperties)
            histogramWrapper.addThreshold(val, ColorToolsFX.getCachedColor(240, 0, 0, 128));
        histogramWrapper.getPane().setPrefHeight(150);
        paneHistogram.add(histogramWrapper.getPane(), 0, 0);
        Tooltip.install(histogramPanel.getChart(), new Tooltip("Distribution of scores"));
        GridPane.setHgrow(histogramWrapper.getPane(), Priority.ALWAYS);
        GridPane.setVgrow(histogramWrapper.getPane(), Priority.ALWAYS);

        NumberAxis xAxis = new NumberAxis();
        xAxis.setLabel("Score threshold");
        NumberAxis yAxis = new NumberAxis();
        yAxis.setLowerBound(0);
        yAxis.setUpperBound(1);
        yAxis.setTickUnit(0.1);
        yAxis.setAutoRanging(false);
        yAxis.setLabel("P-value");
        chartPValues = new LineChart<>(xAxis, yAxis);
        chartPValues.setAnimated(false);
        chartPValues.setLegendVisible(false);

        // Make chart so it can be navigated
        ChartToolsFX.makeChartInteractive(chartPValues, xAxis, yAxis);
        pValuesChanged = true;
        Tooltip.install(chartPValues, new Tooltip(
                "Distribution of p-values (log-rank test) comparing low vs. high for all possible score thresholds"));
        //            chartPValues.getYAxis().setAutoRanging(false);
        pValuesWrapper = new ThresholdedChartWrapper(chartPValues);
        for (ObservableNumberValue val : threshProperties)
            pValuesWrapper.addThreshold(val, ColorToolsFX.getCachedColor(240, 0, 0, 128));

        pValuesWrapper.getPane().setPrefHeight(150);
        paneHistogram.add(pValuesWrapper.getPane(), 0, 1);
        GridPane.setHgrow(pValuesWrapper.getPane(), Priority.ALWAYS);
        GridPane.setVgrow(pValuesWrapper.getPane(), Priority.ALWAYS);

        ContextMenu popup = new ContextMenu();
        ChartToolsFX.addChartExportMenu(chartPValues, popup);

        RadioMenuItem miZoomY1 = new RadioMenuItem("0-1");
        miZoomY1.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(1);
            yAxis.setTickUnit(0.2);
        });
        RadioMenuItem miZoomY05 = new RadioMenuItem("0-0.5");
        miZoomY05.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.5);
            yAxis.setTickUnit(0.1);
        });
        RadioMenuItem miZoomY02 = new RadioMenuItem("0-0.2");
        miZoomY02.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.2);
            yAxis.setTickUnit(0.05);
        });
        RadioMenuItem miZoomY01 = new RadioMenuItem("0-0.1");
        miZoomY01.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.1);
            yAxis.setTickUnit(0.05);
        });
        RadioMenuItem miZoomY005 = new RadioMenuItem("0-0.05");
        miZoomY005.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.05);
            yAxis.setTickUnit(0.01);
        });
        RadioMenuItem miZoomY001 = new RadioMenuItem("0-0.01");
        miZoomY001.setOnAction(e -> {
            yAxis.setAutoRanging(false);
            yAxis.setUpperBound(0.01);
            yAxis.setTickUnit(0.005);
        });
        ToggleGroup tgZoom = new ToggleGroup();
        miZoomY1.setToggleGroup(tgZoom);
        miZoomY05.setToggleGroup(tgZoom);
        miZoomY02.setToggleGroup(tgZoom);
        miZoomY01.setToggleGroup(tgZoom);
        miZoomY005.setToggleGroup(tgZoom);
        miZoomY001.setToggleGroup(tgZoom);
        Menu menuZoomY = new Menu("Set y-axis range");
        menuZoomY.getItems().addAll(miZoomY1, miZoomY05, miZoomY02, miZoomY01, miZoomY005, miZoomY001);

        MenuItem miCopyData = new MenuItem("Copy chart data");
        miCopyData.setOnAction(e -> {
            String dataString = ChartToolsFX.getChartDataAsString(chartPValues);
            ClipboardContent content = new ClipboardContent();
            content.putString(dataString);
            Clipboard.getSystemClipboard().setContent(content);
        });

        popup.getItems().addAll(miCopyData, menuZoomY);
        chartPValues.setOnContextMenuRequested(e -> {
            popup.show(chartPValues, e.getScreenX(), e.getScreenY());
        });

        for (int col = 0; col < tableModel.getColumnCount(); col++) {
            TableColumn<Integer, String> column = new TableColumn<>(tableModel.getColumnName(col));
            int colNumber = col;
            column.setCellValueFactory(
                    new Callback<CellDataFeatures<Integer, String>, ObservableValue<String>>() {
                        @Override
                        public ObservableValue<String> call(CellDataFeatures<Integer, String> p) {
                            return new SimpleStringProperty(
                                    (String) tableModel.getValueAt(p.getValue(), colNumber));
                        }
                    });

            column.setCellFactory(new Callback<TableColumn<Integer, String>, TableCell<Integer, String>>() {

                @Override
                public TableCell<Integer, String> call(TableColumn<Integer, String> param) {
                    TableCell<Integer, String> cell = new TableCell<Integer, String>() {
                        @Override
                        protected void updateItem(String item, boolean empty) {
                            super.updateItem(item, empty);
                            setText(item);
                            setTooltip(new Tooltip(item));
                        }
                    };
                    return cell;
                }
            });

            table.getColumns().add(column);
        }
        table.setPrefHeight(250);
        table.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY);
        table.maxHeightProperty().bind(table.prefHeightProperty());

        params = new ParameterList();
        //         maxTimePoint = 0;
        //         for (TMACoreObject core : hierarchy.getTMAGrid().getTMACoreList()) {
        //            double os = core.getMeasurementList().getMeasurementValue(TMACoreObject.KEY_OVERALL_SURVIVAL);
        //            double rfs = core.getMeasurementList().getMeasurementValue(TMACoreObject.KEY_RECURRENCE_FREE_SURVIVAL);
        //            if (os > maxTimePoint)
        //               maxTimePoint = os;
        //            if (rfs > maxTimePoint)
        //               maxTimePoint = rfs;
        //         }
        params.addIntParameter("censorTimePoints", "Max censored time", (int) (censorThreshold + 0.5), null, 0,
                (int) Math.ceil(maxTimePoint), "Latest time point beyond which data will be censored");
        //            params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Manual", Arrays.asList("Manual", "Median", "Log-rank test"));
        if (calculateAllPValues)
            // Don't include "Lowest smoothed p-value" - it's not an established method and open to misinterpretation...
            params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median",
                    Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles",
                            "Lowest p-value"));
        //            params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median", Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles", "Lowest p-value", "Lowest smoothed p-value"));
        else
            params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median",
                    Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles"));
        params.addDoubleParameter("threshold1", "Threshold 1",
                thresholds.length > 0 ? thresholds[0] : (minVal + maxVal) / 2, null,
                "Threshold to distinguish between patient groups");
        params.addDoubleParameter("threshold2", "Threshold 2",
                thresholds.length > 1 ? thresholds[1] : (minVal + maxVal) / 2, null,
                "Threshold to distinguish between patient groups");
        params.addDoubleParameter("threshold3", "Threshold 3",
                thresholds.length > 2 ? thresholds[2] : (minVal + maxVal) / 2, null,
                "Threshold to distinguish between patient groups");
        params.addBooleanParameter("showAtRisk", "Show at risk", plotter.getShowAtRisk(),
                "Show number of patients at risk below the plot");
        params.addBooleanParameter("showTicks", "Show censored ticks", plotter.getShowCensoredTicks(),
                "Show ticks to indicate censored data");
        params.addBooleanParameter("showKey", "Show key", plotter.getShowKey(),
                "Show key indicating display of each curve");
        //            params.addBooleanParameter("useColor", "Use color", plotter.getUseColor(), "Show each curve in a different color");
        //         params.addBooleanParameter("useStrokes", "Use strokes", plotter.getUseStrokes(), "Show each curve with a differed line stroke");
        // Hide threshold parameters if threshold can't be used
        if (!scoresValid) {
            //               params.setHiddenParameters(true, "scoreThresholdMethod", "scoreThreshold");
            histogramPanel.getChart().setVisible(false);
        }
        panelParams = new ParameterPanelFX(params);
        panelParams.addParameterChangeListener(this);
        updateThresholdsEnabled();

        for (int i = 0; i < threshProperties.length; i++) {
            String p = "threshold" + (i + 1);
            threshProperties[i].addListener((v, o, n) -> {
                if (interactiveThresholds()) {
                    // Need to do a decent double check with tolerance to text field value changing while typing
                    if (!GeneralTools.almostTheSame(params.getDoubleParameterValue(p), n.doubleValue(), 0.0001))
                        panelParams.setNumericParameterValue(p, n);
                }
            });
        }

        BorderPane paneBottom = new BorderPane();
        TitledPane paneOptions = new TitledPane("Options", panelParams.getPane());
        //            paneOptions.setCollapsible(false);
        Pane paneCanvas = new StackPane();
        paneCanvas.getChildren().add(plotter.getCanvas());

        GridPane paneLeft = new GridPane();
        paneLeft.add(paneOptions, 0, 0);
        paneLeft.add(table, 0, 1);
        GridPane.setHgrow(paneOptions, Priority.ALWAYS);
        GridPane.setHgrow(table, Priority.ALWAYS);
        paneBottom.setLeft(paneLeft);
        paneBottom.setCenter(paneHistogram);

        paneMain.setCenter(paneCanvas);
        paneMain.setBottom(paneBottom);

        paneMain.setPadding(new Insets(10, 10, 10, 10));
    } else if (thresholds.length > 0) {
        // Ensure the sliders/text fields are set sensibly
        if (!GeneralTools.almostTheSame(thresholds[0], params.getDoubleParameterValue("threshold1"), 0.0001)) {
            panelParams.setNumericParameterValue("threshold1", thresholds[0]);
        }
        if (thresholds.length > 1 && !GeneralTools.almostTheSame(thresholds[1],
                params.getDoubleParameterValue("threshold2"), 0.0001)) {
            panelParams.setNumericParameterValue("threshold2", thresholds[1]);
        }
        if (thresholds.length > 2 && !GeneralTools.almostTheSame(thresholds[2],
                params.getDoubleParameterValue("threshold3"), 0.0001)) {
            panelParams.setNumericParameterValue("threshold3", thresholds[2]);
        }
    }

    if (histogram != null) {
        histogramPanel.getHistogramData()
                .setAll(HistogramPanelFX.createHistogramData(histogram, false, (Color) null));
        histogramPanel.getChart().getXAxis().setLabel(scoreColumn);
        histogramPanel.getChart().getYAxis().setLabel("Count");

        ChartToolsFX.addChartExportMenu(histogramPanel.getChart(), null);

        //            histogramWrapper.setVerticalLines(thresholds, ColorToolsFX.getCachedColor(240, 0, 0, 128));
        // Deal with threshold adjustment
        //            histogramWrapper.getThresholds().addListener((Observable o) -> generatePlot());
    }

    if (pValues != null) {
        // TODO: Raise earlier where p-value calculation is
        if (pValuesChanged) {
            ObservableList<XYChart.Data<Number, Number>> data = FXCollections.observableArrayList();
            for (int i = 0; i < pValueThresholds.length; i++) {
                double pValue = pValues[i];
                if (Double.isNaN(pValue))
                    continue;
                data.add(new XYChart.Data<>(pValueThresholds[i], pValue, pValueThresholdsObserved[i]));
            }

            ObservableList<XYChart.Data<Number, Number>> dataSmoothed = null;
            if (pValuesSmoothed != null) {
                dataSmoothed = FXCollections.observableArrayList();
                for (int i = 0; i < pValueThresholds.length; i++) {
                    double pValueSmoothed = pValuesSmoothed[i];
                    if (Double.isNaN(pValueSmoothed))
                        continue;
                    dataSmoothed.add(new XYChart.Data<>(pValueThresholds[i], pValueSmoothed));
                }
            }

            // Don't bother showing the smoothed data... it tends to get in the way...
            //            if (dataSmoothed != null)
            //               chartPValues.getData().setAll(new XYChart.Series<>("P-values", data), new XYChart.Series<>("Smoothed P-values", dataSmoothed));
            //            else
            chartPValues.getData().setAll(new XYChart.Series<>("P-values", data));

            // Add line to show 0.05 significance threshold
            if (pValueThresholds.length > 1) {
                Data<Number, Number> sigData1 = new Data<>(pValueThresholds[0], 0.05);
                Data<Number, Number> sigData2 = new Data<>(pValueThresholds[pValueThresholds.length - 1], 0.05);
                XYChart.Series<Number, Number> dataSignificant = new XYChart.Series<>("Signficance 0.05",
                        FXCollections.observableArrayList(sigData1, sigData2));
                chartPValues.getData().add(dataSignificant);
                sigData1.getNode().setVisible(false);
                sigData2.getNode().setVisible(false);
            }

            //               chartPValues.getData().get(0).getNode().setVisible(true);

            //               pValuesWrapper.clearThresholds();
            for (XYChart.Data<Number, Number> dataPoint : data) {
                if (!Boolean.TRUE.equals(dataPoint.getExtraValue()))
                    dataPoint.getNode().setVisible(false);
            }
            //            if (dataSmoothed != null) {
            //               for (XYChart.Data<Number, Number> dataPoint : dataSmoothed) {
            //                  dataPoint.getNode().setVisible(false);
            //               }
            //               chartPValues.getData().get(1).getNode().setOpacity(0.5);
            //            }

            //               int count = 0;               
            //               for (int i = 0; i < pValueThresholds.length; i++) {
            //                  double pValue = pValues[i];
            //                  if (Double.isNaN(pValue))
            //                     continue;
            //                  boolean observed = pValueThresholdsObserved[i];
            ////                  if (observed)
            ////                     pValuesWrapper.addThreshold(new ReadOnlyDoubleWrapper(pValueThresholds[i]), Color.rgb(0, 0, 0, 0.05));
            //                  
            //                  if (!observed) {
            ////                     StackPane pane = (StackPane)data.get(count).getNode();
            ////                     pane.setEffect(new DropShadow());
            //                     data.get(count).getNode().setVisible(false);
            //                  }
            //                  count++;
            //               }
        }

        for (int i = 0; i < threshProperties.length; i++) {
            if (i < thresholds.length)
                threshProperties[i].set(thresholds[i]);
            else
                threshProperties[i].set(Double.NaN);
        }
        boolean isInteractive = interactiveThresholds();
        histogramWrapper.setIsInteractive(isInteractive);
        pValuesWrapper.setIsInteractive(isInteractive);

        chartPValues.setVisible(true);
    }
    //         else
    //            chartPValues.setVisible(false);

    // Store values for next time
    scoreData = newScoreData;
}

---

From source file:com.github.vatbub.tictactoe.view.Main.java

private void initBoard() {
    guiAnimationQueue.submit(() -> {/*from  w  w  w  .  j a  v a 2  s.  c  o m*/
        board = new Board(gameRows, gameCols);
        // set the ai level
        int sliderPos = (int) Math.round(aiLevelSlider.getValue() * 3.0 / 100.0);

        switch (sliderPos) {
        case 0:
            board.setAiLevel(AILevel.COMPLETELY_STUPID);
            break;
        case 1:
            board.setAiLevel(AILevel.SOMEWHAT_GOOD);
            break;
        case 2:
            board.setAiLevel(AILevel.GOOD);
            break;
        case 3:
            board.setAiLevel(AILevel.UNBEATABLE);
            break;
        }

        board.setGameEndCallback((winnerInfo) -> guiAnimationQueue.submit(() -> {
            // disconnect after ending the game
            if (board.getCurrentPlayer().getPlayerMode().equals(PlayerMode.internetHuman) || board
                    .getOpponent(board.getCurrentPlayer()).getPlayerMode().equals(PlayerMode.internetHuman)) {
                KryoGameConnections.resetConnections();
            }
            updateOpponentsTurnHBox(false, false);
            FOKLogger.info(Main.class.getName(), "The winner is: " + winnerInfo.winningPlayer.getName());
            if (winnerInfo.isTie()) {
                showTie();
            } else if (winnerInfo.winningPlayer.getPlayerMode().equals(PlayerMode.localHuman) && !board
                    .getOpponent(winnerInfo.winningPlayer).getPlayerMode().equals(PlayerMode.localHuman)) {
                showWinner(winnerInfo);
            } else if (winnerInfo.winningPlayer.getPlayerMode().equals(PlayerMode.localHuman) && board
                    .getOpponent(winnerInfo.winningPlayer).getPlayerMode().equals(PlayerMode.localHuman)) {
                showWinnerWithTwoHumanPlayers(winnerInfo);
            } else {
                showLooser(winnerInfo);
            }
        }));
        while (gameTable.getColumns().size() > 0) {
            gameTable.getColumns().remove(0);
        }

        for (int i = 0; i < gameCols; i++) {
            TableColumn<Row, String> column = new TableColumn<>(Integer.toString(i + 1));
            //noinspection Convert2Lambda
            int finalI = i;
            column.setCellValueFactory(p -> new SimpleStringProperty(p.getValue().getValues().get(finalI)));

            column.setCellFactory(new Callback<TableColumn<Row, String>, TableCell<Row, String>>() {
                @Override
                public TableCell<Row, String> call(TableColumn col) {
                    TableCell<Row, String> cell = new TableCell<Row, String>() {
                        // The updateItem method is what is called when setting the cell's text.  You can customize formatting here
                        @Override
                        protected void updateItem(String item, boolean empty) {
                            // calling super here is very important - don't skip this!
                            super.updateItem(item, empty);
                            if (item != null) {
                                setText(item);
                            }
                        }
                    };

                    cell.setOnMouseClicked(event -> {
                        if (board.getPlayerAt(cell.getIndex(), gameTable.getColumns().indexOf(col)) == null
                                && !isBlockedForInput()) {
                            setBlockedForInput(true);
                            boolean opponentIsInternetPlayer = board.getOpponent(board.getCurrentPlayer())
                                    .getPlayerMode().equals(PlayerMode.internetHuman);
                            board.doTurn(new Move(cell.getIndex(), gameTable.getColumns().indexOf(col)));
                            updateCurrentPlayerLabel(false, opponentIsInternetPlayer);
                            renderRows();
                        } else if (isBlockedForInput()) {
                            flashOpponentsTurnHBox();
                        }
                    });
                    return cell;
                }
            });

            column.setStyle("-fx-alignment: CENTER; -fx-padding: 0;");
            gameTable.getColumns().add(column);
        }

        renderRows();
    });
}

---

From source file:fr.amap.lidar.amapvox.gui.MainFrameController.java

/**
 * Initializes the controller class.//from   ww w  .  j  a  v  a 2 s.  c om
 */
@Override
public void initialize(URL url, ResourceBundle rb) {

    this.resourceBundle = rb;

    viewer3DPanelController.setResourceBundle(rb);

    initStrings(rb);

    colorPickerSeries.valueProperty().addListener(new ChangeListener<javafx.scene.paint.Color>() {
        @Override
        public void changed(ObservableValue<? extends javafx.scene.paint.Color> observable,
                javafx.scene.paint.Color oldValue, javafx.scene.paint.Color newValue) {
            if (listViewVoxelsFilesChart.getSelectionModel().getSelectedItems().size() == 1) {
                listViewVoxelsFilesChart.getSelectionModel().getSelectedItem().getSeriesParameters()
                        .setColor(new Color((float) newValue.getRed(), (float) newValue.getGreen(),
                                (float) newValue.getBlue(), 1.0f));
            }
        }
    });

    comboboxScript.getItems().setAll("Daniel script");

    vboxWeighting.disableProperty().bind(checkboxEnableWeighting.selectedProperty().not());

    checkboxEnableWeighting.selectedProperty().addListener(new ChangeListener<Boolean>() {
        @Override
        public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
            if (newValue && textAreaWeighting.getText().isEmpty()) {

                int selectedVoxTab = tabPaneVoxelisation.getSelectionModel().getSelectedIndex();

                if (selectedVoxTab == 0) { //ALS
                    fillWeightingData(EchoesWeightParams.DEFAULT_ALS_WEIGHTING);
                } else if (selectedVoxTab == 1) { //TLS
                    fillWeightingData(EchoesWeightParams.DEFAULT_TLS_WEIGHTING);
                }
            }
        }
    });

    /*comboboxTransMode.getItems().setAll(1, 2, 3);
    comboboxTransMode.getSelectionModel().selectFirst();
            
    comboboxPathLengthMode.getItems().setAll("A", "B");
    comboboxPathLengthMode.getSelectionModel().selectFirst();*/

    helpButtonNaNsCorrection.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {
            helpButtonNaNsCorrectionController.showHelpDialog(resourceBundle.getString("help_NaNs_correction"));
        }
    });

    helpButtonAutoBBox.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {
            helpButtonAutoBBoxController.showHelpDialog(resourceBundle.getString("help_bbox"));
        }
    });

    helpButtonHemiPhoto.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {
            helpButtonHemiPhotoController.showHelpDialog(resourceBundle.getString("help_hemiphoto"));
        }
    });

    buttonHelpEmptyShotsFilter.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {
            buttonHelpEmptyShotsFilterController
                    .showHelpDialog(resourceBundle.getString("help_empty_shots_filter"));
        }
    });

    /*work around, the divider positions values are defined in the fxml,
    but when the window is initialized the values are lost*/
    Platform.runLater(new Runnable() {
        @Override
        public void run() {
            splitPaneMain.setDividerPositions(0.75f);
            splitPaneVoxelization.setDividerPositions(0.45f);
        }
    });

    initValidationSupport();
    initPostProcessTab();

    listViewTransmittanceMapSensorPositions.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    listViewTaskList.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);

    MenuItem menuItemPadValue1m = new MenuItem("1m voxel size");
    addMenuItemPadValue(menuItemPadValue1m, 3.536958f);

    MenuItem menuItemPadValue2m = new MenuItem("2m voxel size");
    addMenuItemPadValue(menuItemPadValue2m, 2.262798f);

    MenuItem menuItemPadValue3m = new MenuItem("3m voxel size");
    addMenuItemPadValue(menuItemPadValue3m, 1.749859f);

    MenuItem menuItemPadValue4m = new MenuItem("4m voxel size");
    addMenuItemPadValue(menuItemPadValue4m, 1.3882959f);

    MenuItem menuItemPadValue5m = new MenuItem("5m voxel size");
    addMenuItemPadValue(menuItemPadValue5m, 1.0848f);

    menuButtonAdvisablePADMaxValues.getItems().addAll(menuItemPadValue1m, menuItemPadValue2m,
            menuItemPadValue3m, menuItemPadValue4m, menuItemPadValue5m);

    fileChooserSaveCanopyAnalyserOutputFile = new FileChooserContext();
    fileChooserSaveCanopyAnalyserCfgFile = new FileChooserContext();
    fileChooserSaveTransmittanceSimCfgFile = new FileChooserContext();
    fileChooserOpenCanopyAnalyserInputFile = new FileChooserContext();
    listViewCanopyAnalyzerSensorPositions.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);

    ContextMenu contextMenuProductsList = new ContextMenu();
    MenuItem openImageItem = new MenuItem(RS_STR_OPEN_IMAGE);
    openImageItem.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {
            File selectedFile = listViewProductsFiles.getSelectionModel().getSelectedItem();

            showImage(selectedFile);
        }
    });

    Menu menuEdit = new Menu(RS_STR_EDIT);

    MenuItem menuItemEditVoxels = new MenuItem("Remove voxels (delete key)");
    MenuItem menuItemFitToContent = new MenuItem("Fit to content");
    MenuItem menuItemCrop = new MenuItem("Crop");

    menuEdit.getItems().setAll(menuItemEditVoxels, menuItemFitToContent, menuItemCrop);

    menuItemFitToContent.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {
            File selectedItem = listViewProductsFiles.getSelectionModel().getSelectedItem();

            if (selectedItem != null) {
                fitVoxelSpaceToContent(selectedItem);
            }
        }
    });

    menuItemEditVoxels.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {

            File selectedItem = listViewProductsFiles.getSelectionModel().getSelectedItem();

            if (selectedItem != null) {
                editVoxelSpace(selectedItem);
            }
        }
    });

    menuItemCrop.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {

            File selectedItem = listViewProductsFiles.getSelectionModel().getSelectedItem();

            if (selectedItem != null) {
                try {
                    voxelSpaceCroppingFrameController.setVoxelFile(selectedItem);
                    voxelSpaceCroppingFrame.show();
                } catch (Exception ex) {
                    showErrorDialog(ex);
                }
            }
        }
    });

    Menu menuExport = new Menu(RS_STR_EXPORT);
    MenuItem menuItemExportDartMaket = new MenuItem("Dart (maket.txt)");
    MenuItem menuItemExportDartPlots = new MenuItem("Dart (plots.xml)");
    MenuItem menuItemExportMeshObj = new MenuItem("Mesh (*.obj)");

    menuItemExportDartMaket.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {

            File selectedItem = listViewProductsFiles.getSelectionModel().getSelectedItem();

            if (selectedItem != null) {
                exportDartMaket(selectedItem);
            }
        }
    });

    menuItemExportDartPlots.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {

            File selectedItem = listViewProductsFiles.getSelectionModel().getSelectedItem();

            if (selectedItem != null) {
                exportDartPlots(selectedItem);
            }
        }
    });

    menuItemExportMeshObj.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {

            File selectedItem = listViewProductsFiles.getSelectionModel().getSelectedItem();

            if (selectedItem != null) {
                exportMeshObj(selectedItem);
            }
        }
    });

    menuExport.getItems().setAll(menuItemExportDartMaket, menuItemExportDartPlots, menuItemExportMeshObj);

    MenuItem menuItemInfo = new MenuItem(RS_STR_INFO);

    menuItemInfo.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {

            Alert alert = new Alert(AlertType.INFORMATION);

            File selectedItem = listViewProductsFiles.getSelectionModel().getSelectedItem();

            if (selectedItem != null) {
                VoxelFileReader reader;
                try {
                    reader = new VoxelFileReader(selectedItem);
                    VoxelSpaceInfos voxelSpaceInfos = reader.getVoxelSpaceInfos();
                    alert.setTitle("Information");
                    alert.setHeaderText("Voxel space informations");
                    alert.setContentText(voxelSpaceInfos.toString());
                    alert.show();
                } catch (Exception ex) {
                    showErrorDialog(ex);
                }

            }
        }
    });

    final MenuItem menuItemOpenContainingFolder = new MenuItem(RS_STR_OPEN_CONTAINING_FOLDER);

    menuItemOpenContainingFolder.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent event) {

            final File selectedItem = listViewProductsFiles.getSelectionModel().getSelectedItem();

            if (selectedItem != null) {
                if (Desktop.isDesktopSupported()) {
                    new Thread(() -> {
                        try {
                            Desktop.getDesktop().open(selectedItem.getParentFile());
                        } catch (IOException ex) {
                            logger.error("Cannot open directory " + selectedItem);
                        }
                    }).start();
                }

            }

        }
    });

    listViewProductsFiles.setOnContextMenuRequested(new EventHandler<ContextMenuEvent>() {
        @Override
        public void handle(ContextMenuEvent event) {

            if (listViewProductsFiles.getSelectionModel().getSelectedIndices().size() == 1) {

                File selectedFile = listViewProductsFiles.getSelectionModel().getSelectedItem();
                String extension = FileManager.getExtension(selectedFile);

                switch (extension) {
                case ".png":
                case ".bmp":
                case ".jpg":
                    contextMenuProductsList.getItems().setAll(openImageItem, menuItemOpenContainingFolder);
                    contextMenuProductsList.show(listViewProductsFiles, event.getScreenX(), event.getScreenY());
                    break;
                case ".vox":

                default:
                    if (VoxelFileReader.isFileAVoxelFile(selectedFile)) {
                        contextMenuProductsList.getItems().setAll(menuItemInfo, menuItemOpenContainingFolder,
                                menuEdit, menuExport);
                        contextMenuProductsList.show(listViewProductsFiles, event.getScreenX(),
                                event.getScreenY());
                    }
                }

            }

        }
    });

    ContextMenu contextMenuLidarScanEdit = new ContextMenu();
    MenuItem editItem = new MenuItem("Edit");

    editItem.setOnAction(new EventHandler<ActionEvent>() {

        @Override
        public void handle(ActionEvent event) {

            filterFrameController.setFilters("Reflectance", "Deviation", "Amplitude");
            filterFrame.show();

            filterFrame.setOnHidden(new EventHandler<WindowEvent>() {

                @Override
                public void handle(WindowEvent event) {

                    if (filterFrameController.getFilter() != null) {
                        ObservableList<LidarScan> items = listViewHemiPhotoScans.getSelectionModel()
                                .getSelectedItems();
                        for (LidarScan scan : items) {
                            scan.filters.add(filterFrameController.getFilter());
                        }
                    }
                }
            });
        }
    });

    contextMenuLidarScanEdit.getItems().add(editItem);

    listViewHemiPhotoScans.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    listViewHemiPhotoScans.setOnContextMenuRequested(new EventHandler<ContextMenuEvent>() {

        @Override
        public void handle(ContextMenuEvent event) {
            contextMenuLidarScanEdit.show(listViewHemiPhotoScans, event.getScreenX(), event.getScreenY());
        }
    });

    /**LAD tab initialization**/
    comboboxLADChoice.getItems().addAll(LeafAngleDistribution.Type.UNIFORM, LeafAngleDistribution.Type.SPHERIC,
            LeafAngleDistribution.Type.ERECTOPHILE, LeafAngleDistribution.Type.PLANOPHILE,
            LeafAngleDistribution.Type.EXTREMOPHILE, LeafAngleDistribution.Type.PLAGIOPHILE,
            LeafAngleDistribution.Type.HORIZONTAL, LeafAngleDistribution.Type.VERTICAL,
            LeafAngleDistribution.Type.ELLIPSOIDAL, LeafAngleDistribution.Type.ELLIPTICAL,
            LeafAngleDistribution.Type.TWO_PARAMETER_BETA);

    comboboxLADChoice.getSelectionModel().select(LeafAngleDistribution.Type.SPHERIC);
    comboboxLADChoice.getSelectionModel().selectedItemProperty()
            .addListener(new ChangeListener<LeafAngleDistribution.Type>() {

                @Override
                public void changed(ObservableValue<? extends LeafAngleDistribution.Type> observable,
                        LeafAngleDistribution.Type oldValue, LeafAngleDistribution.Type newValue) {

                    if (newValue == LeafAngleDistribution.Type.TWO_PARAMETER_BETA
                            || newValue == LeafAngleDistribution.Type.ELLIPSOIDAL) {

                        hboxTwoBetaParameters.setVisible(true);

                        if (newValue == LeafAngleDistribution.Type.ELLIPSOIDAL) {
                            labelLADBeta.setVisible(false);
                        } else {
                            labelLADBeta.setVisible(true);
                        }
                    } else {
                        hboxTwoBetaParameters.setVisible(false);
                    }
                }
            });

    ToggleGroup ladTypeGroup = new ToggleGroup();
    radiobuttonLADHomogeneous.setToggleGroup(ladTypeGroup);
    radiobuttonLADLocalEstimation.setToggleGroup(ladTypeGroup);

    /**CHART panel initialization**/

    ToggleGroup profileChartType = new ToggleGroup();
    radiobuttonPreDefinedProfile.setToggleGroup(profileChartType);
    radiobuttonFromVariableProfile.setToggleGroup(profileChartType);

    ToggleGroup profileChartRelativeHeightType = new ToggleGroup();
    radiobuttonHeightFromAboveGround.setToggleGroup(profileChartRelativeHeightType);
    radiobuttonHeightFromBelowCanopy.setToggleGroup(profileChartRelativeHeightType);

    comboboxFromVariableProfile.disableProperty().bind(radiobuttonPreDefinedProfile.selectedProperty());
    comboboxPreDefinedProfile.disableProperty().bind(radiobuttonFromVariableProfile.selectedProperty());

    hboxMaxPADVegetationProfile.visibleProperty().bind(radiobuttonPreDefinedProfile.selectedProperty());

    listViewVoxelsFilesChart.getSelectionModel().selectedIndexProperty()
            .addListener(new ChangeListener<Number>() {

                @Override
                public void changed(ObservableValue<? extends Number> observable, Number oldValue,
                        Number newValue) {

                    if (listViewVoxelsFilesChart.getSelectionModel().getSelectedItems().size() > 1) {
                        colorPickerSeries.setDisable(true);
                    } else if (listViewVoxelsFilesChart.getSelectionModel().getSelectedItems().size() == 1) {

                        VoxelFileChart selectedItem = listViewVoxelsFilesChart.getSelectionModel()
                                .getSelectedItem();
                        Color selectedItemColor = selectedItem.getSeriesParameters().getColor();

                        colorPickerSeries.setDisable(false);
                        colorPickerSeries.setValue(new javafx.scene.paint.Color(
                                selectedItemColor.getRed() / 255.0, selectedItemColor.getGreen() / 255.0,
                                selectedItemColor.getBlue() / 255.0, 1.0));

                        if (newValue.intValue() >= 0) {
                            textfieldLabelVoxelFileChart.setText(
                                    listViewVoxelsFilesChart.getItems().get(newValue.intValue()).label);
                        }
                    }
                }
            });

    textfieldLabelVoxelFileChart.textProperty().addListener(new ChangeListener<String>() {

        @Override
        public void changed(ObservableValue<? extends String> observable, String oldValue, String newValue) {

            if (listViewVoxelsFilesChart.getSelectionModel().getSelectedIndex() >= 0) {
                listViewVoxelsFilesChart.getSelectionModel().getSelectedItem().label = newValue;
            }
        }
    });

    listViewVoxelsFilesChart.getItems().addListener(new ListChangeListener<VoxelFileChart>() {

        @Override
        public void onChanged(ListChangeListener.Change<? extends VoxelFileChart> c) {

            while (c.next()) {
            }

            if (c.wasAdded() && c.getAddedSize() == c.getList().size()) {

                try {
                    VoxelFileReader reader = new VoxelFileReader(c.getList().get(0).file);
                    String[] columnNames = reader.getVoxelSpaceInfos().getColumnNames();
                    comboboxFromVariableProfile.getItems().clear();
                    comboboxFromVariableProfile.getItems().addAll(columnNames);
                    comboboxFromVariableProfile.getSelectionModel().selectFirst();
                } catch (Exception ex) {
                    logger.error("Cannot read voxel file", ex);
                }
            }

        }
    });

    anchorpaneQuadrats.disableProperty().bind(checkboxMakeQuadrats.selectedProperty().not());

    comboboxSelectAxisForQuadrats.getItems().addAll("X", "Y", "Z");
    comboboxSelectAxisForQuadrats.getSelectionModel().select(1);

    comboboxPreDefinedProfile.getItems().addAll("Vegetation (PAD)");
    comboboxPreDefinedProfile.getSelectionModel().selectFirst();

    radiobuttonSplitCountForQuadrats.selectedProperty().addListener(new ChangeListener<Boolean>() {

        @Override
        public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
            textFieldSplitCountForQuadrats.setDisable(!newValue);
            textFieldLengthForQuadrats.setDisable(newValue);
        }
    });

    ToggleGroup chartMakeQuadratsSplitType = new ToggleGroup();
    radiobuttonLengthForQuadrats.setToggleGroup(chartMakeQuadratsSplitType);
    radiobuttonSplitCountForQuadrats.setToggleGroup(chartMakeQuadratsSplitType);

    /**Virtual measures panel initialization**/

    comboboxHemiPhotoBitmapOutputMode.getItems().addAll("Pixel", "Color");
    comboboxHemiPhotoBitmapOutputMode.getSelectionModel().selectFirst();

    ToggleGroup virtualMeasuresChoiceGroup = new ToggleGroup();

    toggleButtonLAI2000Choice.setToggleGroup(virtualMeasuresChoiceGroup);
    toggleButtonLAI2200Choice.setToggleGroup(virtualMeasuresChoiceGroup);

    comboboxChooseCanopyAnalyzerSampling.getItems().setAll(500, 4000, 10000);
    comboboxChooseCanopyAnalyzerSampling.getSelectionModel().selectFirst();

    initEchoFiltering();

    data = FXCollections.observableArrayList();

    tableViewSimulationPeriods.setItems(data);
    tableViewSimulationPeriods.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);

    comboboxChooseDirectionsNumber.getItems().addAll(1, 6, 16, 46, 136, 406);
    comboboxChooseDirectionsNumber.getSelectionModel().select(4);

    ToggleGroup scannerPositionsMode = new ToggleGroup();

    /*radiobuttonScannerPosSquaredArea.setToggleGroup(scannerPositionsMode);
    radiobuttonScannerPosFile.setToggleGroup(scannerPositionsMode);*/

    tableColumnPeriod.setCellValueFactory(
            new Callback<TableColumn.CellDataFeatures<SimulationPeriod, String>, ObservableValue<String>>() {

                @Override
                public ObservableValue<String> call(
                        TableColumn.CellDataFeatures<SimulationPeriod, String> param) {
                    return new SimpleStringProperty(param.getValue().getPeriod().toString());
                }
            });

    tableColumnClearness.setCellValueFactory(
            new Callback<TableColumn.CellDataFeatures<SimulationPeriod, String>, ObservableValue<String>>() {

                @Override
                public ObservableValue<String> call(
                        TableColumn.CellDataFeatures<SimulationPeriod, String> param) {
                    return new SimpleStringProperty(String.valueOf(param.getValue().getClearnessCoefficient()));
                }
            });

    checkboxMultiFiles.selectedProperty().addListener(new ChangeListener<Boolean>() {

        @Override
        public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
            anchorpaneBoundingBoxParameters.setDisable(newValue);
        }
    });

    hboxGenerateBitmapFiles.disableProperty().bind(checkboxGenerateBitmapFile.selectedProperty().not());
    hboxGenerateTextFile.disableProperty().bind(checkboxGenerateTextFile.selectedProperty().not());

    fileChooserOpenConfiguration = new FileChooser();
    fileChooserOpenConfiguration.setTitle("Choose configuration file");

    fileChooserSaveConfiguration = new FileChooserContext("cfg.xml");
    fileChooserSaveConfiguration.fc.setTitle("Choose output file");

    fileChooserOpenInputFileALS = new FileChooser();
    fileChooserOpenInputFileALS.setTitle("Open input file");
    fileChooserOpenInputFileALS.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("Shot files", "*.sht"), new ExtensionFilter("Text Files", "*.txt"),
            new ExtensionFilter("Las Files", "*.las", "*.laz"));

    fileChooserOpenTrajectoryFileALS = new FileChooser();
    fileChooserOpenTrajectoryFileALS.setTitle("Open trajectory file");
    fileChooserOpenTrajectoryFileALS.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("Text Files", "*.txt"));

    fileChooserOpenOutputFileALS = new FileChooser();
    fileChooserOpenOutputFileALS.setTitle("Choose output file");

    fileChooserOpenInputFileTLS = new FileChooserContext();
    fileChooserOpenInputFileTLS.fc.setTitle("Open input file");
    fileChooserOpenInputFileTLS.fc.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("Text Files", "*.txt"), new ExtensionFilter("Rxp Files", "*.rxp"),
            new ExtensionFilter("Project Rsp Files", "*.rsp"));

    directoryChooserOpenOutputPathTLS = new DirectoryChooser();
    directoryChooserOpenOutputPathTLS.setTitle("Choose output path");

    directoryChooserOpenOutputPathALS = new DirectoryChooser();
    directoryChooserOpenOutputPathALS.setTitle("Choose output path");

    fileChooserSaveOutputFileTLS = new FileChooser();
    fileChooserSaveOutputFileTLS.setTitle("Save voxel file");

    fileChooserSaveTransmittanceTextFile = new FileChooser();
    fileChooserSaveTransmittanceTextFile.setTitle("Save text file");

    directoryChooserSaveTransmittanceBitmapFile = new DirectoryChooser();
    directoryChooserSaveTransmittanceBitmapFile.setTitle("Choose output directory");

    fileChooserSaveHemiPhotoOutputBitmapFile = new FileChooserContext("*.png");
    fileChooserSaveHemiPhotoOutputBitmapFile.fc.setTitle("Save bitmap file");

    directoryChooserSaveHemiPhotoOutputBitmapFile = new DirectoryChooser();
    directoryChooserSaveHemiPhotoOutputBitmapFile.setTitle("Choose bitmap files output directory");

    directoryChooserSaveHemiPhotoOutputTextFile = new DirectoryChooser();
    directoryChooserSaveHemiPhotoOutputTextFile.setTitle("Choose text files output directory");

    fileChooserSaveHemiPhotoOutputTextFile = new FileChooser();
    fileChooserSaveHemiPhotoOutputTextFile.setTitle("Save text file");

    fileChooserOpenVoxelFile = new FileChooser();
    fileChooserOpenVoxelFile.setTitle("Open voxel file");
    fileChooserOpenVoxelFile.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("Voxel Files", "*.vox"));

    fileChooserOpenPopMatrixFile = new FileChooser();
    fileChooserOpenPopMatrixFile.setTitle("Choose matrix file");
    fileChooserOpenPopMatrixFile.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("Text Files", "*.txt"));

    fileChooserOpenSopMatrixFile = new FileChooser();
    fileChooserOpenSopMatrixFile.setTitle("Choose matrix file");
    fileChooserOpenSopMatrixFile.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("Text Files", "*.txt"));

    fileChooserOpenVopMatrixFile = new FileChooser();
    fileChooserOpenVopMatrixFile.setTitle("Choose matrix file");
    fileChooserOpenVopMatrixFile.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("Text Files", "*.txt"));

    fileChooserOpenPonderationFile = new FileChooser();
    fileChooserOpenPonderationFile.setTitle("Choose ponderation file");
    fileChooserOpenPonderationFile.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("Text Files", "*.txt"));

    fileChooserOpenDTMFile = new FileChooser();
    fileChooserOpenDTMFile.setTitle("Choose DTM file");
    fileChooserOpenDTMFile.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("DTM Files", "*.asc"));

    fileChooserOpenPointCloudFile = new FileChooser();
    fileChooserOpenPointCloudFile.setTitle("Choose point cloud file");
    fileChooserOpenPointCloudFile.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("TXT Files", "*.txt"));

    fileChooserOpenMultiResVoxelFile = new FileChooser();
    fileChooserOpenMultiResVoxelFile.setTitle("Choose voxel file");
    fileChooserOpenMultiResVoxelFile.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("Voxel Files", "*.vox"));

    fileChooserOpenOutputFileMultiRes = new FileChooser();
    fileChooserOpenOutputFileMultiRes.setTitle("Save voxel file");

    fileChooserAddTask = new FileChooser();
    fileChooserAddTask.setTitle("Choose parameter file");
    fileChooserAddTask.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("XML Files", "*.xml"));

    fileChooserSaveDartFile = new FileChooser();
    fileChooserSaveDartFile.setTitle("Save dart file (.maket)");
    fileChooserSaveDartFile.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("Maket File", "*.maket"));

    fileChooserOpenOutputFileMerging = new FileChooser();
    fileChooserOpenOutputFileMerging.setTitle("Choose voxel file");
    fileChooserOpenOutputFileMerging.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("Voxel Files", "*.vox"));

    fileChooserOpenScriptFile = new FileChooser();
    fileChooserOpenScriptFile.setTitle("Choose script file");

    fileChooserSaveGroundEnergyOutputFile = new FileChooser();
    fileChooserSaveGroundEnergyOutputFile.setTitle("Save ground energy file");

    fileChooserOpenPointsPositionFile = new FileChooser();
    fileChooserOpenPointsPositionFile.setTitle("Choose points file");
    fileChooserOpenPointsPositionFile.getExtensionFilters().addAll(new ExtensionFilter("All Files", "*"),
            new ExtensionFilter("TXT Files", "*.txt"));

    try {
        viewCapsSetupFrame = new Stage();
        FXMLLoader loader = new FXMLLoader(getClass().getResource("/fxml/ViewCapsSetupFrame.fxml"));
        Parent root = loader.load();
        viewCapsSetupFrameController = loader.getController();
        viewCapsSetupFrame.setScene(new Scene(root));
    } catch (IOException ex) {
        logger.error("Cannot load fxml file", ex);
    }

    try {
        FXMLLoader loader = new FXMLLoader(getClass().getResource("/fxml/FilteringPaneComponent.fxml"));
        anchorPaneEchoFilteringRxp = loader.load();
        filteringPaneController = loader.getController();
        filteringPaneController.setFiltersNames("Reflectance", "Amplitude", "Deviation");
    } catch (IOException ex) {
        logger.error("Cannot load fxml file", ex);
    }

    try {
        positionImporterFrame = new Stage();
        FXMLLoader loader = new FXMLLoader(getClass().getResource("/fxml/PositionImporterFrame.fxml"));
        Parent root = loader.load();
        positionImporterFrameController = loader.getController();
        positionImporterFrame.setScene(new Scene(root));
        positionImporterFrameController.setStage(positionImporterFrame);
    } catch (IOException ex) {
        logger.error("Cannot load fxml file", ex);
    }

    try {
        voxelSpaceCroppingFrame = new Stage();
        FXMLLoader loader = new FXMLLoader(getClass().getResource("/fxml/VoxelSpaceCroppingFrame.fxml"));
        Parent root = loader.load();
        voxelSpaceCroppingFrameController = loader.getController();
        voxelSpaceCroppingFrame.setScene(new Scene(root));
    } catch (IOException ex) {
        logger.error("Cannot load fxml file", ex);
    }

    try {
        attributsImporterFrame = new Stage();
        FXMLLoader loader = new FXMLLoader(getClass().getResource("/fxml/AttributsImporterFrame.fxml"));
        Parent root = loader.load();
        attributsImporterFrameController = loader.getController();
        attributsImporterFrame.setScene(new Scene(root));
        attributsImporterFrameController.setStage(attributsImporterFrame);
    } catch (IOException ex) {
        logger.error("Cannot load fxml file", ex);
    }

    try {
        textFileParserFrameController = TextFileParserFrameController.getInstance();
    } catch (Exception ex) {
        logger.error("Cannot load fxml file", ex);
    }

    try {
        transformationFrameController = TransformationFrameController.getInstance();
        transformationFrame = transformationFrameController.getStage();
    } catch (Exception ex) {
        logger.error("Cannot load fxml file", ex);
    }

    updaterFrame = new Stage();

    try {
        FXMLLoader loader = new FXMLLoader(getClass().getResource("/fxml/update/UpdaterFrame.fxml"));
        Parent root = loader.load();
        updaterFrameController = loader.getController();
        updaterFrame.setScene(new Scene(root));

    } catch (IOException ex) {
        logger.error("Cannot load fxml file", ex);
    }

    riscanProjectExtractor = new RiscanProjectExtractor();
    ptxProjectExtractor = new PTXProjectExtractor();
    ptgProjectExtractor = new PTGProjectExtractor();

    dateChooserFrame = new Stage();

    try {
        FXMLLoader loader = new FXMLLoader(getClass().getResource("/fxml/DateChooserFrame.fxml"));
        Parent root = loader.load();
        dateChooserFrameController = loader.getController();
        dateChooserFrame.setScene(new Scene(root));
        dateChooserFrameController.setStage(dateChooserFrame);
    } catch (IOException ex) {
        logger.error("Cannot load fxml file", ex);
    }

    comboboxModeALS.getItems().addAll(RS_STR_INPUT_TYPE_LAS, RS_STR_INPUT_TYPE_LAZ,
            /*RS_STR_INPUT_TYPE_XYZ, */RS_STR_INPUT_TYPE_SHOTS);

    comboboxModeALS.getSelectionModel().selectedItemProperty().addListener(new ChangeListener<String>() {
        @Override
        public void changed(ObservableValue<? extends String> observable, String oldValue, String newValue) {

            if (newValue.equals(RS_STR_INPUT_TYPE_SHOTS)) {
                alsVoxValidationSupport.registerValidator(textFieldTrajectoryFileALS, false,
                        Validators.unregisterValidator);
            } else {
                alsVoxValidationSupport.registerValidator(textFieldTrajectoryFileALS, false,
                        Validators.fileExistValidator);
            }
        }
    });

    comboboxModeTLS.getItems().setAll("Rxp scan", "Rsp project", "PTX",
            "PTG"/*, RS_STR_INPUT_TYPE_XYZ, RS_STR_INPUT_TYPE_SHOTS*/);
    comboboxGroundEnergyOutputFormat.getItems().setAll("txt", "png");

    comboboxLaserSpecification.getItems().addAll(LaserSpecification.getPresets());

    comboboxLaserSpecification.getSelectionModel().selectedItemProperty()
            .addListener(new ChangeListener<LaserSpecification>() {
                @Override
                public void changed(ObservableValue<? extends LaserSpecification> observable,
                        LaserSpecification oldValue, LaserSpecification newValue) {
                    DecimalFormatSymbols symb = new DecimalFormatSymbols();
                    symb.setDecimalSeparator('.');
                    DecimalFormat formatter = new DecimalFormat("#####.######", symb);

                    textFieldBeamDiameterAtExit.setText(formatter.format(newValue.getBeamDiameterAtExit()));
                    textFieldBeamDivergence.setText(formatter.format(newValue.getBeamDivergence()));
                }
            });

    comboboxLaserSpecification.getSelectionModel().select(LaserSpecification.LMS_Q560);

    comboboxLaserSpecification.disableProperty().bind(checkboxCustomLaserSpecification.selectedProperty());
    textFieldBeamDiameterAtExit.disableProperty()
            .bind(checkboxCustomLaserSpecification.selectedProperty().not());
    textFieldBeamDivergence.disableProperty().bind(checkboxCustomLaserSpecification.selectedProperty().not());

    listViewProductsFiles.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);

    listViewProductsFiles.getSelectionModel().selectedIndexProperty().addListener(new ChangeListener<Number>() {

        @Override
        public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
            int size = listViewProductsFiles.getSelectionModel().getSelectedIndices().size();

            if (size == 1) {
                viewer3DPanelController
                        .updateCurrentVoxelFile(listViewProductsFiles.getSelectionModel().getSelectedItem());
            }
        }
    });

    listViewTaskList.getSelectionModel().selectedIndexProperty().addListener(new ChangeListener<Number>() {

        @Override
        public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
            int size = listViewTaskList.getSelectionModel().getSelectedIndices().size();

            if (size == 1) {
                buttonLoadSelectedTask.setDisable(false);
            } else {
                buttonLoadSelectedTask.setDisable(true);
            }

            buttonExecute.setDisable(size == 0);
        }
    });

    resetMatrices();

    calculateMatrixFrame = new Stage();

    try {
        FXMLLoader loader = new FXMLLoader(getClass().getResource("/fxml/CalculateMatrixFrame.fxml"));
        Parent root = loader.load();
        calculateMatrixFrameController = loader.getController();
        calculateMatrixFrameController.setStage(calculateMatrixFrame);
        Scene scene = new Scene(root);
        calculateMatrixFrame.setScene(scene);
    } catch (IOException ex) {
        logger.error("Cannot load fxml file", ex);
    }

    filterFrame = new Stage();

    try {
        FXMLLoader loader = new FXMLLoader(getClass().getResource("/fxml/FilterFrame.fxml"));
        Parent root = loader.load();
        filterFrameController = loader.getController();
        filterFrameController.setStage(filterFrame);
        filterFrameController.setFilters("Angle");
        filterFrame.setScene(new Scene(root));
    } catch (IOException ex) {
        logger.error("Cannot load fxml file", ex);
    }

    try {
        FXMLLoader loader = new FXMLLoader(getClass().getResource("/fxml/export/ObjExporterDialog.fxml"));
        Parent root = loader.load();
        objExporterController = loader.getController();
        Stage s = new Stage();
        objExporterController.setStage(s);
        s.setScene(new Scene(root));
    } catch (IOException ex) {
        logger.error("Cannot load fxml file", ex);
    }

    textFieldResolution.textProperty().addListener(new ChangeListener<String>() {
        @Override
        public void changed(ObservableValue<? extends String> observable, String oldValue, String newValue) {
            voxelSpacePanelVoxelizationController.setResolution(Float.valueOf(newValue));
        }
    });

    textFieldResolution.textProperty().addListener(voxelSpacePanelVoxelizationController.getChangeListener());

    checkboxUseDTMFilter.selectedProperty().addListener(new ChangeListener<Boolean>() {

        @Override
        public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {

            if (checkboxUseDTMFilter.isSelected()) {
                buttonOpenDTMFile.setDisable(false);
                textfieldDTMPath.setDisable(false);
                textfieldDTMValue.setDisable(false);
                checkboxApplyVOPMatrix.setDisable(false);
                labelDTMValue.setDisable(false);
                labelDTMPath.setDisable(false);
            } else {
                buttonOpenDTMFile.setDisable(true);
                textfieldDTMPath.setDisable(true);
                textfieldDTMValue.setDisable(true);
                checkboxApplyVOPMatrix.setDisable(true);
                labelDTMValue.setDisable(true);
                labelDTMPath.setDisable(true);
            }
        }
    });

    checkboxUseVopMatrix.selectedProperty().addListener(new ChangeListener<Boolean>() {

        @Override
        public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
            buttonSetVOPMatrix.setDisable(!newValue);
        }
    });

    checkboxUsePopMatrix.selectedProperty().addListener(new ChangeListener<Boolean>() {

        @Override
        public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
            if (newValue) {
                checkBoxUseDefaultPopMatrix.setDisable(false);
                buttonOpenPopMatrixFile.setDisable(false);
            } else {
                checkBoxUseDefaultPopMatrix.setDisable(true);
                buttonOpenPopMatrixFile.setDisable(true);
            }
        }
    });

    checkboxUseSopMatrix.selectedProperty().addListener(new ChangeListener<Boolean>() {

        @Override
        public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
            if (newValue) {
                checkBoxUseDefaultSopMatrix.setDisable(false);
                buttonOpenSopMatrixFile.setDisable(false);
            } else {
                checkBoxUseDefaultSopMatrix.setDisable(true);
                buttonOpenSopMatrixFile.setDisable(true);
            }
        }
    });

    checkboxCalculateGroundEnergy.selectedProperty().addListener(new ChangeListener<Boolean>() {

        @Override
        public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
            if (newValue) {
                anchorPaneGroundEnergyParameters.setDisable(false);
            } else {
                anchorPaneGroundEnergyParameters.setDisable(true);
            }
        }
    });

    listviewRxpScans.getSelectionModel().selectedItemProperty().addListener(new ChangeListener<LidarScan>() {

        @Override
        public void changed(ObservableValue<? extends LidarScan> observable, LidarScan oldValue,
                LidarScan newValue) {
            if (newValue != null) {
                sopMatrix = newValue.matrix;
                updateResultMatrix();
            }
        }
    });

    comboboxModeTLS.getSelectionModel().selectedIndexProperty().addListener(new ChangeListener<Number>() {

        @Override
        public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {

            switch (newValue.intValue()) {

            case 1:
            case 2:
            case 3:
                listviewRxpScans.setDisable(false);
                checkboxMergeAfter.setDisable(false);
                textFieldMergedFileName.setDisable(false);
                disableSopMatrixChoice(false);
                labelTLSOutputPath.setText("Output path");
                break;

            default:
                listviewRxpScans.setDisable(true);
                checkboxMergeAfter.setDisable(true);
                textFieldMergedFileName.setDisable(true);
                //disableSopMatrixChoice(true);
                labelTLSOutputPath.setText("Output file");
            }

            if (newValue.intValue() == 0 || newValue.intValue() == 1) {
                checkboxEmptyShotsFilter.setDisable(false);
            } else {
                checkboxEmptyShotsFilter.setDisable(true);
            }
        }
    });

    tabPaneVoxelisation.getSelectionModel().selectedIndexProperty().addListener(new ChangeListener<Number>() {

        @Override
        public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {

            switch (newValue.intValue()) {

            case 1:
                disableSopMatrixChoice(false);
                disablePopMatrixChoice(false);
                checkboxEmptyShotsFilter.setDisable(false);
                break;

            default:
                disableSopMatrixChoice(true);
                disablePopMatrixChoice(true);
                checkboxEmptyShotsFilter.setDisable(true);
            }

            switch (newValue.intValue()) {
            case 0:
                checkboxCalculateGroundEnergy.setDisable(false);

                if (checkboxCalculateGroundEnergy.isSelected()) {
                    anchorPaneGroundEnergyParameters.setDisable(true);
                    checkboxCalculateGroundEnergy.setDisable(false);

                }

                anchorPaneEchoFiltering.getChildren().set(0, anchorPaneEchoFilteringClassifications);

                //anchorPaneEchoFilteringClassifications.setVisible(true);
                anchorpaneBoundingBoxParameters.setDisable(checkboxMultiFiles.isSelected());
                hboxAutomaticBBox.setDisable(false);
                break;
            default:
                anchorPaneGroundEnergyParameters.setDisable(true);
                checkboxCalculateGroundEnergy.setDisable(true);
                anchorPaneEchoFiltering.getChildren().set(0, anchorPaneEchoFilteringRxp);
                //anchorPaneEchoFilteringClassifications.setVisible(false);
                anchorpaneBoundingBoxParameters.setDisable(false);
                hboxAutomaticBBox.setDisable(true);
            }
        }
    });

    int availableCores = Runtime.getRuntime().availableProcessors();

    sliderRSPCoresToUse.setMin(1);
    sliderRSPCoresToUse.setMax(availableCores);
    sliderRSPCoresToUse.setValue(availableCores);

    textFieldInputFileALS.setOnDragOver(DragAndDropHelper.dragOverEvent);
    textFieldTrajectoryFileALS.setOnDragOver(DragAndDropHelper.dragOverEvent);
    textFieldOutputFileALS.setOnDragOver(DragAndDropHelper.dragOverEvent);
    textFieldInputFileTLS.setOnDragOver(DragAndDropHelper.dragOverEvent);
    textFieldOutputFileMerging.setOnDragOver(DragAndDropHelper.dragOverEvent);
    textfieldDTMPath.setOnDragOver(DragAndDropHelper.dragOverEvent);
    textFieldOutputFileGroundEnergy.setOnDragOver(DragAndDropHelper.dragOverEvent);
    listViewTaskList.setOnDragOver(DragAndDropHelper.dragOverEvent);
    listViewProductsFiles.setOnDragOver(DragAndDropHelper.dragOverEvent);
    textfieldVoxelFilePathTransmittance.setOnDragOver(DragAndDropHelper.dragOverEvent);
    textfieldOutputTextFilePath.setOnDragOver(DragAndDropHelper.dragOverEvent);
    textfieldOutputBitmapFilePath.setOnDragOver(DragAndDropHelper.dragOverEvent);

    textFieldInputFileALS.setOnDragDropped(new EventHandler<DragEvent>() {
        @Override
        public void handle(DragEvent event) {
            Dragboard db = event.getDragboard();
            boolean success = false;
            if (db.hasFiles() && db.getFiles().size() == 1) {
                success = true;
                for (File file : db.getFiles()) {
                    if (file != null) {
                        textFieldInputFileALS.setText(file.getAbsolutePath());
                        selectALSInputMode(file);
                    }
                }
            }
            event.setDropCompleted(success);
            event.consume();
        }
    });
    textFieldTrajectoryFileALS.setOnDragDropped(new EventHandler<DragEvent>() {
        @Override
        public void handle(DragEvent event) {
            Dragboard db = event.getDragboard();
            boolean success = false;
            if (db.hasFiles() && db.getFiles().size() == 1) {
                success = true;
                for (File file : db.getFiles()) {
                    if (file != null) {
                        onTrajectoryFileChoosed(file);
                    }
                }
            }
            event.setDropCompleted(success);
            event.consume();
        }
    });

    textFieldInputFileTLS.setOnDragDropped(new EventHandler<DragEvent>() {
        @Override
        public void handle(DragEvent event) {
            Dragboard db = event.getDragboard();
            boolean success = false;
            if (db.hasFiles() && db.getFiles().size() == 1) {
                success = true;
                for (File file : db.getFiles()) {
                    if (file != null) {
                        onInputFileTLSChoosed(file);
                    }
                }
            }
            event.setDropCompleted(success);
            event.consume();
        }
    });

    setDragDroppedSingleFileEvent(textFieldOutputFileALS);
    setDragDroppedSingleFileEvent(textFieldOutputFileMerging);
    setDragDroppedSingleFileEvent(textfieldDTMPath);
    setDragDroppedSingleFileEvent(textFieldOutputFileGroundEnergy);
    setDragDroppedSingleFileEvent(textfieldVoxelFilePathTransmittance);
    setDragDroppedSingleFileEvent(textfieldOutputTextFilePath);
    setDragDroppedSingleFileEvent(textfieldOutputBitmapFilePath);

    listViewTaskList.setOnDragDropped(new EventHandler<DragEvent>() {
        @Override
        public void handle(DragEvent event) {
            Dragboard db = event.getDragboard();
            boolean success = false;
            if (db.hasFiles()) {
                success = true;
                for (File file : db.getFiles()) {
                    addFileToTaskList(file);
                }
            }
            event.setDropCompleted(success);
            event.consume();
        }
    });

    listViewProductsFiles.setOnDragDropped(new EventHandler<DragEvent>() {
        @Override
        public void handle(DragEvent event) {
            Dragboard db = event.getDragboard();
            boolean success = false;
            if (db.hasFiles()) {
                success = true;
                for (File file : db.getFiles()) {
                    addFileToProductsList(file);
                }
            }
            event.setDropCompleted(success);
            event.consume();
        }
    });

    listViewProductsFiles.setOnDragDetected(new EventHandler<MouseEvent>() {

        @Override
        public void handle(MouseEvent event) {

            Dragboard db = listViewProductsFiles.startDragAndDrop(TransferMode.COPY);

            ClipboardContent content = new ClipboardContent();
            content.putFiles(listViewProductsFiles.getSelectionModel().getSelectedItems());
            db.setContent(content);

            event.consume();
        }
    });

    addPointcloudFilterComponent();

    checkboxUsePointcloudFilter.selectedProperty().addListener(new ChangeListener<Boolean>() {

        @Override
        public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {

            hBoxPointCloudFiltering.setDisable(!newValue);

            ObservableList<Node> list = vBoxPointCloudFiltering.getChildren();
            for (Node n : list) {
                if (n instanceof PointCloudFilterPaneComponent) {

                    PointCloudFilterPaneComponent panel = (PointCloudFilterPaneComponent) n;
                    panel.disableContent(!newValue);
                }
            }

            buttonAddPointcloudFilter.setDisable(!newValue);

        }
    });

    //displayGThetaAllDistributions();
}

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