Plotting progress for 5-isotopes

TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/AbstractDataView.java

@@ -49,8 +49,9 @@ public abstract class AbstractDataView extends Canvas {
     protected BigDecimal[] ticsX;
     protected BigDecimal[] ticsY;
     //    protected BigDecimal[] ticsYII;
-    private double displayOffsetY = 0;
-    private double displayOffsetX = 0;
+    protected double displayOffsetY = 0;
+    protected double displayOffsetX = 0;
+    protected String xAxisLabel;
 
     private AbstractDataView() {
         super();
@@ -108,9 +109,9 @@ public void labelXAxis(String label) {
 
     public void showTitle(String title) {
         Paint savedPaint = getGraphicsContext2D().getFill();
-        getGraphicsContext2D().setFont(Font.font("SansSerif", 14));
+        getGraphicsContext2D().setFont(Font.font("SansSerif", 10));
         getGraphicsContext2D().setFill(Paint.valueOf("RED"));
-        getGraphicsContext2D().fillText(title, leftMargin + 25, topMargin + 12);
+        getGraphicsContext2D().fillText(title, leftMargin + 25, topMargin + 7);
         getGraphicsContext2D().setFill(savedPaint);
     }
 

TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/GBeamLinePlot.java

@@ -80,7 +80,7 @@ public void paint(GraphicsContext g2d) {
         g2d.beginPath();
         g2d.setStroke(Paint.valueOf("Blue"));
         g2d.setLineDashes(0);
-        // x = magnetMass y = intensity
+        // x = magnetMass y = blockIntensities
 
         for (int i = 0; i < xMass.length; i++) {
             g2d.lineTo(mapX(xMass[i]), mapY(yIntensity[i]));

TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/HistogramPlot.java

@@ -45,12 +45,13 @@ public void preparePanel() {
         minX = xAxisData[0];
         maxX = xAxisData[xAxisData.length - 1];
         if (histogramBuilder.getHistograms().length > 1) {
-            // assume only 2 for now
-            minX = Math.min(minX, histogramBuilder.getHistograms()[1].binCenters()[0]);
-            maxX = Math.max(maxX, histogramBuilder.getHistograms()[1].binCenters()[histogramBuilder.getHistograms()[1].binCount() - 1]);
+            for (int histogramIndex = 0; histogramIndex < histogramBuilder.getHistograms().length; histogramIndex++) {
+                minX = Math.min(minX, histogramBuilder.getHistograms()[histogramIndex].binCenters()[0]);
+                maxX = Math.max(maxX, histogramBuilder.getHistograms()[histogramIndex].binCenters()[histogramBuilder.getHistograms()[histogramIndex].binCount() - 1]);
+            }
         }
 
-        double xMarginStretch = TicGeneratorForAxes.generateMarginAdjustment(minX, maxX, 0.05);
+        double xMarginStretch = TicGeneratorForAxes.generateMarginAdjustment(minX, maxX, 0.25);
         minX -= xMarginStretch;
         maxX += xMarginStretch;
         ticsX = TicGeneratorForAxes.generateTics(minX, maxX, (int) (graphWidth / 40.0));
@@ -64,16 +65,17 @@ public void preparePanel() {
             maxY = StrictMath.max(maxY, yAxisDatum);
         }
         if (histogramBuilder.getHistograms().length > 1) {
-            // assume only 2 for now
-            for (double yAxisDatum : histogramBuilder.getHistograms()[1].binCounts()) {
-                minY = StrictMath.min(minY, yAxisDatum);
-                maxY = StrictMath.max(maxY, yAxisDatum);
+            for (int histogramIndex = 0; histogramIndex < histogramBuilder.getHistograms().length; histogramIndex++) {
+                for (double yAxisDatum : histogramBuilder.getHistograms()[histogramIndex].binCounts()) {
+                    minY = StrictMath.min(minY, yAxisDatum);
+                    maxY = StrictMath.max(maxY, yAxisDatum);
+                }
             }
         }
 
         // customized for histogram
         minY = 0;
-        ticsY = TicGeneratorForAxes.generateTics(minY, maxY, (int) (graphHeight / 10.0));
+        ticsY = TicGeneratorForAxes.generateTics(minY, maxY, (int) (graphHeight / 20.0));
 
         // check for no data
         if ((ticsY != null) && (ticsY.length > 1)) {
@@ -111,11 +113,15 @@ public void paint(GraphicsContext g2d) {
 
         if (histogramBuilder.getHistograms().length > 1) {
             g2d.setFill(Paint.valueOf("GREEN"));
-            xAxisData = histogramBuilder.getHistograms()[1].binCenters();
-            yAxisData = histogramBuilder.getHistograms()[1].binCounts();
-            binWidth = histogramBuilder.getHistograms()[1].binWidth();
-            doFrameBins = (mapX(xAxisData[1]) - mapX(xAxisData[0])) > 1.0;
-            plotData(g2d, binWidth, doFrameBins);
+
+            for (int histogramIndex = 0; histogramIndex < histogramBuilder.getHistograms().length; histogramIndex++) {
+                xAxisData = histogramBuilder.getHistograms()[histogramIndex].binCenters();
+                yAxisData = histogramBuilder.getHistograms()[histogramIndex].binCounts();
+                binWidth = histogramBuilder.getHistograms()[histogramIndex].binWidth();
+                doFrameBins = (mapX(xAxisData[1]) - mapX(xAxisData[0])) > 1.0;
+                plotData(g2d, binWidth, doFrameBins);
+            }
+
             xAxisData = histogramBuilder.getHistograms()[0].binCenters();
             yAxisData = histogramBuilder.getHistograms()[0].binCounts();
         }
@@ -143,7 +149,7 @@ public void paint(GraphicsContext g2d) {
                     text.setText(bigDecimal.toString());
                     textWidth = (int) text.getLayoutBounds().getWidth();
                     g2d.fillText(text.getText(),//
-                            (float) mapX(minX) - textWidth - 5f,
+                            (float) mapX(minX) - textWidth - 2.5f,
                             (float) mapY(bigDecimal.doubleValue()) + verticalTextShift);
 
                     // right side
@@ -181,7 +187,7 @@ private void plotData(GraphicsContext g2d, double binWidth, boolean doFrameBins)
             g2d.fillRect(
                     mapX(xAxisData[i] - binWidth / 2.0) + (doFrameBins ? 1.0 : 0.0),
                     mapY(yAxisData[i]),
-                    mapX(xAxisData[1]) - mapX(xAxisData[0]) - (doFrameBins ? 1.0 : 0.0),
+                    mapX(xAxisData[1]) - mapX(xAxisData[0]) - (doFrameBins ? 1.0 : -0.5),
                     mapY(0.0) - mapY(yAxisData[i]));
         }
     }

TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/MultiLineLinePlot.java

@@ -0,0 +1,141 @@
+package org.cirdles.tripoli.gui.dataViews.plots;
+
+import javafx.scene.canvas.GraphicsContext;
+import javafx.scene.paint.Paint;
+import javafx.scene.shape.Path;
+import javafx.scene.shape.Rectangle;
+import javafx.scene.text.Font;
+import javafx.scene.text.Text;
+import org.cirdles.tripoli.visualizationUtilities.linePlots.MultiLinePlotBuilder;
+
+
+public class MultiLineLinePlot extends AbstractDataView {
+
+    private final MultiLinePlotBuilder multiLinePlotBuilder;
+    private double[][] yData;
+
+    /**
+     * @param bounds
+     * @param linePlotBuilder
+     */
+    public MultiLineLinePlot(Rectangle bounds, MultiLinePlotBuilder multiLinePlotBuilder) {
+        super(bounds, 50, 5);
+        this.multiLinePlotBuilder = multiLinePlotBuilder;
+    }
+
+    @Override
+    public void preparePanel() {
+        xAxisData = multiLinePlotBuilder.getxData();
+        yData = multiLinePlotBuilder.getyData();
+
+        minX = xAxisData[0];
+        maxX = xAxisData[xAxisData.length - 1];
+
+        ticsX = TicGeneratorForAxes.generateTics(minX, maxX, (int) (graphWidth / 40.0));
+        double xMarginStretch = TicGeneratorForAxes.generateMarginAdjustment(minX, maxX, 0.01);
+        minX -= xMarginStretch;
+        maxX += xMarginStretch;
+
+        minY = Double.MAX_VALUE;
+        maxY = -Double.MAX_VALUE;
+
+        for (int i = 0; i < yData.length; i++) {
+            for (int j = 0; j < yData[i].length; j++) {
+                minY = StrictMath.min(minY, yData[i][j]);
+                maxY = StrictMath.max(maxY, yData[i][j]);
+            }
+        }
+        ticsY = TicGeneratorForAxes.generateTics(minY, maxY, (int) (graphHeight / 15.0));
+        if ((ticsY != null) && (ticsY.length > 1)) {
+            // force y to tics
+            minY = ticsY[0].doubleValue();
+            maxY = ticsY[ticsY.length - 1].doubleValue();
+            // adjust margins
+            double yMarginStretch = TicGeneratorForAxes.generateMarginAdjustment(minY, maxY, 0.1);
+            minY -= yMarginStretch * 2.0;
+            maxY += yMarginStretch;
+        }
+
+        setDisplayOffsetY(0.0);
+        setDisplayOffsetX(0.0);
+
+        this.repaint();
+    }
+
+    @Override
+    public void paint(GraphicsContext g2d) {
+        super.paint(g2d);
+
+        Text text = new Text();
+        text.setFont(Font.font("SansSerif", 12));
+        int textWidth = 0;
+
+        showTitle(multiLinePlotBuilder.getTitle());
+
+        // new line plots
+        g2d.setLineWidth(1.0);
+        g2d.setStroke(Paint.valueOf("Black"));
+        for (int lineIndex = 0; lineIndex < yData.length; lineIndex++) {
+            g2d.setLineDashes(8);
+            g2d.beginPath();
+            g2d.moveTo(mapX(xAxisData[0]), mapY(yData[lineIndex][0]));
+            for (int i = 0; i < xAxisData.length; i++) {
+                // line tracing through points
+                g2d.lineTo(mapX(xAxisData[i]), mapY(yData[lineIndex][i]));
+            }
+            g2d.stroke();
+        }
+        g2d.setLineDashes(0);
+
+        if (ticsY.length > 1) {
+            // border and fill
+            g2d.setLineWidth(0.5);
+            g2d.setStroke(Paint.valueOf("BLACK"));
+            g2d.strokeRect(
+                    mapX(minX),
+                    mapY(ticsY[ticsY.length - 1].doubleValue()),
+                    graphWidth,
+                    StrictMath.abs(mapY(ticsY[ticsY.length - 1].doubleValue()) - mapY(ticsY[0].doubleValue())));
+
+            g2d.setFill(Paint.valueOf("BLACK"));
+
+            // ticsY
+            float verticalTextShift = 3.2f;
+            g2d.setFont(Font.font("SansSerif", 10));
+            if (ticsY != null) {
+                for (int i = 0; i < ticsY.length; i++) {
+                    g2d.strokeLine(
+                            mapX(minX), mapY(ticsY[i].doubleValue()), mapX(maxX), mapY(ticsY[i].doubleValue()));
+
+                    // left side
+                    text.setText(ticsY[i].toString());
+                    textWidth = (int) text.getLayoutBounds().getWidth();
+                    g2d.fillText(text.getText(),//
+                            (float) mapX(minX) - textWidth - 5f,
+                            (float) mapY(ticsY[i].doubleValue()) + verticalTextShift);
+
+                }
+                // ticsX
+                if (ticsX != null) {
+                    for (int i = 0; i < ticsX.length - 1; i++) {
+                        try {
+                            g2d.strokeLine(
+                                    mapX(ticsX[i].doubleValue()),
+                                    mapY(ticsY[0].doubleValue()),
+                                    mapX(ticsX[i].doubleValue()),
+                                    mapY(ticsY[0].doubleValue()) + 5);
+
+                            // bottom
+                            String xText = ticsX[i].toPlainString();
+                            g2d.fillText(xText,
+                                    (float) mapX(ticsX[i].doubleValue()) - 5f,
+                                    (float) mapY(ticsY[0].doubleValue()) + 15);
+
+                        } catch (Exception e) {
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/PeakCentresLinePlot.java

@@ -86,7 +86,7 @@ public void paint(GraphicsContext g2d) {
             g2d.beginPath();
             g2d.setStroke(Paint.valueOf("Black"));
             g2d.setLineDashes(0);
-            // x = magnetMass y = intensity
+            // x = magnetMass y = blockIntensities
 
             for (int i = 0; i < xAxisData.length; i++) {
                 g2d.lineTo(mapX(xAxisData[i]), mapY(yAxisData[i]));
@@ -216,4 +216,4 @@ public void handle(MouseEvent mouseEvent) {
         }
     }
 
-}
+}

TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/plotsControllers/RJMCMCPlots/RJMCMCPlotsController.java

@@ -9,6 +9,8 @@
 import javafx.scene.layout.GridPane;
 import javafx.scene.layout.VBox;
 import javafx.scene.shape.Rectangle;
+import org.cirdles.commons.util.ResourceExtractor;
+import org.cirdles.tripoli.Tripoli;
 import org.cirdles.tripoli.gui.dataViews.plots.*;
 import org.cirdles.tripoli.sessions.analysis.methods.AnalysisMethod;
 import org.cirdles.tripoli.sessions.analysis.methods.AnalysisMethodBuiltinFactory;
@@ -99,28 +101,35 @@ public class RJMCMCPlotsController {
     @FXML
     private Button processFileButton;
 
+    @FXML
+    private Button processFileButton2;
+
     @FXML
     private ToolBar toolbar;
 
     private ListView<File> listViewOfSyntheticFiles = new ListView<>();
 
 
     @FXML
-    void demo1ButtonAction(ActionEvent event) throws IOException {
+    void demo1_2IsotopeButtonAction(ActionEvent event) throws IOException {
         processDataFileAndShowPlotsOfRJMCMC(
                 listViewOfSyntheticFiles.getSelectionModel().selectedItemProperty().getValue().toPath(),
                 AnalysisMethodBuiltinFactory.analysisMethodsBuiltinMap.get("BurdickBlSyntheticData"));
-
+        ((Button) event.getSource()).setDisable(true);
+        processFileButton2.setDisable(true);
+    }
+    @FXML
+    void demo1_5IsotopeButtonAction(ActionEvent event) throws IOException {
         // Jim's playground for 5 isotopes
-//        ResourceExtractor RESOURCE_EXTRACTOR= new ResourceExtractor(Tripoli.class);
-//        Path dataFile = RESOURCE_EXTRACTOR
-//                .extractResourceAsFile("/org/cirdles/tripoli/dataProcessors/dataSources/synthetic/fiveIsotopeSyntheticData/SyntheticDataset_01R.txt").toPath();
-//        processDataFileAndShowPlotsOfRJMCMC(
-//                dataFile,
-//                AnalysisMethodBuiltinFactory.analysisMethodsBuiltinMap.get("KU_204_5_6_7_8_Daly_AllFaradayPb"));
-
+        ResourceExtractor RESOURCE_EXTRACTOR = new ResourceExtractor(Tripoli.class);
+        Path dataFile = RESOURCE_EXTRACTOR
+                .extractResourceAsFile("/org/cirdles/tripoli/dataProcessors/dataSources/synthetic/fiveIsotopeSyntheticData/SyntheticDataset_01R.txt").toPath();
+        processDataFileAndShowPlotsOfRJMCMC(
+                dataFile,
+                AnalysisMethodBuiltinFactory.analysisMethodsBuiltinMap.get("KU_204_5_6_7_8_Daly_AllFaradayPb"));
 
         ((Button) event.getSource()).setDisable(true);
+        processFileButton.setDisable(true);
     }
 
     @FXML
@@ -159,6 +168,7 @@ void initialize() {
         populateListOfSyntheticData2IsotopesFiles();
 
         processFileButton.setDisable(listViewOfSyntheticFiles.getItems().isEmpty());
+        processFileButton2.setDisable(listViewOfSyntheticFiles.getItems().isEmpty());
     }
 
     private void populateListOfSyntheticData2IsotopesFiles() {
@@ -242,10 +252,10 @@ public void processDataFileAndShowPlotsOfRJMCMC(Path dataFile, AnalysisMethod an
                             (plotTabPane.getHeight() - TAB_HEIGHT) / ensembleGridPane.getRowCount()),
                     (HistogramBuilder) dalyFaradayHistogramBuilder);
 
-            AbstractDataView intensityLinePlot = new BasicLinePlot(
+            AbstractDataView intensityLinePlot = new MultiLineLinePlot(
                     new Rectangle(ensembleGridPane.getWidth(),
                             (plotTabPane.getHeight() - TAB_HEIGHT) / ensembleGridPane.getRowCount()),
-                    (LinePlotBuilder) intensityLinePlotBuilder
+                    (MultiLinePlotBuilder) intensityLinePlotBuilder
             );
 
             AbstractDataView signalNoiseHistogramPlot = new HistogramPlot(
@@ -400,7 +410,7 @@ public void processDataFileAndShowPlotsOfRJMCMC(Path dataFile, AnalysisMethod an
             intensityLinePlot.preparePanel();
             ensembleGridPane.add(intensityLinePlot, 0, 2, 2, 1);
             signalNoiseHistogramPlot.preparePanel();
-            ensembleGridPane.add(signalNoiseHistogramPlot, 0, 4, 2, 1);
+            ensembleGridPane.add(signalNoiseHistogramPlot, 0, 3, 2, 1);
 
             convergeRatioLinePlot.preparePanel();
             convergeRatioAnchorPane.getChildren().add(convergeRatioLinePlot);