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Additional plots and conversion to ojAlgo matrix library #60

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merged 2 commits into from
Aug 17, 2022
Merged

Additional plots and conversion to ojAlgo matrix library #60

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5ad03f9
additional plots
bowring Aug 17, 2022
e58c4c5
Merged to fix conflicts
bowring Aug 17, 2022
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2 changes: 1 addition & 1 deletion TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/BasicLinePlot.java
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ public void paint(GraphicsContext g2d) {
g2d.fillText(intensityLinePlotBuilder.getTitle(), leftMargin + 25, 15);

g2d.setLineWidth(2.0);
// new line graph
// new line plot
g2d.setStroke(Paint.valueOf("Black"));
g2d.beginPath();
g2d.moveTo(mapX(xAxisData[0]), mapY(yAxisData[0]));
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159 changes: 159 additions & 0 deletions ...oliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/BasicScatterAndLinePlot.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,159 @@
package org.cirdles.tripoli.gui.dataViews.plots;

import javafx.scene.canvas.GraphicsContext;
import javafx.scene.paint.Paint;
import javafx.scene.shape.Rectangle;
import javafx.scene.text.Font;
import javafx.scene.text.FontWeight;
import javafx.scene.text.Text;
import org.cirdles.tripoli.visualizationUtilities.linePlots.ComboPlotBuilder;


public class BasicScatterAndLinePlot extends AbstractDataView {

private final ComboPlotBuilder comboPlotBuilder;
private double[] yAxisData2;
/**
* @param bounds
* @param comboPlotBuilder
*/
public BasicScatterAndLinePlot(Rectangle bounds, ComboPlotBuilder comboPlotBuilder) {
super(bounds, 50, 5);
this.comboPlotBuilder = comboPlotBuilder;
}

@Override
public void preparePanel() {
xAxisData = comboPlotBuilder.getxData();
yAxisData = comboPlotBuilder.getyData();
yAxisData2 = comboPlotBuilder.getyData2();

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 < yAxisData.length; i++) {
minY = StrictMath.min(minY, yAxisData[i]);
maxY = StrictMath.max(maxY, yAxisData[i]);
minY = StrictMath.min(minY, yAxisData2[i]);
maxY = StrictMath.max(maxY, yAxisData2[i]);
if (comboPlotBuilder.isyData2OneSigma()){
minY = StrictMath.min(minY, -yAxisData2[i]);
}
}
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;

g2d.setFont(Font.font("SansSerif", FontWeight.SEMI_BOLD, 12));
g2d.setFill(Paint.valueOf("BLUE"));
g2d.fillText(comboPlotBuilder.getTitle(), leftMargin + 25, 15);

// scatter plot
g2d.setLineWidth(0.75);
g2d.setStroke(Paint.valueOf("Black"));
for (int i = 0; i < xAxisData.length; i++) {
g2d.strokeOval(mapX(xAxisData[i]) - 2f, mapY(yAxisData[i]) -2f, 4f, 4f);
}

// new line plot from yAxisData2
g2d.setStroke(Paint.valueOf("red"));
g2d.beginPath();
g2d.moveTo(mapX(xAxisData[0]), mapY(yAxisData2[0]));
for (int i = 0; i < xAxisData.length; i++) {
// line tracing through points
g2d.lineTo(mapX(xAxisData[i]), mapY(yAxisData2[i]));
}
g2d.stroke();

if (comboPlotBuilder.isyData2OneSigma()){
g2d.beginPath();
g2d.moveTo(mapX(xAxisData[0]), mapY(-yAxisData2[0]));
for (int i = 0; i < xAxisData.length; i++) {
// line tracing through points
g2d.lineTo(mapX(xAxisData[i]), mapY(-yAxisData2[i]));
}
g2d.stroke();
}


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) {
}
}
}
}
}
}
}
2 changes: 1 addition & 1 deletion TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/BasicScatterPlot.java
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ public void paint(GraphicsContext g2d) {
g2d.fillText(intensityLinePlotBuilder.getTitle(), leftMargin + 25, 15);

g2d.setLineWidth(0.5);
// new line graph
// scatter plot
g2d.setStroke(Paint.valueOf("Black"));
for (int i = 0; i < xAxisData.length; i++) {
g2d.strokeOval(mapX(xAxisData[i]) - 2f, mapY(yAxisData[i]) -2f, 4f, 4f);
Expand Down
14 changes: 10 additions & 4 deletions ...dles/tripoli/gui/dataViews/plots/plotsControllers/RJMCMCPlots/RJMCMCPlotBuildersTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,8 @@ public class RJMCMCPlotBuildersTask extends Task<String> implements LoggingCallb

private AbstractPlotBuilder convergeRatioLineBuilder;

private AbstractPlotBuilder ObserveDataLineBuilder;
private AbstractPlotBuilder observedDataLineBuilder;
private AbstractPlotBuilder residualDataLineBuilder;

public RJMCMCPlotBuildersTask(Path dataFile) {
this.dataFile = dataFile;
Expand Down Expand Up @@ -67,8 +68,12 @@ public AbstractPlotBuilder getConvergeRatioLineBuilder() {
return convergeRatioLineBuilder;
}

public AbstractPlotBuilder getObserveDataLineBuilder() {
return ObserveDataLineBuilder;
public AbstractPlotBuilder getObservedDataLineBuilder() {
return observedDataLineBuilder;
}

public AbstractPlotBuilder getResidualDataLineBuilder() {
return residualDataLineBuilder;
}

@Override
Expand All @@ -82,7 +87,8 @@ protected String call() throws Exception {

convergeRatioLineBuilder = plots[5];

ObserveDataLineBuilder = plots[6];
observedDataLineBuilder = plots[6];
residualDataLineBuilder = plots[7];
return "DONE";
}

Expand Down
110 changes: 56 additions & 54 deletions ...rdles/tripoli/gui/dataViews/plots/plotsControllers/RJMCMCPlots/RJMCMCPlotsController.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
package org.cirdles.tripoli.gui.dataViews.plots.plotsControllers.RJMCMCPlots;

import javafx.beans.value.ChangeListener;
import javafx.beans.value.ObservableValue;
import javafx.event.ActionEvent;
import javafx.fxml.FXML;
import javafx.scene.control.*;
Expand All @@ -11,12 +9,10 @@
import javafx.scene.shape.Rectangle;
import org.cirdles.commons.util.ResourceExtractor;
import org.cirdles.tripoli.Tripoli;
import org.cirdles.tripoli.gui.dataViews.plots.AbstractDataView;
import org.cirdles.tripoli.gui.dataViews.plots.BasicScatterPlot;
import org.cirdles.tripoli.gui.dataViews.plots.HistogramPlot;
import org.cirdles.tripoli.gui.dataViews.plots.BasicLinePlot;
import org.cirdles.tripoli.gui.dataViews.plots.*;
import org.cirdles.tripoli.visualizationUtilities.AbstractPlotBuilder;
import org.cirdles.tripoli.visualizationUtilities.histograms.HistogramBuilder;
import org.cirdles.tripoli.visualizationUtilities.linePlots.ComboPlotBuilder;
import org.cirdles.tripoli.visualizationUtilities.linePlots.LinePlotBuilder;

import java.io.IOException;
Expand Down Expand Up @@ -112,7 +108,8 @@ public void processDataFileAndShowPlotsOfRJMCMC() throws IOException {

AbstractPlotBuilder convergeRatioPlotBuilder = ((RJMCMCPlotBuildersTask) service.getPlotBuildersTask()).getConvergeRatioLineBuilder();

AbstractPlotBuilder observedDataPlotBuilder = ((RJMCMCPlotBuildersTask) service.getPlotBuildersTask()).getObserveDataLineBuilder();
AbstractPlotBuilder observedDataPlotBuilder = ((RJMCMCPlotBuildersTask) service.getPlotBuildersTask()).getObservedDataLineBuilder();
AbstractPlotBuilder residualDataPlotBuilder = ((RJMCMCPlotBuildersTask) service.getPlotBuildersTask()).getResidualDataLineBuilder();

AbstractDataView ratiosHistogramPlot = new HistogramPlot(
new Rectangle(ensembleGridPane.getWidth(),
Expand Down Expand Up @@ -145,58 +142,61 @@ public void processDataFileAndShowPlotsOfRJMCMC() throws IOException {
convergeRatioScrollPane.getHeight()),
(LinePlotBuilder) convergeRatioPlotBuilder);

AbstractDataView observedDataLinePlot = new BasicScatterPlot(
AbstractDataView observedDataLinePlot = new BasicScatterAndLinePlot(
new Rectangle(dataFitGridPane.getWidth(),
dataFitGridPane.getHeight() / dataFitGridPane.getRowCount()),
(LinePlotBuilder) observedDataPlotBuilder);


plotTabPane.widthProperty().addListener(new ChangeListener<Number>() {
@Override
public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
if (newValue.intValue() > 100) {
double newWidth = newValue.intValue() - ensembleLegendTextBox.getWidth();
ratiosHistogramPlot.setMyWidth(newWidth);
ratiosHistogramPlot.repaint();
baselineHistogramPlot.setMyWidth(newWidth / ensembleGridPane.getColumnCount());
baselineHistogramPlot.repaint();
dalyFaradayHistogramPlot.setMyWidth(newWidth / ensembleGridPane.getColumnCount());
dalyFaradayHistogramPlot.repaint();
intensityLinePlot.setMyWidth(newWidth);
intensityLinePlot.repaint();
signalNoiseHistogramPlot.setMyWidth(newWidth);
signalNoiseHistogramPlot.repaint();

convergeRatioLinePlot.setMyWidth(newValue.intValue());
convergeRatioLinePlot.repaint();

observedDataLinePlot.setMyWidth(newWidth);
observedDataLinePlot.repaint();
}
(ComboPlotBuilder) observedDataPlotBuilder);

AbstractDataView residualDataLinePlot = new BasicScatterAndLinePlot(
new Rectangle(dataFitGridPane.getWidth(),
dataFitGridPane.getHeight() / dataFitGridPane.getRowCount()),
(ComboPlotBuilder) residualDataPlotBuilder);


plotTabPane.widthProperty().addListener((observable, oldValue, newValue) -> {
if (newValue.intValue() > 100) {
double newWidth = newValue.intValue() - ensembleLegendTextBox.getWidth();
ratiosHistogramPlot.setMyWidth(newWidth);
ratiosHistogramPlot.repaint();
baselineHistogramPlot.setMyWidth(newWidth / ensembleGridPane.getColumnCount());
baselineHistogramPlot.repaint();
dalyFaradayHistogramPlot.setMyWidth(newWidth / ensembleGridPane.getColumnCount());
dalyFaradayHistogramPlot.repaint();
intensityLinePlot.setMyWidth(newWidth);
intensityLinePlot.repaint();
signalNoiseHistogramPlot.setMyWidth(newWidth);
signalNoiseHistogramPlot.repaint();

convergeRatioLinePlot.setMyWidth(newValue.intValue());
convergeRatioLinePlot.repaint();

observedDataLinePlot.setMyWidth(newWidth);
observedDataLinePlot.repaint();
residualDataLinePlot.setMyWidth(newWidth);
residualDataLinePlot.repaint();
}
});

plotTabPane.heightProperty().addListener(new ChangeListener<Number>() {
@Override
public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
if (newValue.intValue() > 100) {
ratiosHistogramPlot.setMyHeight(newValue.intValue() / ensembleGridPane.getRowCount() - 5);
ratiosHistogramPlot.repaint();
baselineHistogramPlot.setMyHeight(newValue.intValue() / ensembleGridPane.getRowCount() - 5);
baselineHistogramPlot.repaint();
dalyFaradayHistogramPlot.setMyHeight(newValue.intValue() / ensembleGridPane.getRowCount() - 5);
dalyFaradayHistogramPlot.repaint();
intensityLinePlot.setMyHeight(newValue.intValue() / ensembleGridPane.getRowCount() - 5);
intensityLinePlot.repaint();
signalNoiseHistogramPlot.setMyHeight(newValue.intValue() / ensembleGridPane.getRowCount() - 5);
signalNoiseHistogramPlot.repaint();

convergeRatioLinePlot.setMyHeight(newValue.intValue());
convergeRatioLinePlot.repaint();

observedDataLinePlot.setMyHeight(newValue.intValue());
observedDataLinePlot.repaint();
}
plotTabPane.heightProperty().addListener((observable, oldValue, newValue) -> {
if (newValue.intValue() > 100) {
ratiosHistogramPlot.setMyHeight(newValue.intValue() / ensembleGridPane.getRowCount() - 5);
ratiosHistogramPlot.repaint();
baselineHistogramPlot.setMyHeight(newValue.intValue() / ensembleGridPane.getRowCount() - 5);
baselineHistogramPlot.repaint();
dalyFaradayHistogramPlot.setMyHeight(newValue.intValue() / ensembleGridPane.getRowCount() - 5);
dalyFaradayHistogramPlot.repaint();
intensityLinePlot.setMyHeight(newValue.intValue() / ensembleGridPane.getRowCount() - 5);
intensityLinePlot.repaint();
signalNoiseHistogramPlot.setMyHeight(newValue.intValue() / ensembleGridPane.getRowCount() - 5);
signalNoiseHistogramPlot.repaint();

convergeRatioLinePlot.setMyHeight(newValue.intValue());
convergeRatioLinePlot.repaint();

observedDataLinePlot.setMyHeight(newValue.intValue() / dataFitGridPane.getRowCount() - 5);
observedDataLinePlot.repaint();
residualDataLinePlot.setMyHeight(newValue.intValue() / dataFitGridPane.getRowCount() - 5);
residualDataLinePlot.repaint();
}
});

Expand All @@ -216,6 +216,8 @@ public void changed(ObservableValue<? extends Number> observable, Number oldValu

observedDataLinePlot.preparePanel();
dataFitGridPane.add(observedDataLinePlot, 0,0);
residualDataLinePlot.preparePanel();
dataFitGridPane.add(residualDataLinePlot, 0,1);


});
Expand Down
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