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Merge pull request #70 from robinsonianr/peak-cleanup
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Peak Refining and Doc
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@bowring
bowring authored Sep 6, 2022
2 parents f7eb7ec + b3f64ba commit 289c889
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Showing 8 changed files with 127 additions and 125 deletions.
6 changes: 3 additions & 3 deletions TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/BeamShapeLinePlot.java
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Original file line number Diff line number Diff line change
Expand Up @@ -96,8 +96,8 @@ public void paint(GraphicsContext g2d) {
g2d.stroke();

g2d.setFill(Paint.valueOf("Red"));
g2d.fillOval(mapX(xAxisData[leftBoundary]) - 2, mapY(yAxisData[leftBoundary]) - 4, 7, 7);
g2d.fillOval(mapX(xAxisData[rightBoundary]) - 2, mapY(yAxisData[rightBoundary]) - 4, 7, 7);
g2d.fillOval(mapX(xAxisData[leftBoundary]) - 3.5, mapY(yAxisData[leftBoundary]) - 3.5, 7, 7);
g2d.fillOval(mapX(xAxisData[rightBoundary]) - 3.5, mapY(yAxisData[rightBoundary]) - 3.5, 7, 7);

g2d.beginPath();
g2d.setLineDashes(0);
Expand Down Expand Up @@ -127,7 +127,7 @@ 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 - 5f,
(float) mapY(bigDecimal.doubleValue()) + verticalTextShift);

}
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2 changes: 1 addition & 1 deletion TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/GBeamLinePlot.java
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Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,7 @@ 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 - 5f,
(float) mapY(bigDecimal.doubleValue()) + verticalTextShift);

}
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214 changes: 119 additions & 95 deletions ...tripoli/gui/dataViews/plots/plotsControllers/peakShapePlots/PeakShapePlotsController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import javafx.collections.ObservableList;
import javafx.fxml.FXML;
import javafx.scene.control.*;
import javafx.scene.input.KeyCode;
import javafx.scene.layout.AnchorPane;
import javafx.scene.layout.VBox;
import javafx.scene.shape.Rectangle;
Expand Down Expand Up @@ -202,20 +203,20 @@ private void populateListOfGroups() {
ObservableList<String> items = FXCollections.observableArrayList(resourceGroups.keySet().stream().toList());
listViewOfGroupResourcesInFolder.setItems(items);



listViewOfGroupResourcesInFolder.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> {
// Files will be manipulated here when group is selected
setCurrentGroup(newValue);
processFilesAndShowPeakCentre(newValue);
populateListOfResources(newValue);
setCurrentGroup(newValue);
gBeamPlotScrollPane.setContent(null);
beamShapePlotScrollPane.setContent(null);
eventLogTextArea.textProperty().unbind();
eventLogTextArea.setText("Select File From Plot");
});

listViewOfGroupResourcesInFolder.getSelectionModel().selectFirst();
setCurrentGroup(listViewOfGroupResourcesInFolder.getSelectionModel().getSelectedItem());


listViewOfGroupResourcesInFolder.getSelectionModel().selectFirst();
listViewOfGroupResourcesInFolder.prefHeightProperty().bind(resourceListAnchorPane.prefHeightProperty());
listViewOfGroupResourcesInFolder.prefWidthProperty().bind(resourceListAnchorPane.prefWidthProperty());
resourceListAnchorPane.getChildren().add(listViewOfGroupResourcesInFolder);
Expand All @@ -238,94 +239,11 @@ private void populateListOfGroups() {

}

private void populateListOfResources(String groupValue) {
listViewOfResourcesInFolder = new ListView<>();
listViewOfResourcesInFolder.setCellFactory(param -> new ResourceDisplayName2());
eventLogTextArea.textProperty().unbind();

ObservableList<File> items = FXCollections.observableArrayList(resourceGroups.get(groupValue));
listViewOfResourcesInFolder.setItems(items);


listViewOfResourcesInFolder.setOnMouseClicked(click -> {
peakCentreLinePlot.repaint();
int index;
if (click.getClickCount() == 1) {
resourceBrowserTarget = listViewOfResourcesInFolder.getSelectionModel().getSelectedItem();
index = listViewOfResourcesInFolder.getSelectionModel().getSelectedIndex();
peakCentreLinePlot.getGraphicsContext2D().setLineWidth(1.0);
peakCentreLinePlot.getGraphicsContext2D().strokeOval(peakCentreLinePlot.mapX(peakCentreLinePlot.getxAxisData()[index]) - 6, peakCentreLinePlot.mapY(peakCentreLinePlot.getyAxisData()[index]) - 6, 12, 12);
processDataFileAndShowPlotsOfPeakShapes();
}
});

listViewOfResourcesInFolder.prefHeightProperty().bind(eventAnchorPane.heightProperty());
listViewOfResourcesInFolder.prefWidthProperty().bind(eventAnchorPane.widthProperty());
eventAnchorPane.getChildren().add(listViewOfResourcesInFolder);
}

public void processFilesAndShowPeakCentre(String groupValue) {

double[] finalYAxis;
double[] finalXAxis;

// PeakShapesService service;
// // Trying to get data from peakShapeTask
// for (int j = 0; j < fileGroups.size(); j++) {
// if (fileGroups.get(j).equalsIgnoreCase(groupValue)) {
// for (int h = 0; h < resourceGroups.get(j).size(); h++) {
// final double[] testXAxis = new double[resourceGroups.get(j).size()];
// final double[] testYAxis = new double[resourceGroups.get(j).size()];
//
// testXAxis[h] = h + 1;
// for (int i = 0; i < resourceGroups.get(j).size(); i++) {
// resourceBrowserTarget = resourceGroups.get(j).get(i);
// service = new PeakShapesService(resourceBrowserTarget.toPath());
// service.start();
// int finalI = i;
// int finalJ = j;
// PeakShapesService finalService = service;
// service.setOnSucceeded(evt -> {
// if (finalI != resourceGroups.get(finalJ).size() - 1) {
// AbstractPlotBuilder beamShapePlotBuilder = ((PeakShapesTask) finalService.getPeakShapesTask()).getBeamShapePlotBuilder();
// AbstractPlotBuilder gBeamPlotBuilder = ((PeakShapesTask) finalService.getPeakShapesTask()).getGBeamPlotBuilder();
// testYAxis[finalI] = ((PeakShapesTask) finalService.getPeakShapesTask()).getPeakWidth();
// } else {
// LinePlotBuilder peakCentrePlotBuilder = LinePlotBuilder.initializeLinePlot(testXAxis, testYAxis, "PeakCentre Plot");
//
// AbstractDataView peakCentreLinePlot = new PeakCentresLinePlot(new Rectangle(peakCentrePlotScrollPane.getWidth(), peakCentrePlotScrollPane.getHeight()), peakCentrePlotBuilder);
//
// peakCentrePlotScrollPane.widthProperty().addListener(new ChangeListener<Number>() {
// @Override
// public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
// peakCentreLinePlot.setMyWidth(newValue.intValue());
// peakCentreLinePlot.repaint();
// }
// });
//
// peakCentrePlotScrollPane.heightProperty().addListener(new ChangeListener<Number>() {
// @Override
// public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
// peakCentreLinePlot.setMyHeight(newValue.intValue());
// peakCentreLinePlot.repaint();
// }
// });
//
// peakCentreLinePlot.preparePanel();
// peakCentrePlotScrollPane.setContent(peakCentreLinePlot);
// resourceBrowserTarget = null;
// }
//
// });
//
// }
// System.out.println(Arrays.toString(testXAxis));
// }
//
// }
// }

// Work in progress todo
double[] xAxis = new double[resourceGroups.get(groupValue).size()];
double[] yAxis = new double[resourceGroups.get(groupValue).size()];
for (int k = 0; k < resourceGroups.get(groupValue).size(); k++) {
Expand Down Expand Up @@ -371,20 +289,68 @@ public void processFilesAndShowPeakCentre(String groupValue) {

}

private void populateListOfResources(String groupValue) {
listViewOfResourcesInFolder = new ListView<>();
listViewOfResourcesInFolder.setCellFactory(param -> new ResourceDisplayName2());
eventLogTextArea.textProperty().unbind();
int initialIndex;

ObservableList<File> items = FXCollections.observableArrayList(resourceGroups.get(groupValue));
listViewOfResourcesInFolder.setItems(items);



listViewOfResourcesInFolder.setOnMouseClicked(click -> {
peakCentreLinePlot.repaint();
int index;
if (click.getClickCount() == 1) {
resourceBrowserTarget = listViewOfResourcesInFolder.getSelectionModel().getSelectedItem();
index = listViewOfResourcesInFolder.getSelectionModel().getSelectedIndex();
peakCentreLinePlot.getGraphicsContext2D().setLineWidth(1.0);
peakCentreLinePlot.getGraphicsContext2D().strokeOval(peakCentreLinePlot.mapX(peakCentreLinePlot.getxAxisData()[index]) - 6, peakCentreLinePlot.mapY(peakCentreLinePlot.getyAxisData()[index]) - 6, 12, 12);
processDataFileAndShowPlotsOfPeakShapes();
}
});

listViewOfResourcesInFolder.setOnKeyPressed(key -> {
peakCentreLinePlot.repaint();
int index;
if (key.getCode() == KeyCode.DOWN || key.getCode() == KeyCode.UP) {
resourceBrowserTarget = listViewOfResourcesInFolder.getSelectionModel().getSelectedItem();
index = listViewOfResourcesInFolder.getSelectionModel().getSelectedIndex();
processDataFileAndShowPlotsOfPeakShapes();
peakCentreLinePlot.getGraphicsContext2D().setLineWidth(1.0);
peakCentreLinePlot.getGraphicsContext2D().strokeOval(peakCentreLinePlot.mapX(peakCentreLinePlot.getxAxisData()[index]) - 6, peakCentreLinePlot.mapY(peakCentreLinePlot.getyAxisData()[index]) - 6, 12, 12);
}
});

listViewOfResourcesInFolder.getSelectionModel().selectFirst();
initialIndex = listViewOfResourcesInFolder.getSelectionModel().getSelectedIndex();
resourceBrowserTarget = listViewOfResourcesInFolder.getSelectionModel().getSelectedItem();
peakCentreLinePlot.getGraphicsContext2D().setLineWidth(1.0);
peakCentreLinePlot.getGraphicsContext2D().strokeOval(peakCentreLinePlot.mapX(peakCentreLinePlot.getxAxisData()[initialIndex]) - 6, peakCentreLinePlot.mapY(peakCentreLinePlot.getyAxisData()[initialIndex]) - 6, 12, 12);
processDataFileAndShowPlotsOfPeakShapes();

listViewOfResourcesInFolder.prefHeightProperty().bind(eventAnchorPane.heightProperty());
listViewOfResourcesInFolder.prefWidthProperty().bind(eventAnchorPane.widthProperty());
eventAnchorPane.getChildren().add(listViewOfResourcesInFolder);
}



public void processDataFileAndShowPlotsOfPeakShapes() {


if (resourceBrowserTarget != null && resourceBrowserTarget.isFile()) {
final PeakShapesService service = new PeakShapesService(resourceBrowserTarget.toPath());
eventLogTextArea.textProperty().bind(service.valueProperty());
service.start();
service.setOnSucceeded(evt -> {
AbstractPlotBuilder gBeamPlotBuilder = ((PeakShapesTask) service.getPeakShapesTask()).getGBeamPlotBuilder();
try {
AbstractPlotBuilder[] plots = BeamDataOutputDriverExperiment.modelTest(resourceBrowserTarget.toPath(), this::processFilesAndShowPeakCentre);

AbstractDataView gBeamLinePlot = new GBeamLinePlot(
new Rectangle(gBeamPlotScrollPane.getWidth(),
gBeamPlotScrollPane.getHeight()),
(GBeamLinePlotBuilder) gBeamPlotBuilder
(GBeamLinePlotBuilder) plots[1]
);

gBeamPlotScrollPane.widthProperty().addListener((observable, oldValue, newValue) -> {
Expand All @@ -405,12 +371,11 @@ public void processDataFileAndShowPlotsOfPeakShapes() {
gBeamPlotScrollPane.setContent(gBeamLinePlot);


AbstractPlotBuilder beamShapePlotBuilder = ((PeakShapesTask) service.getPeakShapesTask()).getBeamShapePlotBuilder();

AbstractDataView beamShapeLinePlot = new BeamShapeLinePlot(
new Rectangle(beamShapePlotScrollPane.getWidth(),
beamShapePlotScrollPane.getHeight()),
(BeamShapeLinePlotBuilder) beamShapePlotBuilder
(BeamShapeLinePlotBuilder) plots[0]
);

beamShapePlotScrollPane.widthProperty().addListener((observable, oldValue, newValue) -> {
Expand All @@ -429,7 +394,66 @@ public void processDataFileAndShowPlotsOfPeakShapes() {

beamShapeLinePlot.preparePanel();
beamShapePlotScrollPane.setContent(beamShapeLinePlot);
});
}catch (Exception e){
e.printStackTrace();
}




// service.start();
// service.setOnSucceeded(evt -> {
// AbstractPlotBuilder gBeamPlotBuilder = ((PeakShapesTask) service.getPeakShapesTask()).getGBeamPlotBuilder();
//
// AbstractDataView gBeamLinePlot = new GBeamLinePlot(
// new Rectangle(gBeamPlotScrollPane.getWidth(),
// gBeamPlotScrollPane.getHeight()),
// (GBeamLinePlotBuilder) gBeamPlotBuilder
// );
//
// gBeamPlotScrollPane.widthProperty().addListener((observable, oldValue, newValue) -> {
// if (newValue.intValue() > 100) {
// gBeamLinePlot.setMyWidth(newValue.intValue() - SCROLLBAR_THICKNESS);
// gBeamLinePlot.repaint();
// }
// });
//
// gBeamPlotScrollPane.heightProperty().addListener((observable, oldValue, newValue) -> {
// if (newValue.intValue() > 100) {
// gBeamLinePlot.setMyHeight(newValue.intValue() - SCROLLBAR_THICKNESS);
// gBeamLinePlot.repaint();
// }
// });
//
// gBeamLinePlot.preparePanel();
// gBeamPlotScrollPane.setContent(gBeamLinePlot);
//
//
// AbstractPlotBuilder beamShapePlotBuilder = ((PeakShapesTask) service.getPeakShapesTask()).getBeamShapePlotBuilder();
//
// AbstractDataView beamShapeLinePlot = new BeamShapeLinePlot(
// new Rectangle(beamShapePlotScrollPane.getWidth(),
// beamShapePlotScrollPane.getHeight()),
// (BeamShapeLinePlotBuilder) beamShapePlotBuilder
// );
//
// beamShapePlotScrollPane.widthProperty().addListener((observable, oldValue, newValue) -> {
// if (newValue.intValue() > 100) {
// beamShapeLinePlot.setMyWidth(newValue.intValue() - SCROLLBAR_THICKNESS);
// beamShapeLinePlot.repaint();
// }
// });
//
// beamShapePlotScrollPane.heightProperty().addListener((observable, oldValue, newValue) -> {
// if (newValue.intValue() > 100) {
// beamShapeLinePlot.setMyHeight(newValue.intValue() - SCROLLBAR_THICKNESS);
// beamShapeLinePlot.repaint();
// }
// });
//
// beamShapeLinePlot.preparePanel();
// beamShapePlotScrollPane.setContent(beamShapeLinePlot);
// });
} else {
eventLogTextArea.textProperty().unbind();
eventLogTextArea.setText("Please Choose Folder");
Expand Down
4 changes: 2 additions & 2 deletions ...les/tripoli/gui/dataViews/plots/plotsControllers/peakShapePlots/PeakShapePlotsWindow.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,8 +35,8 @@ public class PeakShapePlotsWindow {
public static final double PLOT_WINDOW_HEIGHT = 600.0;
public static final double SCROLLBAR_THICKNESS = 15.0;
public static Window plottingWindow;
private final double xOffset = 0;
private final double yOffset = 0;
// private final double xOffset = 0;
// private final double yOffset = 0;
public Stage plottingStage;
private Stage primaryStage;

Expand Down
4 changes: 0 additions & 4 deletions ...tripoli/gui/dataViews/plots/plotsControllers/peakShapePlots/PeakShapesTaskExperiment.java
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This file was deleted.

2 changes: 2 additions & 0 deletions ...ns/analysis/massSpectrometerModels/dataSourceProcessors/PeakShapeProcessor_OPPhoenix.java
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,8 @@ public PeakShapeOutputDataRecord prepareInputDataModelFromFile(Path inputDataFil
intensity.add(Double.parseDouble(cols[1]));
}
default -> {
masses = null;
intensity = null;
}
}

Expand Down
10 changes: 0 additions & 10 deletions TripoliCore/src/test/java/org/cirdles/tripoli/utilities/mathUtilities/MatLabTest.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
package org.cirdles.tripoli.utilities.mathUtilities;

import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.ojalgo.matrix.store.MatrixStore;
import org.ojalgo.matrix.store.PhysicalStore;
Expand All @@ -14,14 +12,6 @@

class MatLabTest {

@BeforeEach
void setUp() {
}

@AfterEach
void tearDown() {
}

@Test
void kronTest() {
PhysicalStore.Factory<Double, Primitive64Store> storeFactory = Primitive64Store.FACTORY;
Expand Down
10 changes: 0 additions & 10 deletions ...iCore/src/test/java/org/cirdles/tripoli/utilities/mathUtilities/SplineBasisModelTest.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
package org.cirdles.tripoli.utilities.mathUtilities;

import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.ojalgo.matrix.store.MatrixStore;
import org.ojalgo.matrix.store.Primitive64Store;
Expand All @@ -12,14 +10,6 @@

class SplineBasisModelTest {

@BeforeEach
void setUp() {
}

@AfterEach
void tearDown() {
}

@Test
void bBase() {
Primitive64Store test = MatLab.linspace(204.83994725925928, 205.10565274074074, 1000);
Expand Down

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