Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Peak Refining and Doc #70

Merged
merged 6 commits into from
Sep 6, 2022
Merged

Peak Refining and Doc #70

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
0ddaac2
initial cleanup
robinsonianr Aug 31, 2022
90a7cd4
Merge branch 'main' of https://github.com/CIRDLES/Tripoli into peak-c…
robinsonianr Aug 31, 2022
5cbebce
codacy cleanup
robinsonianr Sep 1, 2022
dd783d3
PeakProcessor fix and key pressed added
robinsonianr Sep 1, 2022
e1996e1
potential auto-selection fix
robinsonianr Sep 3, 2022
b3f64ba
Merge branch 'main' into peak-cleanup
bowring Sep 6, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/BeamShapeLinePlot.java
View file
Open in desktop
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);

}
Expand Down
2 changes: 1 addition & 1 deletion TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/GBeamLinePlot.java
View file
Open in desktop
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);

}
Expand Down
214 changes: 119 additions & 95 deletions ...tripoli/gui/dataViews/plots/plotsControllers/peakShapePlots/PeakShapePlotsController.java
View file
Open in desktop
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
View file
Open in desktop
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
View file
Open in desktop

This file was deleted.

2 changes: 2 additions & 0 deletions ...ns/analysis/massSpectrometerModels/dataSourceProcessors/PeakShapeProcessor_OPPhoenix.java
View file
Open in desktop
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
View file
Open in desktop
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
View file
Open in desktop
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