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Merge pull request #161 from bowring/converge
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Interactive converge and various improvements to plots.
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@bowring
bowring authored Sep 24, 2023
2 parents e4fd914 + 8069df3 commit 61a762b
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Showing 52 changed files with 1,548 additions and 844 deletions.
2 changes: 2 additions & 0 deletions TripoliApp/src/main/java/org/cirdles/tripoli/gui/AnalysisManagerCallbackI.java
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Expand Up @@ -2,4 +2,6 @@

public interface AnalysisManagerCallbackI {
public void callbackRefreshBlocksStatus();

public void reviewAndSculptDataAction();
}
42 changes: 36 additions & 6 deletions TripoliApp/src/main/java/org/cirdles/tripoli/gui/AnalysisManagerController.java
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Expand Up @@ -61,6 +61,7 @@ public class AnalysisManagerController implements Initializable, AnalysisManager
public static AnalysisInterface analysis;
public static MCMCPlotsWindow MCMCPlotsWindow;
public static OGTripoliPlotsWindow ogTripoliPlotsWindow;
public static OGTripoliPlotsWindow ogTripoliPreviewPlotsWindow;
private final Map<String, boolean[][]> mapOfGridPanesToCellUse = new TreeMap<>();
public Tab detectorDetailTab;
public TabPane analysiMethodTabPane;
Expand Down Expand Up @@ -112,6 +113,18 @@ public class AnalysisManagerController implements Initializable, AnalysisManager
@FXML
private Button addRatioButton;

public static void closePlotWindows() {
if (ogTripoliPreviewPlotsWindow != null) {
ogTripoliPreviewPlotsWindow.close();
}
if (ogTripoliPlotsWindow != null) {
ogTripoliPlotsWindow.close();
}
if (MCMCPlotsWindow != null) {
MCMCPlotsWindow.close();
}
}

public static StackPane makeMassStackPane(String massName, String color) {
Text massText = new Text(massName);
massText.setFont(new Font("Monospaced Bold", 14));
Expand Down Expand Up @@ -375,6 +388,8 @@ private void populateAnalysisMethodRatioSelectorPane() {

private void populateAnalysisMethodRatioBuilderPane() {
addRatioButton.setStyle(addRatioButton.getStyle() + ";-fx-font-size:15");
numeratorMassesListTextFlow.getChildren().clear();
denominatorMassesListTextFlow.getChildren().clear();
if (null != analysis.getAnalysisMethod()) {
activeRatiosList = new TreeSet<>();
List<SpeciesRecordInterface> species = analysis.getAnalysisMethod().getSpeciesListSortedByMass();
Expand Down Expand Up @@ -590,7 +605,7 @@ private void selectDataFileButtonAction() {
@FXML
private void selectMethodFileButtonAction() {
try {
File selectedFile = selectMethodFile(TripoliGUI.primaryStage);
File selectedFile = selectMethodFile(null);
if ((null != selectedFile) && (selectedFile.exists())) {
AnalysisMethod analysisMethod = analysis.extractAnalysisMethodfromPath(Path.of(selectedFile.toURI()));
String compareInfo = compareAnalysisMethodToDataFileSpecs(analysisMethod, analysis.getMassSpecExtractedData());
Expand All @@ -615,6 +630,7 @@ private void selectMethodFileButtonAction() {
// initialize block processing state
for (Integer blockID : analysis.getMassSpecExtractedData().getBlocksData().keySet()) {
analysis.getMapOfBlockIdToProcessStatus().put(blockID, RUN);
analysis.getMapOfBlockIdToModelsBurnCount().put(blockID, 0);
}
populateAnalysisManagerGridPane();
}
Expand All @@ -635,18 +651,29 @@ final void initializeMonteCarloTechniqueAction() {
}


public void reviewAndSculptDataAction() throws TripoliException {
public void previewAndSculptDataAction() throws TripoliException {
// ogTripoli view
if (null != ogTripoliPlotsWindow) {
ogTripoliPlotsWindow.close();
if (null != ogTripoliPreviewPlotsWindow) {
ogTripoliPreviewPlotsWindow.close();
}
ogTripoliPlotsWindow = new OGTripoliPlotsWindow(TripoliGUI.primaryStage);
ogTripoliPreviewPlotsWindow = new OGTripoliPlotsWindow(TripoliGUI.primaryStage, this);
OGTripoliViewController.analysis = analysis;
OGTripoliViewController.plottingData = AllBlockInitForOGTripoli.initBlockModels(analysis);
ogTripoliPlotsWindow.loadPlotsWindow();
ogTripoliPreviewPlotsWindow.loadPlotsWindow();

}

public void reviewAndSculptDataAction() {
// fire up OGTripoli style session plots
if (null != ogTripoliPlotsWindow) {
ogTripoliPlotsWindow.close();
}
ogTripoliPlotsWindow = new OGTripoliPlotsWindow(TripoliGUI.primaryStage, this);
AllBlockInitForOGTripoli.PlottingData plottingData = analysis.assemblePostProcessPlottingData();
OGTripoliViewController.plottingData = plottingData;
ogTripoliPlotsWindow.loadPlotsWindow();
}

public void selectRunAllAction() {
for (Node button : blockStatusHBox.getChildren()) {
if (button instanceof Button) {
Expand All @@ -672,6 +699,9 @@ public void selectShowsAction() {
}
}

/**
* Restores block status buttons to their saved state
*/
public void restoreAllAction() {
for (Node button : blockStatusHBox.getChildren()) {
if ((button instanceof Button) && (null != analysis.getMapOfBlockIdToProcessStatus().get(Integer.parseInt(button.getId())))) {
Expand Down
16 changes: 5 additions & 11 deletions TripoliApp/src/main/java/org/cirdles/tripoli/gui/OGTripoliPlotsWindow.java
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Expand Up @@ -33,31 +33,24 @@ public class OGTripoliPlotsWindow {

public static final double PLOT_WINDOW_WIDTH = 1000.0;
public static final double PLOT_WINDOW_HEIGHT = 700.0;
public static final double SCROLLBAR_THICKNESS = 15.0;

private final double xOffset = 0;
private final double yOffset = 0;
public Stage plottingStage;
public Window plottingWindow;
private Stage primaryStage;

private OGTripoliPlotsWindow() {
}

public OGTripoliPlotsWindow(Stage primaryStage) {//}, AnalysisManagerCallbackI analysisManagerCallbackI) {
public OGTripoliPlotsWindow(Stage primaryStage, AnalysisManagerCallbackI analysisManagerCallbackI) {
this.primaryStage = primaryStage;
plottingStage = new Stage();
plottingStage.setMinWidth(PLOT_WINDOW_WIDTH);
plottingStage.setMinHeight(PLOT_WINDOW_HEIGHT);
// plottingStage.setTitle("Tripoli Preview and Sculpt Data");

plottingStage.setOnCloseRequest((WindowEvent e) -> {
plottingStage.hide();
plottingStage.setScene(null);
e.consume();
});

// MCMCPlotsController.analysisManagerCallbackI = analysisManagerCallbackI;
OGTripoliViewController.analysisManagerCallbackI = analysisManagerCallbackI;
}

public void close() {
Expand All @@ -66,17 +59,18 @@ public void close() {

public void loadPlotsWindow() {
if (!plottingStage.isShowing()) {
FXMLLoader loader = new FXMLLoader(getClass().getResource("/org/cirdles/tripoli/gui/OGTripoliView.fxml"));
try {
FXMLLoader loader = new FXMLLoader(getClass().getResource("/org/cirdles/tripoli/gui/OGTripoliView.fxml"));
Scene scene = new Scene(loader.load());
plottingStage.setScene(scene);

} catch (IOException iOException) {
iOException.printStackTrace();
}
plottingWindow = plottingStage.getScene().getWindow();
plottingStage.setTitle("Tripoli " + (plottingData.preview() ? "PREVIEW" : "REVIEW") + " and Sculpt Data");
// ((OGTripoliViewController) loader.getController()).populatePlots();
plottingStage.show();

}

// center on app window
Expand Down
73 changes: 66 additions & 7 deletions TripoliApp/src/main/java/org/cirdles/tripoli/gui/OGTripoliViewController.java
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Original file line number Diff line number Diff line change
@@ -1,9 +1,13 @@
package org.cirdles.tripoli.gui;

import javafx.beans.value.ChangeListener;
import javafx.beans.value.ObservableValue;
import javafx.fxml.FXML;
import javafx.scene.control.TabPane;
import javafx.scene.layout.AnchorPane;
import javafx.scene.layout.Background;
import javafx.scene.layout.BackgroundFill;
import javafx.scene.layout.VBox;
import javafx.scene.paint.Paint;
import javafx.scene.shape.Rectangle;
import org.cirdles.tripoli.gui.dataViews.plots.AbstractPlot;
Expand Down Expand Up @@ -35,29 +39,61 @@
public class OGTripoliViewController {
public static AnalysisInterface analysis;
public static AllBlockInitForOGTripoli.PlottingData plottingData;
public static AnalysisManagerCallbackI analysisManagerCallbackI;
@FXML
public VBox plotWindowVBox;
@FXML
public TabPane plotTabPane;
@FXML
public AnchorPane ogtSpeciesIntensitiesPlotAnchorPane;
@FXML
private AnchorPane ogtCycleRatioPlotsAnchorPane;

@FXML
void initialize() {
public void initialize() {
plotWindowVBox.widthProperty().addListener((observable, oldValue, newValue) -> {
plotTabPane.setMinWidth((Double) newValue);
ogtCycleRatioPlotsAnchorPane.setMinWidth((Double) newValue);
ogtSpeciesIntensitiesPlotAnchorPane.setMinWidth((Double) newValue);
});

plotWindowVBox.heightProperty().addListener((observable, oldValue, newValue) -> {
plotTabPane.setMinHeight(((Double) newValue) - 30.0);
ogtCycleRatioPlotsAnchorPane.setMinHeight(((Double) newValue) - 65.0);
ogtSpeciesIntensitiesPlotAnchorPane.setMinHeight(((Double) newValue) - 100.0);
});

populatePlots();
}

private void populatePlots() {
public void populatePlots() {
plotRatios();
plotOnPeakIntensities();
}

private void plotRatios() {
public void plotRatios() {
ogtCycleRatioPlotsAnchorPane.getChildren().clear();

PlotWallPane plotsWallPane = PlotWallPane.createPlotWallPane("OGTripoliSession");
PlotWallPane plotsWallPane = PlotWallPane.createPlotWallPane("OGTripoliSession", analysis, null, analysisManagerCallbackI);
PlotWallPane.menuOffset = 0.0;
plotsWallPane.setBackground(new Background(new BackgroundFill(Paint.valueOf("LINEN"), null, null)));
plotsWallPane.setPrefSize(ogtCycleRatioPlotsAnchorPane.getPrefWidth(), ogtCycleRatioPlotsAnchorPane.getPrefHeight());

plotsWallPane.prefWidthProperty().bind(ogtCycleRatioPlotsAnchorPane.widthProperty());
plotsWallPane.prefHeightProperty().bind(ogtCycleRatioPlotsAnchorPane.heightProperty());

ogtCycleRatioPlotsAnchorPane.getChildren().add(plotsWallPane);
plotWindowVBox.widthProperty().addListener(new ChangeListener<Number>() {
@Override
public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
plotsWallPane.stackPlots();
}
});
plotWindowVBox.heightProperty().addListener(new ChangeListener<Number>() {
@Override
public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
plotsWallPane.stackPlots();
}
});

SingleBlockModelRecord[] singleBlockModelRecords = plottingData.singleBlockModelRecords();
int countOfOnPeakCycles = singleBlockModelRecords[0].cycleCount();
Expand All @@ -82,6 +118,7 @@ private void plotRatios() {

for (IsotopicRatio isotopicRatio : ratiosToPlot) {
TripoliPlotPane tripoliPlotPane = TripoliPlotPane.makePlotPane(plotsWallPane);

List<BlockRatioCyclesRecord> blockRatioCyclesRecords = new ArrayList<>();
for (int blockIndex = 0; blockIndex < singleBlockModelRecords.length; blockIndex++) {
int blockStatus = analysis.getMapOfBlockIdToProcessStatus().get(blockIndex + 1);
Expand All @@ -102,8 +139,11 @@ private void plotRatios() {
blockRatioCyclesRecords, new String[]{isotopicRatio.prettyPrint()},
"Blocks & Cycles by Time", "Ratio");
AbstractPlot plot = BlockRatioCyclesSessionPlot.generatePlot(
new Rectangle(minPlotWidth, minPlotHeight), blockRatioCyclesSessionBuilder.getBlockRatioCyclesSessionRecord());
new Rectangle(minPlotWidth, minPlotHeight), blockRatioCyclesSessionBuilder.getBlockRatioCyclesSessionRecord(), plotsWallPane);

tripoliPlotPane.addPlot(plot);
plot.refreshPanel(false, false);

}
plotsWallPane.buildScaleControlsToolbar();
plotsWallPane.stackPlots();
Expand All @@ -115,8 +155,25 @@ private void plotOnPeakIntensities() {
PlotWallPane.menuOffset = 0.0;
plotsWallPane.setBackground(new Background(new BackgroundFill(Paint.valueOf("LINEN"), null, null)));
plotsWallPane.setPrefSize(ogtSpeciesIntensitiesPlotAnchorPane.getPrefWidth(), ogtSpeciesIntensitiesPlotAnchorPane.getPrefHeight() + PlotWallPaneOGTripoli.toolBarHeight * 2.0);

plotsWallPane.prefWidthProperty().bind(ogtSpeciesIntensitiesPlotAnchorPane.widthProperty());
plotsWallPane.prefHeightProperty().bind(ogtSpeciesIntensitiesPlotAnchorPane.heightProperty());

ogtSpeciesIntensitiesPlotAnchorPane.getChildren().add(plotsWallPane);

plotWindowVBox.widthProperty().addListener(new ChangeListener<Number>() {
@Override
public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
plotsWallPane.stackPlots();
}
});
plotWindowVBox.heightProperty().addListener(new ChangeListener<Number>() {
@Override
public void changed(ObservableValue<? extends Number> observable, Number oldValue, Number newValue) {
plotsWallPane.stackPlots();
}
});

SingleBlockRawDataSetRecord[] singleBlockRawDataSetRecords = plottingData.singleBlockRawDataSetRecords();
SingleBlockModelRecord[] singleBlockModelRecords = plottingData.singleBlockModelRecords();
// only plotting onPeaks
Expand Down Expand Up @@ -195,11 +252,13 @@ private void plotOnPeakIntensities() {
}

PlotBuilder plotBuilder = SpeciesIntensitySessionBuilder.initializeSpeciesIntensitySessionPlot(
xAxis, onPeakDataCounts, onPeakDataAmpResistance, onPeakBaseline, onPeakGain, new String[]{"Species Intensity by Session"}, "Time", "Intensity (counts)");
xAxis, onPeakDataCounts, onPeakDataAmpResistance, onPeakBaseline, onPeakGain, new String[]{"Species Intensity by Session"}, "Time (secs)", "Intensity (counts)");

TripoliPlotPane tripoliPlotPane = TripoliPlotPane.makePlotPane(plotsWallPane);
AbstractPlot plot = SpeciesIntensitySessionPlot.generatePlot(new Rectangle(minPlotWidth, minPlotHeight), (SpeciesIntensitySessionBuilder) plotBuilder);
tripoliPlotPane.addPlot(plot);
plot.refreshPanel(false, false);

plotsWallPane.buildOGTripoliToolBar(analysis.getAnalysisMethod().getSpeciesList());
plotsWallPane.buildScaleControlsToolbar();
plotsWallPane.stackPlots();
Expand Down
4 changes: 3 additions & 1 deletion TripoliApp/src/main/java/org/cirdles/tripoli/gui/TripoliGUIController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ public static void quit() {
} catch (TripoliException squidException) {
TripoliMessageDialog.showWarningDialog(squidException.getMessage(), primaryStageWindow);
}
// todo: confirmSaveOnProjectClose();
// todo: confirmSaveOnSessionClose();
System.out.println("Tripoli quitting normally.");
Platform.exit();
System.exit(0);
Expand Down Expand Up @@ -156,6 +156,8 @@ private void removeAllManagers() throws TripoliException {
manager.setVisible(false);
}

AnalysisManagerController.closePlotWindows();

// prevent stacking of panes
splashAnchor.getChildren().remove(sessionManagerUI);
splashAnchor.getChildren().remove(analysesManagerUI);
Expand Down
8 changes: 8 additions & 0 deletions TripoliApp/src/main/java/org/cirdles/tripoli/gui/constants/ConstantsTripoliApp.java
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,8 @@ public enum ConstantsTripoliApp {
//https://docs.oracle.com/javase/8/javafx/api/javafx/scene/paint/Color.html
public static final String[] TRIPOLI_PALLETTE_FOUR = {"RED", "BLUE", "GREEN", "BLACK", "ORANGE", "INDIGO", "#35978f", "#01665e"};

public static final Color TRIPOLI_MOVING_SHADE = new Color(255.0 / 256.0, 182.0 / 256.0, 193.0 / 256.0, 0.5);

public static @NonNls String convertColorToHex(Color color) {
String red = Integer.toHexString((int) (color.getRed() * 255));
String green = Integer.toHexString((int) (color.getGreen() * 255));
Expand All @@ -49,5 +51,11 @@ public enum ConstantsTripoliApp {
return "#" + red + green + blue;
}

public static enum PlotLayoutStyle {
TILE(),
STACK(),
CASCADE();
}


}
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