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Weighted Means and various improvements #187

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Nov 11, 2023
Merged

Weighted Means and various improvements #187

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7a3c2ca
Fixed misc bugs, refactored, and prespped for weighted means
bowring Nov 8, 2023
8f33798
Implemented weighted means of ratios, various improvements to look an…
bowring Nov 11, 2023
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2 changes: 1 addition & 1 deletion TripoliApp/src/main/java/org/cirdles/tripoli/gui/AnalysisManagerController.java
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Expand Up @@ -31,7 +31,7 @@
import org.cirdles.tripoli.gui.dialogs.TripoliMessageDialog;
import org.cirdles.tripoli.sessions.analysis.Analysis;
import org.cirdles.tripoli.sessions.analysis.AnalysisInterface;
import org.cirdles.tripoli.sessions.analysis.massSpectrometerModels.dataModels.mcmc.AllBlockInitForOGTripoli;
import org.cirdles.tripoli.sessions.analysis.massSpectrometerModels.dataModels.mcmc.initializers.AllBlockInitForOGTripoli;
import org.cirdles.tripoli.sessions.analysis.massSpectrometerModels.dataSourceProcessors.MassSpecOutputSingleBlockRecord;
import org.cirdles.tripoli.sessions.analysis.massSpectrometerModels.detectorSetups.Detector;
import org.cirdles.tripoli.sessions.analysis.methods.AnalysisMethod;
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2 changes: 1 addition & 1 deletion TripoliApp/src/main/java/org/cirdles/tripoli/gui/TripoliGUIController.java
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Expand Up @@ -227,7 +227,7 @@ private void launchSessionManager() throws IOException, TripoliException {
sessionManagerMenuItem.setDisable(false);
saveSessionAsMenuItem.setDisable(false);
closeSessionMenuItem.setDisable(false);
analysisMenu.setDisable(false);
analysisMenu.setDisable(true);
}

private void buildSessionMenuMRU() {
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7 changes: 4 additions & 3 deletions TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/AbstractPlot.java
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Expand Up @@ -355,17 +355,18 @@ private void drawAxes(GraphicsContext g2d) {

public void showTitle(GraphicsContext g2d) {
Paint savedPaint = g2d.getFill();
Font titleFont = Font.font("Monospaced Bold", 12);
Font titleFont = Font.font("Courier Bold", 12);
g2d.setFont(titleFont);
g2d.setFill(Paint.valueOf("RED"));
g2d.fillText(plotTitle[0], leftMargin, 12);
double titleLeftX = 15;
g2d.fillText(plotTitle[0], titleLeftX, 12);
if (2 == plotTitle.length) {
Text textTitle1 = new Text(plotTitle[0].split("\\.")[0]);
textTitle1.setFont(titleFont);
Text textTitle2 = new Text(plotTitle[1].split("\\.")[0]);
textTitle2.setFont(titleFont);
double offset = textTitle1.getLayoutBounds().getWidth() - textTitle2.getLayoutBounds().getWidth();
g2d.fillText(plotTitle[1], leftMargin + offset, 22);
g2d.fillText(plotTitle[1], titleLeftX + offset, 22);
}
g2d.setFill(savedPaint);
}
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32 changes: 18 additions & 14 deletions TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/PlotWallPane.java
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Expand Up @@ -47,20 +47,20 @@ public class PlotWallPane extends Pane implements PlotWallPaneInterface {
private final String iD;
private final boolean[] zoomFlagsXY = new boolean[2];
private final AnalysisInterface analysis;
private final MCMCPlotsControllerInterface mcmcPlotsControllerInterface;
private final MCMCPlotsControllerInterface mcmcPlotsController;
AnalysisManagerCallbackI analysisManagerCallbackI;
private double toolBarHeight;
private int toolBarCount;
private boolean logScale;
private ConstantsTripoliApp.PlotLayoutStyle plotLayoutStyle;


private PlotWallPane(String iD, AnalysisInterface analysis, MCMCPlotsControllerInterface mcmcPlotsControllerInterface, AnalysisManagerCallbackI analysisManagerCallbackI) {
private PlotWallPane(String iD, AnalysisInterface analysis, MCMCPlotsControllerInterface mcmcPlotsController, AnalysisManagerCallbackI analysisManagerCallbackI) {
this.iD = iD;
zoomFlagsXY[0] = true;
zoomFlagsXY[1] = true;
this.analysis = analysis;
this.mcmcPlotsControllerInterface = mcmcPlotsControllerInterface;
this.mcmcPlotsController = mcmcPlotsController;
this.analysisManagerCallbackI = analysisManagerCallbackI;
plotLayoutStyle = ConstantsTripoliApp.PlotLayoutStyle.TILE;

Expand All @@ -69,12 +69,12 @@ private PlotWallPane(String iD, AnalysisInterface analysis, MCMCPlotsControllerI
public static PlotWallPaneInterface createPlotWallPane(
String iD,
AnalysisInterface analysis,
MCMCPlotsControllerInterface mcmcPlotsControllerInterface,
MCMCPlotsControllerInterface mcmcPlotsController,
AnalysisManagerCallbackI analysisManagerCallbackI) {
if (null == iD) {
return new PlotWallPane("NONE", analysis, mcmcPlotsControllerInterface, analysisManagerCallbackI);
return new PlotWallPane("NONE", analysis, mcmcPlotsController, analysisManagerCallbackI);
} else {
return new PlotWallPane(iD, analysis, mcmcPlotsControllerInterface, analysisManagerCallbackI);
return new PlotWallPane(iD, analysis, mcmcPlotsController, analysisManagerCallbackI);
}
}

Expand Down Expand Up @@ -223,12 +223,14 @@ public void toggleRatiosLogRatios() {
}

public void applyBurnIn() {
int burnIn = (int) analysis.getMapOfBlockIdToPlots().get(mcmcPlotsControllerInterface.getCurrentBlockID())[5][0].getShadeWidthForModelConvergence();
int blockID = mcmcPlotsControllerInterface.getCurrentBlockID();
int burnIn = (int) analysis.getMapOfBlockIdToPlots().get(mcmcPlotsController.getCurrentBlockID())[5][0].getShadeWidthForModelConvergence();
int blockID = mcmcPlotsController.getCurrentBlockID();
analysis.getMapOfBlockIdToModelsBurnCount().put(blockID, burnIn);

blockEnsemblePlotEngine(blockID, analysis);
mcmcPlotsControllerInterface.plotEnsemblesEngine(analysis.getMapOfBlockIdToPlots().get(blockID));
mcmcPlotsControllerInterface.plotRatioSessionEngine();
mcmcPlotsController.plotEnsemblesEngine(analysis.getMapOfBlockIdToPlots().get(blockID));
((Analysis) analysis).analysisRatioEngine();
mcmcPlotsController.plotAnalysisRatioEngine();
EnsemblesStore.produceSummaryModelFromEnsembleStore(blockID, analysis);

// fire up OGTripoli style analysis plots
Expand All @@ -238,18 +240,20 @@ public void applyBurnIn() {
}

public void applyBurnInAllBlocks() {
int burnIn = (int) analysis.getMapOfBlockIdToPlots().get(mcmcPlotsControllerInterface.getCurrentBlockID())[5][0].getShadeWidthForModelConvergence();
int burnIn = (int) analysis.getMapOfBlockIdToPlots().get(mcmcPlotsController.getCurrentBlockID())[5][0].getShadeWidthForModelConvergence();
int blockIDCount = analysis.getMapOfBlockIdToPlots().keySet().size() + 1;

for (int blockID = 1; blockID < blockIDCount; blockID++) {
((Analysis) analysis).updateShadeWidthsForConvergenceLinePlots(blockID, burnIn);
analysis.getMapOfBlockIdToModelsBurnCount().put(blockID, burnIn);
blockEnsemblePlotEngine(blockID, analysis);
mcmcPlotsControllerInterface.plotEnsemblesEngine(analysis.getMapOfBlockIdToPlots().get(blockID));
// mcmcPlotsControllerInterface.plotRatioSessionEngine();
mcmcPlotsController.plotEnsemblesEngine(analysis.getMapOfBlockIdToPlots().get(blockID));
// mcmcPlotsController.analysisRatioEngine();
EnsemblesStore.produceSummaryModelFromEnsembleStore(blockID, analysis);
}

mcmcPlotsControllerInterface.plotRatioSessionEngine();
((Analysis) analysis).analysisRatioEngine();
mcmcPlotsController.plotAnalysisRatioEngine();

// fire up OGTripoli style analysis plots
if (null != analysisManagerCallbackI) {
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4 changes: 4 additions & 0 deletions TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/PlotWallPaneInterface.java
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Expand Up @@ -15,4 +15,8 @@ public interface PlotWallPaneInterface {

public void stackPlots();

public void tilePlots();

public void toggleShowStatsAllPlots();

}
16 changes: 16 additions & 0 deletions TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/PlotWallPaneOGTripoli.java
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Expand Up @@ -101,6 +101,22 @@ public void stackPlots() {
}
}

/**
*
*/
@Override
public void tilePlots() {
// not applicable
}

/**
*
*/
@Override
public void toggleShowStatsAllPlots() {
// not used
}

public void buildOGTripoliToolBar(List<SpeciesRecordInterface> species) {
ToolBar toolBar = new ToolBar();
toolBar.setPrefHeight(toolBarHeight);
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8 changes: 7 additions & 1 deletion TripoliApp/src/main/java/org/cirdles/tripoli/gui/dataViews/plots/TripoliPlotPane.java
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Expand Up @@ -27,6 +27,7 @@
import org.cirdles.tripoli.gui.dataViews.plots.plotsControllers.ogTripoliPlots.analysisPlots.BlockRatioCyclesAnalysisPlot;
import org.cirdles.tripoli.gui.dataViews.plots.plotsControllers.ogTripoliPlots.analysisPlots.SpeciesIntensityAnalysisPlot;
import org.cirdles.tripoli.gui.dataViews.plots.plotsControllers.tripoliPlots.RatioHistogramPlot;
import org.cirdles.tripoli.gui.dataViews.plots.plotsControllers.tripoliPlots.analysisPlots.AnalysisRatioPlot;
import org.cirdles.tripoli.gui.utilities.TripoliColor;

import static org.cirdles.tripoli.gui.dataViews.plots.PlotWallPane.gridCellDim;
Expand Down Expand Up @@ -253,8 +254,13 @@ public void toggleShowStats() {
public void toggleRatiosLogRatios() {
if (!getChildren().isEmpty() && (getChildren().get(0) instanceof RatioHistogramPlot)) {
((RatioHistogramPlot) getChildren().get(0)).toggleRatiosLogRatios();
((RatioHistogramPlot) getChildren().get(0)).repaint();
// ((RatioHistogramPlot) getChildren().get(0)).repaint();
}
if (!getChildren().isEmpty() && (getChildren().get(0) instanceof AnalysisRatioPlot)) {
((AnalysisRatioPlot) getChildren().get(0)).toggleRatiosLogRatios();
// ((AnalysisRatioPlot) getChildren().get(0)).repaint();
}

}

public void restorePlot() {
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2 changes: 1 addition & 1 deletion .../cirdles/tripoli/gui/dataViews/plots/plotsControllers/mcmcPlots/MCMCPlotBuildersTask.java
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Expand Up @@ -26,7 +26,7 @@
/**
* @author James F. Bowring
*/
public class MCMCPlotBuildersTask extends Task<String> implements LoggingCallbackInterface, PlotBuildersTaskInterface {
public class MCMCPlotBuildersTask extends Task<String> implements LoggingCallbackInterface, MCMCPlotBuildersTaskInterface {
public static AnalysisInterface analysis;
private final int blockID;
// plotBuilders
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2 changes: 1 addition & 1 deletion .../mcmcPlots/PlotBuildersTaskInterface.java → ...cPlots/MCMCPlotBuildersTaskInterface.java
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Expand Up @@ -2,7 +2,7 @@

import org.cirdles.tripoli.plots.PlotBuilder;

public interface PlotBuildersTaskInterface {
public interface MCMCPlotBuildersTaskInterface {
boolean healthyPlotbuilder();

PlotBuilder[] getPeakShapesBuilder();
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