Plot_XY_Data.bsh

/* Plot XY_Data.bsh
 * IJ BAR: https://github.com/tferr/Scripts#scripts
 *
 * Interactively creates a multi-series plot (XY with or without error bars,
 * and vector fields) from ImageJ measurements or imported spreadsheet data.
 *
 * Requires BAR_-X.X.X.jar. To use it without BAR append the getResultsTable()
 * method in bar.Utils to this file, replacing its calls accordingly.
 *
 * TF, v2016.04
 */

import bar.Utils;
import ij.IJ;
import ij.Prefs;
import ij.gui.DialogListener;
import ij.gui.ImageWindow;
import ij.gui.GenericDialog;
import ij.gui.NonBlockingGenericDialog;
import ij.gui.Plot;
import ij.gui.PlotDialog;
import ij.gui.PlotWindow;
import ij.measure.ResultsTable;
import ij.plugin.Colors;
import ij.plugin.frame.Recorder;
import ij.text.TextWindow;
import ij.util.Tools;
import ij.WindowManager;

/**
 * Adds a dataset to the script's plot according to the settings
 * retrieved by the dialog listener. Plot is created if it does
 * not exist, i.e., if the method has not been called before.
 */
void addDataset(String datasetLabel, double[]x1, double[]y1, double[]x2, double[]y2, boolean vectorField) {

	// Create and display plot with ajusted limits if first dataset
	boolean firstRun = false;

	if (super.plot==null || super.pw==null) {
		firstRun = true;
		super.plot = new Plot(WindowManager.makeUniqueName("Plotted Results"),
				"", "", Plot.DEFAULT_FLAGS);
		if (super.font!=null)
			super.plot.setFont(super.font);
		xLimits = Tools.getMinMax(x1);
		yLimits = Tools.getMinMax(y1);
		super.plot.setLimits(xLimits[0], xLimits[1], yLimits[0], yLimits[1]);
		super.pw = PWindowWithListener(plot);
	}

	// Add the dataset (with vectors, all column choices must be valid)
	super.plot.setColor(super.dColor, super.dColor2);
	if (vectorField)
		super.plot.drawVectors(x1, y1, x2, y2);
	else {
		super.plot.addPoints(x1, y1, Plot.toShape(super.dShape));
		if (super.x2!=null)
			super.plot.addHorizontalErrorBars(x2);
		if (y2!=null)
			super.plot.addErrorBars(y2);
	}

	// Update plot legend, dataset tally, and axis limits
	if (!firstRun)
		super.legend += "\n";
	super.legend += datasetLabel;
	super.plot.setColor(Color.BLACK);
	super.plot.addLegend(super.legend);
	super.plot.setLimitsToFit(true);
	super.datasetCounter++;
}

/**
 * Generates abscissae from row numbers of the specified ResultsTable.
 * Useful for datasets in which only Y-values need to be plotted.
 */
 double[] generateX(ResultsTable rt) {
 	int size = rt.getCounter();
	double[] incX = new double[size];
	for (int i=0; i<size; i++)
		incX[i] = (double)i;
	return incX;
}

/**
 * Retrieves a list of column choices for the specified ResultsTable.
 * The "Label" column (containing non-numeric data) is excluded).
 */
String[] getColumnChoices(ResultsTable rt) {
	n = rt.getLastColumn();
	cChoices = new String[n+2];
	for (int i=0; i<=n; i++)
		cChoices[i] = rt.getColumnHeading(i);
	cChoices[n+1] = "*None*";
	return cChoices;
}

/**
 * Activates the Checkbox of a RadioButtonGroup() in a GenericDialog
 * associated with the specified label. <code>panel</code> is the
 * java.awt.Panel to which the RadioButtonGroup (java.awt.CheckboxGroup)
 * was added as per ij.gui.GenericDialog.addRadioButtonGroup().
 */
void activateRadioCheckbox(Panel panel, String label) {
	Component[] components = panel.getComponents();
	for (int i = 0; i<components.length; i++) {
		Component c = components[i];
		if (c instanceof Checkbox) {
			Checkbox cb = (Checkbox)c;
			if (cb.getLabel().equals(label)) {
				cb.setState(true);
				return;
			}
		}
	}
	return;
}

/**
 * Prompts the user for settings. Position of dialog is stored using
 * the ImageJ preferences mechanism. All the values in the prompt are
 * retrieved in real time by scripting the ij.gui.DialogListener
 * interface (see anonymous inner class <code>dl</code> below).
 */
void promptForData() {

	// Do nothing if table is not available
	if (super.rt==null) {
			IJ.showMessage("No Data to Be Plotted",
				"Since no data is available, Plot Builder will now quit.");
		return;
	}

	// Define column choices for drop-down menus
	super.colChoices = getColumnChoices(super.rt);

	// Build prompt if it is not being displayed
	gdWindow = WindowManager.getWindow("Plot Builder");
	if (!IJ.macroRunning() && gdWindow!=null) {
		gdWindow.toFront();
		return;
	}
	gd = new NonBlockingGenericDialog("Plot Builder");
	gd.addChoice("      X-values", super.colChoices, "*None*");
	gd.addChoice(" X-error bars", super.colChoices, "*None*");
	gd.addChoice("      Y-values", super.colChoices, super.colChoices[0]);
	gd.addChoice(" Y-error bars", super.colChoices, "*None*");
	gd.setInsets(0, 20, 0);
	gd.addCheckbox("Vector field dataset", super.vectorData);
	gd.addMessage("");
	gd.addRadioButtonGroup("Style:", super.S_LABELS, 4, 2, super.dShape);
	gd.addRadioButtonGroup("Color:", Colors.colors, 5, 2, super.dColor);

	// Add the "Add Dataset" button to the dialog
	super.datasetButton = new Button("       Add Dataset "
			+ String.valueOf(super.datasetCounter+1) + "       ");
	super.datasetButton.addActionListener(gd);
	buttonPanel = new Panel();
	buttonPanel.add(super.datasetButton);
	gd.addPanel(buttonPanel, GridBagConstraints.SOUTH, new Insets(10,0,0,0));

	// Generate a 3-button prompt
	gd.addHelp("");
	gd.setHelpLabel("Options");
	gd.enableYesNoCancel("Close", "Data...");
	gd.hideCancelButton();
	gd.addDialogListener(dl);
	gd.addWindowFocusListener(WListener);

	// Display prompt at last screen position
	LOC_KEY = "bar.PRloc";
	loc = Prefs.getLocation(LOC_KEY);
	if (loc!=null) {
		gd.centerDialog(false);
		gd.setLocation(loc);
	}

	// Update prompt before displaying it
	if (!IJ.macroRunning())
		dl.dialogItemChanged(gd, null);
	gd.showDialog();
	Prefs.saveLocation(LOC_KEY, gd.getLocation());

	// Dialog closure: Update plot if user pressed "OK",
	// plot dataset if a macro/script "OKayed" the prompt
	if (gd.wasCanceled()) { // Dialog dismissed
		return;
	} if (gd.wasOKed()) { // "Close" button pressed
		if (super.plot!=null)
			super.plot.setLimitsToFit(true);
	} else { // "Reload" button pressed

		// Replace data source only if it is valid
		newRt = getTableWithListener();
		if (newRT != null)
			super.rt = newRt;
		promptForData();
		// Re-displaying the prompt is problematic when recording macros
		// due to duplicated keywords. So, we'll reset the recording
		if (Recorder.record)
			Recorder.setCommand(Recorder.getCommand());

	}
	return;
}

/** Assesses if the specified ResultsTable heading contains numeric data */
boolean validColumn(String columnHeading) {
	return !columnHeading.equals("Label") && !columnHeading.equals("*None*") &&
		super.rt.getColumnIndex(columnHeading)!=ResultsTable.COLUMN_NOT_FOUND;
}

/**
 * Inner class scripting the ij.gui.DialogListener interface. We'll
 * use it to read in real-time all of the options in the prompt.
 */
DialogListener dl = new DialogListener() {

	// This method is invoked by the GenericDialog upon changes
	public boolean dialogItemChanged(GenericDialog gd, java.awt.AWTEvent e) {

		// Read parameters from dialog
		x1Col = gd.getNextChoiceIndex();
		x2Col = gd.getNextChoiceIndex();
		y1Col = gd.getNextChoiceIndex();
		y2Col = gd.getNextChoiceIndex();
		vectorData = gd.getNextBoolean();
		dShape = gd.getNextRadioButton();
		dColor = gd.getNextRadioButton();

		// Define the dataset: A vector field or a X,Y series (using
		// incremental x-values if user chose a non-numeric column)
		x1 = validColumn(super.colChoices[x1Col])?super.rt.getColumnAsDoubles(x1Col):null;
		if (!vectorData && x1==null)
			x1 = generateX(super.rt);
		validX1 = x1 != null;
		datasetLabel = super.colChoices[y1Col];
		y1 = validColumn(datasetLabel)?super.rt.getColumnAsDoubles(y1Col):null;
		validY1 = y1 != null;
		x2 = validColumn(super.colChoices[x2Col])?super.rt.getColumnAsDoubles(x2Col):null;
		validX2 = x2 != null;
		y2 = validColumn(super.colChoices[y2Col])?super.rt.getColumnAsDoubles(y2Col):null;
		validY2 = y2 != null;

		// Assess if all dataset values are valid and plot/table remain available
		boolean validData = true;
		if (vectorData)
			validData = validX1 && validY1 && validX2 && validY2;
		else
			validData = validX1 && validY1;

		// Set parameters
		super.vectorData = vectorData;
		super.dShape = dShape;
		super.dColor = dColor;

		// Update dialog components if dialog is being displayed
		if (e != null && !IJ.macroRunning()) {

			super.datasetButton.setEnabled(!super.rtClosed && validData);

			// Update choice labels
			gd.getComponent(0).setText(vectorData?"X-start (X1)":"X-values");
			gd.getComponent(0).setForeground(validX1?Color.BLACK:Color.GRAY);
			gd.getComponent(2).setText(vectorData?"X-end (X2)":"X-error bars");
			gd.getComponent(2).setForeground(validX2?Color.BLACK:Color.GRAY);
			gd.getComponent(4).setText(vectorData?"Y-start (Y1)":"Y-values");
			gd.getComponent(4).setForeground(validY1?Color.BLACK:Color.GRAY);
			gd.getComponent(6).setText(vectorData?"Y-end (Y2)":"Y-error bars");
			gd.getComponent(6).setForeground(validY2?Color.BLACK:Color.GRAY);

		}

		// Check if the 'Add dataset' button has been pressed
		if (e != null && e.getSource()==super.datasetButton) {
			if (super.pwClosed) {
				super.pw = PWindowWithListener(super.plot); // Redisplay plot
			} else if (!super.rtClosed) {

				// Plot data and auto-select new defaults for next dataset
				if (validData) {
					addDataset(datasetLabel, x1, y1, x2, x2, vectorData);
					super.datasetButton.setLabel("Add Dataset "+ (super.datasetCounter+1));

				} else {
					IJ.showMessage("Invalid data",
						"Chosen column(s) do not seem to contain numeric data.");
					return;
				}
				choices = gd.getChoices();
				y1idx = (super.datasetCounter % (super.colChoices.length-1));
				choices.elementAt(2).select(y1idx);
				cIdx = (super.datasetCounter % (Colors.colors.length-1));
				colorRadioButtonGroupPanel = gd.getComponent(13); // empirically determined
				activateRadioCheckbox(colorRadioButtonGroupPanel, Colors.colors[cIdx]);
				//x1idx = (y1idx+1 % super.colChoices.length);
				//choices.elementAt(0).select(x1idx);
				//shapeRadioButtonGroupPanel = gd.getComponent(11);
				//activateRadioCheckbox(shapeRadioButtonGroupPanel, S_LABELS[cIdx])
			}


		// Check if the 'Options' button has been pressed
		} else if (e != null && e.toString().contains("Options")) {
			showOptions(gd.getParent());

		// Plot a single dataset if called from macro
		} else if (validData && IJ.macroRunning())
			addDataset(datasetLabel, x1, y1, x2, x2, vectorData);

		return validData;
	}

};

/** Displays the "Options" dialog for plot customization */
public static void showOptions(Frame parentFrame) {

	FONTS = new String[]{Font.SANS_SERIF, Font.MONOSPACED, Font.SERIF};
	ogd = new GenericDialog("Plot Builder Options", parentFrame);
	ogd.addChoice("Font for new plots:", FONTS, FONTS[0]);
	ogd.addChoice("Secondary color:", Colors.colors, super.dColor2);
	if (super.plot!=null) {
		ogd.addMessage("\n \nOptions below apply only to the current plot:");
		ogd.addNumericField("Line width:", 1, 0, 3, "(Default: 1 pixel)");
		ogd.addNumericField("Major ticks length:", 7, 0, 3, "(Default: 7 pixels)");
		ogd.addNumericField("Minor ticks length:", 3, 0, 3, "(Default: 3 pixels)");
		ogd.addNumericField("Maximum n. of intervals:", 12, 0, 3, "(Default: 12)");
	}
	ogd.enableYesNoCancel("Apply", "Start New Plot");
	ogd.hideCancelButton();
	ogd.showDialog();
	if (ogd.wasOKed()) {
		return;
	} else if (ogd.wasOKed()) {
		super.font = new Font(FONTS[ogd.getNextChoiceIndex()], Font.PLAIN, ij.gui.PlotWindow.fontSize);
		super.dColor2 = Colors.colors[ogd.getNextChoiceIndex()];
		if (super.plot!=null) {
			super.plot.setLineWidth((int)ogd.getNextNumber());
			super.plot.setTickLength((int)ogd.getNextNumber());
			super.plot.setMinorTickLength((int)ogd.getNextNumber());
			super.plot.setMaxIntervals((int)ogd.getNextNumber());
			super.plot.updateImage();
		}
	} else { // Start new plot
		super.datasetCounter = 0;
		super.legend = "";
		super.plot = null;
		super.pw = null;
	}

}

/**
 * Inner class scripting the java.awt.event.WindowFocusListener
 * interface. We'll use it to update the main dialog on every
 * focus change.
 */
WindowFocusListener WListener = new WindowFocusListener() {
	public void windowGainedFocus(WindowEvent e) {
		updateDatasetButton();
	}
	public void windowLostFocus(WindowEvent e) {
		updateDatasetButton();
	}
};

/**
 * Inner class scripting java.awt.WindowAdapter, the adapter that
 * receives window events. We'll use it to keep track of which windows
 * have been closed, so that main prompt can be updated accordingly.
 */
WindowAdapter WinAdapter = new WindowAdapter() {
	public void windowClosed(WindowEvent e) {
		if (e.getSource() instanceof ij.text.TextWindow) // ResultsTable
			super.rtClosed = true;
		else // Plot Window
			super.pwClosed = true;
		updateDatasetButton();
	}
};

/**
 * Displays the specified plot and returns its PlotWindow.
 * A WindowListener is used to monitor it is closure.
 */
PlotWindow PWindowWithListener(Plot plot) {
	PlotWindow pw = null;
	if (plot!=null) {
		super.pwClosed = false;
		pw = plot.show();
		pw.addWindowListener(WinAdapter);
	}
	return pw;
}

/**
 * Returns the ResultsTable to be used as data input.
 * A WindowListener is used to monitor it is closure.
 */
ResultsTable getTableWithListener() {
	ResultsTable rt = null;
	rt = Utils.getTable(false, WinAdapter);
	if (rt!=null)
		super.rtClosed = false;
	return rt;
}

/**
 * Updates <tt>datasetButton</tt> according to the availability
 * of required windows when running in interactive mode.
 */
void updateDatasetButton() {
	if (!IJ.macroRunning()) {
		if (super.pwClosed)
			super.datasetButton.setLabel("Reopen Closed Plot");
		else if (super.rtClosed)
			super.datasetButton.setLabel("Table Closed...");
		else
			super.datasetButton.setLabel("Add Dataset "+ (super.datasetCounter+1));
		super.datasetButton.setEnabled(!super.rtClosed || super.pwClosed);
	}
}

/** Definitions of dataset shapes as per ij.gui.Plot.toShape() */
String[] S_LABELS = {"line","x","box","connected","triangle","dot","circle","cross"};

/** Parameters */
ResultsTable rt;			// ResultsTable from which data is retrieved
String[] colChoices;		// Array holding choices for ResultsTable columns
boolean vectorData = false;	// Flag setting vector field data
boolean pwClosed = false;	// Flag monitoring if Plotwindow has been closed
boolean rtClosed = false;	// Flag monitoring if ResultsTable has been closed
String dShape = "line";		// Descriptive label of the dataset shape
String dColor = "red";		// Descriptive label of the dataset main color
String dColor2 = "black";	// Descriptive label of the dataset secondary color
int datasetCounter = 0;		// The number of datasets being plotted
Plot plot = null;			// The plot produced by this script
PlotWindow pw = null;		// The plot's window
String legend = "";			// The plot legend
Button datasetButton;		// The dialog button used to append datasets to the plot
Font font = null;			// The custom plot font (Advanced Options prompt)


// After setting-up everything, we try retrieve valid data
// from an opened ResultsTable and display the prompt
super.rt = getTableWithListener();
promptForData();