Java Code Examples for ij.gui.GenericDialog#setInsets()

private void createSettingsDialog() {
	settingsDialog = new GenericDialog("Analyze Skeleton");
	Font headerFont = new Font("SansSerif", Font.BOLD, 12);

	settingsDialog.setInsets(0, 0, 0);
	settingsDialog.addMessage("Elimination of Loops:", headerFont);
	settingsDialog.addChoice("Prune cycle method: ", AnalyzeSkeleton_.pruneCyclesModes,
			AnalyzeSkeleton_.pruneCyclesModes[pruneIndex]);

	settingsDialog.setInsets(20, 0, -15); //default top inset for 1st checkbox is 15
	settingsDialog.addMessage("Elimination of End-points:", headerFont);
	settingsDialog.addCheckbox("Prune ends", pruneEnds);
	settingsDialog.addCheckbox("Exclude ROI from pruning", protectRoi);

	settingsDialog.setInsets(20, 0, 0); //default top inset for subsequent checkboxes is 0
	settingsDialog.addMessage("Results and Output:", headerFont);
	settingsDialog.addCheckbox("Calculate largest shortest path", calculateShortestPath);
	settingsDialog.addCheckbox("Show detailed info", verbose);
	settingsDialog.addCheckbox("Display labeled skeletons", displaySkeletons);

	settingsDialog.addHelp(HELP_URL);
	dialogItemChanged(settingsDialog, null);
}
 

private void setPreferences() {
	final GenericDialog gd = new GenericDialog("Preferences");
	gd.addChoice("Secondary style color:", Colors.colors, dColor2);
	gd.setInsets(0, 0, 0);
	gd.addMessage("(Used by styles 'box', 'circle', 'connected', etc.)");
	gd.setInsets(30, 0, 0);
	gd.addMessage("After plotting a series:");
	gd.setInsets(0, 20, 0);
	gd.addCheckbox("Auto-select_next_Y-values", autoNextValues);
	gd.addCheckbox("Auto-select_next_shape", autoNextShape);
	gd.addCheckbox("Auto-select_next_color", autoNextColor);
	showAsSubDialog(gd);
	if (gd.wasOKed()) {
		dColor2 = Colors.colors[gd.getNextChoiceIndex()];
		autoNextValues = gd.getNextBoolean();
		autoNextShape = gd.getNextBoolean();
		autoNextColor = gd.getNextBoolean();
	}
}
 

private boolean showDialog() {

		gd = new GenericDialog("Render Paths as Topographic Skeletons");
		final String[] pwScopes = { "Render all paths", "Render only selected paths" };
		gd.addRadioButtonGroup("Path selection:", pwScopes, 2, 1, pwScopes[useOnlySelectedPaths ? 1 : 0]);
		final String[] roiScopes = { "None", "Render only segments contained by ROI" };
		gd.addRadioButtonGroup("ROI filtering:", roiScopes, 2, 1, roiScopes[restrictByRoi ? 1 : 0]);

		// Assemble SWC choices
		final ArrayList<String> swcTypeNames = Path.getSWCtypeNames();
		final int nTypes = swcTypeNames.size();
		final String[] typeNames = swcTypeNames.toArray(new String[nTypes]);
		final boolean[] typeChoices = new boolean[nTypes];
		for (int i = 0; i < nTypes; i++)
			typeChoices[i] = typeNames[i].contains("dendrite");
		final String[] swcScopes = { "None", "Include only the following SWC types:" };
		gd.addRadioButtonGroup("SWC filtering:", swcScopes, 2, 1, swcScopes[restrictBySWCType ? 1 : 0]);
		gd.setInsets(0, 40, 0);
		gd.addCheckboxGroup(nTypes / 2, 2, typeNames, typeChoices);

		final String[] analysisScopes = { "None", "Obtain summary", "Run \"Analyze Skeleton\" plugin" };
		gd.addRadioButtonGroup("Analysis of rendered paths:", analysisScopes, 3, 1, analysisScopes[0]);
		gd.addDialogListener(this);
		dialogItemChanged(gd, null);
		gd.showDialog();
		if (gd.wasCanceled())
			return false;
		else if (gd.wasOKed()) {
			return dialogItemChanged(gd, null);
		}
		return false;

	}
 

protected void promptForOptions() {

		final int startupOptions = 7;
		final int pluginOptions = 2;

		final String[] startupLabels = new String[startupOptions];
		final int[] startupItems = new int[startupOptions];
		final boolean[] startupStates = new boolean[startupOptions];
		int idx = 0;

		startupItems[idx] = ENFORCE_LUT;
		startupLabels[idx] = "Enforce non-inverted grayscale LUT";
		startupStates[idx++] = snt.forceGrayscale;

		startupItems[idx] = USE_THREE_PANE;
		startupLabels[idx] = "Use_three-pane view";
		startupStates[idx++] = !snt.getSinglePane();

		startupItems[idx] = USE_3D_VIEWER;
		startupLabels[idx] = "Use_3D Viewer";
		startupStates[idx++] = snt.use3DViewer;

		startupItems[idx] = LOOK_FOR_TUBES;
		startupLabels[idx] = "Load_Tubeness \".tubes.tif\" pre-processed file (if present)";
		startupStates[idx++] = snt.look4tubesFile;

		startupItems[idx] = LOOK_FOR_OOF;
		startupLabels[idx] = "Load_Tubular_Geodesics \".oof.ext\" pre-processed file (if present)";
		startupStates[idx++] = snt.look4oofFile;

		startupItems[idx] = LOOK_FOR_TRACES;
		startupLabels[idx] = "Load_default \".traces\" file (if present)";
		startupStates[idx++] = snt.look4tracesFile;

		startupItems[idx] = STORE_WIN_LOCATIONS;
		startupLabels[idx] = "Remember window locations across restarts";
		startupStates[idx++] = isSaveWinLocations();

		final String[] pluginLabels = new String[pluginOptions];
		final int[] pluginItems = new int[pluginOptions];
		final boolean[] pluginStates = new boolean[pluginOptions];
		idx = 0;

		pluginItems[idx] = COMPRESSED_XML;
		pluginLabels[idx] = "Use compression when saving traces";
		pluginStates[idx++] = snt.useCompressedXML;

		pluginItems[idx] = DEBUG;
		pluginLabels[idx] = "Enable_debug mode";
		pluginStates[idx++] = SimpleNeuriteTracer.verbose;

		final GenericDialog gd = new GenericDialog("SNT v" + SNT.VERSION + " Preferences");
		final Font font = new Font("SansSerif", Font.BOLD, 12);
		gd.setInsets(0, 0, 0);
		gd.addMessage("Startup Options:", font);
		gd.setInsets(0, 0, 0);
		gd.addCheckboxGroup(startupOptions, 1, startupLabels, startupStates);
		gd.setInsets(20, 0, 0);
		gd.addMessage("Advanced Options:", font);
		gd.setInsets(0, 0, 0);
		gd.addCheckboxGroup(pluginOptions, 1, pluginLabels, pluginStates);

		gd.enableYesNoCancel("OK", "Revert to Defaults");
		gd.showDialog();
		if (gd.wasCanceled()) {
			return;
		} else if (gd.wasOKed()) {

			for (int i = 0; i < startupOptions; i++) {
				if (gd.getNextBoolean())
					currentBooleans |= startupItems[i];
				else
					currentBooleans &= ~startupItems[i];
			}
			for (int i = 0; i < pluginOptions; i++) {
				if (gd.getNextBoolean())
					currentBooleans |= pluginItems[i];
				else
					currentBooleans &= ~pluginItems[i];
			}
			Prefs.set(BOOLEANS, currentBooleans);

		} else {
			resetOptions();
		}

		Prefs.savePreferences();
		loadPluginPrefs();

	}
 

public int showDialog(
		ImagePlus imp,
		String command,
		PlugInFilterRunner pfr )
{
	if( !BinaryImages.isBinaryImage( imp ) )
	{
		IJ.error( "Distance Transform Watershed", "Input image is not"
				+ " binary (8-bit with only 0 or 255 values)" );
		return DONE;
	}
	// Store user data
	this.imagePlus = imp;
	this.baseImage = imp.getProcessor().duplicate();
	this.pfr = pfr;

	// Create a new generic dialog with appropriate options
	GenericDialog gd = new GenericDialog( "Distance Transform Watershed" );
	gd.setInsets( 0, 0, 0 );
	gd.addMessage( "Distance map options:",
			new Font( "SansSerif", Font.BOLD, 12 ) );
	gd.addChoice( "Distances", ChamferWeights.getAllLabels(), weightLabel );
	String[] outputTypes = new String[]{"32 bits", "16 bits"};
	gd.addChoice( "Output Type", outputTypes, outputTypes[ floatProcessing ? 0:1 ]);
	gd.setInsets( 0, 0, 0 );
	gd.addCheckbox( "Normalize weights", normalize );
	gd.setInsets( 20, 0, 0 );
	gd.addMessage( "Watershed options:",
			new Font( "SansSerif", Font.BOLD, 12 ) );
	gd.addNumericField( "Dynamic", dynamic, 2 );
	gd.addChoice( "Connectivity", Conn2D.getAllLabels(), connLabel );
	gd.setInsets( 20, 0, 0 );
	gd.addPreviewCheckbox( pfr );
	gd.addDialogListener(this);
	previewing = true;
	gd.addHelp( "http://imagej.net/MorphoLibJ#Utilities_for_binary_images" );
	gd.showDialog();
	previewing = false;

	// test cancel
	if (gd.wasCanceled())
		return DONE;

	// set up current parameters
	weightLabel = gd.getNextChoice();
	floatProcessing = gd.getNextChoiceIndex() == 0;
	normalize = gd.getNextBoolean();
	dynamic = (int) gd.getNextNumber();
	connLabel = gd.getNextChoice();
	connectivity = Conn2D.fromLabel( connLabel ).getValue();

	// identify which weights should be used
	weights = ChamferWeights.fromLabel( weightLabel );

	return flags;
}
 

/**
 * Plugin run method
 */
public void run(String arg) {
	
	ImagePlus image = WindowManager.getCurrentImage();
	if ( image == null ) 
	{
		IJ.error("Distance Transform Watershed 3D",
				"Need at least one image to work");
		return;
	}

	if( !BinaryImages.isBinaryImage( image ) )
	{
		IJ.error( "Distance Transform Watershed 3D", "Input image is not"
				+ " binary (8-bit with only 0 or 255 values)" );
	}

	// Create a new generic dialog with appropriate options
	GenericDialog gd = new GenericDialog( "Distance Transform Watershed 3D" );
	gd.setInsets( 0, 0, 0 );
	gd.addMessage( "Distance map options:",
			new Font( "SansSerif", Font.BOLD, 12 ) );
	gd.addChoice( "Distances", ChamferWeights3D.getAllLabels(), weightLabel );
	String[] outputTypes = new String[]{"32 bits", "16 bits"};
	gd.addChoice( "Output Type", outputTypes, outputTypes[ floatProcessing ? 0:1 ]);
	gd.setInsets( 0, 0, 0 );
	gd.addCheckbox( "Normalize weights", normalize );
	gd.setInsets( 20, 0, 0 );
	gd.addMessage( "Watershed options:",
			new Font( "SansSerif", Font.BOLD, 12 ) );
	gd.addNumericField( "Dynamic", dynamic, 2 );
	gd.addChoice( "Connectivity", Conn3D.getAllLabels(),
			connectivity.label );
	gd.addHelp( "http://imagej.net/MorphoLibJ#Utilities_for_binary_images" );
	gd.showDialog();

	// test cancel
	if ( gd.wasCanceled() )
		return;

	// set up current parameters
	weightLabel = gd.getNextChoice();
	floatProcessing = gd.getNextChoiceIndex() == 0;
	normalize = gd.getNextBoolean();
	dynamic = (int) gd.getNextNumber();
	connectivity = Conn3D.fromLabel( gd.getNextChoice() );

	// identify which weights should be used
	weights = ChamferWeights3D.fromLabel( weightLabel );

	long t0 = System.currentTimeMillis();

	final ImagePlus result;
	if (floatProcessing)
		result = processFloat( image, weights.getFloatWeights(), normalize );
	else
		result = processShort( image, weights.getShortWeights(), normalize );

	Images3D.optimizeDisplayRange( result );

	// Display the result image
	result.show();
	result.setSlice( image.getCurrentSlice() );

	// Display elapsed time
	long t1 = System.currentTimeMillis();
	IJUtils.showElapsedTime( "Distance Transform Watershed 3D",
			t1 - t0, image );
}
 

private void setPlotOptions() {

		if (plot == null)
			return;

		final int DEF_LINE_WIDTH = 1;
		final int DEF_MAX_INTERVALS = 12;
		final int DEF_TICK_LENGTH = 7;
		final int DEF_MINOR_TICK_LENGTH = 3;
		final int[] NUM_DEFAULTS = { DEF_LINE_WIDTH, DEF_MAX_INTERVALS, DEF_TICK_LENGTH, DEF_MINOR_TICK_LENGTH };
		final String DEF_BACKGROUND_COLOR = "white";
		final String title = plot.getTitle();
		final GenericDialog ogd = new GenericDialog("Options for " + title);
		ogd.setInsets(0, 10, 10);
		ogd.addMessage("This prompt allows you access customizations that\n"
				+ "are not accessible through the plot's \"More \u00bb\" menu");
		if (!pwClosed)
			ogd.addStringField("Plot title:", title, 27);
		ogd.addSlider("Line width:", 1, 20, 1);
		ogd.addSlider("Max. n. of intervals:", 1, 40, 12);
		ogd.addSlider("Major ticks length:", 1, 14, 7);
		ogd.addSlider("Minor ticks length:", 1, 14, 3);
		ogd.addChoice("Backgrond color:", Colors.colors, DEF_BACKGROUND_COLOR);
		final Panel buttonPanel = new Panel();
		final Button fontButton = new Button("  Text & Font...  ");
		fontButton.addActionListener(ogd);
		buttonPanel.add(fontButton);
		final Button templateButton = new Button("Apply Template...");
		templateButton.addActionListener(ogd);
		buttonPanel.add(templateButton);
		ogd.addPanel(buttonPanel, GridBagConstraints.EAST, new Insets(0, 0, 0, 0));
		ogd.hideCancelButton();
		ogd.addHelp("");
		ogd.setHelpLabel("Apply Defaults");
		ogd.addDialogListener(new DialogListener() {
			@Override
			public boolean dialogItemChanged(final GenericDialog gd, final AWTEvent e) {

				if (e != null && e.toString().contains("Apply Defaults")) {
					@SuppressWarnings("unchecked")
					final Vector<TextField> nFields = gd.getNumericFields();
					for (final TextField field : nFields)
						field.setText(Integer.toString(NUM_DEFAULTS[nFields.indexOf(field)]));
					@SuppressWarnings("unchecked")
					final Vector<Choice> nChoices = gd.getChoices();
					nChoices.firstElement().select(DEF_BACKGROUND_COLOR);
				} else if (e != null && e.toString().contains("Font")) {
					setPlotFont();
					return true;
				} else if (e != null && e.toString().contains("Template")) {
					setTemplate();
					return true;
				}

				plot.setLineWidth((int) ogd.getNextNumber());
				plot.setMaxIntervals((int) ogd.getNextNumber());
				plot.setTickLength((int) ogd.getNextNumber());
				plot.setBackgroundColor(Colors.colors[ogd.getNextChoiceIndex()]);
				plot.updateImage();
				return true;

			}
		});
		showAsSubDialog(ogd);
		if (!ogd.wasOKed())
			return;
		if (!pwClosed)
			plot.getImagePlus().setTitle(WindowManager.makeUniqueName(ogd.getNextString()));

	}
 

private void setPlotFont() {

		if (plot == null)
			return;

		final String[] FONTS = new String[] { Font.SANS_SERIF, Font.MONOSPACED, Font.SERIF };
		final String[] STYLES = { "Plain", "Bold", "Italic", "Bold+Italic" };
		final String[] JUSTIFICATIONS = { "Left", "Center", "Right" };
		final String[] SCOPES = { "Plot", "Both Axes Titles", "X-axis Title", "Y-axis Title" };
		final String[] CHOICE_DEFAULTS = { FONTS[0], STYLES[0], JUSTIFICATIONS[0], SCOPES[0] };
		final int[] INT_STYLES = { Font.PLAIN, Font.BOLD, Font.ITALIC, Font.BOLD + Font.ITALIC };
		final int[] INT_JUSTIFICATIONS = { Plot.LEFT, Plot.CENTER, Plot.RIGHT };
		final int DEF_SIZE = 12;
		final boolean DEF_ANTIALISED = true;

		final GenericDialog fgd = new GenericDialog("Font Options");
		fgd.addChoice("Type:", FONTS, CHOICE_DEFAULTS[0]);
		fgd.addChoice("Style:", STYLES, CHOICE_DEFAULTS[1]);
		fgd.addChoice("Justification:", JUSTIFICATIONS, CHOICE_DEFAULTS[2]);
		fgd.addSlider("Size:", 9, 24, DEF_SIZE);
		fgd.setInsets(0, 20, 15);
		fgd.addCheckbox("Antialiased text", DEF_ANTIALISED);
		fgd.addChoice("Apply to:", SCOPES, CHOICE_DEFAULTS[3]);
		fgd.hideCancelButton();
		fgd.addHelp("");
		fgd.setHelpLabel("Apply Defaults");
		fgd.addDialogListener(new DialogListener() {
			@Override
			public boolean dialogItemChanged(final GenericDialog gd, final AWTEvent e) {
				if (e != null && e.toString().contains("Apply Defaults")) {
					@SuppressWarnings("unchecked")
					final Vector<Choice> nChoices = gd.getChoices();
					for (final Choice choice : nChoices)
						choice.select(CHOICE_DEFAULTS[nChoices.indexOf(choice)]);
					((TextField) gd.getNumericFields().get(0)).setText(Integer.toString(DEF_SIZE));
					((Checkbox) gd.getCheckboxes().get(0)).setState(DEF_ANTIALISED);
				}

				final String type = FONTS[fgd.getNextChoiceIndex()];
				final int style = INT_STYLES[fgd.getNextChoiceIndex()];
				final int justification = INT_JUSTIFICATIONS[fgd.getNextChoiceIndex()];
				final int size = (int) fgd.getNextNumber();
				final int scopeIdx = fgd.getNextChoiceIndex();

				plot.setJustification(justification);
				plot.setAntialiasedText(fgd.getNextBoolean());
				final Font font = new Font(type, style, size);
				switch (scopeIdx) {
				case 1: // SCOPES[1]
					plot.setXLabelFont(font);
					plot.setYLabelFont(font);
					break;
				case 2: // SCOPES[2]
					plot.setXLabelFont(font);
					break;
				case 3: // SCOPES[3]
					plot.setYLabelFont(font);
					break;
				default:
					plot.setFont(font);
					plot.setXLabelFont(font);
					plot.setYLabelFont(font);
					break;
				}

				plot.updateImage();
				return true;
			}
		});
		showAsSubDialog(fgd);
		if (!fgd.wasOKed())
			return;
	}