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

@Override
public void run(String arg0) 
{
	ImagePlus imagePlus = IJ.getImage();
	
	GenericDialog gd = new GenericDialog("Remove/Replace Label(s)");
	gd.addStringField("Label(s)", "1", 12);
	gd.addMessage("Separate label values by \",\"");
	gd.addNumericField("Final Value", 0, 0);
	gd.addMessage("Replacing by value 0\n will remove labels");
	gd.showDialog();
	
	if (gd.wasCanceled())
		return;
	
	String labelListString = gd.getNextString();
	double finalValue = gd.getNextNumber();

	float[] labelArray = parseLabels(labelListString);
	
	// replace values in original image
	LabelImages.replaceLabels(imagePlus, labelArray, (float) finalValue);
	imagePlus.updateAndDraw();
}
 

@Override
public void queryAdditionalParameters( final GenericDialog gd, final SpimData2 spimData )
{
	if ( defaultPath == null || defaultPath.length() == 0 )
	{
		defaultPath = spimData.getBasePath().getAbsolutePath();
		
		if ( defaultPath.endsWith( "/." ) )
			defaultPath = defaultPath.substring( 0, defaultPath.length() - 1 );
		
		if ( defaultPath.endsWith( "/./" ) )
			defaultPath = defaultPath.substring( 0, defaultPath.length() - 2 );
	}

	gd.addStringField( "Output_file_directory", defaultPath, 50 );
}
 

protected Tag askForNewTag(final int keyCode) {
	GenericDialog gd = new GenericDialog("Define new tag");
	gd.addMessage("Define new tag for key: " + ((char)keyCode));
	TreeSet<Tag> ts = getTags(keyCode);
	gd.addStringField("New tag:", "", 40);
	if (null != ts && ts.size() > 0) {
		String[] names = new String[ts.size()];
		int next = 0;
		for (Tag t : ts) names[next++] = t.toString();
		gd.addChoice("Existing tags for " + ((char)keyCode) + ":", names, names[0]);
	}
	gd.showDialog();
	if (gd.wasCanceled()) return null;
	String tag = gd.getNextString().trim();
	if (0 == tag.length()) {
		Utils.logAll("Invalid tag " + tag);
		return null;
	}
	return putTag(tag, keyCode);
}
 

boolean setParametersFromDialog() {

            final GenericDialog dialog = new GenericDialog("Export Parameters");

            final int defaultTextColumns = 100;
            dialog.addStringField("Render Web Services Base URL", baseDataUrl, defaultTextColumns);
            dialog.addStringField("Basis Render Stack Owner", basisRenderOwner, defaultTextColumns);
            dialog.addStringField("Basis Render Stack Project", basisRenderProject, defaultTextColumns);
            dialog.addStringField("Basis Render Stack Name", basisRenderStack, defaultTextColumns);
            layerRange.addFieldsToDialog(dialog);
            dialog.addStringField("Target Render Stack Owner", targetRenderOwner, defaultTextColumns);
            dialog.addStringField("Target Render Stack Project", targetRenderProject, defaultTextColumns);
            dialog.addStringField("Target Render Stack Name", targetRenderStack, defaultTextColumns);
            dialog.addStringField("TrakEM2 Z to Target Z Map", trakZToTargetZMapString, defaultTextColumns);
            dialog.addMessage("  note: leave empty to skip mapping, format is a=b,c=d");
            dialog.addCheckbox("Complete Stack After Export", completeStackAfterExport);

            dialog.showDialog();
            dialog.repaint(); // seems to help with missing dialog elements, but shouldn't be necessary

            final boolean wasCancelled = dialog.wasCanceled();

            if (! wasCancelled) {
                baseDataUrl = dialog.getNextString().trim();
                basisRenderOwner = dialog.getNextString().trim();
                basisRenderProject = dialog.getNextString().trim();
                basisRenderStack =  dialog.getNextString().trim();
                layerRange.setFieldsFromDialog(dialog);
                targetRenderOwner = dialog.getNextString().trim();
                targetRenderProject = dialog.getNextString().trim();
                targetRenderStack =  dialog.getNextString().trim();
                trakZToTargetZMapString =  dialog.getNextString().trim();
                completeStackAfterExport = dialog.getNextBoolean();

                sectionIdToDataMap.clear();
                trakZToTargetZMap.clear();
            }

            return wasCancelled;
        }
 

boolean setParametersFromDialog() {

            final GenericDialog dialog = new GenericDialog("Export Parameters");

            final int defaultTextColumns = 100;
            dialog.addStringField("Render Web Services Base URL", baseDataUrl, defaultTextColumns);
            layerRange.addFieldsToDialog(dialog);
            dialog.addCheckbox("Only Export Visible Patches", onlyExportVisiblePatches);
            dialog.addCheckbox("Use Patch Title For Tile ID", usePatchTitleForTileId);
            dialog.addMessage("  note: leave unchecked to use TrakEM2 patch object ID as tile ID");
            dialog.addStringField("Target Render Stack Owner", targetRenderOwner, defaultTextColumns);
            dialog.addStringField("Target Render Stack Project", targetRenderProject, defaultTextColumns);
            dialog.addStringField("Target Render Stack Name", targetRenderStack, defaultTextColumns);
            dialog.addNumericField("Stack Resolution X (nm/pixel)", stackResolutionX, 0);
            dialog.addNumericField("Stack Resolution Y (nm/pixel)", stackResolutionY, 0);
            dialog.addNumericField("Stack Resolution Z (nm/pixel)", stackResolutionZ, 0);
            dialog.addCheckbox("Complete Stack After Export", completeStackAfterExport);

            dialog.showDialog();
            dialog.repaint(); // seems to help with missing dialog elements, but shouldn't be necessary

            final boolean wasCancelled = dialog.wasCanceled();

            if (! wasCancelled) {
                baseDataUrl = dialog.getNextString().trim();
                layerRange.setFieldsFromDialog(dialog);
                onlyExportVisiblePatches = dialog.getNextBoolean();
                usePatchTitleForTileId = dialog.getNextBoolean();
                targetRenderOwner = dialog.getNextString().trim();
                targetRenderProject = dialog.getNextString().trim();
                targetRenderStack =  dialog.getNextString().trim();
                stackResolutionX = dialog.getNextNumber();
                stackResolutionY = dialog.getNextNumber();
                stackResolutionZ = dialog.getNextNumber();
                completeStackAfterExport = dialog.getNextBoolean();
            }

            return wasCancelled;
        }
 

public void run(String args) {
    ImagePlus imagePlus = IJ.getImage();
    
    // create the dialog, with operator options
    GenericDialog gd = new GenericDialog("Select Label(s)");
    gd.addMessage("Add labels seperated by comma.\nEx: [1, 2, 6, 9]");
    gd.addStringField("Label(s)", "1");
    gd.showDialog();
    
    // If cancel was clicked, do nothing
    if (gd.wasCanceled())
        return;
    
    // extract label index, and number of pixel border to add
    String labelString = (String) gd.getNextString();
  
    int[] labels = IJUtils.parseLabelList(labelString);
    ImagePlus selectedPlus = LabelImages.keepLabels(imagePlus, labels);
    		
    // copy settings
    selectedPlus.copyScale(imagePlus);
    selectedPlus.setDisplayRange(imagePlus.getDisplayRangeMin(), imagePlus.getDisplayRangeMax());
    selectedPlus.setLut( imagePlus.getProcessor().getLut() );

    // display and adapt visible slice
    selectedPlus.show();
    if (imagePlus.getStackSize() > 1)
    {	
    	selectedPlus.setSlice(imagePlus.getCurrentSlice());
    }
}
 

public static boolean queryNewCal( final ArrayList< Cal > calibrations, final Cal maxCal )
{
	final GenericDialog gd = new GenericDialog( "Define new calibration" );
	
	gd.addNumericField( "Calibration_x", maxCal.getCal()[ 0 ], 40, 20, "" );
	// ImageJ cuts of part of the number otherwise
	((TextField)gd.getNumericFields().lastElement()).setText( "" + maxCal.getCal()[ 0 ] );
	gd.addNumericField( "Calibration_y", maxCal.getCal()[ 1 ], 40, 20, "" );
	// ImageJ cuts of part of the number otherwise
	((TextField)gd.getNumericFields().lastElement()).setText( "" + maxCal.getCal()[ 1 ] );
	gd.addNumericField( "Calibration_z", maxCal.getCal()[ 2 ], 40, 20, "" );
	// ImageJ cuts of part of the number otherwise
	((TextField)gd.getNumericFields().lastElement()).setText( "" + maxCal.getCal()[ 2 ] );
	gd.addStringField( "Unit", maxCal.unit() );

	if ( calibrations.size() > 1 )
		gd.addMessage( "WARNING: Calibrations are not the same for all\n" +
					   "view setups! All calibrations will be overwritten\n" +
					   "for all view setups if defined here.",
					   GUIHelper.mediumstatusfont, GUIHelper.warning );

	gd.addMessage( "Note: These values will be applied to selected view\n" +
				   "setups, existing registration are not affected and\n" +
				   "will need to be recomputed if necessary.",
				   GUIHelper.mediumstatusfont );

	gd.showDialog();
	
	if ( gd.wasCanceled() )
		return false;
	
	maxCal.getCal()[ 0 ] = gd.getNextNumber();
	maxCal.getCal()[ 1 ] = gd.getNextNumber();
	maxCal.getCal()[ 2 ] = gd.getNextNumber();
	maxCal.setUnit( gd.getNextString() );

	return true;
}
 

public void rename(final ProjectThing thing) {
	final Object ob = thing.getObject();
	final String old_title;
	if (null == ob) old_title = thing.getType();
	else if (ob instanceof DBObject) old_title = ((DBObject)ob).getTitle();
	else old_title = ob.toString();
	GenericDialog gd = ControlWindow.makeGenericDialog("New name");
	gd.addMessage("Old name: " + old_title);
	gd.addStringField("New name: ", old_title, 40);
	gd.showDialog();
	if (gd.wasCanceled()) return;
	String title = gd.getNextString();
	if (null == title) {
		Utils.log("WARNING: avoided setting the title to null for " + thing);
		return;
	}
	title = title.replace('"', '\'').trim(); // avoid XML problems - could also replace by double '', then replace again by " when reading.
	project.getRootLayerSet().addUndoStep(new RenameThingStep(thing));
	if (title.length() == 0) {
		// Set the title to the template type
		thing.setTitle(thing.getTemplate().getType());
		return;
	}
	thing.setTitle(title);
	this.updateUILater();
	project.getRootLayerSet().addUndoStep(new RenameThingStep(thing));
}
 

boolean setParametersFromDialog() {

            final GenericDialog dialog = new GenericDialog("Import Parameters");

            final int defaultTextColumns = 80;
            dialog.addStringField("Render Web Services Base URL", baseDataUrl, defaultTextColumns);
            dialog.addStringField("Render Stack Owner", renderOwner, defaultTextColumns);
            dialog.addStringField("Render Stack Project", renderProject, defaultTextColumns);
            dialog.addStringField("Render Stack Name", renderStack, defaultTextColumns);
            dialog.addStringField("Channel (empty for default)", "", defaultTextColumns);
            dialog.addNumericField("Min Z", minZ, 1);
            dialog.addNumericField("Max Z", maxZ, 1);
            dialog.addNumericField("Image Plus Type (use '-1' to slowly derive dynamically)", imagePlusType, 0);
            dialog.addMessage("  note: image plus type values are: 0:GRAY8, 1:GRAY16, 2:GRAY32, 3:COLOR_256, 4:COLOR_RGB");
            dialog.addCheckbox("Load Masks", loadMasks);
            dialog.addCheckbox("Split Sections", splitSections);
            dialog.addCheckbox("Replace Last Transform With Stage", replaceLastWithStage);
            dialog.addNumericField("Number of threads for mipmaps", numberOfMipmapThreads, 0);

            dialog.showDialog();
            dialog.repaint(); // seems to help with missing dialog elements, but shouldn't be necessary

            final boolean wasCancelled = dialog.wasCanceled();

            if (! wasCancelled) {
                baseDataUrl = dialog.getNextString();
                renderOwner = dialog.getNextString();
                renderProject = dialog.getNextString();
                renderStack =  dialog.getNextString();
                String channelString = dialog.getNextString();
                if (channelString != null && channelString.length() > 0) {
                    channels.add(channelString);
                }
                minZ = dialog.getNextNumber();
                maxZ = dialog.getNextNumber();
                imagePlusType = new Double(dialog.getNextNumber()).intValue();
                loadMasks = dialog.getNextBoolean();
                splitSections = dialog.getNextBoolean();
                replaceLastWithStage = dialog.getNextBoolean();
                numberOfMipmapThreads = (int) dialog.getNextNumber();
            }

            return wasCancelled;
        }
 

public BoundingBox defineBoundingBox(
		final SpimData2 data,
		final List< ViewId > viewIds,
		final String clusterExtension,
		final String xmlFileName,
		final boolean saveXML )
{
	final String[] boundingBoxDescriptions = new String[ staticBoundingBoxAlgorithms.size() ];

	for ( int i = 0; i < staticBoundingBoxAlgorithms.size(); ++i )
		boundingBoxDescriptions[ i ] = staticBoundingBoxAlgorithms.get( i ).getDescription();

	if ( defaultBoundingBoxAlgorithm >= boundingBoxDescriptions.length )
		defaultBoundingBoxAlgorithm = 0;

	final GenericDialog gd = new GenericDialog( "Image Fusion" );

	gd.addChoice( "Bounding_Box", boundingBoxDescriptions, boundingBoxDescriptions[ defaultBoundingBoxAlgorithm ] );
	gd.addStringField( "Bounding_Box_Name", defaultName, 30 );

	// assemble the last registration names of all viewsetups involved
	final HashMap< String, Integer > names = GUIHelper.assembleRegistrationNames( data, viewIds );
	gd.addMessage( "" );
	GUIHelper.displayRegistrationNames( gd, names );
	gd.addMessage( "" );

	GUIHelper.addWebsite( gd );

	if ( names.keySet().size() > 5 )
		GUIHelper.addScrollBars( gd );
	
	gd.showDialog();

	if ( gd.wasCanceled() )
		return null;

	final int boundingBoxAlgorithm = defaultBoundingBoxAlgorithm = gd.getNextChoiceIndex();
	final String boundingBoxName = gd.getNextString();

	for ( final BoundingBox bb : data.getBoundingBoxes().getBoundingBoxes() )
	{
		if ( bb.getTitle().equals( boundingBoxName ) )
		{
			IOFunctions.println( "A bounding box with the name '" + boundingBoxName + "' already exists." );
			defaultName = boundingBoxName + "1";
			return null;
		}
	}

	final BoundingBoxGUI boundingBox = staticBoundingBoxAlgorithms.get( boundingBoxAlgorithm ).newInstance( data, viewIds );

	if ( !boundingBox.queryParameters( null, null ) )
		return null;

	boundingBox.setTitle( boundingBoxName );
	defaultName = boundingBoxName + "1";

	data.getBoundingBoxes().addBoundingBox( boundingBox );

	if ( saveXML )
		SpimData2.saveXML( data, xmlFileName, clusterExtension );

	return boundingBox;
}
 

/**
 * Querys a pattern of element from the list
 * 
 * @param name - type of elements (e.g. "Timepoints")
 * @param list - list of available elements
 * @param defaultSelectionArray - default selection (array of size 1 to be able to return it)
 * @return the selection or null if cancelled
 */
public static boolean[] queryPattern( final String name, final String[] list, final String[] defaultSelectionArray )
{
	String defaultSelection = defaultSelectionArray[ 0 ];

	if ( defaultSelection == null || defaultSelection.length() == 0 )
	{
		defaultSelection = list[ 0 ];
		
		for ( int i = 1; i < Math.min( list.length, 3 ); ++i )
			defaultSelection += "," + list[ i ];
	}
	
	final GenericDialog gd = new GenericDialog( "Select Range of " + name );
	
	gd.addMessage( "" );
	gd.addStringField( "Process_following_" + name, defaultSelection, 30 );
	gd.addMessage( "" );
	gd.addMessage( "Available " + name + ":" );
	
	final String singular = name.substring( 0, name.length() - 1 ) + " ";
	String allTps = singular + list[ 0 ];
	
	for ( int i = 1; i < list.length; ++i )
		allTps += "\n" + singular + list[ i ];
	
	gd.addMessage( allTps, GUIHelper.smallStatusFont );
	
	GUIHelper.addScrollBars( gd );
	gd.showDialog();
	
	if ( gd.wasCanceled() )
		return null;
	
	// the result
	final boolean[] selected = new boolean[ list.length ];
	
	for ( int i = 0; i < list.length; ++i )
		selected[ i ] = false;
	
	try 
	{
		final ArrayList< String > nameList = NamePattern.parseNameString( defaultSelection = gd.getNextString(), true );
		
		for ( final String entry : nameList )
		{
			boolean found = false;
			
			for ( int i = 0; i < list.length && !found; ++i )
			{
				if ( entry.equals( list[ i ] ) )
				{
					selected[ i ] = true;
					found = true;
				}
			}
			
			if ( !found )
				IOFunctions.println( name + " " + entry + " not part of the list of " + name + "s. Ignoring it." );
		}				
	} 
	catch ( final ParseException e ) 
	{
		IOFunctions.println( "Cannot parse pattern '" + defaultSelection + "': " + e );
		return null;
	}
	
	defaultSelectionArray[ 0 ] = defaultSelection;
	
	return selected;
}
 

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()));

	}
 

protected GenericDialog makeAdjustPropertiesDialog() {
	Rectangle box = getBoundingBox(null);
	GenericDialog gd = new GD("Properties of #" + id, this);
	gd.addStringField("title: ", title);
	gd.addNumericField("x: ", box.x, 2);
	gd.addNumericField("y: ", box.y, 2);
	gd.addNumericField("scale_x: ", 1, 2);
	gd.addNumericField("scale_y: ", 1, 2);
	gd.addNumericField("rot (degrees): ", 0, 2);
	gd.addSlider("alpha: ", 0, 100, (int)(alpha*100));
	gd.addCheckbox("visible", visible);
	gd.addSlider("Red: ", 0, 255, color.getRed());
	gd.addSlider("Green: ", 0, 255, color.getGreen());
	gd.addSlider("Blue: ", 0, 255, color.getBlue());
	gd.addCheckbox("locked", locked);
	// add slider listener
	final Scrollbar alp = (Scrollbar)gd.getSliders().get(0);
	final Scrollbar red = (Scrollbar)gd.getSliders().get(1);
	final Scrollbar green = (Scrollbar)gd.getSliders().get(2);
	final Scrollbar blue = (Scrollbar)gd.getSliders().get(3);
	final TextField talp = (TextField)gd.getNumericFields().get(5);
	final TextField tred = (TextField)gd.getNumericFields().get(6);
	final TextField tgreen = (TextField)gd.getNumericFields().get(7);
	final TextField tblue = (TextField)gd.getNumericFields().get(8);
	SliderListener sla = new SliderListener() {
		public void update() {
			setAlpha((float)alp.getValue()/100);
		}
	};
	SliderListener slc = new SliderListener() {
		public void update() {
			setColor(new Color(red.getValue(), green.getValue(), blue.getValue()));
		}
	};
	alp.addAdjustmentListener(sla);
	red.addAdjustmentListener(slc);
	green.addAdjustmentListener(slc);
	blue.addAdjustmentListener(slc);
	talp.addTextListener(sla);
	tred.addTextListener(slc);
	tgreen.addTextListener(slc);
	tblue.addTextListener(slc);
	
	gd.addChoice( "composite mode: ", compositeModes, compositeModes[ compositeMode ] );
	return gd;
}
 

public boolean setup(final boolean to_file, final String regex, final boolean plot, final boolean condense) {
	final GenericDialog gd = new GenericDialog("All to all");
	gd.addMessage("Choose a point interdistance to resample to, or 0 for the average of all.");
	gd.addNumericField("point_interdistance: ", delta, 2);
	gd.addCheckbox("skip insertion/deletion strings at ends when scoring", skip_ends);
	gd.addNumericField("maximum_ignorable consecutive muts in endings: ", max_mut, 0);
	gd.addNumericField("minimum_percentage that must remain: ", min_chunk, 2);
	gd.addCheckbox("Score mutations only", score_mut_only);
	Utils.addEnablerListener((Checkbox)gd.getCheckboxes().get(0), new Component[]{(Component)gd.getNumericFields().get(0), (Component)gd.getNumericFields().get(1)}, null);

	final String[] transforms = {"translate and rotate",
				     "translate, rotate and scale",
				     "translate, rotate, scale and shear",
				     "moving least squares",
				     "relative",
				     "direct"};
	gd.addChoice("Transform_type: ", transforms, transforms[transform_type]);
	gd.addCheckbox("Chain_branches", chain_branches);

	gd.addChoice("Presets: ", preset_names, preset_names[0]);
	gd.addMessage("");
	gd.addChoice("Scoring type: ", distance_types, distance_types[distance_type]);
	final String[] distance_types2 = {"Levenshtein", "Dissimilarity", "Average physical distance", "Median physical distance", "Cummulative physical distance", "Standard deviation", "Combined SLM", "Proximity", "Proximity of mutation pairs", "None"}; // CAREFUL when adding more entries: index 9 is used as None for sortMatches and as a conditional.
	gd.addChoice("Resort scores by: ", distance_types2, distance_types2[distance_type_2]);
	gd.addNumericField("Min_matches: ", min_matches, 0);
	if (to_file) {
		gd.addChoice("File format: ", formats, formats[2]);
	}
	gd.addCheckbox("normalize", normalize);
	gd.addCheckbox("direct", direct);
	gd.addCheckbox("substring_matching", substring_matching);
	gd.addStringField("regex: ", null != regex ? regex : "");
	if (plot) {
		gd.addNumericField("plot_width: ", plot_width, 0);
		gd.addNumericField("plot_height: ", plot_height, 0);
		gd.addNumericField("plot_max_x: ", plot_max_x, 2);
		gd.addNumericField("plot_max_y: ", plot_max_y, 2);
	}
	if (condense) {
		gd.addCheckbox("cut_uneven_ends", cut_uneven_ends);
		final String[] env = {"1 std dev", "2 std dev", "3 std dev", "average", "maximum"};
		gd.addChoice("envelope", env, env[envelope_type]);
		gd.addNumericField("delta envelope:", delta_envelope, 1);
	}

	//////

	gd.showDialog();
	if (gd.wasCanceled()) return false;

	delta = gd.getNextNumber();
	skip_ends = gd.getNextBoolean();
	max_mut = (int)gd.getNextNumber();
	min_chunk = (float)gd.getNextNumber();
	score_mut_only = gd.getNextBoolean();
	if (skip_ends) {
		if (max_mut < 0) max_mut = 0;
		if (min_chunk <= 0) skip_ends = false;
		if (min_chunk > 1) min_chunk = 1;
	}
	transform_type = gd.getNextChoiceIndex();
	chain_branches = gd.getNextBoolean();
	preset = presets[gd.getNextChoiceIndex()];

	distance_type = gd.getNextChoiceIndex();
	distance_type_2 = gd.getNextChoiceIndex();
	min_matches = (int) gd.getNextNumber();
	if (min_matches < 0) {
		Utils.log("Using 0 min_matches!");
		min_matches = 0;
	}

	format = formats[0];
	if (to_file) format = gd.getNextChoice().trim();

	normalize = gd.getNextBoolean();
	direct = gd.getNextBoolean();
	substring_matching = gd.getNextBoolean();

	this.regex = gd.getNextString().trim();
	if (0 == this.regex.length()) this.regex = null;

	if (plot) {
		plot_width = (int)gd.getNextNumber();
		plot_height = (int)gd.getNextNumber();
		plot_max_x = gd.getNextNumber();
		plot_max_y = gd.getNextNumber();
	}
	if (condense) {
		cut_uneven_ends = gd.getNextBoolean();
		envelope_type = gd.getNextChoiceIndex();
		delta_envelope = gd.getNextNumber();
		Utils.log2("delta_envelope has been set to " + delta_envelope);
	}

	return true;
}
 

/**
 * Setup as a three step dialog.
 */
@Override
public boolean setup( final String title )
{
	source_dir = "";
	while ( source_dir == "" )
	{
		final DirectoryChooser dc = new DirectoryChooser( "Calibration Images" );
		source_dir = dc.getDirectory();
		if ( null == source_dir ) return false;

		source_dir = source_dir.replace( '\\', '/' );
		if ( !source_dir.endsWith( "/" ) ) source_dir += "/";
	}

	final String exts = ".tif.jpg.png.gif.tiff.jpeg.bmp.pgm";
	names = new File( source_dir ).list(
			new FilenameFilter()
			{
				@Override
                      public boolean accept( final File dir, final String name )
				{
					final int idot = name.lastIndexOf( '.' );
					if ( -1 == idot ) return false;
					return exts.contains( name.substring( idot ).toLowerCase() );
				}
			} );
	Arrays.sort( names );

	final GenericDialog gd = new GenericDialog( title );

	gd.addNumericField( "number_of_images :", 9, 0 );
	gd.addChoice( "first_image :", names, names[ 0 ] );
	gd.addNumericField( "power_of_polynomial_kernel :", dimension, 0 );
	gd.addNumericField( "lambda :", lambda, 6 );
	gd.addCheckbox( "apply_correction_to_images", applyCorrection );
	gd.addCheckbox( "visualize results", visualizeResults );
	final String[] options = new String[]{ "save", "load" };
	gd.addChoice( "What to do? ", options, options[ saveOrLoad ] );
	gd.addStringField( "file_name: ", saveFileName );
	gd.showDialog();

	if (gd.wasCanceled()) return false;

	numberOfImages = ( int )gd.getNextNumber();
	firstImageIndex = gd.getNextChoiceIndex();
	dimension = ( int )gd.getNextNumber();
	lambda = gd.getNextNumber();
	applyCorrection = gd.getNextBoolean();
	visualizeResults = gd.getNextBoolean();
	saveOrLoad = gd.getNextChoiceIndex();
	saveFileName = gd.getNextString();

	if ( saveOrLoad == 0 || visualizeResults )
	{
		final GenericDialog gds = new GenericDialog( title );
		SIFT.addFields( gds, sift );

		gds.addNumericField( "closest/next_closest_ratio :", rod, 2 );

		gds.addMessage( "Geometric Consensus Filter:" );
		gds.addNumericField( "maximal_alignment_error :", maxEpsilon, 2, 6, "px" );
		gds.addNumericField( "inlier_ratio :", minInlierRatio, 2 );
		gds.addChoice( "expected_transformation :", modelStrings, modelStrings[ expectedModelIndex ] );

		gds.showDialog();
		if ( gds.wasCanceled() ) return false;

		SIFT.readFields( gds, sift );

		rod = ( float )gds.getNextNumber();

		maxEpsilon = ( float )gds.getNextNumber();
		minInlierRatio = ( float )gds.getNextNumber();
		expectedModelIndex = gds.getNextChoiceIndex();

		return !( gd.invalidNumber() || gds.invalidNumber() );
	}

	return !gd.invalidNumber();
}