fiji.util.gui.GenericDialogPlus Java Examples

@Override
public void run(ImageProcessor ip) {
	GenericDialogPlus gd = new GenericDialogPlus("Povray Animator");
	gd.addDirectoryField("Output_folder", "");
	gd.addNumericField("Target_width", 640, 0);
	gd.addNumericField("Target_height", 480, 0);
	gd.showDialog();

	if(gd.wasCanceled())
		return;

	String outputFolder = gd.getNextString();
	int tgtW = (int)gd.getNextNumber();
	int tgtH = (int)gd.getNextNumber();

	run(image, outputFolder, tgtW, tgtH);
}
 

protected File queryMMFile()
{
	GenericDialogPlus gd = new GenericDialogPlus( "Define MicroMananger diSPIM Dataset" );

	gd.addFileField( "MicroManager OME TIFF file", defaultFirstFile, 50 );

	gd.showDialog();

	if ( gd.wasCanceled() )
		return null;

	final File firstFile = new File( defaultFirstFile = gd.getNextString() );

	if ( !firstFile.exists() )
	{
		IOFunctions.println( "File '" + firstFile.getAbsolutePath() + "' does not exist. Stopping" );
		return null;
	}
	else
	{
		IOFunctions.println( "Investigating file '" + firstFile.getAbsolutePath() + "'." );
		return firstFile;
	}
}
 

protected File querySLDFile() {
    GenericDialogPlus gd = new GenericDialogPlus("Define SlideBook6 diSPIM Dataset");

    gd.addFileField("SlideBook6 SLD file", defaultFilePath, 50);
    gd.showDialog();

    if (gd.wasCanceled())
        return null;

    final File firstFile = new File(defaultFilePath = gd.getNextString());
    if (!firstFile.exists()) {
        IOFunctions.println("File '" + firstFile.getAbsolutePath() + "' does not exist. Stopping");
        return null;
    } else {
        IOFunctions.println("Investigating file '" + firstFile.getAbsolutePath() + "'.");
        return firstFile;
    }
}
 

protected File queryCZIFile()
{
	GenericDialogPlus gd = new GenericDialogPlus( "Define Lightsheet Z.1 Dataset" );

	gd.addFileField( "First_CZI file of the dataset", defaultFirstFile, 50 );

	gd.showDialog();

	if ( gd.wasCanceled() )
		return null;

	final File firstFile = new File( defaultFirstFile = gd.getNextString() );

	if ( !firstFile.exists() )
	{
		IOFunctions.println( "File '" + firstFile.getAbsolutePath() + "' does not exist. Stopping" );
		return null;
	}
	else
	{
		IOFunctions.println( "Investigating file '" + firstFile.getAbsolutePath() + "'." );
		return firstFile;
	}
}
 

public static void addSaveAsFileField( final GenericDialogPlus dialog, final String label, final String defaultPath, final int columns) {
	dialog.addStringField( label, defaultPath, columns );

	final TextField text = ( TextField ) dialog.getStringFields().lastElement();
	final GridBagLayout layout = ( GridBagLayout ) dialog.getLayout();
	final GridBagConstraints constraints = layout.getConstraints( text );

	final Button button = new Button( "Browse..." );
	final ChooseXmlFileListener listener = new ChooseXmlFileListener( text );
	button.addActionListener( listener );
	button.addKeyListener( dialog );

	final Panel panel = new Panel();
	panel.setLayout( new FlowLayout( FlowLayout.LEFT, 0, 0 ) );
	panel.add( text );
	panel.add( button );

	layout.setConstraints( panel, constraints );
	dialog.add( panel );
}
 

@Override
public void run(String arg)
{
	// load SpimData
	final LoadParseQueryXML result = new LoadParseQueryXML();
	if ( !result.queryXML( "to load a TileConfiguration for", false, false, false, false, false ) )
		return;
	final SpimData2 data = result.getData();

	// ask for parameters
	final GenericDialogPlus gd = new GenericDialogPlus( "" );
	gd.addFileField( "TileConfiguration file", defaultTCFile );
	gd.addCheckbox( "Use_pixel_units", true );
	gd.addCheckbox( "Keep_metadata_rotation", true );

	gd.showDialog();

	if ( gd.wasCanceled() )
		return;

	defaultTCFile = gd.getNextString();
	final boolean pixelUnits = gd.getNextBoolean();
	final boolean metadataRotate = gd.getNextBoolean();

	// apply
	final Map< ViewId, Translation3D > tcParsed = TileConfigurationHelpers.parseTileConfiguration( new File( defaultTCFile ) );
	final Map< ViewId, Translation3D > transformsForData = TileConfigurationHelpers.getTransformsForData( tcParsed, pixelUnits, data );
	TileConfigurationHelpers.applyToData( transformsForData, pixelUnits, metadataRotate, data );

	// save result
	SpimData2.saveXML( data, result.getXMLFileName(), result.getClusterExtension() );
}
 

protected DHMMetaData queryDirectoryAndRatio()
{
	GenericDialogPlus gd = new GenericDialogPlus( "Specify Holographic Acquistion Directory" );

	gd.addDirectoryField( "Holographic_Acquisition main directory", defaultDir, 50 );

	gd.addMessage( "" );
	gd.addMessage( "Camera pixel size (e.g. 3.45um) / Magnification (e.g. 20):" );
	gd.addNumericField( "Pixel_distance_x", defaulCalX, 5 );
	gd.addNumericField( "Pixel_distance_y", defaulCalY, 5 );
	gd.addMessage( "Depth between planes (e.g. 0.5mm) / Magnification^2 (e.g. 20^2) * 1000 (mm to um):" );
	gd.addNumericField( "Pixel_distance_z", defaulCalZ, 5 );
	gd.addStringField( "Pixel_unit", defaulCalUnit );
	gd.addMessage( "" );
	gd.addCheckbox( "Open_all planes to ensure they have the same dimensions (takes time!)", defaultOpenAll );
	gd.showDialog();

	if ( gd.wasCanceled() )
		return null;

	return new DHMMetaData(
			new File( defaultDir = gd.getNextString() ),
			defaulCalX = gd.getNextNumber(),
			defaulCalY = gd.getNextNumber(),
			defaulCalZ = gd.getNextNumber(),
			defaulCalUnit = gd.getNextString(),
			defaultOpenAll = gd.getNextBoolean() );
}
 

public static Parameters getParameters()
{
	final GenericDialogPlus gd = new GenericDialogPlus( "Resave dataset as TIFF" );

	if ( defaultPath == null )
		defaultPath = LoadParseQueryXML.defaultXMLfilename;

	PluginHelper.addSaveAsFileField( gd, "Select new XML", defaultPath, 80 );
	
	gd.addChoice( "ImgLib2_data_container", StackList.imglib2Container, StackList.imglib2Container[ defaultContainer ] );
	gd.addCheckbox( "Lossless compression of TIFF files (ZIP)", defaultCompress );
	gd.addMessage( "Use ArrayImg if -ALL- input views are smaller than ~2048x2048x500 px (2^31 px), or if the\n" +
				   "program throws an OutOfMemory exception while processing.  CellImg is slower, but more\n" +
			       "memory efficient and supports much larger file sizes only limited by the RAM of the machine.", 
			       new Font( Font.SANS_SERIF, Font.ITALIC, 11 ) );

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

	final Parameters params = new Parameters();
	
	params.xmlFile = gd.getNextString();
	
	if ( !params.xmlFile.endsWith( ".xml" ) )
		params.xmlFile += ".xml";

	params.compress = defaultCompress = gd.getNextBoolean();

	defaultPath = LoadParseQueryXML.defaultXMLfilename = params.xmlFile;

	if ( ( defaultContainer = gd.getNextChoiceIndex() ) == 0 )
		params.imgFactory = new ArrayImgFactory< FloatType >();
	else
		params.imgFactory = new CellImgFactory< FloatType >();

	return params;
}
 

/**
 * Can be called with values[ 3 ], i.e. [r1, r2, threshold] (r2 is only written as result)
 * 
 * The results are stored in the same array.
 * 
 * @param text - the text which is shown when asking for the file
 * @param values - the intial values and also contains the result
 */
public static void getInteractiveIntegralParameters( final String text, final double values[] )
{
	final GenericDialogPlus gd = new GenericDialogPlus( text );		
	gd.addFileField( "", spimDataDirectory, 50 );		
	gd.showDialog();
	
	if ( gd.wasCanceled() )
		return;
	
	final String file = gd.getNextString();
	
	IOFunctions.println( "Loading " + file );
	final Image<FloatType> img = LOCI.openLOCIFloatType( file, new ArrayContainerFactory() );
	
	if ( img == null )
	{
		IOFunctions.println( "File not found: " + file );
		return;
	}
	
	img.getDisplay().setMinMax();
	final ImagePlus imp = ImageJFunctions.copyToImagePlus( img );
	img.close();
	
	imp.show();		
	imp.setSlice( imp.getStackSize() / 2 );	
	
	final InteractiveIntegral ii = new InteractiveIntegral();
	
	ii.setInitialRadius( Math.round( (float)values[ 0 ] ) );
	ii.setThreshold( (float)values[ 2 ] );
	
	ii.run( null );
	
	while ( !ii.isFinished() )
		SimpleMultiThreading.threadWait( 100 );
	
	imp.close();
	
	values[ 0 ] = ii.getRadius1();
	values[ 1 ] = ii.getRadius2();
	values[ 2 ] = ii.getThreshold();
}
 

/**
 * Can be called with values[ 3 ], i.e. [initialsigma, sigma2, threshold] or
 * values[ 2 ], i.e. [initialsigma, threshold]
 * 
 * The results are stored in the same array.
 * If called with values[ 2 ], sigma2 changing will be disabled
 * 
 * @param text - the text which is shown when asking for the file
 * @param values - the intial values and also contains the result
 */
public static void getInteractiveDoGParameters( final String text, final double values[] )
{
	final GenericDialogPlus gd = new GenericDialogPlus( text );		
	gd.addFileField( "", spimDataDirectory, 50 );		
	gd.showDialog();
	
	if ( gd.wasCanceled() )
		return;
	
	final String file = gd.getNextString();
	
	IOFunctions.println( "Loading " + file );
	final Image<FloatType> img = LOCI.openLOCIFloatType( file, new ArrayContainerFactory() );
	
	if ( img == null )
	{
		IOFunctions.println( "File not found: " + file );
		return;
	}
	
	img.getDisplay().setMinMax();
	final ImagePlus imp = ImageJFunctions.copyToImagePlus( img );
	img.close();
	
	imp.show();		
	imp.setSlice( imp.getStackSize() / 2 );	
	imp.setRoi( 0, 0, imp.getWidth()/3, imp.getHeight()/3 );		
	
	final InteractiveDoG idog = new InteractiveDoG();
	
	if ( values.length == 2 )
	{
		idog.setSigma2isAdjustable( false );
		idog.setInitialSigma( (float)values[ 0 ] );
		idog.setThreshold( (float)values[ 1 ] );
	}
	else
	{
		idog.setInitialSigma( (float)values[ 0 ] );
		idog.setThreshold( (float)values[ 2 ] );			
	}
	
	idog.run( null );
	
	while ( !idog.isFinished() )
		SimpleMultiThreading.threadWait( 100 );
	
	imp.close();
	
	if ( values.length == 2)
	{
		values[ 0 ] = idog.getInitialSigma();
		values[ 1 ] = idog.getThreshold();
	}
	else
	{
		values[ 0 ] = idog.getInitialSigma();
		values[ 1 ] = idog.getSigma2();						
		values[ 2 ] = idog.getThreshold();			
	}
}
 

public Pair< SpimData2, String > defineDataset( final boolean save )
{
	final ArrayList< MultiViewDatasetDefinition > datasetDefinitions = new ArrayList< MultiViewDatasetDefinition >();
	
	for ( final MultiViewDatasetDefinition mvd : staticDatasetDefinitions )
		datasetDefinitions.add( mvd.newInstance() );
	
	// verify that there are definitions
	final int numDatasetDefinitions = datasetDefinitions.size();
	
	if ( numDatasetDefinitions == 0 )
	{
		IJ.log( "No Multi-View Dataset Definitions available." );
		return null;
	}
	
	// get their names
	final String[] titles = new String[ numDatasetDefinitions ];
	
	for ( int i = 0; i < datasetDefinitions.size(); ++i )
		titles[ i ] = datasetDefinitions.get( i ).getTitle();
	
	// query the dataset definition to use
	final GenericDialogPlus gd1 = new GenericDialogPlus( "Select type of multi-view dataset" );

	if ( defaultDatasetDef >= numDatasetDefinitions )
		defaultDatasetDef = 0;
	
	gd1.addChoice( "Type_of_dataset: ", titles, titles[ defaultDatasetDef ] );
	//Choice choice = (Choice)gd1.getChoices().lastElement();
	gd1.addStringField( "XML_filename", defaultXMLName, 30 );
	/*
	final MyMultiLineLabel label = MyMultiLineLabel.addMessage( gd1,
			formatEntry( datasetDefinitions.get( defaultDatasetDef ).getExtendedDescription(), numCharacters, numLinesDocumentation ),
			new Font( Font.MONOSPACED, Font.PLAIN, 11 ),
			Color.BLACK );
					
	addListeners( gd1, choice, label, datasetDefinitions );*/
	
	GUIHelper.addWebsite( gd1 );
	
	gd1.showDialog();
	if ( gd1.wasCanceled() )
		return null;
	
	defaultDatasetDef = gd1.getNextChoiceIndex();
	final String xmlFileName = defaultXMLName = gd1.getNextString();
	
	// run the definition
	final MultiViewDatasetDefinition def = datasetDefinitions.get( defaultDatasetDef );
	
	IOFunctions.println( defaultDatasetDef );
	
	final SpimData2 spimData = def.createDataset();
	
	if ( spimData == null )
	{
		IOFunctions.println( "Defining multi-view dataset failed." );
		return null;
	}
	else
	{
		final String xml = SpimData2.saveXML( spimData, xmlFileName, "" );

		if ( xml != null )
		{
			GenericLoadParseQueryXML.defaultXMLfilename = xml;
			return new ValuePair< SpimData2, String >( spimData, xml );
		}
		else
		{
			return null;
		}
	}
}
 

@Override
public void run(String arg0)
{
	GenericDialogPlus gd = new GenericDialogPlus("Stitch Image Grid");
	GridLayout gridLayout = new GridLayout();
	
	gd.addNumericField("grid_size_x", gridSizeXStatic, 0);
	gd.addNumericField("grid_size_y", gridSizeYStatic, 0);
	//gd.addChoice("order_of_storage", arrangement, arrangmentStatic );
	
	gd.addSlider("overlap [%]", 0, 100, overlapStatic);
	gd.addDirectoryField("directory", directoryStatic, 50);
	gd.addStringField("file_names", fileNamesStatic, 50);
	gd.addChoice("rgb_order", rgbTypes, rgbOrderStatic);
	gd.addStringField("Output_file_name", tileConfStatic, 50);
	gd.addCheckbox("Save_Only_Tile_Configuration", writeOnlyTileConfStatic);
	gd.addNumericField("start_x", startXStatic, 0);
	gd.addNumericField("start_y", startYStatic, 0);
	gd.addNumericField("start_i", startIStatic, 0);
	gd.addChoice("channels_for_registration", colorList, handleRGBStatic);
	gd.addChoice("fusion_method", methodListCollection, fusionMethodStatic);
	gd.addNumericField("fusion_alpha", alphaStatic, 2);
	gd.addNumericField("regression_threshold", thresholdRStatic, 2);
	gd.addNumericField("max/avg_displacement_threshold", thresholdDisplacementRelativeStatic, 2);		
	gd.addNumericField("absolute_displacement_threshold", thresholdDisplacementAbsoluteStatic, 2);		
	gd.addCheckbox("create_only_preview", previewOnlyStatic);
	gd.addCheckbox("compute_overlap (otherwise use the coordinates given in the layout file)", computeOverlapStatic );
	gd.addMessage("");
	gd.addMessage("This Plugin is developed by Stephan Preibisch\n" + myURL);

	MultiLineLabel text = (MultiLineLabel) gd.getMessage();
	addHyperLinkListener(text, myURL);

	gd.showDialog();
	if (gd.wasCanceled()) return;
	
	gridLayout.sizeX = (int)Math.round(gd.getNextNumber());
	gridLayout.sizeY = (int)Math.round(gd.getNextNumber());
	gridSizeXStatic = gridLayout.sizeX;
	gridSizeYStatic = gridLayout.sizeY;

	//gridLayout.arrangement = gd.getNextChoice();
	//arrangmentStatic = gridLayout.arrangement;
	
	double overlap = gd.getNextNumber()/100;
	overlapStatic = overlap*100;
	
	String directory = gd.getNextString();
	directoryStatic = directory;
	
	String filenames = gd.getNextString();
	fileNamesStatic = filenames;
	
	gridLayout.rgbOrder = gd.getNextChoice();
	rgbOrderStatic = gridLayout.rgbOrder;
	
	String output = gd.getNextString();
	tileConfStatic = output;
	
	boolean writeOnlyOutput = gd.getNextBoolean();
	writeOnlyTileConfStatic = writeOnlyOutput;
	
	int startX = (int)Math.round(gd.getNextNumber());
	startXStatic = startX;
	
	int startY = (int)Math.round(gd.getNextNumber());
	startYStatic = startY;
	
	int startI = (int)Math.round(gd.getNextNumber());
	startIStatic = startI;
	
	String handleRGB = gd.getNextChoice();
	handleRGBStatic = handleRGB;
	
	String fusionMethod = gd.getNextChoice();
	fusionMethodStatic = fusionMethod;
	
	gridLayout.alpha = gd.getNextNumber();
	alphaStatic = gridLayout.alpha;
	
	gridLayout.thresholdR = gd.getNextNumber();
	thresholdRStatic = gridLayout.thresholdR;
	
	gridLayout.thresholdDisplacementRelative = gd.getNextNumber();
	thresholdDisplacementRelativeStatic = gridLayout.thresholdDisplacementRelative;
	
	gridLayout.thresholdDisplacementAbsolute = gd.getNextNumber();
	thresholdDisplacementAbsoluteStatic = gridLayout.thresholdDisplacementAbsolute;
	
	boolean previewOnly = gd.getNextBoolean();
	previewOnlyStatic = previewOnly;
	
	boolean computeOverlap = gd.getNextBoolean();
	computeOverlapStatic = computeOverlap;
	
	stitchImageGrid(filenames, directory, gridLayout, handleRGB, 
			fusionMethod, output, overlap, startX, startY, startI, 
			writeOnlyOutput, previewOnly, computeOverlap);

}
 

/**
 * Displays a dialog to harvest user input, allowing scaling from a
 * specified image width and height.
 * 
 * @param imgWidth Base image width
 * @param imgHeight Base image height
 */
public void getInput(int imgWidth, int imgHeight) {
	originalWidth = imgWidth;
	originalHeight = imgHeight;
	final GenericDialogPlus gdDownSample = new GenericDialogPlus("Downsample");
	String[] methods = ImageProcessor.getInterpolationMethods();

	gdDownSample.addNumericField("x scale", 1, 1);
	gdDownSample.addNumericField("y scale", 1, 1);
	gdDownSample.addNumericField("width (pixels)", imgWidth, 0);
	gdDownSample.addNumericField("height (pixels)", imgHeight, 0);
	gdDownSample.addChoice("Interpolation:", methods,
		methods[methods.length - 1]);
	gdDownSample.addCheckbox("Average when downsizing", true);
	Vector<?> fields = gdDownSample.getNumericFields();
	xField = (TextComponent) fields.get(0);
	yField = (TextComponent) fields.get(1);
	widthField = (TextComponent) fields.get(2);
	heightField = (TextComponent) fields.get(3);

	xField.addTextListener(textListener);
	xField.addFocusListener(focusListener);
	yField.addTextListener(textListener);
	yField.addFocusListener(focusListener);
	widthField.addTextListener(textListener);
	widthField.addFocusListener(focusListener);
	heightField.addTextListener(textListener);
	heightField.addFocusListener(focusListener);
	gdDownSample.showDialog();

	if (gdDownSample.wasOKed()) {
		xScale = gdDownSample.getNextNumber();
		yScale = gdDownSample.getNextNumber();
		double width = gdDownSample.getNextNumber();
		double height = gdDownSample.getNextNumber();
		String method = gdDownSample.getNextChoice();
		String average = gdDownSample.getNextBoolean() ? " average" : "";
		params =
			"width=" + width + " height=" +
				height + average + " interpolation=" + method;
	}
}
 

/**
 * Manages the dialog for stitching a collection of images defined by a Tileconfiguration file
 */
public void stitchCollection()
{
	final GenericDialogPlus gd = new GenericDialogPlus("Stitch Image Collection");
	
	//gd.addStringField("Layout file", fileNameStatic, 50);
	gd.addFileField( "Layout file", fileNameStatic, 50 );		
	gd.addCheckbox( "compute_overlap (otherwise use the coordinates given in the layout file)", computeOverlapStatic );
	gd.addChoice( "Channels_for_Registration", colorList, handleRGBStatic );
	gd.addChoice( "rgb_order", rgbTypes, rgbOrderStatic );
	gd.addChoice( "Fusion_Method", methodListCollection, methodListCollection[LIN_BLEND] );
	gd.addNumericField( "Fusion alpha", alphaStatic, 2 );
	gd.addNumericField( "Regression Threshold", thresholdRStatic, 2 );
	gd.addNumericField( "Max/Avg Displacement Threshold", thresholdDisplacementRelativeStatic, 2 );		
	gd.addNumericField( "Absolute Avg Displacement Threshold", thresholdDisplacementAbsoluteStatic, 2 );		
	gd.addCheckbox( "Create_only_Preview", previewOnlyStatic );
	gd.addMessage( "");
	gd.addMessage( "This Plugin is developed by Stephan Preibisch\n" + myURL );

	MultiLineLabel text = (MultiLineLabel) gd.getMessage();
	addHyperLinkListener(text, myURL);

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

	String fileName = gd.getNextString();
	fileNameStatic = fileName;

	boolean computeOverlap = gd.getNextBoolean();
	computeOverlapStatic = computeOverlap;

	String handleRGB = gd.getNextChoice();
	handleRGBStatic = handleRGB;
	
	String rgbOrder = gd.getNextChoice();
	rgbOrderStatic = rgbOrder;
	
	String fusionMethod = gd.getNextChoice();
	fusionMethodStatic = fusionMethod;
	
	double alpha = gd.getNextNumber();
	alphaStatic = alpha;
	
	double thresholdR = gd.getNextNumber();
	thresholdRStatic = thresholdR;
	
	double thresholdDisplacementRelative = gd.getNextNumber();
	thresholdDisplacementRelativeStatic = thresholdDisplacementRelative;
	
	double thresholdDisplacementAbsolute = gd.getNextNumber();
	thresholdDisplacementAbsoluteStatic = thresholdDisplacementAbsolute;
	
	boolean previewOnly = gd.getNextBoolean();
	previewOnlyStatic = previewOnly;	
	
	runStitching();
}
 

@Override
public void run(String arg0)
{
	GenericDialogPlus gd = new GenericDialogPlus("Stitch Image Collection");
	
	//gd.addStringField("Layout file", fileNameStatic, 50);
	gd.addFileField("Layout file", fileNameStatic, 50);		
	gd.addCheckbox("compute_overlap (otherwise use the coordinates given in the layout file)", computeOverlapStatic );
	gd.addChoice("Channels_for_Registration", colorList, handleRGBStatic);
	gd.addChoice("rgb_order", rgbTypes, rgbOrderStatic);
	gd.addChoice("Fusion_Method", methodListCollection, methodListCollection[LIN_BLEND]);
	gd.addNumericField("Fusion alpha", alphaStatic, 2);
	gd.addNumericField("Regression Threshold", thresholdRStatic, 2);
	gd.addNumericField("Max/Avg Displacement Threshold", thresholdDisplacementRelativeStatic, 2);		
	gd.addNumericField("Absolute Avg Displacement Threshold", thresholdDisplacementAbsoluteStatic, 2);		
	gd.addCheckbox("Create_only_Preview", previewOnlyStatic);
	gd.addMessage("");
	gd.addMessage("This Plugin is developed by Stephan Preibisch\n" + myURL);

	MultiLineLabel text = (MultiLineLabel) gd.getMessage();
	addHyperLinkListener(text, myURL);

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

	String fileName = gd.getNextString();
	fileNameStatic = fileName;

	boolean computeOverlap = gd.getNextBoolean();
	computeOverlapStatic = computeOverlap;

	String handleRGB = gd.getNextChoice();
	handleRGBStatic = handleRGB;
	
	this.rgbOrder = gd.getNextChoice();
	rgbOrderStatic = rgbOrder;
	
	String fusionMethod = gd.getNextChoice();
	fusionMethodStatic = fusionMethod;
	
	this.alpha = gd.getNextNumber();
	alphaStatic = alpha;
	
	this.thresholdR = gd.getNextNumber();
	thresholdRStatic = thresholdR;
	
	this.thresholdDisplacementRelative = gd.getNextNumber();
	thresholdDisplacementRelativeStatic = thresholdDisplacementRelative;
	
	this.thresholdDisplacementAbsolute = gd.getNextNumber();
	thresholdDisplacementAbsoluteStatic = thresholdDisplacementAbsolute;
	
	boolean previewOnly = gd.getNextBoolean();
	previewOnlyStatic = previewOnly;
	
	work(fileName, previewOnly, computeOverlap, fusionMethod, handleRGB, true);		
}
 

@Override
public void run(String arg0)
{
	GenericDialogPlus gd = new GenericDialogPlus( "Stitch Multiple Series File" );
	
	gd.addFileField( "File", fileNameStatic, 50 );		
	gd.addCheckbox( "Compute_overlap (or trust coordinates in the file)", computeOverlapStatic );
	gd.addCheckbox( "Ignore_Calibration", ignoreCalibrationStatic );
	gd.addSlider( "Increase_overlap [%]", 0, 100, overlapStatic );
	gd.addCheckbox( "Invert_X coordinates", invertXStatic );
	gd.addCheckbox( "Invert_Y coordinates", invertYStatic );
	gd.addCheckbox("Ignore_Z_stage position", ignoreZStageStatic);
	             
	gd.addChoice( "Fusion_Method", methodListCollection, fusionMethodStatic );
	gd.addNumericField( "Fusion alpha", alphaStatic, 2 );
	gd.addNumericField( "Regression Threshold", thresholdRStatic, 2 );
	gd.addNumericField( "Max/Avg Displacement Threshold", thresholdDisplacementRelativeStatic, 2 );		
	gd.addNumericField( "Absolute Avg Displacement Threshold", thresholdDisplacementAbsoluteStatic, 2 );		
	gd.addCheckbox("Create_only_preview", previewOnlyStatic);
	gd.addMessage( "" );
	gd.addMessage( "This Plugin is developed by Stephan Preibisch\n" + myURL );

	MultiLineLabel text = (MultiLineLabel) gd.getMessage();
	addHyperLinkListener(text, myURL);

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

	String fileName = gd.getNextString();
	fileNameStatic = fileName;

	boolean computeOverlap = gd.getNextBoolean();
	computeOverlapStatic = computeOverlap;

	boolean ignoreCalibration = gd.getNextBoolean();
	ignoreCalibrationStatic = ignoreCalibration;
	
	double overlap = gd.getNextNumber();
	overlapStatic = overlap;

	boolean invertX = gd.getNextBoolean();
	invertXStatic = invertX;

	boolean invertY = gd.getNextBoolean();
	invertYStatic = invertY;

	boolean ignoreZStage = gd.getNextBoolean();
	ignoreZStageStatic = ignoreZStage;

	String fusionMethod = gd.getNextChoice();
	fusionMethodStatic = fusionMethod;
	
	this.alpha = gd.getNextNumber();
	alphaStatic = alpha;
	
	this.thresholdR = gd.getNextNumber();
	thresholdRStatic = thresholdR;
	
	this.thresholdDisplacementRelative = gd.getNextNumber();
	thresholdDisplacementRelativeStatic = thresholdDisplacementRelative;
	
	this.thresholdDisplacementAbsolute = gd.getNextNumber();
	thresholdDisplacementAbsoluteStatic = thresholdDisplacementAbsolute;
	
	boolean previewOnly = gd.getNextBoolean();
	previewOnlyStatic = previewOnly;

	ArrayList<ImageInformation> imageInformationList = parseMultiSeriesFile( fileName, overlap,  ignoreCalibration, invertX, invertY, ignoreZStage );
	
	if ( imageInformationList == null )
		return;
	
	for ( ImageInformation iI : imageInformationList )
	{
		Log.info( iI.imageName );
		
		String offset = "";
		for ( int d = 0; d < iI.offset.length; ++d )
			offset += iI.offset[ d ] + ", ";
		
		Log.info( offset );
	}

	final GridLayout gridLayout = new GridLayout();

	gridLayout.imageInformationList = imageInformationList;
	gridLayout.fusionMethod = fusionMethod;
	gridLayout.alpha = this.alpha;
	gridLayout.thresholdR = this.thresholdR;
	gridLayout.thresholdDisplacementRelative = this.thresholdDisplacementRelative;
	gridLayout.thresholdDisplacementAbsolute = this.thresholdDisplacementAbsolute;
	gridLayout.dim = imageInformationList.get( 0 ).dim;
	gridLayout.rgbOrder = rgbTypes[0];

	new Stitch_Image_Collection().work( gridLayout, previewOnly, computeOverlap, fileName + ".txt", true );
}
 

protected ArrayList< ImageCollectionElement > getAllFilesInDirectory( final String directory, final boolean confirmFiles )
{
	// get all files from the directory
	final File dir = new File( directory );
	if ( !dir.isDirectory() )
	{
		Log.error( "'" + directory + "' is not a directory. stop.");
		return null;
	}
	
	final String[] imageFiles = dir.list();
	final ArrayList<String> files = new ArrayList<String>();
	for ( final String fileName : imageFiles )
	{
		File file = new File( dir, fileName );
		
		if ( file.isFile() && !file.isHidden() && !fileName.endsWith( ".txt" ) && !fileName.endsWith( ".TXT" ) )
		{
			Log.info( file.getPath() );
			files.add( fileName );
		}
	}
	
	Log.info( "Found " + files.size() + " files (we ignore hidden and .txt files)." );
	
	if ( files.size() < 2 )
	{
		Log.error( "Only " + files.size() + " files found in '" + dir.getPath() + "', you need at least 2 - stop." );
		return null ;
	}
	
	final boolean[] useFile = new boolean[ files.size() ];
	for ( int i = 0; i < files.size(); ++i )
		useFile[ i ] = true;
	
	if ( confirmFiles )
	{
		final GenericDialogPlus gd = new GenericDialogPlus( "Confirm files" );
		
		for ( final String name : files )
			gd.addCheckbox( name, true );
		
		gd.showDialog();
		
		if ( gd.wasCanceled() )
			return null;
		
		for ( int i = 0; i < files.size(); ++i )
			useFile[ i ] = gd.getNextBoolean();
	}

	final ArrayList< ImageCollectionElement > elements = new ArrayList< ImageCollectionElement >();

	for ( int i = 0; i < files.size(); ++i )
		if ( useFile [ i ] )
			elements.add( new ImageCollectionElement( new File( directory, files.get( i ) ), i ) );
	
	if ( elements.size() < 2 )
	{
		Log.error( "Only " + elements.size() + " files selected, you need at least 2 - stop." );
		return null ;			
	}
	
	return elements;
}