ij.gui.ImageWindow Java Examples

/**
 * Segment current image (GUI needs to be running)
 * 
 * @param dynamic string containing dynamic value (format: "dynamic=[integer value]")
 * @param calculateDams string containing boolean flag to create dams (format: "calculateDams=[boolean])
 * @param connectivity string containing connectivity value (format: "connectivity=[4 or 8 / 6 or 26])
 * @param usePriorityQueue string containing boolean flag to use priority queue (format: "usePriorityQueue=[boolean])
 * 
 * @deprecated the priority queue method is now the only one
 */
public static void segment(
		String dynamic,
		String calculateDams,
		String connectivity,
		String usePriorityQueue )
{		
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		//IJ.log( "GUI detected" );			
		final CustomWindow win = (CustomWindow) iw;
		win.setDynamic( Double.parseDouble( dynamic.replace( "tolerance=", "" ) ) );
		win.setCalculateDams( calculateDams.contains( "true" ) );
		win.setConnectivity( Integer.parseInt( connectivity.replace( "connectivity=", "" ) ) );
		win.runSegmentation( win.getSegmentText() );			
	}
	else
		IJ.log( "Error: Morphological Segmentation GUI not detected." );
}
 

private ArrayList<PlotInstance> getPlots() {
	final ArrayList<PlotInstance> plots = new ArrayList<>();
	final int[] ids = WindowManager.getIDList();
	if (ids != null) {
		for (final int id : ids) {
			final ImagePlus pImp = WindowManager.getImage(id);
			if (pImp == null)
				continue;
			final ImageWindow win = pImp.getWindow();
			if (win == null)
				continue;
			if (win instanceof PlotWindow) {
				if (win.equals(pw))
					continue;
				plots.add(new PlotInstance((PlotWindow) win));
			}
		}
	}
	return plots;
}
 

/**
 * Segment current image (GUI needs to be running)
 *
 * @param calculateDams string containing boolean flag to create dams (format: "calculateDams=[boolean])
 * @param connectivity string containing connectivity value (format: "connectivity=[4 or 8 / 6 or 26])
 */
public static void segment(
		String calculateDams,
		String connectivity )
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		win.setCalculateDams( calculateDams.contains( "true" ) );
		win.setConnectivity( Integer.parseInt( connectivity.replace( "connectivity=", "" ) ) );
		win.runSegmentation( win.getSegmentText() );
	}
	else
		IJ.log( "Error: Interactive Marker-controlled Watershed GUI not detected." );
}
 

/**
 * Segment current image (GUI needs to be running)
 * 
 * @param dynamic string containing dynamic value (format: "dynamic=[integer value]")
 * @param calculateDams string containing boolean flag to create dams (format: "calculateDams=[boolean])
 * @param connectivity string containing connectivity value (format: "connectivity=[4 or 8 / 6 or 26])
 */
public static void segment(
		String dynamic,
		String calculateDams,
		String connectivity )
{		
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		//IJ.log( "GUI detected" );			
		final CustomWindow win = (CustomWindow) iw;
		win.setDynamic( Double.parseDouble( dynamic.replace( "tolerance=", "" ) ) );
		win.setCalculateDams( calculateDams.contains( "true" ) );
		win.setConnectivity( Integer.parseInt( connectivity.replace( "connectivity=", "" ) ) );
		win.runSegmentation( win.getSegmentText() );			
	}
	else
		IJ.log( "Error: Morphological Segmentation GUI not detected." );
}
 

/**
 * Toggle current result overlay image
 */
public static void toggleOverlay()
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		win.toggleOverlay();
	}
}
 

/**
 * Merge labels that are selected either by a freehand or a point ROI.
 * Label of value 0 (watershed line) is skipped.
 */
public static void mergeLabels()
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		win.mergeLabels();
	}
}
 

/**
 * Shuffle LUT of current display image.
 */
public static void shuffleColors()
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		win.shuffleColors();
	}
}
 

/**
 * Show current result in a new image
 */
public static void createResultImage()
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		String mode = win.getResultDisplayOption();
		
		ImagePlus result = null;

		if( mode.equals( MorphologicalSegmentation.catchmentBasinsText) )
			result = win.getResult( ResultMode.BASINS );
		else if( mode.equals( MorphologicalSegmentation.overlaidBasinsText ) )
			result = win.getResult( ResultMode.OVERLAID_BASINS );
		else if( mode.equals( MorphologicalSegmentation.watershedLinesText ) )
			result = win.getResult( ResultMode.LINES );
		else if( mode.equals( MorphologicalSegmentation.overlaidDamsText ))
			result = win.getResult( ResultMode.OVERLAID_DAMS );

		if( null != result )
		{
			result.show();
			result.setSlice( win.getImagePlus().getCurrentSlice() );
		}
	}
}
 

/**
 * Set input image type 
 * @param type input image type (border or object)
 */
public static void setInputImageType( String type )
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		
		if( type.equals( "object" ) )
			win.setInputImageType( objectImageText );
		else if( type.equals( "border" ) )
			win.setInputImageType( borderImageText );
	}			
}
 

/**
 * Set GUI to show gradient image in the main canvas
 * @param bool true to display gradient image and false to display input image
 */
public static void setShowGradient( String bool )
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		if( bool.equals( "true" ) )
			win.setShowGradient( true );
		else if( bool.equals( "false" ) )
			win.setShowGradient( false );	
	}
}
 

/**
 * Set the display format in the GUI
 * @param format output mode ("Overlaid basins", "Overlaid dams", "Catchment basins", "Watershed lines")
 */
public static void setDisplayFormat( String format )
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		win.setResultDisplayOption( format );
		if( win.isShowResultOverlaySelected() )
			win.updateResultOverlay();
	}
}
 

/**
 * Set the gradient radius
 * @param radius gradient radius size (in pixels)
 */
public static void setGradientRadius( String radius )
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		win.setGradientRadius( Integer.parseInt( radius ) );			
	}
}
 

/**
 * Set the gradient method to use
 * @param method name of the gradient method to use
 */
public static void setGradientType( String method )
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		win.setGradientType( method );
	}
}
 

/**
 * Toggle current result overlay image
 */
public static void toggleOverlay()
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		win.toggleOverlay();
	}
}
 

/**
 * Merge labels that are selected either by a freehand or a point ROI.
 * Label of value 0 (watershed line) is skipped.
 */
public static void mergeLabels()
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		win.mergeLabels();
	}
}
 

/**
 * Shuffle LUT of current display image.
 */
public static void shuffleColors()
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		win.shuffleColors();
	}
}
 

/**
 * Show current result in a new image
 */
public static void createResultImage()
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		String mode = win.getResultDisplayOption();

		ImagePlus result = null;

		if( mode.equals( InteractiveMarkerControlledWatershed.catchmentBasinsText) )
			result = win.getResult( ResultMode.BASINS );
		else if( mode.equals( InteractiveMarkerControlledWatershed.overlaidBasinsText ) )
			result = win.getResult( ResultMode.OVERLAID_BASINS );
		else if( mode.equals( InteractiveMarkerControlledWatershed.watershedLinesText ) )
			result = win.getResult( ResultMode.LINES );
		else if( mode.equals( InteractiveMarkerControlledWatershed.overlaidDamsText ))
			result = win.getResult( ResultMode.OVERLAID_DAMS );

		if( null != result )
		{
			result.show();
			result.setSlice( win.getImagePlus().getCurrentSlice() );
		}
	}
}
 

/**
 * Set the display format in the GUI
 * @param format output mode ("Overlaid basins", "Overlaid dams", "Catchment basins", "Watershed lines")
 */
public static void setDisplayFormat( String format )
{
	final ImageWindow iw = WindowManager.getCurrentImage().getWindow();
	if( iw instanceof CustomWindow )
	{
		final CustomWindow win = (CustomWindow) iw;
		win.setResultDisplayOption( format );
		if( win.isShowResultOverlaySelected() )
			win.updateResultOverlay();
	}
}
 

/**
 * Functional method of the RoiPicker. Determines which Rois match the x,y
 * coordinates of the received MouseEvent and the C,Z,T coordinates of the
 * active image. The user can cycle through these Rois with repeated clicks.
 */
@Override
public void mouseReleased(MouseEvent e) {
	ImageCanvas source = (ImageCanvas) e.getSource();
	if (source != canvas) {
		// We changed image window. Update fields accordingly
		ImageWindow window = (ImageWindow) source.getParent();
		imp = window.getImagePlus();
		canvas = source;
	}
	// Convert global coords to local
	double x = canvas.offScreenXD(e.getX());
	double y = canvas.offScreenYD(e.getY());
	// Get the RoiManager
	RoiManager rm = RoiManager.getInstance();
	if (rm == null) return;

	Roi[] rois = rm.getRoisAsArray();
	// Get the active ImagePlus's current z,c,t coords
	int[] position = imp.convertIndexToPosition(imp.getCurrentSlice());

	Set<Integer> matchedSet = new HashSet<Integer>();
	List<Integer> matchedIndices = new ArrayList<Integer>();

	// generate list of all rois containing x,y and matching the ImagePlus's
	// position
	for (int i = 0; i < rois.length; i++) {
		Roi r = rois[i];
		// Check position
		if (containsPoint(r, position, x, y)) {
			// Matched. Add to the matched set and list
			Integer index = i;
			matchedSet.add(index);
			matchedIndices.add(index);
		}
	}

	// If we discovered the currently known roi set, display the next roi in
	// the series
	if (same(roiSet, matchedSet)) {
		incrementIndex();
	}
	else {
		// otherwise, update the cached indices and display the union of the rois
		roiSet = matchedSet;
		roiIndices = matchedIndices;
		roiIndex = roiIndices.size();
	}

	// Perform the roi selection
	if (matchedIndices.size() > 0) selectRois(rm);
}