plugins/Align_ComplexEdgeFiltering.java

@@ -0,0 +1,154 @@
+import ij.*;
+import ij.ImagePlus;
+import ij.ImageStack;
+import ij.plugin.filter.PlugInFilter;
+import ij.process.ImageProcessor;
+import ij.plugin.filter.GaussianBlur;
+import ij.gui.GenericDialog;
+
+/**
+ * This is a template for a plugin that requires one image to
+ * be opened, and takes it as parameter.
+ */
+public class Align_ComplexEdgeFiltering implements PlugInFilter {
+	protected ImagePlus imp;
+	private static double g_sigma = 3.0, g_resolution = 1e-4; //filter parameters
+	private static int filter_output;
+	//private static int filter_type = 0;
+	private GaussianBlur gb = new GaussianBlur();
+	private int[] sobel_r = new int[] {1,0,-1, 2,0,-2, 1,0,-1};
+	private int[] sobel_i = new int[] {1,2,1, 0,0,0, -1,-2,-1};
+
+    String arg;
+    final  java.util.List output = new java.util.ArrayList();
+    public java.util.List getOutput(){
+        return output;
+    }
+    boolean show=true;
+	
+	/**
+	 * This method gets called by ImageJ / Fiji to determine
+	 * whether the current image is of an appropriate type.
+	 *
+	 * @param arg can be specified in plugins.config
+	 * @param image is the currently opened image
+	 */
+	public int setup(String arg, ImagePlus image) {
+		this.imp = image;
+        this.arg = arg;
+		/*
+		 * The current return value accepts all gray-scale
+		 * images (if you access the pixels with ip.getf(x, y)
+		 * anyway, that works quite well.
+		 *
+		 * It could also be DOES_ALL; you can add "| NO_CHANGES"
+		 * to indicate that the current image will not be
+		 * changed by this plugin.
+		 *
+		 * Beware of DOES_STACKS: this will call the run()
+		 * method with all slices of the current image
+		 * (channels, z-slices and frames, all). Most likely
+		 * not what you want.
+		 */
+		return DOES_8G | DOES_16 | DOES_32 | NO_CHANGES;// | DOES_STACKS;
+	}
+
+	/**
+	 * This method is run when the current image was accepted.
+	 *
+	 * @param ip is the current slice (typically, plugins use
+	 * the ImagePlus set above instead).
+	 */
+	public void run(ImageProcessor ip) {
+        if ((arg !=null) && (!arg.isBlank())){
+            String[] tokens = arg.trim().split(",");
+            g_sigma = Double.valueOf(tokens[0].trim());
+            filter_output = Boolean.valueOf(tokens[1].trim().toLowerCase()) ? 0 : 1;
+            try{
+                show = Boolean.valueOf(tokens[2].trim().toLowerCase());
+            } catch (Exception ex){
+                show = false;
+            }
+        } else {
+    		String[] filter_outputs = {"complex", "real"};
+    		GenericDialog gd = new GenericDialog("Complex Edge Filtering Options:");
+    		gd.addSlider("Gaussian blur radius", 0, 20.0, g_sigma);
+    		gd.addChoice("Edge filter output:", filter_outputs, filter_outputs[0]);
+    		//String[] edge_filters = {"Sobel"};//, "Frei&Chen"};
+    		//gd.addChoice("Task:", edge_filters, edge_filters[0]);
+            	gd.showDialog();                		// display the dialog; preview runs in the background now
+    		if (gd.wasCanceled()) return;
+    		g_sigma = gd.getNextNumber();
+    		filter_output = gd.getNextChoiceIndex();
+        }
+         	//filter_type = gd.getNextChoiceIndex();
+         	exec();
+	}
+
+	private void exec() {
+		// display the results
+		if (filter_output == 1) {
+			ImagePlus imp_r = imp.createImagePlus();
+			ImageStack stack_r = new ImageStack(imp.getWidth(), imp.getHeight());
+		
+			for (int i = 1; i <= imp.getImageStackSize(); i++) {
+				ImageProcessor ip_r = imp.getStack().getProcessor(i).duplicate().convertToFloat();
+				// Gaussian blurring
+				gb.blurGaussian(ip_r, g_sigma, g_sigma, g_resolution);
+				// Sobel edge filtering
+				ip_r.filter(ImageProcessor.FIND_EDGES);
+			
+				stack_r.addSlice(imp.getStack().getSliceLabel(i), ip_r);
+				IJ.showProgress(i, imp.getImageStackSize());
+			}
+			
+			//real
+			imp_r.setStack("EdgeReal_" + imp.getTitle(), stack_r);
+			imp_r.resetDisplayRange();
+            if (show){
+			    imp_r.show();
+			    imp_r.updateAndDraw();
+            }
+            output.add(imp_r);
+			
+		} else {
+			ImagePlus imp_r = imp.createImagePlus();
+			ImageStack stack_r = new ImageStack(imp.getWidth(), imp.getHeight());
+
+			ImagePlus imp_i = imp.createImagePlus();
+			ImageStack stack_i = new ImageStack(imp.getWidth(), imp.getHeight());
+		
+			for (int i = 1; i <= imp.getImageStackSize(); i++) {
+				ImageProcessor ip_r = imp.getStack().getProcessor(i).duplicate().convertToFloat();
+				// Gaussian blurring
+				gb.blurGaussian(ip_r, g_sigma, g_sigma, g_resolution);
+				ImageProcessor ip_i = ip_r.duplicate();
+				// Sobel edge filtering
+				ip_r.convolve3x3(sobel_r);
+				ip_i.convolve3x3(sobel_i);
+			
+				stack_r.addSlice(imp.getStack().getSliceLabel(i), ip_r);
+				stack_i.addSlice(imp.getStack().getSliceLabel(i), ip_i);
+				IJ.showProgress(i, imp.getImageStackSize());
+			}
+						
+			//real
+			imp_r.setStack("EdgeReal_" + imp.getTitle(), stack_r);
+			imp_r.resetDisplayRange();
+            if (show){
+			    imp_r.show();
+			    imp_r.updateAndDraw();
+            }
+            output.add(imp_r);
+		
+			//imag
+			imp_i.setStack("EdgeImag_" + imp.getTitle(), stack_i);
+			imp_i.resetDisplayRange();
+            if (show){
+			    imp_i.show();
+			    imp_i.updateAndDraw();
+            }
+            output.add(imp_i);
+		}
+	}
+}

plugins/Align_ComputeShifts.java

@@ -0,0 +1,728 @@
+import ij.*;
+import ij.process.*;
+import ij.gui.*;
+import java.awt.*;
+import ij.plugin.PlugIn;
+import ij.WindowManager;
+//import edu.emory.mathcs.jtransforms.fft.*;
+//import edu.emory.mathcs.utils.*;
+import org.jtransforms.fft.*;
+import org.jtransforms.utils.*;
+import flanagan.complex.*;
+import flanagan.math.*;
+import ij.plugin.frame.RoiManager;
+import ij.gui.Roi;
+
+
+public class Align_ComputeShifts implements PlugIn {
+	protected ImagePlus imp_r, imp_i;
+	protected int reference_slide;
+	protected Roi roi;
+	protected int usfac;
+	protected boolean debug = true;
+
+	public void run(String arg) {
+		int[] wList = WindowManager.getIDList();
+
+		if (null == wList) { //there are no images
+			IJ.error("There must be at least one open image");
+			return;
+		}
+
+		//get all the image titles so they can be shown in the dialog
+		String[] titles = new String[wList.length+1];
+		ImagePlus[] limps = new ImagePlus[wList.length+1];
+
+		titles[0] = "None";
+		limps[0] = null;
+		for (int i=0, k=1; i<wList.length; i++) {
+			ImagePlus limp = WindowManager.getImage(wList[i]);
+			if (limp != null) {
+				titles[k] = limp.getTitle();
+				limps[k] = limp;
+				k++;
+			}
+		}
+
+		GenericDialog gd = new GenericDialog("Alignement Procedure");
+		String[] tasks = {"Calculate direct shifts", "Calculate all shifts"};
+		gd.addChoice("Task:", tasks, tasks[0]);
+		gd.addChoice("Real part image:", titles, titles[1]);
+		gd.addChoice("Imag part image (optional):", titles, titles[0]);
+		gd.addNumericField("Upscale factor (1 < integer < 100)", 100, 0);
+		
+		gd.showDialog();
+      		if (gd.wasCanceled()) return;
+      		
+      		this.usfac = (int)Math.round(gd.getNextNumber());
+		int task =  gd.getNextChoiceIndex();
+		int i1Index = gd.getNextChoiceIndex();
+		int i2Index = gd.getNextChoiceIndex();
+
+		//get the images stack(s)
+		if (i1Index == 0) {
+			IJ.error("Real part image must exist!");
+			return;
+		}
+
+		imp_r = limps[i1Index];
+		if (i2Index == 0) {
+			imp_i = null;
+		} else {
+			imp_i = limps[i2Index];
+		}
+
+		//get the reference slide
+		reference_slide = imp_r.getCurrentSlice();
+
+		// get the ROI
+		RoiManager manager = RoiManager.getInstance();
+		if (manager == null) {
+			IJ.error("No ROI manager opened");
+			return;
+		}
+
+		Roi rois[] = manager.getSelectedRoisAsArray();
+		if (rois.length != 1) {
+			IJ.error("There must be one and only one ROI selected");
+			return;
+		}
+		
+		roi = rois[0];
+		if (roi.getType()!=Roi.RECTANGLE) {
+			IJ.error("The selected ROI must be a rectangle");
+			return;
+		}
+		
+		Rectangle box = roi.getBounds();
+		if (!ConcurrencyUtils.isPowerOf2(box.height)
+			|| !ConcurrencyUtils.isPowerOf2(box.width)) {
+			IJ.error("The selected ROI height and with must be a power of 2");
+			return;
+		}
+		
+      		if (task == 0) {
+      			calculateShiftsRun();
+      		} else {
+      			calculateAllShiftsRun();
+      		}
+      		
+      		return;
+	}
+
+	private void calculateShiftsRun() {
+		// perform the FFT of each slice
+        
+		IJ.showStatus("1/2 Perform FFT of each slice");
+		ComplexMatrix[] ffts = computeFFT();
+        
+		// calculate shifts
+		IJ.showStatus("2/2 Calculate shifts between slices");
+		double[][] shifts = calculateShifts(ffts);
+		
+		// save shifts
+		ShiftsIO sio = new ShiftsIO();
+		sio.save(shifts, "directshifts");
+       
+	}
+
+	private void calculateAllShiftsRun() {
+		// perform the FFT of each slice
+		IJ.showStatus("1/2 Perform FFT of each slice");
+		ComplexMatrix[] ffts = computeFFT();
+
+		// calculate shifts
+		IJ.showStatus("2/2 Calculate shifts between slices");
+		double[][] shifts = calculateAllShifts(ffts);
+		// save shifts
+		ShiftsIO sio = new ShiftsIO();
+		sio.save(shifts, "allshifts");
+	}
+
+	// perform the FFT of each slice
+	private ComplexMatrix[] computeFFT() {
+		
+		int slices = imp_r.getStackSize();
+		
+		ComplexMatrix[] ffts = new ComplexMatrix[slices];
+		for (int i=1; i <= slices; i++) {
+			if (imp_i == null) {
+				ImageProcessor ip = imp_r.getStack().getProcessor(i);
+				ip.setRoi(roi);
+				ImageProcessor curr = ip.crop().convertToFloat();
+				double[][] data = ImageProcessor_to_FFTArray2D(curr);	
+				ffts[i-1] = fft2(data);
+			} else {
+				ImageProcessor ip1, ip2;
+				ip1 = imp_r.getStack().getProcessor(i);
+				ip1.setRoi(roi);
+				ImageProcessor curr_r = ip1.crop().convertToFloat();
+				ip2 = imp_i.getStack().getProcessor(i);
+				ip2.setRoi(roi);
+				ImageProcessor curr_i = ip2.crop().convertToFloat();
+				double[][] data = ImageProcessor_to_FFTComplexArray2D(curr_r, curr_i);
+				ffts[i-1] = cfft2(data);
+			}
+			IJ.showProgress(i, slices);
+		}
+
+		return ffts;
+	}
+
+	//calculate the shifts between ffts
+	private double[][] calculateShifts(ComplexMatrix[] ffts) {
+        
+		double[][] shifts = new double[ffts.length][6];        
+		for (int i = 0; i < ffts.length; i++) {
+			shifts[i][0] = reference_slide; shifts[i][1] = i+1;
+			double[] temp = DFTRegistration(ffts[reference_slide - 1], ffts[i]);
+			shifts[i][2] = temp[2]; shifts[i][3] = temp[3];
+			shifts[i][4] = temp[0]; shifts[i][5] = temp[1];            
+			IJ.showProgress(i + 1, ffts.length);
+		}
+		return shifts; // [ref, drifted, dr, dc, error, diffphase]
+	
+	}
+
+	//calculate all the shifts between ffts
+	private double[][] calculateAllShifts(ComplexMatrix[] ffts) {
+
+		double[][] shifts = new double[ffts.length*(ffts.length-1)/2][6];
+		int id = 0;
+		for (int i = 0; i < ffts.length-1; i++) {
+			for (int j = i+1; j < ffts.length; j++) {
+				shifts[id][0] = i+1; shifts[id][1] = j+1;
+				double[] temp = DFTRegistration(ffts[i], ffts[j]);
+				shifts[id][2] = temp[2]; shifts[id][3] = temp[3];
+				shifts[id][4] = temp[0]; shifts[id][5] = temp[1];
+				id = id + 1;
+				IJ.showProgress(id + 1, ffts.length*(ffts.length-1)/2);
+			}
+		}
+		
+		return shifts; // [ref,drifted,dr,dc,error, diffphase]
+	}
+	
+	// compute 2D fft from an image
+	private ComplexMatrix fft2(double[][] data) {
+
+		int h = data.length;
+		int w = data[0].length;
+		DoubleFFT_2D fft = new DoubleFFT_2D(h, w);
+		
+		fft.realForward(data);
+		ComplexMatrix m = FFTArray2D_to_ComplexMatrix(data, h, w);
+
+		return m;
+	}
+
+	// compute complex 2D fft from an image
+	private ComplexMatrix cfft2(double[][] data) {
+
+		int h = data.length;
+		int w = data[0].length;
+		DoubleFFT_2D fft = new DoubleFFT_2D(h, w/2);
+		
+		fft.complexForward(data);
+		ComplexMatrix m = FFTComplexArray2D_to_ComplexMatrix(data, h, w/2);
+
+		return m;
+	}
+	
+	// compute inverse 2D fft from a complex matrix
+	private double[][] ifft2(ComplexMatrix m) {
+		int w = m.getNcol();
+		int h = m.getNrow();
+		
+		DoubleFFT_2D fft = new DoubleFFT_2D(h, w);
+		
+		double[][] data = ComplexMatrix_to_FFTArray2D(m);	
+		fft.realInverse(data, true);
+
+		return data;
+	}
+	
+	// compute complex inverse 2D fft from a complex matrix
+	private ComplexMatrix cifft2(ComplexMatrix m) {
+		int w = m.getNcol();
+		int h = m.getNrow();
+		
+		DoubleFFT_2D fft = new DoubleFFT_2D(h, w);
+		
+		double[][] data = new double[h][2*w];
+		for (int j=0; j<h; j++) {
+			for (int i=0; i<w; i++) {
+				data[j][2*i] = m.getElementReference(j, i).getReal();
+				data[j][2*i+1] = m.getElementReference(j, i).getImag();				
+			}
+		}
+
+		fft.complexInverse(data, true);
+
+		ComplexMatrix out = new ComplexMatrix(h, w);
+		for (int j=0; j<h; j++) {
+			for (int i=0; i<w; i++) {
+				out.setElement(j, i, data[j][2*i], data[j][2*i+1]);			
+			}
+		}
+
+		return out;
+	}
+	
+	private double[] DFTRegistration(ComplexMatrix ref, ComplexMatrix drifted) {
+		int m = ref.getNrow();
+		int n = ref.getNcol();
+		double[] output = new double[4];
+		
+		// First upsample by a factor of 2 to obtain initial estimate
+    		// Embed Fourier data in a 2x larger array
+    		int mlarge = m*2;
+    		int nlarge = n*2;
+    		ComplexMatrix large = new ComplexMatrix(mlarge, nlarge);
+    		ComplexMatrix c = fftshift(ElementProduct(ref, drifted.conjugate()));
+
+    		for (int j = 0; j < m; j++) {
+    			for (int i = 0; i < n; i++) {
+    				large.setElement((int)(j + m - Math.floor(m/2.0)), (int)(i + n - Math.floor(n/2.0)), c.getElementReference(j, i));
+    			}
+    		}
+  
+    		// Compute crosscorrelation and locate the peak
+    		ComplexMatrix CC = cifft2(ifftshift(large));
+    		double[] peak = cFindPeak(CC); //max, r, c, max_r, max_c
+    		    
+    		// Obtain shift in original pixel grid from the position of the
+    		// crosscorrelation peak 
+    		if (peak[1] > m) { 
+        		peak[1] = peak[1] - mlarge;
+    		}
+		if (peak[2] > n) {
+			peak[2] = peak[2] - nlarge;
+		}
+
+    		//% If upsampling > 2, then refine estimate with matrix multiply DFT
+    		if (this.usfac > 2) {
+     			//   %%% DFT computation %%%
+     			//   % Initial shift estimate in upsampled grid
+     			double row_shift = Math.round(peak[1]/2.0*this.usfac)/this.usfac; 
+     			double col_shift = Math.round(peak[2]/2.0*this.usfac)/this.usfac;     
+     			int dftshift = (int)Math.floor(Math.ceil(this.usfac*1.5)/2); // Center of output array at dftshift+1
+     			//   % Matrix multiply DFT around the current shift estimate
+    			ComplexMatrix in = ElementProduct(drifted, ref.conjugate());
+     			ComplexMatrix nCC = dftups(in, (int)Math.ceil(this.usfac*1.5), (int)Math.ceil(this.usfac*1.5),
+     					dftshift-row_shift*this.usfac, dftshift-col_shift*this.usfac);
+     		     	nCC = nCC.times(1.0/(m*n*this.usfac*this.usfac)).conjugate();
+     			//   % Locate maximum and map back to original pixel grid 
+     			double[] npeak = cFindPeak(nCC); //max_r, max_i, r, c
+    
+ 			ComplexMatrix mrg00 = dftups(ElementProduct(ref, ref.conjugate()),1,1,0,0);
+ 			double rg00 = mrg00.getElementReference(0, 0).abs()/(m*n*this.usfac*this.usfac);
+     			ComplexMatrix mrf00 = dftups(ElementProduct(drifted, drifted.conjugate()),1,1,0,0);
+     			double rf00 = mrf00.getElementReference(0, 0).abs()/(m*n*this.usfac*this.usfac);
+     			
+     			npeak[1] = npeak[1] - dftshift;
+     			npeak[2] = npeak[2] - dftshift;
+     			output[0] = Math.sqrt(Math.abs(1.0 - npeak[0]*npeak[0]/(rg00*rf00)));	//error
+			output[1] = Math.atan2(npeak[4], npeak[3]);				//diffphase		
+     			output[2] = row_shift + npeak[1]/this.usfac;			//delta row
+     			output[3] = col_shift + npeak[2]/this.usfac;			//delta col
+     			
+    		} else {
+   			// % If upsampling = 2, no additional pixel shift refinement
+   			double rg00 = SumSquareAbs(ref)/(mlarge*nlarge);
+			double rf00 = SumSquareAbs(drifted)/(mlarge*nlarge);
+			
+			output[0] = Math.sqrt(Math.abs(1.0 - peak[0]*peak[0]/(rg00*rf00)));	//error
+			output[1] = Math.atan2(peak[4], peak[3]);				//diffphase		
+			output[2] = peak[1]/2.0;					//delta row
+    			output[3] = peak[2]/2.0;					//delta col
+    		}
+    		
+		return output;	
+	}
+
+	private double SumSquareAbs(ComplexMatrix m) {
+		double sum = 0.0;
+
+		for (int j = 0; j < m.getNrow(); j ++){
+			for (int i = 0; i < m.getNcol(); i++) {
+				sum += m.getElementReference(j, i).squareAbs();
+			}
+		}
+
+		return sum;
+	}
+	
+	private double[] cFindPeak(ComplexMatrix m) {
+		double max = 0.0;
+		double realmax = 0.0;
+		double imagmax = 0.0;
+		int cmax = 0, rmax = 0;
+		
+		for (int j = 0; j < m.getNrow(); j ++){
+			for (int i = 0; i < m.getNcol(); i++) {
+				if (m.getElementReference(j, i).abs() > max) {
+					max = m.getElementReference(j, i).abs();
+					realmax = m.getElementReference(j, i).getReal();
+					imagmax = m.getElementReference(j, i).getImag();
+					rmax = j;
+					cmax = i;
+				}
+			}
+		}
+
+		double[] res = new double[5];
+		res[0] = Math.sqrt(realmax*realmax+imagmax*imagmax); res[1] = rmax; res[2] = cmax;
+		res[3] = realmax; res[4] = imagmax;
+		return res;
+	}
+	
+	private ComplexMatrix fftshift(ComplexMatrix in) {
+		int nc = in.getNcol();
+		int nr = in.getNrow();
+
+		ComplexMatrix out = new ComplexMatrix (nr, nc);
+		
+		int midi = (int)Math.floor(nc/2.0);
+		int offi = (int)Math.ceil(nc/2.0);
+		int midj = (int)Math.floor(nr/2.0);
+		int offj = (int)Math.ceil(nr/2.0);
+		
+		for (int j = 0; j < nr; j ++){
+			for (int i = 0; i < nc; i++) {
+				if (j < midj) {
+					if (i < midi) {
+						out.setElement(j, i, in.getElementReference(j+offj, i+offi));
+					} else {
+						out.setElement(j, i, in.getElementReference(j+offj, i-midi));		
+					}
+				} else {
+					if (i < midi) {
+						out.setElement(j, i, in.getElementReference(j-midj, i+offi));
+					} else {
+						out.setElement(j, i, in.getElementReference(j-midj, i-midi));		
+					}
+				}
+			}
+		}
+
+		return out;
+	}
+
+	private ComplexMatrix ifftshift(ComplexMatrix in) {
+		int nc = in.getNcol();
+		int nr = in.getNrow();
+
+		ComplexMatrix out = new ComplexMatrix (nr, nc);
+		
+		int midi = (int)Math.ceil(nc/2.0);
+		int offi = (int)Math.floor(nc/2.0);
+		int midj = (int)Math.ceil(nr/2.0);
+		int offj = (int)Math.floor(nr/2.0);
+		
+		for (int j = 0; j < nr; j ++){
+			for (int i = 0; i < nc; i++) {
+				if (j < midj) {
+					if (i < midi) {
+						out.setElement(j, i, in.getElementReference(j+offj, i+offi));
+					} else {
+						out.setElement(j, i, in.getElementReference(j+offj, i-midi));		
+					}
+				} else {
+					if (i < midi) {
+						out.setElement(j, i, in.getElementReference(j-midj, i+offi));
+					} else {
+						out.setElement(j, i, in.getElementReference(j-midj, i-midi));		
+					}
+				}
+			}
+		}
+
+		return out;
+	}
+	
+	private Matrix ifftshift(Matrix in) {
+		int nc = in.getNcol();
+		int nr = in.getNrow();
+
+		Matrix out = new Matrix (nr, nc);
+		
+		int midi = (int)Math.ceil(nc/2.0);
+		int offi = (int)Math.floor(nc/2.0);
+		int midj = (int)Math.ceil(nr/2.0);
+		int offj = (int)Math.floor(nr/2.0);
+		
+		for (int j = 0; j < nr; j ++){
+			for (int i = 0; i < nc; i++) {
+				if (j < midj) {
+					if (i < midi) {
+						out.setElement(j, i, in.getElement(j+offj, i+offi));
+					} else {
+						out.setElement(j, i, in.getElement(j+offj, i-midi));		
+					}
+				} else {
+					if (i < midi) {
+						out.setElement(j, i, in.getElement(j-midj, i+offi));
+					} else {
+						out.setElement(j, i, in.getElement(j-midj, i-midi));		
+					}
+				}
+			}
+		}
+
+		return out;
+	}
+	
+	private ComplexMatrix dftups(ComplexMatrix in, int nor, int noc, double roff, double coff) {
+		// function out=dftups(in,nor,noc,usfac,roff,coff);
+		// Upsampled DFT by matrix multiplies, can compute an upsampled DFT in just
+		// a small region.
+		// usfac         Upsampling factor (default usfac = 1)
+		// [nor,noc]     Number of pixels in the output upsampled DFT, in
+		//               units of upsampled pixels (default = size(in))
+		// roff, coff    Row and column offsets, allow to shift the output array to
+		//               a region of interest on the DFT (default = 0)
+		// Recieves DC in upper left corner, image center must be in (1,1)
+		// Loïc Le Guyader - Jun 11, 2011 Java version for ImageJ plugin 
+		// Manuel Guizar - Dec 13, 2007
+		// Modified from dftus, by J.R. Fienup 7/31/06
+
+		// This code is intended to provide the same result as if the following
+		// operations were performed
+		//   - Embed the array "in" in an array that is usfac times larger in each
+		//     dimension. ifftshift to bring the center of the image to (1,1).
+		//   - Take the FFT of the larger array
+		//   - Extract an [nor, noc] region of the result. Starting with the 
+		//     [roff+1 coff+1] element.
+
+		// It achieves this result by computing the DFT in the output array without
+		// the need to zeropad. Much faster and memory efficient than the
+		// zero-padded FFT approach if [nor noc] are much smaller than [nr*usfac nc*usfac]
+
+		
+		int nr = in.getNrow();
+		int nc = in.getNcol();
+	
+		// Compute kernels and obtain DFT by matrix products
+		double amplitude = -2.0*Math.PI/(nc*usfac);
+		
+		Matrix u = new Matrix(nc, 1);
+		for (int i = 0; i < nc; i++) {
+			u.setElement(i, 0, i - Math.floor(nc/2.0));
+		}
+		u = ifftshift(u);
+
+		Matrix v = new Matrix(1, noc);
+		for (int i = 0; i < noc; i++) {
+			v.setElement(0, i, i-coff);
+		}
+
+		Matrix phase = u.times(v);
+		ComplexMatrix kernc = new ComplexMatrix(nc, noc);
+		for (int j = 0; j < nc; j++) {
+			for (int i = 0; i < noc; i++) {
+				Complex t = new Complex();
+				t.polar(1.0, amplitude*phase.getElement(j, i));
+				kernc.setElement(j, i, t);
+			}		
+		}
+		//ComplexMatrixPrint(kernc);
+		
+		amplitude = -2.0*Math.PI/(nr*usfac);
+		
+		Matrix w = new Matrix(nor, 1); 
+		for (int i = 0; i < nor; i++) {
+			w.setElement(i, 0, i - roff);
+		}
+		
+		Matrix x = new Matrix(1, nr);
+		for (int i = 0; i < nr; i++) {
+			x.setElement(0, i, i - Math.floor(nr/2.0));
+		}
+		x = ifftshift(x);
+
+		Matrix nphase = w.times(x);
+		ComplexMatrix kernr = new ComplexMatrix(nor, nr);
+		for (int j = 0; j < nor; j++) {
+			for (int i = 0; i < nr; i++) {
+				Complex t = new Complex();
+				t.polar(1.0, amplitude*nphase.getElement(j, i));
+				kernr.setElement(j, i, t);
+			}		
+		}
+		//ComplexMatrixPrint(kernr);
+		
+		ComplexMatrix out = kernr.times(in.times(kernc));
+
+		return out;
+	}
+	
+	private double[][] CrossCorrelation(ComplexMatrix ref, ComplexMatrix drifted) {
+		int h = ref.getNrow();
+		int w = ref.getNcol();
+		ComplexMatrix b = drifted.conjugate();
+		ComplexMatrix res = ElementProduct(ref, b);
+		
+		double[][] data = ComplexMatrix_to_FFTArray2D(res);
+		DoubleFFT_2D fft = new DoubleFFT_2D(h, w);
+		fft.realInverse(data, true);
+		
+		return data;
+	}
+
+	private ComplexMatrix ElementProduct(ComplexMatrix a, ComplexMatrix b) {
+		int nr = a.getNrow();
+		int nc = a.getNcol();
+		
+		ComplexMatrix res = new ComplexMatrix(nr, nc);
+
+		for(int j = 0; j < nr; j++) {
+			for(int i = 0; i < nc; i++) {
+				res.setElement(j, i, a.getElementReference(j, i).times(b.getElementReference(j, i)));
+			}
+		}
+
+		return res;
+	}
+	
+	private double[][] ImageProcessor_to_FFTArray2D(ImageProcessor ip) {
+
+		float[] pixels = (float[])ip.getPixels();
+		int w = ip.getWidth();
+		int h = ip.getHeight();
+		double[][] data = new double[h][w];
+		
+		for (int j = 0; j < h; j++) { 
+			for (int i = 0; i < w; i++) {
+				data[j][i] = (double)pixels[j*w + i];
+    			}
+		}
+
+		return data;
+	}
+	
+	private double[][] ImageProcessor_to_FFTComplexArray2D(ImageProcessor ip_r, ImageProcessor ip_i) {
+
+		float[] pixels_r = (float[])ip_r.getPixels();
+		float[] pixels_i = (float[])ip_i.getPixels();
+		int w = ip_r.getWidth();
+		int h = ip_r.getHeight();
+		double[][] data = new double[h][2*w];
+		
+		for (int j = 0; j < h; j++) { 
+			for (int i = 0; i < w; i++) {
+				data[j][2*i] = (double)pixels_r[j*w + i];
+				data[j][2*i+1] = (double)pixels_i[j*w + i];
+    			}
+		}
+
+		return data;
+	}
+	
+	private ComplexMatrix FFTArray2D_to_ComplexMatrix(double[][] data, int h, int w) {
+	
+		ComplexMatrix m = new ComplexMatrix(h,w);
+
+		for (int j = 0; j < h; j++) {
+			for (int i = 0; i <= w/2; i++) {
+				if (j > 0 && i > 0 && i < w/2) { 
+      					m.setElement(j,i, new Complex(data[j][2*i], data[j][2*i+1]));
+      					m.setElement(h-j, w-i, new Complex(data[j][2*i], -data[j][2*i+1]));
+				}
+				if (j == 0 && i > 0 && i < w/2) {
+					m.setElement(0, i, new Complex(data[0][2*i], data[0][2*i+1]));
+      					m.setElement(0, w-i, new Complex(data[0][2*i], -data[0][2*i+1]));
+				}
+				if (i == 0 && j > 0 && j < h/2) {
+					m.setElement(j,0, new Complex(data[j][0], data[j][1]));
+      					m.setElement(h-j, 0, new Complex(data[j][0], -data[j][1]));
+      					m.setElement(j, w/2, new Complex(data[h-j][1], -data[h-j][0]));
+      					m.setElement(h-j, w/2, new Complex(data[h-j][1], data[h-j][0]));	
+				}
+				if (j == 0 && i == 0) {
+					m.setElement(0, 0, new Complex(data[0][0], 0));
+				}
+				if (j == 0 && i == w/2) {
+					m.setElement(0, w/2, new Complex(data[0][1], 0));
+				}
+				if (j == h/2 && i == 0) {
+					m.setElement(h/2, 0, new Complex(data[h/2][0], 0));
+				}
+				if (j == h/2 && i == w/2) {
+					m.setElement(h/2, w/2, new Complex(data[h/2][1], 0));
+				}
+			}
+		}
+
+		return m;
+	}
+
+	private ComplexMatrix FFTComplexArray2D_to_ComplexMatrix(double[][] data, int h, int w) {
+	
+		ComplexMatrix m = new ComplexMatrix(h,w);
+
+		for (int j = 0; j < h; j++) {
+			for (int i = 0; i < w; i++) {
+				m.setElement(j,i, new Complex(data[j][2*i], data[j][2*i+1]));
+			}
+		}
+
+		return m;
+	}
+
+	private double[][] ComplexMatrix_to_FFTArray2D(ComplexMatrix m) {
+		int w = m.getNcol();
+		int h = m.getNrow();
+		double[][] data = new double[h][w];
+
+		for (int j = 0; j < h; j++) {
+			for (int i = 0; i <= w/2; i++) {
+				if (j > 0 && i > 0 && i < w/2) {
+      					data[j][2*i] = m.getElementReference(j,i).getReal();
+      					data[j][2*i+1] = m.getElementReference(j,i).getImag();
+				}
+				if (j == 0 && i > 0 && i < w/2) {
+					data[0][2*i] = m.getElementReference(0,i).getReal();
+      					data[0][2*i+1] = m.getElementReference(0,i).getImag();
+				}
+				if (i == 0 && j > 0 && j < h/2) {
+					data[j][0] = m.getElementReference(j,0).getReal();
+      					data[j][1] = m.getElementReference(j,0).getImag();
+      					data[h-j][1] = m.getElementReference(j,w/2).getReal();
+      					data[h-j][0] = m.getElementReference(h-j,w/2).getImag();	
+				}
+				if (j == 0 && i == 0) {
+					data[0][0] = m.getElementReference(0,0).getReal();
+				}
+				if (j == 0 && i == w/2) {
+					data[0][1] = m.getElementReference(0,w/2).getReal();
+				}
+				if (j == h/2 && i == 0) {
+					data[h/2][0] = m.getElementReference(h/2,0).getReal();
+				}
+				if (j == h/2 && i == w/2) {
+					data[h/2][1] = m.getElementReference(h/2,w/2).getReal();
+				}
+			}
+		}
+
+		return data;
+	}
+
+	// convert a Complex Matrix into an 2d real part array data[0][][]
+	// and 2d imaginary part data[1][][]
+	private double[][][] ComplexMatrix_to_RealArray2D(ComplexMatrix m) {
+		int w = m.getNcol();
+		int h = m.getNrow();
+		double[][][] data = new double[2][h][w];
+
+		for (int j = 0; j < h; j++) {
+			for (int i = 0; i < w; i++) {
+				data[0][j][i] = m.getElementReference(j,i).getReal();
+      				data[1][j][i] = m.getElementReference(j,i).getImag();
+			}
+		}
+		
+		return data;
+	}
+}

plugins/Align_ComputeShifts2.java

@@ -0,0 +1,701 @@
+import ij.*;
+import ij.process.*;
+import ij.gui.*;
+import java.awt.*;
+import ij.plugin.PlugIn;
+import ij.WindowManager;
+//import edu.emory.mathcs.jtransforms.fft.*;
+//import edu.emory.mathcs.utils.*;
+import org.jtransforms.fft.*;
+import org.jtransforms.utils.*;
+import flanagan.complex.*;
+import flanagan.math.*;
+import ij.plugin.frame.RoiManager;
+import ij.gui.Roi;
+
+
+public class Align_ComputeShifts2 implements PlugIn {
+	protected ImagePlus imp_r, imp_i;
+	protected int reference_slide;
+	protected Roi roi;
+	protected int usfac;
+	protected boolean debug = true;
+    double[][] shifts;
+    boolean allShifts;
+
+     public void setup(int upscaleFactor, boolean allShifts, ImagePlus imp_r, ImagePlus imp_i, 
+            int reference_slide,  Roi roi) {
+         if (imp_r==null){
+            throw new RuntimeException("Real part image must exist!");
+         }
+
+         if (roi==null){
+            roi = new Roi(0,0,imp_r.getWidth(), imp_r.getHeight());
+         }
+        Rectangle box = roi.getBounds();
+        if (!ConcurrencyUtils.isPowerOf2(box.height)
+            || !ConcurrencyUtils.isPowerOf2(box.width)) {
+            throw new RuntimeException("The selected ROI height and with must be a power of 2");
+        }
+
+         this.usfac = upscaleFactor;
+         this.allShifts = allShifts;
+         this.imp_r = imp_r;
+         this.imp_i = imp_i;
+         this.reference_slide=reference_slide;
+         this.roi = roi;
+        
+     }
+
+	public void run(String arg) {	
+      		if (allShifts) {
+                calculateAllShiftsRun();
+      			
+      		} else {
+      			calculateShiftsRun();
+      		}
+      		return;
+	}
+
+	private void calculateShiftsRun() {
+		// perform the FFT of each slice
+        
+		IJ.showStatus("1/2 Perform FFT of each slice");
+		ComplexMatrix[] ffts = computeFFT();
+        
+		// calculate shifts
+		IJ.showStatus("2/2 Calculate shifts between slices");
+		shifts = calculateShifts(ffts);
+
+        /*
+		// save shifts
+		ShiftsIO sio = new ShiftsIO();
+		sio.save(shifts, "directshifts");
+       */
+	}
+
+   public double[][] getShifts(){
+        return shifts;
+   }
+
+	private void calculateAllShiftsRun() {
+		// perform the FFT of each slice
+		IJ.showStatus("1/2 Perform FFT of each slice");
+		ComplexMatrix[] ffts = computeFFT();
+
+		// calculate shifts
+		IJ.showStatus("2/2 Calculate shifts between slices");
+		double[][] shifts = calculateAllShifts(ffts);
+		// save shifts
+		ShiftsIO sio = new ShiftsIO();
+		sio.save(shifts, "allshifts");
+	}
+
+	// perform the FFT of each slice
+	private ComplexMatrix[] computeFFT() {
+		
+		int slices = imp_r.getStackSize();
+		
+		ComplexMatrix[] ffts = new ComplexMatrix[slices];
+		for (int i=1; i <= slices; i++) {
+			if (imp_i == null) {
+				ImageProcessor ip = imp_r.getStack().getProcessor(i);
+				ip.setRoi(roi);
+				ImageProcessor curr = ip.crop().convertToFloat();
+				double[][] data = ImageProcessor_to_FFTArray2D(curr);	
+				ffts[i-1] = fft2(data);
+			} else {
+				ImageProcessor ip1, ip2;
+				ip1 = imp_r.getStack().getProcessor(i);
+				ip1.setRoi(roi);
+				ImageProcessor curr_r = ip1.crop().convertToFloat();
+				ip2 = imp_i.getStack().getProcessor(i);
+				ip2.setRoi(roi);
+				ImageProcessor curr_i = ip2.crop().convertToFloat();
+				double[][] data = ImageProcessor_to_FFTComplexArray2D(curr_r, curr_i);
+				ffts[i-1] = cfft2(data);
+			}
+			IJ.showProgress(i, slices);
+		}
+
+		return ffts;
+	}
+
+	//calculate the shifts between ffts
+	private double[][] calculateShifts(ComplexMatrix[] ffts) {
+        
+		double[][] shifts = new double[ffts.length][6];        
+		for (int i = 0; i < ffts.length; i++) {
+			shifts[i][0] = reference_slide; shifts[i][1] = i+1;
+			double[] temp = DFTRegistration(ffts[reference_slide - 1], ffts[i]);
+			shifts[i][2] = temp[2]; shifts[i][3] = temp[3];
+			shifts[i][4] = temp[0]; shifts[i][5] = temp[1];            
+			IJ.showProgress(i + 1, ffts.length);
+		}
+		return shifts; // [ref, drifted, dr, dc, error, diffphase]
+	
+	}
+
+	//calculate all the shifts between ffts
+	private double[][] calculateAllShifts(ComplexMatrix[] ffts) {
+
+		double[][] shifts = new double[ffts.length*(ffts.length-1)/2][6];
+		int id = 0;
+		for (int i = 0; i < ffts.length-1; i++) {
+			for (int j = i+1; j < ffts.length; j++) {
+				shifts[id][0] = i+1; shifts[id][1] = j+1;
+				double[] temp = DFTRegistration(ffts[i], ffts[j]);
+				shifts[id][2] = temp[2]; shifts[id][3] = temp[3];
+				shifts[id][4] = temp[0]; shifts[id][5] = temp[1];
+				id = id + 1;
+				IJ.showProgress(id + 1, ffts.length*(ffts.length-1)/2);
+			}
+		}
+		
+		return shifts; // [ref,drifted,dr,dc,error, diffphase]
+	}
+	
+	// compute 2D fft from an image
+	private ComplexMatrix fft2(double[][] data) {
+
+		int h = data.length;
+		int w = data[0].length;
+		DoubleFFT_2D fft = new DoubleFFT_2D(h, w);
+		
+		fft.realForward(data);
+		ComplexMatrix m = FFTArray2D_to_ComplexMatrix(data, h, w);
+
+		return m;
+	}
+
+	// compute complex 2D fft from an image
+	private ComplexMatrix cfft2(double[][] data) {
+
+		int h = data.length;
+		int w = data[0].length;
+		DoubleFFT_2D fft = new DoubleFFT_2D(h, w/2);
+		
+		fft.complexForward(data);
+		ComplexMatrix m = FFTComplexArray2D_to_ComplexMatrix(data, h, w/2);
+
+		return m;
+	}
+	
+	// compute inverse 2D fft from a complex matrix
+	private double[][] ifft2(ComplexMatrix m) {
+		int w = m.getNcol();
+		int h = m.getNrow();
+		
+		DoubleFFT_2D fft = new DoubleFFT_2D(h, w);
+		
+		double[][] data = ComplexMatrix_to_FFTArray2D(m);	
+		fft.realInverse(data, true);
+
+		return data;
+	}
+	
+	// compute complex inverse 2D fft from a complex matrix
+	private ComplexMatrix cifft2(ComplexMatrix m) {
+		int w = m.getNcol();
+		int h = m.getNrow();
+		
+		DoubleFFT_2D fft = new DoubleFFT_2D(h, w);
+		
+		double[][] data = new double[h][2*w];
+		for (int j=0; j<h; j++) {
+			for (int i=0; i<w; i++) {
+				data[j][2*i] = m.getElementReference(j, i).getReal();
+				data[j][2*i+1] = m.getElementReference(j, i).getImag();				
+			}
+		}
+
+		fft.complexInverse(data, true);
+
+		ComplexMatrix out = new ComplexMatrix(h, w);
+		for (int j=0; j<h; j++) {
+			for (int i=0; i<w; i++) {
+				out.setElement(j, i, data[j][2*i], data[j][2*i+1]);			
+			}
+		}
+
+		return out;
+	}
+	
+	private double[] DFTRegistration(ComplexMatrix ref, ComplexMatrix drifted) {
+		int m = ref.getNrow();
+		int n = ref.getNcol();
+		double[] output = new double[4];
+		
+		// First upsample by a factor of 2 to obtain initial estimate
+    		// Embed Fourier data in a 2x larger array
+    		int mlarge = m*2;
+    		int nlarge = n*2;
+    		ComplexMatrix large = new ComplexMatrix(mlarge, nlarge);
+    		ComplexMatrix c = fftshift(ElementProduct(ref, drifted.conjugate()));
+
+    		for (int j = 0; j < m; j++) {
+    			for (int i = 0; i < n; i++) {
+    				large.setElement((int)(j + m - Math.floor(m/2.0)), (int)(i + n - Math.floor(n/2.0)), c.getElementReference(j, i));
+    			}
+    		}
+  
+    		// Compute crosscorrelation and locate the peak
+    		ComplexMatrix CC = cifft2(ifftshift(large));
+    		double[] peak = cFindPeak(CC); //max, r, c, max_r, max_c
+    		    
+    		// Obtain shift in original pixel grid from the position of the
+    		// crosscorrelation peak 
+    		if (peak[1] > m) { 
+        		peak[1] = peak[1] - mlarge;
+    		}
+		if (peak[2] > n) {
+			peak[2] = peak[2] - nlarge;
+		}
+
+    		//% If upsampling > 2, then refine estimate with matrix multiply DFT
+    		if (this.usfac > 2) {
+     			//   %%% DFT computation %%%
+     			//   % Initial shift estimate in upsampled grid
+     			double row_shift = Math.round(peak[1]/2.0*this.usfac)/this.usfac; 
+     			double col_shift = Math.round(peak[2]/2.0*this.usfac)/this.usfac;     
+     			int dftshift = (int)Math.floor(Math.ceil(this.usfac*1.5)/2); // Center of output array at dftshift+1
+     			//   % Matrix multiply DFT around the current shift estimate
+    			ComplexMatrix in = ElementProduct(drifted, ref.conjugate());
+     			ComplexMatrix nCC = dftups(in, (int)Math.ceil(this.usfac*1.5), (int)Math.ceil(this.usfac*1.5),
+     					dftshift-row_shift*this.usfac, dftshift-col_shift*this.usfac);
+     		     	nCC = nCC.times(1.0/(m*n*this.usfac*this.usfac)).conjugate();
+     			//   % Locate maximum and map back to original pixel grid 
+     			double[] npeak = cFindPeak(nCC); //max_r, max_i, r, c
+    
+ 			ComplexMatrix mrg00 = dftups(ElementProduct(ref, ref.conjugate()),1,1,0,0);
+ 			double rg00 = mrg00.getElementReference(0, 0).abs()/(m*n*this.usfac*this.usfac);
+     			ComplexMatrix mrf00 = dftups(ElementProduct(drifted, drifted.conjugate()),1,1,0,0);
+     			double rf00 = mrf00.getElementReference(0, 0).abs()/(m*n*this.usfac*this.usfac);
+     			
+     			npeak[1] = npeak[1] - dftshift;
+     			npeak[2] = npeak[2] - dftshift;
+     			output[0] = Math.sqrt(Math.abs(1.0 - npeak[0]*npeak[0]/(rg00*rf00)));	//error
+			output[1] = Math.atan2(npeak[4], npeak[3]);				//diffphase		
+     			output[2] = row_shift + npeak[1]/this.usfac;			//delta row
+     			output[3] = col_shift + npeak[2]/this.usfac;			//delta col
+     			
+    		} else {
+   			// % If upsampling = 2, no additional pixel shift refinement
+   			double rg00 = SumSquareAbs(ref)/(mlarge*nlarge);
+			double rf00 = SumSquareAbs(drifted)/(mlarge*nlarge);
+			
+			output[0] = Math.sqrt(Math.abs(1.0 - peak[0]*peak[0]/(rg00*rf00)));	//error
+			output[1] = Math.atan2(peak[4], peak[3]);				//diffphase		
+			output[2] = peak[1]/2.0;					//delta row
+    			output[3] = peak[2]/2.0;					//delta col
+    		}
+    		
+		return output;	
+	}
+
+	private double SumSquareAbs(ComplexMatrix m) {
+		double sum = 0.0;
+
+		for (int j = 0; j < m.getNrow(); j ++){
+			for (int i = 0; i < m.getNcol(); i++) {
+				sum += m.getElementReference(j, i).squareAbs();
+			}
+		}
+
+		return sum;
+	}
+	
+	private double[] cFindPeak(ComplexMatrix m) {
+		double max = 0.0;
+		double realmax = 0.0;
+		double imagmax = 0.0;
+		int cmax = 0, rmax = 0;
+		
+		for (int j = 0; j < m.getNrow(); j ++){
+			for (int i = 0; i < m.getNcol(); i++) {
+				if (m.getElementReference(j, i).abs() > max) {
+					max = m.getElementReference(j, i).abs();
+					realmax = m.getElementReference(j, i).getReal();
+					imagmax = m.getElementReference(j, i).getImag();
+					rmax = j;
+					cmax = i;
+				}
+			}
+		}
+
+		double[] res = new double[5];
+		res[0] = Math.sqrt(realmax*realmax+imagmax*imagmax); res[1] = rmax; res[2] = cmax;
+		res[3] = realmax; res[4] = imagmax;
+		return res;
+	}
+	
+	private ComplexMatrix fftshift(ComplexMatrix in) {
+		int nc = in.getNcol();
+		int nr = in.getNrow();
+
+		ComplexMatrix out = new ComplexMatrix (nr, nc);
+		
+		int midi = (int)Math.floor(nc/2.0);
+		int offi = (int)Math.ceil(nc/2.0);
+		int midj = (int)Math.floor(nr/2.0);
+		int offj = (int)Math.ceil(nr/2.0);
+		
+		for (int j = 0; j < nr; j ++){
+			for (int i = 0; i < nc; i++) {
+				if (j < midj) {
+					if (i < midi) {
+						out.setElement(j, i, in.getElementReference(j+offj, i+offi));
+					} else {
+						out.setElement(j, i, in.getElementReference(j+offj, i-midi));		
+					}
+				} else {
+					if (i < midi) {
+						out.setElement(j, i, in.getElementReference(j-midj, i+offi));
+					} else {
+						out.setElement(j, i, in.getElementReference(j-midj, i-midi));		
+					}
+				}
+			}
+		}
+
+		return out;
+	}
+
+	private ComplexMatrix ifftshift(ComplexMatrix in) {
+		int nc = in.getNcol();
+		int nr = in.getNrow();
+
+		ComplexMatrix out = new ComplexMatrix (nr, nc);
+		
+		int midi = (int)Math.ceil(nc/2.0);
+		int offi = (int)Math.floor(nc/2.0);
+		int midj = (int)Math.ceil(nr/2.0);
+		int offj = (int)Math.floor(nr/2.0);
+		
+		for (int j = 0; j < nr; j ++){
+			for (int i = 0; i < nc; i++) {
+				if (j < midj) {
+					if (i < midi) {
+						out.setElement(j, i, in.getElementReference(j+offj, i+offi));
+					} else {
+						out.setElement(j, i, in.getElementReference(j+offj, i-midi));		
+					}
+				} else {
+					if (i < midi) {
+						out.setElement(j, i, in.getElementReference(j-midj, i+offi));
+					} else {
+						out.setElement(j, i, in.getElementReference(j-midj, i-midi));		
+					}
+				}
+			}
+		}
+
+		return out;
+	}
+	
+	private Matrix ifftshift(Matrix in) {
+		int nc = in.getNcol();
+		int nr = in.getNrow();
+
+		Matrix out = new Matrix (nr, nc);
+		
+		int midi = (int)Math.ceil(nc/2.0);
+		int offi = (int)Math.floor(nc/2.0);
+		int midj = (int)Math.ceil(nr/2.0);
+		int offj = (int)Math.floor(nr/2.0);
+		
+		for (int j = 0; j < nr; j ++){
+			for (int i = 0; i < nc; i++) {
+				if (j < midj) {
+					if (i < midi) {
+						out.setElement(j, i, in.getElement(j+offj, i+offi));
+					} else {
+						out.setElement(j, i, in.getElement(j+offj, i-midi));		
+					}
+				} else {
+					if (i < midi) {
+						out.setElement(j, i, in.getElement(j-midj, i+offi));
+					} else {
+						out.setElement(j, i, in.getElement(j-midj, i-midi));		
+					}
+				}
+			}
+		}
+
+		return out;
+	}
+
+        public Matrix times(Matrix amat, Matrix bmat){
+            
+            if(amat.getNumberOfColumns()!=bmat.getNumberOfRows())throw new IllegalArgumentException("Nonconformable matrices");
+
+            Matrix cmat = new Matrix(amat.getNumberOfRows(), bmat.getNumberOfColumns());
+            double [][] aarray = amat.getArrayReference();
+            double [][] barray = bmat.getArrayReference();
+            double [][] carray = cmat.getArrayReference();
+            double sum = 0.0D;
+
+            for(int i=0; i<amat.getNumberOfRows(); i++){
+                    for(int j=0; j<bmat.getNumberOfColumns(); j++){
+                        sum=0.0D;
+                        for(int k=0; k<amat.getNumberOfColumns(); k++){
+                                sum += aarray[i][k]*barray[k][j];
+                        }
+                        carray[i][j]=sum;
+                    }
+            }
+            return cmat;
+        }   
+	
+	private ComplexMatrix dftups(ComplexMatrix in, int nor, int noc, double roff, double coff) {
+		// function out=dftups(in,nor,noc,usfac,roff,coff);
+		// Upsampled DFT by matrix multiplies, can compute an upsampled DFT in just
+		// a small region.
+		// usfac         Upsampling factor (default usfac = 1)
+		// [nor,noc]     Number of pixels in the output upsampled DFT, in
+		//               units of upsampled pixels (default = size(in))
+		// roff, coff    Row and column offsets, allow to shift the output array to
+		//               a region of interest on the DFT (default = 0)
+		// Recieves DC in upper left corner, image center must be in (1,1)
+		// Loïc Le Guyader - Jun 11, 2011 Java version for ImageJ plugin 
+		// Manuel Guizar - Dec 13, 2007
+		// Modified from dftus, by J.R. Fienup 7/31/06
+
+		// This code is intended to provide the same result as if the following
+		// operations were performed
+		//   - Embed the array "in" in an array that is usfac times larger in each
+		//     dimension. ifftshift to bring the center of the image to (1,1).
+		//   - Take the FFT of the larger array
+		//   - Extract an [nor, noc] region of the result. Starting with the 
+		//     [roff+1 coff+1] element.
+
+		// It achieves this result by computing the DFT in the output array without
+		// the need to zeropad. Much faster and memory efficient than the
+		// zero-padded FFT approach if [nor noc] are much smaller than [nr*usfac nc*usfac]
+
+		int nr = in.getNrow();
+		int nc = in.getNcol();
+		// Compute kernels and obtain DFT by matrix products
+		double amplitude = -2.0*Math.PI/(nc*usfac);
+		
+		Matrix u = new Matrix(nc, 1);
+		for (int i = 0; i < nc; i++) {
+			u.setElement(i, 0, i - Math.floor(nc/2.0));
+		}
+		u = ifftshift(u);
+
+		Matrix v = new Matrix(1, noc);
+		for (int i = 0; i < noc; i++) {
+			v.setElement(0, i, i-coff);
+		}
+		Matrix phase = u.times(v);
+        //Matrix phase = times(u,v);
+      
+		ComplexMatrix kernc = new ComplexMatrix(nc, noc);
+		for (int j = 0; j < nc; j++) {
+			for (int i = 0; i < noc; i++)  {
+				Complex t = new Complex();
+				t.polar(1.0, amplitude*phase.getElement(j, i));
+				kernc.setElement(j, i, t);
+			}		
+		}
+		//ComplexMatrixPrint(kernc);
+		
+		amplitude = -2.0*Math.PI/(nr*usfac);
+		
+		Matrix w = new Matrix(nor, 1); 
+		for (int i = 0; i < nor; i++) {
+			w.setElement(i, 0, i - roff);
+		}
+		
+		Matrix x = new Matrix(1, nr);
+		for (int i = 0; i < nr; i++) {
+			x.setElement(0, i, i - Math.floor(nr/2.0));
+		}
+		x = ifftshift(x);
+
+		Matrix nphase = w.times(x);
+       //Matrix nphase = times(w,x);
+		ComplexMatrix kernr = new ComplexMatrix(nor, nr);
+		for (int j = 0; j < nor; j++) {
+			for (int i = 0; i < nr; i++) {
+				Complex t = new Complex();
+				t.polar(1.0, amplitude*nphase.getElement(j, i));
+				kernr.setElement(j, i, t);
+			}		
+		}
+		//ComplexMatrixPrint(kernr);
+		
+		ComplexMatrix out = kernr.times(in.times(kernc));     
+		return out;
+	}
+	
+	private double[][] CrossCorrelation(ComplexMatrix ref, ComplexMatrix drifted) {
+		int h = ref.getNrow();
+		int w = ref.getNcol();
+		ComplexMatrix b = drifted.conjugate();
+		ComplexMatrix res = ElementProduct(ref, b);
+		
+		double[][] data = ComplexMatrix_to_FFTArray2D(res);
+		DoubleFFT_2D fft = new DoubleFFT_2D(h, w);
+		fft.realInverse(data, true);
+		
+		return data;
+	}
+
+	private ComplexMatrix ElementProduct(ComplexMatrix a, ComplexMatrix b) {
+		int nr = a.getNrow();
+		int nc = a.getNcol();
+		
+		ComplexMatrix res = new ComplexMatrix(nr, nc);
+
+		for(int j = 0; j < nr; j++) {
+			for(int i = 0; i < nc; i++) {
+				res.setElement(j, i, a.getElementReference(j, i).times(b.getElementReference(j, i)));
+			}
+		}
+
+		return res;
+	}
+	
+	private double[][] ImageProcessor_to_FFTArray2D(ImageProcessor ip) {
+
+		float[] pixels = (float[])ip.getPixels();
+		int w = ip.getWidth();
+		int h = ip.getHeight();
+		double[][] data = new double[h][w];
+		
+		for (int j = 0; j < h; j++) { 
+			for (int i = 0; i < w; i++) {
+				data[j][i] = (double)pixels[j*w + i];
+    			}
+		}
+
+		return data;
+	}
+	
+	private double[][] ImageProcessor_to_FFTComplexArray2D(ImageProcessor ip_r, ImageProcessor ip_i) {
+
+		float[] pixels_r = (float[])ip_r.getPixels();
+		float[] pixels_i = (float[])ip_i.getPixels();
+		int w = ip_r.getWidth();
+		int h = ip_r.getHeight();
+		double[][] data = new double[h][2*w];
+		
+		for (int j = 0; j < h; j++) { 
+			for (int i = 0; i < w; i++) {
+				data[j][2*i] = (double)pixels_r[j*w + i];
+				data[j][2*i+1] = (double)pixels_i[j*w + i];
+    			}
+		}
+
+		return data;
+	}
+	
+	private ComplexMatrix FFTArray2D_to_ComplexMatrix(double[][] data, int h, int w) {
+	
+		ComplexMatrix m = new ComplexMatrix(h,w);
+
+		for (int j = 0; j < h; j++) {
+			for (int i = 0; i <= w/2; i++) {
+				if (j > 0 && i > 0 && i < w/2) { 
+      					m.setElement(j,i, new Complex(data[j][2*i], data[j][2*i+1]));
+      					m.setElement(h-j, w-i, new Complex(data[j][2*i], -data[j][2*i+1]));
+				}
+				if (j == 0 && i > 0 && i < w/2) {
+					m.setElement(0, i, new Complex(data[0][2*i], data[0][2*i+1]));
+      					m.setElement(0, w-i, new Complex(data[0][2*i], -data[0][2*i+1]));
+				}
+				if (i == 0 && j > 0 && j < h/2) {
+					m.setElement(j,0, new Complex(data[j][0], data[j][1]));
+      					m.setElement(h-j, 0, new Complex(data[j][0], -data[j][1]));
+      					m.setElement(j, w/2, new Complex(data[h-j][1], -data[h-j][0]));
+      					m.setElement(h-j, w/2, new Complex(data[h-j][1], data[h-j][0]));	
+				}
+				if (j == 0 && i == 0) {
+					m.setElement(0, 0, new Complex(data[0][0], 0));
+				}
+				if (j == 0 && i == w/2) {
+					m.setElement(0, w/2, new Complex(data[0][1], 0));
+				}
+				if (j == h/2 && i == 0) {
+					m.setElement(h/2, 0, new Complex(data[h/2][0], 0));
+				}
+				if (j == h/2 && i == w/2) {
+					m.setElement(h/2, w/2, new Complex(data[h/2][1], 0));
+				}
+			}
+		}
+
+		return m;
+	}
+
+	private ComplexMatrix FFTComplexArray2D_to_ComplexMatrix(double[][] data, int h, int w) {
+	
+		ComplexMatrix m = new ComplexMatrix(h,w);
+
+		for (int j = 0; j < h; j++) {
+			for (int i = 0; i < w; i++) {
+				m.setElement(j,i, new Complex(data[j][2*i], data[j][2*i+1]));
+			}
+		}
+
+		return m;
+	}
+
+	private double[][] ComplexMatrix_to_FFTArray2D(ComplexMatrix m) {
+		int w = m.getNcol();
+		int h = m.getNrow();
+		double[][] data = new double[h][w];
+
+		for (int j = 0; j < h; j++) {
+			for (int i = 0; i <= w/2; i++) {
+				if (j > 0 && i > 0 && i < w/2) {
+      					data[j][2*i] = m.getElementReference(j,i).getReal();
+      					data[j][2*i+1] = m.getElementReference(j,i).getImag();
+				}
+				if (j == 0 && i > 0 && i < w/2) {
+					data[0][2*i] = m.getElementReference(0,i).getReal();
+      					data[0][2*i+1] = m.getElementReference(0,i).getImag();
+				}
+				if (i == 0 && j > 0 && j < h/2) {
+					data[j][0] = m.getElementReference(j,0).getReal();
+      					data[j][1] = m.getElementReference(j,0).getImag();
+      					data[h-j][1] = m.getElementReference(j,w/2).getReal();
+      					data[h-j][0] = m.getElementReference(h-j,w/2).getImag();	
+				}
+				if (j == 0 && i == 0) {
+					data[0][0] = m.getElementReference(0,0).getReal();
+				}
+				if (j == 0 && i == w/2) {
+					data[0][1] = m.getElementReference(0,w/2).getReal();
+				}
+				if (j == h/2 && i == 0) {
+					data[h/2][0] = m.getElementReference(h/2,0).getReal();
+				}
+				if (j == h/2 && i == w/2) {
+					data[h/2][1] = m.getElementReference(h/2,w/2).getReal();
+				}
+			}
+		}
+
+		return data;
+	}
+
+	// convert a Complex Matrix into an 2d real part array data[0][][]
+	// and 2d imaginary part data[1][][]
+	private double[][][] ComplexMatrix_to_RealArray2D(ComplexMatrix m) {
+		int w = m.getNcol();
+		int h = m.getNrow();
+		double[][][] data = new double[2][h][w];
+
+		for (int j = 0; j < h; j++) {
+			for (int i = 0; i < w; i++) {
+				data[0][j][i] = m.getElementReference(j,i).getReal();
+      				data[1][j][i] = m.getElementReference(j,i).getImag();
+			}
+		}
+		
+		return data;
+	}
+}

plugins/Align_TranslationFilter.java

@@ -0,0 +1,115 @@
+import ij.plugin.filter.ExtendedPlugInFilter;
+import ij.plugin.filter.PlugInFilterRunner;
+import ij.plugin.filter.GaussianBlur;
+import ij.*;
+import ij.process.*;
+
+import ij.io.OpenDialog;
+import ij.io.SaveDialog;
+import java.util.ArrayList;
+import java.io.IOException;
+import java.io.File;
+import jmatio.types.*;
+import jmatio.io.*;
+import ij.gui.GenericDialog;
+import ij.IJ;
+import ij.Prefs;
+
+public class Align_TranslationFilter implements ExtendedPlugInFilter {
+     private double[][] shifts;
+     private final int flags = (DOES_ALL-DOES_RGB)|DOES_STACKS|NO_CHANGES|FINAL_PROCESSING;
+     private ImagePlus imp;
+     private ImagePlus registred;
+     private ImageStack translated;
+     private PlugInFilterRunner pifr;
+     private int nbslices = 0;
+     private int processed = 0;  
+
+     public void setShifts(double[][] shifts){
+        this.shifts = shifts;
+     }
+
+     public double[][] getShifts(){
+        return shifts;
+     }
+
+     public ImagePlus getOutput(){
+        return registred;
+     }
+
+     public void  setImp(ImagePlus imp){
+        this.imp = imp;
+     }
+
+     /**
+      * This method is called by ImageJ for initialization.
+      * @param arg Unused here. For plugins in a .jar file this argument string can
+      *            be specified in the plugins.config file of the .jar archive.
+      * @param imp The ImagePlus containing the image (or stack) to process.
+      * @return    The method returns flags (i.e., a bit mask) specifying the
+      *            capabilities (supported formats, etc.) and needs of the filter.
+      *            See PlugInFilter.java and ExtendedPlugInFilter in the ImageJ
+      *            sources for details.
+      */
+     public int setup(String arg, ImagePlus imp) {
+        System.out.println("Setup " + arg);
+         if ("final".equals(arg)) {
+         	registred.setStack("REG_" + this.imp.getTitle(), translated);
+    		return DONE;
+         } else {
+            if (imp==null ){
+         	    this.imp = imp;
+            }
+         	return flags;
+         }
+     }
+
+	/** Called by ImageJ after setup. */
+	public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
+		pifr = pfr;
+        
+		//ShiftsIO sio = new ShiftsIO();
+    	//shifts = sio.load(null, "directshifts");
+    	//if (shifts == null) return DONE;
+         
+        //IJ.register(this.getClass());   		// protect static class variables (filter parameters) from garbage collection
+        //return IJ.setupDialog(imp, flags);  	// ask whether to process all slices of stack (if a stack)
+        return flags;
+	}
+
+     /** Process a FloatProcessor (with the CONVERT_TO_FLOAT flag, ImageJ does the conversion to float).
+      *  Called by ImageJ for each stack slice (when processing a full stack); for RGB also called once for each color. */
+     public void run(ImageProcessor ip) {
+     	        // translate from shifts
+     	        if (Thread.currentThread().isInterrupted()) return;
+		
+		int thisone = pifr.getSliceNumber();
+		
+		ImageProcessor nip = ip.duplicate().convertToFloat();
+		nip.setInterpolationMethod(ImageProcessor.BICUBIC);
+		if (shifts.length != nbslices) {
+			nip.translate(shifts[1][3], shifts[1][2]); // translate all the frame by the
+								// same shifts
+		} else {
+			nip.translate(shifts[thisone-1][3], shifts[thisone-1][2]);
+		}
+		
+		String lbl = imp.getStack().getSliceLabel(thisone);
+		if (lbl != null) {
+			translated.addSlice(lbl, nip, thisone - 1);
+		} else {
+			translated.addSlice("" + thisone, nip, thisone - 1);
+		}
+		translated.deleteSlice(thisone + 1);
+
+		processed++;
+		IJ.showProgress(processed, nbslices);
+	}
+
+     /** Called by ImageJ to set the number of calls to run(ip) corresponding to 100% of the progress bar */
+     public void setNPasses(int nPasses) {
+         nbslices = nPasses;
+         registred = imp.createImagePlus();
+         translated = new ImageStack(imp.getWidth(), imp.getHeight(), nbslices);
+     }     
+}

plugins/Align_TranslationFilter2.java

@@ -0,0 +1,91 @@
+import ij.plugin.filter.PlugInFilter;
+import ij.plugin.filter.PlugInFilterRunner;
+import ij.plugin.filter.GaussianBlur;
+import ij.*;
+import ij.process.*;
+import com.jmatio.types.*;
+import com.jmatio.io.*;
+
+public class Align_TranslationFilter2 implements PlugInFilter {
+     private final int flags = (DOES_ALL-DOES_RGB)|DOES_STACKS|NO_CHANGES|FINAL_PROCESSING;
+     private ImagePlus imp;
+     private ImagePlus registred;
+     private ImageStack translated;
+     private int nbslices = 0;
+     private int processed = 0;  
+
+     double[][] shifts;
+    
+     public void setShifts(double[][] shifts){
+        this.shifts = shifts;
+    }
+
+    public double[][] getShifts(){
+        return this.shifts;
+    }
+
+    
+
+     /**
+      * This method is called by ImageJ for initialization.
+      * @param arg Unused here. For plugins in a .jar file this argument string can
+      *            be specified in the plugins.config file of the .jar archive.
+      * @param imp The ImagePlus containing the image (or stack) to process.
+      * @return    The method returns flags (i.e., a bit mask) specifying the
+      *            capabilities (supported formats, etc.) and needs of the filter.
+      *            See PlugInFilter.java and ExtendedPlugInFilter in the ImageJ
+      *            sources for details.
+      */
+       
+     public int setup(String arg, ImagePlus imp) {
+         nbslices = imp.getImageStackSize();
+         registred = imp.createImagePlus();
+         translated = new ImageStack(imp.getWidth(), imp.getHeight(), nbslices);
+         this.imp = imp;
+                 
+         
+         if (shifts == null) return DONE;         
+         //int ret = IJ.setupDialog(imp, flags);      // ask whether to process all slices of stack (if a stack)      
+         return flags;
+     }
+
+    public ImagePlus getRegistred(){
+        return registred;
+    }
+    
+    public ImageStack getTranslated(){
+        return translated;
+    }     
+
+     /** Process a FloatProcessor (with the CONVERT_TO_FLOAT flag, ImageJ does the conversion to float).
+      *  Called by ImageJ for each stack slice (when processing a full stack); for RGB also called once for each color. */
+     public void run(ImageProcessor ip) {
+     	       	        
+        for (int slice =1; slice<= nbslices; slice++){
+            if (Thread.currentThread().isInterrupted()) return;
+            
+    		ImageProcessor nip = ip.duplicate().convertToFloat();
+    		nip.setInterpolationMethod(ImageProcessor.BICUBIC);
+    		if (shifts.length != nbslices) {
+    			nip.translate(shifts[1][3], shifts[1][2]); // translate all the frame by the
+    								// same shifts
+    		} else {
+    			nip.translate(shifts[slice-1][3], shifts[slice-1][2]);
+    		}
+    		
+    		String lbl = imp.getStack().getSliceLabel(slice);
+    		if (lbl != null) {
+    			translated.addSlice(lbl, nip, slice - 1);
+    		} else {
+    			translated.addSlice("" + slice, nip, slice - 1);
+    		}
+    		translated.deleteSlice(slice + 1);
+    
+    		processed++;
+    		IJ.showProgress(processed, nbslices);
+         }
+         registred.setStack("REG_" + imp.getTitle(), translated);
+       
+	}
+
+}

plugins/ManipulatorScan.form

@@ -510,6 +510,7 @@
                   <Group type="103" groupAlignment="0" attributes="0">
                       <Component id="buttonStart" max="32767" attributes="0"/>
                       <Component id="buttonAbort" pref="244" max="32767" attributes="0"/>
+                      <Component id="buttonAddToQueue" pref="244" max="32767" attributes="0"/>
                   </Group>
                   <EmptySpace max="-2" attributes="0"/>
               </Group>
@@ -528,6 +529,8 @@
                   <EmptySpace type="separate" max="-2" attributes="0"/>
                   <Component id="buttonAbort" min="-2" max="-2" attributes="0"/>
                   <EmptySpace max="32767" attributes="0"/>
+                  <Component id="buttonAddToQueue" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace min="-2" pref="36" max="-2" attributes="0"/>
                   <Component id="jButton1" min="-2" max="-2" attributes="0"/>
                   <EmptySpace min="-2" pref="143" max="-2" attributes="0"/>
               </Group>
@@ -556,6 +559,14 @@
             <Property name="text" type="java.lang.String" value="jButton1"/>
           </Properties>
         </Component>
+        <Component class="javax.swing.JButton" name="buttonAddToQueue">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="Add To Queue"/>
+          </Properties>
+          <Events>
+            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonAddToQueueActionPerformed"/>
+          </Events>
+        </Component>
       </SubComponents>
     </Container>
   </SubComponents>

plugins/ManipulatorScan.java

@@ -1,15 +1,19 @@
 /*
  * Copyright (c) 2014 Paul Scherrer Institute. All rights reserved.
- */
+ */
  
 
 import ch.psi.pshell.device.Motor;
+import ch.psi.pshell.ui.Panel;
 import ch.psi.pshell.ui.ScriptProcessor;
+import ch.psi.pshell.ui.Plugin;
 import ch.psi.pshell.ui.QueueProcessor;
 import ch.psi.utils.State;
 import ch.psi.utils.swing.SwingUtils;
 import java.awt.Component;
 import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
@@ -18,7 +22,7 @@ import javax.swing.SpinnerNumberModel;
 
 /**
  *
-public class ManipulatorScan extends Panel {
+ */
 public class ManipulatorScan extends ScriptProcessor {
 
     public ManipulatorScan() {
@@ -64,8 +68,14 @@ public class ManipulatorScan extends Panel {
     
     void updateTable(){
         
-
-    void startScan() throws Exception {
+    }
+    
+    @Override
+    public String getScript() {
+        return "ManipulatorScan";
+    }     
+    
+    @Override
     public Map<String, Object> getArgs(){
         HashMap<String, Object> args = new HashMap<>();
         args.put("MOTOR", comboMotor.getSelectedItem().toString());
@@ -89,45 +99,10 @@ public class ManipulatorScan extends Panel {
             args.put("STEPS", (Integer) spinnerSteps.getValue());
         }
         args.put("LATENCY", (Double) spinnerLatency.getValue());
-        
-        runAsync("ManipulatorScan", args);
-
-        /*
-         getContext().setExecutingContext("manip_scan");
-         String scan ="lscan(" + comboMotor.getSelectedItem().toString() + ", ( " ; 
-         for (Component c : panelSensors.getComponents()) {
-         if ((c instanceof JCheckBox) && ((JCheckBox)c).isSelected())
-         scan += c.getName() + ", ";
-         }          
-         scan+="), ";
-         if (radioRelative.isSelected()){
-         double halfRange = (Double)spinnerRange.getValue()/2;
-         scan+= (-halfRange) + ", " + (halfRange)+ ", ";
-         } else {
-         Double from = (Double)spinnerFrom.getValue();
-         Double to = (Double)spinnerTo.getValue();
-
-         if (to <= from){
-         throw new Exception ("Invalid range");
-         }
-         scan+= from + ", " + to + ", ";
-         }
-
-         scan+= (radioStepSize.isSelected()) ? "(" +((Double)spinnerStepSize.getValue())+",)" :((Integer)spinnerSteps.getValue());
-         scan+=", " + (Double)spinnerLatency.getValue() + ", ";
-         if (radioRelative.isSelected()){
-         scan+="True, "; //Relative            
-         }
-         scan+="before_read=trig_scienta)"; //Relative   
-
-         if (checkImageIntegration.isSelected()){
-         scan = "set_preference(Preference.PLOT_TYPES,{'integration':1}); " + scan;
-         }
-
-         evalAsync(scan);
-         */
+        args.put("RELATIVE", radioRelative.isSelected());
         return args;
     }
+
 
     @SuppressWarnings("unchecked")
     // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
@@ -173,6 +148,7 @@ public class ManipulatorScan extends Panel {
         jPanel3 = new javax.swing.JPanel();
         buttonStart = new javax.swing.JButton();
         buttonAbort = new javax.swing.JButton();
+        jButton1 = new javax.swing.JButton();
         buttonAddToQueue = new javax.swing.JButton();
 
         panelPositioner.setBorder(javax.swing.BorderFactory.createTitledBorder("Positioner"));
@@ -473,6 +449,13 @@ public class ManipulatorScan extends Panel {
         });
 
         jButton1.setText("jButton1");
+
+        buttonAddToQueue.setText("Add To Queue");
+        buttonAddToQueue.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                buttonAddToQueueActionPerformed(evt);
+            }
+        });
 
         javax.swing.GroupLayout jPanel3Layout = new javax.swing.GroupLayout(jPanel3);
         jPanel3.setLayout(jPanel3Layout);
@@ -481,7 +464,8 @@ public class ManipulatorScan extends Panel {
             .addGroup(jPanel3Layout.createSequentialGroup()
                 .addContainerGap()
                 .addGroup(jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                    .addComponent(buttonAbort, javax.swing.GroupLayout.DEFAULT_SIZE, 244, Short.MAX_VALUE))
+                    .addComponent(buttonStart, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                    .addComponent(buttonAbort, javax.swing.GroupLayout.DEFAULT_SIZE, 244, Short.MAX_VALUE)
                     .addComponent(buttonAddToQueue, javax.swing.GroupLayout.DEFAULT_SIZE, 244, Short.MAX_VALUE))
                 .addContainerGap())
             .addGroup(jPanel3Layout.createSequentialGroup()
@@ -496,6 +480,8 @@ public class ManipulatorScan extends Panel {
                 .addComponent(buttonStart)
                 .addGap(18, 18, 18)
                 .addComponent(buttonAbort)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addComponent(buttonAddToQueue)
                 .addGap(36, 36, 36)
                 .addComponent(jButton1)
                 .addGap(143, 143, 143))
@@ -538,7 +524,7 @@ public class ManipulatorScan extends Panel {
     }//GEN-LAST:event_buttonScientaSetupActionPerformed
 
     private void buttonStartActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonStartActionPerformed
-            startScan();
+        try {
             execute();
         } catch (Exception ex) {
             SwingUtils.showException(this, ex);
@@ -566,7 +552,7 @@ public class ManipulatorScan extends Panel {
             txtSize.setText("Size (" + motor.getUnit() +")");
             //spinnerFrom.setModel(new javax.swing.SpinnerNumberModel(3.0, 0.001, 100.0, 1.0));
             //spinnerTo.setModel(new javax.swing.SpinnerNumberModel(2.0, 0.001, 100.0, 1.0));
-            SwingUtils.showException(this, ex);
+        } catch (Exception ex) {
             showException(ex);
         }
     }//GEN-LAST:event_comboMotorActionPerformed
@@ -574,8 +560,20 @@ public class ManipulatorScan extends Panel {
     private void radioAbsoluteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_radioAbsoluteActionPerformed
         setEnabled(isEnabled());
     }//GEN-LAST:event_radioAbsoluteActionPerformed
+
+    private void buttonAddToQueueActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonAddToQueueActionPerformed
+        try {
+            List<QueueProcessor> queues = getView().getQueues();
+            QueueProcessor tq =  (queues.size() == 0) ?  getView().openProcessor(QueueProcessor.class, null) : queues.get(0);
+            getView().getDocumentsTab().setSelectedComponent(tq);
+            tq.addNewFile(getScript(), getArgs());
+        } catch (Exception ex) {
+            showException( ex);
+        }                
+    }//GEN-LAST:event_buttonAddToQueueActionPerformed
 
     // Variables declaration - do not modify//GEN-BEGIN:variables
+    private javax.swing.JButton buttonAbort;
     private javax.swing.JButton buttonAddToQueue;
     private javax.swing.ButtonGroup buttonGroup1;
     private javax.swing.ButtonGroup buttonGroup2;
@@ -617,4 +615,5 @@ public class ManipulatorScan extends Panel {
     private javax.swing.JSpinner spinnerSteps;
     private javax.swing.JSpinner spinnerTo;
     private javax.swing.JLabel txtSize;
+    // End of variables declaration//GEN-END:variables
 

plugins/PanelPlugin.form

@@ -22,39 +22,51 @@
       <Group type="103" groupAlignment="0" attributes="0">
           <Group type="102" attributes="0">
               <Group type="103" groupAlignment="0" attributes="0">
-                  <Group type="102" attributes="0">
+                  <Group type="102" alignment="0" attributes="0">
                       <EmptySpace max="-2" attributes="0"/>
                       <Group type="103" groupAlignment="0" attributes="0">
                           <Component id="scriptButton2" alignment="0" min="-2" max="-2" attributes="0"/>
-                          <Group type="102" alignment="0" attributes="0">
-                              <Group type="103" groupAlignment="1" attributes="0">
-                                  <Component id="jSpinner1" min="-2" max="-2" attributes="0"/>
-                                  <Component id="motorPanel2" min="-2" max="-2" attributes="0"/>
-                                  <Component id="jSpinner2" alignment="1" min="-2" max="-2" attributes="0"/>
-                                  <Component id="jSpinner3" alignment="1" min="-2" max="-2" attributes="0"/>
+                          <Group type="103" alignment="0" groupAlignment="1" max="-2" attributes="0">
+                              <Component id="jSpinner1" min="-2" max="-2" attributes="0"/>
+                              <Component id="motorPanel2" min="-2" max="-2" attributes="0"/>
+                              <Component id="jSpinner2" alignment="1" min="-2" max="-2" attributes="0"/>
+                              <Group type="102" alignment="1" attributes="0">
+                                  <Group type="103" groupAlignment="1" attributes="0">
+                                      <Component id="buttonExecShellCmd" min="-2" max="-2" attributes="0"/>
+                                      <Group type="103" alignment="1" groupAlignment="0" attributes="0">
+                                          <Component id="jRadioButton2" min="-2" max="-2" attributes="0"/>
+                                          <Component id="jRadioButton1" min="-2" max="-2" attributes="0"/>
+                                      </Group>
+                                  </Group>
+                                  <EmptySpace max="-2" attributes="0"/>
+                                  <Component id="jButton2" min="-2" max="-2" attributes="0"/>
+                                  <EmptySpace max="32767" attributes="0"/>
+                                  <Component id="jSpinner3" min="-2" max="-2" attributes="0"/>
                               </Group>
-                              <EmptySpace max="-2" attributes="0"/>
-                              <Component id="scriptButton1" min="-2" max="-2" attributes="0"/>
                           </Group>
                       </Group>
                   </Group>
                   <Group type="102" alignment="0" attributes="0">
-                      <EmptySpace min="-2" pref="36" max="-2" attributes="0"/>
+                      <EmptySpace min="-2" pref="86" max="-2" attributes="0"/>
                       <Group type="103" groupAlignment="0" attributes="0">
-                          <Component id="jRadioButton2" min="-2" max="-2" attributes="0"/>
-                          <Component id="jRadioButton1" min="-2" max="-2" attributes="0"/>
+                          <Group type="102" alignment="0" attributes="0">
+                              <Component id="panelSetp" min="-2" pref="95" max="-2" attributes="0"/>
+                              <EmptySpace max="-2" attributes="0"/>
+                              <Component id="panelRbck" min="-2" pref="82" max="-2" attributes="0"/>
+                          </Group>
+                          <Component id="scriptButton1" min="-2" max="-2" attributes="0"/>
                       </Group>
                   </Group>
               </Group>
-              <EmptySpace pref="168" max="32767" attributes="0"/>
-          </Group>
-          <Group type="102" alignment="1" attributes="0">
-              <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
+              <EmptySpace type="unrelated" max="-2" attributes="0"/>
               <Group type="103" groupAlignment="0" attributes="0">
-                  <Component id="jButton2" min="-2" max="-2" attributes="0"/>
-                  <Component id="buttonExecShellCmd" min="-2" max="-2" attributes="0"/>
+                  <Component id="line" min="-2" max="-2" attributes="0"/>
+                  <Group type="102" attributes="0">
+                      <EmptySpace min="6" pref="6" max="-2" attributes="0"/>
+                      <Component id="time" min="-2" max="-2" attributes="0"/>
+                  </Group>
               </Group>
-              <EmptySpace min="-2" pref="225" max="-2" attributes="0"/>
+              <EmptySpace max="32767" attributes="0"/>
           </Group>
       </Group>
     </DimensionLayout>
@@ -62,10 +74,7 @@
       <Group type="103" groupAlignment="0" attributes="0">
           <Group type="102" alignment="0" attributes="0">
               <EmptySpace max="-2" attributes="0"/>
-              <Group type="103" groupAlignment="0" attributes="0">
-                  <Component id="scriptButton1" min="-2" max="-2" attributes="0"/>
-                  <Component id="motorPanel2" min="-2" max="-2" attributes="0"/>
-              </Group>
+              <Component id="motorPanel2" min="-2" max="-2" attributes="0"/>
               <EmptySpace type="separate" max="-2" attributes="0"/>
               <Group type="103" groupAlignment="0" attributes="0">
                   <Component id="scriptButton2" min="-2" max="-2" attributes="0"/>
@@ -73,17 +82,37 @@
               </Group>
               <EmptySpace max="-2" attributes="0"/>
               <Component id="jSpinner2" min="-2" max="-2" attributes="0"/>
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="jSpinner3" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <Group type="102" alignment="0" attributes="0">
+                      <EmptySpace min="-2" pref="21" max="-2" attributes="0"/>
+                      <Component id="jRadioButton1" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="jRadioButton2" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace type="separate" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="3" attributes="0">
+                          <Component id="buttonExecShellCmd" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="jButton2" alignment="3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                  </Group>
+              </Group>
+              <EmptySpace max="32767" attributes="0"/>
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Component id="panelSetp" linkSize="1" alignment="1" min="-2" max="-2" attributes="0"/>
+                  <Component id="panelRbck" linkSize="1" alignment="1" min="-2" max="-2" attributes="0"/>
+              </Group>
+              <EmptySpace min="-2" pref="44" max="-2" attributes="0"/>
+              <Component id="scriptButton1" min="-2" max="-2" attributes="0"/>
+              <EmptySpace min="-2" pref="25" max="-2" attributes="0"/>
+          </Group>
+          <Group type="102" alignment="0" attributes="0">
+              <Component id="line" min="-2" max="-2" attributes="0"/>
               <EmptySpace max="-2" attributes="0"/>
-              <Component id="jSpinner3" min="-2" max="-2" attributes="0"/>
-              <EmptySpace type="separate" max="-2" attributes="0"/>
-              <Component id="jRadioButton1" min="-2" max="-2" attributes="0"/>
-              <EmptySpace max="-2" attributes="0"/>
-              <Component id="jRadioButton2" min="-2" max="-2" attributes="0"/>
-              <EmptySpace type="separate" max="-2" attributes="0"/>
-              <Component id="buttonExecShellCmd" min="-2" max="-2" attributes="0"/>
-              <EmptySpace type="separate" max="-2" attributes="0"/>
-              <Component id="jButton2" min="-2" max="-2" attributes="0"/>
-              <EmptySpace pref="35" max="32767" attributes="0"/>
+              <Component id="time" min="-2" max="-2" attributes="0"/>
+              <EmptySpace min="0" pref="12" max="32767" attributes="0"/>
           </Group>
       </Group>
     </DimensionLayout>
@@ -166,5 +195,19 @@
         <Property name="text" type="java.lang.String" value="Exec Sync"/>
       </Properties>
     </Component>
+    <Component class="ch.psi.pshell.plot.LinePlotJFree" name="line">
+    </Component>
+    <Component class="ch.psi.pshell.plot.TimePlotJFree" name="time">
+    </Component>
+    <Component class="ch.psi.pshell.swing.RegisterPanel" name="panelSetp">
+      <Properties>
+        <Property name="name" type="java.lang.String" value="TESTIOC:TESTCALCOUT:Input" noResource="true"/>
+      </Properties>
+    </Component>
+    <Component class="ch.psi.pshell.swing.DeviceValuePanel" name="panelRbck">
+      <Properties>
+        <Property name="name" type="java.lang.String" value="TESTIOC:TESTCALCOUT:Input" noResource="true"/>
+      </Properties>
+    </Component>
   </SubComponents>
 </Form>

plugins/PanelPlugin.java

@@ -3,9 +3,14 @@
  */
 
 import ch.psi.pshell.core.Context;
+import ch.psi.pshell.epics.ChannelDouble;
+import ch.psi.pshell.epics.GenericChannel;
+import ch.psi.pshell.plot.Plot;
+import ch.psi.pshell.swing.DevicePanel;
 import ch.psi.pshell.ui.Panel;
 import ch.psi.utils.State;
 import java.awt.Component;
+import java.io.IOException;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import javax.swing.JButton;
@@ -18,13 +23,29 @@ public class PanelPlugin extends Panel {
     public PanelPlugin() {
         initComponents();
         this.setPersistedComponents(new Component[]{jRadioButton1, jRadioButton2});
+        line.getAxis(Plot.AxisId.Y).setLabel("LinePlot");
+        time.getAxis(Plot.AxisId.Y).setLabel("TimePlot");
+        time.setTitle("Test");
+        
     }
 
     //Overridables
+
     @Override
     public void onInitialize(int runCount) {
-
+        DevicePanel[] panels = new DevicePanel[]{panelSetp, panelRbck};
+        for (DevicePanel p : panels){
+            GenericChannel channel = new GenericChannel(p.getName(), p.getName(), 3);
+            channel.setMonitored(true);
+            try {
+                channel.initialize();
+                p.setDevice(channel);
+            } catch (Exception ex) {
+                Logger.getLogger(PanelPlugin.class.getName()).log(Level.SEVERE, null, ex);
+            }    
+        }
     }
+    
 
     @Override
     public void onStateChange(State state, State former) {
@@ -56,6 +77,10 @@ public class PanelPlugin extends Panel {
         jRadioButton2 = new javax.swing.JRadioButton();
         buttonExecShellCmd = new javax.swing.JButton();
         jButton2 = new javax.swing.JButton();
+        line = new ch.psi.pshell.plot.LinePlotJFree();
+        time = new ch.psi.pshell.plot.TimePlotJFree();
+        panelSetp = new ch.psi.pshell.swing.RegisterPanel();
+        panelRbck = new ch.psi.pshell.swing.DeviceValuePanel();
 
         motorPanel2.setDeviceName("m1");
 
@@ -90,6 +115,10 @@ public class PanelPlugin extends Panel {
 
         jButton2.setText("Exec Sync");
 
+        panelSetp.setName("TESTIOC:TESTCALCOUT:Input"); // NOI18N
+
+        panelRbck.setName("TESTIOC:TESTCALCOUT:Input"); // NOI18N
+
         javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
         this.setLayout(layout);
         layout.setHorizontalGroup(
@@ -100,52 +129,76 @@ public class PanelPlugin extends Panel {
                         .addContainerGap()
                         .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                             .addComponent(scriptButton2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                            .addGroup(layout.createSequentialGroup()
-                                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
-                                    .addComponent(jSpinner1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                    .addComponent(motorPanel2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                    .addComponent(jSpinner2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                    .addComponent(jSpinner3, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
-                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                .addComponent(scriptButton1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))))
+                            .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
+                                .addComponent(jSpinner1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                .addComponent(motorPanel2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                .addComponent(jSpinner2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                .addGroup(layout.createSequentialGroup()
+                                    .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
+                                        .addComponent(buttonExecShellCmd)
+                                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                                            .addComponent(jRadioButton2)
+                                            .addComponent(jRadioButton1)))
+                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                                    .addComponent(jButton2)
+                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                                    .addComponent(jSpinner3, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))))
                     .addGroup(layout.createSequentialGroup()
-                        .addGap(36, 36, 36)
+                        .addGap(86, 86, 86)
                         .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                            .addComponent(jRadioButton2)
-                            .addComponent(jRadioButton1))))
-                .addContainerGap(168, Short.MAX_VALUE))
-            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
-                .addGap(0, 0, Short.MAX_VALUE)
+                            .addGroup(layout.createSequentialGroup()
+                                .addComponent(panelSetp, javax.swing.GroupLayout.PREFERRED_SIZE, 95, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                                .addComponent(panelRbck, javax.swing.GroupLayout.PREFERRED_SIZE, 82, javax.swing.GroupLayout.PREFERRED_SIZE))
+                            .addComponent(scriptButton1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                    .addComponent(jButton2)
-                    .addComponent(buttonExecShellCmd))
-                .addGap(225, 225, 225))
+                    .addComponent(line, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                    .addGroup(layout.createSequentialGroup()
+                        .addGap(6, 6, 6)
+                        .addComponent(time, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
+                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
         );
         layout.setVerticalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
             .addGroup(layout.createSequentialGroup()
                 .addContainerGap()
-                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                    .addComponent(scriptButton1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                    .addComponent(motorPanel2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addComponent(motorPanel2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                 .addGap(18, 18, 18)
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                     .addComponent(scriptButton2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                     .addComponent(jSpinner1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                 .addComponent(jSpinner2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addGroup(layout.createSequentialGroup()
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(jSpinner3, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                    .addGroup(layout.createSequentialGroup()
+                        .addGap(21, 21, 21)
+                        .addComponent(jRadioButton1)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(jRadioButton2)
+                        .addGap(18, 18, 18)
+                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                            .addComponent(buttonExecShellCmd)
+                            .addComponent(jButton2))))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(panelSetp, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                    .addComponent(panelRbck, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addGap(44, 44, 44)
+                .addComponent(scriptButton1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addGap(25, 25, 25))
+            .addGroup(layout.createSequentialGroup()
+                .addComponent(line, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                .addComponent(jSpinner3, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                .addGap(18, 18, 18)
-                .addComponent(jRadioButton1)
-                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                .addComponent(jRadioButton2)
-                .addGap(18, 18, 18)
-                .addComponent(buttonExecShellCmd)
-                .addGap(18, 18, 18)
-                .addComponent(jButton2)
-                .addContainerGap(35, Short.MAX_VALUE))
+                .addComponent(time, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addGap(0, 12, Short.MAX_VALUE))
         );
+
+        layout.linkSize(javax.swing.SwingConstants.VERTICAL, new java.awt.Component[] {panelRbck, panelSetp});
+
     }// </editor-fold>//GEN-END:initComponents
 
     private void buttonExecShellCmdActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonExecShellCmdActionPerformed
@@ -178,8 +231,12 @@ public class PanelPlugin extends Panel {
     private javax.swing.JSpinner jSpinner1;
     private javax.swing.JSpinner jSpinner2;
     private javax.swing.JSpinner jSpinner3;
+    private ch.psi.pshell.plot.LinePlotJFree line;
     private ch.psi.pshell.swing.MotorPanel motorPanel2;
+    private ch.psi.pshell.swing.DeviceValuePanel panelRbck;
+    private ch.psi.pshell.swing.RegisterPanel panelSetp;
     private ch.psi.pshell.swing.ScriptButton scriptButton1;
     private ch.psi.pshell.swing.ScriptButton scriptButton2;
+    private ch.psi.pshell.plot.TimePlotJFree time;
     // End of variables declaration//GEN-END:variables
 }

plugins/README

@@ -0,0 +1,5 @@
+This plugin for the analysis of PEEM images requires the following additional
+libraries:
+JTransform, http://sites.google.com/site/piotrwendykier/software/jtransforms
+Michael Thomas Flanagan's Java Scientific Library, http://www.ee.ucl.ac.uk/~mflanaga/java/
+JMatIO, http://www.mathworks.com/matlabcentral/fileexchange/10759

plugins/Regine.form

@@ -297,6 +297,9 @@
         <Component class="javax.swing.JTextField" name="textExposures">
         </Component>
         <Component class="javax.swing.JCheckBox" name="checkZigZag">
+          <Properties>
+            <Property name="selected" type="boolean" value="true"/>
+          </Properties>
         </Component>
         <Component class="javax.swing.JLabel" name="jLabel12">
           <Properties>

plugins/Regine.java

@@ -212,6 +212,8 @@ public class Regine extends ScriptProcessor {
         jLabel11.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
         jLabel11.setText("Exposures(s):");
 
+        checkZigZag.setSelected(true);
+
         jLabel12.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
         jLabel12.setText("ZigZag:");
 

plugins/SIStem.form

@@ -0,0 +1,395 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<Form version="1.6" maxVersion="1.9" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
+  <AuxValues>
+    <AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
+    <AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="1"/>
+    <AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
+  </AuxValues>
+
+  <Layout>
+    <DimensionLayout dim="0">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Component id="jPanel2" alignment="1" max="32767" attributes="0"/>
+          <Group type="102" alignment="0" attributes="0">
+              <EmptySpace max="-2" attributes="0"/>
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="0" attributes="0">
+                      <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
+                      <Component id="buttonAddToQueue" linkSize="1" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace type="unrelated" max="-2" attributes="0"/>
+                      <Component id="buttonStart" linkSize="1" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace type="unrelated" max="-2" attributes="0"/>
+                      <Component id="buttonAbort" linkSize="1" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace pref="137" max="32767" attributes="0"/>
+                  </Group>
+                  <Group type="102" alignment="0" attributes="0">
+                      <Component id="buttonScienta" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="32767" attributes="0"/>
+                      <Component id="jLabel2" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="textFileId" min="-2" pref="67" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="buttonResetId" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+          </Group>
+      </Group>
+    </DimensionLayout>
+    <DimensionLayout dim="1">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Group type="102" alignment="1" attributes="0">
+              <Component id="jPanel2" max="32767" attributes="0"/>
+              <EmptySpace type="separate" max="-2" attributes="0"/>
+              <Group type="103" groupAlignment="3" attributes="0">
+                  <Component id="buttonScienta" alignment="3" min="-2" max="-2" attributes="0"/>
+                  <Component id="buttonResetId" alignment="3" min="-2" max="-2" attributes="0"/>
+                  <Component id="jLabel2" alignment="3" min="-2" max="-2" attributes="0"/>
+                  <Component id="textFileId" alignment="3" min="-2" max="-2" attributes="0"/>
+              </Group>
+              <EmptySpace type="separate" max="-2" attributes="0"/>
+              <Group type="103" groupAlignment="3" attributes="0">
+                  <Component id="buttonStart" alignment="3" min="-2" max="-2" attributes="0"/>
+                  <Component id="buttonAbort" alignment="3" min="-2" max="-2" attributes="0"/>
+                  <Component id="buttonAddToQueue" alignment="3" min="-2" max="-2" attributes="0"/>
+              </Group>
+              <EmptySpace max="-2" attributes="0"/>
+          </Group>
+      </Group>
+    </DimensionLayout>
+  </Layout>
+  <SubComponents>
+    <Component class="javax.swing.JButton" name="buttonScienta">
+      <Properties>
+        <Property name="text" type="java.lang.String" value="Scienta Panel"/>
+      </Properties>
+      <Events>
+        <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonScientaActionPerformed"/>
+      </Events>
+    </Component>
+    <Component class="javax.swing.JLabel" name="jLabel2">
+      <Properties>
+        <Property name="text" type="java.lang.String" value="File ID:"/>
+      </Properties>
+    </Component>
+    <Component class="javax.swing.JTextField" name="textFileId">
+      <Properties>
+        <Property name="editable" type="boolean" value="false"/>
+        <Property name="horizontalAlignment" type="int" value="0"/>
+      </Properties>
+    </Component>
+    <Component class="javax.swing.JButton" name="buttonResetId">
+      <Properties>
+        <Property name="text" type="java.lang.String" value="Reset"/>
+      </Properties>
+      <Events>
+        <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonResetIdActionPerformed"/>
+      </Events>
+    </Component>
+    <Component class="javax.swing.JButton" name="buttonStart">
+      <Properties>
+        <Property name="text" type="java.lang.String" value="Start"/>
+      </Properties>
+      <Events>
+        <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonStartActionPerformed"/>
+      </Events>
+    </Component>
+    <Component class="javax.swing.JButton" name="buttonAbort">
+      <Properties>
+        <Property name="text" type="java.lang.String" value="Abort"/>
+      </Properties>
+      <Events>
+        <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonAbortActionPerformed"/>
+      </Events>
+    </Component>
+    <Container class="javax.swing.JPanel" name="jPanel2">
+      <Properties>
+        <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+          <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+            <TitledBorder title="Parameters"/>
+          </Border>
+        </Property>
+      </Properties>
+
+      <Layout>
+        <DimensionLayout dim="0">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" attributes="0">
+                  <Group type="103" groupAlignment="0" attributes="0">
+                      <Group type="102" alignment="0" attributes="0">
+                          <EmptySpace max="-2" attributes="0"/>
+                          <Component id="jPanel1" max="32767" attributes="0"/>
+                      </Group>
+                      <Group type="102" alignment="0" attributes="0">
+                          <EmptySpace min="-2" pref="17" max="-2" attributes="0"/>
+                          <Group type="103" groupAlignment="0" attributes="0">
+                              <Group type="102" alignment="0" attributes="0">
+                                  <EmptySpace min="0" pref="98" max="32767" attributes="0"/>
+                                  <Component id="checkZigzag" min="-2" max="-2" attributes="0"/>
+                                  <EmptySpace type="separate" max="-2" attributes="0"/>
+                                  <Component id="jLabel4" min="-2" max="-2" attributes="0"/>
+                                  <EmptySpace max="-2" attributes="0"/>
+                                  <Component id="spinnerLatency" linkSize="3" min="-2" max="-2" attributes="0"/>
+                                  <EmptySpace type="separate" max="-2" attributes="0"/>
+                                  <Component id="jLabel1" min="-2" max="-2" attributes="0"/>
+                                  <EmptySpace max="-2" attributes="0"/>
+                                  <Component id="spinnerPasses" linkSize="3" min="-2" max="-2" attributes="0"/>
+                              </Group>
+                              <Group type="102" attributes="0">
+                                  <Component id="jLabel3" min="-2" max="-2" attributes="0"/>
+                                  <EmptySpace min="-2" max="-2" attributes="0"/>
+                                  <Component id="textFile" max="32767" attributes="0"/>
+                                  <EmptySpace min="-2" max="-2" attributes="0"/>
+                                  <Component id="buttonOpen" linkSize="2" min="-2" max="-2" attributes="0"/>
+                                  <EmptySpace min="-2" max="-2" attributes="0"/>
+                                  <Component id="buttonSave" linkSize="2" min="-2" max="-2" attributes="0"/>
+                                  <EmptySpace max="-2" attributes="0"/>
+                                  <Component id="buttonClear" linkSize="2" min="-2" max="-2" attributes="0"/>
+                              </Group>
+                          </Group>
+                      </Group>
+                  </Group>
+                  <EmptySpace max="-2" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
+        <DimensionLayout dim="1">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" alignment="0" attributes="0">
+                  <EmptySpace min="-2" max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="3" attributes="0">
+                      <Component id="buttonOpen" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="buttonSave" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel3" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="textFile" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="buttonClear" alignment="3" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="0" attributes="0">
+                      <Group type="103" alignment="0" groupAlignment="3" attributes="0">
+                          <Component id="jLabel4" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="spinnerLatency" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="checkZigzag" alignment="3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <Group type="103" groupAlignment="3" attributes="0">
+                          <Component id="jLabel1" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="spinnerPasses" alignment="3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                  </Group>
+                  <EmptySpace min="-2" pref="2" max="-2" attributes="0"/>
+                  <Component id="jPanel1" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace pref="56" max="32767" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
+      </Layout>
+      <SubComponents>
+        <Component class="javax.swing.JButton" name="buttonOpen">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="Open"/>
+          </Properties>
+          <Events>
+            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonOpenActionPerformed"/>
+          </Events>
+        </Component>
+        <Component class="javax.swing.JButton" name="buttonSave">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="Save"/>
+          </Properties>
+          <Events>
+            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonSaveActionPerformed"/>
+          </Events>
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel3">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="File:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JTextField" name="textFile">
+          <Properties>
+            <Property name="disabledTextColor" type="java.awt.Color" editor="org.netbeans.beaninfo.editors.ColorEditor">
+              <Color blue="0" green="0" id="TextField.foreground" palette="3" red="0" type="palette"/>
+            </Property>
+            <Property name="enabled" type="boolean" value="false"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JButton" name="buttonClear">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="Clear"/>
+          </Properties>
+          <Events>
+            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonClearActionPerformed"/>
+          </Events>
+        </Component>
+        <Container class="javax.swing.JPanel" name="jPanel1">
+          <Properties>
+            <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+              <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+                <TitledBorder title="Positioners"/>
+              </Border>
+            </Property>
+          </Properties>
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="0" attributes="0">
+                      <EmptySpace min="-2" max="-2" attributes="0"/>
+                      <Component id="jScrollPane1" pref="0" max="32767" attributes="0"/>
+                      <EmptySpace min="-2" max="-2" attributes="0"/>
+                      <Component id="jScrollPane2" pref="0" max="32767" attributes="0"/>
+                      <EmptySpace min="-2" max="-2" attributes="0"/>
+                      <Component id="jScrollPane3" pref="0" max="32767" attributes="0"/>
+                      <EmptySpace min="-2" max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+            <DimensionLayout dim="1">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="jScrollPane1" pref="0" max="32767" attributes="0"/>
+                          <Component id="jScrollPane2" pref="183" max="32767" attributes="0"/>
+                          <Component id="jScrollPane3" pref="183" max="32767" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="-2" pref="12" max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+          </Layout>
+          <SubComponents>
+            <Container class="javax.swing.JScrollPane" name="jScrollPane1">
+              <Properties>
+                <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+                  <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+                    <TitledBorder title="Inactive"/>
+                  </Border>
+                </Property>
+              </Properties>
+              <AuxValues>
+                <AuxValue name="autoScrollPane" type="java.lang.Boolean" value="true"/>
+              </AuxValues>
+
+              <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+              <SubComponents>
+                <Component class="javax.swing.JTable" name="tableInactive">
+                  <Properties>
+                    <Property name="model" type="javax.swing.table.TableModel" editor="org.netbeans.modules.form.editors2.TableModelEditor">
+                      <Table columnCount="1" rowCount="0">
+                        <Column editable="false" title="Name" type="java.lang.String"/>
+                      </Table>
+                    </Property>
+                    <Property name="selectionMode" type="int" value="0"/>
+                  </Properties>
+                </Component>
+              </SubComponents>
+            </Container>
+            <Container class="javax.swing.JScrollPane" name="jScrollPane2">
+              <Properties>
+                <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+                  <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+                    <TitledBorder title="Fixed"/>
+                  </Border>
+                </Property>
+              </Properties>
+              <AuxValues>
+                <AuxValue name="autoScrollPane" type="java.lang.Boolean" value="true"/>
+              </AuxValues>
+
+              <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+              <SubComponents>
+                <Component class="javax.swing.JTable" name="tableFixed">
+                  <Properties>
+                    <Property name="model" type="javax.swing.table.TableModel" editor="org.netbeans.modules.form.editors2.TableModelEditor">
+                      <Table columnCount="3" rowCount="0">
+                        <Column editable="false" title="Name" type="java.lang.String"/>
+                        <Column editable="true" title="Value" type="java.lang.Double"/>
+                        <Column editable="false" title="Units" type="java.lang.String"/>
+                      </Table>
+                    </Property>
+                    <Property name="selectionMode" type="int" value="0"/>
+                  </Properties>
+                </Component>
+              </SubComponents>
+            </Container>
+            <Container class="javax.swing.JScrollPane" name="jScrollPane3">
+              <Properties>
+                <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+                  <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+                    <TitledBorder title="Scanned"/>
+                  </Border>
+                </Property>
+              </Properties>
+              <AuxValues>
+                <AuxValue name="autoScrollPane" type="java.lang.Boolean" value="true"/>
+              </AuxValues>
+
+              <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+              <SubComponents>
+                <Component class="javax.swing.JTable" name="tableScanned">
+                  <Properties>
+                    <Property name="model" type="javax.swing.table.TableModel" editor="org.netbeans.modules.form.editors2.TableModelEditor">
+                      <Table columnCount="6" rowCount="0">
+                        <Column editable="false" title="Name" type="java.lang.String"/>
+                        <Column editable="true" title="Start" type="java.lang.Double"/>
+                        <Column editable="true" title="Stop" type="java.lang.Double"/>
+                        <Column editable="true" title="Points" type="java.lang.Integer"/>
+                        <Column editable="false" title="Step" type="java.lang.Double"/>
+                        <Column editable="false" title="Units" type="java.lang.String"/>
+                      </Table>
+                    </Property>
+                    <Property name="selectionMode" type="int" value="0"/>
+                  </Properties>
+                </Component>
+              </SubComponents>
+            </Container>
+          </SubComponents>
+        </Container>
+        <Component class="javax.swing.JLabel" name="jLabel1">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="Passes:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JSpinner" name="spinnerPasses">
+          <Properties>
+            <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+              <SpinnerModel initial="1" maximum="1000" minimum="1" numberType="java.lang.Integer" stepSize="1" type="number"/>
+            </Property>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JCheckBox" name="checkZigzag">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="Zigzag"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel4">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="Settling Time:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JSpinner" name="spinnerLatency">
+          <Properties>
+            <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+              <SpinnerModel initial="0.0" maximum="1000.0" minimum="0.0" numberType="java.lang.Double" stepSize="1.0" type="number"/>
+            </Property>
+          </Properties>
+        </Component>
+      </SubComponents>
+    </Container>
+    <Component class="javax.swing.JButton" name="buttonAddToQueue">
+      <Properties>
+        <Property name="text" type="java.lang.String" value="Add to Queue"/>
+      </Properties>
+      <Events>
+        <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonAddToQueueActionPerformed"/>
+      </Events>
+    </Component>
+  </SubComponents>
+</Form>

plugins/SIStem.java

@@ -0,0 +1,813 @@
+import ch.psi.pshell.core.JsonSerializer;
+import ch.psi.pshell.device.Positioner;
+import ch.psi.pshell.ui.Panel;
+import ch.psi.pshell.ui.PanelProcessor;
+import ch.psi.pshell.ui.QueueProcessor;
+import ch.psi.utils.Arr; 
+import ch.psi.utils.IO;
+import ch.psi.utils.State;
+import ch.psi.utils.swing.SwingUtils;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import javax.swing.DropMode;
+import javax.swing.JComponent;
+import javax.swing.JFileChooser;
+import javax.swing.JTable;
+import javax.swing.TransferHandler;
+import javax.swing.filechooser.FileNameExtensionFilter;
+import javax.swing.table.DefaultTableModel;
+
+/**
+ *
+ */
+public class SIStem extends PanelProcessor {
+    File currentFile;
+    final DefaultTableModel modelInactive;
+    final DefaultTableModel modelFixed;
+    final DefaultTableModel modelScanned;
+    
+    
+    public static final String FILE_EXTENSION = "json";
+    
+    public SIStem() {
+        initComponents();
+        modelInactive = (DefaultTableModel) tableInactive.getModel();
+        modelFixed = (DefaultTableModel) tableFixed.getModel();
+        modelScanned = (DefaultTableModel) tableScanned.getModel();
+        clear();
+        Standard st = new Standard(); st.run();
+
+        
+        abstract class PositinerTransferHandler extends TransferHandler{
+            @Override
+            public int getSourceActions(JComponent c) {
+                return DnDConstants.ACTION_COPY_OR_MOVE;
+            }
+            @Override
+            public Transferable createTransferable(JComponent comp) {
+                try{
+                    JTable table = (JTable) comp;
+                    return new StringSelection((String) table.getModel().getValueAt(table.getSelectedRow(),0));
+                } catch(Exception ex){
+                    return null;
+                }
+            }
+            @Override
+            public boolean canImport(TransferHandler.TransferSupport support) {
+                return support.isDataFlavorSupported(DataFlavor.stringFlavor);
+            }
+            @Override
+            public boolean importData(TransferHandler.TransferSupport support) {
+                if (support.isDrop() && canImport(support)) {
+                    try {
+                        JTable.DropLocation dl = (JTable.DropLocation)support.getDropLocation();
+                        String name = (String) support.getTransferable().getTransferData(DataFlavor.stringFlavor);         
+                        Positioner pos = getContext().getDevicePool().getByName(name, Positioner.class);               
+                        DefaultTableModel model = ((DefaultTableModel)((JTable)support.getComponent()).getModel());
+                        addPositioner(pos, model, dl.getRow(), getRowData(pos));
+                    } catch (Exception ex) {
+                        return false;
+                    }                
+                }
+                return true;
+            }      
+            abstract Object[] getRowData(Positioner pos);
+        };
+        
+        tableInactive.setDragEnabled(true);              
+        tableInactive.setDropMode(DropMode.INSERT_ROWS);
+        tableInactive.setFillsViewportHeight(true);        
+        tableInactive.setTransferHandler(new PositinerTransferHandler() {
+            @Override
+            Object[] getRowData(Positioner pos) {
+                return new Object[]{pos.getName()};
+            }
+        });
+        
+        tableFixed.setDragEnabled(true);
+        tableFixed.setDropMode(DropMode.INSERT_ROWS);
+        tableFixed.setFillsViewportHeight(true);
+        tableFixed.setTransferHandler(new PositinerTransferHandler() {
+            @Override
+            Object[] getRowData(Positioner pos) {
+                return new Object[]{pos.getName(), Double.NaN, pos.getUnit()};     
+            }
+        });
+        
+        tableScanned.setDragEnabled(true);
+        tableScanned.setDropMode(DropMode.INSERT_ROWS);
+        tableScanned.setFillsViewportHeight(true);
+        tableScanned.setTransferHandler(new PositinerTransferHandler() {
+            @Override
+            Object[] getRowData(Positioner pos) {
+                return new Object[]{pos.getName(), Double.NaN, Double.NaN, 0, Double.NaN, pos.getUnit()};     
+            }
+        });        
+    }
+
+    void addPositioner(Positioner pos, DefaultTableModel model, int row, Object[] data){
+        if (row<0){
+            row = model.getRowCount();
+        }
+        model.insertRow(row, data);                                                
+        removePositioner(pos, modelInactive, (model==modelInactive) ? row : -1);                        
+        removePositioner(pos, modelFixed, (model==modelFixed) ? row : -1);                      
+        removePositioner(pos, modelScanned, (model==modelScanned) ?row : -1);                      
+    }
+    
+    void removePositioner(Positioner pos, DefaultTableModel model, int except){
+        for (int i=0; i< model.getRowCount(); i++){
+            if ((except<0) || (i!=except)){
+                if (model.getValueAt(i, 0).equals(pos.getName())){
+                    model.removeRow(i);
+                    break;
+                }
+            }
+        }
+    }
+
+    //Overridable callbacks
+    @Override
+    public void onInitialize(int runCount) {        
+
+    }
+
+    
+    @Override
+    public void onStateChange(State state, State former) {
+        updateControls();
+    }
+
+    @Override
+    public void onExecutedFile(String fileName, Object result) {
+    }
+
+    
+    //Callback to perform update - in event thread
+    @Override
+    protected void doUpdate() {
+    }
+    
+    
+    @Override
+    public String getFileName(){
+        return (currentFile==null) ? null : currentFile.toString();
+    }  
+    
+    @Override
+    public  boolean isTabNameUpdated() {
+        return false;
+    }
+
+    @Override
+    public String getType() {
+        return "SIStem";
+    }    
+    
+    @Override
+    public boolean createMenuNew() {
+        return true;
+    }
+    
+    @Override
+    public boolean createFilePanel() {
+        return true;
+    }    
+    
+    @Override
+    public String getDescription() {
+        return "SIStem Scan definition file (*." + FILE_EXTENSION + ")";
+    }
+
+    @Override
+    public String[] getExtensions() {
+        return new String[]{FILE_EXTENSION};
+    }
+
+    @Override
+    public String getHomePath() {
+        return "{home}/scans";
+    }        
+    
+    @Override
+    public void saveAs(String fileName) throws IOException {    
+        currentFile = new File(fileName);
+        Map preActions = new HashMap();    
+        for (int i=0; i< modelFixed.getRowCount(); i++){
+            preActions.put(modelFixed.getValueAt(i, 0), modelFixed.getValueAt(i, 1));
+        }     
+        String[] positioners = new String[modelScanned.getRowCount()];
+        Double[] start = new Double[modelScanned.getRowCount()];
+        Double[] stop = new Double[modelScanned.getRowCount()];
+        Integer[] steps = new Integer[modelScanned.getRowCount()];
+        for (int i=0; i< modelScanned.getRowCount(); i++){
+            positioners[i] = (String) modelScanned.getValueAt(i, 0);
+            start[i] = (Double) modelScanned.getValueAt(i, 1);
+            stop[i] = (Double) modelScanned.getValueAt(i, 2);
+            steps[i] = (Integer) modelScanned.getValueAt(i, 3) -1;
+        }
+        
+        Map config = new HashMap();
+        config.put("PRE_ACTIONS", preActions);
+        config.put("POSITIONERS", positioners);
+        config.put("START", start);
+        config.put("STOP", stop);
+        config.put("STEPS", steps);
+        
+        //TODO:
+        config.put("SENSORS", Arr.toList(new String[]{"scienta.dataMatrix", "sin"}));
+        config.put("SETTLING_TIME", spinnerLatency.getValue() );
+        config.put("PASSES", spinnerPasses.getValue());
+        config.put("ZIGZAG", checkZigzag.isSelected());
+        config.put("COMPRESSION", true);
+        
+        String json = JsonSerializer.encode(config, true);
+        Files.write(currentFile.toPath(), json.getBytes());
+        updateControls();
+    }
+
+    @Override
+    public void open(String fileName) throws IOException {
+        clear();
+        if (fileName!=null){
+            Path path = Paths.get(fileName);
+            String json = new String(Files.readAllBytes(path));
+            currentFile = path.toFile();
+            Map config = (Map) JsonSerializer.decode(json, Map.class);
+            
+            Map<String, Double> preActions = (Map) config.get("PRE_ACTIONS");
+            
+            List<String> positioners = (List)config.get("POSITIONERS");
+            List<Double> start = (List)config.get("START");
+            List<Double> stop = (List)config.get("STOP");
+            List<Integer> steps = (List) config.get("STEPS");
+            
+            for (String name:preActions.keySet()){
+                Positioner pos = getContext().getDevicePool().getByName(name, Positioner.class);   
+                if (pos!=null){
+                    addPositioner(pos, modelFixed, -1, new Object[]{name, preActions.get(name), pos.getUnit()});
+                }
+            }
+            for (int i=0; i< positioners.size(); i++){
+                String name = positioners.get(i);                
+                Positioner pos = getContext().getDevicePool().getByName(name, Positioner.class);   
+                if (pos!=null){
+                    addPositioner(pos, modelScanned, -1, new Object[]{name, start.get(i), stop.get(i), steps.get(i), 0, pos.getUnit()});
+                }
+            }
+            spinnerLatency.setValue(config.get("SETTLING_TIME"));
+            spinnerPasses.setValue(config.get("PASSES"));
+            checkZigzag.setSelected((Boolean) config.get("ZIGZAG"));       
+        }
+        updateControls();
+    }
+    
+    public void clear(){
+        currentFile = null;           
+        modelInactive.setRowCount(0);
+        modelFixed.setRowCount(0);
+        modelScanned.setRowCount(0);    
+        Positioner[] positioners = getContext().getDevicePool().getAllDevicesOrderedByName(Positioner.class);
+        for (Positioner pos: positioners){
+            modelInactive.addRow(new Object[]{pos.getName()});
+        }
+        updateControls();
+    }
+    
+    @Override
+    public void execute() throws Exception {
+        checkValues();
+        
+        HashMap args = new HashMap();
+        if (currentFile == null) {
+            throw new Exception("TODO");
+        }
+        args.put("NAME", getScanName());
+        
+        this.runAsync("SIStem", args).handle((ret, ex) -> {
+            if (ex != null) {
+            }
+            try {
+            } catch (Exception e) {
+                Logger.getLogger(SIStem.class.getName()).log(Level.SEVERE, null, e);
+            }
+            return ret;
+        });
+        
+    }    
+
+    String getScanName() {
+        if (currentFile != null) {
+            return IO.getPrefix(currentFile);
+        }
+        return null;
+    }
+    
+    void updateControls() {
+        State state = getState();
+        try {
+            textFileId.setText(String.valueOf(getContext().getFileSequentialNumber()));
+        } catch (Exception ex) {
+            textFileId.setText("");
+        }
+        
+        String fileName = getFileName();
+        if (fileName == null){
+            textFile.setText("");
+        } else {
+            String home = getContext().getSetup().expandPath(getHomePath());
+            if (IO.isSubPath(fileName, home)) {
+                fileName = IO.getRelativePath(fileName, home);
+            }
+            textFile.setText(fileName);
+        }        
+        
+        buttonStart.setEnabled((state == State.Ready) && (currentFile != null));
+        buttonAddToQueue.setEnabled((state == State.Ready) && (currentFile != null));
+        buttonAbort.setEnabled(state.isProcessing());
+        buttonScienta.setEnabled(state.isInitialized());
+        
+    }      
+    
+    void checkValues(){                
+        for (int i=0; i< modelFixed.getRowCount(); i++){
+            if (Double.isNaN((Double)modelFixed.getValueAt(i, 1))){
+                throw new IllegalArgumentException("Invalid value for " + modelFixed.getValueAt(i, 0));
+            }
+        }
+        for (int i=0; i< modelScanned.getRowCount(); i++){
+            if (Double.isNaN((Double)modelScanned.getValueAt(i, 1))){
+                throw new IllegalArgumentException("Invalid start for " + modelFixed.getValueAt(i, 0));
+            }
+            if (Double.isNaN((Double)modelScanned.getValueAt(i, 2))){
+                throw new IllegalArgumentException("Invalid stop for " + modelFixed.getValueAt(i, 0));
+            }
+            if (((Integer)modelScanned.getValueAt(i, 3)) < 1){
+                throw new IllegalArgumentException("Invalid points for " + modelFixed.getValueAt(i, 0));
+            }
+        }
+    }
+    
+    @SuppressWarnings("unchecked")
+    // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
+    private void initComponents() {
+
+        buttonScienta = new javax.swing.JButton();
+        jLabel2 = new javax.swing.JLabel();
+        textFileId = new javax.swing.JTextField();
+        buttonResetId = new javax.swing.JButton();
+        buttonStart = new javax.swing.JButton();
+        buttonAbort = new javax.swing.JButton();
+        jPanel2 = new javax.swing.JPanel();
+        buttonOpen = new javax.swing.JButton();
+        buttonSave = new javax.swing.JButton();
+        jLabel3 = new javax.swing.JLabel();
+        textFile = new javax.swing.JTextField();
+        buttonClear = new javax.swing.JButton();
+        jPanel1 = new javax.swing.JPanel();
+        jScrollPane1 = new javax.swing.JScrollPane();
+        tableInactive = new javax.swing.JTable();
+        jScrollPane2 = new javax.swing.JScrollPane();
+        tableFixed = new javax.swing.JTable();
+        jScrollPane3 = new javax.swing.JScrollPane();
+        tableScanned = new javax.swing.JTable();
+        jLabel1 = new javax.swing.JLabel();
+        spinnerPasses = new javax.swing.JSpinner();
+        checkZigzag = new javax.swing.JCheckBox();
+        jLabel4 = new javax.swing.JLabel();
+        spinnerLatency = new javax.swing.JSpinner();
+        buttonAddToQueue = new javax.swing.JButton();
+
+        buttonScienta.setText("Scienta Panel");
+        buttonScienta.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                buttonScientaActionPerformed(evt);
+            }
+        });
+
+        jLabel2.setText("File ID:");
+
+        textFileId.setEditable(false);
+        textFileId.setHorizontalAlignment(javax.swing.JTextField.CENTER);
+
+        buttonResetId.setText("Reset");
+        buttonResetId.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                buttonResetIdActionPerformed(evt);
+            }
+        });
+
+        buttonStart.setText("Start");
+        buttonStart.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                buttonStartActionPerformed(evt);
+            }
+        });
+
+        buttonAbort.setText("Abort");
+        buttonAbort.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                buttonAbortActionPerformed(evt);
+            }
+        });
+
+        jPanel2.setBorder(javax.swing.BorderFactory.createTitledBorder("Parameters"));
+
+        buttonOpen.setText("Open");
+        buttonOpen.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                buttonOpenActionPerformed(evt);
+            }
+        });
+
+        buttonSave.setText("Save");
+        buttonSave.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                buttonSaveActionPerformed(evt);
+            }
+        });
+
+        jLabel3.setText("File:");
+
+        textFile.setDisabledTextColor(javax.swing.UIManager.getDefaults().getColor("TextField.foreground"));
+        textFile.setEnabled(false);
+
+        buttonClear.setText("Clear");
+        buttonClear.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                buttonClearActionPerformed(evt);
+            }
+        });
+
+        jPanel1.setBorder(javax.swing.BorderFactory.createTitledBorder("Positioners"));
+
+        jScrollPane1.setBorder(javax.swing.BorderFactory.createTitledBorder("Inactive"));
+
+        tableInactive.setModel(new javax.swing.table.DefaultTableModel(
+            new Object [][] {
+
+            },
+            new String [] {
+                "Name"
+            }
+        ) {
+            Class[] types = new Class [] {
+                java.lang.String.class
+            };
+            boolean[] canEdit = new boolean [] {
+                false
+            };
+
+            public Class getColumnClass(int columnIndex) {
+                return types [columnIndex];
+            }
+
+            public boolean isCellEditable(int rowIndex, int columnIndex) {
+                return canEdit [columnIndex];
+            }
+        });
+        tableInactive.setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
+        jScrollPane1.setViewportView(tableInactive);
+
+        jScrollPane2.setBorder(javax.swing.BorderFactory.createTitledBorder("Fixed"));
+
+        tableFixed.setModel(new javax.swing.table.DefaultTableModel(
+            new Object [][] {
+
+            },
+            new String [] {
+                "Name", "Value", "Units"
+            }
+        ) {
+            Class[] types = new Class [] {
+                java.lang.String.class, java.lang.Double.class, java.lang.String.class
+            };
+            boolean[] canEdit = new boolean [] {
+                false, true, false
+            };
+
+            public Class getColumnClass(int columnIndex) {
+                return types [columnIndex];
+            }
+
+            public boolean isCellEditable(int rowIndex, int columnIndex) {
+                return canEdit [columnIndex];
+            }
+        });
+        tableFixed.setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
+        jScrollPane2.setViewportView(tableFixed);
+
+        jScrollPane3.setBorder(javax.swing.BorderFactory.createTitledBorder("Scanned"));
+
+        tableScanned.setModel(new javax.swing.table.DefaultTableModel(
+            new Object [][] {
+
+            },
+            new String [] {
+                "Name", "Start", "Stop", "Points", "Step", "Units"
+            }
+        ) {
+            Class[] types = new Class [] {
+                java.lang.String.class, java.lang.Double.class, java.lang.Double.class, java.lang.Integer.class, java.lang.Double.class, java.lang.String.class
+            };
+            boolean[] canEdit = new boolean [] {
+                false, true, true, true, false, false
+            };
+
+            public Class getColumnClass(int columnIndex) {
+                return types [columnIndex];
+            }
+
+            public boolean isCellEditable(int rowIndex, int columnIndex) {
+                return canEdit [columnIndex];
+            }
+        });
+        tableScanned.setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
+        jScrollPane3.setViewportView(tableScanned);
+
+        javax.swing.GroupLayout jPanel1Layout = new javax.swing.GroupLayout(jPanel1);
+        jPanel1.setLayout(jPanel1Layout);
+        jPanel1Layout.setHorizontalGroup(
+            jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(jPanel1Layout.createSequentialGroup()
+                .addContainerGap()
+                .addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addComponent(jScrollPane2, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addComponent(jScrollPane3, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE)
+                .addContainerGap())
+        );
+        jPanel1Layout.setVerticalGroup(
+            jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(jPanel1Layout.createSequentialGroup()
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE)
+                    .addComponent(jScrollPane2, javax.swing.GroupLayout.DEFAULT_SIZE, 183, Short.MAX_VALUE)
+                    .addComponent(jScrollPane3, javax.swing.GroupLayout.DEFAULT_SIZE, 183, Short.MAX_VALUE))
+                .addGap(12, 12, 12))
+        );
+
+        jLabel1.setText("Passes:");
+
+        spinnerPasses.setModel(new javax.swing.SpinnerNumberModel(1, 1, 1000, 1));
+
+        checkZigzag.setText("Zigzag");
+
+        jLabel4.setText("Settling Time:");
+
+        spinnerLatency.setModel(new javax.swing.SpinnerNumberModel(0.0d, 0.0d, 1000.0d, 1.0d));
+
+        javax.swing.GroupLayout jPanel2Layout = new javax.swing.GroupLayout(jPanel2);
+        jPanel2.setLayout(jPanel2Layout);
+        jPanel2Layout.setHorizontalGroup(
+            jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(jPanel2Layout.createSequentialGroup()
+                .addGroup(jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addGroup(jPanel2Layout.createSequentialGroup()
+                        .addContainerGap()
+                        .addComponent(jPanel1, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+                    .addGroup(jPanel2Layout.createSequentialGroup()
+                        .addGap(17, 17, 17)
+                        .addGroup(jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                            .addGroup(jPanel2Layout.createSequentialGroup()
+                                .addGap(0, 98, Short.MAX_VALUE)
+                                .addComponent(checkZigzag)
+                                .addGap(18, 18, 18)
+                                .addComponent(jLabel4)
+                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                                .addComponent(spinnerLatency, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                .addGap(18, 18, 18)
+                                .addComponent(jLabel1)
+                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                                .addComponent(spinnerPasses, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                            .addGroup(jPanel2Layout.createSequentialGroup()
+                                .addComponent(jLabel3)
+                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                                .addComponent(textFile)
+                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                                .addComponent(buttonOpen)
+                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                                .addComponent(buttonSave)
+                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                                .addComponent(buttonClear)))))
+                .addContainerGap())
+        );
+
+        jPanel2Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {buttonClear, buttonOpen, buttonSave});
+
+        jPanel2Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {spinnerLatency, spinnerPasses});
+
+        jPanel2Layout.setVerticalGroup(
+            jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(jPanel2Layout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(buttonOpen)
+                    .addComponent(buttonSave)
+                    .addComponent(jLabel3)
+                    .addComponent(textFile, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                    .addComponent(buttonClear))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addGroup(jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                        .addComponent(jLabel4)
+                        .addComponent(spinnerLatency, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                        .addComponent(checkZigzag))
+                    .addGroup(jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                        .addComponent(jLabel1)
+                        .addComponent(spinnerPasses, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
+                .addGap(2, 2, 2)
+                .addComponent(jPanel1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addContainerGap(56, Short.MAX_VALUE))
+        );
+
+        buttonAddToQueue.setText("Add to Queue");
+        buttonAddToQueue.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                buttonAddToQueueActionPerformed(evt);
+            }
+        });
+
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
+        this.setLayout(layout);
+        layout.setHorizontalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addComponent(jPanel2, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+            .addGroup(layout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addGroup(layout.createSequentialGroup()
+                        .addGap(0, 0, Short.MAX_VALUE)
+                        .addComponent(buttonAddToQueue)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                        .addComponent(buttonStart)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                        .addComponent(buttonAbort)
+                        .addContainerGap(137, Short.MAX_VALUE))
+                    .addGroup(layout.createSequentialGroup()
+                        .addComponent(buttonScienta)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                        .addComponent(jLabel2)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(textFileId, javax.swing.GroupLayout.PREFERRED_SIZE, 67, javax.swing.GroupLayout.PREFERRED_SIZE)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(buttonResetId)
+                        .addContainerGap())))
+        );
+
+        layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {buttonAbort, buttonAddToQueue, buttonStart});
+
+        layout.setVerticalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
+                .addComponent(jPanel2, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addGap(18, 18, 18)
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(buttonScienta)
+                    .addComponent(buttonResetId)
+                    .addComponent(jLabel2)
+                    .addComponent(textFileId, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addGap(18, 18, 18)
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(buttonStart)
+                    .addComponent(buttonAbort)
+                    .addComponent(buttonAddToQueue))
+                .addContainerGap())
+        );
+    }// </editor-fold>//GEN-END:initComponents
+
+    private void buttonScientaActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonScientaActionPerformed
+        try {
+            this.showDevicePanel("scienta");
+        } catch (Exception ex) {
+            showException(ex);
+        }
+    }//GEN-LAST:event_buttonScientaActionPerformed
+
+    private void buttonResetIdActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonResetIdActionPerformed
+        try {
+            this.getContext().setFileSequentialNumber(0);
+           updateControls();
+        } catch (Exception ex) {
+            showException(ex);
+        }
+    }//GEN-LAST:event_buttonResetIdActionPerformed
+
+    private void buttonStartActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonStartActionPerformed
+        try {
+            execute();
+        } catch (Exception ex) {
+            showException(ex);
+        }
+    }//GEN-LAST:event_buttonStartActionPerformed
+
+    private void buttonAbortActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonAbortActionPerformed
+        try {
+            abort();
+        } catch (Exception ex) {
+            showException(ex);
+        }
+    }//GEN-LAST:event_buttonAbortActionPerformed
+
+    private void buttonOpenActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonOpenActionPerformed
+        try {
+            open();
+        } catch (Exception ex) {
+            showException(ex);
+        }
+    }//GEN-LAST:event_buttonOpenActionPerformed
+
+    private void buttonSaveActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonSaveActionPerformed
+        try {
+            JFileChooser chooser = new JFileChooser(getContext().getSetup().expandPath(getHomePath()));
+            FileNameExtensionFilter filter = new FileNameExtensionFilter(getDescription(), getExtensions());
+            chooser.setFileFilter(filter);
+            try {
+                if (currentFile != null) {
+                    chooser.setSelectedFile(currentFile);
+                } 
+            } catch (Exception ex) {
+                this.showException(ex);
+            }
+            int rVal = chooser.showSaveDialog(this);
+            if (rVal == JFileChooser.APPROVE_OPTION) {
+                String fileName = chooser.getSelectedFile().getAbsolutePath();
+                if (IO.getExtension(chooser.getSelectedFile().getAbsolutePath()).isEmpty()) {
+                    fileName += "." + FILE_EXTENSION;
+                }
+                saveAs(fileName);
+            }
+        } catch (Exception ex) {
+            showException(ex);
+        }
+    }//GEN-LAST:event_buttonSaveActionPerformed
+
+    private void buttonAddToQueueActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonAddToQueueActionPerformed
+        try {
+            QueueProcessor tq = null;
+            List<QueueProcessor> queues = getView().getQueues();
+            if (queues.size()==0){
+                tq = getView().openProcessor(QueueProcessor.class, null);
+            } else {
+                tq = queues.get(0);                
+            }
+            getView().getDocumentsTab().setSelectedComponent(tq);
+            tq.addNewFile(currentFile.getPath());
+            
+        } catch (Exception ex) {
+             showException(ex);
+        }
+    }//GEN-LAST:event_buttonAddToQueueActionPerformed
+
+    private void buttonClearActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonClearActionPerformed
+        try {
+            clear();
+        } catch (Exception ex) {
+             showException(ex);        
+        }
+    }//GEN-LAST:event_buttonClearActionPerformed
+
+
+
+    // Variables declaration - do not modify//GEN-BEGIN:variables
+    private javax.swing.JButton buttonAbort;
+    private javax.swing.JButton buttonAddToQueue;
+    private javax.swing.JButton buttonClear;
+    private javax.swing.JButton buttonOpen;
+    private javax.swing.JButton buttonResetId;
+    private javax.swing.JButton buttonSave;
+    private javax.swing.JButton buttonScienta;
+    private javax.swing.JButton buttonStart;
+    private javax.swing.JCheckBox checkZigzag;
+    private javax.swing.JLabel jLabel1;
+    private javax.swing.JLabel jLabel2;
+    private javax.swing.JLabel jLabel3;
+    private javax.swing.JLabel jLabel4;
+    private javax.swing.JPanel jPanel1;
+    private javax.swing.JPanel jPanel2;
+    private javax.swing.JScrollPane jScrollPane1;
+    private javax.swing.JScrollPane jScrollPane2;
+    private javax.swing.JScrollPane jScrollPane3;
+    private javax.swing.JSpinner spinnerLatency;
+    private javax.swing.JSpinner spinnerPasses;
+    private javax.swing.JTable tableFixed;
+    private javax.swing.JTable tableInactive;
+    private javax.swing.JTable tableScanned;
+    private javax.swing.JTextField textFile;
+    private javax.swing.JTextField textFileId;
+    // End of variables declaration//GEN-END:variables
+}

plugins/ScreenPanel.java

@@ -37,6 +37,7 @@ import javax.swing.JComboBox;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JTextField;
+import javax.swing.SwingUtilities;
 
 /**
  *
@@ -103,20 +104,30 @@ public class ScreenPanel extends Panel implements CamServerViewer.CamServerViewe
         if (App.hasArgument("instance_format")) {
             camServerViewer.setInstanceNameFormat(App.getArgumentValue("instance_format"));
         } 
+        camServerViewer.setShowFit(true);
+        camServerViewer.setShowProfile(true);
+        camServerViewer.setShowReticle(true);
     }
 
     @Override
     public void onStart() {
-        super.onStart();
+        super.onStart();        
         try {            
             camServerViewer.setCameraServerUrl(App.getArgumentValue(ARG_CAMERA_SERVER));
             camServerViewer.setPipelineServerUrl(App.getArgumentValue(ARG_PIPELINE_SERVER));
             camServerViewer.setStartupStream(App.getArgumentValue(ARG_CAMERA));        
-            camServerViewer.initialize(CamServerViewer.SourceSelecionMode.Cameras);            
+            SwingUtilities.invokeLater(()->{
+                try {            
+                    camServerViewer.initialize(CamServerViewer.SourceSelecionMode.Cameras);
+                } catch (Exception ex) {
+                    Logger.getLogger(ScreenPanel.class.getName()).log(Level.SEVERE, null, ex);
+                }
+                updateDialogTitle();
+            });
+            
         } catch (Exception ex) {
             logger.log(Level.SEVERE, null, ex);
-        }
-        updateDialogTitle();
+        }        
     }
 
     @Override
@@ -195,7 +206,7 @@ public class ScreenPanel extends Panel implements CamServerViewer.CamServerViewe
 
     @Override
     public void onOpeningStream(String name) throws Exception {
-        System.out.println("Initializing stream " + name);        
+        System.out.println("Initializing stream " + name);              
         if ((devicesInitTask != null) && (devicesInitTask.isAlive())) {
             devicesInitTask.interrupt();
         }
@@ -207,6 +218,7 @@ public class ScreenPanel extends Panel implements CamServerViewer.CamServerViewe
             filter.close();
             filter = null;
         }        
+        updateDialogTitle();
     }    
     
 
@@ -272,7 +284,7 @@ public class ScreenPanel extends Panel implements CamServerViewer.CamServerViewe
                 devicesInitTask.start();
             }
         }
-        
+        updateDialogTitle();
     }    
 
     public void onSavedSnapshot(String name, String instancee, String snapshotFile) throws Exception {

plugins/ScreenPanel1.form

@@ -0,0 +1,960 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<Form version="1.5" maxVersion="1.9" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
+  <NonVisualComponents>
+    <Component class="javax.swing.ButtonGroup" name="buttonGroup1">
+    </Component>
+    <Component class="javax.swing.ButtonGroup" name="buttonGroup2">
+    </Component>
+    <Component class="javax.swing.ButtonGroup" name="buttonGroup3">
+    </Component>
+    <Component class="javax.swing.ButtonGroup" name="buttonGroup4">
+    </Component>
+    <Component class="javax.swing.JProgressBar" name="jProgressBar1">
+    </Component>
+  </NonVisualComponents>
+  <Properties>
+    <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+      <Dimension value="[873, 600]"/>
+    </Property>
+  </Properties>
+  <AuxValues>
+    <AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
+    <AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="1"/>
+    <AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
+  </AuxValues>
+
+  <Layout>
+    <DimensionLayout dim="0">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Group type="102" alignment="1" attributes="0">
+              <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+              <Component id="jPanel4" min="-2" max="-2" attributes="0"/>
+              <EmptySpace max="-2" attributes="0"/>
+              <Component id="jPanel1" max="32767" attributes="0"/>
+          </Group>
+      </Group>
+    </DimensionLayout>
+    <DimensionLayout dim="1">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Group type="102" alignment="0" attributes="0">
+              <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Component id="jPanel1" max="32767" attributes="0"/>
+                  <Component id="jPanel4" max="32767" attributes="0"/>
+              </Group>
+          </Group>
+      </Group>
+    </DimensionLayout>
+  </Layout>
+  <SubComponents>
+    <Container class="javax.swing.JPanel" name="jPanel1">
+
+      <Layout>
+        <DimensionLayout dim="0">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" alignment="1" attributes="0">
+                  <Group type="103" groupAlignment="1" attributes="0">
+                      <Component id="renderer" max="32767" attributes="0"/>
+                      <Component id="jPanel7" alignment="1" max="32767" attributes="0"/>
+                      <Component id="jPanel6" alignment="1" max="32767" attributes="0"/>
+                  </Group>
+                  <EmptySpace max="-2" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
+        <DimensionLayout dim="1">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" attributes="0">
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Component id="jPanel6" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace type="unrelated" max="-2" attributes="0"/>
+                  <Component id="renderer" max="32767" attributes="0"/>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Component id="jPanel7" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace max="-2" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
+      </Layout>
+      <SubComponents>
+        <Container class="javax.swing.JPanel" name="jPanel7">
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                      <Component id="buttonPause" linkSize="5" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="buttonMarker" linkSize="5" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="buttonProfile" linkSize="5" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="buttonFit" linkSize="5" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="buttonReticle" linkSize="5" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace type="separate" max="32767" attributes="0"/>
+                      <Component id="buttonGrabBackground" linkSize="6" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="buttonSave" linkSize="6" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+            <DimensionLayout dim="1">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="3" attributes="0">
+                          <Component id="buttonPause" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonFit" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonMarker" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonSave" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonReticle" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonGrabBackground" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonProfile" alignment="3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+          </Layout>
+          <SubComponents>
+            <Component class="javax.swing.JToggleButton" name="buttonMarker">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Marker"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonMarkerActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JButton" name="buttonGrabBackground">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Grab Background"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonGrabBackgroundActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JToggleButton" name="buttonSave">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Save Snapshot"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonSaveActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JToggleButton" name="buttonFit">
+              <Properties>
+                <Property name="selected" type="boolean" value="true"/>
+                <Property name="text" type="java.lang.String" value="Fit"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonFitActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JToggleButton" name="buttonReticle">
+              <Properties>
+                <Property name="selected" type="boolean" value="true"/>
+                <Property name="text" type="java.lang.String" value="Reticle"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonReticleActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JToggleButton" name="buttonPause">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Pause"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonPauseActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JToggleButton" name="buttonProfile">
+              <Properties>
+                <Property name="selected" type="boolean" value="true"/>
+                <Property name="text" type="java.lang.String" value="Profile"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonProfileActionPerformed"/>
+              </Events>
+            </Component>
+          </SubComponents>
+        </Container>
+        <Container class="javax.swing.JPanel" name="jPanel6">
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                      <Component id="jLabel1" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace min="-2" max="-2" attributes="0"/>
+                      <Component id="comboCameras" max="32767" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="buttonArgs" linkSize="3" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="buttonConfig" linkSize="3" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="buttonStop" linkSize="3" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace type="separate" max="-2" attributes="0"/>
+                      <Component id="jLabel2" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="textState" min="-2" pref="100" max="-2" attributes="0"/>
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+            <DimensionLayout dim="1">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="3" attributes="0">
+                          <Component id="jLabel1" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="comboCameras" linkSize="2" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="jLabel2" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="textState" linkSize="2" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonArgs" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonConfig" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonStop" alignment="3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+          </Layout>
+          <SubComponents>
+            <Component class="javax.swing.JTextField" name="textState">
+              <Properties>
+                <Property name="editable" type="boolean" value="false"/>
+                <Property name="horizontalAlignment" type="int" value="0"/>
+                <Property name="disabledTextColor" type="java.awt.Color" editor="org.netbeans.beaninfo.editors.ColorEditor">
+                  <Color blue="0" green="0" red="0" type="rgb"/>
+                </Property>
+                <Property name="enabled" type="boolean" value="false"/>
+              </Properties>
+            </Component>
+            <Component class="javax.swing.JLabel" name="jLabel2">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="State:"/>
+              </Properties>
+            </Component>
+            <Component class="javax.swing.JComboBox" name="comboCameras">
+              <Properties>
+                <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
+                  <Font name="Dialog" size="14" style="1"/>
+                </Property>
+                <Property name="maximumRowCount" type="int" value="30"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="comboCamerasActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JButton" name="buttonConfig">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Config"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonConfigActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JLabel" name="jLabel1">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Camera:"/>
+              </Properties>
+            </Component>
+            <Component class="javax.swing.JButton" name="buttonArgs">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Setup"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonArgsActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JButton" name="buttonStop">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Stop"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonStopActionPerformed"/>
+              </Events>
+            </Component>
+          </SubComponents>
+        </Container>
+        <Component class="ch.psi.pshell.imaging.Renderer" name="renderer">
+        </Component>
+      </SubComponents>
+    </Container>
+    <Container class="javax.swing.JPanel" name="jPanel4">
+
+      <Layout>
+        <DimensionLayout dim="0">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" alignment="0" attributes="0">
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="1" max="-2" attributes="0">
+                      <Component id="jPanel5" max="32767" attributes="0"/>
+                      <Component id="panelScreen" alignment="0" max="32767" attributes="0"/>
+                      <Component id="panelScreen1" alignment="0" max="32767" attributes="0"/>
+                      <Component id="jPanel3" alignment="0" max="32767" attributes="0"/>
+                      <Component id="jPanel2" alignment="0" max="32767" attributes="0"/>
+                      <Component id="pauseSelection" alignment="1" pref="0" max="32767" attributes="0"/>
+                      <Component id="panelScreen2" alignment="0" max="32767" attributes="0"/>
+                  </Group>
+                  <EmptySpace max="32767" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
+        <DimensionLayout dim="1">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" attributes="0">
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Component id="jPanel5" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Component id="panelScreen" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Component id="panelScreen1" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Component id="panelScreen2" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Component id="jPanel3" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Component id="jPanel2" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace type="unrelated" max="32767" attributes="0"/>
+                  <Component id="pauseSelection" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace max="-2" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
+      </Layout>
+      <SubComponents>
+        <Container class="javax.swing.JPanel" name="jPanel3">
+          <Properties>
+            <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+              <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+                <TitledBorder title="Zoom"/>
+              </Border>
+            </Property>
+          </Properties>
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="buttonZoomFit" alignment="0" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonZoomNormal" alignment="0" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonZoomStretch" alignment="0" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace max="32767" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="buttonZoom025" alignment="0" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonZoom05" alignment="0" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonZoom2" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace max="32767" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+            <DimensionLayout dim="1">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="0" attributes="0">
+                      <EmptySpace min="-2" pref="4" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="2" attributes="0">
+                          <Component id="buttonZoomNormal" alignment="2" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonZoom025" alignment="2" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="2" attributes="0">
+                          <Component id="buttonZoomFit" alignment="2" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonZoom05" alignment="2" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="2" attributes="0">
+                          <Component id="buttonZoomStretch" alignment="2" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonZoom2" alignment="2" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+          </Layout>
+          <SubComponents>
+            <Component class="javax.swing.JRadioButton" name="buttonZoomFit">
+              <Properties>
+                <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                  <ComponentRef name="buttonGroup1"/>
+                </Property>
+                <Property name="text" type="java.lang.String" value="Fit"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonZoomFitActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JRadioButton" name="buttonZoomStretch">
+              <Properties>
+                <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                  <ComponentRef name="buttonGroup1"/>
+                </Property>
+                <Property name="text" type="java.lang.String" value="Stretch"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonZoomStretchActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JRadioButton" name="buttonZoomNormal">
+              <Properties>
+                <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                  <ComponentRef name="buttonGroup1"/>
+                </Property>
+                <Property name="text" type="java.lang.String" value="Normal"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonZoomNormalActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JRadioButton" name="buttonZoom025">
+              <Properties>
+                <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                  <ComponentRef name="buttonGroup1"/>
+                </Property>
+                <Property name="text" type="java.lang.String" value="1/4"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonZoom025ActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JRadioButton" name="buttonZoom05">
+              <Properties>
+                <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                  <ComponentRef name="buttonGroup1"/>
+                </Property>
+                <Property name="text" type="java.lang.String" value="1/2"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonZoom05ActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JRadioButton" name="buttonZoom2">
+              <Properties>
+                <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                  <ComponentRef name="buttonGroup1"/>
+                </Property>
+                <Property name="text" type="java.lang.String" value="2"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonZoom2ActionPerformed"/>
+              </Events>
+            </Component>
+          </SubComponents>
+        </Container>
+        <Container class="javax.swing.JPanel" name="jPanel2">
+          <Properties>
+            <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+              <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+                <TitledBorder title="Colormap"/>
+              </Border>
+            </Property>
+          </Properties>
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="0" attributes="0">
+                      <EmptySpace min="-2" pref="4" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="jLabel3" linkSize="9" alignment="0" min="-2" max="-2" attributes="0"/>
+                          <Component id="jLabel4" linkSize="9" alignment="0" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="-2" pref="4" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="buttonAutomatic" alignment="0" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonFullRange" alignment="0" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonManual" alignment="0" min="-2" max="-2" attributes="0"/>
+                          <Component id="comboColormap" alignment="0" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace pref="12" max="32767" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Group type="102" alignment="1" attributes="0">
+                              <Component id="labelMax" min="-2" max="-2" attributes="0"/>
+                              <EmptySpace min="-2" pref="2" max="-2" attributes="0"/>
+                              <Component id="spinnerMax" linkSize="7" min="-2" max="-2" attributes="0"/>
+                          </Group>
+                          <Component id="checkHistogram" alignment="1" min="-2" max="-2" attributes="0"/>
+                          <Group type="102" alignment="1" attributes="0">
+                              <Component id="labelMin" min="-2" max="-2" attributes="0"/>
+                              <EmptySpace min="-2" pref="2" max="-2" attributes="0"/>
+                              <Group type="103" groupAlignment="0" max="-2" attributes="0">
+                                  <Component id="btFixColormapRange" linkSize="7" alignment="1" max="-2" attributes="0"/>
+                                  <Component id="spinnerMin" linkSize="7" alignment="1" max="32767" attributes="0"/>
+                              </Group>
+                          </Group>
+                      </Group>
+                      <EmptySpace max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+            <DimensionLayout dim="1">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="1" attributes="0">
+                      <EmptySpace min="-2" pref="4" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="3" attributes="0">
+                          <Component id="comboColormap" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="jLabel3" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="checkHistogram" alignment="3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="3" attributes="0">
+                          <Component id="buttonAutomatic" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="jLabel4" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="btFixColormapRange" alignment="3" min="-2" pref="26" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="2" attributes="0">
+                          <Component id="labelMin" alignment="2" min="-2" max="-2" attributes="0"/>
+                          <Component id="spinnerMin" alignment="2" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonFullRange" alignment="2" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <Group type="103" groupAlignment="2" attributes="0">
+                          <Component id="buttonManual" alignment="2" min="-2" max="-2" attributes="0"/>
+                          <Component id="labelMax" alignment="2" min="-2" max="-2" attributes="0"/>
+                          <Component id="spinnerMax" alignment="2" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+          </Layout>
+          <SubComponents>
+            <Component class="javax.swing.JCheckBox" name="checkHistogram">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Histogram"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="checkHistogramActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JComboBox" name="comboColormap">
+              <Properties>
+                <Property name="model" type="javax.swing.ComboBoxModel" editor="org.netbeans.modules.form.editors2.ComboBoxModelEditor">
+                  <StringArray count="0"/>
+                </Property>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="onChangeColormap"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JLabel" name="jLabel3">
+              <Properties>
+                <Property name="horizontalAlignment" type="int" value="11"/>
+                <Property name="text" type="java.lang.String" value="Type:"/>
+              </Properties>
+            </Component>
+            <Component class="javax.swing.JLabel" name="jLabel4">
+              <Properties>
+                <Property name="horizontalAlignment" type="int" value="11"/>
+                <Property name="text" type="java.lang.String" value="Range:"/>
+              </Properties>
+            </Component>
+            <Component class="javax.swing.JRadioButton" name="buttonFullRange">
+              <Properties>
+                <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                  <ComponentRef name="buttonGroup3"/>
+                </Property>
+                <Property name="text" type="java.lang.String" value="Full"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="onChangeColormap"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JRadioButton" name="buttonManual">
+              <Properties>
+                <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                  <ComponentRef name="buttonGroup3"/>
+                </Property>
+                <Property name="text" type="java.lang.String" value="Manual"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="onChangeColormap"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JRadioButton" name="buttonAutomatic">
+              <Properties>
+                <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                  <ComponentRef name="buttonGroup3"/>
+                </Property>
+                <Property name="text" type="java.lang.String" value="Automatic"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="onChangeColormap"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JLabel" name="labelMin">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Min:"/>
+              </Properties>
+            </Component>
+            <Component class="javax.swing.JSpinner" name="spinnerMin">
+              <Properties>
+                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                  <SpinnerModel initial="0" maximum="65535" minimum="0" numberType="java.lang.Integer" stepSize="1" type="number"/>
+                </Property>
+                <Property name="enabled" type="boolean" value="false"/>
+                <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+                  <Dimension value="[77, 20]"/>
+                </Property>
+              </Properties>
+              <Events>
+                <EventHandler event="stateChanged" listener="javax.swing.event.ChangeListener" parameters="javax.swing.event.ChangeEvent" handler="onChangeColormapRange"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JSpinner" name="spinnerMax">
+              <Properties>
+                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                  <SpinnerModel initial="255" maximum="65535" minimum="0" numberType="java.lang.Integer" stepSize="1" type="number"/>
+                </Property>
+                <Property name="enabled" type="boolean" value="false"/>
+                <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+                  <Dimension value="[77, 20]"/>
+                </Property>
+              </Properties>
+              <Events>
+                <EventHandler event="stateChanged" listener="javax.swing.event.ChangeListener" parameters="javax.swing.event.ChangeEvent" handler="onChangeColormapRange"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JLabel" name="labelMax">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Max:"/>
+              </Properties>
+            </Component>
+            <Component class="javax.swing.JButton" name="btFixColormapRange">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Fix"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="btFixColormapRangeActionPerformed"/>
+              </Events>
+            </Component>
+          </SubComponents>
+        </Container>
+        <Container class="javax.swing.JPanel" name="jPanel5">
+          <Properties>
+            <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+              <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+                <TitledBorder title="Source"/>
+              </Border>
+            </Property>
+          </Properties>
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="0" attributes="0">
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="buttonServer" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="32767" attributes="0"/>
+                      <Component id="buttonDirect" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="32767" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+            <DimensionLayout dim="1">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="0" attributes="0">
+                      <EmptySpace min="-2" pref="4" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="3" attributes="0">
+                          <Component id="buttonServer" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="buttonDirect" alignment="3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+          </Layout>
+          <SubComponents>
+            <Component class="javax.swing.JRadioButton" name="buttonServer">
+              <Properties>
+                <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                  <ComponentRef name="buttonGroup4"/>
+                </Property>
+                <Property name="selected" type="boolean" value="true"/>
+                <Property name="text" type="java.lang.String" value="Server"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonServerActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JRadioButton" name="buttonDirect">
+              <Properties>
+                <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                  <ComponentRef name="buttonGroup4"/>
+                </Property>
+                <Property name="text" type="java.lang.String" value="Direct"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonDirectActionPerformed"/>
+              </Events>
+            </Component>
+          </SubComponents>
+        </Container>
+        <Container class="javax.swing.JPanel" name="panelScreen">
+          <Properties>
+            <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+              <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+                <TitledBorder title="Screen"/>
+              </Border>
+            </Property>
+          </Properties>
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="valueScreen" max="32767" attributes="0"/>
+                          <Component id="comboScreen" max="32767" attributes="0"/>
+                      </Group>
+                      <EmptySpace max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+            <DimensionLayout dim="1">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="1" attributes="0">
+                      <EmptySpace min="-2" pref="4" max="-2" attributes="0"/>
+                      <Component id="comboScreen" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="valueScreen" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+          </Layout>
+          <SubComponents>
+            <Component class="ch.psi.pshell.swing.DeviceValuePanel" name="valueScreen">
+            </Component>
+            <Component class="javax.swing.JComboBox" name="comboScreen">
+              <Properties>
+                <Property name="model" type="javax.swing.ComboBoxModel" editor="org.netbeans.modules.form.editors2.ComboBoxModelEditor">
+                  <StringArray count="0"/>
+                </Property>
+                <Property name="enabled" type="boolean" value="false"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="comboScreenActionPerformed"/>
+              </Events>
+            </Component>
+          </SubComponents>
+        </Container>
+        <Container class="javax.swing.JPanel" name="panelScreen1">
+          <Properties>
+            <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+              <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+                <TitledBorder title="Filter"/>
+              </Border>
+            </Property>
+          </Properties>
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="0" attributes="0">
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="valueFilter" alignment="0" max="32767" attributes="0"/>
+                          <Component id="comboFilter" alignment="0" max="32767" attributes="0"/>
+                      </Group>
+                      <EmptySpace max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+            <DimensionLayout dim="1">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="1" attributes="0">
+                      <EmptySpace min="-2" pref="4" max="-2" attributes="0"/>
+                      <Component id="comboFilter" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="valueFilter" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="32767" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+          </Layout>
+          <SubComponents>
+            <Component class="ch.psi.pshell.swing.DeviceValuePanel" name="valueFilter">
+            </Component>
+            <Component class="javax.swing.JComboBox" name="comboFilter">
+              <Properties>
+                <Property name="model" type="javax.swing.ComboBoxModel" editor="org.netbeans.modules.form.editors2.ComboBoxModelEditor">
+                  <StringArray count="0"/>
+                </Property>
+                <Property name="enabled" type="boolean" value="false"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="comboFilterActionPerformed"/>
+              </Events>
+            </Component>
+          </SubComponents>
+        </Container>
+        <Component class="ch.psi.pshell.swing.ValueSelection" name="pauseSelection">
+          <Properties>
+            <Property name="decimals" type="int" value="0"/>
+          </Properties>
+        </Component>
+        <Container class="javax.swing.JPanel" name="panelScreen2">
+          <Properties>
+            <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+              <Border info="org.netbeans.modules.form.compat2.border.TitledBorderInfo">
+                <TitledBorder title="Image"/>
+              </Border>
+            </Property>
+          </Properties>
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="0" attributes="0">
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Group type="102" alignment="1" attributes="0">
+                              <Component id="checkGoodRegion" min="-2" max="-2" attributes="0"/>
+                              <EmptySpace max="32767" attributes="0"/>
+                              <Component id="labelGrScale" min="-2" max="-2" attributes="0"/>
+                              <EmptySpace min="-2" pref="2" max="-2" attributes="0"/>
+                              <Component id="spinnerGrScale" linkSize="8" min="-2" max="-2" attributes="0"/>
+                          </Group>
+                          <Group type="102" alignment="1" attributes="0">
+                              <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
+                              <Component id="labelGrThreshold" min="-2" max="-2" attributes="0"/>
+                              <EmptySpace min="-2" pref="2" max="-2" attributes="0"/>
+                              <Component id="spinnerGrThreshold" linkSize="8" min="-2" max="-2" attributes="0"/>
+                          </Group>
+                          <Group type="102" attributes="0">
+                              <Component id="checkBackground" min="-2" max="-2" attributes="0"/>
+                              <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
+                          </Group>
+                          <Group type="102" attributes="0">
+                              <Component id="checkThreshold" min="-2" max="-2" attributes="0"/>
+                              <EmptySpace max="32767" attributes="0"/>
+                              <Component id="spinnerThreshold" linkSize="8" min="-2" max="-2" attributes="0"/>
+                          </Group>
+                      </Group>
+                      <EmptySpace max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+            <DimensionLayout dim="1">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="1" attributes="0">
+                      <EmptySpace min="-2" pref="4" max="-2" attributes="0"/>
+                      <Component id="checkBackground" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace min="-2" pref="2" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="3" attributes="0">
+                          <Component id="checkThreshold" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="spinnerThreshold" alignment="3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="-2" pref="2" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="3" attributes="0">
+                          <Component id="checkGoodRegion" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="spinnerGrScale" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="labelGrScale" alignment="3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="-2" pref="2" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="3" attributes="0">
+                          <Component id="spinnerGrThreshold" alignment="3" min="-2" max="-2" attributes="0"/>
+                          <Component id="labelGrThreshold" alignment="3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+          </Layout>
+          <SubComponents>
+            <Component class="javax.swing.JCheckBox" name="checkThreshold">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Threshold"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="checkThresholdActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JSpinner" name="spinnerThreshold">
+              <Properties>
+                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                  <SpinnerModel initial="0.0" maximum="99999.0" minimum="0.0" numberType="java.lang.Double" stepSize="1.0" type="number"/>
+                </Property>
+                <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+                  <Dimension value="[77, 20]"/>
+                </Property>
+              </Properties>
+              <Events>
+                <EventHandler event="stateChanged" listener="javax.swing.event.ChangeListener" parameters="javax.swing.event.ChangeEvent" handler="spinnerThresholdonChange"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JCheckBox" name="checkBackground">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Subtract Background"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="checkBackgroundActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JCheckBox" name="checkGoodRegion">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Good Region"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="checkGoodRegionActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JSpinner" name="spinnerGrScale">
+              <Properties>
+                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                  <SpinnerModel initial="3.0" maximum="100.0" minimum="0.01" numberType="java.lang.Double" stepSize="1.0" type="number"/>
+                </Property>
+                <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+                  <Dimension value="[77, 20]"/>
+                </Property>
+              </Properties>
+              <Events>
+                <EventHandler event="stateChanged" listener="javax.swing.event.ChangeListener" parameters="javax.swing.event.ChangeEvent" handler="spinnerGrThresholdonChange"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JSpinner" name="spinnerGrThreshold">
+              <Properties>
+                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                  <SpinnerModel initial="0.5" maximum="1.0" minimum="0.04" numberType="java.lang.Double" stepSize="0.1" type="number"/>
+                </Property>
+                <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+                  <Dimension value="[77, 20]"/>
+                </Property>
+              </Properties>
+              <Events>
+                <EventHandler event="stateChanged" listener="javax.swing.event.ChangeListener" parameters="javax.swing.event.ChangeEvent" handler="spinnerGrThresholdonChange"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JLabel" name="labelGrThreshold">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Threshold:"/>
+              </Properties>
+            </Component>
+            <Component class="javax.swing.JLabel" name="labelGrScale">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Scale:"/>
+              </Properties>
+            </Component>
+          </SubComponents>
+        </Container>
+      </SubComponents>
+    </Container>
+  </SubComponents>
+</Form>

plugins/ScreenPanel9.form

@@ -1177,7 +1177,6 @@
       <SubComponents>
         <Container class="javax.swing.JToolBar" name="toolBar">
           <Properties>
-            <Property name="floatable" type="boolean" value="false"/>
             <Property name="rollover" type="boolean" value="true"/>
           </Properties>
 

plugins/ScreenPanel9.java

@@ -1320,7 +1320,7 @@ public class ScreenPanel9 extends Panel {
             updatePipelineControls();
             if (renderer.getDevice() == null) {
                 //renderer.setZoom(1.0);
-                //renderer.setMode(RendererMode.Zoom);
+                //renderer.setMode(RenderegetDisplayNamerMode.Zoom);
                 errorOverlay = new Text(renderer.getPenErrorText(), ex.toString(), new Font("Verdana", Font.PLAIN, 12), new Point(20, 20));
                 errorOverlay.setFixed(true);
                 errorOverlay.setAnchor(Overlay.ANCHOR_VIEWPORT_TOP_LEFT);
@@ -2832,13 +2832,18 @@ public class ScreenPanel9 extends Panel {
             dm.setItem(pathTimestampStr, Chrono.getTimeStr(streamValue.getTimestamp(), "YYYY-MM-dd HH:mm:ss.SSS"), index);
 
             for (String id : streamValue.getIdentifiers()) {
-                Object val = streamValue.getValue(id);
-                if (id.equals("image")) {
-                } else if (id.equals("processing_parameters")) {
-                } else if (val.getClass().isArray()) {
-                    dm.setItem(pathRoot + id, val, index);
-                } else {
-                    dm.setItem(pathRoot + id, val, index);
+                try{
+                    Object val = streamValue.getValue(id);
+                    if (id.equals("image")) {
+                    } else if (id.equals("processing_parameters")) {
+                    } else if (val.getClass().isArray()) {
+                        dm.setItem(pathRoot + id, val, index);
+                    } else {
+                        dm.setItem(pathRoot + id, val, index);
+                    }
+                } catch (Exception ex){
+                    logger.log(Level.WARNING, null, ex);
+                    System.out.println("Error saving " + id + " index " + index + ": " + ex.getMessage());
                 }
             }
         }
@@ -2998,7 +3003,7 @@ public class ScreenPanel9 extends Panel {
                 Frame frame = getCurrentFrame();
                 int[] sel_rows = (dataTable == null) ? null : dataTable.getSelectedRows();
                 int[] sel_cols = (dataTable == null) ? null : dataTable.getSelectedColumns();
-                List<String> ids = (value == null) ? new ArrayList<>() : new ArrayList(value.getIdentifiers());
+                List<String> ids = (value == null) ? new ArrayList<>() : value.getIdentifiers();//### TODO
                 if (ids.size() + 4 != dataTableModel.getRowCount()) {
                     dataTableModel.setNumRows(0);
                     try {

plugins/ShiftsIO.java

@@ -0,0 +1,109 @@
+import ij.io.OpenDialog;
+import ij.io.SaveDialog;
+import java.util.ArrayList;
+import java.io.IOException;
+import java.io.File;
+import jmatio.types.*;
+import jmatio.io.*;
+import ij.gui.GenericDialog;
+import ij.IJ;
+import ij.Prefs;
+
+public class ShiftsIO {
+    
+    public ShiftsIO () {}
+
+    public double[][] load(String filename, String varname) {
+        if (filename==null){
+                String analysis_dir =  Prefs.get("peem.analysis_dir", "");
+                OpenDialog od = new OpenDialog("Open_shifts .mat file:", analysis_dir, "shifts.mat");
+                String dir = od.getDirectory();
+                if (null == dir) return null; // dialog was canceled
+                if (!dir.endsWith(File.separator)) dir += File.separator;
+                filename = dir + od.getFileName();
+                Prefs.set("peem.analysis_dir", dir);
+            }
+            return low_load(filename, varname);
+    }
+
+       private double[][] low_load(String filename, String varname) {
+        MatFileReader mfr = null;
+        try {
+            mfr = new MatFileReader(filename);
+        } catch (IOException e) {
+                System.err.println("Caught IOException: "
+                    + e.getMessage());
+        }
+
+        if (mfr != null) {
+            MLDouble array = (MLDouble)mfr.getMLArray(varname);
+            if (array != null){
+                return array.getArray();
+            } else {
+                return null;
+            }
+        } else {
+            return null;
+        }
+    }
+
+    public void save(String filename, double[][] shifts, String varname) {
+        boolean update = false;
+        if (filename==null){
+        String analysis_dir =  Prefs.get("peem.analysis_dir", "");
+        SaveDialog sd = new SaveDialog("Save_shifts .mat file:", analysis_dir, "shifts.mat", ".mat");
+            String dir = sd.getDirectory();
+            String fname = sd.getFileName();
+            if (null == fname) return; // user canceled dialog
+            if (!dir.endsWith(File.separator)) dir += File.separator;
+            Prefs.set("peem.analysis_dir", dir);       
+        
+            if ((new File(dir + fname)).exists()) { // if file exist, overwrite or update shifts ?
+                GenericDialog gd = new GenericDialog("Update");
+                String[] options = {"overwrite","update"};
+            gd.addChoice("Mode of operation with existing file. You want to: ", options, options[0]);
+            gd.showDialog();
+            if (gd.wasCanceled()) return;
+            if (gd.getNextChoiceIndex() == 1) update = true;
+            }
+            filename = dir + fname;
+        } 
+        double[][] final_shifts;
+            if (update) {
+                double[][] prev_shifts = low_load(filename, "directshifts");
+                if (prev_shifts == null) {
+                    IJ.error("Can't read the direct shifts in this file");
+                    return;
+                }
+
+            if (prev_shifts.length == shifts.length) {
+                    for (int j = 0; j < prev_shifts.length; j++) {
+                        prev_shifts[j][3] += shifts[j][3];
+                        prev_shifts[j][4] += shifts[j][4];
+                    }
+            } else if (shifts.length == 2) {// 2 shifts, like between two slices of different
+                            // sequences
+                 for (int j = 0; j < prev_shifts.length; j++) {
+                        prev_shifts[j][3] += shifts[1][3];
+                        prev_shifts[j][4] += shifts[1][4];
+                    }
+            } else {
+                IJ.error("Old and new shifts have incompatible length !");
+                return;
+            }
+            final_shifts = prev_shifts;
+            } else {
+            final_shifts = shifts;
+            }
+            
+            MLDouble mlDouble = new MLDouble(varname, final_shifts);
+            ArrayList<MLArray> list = new ArrayList<MLArray>();
+        list.add(mlDouble);
+        try {
+            new MatFileWriter(filename, list);
+        } catch (IOException e) {
+                System.err.println("Caught IOException: "
+                            + e.getMessage());
+        }       
+    }
+}

plugins/SpinnerLayoutTest.java

@@ -19,7 +19,7 @@ public class SpinnerLayoutTest {
         super.setLayout(new SpinnerLayout());
       }
     };
-    spinner.set
+    
     JPanel p = new JPanel(new BorderLayout(5,5));
     p.add(new JSpinner(m), BorderLayout.NORTH);
     p.add(spinner, BorderLayout.SOUTH);

plugins/Standard.java

@@ -0,0 +1,6 @@
+public class Standard{
+
+    public void run() {
+        System.out.println("run");
+    }        
+} 

plugins/TstProc.form

@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<Form version="1.5" maxVersion="1.9" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
+  <AuxValues>
+    <AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
+    <AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="1"/>
+    <AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
+  </AuxValues>
+
+  <Layout>
+    <DimensionLayout dim="0">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <EmptySpace min="0" pref="449" max="32767" attributes="0"/>
+      </Group>
+    </DimensionLayout>
+    <DimensionLayout dim="1">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <EmptySpace min="0" pref="137" max="32767" attributes="0"/>
+      </Group>
+    </DimensionLayout>
+  </Layout>
+</Form>

plugins/TstProc.java

@@ -0,0 +1,195 @@
+
+import ch.psi.pshell.core.JsonSerializer;
+import ch.psi.pshell.ui.PanelProcessor;
+import ch.psi.pshell.ui.Task;
+import ch.psi.utils.State;
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Template for a processor plugin backed by json files.
+ */
+public class TstProc extends PanelProcessor {
+
+    public static final String TYPE = "TstProc";
+    public static final String FILE_EXTENSION = "json";
+    public static final String HOME_PATH = "{home}/" + TYPE;
+
+    File currentFile;
+
+    public TstProc() {
+        initComponents();
+    }
+
+    //Overridable callbacks
+    @Override
+    public void onInitialize(int runCount) {
+
+    }
+
+    @Override
+    public void onStateChange(State state, State former) {
+
+    }
+
+    @Override
+    public void onExecutedFile(String fileName, Object result) {
+    }
+
+    @Override
+    public void onTaskFinished(Task task) {
+    }
+
+    @Override
+    protected void onTimer() {
+    }
+
+    @Override
+    protected void onLoaded() {
+
+    }
+
+    @Override
+    protected void onUnloaded() {
+
+    }
+
+    //Invoked by 'update()' to update components in the event thread
+    @Override
+    protected void doUpdate() {
+    }
+
+    //Processor Configuration
+    @Override
+    public String getType() {
+        return TYPE;
+    }
+
+    @Override
+    public String getDescription() {
+        return getType() + " definition file (*." + FILE_EXTENSION + ")";
+    }
+
+    @Override
+    public String getHomePath() {
+        return HOME_PATH;
+    }
+
+    @Override
+    public String[] getExtensions() {
+        return new String[]{FILE_EXTENSION};
+    }
+
+    @Override
+    public String getFileName() {
+        return (currentFile == null) ? null : currentFile.toString();
+    }
+
+    @Override
+    public boolean createFilePanel() {
+        return true;
+    }
+
+    @Override
+    public boolean createMenuNew() {
+        return true;
+    }
+
+    @Override
+    public boolean canStep() {
+        return false;
+    }
+
+    @Override
+    public boolean canPause() {
+        return false;
+    }
+
+    @Override
+    public boolean isTabNameUpdated() {
+        return false;
+    }
+
+    @Override
+    public void saveAs(String fileName) throws IOException {
+        currentFile = new File(fileName);
+        Map config = getConfig();
+        String json = JsonSerializer.encode(config, true);
+        Files.write(currentFile.toPath(), json.getBytes());
+    }
+
+    @Override
+    public void open(String fileName) throws IOException {
+        clear();
+        if (fileName != null) {
+            Path path = Paths.get(fileName);
+            String json = new String(Files.readAllBytes(path));
+            Map config = (Map) JsonSerializer.decode(json, Map.class);
+            currentFile = path.toFile();
+            setConfig(config);
+        }
+    }
+
+    //Component update 
+    public void clear() throws IOException {
+        currentFile=null;        
+        //TODO
+    }
+
+    Map getConfig() throws IOException {
+        //TODO
+        return new HashMap();
+    }
+
+    void setConfig(Map config) throws IOException {
+        //TODO
+    }
+
+    //Workbench actions
+    @Override
+    public void plotDataFile(File file) throws Exception {
+        throw new Exception("Not implemented");
+    }
+
+    @Override
+    public void step() {
+    }
+
+    @Override
+    public void pause() {
+    }
+
+    @Override
+    public void abort() throws InterruptedException {
+        super.abort();
+    }
+
+    @Override
+    public void execute() throws Exception {
+        this.evalAsync("tscan(sin,10,0.2)");
+    }
+
+    @SuppressWarnings("unchecked")
+    // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
+    private void initComponents() {
+
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
+        this.setLayout(layout);
+        layout.setHorizontalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGap(0, 449, Short.MAX_VALUE)
+        );
+        layout.setVerticalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGap(0, 137, Short.MAX_VALUE)
+        );
+    }// </editor-fold>//GEN-END:initComponents
+
+    // Variables declaration - do not modify//GEN-BEGIN:variables
+    // End of variables declaration//GEN-END:variables
+}

plugins/sc.form

@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<Form version="1.5" maxVersion="1.9" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
+  <AuxValues>
+    <AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
+    <AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="1"/>
+    <AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
+  </AuxValues>
+
+  <Layout>
+    <DimensionLayout dim="0">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Group type="102" alignment="1" attributes="0">
+              <EmptySpace max="-2" attributes="0"/>
+              <Component id="plotPanel" max="32767" attributes="0"/>
+              <EmptySpace max="-2" attributes="0"/>
+          </Group>
+      </Group>
+    </DimensionLayout>
+    <DimensionLayout dim="1">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Group type="102" alignment="0" attributes="0">
+              <Component id="plotPanel" pref="232" max="32767" attributes="0"/>
+              <EmptySpace min="-2" pref="170" max="-2" attributes="0"/>
+          </Group>
+      </Group>
+    </DimensionLayout>
+  </Layout>
+  <SubComponents>
+    <Container class="javax.swing.JPanel" name="plotPanel">
+
+      <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout"/>
+    </Container>
+  </SubComponents>
+</Form>

plugins/sc.java

@@ -0,0 +1,91 @@
+
+import ch.psi.pshell.ui.App;
+import ch.psi.pshell.ui.Panel;
+import ch.psi.pshell.ui.StripChart;
+import ch.psi.utils.State;
+import ch.psi.utils.Sys;
+import java.io.File;
+
+/**
+ *
+ */
+public class sc extends Panel {
+    StripChart stripChart;
+    public sc() {
+        initComponents();
+        
+        /*
+        stripChart = new StripChart(this.getTopLevel(),false, null); 
+        this.add(stripChart.getPlotPanel());
+        try { 
+            stripChart.open(new File("test.scd")); 
+            stripChart.start(); 
+        } catch  (Exception ex) { showException(ex); 
+        } 
+        */
+    }
+
+    //Overridable callbacks
+    @Override
+    public void onInitialize(int runCount) {
+        plotPanel.removeAll();
+        plotPanel.add(StripChart.getPlotPanel(new File("test.scd")));
+    }
+
+    @Override
+    public void onStateChange(State state, State former) {
+
+    }
+
+    @Override
+    public void onExecutedFile(String fileName, Object result) {
+    }
+
+    @Override
+    protected void onTimer() {
+    }
+
+    @Override
+    protected void onLoaded() {
+
+    }
+
+    @Override
+    protected void onUnloaded() {
+
+    }
+
+    //Invoked by 'update()' to update components in the event thread
+    @Override
+    protected void doUpdate() {
+    }
+
+    @SuppressWarnings("unchecked")
+    // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
+    private void initComponents() {
+
+        plotPanel = new javax.swing.JPanel();
+
+        plotPanel.setLayout(new java.awt.BorderLayout());
+
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
+        this.setLayout(layout);
+        layout.setHorizontalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
+                .addContainerGap()
+                .addComponent(plotPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addContainerGap())
+        );
+        layout.setVerticalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(layout.createSequentialGroup()
+                .addComponent(plotPanel, javax.swing.GroupLayout.DEFAULT_SIZE, 232, Short.MAX_VALUE)
+                .addGap(170, 170, 170))
+        );
+    }// </editor-fold>//GEN-END:initComponents
+
+    // Variables declaration - do not modify//GEN-BEGIN:variables
+    private javax.swing.JPanel plotPanel;
+    // End of variables declaration//GEN-END:variables
+}