| Slicer |

    package ij.plugin;
    import ij.*;
    import ij.process.*;
    import ij.gui.*;
    import ij.measure.*;
    import ij.plugin.filter.RGBStackSplitter;
    import ij.util.Tools;
    import java.awt.*;
    import java.awt.event.*;
    import java.util.*;

    /** Implements the Image/Stacks/Reslice command. */
    public class Slicer implements PlugIn, TextListener {

        private static final String[] starts = {"Top", "Left", "Bottom", "Right"};
        private static String startAt = starts[0];
        private static boolean rotate;
        private static boolean flip;
        private double outputZSpacing = 1.0;
        private int outputSlices = 1;
        private boolean noRoi;
        private boolean rgb;
        private Vector fields;
        private Label message;
        private ImagePlus imp;
        private double gx1, gy1, gx2, gy2, gLength;

        // Variables used by getIrregularProfile and doIrregularSetup
        private int n;
        private double[] x;
        private  double[] y;
        private int xbase;
        private int ybase;
        private double length;
        private double[] segmentLengths;
        private double[] dx;
        private double[] dy;

        public void run(String arg) {
            imp = WindowManager.getCurrentImage();
            if (imp==null) {
                IJ.noImage();
                return;
            }
            int stackSize = imp.getStackSize();
            Roi roi = imp.getRoi();
            if (stackSize<2 && !(roi==null||roi.getType()==Roi.RECTANGLE)) {
                IJ.error("Reslicer", "Stack required");
                return;
            }
            if (!showDialog(imp))
                return;
            long startTime = System.currentTimeMillis();
            ImagePlus imp2 = null;
            rgb = imp.getType()==ImagePlus.COLOR_RGB;
            imp2 = reslice(imp);
            if (imp2==null)
                return;
            ImageProcessor ip = imp.getProcessor();
            double min = ip.getMin();
            double max = ip.getMax();
            imp2.setCalibration(imp.getCalibration());
            Calibration cal = imp2.getCalibration();
            cal.pixelDepth = outputZSpacing*cal.pixelWidth;
            if (!rgb) imp2.getProcessor().setMinAndMax(min, max);
            imp2.show();
            if (noRoi)
                imp.killRoi();
            else
               imp.draw();
            IJ.showStatus(IJ.d2s(((System.currentTimeMillis()-startTime)/1000.0),2)+" seconds");
        }

        public ImagePlus reslice(ImagePlus imp) {
            Roi roi = imp.getRoi();
            int roiType = roi!=null?roi.getType():0;
            if (roi==null || roiType==Roi.RECTANGLE || roiType==Roi.LINE)
                return resliceRectOrLine(imp);
            else if (roiType==Roi.POLYLINE || roiType==Roi.FREELINE) {
                 String status = imp.getStack().isVirtual()?"":null;
                 IJ.showStatus("Reslice...");
                 ImageProcessor ip2 = getSlice(imp, 0.0, 0.0, 0.0, 0.0, status);
                 return new ImagePlus("Reslice of  "+imp.getShortTitle(), ip2);
            } else {
                IJ.error("Reslice...", "Line or rectangular selection required");
                return null;
            }
        }

       boolean showDialog(ImagePlus imp) {
            Calibration cal = imp.getCalibration();
            String units = cal.getUnits();
            if (cal.pixelWidth==0.0)
                cal.pixelWidth = 1.0;
            double outputSpacing = cal.pixelDepth;
            Roi roi = imp.getRoi();
            boolean line = roi!=null && roi.getType()==Roi.LINE;
            if (line)
                saveLineInfo(roi);
            GenericDialog gd = new GenericDialog("Reslice");
            gd.addNumericField("Input Z Spacing ("+units+"):", cal.pixelDepth, 3);
            gd.addNumericField("Output Z Spacing ("+units+"):", outputSpacing, 3);
            if (line)
                gd.addNumericField("Slice Count:", outputSlices, 0);
            else
               gd.addChoice("Start At:", starts, startAt);
            gd.addCheckbox("Flip Vertically", flip);
            gd.addCheckbox("Rotate 90 Degrees", rotate);
            gd.addMessage(getSize(cal.pixelDepth,outputSpacing,outputSlices)+"          ");
            fields = gd.getNumericFields();
            for (int i=0; i<fields.size(); i++)
                ((TextField)fields.elementAt(i)).addTextListener(this);
            message = (Label)gd.getMessage();
            gd.showDialog();
            if(gd.wasCanceled())
                return false;
            cal.pixelDepth = gd.getNextNumber();
            if (cal.pixelDepth==0.0) cal.pixelDepth = 1.0;
            outputZSpacing = gd.getNextNumber()/cal.pixelWidth;
            if (line) {
                outputSlices = (int)gd.getNextNumber();
                imp.setRoi(roi);
            } else
                startAt = gd.getNextChoice();
            flip = gd.getNextBoolean();
            rotate = gd.getNextBoolean();
            return true;
        }

        void saveLineInfo(Roi roi) {
            Line line = (Line)roi;
            gx1 = line.x1;
            gy1 = line.y1;
            gx2 = line.x2;
            gy2 = line.y2;
            gLength = line.getRawLength();
        }

        ImagePlus resliceRectOrLine(ImagePlus imp) {
            double x1 = 0.0;
            double y1 = 0.0;
            double x2 = 0.0;
            double y2 = 0.0;
            double xInc = 0.0;
            double yInc = 0.0;
            noRoi = false;

            Roi roi = imp.getRoi();
            if (roi==null) {
                noRoi = true;
                imp.setRoi(0, 0, imp.getWidth(), imp.getHeight());
                roi = imp.getRoi();
            }
            if (roi.getType()==Roi.RECTANGLE) {
                Rectangle r = roi.getBounds();
                if (startAt.equals(starts[0])) { // top
                    x1 = r.x;
                    y1 = r.y;
                    x2 = r.x + r.width;
                    y2 = r.y;
                    xInc = 0.0;
                    yInc = outputZSpacing;
                    outputSlices =  (int)(r.height/outputZSpacing);
               } else if (startAt.equals(starts[1])) { // left
                    x1 = r.x;
                    y1 = r.y;
                    x2 = r.x;
                    y2 = r.y + r.height;
                    xInc = outputZSpacing;
                    yInc = 0.0;
                    outputSlices =  (int)(r.width/outputZSpacing);
                } else if (startAt.equals(starts[2])) { // bottom
                    x1 = r.x;
                    y1 = r.y + r.height-1;
                    x2 = r.x + r.width;
                    y2 = r.y + r.height-1;
                    xInc = 0.0;
                    yInc = -outputZSpacing;
                    outputSlices =  (int)(r.height/outputZSpacing);
                } else if (startAt.equals(starts[3])) { // right
                    x1 = r.x + r.width-1;
                    y1 = r.y;
                    x2 = r.x + r.width-1;
                    y2 = r.y + r.height;
                    xInc = -outputZSpacing;
                    yInc = 0.0;
                    outputSlices =  (int)(r.width/outputZSpacing);
                }
            } else if (roi.getType()==Roi.LINE) {
                    Line line = (Line)roi;
                    x1 = line.x1;
                    y1 = line.y1;
                    x2 = line.x2;
                    y2 = line.y2;
                    double dx = x2 - x1;
                    double dy = y2 - y1;
                    double nrm = Math.sqrt(dx*dx + dy*dy)/outputZSpacing;
                    xInc = -(dy/nrm);
                    yInc = (dx/nrm);
           } else
                return null;

            if (outputSlices==0) {
               IJ.error("Reslicer", "Output Z spacing ("+IJ.d2s(outputZSpacing,0)+" pixels) is too large.");
               return null;
            }
            boolean virtualStack = imp.getStack().isVirtual();
            String status = null;
            ImagePlus imp2 = null;
            ImageStack stack2 = null;
            boolean isStack = imp.getStackSize()>1;
            IJ.resetEscape();
            for (int i=0; i<outputSlices; i++)  {
                if (virtualStack)
                    status = outputSlices>1?(i+1)+"/"+outputSlices+", ":"";
                ImageProcessor ip = getSlice(imp, x1, y1, x2, y2, status);
                if (isStack) drawLine(x1, y1, x2, y2, imp);
                if (stack2==null) {
                    stack2 = createOutputStack(imp, ip);
                    if (stack2==null || stack2.getSize()<outputSlices) return null; // out of memory
                }
                stack2.setPixels(ip.getPixels(), i+1);
                x1 += xInc;
                x2 += xInc;
                y1 += yInc;
                y2 += yInc;
                if (IJ.escapePressed())
                    {IJ.beep(); imp.draw(); return null;}
            }
            return new ImagePlus("Reslice of  "+imp.getShortTitle(), stack2);
        }

        ImageStack createOutputStack(ImagePlus imp, ImageProcessor ip) {
            int bitDepth = imp.getBitDepth();
            int w2=ip.getWidth(), h2=ip.getHeight(), d2=outputSlices;
            int flags = NewImage.FILL_BLACK + NewImage.CHECK_AVAILABLE_MEMORY;
            ImagePlus imp2 = NewImage.createImage("temp", w2, h2, d2, bitDepth, flags);
            if (imp2!=null && imp2.getStackSize()==d2)
                IJ.showStatus("Reslice... (press 'Esc' to abort)");
            if (imp2==null)
                return null;
            else {
                ImageStack stack2 = imp2.getStack();
                stack2.setColorModel(ip.getColorModel());
                return stack2;
            }
        }

       ImageProcessor getSlice(ImagePlus imp, double x1, double y1, double x2, double y2, String status) {
            Roi roi = imp.getRoi();
            int roiType = roi!=null?roi.getType():0;
            ImageStack stack = imp.getStack();
            int stackSize = stack.getSize();
            ImageProcessor ip,ip2=null;
            float[] line = null;
            boolean ortho = (int)x1==x1&&(int)y1==y1&&x1==x2||y1==y2;
            //IJ.log("ortho: "+ortho);
            for (int i=0; i<stackSize; i++) {
                ip = stack.getProcessor(flip?stackSize-i:i+1);
                if (roiType==Roi.POLYLINE || roiType==Roi.FREELINE)
                    line = getIrregularProfile(roi, ip);
                 else if (ortho)
                    line = getOrthoLine(ip, (int)x1, (int)y1, (int)x2, (int)y2, line);
                else
                    line = getLine(ip, x1, y1, x2, y2, line);
                if (rotate) {
                    if (i==0) ip2 = ip.createProcessor(stackSize, line.length);
                    putColumn(ip2, i, 0, line, line.length);
                } else {
                    if (i==0) ip2 = ip.createProcessor(line.length, stackSize);
                    putRow(ip2, 0, i, line, line.length);
                }
                if (status!=null) IJ.showStatus("Slicing: "+status +i+"/"+stackSize);
            }
            Calibration cal = imp.getCalibration();
            double zSpacing = cal.pixelDepth/cal.pixelWidth;
            if (zSpacing!=1.0) {
                ip2.setInterpolate(true);
                if (rotate)
                    ip2 = ip2.resize((int)(stackSize*zSpacing), line.length);
                else
                    ip2 = ip2.resize(line.length, (int)(stackSize*zSpacing));
            }
            return ip2;
        }

        public void putRow(ImageProcessor ip, int x, int y, float[] data, int length) {
            if (rgb) {
                for (int i=0; i<length; i++)
                    ip.putPixel(x++, y, Float.floatToIntBits(data[i]));
            } else {
                for (int i=0; i<length; i++)
                    ip.putPixelValue(x++, y, data[i]);
            }
        }

        public void putColumn(ImageProcessor ip, int x, int y, float[] data, int length) {
            if (rgb) {
                for (int i=0; i<length; i++)
                    ip.putPixel(x, y++, Float.floatToIntBits(data[i]));
            } else {
                for (int i=0; i<length; i++)
                    ip.putPixelValue(x, y++, data[i]);
            }
        }

        float[] getIrregularProfile(Roi roi, ImageProcessor ip) {
            if (x==null)
                doIrregularSetup(roi);
            float[] values = new float[(int)length];
            double leftOver = 1.0;
            double distance = 0.0;
            int index;
            double oldx=xbase, oldy=ybase;
            for (int i=0; i<n; i++) {
                double len = segmentLengths[i];
                if (len==0.0)
                    continue;
                double xinc = dx[i]/len;
                double yinc = dy[i]/len;
                double start = 1.0-leftOver;
                double rx = xbase+x[i]+start*xinc;
                double ry = ybase+y[i]+start*yinc;
                double len2 = len - start;
                int n2 = (int)len2;
                //double d=0;;
                //IJ.write("new segment: "+IJ.d2s(xinc)+" "+IJ.d2s(yinc)+" "+IJ.d2s(len)+" "+IJ.d2s(len2)+" "+IJ.d2s(n2)+" "+IJ.d2s(leftOver));
                for (int j=0; j<=n2; j++) {
                    index = (int)distance+j;
                    if (index<values.length) {
                        if (rgb) {
                            int rgbPixel = ((ColorProcessor)ip).getInterpolatedRGBPixel(rx, ry);
                            values[index] = Float.intBitsToFloat(rgbPixel&0xffffff);
                        } else
                            values[index] = (float)ip.getInterpolatedValue(rx, ry);
                    }
                    //d = Math.sqrt((rx-oldx)*(rx-oldx)+(ry-oldy)*(ry-oldy));
                    //IJ.write(IJ.d2s(rx)+"    "+IJ.d2s(ry)+"    "+IJ.d2s(d));
                    //oldx = rx; oldy = ry;
                    rx += xinc;
                    ry += yinc;
                }
                distance += len;
                leftOver = len2 - n2;
            }

            return values;

        }

        void doIrregularSetup(Roi roi) {
            n = ((PolygonRoi)roi).getNCoordinates();
            int[] ix = ((PolygonRoi)roi).getXCoordinates();
            int[] iy = ((PolygonRoi)roi).getYCoordinates();
            x = new double[n];
            y = new double[n];
            for (int i=0; i<n; i++) {
                x[i] = ix[i];
                y[i] = iy[i];
            }
            if (roi.getType()==Roi.FREELINE) {
                // smooth line
                for (int i=1; i<n-1; i++) {
                    x[i] = (x[i-1] + x[i] + x[i+1])/3.0+0.5;
                    y[i] = (y[i-1] + y[i] + y[i+1])/3.0+0.5;
                }
            }
            Rectangle r = roi.getBounds();
            xbase = r.x;
            ybase = r.y;
            length = 0.0;
            double segmentLength;
            double xdelta, ydelta;
            segmentLengths = new double[n];
            dx = new double[n];
            dy = new double[n];
            for (int i=0; i<(n-1); i++) {
                xdelta = x[i+1] - x[i];
                ydelta = y[i+1] - y[i];
                segmentLength = Math.sqrt(xdelta*xdelta+ydelta*ydelta);
                length += segmentLength;
                segmentLengths[i] = segmentLength;
                dx[i] = xdelta;
                dy[i] = ydelta;
            }
        }

        private float[] getLine(ImageProcessor ip, double x1, double y1, double x2, double y2, float[] data) {
            double dx = x2-x1;
            double dy = y2-y1;
            int n = (int)Math.round(Math.sqrt(dx*dx + dy*dy));
            if (data==null)
                data = new float[n];
            double xinc = dx/n;
            double yinc = dy/n;
            double rx = x1;
            double ry = y1;
            for (int i=0; i<n; i++) {
                if (rgb) {
                    int rgbPixel = ((ColorProcessor)ip).getInterpolatedRGBPixel(rx, ry);
                    data[i] = Float.intBitsToFloat(rgbPixel&0xffffff);
                } else
                    data[i] = (float)ip.getInterpolatedValue(rx, ry);
                rx += xinc;
                ry += yinc;
            }
            return data;
        }

        private float[] getOrthoLine(ImageProcessor ip, int x1, int y1, int x2, int y2, float[] data) {
            int dx = x2-x1;
            int dy = y2-y1;
            int n = Math.max(dx, dy);
            if (data==null) data = new float[n];
            int xinc = dx/n;
            int yinc = dy/n;
            int rx = x1;
            int ry = y1;
            for (int i=0; i<n; i++) {
                if (rgb) {
                    int rgbPixel = ((ColorProcessor)ip).getPixel(rx, ry);
                    data[i] = Float.intBitsToFloat(rgbPixel&0xffffff);
                } else
                    data[i] = (float)ip.getPixelValue(rx, ry);
                rx += xinc;
                ry += yinc;
            }
            return data;
        }

        void drawLine(double x1, double y1, double x2, double y2, ImagePlus imp) {
            ImageCanvas ic = imp.getCanvas();
            if (ic==null) return;
            Graphics g = ic.getGraphics();
            g.setColor(Roi.getColor());
            g.setXORMode(Color.black);
            g.drawLine(ic.screenX((int)(x1+0.5)), ic.screenY((int)(y1+0.5)), ic.screenX((int)(x2+0.5)), ic.screenY((int)(y2+0.5)));
        }

        public void textValueChanged(TextEvent e) {
            double inSpacing = Tools.parseDouble(((TextField)fields.elementAt(0)).getText(),0.0);
            double outSpacing = Tools.parseDouble(((TextField)fields.elementAt(1)).getText(),0.0);
            int count = 0;
            boolean lineSelection = fields.size()==3;
            if (lineSelection) {
                count = (int)Tools.parseDouble(((TextField)fields.elementAt(2)).getText(), 0.0);
                if (count>0) makePolygon(count, outSpacing);
            }
            String size = getSize(inSpacing, outSpacing, count);
            message.setText(size);
        }

        String getSize(double inSpacing, double outSpacing, int count) {
            int size = getOutputStackSize(inSpacing, outSpacing, count);
            int mem = getAvailableMemory();
            String available = mem!=-1?" ("+mem+"MB)":"";
            if (message!=null)
                message.setForeground(mem!=-1&&size>mem?Color.red:Color.black);
            if (size>0)
                return size+"MB"+available;
            else
                return "<1MB"+available;
        }

        void makePolygon(int count, double outSpacing) {
            int[] x = new int[4];
            int[] y = new int[4];
            x[0] = (int)gx1;
            y[0] = (int)gy1;
            x[1] = (int)gx2;
            y[1] = (int)gy2;
            double dx = gx2 - gx1;
            double dy = gy2 - gy1;
            double nrm = Math.sqrt(dx*dx + dy*dy)/outSpacing;
            double xInc = -(dy/nrm);
            double yInc = (dx/nrm);
            x[2] = x[1] + (int)(xInc*count);
            y[2] = y[1] + (int)(yInc*count);
            x[3] = x[0] + (int)(xInc*count);
            y[3] = y[0] + (int)(yInc*count);
            imp.setRoi(new PolygonRoi(x, y, 4, PolygonRoi.FREEROI));
        }

        int getOutputStackSize(double inSpacing, double outSpacing, int count) {
            Roi roi = imp.getRoi();
            int width = imp.getWidth();
            int height = imp.getHeight();
            if (roi!=null) {
                Rectangle r = roi.getBounds();
                width = r.width;
                width = r.height;
            }
            int type = roi!=null?roi.getType():0;
            int stackSize = imp.getStackSize();
            double size = 0.0;
            if (type==Roi.RECTANGLE) {
                size = width*height*stackSize;
                if (outSpacing>0) size /= outSpacing;
            } else
                size = gLength*count*stackSize;
            Calibration cal = imp.getCalibration();
            double zSpacing = inSpacing/cal.pixelWidth;
            if (zSpacing!=0.0 && zSpacing!=1.0)
                size *= zSpacing;
            return (int)Math.round(size/1048576.0);
        }

        int getAvailableMemory() {
                long max = IJ.maxMemory();
                if (max==0) return -1;
                long inUse = IJ.currentMemory();
                long available = max - inUse;
                return (int)((available+524288L)/1048576L);
        }
    }

| Slicer |