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package ij.plugin;
import ij.*;
import ij.gui.*;
import ij.process.*;
import ij.measure.Calibration;
import java.awt.*;
/** This plugin implements the Edit/Selection/Straighten command. */
public class Straightener implements PlugIn {
static boolean processStack;
public void run(String arg) {
ImagePlus imp = IJ.getImage();
Roi roi = imp.getRoi();
boolean rotatedRectangle = roi!=null && (roi instanceof RotatedRectRoi);
if (roi==null || !(roi.isLine()||rotatedRectangle)) {
IJ.error("Straightener", "Line, or rotated rectangle, selection required");
return;
}
if (rotatedRectangle) {
IJ.run(imp, "Duplicate...", " ");
return;
}
int width = (int)Math.round(roi.getStrokeWidth());
int originalWidth = width;
boolean isMacro = IJ.macroRunning() && Macro.getOptions()!=null;
int stackSize = imp.getStackSize();
if (stackSize==1) processStack = false;
String newTitle = WindowManager.getUniqueName(imp.getTitle());
if (width<=1 || isMacro || stackSize>1) {
if (width<=1) width = 20;
GenericDialog gd = new GenericDialog("Straightener");
gd.addStringField("Title:", newTitle, 15);
gd.addNumericField("Line Width:", width, 0, 3, "pixels");
if (stackSize>1)
gd.addCheckbox("Process Entire Stack", processStack);
gd.showDialog();
if (gd.wasCanceled()) return;
newTitle = gd.getNextString();
width = (int)gd.getNextNumber();
Line.setWidth(width);
if (stackSize>1)
processStack = gd.getNextBoolean();
}
roi = (Roi)imp.getRoi().clone();
int type = roi.getType();
if (type==Roi.FREELINE)
IJ.run(imp, "Fit Spline", "");
ImageProcessor ip2 = null;
ImagePlus imp2 = null;
if (processStack) {
ImageStack stack2 = straightenStack(imp, roi, width);
imp2 = new ImagePlus(newTitle, stack2);
} else {
ip2 = straighten(imp, roi, width);
imp2 = new ImagePlus(newTitle, ip2);
}
if (imp2==null)
return;
Calibration cal = imp.getCalibration();
if (cal.pixelWidth==cal.pixelHeight)
imp2.setCalibration(cal);
imp2.show();
if (isMacro) Line.setWidth(originalWidth);
}
public ImageProcessor straighten(ImagePlus imp, Roi roi, int width) {
ImageProcessor ip2;
if (imp.getBitDepth()==24 && roi.getType()!=Roi.LINE)
ip2 = straightenRGB(imp, width);
else if (imp.isComposite() && ((CompositeImage)imp).getMode()==IJ.COMPOSITE) {
if (roi.getType()==Roi.LINE)
ip2 = rotateCompositeLine(imp, width);
else
ip2 = straightenComposite(imp, width);
} else if (roi.getType()==Roi.LINE)
ip2 = rotateLine(imp, width);
else
ip2 = straightenLine(imp, width);
return ip2;
}
public ImageStack straightenStack(ImagePlus imp, Roi roi, int width) {
int current = imp.getCurrentSlice();
int n = imp.getStackSize();
ImageStack stack2 = null;
for (int i=1; i<=n; i++) {
IJ.showProgress(i, n);
imp.setSlice(i);
ImageProcessor ip2 = straighten(imp, roi, width);
if (stack2==null)
stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight());
stack2.addSlice(null, ip2);
}
imp.setSlice(current);
return stack2;
}
public ImageProcessor straightenLine(ImagePlus imp, int width) {
Roi tempRoi = imp.getRoi();
if (!(tempRoi instanceof PolygonRoi))
return null;
PolygonRoi roi = (PolygonRoi)tempRoi;
if (roi==null)
return null;
if (roi.getState()==Roi.CONSTRUCTING)
roi.exitConstructingMode();
if (roi.isSplineFit())
roi.removeSplineFit();
int type = roi.getType();
int n = roi.getNCoordinates();
double len = roi.getLength();
roi.fitSplineForStraightening();
if (roi.getNCoordinates()<2)
return null;
FloatPolygon p = roi.getFloatPolygon();
n = p.npoints;
ImageProcessor ip = imp.getProcessor();
ImageProcessor ip2 = new FloatProcessor(n, width);
//ImageProcessor distances = null;
//if (IJ.debugMode) distances = new FloatProcessor(n, 1);
float[] pixels = (float[])ip2.getPixels();
double x1, y1;
double x2=p.xpoints[0]-(p.xpoints[1]-p.xpoints[0]);
double y2=p.ypoints[0]-(p.ypoints[1]-p.ypoints[0]);
if (width==1)
ip2.putPixelValue(0, 0, ip.getInterpolatedValue(x2, y2));
for (int i=0; i<n; i++) {
if (!processStack&&(i%10)==0) IJ.showProgress(i, n);
x1=x2; y1=y2;
x2=p.xpoints[i]; y2=p.ypoints[i];
//if (distances!=null) distances.putPixelValue(i, 0, (float)Math.sqrt((x2-x1)*(x2-x1)+(y2-y1)*(y2-y1)));
if (width==1) {
ip2.putPixelValue(i, 0, ip.getInterpolatedValue(x2, y2));
continue;
}
double dx = x2-x1;
double dy = y1-y2;
double length = (float)Math.sqrt(dx*dx+dy*dy);
dx /= length;
dy /= length;
//IJ.log(i+" "+x2+" "+dy+" "+(dy*width/2f)+" "+y2+" "+dx+" "+(dx*width/2f));
double x = x2-dy*width/2.0;
double y = y2-dx*width/2.0;
int j = 0;
int n2 = width;
do {
ip2.putPixelValue(i, j++, ip.getInterpolatedValue(x, y));;
//ip.drawDot((int)x, (int)y);
x += dy;
y += dx;
} while (--n2>0);
}
if (!processStack) IJ.showProgress(n, n);
if (type==Roi.FREELINE)
roi.removeSplineFit();
else
imp.draw();
if (imp.getBitDepth()!=24) {
ip2.setColorModel(ip.getColorModel());
ip2.resetMinAndMax();
}
return ip2;
}
public ImageProcessor rotateLine(ImagePlus imp, int width) {
Roi roi = imp.getRoi();
if (roi==null || roi.getType()!=Roi.LINE)
throw new IllegalArgumentException("Straight line selection expected");
Polygon p = ((Line)roi).getPoints();
imp.setRoi(new PolygonRoi(p.xpoints, p.ypoints, 2, Roi.POLYLINE));
ImageProcessor ip2 = imp.getBitDepth()==24?straightenRGB(imp, width):straightenLine(imp, width);
imp.setRoi(roi);
return ip2;
}
ImageProcessor straightenRGB(ImagePlus imp, int width) {
int w=imp.getWidth(), h=imp.getHeight();
int size = w*h;
byte[] r = new byte[size];
byte[] g = new byte[size];
byte[] b = new byte[size];
ColorProcessor cp = (ColorProcessor)imp.getProcessor();
cp.getRGB(r, g, b);
ImagePlus imp2 = new ImagePlus("red", new ByteProcessor(w, h, r, null));
imp2.setRoi((Roi)imp.getRoi().clone());
ImageProcessor red = straightenLine(imp2, width);
if (red==null) return null;
imp2 = new ImagePlus("green", new ByteProcessor(w, h, g, null));
imp2.setRoi((Roi)imp.getRoi().clone());
ImageProcessor green = straightenLine(imp2, width);
if (green==null) return null;
imp2 = new ImagePlus("blue", new ByteProcessor(w, h, b, null));
imp2.setRoi((Roi)imp.getRoi().clone());
ImageProcessor blue = straightenLine(imp2, width);
if (blue==null) return null;
ColorProcessor cp2 = new ColorProcessor(red.getWidth(), red.getHeight());
red = red.convertToByte(false);
green = green.convertToByte(false);
blue = blue.convertToByte(false);
cp2.setRGB((byte[])red.getPixels(), (byte[])green.getPixels(), (byte[])blue.getPixels());
imp.setRoi(imp2.getRoi());
return cp2;
}
ImageProcessor straightenComposite(ImagePlus imp, int width) {
Image img = imp.getImage();
ImagePlus imp2 = new ImagePlus("temp", new ColorProcessor(img));
imp2.setRoi(imp.getRoi());
ImageProcessor ip2 = straightenRGB(imp2, width);
imp.setRoi(imp2.getRoi());
return ip2;
}
ImageProcessor rotateCompositeLine(ImagePlus imp, int width) {
Image img = imp.getImage();
ImagePlus imp2 = new ImagePlus("temp", new ColorProcessor(img));
imp2.setRoi(imp.getRoi());
ImageProcessor ip2 = rotateLine(imp2, width);
return ip2;
}
}
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