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package ij.plugin;
import java.awt.*;
import java.awt.image.*;
import java.util.Vector;
import java.io.*;
import ij.*;
import ij.process.*;
import ij.io.*;
import ij.gui.*;
/** Writes the XY coordinates and pixel values of all non-background pixels
to a tab-delimited text file. Backround is assumed to be the value of
the pixel in the upper left corner of the image. */
public class XYCoordinates implements PlugIn {
static boolean processStack;
static boolean invertY;
static boolean suppress;
public void run(String arg) {
ImagePlus imp = IJ.getImage();
ImageProcessor ip = imp.getProcessor();
int width = imp.getWidth();
int height = imp.getHeight();
double background = ip.getPixelValue(0,0);
String bg = " \n";
boolean rgb = imp.getBitDepth()==24;
if (rgb) {
int c = ip.getPixel(0,0);
int r = (c&0xff0000)>>16;
int g = (c&0xff00)>>8;
int b = c&0xff;
bg = r+","+g+","+b;
bg = " \n Background value: " + bg + "\n";
}
imp.killRoi();
int slices = imp.getStackSize();
String msg =
"This plugin writes to a text file the XY coordinates and\n"
+ "pixel value of all non-background pixels. Backround\n"
+ "defaults to be the value of the pixel in the upper\n"
+ "left corner of the image.\n"
+ bg;
GenericDialog gd = new GenericDialog("Save XY Coordinates");
gd.addMessage(msg);
int digits = (int)background==background?0:4;
if (!rgb) {
gd.setInsets(5, 35, 3);
gd.addNumericField("Background value:", background, digits);
}
gd.setInsets(10, 35, 0);
gd.addCheckbox("Invert y coordinates off (0 at top of image)", invertY);
gd.setInsets(0, 35, 0);
gd.addCheckbox("Suppress Log output", suppress);
if (slices>1) {
gd.setInsets(0, 35, 0);
gd.addCheckbox("Process all "+slices+" images", processStack);
}
gd.showDialog();
if (gd.wasCanceled())
return;
if (!rgb)
background = gd.getNextNumber();
invertY = gd.getNextBoolean();
suppress = gd.getNextBoolean();
if (slices>1)
processStack = gd.getNextBoolean();
else
processStack = false;
if (!processStack) slices = 1;
SaveDialog sd = new SaveDialog("Save Coordinates as Text...", imp.getTitle(), ".txt");
String name = sd.getFileName();
if (name == null)
return;
String directory = sd.getDirectory();
PrintWriter pw = null;
try {
FileOutputStream fos = new FileOutputStream(directory+name);
BufferedOutputStream bos = new BufferedOutputStream(fos);
pw = new PrintWriter(bos);
}
catch (IOException e) {
IJ.write("" + e);
return;
}
IJ.showStatus("Saving coordinates...");
int count = 0;
float v;
int c,r,g,b;
int type = imp.getType();
ImageStack stack = imp.getStack();
for (int z=0; z<slices; z++) {
if (slices>1) ip = stack.getProcessor(z+1);
String zstr = slices>1?z+"\t":"";
for (int i=0; i<height; i++) {
int y = invertY?i:height-1-i;
for (int x=0; x<width; x++) {
v = ip.getPixelValue(x,y);
if (v!=background) {
if (type==ImagePlus.GRAY32)
pw.println(x+"\t"+(invertY?y:height-1-y)+"\t"+zstr+v);
else if (rgb) {
c = ip.getPixel(x,y);
r = (c&0xff0000)>>16;
g = (c&0xff00)>>8;
b = c&0xff;
pw.println(x+"\t"+(invertY?y:height-1-y)+"\t"+zstr+r+"\t"+g+"\t"+b);
} else
pw.println(x+"\t"+(invertY?y:height-1-y)+"\t"+zstr+(int)v);
count++;
}
} // x
if (slices==1&&y%10==0) IJ.showProgress((double)(height-y)/height);
} // y
if (slices>1) IJ.showProgress(z+1, slices);
String img = slices>1?"-"+(z+1):"";
if (!suppress)
IJ.log(imp.getTitle() + img+": " + count + " pixels (" + IJ.d2s(count*100.0/(width*height)) + "%)\n");
count = 0;
} // z
IJ.showProgress(1.0);
IJ.showStatus("");
pw.close();
}
}
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