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package ij.plugin;
import ij.*;
import ij.gui.*;
import ij.util.Tools;
import ij.process.*;
import java.awt.*;
/** This plugin implements the File/New/Hyperstack command. */
public class HyperStackMaker implements PlugIn {
private static String defaults = "8-bit Color 400 300 3 4 5 1";
private static String[] types = {"8-bit", "16-bit", "32-bit", "RGB"};
private static String[] modes = {"Composite", "Color", "Grayscale"};
private static String title = "HyperStack";
private String type, mode;
private int width, height, c, z, t;
private boolean label;
public void run(String arg) {
String defaults2 = Prefs.get("hyperstack.new", defaults);
if (Macro.getOptions()!=null)
defaults2 = defaults;
String[] prefs = Tools.split(defaults2);
if (prefs.length<8)
prefs = Tools.split(defaults);
type = prefs[0];
mode = prefs[1];
width = (int)Tools.parseDouble(prefs[2], 400);
height = (int)Tools.parseDouble(prefs[3], 300);
c = (int)Tools.parseDouble(prefs[4], 3);
z = (int)Tools.parseDouble(prefs[5], 4);
t = (int)Tools.parseDouble(prefs[6], 5);
int labelInt = (int)Tools.parseDouble(prefs[7], 1);
label = labelInt==1?true:false;
if (!showDialog())
return;
String type2 = type;
if (label)
type2 += " ramp label";
if (mode.equals("Composite"))
type2 += " composite";
else if (mode.equals("Color"))
type2 += " color";
else if (mode.equals("Grayscale"))
type2 += " grayscale";
ImagePlus imp = IJ.createImage(title, type2, width, height, c, z, t);
WindowManager.checkForDuplicateName = true;
imp.show();
if (Macro.getOptions()==null) {
defaults2 = type+" "+mode+" "+width+" "+height+" "+c+" "+z+" "+t+" "+(label?"1":"0");
Prefs.set("hyperstack.new", defaults2);
}
}
private boolean showDialog() {
String options = IJ.isMacro()?Macro.getOptions():null;
if (options!=null && options.contains("title="))
Macro.setOptions(options.replace("title=", "name="));
GenericDialog gd = new GenericDialog("New Hyperstack...");
gd.addStringField("Name:", title, 12);
gd.addChoice("Type:", types, type);
gd.addChoice("Display mode:", modes, mode);
gd.addNumericField("Width:", width, 0, 5, "pixels");
gd.addNumericField("Height:", height, 0, 5, "pixels");
gd.addNumericField("Channels (c):", c, 0, 5, "");
gd.addNumericField("Slices (z):", z, 0, 5, "");
gd.addNumericField("Frames (t):", t, 0, 5, "");
gd.addCheckbox("Label images", label);
gd.showDialog();
if (gd.wasCanceled())
return false;
title = gd.getNextString();
type = gd.getNextChoice();
mode = gd.getNextChoice();
width = (int)gd.getNextNumber();
height = (int)gd.getNextNumber();
c = (int)gd.getNextNumber();
if (c<1) c=1;
z = (int)gd.getNextNumber();
if (z<1) z=1;
t = (int)gd.getNextNumber();
if (t<1) t=1;
label = gd.getNextBoolean();
if (width<1 || height<1) {
IJ.error("New Image", "Width and height must be >0");
return false;
} else
return true;
}
public static void labelHyperstack(ImagePlus imp) {
int width = imp.getWidth();
int height = imp.getHeight();
int c = imp.getNChannels();
int z = imp.getNSlices();
int t = imp.getNFrames();
ImageStack stack = imp.getStack();
Overlay overlay = new Overlay();
int n = stack.getSize();
int channel=1, slice=1, frame=1;
boolean hyperstack = imp.isHyperStack();
for (int i=1; i<=n; i++) {
int yloc = 30;
IJ.showProgress(i, n);
ImageProcessor ip = stack.getProcessor(i);
ip.setAntialiasedText(true);
ip.setColor(Color.black);
ip.setRoi(0, 0, width, yloc);
ip.fill();
ip.setRoi(0, yloc+25, width, height-(yloc+25));
ip.fill();
ip.setColor(Color.white);
Font font = new Font("SansSerif",Font.PLAIN,24);
ip.setFont(font);
String text = "c="+IJ.pad(channel,3)+", z="+IJ.pad(slice,3)+", t="+IJ.pad(frame,3)+", i="+IJ.pad(i,4);
if (!hyperstack)
text = IJ.pad(i,4);
TextRoi roi = new TextRoi(5, yloc-28, text, font);
roi.setStrokeColor(Color.white);
if (hyperstack || c>1)
roi.setPosition(channel, slice, frame);
else
roi.setPosition(i);
overlay.add(roi);
ip.drawString(text, 5, yloc+27);
// embed channel, slice, frame and stack index into pixel data
yloc += 30;;
int size = 20;
ip.setValue(channel); ip.setRoi(size,yloc,size,size); ip.fill();
ip.setColor(Color.white); ip.drawRect(size,yloc,size,size);
ip.setValue(slice); ip.setRoi(size*3,yloc,size,size); ip.fill();
ip.setColor(Color.white); ip.drawRect(size*3,yloc,size,size);
ip.setValue(frame); ip.setRoi(size*5,yloc,size,size); ip.fill();
ip.setColor(Color.white); ip.drawRect(size*5,yloc,size,size);
ip.setValue(i); ip.setRoi(size*7,yloc,size,size); ip.fill();
ip.setColor(Color.white); ip.drawRect(size*7,yloc,size,size);
yloc = 90;
if (i==1 && hyperstack) {
String msg = "Press shift-z (Image>Color>Channels Tool)\n"+
"to open the \"Channels\" window, which will\n"+
"allow you switch to composite color mode\n"+
"and to enable/disable channels.\n";
font = new Font("SansSerif", Font.PLAIN, imp.getWidth()>399?14:12);
roi = new TextRoi(25, yloc, msg, font);
roi.setStrokeColor(Color.white);
roi.setPosition(0, 1, 1);
overlay.add(roi);
}
channel++;
if (channel>c) {
channel = 1;
slice++;
if (slice>z) {
slice = 1;
frame++;
if (frame>t) frame = 1;
}
}
}
imp.setOverlay(overlay);
}
}
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