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package ij.plugin;
import ij.*;
import ij.process.*;
import ij.gui.*;
/**
* This plugin implements the Image/Stacks/Tools/Make Substack command.
* What it does is extracts selected images from a stack to make a new substack.
* It takes three types of inputs: a range of images (e.g. 2-14), a range of images
* with an increment (e.g. 2-14-3), or a list of images (e.g. 7,9,25,27,34,132).
* It then copies those images from the active stack to a new stack in the order
* of listing or range.
*
* @author Anthony Padua
* @author Daniel Barboriak, MD
* @author Neuroradiology
* @author Duke University Medical Center
*
* @author Ved P. Sharma, Ph.D.
* @author Anatomy and Structural Biology
* @author Albert Einstein College of Medicine
*
*/
public class SubstackMaker implements PlugIn {
private static boolean delete = false;
public void run(String arg) {
ImagePlus imp = IJ.getImage();
if (imp.isHyperStack() || imp.isComposite()) {
IJ.error("Make Substack", "This command does not currently work with hyperstacks.");
return;
}
String userInput = showDialog();
if (userInput==null)
return;
ImagePlus imp2 = makeSubstack(imp, userInput);
if (imp2!=null)
imp2.show();
}
public ImagePlus makeSubstack(ImagePlus imp, String userInput) {
String stackTitle = "Substack ("+userInput+")";
if (stackTitle.length()>25) {
int idxA = stackTitle.indexOf(",",18);
int idxB = stackTitle.lastIndexOf(",");
if(idxA>=1 && idxB>=1){
String strA = stackTitle.substring(0,idxA);
String strB = stackTitle.substring(idxB+1);
stackTitle = strA + ", ... " + strB;
}
}
ImagePlus imp2 = null;
try {
int idx1 = userInput.indexOf("-");
if (idx1>=1) { // input displayed in range
String rngStart = userInput.substring(0, idx1);
String rngEnd = userInput.substring(idx1+1);
Integer obj = new Integer(rngStart);
int first = obj.intValue();
int inc = 1;
int idx2 = rngEnd.indexOf("-");
if (idx2>=1) {
String rngEndAndInc = rngEnd;
rngEnd = rngEndAndInc.substring(0, idx2);
String rngInc = rngEndAndInc.substring(idx2+1);
obj = new Integer(rngInc);
inc = obj.intValue();
}
obj = new Integer(rngEnd);
int last = obj.intValue();
imp2 = stackRange(imp, first, last, inc, stackTitle);
} else {
int count = 1; // count # of slices to extract
for (int j=0; j<userInput.length(); j++) {
char ch = Character.toLowerCase(userInput.charAt(j));
if (ch==',') {count += 1;}
}
int[] numList = new int[count];
for(int i=0; i<count; i++) {
int idx2 = userInput.indexOf(",");
if(idx2>0) {
String num = userInput.substring(0,idx2);
Integer obj = new Integer(num);
numList[i] = obj.intValue();
userInput = userInput.substring(idx2+1);
}
else{
String num = userInput;
Integer obj = new Integer(num);
numList[i] = obj.intValue();
}
}
imp2 = stackList(imp, count, numList, stackTitle);
}
} catch (Exception e) {
IJ.error("Substack Maker", "Invalid input string: \n \n \""+userInput+"\"");
}
return imp2;
}
String showDialog() {
GenericDialog gd = new GenericDialog("Substack Maker");
gd.setInsets(10,45,0);
gd.addMessage("Enter a range (e.g. 2-14), a range with increment\n(e.g. 1-100-2) or a list (e.g. 7,9,25,27)");
gd.addStringField("Slices:", "", 40);
gd.addCheckbox("Delete slices from original stack", delete);
gd.showDialog();
if (gd.wasCanceled())
return null;
else {
delete = gd.getNextBoolean();
return gd.getNextString();
}
}
// extract specific slices
ImagePlus stackList(ImagePlus imp, int count, int[] numList, String stackTitle) throws Exception {
ImageStack stack = imp.getStack();
ImageStack stack2 = null;
Roi roi = imp.getRoi();
for (int i=0, j=0; i<count; i++) {
int currSlice = numList[i]-j;
ImageProcessor ip2 = stack.getProcessor(currSlice);
ip2.setRoi(roi);
ip2 = ip2.crop();
if (stack2==null)
stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight());
stack2.addSlice(stack.getSliceLabel(currSlice), ip2);
if (delete) {
stack.deleteSlice(currSlice);
j++;
}
}
if (delete) {
imp.setStack(stack);
// next three lines for updating the scroll bar
ImageWindow win = imp.getWindow();
StackWindow swin = (StackWindow) win;
swin.updateSliceSelector();
}
ImagePlus impSubstack = imp.createImagePlus();
impSubstack.setStack(stackTitle, stack2);
impSubstack.setCalibration(imp.getCalibration());
return impSubstack;
}
// extract range of slices
ImagePlus stackRange(ImagePlus imp, int first, int last, int inc, String title) throws Exception {
ImageStack stack = imp.getStack();
ImageStack stack2 = null;
Roi roi = imp.getRoi();
for (int i= first, j=0; i<= last; i+=inc) {
//IJ.log(first+" "+last+" "+inc+" "+i);
int currSlice = i-j;
ImageProcessor ip2 = stack.getProcessor(currSlice);
ip2.setRoi(roi);
ip2 = ip2.crop();
if (stack2==null)
stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight());
stack2.addSlice(stack.getSliceLabel(currSlice), ip2);
if (delete) {
stack.deleteSlice(currSlice);
j++;
}
}
if (delete) {
imp.setStack(stack);
// next three lines for updating the scroll bar
ImageWindow win = imp.getWindow();
StackWindow swin = (StackWindow) win;
swin.updateSliceSelector();
}
ImagePlus substack = imp.createImagePlus();
substack.setStack(title, stack2);
substack.setCalibration(imp.getCalibration());
return substack;
}
}
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