ij.plugin.StackWriter Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of ij Show documentation
ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh.
There is a newer version: 1.54p
package ij.plugin;
import java.awt.*;
import java.io.*;
import java.text.DecimalFormat;	
import java.util.*;
import ij.*;
import ij.io.*;
import ij.gui.*;
import ij.measure.Calibration;
import ij.process.*;
import ij.plugin.frame.Recorder;
import ij.macro.Interpreter;
import ij.util.Tools;

/** This plugin, which saves the images in a stack as separate files, 
	implements the File/Save As/Image Sequence command. */
public class StackWriter implements PlugIn {
	private static final String DIR_KEY = "save.sequence.dir";
	private static String[] choices = {"BMP",  "FITS", "GIF", "JPEG", "PGM", "PNG", "Raw", "Text", "TIFF",  "ZIP"};
	private static String staticFileType = "TIFF";
	private String fileType = "TIFF";
	private int ndigits = 4;
	private boolean useLabels;
	private boolean firstTime = true;
	private int startAt;
	private boolean hyperstack;
	private int[] dim;
	private ImagePlus imp;
	private String directory;
	private String format = "tiff";
	private String name;
	
	/** Saves the specified image as a sequence of images. */
	public static void save(ImagePlus imp, String directoryPath, String options) {
		StackWriter sw = new StackWriter();
		sw.imp = imp;
		sw.format = Tools.getStringFromList(options, "format=", sw.format);
		sw.name = Tools.getStringFromList(options, "name=");
		sw.ndigits = (int)Tools.getNumberFromList(options, "digits=", sw.ndigits);
		sw.useLabels = options.contains(" use");
		sw.run(directoryPath);
	}


	public void run(String arg) {
		if (imp==null)
			imp = WindowManager.getCurrentImage();
		if (imp==null || (imp!=null && imp.getStackSize()<2&&!IJ.isMacro())) {
			IJ.error("Stack Writer", "This command requires a stack.");
			return;
		}
		int stackSize = imp.getStackSize();
		if (name==null) {
			name = imp.getTitle();
			int dotIndex = name.lastIndexOf(".");
			if (dotIndex>=0)
				name = name.substring(0, dotIndex);
		}
		hyperstack = imp.isHyperStack();
		LUT[] luts = null;
		int lutIndex = 0;
		int nChannels = imp.getNChannels();
		if (hyperstack) {
			dim = imp.getDimensions();
			if (imp.isComposite())
				luts = ((CompositeImage)imp).getLuts();
			if (firstTime && ndigits==4) {
				ndigits = 3;
				firstTime = false;
			}
		}
		if (arg!=null && arg.length()>0)
			directory = arg;
		else {		
			if (!showDialog(imp))
				return;
		}		
		File d = new File(directory);
		if (d==null || !d.isDirectory()) {
			IJ.error("File>Save As>Image Sequence", "Directory not found: "+directory);
			return;
		}
		int number = 0;
		if (ndigits<1) ndigits = 1;
		if (ndigits>8) ndigits = 8;
		int maxImages = (int)Math.pow(10,ndigits);
		if (stackSize>maxImages && !useLabels && !hyperstack) {
			IJ.error("Stack Writer", "More than " + ndigits
				+" digits are required to generate \nunique file names for "+stackSize+" images.");
			return;			
		}
		if (format.equals("fits") && !FileSaver.okForFits(imp))
			return;			
		if (format.equals("text"))
			format = "text image";
		String extension = "." + format;
		if (format.equals("tiff"))
			extension = ".tif";
		else if (format.equals("text image"))
			extension = ".txt";					
		Overlay overlay = imp.getOverlay();
		boolean isOverlay = overlay!=null && !imp.getHideOverlay();
		if (!(format.equals("jpeg")||format.equals("png")))
			isOverlay = false;
		ImageStack stack = imp.getStack();
		ImagePlus imp2 = new ImagePlus();
		imp2.setTitle(imp.getTitle());
		Calibration cal = imp.getCalibration();
		int nSlices = stack.size();
		String path,label=null;
		imp.lock();
		for (int i=1; i<=nSlices; i++) {
			IJ.showStatus("writing: "+i+"/"+nSlices);
			IJ.showProgress(i, nSlices);
			ImageProcessor ip = stack.getProcessor(i);
			if (isOverlay) {
				imp.setSliceWithoutUpdate(i);
				ip = imp.flatten().getProcessor();
			} else if (luts!=null && nChannels>1 && hyperstack) {
				ip.setColorModel(luts[lutIndex++]);
				if (lutIndex>=luts.length) lutIndex = 0;
			}
			imp2.setProcessor(null, ip);
			String label2 = stack.getSliceLabel(i);
			imp2.setProp("Slice_Label", null);
			if (label2!=null) {
				if (label2.contains("\n"))
					imp2.setProperty("Info", label2);
				else
					imp2.setProp("Slice_Label", label2);;
			} else {
				Properties props = imp2.getProperties();
				if (props!=null) props.remove("Info");
			}
			imp2.setCalibration(cal);
			String digits = getDigits(number++);
			if (useLabels) {
				label = stack.getShortSliceLabel(i, 111);
				if (label!=null && label.equals("")) label = null;
				if (label!=null) label = label.replaceAll("/","-");
			}
			if (label==null)
				path = directory+name+digits+extension;
			else
				path = directory+label+extension;
			if (i==1) {
				File f = new File(path);
				if (f.exists()) {
					if (!IJ.isMacro() && !IJ.showMessageWithCancel("Overwrite files?",
						"One or more files will be overwritten if you click \"OK\".\n \n"+path)) {
						imp.unlock();
						IJ.showStatus("");
						IJ.showProgress(1.0);
						return;
					}
				}
			}
			if (IJ.recording())
				Recorder.disablePathRecording();
			imp2.setOverlay(null);
			if (overlay!=null && format.equals("tiff")) {
				Overlay overlay2 = overlay.duplicate();
				overlay2.crop(i, i);
				if (overlay2.size()>0) {
					for (int j=0; j1) {
				cs = "00000000"+c;
				cs = "_c"+cs.substring(cs.length()-ndigits);
			}
			if (dim[3]>1) {
				zs = "00000000"+z;
				zs = "_z"+zs.substring(zs.length()-ndigits);
			}
			if (dim[4]>1) {
				ts = "00000000"+t;
				ts = "_t"+ts.substring(ts.length()-ndigits);
			}
			return ts+zs+cs;
		} else {
			String digits = "00000000"+(startAt+n);
			return digits.substring(digits.length()-ndigits);
		}
	}
	
}