ij.VirtualStack Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of ij
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;
import ij.process.*;
import ij.io.*;
import ij.gui.ImageCanvas;
import ij.util.Tools;
import java.io.*;
import java.awt.Font;
import java.awt.image.ColorModel;

/** This class represents an array of disk-resident images. */
public class VirtualStack extends ImageStack {
	private static final int INITIAL_SIZE = 100;
	private String path;
	private int nSlices;
	private String[] names;
	private String[] labels;
	private int bitDepth;
	
	/** Default constructor. */
	public VirtualStack() { }

	/** Creates a new, empty virtual stack. */
	public VirtualStack(int width, int height, ColorModel cm, String path) {
		super(width, height, cm);
		this.path = path;
		names = new String[INITIAL_SIZE];
		labels = new String[INITIAL_SIZE];
		//IJ.log("VirtualStack: "+path);
	}

	 /** Adds an image to the end of the stack. */
	public void addSlice(String name) {
		if (name==null) 
			throw new IllegalArgumentException("'name' is null!");
		nSlices++;
	   //IJ.log("addSlice: "+nSlices+"	"+name);
	   if (nSlices==names.length) {
			String[] tmp = new String[nSlices*2];
			System.arraycopy(names, 0, tmp, 0, nSlices);
			names = tmp;
			tmp = new String[nSlices*2];
			System.arraycopy(labels, 0, tmp, 0, nSlices);
			labels = tmp;
		}
		names[nSlices-1] = name;
	}

   /** Does nothing. */
	public void addSlice(String sliceLabel, Object pixels) {
	}

	/** Does nothing.. */
	public void addSlice(String sliceLabel, ImageProcessor ip) {
	}
	
	/** Does noting. */
	public void addSlice(String sliceLabel, ImageProcessor ip, int n) {
	}

	/** Deletes the specified slice, were 1<=n<=nslices. */
	public void deleteSlice(int n) {
		if (n<1 || n>nSlices)
			throw new IllegalArgumentException("Argument out of range: "+n);
			if (nSlices<1)
				return;
			for (int i=n; i0)
			deleteSlice(nSlices);
	}
	   
   /** Returns the pixel array for the specified slice, were 1<=n<=nslices. */
	public Object getPixels(int n) {
		ImageProcessor ip = getProcessor(n);
		if (ip!=null)
			return ip.getPixels();
		else
			return null;
	}		
	
	 /** Assigns a pixel array to the specified slice,
		were 1<=n<=nslices. */
	public void setPixels(Object pixels, int n) {
	}

   /** Returns an ImageProcessor for the specified slice,
		were 1<=n<=nslices. Returns null if the stack is empty.
	*/
	public ImageProcessor getProcessor(int n) {
		//IJ.log("getProcessor: "+n+"  "+names[n-1]+"  "+bitDepth);
		Opener opener = new Opener();
		opener.setSilentMode(true);
		IJ.redirectErrorMessages(true);
		ImagePlus imp = opener.openImage(path, names[n-1]);
		IJ.redirectErrorMessages(false);
		ImageProcessor ip = null;
		int depthThisImage = 0;
		if (imp!=null) {
			int w = imp.getWidth();
			int h = imp.getHeight();
			int type = imp.getType();
			ColorModel cm = imp.getProcessor().getColorModel();
			String info = (String)imp.getProperty("Info");
			if (info!=null && !(info.startsWith("Software")||info.startsWith("ImageDescription")))
				labels[n-1] = info;
			depthThisImage = imp.getBitDepth();
			ip = imp.getProcessor();
			ip.setOverlay(imp.getOverlay());
		} else {
			File f = new File(path, names[n-1]);
			String msg = f.exists()?"Error opening ":"File not found: ";
			ip = new ByteProcessor(getWidth(), getHeight());
			ip.invert();
			int size = getHeight()/20;
			if (size<9) size=9;
			Font font = new Font("Helvetica", Font.PLAIN, size);
			ip.setFont(font);
			ip.setAntialiasedText(true);
			ip.setColor(0);
			ip.drawString(msg+names[n-1], size, size*2);
			depthThisImage = 8;
		}
		if (depthThisImage!=bitDepth) {
			switch (bitDepth) {
				case 8: ip=ip.convertToByte(true); break;
				case 16: ip=ip.convertToShort(true); break;
				case 24:  ip=ip.convertToRGB(); break;
				case 32: ip=ip.convertToFloat(); break;
			}
		}
		if (ip.getWidth()!=getWidth() || ip.getHeight()!=getHeight()) {
			ImageProcessor ip2 = ip.createProcessor(getWidth(), getHeight());
			ip2.insert(ip, 0, 0);
			ip = ip2;
		}
		return ip;
	 }
 
	/** Currently not implemented */
	public int saveChanges(int n) {
		return -1;
	}

	 /** Returns the number of slices in this stack. */
	public int getSize() {
		return nSlices;
	}

	/** Returns the label of the Nth image. */
	public String getSliceLabel(int n) {
		String label = labels[n-1];
		if (label==null)
			return names[n-1];
		else if (label.length()<=60)
			return label;
		else
			return names[n-1]+"\n"+label;
	}
	
	/** Returns null. */
	public Object[] getImageArray() {
		return null;
	}

   /** Does nothing. */
	public void setSliceLabel(String label, int n) {
	}

	/** Always return true. */
	public boolean isVirtual() {
		return true;
	}

   /** Does nothing. */
	public void trim() {
	}
	
	/** Returns the path to the directory containing the images. */
	public String getDirectory() {
		return path;
	}
		
	/** Returns the file name of the specified slice, were 1<=n<=nslices. */
	public String getFileName(int n) {
		return names[n-1];
	}
	
	/** Sets the bit depth (8, 16, 24 or 32). */
	public void setBitDepth(int bitDepth) {
		this.bitDepth = bitDepth;
	}

	/** Returns the bit depth (8, 16, 24 or 32), or 0 if the bit depth is not known. */
	public int getBitDepth() {
		return bitDepth;
	}
	
	public ImageStack sortDicom(String[] strings, String[] info, int maxDigits) {
		int n = getSize();
		String[] names2 = new String[n];
		for (int i=0; i