/* HSTVolReader_.java
 * Greg Johnson, November 2005
 * Corrections and evolutions from 06/2006 on: P. Cloetens
 * 
 * This is a simple plugin for ImageJ that attempts to use the .XML files that coexist with volumes
 * to automate the reading of them.  The features and known problems
 * are below:
 * 1.  32bit floating point files (.vol) or 8bit unsigned integer files (.raw) which have one or more slices. 
 *     With multi-slice volumes, a VOI may be specified or the volume is opened as virtual stack.
 *     In the case of a VOI, the z-slices are correctly cropped, but the X/Y cropping only generates a ROI
 *     that the user must crop themselves using the Image/Crop tool.  This is not by design!
 *     Otherwise the single slice is read into without further hesitation.
 *
 * modified March 2006 to handle volumes with larger size (offsets>integer (31 bits)).  Now using .longOffset 
 * instead of .offset.  GJ
 *
 * 29/06/2006 PC
 *      call to OpenDialog without third argument ".xml"
 *      this seems to solve:    HandleExtraFileTypes issue
 *                              next call of plugin remembers previous directory
 *      make roi selection consistent (seems to start from 1 not 0)
 *      do roi selection only if needed, user can correct before applying crop
 *
 * 13/04/2007 PC
 *      correct readHeader: do not read BYTE_ORDER of an 8-bits file (info does not exist)
 *      clean up
 *
 * 09/01/2008 PC
 *      make compatible with virtual stack that appeared in v1.39
 *      cleanup
 *      it seems necessary to do the compilation with jdom.jar in the CLASSPATH when compiling
 */

import java.io.*; 

import ij.*; 
import ij.plugin.*;
import ij.io.*;
import ij.gui.*;

import org.jdom.*;
import org.jdom.input.*;

public class HSTVolReader_ implements PlugIn {
    public boolean littleEndian = false;
    private static boolean virtual;
    private int xMin,xMax,yMin,yMax,zMin,zMax;

	public void run(String arg) {
    	if (IJ.versionLessThan("1.39o")){
	        IJ.showMessage("Please upgrade ImageJ to at least version 1.39o");
	        return;
	    }
		OpenDialog od = new OpenDialog("Select an XML file...", arg);
		String directory = od.getDirectory();
		String name = od.getFileName();
		if (name==null)
			return;
		IJ.showStatus("Opening: " + directory + name);
		
		FileInfo fi = getVolumeInfo(directory, name);
		if (virtual)
			new FileInfoVirtualStack(fi);
		else {
			FileOpener fo = new FileOpener(fi);
			ImagePlus imp = fo.open(false);
            if ((xMin!=1)||(xMax!=fi.width)||(yMin!=1)||(yMax!=fi.height))
                imp.setRoi(xMin-1,yMin-1,xMax-xMin+1,yMax-yMin+1);
            if (imp!=null)
			    imp.show();
		}
	}
	
	public FileInfo getVolumeInfo(String directory, String name) {
		
		FileInfo fi = new FileInfo(); 
		if ((name == null) || (name == "")) return null;
		IJ.showStatus("Loading HST Volume File: " + directory + name);
		
		try {
			fi = readHeader(directory+name);
		}
		catch (IOException e) { IJ.log("HST Volume Reader: "+ e.getMessage()); }
		
		fi.directory = directory;
		fi.fileFormat = FileInfo.RAW;
		
		xMin=1;
		xMax=fi.width;
		yMin=1;
		yMax=fi.height;
		zMin=1;
		zMax=fi.nImages;
		
		if (fi.nImages!=1) {
			GenericDialog gd = new GenericDialog("VOI Selection");
			gd.addNumericField("X minimum: ", xMin, 0);
			gd.addNumericField("X maximum: ", xMax, 0);
			gd.addNumericField("Y minimum: ", yMin, 0);
			gd.addNumericField("Y maximum: ", yMax, 0);
			gd.addNumericField("Z minimum: ", zMin, 0);
			gd.addNumericField("Z maximum: ", zMax, 0);
			gd.addCheckbox("Use Virtual Stack", virtual);
			gd.addMessage("Please enter VOI or use Virtual Stack.");
            gd.addMessage("Starts at 1 (not zero)");
			gd.showDialog();
			if (gd.wasCanceled())
				return null;	
			xMin=(int)gd.getNextNumber();
			xMax=(int)gd.getNextNumber();
			yMin=(int)gd.getNextNumber();
			yMax=(int)gd.getNextNumber();
			zMin=(int)gd.getNextNumber();
			zMax=(int)gd.getNextNumber();
			virtual = gd.getNextBoolean();
		} else
		    virtual = false;
		
		fi.longOffset=((long)zMin-1)*(long)fi.getBytesPerPixel()*(long)fi.width*(long)fi.height;
		fi.nImages=zMax-(zMin-1);
		if (IJ.debugMode) 
		    IJ.log("DEBUG: longOffset " + Long.toString(fi.longOffset) + " nImages " + Integer.toString(fi.nImages)); 
        return fi;
	} 
	
	public FileInfo readHeader( String hdrfile ) throws IOException 
	{
		FileInfo fi = new FileInfo();
		SAXBuilder builder = new SAXBuilder();
		if (IJ.debugMode) {
		    IJ.log("Starting HSTVolReader");	
		}
		try {
			Document doc = builder.build(hdrfile);
			Element root = doc.getRootElement();
			Element reconstruction = root.getChild("reconstruction");
			Element listSubVolume = reconstruction.getChild("listSubVolume");
			Element subVolume = listSubVolume.getChild("subVolume");
			Element volName = subVolume.getChild("SUBVOLUME_NAME");
			String strName = volName.getTextTrim();
			IJ.showStatus("Volume: " + strName);
			
			// the next element may not exist!
			Element rawName = subVolume.getChild("RAW_NAME");
			String strRawName = new String();
			if (rawName==null) {
			    if (IJ.debugMode)
				    IJ.log("Probably a 32 bit volume");
				fi.fileName=strName;
				fi.fileType=FileInfo.GRAY32_FLOAT;  // presume it is 32 bit float data
                // check low/bigendian
                String volEndian = subVolume.getChild("BYTE_ORDER").getText();
                if (volEndian.equals("LOWBYTEFIRST"))
				    fi.intelByteOrder=true;
                else
				    fi.intelByteOrder=false;
			} else {
				strRawName= rawName.getTextTrim();
				if (IJ.debugMode)
				    IJ.log("Filename: "+ strRawName);
				fi.fileName=strRawName;
				fi.fileType=FileInfo.GRAY8; // presume it is 8 bit uint (how to specify signage??)
				// assume lowendian, not relevant
                fi.intelByteOrder=true;
			}
			
			int volSizeX = Integer.parseInt(subVolume.getChild("SIZEX").getText());
			int volSizeY = Integer.parseInt(subVolume.getChild("SIZEY").getText());
			int volSizeZ = Integer.parseInt(subVolume.getChild("SIZEZ").getText());
			
			fi.width=volSizeX;
			fi.height=volSizeY;
			fi.nImages=volSizeZ;

		}
		catch (JDOMException e) {
			IJ.showStatus("Barf");
		}
		return fi;
	}
}