import ij.*;
import ij.gui.*;
import ij.process.*;
import ij.plugin.*;
import ij.io.*;
import java.io.*;
import java.io.RandomAccessFile;
import java.lang.String;

/**
Imports 3rrr and 3iii files from Bruker
written by Bertram Manz,
           Arbeitsgruppe Magnetische Resonanz,
           Fraunhofer-Institut für Biomedizinische Technik
           Enheimer Str. 48
           66386 St. Ingbert
           Germany
           bertram dot manz at ibmt dot fraunhofer dot de
Version 29/07/04
*/

public class rrr3iiiOpener extends ImagePlus implements PlugIn {

        private static final int UINT32=0, INT32=1;
        private static final String[] types = {"uint32","int32"};
    	private static int xsize=1;
    	private static int ysize=1;
    	private static int zsize=1;
    	private static int xdim=1;
    	private static int ydim=1;
    	private static int zdim=1;
    	private static int ymin=0;

    public void run(String path) {
        String FileLine;

	File theFile=new File(path);
	String directory = theFile.getParent();
	String fileName = theFile.getName();
	File procs = new File(directory, "procs");
	try {
            RandomAccessFile f = new RandomAccessFile(procs, "r");
	    while ((FileLine = f.readLine()) != null) {
	      if (FileLine.startsWith("##$SI= ")) {
 	      	 xsize = getiValue(FileLine.substring(7, FileLine.length()));
	      }
	      if (FileLine.startsWith("##$XDIM= ")) {
 	      	 xdim = getiValue(FileLine.substring(9, FileLine.length()));
	      }
	      if (FileLine.startsWith("##$YMIN_p= ")) {
 	      	 ymin = getiValue(FileLine.substring(11, FileLine.length()));
	      }
	    }
	    f.close();
	}
	catch (IOException e) {
	    IJ.showMessage("rrr3iiiOpener", "File procs not found.");
	    xsize = 0;
	    xdim = 0;
	}
	File proc2s = new File(directory, "proc2s");
	try {
            RandomAccessFile f = new RandomAccessFile(proc2s, "r");
	    while ((FileLine = f.readLine()) != null) {
	      if (FileLine.startsWith("##$SI= ")) {
 	      	 ysize = getiValue(FileLine.substring(7, FileLine.length()));
	      }
	      if (FileLine.startsWith("##$XDIM= ")) {
 	      	 ydim = getiValue(FileLine.substring(9, FileLine.length()));
	      }
	    }
	    f.close();
	}
	catch (IOException e) {
	    IJ.showMessage("rrr3iiiOpener", "File proc2s not found.");
	    ysize = 0;
	    ydim = 0;
	}
	File proc3s = new File(directory, "proc3s");
	try {
            RandomAccessFile f = new RandomAccessFile(proc3s, "r");
	    while ((FileLine = f.readLine()) != null) {
	      if (FileLine.startsWith("##$SI= ")) {
 	      	 zsize = getiValue(FileLine.substring(7, FileLine.length()));
	      }
	      if (FileLine.startsWith("##$XDIM= ")) {
 	      	 zdim = getiValue(FileLine.substring(9, FileLine.length()));
	      }
	    }
	    f.close();
	}
	catch (IOException e) {
	    IJ.showMessage("rrr3iiiOpener", "File proc3s not found.");
	    zsize = 0;
	    zdim = 0;
	}

	File titlefile = new File(directory, "title");
	try {
            RandomAccessFile f = new RandomAccessFile(titlefile, "r");
	    FileLine = f.readLine();
	    f.close();
	}
	catch (IOException e) {
	    FileLine = fileName;
	}

	if ((xsize == 0) || (ysize ==0) || (zsize == 0)) {
	    ImportDialog id = new ImportDialog(fileName, directory);
	    id.openImage();
	} else {
	    if (ymin < 0) {
	       IJ.run("Raw...", "open='" +path +"' image='32-bit Signed' width=" +xsize +" height=" + ysize +" offset=0 number=" +zsize +" gap=0");
	    } else {
	       IJ.run("Raw...", "open='" +path +"' image='32-bit Unsigned' width=" +xsize +" height=" + ysize +" offset=0 number=" +zsize +" gap=0");
	    }
	}
	IJ.run("Rename...", "title='" +FileLine +"'");
	ImagePlus imp = WindowManager.getCurrentImage();
	if ((xdim > 0) && (ydim > 0) && (zdim > 0)) Order(imp, xdim, ydim, zdim);
    }

    double getdValue(String theText) {
        Double d;
        try {d = new Double(theText);}
        catch (NumberFormatException e){
	    IJ.showMessage("rrr3iiiOpener", "Cannot convert " +theText +" to double.");
            d = null;
        }
        return d.doubleValue();
    }

    int getiValue(String theText) {
        Integer d;
        try {d = new Integer(theText);}
        catch (NumberFormatException e){
	    IJ.showMessage("rrr3iiiOpener", "Cannot convert " +theText +" to int.");
            d = null;
        }
        return d.intValue();
    }

    void Order(ImagePlus imp, int xd1, int xd2, int xd3)
    {
         float[] DataArray1, DataArray2;
         int width, height, slices;
         int h1, i1, j1, h2, i2, j2,l;
         float helpf;
         ImageProcessor ip;
         ImageStack is;
         String s1;

         width = imp.getWidth();
         height = imp.getHeight();
         slices = imp.getStackSize();
         is = imp.getStack();
         DataArray1 = new float[width*height*slices];
         DataArray2 = new float[width*height*slices];
         for (h1=0; h1<slices; h1++) {
             ip = is.getProcessor(h1+1);
             for (i1=0; i1<width; i1++) {
                for (j1=0; j1<height; j1++) {
                    DataArray1[i1 + j1*width + h1*width*height] = ip.getPixelValue(i1, j1);
                }
             }
         }
         l = 0;
         int numl = slices/xd3*height/xd2*width/xd1;
         for (h1=0; h1<slices/xd3; h1++) {
             for (i1=0; i1<height/xd2; i1++) {
                for (j1=0; j1<width/xd1; j1++) {
                    ij.IJ.showStatus(l + "/" + numl);
                    for (h2=0; h2<xd3; h2++) {
                        for (i2=0; i2<xd2; i2++) {
                            for (j2=0; j2<xd1; j2++) {
                                DataArray2[h1*xd3*width*height + h2*width*height + i1*xd2*width + i2*width + j1*xd1 + j2] = DataArray1[l*xd3*xd2*xd1 + h2*xd2*xd1 + i2*xd1 + j2];
                            }
                        }
                    }
                    l++;
                }
             }
         }
         for (h1=0; h1<slices; h1++) {
             ip = is.getProcessor(h1+1);
             l = 0;
             for (i1=0; i1<width; i1++) {
                for (j1=0; j1<height; j1++) {
                    ip.putPixelValue(i1, j1, DataArray2[i1 + j1*width + h1*width*height]);
                }
             }
         }
         imp.updateAndDraw();
    }
}