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 a 2dseq file 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 03/08/04
*/

public class seqOpener extends ImagePlus implements PlugIn {

    	private static int xsize=1;
    	private static int ysize=1;
    	private static int zsize=1;
    	private static int ymin=0;
    	private static int dattype=0;
    	private static int imagetype=0;
    	private String byteOrder = "";

    public void run(String path) {
        String FileLine;
        int index;

	File theFile=new File(path);
	String directory = theFile.getParent();
	String fileName = theFile.getName();
	File reco = new File(directory, "reco");
	File proc2s = new File(directory, "proc2s");
	File d3proc = new File(directory, "d3proc");
	if (reco.exists()) read_reco(reco);  // this seems to be a ParaVision file
	else if (proc2s.exists()) read_proc2s(proc2s); // this seems to be a XWinNMR file
	try {
            RandomAccessFile f = new RandomAccessFile(d3proc, "r");
//	IJ.log("reading " +d3proc.getPath());
	    while ((FileLine = f.readLine()) != null) {
              index = FileLine.indexOf("=");
	      if (FileLine.startsWith("##$IM_SIX=")) {
 	      	 xsize = getiValue(FileLine.substring(index+1).trim());
	      }
	      if (FileLine.startsWith("##$IM_SIY=")) {
 	      	 ysize = getiValue(FileLine.substring(index+1).trim());
	      }
	      if (FileLine.startsWith("##$IM_SIZ=")) {
 	      	 zsize = getiValue(FileLine.substring(index+1).trim());
	      }
	      if (FileLine.startsWith("##$DATTYPE= ")) {
 	      	 dattype = getiValue(FileLine.substring(index+1).trim());
	      }

	    }
	    f.close();
	}
	catch (IOException e) {
	    IJ.showMessage("seqOpener", "File d3proc not found.");
	    dattype = 0;
	}

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

	switch (dattype)
	{
	  case 0:
	   ImportDialog id = new ImportDialog(fileName, directory);
	   id.openImage();
	   break;
	  case 1:
	   IJ.run("Raw...", "open='" +path +"' image='8-bit' width=" +xsize +" height=" + ysize +" offset=0 number=" +zsize +" gap=0" +byteOrder);
	   break;
	  case 2:
	   IJ.run("Raw...", "open='" +path +"' image='16-bit Signed' width=" +xsize +" height=" + ysize +" offset=0 number=" +zsize +" gap=0" +byteOrder);
	   break;
	  case 12:
	   IJ.run("Raw...", "open='" +path +"' image='16-bit Signed' width=" +xsize +" height=" + ysize +" offset=0 number=" +zsize +" gap=0" +byteOrder);
	   break;
	  case 3:
	   IJ.run("Raw...", "open='" +path +"' image='16-bit Unsigned' width=" +xsize +" height=" + ysize +" offset=0 number=" +zsize +" gap=0" +byteOrder);
	   break;
	  case 4:
	   IJ.run("Raw...", "open='" +path +"' image='32-bit Signed' width=" +xsize +" height=" + ysize +" offset=0 number=" +zsize +" gap=0" +byteOrder);
	   break;
	  case 5:
	   IJ.run("Raw...", "open='" +path +"' image='32-bit Unsigned' width=" +xsize +" height=" + ysize +" offset=0 number=" +zsize +" gap=0" +byteOrder);
	   break;
	   default:
	   IJ.run("Raw...", "open='" +path +"' image='32-bit Unsigned' width=" +xsize +" height=" + ysize +" offset=0 number=" +zsize +" gap=0" +byteOrder);
	   break;
	}

	IJ.run("Rename...", "title='" +FileLine +"'");
    }

    void read_reco(File reco) {
        String FileLine;
        int index;
//	IJ.log("reading " +reco.getPath());
    	if (!reco.canRead()) {
	    IJ.showMessage("seqOpener", "Cannot read " +reco.getPath() +".");
	    return;
    	}
	try {
        RandomAccessFile f = new RandomAccessFile(reco, "r");
	while ((FileLine = f.readLine()) != null) {
          index = FileLine.indexOf("=");
	  if (FileLine.startsWith("##$RECO_wordtype=")) {
 	     if (FileLine.substring(index+1).equalsIgnoreCase("_8bit_unsgn_int")) dattype = 1;
 	     if (FileLine.substring(index+1).equalsIgnoreCase("_16bit_sgn_int")) dattype = 2;
 	     if (FileLine.substring(index+1).equalsIgnoreCase("_32bit_sgn_int")) dattype = 4;
	  }
	  if (FileLine.startsWith("##$RECO_image_type=")) {
 	     if (FileLine.substring(index+1).equalsIgnoreCase("magnitude_image")) imagetype = 0;
 	     else imagetype = 1;
	  }
	  if (FileLine.startsWith("##$RECO_byte_order=")) {
 	     if (FileLine.substring(index+1).equalsIgnoreCase("bigendian")) byteOrder = "";
 	     if (FileLine.substring(index+1).equalsIgnoreCase("littleendian")) byteOrder = " little-endian";
	  }
	}
	f.close();
	}
	catch (IOException e) {
	    IJ.showMessage("seqOpener", "File reco not found.");
	    dattype = 0;
	}
    }

    void read_proc2s(File proc2s) {
        String FileLine;
        int index, ivalue;
    	if (!proc2s.canRead()) {
	    IJ.showMessage("seqOpener", "Cannot read " +proc2s.getPath() +".");
	    return;
    	}
//	IJ.log("reading " +proc2s.getPath());
	try {
        RandomAccessFile f = new RandomAccessFile(proc2s, "r");
	while ((FileLine = f.readLine()) != null) {
              index = FileLine.indexOf("=");
	      if (FileLine.startsWith("##$BYTORDP=")) {
	         ivalue = getiValue(FileLine.substring(index+1).trim());
	         if (ivalue < 1) byteOrder = "";
	         else byteOrder = " little-endian";
	      }
	}
	}
	catch (IOException e) {
	    IJ.showMessage("seqOpener", "File proc2s not found.");
	    dattype = 0;
	}

    }

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

}