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 ser 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 29/07/04
*/

public class serOpener extends ImagePlus implements PlugIn {

    	private static int xsize=1;
    	private static int ysize=1;
    	private static int zsize=1;

    public void run(String path) {
        String FileLine;

	File theFile=new File(path);
	String directory = theFile.getParent();
	String fileName = theFile.getName();
	String fileSeparator = (String)System.getProperty("file.separator");
	File acqu = new File(directory, "acqu");
	try {
            RandomAccessFile f = new RandomAccessFile(acqu, "r");
	    while ((FileLine = f.readLine()) != null) {
	      if (FileLine.startsWith("##$TD= ")) {
 	      	 xsize = getiValue(FileLine.substring(7, FileLine.length()));
	      }
	    }
	    f.close();
	}
	catch (IOException e) {
	    IJ.showMessage("serOpener", "File acqu not found.");
	    zsize = 0;
	}

	if (xsize < 256) xsize = 256;

	File acqu2 = new File(directory, "acqu2");
	try {
            RandomAccessFile f = new RandomAccessFile(acqu2, "r");
	    while ((FileLine = f.readLine()) != null) {
	      if (FileLine.startsWith("##$TD= ")) {
 	      	 ysize = getiValue(FileLine.substring(7, FileLine.length()));
	      }
	    }
	    f.close();
	}
	catch (IOException e) {
	    IJ.showMessage("serOpener", "File acqu2 not found.");
            ysize = 0;
	}
	File acqu3 = new File(directory, "acqu3");
	try {
            RandomAccessFile f = new RandomAccessFile(acqu3, "r");
	    while ((FileLine = f.readLine()) != null) {
	      if (FileLine.startsWith("##$TD= ")) {
 	      	 zsize = getiValue(FileLine.substring(7, FileLine.length()));
	      }
	    }
	    f.close();
	}
	catch (IOException e) {
            zsize = 1;  // This is a 2D file
	}

	String titledirectory = directory + fileSeparator +"pdata" +fileSeparator +"1";
	File titlefile = new File(titledirectory, "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 {
	    IJ.run("Raw...", "open='" +path +"' image='32-bit Signed' width=" +xsize +" height=" + ysize +" offset=0 number=" +zsize +" gap=0");
	}
	IJ.run("Rename...", "title='" +FileLine +"'");
//	IJ.run("ExtractReal Imag");
//	IJ.run("Close");
    }

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

}