import ij.plugin.*;
import ij.*;
import ij.io.*;
import ij.process.*;
import java.io.*;

/** This plugin opens images in the Isee/Unix (.ISE)  format. 
    modifited by arvonn tully from the  IPLab_Reader source  
    so that we can read ISee/Inovision Files Directly         */
 
public class Isee_Reader extends ImagePlus implements PlugIn {
    boolean littleEndian;
    BufferedInputStream f;

    public void run(String arg) {
	if (arg ==""){
	    OpenDialog od = new OpenDialog("Open Isee...", arg);
	    String directory = od.getDirectory();
	    String name = od.getFileName();
	    if (name==null)
		return;
	    IJ.showStatus("Opening: " + directory + name);
	    open(directory, name, arg);
	}
	if (arg!=""){
	    File theFile=new File(arg);
	    //used to be theFile.getParent();
	    String directory = theFile.getParent()+'/';
	    String name = theFile.getName();
	    if (directory==null) return;
	    open(directory, name, arg);
	}	
    }//run
  
    void open(String directory, String name, String arg) {
        FileInfo fi = null;
        try {
	    fi = getFileInfo(directory, name);
        } catch (IOException e) {
            String error = e.getMessage();
            if (error==null || error.equals(""))
                error = ""+e;
            IJ.showMessage("Isee Reader failed because ", ""+error);
            return;
	}
	if (fi!=null) {
            FileOpener fo = new FileOpener(fi);
            ImagePlus imp = fo.open(false);
            if (imp==null)
                return;
	    setStack(name,  imp.getStack());
            setCalibration(imp.getCalibration());
	    show();
        }
    }//open

    FileInfo getFileInfo(String directory, String name) throws IOException {
        FileInfo fi = new FileInfo();
        f = new BufferedInputStream(new FileInputStream(directory+name));

	// we know that all isee files will be GRAY16_UNSIGNED
	fi.fileType = FileInfo.GRAY16_UNSIGNED;
        fi.fileFormat = fi.RAW;
        fi.fileName = name;
        fi.directory = directory;
  
	littleEndian = false; //Inovision file format is BigEndian
        fi.intelByteOrder = littleEndian;
	
	// we know that all isee images have a 512 byte offset
	// actually this is in the first four bytes
	
	int chomp = getInt();//first four bytes
	fi.offset = chomp;
	chomp = getInt();//second four bytes
	chomp = getInt();//third four bytes
	chomp = getInt();//fourth four bytes

	//fifth four bytes should be X resolution
	fi.width = getInt();
	
	//sixth four bytes should be Y resolution
	fi.height = getInt();
	
	f.close();
        return fi;
    }//getFileInfo
   
    int getByte() throws IOException {
        int b = f.read();
        if (b ==-1) throw new IOException("unexpected EOF");
        return b;
    }//getByte
    
    final int getInt() throws IOException {
        int b0 = getByte();
        int b1 = getByte();
        int b2 = getByte();
        int b3 = getByte();
        if (littleEndian)
            return ((b3<<24) + (b2<<16) + (b1<<8) + b0);
        else
            return ((b0<<24) + (b1<<16) + (b2<<8) + b3);
    }//getInt
}//Isee_Reader