This class deals with running the actual 3B code It should be run in a separate thread It will make calls back to a viewer, and accepts termination calls as well. More...

Public Member Functions
void	register (EControlPanel c)
void	run ()
Static Public Member Functions
static void	addLibraryPath (String pathToAdd) throws Exception
Package Functions
	ThreeBRunner (ByteProcessor mask_, ImageStack s, String cfg_, String filename_, int firstfr, int lastfr)
void	stop_thread ()
boolean	has_stopped ()
void	send_message_string (String s)
void	send_new_points (float[] points)
void	die (String err)
boolean	should_stop ()
native void	call (String cfg, float[][] images, byte[] mask, int n_images, int rows, int cols, String file)
Static Package Functions
static String	get_plugin_dir ()
static UnsatisfiedLinkError	try_to_load_dlls (String[] s)
	[static initializer]
Package Attributes
ByteProcessor	mask
float[][]	pixels
EControlPanel	cp
String	config
String	filename
long	start_time
int	its
Static Private Member Functions
static String	decodePercent (String str)
Private Attributes
volatile boolean	stop = false
volatile boolean	stopped = false
boolean	fatal = false

Detailed Description

This class deals with running the actual 3B code It should be run in a separate thread It will make calls back to a viewer, and accepts termination calls as well.

Definition at line 1283 of file three_B.java.

Constructor & Destructor Documentation

ThreeBRunner::ThreeBRunner	(	ByteProcessor	mask_,
		ImageStack	s,
		String	cfg_,
		String	filename_,
		int	firstfr,
		int	lastfr
	)		`[inline, package]`

Definition at line 1296 of file three_B.java.

References config, filename, mask, and pixels.

    {
        config = cfg_;
        filename = filename_;
        
        //Take a copy of the mask to stop it getting trashed by other threads
        mask = (ByteProcessor)mask_.duplicate();
        
        //Convert all the input images into float as a common
        //format. They will be scaled differently from float images 
        //loaded by libcvd, but the later normalization will take care of that
        //
        //Oh, and ImageStack counts from 1, not 0
        pixels = new float[lastfr - firstfr + 1][];
        for(int i=firstfr; i <= lastfr; i++)
            pixels[i-firstfr] = (float[])s.getProcessor(i+1).convertToFloat().getPixels();
    }

Member Function Documentation

void ThreeBRunner::register ( EControlPanel c ) [inline]

Definition at line 1314 of file three_B.java.

References cp.

Referenced by EControlPanel::EControlPanel().

    {
        cp = c;
    }

void ThreeBRunner::stop_thread ( ) [inline, package]

Definition at line 1319 of file three_B.java.

References send_message_string(), and stop.

Referenced by EControlPanel::issue_stop(), and EControlPanel::windowClosing().

    {
        stop=true;
        send_message_string("stopping...");
    }

boolean ThreeBRunner::has_stopped ( ) [inline, package]

Definition at line 1325 of file three_B.java.

References stopped.

Referenced by EControlPanel::windowClosing().

    {
        return stopped;
    }

void ThreeBRunner::send_message_string ( String s ) [inline, package]

Definition at line 1332 of file three_B.java.

References cp, and EControlPanel::send_status_text_message().

Referenced by stop_thread().

    {
        cp.send_status_text_message(s);
    }

void ThreeBRunner::send_new_points ( float[] points ) [inline, package]

Definition at line 1337 of file three_B.java.

References EControlPanel::append(), cp, ThreeBGlobalConstants::critical_iterations, its, EControlPanel::send_time_text_message(), EControlPanel::send_update_canvas_event(), start_time, Spot::x, and Spot::y.

    {
        //New points are sent in the form x, y, x, y
        ArrayList<Spot> tmp = new ArrayList<Spot>();
        for(int i=0; i < points.length; i+=2)
        {
            Spot s = new Spot();
            s.x = points[i];
            s.y = points[i+1];
            tmp.add(s);
        }

        cp.append(tmp, its);
        cp.send_update_canvas_event();
            
        //This happens each "iteration", i.e. each pass.
        long current = (new java.util.Date()).getTime();

        if(its > 0)
        {
            if(its < 8)
                cp.send_time_text_message("computing...");
            else
            {
                long time_per_it = (current -start_time) / its;
                int target = (int)Math.ceil(its * 1.0 / ThreeBGlobalConstants.critical_iterations) * ThreeBGlobalConstants.critical_iterations;
                int its_remaining = target-its;

                System.out.println("Its = " + its);
                System.out.println("rem = " + its_remaining);
                System.out.println("time_per_it = " + time_per_it);

                
                long time_remaining_s = (its_remaining * time_per_it)/1000;
                
                long s = time_remaining_s % 60;
                long m = (time_remaining_s / 60)%60;
                long h = time_remaining_s / 3600;

                cp.send_time_text_message( h + "h" + m + "m (for " + target + " iterations)");
            }
            
        }
        
        //Increment after, since it outputs the initial spots as well
        its++;
    }

void ThreeBRunner::die ( String err ) [inline, package]

Definition at line 1385 of file three_B.java.

References cp, EControlPanel::die(), and fatal.

    {
        cp.die(err);
        fatal=true;
    }

boolean ThreeBRunner::should_stop ( ) [inline, package]

Definition at line 1391 of file three_B.java.

References stop.

    {
        return stop;
    }

native void ThreeBRunner::call	(	String	cfg,
		float	images[][],
		byte[]	mask,
		int	n_images,
		int	rows,
		int	cols,
		String	file
	)		`[package]`

Referenced by run().

void ThreeBRunner::run ( ) [inline]

Definition at line 1398 of file three_B.java.

References call(), config, cp, fatal, filename, its, mask, pixels, EControlPanel::send_status_text_message(), start_time, and stopped.

    {
        System.out.println("About to call...");
        start_time = (new java.util.Date()).getTime();
        its=0;

        call(config, pixels, (byte[])mask.getPixels(), pixels.length, mask.getHeight(), mask.getWidth(), filename);

        System.out.println("Finished.");
        
        if(!fatal)
        {
            cp.send_status_text_message("Finished\n");
            ij.IJ.showStatus("3B run terminated");
        }

        stopped=true;
    }

static String ThreeBRunner::decodePercent ( String str ) [inline, static, private]

Definition at line 1420 of file three_B.java.

    {
        StringBuffer sb = new StringBuffer();
        for (int i = 0; i < str.length(); i++) 
        {
            char c = str.charAt(i);
            if(c == '+')
                sb.append(' ');
            else if(c == '%')
            {
                sb.append((char) Integer.parseInt(str.substring(i + 1, i + 3), 16));
                i += 2;
            }
            else
                sb.append(c);
        }
        return sb.toString();
    }

static void ThreeBRunner::addLibraryPath ( String pathToAdd ) throws Exception [inline, static]

Adds the specified path to the java library path.

Parameters:

pathToAdd the path to add

Exceptions:

Exception

Definition at line 1445 of file three_B.java.

                                                                        {
        final Field usrPathsField = ClassLoader.class.getDeclaredField("usr_paths");
        usrPathsField.setAccessible(true);
     
        //get array of paths
        final String[] paths = (String[])usrPathsField.get(null);
     
        //check if the path to add is already present
        for(String path : paths) {
            if(path.equals(pathToAdd)) {
                return;
            }
        }
     
        //add the new path
        final String[] newPaths = Arrays.copyOf(paths, paths.length + 1);
        newPaths[newPaths.length-1] = pathToAdd;
        usrPathsField.set(null, newPaths);
    }

static String ThreeBRunner::get_plugin_dir ( ) [inline, static, package]

Definition at line 1489 of file three_B.java.

Referenced by try_to_load_dlls().

    {
        try{
            String img_url = (new SPair()).getClass().getResource("img").getFile();
            URI jar_url = null;
            
            jar_url= new URI(img_url.substring(0, img_url.length()-5));

            File jar = new File(jar_url);

            System.out.println("File: " + jar.getCanonicalPath());


            String dir = jar.getParentFile().getCanonicalPath() + File.separator;
            System.out.println("Dir: " + dir);

            return dir;
            
        }
        catch(Exception e){
            return "";
        }
    }

static UnsatisfiedLinkError ThreeBRunner::try_to_load_dlls ( String[] s ) [inline, static, package]

Definition at line 1514 of file three_B.java.

References get_plugin_dir().

    {
        String dir = get_plugin_dir();
        
        try{
            for(int i=0; i < s.length; i++)
            {
                System.out.println("Loading " + dir+s[i]);
                System.load(dir + s[i]);
            }
            
            return null;
        }
        catch(UnsatisfiedLinkError e)
        {
            System.out.println("Link error: " + e.getMessage());
            return e;
        }

    }