Javascript console examples

Using the javascript exposes many of the actions that are difficult to include in a graphical interface. Each one can increase the complexity of the interface significantly. There can also be parameters that need to be passed. Or actions that can be done repetively.

A handy feature of the javascript console is that it has auto complete. Start by typing a command, especially by using the ‘controls’ object, and press tab and a selection of options will be shown.

The API

The main entry point is the SegmentationController object that handles most of the data. All of the public methods are accessible.

Detecting meshes automatically.

controls.guessMeshes(1);

This will go through each image in the current volume and apply a threshold of 1. It will then do a 3D connected components to find candidate meshes. Then meshes are initialized by racasting at each connected component.

Creating 3D training data.

controls.generateTrainingData( 0, 5 );

Creates a folder labels and a folder images

Changing the color scheme

mf3d = controls.getMeshFrame3D();
mf3d.setBackgroundColor(Color.BLACK);
controls.setVolumeColor(Color.GREEN);

set it back.

mf3d.setBackgroundColor(Color.WHITE);
controls.setVolumeColor(Color.BLUE);

Remove all tracks outside of a certain track range. **This modifies

tracks so it can clear an undo stack.**

function clearRemainingMeshes(first, last){
    tracks = controls.getAllTracks();
    tracks.removeIf( function(track){
		fi = track.getFirstFrame();
        li = track.getLastFrame();
        return fi > last || li < first;
    });
    controls.setMeshTracks(tracks);
    
    tracks = controls.getAllTracks();
    for(i = 0; i<tracks.size(); i++){
        track = tracks.get(i);
        for( j = track.getFirstFrame() ; j<=track.getLastFrame(); j++){
            if(j < first || j > last){
                controls.clearMeshFromTrack(track, j, track.getMesh(j));
            }
        }
    }
}

Surface Plots

There are two surface plots available. Intensity or Curvature.

sp = controls.intensitySurfacePlot();
sp.processAndShow();

We can set a clipping range, and change the colors used. We also can access the MeshFrame and set the background color.

  cp = controls.curvatureSurfacePlot();
  cp.process();
  cp.setMax(cp.getMax()*0.8);
  cp.setHighColor(Color.YELLOW);
  cp.setLow(Color.BLUE);
  cp.show();

The surface plots have quite a few controls.

Iterating through all of the frames and deforming each existing mesh 100 steps.

n = controls.getNFrames();
tracks = controls.getAllTracks();
for(var i = 0; i<n; i++){
    controls.toFrame(i)
    ts = tracks.size();
    for( var j = 0; j<ts; j++){
        track = tracks.get(j);
        if(track.containsKey(i)){
            mesh = track.getMesh(i);
            echo(i + ", " + j + ", " + mesh);
            controls.selectMesh(mesh);
            controls.deformMesh(100);
        }
    }
}

Creates a movie by taking a snapshot and rotating the viewing platform each frame.

ImageStack = Java.type("ij.ImageStack");
ColorProcessor = Java.type("ij.process.ColorProcessor");
ImageStack = Java.type("ij.ImageStack");

mf3d = controls.getMeshFrame3D();
stack = 0;
for(var i = 0; i<360; i++){
	c = Math.cos(i*3.14/180)*Math.cos(0.1);
	s = Math.sin(i*3.14/180)*Math.cos(0.1);
	z = Math.sin(0.1)
	controls.nextFrame();
	mf3d.lookTowards([c, s, z], [0, 0, 1]);
	img = mf3d.snapShot();
	proc = new ColorProcessor(img);
	if(stack==0){
		stack = new ImageStack(proc.getWidth(), proc.getHeight());
	}
	stack.addSlice(proc);
}
plus = new ImagePlus();
plus.setStack(stack);
plus.show();

Create a movie of the current mesh deforming. Frames determines how many frames will be in the resulting movie. and steps is how many steps of deformation between frames. Warning, this will effectively erase your undo history.

ImageStack = Java.type("ij.ImageStack");
ColorProcessor = Java.type("ij.process.ColorProcessor");
ImageStack = Java.type("ij.ImageStack");
frames = 100;
steps = 3;

mf3d = controls.getMeshFrame3D();
stack = 0;
for(var i = 0; i<frames; i++){
	controls.deformMesh(steps);
	img = mf3d.snapShot();
	proc = new ColorProcessor(img);
	if(stack==0){
		stack = new ImageStack(proc.getWidth(), proc.getHeight());
	}
	stack.addSlice(proc);
}
plus = new ImagePlus();
plus.setStack(stack);
plus.show();

Find and select a mesh based on volume.

Finds the first mesh with a volume less than a threshold value.

stopping = false;
tracks = controls.getAllTracks();
threshold = 0;
for( key in tracks){
    track = tracks[key];
    map = track.getTrack();
    for( frame in map){
        mesh = track.getMesh( frame );
        if( mesh.calculateVolume() < threshold){
            controls.toFrame(frame);
             controls.selectMesh(mesh);
             stopping = true;
             break;
        }
    }
    if(stopping){
         break;
    }
}

if(stopping){
    echo("found small mesh!");
}	

Goes through each frame and auto tracks any unlinked meshes. Autotracking tries to link any tracks that do not exist in the current frame, but do exist in the next frame.

for( i = 0; i<controls.getNFrames() - 1; i++){
  controls.toFrame(i);
  controls.autotrackAvailableTracks();
  }