deformablemesh.util

Class Create3DTrainingDataFromMeshes

java.lang.Object

deformablemesh.util.Create3DTrainingDataFromMeshes

public class Create3DTrainingDataFromMeshes
extends Object

Constructor Summary

Constructors

Constructor and Description
Create3DTrainingDataFromMeshes(List<Track> tracks, ij.ImagePlus plus)

Method Summary

Modifier and Type	Method and Description
ij.ImageStack	createDistanceMapImage(ij.ImageStack mosaic)
ij.ImageStack	createMaskImage(ij.ImageStack mosaic) Creates a binary stack (ByteProcessor#threshold(int)) from the provided labelled image.
ij.ImageStack	createMembraneImage(ij.ImageStack mosaic) Creates a "binary" image, 255 or 0, of the membrane by checking neighboring neighboring pixels for either being background or another blob.
void	fillHoles(ij.process.ImageProcessor p) Fills holes, by inverting the processor (1-> 0 and 0->1) then labels the connected components.
ij.ImageStack	getLabeledStack()
ij.ImagePlus	getOriginalFrame(Integer tp)
static void	main(String[] args) Creates Cerberus training data.
void	run(int meshFrameNumber)
void	showCurrent()
boolean	touchesEdge(List<int[]> pixels, int width, int height) checks if *any* of the provided pixels touch the edge of the box bound by x ∈ [0, width) and y ∈ [0, height)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Create3DTrainingDataFromMeshes

public Create3DTrainingDataFromMeshes(List<Track> tracks,
                                      ij.ImagePlus plus)

Method Detail

showCurrent

public void showCurrent()

run

public void run(int meshFrameNumber)

createMaskImage

public ij.ImageStack createMaskImage(ij.ImageStack mosaic)

Creates a binary stack (ByteProcessor#threshold(int)) from the provided labelled image. First a threshold is used, then a fill holes is used.

Parameters:

mosaic - labelled image, where non-zero values represent a different cell/mesh

Returns:

stack of masked images.

fillHoles

public void fillHoles(ij.process.ImageProcessor p)

Fills holes, by inverting the processor (1-> 0 and 0->1) then labels the connected components. All of the regions that do not touch the edge are set to 255.

Parameters:

p - binary in put processor.

touchesEdge

public boolean touchesEdge(List<int[]> pixels,
                           int width,
                           int height)

checks if *any* of the provided pixels touch the edge of the box bound by x ∈ [0, width) and y ∈ [0, height)

Parameters:

pixels - x,y pairs of points.

width - upper bounds for x. x=0 or x=width-1 touches.

height - upper bounds for y. y=0 or y=height-1 touches.

Returns:

true if any pixel touches and edge, false otherwise.

createMembraneImage

public ij.ImageStack createMembraneImage(ij.ImageStack mosaic)

Creates a "binary" image, 255 or 0, of the membrane by checking neighboring neighboring pixels for either being background or another blob.

Parameters:

mosaic - stack of Labelled images. Each label corresponds to a separate cell/mesh

Returns:

stack stack of images with 255 for membrane and 0 for non-membrane.

createDistanceMapImage

public ij.ImageStack createDistanceMapImage(ij.ImageStack mosaic)

main

public static void main(String[] args)
                 throws IOException

Creates Cerberus training data. Which will be isotropic in dimension and contain 3 aspects. Distance Transform Membrane and

Parameters:

args -

Throws:

IOException

getOriginalFrame

public ij.ImagePlus getOriginalFrame(Integer tp)

getLabeledStack

public ij.ImageStack getLabeledStack()