jp.ac.keio.bio.fun.xitosbml.image

Class Filler

java.lang.Object

jp.ac.keio.bio.fun.xitosbml.image.Filler

public class Filler
extends Object

The class Filler, which provides several morphological operations for filling holes in the image. Date Created: Feb 21, 2017

Author:

Kaito Ii <ii@fun.bio.keio.ac.jp>, Akira Funahashi <funa@bio.keio.ac.jp>

Constructor Summary

Constructors

Constructor and Description
Filler()

Method Summary

Modifier and Type	Method and Description
byte	checkAdjacentsLabel(int w, int h, int d, int labelNum) Check adjacent pixels whether it contains the given label (labelNum).
boolean	checkHole() Check whether a hole exists in the hashmap of pixels (HashMap<label number, pixel value>).
ij.ImagePlus	fill(ij.ImagePlus image) Fill a hole in the given image (ImagePlus object) by morphology operation, and returns the filled image.
void	fill(int labelNum) Fill a hole in the hashmap of pixels (HashMap<label number, pixel value> by morphology operation.
ij.ImagePlus	fill(SpatialImage spImg) Fill a hole in the given image (SpatialImage object) by morphology operation, and returns the filled image as ImageJ image object.
void	fillHole() Fill a hole in the hashmap of pixels (HashMap<label number, pixel value> by morphology operation.
void	label() Assign a label (label number) to each pixel.

Methods inherited from class java.lang.Object

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

Constructor Detail

Filler

public Filler()

Method Detail

fill

public ij.ImagePlus fill(ij.ImagePlus image)

Fill a hole in the given image (ImagePlus object) by morphology operation, and returns the filled image.

Parameters:

image - the ImageJ image object

Returns:

the filled ImageJ image (ImagePlus) object

fill

public ij.ImagePlus fill(SpatialImage spImg)

Fill a hole in the given image (SpatialImage object) by morphology operation, and returns the filled image as ImageJ image object.

Parameters:

spImg - the SpatialImage object

Returns:

the filled ImageJ image (ImagePlus) object

label

public void label()

Assign a label (label number) to each pixel. The label number will be stored in mask[] array. The domain which has pixel value = 0 will have a label = 1.

checkHole

public boolean checkHole()

Check whether a hole exists in the hashmap of pixels (HashMap<label number, pixel value>).

Returns:

true, if a hole exists

fillHole

public void fillHole()

Fill a hole in the hashmap of pixels (HashMap<label number, pixel value> by morphology operation. The fill operation will be applied to each domain (which has unique label number).

fill

public void fill(int labelNum)

Fill a hole in the hashmap of pixels (HashMap<label number, pixel value> by morphology operation. The hole will be filled with the pixel value of adjacent pixel.

Parameters:

labelNum - the label number

checkAdjacentsLabel

public byte checkAdjacentsLabel(int w,
                                int h,
                                int d,
                                int labelNum)

Check adjacent pixels whether it contains the given label (labelNum). If all the adjacent pixels have same label with given label, then return 0. If the adjacent pixels contain different labels, then returns the pixel value of most enclosing adjacent domain.

Parameters:

w - the x offset

h - the y offset

d - the z offset

labelNum - the label number

Returns:

the pixel value of most enclosing adjacent domain if different domain exists, otherwise 0