net.sf.ij_plugins.im3d.grow

Class SRG3D

java.lang.Object

net.sf.ij_plugins.util.progress.DefaultProgressReporter

net.sf.ij_plugins.im3d.grow.SRG3D

All Implemented Interfaces:

ProgressReporter

public final class SRG3D
extends DefaultProgressReporter

Seeded region growing algorithm based on article by Rolf Adams and Leanne Bischof, "Seeded Region Growing", IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 16, no. 6, June 1994.

The algorithm assumes that seeds for objects and the background be provided. Seeds are used to compute initial mean gray level for each region. The condition of growth is difference of a gray level of a candidate pixel and mean grey level intensity of a neighboring region. At each step of the algorithm a candidate with a smallest difference to some neighboring region is added to that region and all neighboring points of that that are not yet assigned to any region are added to candidate list.

Part of the image that will be segmented can be restricted by setting a mask.

Progress of segmentation can be recorded on a animation stack. To enable recording set numberOfAnimationFrames to a value larger than 0.

An example of segmenting an image is below. Seeds are set for three regions: background, blob 1, and blob 2.

 // Setup growing
 final ImageStack image = ...;
 final Point3DInt[][] seeds = {
         {new Point3DInt(107, 144, 1)},   // Background
         {new Point3DInt(91, 159, 100)},  // Blob 1
         {new Point3DInt(119, 143, 51)},  // Blob 2
     };
 final SRG3D srg = new SRG3D();
 srg.setImage(image);
 srg.setSeeds(seeds);
 // Run growing
 srg.run();
 // Extract results
 final ImageStack regionMask = srg.getRegionMarkers();
 

If ImageJ is set to debug mode (IJ.debugMode property is true) additional information will be printed to output window (using IJ.log()).

History of growing can be saved using setGrowHistoryEnabled(boolean) and setGrowHistoryDirectory(java.io.File). Saved images represent internal representation of growing regions including 0xff marking of candidate voxels (that were not yet assigned to a region).

Author:

Jarek Sacha

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	GROW_HISTORY_FILE_FORMAT

Constructor Summary

Constructors

Constructor and Description
SRG3D()

Method Summary

Methods

Modifier and Type	Method and Description
java.io.File	getGrowHistoryDirectory()
ij.ImageStack	getRegionMarkers()
boolean	isGrowHistoryEnabled()
void	run() Perform region growing.
void	setGrowHistoryDirectory(java.io.File growHistoryDirectory) Directory where to save marker history growth.
void	setGrowHistoryEnabled(boolean growHistoryEnabled) Enable saving of images containing grow markers.
void	setImage(ij.ImageStack image) Set image to be segmented.
void	setMask(ij.ImageStack mask) Set ROI mask, if not set full image is processed.
void	setSeeds(ij.ImageStack seeds)
static ij.ImageStack	toSeedImage(Point3DInt[][] seeds, int xSize, int ySize, int zSize) Convert array of point seeds to a seed image.

Methods inherited from class net.sf.ij_plugins.util.progress.DefaultProgressReporter

addProgressListener, currentProgress, notifyProgressListeners, notifyProgressListeners, notifyProgressListeners, removeAllProgressListener, removeProgressListener, setCurrentProgress

Methods inherited from class java.lang.Object

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

Field Detail

GROW_HISTORY_FILE_FORMAT

public static final java.lang.String GROW_HISTORY_FILE_FORMAT

See Also:

Constant Field Values

Constructor Detail

SRG3D

public SRG3D()

Method Detail

setImage

public void setImage(ij.ImageStack image)

Set image to be segmented.

Parameters:

image - image.

setSeeds

public void setSeeds(ij.ImageStack seeds)

setMask

public void setMask(ij.ImageStack mask)

Set ROI mask, if not set full image is processed.

Parameters:

mask - Mask of the region of interest used for processing.

getRegionMarkers

public ij.ImageStack getRegionMarkers()

isGrowHistoryEnabled

public boolean isGrowHistoryEnabled()

setGrowHistoryEnabled

public void setGrowHistoryEnabled(boolean growHistoryEnabled)

Enable saving of images containing grow markers. Output directory has to be selected using setGrowHistoryDirectory(java.io.File) .

Parameters:

growHistoryEnabled - if true saving is enabled.

getGrowHistoryDirectory

public java.io.File getGrowHistoryDirectory()

setGrowHistoryDirectory

public void setGrowHistoryDirectory(java.io.File growHistoryDirectory)

Directory where to save marker history growth. Format of each file name is: "SRG_markers_%03d.tif".

Parameters:

growHistoryDirectory - grow history directory.

See Also:

setGrowHistoryEnabled(boolean)

run

public void run()

Perform region growing.

toSeedImage

public static ij.ImageStack toSeedImage(Point3DInt[][] seeds,
                        int xSize,
                        int ySize,
                        int zSize)

Convert array of point seeds to a seed image. The first index in the seeds array refers to the region. Region number if the first index + 1. Second index is a seeds with a region.

Conditions: .

1. Argument seeds cannot be link null.
2. There must be at least 2 regions.
3. There must be at most 253 regions.
4. Each region has to have at least one seed point.
5. All seed points have to be unique.

Parameters:

seeds - region seeds.

xSize - width of the seed image

ySize - height of the seed image

zSize - number of slices

Returns:

seed image.