inra.ijpb.watershed

Class WatershedTransform3D

java.lang.Object

inra.ijpb.watershed.WatershedTransform3D

Direct Known Subclasses:

MarkerControlledWatershedTransform3D

public class WatershedTransform3D
extends Object

Class to apply the watershed algorithm in 3D to an image. It allows specifying a binary mask to restrict the regions of interest.

Author:

Ignacio Arganda-Carreras

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	verbose flag to output the transform steps and their execution times in the log window

Constructor Summary

Constructors

Constructor and Description
WatershedTransform3D(ij.ImagePlus input, ij.ImagePlus mask) Construct a watershed transform
WatershedTransform3D(ij.ImagePlus input, ij.ImagePlus mask, int connectivity) Construct a watershed transform

Method Summary

Modifier and Type	Method and Description
ij.ImagePlus	apply() Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M.
ij.ImagePlus	apply(double hMin, double hMax) Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M.
ArrayList<VoxelRecord>	extractVoxelValues(ij.ImageStack inputStack, double hMin, double hMax) Extract voxel values from input image such that they have value h, hMin <= h <= hMax.
int	getConnectivity() Get the voxel connectivity (6 or 26)
void	setConnectivity(int conn) Set the voxel connectivity (6 or 26)
void	setVerbose(boolean verbose) Set verbose flag

Methods inherited from class java.lang.Object

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

Field Detail

verbose

protected boolean verbose

flag to output the transform steps and their execution times in the log window

Constructor Detail

WatershedTransform3D

public WatershedTransform3D(ij.ImagePlus input,
                            ij.ImagePlus mask)

Construct a watershed transform

Parameters:

input - input image (usually a gradient image)

mask - binary mask to restrict the region of interest (null to use whole input image)

WatershedTransform3D

public WatershedTransform3D(ij.ImagePlus input,
                            ij.ImagePlus mask,
                            int connectivity)

Construct a watershed transform

Parameters:

input - grayscale image (usually a gradient image)

mask - binary mask to restrict the region of interest (null to use whole input image)

connectivity - voxel connectivity (6 or 26)

Method Detail

getConnectivity

public int getConnectivity()

Get the voxel connectivity (6 or 26)

Returns:

voxel connectivity

setConnectivity

public void setConnectivity(int conn)

Set the voxel connectivity (6 or 26)

Parameters:

conn - voxel connectivity

setVerbose

public void setVerbose(boolean verbose)

Set verbose flag

Parameters:

verbose - new verbose flag

apply

public ij.ImagePlus apply()

Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M. Vincent. "Determining watersheds in digital pictures via flooding simulations." Lausanne-DL tentative. International Society for Optics and Photonics, 1990.

Returns:

image of labeled catchment basins (with dams)

apply

public ij.ImagePlus apply(double hMin,
                          double hMax)

Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M. Vincent. "Determining watersheds in digital pictures via flooding simulations." Lausanne-DL tentative. International Society for Optics and Photonics, 1990.

Parameters:

hMin - the minimum value for dynamic

hMax - the maximum value for dynamic

Returns:

image of labeled catchment basins (with dams)

extractVoxelValues

public ArrayList<VoxelRecord> extractVoxelValues(ij.ImageStack inputStack,
                                                 double hMin,
                                                 double hMax)

Extract voxel values from input image such that they have value h, hMin <= h <= hMax. A binary mask is used if it exists.

Parameters:

inputStack - input stack

hMin - minimum grayscale height value

hMax - maximum grayscale height value

Returns:

list of input voxel values