inra.ijpb.plugins

Class InteractiveMarkerControlledWatershed

java.lang.Object

inra.ijpb.plugins.InteractiveMarkerControlledWatershed

All Implemented Interfaces:

ij.plugin.PlugIn

public class InteractiveMarkerControlledWatershed
extends Object
implements ij.plugin.PlugIn

Plugin to perform automatic segmentation of 2D and 3D images using marker-controlled watershed with manually selected seeds. References: [1] Soille, P., Morphological Image Analysis: Principles and Applications, Springer-Verlag, 1999, pp. 170-171.

Author:

Ignacio Arganda-Carreras

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	InteractiveMarkerControlledWatershed.ResultMode enumeration of result modes

Field Summary

Fields

Modifier and Type	Field and Description
static String	CREATE_IMAGE name of the macro method to show current segmentation result in a new window
static String	MERGE_LABELS name of the macro method to merge selected labels
static String	RUN_SEGMENTATION name of the macro method to segment the current image based on the current parameters
static String	SET_DISPLAY name of the macro method to set the output display format
static String	SET_INPUT_TYPE name of the macro method to set the input image type
static String	SET_RADIUS name of the macro method to set the gradient radius
static String	SHOW_GRADIENT name of the macro method to set the flag to show the gradient image
static String	SHOW_RESULT_OVERLAY name of the macro method to toggle the current overlay
static String	SHUFFLE_COLORS name of the macro method to shuffle color labels

Constructor Summary

Constructors

Constructor and Description
InteractiveMarkerControlledWatershed()

Method Summary

Modifier and Type	Method and Description
static void	createResultImage() Show current result in a new image
static void	mergeLabels() Merge labels that are selected either by a freehand or a point ROI.
static void	record(String command, String... args) Macro-record a specific command.
void	run(String arg0)
static void	segment(String calculateDams, String compactness, String connectivity) Segment current image (GUI needs to be running)
static void	setDisplayFormat(String format) Set the display format in the GUI
static void	shuffleColors() Shuffle LUT of current display image.
static void	toggleOverlay() Toggle current result overlay image

Methods inherited from class java.lang.Object

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

Field Detail

RUN_SEGMENTATION

public static String RUN_SEGMENTATION

name of the macro method to segment the current image based on the current parameters

SHOW_RESULT_OVERLAY

public static String SHOW_RESULT_OVERLAY

name of the macro method to toggle the current overlay

CREATE_IMAGE

public static String CREATE_IMAGE

name of the macro method to show current segmentation result in a new window

SET_INPUT_TYPE

public static String SET_INPUT_TYPE

name of the macro method to set the input image type

SHOW_GRADIENT

public static String SHOW_GRADIENT

name of the macro method to set the flag to show the gradient image

SET_DISPLAY

public static String SET_DISPLAY

name of the macro method to set the output display format

SET_RADIUS

public static String SET_RADIUS

name of the macro method to set the gradient radius

MERGE_LABELS

public static String MERGE_LABELS

name of the macro method to merge selected labels

SHUFFLE_COLORS

public static String SHUFFLE_COLORS

name of the macro method to shuffle color labels

Constructor Detail

InteractiveMarkerControlledWatershed

public InteractiveMarkerControlledWatershed()

Method Detail

run

public void run(String arg0)

Specified by:

run in interface ij.plugin.PlugIn

record

public static void record(String command,
                          String... args)

Macro-record a specific command. The command names match the static methods that reproduce that part of the code.

Parameters:

command - name of the command including package info

args - set of arguments for the command

segment

public static void segment(String calculateDams,
                           String compactness,
                           String connectivity)

Segment current image (GUI needs to be running)

Parameters:

calculateDams - string containing boolean flag to create dams (format: "calculateDams=[boolean])

compactness - compactness constrain parameter (values larger than 0 imply using compact watershed)

connectivity - string containing connectivity value (format: "connectivity=[4 or 8 / 6 or 26])

toggleOverlay

public static void toggleOverlay()

Toggle current result overlay image

mergeLabels

public static void mergeLabels()

Merge labels that are selected either by a freehand or a point ROI. Label of value 0 (watershed line) is skipped.

shuffleColors

public static void shuffleColors()

Shuffle LUT of current display image.

createResultImage

public static void createResultImage()

Show current result in a new image

setDisplayFormat

public static void setDisplayFormat(String format)

Set the display format in the GUI

Parameters:

format - output mode ("Overlaid basins", "Overlaid dams", "Catchment basins", "Watershed lines")