MorphologicalSegmentation (MorphoLibJ 1.6.0.1 API)

java.lang.Object
- inra.ijpb.plugins.MorphologicalSegmentation

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class MorphologicalSegmentation
extends Object
implements ij.plugin.PlugIn
```
Plugin to perform automatic segmentation of 2D and 3D images based on morphological operations, mainly extended minima and watershed transforms. 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 MorphologicalSegmentation.ResultMode
enumeration of result modes

Nested Classes
Modifier and Type	Class and Description
`static class`	`MorphologicalSegmentation.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_GRADIENT_TYPE` name of the macro method to set the gradient method
`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

MorphologicalSegmentation()

Constructors
Constructor and Description
`MorphologicalSegmentation()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
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 dynamic, String calculateDams, String connectivity)` Segment current image (GUI needs to be running)
`static void`	`segment(String dynamic, String calculateDams, String connectivity, String usePriorityQueue)` Deprecated. the priority queue method is now the only one
`static void`	`setDisplayFormat(String format)` Set the display format in the GUI
`static void`	`setGradientRadius(String radius)` Set the gradient radius
`static void`	`setGradientType(String method)` Set the gradient method to use
`static void`	`setInputImageType(String type)` Set input image type
`static void`	`setShowGradient(String bool)` Set GUI to show gradient image in the main canvas
`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
  - SET_GRADIENT_TYPE
```
public static String SET_GRADIENT_TYPE
```
    name of the macro method to set the gradient method
  - 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
  - MorphologicalSegmentation
```
public MorphologicalSegmentation()
```
- 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 dynamic,
                           String calculateDams,
                           String connectivity,
                           String usePriorityQueue)
```
    Deprecated. the priority queue method is now the only one
    
    Segment current image (GUI needs to be running)
    
    Parameters:
    
    dynamic - string containing dynamic value (format: "dynamic=[integer value]")
    
    calculateDams - string containing boolean flag to create dams (format: "calculateDams=[boolean])
    
    connectivity - string containing connectivity value (format: "connectivity=[4 or 8 / 6 or 26])
    
    usePriorityQueue - string containing boolean flag to use priority queue (format: "usePriorityQueue=[boolean])
  - segment
```
public static void segment(String dynamic,
                           String calculateDams,
                           String connectivity)
```
    Segment current image (GUI needs to be running)
    
    Parameters:
    
    dynamic - string containing dynamic value (format: "dynamic=[integer value]")
    
    calculateDams - string containing boolean flag to create dams (format: "calculateDams=[boolean])
    
    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
  - setInputImageType
```
public static void setInputImageType(String type)
```
    Set input image type
    
    Parameters:
    
    type - input image type (border or object)
  - setShowGradient
```
public static void setShowGradient(String bool)
```
    Set GUI to show gradient image in the main canvas
    
    Parameters:
    
    bool - true to display gradient image and false to display input 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")
  - setGradientRadius
```
public static void setGradientRadius(String radius)
```
    Set the gradient radius
    
    Parameters:
    
    radius - gradient radius size (in pixels)
  - setGradientType
```
public static void setGradientType(String method)
```
    Set the gradient method to use
    
    Parameters:
    
    method - name of the gradient method to use

Class MorphologicalSegmentation

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

RUN_SEGMENTATION

SHOW_RESULT_OVERLAY

CREATE_IMAGE

SET_INPUT_TYPE

SHOW_GRADIENT

SET_DISPLAY

SET_RADIUS

SET_GRADIENT_TYPE

MERGE_LABELS

SHUFFLE_COLORS

Constructor Detail

MorphologicalSegmentation

Method Detail

run

record

segment

segment

toggleOverlay

mergeLabels

shuffleColors

createResultImage

setInputImageType

setShowGradient

setDisplayFormat

setGradientRadius

setGradientType