Binarize (ImageJ2 Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.scijava.AbstractContextual
- - org.scijava.command.ContextCommand
  - - net.imagej.plugins.commands.binary.Binarize<T>

All Implemented Interfaces:

Runnable, Cancelable, Command, Contextual, SciJavaPlugin
```
public class Binarize<T extends RealType<T>>
extends ContextCommand
```
Creates or updates a mask Dataset of type BitType. Uses an input Dataset that will be thresholded. Thresholding options can be specified which are used to discriminate pixel values. The input Dataset can become the mask if desired.

Author:

Barry DeZonia

Field Summary

Fields
Modifier and Type Field and Description

static String BLACK

static String DEFAULT_METHOD

static String INSIDE

static String OUTSIDE

static String WHITE

Fields
Modifier and Type	Field and Description
`static String`	`BLACK`
`static String`	`DEFAULT_METHOD`
`static String`	`INSIDE`
`static String`	`OUTSIDE`
`static String`	`WHITE`

Constructor Summary

Constructors
Constructor and Description

Binarize()

Constructors
Constructor and Description
`Binarize()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`changeInput()` Gets whether to change input data to contain the output mask.
`boolean`	`fillMaskBackground()` Gets whether to fill background pixels of binary mask or not.
`boolean`	`fillMaskForeground()` Gets whether to fill foreground pixels of binary mask or not.
`Dataset`	`inputData()` Gets the reference input data.
`Dataset`	`inputMask()` Gets the preexisting mask (if any).
`String`	`maskColor()` Gets the color of the mask pixels.
`String`	`maskPixels()` Gets which pixels are considered part of the mask.
`Dataset`	`outputMask()` Gets the output mask.
`void`	`run()`
`void`	`setChangeInput(boolean val)` Sets whether to change input data to contain the output mask.
`void`	`setDefaultThresholdMethod()` Sets the threshold method to the default algorithm.
`void`	`setFillMaskBackground(boolean val)` Sets whether to fill background pixels of binary mask or not to the given specified value.
`void`	`setFillMaskForeground(boolean val)` Sets whether to fill foreground pixels of binary mask or not to the given specified value.
`void`	`setInputData(Dataset dataset)` Sets the reference input data.
`void`	`setInputMask(Dataset dataset)` Sets the preexisting mask (if any).
`void`	`setMaskColor(String blackOrWhite)` Sets the color of the mask pixels.
`void`	`setMaskPixels(String insideOrOutside)` Sets which pixels are considered part of the mask.
`void`	`setThresholdEachPlane(boolean val)` Set whether to threshold each plane separately or to threshold the whole image at once.
`void`	`setThresholdMethod(net.imagej.threshold.ThresholdMethod thresholdMethod)` Sets the threshold method to use for pixel discrimination.
`boolean`	`thresholdEachPlane()` Gets whether to threshold each plane separately or to threshold the whole image at once.
`net.imagej.threshold.ThresholdMethod`	`thresholdMethod()` Gets the threshold method used for pixel discrimination.

Methods inherited from class org.scijava.command.ContextCommand
cancel, getCancelReason, isCanceled

Methods inherited from class org.scijava.AbstractContextual
context, getContext

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.scijava.Contextual
setContext

- Field Detail
  - INSIDE
```
public static final String INSIDE
```
    See Also:
    
    Constant Field Values
  - OUTSIDE
```
public static final String OUTSIDE
```
    See Also:
    
    Constant Field Values
  - WHITE
```
public static final String WHITE
```
    See Also:
    
    Constant Field Values
  - BLACK
```
public static final String BLACK
```
    See Also:
    
    Constant Field Values
  - DEFAULT_METHOD
```
public static final String DEFAULT_METHOD
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Binarize
```
public Binarize()
```
- Method Detail
  - setThresholdMethod
```
public void setThresholdMethod(net.imagej.threshold.ThresholdMethod thresholdMethod)
```
    Sets the threshold method to use for pixel discrimination.
    
    Parameters:
    
    thresholdMethod - The name of the threshold method to use.
  - thresholdMethod
```
public net.imagej.threshold.ThresholdMethod thresholdMethod()
```
    Gets the threshold method used for pixel discrimination.
  - setMaskPixels
```
public void setMaskPixels(String insideOrOutside)
```
    Sets which pixels are considered part of the mask. Those either inside or outside the threshold range. Use the constants MakeBinary.INSIDE or MakeBinary.OUTSIDE.
    
    Parameters:
    
    insideOrOutside - One of the values INSIDE or OUTSIDE.
  - maskPixels
```
public String maskPixels()
```
    Gets which pixels are considered part of the mask. Either inside or outside the threshold range. Returns one of the constants MakeBinary.INSIDE or MakeBinary.OUTSIDE.
  - setMaskColor
```
public void setMaskColor(String blackOrWhite)
```
    Sets the color of the mask pixels. Either black or white. Use the constants MakeBinary.BLACK or MakeBinary.WHITE.
    
    Parameters:
    
    blackOrWhite - One of the values BLACK or WHITE.
  - maskColor
```
public String maskColor()
```
    Gets the color of the mask pixels. Either black or white. One of the constants MakeBinary.BLACK or MakeBinary.WHITE.
  - setThresholdEachPlane
```
public void setThresholdEachPlane(boolean val)
```
    Set whether to threshold each plane separately or to threshold the whole image at once.
  - thresholdEachPlane
```
public boolean thresholdEachPlane()
```
    Gets whether to threshold each plane separately or to threshold the whole image at once.
  - setFillMaskForeground
```
public void setFillMaskForeground(boolean val)
```
    Sets whether to fill foreground pixels of binary mask or not to the given specified value.
    
    Parameters:
    
    val - The specified value.
  - fillMaskForeground
```
public boolean fillMaskForeground()
```
    Gets whether to fill foreground pixels of binary mask or not.
  - setFillMaskBackground
```
public void setFillMaskBackground(boolean val)
```
    Sets whether to fill background pixels of binary mask or not to the given specified value.
    
    Parameters:
    
    val - The specified value.
  - fillMaskBackground
```
public boolean fillMaskBackground()
```
    Gets whether to fill background pixels of binary mask or not.
  - setInputData
```
public void setInputData(Dataset dataset)
```
    Sets the reference input data.
    
    Parameters:
    
    dataset -
  - inputData
```
public Dataset inputData()
```
    Gets the reference input data.
  - setInputMask
```
public void setInputMask(Dataset dataset)
```
    Sets the preexisting mask (if any).
  - inputMask
```
public Dataset inputMask()
```
    Gets the preexisting mask (if any).
  - outputMask
```
public Dataset outputMask()
```
    Gets the output mask.
  - setChangeInput
```
public void setChangeInput(boolean val)
```
    Sets whether to change input data to contain the output mask.
  - changeInput
```
public boolean changeInput()
```
    Gets whether to change input data to contain the output mask.
  - setDefaultThresholdMethod
```
public void setDefaultThresholdMethod()
```
    Sets the threshold method to the default algorithm.
  - run
```
public void run()
```

Class Binarize<T extends RealType<T>>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.scijava.command.ContextCommand

Methods inherited from class org.scijava.AbstractContextual

Methods inherited from class java.lang.Object

Methods inherited from interface org.scijava.Contextual

Field Detail

INSIDE

OUTSIDE

WHITE

BLACK

DEFAULT_METHOD

Constructor Detail

Binarize

Method Detail

setThresholdMethod

thresholdMethod

setMaskPixels

maskPixels

setMaskColor

maskColor

setThresholdEachPlane

thresholdEachPlane

setFillMaskForeground

fillMaskForeground

setFillMaskBackground

fillMaskBackground

setInputData

inputData

setInputMask

inputMask

outputMask

setChangeInput

changeInput

setDefaultThresholdMethod

run