ChannelMasker (Incenp.org ImageJ Plugins 0.9.6 API)

java.lang.Object
- org.incenp.imagej.ChannelMasker

```
public class ChannelMasker
extends Object
```
A helper class to create and apply binary masks. A ChannelMasker object is defined by a list of “operations” that describes how to generate a new image from a given source image. The generated image will contain as many channels as there are operations in the list.
Four different types of operations are supported:
- copying a channel verbatim from the source image;
- creating a binary mask from one the channel of the source image;
- applying a binary mask to one of the channel of the source image; the binary mask itself is also taken from a channel of the source image;
- inverting a binary mask.

Constructor Summary

Constructors
Constructor and Description

ChannelMasker(org.incenp.imagej.ChannelMasker.ChannelOperation[] operations)
Creates a new ChannelMasker object with the given list of operations.

Constructors
Constructor and Description
`ChannelMasker(org.incenp.imagej.ChannelMasker.ChannelOperation[] operations)` Creates a new ChannelMasker object with the given list of operations.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`ij.ImagePlus`	`apply(ij.ImagePlus image, String name)` Apply this ChannelMasker object to an image.
`ij.ImagePlus`	`apply(ij.ImagePlus image, String name, String order)` Apply this ChannelMasker object to an image.
`static ij.ImagePlus`	`applyMasker(ij.ImagePlus image, String command, String name, String order)` Apply a list of operations to an image.
`ChannelMasker`	`chain(ChannelMasker next)` Sets a ChannelMasker to apply after the current one.
`static ChannelMasker`	`createMasker(String command)` Creates a ChannelMasker object from a text description of the operations.
`static ChannelMasker`	`createMasker(String command, String order)` Creates a ChannelMasker object from a text description of the operations.
`static ChannelMasker`	`createMasker(String command, String order, int options)` Creates a ChannelMasker from a text description of the operations.
`String`	`getChannelOrder()` Gets the default channel order specification.
`int`	`getMaskingOptions()` Gets the masking options currently used by this object.
`void`	`setChannelOrder(String order)` Sets the default channel order specification.
`void`	`setMaskingOptions(int options)` Sets the masking options used by this object.

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

- Constructor Detail
  - ChannelMasker
```
public ChannelMasker(org.incenp.imagej.ChannelMasker.ChannelOperation[] operations)
```
    Creates a new ChannelMasker object with the given list of operations. This constructor is public and may be called directly, but the createMasker(String) static method is the preferred high-level interface to create a ChannelMasker.
    
    Parameters:
    
    operations - the list of operations to apply
- Method Detail
  - setChannelOrder
```
public void setChannelOrder(String order)
```
    Sets the default channel order specification. A channel order specification is a string of one-letter channel codes; those channel codes may then be used when calling the createMasker(java.lang.String, java.lang.String, int) method to refer to channels without knowing the position of the channels in the images the masker will be applied to.
    For example, a masker object created with the "A:MASK(Huang),B:COPY()" command and applied to an image with channel order "ABC" will perform the MASK operation to the first channel and the COPY operation to the second channel; the same masker applied to an image with channel order "CADB" will perform the MASK operation on the second channel and the COPY operation to the fourth channel.
    
    Parameters:
    
    order - the default channel order to use when applying the masker
  - getChannelOrder
```
public String getChannelOrder()
```
    Gets the default channel order specification.
    
    Returns:
    
    the default channel order used by this masker
    
    See Also:
    
    setChannelOrder(String)
  - setMaskingOptions
```
public void setMaskingOptions(int options)
```
    Sets the masking options used by this object. See the constant fields in Masking for available options. By default ChannelMasker objects uses the CLOSE_OPEN_MASK option.
    
    Parameters:
    
    options - the new masking options
  - getMaskingOptions
```
public int getMaskingOptions()
```
    Gets the masking options currently used by this object.
    
    Returns:
    
    the current masking options
  - apply
```
public ij.ImagePlus apply(ij.ImagePlus image,
                          String name,
                          String order)
```
    Apply this ChannelMasker object to an image. This method will create a new image by performing all the operations defined in the object’s operations list.
    
    Parameters:
    
    image - the source image to apply the operations to
    
    name - the name to give to the new image
    
    order - the order of channels in the source image (may be null, in which case the default channel order will be used)
    
    Returns:
    
    the resulting image
  - apply
```
public ij.ImagePlus apply(ij.ImagePlus image,
                          String name)
```
    Apply this ChannelMasker object to an image. This method will create a new image by performing all the operations defined in the object’s operations list. If the ChannelMasker uses channel codes instead of channel indexes, they will be translated using the default channel order specification.
    
    Parameters:
    
    image - the source image to apply the operations to
    
    name - the name to give to the new image
    
    Returns:
    
    the resulting image
  - chain
```
public ChannelMasker chain(ChannelMasker next)
```
    Sets a ChannelMasker to apply after the current one. When the apply(ij.ImagePlus, java.lang.String, java.lang.String) method is called, the specified ChannelMasker will be applied to the resulting image, and the output of that application is what will be returned.
    The method returns the object it is called on, allowing to create a chain as follows:
```
 CM1.chain(CM2.chain(CM3))
 
```
    When CM1.apply(...) is called, it will return the output of CM3 applied to the output of CM2 applied to the output of CM1 applied to the original image.
    Parameters:
    
    next - the ChannelMasker object to apply after this one
    
    Returns:
    
    the current ChannelMasker object
  - createMasker
```
public static ChannelMasker createMasker(String command,
                                         String order,
                                         int options)
```
    Creates a ChannelMasker from a text description of the operations. This is the preferred way to instanciate a ChannelMasker. The command parameter is a comma-separated list of operation descriptors, each descriptor being one of the following:
    - "X:COPY()": Copy verbatim channel number X of the source image.
    - "X:MASK(algo[,param])": Create a binary mask by applying the specified automatic thresholding algorithm to channel number X (see ThresholdingMethod for possible values of "algo"; values are matched in a case-insensitive way). The optional "param" value is either the actual threshold to use (when using the FIXED method) or the radius to consider when using one of the local thresholding methods (defaulting to 15 if no value is specified).
    - "X:APPLY(Y[,Z...],OP)": Apply the binary mask found in channel number Y, Z, etc. to channel number X, using the binary operator OP which can be one of AND, NAND, OR, NOR, XOR, or XNOR. If only one channel is specified, the operator may be omitted, in which case it defaults to AND.
    - "X:INVERT()": Invert channel number X of the source image.
    For example, the command "2:MASK(MaxEntropy),1:COPY()" will create a ChannelMasker that, when applied to an image, will produce an output image with two channels: the first channel will be a binary mask created by thresholding the second channel of the source image with the “Max Entropy” algorithm, and the second channel will be a copy of the first channel of the source image.
    The command "2:APPLY(1)" will create a ChannelMasker that, when applied to an image, will produce an output image containing a single channel, which will be result of applying the binary mask found in the first channel of the source image to the second channel of that same image, with the AND operator.
    The order parameter, if non-null, is expected to be a list of letters. Channels in the command string may then be specified by a letter from that list instead of a numerical index. The rationale behind this parameter is to allow to use command strings that are independent of the orders of the channels in the source image.
    For example, if the order parameter is "GRB", then the command "R:MASK(MaxEntropy),G:COPY()" will be equivalent to the first example above.
    Parameters:
    
    command - a text description of the operations to perform
    
    order - the default channel order specification, as described in setChannelOrder(String) (may be null)
    
    options - flags for masking operation (see constant fields in Masking for available flags)
    
    Returns:
    
    a ChannelMasker object
  - createMasker
```
public static ChannelMasker createMasker(String command,
                                         String order)
```
    Creates a ChannelMasker object from a text description of the operations. This method is similar to createMasker(String, String, int) but uses the default option CLOSE_OPEN_MASK.
    
    Parameters:
    
    command - a text description of the operations to perform
    
    order - the default channel order specification, as described in setChannelOrder(String) (may be null)
    
    Returns:
    
    a ChannelMasker object
  - createMasker
```
public static ChannelMasker createMasker(String command)
```
    Creates a ChannelMasker object from a text description of the operations. This method is similar to createMasker(String, String) but does not allow to set a default channel order.
    
    Parameters:
    
    command - a text description of the operations to perform
    
    Returns:
    
    a ChannelMasker object
  - applyMasker
```
public static ij.ImagePlus applyMasker(ij.ImagePlus image,
                                       String command,
                                       String name,
                                       String order)
```
    Apply a list of operations to an image. This is a convenience method to apply a list of operations (defined in a string as in the createMasker(String, String) method) directly to an image without having to manipulate a ChannelMasker object.
    
    Parameters:
    
    image - the image to apply the operations to
    
    command - the list of operations to apply
    
    name - the name to give to the new image
    
    order - the order of channels in the source image (may be null)
    
    Returns:
    
    the resulting image

Class ChannelMasker

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ChannelMasker

Method Detail

setChannelOrder

getChannelOrder

setMaskingOptions

getMaskingOptions

apply

apply

chain

createMasker

createMasker

createMasker

applyMasker