Channel (Anchor - merged Javadoc across key repositories. This documentation is a work-in-progress. 0.0.1-SNAPSHOT API)

Object
- Channel

```
public class Channel
extends Object
```
A channel from an image.
This is one of the key image-processing classes in Anchor. An image may have one channel (grayscale) or several. Channels of identical size can be bundled together to form a Stack.
The channel's voxels have an underlying data-type that is not exposed as a templated parameter, but can be accessed via getVoxelDataType(). This is deliberate weak-typing.
Each channel has an associated size and optionally defines a physical size for each voxel, as stored in the associated Dimensions structure.

Author:

Owen Feehan

Constructor Summary

Constructors
Constructor and Description

Channel(Voxels<?> voxels, Optional<Resolution> resolution)
Creates for particular voxels and resolution.

Constructors
Constructor and Description
`Channel(Voxels<?> voxels, Optional<Resolution> resolution)` Creates for particular voxels and resolution.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`VoxelsArithmetic`	`arithmetic()` Interface that allows manipulation of voxel intensities via arithmetic operations.
`void`	`assignResolution(Optional<Resolution> resolution)` Assigns a new resolution.
`VoxelsAssigner`	`assignValue(int valueToAssign)` Interface that allows assignment of a particular value to all or subsets of the voxels.
`Dimensions`	`dimensions()` The size and voxel-resolution of the channel.
`Channel`	`duplicate()` A deep-copy.
`ObjectMask`	`equalMask(BoundingBox box, int equalValue)` Creates a `ObjectMask` representing all the voxels in `box` equal to `equalValue`.
`boolean`	`equalsDeep(Channel other, boolean compareResolution)` Are the two channels equal using a deep voxel by voxel comparison?
`Extent`	`extent()` The size of the voxels across three dimensions.
`VoxelsExtracter<?>`	`extract()` Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
`Channel`	`extractSlice(int sliceIndex)` Creates a new `Channel` containing only one particular slice.
`VoxelDataType`	`getVoxelDataType()` The underlying data-type of the voxels in the channel, represented by a `VoxelDataType` instance.
`Channel`	`projectMax()` A maximum-intensity projection across the z-slices.
`Channel`	`projectMean()` A mean-intensity projection across the z-slices.
`void`	`replaceVoxels(Voxels<?> voxelsToAssign)` Assigns new voxels to replace the existing voxels.
`Channel`	`resizeXY(Extent extentToAssign, VoxelsResizer resizer)` Resizes the dimensions of the channel, interpolating the existing voxel values to match.
`Channel`	`resizeXY(int x, int y, VoxelsResizer resizer)` Like `resizeXY(Extent, VoxelsResizer)` but specifies the size via `int` parameters.
`Optional<Resolution>`	`resolution()` The resolution of the voxel that describes a physical size for each voxel.
`Channel`	`scaleXY(ScaleFactor scaleFactor, VoxelsResizer resizer)` Resizes the dimensions of the channel, by scaling the existing size by a factor.
`String`	`toString()` A string representation of a histogram of voxel-intensities in the channel.
`VoxelsUntyped`	`voxels()` The underlying voxels in the channel.
`VoxelsPredicate`	`voxelsEqualTo(int equalToValue)` Operations on whether particular voxels are equal to a particular value.
`VoxelsPredicate`	`voxelsGreaterThan(int threshold)` Operations on whether particular voxels are greater than a threshold (but not equal to).

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - Channel
```
public Channel(Voxels<?> voxels,
               Optional<Resolution> resolution)
```
    Creates for particular voxels and resolution.
    
    Parameters:
    
    voxels - the voxels.
    
    resolution - the resolution, if it is known.
- Method Detail
  - equalMask
```
public ObjectMask equalMask(BoundingBox box,
                            int equalValue)
```
    Creates a ObjectMask representing all the voxels in box equal to equalValue.
    The equal values in the box are assigned an on state, and all other values an off state.
    
    Parameters:
    
    box - the bounding-box to consider voxels within, and which forms the bounding-box for the created ObjectMask.
    
    equalValue - the value voxels must be equal to, so to be assigned an on state in the ObjectMask.
    
    Returns:
    
    a newly created ObjectMask as per above.
  - voxels
```
public VoxelsUntyped voxels()
```
    The underlying voxels in the channel.
    
    Returns:
    
    the voxels, wrapped in a class that facilitates friendly conversion.
  - replaceVoxels
```
public void replaceVoxels(Voxels<?> voxelsToAssign)
                   throws IncorrectImageSizeException
```
    Assigns new voxels to replace the existing voxels.
    
    Parameters:
    
    voxelsToAssign - voxels to be assigned.
    
    Throws:
    
    IncorrectImageSizeException - if voxelsToAssign has a different size to the dimensions of the channel.
  - extractSlice
```
public Channel extractSlice(int sliceIndex)
```
    Creates a new Channel containing only one particular slice.
    The existing Voxels are reused, without creating new buffers.
    
    Parameters:
    
    sliceIndex - the index of the slice to extract (index in z-dimension).
    
    Returns:
    
    a newly created Channel consisting of the slice at sliceIndex only.
  - scaleXY
```
public Channel scaleXY(ScaleFactor scaleFactor,
                       VoxelsResizer resizer)
```
    Resizes the dimensions of the channel, by scaling the existing size by a factor.
    Existing voxel values are interpolated to match the new size.
    This is useful for quickly downscaling or upscaling by a particular factor.
    It is an immutable operation, and the existing object state remains unchanged.
    The z-dimension remains unchanged.
    
    Parameters:
    
    scaleFactor - the scaling-factor to be applied to the sizes.
    
    resizer - an interpolator for resizing voxels.
    
    Returns:
    
    a newly created Channel containing a resized version of the current.
  - resizeXY
```
public Channel resizeXY(Extent extentToAssign,
                        VoxelsResizer resizer)
```
    Resizes the dimensions of the channel, interpolating the existing voxel values to match.
    It is an immutable operation, and the existing object state remains unchanged.
    The z-dimension remains unchanged.
    
    Parameters:
    
    extentToAssign - the new size to assign. The z-component is ignored.
    
    resizer - an interpolator for resizing voxels.
    
    Returns:
    
    a newly created Channel containing a resized version of the current.
  - resizeXY
```
public Channel resizeXY(int x,
                        int y,
                        VoxelsResizer resizer)
```
    Like resizeXY(Extent, VoxelsResizer) but specifies the size via int parameters.
    
    Parameters:
    
    x - the size along the x-axis.
    
    y - the size along the y-axis.
    
    resizer - an interpolator for resizing voxels.
    
    Returns:
    
    a newly created Channel containing a resized version of the current.
  - projectMax
```
public Channel projectMax()
```
    A maximum-intensity projection across the z-slices.
    
    Returns:
    
    a newly created Channel with a newly created voxel-buffer.
  - projectMean
```
public Channel projectMean()
```
    A mean-intensity projection across the z-slices.
    
    Returns:
    
    a newly created Channel with a newly created voxel-buffer.
  - duplicate
```
public Channel duplicate()
```
    A deep-copy.
    
    Returns:
    
    newly created deep-copy.
  - voxelsEqualTo
```
public VoxelsPredicate voxelsEqualTo(int equalToValue)
```
    Operations on whether particular voxels are equal to a particular value.
    
    Parameters:
    
    equalToValue - the value all voxels should be equal to.
    
    Returns:
    
    a newly instantiated object to perform queries on voxels who fulfill the above condition.
  - voxelsGreaterThan
```
public VoxelsPredicate voxelsGreaterThan(int threshold)
```
    Operations on whether particular voxels are greater than a threshold (but not equal to).
    
    Parameters:
    
    threshold - voxel-values greater than this threshold are included.
    
    Returns:
    
    a newly instantiated object to perform queries on voxels who fulfill the above condition.
  - assignResolution
```
public void assignResolution(Optional<Resolution> resolution)
```
    Assigns a new resolution.
    This is a mutable operation that replaces existing state.
    
    Parameters:
    
    resolution - the resolution to assign.
  - getVoxelDataType
```
public VoxelDataType getVoxelDataType()
```
    The underlying data-type of the voxels in the channel, represented by a VoxelDataType instance.
    
    Returns:
    
    an instance of VoxelDataType.
  - toString
```
public String toString()
```
    A string representation of a histogram of voxel-intensities in the channel.
    
    Overrides:
    
    toString in class Object
  - equalsDeep
```
public boolean equalsDeep(Channel other,
                          boolean compareResolution)
```
    Are the two channels equal using a deep voxel by voxel comparison?
    
    Parameters:
    
    other - the channel to compare with.
    
    compareResolution - if true, image-resolution must also be equal, otherwise it is not compared.
    
    Returns:
    
    true if they are deemed equal, false otherwise.
  - arithmetic
```
public VoxelsArithmetic arithmetic()
```
    Interface that allows manipulation of voxel intensities via arithmetic operations.
    
    Returns:
    
    the interface.
  - assignValue
```
public VoxelsAssigner assignValue(int valueToAssign)
```
    Interface that allows assignment of a particular value to all or subsets of the voxels.
    
    Parameters:
    
    valueToAssign - the value to assign.
    
    Returns:
    
    the interface.
  - extract
```
public VoxelsExtracter<?> extract()
```
    Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
    
    Returns:
    
    the interface.
  - extent
```
public Extent extent()
```
    The size of the voxels across three dimensions.
    
    Returns:
    
    the size.
  - resolution
```
public Optional<Resolution> resolution()
```
    The resolution of the voxel that describes a physical size for each voxel.
    
    Returns:
    
    the resolution, if it exists.
  - dimensions
```
public Dimensions dimensions()
```
    The size and voxel-resolution of the channel.

Class Channel

Constructor Summary

Method Summary

Methods inherited from class Object

Constructor Detail

Channel

Method Detail

equalMask

voxels

replaceVoxels

extractSlice

scaleXY

resizeXY

resizeXY

projectMax

projectMean

duplicate

voxelsEqualTo

voxelsGreaterThan

assignResolution

getVoxelDataType

toString

equalsDeep

arithmetic

assignValue

extract

extent

resolution

dimensions