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

Object
- DisplayStack

```
public class DisplayStack
extends Object
```
Stack that contains 1 or 3 channels so that we and display it as either grayscale or as an RGB unsigned 8-bit image, respectively.
A converter is optionally associated with each channel, used to convert the source images into unsigned 8-bit.
When only two channels are present, one particular channel (with index=) is left blank.

Author:

Owen Feehan

Field Summary

Fields
Modifier and Type Field and Description

static int CHANNEL_TO_SKIP_WHEN_TWO
Index of channel to leave blank when there are only two channels.

Fields
Modifier and Type	Field and Description
`static int`	`CHANNEL_TO_SKIP_WHEN_TWO` Index of channel to leave blank when there are only two channels.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`copyPixelsTo(int channelIndex, BoundingBox sourceBox, Voxels<UnsignedByteBuffer> destinationVoxels, BoundingBox destinationBox)` Copies pixels from a particular channel to an output buffer.
`static DisplayStack`	`create(Channel channel)` Creates from a `Channel`.
`static DisplayStack`	`create(RGBStack rgbStack)` Creates from a `RGBStack`.
`static DisplayStack`	`create(Stack stack)` Creates from a `RGBStack`.
`Channel`	`createChannel(int index, boolean alwaysNew)` Create `Channel` for a particular `index` after applying conversion.
`Stack`	`deriveStack(boolean alwaysNew)` Derives a `Stack` from the display-stack that will be converted to 8-bit if necessary.
`Dimensions`	`dimensions()` The dimensions of all channels in the stack.
`Extent`	`extent()` The width and height and depth of all channels in the `Stack`.
`Channel`	`extractChannelForBoundingBox(int index, BoundingBox box)` Creates a new `Channel` that refers to only a `BoundingBox` portion of the `DisplayStack`.
`DisplayStack`	`extractSlice(int z)` Extract a particular z-slice from the `DisplayStack` as a new stack, applying any applicable conversion.
`List<Optional<ChannelConverterAttached<Channel,UnsignedByteBuffer>>>`	`getConverters()` A list of optional converters that will be applied to the respective channel in `stack` if they exist.
`int`	`getNumberChannels()` The number of channels in the stack.
`Stack`	`getStack()` The underlying stack that will be displayed, possibly after conversion.
`int`	`getUnconvertedVoxelAt(int channelIndex, Point3i point)` Retrieve the intensity of a voxel at a particular point, before any conversion is applied.
`boolean`	`isRGB()` Does the display-stack contain an RGB image?
`DisplayStack`	`projectMax()` Creates a Maximum Intensity Projection of each channel.
`Optional<Resolution>`	`resolution()` Resolution of voxels to physical measurements.
`Optional<VoxelDataType>`	`unconvertedDataType()` The data-type of the underlying voxels before they are converted to 8-bit.

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

- Field Detail
  - CHANNEL_TO_SKIP_WHEN_TWO
```
public static final int CHANNEL_TO_SKIP_WHEN_TWO
```
    Index of channel to leave blank when there are only two channels. 0=first, 1=second, 2=third.
    
    See Also:
    
    Constant Field Values
- Method Detail
  - create
```
public static DisplayStack create(Channel channel)
                           throws CreateException
```
    Creates from a Channel.
    
    Parameters:
    
    channel - the stack to create from.
    
    Returns:
    
    a newly created DisplayStack, after applying any applicable conversion.
    
    Throws:
    
    CreateException - if a converter cannot be associated with a particular channel.
  - create
```
public static DisplayStack create(Stack stack)
                           throws CreateException
```
    Creates from a RGBStack.
    
    Parameters:
    
    stack - the stack to create from, which should have either 1 or 3 channels (corresponding to RGB).
    
    Returns:
    
    a newly created DisplayStack, after applying any applicable conversion.
    
    Throws:
    
    CreateException - with an incorrect number of channels, or if a converter cannot be associated with a particular channel.
  - create
```
public static DisplayStack create(RGBStack rgbStack)
                           throws CreateException
```
    Creates from a RGBStack.
    
    Parameters:
    
    rgbStack - the stack to create from.
    
    Returns:
    
    a newly created DisplayStack, after applying any applicable conversion.
    
    Throws:
    
    CreateException - if a converter cannot be associated with a particular channel.
  - isRGB
```
public boolean isRGB()
```
    Does the display-stack contain an RGB image?
    
    Returns:
    
    true if the contained image is RGB, false if it is grayscale.
  - dimensions
```
public Dimensions dimensions()
```
    The dimensions of all channels in the stack.
    
    Returns:
    
    the dimensions.
  - extent
```
public Extent extent()
```
    The width and height and depth of all channels in the Stack.
    i.e. the size of each of the three possible dimensions.
    
    Returns:
    
    the extent.
  - getNumberChannels
```
public final int getNumberChannels()
```
    The number of channels in the stack.
    
    Returns:
    
    the number of channels.
  - resolution
```
public Optional<Resolution> resolution()
```
    Resolution of voxels to physical measurements.
    e.g. physical size of each voxel in a particular dimension.
    
    Returns:
    
    the resolution.
  - createChannel
```
public Channel createChannel(int index,
                             boolean alwaysNew)
```
    Create Channel for a particular index after applying conversion.
    
    Parameters:
    
    index - the index of the channel in the Stack to create a converted version of.
    
    alwaysNew - if true, a new channel is always created. Otherwise it is created, only if needs be.
    
    Returns:
    
    the Channel after extracting from the stack and applying conversion.
  - extractChannelForBoundingBox
```
public Channel extractChannelForBoundingBox(int index,
                                            BoundingBox box)
```
    Creates a new Channel that refers to only a BoundingBox portion of the DisplayStack.
    Existing voxels are always duplicated, and never reused.
    
    Parameters:
    
    index - the index of the channel.
    
    box - the bounding-box portion to extract.
    
    Returns:
    
    a newly created Channel containing extracted voxels, corresponding to box.
  - deriveStack
```
public Stack deriveStack(boolean alwaysNew)
```
    Derives a Stack from the display-stack that will be converted to 8-bit if necessary.
    
    Parameters:
    
    alwaysNew - iff true channels are always created new during conversion, otherwise only if needed.
    
    Returns:
    
    a stack with either 1 or 3 channels (depending on what's passed into display-stack), all of which are unsigned 8-bit.
  - copyPixelsTo
```
public void copyPixelsTo(int channelIndex,
                         BoundingBox sourceBox,
                         Voxels<UnsignedByteBuffer> destinationVoxels,
                         BoundingBox destinationBox)
```
    Copies pixels from a particular channel to an output buffer.
    
    Parameters:
    
    channelIndex - the index of the source channel to copy from.
    
    sourceBox - the bounding-box in the source channel to copy from.
    
    destinationVoxels - where to copy the pixels to.
    
    destinationBox - the bounding-box in the destination channel to copy to.
  - unconvertedDataType
```
public Optional<VoxelDataType> unconvertedDataType()
```
    The data-type of the underlying voxels before they are converted to 8-bit.
    
    Returns:
    
    the data-type if all channels have identical data-type, or Optional.empty() if they vary.
  - getUnconvertedVoxelAt
```
public int getUnconvertedVoxelAt(int channelIndex,
                                 Point3i point)
```
    Retrieve the intensity of a voxel at a particular point, before any conversion is applied.
    
    Parameters:
    
    channelIndex - the index of the channel in which the voxel resides.
    
    point - the point in the channel corresponding to the voxel.
    
    Returns:
    
    the intensity value, before any conversion.
  - projectMax
```
public DisplayStack projectMax()
```
    Creates a Maximum Intensity Projection of each channel.
    Note that if the channels do not need projections, the existing Channel is reused in the newly created Stack. But if a projection is needed, it is always freshly created as a new channel.
    
    Returns:
    
    a newly created Stack, with maximum intensity projections of each Channel.
  - extractSlice
```
public DisplayStack extractSlice(int z)
                          throws CreateException
```
    Extract a particular z-slice from the DisplayStack as a new stack, applying any applicable conversion.
    The existing voxels may be reused, if no conversion needs to be applied.
    
    Parameters:
    
    z - the index in the Z-dimension of the slice to extract.
    
    Returns:
    
    the extracted slice, as a new DisplayStack after any applicable conversion.
    
    Throws:
    
    CreateException - if a channel cannot be attached to a converter.
  - getStack
```
public Stack getStack()
```
    The underlying stack that will be displayed, possibly after conversion.
  - getConverters
```
public List<Optional<ChannelConverterAttached<Channel,UnsignedByteBuffer>>> getConverters()
```
    A list of optional converters that will be applied to the respective channel in stack if they exist.

Class DisplayStack

Field Summary

Method Summary

Methods inherited from class Object

Field Detail

CHANNEL_TO_SKIP_WHEN_TWO

Method Detail

create

create

create

isRGB

dimensions

extent

getNumberChannels

resolution

createChannel

extractChannelForBoundingBox

deriveStack

copyPixelsTo

unconvertedDataType

getUnconvertedVoxelAt

projectMax

extractSlice

getStack

getConverters