org.anchoranalysis.image.core.stack

Class Stack

Object

Stack

All Implemented Interfaces:

Iterable<Channel>

public class Stack
extends Object
implements Iterable<Channel>

One or more single-channel images that all have the same dimensions.

This is one of the fundamental image data structures in Anchor.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor and Description
Stack()
Stack(boolean rgb)
Stack(boolean rgb, Channel... channels)
Stack(boolean rgb, java.util.stream.Stream<Channel> channelStream)
Stack(Channel channel)
Stack(Dimensions dimensions, ChannelFactorySingleType factory, int numberChannels, boolean rgb)
Stack(java.util.stream.Stream<Channel> channelStream)

Method Summary

Modifier and Type	Method and Description
void	addBlankChannel()
void	addChannel(Channel channel)
void	addChannelsFrom(Stack stack)
boolean	allChannelsHaveIdenticalType() Determines if all channels have an identical voxel data-type.
boolean	allChannelsHaveType(VoxelDataType channelDataType) Determines if all channels have a specific data-type.
List<Channel>	asListChannels()
Dimensions	dimensions()
Stack	duplicateDeep() Performs a deep copy of the stack, so that all channels are duplicated.
Stack	duplicateShallow() Performs a shallow copy of the stack, so that all channels are reused.
boolean	equals(Object obj)
boolean	equalsDeep(Stack other, boolean compareResolution) Are the two stack equal using a deep voxel by voxel comparison of each channel?
Extent	extent()
Stack	extractSlice(int z)
Stack	extractUpToThreeChannels()
Channel	getChannel(int index)
int	getNumberChannels()
int	hashCode()
boolean	hasMoreThanOneSlice() Does the stack have more than one slice in the z-dimension?
boolean	isRGB() If true, and the stack has exactly three channels, this stack can be interpreted as a RGB image.
Iterator<Channel>	iterator()
Stack	mapChannel(CheckedUnaryOperator<Channel,OperationFailedException> mapping) Produces a new stack with a particular mapping applied to each channel.
Stack	mapChannelWithIndex(CheckedBiFunction<Channel,Integer,Channel,OperationFailedException> mapping) Produces a new stack with a particular mapping applied to each channel (with an index of the channel also available)
Stack	projectMax() Creates a Maximum Intensity Projection of each channel.
Optional<Resolution>	resolution()
void	updateResolution(Resolution resolution)

Methods inherited from class Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface Iterable

forEach, spliterator

Constructor Detail

Stack

public Stack(boolean rgb)

Stack

public Stack()

Stack

public Stack(Channel channel)

Stack

public Stack(Dimensions dimensions,
             ChannelFactorySingleType factory,
             int numberChannels,
             boolean rgb)

Stack

public Stack(boolean rgb,
             Channel... channels)
      throws IncorrectImageSizeException

Throws:

IncorrectImageSizeException

Stack

public Stack(java.util.stream.Stream<Channel> channelStream)
      throws IncorrectImageSizeException

Throws:

IncorrectImageSizeException

Stack

public Stack(boolean rgb,
             java.util.stream.Stream<Channel> channelStream)
      throws IncorrectImageSizeException

Throws:

IncorrectImageSizeException

Method Detail

mapChannel

public Stack mapChannel(CheckedUnaryOperator<Channel,OperationFailedException> mapping)
                 throws OperationFailedException

Produces a new stack with a particular mapping applied to each channel.

The function applied to the channel should ensure it produces uniform sizes.

Parameters:

mapping - performs an operation on a channel and produces a modified channel (or a different one entirely)

Returns:

a new stack (after any modification by mapping) preserving the channel order

Throws:

OperationFailedException - if the channels produced have non-uniform sizes

mapChannelWithIndex

public Stack mapChannelWithIndex(CheckedBiFunction<Channel,Integer,Channel,OperationFailedException> mapping)
                          throws OperationFailedException

Produces a new stack with a particular mapping applied to each channel (with an index of the channel also available)

The function applied to the channel should ensure it produces uniform sizes.

Parameters:

mapping - performs an operation on a channel and produces a modified channel (or a different one entirely)

Returns:

a new stack (after any modification by mapping) preserving the channel order

Throws:

OperationFailedException - if the channels produced have non-uniform sizes

extractSlice

public Stack extractSlice(int z)

projectMax

public Stack 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.

addBlankChannel

public void addBlankChannel()
                     throws OperationFailedException

Throws:

OperationFailedException

addChannel

public final void addChannel(Channel channel)
                      throws IncorrectImageSizeException

Throws:

IncorrectImageSizeException

addChannelsFrom

public final void addChannelsFrom(Stack stack)
                           throws IncorrectImageSizeException

Throws:

IncorrectImageSizeException

getChannel

public final Channel getChannel(int index)

getNumberChannels

public final int getNumberChannels()

dimensions

public Dimensions dimensions()

resolution

public Optional<Resolution> resolution()

extent

public Extent extent()

duplicateDeep

public Stack duplicateDeep()

Performs a deep copy of the stack, so that all channels are duplicated.

Returns:

a new stack with deep-copied channels.

duplicateShallow

public Stack duplicateShallow()

Performs a shallow copy of the stack, so that all channels are reused.

Returns:

a new stack with reused channels.

extractUpToThreeChannels

public Stack extractUpToThreeChannels()

hasMoreThanOneSlice

public boolean hasMoreThanOneSlice()

Does the stack have more than one slice in the z-dimension?

Returns:

true if there is more than one z slice, false if there is 1

iterator

public Iterator<Channel> iterator()

Specified by:

iterator in interface Iterable<Channel>

asListChannels

public List<Channel> asListChannels()

allChannelsHaveIdenticalType

public boolean allChannelsHaveIdenticalType()

Determines if all channels have an identical voxel data-type.

Returns:

true iff all channels have an identical voxel data-type.

allChannelsHaveType

public boolean allChannelsHaveType(VoxelDataType channelDataType)

Determines if all channels have a specific data-type.

Parameters:

channelDataType - the specific data-type

Returns:

true iff all channels have channelDataType as their voxel data-type.

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

equalsDeep

public boolean equalsDeep(Stack other,
                          boolean compareResolution)

Are the two stack equal using a deep voxel by voxel comparison of each channel?

Parameters:

other - the stack to compare with

compareResolution - if true, the image-resolution is also compared for each channel.

Returns:

true if they are deemed equals, false otherwise.

hashCode

public int hashCode()

Overrides:

hashCode in class Object

updateResolution

public void updateResolution(Resolution resolution)

isRGB

public boolean isRGB()

If true, and the stack has exactly three channels, this stack can be interpreted as a RGB image.

This is an important flag for determining how a stack is displayed visually, determining whether a stack is portrayed as a color image or composite grayscale channels.