Package org.anchoranalysis.image.io.channel.map

Class OpenedNamedChannels

Object

OpenedNamedChannels

All Implemented Interfaces:

ChannelGetter, NamedChannelsMap

public class OpenedNamedChannels
extends Object
implements NamedChannelsMap

A set of named Channels available from an OpenedImageFile.

Channels are added to a Stack in the order they appear in the channelMap.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
OpenedNamedChannels(OpenedImageFile openedFile, ChannelMap channelMap, int seriesIndex)	Creates a new OpenedNamedChannels instance.

Method Summary

Modifier and Type	Method	Description
void	addAsSeparateChannels(NamedProviderStore<TimeSeries> destination, int timeIndex, Logger logger)	Adds each Channel as a separate TimeSeries in a NamedProviderStore.
void	addAsSeparateChannels(NamedStacks destination, int timeIndex, Logger logger)	Adds each Channel as a separate Stack in a NamedStacks.
StoreSupplier<Stack>	allChannelsAsStack(int t, Logger logger)	Combines all channels as a single Stack at a particular time-frame.
Set<String>	channelNames()	All channel-names.
Dimensions	dimensions(Logger logger)	The dimensions of each Channel.
Channel	getChannel(String channelName, int timeIndex, Logger logger)	Retrieve the Channel corresponding to channelName at a particular time-frame.
Optional<Channel>	getChannelOptional(String channelName, int timeIndex, Logger logger)	Gets a channel if it exists, returning empty if it doesn't.
boolean	hasChannel(String channelName)	Does a particular channel-name exist?
boolean	isRGB(Logger logger)	Whether the channels describe an RGB image.
int	numberChannels()	The number of channels that exist for the series.
int	sizeT(Logger logger)	The number of frames along the time-axis.

Methods inherited from class java.lang.Object

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

Constructor Details

OpenedNamedChannels

public OpenedNamedChannels(OpenedImageFile openedFile,
 ChannelMap channelMap,
 int seriesIndex)

Creates a new OpenedNamedChannels instance.

Parameters:

openedFile - The underlying opened image-file that provides the channels.

channelMap - A mapping between names to indices of Channels.

seriesIndex - Which series to open in OpenedImageFile.

Method Details

dimensions

public Dimensions dimensions(Logger logger)
                      throws ImageIOException

Description copied from interface: NamedChannelsMap

The dimensions of each Channel.

Specified by:

dimensions in interface NamedChannelsMap

Parameters:

logger - a logger for any non-fatal errors. Fatal errors throw an exception.

Returns:

the dimensions.

Throws:

ImageIOException - if unable to successfully determine the dimensions.

getChannel

public Channel getChannel(String channelName,
 int timeIndex,
 Logger logger)
                   throws GetOperationFailedException

Description copied from interface: ChannelGetter

Retrieve the Channel corresponding to channelName at a particular time-frame.

Specified by:

getChannel in interface ChannelGetter

Parameters:

channelName - the name of the Channel.

timeIndex - the index (beginning at 0) of the frame.

logger - logger to write informative messes or non-fatal errors.

Returns:

the retrieved Channel.

Throws:

GetOperationFailedException - if no channel exists with channelName at time-point timeIndex.

getChannelOptional

public Optional<Channel> getChannelOptional(String channelName,
 int timeIndex,
 Logger logger)
                                     throws GetOperationFailedException

Description copied from interface: NamedChannelsMap

Gets a channel if it exists, returning empty if it doesn't.

Specified by:

getChannelOptional in interface NamedChannelsMap

Parameters:

channelName - name of channel.

timeIndex - point in time-series.

logger - a logger for any non-fatal errors. Fatal errors throw an exception.

Returns:

the channel if it exists, or empty otherwise.

Throws:

GetOperationFailedException - if something goes wrong getting an existing channel (but never if a channel doesn't exist).

sizeT

public int sizeT(Logger logger)
          throws ImageIOException

Description copied from interface: NamedChannelsMap

The number of frames along the time-axis.

Specified by:

sizeT in interface NamedChannelsMap

Parameters:

logger - a logger for any non-fatal errors. Fatal errors throw an exception.

Returns:

the number of time-frames.

Throws:

ImageIOException - if unable to successfully determine the number of frames.

channelNames

public Set<String> channelNames()

Description copied from interface: NamedChannelsMap

All channel-names.

Specified by:

channelNames in interface NamedChannelsMap

Returns:

a set view of all channel-names in the map.

numberChannels

public int numberChannels()

Description copied from interface: NamedChannelsMap

The number of channels that exist for the series.

Specified by:

numberChannels in interface NamedChannelsMap

Returns:

the number of channels.

hasChannel

public boolean hasChannel(String channelName)

Description copied from interface: ChannelGetter

Does a particular channel-name exist?

Specified by:

hasChannel in interface ChannelGetter

Parameters:

channelName - the name of the channel to check.

Returns:

true iff the channel-name exists.

addAsSeparateChannels

public void addAsSeparateChannels(NamedStacks destination,
 int timeIndex,
 Logger logger)
                           throws OperationFailedException

Description copied from interface: NamedChannelsMap

Adds each Channel as a separate Stack in a NamedStacks.

Specified by:

addAsSeparateChannels in interface NamedChannelsMap

Parameters:

destination - the NamedStacks into which each Channel is copied.

timeIndex - the index of the time-frame, beginning at zero.

logger - a logger for any non-fatal errors. Fatal errors throw an exception.

Throws:

OperationFailedException - if unable to add a Channel.

addAsSeparateChannels

public void addAsSeparateChannels(NamedProviderStore<TimeSeries> destination,
 int timeIndex,
 Logger logger)
                           throws OperationFailedException

Description copied from interface: NamedChannelsMap

Adds each Channel as a separate TimeSeries in a NamedProviderStore.

Although added as a TimeSeries, each added Stack will have only a single-time frame at point 0, representing the channel found at timeIndex.

Specified by:

addAsSeparateChannels in interface NamedChannelsMap

Parameters:

destination - the NamedStacks into which each Channel is copied.

timeIndex - the index of the time-frame, beginning at zero.

logger - a logger for any non-fatal errors. Fatal errors throw an exception.

Throws:

OperationFailedException - if unable to add a Channel.

isRGB

public boolean isRGB(Logger logger)
              throws ImageIOException

Description copied from interface: NamedChannelsMap

Whether the channels describe an RGB image.

In this case, there should be exactly three channels, named "red", "green" and "blue".

Specified by:

isRGB in interface NamedChannelsMap

Parameters:

logger - a logger for any non-fatal errors. Fatal errors throw an exception.

Returns:

true if the channels describe an RGB image.

Throws:

ImageIOException - if this cannot be successfully inferred.

allChannelsAsStack

public StoreSupplier<Stack> allChannelsAsStack(int t,
 Logger logger)

Description copied from interface: NamedChannelsMap

Combines all channels as a single Stack at a particular time-frame.

Specified by:

allChannelsAsStack in interface NamedChannelsMap

Parameters:

t - the index of the time-frame, beginning at zero.

logger - a logger for any non-fatal errors. Fatal errors throw an exception.

Returns:

a supplier for a newly created Stack, containing all Channels. The order depends on implementation.