Package org.anchoranalysis.image.io.channel.input

Class NamedChannelsInput

Object

NamedChannelsInput

All Implemented Interfaces:

ProvidesStackInput, InputFromManager

Direct Known Subclasses:

NamedChannelsInputPart

public abstract class NamedChannelsInput
extends Object
implements ProvidesStackInput

Provides a set of channels as an input, with each channel having a name.

Only the first time-point is considered from each series.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
NamedChannelsInput()

Method Summary

Modifier and Type	Method	Description
void	addToStoreInferNames(NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)	Adds any stacks exposed by the current element to a named-store of stacks - inferring the names of the Stacks.
void	addToStoreWithName(String name, NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)	Adds any stacks exposed by the current element to a named-store of stacks - with a particular name.
abstract int	bitDepth(Logger logger)	Bit-depth of image.
abstract NamedChannelsMap	createChannelsForSeries(int seriesIndex, Logger logger)	Creates a NamedChannelsMap representing the channels for a particular series in this input.
abstract Dimensions	dimensions(int seriesIndex, Logger logger)	Dimensions of a particular series.
abstract ImageMetadata	metadata(int seriesIndex, Logger logger)	The image-metadata associated with a particular series.
abstract int	numberChannels(Logger logger)	Number of channels.
int	numberFrames()	The number of time-frames in the underlying input image.
abstract int	numberSeries()	Number of series that exist.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.anchoranalysis.io.input.InputFromManager

allAssociatedPaths, asFile, close, identifier, identifierAsPath, pathForBinding, pathForBindingRequired

Methods inherited from interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput

addToStoreInferNames, asSet, asStack

Constructor Details

NamedChannelsInput

public NamedChannelsInput()

Method Details

numberSeries

public abstract int numberSeries()
                          throws ImageIOException

Number of series that exist.

Returns:

the number of series.

Throws:

ImageIOException - if the information cannot be successfully retrieved from the underlying image.

dimensions

public abstract Dimensions dimensions(int seriesIndex,
 Logger logger)
                               throws ImageIOException

Dimensions of a particular series.

Parameters:

seriesIndex - the index of the series.

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

Returns:

the corresponding dimensions.

Throws:

ImageIOException - if the information cannot be successfully retrieved from the underlying image.

numberChannels

public abstract int numberChannels(Logger logger)
                            throws ImageIOException

Number of channels.

Parameters:

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

Returns:

the number of channels.

Throws:

ImageIOException - if the information cannot be successfully retrieved from the underlying image.

bitDepth

public abstract int bitDepth(Logger logger)
                      throws ImageIOException

Bit-depth of image.

Parameters:

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

Returns:

the bit-depth.

Throws:

ImageIOException - if the information cannot be successfully retrieved from the underlying image.

createChannelsForSeries

public abstract NamedChannelsMap createChannelsForSeries(int seriesIndex,
 Logger logger)
                                                  throws ImageIOException

Creates a NamedChannelsMap representing the channels for a particular series in this input.

Parameters:

seriesIndex - the index of the series to use (beginning at 0).

logger - the logger where informative or non-fatal error messages amy be written.

Returns:

a newly created NamedChannelsMap bound to seriesIndex.

Throws:

ImageIOException - if the operation cannot successfully complete.

metadata

public abstract ImageMetadata metadata(int seriesIndex,
 Logger logger)
                                throws ImageIOException

The image-metadata associated with a particular series.

Parameters:

seriesIndex - the index of the series.

logger - the logger.

Returns:

the metadata.

Throws:

ImageIOException - if the metadata cannot be calculated.

addToStoreInferNames

public void addToStoreInferNames(NamedProviderStore<TimeSeries> stacks,
 int seriesIndex,
 Logger logger)
                          throws OperationFailedException

Description copied from interface: ProvidesStackInput

Adds any stacks exposed by the current element to a named-store of stacks - inferring the names of the Stacks.

Specified by:

addToStoreInferNames in interface ProvidesStackInput

Parameters:

stacks - the named-store of stacks.

seriesIndex - the index of the series (beginning at 0) to retrieve stacks from the TimeSeries.

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

Throws:

OperationFailedException - if the operation cannot successfully complete.

addToStoreWithName

public void addToStoreWithName(String name,
 NamedProviderStore<TimeSeries> stacks,
 int seriesIndex,
 Logger logger)
                        throws OperationFailedException

Description copied from interface: ProvidesStackInput

Adds any stacks exposed by the current element to a named-store of stacks - with a particular name.

Specified by:

addToStoreWithName in interface ProvidesStackInput

Parameters:

name - the name to use for the added stack.

stacks - the named-store of stacks.

seriesIndex - the index of the series (beginning at 0) to retrieve stacks from the TimeSeries.

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

Throws:

OperationFailedException - if the operation cannot successfully complete.

numberFrames

public int numberFrames()

Description copied from interface: ProvidesStackInput

The number of time-frames in the underlying input image.

Specified by:

numberFrames in interface ProvidesStackInput

Returns:

the number of time-frames.