Package org.anchoranalysis.mpp.io.input

Class MultiInput

Object

MultiInput

All Implemented Interfaces:

ProvidesStackInput, InputFromManager, ExportSharedObjects

public class MultiInput
extends Object
implements ProvidesStackInput, ExportSharedObjects

An input to an experiment that combines a particular Stack with other types of entities.

These entities each have a unique name, and must be one of the following types:

1. Stack (in addition to the primary stack that forms the input).
2. MarkCollection.
3. ObjectCollection.
4. Dictionary.
5. Histogram.
6. Path.

Author:

Owen Feehan

Field Summary

Fields

Modifier and Type	Field	Description
static final String	DEFAULT_IMAGE_INPUT_NAME	The default name for the input image stack.

Constructor Summary

Constructors

Constructor	Description
MultiInput(String mainObjectName, ProvidesStackInput mainInputObject)	Creates a new MultiInput with a specified name for the main input object.
MultiInput(ProvidesStackInput mainInputObject)	Creates a new MultiInput with a default name for the main input object.

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.
void	close(ErrorReporter errorReporter)	Performs all tidying up, file-closing etc. after we are finished using the InputFromManager
void	copyTo(SharedObjects target, Logger logger)	Adds any exported shared objects to the target container.
MultiInputSubMap<Dictionary>	dictionary()	Gets the map of Dictionarys.
MultiInputSubMap<Path>	filePath()	Gets the map of Paths.
String	getMainObjectName()	Gets the name of the main input object.
MultiInputSubMap<Histogram>	histogram()	Gets the map of Histograms.
String	identifier()	A unique name associated with the input.
MultiInputSubMap<MarkCollection>	marks()	Gets the map of MarkCollections.
int	numberFrames()	The number of time-frames in the underlying input image.
MultiInputSubMap<ObjectCollection>	objects()	Gets the map of ObjectCollections.
Optional<Path>	pathForBinding()	A path to a file from which this input originated.
MultiInputSubMap<TimeSeries>	stack()	Gets the map of TimeSeries (stacks).

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, identifierAsPath, pathForBindingRequired

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

addToStoreInferNames, asSet, asStack

Field Details

DEFAULT_IMAGE_INPUT_NAME

public static final String DEFAULT_IMAGE_INPUT_NAME

The default name for the input image stack.

See Also:

• Constant Field Values

Constructor Details

MultiInput

public MultiInput(ProvidesStackInput mainInputObject)

Creates a new MultiInput with a default name for the main input object.

Parameters:

mainInputObject - the main input object that provides the stack

MultiInput

public MultiInput(String mainObjectName,
 ProvidesStackInput mainInputObject)

Creates a new MultiInput with a specified name for the main input object.

Parameters:

mainObjectName - the name for the main input object

mainInputObject - the main input object that provides the stack

Method Details

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.

copyTo

public void copyTo(SharedObjects target,
 Logger logger)
            throws OperationFailedException

Description copied from interface: ExportSharedObjects

Adds any exported shared objects to the target container.

This method is responsible for copying the relevant shared objects from the implementing class to the provided target container. Non-fatal errors should be logged using the provided logger, while fatal errors should throw an OperationFailedException.

Specified by:

copyTo in interface ExportSharedObjects

Parameters:

target - the SharedObjects container where the exported objects will be added

logger - a Logger for reporting non-fatal errors

Throws:

OperationFailedException - if a fatal error occurs during the export process

identifier

public String identifier()

Description copied from interface: InputFromManager

A unique name associated with the input.

The name should never begin with or end with whitespace.

It should never contain backslashes, but forward-slashes are permitted.

Specified by:

identifier in interface InputFromManager

Returns:

a string uniquely (in the current dataset) identifying the input in a meaningful way.

pathForBinding

public Optional<Path> pathForBinding()

Description copied from interface: InputFromManager

A path to a file from which this input originated.

This path is not guaranteed to be unique for each input i.e. multiple inputs may originate from the same path.

Specified by:

pathForBinding in interface InputFromManager

Returns:

the primary path associated with the input, if it exists.

close

public void close(ErrorReporter errorReporter)

Description copied from interface: InputFromManager

Performs all tidying up, file-closing etc. after we are finished using the InputFromManager

Specified by:

close in interface InputFromManager

Parameters:

errorReporter - whether errors are reported to.

marks

public MultiInputSubMap<MarkCollection> marks()

Gets the map of MarkCollections.

Returns:

the MultiInputSubMap of MarkCollections

objects

public MultiInputSubMap<ObjectCollection> objects()

Gets the map of ObjectCollections.

Returns:

the MultiInputSubMap of ObjectCollections

dictionary

public MultiInputSubMap<Dictionary> dictionary()

Gets the map of Dictionarys.

Returns:

the MultiInputSubMap of Dictionarys

histogram

public MultiInputSubMap<Histogram> histogram()

Gets the map of Histograms.

Returns:

the MultiInputSubMap of Histograms

filePath

public MultiInputSubMap<Path> filePath()

Gets the map of Paths.

Returns:

the MultiInputSubMap of Paths

stack

public MultiInputSubMap<TimeSeries> stack()

Gets the map of TimeSeries (stacks).

Returns:

the MultiInputSubMap of TimeSeries

getMainObjectName

public String getMainObjectName()

Gets the name of the main input object.

Returns:

the name of the main input object

numberFrames

public int numberFrames()
                 throws OperationFailedException

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.

Throws:

OperationFailedException - if the operation cannot successfully complete.