Package org.anchoranalysis.image.bean.nonbean.init

Class ImageInitialization

Object

ImageInitialization

All Implemented Interfaces:

BeanInitialization

public class ImageInitialization
extends Object
implements BeanInitialization

The state used to initialize a ImageBean.

It contains several NamedProviderStores for particular types of entities.

Author:

Owen

Field Summary

Fields

Modifier and Type	Field	Description
static final String	DICTIONARY_IDENTIFIER	The name of the dictionary added by addSharedObjectsDictionary(java.util.Optional<org.anchoranalysis.core.identifier.provider.store.SharedObjects>, java.util.Optional<org.anchoranalysis.core.value.Dictionary>).

Constructor Summary

Constructors

Constructor	Description
ImageInitialization(SharedObjects sharedObjects)	Create with shared-objects.
ImageInitialization(SharedObjects sharedObjects, Optional<ImageSizeSuggestion> suggestedSize)	Create with shared-objects and a resizing suggestion.

Method Summary

Modifier and Type	Method	Description
void	addDictionary(String identifier, Dictionary toAdd)	Adds a Dictionary to the corresponding named-collection of dictionaries.
void	addObjectsFrom(NamedProvider<ObjectCollection> source)	Adds all the ObjectCollections available in a NamedProvider using the corresponding identifiers.
void	addSharedObjectsDictionary(Optional<SharedObjects> sharedObjects, Optional<Dictionary> dictionary)	Adds stacks and object-collections from a SharedObjects using the respective identifiers, and also adds a Dictionary.
void	addStack(String identifier, Stack toAdd)	Adds a Stack to the corresponding named-collection of stacks.
void	addStacksFrom(NamedProvider<Stack> source)	Adds all the Stacks available in a NamedProvider using the corresponding identifiers.
NamedProviderStore<BinarySegmentation>	binarySegmentations()	A collection of BinarySegmentations, indexed by name.
NamedProviderStore<Channel>	channels()	A collection of Channels, indexed by name.
NamedProvider<Stack>	combinedStacks()	Exposes several entities that have natural Stack representations as a unified NamedProvider.
NamedProviderStore<Dictionary>	dictionaries()	Named-store of Dictionarys.
DictionaryInitialization	dictionaryInitialization()	The associated initialization for a DictionaryBean.
FeatureRelatedInitialization	featuresInitialization()	The associated initialization for a FeatureRelatedBean.
NamedProviderStore<Path>	filePaths()	Named-store of file-paths.
NamedProviderStore<Histogram>	histograms()	A collection of Histograms, indexed by name.
NamedProviderStore<Mask>	masks()	A collection of Masks, indexed by name.
Path	modelDirectory()	Directory where machine-learning models can be found.
NamedProviderStore<ObjectCollection>	objects()	A collection of ObjectCollections, indexed by name.
void	populate(BeanInitializer<?> propertyInitializer, Define define, Logger logger)	Adds diverse entities from a Define into the corresponding name-collections.
SharedObjects	sharedObjects()	Objects shared between different components, a form of shared memory between them.
NamedProviderStore<Stack>	stacks()	A collection of Stacks, indexed by name.
Optional<ImageSizeSuggestion>	suggestedSize()	A suggested input on how to resize an image, if one is provided.

Methods inherited from class java.lang.Object

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

Field Details

DICTIONARY_IDENTIFIER

public static final String DICTIONARY_IDENTIFIER

The name of the dictionary added by addSharedObjectsDictionary(java.util.Optional<org.anchoranalysis.core.identifier.provider.store.SharedObjects>, java.util.Optional<org.anchoranalysis.core.value.Dictionary>).

See Also:

• Constant Field Values

Constructor Details

ImageInitialization

public ImageInitialization(SharedObjects sharedObjects)

Create with shared-objects.

Parameters:

sharedObjects - objects shared between different components, a form of shared memory between them.

ImageInitialization

public ImageInitialization(SharedObjects sharedObjects,
 Optional<ImageSizeSuggestion> suggestedSize)

Create with shared-objects and a resizing suggestion.

Parameters:

sharedObjects - objects shared between different components, a form of shared memory between them.

suggestedSize - a suggested input on how to resize an image, if one is provided.

Method Details

filePaths

public NamedProviderStore<Path> filePaths()

Named-store of file-paths.

Returns:

the store.

dictionaries

public NamedProviderStore<Dictionary> dictionaries()

Named-store of Dictionarys.

Returns:

the store.

modelDirectory

public Path modelDirectory()

Directory where machine-learning models can be found.

Returns:

the path.

dictionaryInitialization

public DictionaryInitialization dictionaryInitialization()

The associated initialization for a DictionaryBean.

Returns:

the associated initialization.

featuresInitialization

public FeatureRelatedInitialization featuresInitialization()

The associated initialization for a FeatureRelatedBean.

Returns:

the associated initialization.

combinedStacks

public NamedProvider<Stack> combinedStacks()

Exposes several entities that have natural Stack representations as a unified NamedProvider.

These are the:

• stacks()
• channels()
• masks()

If multiple sources have the same identifier, only one identifier (arbitrarily selected) will exist in the unified NamedProvider.

Returns:

a newly created NamedProvider combining the above entities as Stacks.

addDictionary

public void addDictionary(String identifier,
 Dictionary toAdd)
                   throws OperationFailedException

Adds a Dictionary to the corresponding named-collection of dictionaries.

Parameters:

identifier - the unique name of the dictionary.

toAdd - the dictionary to add.

Throws:

OperationFailedException - if the identifier already exists, or otherwise the add operation fails.

addStack

public void addStack(String identifier,
 Stack toAdd)
              throws OperationFailedException

Adds a Stack to the corresponding named-collection of stacks.

Parameters:

identifier - the unique name of the stack.

toAdd - the stack to add.

Throws:

OperationFailedException - if the identifier already exists, or otherwise the add operation fails.

addStacksFrom

public void addStacksFrom(NamedProvider<Stack> source)
                   throws OperationFailedException

Adds all the Stacks available in a NamedProvider using the corresponding identifiers.

Parameters:

source - the NamedProvider to add from.

Throws:

OperationFailedException - if an identifier already exists, or otherwise the add operation fails.

addObjectsFrom

public void addObjectsFrom(NamedProvider<ObjectCollection> source)
                    throws OperationFailedException

Adds all the ObjectCollections available in a NamedProvider using the corresponding identifiers.

Parameters:

source - the NamedProvider to add from.

Throws:

OperationFailedException - if an identifier already exists, or otherwise the add operation fails.

populate

public void populate(BeanInitializer<?> propertyInitializer,
 Define define,
 Logger logger)
              throws OperationFailedException

Adds diverse entities from a Define into the corresponding name-collections.

Parameters:

propertyInitializer - initializes the properties of objects, where initialization is required.

define - the Define from which entities are added.

logger - a logger to report messages or errors.

Throws:

OperationFailedException - if the identifier for an entity already exists, or otherwise the add operation fails.

addSharedObjectsDictionary

public void addSharedObjectsDictionary(Optional<SharedObjects> sharedObjects,
 Optional<Dictionary> dictionary)
                                throws OperationFailedException

Adds stacks and object-collections from a SharedObjects using the respective identifiers, and also adds a Dictionary.

The dictionary is assigned the identifier "input_dictionary".

Parameters:

sharedObjects - the shared-objects to add entities from, if it exists.

dictionary - the dictionary to add, if it exists.

Throws:

OperationFailedException - if the identifier for an entity already exists, or otherwise the add operation fails.

sharedObjects

public SharedObjects sharedObjects()

Objects shared between different components, a form of shared memory between them.

suggestedSize

public Optional<ImageSizeSuggestion> suggestedSize()

A suggested input on how to resize an image, if one is provided.

stacks

public NamedProviderStore<Stack> stacks()

A collection of Stacks, indexed by name.

histograms

public NamedProviderStore<Histogram> histograms()

A collection of Histograms, indexed by name.

objects

public NamedProviderStore<ObjectCollection> objects()

A collection of ObjectCollections, indexed by name.

channels

public NamedProviderStore<Channel> channels()

A collection of Channels, indexed by name.

masks

public NamedProviderStore<Mask> masks()

A collection of Masks, indexed by name.

binarySegmentations

public NamedProviderStore<BinarySegmentation> binarySegmentations()

A collection of BinarySegmentations, indexed by name.