org.anchoranalysis.image.bean.nonbean.init.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 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<org.anchoranalysis.image.voxel.object.ObjectCollection> source)`	Adds all the `ObjectCollection`s 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 `Stack`s available in a `NamedProvider` using the corresponding identifiers.
`NamedProviderStore<BinarySegmentation>`	`binarySegmentations()`	A collection of `BinarySegmentation`s, indexed by name.
`NamedProviderStore<Channel>`	`channels()`	A collection of `Channel`s, indexed by name.
`NamedProvider<Stack>`	`combinedStacks()`	Exposes several entities that have natural `Stack` representations as a unified `NamedProvider`.
`NamedProviderStore<Dictionary>`	`dictionaries()`	Named-store of `Dictionary`s.
`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<org.anchoranalysis.math.histogram.Histogram>`	`histograms()`	A collection of `Histogram`s, indexed by name.
`NamedProviderStore<Mask>`	`masks()`	A collection of `Mask`s, indexed by name.
`Path`	`modelDirectory()`	Directory where machine-learning models can be found.
`NamedProviderStore<org.anchoranalysis.image.voxel.object.ObjectCollection>`	`objects()`	A collection of `ObjectCollection`s, 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 `Stack`s, 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<org.anchoranalysis.image.voxel.object.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<org.anchoranalysis.math.histogram.Histogram> histograms()
  
  A collection of Histograms, indexed by name.
- objects
  
  public NamedProviderStore<org.anchoranalysis.image.voxel.object.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.

Class ImageInitialization

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

Constructor Details

Method Details