io.scif.services

Interface InitializeService

All Superinterfaces:

Comparable<org.scijava.Prioritized>, org.scijava.Contextual, org.scijava.Disposable, org.scijava.plugin.HasPluginInfo, org.scijava.Identifiable, org.scijava.Initializable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.Prioritized, org.scijava.plugin.RichPlugin, SCIFIOService, org.scijava.plugin.SciJavaPlugin, org.scijava.service.Service, org.scijava.Versioned

All Known Implementing Classes:

DefaultInitializeService

public interface InitializeService
extends SCIFIOService

A collection of methods for initializing the IO components of SCIFIO (Readers and Writers). All parsing and Metadata setup is done automatically.

NB: The initializeReader(org.scijava.io.location.Location) line of methods return a ReaderFilter instead of a basic Reader. This is a convenience to allow filters to be enabled if desired.

Author:

Mark Hiner

See Also:

Reader, Writer, ReaderFilter

Method Summary

Modifier and Type	Method and Description
ReaderFilter	initializeReader(org.scijava.io.location.Location id) See initializeReader(Location, SCIFIOConfig).
ReaderFilter	initializeReader(org.scijava.io.location.Location id, SCIFIOConfig config) Convenience method for creating a Reader component that is ready to open planes of the provided image source.
Writer	initializeWriter(org.scijava.io.location.Location source, org.scijava.io.location.Location destination) See initializeWriter(Location, Location, SCIFIOConfig).
Writer	initializeWriter(org.scijava.io.location.Location source, org.scijava.io.location.Location destination, SCIFIOConfig config) As initializeWriter(Location, Location) with configuration options.
Writer	initializeWriter(Metadata sourceMeta, org.scijava.io.location.Location destination) See initializeWriter(Location, Location, SCIFIOConfig).
Writer	initializeWriter(Metadata sourceMeta, org.scijava.io.location.Location destination, SCIFIOConfig config) As initializeWriter(Metadata, Location) with configuration options.
Metadata	parseMetadata(org.scijava.io.location.Location id) Convenience method to parse Metadata without reading the underlying pixels.
Metadata	parseMetadata(org.scijava.io.location.Location id, SCIFIOConfig config) As parseMetadata(Location) with a flag to open the underlying dataset when parsing, if desired.

Methods inherited from interface org.scijava.service.Service

initialize, registerEventHandlers

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier, log

Methods inherited from interface org.scijava.Contextual

context, getContext, setContext

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Methods inherited from interface org.scijava.Versioned

getVersion

Methods inherited from interface org.scijava.Disposable

dispose

Method Detail

initializeReader

ReaderFilter initializeReader(org.scijava.io.location.Location id)
                       throws FormatException,
                              IOException

See initializeReader(Location, SCIFIOConfig). Will not open the image source while parsing metadata.

Parameters:

id - Name of the image source to be read.

Returns:

An initialized Reader.

Throws:

FormatException

IOException

initializeReader

ReaderFilter initializeReader(org.scijava.io.location.Location id,
                              SCIFIOConfig config)
                       throws FormatException,
                              IOException

Convenience method for creating a Reader component that is ready to open planes of the provided image source. The reader's Metadata and source fields will be populated.

Parameters:

id - Name of the image source to be read.

config - Configuration for this method execution.

Returns:

An initialized Reader.

Throws:

FormatException

IOException

initializeWriter

Writer initializeWriter(org.scijava.io.location.Location source,
                        org.scijava.io.location.Location destination)
                 throws FormatException,
                        IOException

See initializeWriter(Location, Location, SCIFIOConfig). Will not open the image source while parsing metadata.

Parameters:

source - Name of the image source to use for parsing metadata.

destination - Name of the writing destination.

Returns:

An initialized Writer.

Throws:

FormatException

IOException

initializeWriter

Writer initializeWriter(org.scijava.io.location.Location source,
                        org.scijava.io.location.Location destination,
                        SCIFIOConfig config)
                 throws FormatException,
                        IOException

As initializeWriter(Location, Location) with configuration options.

Parameters:

source - Name of the image source to use for parsing metadata.

destination - Name of the writing destination.

config - Configuration for this method execution.

Returns:

An initialized Writer.

Throws:

FormatException

IOException

initializeWriter

Writer initializeWriter(Metadata sourceMeta,
                        org.scijava.io.location.Location destination)
                 throws FormatException,
                        IOException

See initializeWriter(Location, Location, SCIFIOConfig). Will not open the image source while parsing metadata.

Parameters:

sourceMeta - Name of the image source to use for parsing metadata.

destination - Name of the writing destination.

Returns:

An initialized Writer.

Throws:

FormatException

IOException

initializeWriter

Writer initializeWriter(Metadata sourceMeta,
                        org.scijava.io.location.Location destination,
                        SCIFIOConfig config)
                 throws FormatException,
                        IOException

As initializeWriter(Metadata, Location) with configuration options.

Parameters:

sourceMeta - Name of the image source to use for parsing metadata.

destination - Name of the writing destination.

config - Configuration information to use for this parse.

Returns:

An initialized Writer.

Throws:

FormatException

IOException

parseMetadata

Metadata parseMetadata(org.scijava.io.location.Location id)
                throws IOException,
                       FormatException

Convenience method to parse Metadata without reading the underlying pixels. Useful when translating to other formats, or simply extracting image metadata. Will not open the image source when determining format compatibility.

Parameters:

id - Name of the image source to be read.

Returns:

Parsed Metadata for the given source.

Throws:

FormatException

IOException

parseMetadata

Metadata parseMetadata(org.scijava.io.location.Location id,
                       SCIFIOConfig config)
                throws FormatException,
                       IOException

As parseMetadata(Location) with a flag to open the underlying dataset when parsing, if desired.

Parameters:

id - Name of the image source to be read.

config - Configuration for this method execution.

Returns:

Parsed Metadata for the given source.

Throws:

FormatException

IOException