io.scif

Interface Parser

All Superinterfaces:

Comparable<org.scijava.Prioritized>, org.scijava.Contextual, Groupable, HasFormat, org.scijava.plugin.HasPluginInfo, HasSource, org.scijava.Identifiable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.Prioritized, org.scijava.plugin.RichPlugin, SCIFIOPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Versioned

All Known Subinterfaces:

TypedParser<M>

All Known Implementing Classes:

AbstractParser, APNGFormat.Parser, AVIFormat.Parser, BMPFormat.Parser, DefaultParser, DICOMFormat.Parser, EPSFormat.Parser, FITSFormat.Parser, GIFFormat.Parser, ICSFormat.Parser, ImageIOFormat.Parser, JPEG2000Format.Parser, JPEGFormat.Parser, JPEGTileFormat.Parser, KontronFormat.Parser, LegacyQTFormat.Parser, MicromanagerFormat.Parser, MinimalTIFFFormat.Parser, MNGFormat.Parser, NativeQTFormat.Parser, NRRDFormat.Parser, PCXFormat.Parser, PGMFormat.Parser, PICTFormat.Parser, ScancoISQFormat.Parser, StratecPQCTFormat.Parser, TestImgFormat.Parser, TIFFFormat.BaseTIFFParser, TIFFFormat.Parser, TIFFJAIFormat.Parser

public interface Parser
extends HasFormat, HasSource, Groupable

Interface for all SCIFIO Parsers.

Parsers are used to create type-specific Metadata appropriate for their Format by reading from an image source.

Author:

Mark Hiner

See Also:

Format

Method Summary

Modifier and Type	Method and Description
LocationInfo[]	getAdvancedImageUsedLocations(int imageIndex, boolean noPixels) Returns an array of LocationInfo objects representing the Locations needed to open the current series.
LocationInfo[]	getAdvancedUsedLocations(boolean noPixels) Returns an array of LocationInfo objects representing the Locations needed to open this dataset.
org.scijava.io.location.Location[]	getImageUsedFiles(int imageIndex) Returns an array of filenames needed to open the indicated image index.
org.scijava.io.location.Location[]	getImageUsedFiles(int imageIndex, boolean noPixels) Returns an array of filenames needed to open the indicated image.
Metadata	getMetadata()
org.scijava.io.handle.DataHandle<org.scijava.io.location.Location>	getSource()
org.scijava.io.location.Location	getSourceLocation()
Set<MetadataLevel>	getSupportedMetadataLevels() Returns a list of MetadataLevel options for determining the granularity of Metadata collection.
org.scijava.io.location.Location[]	getUsedFiles() Returns an array of filenames needed to open this dataset.
org.scijava.io.location.Location[]	getUsedLocations(boolean noPixels) Returns an array of filenames needed to open this dataset.
Metadata	parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream) Creates a Metadata object from the provided image source.
Metadata	parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, Metadata meta) Parses metadata from the provided image source to an existing Metadata object (overwriting may occur).
Metadata	parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, Metadata meta, SCIFIOConfig config) /** As parse(DataHandle, Metadata) with configuration options.
Metadata	parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, SCIFIOConfig config) As parse(DataHandle) with configuration options.
Metadata	parse(org.scijava.io.location.Location location) Creates a Metadata object using the provided location of an image source.
Metadata	parse(org.scijava.io.location.Location location, Metadata meta) Parses metadata using the provided name of an image source, and writes to an existing Metadata object (overwriting may occur).
Metadata	parse(org.scijava.io.location.Location fileName, Metadata meta, SCIFIOConfig config) As parse(Location, Metadata) with configuration options.
Metadata	parse(org.scijava.io.location.Location fileName, SCIFIOConfig config) As parse(Location) with configuration options.
void	updateSource(org.scijava.io.location.Location source) Updates the source being operated on by this parser (e.g. in multi-file formats).

Methods inherited from interface io.scif.HasFormat

getFormat, getFormatName

Methods inherited from interface io.scif.SCIFIOPlugin

getVersion, log

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier

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 io.scif.HasSource

close, close

Methods inherited from interface io.scif.Groupable

fileGroupOption, hasCompanionFiles, isSingleFile

Method Detail

parse

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

Creates a Metadata object using the provided location of an image source.

Parameters:

location - the Location of the image source to parse.

Returns:

A new Metadata object of the appropriate type.

Throws:

IOException

FormatException

parse

Metadata parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream)
        throws IOException,
               FormatException

Creates a Metadata object from the provided image source.

Parameters:

stream - a random access handle to the image source to parse.

Returns:

A new Metadata object of the appropriate type.

Throws:

IOException

FormatException

parse

Metadata parse(org.scijava.io.location.Location location,
               Metadata meta)
        throws IOException,
               FormatException

Parses metadata using the provided name of an image source, and writes to an existing Metadata object (overwriting may occur).

Parameters:

location - the Location of the image source to parse.

meta - A base Metadata to fill.

Returns:

The provided Metadata after parsing.

Throws:

IllegalArgumentException - if meta is not assignable from the Metadata associated with this Parser's Format

IOException

FormatException

parse

Metadata parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream,
               Metadata meta)
        throws IOException,
               FormatException

Parses metadata from the provided image source to an existing Metadata object (overwriting may occur).

Parameters:

stream - A DataHandle to the image source to parse.

meta - A base Metadata to fill.

Returns:

The provided Metadata after parsing.

Throws:

IllegalArgumentException - if meta is not assignable from the Metadata associated with this Parser's Format

IOException

FormatException

parse

Metadata parse(org.scijava.io.location.Location fileName,
               SCIFIOConfig config)
        throws IOException,
               FormatException

As parse(Location) with configuration options.

Parameters:

fileName - Name of the image source to parse.

config - Configuration information to use for this parse.

Returns:

A new Metadata object of the appropriate type.

Throws:

IOException

FormatException

parse

Metadata parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle,
               SCIFIOConfig config)
        throws IOException,
               FormatException

As parse(DataHandle) with configuration options.

Parameters:

handle - a DataHandle to the image source to parse.

config - Configuration information to use for this parse.

Returns:

A new Metadata object of the appropriate type.

Throws:

IOException

FormatException

parse

Metadata parse(org.scijava.io.location.Location fileName,
               Metadata meta,
               SCIFIOConfig config)
        throws IOException,
               FormatException

As parse(Location, Metadata) with configuration options.

Parameters:

fileName - the Location of the image source to parse.

meta - A base Metadata to fill.

config - Configuration information to use for this parse.

Returns:

The provided Metadata after parsing.

Throws:

IllegalArgumentException - if meta is not assignable from the Metadata associated with this Parser's Format

IOException

FormatException

parse

Metadata parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream,
               Metadata meta,
               SCIFIOConfig config)
        throws IOException,
               FormatException

/** As parse(DataHandle, Metadata) with configuration options.

Parameters:

stream - a random access handle to the image source to parse.

meta - A base Metadata to fill.

config - Configuration information to use for this parse.

Returns:

The provided Metadata after parsing.

Throws:

IllegalArgumentException - if meta is not assignable from the Metadata associated with this Parser's Format

IOException

FormatException

getMetadata

Metadata getMetadata()

Returns:

The last metadata instance parsed by this parser.

getSource

org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> getSource()

Returns:

The last DataHandle read by this parser.

getSourceLocation

org.scijava.io.location.Location getSourceLocation()

Returns:

The last Location read from by this parser.

updateSource

void updateSource(org.scijava.io.location.Location source)
           throws IOException

Updates the source being operated on by this parser (e.g. in multi-file formats).

Throws:

IOException

getUsedFiles

org.scijava.io.location.Location[] getUsedFiles()

Returns an array of filenames needed to open this dataset.

getUsedLocations

org.scijava.io.location.Location[] getUsedLocations(boolean noPixels)

Returns an array of filenames needed to open this dataset. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.

getImageUsedFiles

org.scijava.io.location.Location[] getImageUsedFiles(int imageIndex)

Returns an array of filenames needed to open the indicated image index.

getImageUsedFiles

org.scijava.io.location.Location[] getImageUsedFiles(int imageIndex,
                                                     boolean noPixels)

Returns an array of filenames needed to open the indicated image. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.

getAdvancedUsedLocations

LocationInfo[] getAdvancedUsedLocations(boolean noPixels)

Returns an array of LocationInfo objects representing the Locations needed to open this dataset. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.

getAdvancedImageUsedLocations

LocationInfo[] getAdvancedImageUsedLocations(int imageIndex,
                                             boolean noPixels)

Returns an array of LocationInfo objects representing the Locations needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.

getSupportedMetadataLevels

Set<MetadataLevel> getSupportedMetadataLevels()

Returns a list of MetadataLevel options for determining the granularity of Metadata collection.