io.scif

Class AbstractParser<M extends TypedMetadata>

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

io.scif.AbstractSCIFIOPlugin

io.scif.AbstractHasFormat

io.scif.AbstractHasSource

io.scif.AbstractGroupable

io.scif.AbstractParser<M>

Type Parameters:

M - - The Metadata type returned by this Parser.

All Implemented Interfaces:

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

Direct Known Subclasses:

APNGFormat.Parser, AVIFormat.Parser, BMPFormat.Parser, DefaultParser, DICOMFormat.Parser, EPSFormat.Parser, FITSFormat.Parser, GIFFormat.Parser, ICSFormat.Parser, ImageIOFormat.Parser, JPEG2000Format.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, TIFFJAIFormat.Parser

public abstract class AbstractParser<M extends TypedMetadata>
extends AbstractGroupable
implements TypedParser<M>

Abstract superclass of all SCIFIO Parser implementations.

Author:

Mark Hiner

See Also:

Parser, Metadata, HasFormat

Constructor Summary

Constructors

Constructor and Description
AbstractParser()

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.
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.
M	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.
M	parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream) Creates a Metadata object from the provided image source.
M	parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, M meta) Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(DataHandle, Metadata).
M	parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, Metadata meta) Parses metadata from the provided image source to an existing Metadata object (overwriting may occur).
M	parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, Metadata meta, SCIFIOConfig config) /** As Parser.parse(DataHandle, Metadata) with configuration options.
M	parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, M meta, SCIFIOConfig config) Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(DataHandle, Metadata).
M	parse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, SCIFIOConfig config) As Parser.parse(DataHandle) with configuration options.
M	parse(org.scijava.io.location.Location fileName) Creates a Metadata object using the provided location of an image source.
M	parse(org.scijava.io.location.Location loc, Metadata meta) Parses metadata using the provided name of an image source, and writes to an existing Metadata object (overwriting may occur).
M	parse(org.scijava.io.location.Location loc, Metadata meta, SCIFIOConfig config) As Parser.parse(Location, Metadata) with configuration options.
M	parse(org.scijava.io.location.Location loc, M meta, SCIFIOConfig config) Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(Location, Metadata).
M	parse(org.scijava.io.location.Location loc, SCIFIOConfig config) As Parser.parse(Location) with configuration options.
protected void	setMetaData(Metadata meta) Allows implementations of this class that override parse(Location, Metadata, SCIFIOConfig) to set the metadata.
protected abstract void	typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, M meta, SCIFIOConfig config) A helper method, called by parse(DataHandle, TypedMetadata).
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 class io.scif.AbstractGroupable

fileGroupOption, hasCompanionFiles, isSingleFile

Methods inherited from class io.scif.AbstractHasSource

close

Methods inherited from class io.scif.AbstractHasFormat

asBrowsableLocation, asBrowsableLocation, getFormat, getFormatName

Methods inherited from class io.scif.AbstractSCIFIOPlugin

getVersion, log

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

getInfo, getPriority, setInfo, setPriority, toString

Methods inherited from class org.scijava.AbstractContextual

context, getContext

Methods inherited from class java.lang.Object

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

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

Methods inherited from interface io.scif.Groupable

fileGroupOption, hasCompanionFiles, isSingleFile

Constructor Detail

AbstractParser

public AbstractParser()

Method Detail

parse

public M parse(org.scijava.io.location.Location fileName)
        throws IOException,
               FormatException

Description copied from interface: Parser

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

Specified by:

parse in interface Parser

Specified by:

parse in interface TypedParser<M extends TypedMetadata>

Parameters:

fileName - the Location of the image source to parse.

Returns:

A new Metadata object of the appropriate type.

Throws:

IOException

FormatException

parse

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

Description copied from interface: Parser

Creates a Metadata object from the provided image source.

Specified by:

parse in interface Parser

Specified by:

parse in interface TypedParser<M extends TypedMetadata>

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

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

Description copied from interface: Parser

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

Specified by:

parse in interface Parser

Parameters:

loc - the Location of the image source to parse.

meta - A base Metadata to fill.

Returns:

The provided Metadata after parsing.

Throws:

IOException

FormatException

parse

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

Description copied from interface: Parser

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

Specified by:

parse in interface Parser

Parameters:

handle - A DataHandle to the image source to parse.

meta - A base Metadata to fill.

Returns:

The provided Metadata after parsing.

Throws:

IOException

FormatException

getMetadata

public M getMetadata()

Specified by:

getMetadata in interface Parser

Returns:

The last metadata instance parsed by this parser.

getSource

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

Specified by:

getSource in interface Parser

Returns:

The last DataHandle read by this parser.

getSourceLocation

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

Specified by:

getSourceLocation in interface Parser

Returns:

The last Location read from by this parser.

updateSource

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

Description copied from interface: Parser

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

Specified by:

updateSource in interface Parser

Throws:

IOException

getUsedFiles

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

Description copied from interface: Parser

Returns an array of filenames needed to open this dataset.

Specified by:

getUsedFiles in interface Parser

getUsedLocations

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

Description copied from interface: Parser

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.

Specified by:

getUsedLocations in interface Parser

getImageUsedFiles

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

Description copied from interface: Parser

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

Specified by:

getImageUsedFiles in interface Parser

getImageUsedFiles

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

Description copied from interface: Parser

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.

Specified by:

getImageUsedFiles in interface Parser

getAdvancedUsedLocations

public LocationInfo[] getAdvancedUsedLocations(boolean noPixels)

Description copied from interface: Parser

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.

Specified by:

getAdvancedUsedLocations in interface Parser

getAdvancedImageUsedLocations

public LocationInfo[] getAdvancedImageUsedLocations(int imageIndex,
                                                    boolean noPixels)

Description copied from interface: Parser

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.

Specified by:

getAdvancedImageUsedLocations in interface Parser

getSupportedMetadataLevels

public Set<MetadataLevel> getSupportedMetadataLevels()

Description copied from interface: Parser

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

Specified by:

getSupportedMetadataLevels in interface Parser

parse

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

Description copied from interface: TypedParser

Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(DataHandle, Metadata).

Specified by:

parse in interface TypedParser<M extends TypedMetadata>

Throws:

IOException

FormatException

See Also:

Parser.parse(DataHandle, Metadata)

parse

public M parse(org.scijava.io.location.Location loc,
               M meta,
               SCIFIOConfig config)
        throws IOException,
               FormatException

Description copied from interface: TypedParser

Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(Location, Metadata).

Specified by:

parse in interface TypedParser<M extends TypedMetadata>

Throws:

IOException

FormatException

See Also:

Parser.parse(Location, Metadata, SCIFIOConfig)

parse

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

Description copied from interface: TypedParser

Generic-parameterized parse method, using TypedMetadata to avoid type erasure conflicts with Parser.parse(DataHandle, Metadata).

Specified by:

parse in interface TypedParser<M extends TypedMetadata>

Throws:

IOException

FormatException

See Also:

Parser.parse(DataHandle, Metadata, SCIFIOConfig)

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: HasSource

Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.

Specified by:

close in interface HasSource

Parameters:

fileOnly - - If true, only the associated source(s) are closed.

Throws:

IOException

typedParse

protected abstract void typedParse(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle,
                                   M meta,
                                   SCIFIOConfig config)
                            throws IOException,
                                   FormatException

A helper method, called by parse(DataHandle, TypedMetadata). Allows for boilerplate code to come after parsing, specifically calls to Metadata.populateImageMetadata().

This method should be implemented to populate any format-specific Metadata.

NB: if a Format requires type-specific parsing to occur before the Abstract layer, Override #parse(String, TypedMetadata) instead.

Throws:

IOException

FormatException

parse

public M parse(org.scijava.io.location.Location loc,
               SCIFIOConfig config)
        throws IOException,
               FormatException

Description copied from interface: Parser

As Parser.parse(Location) with configuration options.

Specified by:

parse in interface Parser

Specified by:

parse in interface TypedParser<M extends TypedMetadata>

Parameters:

loc - 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

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

Description copied from interface: Parser

As Parser.parse(DataHandle) with configuration options.

Specified by:

parse in interface Parser

Specified by:

parse in interface TypedParser<M extends TypedMetadata>

Parameters:

stream - 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

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

Description copied from interface: Parser

As Parser.parse(Location, Metadata) with configuration options.

Specified by:

parse in interface Parser

Parameters:

loc - 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:

IOException

FormatException

parse

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

Description copied from interface: Parser

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

Specified by:

parse in interface Parser

Parameters:

handle - 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:

IOException

FormatException

setMetaData

protected void setMetaData(Metadata meta)

Allows implementations of this class that override parse(Location, Metadata, SCIFIOConfig) to set the metadata.

Parameters:

meta - the metadata object for this parser