loci.formats

Class DelegateReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.DelegateReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

Direct Known Subclasses:

JPEGReader, ND2Reader, QTReader, TiffDelegateReader

public abstract class DelegateReader
extends FormatReader

DelegateReader is a file format reader that selects which reader to use for a format if there are two readers which handle the same format.

Source code:

Trac, Gitweb

Field Summary

Fields

Modifier and Type	Field and Description
protected IFormatReader	legacyReader Legacy reader.
protected boolean	legacyReaderInitialized Flag indicating that the legacy reader was successfully initialized.
protected IFormatReader	nativeReader Native reader.
protected boolean	nativeReaderInitialized Flag indicating that the native reader was successfully initialized.
protected boolean	useLegacy Flag indicating whether to use legacy reader by default.

Fields inherited from class loci.formats.FormatReader

core, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
DelegateReader(String format, String suffix) Constructs a new delegate reader.
DelegateReader(String format, String[] suffixes) Constructs a new delegate reader.

Method Summary

Methods

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
short[][]	get16BitLookupTable() Gets the 16-bit color lookup table associated with the most recently opened image.
byte[][]	get8BitLookupTable() Gets the 8-bit color lookup table associated with the most recently opened image.
MetadataOptions	getMetadataOptions()
int	getOptimalTileHeight() Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth() Returns the optimal sub-image width for use with openBytes.
Set<MetadataLevel>	getSupportedMetadataLevels()
boolean	isLegacy() Gets whether to use the legacy reader by default.
boolean	isThisType(RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
boolean	isThisType(String name, boolean open) Checks if a file matches the type of this format reader.
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h) Obtains a sub-image of the specified image plane into a pre-allocated byte array.
void	setFlattenedResolutions(boolean flattened) Set whether or not to flatten resolutions into individual series.
void	setGroupFiles(boolean group) Specifies whether or not to force grouping in multi-file formats.
void	setId(String id) Sets the current file name.
void	setLegacy(boolean legacy) Sets whether to use the legacy reader by default.
void	setMetadataCollected(boolean collect) Deprecated.
void	setMetadataFiltered(boolean filter) Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.
void	setMetadataOptions(MetadataOptions options)
void	setMetadataStore(MetadataStore store) Sets the default metadata store for this reader.
void	setNormalized(boolean normalize) Specifies whether or not to normalize float data.
void	setOriginalMetadataPopulated(boolean populate) Specifies whether or not to save proprietary metadata in the MetadataStore.
void	setResolution(int resolution) Set the resolution level.
void	setSeries(int no) Activates the specified series.

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, close, coreIndexToSeries, fileGroupOption, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCompression, getContrastMethod, getCoreIndex, getCoreMetadata, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadata, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, hasCompanionFiles, hasFlattenedResolutions, initFile, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, seriesToCoreIndex

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes

Methods inherited from class java.lang.Object

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

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Field Detail

useLegacy

protected boolean useLegacy

Flag indicating whether to use legacy reader by default.

nativeReader

protected IFormatReader nativeReader

Native reader.

legacyReader

protected IFormatReader legacyReader

Legacy reader.

nativeReaderInitialized

protected boolean nativeReaderInitialized

Flag indicating that the native reader was successfully initialized.

legacyReaderInitialized

protected boolean legacyReaderInitialized

Flag indicating that the legacy reader was successfully initialized.

Constructor Detail

DelegateReader

public DelegateReader(String format,
              String suffix)

Constructs a new delegate reader.

DelegateReader

public DelegateReader(String format,
              String[] suffixes)

Constructs a new delegate reader.

Method Detail

setLegacy

public void setLegacy(boolean legacy)

Sets whether to use the legacy reader by default.

isLegacy

public boolean isLegacy()

Gets whether to use the legacy reader by default.

getSupportedMetadataLevels

public Set<MetadataLevel> getSupportedMetadataLevels()

Specified by:

getSupportedMetadataLevels in interface IMetadataConfigurable

Overrides:

getSupportedMetadataLevels in class FormatReader

getMetadataOptions

public MetadataOptions getMetadataOptions()

Specified by:

getMetadataOptions in interface IMetadataConfigurable

Overrides:

getMetadataOptions in class FormatReader

setMetadataOptions

public void setMetadataOptions(MetadataOptions options)

Specified by:

setMetadataOptions in interface IMetadataConfigurable

Overrides:

setMetadataOptions in class FormatReader

isThisType

public boolean isThisType(String name,
                 boolean open)

Description copied from class: FormatReader

Checks if a file matches the type of this format reader. Checks filename suffixes against those known for this format. If the suffix check is inconclusive and the open parameter is true, the file is opened and tested with FormatReader.isThisType(RandomAccessInputStream).

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis.

isThisType

public boolean isThisType(RandomAccessInputStream stream)
                   throws IOException

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Throws:

IOException

setSeries

public void setSeries(int no)

Description copied from interface: IFormatReader

Activates the specified series.

Specified by:

setSeries in interface IFormatReader

Overrides:

setSeries in class FormatReader

setResolution

public void setResolution(int resolution)

Description copied from interface: IFormatReader

Set the resolution level.

Specified by:

setResolution in interface IFormatReader

Overrides:

setResolution in class FormatReader

See Also:

IFormatReader.getResolutionCount()

setNormalized

public void setNormalized(boolean normalize)

Description copied from interface: IFormatReader

Specifies whether or not to normalize float data.

Specified by:

setNormalized in interface IFormatReader

Overrides:

setNormalized in class FormatReader

setMetadataCollected

public void setMetadataCollected(boolean collect)

Deprecated.

Description copied from interface: IFormatReader

Specifies whether or not to collect metadata.

Specified by:

setMetadataCollected in interface IFormatReader

Overrides:

setMetadataCollected in class FormatReader

See Also:

IFormatReader.setMetadataCollected(boolean)

setOriginalMetadataPopulated

public void setOriginalMetadataPopulated(boolean populate)

Description copied from interface: IFormatReader

Specifies whether or not to save proprietary metadata in the MetadataStore.

Specified by:

setOriginalMetadataPopulated in interface IFormatReader

Overrides:

setOriginalMetadataPopulated in class FormatReader

setGroupFiles

public void setGroupFiles(boolean group)

Description copied from interface: IFormatReader

Specifies whether or not to force grouping in multi-file formats.

Specified by:

setGroupFiles in interface IFormatReader

Overrides:

setGroupFiles in class FormatReader

setFlattenedResolutions

public void setFlattenedResolutions(boolean flattened)

Description copied from interface: IFormatReader

Set whether or not to flatten resolutions into individual series.

Specified by:

setFlattenedResolutions in interface IFormatReader

Overrides:

setFlattenedResolutions in class FormatReader

setMetadataFiltered

public void setMetadataFiltered(boolean filter)

Description copied from interface: IFormatReader

Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.

Specified by:

setMetadataFiltered in interface IFormatReader

Overrides:

setMetadataFiltered in class FormatReader

setMetadataStore

public void setMetadataStore(MetadataStore store)

Description copied from interface: IFormatReader

Sets the default metadata store for this reader.

Specified by:

setMetadataStore in interface IFormatReader

Overrides:

setMetadataStore in class FormatReader

Parameters:

store - a metadata store implementation.

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   IOException

Description copied from interface: IFormatReader

Gets the 8-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT8 or FormatTools.UINT8, this method will return null.

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class FormatReader

Throws:

FormatException

IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
                                     IOException

Description copied from interface: IFormatReader

Gets the 16-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT16 or FormatTools.UINT16, this method will return null.

Specified by:

get16BitLookupTable in interface IFormatReader

Overrides:

get16BitLookupTable in class FormatReader

Throws:

FormatException

IOException

openBytes

public byte[] openBytes(int no,
               byte[] buf,
               int x,
               int y,
               int w,
               int h)
                 throws FormatException,
                        IOException

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Parameters:

no - the image index within the file.

buf - a pre-allocated buffer.

x - X coordinate of the upper-left corner of the sub-image

y - Y coordinate of the upper-left corner of the sub-image

w - width of the sub-image

h - height of the sub-image

Returns:

the pre-allocated buffer buf for convenience.

Throws:

FormatException - if there was a problem parsing the metadata of the file.

IOException - if there was a problem reading the file.

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: IFormatReader

Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().

Specified by:

close in interface IFormatReader

Overrides:

close in class FormatReader

Throws:

IOException

getOptimalTileWidth

public int getOptimalTileWidth()

Description copied from interface: IFormatReader

Returns the optimal sub-image width for use with openBytes.

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class FormatReader

getOptimalTileHeight

public int getOptimalTileHeight()

Description copied from interface: IFormatReader

Returns the optimal sub-image height for use with openBytes.

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight in class FormatReader

setId

public void setId(String id)
           throws FormatException,
                  IOException

Description copied from interface: IFormatHandler

Sets the current file name.

Specified by:

setId in interface IFormatHandler

Overrides:

setId in class FormatReader

Throws:

FormatException

IOException