Package loci.formats.in

Class ND2Reader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.ND2Reader

All Implemented Interfaces:

Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class ND2Reader
extends SubResolutionFormatReader

ND2Reader is the file format reader for Nikon ND2 files. The JAI ImageIO library is required to use this reader; it is available from http://jai-imageio.dev.java.net. Note that JAI ImageIO is bundled with a version of the JJ2000 library, so it is important that either: (1) the JJ2000 jar file is *not* in the classpath; or (2) the JAI jar file precedes JJ2000 in the classpath. Thanks to Tom Caswell for additions to the ND2 metadata parsing logic.

Field Summary

Fields

Modifier and Type	Field	Description
static final long	ND2_MAGIC_BYTES_1
static final long	ND2_MAGIC_BYTES_2
static final boolean	USE_CHUNKMAP_DEFAULT
static final String	USE_CHUNKMAP_KEY
static final String	USE_CHUNKMAP_LEGACY_KEY	Deprecated.

Fields inherited from class loci.formats.SubResolutionFormatReader

core

Fields inherited from class loci.formats.FormatReader

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

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
ND2Reader()	Constructs a new ND2 reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)
short[][]	get16BitLookupTable()
byte[][]	get8BitLookupTable()
protected ArrayList<String>	getAvailableOptions()
long[][]	getOffsets()
protected void	initFile(String id)
boolean	isThisType(RandomAccessInputStream stream)
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)
static String	sanitizeControl(String s)	Remove control and invalid characters from the given string.
void	setOffsets(String file, long[][] newOffsets)	Change the underlying file path and pixel data offsets, keeping all other metadata the same.
boolean	useChunkMap()

Methods inherited from class loci.formats.SubResolutionFormatReader

coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution, setSeries

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, fileGroupOption, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, updateMetadataLists

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from class java.lang.Object

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

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

ND2_MAGIC_BYTES_1

public static final long ND2_MAGIC_BYTES_1

See Also:

• Constant Field Values

ND2_MAGIC_BYTES_2

public static final long ND2_MAGIC_BYTES_2

See Also:

• Constant Field Values

USE_CHUNKMAP_LEGACY_KEY

@Deprecated
public static final String USE_CHUNKMAP_LEGACY_KEY

Deprecated.

Legacy chunkmap option key will be removed in Bio-Formats 8.0.0.

See Also:

• Constant Field Values

USE_CHUNKMAP_KEY

public static final String USE_CHUNKMAP_KEY

See Also:

• Constant Field Values

USE_CHUNKMAP_DEFAULT

public static final boolean USE_CHUNKMAP_DEFAULT

See Also:

• Constant Field Values

Constructor Details

ND2Reader

public ND2Reader()

Constructs a new ND2 reader.

Method Details

useChunkMap

public boolean useChunkMap()

isThisType

public boolean isThisType(RandomAccessInputStream stream)
                   throws IOException

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Throws:

IOException

get8BitLookupTable

public byte[][] get8BitLookupTable()

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class FormatReader

get16BitLookupTable

public short[][] get16BitLookupTable()

Specified by:

get16BitLookupTable in interface IFormatReader

Overrides:

get16BitLookupTable in class FormatReader

openBytes

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

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Throws:

FormatException

IOException

See Also:

• IFormatReader.openBytes(int, byte[], int, int, int, int)

close

public void close(boolean fileOnly)
           throws IOException

Specified by:

close in interface IFormatReader

Overrides:

close in class SubResolutionFormatReader

Throws:

IOException

getAvailableOptions

protected ArrayList<String> getAvailableOptions()

Overrides:

getAvailableOptions in class FormatReader

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Overrides:

initFile in class SubResolutionFormatReader

Throws:

FormatException

IOException

sanitizeControl

public static String sanitizeControl(String s)

Remove control and invalid characters from the given string.

getOffsets

public long[][] getOffsets()

Returns:

offsets to pixel data

setOffsets

public void setOffsets(String file,
 long[][] newOffsets)
                throws IOException

Change the underlying file path and pixel data offsets, keeping all other metadata the same.

Throws:

IOException