loci.formats.in

Class NativeND2Reader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.NativeND2Reader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class NativeND2Reader
extends SubResolutionFormatReader

NativeND2Reader 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.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static class	NativeND2Reader.ChunkMapEntry

Field Summary

Fields

Modifier and Type	Field and Description
private ND2Handler	backupHandler
private static int	BUFFER_SIZE
private java.util.Map<java.lang.String,java.lang.Integer>	channelColors
private Codec	codec Codec to use when decompressing pixel data.
private int[]	colors
private java.util.ArrayList<java.lang.Double>	exposureTime
private int	fieldIndex
(package private) java.lang.String	imageMetadataLVOrder
(package private) java.lang.Boolean	imageMetadataLVProcessed
private boolean	isJPEG Whether or not the pixel data is compressed using JPEG 2000.
private boolean	isLossless Whether or not the pixel data is losslessly compressed.
private int	lastChannel
private java.lang.Double	lensNA
static long	ND2_MAGIC_BYTES_1
static long	ND2_MAGIC_BYTES_2
private int	nXFields
private java.lang.Double	objectiveMag
private java.lang.String	objectiveModel
private long[][]	offsets Array of image offsets.
private long	pfsOffset
private long	pfsStateOffset
private int	positionCount
private java.util.ArrayList<ome.units.quantity.Length>	posX
private java.util.ArrayList<ome.units.quantity.Length>	posY
private java.util.ArrayList<ome.units.quantity.Length>	posZ
private java.lang.Double	refractiveIndex
private boolean	split
private java.util.ArrayList<java.lang.String>	textChannelNames
private boolean	textData
private java.util.ArrayList<java.lang.Double>	textEmissionWavelengths
private double	trueSizeX
private double	trueSizeY
private java.lang.Double	trueSizeZ
private java.util.ArrayList<java.lang.Double>	tsT
static boolean	USE_CHUNKMAP_DEFAULT
static java.lang.String	USE_CHUNKMAP_KEY
private java.lang.Boolean	useZ
private long	xOffset
private long	yOffset
private long	zOffset

Fields inherited from class loci.formats.SubResolutionFormatReader

core

Fields inherited from class loci.formats.FormatReader

coreIndex, datasetDescription, domains, 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 and Description
NativeND2Reader() Constructs a new ND2 reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
private void	copyPixels(int x, int y, int w, int h, int bpp, int scanlinePad, byte[] pix, byte[] buf, boolean split)
private Codec	createCodec(boolean isJPEG)
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.
protected java.util.ArrayList<java.lang.String>	getAvailableOptions() Returns the list of available metadata options.
long[][]	getOffsets()
private int	getScanlinePad()
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
boolean	isThisType(loci.common.RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
private java.util.ArrayList<java.lang.String>	iterateIn(loci.common.RandomAccessInputStream in, java.lang.Long stop) Function for iterating through ND2 metaAttributes
private java.util.ArrayList<java.lang.String>	iterateIn(loci.common.RandomAccessInputStream in, java.lang.Long stop, boolean minimal) Function for iterating through ND2 metaAttributes
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.
private void	parseText(java.lang.String textString, int offsetCount, boolean useDimensions)
private void	populateMetadataStore(ND2Handler handler)
static java.lang.String	sanitizeControl(java.lang.String s) Remove control and invalid characters from the given string.
private void	setDimensions(int numT, int numZ, int numSeries)
void	setOffsets(java.lang.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, 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, 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, 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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Detail

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

BUFFER_SIZE

private static final int BUFFER_SIZE

See Also:

Constant Field Values

USE_CHUNKMAP_KEY

public static final java.lang.String USE_CHUNKMAP_KEY

See Also:

Constant Field Values

USE_CHUNKMAP_DEFAULT

public static final boolean USE_CHUNKMAP_DEFAULT

See Also:

Constant Field Values

offsets

private long[][] offsets

Array of image offsets.

isJPEG

private boolean isJPEG

Whether or not the pixel data is compressed using JPEG 2000.

codec

private Codec codec

Codec to use when decompressing pixel data.

isLossless

private boolean isLossless

Whether or not the pixel data is losslessly compressed.

tsT

private java.util.ArrayList<java.lang.Double> tsT

positionCount

private int positionCount

fieldIndex

private int fieldIndex

xOffset

private long xOffset

yOffset

private long yOffset

zOffset

private long zOffset

pfsOffset

private long pfsOffset

pfsStateOffset

private long pfsStateOffset

posX

private java.util.ArrayList<ome.units.quantity.Length> posX

posY

private java.util.ArrayList<ome.units.quantity.Length> posY

posZ

private java.util.ArrayList<ome.units.quantity.Length> posZ

exposureTime

private java.util.ArrayList<java.lang.Double> exposureTime

channelColors

private java.util.Map<java.lang.String,java.lang.Integer> channelColors

split

private boolean split

lastChannel

private int lastChannel

colors

private int[] colors

useZ

private java.lang.Boolean useZ

nXFields

private int nXFields

backupHandler

private ND2Handler backupHandler

trueSizeX

private double trueSizeX

trueSizeY

private double trueSizeY

trueSizeZ

private java.lang.Double trueSizeZ

textChannelNames

private java.util.ArrayList<java.lang.String> textChannelNames

textEmissionWavelengths

private java.util.ArrayList<java.lang.Double> textEmissionWavelengths

textData

private boolean textData

refractiveIndex

private java.lang.Double refractiveIndex

imageMetadataLVProcessed

java.lang.Boolean imageMetadataLVProcessed

imageMetadataLVOrder

java.lang.String imageMetadataLVOrder

lensNA

private transient java.lang.Double lensNA

objectiveMag

private transient java.lang.Double objectiveMag

objectiveModel

private transient java.lang.String objectiveModel

Constructor Detail

NativeND2Reader

public NativeND2Reader()

Constructs a new ND2 reader.

Method Detail

useChunkMap

public boolean useChunkMap()

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws java.io.IOException

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Parameters:

stream - A RandomAccessInputStream representing the file to check. The first byte in the stream is assumed to be the first byte in the file.

Returns:

true if the file represented by the stream can be read by this reader; false otherwise.

Throws:

java.io.IOException

get8BitLookupTable

public byte[][] get8BitLookupTable()

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

get16BitLookupTable

public short[][] get16BitLookupTable()

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

openBytes

public byte[] openBytes(int no,
                        byte[] buf,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        java.io.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 plane index within the current series.

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.

java.io.IOException - if there was a problem reading the file.

See Also:

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

close

public void close(boolean fileOnly)
           throws java.io.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 SubResolutionFormatReader

Throws:

java.io.IOException

getAvailableOptions

protected java.util.ArrayList<java.lang.String> getAvailableOptions()

Description copied from class: FormatReader

Returns the list of available metadata options.

Overrides:

getAvailableOptions in class FormatReader

initFile

protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.IOException

Description copied from class: SubResolutionFormatReader

Initializes the given file (parsing header information, etc.). Most subclasses should override this method to perform initialization operations such as parsing metadata.

Overrides:

initFile in class SubResolutionFormatReader

Throws:

FormatException - if a parsing error occurs processing the file.

java.io.IOException - if an I/O error occurs processing the file

iterateIn

private java.util.ArrayList<java.lang.String> iterateIn(loci.common.RandomAccessInputStream in,
                                                        java.lang.Long stop)

Function for iterating through ND2 metaAttributes

Parameters:

in - stream of bytes from file

stop - position where to stop

Returns:

text info values, if found

iterateIn

private java.util.ArrayList<java.lang.String> iterateIn(loci.common.RandomAccessInputStream in,
                                                        java.lang.Long stop,
                                                        boolean minimal)

Function for iterating through ND2 metaAttributes

Parameters:

in - stream of bytes from file

stop - position where to stop

minimal - true if values should be read with no additional metadata parsing

Returns:

text info values, if found

populateMetadataStore

private void populateMetadataStore(ND2Handler handler)
                            throws FormatException

Throws:

FormatException

createCodec

private Codec createCodec(boolean isJPEG)

copyPixels

private void copyPixels(int x,
                        int y,
                        int w,
                        int h,
                        int bpp,
                        int scanlinePad,
                        byte[] pix,
                        byte[] buf,
                        boolean split)
                 throws java.io.IOException

Throws:

java.io.IOException

sanitizeControl

public static java.lang.String sanitizeControl(java.lang.String s)

Remove control and invalid characters from the given string.

getScanlinePad

private int getScanlinePad()

parseText

private void parseText(java.lang.String textString,
                       int offsetCount,
                       boolean useDimensions)

setDimensions

private void setDimensions(int numT,
                           int numZ,
                           int numSeries)

getOffsets

public long[][] getOffsets()

Returns:

offsets to pixel data

setOffsets

public void setOffsets(java.lang.String file,
                       long[][] newOffsets)
                throws java.io.IOException

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

Throws:

java.io.IOException