Package loci.formats.in

Class NikonReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.MinimalTiffReader

loci.formats.in.BaseTiffReader

loci.formats.in.NikonReader

All Implemented Interfaces:

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

public class NikonReader
extends BaseTiffReader

NikonReader is the file format reader for Nikon NEF (TIFF) files.

Author:

Melissa Linkert melissa at glencoesoftware.com

Field Summary

Fields

Modifier and Type	Field	Description
private static final int	CAPTURE_EDITOR_DATA
private Object	cfaPattern
private static final int	COLOR_MAP
private static final int	COLOR_MODE
private int[]	curve
private static final int	CURVE
private static final int	FIRMWARE_VERSION
private static final int	FLASH_COMPENSATION
private static final int	FLASH_MODE
private static final int	FLASH_SETTING
private static final int	FLASH_USED
private static final int	FOCUS_MODE
private static final int	HUE
private static final int	ISO
private int	lastIndex
private byte[]	lastPlane
private static final int	LENS
private static final int	LENS_TYPE
private static final int	LIGHT_TYPE
private static final org.slf4j.Logger	LOGGER	Logger for this class.
private boolean	lossyCompression
private static final int	MAKER_WHITE_BALANCE
protected int	makerNoteOffset	Offset to the Nikon Maker Note.
static final String[]	NEF_SUFFIX
protected IFD	original	The original IFD.
private static final int	QUALITY
private static final int	SHARPENING
private int	split
private static final int	TIFF_EPS_STANDARD
private static final int	TONE_COMPENSATION
private int[]	vPredictor
private static final int	WHITE_BALANCE_FINE
private static final int	WHITE_BALANCE_RGB_COEFFS
private TiffRational[]	whiteBalance

Fields inherited from class loci.formats.in.BaseTiffReader

DATE_FORMATS

Fields inherited from class loci.formats.in.MinimalTiffReader

canSeparateSeries, equalStrips, ifds, mergeSubIFDs, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit

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, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
NikonReader()	Constructs a new Nikon reader.

Method Summary

Modifier and Type	Method	Description
private short	adjustForWhiteBalance(short val, int index)
void	close(boolean fileOnly)	Closes the currently open file.
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
protected void	initStandardMetadata()	Parses standard metadata.
boolean	isThisType(String name, boolean open)	Checks if a file matches the type of this format reader.
boolean	isThisType(loci.common.RandomAccessInputStream stream)	Checks if the given stream is a valid stream for this file format.
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.

Methods inherited from class loci.formats.in.BaseTiffReader

getExifTagName, getImageCreationDate, initMetadata, initMetadataStore, put, put, put, put, put, put, put, put, put, put, putDouble, putInt, putString

Methods inherited from class loci.formats.in.MinimalTiffReader

copyTile, get16BitLookupTable, get8BitLookupTable, getCompressedByteCount, getIFDs, getOptimalTileHeight, getOptimalTileWidth, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, getTileIndex, initTiffParser, openThumbBytes, reopenFile, setResolutionLevel

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, getAvailableOptions, 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, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, readPlane, readPlane, readPlane, 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

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

NEF_SUFFIX

public static final String[] NEF_SUFFIX

TIFF_EPS_STANDARD

private static final int TIFF_EPS_STANDARD

See Also:

• Constant Field Values

COLOR_MAP

private static final int COLOR_MAP

See Also:

• Constant Field Values

FIRMWARE_VERSION

private static final int FIRMWARE_VERSION

See Also:

• Constant Field Values

ISO

private static final int ISO

See Also:

• Constant Field Values

QUALITY

private static final int QUALITY

See Also:

• Constant Field Values

MAKER_WHITE_BALANCE

private static final int MAKER_WHITE_BALANCE

See Also:

• Constant Field Values

SHARPENING

private static final int SHARPENING

See Also:

• Constant Field Values

FOCUS_MODE

private static final int FOCUS_MODE

See Also:

• Constant Field Values

FLASH_SETTING

private static final int FLASH_SETTING

See Also:

• Constant Field Values

FLASH_MODE

private static final int FLASH_MODE

See Also:

• Constant Field Values

WHITE_BALANCE_FINE

private static final int WHITE_BALANCE_FINE

See Also:

• Constant Field Values

WHITE_BALANCE_RGB_COEFFS

private static final int WHITE_BALANCE_RGB_COEFFS

See Also:

• Constant Field Values

FLASH_COMPENSATION

private static final int FLASH_COMPENSATION

See Also:

• Constant Field Values

TONE_COMPENSATION

private static final int TONE_COMPENSATION

See Also:

• Constant Field Values

LENS_TYPE

private static final int LENS_TYPE

See Also:

• Constant Field Values

LENS

private static final int LENS

See Also:

• Constant Field Values

FLASH_USED

private static final int FLASH_USED

See Also:

• Constant Field Values

CURVE

private static final int CURVE

See Also:

• Constant Field Values

COLOR_MODE

private static final int COLOR_MODE

See Also:

• Constant Field Values

LIGHT_TYPE

private static final int LIGHT_TYPE

See Also:

• Constant Field Values

HUE

private static final int HUE

See Also:

• Constant Field Values

CAPTURE_EDITOR_DATA

private static final int CAPTURE_EDITOR_DATA

See Also:

• Constant Field Values

makerNoteOffset

protected int makerNoteOffset

Offset to the Nikon Maker Note.

original

protected IFD original

The original IFD.

whiteBalance

private TiffRational[] whiteBalance

cfaPattern

private Object cfaPattern

curve

private int[] curve

vPredictor

private int[] vPredictor

lossyCompression

private boolean lossyCompression

split

private int split

lastPlane

private byte[] lastPlane

lastIndex

private int lastIndex

Constructor Details

NikonReader

public NikonReader()

Constructs a new Nikon reader.

Method Details

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

Parameters:

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(loci.common.RandomAccessInputStream stream)
                   throws 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 MinimalTiffReader

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:

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

Overrides:

openBytes in class MinimalTiffReader

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.

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 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 MinimalTiffReader

Throws:

IOException

initStandardMetadata

protected void initStandardMetadata()
                             throws FormatException,
IOException

Description copied from class: BaseTiffReader

Parses standard metadata. NOTE: Absolutely no calls to the metadata store should be made in this method or methods that override this method. Data will be overwritten if you do so.

Overrides:

initStandardMetadata in class BaseTiffReader

Throws:

FormatException

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
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 BaseTiffReader

Throws:

FormatException - if a parsing error occurs processing the file.

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

adjustForWhiteBalance

private short adjustForWhiteBalance(short val,
 int index)