loci.formats.in

Class GIFReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.GIFReader

All Implemented Interfaces:

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

public class GIFReader
extends FormatReader

GIFReader is the file format reader for Graphics Interchange Format (GIF) files. Much of this code was adapted from the Animated GIF Reader plugin for ImageJ (http://rsb.info.nih.gov/ij).

Field Summary

Fields

Modifier and Type	Field and Description
private int[]	act Active color table.
private int	blockSize Block size.
private java.util.Vector<int[]>	colorTables
private byte[]	dBlock Current data block.
private int	dispose
private static int	END
private static int	EXTENSION
private int[]	gct Global color table.
static java.lang.String	GIF_MAGIC_STRING
private static int	GRAPHICS
private int	ih Current image rectangle.
private static int	IMAGE_SEPARATOR
private java.util.Vector<byte[]>	images
private boolean	interlace Interlace flag.
private int	iw Current image rectangle.
private int	ix Current image rectangle.
private int	iy Current image rectangle.
private int	lastDispose
private static int	MAX_STACK_SIZE Maximum buffer size.
private byte[]	pixels
private byte[]	pixelStack
private java.util.Set<java.lang.Integer>	planesRead
private short[]	prefix
private byte[]	suffix
private int	transIndex Transparent color index.
private boolean	transparency Use transparent color.

Fields inherited from class loci.formats.FormatReader

core, 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 and Description
GIFReader() Constructs a new GIF reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
private void	decodeImageData() Decodes LZW image data into a pixel array.
byte[][]	get8BitLookupTable() Gets the 8-bit color lookup table associated with the most recently opened image.
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.
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 int	readBlock() Reads the next variable length block.
private void	readImageBlock()
private int[]	readLut(int size) Read a color lookup table of the specified size.
private void	setPixels()
private void	skipBlocks()

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, coreIndexToSeries, fileGroupOption, flattenHashtables, get16BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, 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, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, 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, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, 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

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Field Detail

GIF_MAGIC_STRING

public static final java.lang.String GIF_MAGIC_STRING

See Also:

Constant Field Values

MAX_STACK_SIZE

private static final int MAX_STACK_SIZE

Maximum buffer size.

See Also:

Constant Field Values

IMAGE_SEPARATOR

private static final int IMAGE_SEPARATOR

See Also:

Constant Field Values

EXTENSION

private static final int EXTENSION

See Also:

Constant Field Values

END

private static final int END

See Also:

Constant Field Values

GRAPHICS

private static final int GRAPHICS

See Also:

Constant Field Values

gct

private int[] gct

Global color table.

act

private int[] act

Active color table.

interlace

private boolean interlace

Interlace flag.

ix

private int ix

Current image rectangle.

iy

private int iy

Current image rectangle.

iw

private int iw

Current image rectangle.

ih

private int ih

Current image rectangle.

dBlock

private byte[] dBlock

Current data block.

blockSize

private int blockSize

Block size.

dispose

private int dispose

lastDispose

private int lastDispose

transparency

private boolean transparency

Use transparent color.

transIndex

private int transIndex

Transparent color index.

prefix

private short[] prefix

suffix

private byte[] suffix

pixelStack

private byte[] pixelStack

pixels

private byte[] pixels

images

private java.util.Vector<byte[]> images

colorTables

private java.util.Vector<int[]> colorTables

planesRead

private transient java.util.Set<java.lang.Integer> planesRead

Constructor Detail

GIFReader

public GIFReader()

Constructs a new GIF reader.

Method Detail

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()
                            throws FormatException,
                                   java.io.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

java.io.IOException

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 FormatReader

Throws:

java.io.IOException

initFile

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

Description copied from class: FormatReader

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 FormatReader

Throws:

FormatException - if a parsing error occurs processing the file.

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

readBlock

private int readBlock()
               throws java.io.IOException

Reads the next variable length block.

Throws:

java.io.IOException

decodeImageData

private void decodeImageData()
                      throws java.io.IOException

Decodes LZW image data into a pixel array. Adapted from ImageMagick.

Throws:

java.io.IOException

setPixels

private void setPixels()

skipBlocks

private void skipBlocks()
                 throws java.io.IOException

Throws:

java.io.IOException

readImageBlock

private void readImageBlock()
                     throws FormatException,
                            java.io.IOException

Throws:

FormatException

java.io.IOException

readLut

private int[] readLut(int size)
               throws FormatException

Read a color lookup table of the specified size.

Throws:

FormatException