loci.formats.in

Class APNGReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.APNGReader

All Implemented Interfaces:

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

public class APNGReader
extends FormatReader

APNGReader is the file format reader for Animated Portable Network Graphics (APNG) images.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	APNGReader.PNGBlock
(package private) class	APNGReader.PNGInputStream InputStream implementation that stitches together IDAT blocks into a seamless zlib stream.

Field Summary

Fields

Modifier and Type	Field and Description
private static int	AVERAGE
private java.util.Vector<APNGReader.PNGBlock>	blocks
private int	compression
private java.util.Vector<int[]>	frameCoordinates
private static int	GRAY_ALPHA
private static int	GRAYSCALE Color types.
private int	idatCount
private static int	INDEXED
private int	interlace
private byte[]	lastImage
private int	lastImageIndex
private int	lastImageRow
private byte[][]	lut
private static int	NONE Filter types.
private static int	PAETH
private static int[]	PASS_HEIGHTS
private static int[]	PASS_WIDTHS Interlacing pass dimensions.
private static int	SUB
private static int	TRUE_ALPHA
private static int	TRUE_COLOR
private static int	UP

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
APNGReader() Constructs a new APNGReader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
private byte[]	decode(APNGReader.PNGInputStream bytes)
private byte[]	decode(APNGReader.PNGInputStream bytes, int width, int height)
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 void	unfilter(byte[] filters, byte[] image, int width, int height) See http://www.w3.org/TR/PNG/#9Filters.

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, 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

Field Detail

GRAYSCALE

private static final int GRAYSCALE

Color types.

See Also:

Constant Field Values

TRUE_COLOR

private static final int TRUE_COLOR

See Also:

Constant Field Values

INDEXED

private static final int INDEXED

See Also:

Constant Field Values

GRAY_ALPHA

private static final int GRAY_ALPHA

See Also:

Constant Field Values

TRUE_ALPHA

private static final int TRUE_ALPHA

See Also:

Constant Field Values

NONE

private static final int NONE

Filter types.

See Also:

Constant Field Values

SUB

private static final int SUB

See Also:

Constant Field Values

UP

private static final int UP

See Also:

Constant Field Values

AVERAGE

private static final int AVERAGE

See Also:

Constant Field Values

PAETH

private static final int PAETH

See Also:

Constant Field Values

PASS_WIDTHS

private static final int[] PASS_WIDTHS

Interlacing pass dimensions.

PASS_HEIGHTS

private static final int[] PASS_HEIGHTS

blocks

private java.util.Vector<APNGReader.PNGBlock> blocks

frameCoordinates

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

lut

private byte[][] lut

lastImage

private byte[] lastImage

lastImageIndex

private int lastImageIndex

lastImageRow

private int lastImageRow

compression

private int compression

interlace

private int interlace

idatCount

private int idatCount

Constructor Detail

APNGReader

public APNGReader()

Constructs a new APNGReader.

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()

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

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

decode

private byte[] decode(APNGReader.PNGInputStream bytes)
               throws FormatException,
                      java.io.IOException

Throws:

FormatException

java.io.IOException

decode

private byte[] decode(APNGReader.PNGInputStream bytes,
                      int width,
                      int height)
               throws FormatException,
                      java.io.IOException

Throws:

FormatException

java.io.IOException

unfilter

private void unfilter(byte[] filters,
                      byte[] image,
                      int width,
                      int height)
               throws FormatException

See http://www.w3.org/TR/PNG/#9Filters.

Throws:

FormatException