loci.formats.in

Class AVIReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.AVIReader

All Implemented Interfaces:

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

public class AVIReader
extends FormatReader

AVIReader is the file format reader for AVI files. Much of this code was adapted from Wayne Rasband's AVI Movie Reader plugin for ImageJ (available at http://rsb.info.nih.gov/ij).

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	AVI_MAGIC_STRING
private short	bmpBitsPerPixel
private int	bmpColorsUsed
private int	bmpCompression
private int	bmpScanLineSize
private int	bmpWidth
private int	bytesPerPlane
private java.lang.String	fcc
private static int	JPEG
private byte[]	lastImage
private int	lastImageNo
private java.util.List<java.lang.Long>	lengths Number of bytes in each plane.
private java.lang.String	listString
private byte[][]	lut
private static byte[]	MJPEG_HUFFMAN_TABLE Huffman table for MJPEG data.
private static int	MS_VIDEO
private static int	MSRLE Supported compression types.
private java.util.List<java.lang.Long>	offsets Offset to each plane.
private long	pos
private int	size
private java.lang.String	type
private static int	Y8

Fields inherited from class loci.formats.FormatReader

core, 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
AVIReader() Constructs a new AVI reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
byte[][]	get8BitLookupTable() Gets the 8-bit color lookup table associated with the most recently opened image.
private java.lang.String	getCodecName(int bmpCompression)
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	readChunk()
private void	readChunkHeader()
private void	readTypeAndSize()
private byte[]	uncompress(int no, byte[] buf)

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, 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, 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

AVI_MAGIC_STRING

public static final java.lang.String AVI_MAGIC_STRING

See Also:

Constant Field Values

MSRLE

private static final int MSRLE

Supported compression types.

See Also:

Constant Field Values

MS_VIDEO

private static final int MS_VIDEO

See Also:

Constant Field Values

JPEG

private static final int JPEG

See Also:

Constant Field Values

Y8

private static final int Y8

See Also:

Constant Field Values

MJPEG_HUFFMAN_TABLE

private static final byte[] MJPEG_HUFFMAN_TABLE

Huffman table for MJPEG data.

offsets

private java.util.List<java.lang.Long> offsets

Offset to each plane.

lengths

private java.util.List<java.lang.Long> lengths

Number of bytes in each plane.

listString

private java.lang.String listString

type

private java.lang.String type

fcc

private java.lang.String fcc

size

private int size

pos

private long pos

bytesPerPlane

private int bytesPerPlane

bmpColorsUsed

private int bmpColorsUsed

bmpWidth

private int bmpWidth

bmpCompression

private int bmpCompression

bmpScanLineSize

private int bmpScanLineSize

bmpBitsPerPixel

private short bmpBitsPerPixel

lut

private byte[][] lut

lastImage

private byte[] lastImage

lastImageNo

private int lastImageNo

Constructor Detail

AVIReader

public AVIReader()

Constructs a new AVI 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()

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

uncompress

private byte[] uncompress(int no,
                          byte[] buf)
                   throws FormatException,
                          java.io.IOException

Throws:

FormatException

java.io.IOException

readChunkHeader

private void readChunkHeader()
                      throws java.io.IOException

Throws:

java.io.IOException

readTypeAndSize

private void readTypeAndSize()
                      throws java.io.IOException

Throws:

java.io.IOException

readChunk

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

Throws:

FormatException

java.io.IOException

getCodecName

private java.lang.String getCodecName(int bmpCompression)