loci.formats.in

Class NativeQTReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.NativeQTReader

All Implemented Interfaces:

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

public class NativeQTReader
extends FormatReader

NativeQTReader is the file format reader for QuickTime movie files. It does not require any external libraries to be installed. Video codecs currently supported: raw, rle, jpeg, mjpb, rpza. Additional video codecs will be added as time permits.

Author:

Melissa Linkert melissa at glencoesoftware.com

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	altCodec Some movies use two video codecs -- this is the second codec.
private int	altPlanes Number of frames that use the alternate codec.
private int	bitsPerPixel Pixel depth.
private boolean	canUsePrevious Flag indicating whether we can safely use prevPixels.
private java.util.Vector<java.lang.Integer>	chunkSizes Number of bytes in each plane.
private java.lang.String	codec Video codec used by this movie.
private static java.lang.String[]	CONTAINER_TYPES List of identifiers for each container atom.
private boolean	flip
private java.lang.String	forkFile
private boolean	interlaced Set to true if the scanlines in a plane are interlaced (mjpb only).
private java.util.Vector<java.lang.Integer>	offsets Offsets to each plane's pixel data.
private long	pixelBytes Total number of bytes of pixel data.
private long	pixelOffset Offset to start of pixel data.
private byte[]	prevPixels Pixel data for the previous image plane.
private int	prevPlane Previous plane number.
private int	rawSize Raw plane size, in bytes.
private int	scale Amount to subtract from each offset.
private boolean	separatedFork Flag indicating whether the resource and data fork are separated.

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
NativeQTReader() Constructs a new QuickTime reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
private boolean	isContainer(java.lang.String type) Checks if the given String is a container atom type.
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	parse(int depth, long offset, long length) Parse all of the atoms in the file.
private void	print(int depth, long size, java.lang.String type) Debugging method; prints information on an atom.
private void	stripHeader() Cut off header bytes from a resource fork file.
private byte[]	uncompress(byte[] pixs, java.lang.String code) Uncompresses an image plane according to the the codec identifier.

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, get8BitLookupTable, 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, 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

CONTAINER_TYPES

private static final java.lang.String[] CONTAINER_TYPES

List of identifiers for each container atom.

pixelOffset

private long pixelOffset

Offset to start of pixel data.

pixelBytes

private long pixelBytes

Total number of bytes of pixel data.

bitsPerPixel

private int bitsPerPixel

Pixel depth.

rawSize

private int rawSize

Raw plane size, in bytes.

offsets

private java.util.Vector<java.lang.Integer> offsets

Offsets to each plane's pixel data.

prevPixels

private byte[] prevPixels

Pixel data for the previous image plane.

prevPlane

private int prevPlane

Previous plane number.

canUsePrevious

private boolean canUsePrevious

Flag indicating whether we can safely use prevPixels.

codec

private java.lang.String codec

Video codec used by this movie.

altCodec

private java.lang.String altCodec

Some movies use two video codecs -- this is the second codec.

altPlanes

private int altPlanes

Number of frames that use the alternate codec.

scale

private int scale

Amount to subtract from each offset.

chunkSizes

private java.util.Vector<java.lang.Integer> chunkSizes

Number of bytes in each plane.

interlaced

private boolean interlaced

Set to true if the scanlines in a plane are interlaced (mjpb only).

separatedFork

private boolean separatedFork

Flag indicating whether the resource and data fork are separated.

forkFile

private java.lang.String forkFile

flip

private boolean flip

Constructor Detail

NativeQTReader

public NativeQTReader()

Constructs a new QuickTime 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

getSeriesUsedFiles

public java.lang.String[] getSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles 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

parse

private void parse(int depth,
                   long offset,
                   long length)
            throws FormatException,
                   java.io.IOException

Parse all of the atoms in the file.

Throws:

FormatException

java.io.IOException

isContainer

private boolean isContainer(java.lang.String type)

Checks if the given String is a container atom type.

print

private void print(int depth,
                   long size,
                   java.lang.String type)

Debugging method; prints information on an atom.

uncompress

private byte[] uncompress(byte[] pixs,
                          java.lang.String code)
                   throws FormatException,
                          java.io.IOException

Uncompresses an image plane according to the the codec identifier.

Throws:

FormatException

java.io.IOException

stripHeader

private void stripHeader()
                  throws java.io.IOException

Cut off header bytes from a resource fork file.

Throws:

java.io.IOException