loci.formats.in

Class MinimalTiffReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.MinimalTiffReader

All Implemented Interfaces:

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

Direct Known Subclasses:

BaseTiffReader

public class MinimalTiffReader
extends SubResolutionFormatReader

MinimalTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.

Author:

Melissa Linkert melissa at glencoesoftware.com

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	canSeparateSeries Whether or not IFDs with different dimensions can be split into separate series.
protected boolean	equalStrips
protected IFDList	ifds List of IFDs for the current TIFF.
private JPEG2000CodecOptions	j2kCodecOptions Codec options to use when decoding JPEG 2000 data.
protected int	lastPlane
private static org.slf4j.Logger	LOGGER Logger for this class.
protected boolean	mergeSubIFDs Merge SubIFDs into the main IFD list.
protected boolean	noSubresolutions
private java.lang.Integer	resolutionLevels Number of JPEG 2000 resolution levels.
protected boolean	seriesToIFD
protected java.util.List<IFDList>	subResolutionIFDs List of sub-resolution IFDs for each IFD in the current TIFF with the same order as ifds.
protected IFDList	thumbnailIFDs List of thumbnail IFDs for the current TIFF.
protected TiffParser	tiffParser
protected boolean	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 and Description
MinimalTiffReader() Constructs a new MinimalTiffReader.
MinimalTiffReader(java.lang.String name, java.lang.String suffix) Constructs a new MinimalTiffReader.
MinimalTiffReader(java.lang.String name, java.lang.String[] suffixes) Constructs a new MinimalTiffReader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
protected byte[]	copyTile(IFD ifd, byte[] buf, int x, int y)
short[][]	get16BitLookupTable() Gets the 16-bit color lookup table associated with the most recently opened image.
byte[][]	get8BitLookupTable() Gets the 8-bit color lookup table associated with the most recently opened image.
protected long	getCompressedByteCount(IFD ifd, int x, int y)
IFDList	getIFDs() Gets the list of IFDs associated with the current TIFF's image planes.
int	getOptimalTileHeight() Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth() Returns the optimal sub-image width for use with openBytes.
IFDList	getThumbnailIFDs() Gets the list of IFDs associated with the current TIFF's thumbnails.
int	getThumbSizeX() Get the size of the X dimension for the thumbnail.
int	getThumbSizeY() Get the size of the Y dimension for the thumbnail.
protected int	getTileIndex(IFD ifd, int x, int y) Get the index of the tile corresponding to given IFD (plane) and tile XY indexes.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
protected void	initTiffParser() Reinitialize the underlying TiffParser.
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.
byte[]	openThumbBytes(int no) Obtains a thumbnail for the specified image plane from the current file, as a byte array.
void	reopenFile() Reopen any files that were closed, and which are expected to be open while the reader is open.
protected void	setResolutionLevel(IFD ifd) Sets the resolution level when we have JPEG 2000 compressed data.

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, 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.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

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

ifds

protected IFDList ifds

List of IFDs for the current TIFF.

thumbnailIFDs

protected IFDList thumbnailIFDs

List of thumbnail IFDs for the current TIFF.

subResolutionIFDs

protected java.util.List<IFDList> subResolutionIFDs

List of sub-resolution IFDs for each IFD in the current TIFF with the same order as ifds.

tiffParser

protected transient TiffParser tiffParser

equalStrips

protected boolean equalStrips

use64Bit

protected boolean use64Bit

lastPlane

protected int lastPlane

noSubresolutions

protected boolean noSubresolutions

seriesToIFD

protected boolean seriesToIFD

mergeSubIFDs

protected transient boolean mergeSubIFDs

Merge SubIFDs into the main IFD list.

canSeparateSeries

protected transient boolean canSeparateSeries

Whether or not IFDs with different dimensions can be split into separate series.

resolutionLevels

private java.lang.Integer resolutionLevels

Number of JPEG 2000 resolution levels.

j2kCodecOptions

private JPEG2000CodecOptions j2kCodecOptions

Codec options to use when decoding JPEG 2000 data.

Constructor Detail

MinimalTiffReader

public MinimalTiffReader()

Constructs a new MinimalTiffReader.

MinimalTiffReader

public MinimalTiffReader(java.lang.String name,
                         java.lang.String suffix)

Constructs a new MinimalTiffReader.

MinimalTiffReader

public MinimalTiffReader(java.lang.String name,
                         java.lang.String[] suffixes)

Constructs a new MinimalTiffReader.

Method Detail

getIFDs

public IFDList getIFDs()

Gets the list of IFDs associated with the current TIFF's image planes.

getThumbnailIFDs

public IFDList getThumbnailIFDs()

Gets the list of IFDs associated with the current TIFF's thumbnails.

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

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
                                     java.io.IOException

Description copied from interface: IFormatReader

Gets the 16-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.INT16 or FormatTools.UINT16, this method will return null.

Specified by:

get16BitLookupTable in interface IFormatReader

Overrides:

get16BitLookupTable in class FormatReader

Throws:

FormatException

java.io.IOException

getThumbSizeX

public int getThumbSizeX()

Description copied from interface: IFormatReader

Get the size of the X dimension for the thumbnail.

Specified by:

getThumbSizeX in interface IFormatReader

Overrides:

getThumbSizeX in class FormatReader

getThumbSizeY

public int getThumbSizeY()

Description copied from interface: IFormatReader

Get the size of the Y dimension for the thumbnail.

Specified by:

getThumbSizeY in interface IFormatReader

Overrides:

getThumbSizeY in class FormatReader

openThumbBytes

public byte[] openThumbBytes(int no)
                      throws FormatException,
                             java.io.IOException

Description copied from interface: IFormatReader

Obtains a thumbnail for the specified image plane from the current file, as a byte array.

Specified by:

openThumbBytes in interface IFormatReader

Overrides:

openThumbBytes 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:

FormatReader.openBytes(int, byte[], int, int, int, int)

reopenFile

public void reopenFile()
                throws java.io.IOException

Description copied from interface: IFormatReader

Reopen any files that were closed, and which are expected to be open while the reader is open. This assumes that IFormatHandler.setId(java.lang.String) has been called, but close(false) has not been called.

Specified by:

reopenFile in interface IFormatReader

Overrides:

reopenFile in class FormatReader

Throws:

java.io.IOException

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 SubResolutionFormatReader

Throws:

java.io.IOException

getOptimalTileWidth

public int getOptimalTileWidth()

Description copied from interface: IFormatReader

Returns the optimal sub-image width for use with openBytes.

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class FormatReader

getOptimalTileHeight

public int getOptimalTileHeight()

Description copied from interface: IFormatReader

Returns the optimal sub-image height for use with openBytes.

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight in class FormatReader

initFile

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

Throws:

FormatException - if a parsing error occurs processing the file.

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

setResolutionLevel

protected void setResolutionLevel(IFD ifd)

Sets the resolution level when we have JPEG 2000 compressed data.

Parameters:

ifd - The active IFD that is being used in our current openBytes() calling context. It will be the sub-resolution IFD if currentSeries > 0.

initTiffParser

protected void initTiffParser()

Reinitialize the underlying TiffParser.

getTileIndex

protected int getTileIndex(IFD ifd,
                           int x,
                           int y)
                    throws FormatException

Get the index of the tile corresponding to given IFD (plane) and tile XY indexes.

Parameters:

ifd - IFD for the requested tile's plane

x - tile X index

y - tile Y index

Returns:

corresponding tile index

Throws:

FormatException

getCompressedByteCount

protected long getCompressedByteCount(IFD ifd,
                                      int x,
                                      int y)
                               throws FormatException,
                                      java.io.IOException

Throws:

FormatException

java.io.IOException

copyTile

protected byte[] copyTile(IFD ifd,
                          byte[] buf,
                          int x,
                          int y)
                   throws FormatException,
                          java.io.IOException

Throws:

FormatException

java.io.IOException