loci.formats.in

Class OpenlabReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.OpenlabReader

All Implemented Interfaces:

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

public class OpenlabReader
extends FormatReader

OpenlabReader is the file format reader for Openlab LIFF files.

Author:

Melissa Linkert melissa at glencoesoftware.com, Eric Kjellman egkjellman at wisc.edu, Curtis Rueden ctrueden at wisc.edu, Jim Paris jim at jtan.com

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	OpenlabReader.PlaneInfo Helper class for storing plane info.

Field Summary

Fields

Modifier and Type	Field and Description
private static int	CALIBRATION
private static int	DEEP_GREY_10
private static int	DEEP_GREY_11
private static int	DEEP_GREY_12
private static int	DEEP_GREY_13
private static int	DEEP_GREY_14
private static int	DEEP_GREY_15
private static int	DEEP_GREY_16
private static int	DEEP_GREY_9
private java.lang.String	detectorOffset
private java.lang.String	fmt
private java.lang.String	gain
private static int	IMAGE_TYPE_1 Tag types.
private static int	IMAGE_TYPE_2
private int	lastPlane
static long	LIFF_MAGIC_BYTES
private java.util.List<byte[][]>	luts
private static int	MAC_1_BIT Image types.
private static int	MAC_16_BIT_COLOR
private static int	MAC_16_COLORS
private static int	MAC_16_GREYS
private static int	MAC_24_BIT_COLOR
private static int	MAC_256_COLORS
private static int	MAC_256_GREYS
private static int	MAC_4_GREYS
private long	nextTag
private PictReader	pict Helper reader to read PICT data.
private int[][]	planeOffsets
private OpenlabReader.PlaneInfo[]	planes
private boolean	specialPlateNames
private int	subTag
private int	tag
private static int	USER
private int	version LIFF version (should be 2 or 5).
private float	xcal
private java.lang.String	xPos
private float	ycal
private java.lang.String	yPos
private java.lang.String	zPos

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
OpenlabReader() Constructs a new OpenlabReader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
private void	findNextBlock()
byte[][]	get8BitLookupTable() Gets the 8-bit color lookup table associated with the most recently opened image.
int	getOptimalTileHeight() Returns the optimal sub-image height for use with openBytes.
private OpenlabReader.PlaneInfo	getPlane(int[] zct)
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	parseImageNames(int s)
private java.lang.String	readCString()
private void	readTagHeader() Read the next tag.
private void	readVariable()

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, 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

LIFF_MAGIC_BYTES

public static final long LIFF_MAGIC_BYTES

See Also:

Constant Field Values

MAC_1_BIT

private static final int MAC_1_BIT

Image types.

See Also:

Constant Field Values

MAC_4_GREYS

private static final int MAC_4_GREYS

See Also:

Constant Field Values

MAC_16_GREYS

private static final int MAC_16_GREYS

See Also:

Constant Field Values

MAC_16_COLORS

private static final int MAC_16_COLORS

See Also:

Constant Field Values

MAC_256_GREYS

private static final int MAC_256_GREYS

See Also:

Constant Field Values

MAC_256_COLORS

private static final int MAC_256_COLORS

See Also:

Constant Field Values

MAC_16_BIT_COLOR

private static final int MAC_16_BIT_COLOR

See Also:

Constant Field Values

MAC_24_BIT_COLOR

private static final int MAC_24_BIT_COLOR

See Also:

Constant Field Values

DEEP_GREY_9

private static final int DEEP_GREY_9

See Also:

Constant Field Values

DEEP_GREY_10

private static final int DEEP_GREY_10

See Also:

Constant Field Values

DEEP_GREY_11

private static final int DEEP_GREY_11

See Also:

Constant Field Values

DEEP_GREY_12

private static final int DEEP_GREY_12

See Also:

Constant Field Values

DEEP_GREY_13

private static final int DEEP_GREY_13

See Also:

Constant Field Values

DEEP_GREY_14

private static final int DEEP_GREY_14

See Also:

Constant Field Values

DEEP_GREY_15

private static final int DEEP_GREY_15

See Also:

Constant Field Values

DEEP_GREY_16

private static final int DEEP_GREY_16

See Also:

Constant Field Values

IMAGE_TYPE_1

private static final int IMAGE_TYPE_1

Tag types.

See Also:

Constant Field Values

IMAGE_TYPE_2

private static final int IMAGE_TYPE_2

See Also:

Constant Field Values

CALIBRATION

private static final int CALIBRATION

See Also:

Constant Field Values

USER

private static final int USER

See Also:

Constant Field Values

pict

private PictReader pict

Helper reader to read PICT data.

version

private int version

LIFF version (should be 2 or 5).

planes

private OpenlabReader.PlaneInfo[] planes

xcal

private float xcal

ycal

private float ycal

nextTag

private long nextTag

tag

private int tag

subTag

private int subTag

fmt

private java.lang.String fmt

planeOffsets

private int[][] planeOffsets

luts

private java.util.List<byte[][]> luts

lastPlane

private int lastPlane

gain

private java.lang.String gain

detectorOffset

private java.lang.String detectorOffset

xPos

private java.lang.String xPos

yPos

private java.lang.String yPos

zPos

private java.lang.String zPos

specialPlateNames

private boolean specialPlateNames

Constructor Detail

OpenlabReader

public OpenlabReader()

Constructs a new OpenlabReader.

Method Detail

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

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

readTagHeader

private void readTagHeader()
                    throws java.io.IOException

Read the next tag.

Throws:

java.io.IOException

readVariable

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

Throws:

FormatException

java.io.IOException

parseImageNames

private void parseImageNames(int s)

getPlane

private OpenlabReader.PlaneInfo getPlane(int[] zct)

findNextBlock

private void findNextBlock()
                    throws java.io.IOException

Throws:

java.io.IOException

readCString

private java.lang.String readCString()
                              throws java.io.IOException

Throws:

java.io.IOException