Package loci.formats.in

Class LIFReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.LIFReader

All Implemented Interfaces:

Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class LIFReader
extends FormatReader

LIFReader is the file format reader for Leica LIF files.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	LIFReader.MemoryBlock
(package private) class	LIFReader.ROI

Field Summary

Fields

Modifier and Type	Field	Description
private double[]	acquiredDate
private List[]	activeDetector
private boolean	alternateCenter
private static final com.google.common.collect.ImmutableMap<String,Integer>	CHANNEL_PRIORITIES
private String[][]	channelNames
private String[]	corrections
private List[]	cutIns
private List[]	cutOuts
private String[]	descriptions
private HashMap[]	detectorIndexes
private List[]	detectorModels
private Double[][]	detectorOffsets
private static final String	ENCODING	The encoding used in this file.
private long	endPointer
private Double[][]	expTimes
private Double[][]	exWaves
private List<ome.units.quantity.Length>	fieldPosX
private List<ome.units.quantity.Length>	fieldPosY
private List[]	filterModels
private boolean[]	flipX
private boolean[]	flipY
private Double[][]	gains
private String[]	imageNames
private LIFReader.ROI[][]	imageROIs
private String[]	immersions
private List[]	laserActive
private List[]	laserFrap
private List[]	laserIntensity
private List[]	laserWavelength
private int	lastChannel
private Double[]	lensNA
static final byte	LIF_MAGIC_BYTE
static final byte	LIF_MEMORY_BYTE
private static final String	LOGO_FILE
private List<String>	lutNames
private Double[]	magnification
private List<LIFReader.MemoryBlock>	memoryBlocks	Memory blocks including offsets and ID
private static final long	METER_MULTIPLY
private String[]	microscopeModels
private String[]	objectiveModels
static final boolean	OLD_PHYSICAL_SIZE_DEFAULT
static final String	OLD_PHYSICAL_SIZE_KEY
private List<Double>	physicalSizeXs
private List<Double>	physicalSizeYs
private Double[]	pinholes
private ome.units.quantity.Length[]	posX
private ome.units.quantity.Length[]	posY
private ome.units.quantity.Length[]	posZ
private int[][]	realChannel
private Double[]	refractiveIndex
private String[]	serialNumber
private static final String	STYLESHEET_FILE
private boolean[]	swapXY
private long[]	tileBytesInc
private int[]	tileCount
private Double[][]	timestamps
private Double[]	tSteps
private Double[]	zooms
private Double[]	zSteps

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	Description
LIFReader()	Constructs a new Leica LIF reader.

Method Summary

Modifier and Type	Method	Description
private void	addUserCommentMeta(Element imageNode, int image)
private ome.units.quantity.Length	checkFlip(boolean flip, ome.units.quantity.Length pos)
void	close(boolean fileOnly)	Closes the currently open file.
private static com.google.common.collect.ImmutableMap<String,Integer>	createChannelPriorities()
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 ArrayList<String>	getAvailableOptions()	Returns the list of available metadata options.
private ome.xml.model.primitives.Color	getChannelColor(int colorCode)
private NodeList	getChannelDescriptionNodes(Element root)
private int	getChannelIndex(Element filterSetting)
private NodeList	getDimensionDescriptionNodes(Element root)
private Element	getImageDescription(Element root)
private Element	getMetadataRoot(String xml)
private NodeList	getNodes(Element root, String nodeName)
int	getOptimalTileHeight()	Returns the optimal sub-image height for use with openBytes.
String[]	getSeriesUsedFiles(boolean noPixels)	Returns an array of filenames needed to open the current series.
private int	getTileIndex(int coreIndex)
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
private void	initMetadata(String xml)	Parses a string of XML and puts the values in a Hashtable.
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	populateOriginalMetadata(Element root, Deque<String> nameStack, int[] key_index, int jj)
private void	seekStartOfPlane(int no, long dataOffset, long planeSize)
private void	translateAttachmentNodes(Element imageNode, int image)
private void	translateDetectors(Element imageNode, int image)
private void	translateFilterSettings(Element imageNode, int image)
private void	translateImageNames(Element imageNode, int image)
private void	translateImageNodes(Element imageNode, int i)
private void	translateLaserLines(Element imageNode, int image)
private void	translateMetadata(Element root)
private void	translateROIs(Element imageNode, int image)
private void	translateScannerSettings(Element imageNode, int image)
private void	translateSingleROIs(Element imageNode, int image)
private double	translateSingleTimestamp(String timestamp)
private double	translateSingleTimestamp(Element timestamp)
private void	translateTimestamps(Element imageNode, int image)
boolean	useOldPhysicalSizeCalculation()

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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, 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, 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.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

OLD_PHYSICAL_SIZE_KEY

public static final String OLD_PHYSICAL_SIZE_KEY

See Also:

• Constant Field Values

OLD_PHYSICAL_SIZE_DEFAULT

public static final boolean OLD_PHYSICAL_SIZE_DEFAULT

See Also:

• Constant Field Values

LIF_MAGIC_BYTE

public static final byte LIF_MAGIC_BYTE

See Also:

• Constant Field Values

LIF_MEMORY_BYTE

public static final byte LIF_MEMORY_BYTE

See Also:

• Constant Field Values

ENCODING

private static final String ENCODING

The encoding used in this file.

See Also:

• Constant Field Values

LOGO_FILE

private static final String LOGO_FILE

See Also:

• Constant Field Values

STYLESHEET_FILE

private static final String STYLESHEET_FILE

See Also:

• Constant Field Values

CHANNEL_PRIORITIES

private static final com.google.common.collect.ImmutableMap<String,Integer> CHANNEL_PRIORITIES

METER_MULTIPLY

private static final long METER_MULTIPLY

See Also:

• Constant Field Values

memoryBlocks

private List<LIFReader.MemoryBlock> memoryBlocks

Memory blocks including offsets and ID

realChannel

private int[][] realChannel

lastChannel

private int lastChannel

lutNames

private List<String> lutNames

physicalSizeXs

private List<Double> physicalSizeXs

physicalSizeYs

private List<Double> physicalSizeYs

fieldPosX

private List<ome.units.quantity.Length> fieldPosX

fieldPosY

private List<ome.units.quantity.Length> fieldPosY

descriptions

private String[] descriptions

microscopeModels

private String[] microscopeModels

serialNumber

private String[] serialNumber

pinholes

private Double[] pinholes

zooms

private Double[] zooms

zSteps

private Double[] zSteps

tSteps

private Double[] tSteps

lensNA

private Double[] lensNA

flipX

private boolean[] flipX

flipY

private boolean[] flipY

swapXY

private boolean[] swapXY

expTimes

private Double[][] expTimes

gains

private Double[][] gains

detectorOffsets

private Double[][] detectorOffsets

channelNames

private String[][] channelNames

detectorModels

private List[] detectorModels

exWaves

private Double[][] exWaves

activeDetector

private List[] activeDetector

detectorIndexes

private HashMap[] detectorIndexes

immersions

private String[] immersions

corrections

private String[] corrections

objectiveModels

private String[] objectiveModels

magnification

private Double[] magnification

posX

private ome.units.quantity.Length[] posX

posY

private ome.units.quantity.Length[] posY

posZ

private ome.units.quantity.Length[] posZ

refractiveIndex

private Double[] refractiveIndex

cutIns

private List[] cutIns

cutOuts

private List[] cutOuts

filterModels

private List[] filterModels

timestamps

private Double[][] timestamps

laserWavelength

private List[] laserWavelength

laserIntensity

private List[] laserIntensity

laserActive

private List[] laserActive

laserFrap

private List[] laserFrap

imageROIs

private LIFReader.ROI[][] imageROIs

alternateCenter

private boolean alternateCenter

imageNames

private String[] imageNames

acquiredDate

private double[] acquiredDate

tileCount

private int[] tileCount

tileBytesInc

private long[] tileBytesInc

endPointer

private long endPointer

Constructor Details

LIFReader

public LIFReader()

Constructs a new Leica LIF reader.

Method Details

createChannelPriorities

private static com.google.common.collect.ImmutableMap<String,Integer> createChannelPriorities()

useOldPhysicalSizeCalculation

public boolean useOldPhysicalSizeCalculation()

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 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:

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

get16BitLookupTable

public short[][] get16BitLookupTable()

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

openBytes

public byte[] openBytes(int no,
 byte[] buf,
 int x,
 int y,
 int w,
 int h)
                 throws FormatException,
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.

IOException - if there was a problem reading the file.

See Also:

• IFormatReader.openBytes(int, byte[], int, int, int, int)

seekStartOfPlane

private void seekStartOfPlane(int no,
 long dataOffset,
 long planeSize)
                       throws IOException

Throws:

IOException

getSeriesUsedFiles

public 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

close

public void close(boolean fileOnly)
           throws 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:

IOException

getAvailableOptions

protected ArrayList<String> getAvailableOptions()

Description copied from class: FormatReader

Returns the list of available metadata options.

Overrides:

getAvailableOptions in class FormatReader

initFile

protected void initFile(String id)
                 throws FormatException,
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.

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

initMetadata

private void initMetadata(String xml)
                   throws FormatException,
IOException

Parses a string of XML and puts the values in a Hashtable.

Throws:

FormatException

IOException

checkFlip

private ome.units.quantity.Length checkFlip(boolean flip,
 ome.units.quantity.Length pos)

getMetadataRoot

private Element getMetadataRoot(String xml)
                         throws FormatException,
IOException

Throws:

FormatException

IOException

translateMetadata

private void translateMetadata(Element root)
                        throws FormatException

Throws:

FormatException

populateOriginalMetadata

private void populateOriginalMetadata(Element root,
 Deque<String> nameStack,
 int[] key_index,
 int jj)

translateImageNames

private void translateImageNames(Element imageNode,
 int image)

translateDetectors

private void translateDetectors(Element imageNode,
 int image)
                         throws FormatException

Throws:

FormatException

translateROIs

private void translateROIs(Element imageNode,
 int image)
                    throws FormatException

Throws:

FormatException

translateSingleROIs

private void translateSingleROIs(Element imageNode,
 int image)
                          throws FormatException

Throws:

FormatException

translateLaserLines

private void translateLaserLines(Element imageNode,
 int image)
                          throws FormatException

Throws:

FormatException

translateTimestamps

private void translateTimestamps(Element imageNode,
 int image)
                          throws FormatException

Throws:

FormatException

translateSingleTimestamp

private double translateSingleTimestamp(String timestamp)

translateSingleTimestamp

private double translateSingleTimestamp(Element timestamp)

translateFilterSettings

private void translateFilterSettings(Element imageNode,
 int image)
                              throws FormatException

Throws:

FormatException

translateScannerSettings

private void translateScannerSettings(Element imageNode,
 int image)
                               throws FormatException

Throws:

FormatException

translateAttachmentNodes

private void translateAttachmentNodes(Element imageNode,
 int image)
                               throws FormatException

Throws:

FormatException

addUserCommentMeta

private void addUserCommentMeta(Element imageNode,
 int image)
                         throws FormatException

Throws:

FormatException

translateImageNodes

private void translateImageNodes(Element imageNode,
 int i)
                          throws FormatException

Throws:

FormatException

getNodes

private NodeList getNodes(Element root,
 String nodeName)

getImageDescription

private Element getImageDescription(Element root)

getChannelDescriptionNodes

private NodeList getChannelDescriptionNodes(Element root)

getDimensionDescriptionNodes

private NodeList getDimensionDescriptionNodes(Element root)

getChannelIndex

private int getChannelIndex(Element filterSetting)

getChannelColor

private ome.xml.model.primitives.Color getChannelColor(int colorCode)

getTileIndex

private int getTileIndex(int coreIndex)