Package loci.formats.in

Class LiFlimReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.LiFlimReader

All Implemented Interfaces:

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

public class LiFlimReader
extends FormatReader

LiFlimReader is the file format reader for LI-FLIM files.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	LiFlimReader.ROI

Field Summary

Fields

Modifier and Type	Field	Description
static final String	BACKGROUND_TABLE
private String	backgroundC
private String	backgroundDatatype
private String	backgroundF
private String	backgroundP
private String	backgroundT
private String	backgroundX
private String	backgroundY
private String	backgroundZ
static final String	C_KEY
private String	channels
private String	compression
static final String	COMPRESSION_GZIP
static final String	COMPRESSION_KEY
static final String	COMPRESSION_NONE
private String	DarkImage
static final String	DarkImage_KEY
private long	dataOffset	Offset to start of pixel data.
private String	datatype
static final String	DATATYPE_INT16
static final String	DATATYPE_INT32
static final String	DATATYPE_INT8
static final String	DATATYPE_KEY
static final String	DATATYPE_REAL32
static final String	DATATYPE_REAL64
static final String	DATATYPE_UINT12
static final String	DATATYPE_UINT16
static final String	DATATYPE_UINT32
static final String	DATATYPE_UINT8
private Double	exposureTime
private ome.units.unit.Unit<ome.units.quantity.Time>	exposureTimeUnit
static final String	F_KEY
private String	frequencies
private DataInputStream	gz	Stream to use for reading gzip-compressed pixel data.
private boolean	gzip	True if gzip compression was used to deflate the pixels.
private int	gzPos	Image number indicating position in gzip stream.
private int	gzSeries	Series number indicating position in gzip stream.
static final String	INFO_TABLE
private loci.common.IniList	ini	Parsed configuration data.
static final String[]	KNOWN_VERSIONS
static final String	LAYOUT_TABLE
static final String	NUMBEROFDARKIMAGES_KEY
static final String	NUMBEROFFRAMES_KEY
private int	numRegions
static final String	P_KEY
private String	packing
static final String	PACKING_KEY
private String	phases
static final String	PIXELFORMAT_KEY
private Map<Integer,LiFlimReader.ROI>	rois
private Map<Integer,String>	stampValues
static final String	T_KEY
static final String	TIMESTAMP_KEY
private String	timestamps
private boolean	TypeUINT12	if DataType is UINT12, data is compressed in 12 bits.
private DataInputStream	UINT12stream
private int	UINT12streamPos
private int	UINT12streamSeries
private String	version
static final String	VERSION_KEY
static final String	X_KEY
private String	xLen
static final String	Y_KEY
private String	yLen
static final String	Z_KEY
private String	zLen

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
LiFlimReader()	Constructs a new LI-FLIM reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
private static byte[]	convert12to16LSB(byte[] image)
private static byte[]	convert12to16MSB(byte[] image)
private int	getPixelTypeFromString(String type)
private String	getVersion()
private void	initCoreMetadata()
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
private void	initOMEMetadata()
private void	initOriginalMetadata()
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	parseHeader()
private void	prepareGZipStream(int no)
private void	prepareUINT12Stream(int no)	Similar to Gzip, make a DataInputstream for UINT12 data
private void	skip(InputStream is, long num)

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, 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, 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, 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, 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

INFO_TABLE

public static final String INFO_TABLE

See Also:

• Constant Field Values

LAYOUT_TABLE

public static final String LAYOUT_TABLE

See Also:

• Constant Field Values

BACKGROUND_TABLE

public static final String BACKGROUND_TABLE

See Also:

• Constant Field Values

VERSION_KEY

public static final String VERSION_KEY

See Also:

• Constant Field Values

COMPRESSION_KEY

public static final String COMPRESSION_KEY

See Also:

• Constant Field Values

DATATYPE_KEY

public static final String DATATYPE_KEY

See Also:

• Constant Field Values

PACKING_KEY

public static final String PACKING_KEY

See Also:

• Constant Field Values

C_KEY

public static final String C_KEY

See Also:

• Constant Field Values

X_KEY

public static final String X_KEY

See Also:

• Constant Field Values

Y_KEY

public static final String Y_KEY

See Also:

• Constant Field Values

Z_KEY

public static final String Z_KEY

See Also:

• Constant Field Values

P_KEY

public static final String P_KEY

See Also:

• Constant Field Values

F_KEY

public static final String F_KEY

See Also:

• Constant Field Values

T_KEY

public static final String T_KEY

See Also:

• Constant Field Values

DarkImage_KEY

public static final String DarkImage_KEY

See Also:

• Constant Field Values

TIMESTAMP_KEY

public static final String TIMESTAMP_KEY

See Also:

• Constant Field Values

NUMBEROFFRAMES_KEY

public static final String NUMBEROFFRAMES_KEY

See Also:

• Constant Field Values

NUMBEROFDARKIMAGES_KEY

public static final String NUMBEROFDARKIMAGES_KEY

See Also:

• Constant Field Values

PIXELFORMAT_KEY

public static final String PIXELFORMAT_KEY

See Also:

• Constant Field Values

KNOWN_VERSIONS

public static final String[] KNOWN_VERSIONS

COMPRESSION_NONE

public static final String COMPRESSION_NONE

See Also:

• Constant Field Values

COMPRESSION_GZIP

public static final String COMPRESSION_GZIP

See Also:

• Constant Field Values

DATATYPE_UINT8

public static final String DATATYPE_UINT8

See Also:

• Constant Field Values

DATATYPE_INT8

public static final String DATATYPE_INT8

See Also:

• Constant Field Values

DATATYPE_UINT16

public static final String DATATYPE_UINT16

See Also:

• Constant Field Values

DATATYPE_INT16

public static final String DATATYPE_INT16

See Also:

• Constant Field Values

DATATYPE_UINT32

public static final String DATATYPE_UINT32

See Also:

• Constant Field Values

DATATYPE_INT32

public static final String DATATYPE_INT32

See Also:

• Constant Field Values

DATATYPE_REAL32

public static final String DATATYPE_REAL32

See Also:

• Constant Field Values

DATATYPE_REAL64

public static final String DATATYPE_REAL64

See Also:

• Constant Field Values

DATATYPE_UINT12

public static final String DATATYPE_UINT12

See Also:

• Constant Field Values

dataOffset

private long dataOffset

Offset to start of pixel data.

ini

private loci.common.IniList ini

Parsed configuration data.

version

private String version

compression

private String compression

datatype

private String datatype

packing

private String packing

channels

private String channels

xLen

private String xLen

yLen

private String yLen

zLen

private String zLen

phases

private String phases

frequencies

private String frequencies

timestamps

private String timestamps

DarkImage

private String DarkImage

backgroundDatatype

private String backgroundDatatype

backgroundX

private String backgroundX

backgroundY

private String backgroundY

backgroundC

private String backgroundC

backgroundZ

private String backgroundZ

backgroundT

private String backgroundT

backgroundP

private String backgroundP

backgroundF

private String backgroundF

numRegions

private int numRegions

rois

private Map<Integer,LiFlimReader.ROI> rois

stampValues

private Map<Integer,String> stampValues

exposureTime

private Double exposureTime

exposureTimeUnit

private ome.units.unit.Unit<ome.units.quantity.Time> exposureTimeUnit

gzip

private boolean gzip

True if gzip compression was used to deflate the pixels.

gz

private DataInputStream gz

Stream to use for reading gzip-compressed pixel data.

gzPos

private int gzPos

Image number indicating position in gzip stream.

gzSeries

private int gzSeries

Series number indicating position in gzip stream.

TypeUINT12

private boolean TypeUINT12

if DataType is UINT12, data is compressed in 12 bits. Similar to Gzipstream make use of a DataInputStream to unpack the compressed UINT12 pixel data into 16 bits.

UINT12stream

private DataInputStream UINT12stream

UINT12streamPos

private int UINT12streamPos

UINT12streamSeries

private int UINT12streamSeries

Constructor Details

LiFlimReader

public LiFlimReader()

Constructs a new LI-FLIM reader.

Method Details

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)

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

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

getVersion

private String getVersion()

parseHeader

private void parseHeader()
                  throws IOException

Throws:

IOException

initOriginalMetadata

private void initOriginalMetadata()

initCoreMetadata

private void initCoreMetadata()
                       throws FormatException

Throws:

FormatException

initOMEMetadata

private void initOMEMetadata()

getPixelTypeFromString

private int getPixelTypeFromString(String type)
                            throws FormatException

Throws:

FormatException

prepareGZipStream

private void prepareGZipStream(int no)
                        throws IOException

Throws:

IOException

prepareUINT12Stream

private void prepareUINT12Stream(int no)
                          throws IOException

Similar to Gzip, make a DataInputstream for UINT12 data

Throws:

IOException

convert12to16LSB

private static byte[] convert12to16LSB(byte[] image)

convert12to16MSB

private static byte[] convert12to16MSB(byte[] image)

skip

private void skip(InputStream is,
 long num)
           throws IOException

Throws:

IOException