loci.formats.in

Class LiFlimReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.LiFlimReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, 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 and Description
private class	LiFlimReader.ROI

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BACKGROUND_TABLE
private java.lang.String	backgroundC
private java.lang.String	backgroundDatatype
private java.lang.String	backgroundF
private java.lang.String	backgroundP
private java.lang.String	backgroundT
private java.lang.String	backgroundX
private java.lang.String	backgroundY
private java.lang.String	backgroundZ
static java.lang.String	C_KEY
private java.lang.String	channels
private java.lang.String	compression
static java.lang.String	COMPRESSION_GZIP
static java.lang.String	COMPRESSION_KEY
static java.lang.String	COMPRESSION_NONE
private java.lang.String	DarkImage
static java.lang.String	DarkImage_KEY
private long	dataOffset Offset to start of pixel data.
private java.lang.String	datatype
static java.lang.String	DATATYPE_INT16
static java.lang.String	DATATYPE_INT32
static java.lang.String	DATATYPE_INT8
static java.lang.String	DATATYPE_KEY
static java.lang.String	DATATYPE_REAL32
static java.lang.String	DATATYPE_REAL64
static java.lang.String	DATATYPE_UINT12
static java.lang.String	DATATYPE_UINT16
static java.lang.String	DATATYPE_UINT32
static java.lang.String	DATATYPE_UINT8
private java.lang.Double	exposureTime
private ome.units.unit.Unit<ome.units.quantity.Time>	exposureTimeUnit
static java.lang.String	F_KEY
private java.lang.String	frequencies
private java.io.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 java.lang.String	INFO_TABLE
private loci.common.IniList	ini Parsed configuration data.
static java.lang.String[]	KNOWN_VERSIONS
static java.lang.String	LAYOUT_TABLE
private int	numRegions
static java.lang.String	P_KEY
private java.lang.String	phases
private java.util.Map<java.lang.Integer,LiFlimReader.ROI>	rois
private java.util.Map<java.lang.Integer,java.lang.String>	stampValues
static java.lang.String	T_KEY
static java.lang.String	TIMESTAMP_KEY
private java.lang.String	timestamps
private boolean	TypeUINT12 if DataType is UINT12, data is compressed in 12 bits.
private java.io.DataInputStream	UINT12stream
private int	UINT12streamPos
private int	UINT12streamSeries
private java.lang.String	version
static java.lang.String	VERSION_KEY
static java.lang.String	X_KEY
private java.lang.String	xLen
static java.lang.String	Y_KEY
private java.lang.String	yLen
static java.lang.String	Z_KEY
private java.lang.String	zLen

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
LiFlimReader() Constructs a new LI-FLIM reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
private static byte[]	convert12to16(byte[] image)
private int	getPixelTypeFromString(java.lang.String type)
private void	initCoreMetadata()
protected void	initFile(java.lang.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(java.io.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, 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, 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, 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

INFO_TABLE

public static final java.lang.String INFO_TABLE

See Also:

Constant Field Values

LAYOUT_TABLE

public static final java.lang.String LAYOUT_TABLE

See Also:

Constant Field Values

BACKGROUND_TABLE

public static final java.lang.String BACKGROUND_TABLE

See Also:

Constant Field Values

VERSION_KEY

public static final java.lang.String VERSION_KEY

See Also:

Constant Field Values

COMPRESSION_KEY

public static final java.lang.String COMPRESSION_KEY

See Also:

Constant Field Values

DATATYPE_KEY

public static final java.lang.String DATATYPE_KEY

See Also:

Constant Field Values

C_KEY

public static final java.lang.String C_KEY

See Also:

Constant Field Values

X_KEY

public static final java.lang.String X_KEY

See Also:

Constant Field Values

Y_KEY

public static final java.lang.String Y_KEY

See Also:

Constant Field Values

Z_KEY

public static final java.lang.String Z_KEY

See Also:

Constant Field Values

P_KEY

public static final java.lang.String P_KEY

See Also:

Constant Field Values

F_KEY

public static final java.lang.String F_KEY

See Also:

Constant Field Values

T_KEY

public static final java.lang.String T_KEY

See Also:

Constant Field Values

DarkImage_KEY

public static final java.lang.String DarkImage_KEY

See Also:

Constant Field Values

TIMESTAMP_KEY

public static final java.lang.String TIMESTAMP_KEY

See Also:

Constant Field Values

KNOWN_VERSIONS

public static final java.lang.String[] KNOWN_VERSIONS

COMPRESSION_NONE

public static final java.lang.String COMPRESSION_NONE

See Also:

Constant Field Values

COMPRESSION_GZIP

public static final java.lang.String COMPRESSION_GZIP

See Also:

Constant Field Values

DATATYPE_UINT8

public static final java.lang.String DATATYPE_UINT8

See Also:

Constant Field Values

DATATYPE_INT8

public static final java.lang.String DATATYPE_INT8

See Also:

Constant Field Values

DATATYPE_UINT16

public static final java.lang.String DATATYPE_UINT16

See Also:

Constant Field Values

DATATYPE_INT16

public static final java.lang.String DATATYPE_INT16

See Also:

Constant Field Values

DATATYPE_UINT32

public static final java.lang.String DATATYPE_UINT32

See Also:

Constant Field Values

DATATYPE_INT32

public static final java.lang.String DATATYPE_INT32

See Also:

Constant Field Values

DATATYPE_REAL32

public static final java.lang.String DATATYPE_REAL32

See Also:

Constant Field Values

DATATYPE_REAL64

public static final java.lang.String DATATYPE_REAL64

See Also:

Constant Field Values

DATATYPE_UINT12

public static final java.lang.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 java.lang.String version

compression

private java.lang.String compression

datatype

private java.lang.String datatype

channels

private java.lang.String channels

xLen

private java.lang.String xLen

yLen

private java.lang.String yLen

zLen

private java.lang.String zLen

phases

private java.lang.String phases

frequencies

private java.lang.String frequencies

timestamps

private java.lang.String timestamps

DarkImage

private java.lang.String DarkImage

backgroundDatatype

private java.lang.String backgroundDatatype

backgroundX

private java.lang.String backgroundX

backgroundY

private java.lang.String backgroundY

backgroundC

private java.lang.String backgroundC

backgroundZ

private java.lang.String backgroundZ

backgroundT

private java.lang.String backgroundT

backgroundP

private java.lang.String backgroundP

backgroundF

private java.lang.String backgroundF

numRegions

private int numRegions

rois

private java.util.Map<java.lang.Integer,LiFlimReader.ROI> rois

stampValues

private java.util.Map<java.lang.Integer,java.lang.String> stampValues

exposureTime

private java.lang.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 java.io.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 java.io.DataInputStream UINT12stream

UINT12streamPos

private int UINT12streamPos

UINT12streamSeries

private int UINT12streamSeries

Constructor Detail

LiFlimReader

public LiFlimReader()

Constructs a new LI-FLIM reader.

Method Detail

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

parseHeader

private void parseHeader()
                  throws java.io.IOException

Throws:

java.io.IOException

initOriginalMetadata

private void initOriginalMetadata()

initCoreMetadata

private void initCoreMetadata()
                       throws FormatException

Throws:

FormatException

initOMEMetadata

private void initOMEMetadata()

getPixelTypeFromString

private int getPixelTypeFromString(java.lang.String type)
                            throws FormatException

Throws:

FormatException

prepareGZipStream

private void prepareGZipStream(int no)
                        throws java.io.IOException

Throws:

java.io.IOException

prepareUINT12Stream

private void prepareUINT12Stream(int no)
                          throws java.io.IOException

Similar to Gzip, make a DataInputstream for UINT12 data

Throws:

java.io.IOException

convert12to16

private static byte[] convert12to16(byte[] image)

skip

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

Throws:

java.io.IOException