loci.formats.in

Class LiFlimReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.LiFlimReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

public class LiFlimReader
extends FormatReader

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

Source code:

Trac, Gitweb

Field Summary

Fields

Modifier and Type	Field and Description
static String	BACKGROUND_TABLE
static String	C_KEY
static String	COMPRESSION_GZIP
static String	COMPRESSION_KEY
static String	COMPRESSION_NONE
static String	DATATYPE_INT16
static String	DATATYPE_INT32
static String	DATATYPE_INT8
static String	DATATYPE_KEY
static String	DATATYPE_REAL32
static String	DATATYPE_REAL64
static String	DATATYPE_UINT16
static String	DATATYPE_UINT32
static String	DATATYPE_UINT8
static String	F_KEY
static String	INFO_TABLE
static String[]	KNOWN_VERSIONS
static String	LAYOUT_TABLE
static String	P_KEY
static String	T_KEY
static String	TIMESTAMP_KEY
static String	VERSION_KEY
static String	X_KEY
static String	Y_KEY
static String	Z_KEY

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, 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

Methods

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
protected void	initFile(String id) Initializes the given file (parsing header information, etc.).
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.

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, fileGroupOption, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCompression, getContrastMethod, getCoreIndex, getCoreMetadata, getCoreMetadataList, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadataOptions, 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, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, 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, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes

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

Field Detail

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

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

TIMESTAMP_KEY

public static final String TIMESTAMP_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

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,
                        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 image index within the file.

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