Package loci.formats.in

Class FV1000Reader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.FV1000Reader

All Implemented Interfaces:

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

public class FV1000Reader
extends FormatReader

FV1000Reader is the file format reader for Fluoview FV 1000 OIB and Fluoview FV 1000 OIF files.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	DATE_FORMAT
static final String	FV1000_MAGIC_STRING_1
static final String	FV1000_MAGIC_STRING_2
static final String[]	FV1000_SUFFIXES
static final String[]	OIB_SUFFIX
static final String[]	OIF_SUFFIX
static final String[]	PREVIEWNAME_PREFIXES

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
FV1000Reader()	Constructs a new FV1000 reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)
int	fileGroupOption(String id)
short[][]	get16BitLookupTable()
int	getOptimalTileHeight()
int	getOptimalTileWidth()
String[]	getSeriesUsedFiles(boolean noPixels)
protected void	initFile(String id)
boolean	isSingleFile(String id)
boolean	isThisType(String name, boolean open)
boolean	isThisType(RandomAccessInputStream stream)
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)

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, flattenHashtables, 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, 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, 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

FV1000_MAGIC_STRING_1

public static final String FV1000_MAGIC_STRING_1

See Also:

• Constant Field Values

FV1000_MAGIC_STRING_2

public static final String FV1000_MAGIC_STRING_2

See Also:

• Constant Field Values

OIB_SUFFIX

public static final String[] OIB_SUFFIX

OIF_SUFFIX

public static final String[] OIF_SUFFIX

FV1000_SUFFIXES

public static final String[] FV1000_SUFFIXES

PREVIEWNAME_PREFIXES

public static final String[] PREVIEWNAME_PREFIXES

DATE_FORMAT

public static final String DATE_FORMAT

See Also:

• Constant Field Values

Constructor Details

FV1000Reader

public FV1000Reader()

Constructs a new FV1000 reader.

Method Details

getOptimalTileWidth

public int getOptimalTileWidth()

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class FormatReader

getOptimalTileHeight

public int getOptimalTileHeight()

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight in class FormatReader

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
IOException

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

IOException

isThisType

public boolean isThisType(String name,
 boolean open)

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

isThisType

public boolean isThisType(RandomAccessInputStream stream)
                   throws IOException

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Throws:

IOException

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
IOException

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Throws:

FormatException

IOException

get16BitLookupTable

public short[][] get16BitLookupTable()

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

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Throws:

FormatException

IOException

See Also:

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

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

close

public void close(boolean fileOnly)
           throws IOException

Specified by:

close in interface IFormatReader

Overrides:

close in class FormatReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Overrides:

initFile in class FormatReader

Throws:

FormatException

IOException