Package loci.formats.in

Class BioRadReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.BioRadReader

All Implemented Interfaces:

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

public class BioRadReader
extends FormatReader

BioRadReader is the file format reader for Bio-Rad PIC files.

Field Summary

Fields

Modifier and Type	Field	Description
static final int	LUT_LENGTH
static final String[]	NOTE_NAMES	List of note types.
static final int	NOTE_TYPE_4D_SERIES
static final int	NOTE_TYPE_ARROW
static final int	NOTE_TYPE_COLLECT
static final int	NOTE_TYPE_FILE1
static final int	NOTE_TYPE_FILE2
static final int	NOTE_TYPE_LINE
static final int	NOTE_TYPE_LIVE
static final int	NOTE_TYPE_MERGE
static final int	NOTE_TYPE_NUMBER
static final int	NOTE_TYPE_SCALEBAR
static final int	NOTE_TYPE_STRUCTURE
static final int	NOTE_TYPE_THRUVIEW
static final int	NOTE_TYPE_USER
static final int	NOTE_TYPE_VARIABLE
static final String[]	PIC_SUFFIX
static final String[]	STRUCTURE_LABELS_1	Structure labels.
static final String[]	STRUCTURE_LABELS_2
static final String[]	STRUCTURE_LABELS_3
static final String[]	STRUCTURE_LABELS_4
static final String[]	STRUCTURE_LABELS_5
static final String[]	STRUCTURE_LABELS_6

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
BioRadReader()	Constructs a new BioRadReader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)
int	fileGroupOption(String id)
byte[][]	get8BitLookupTable()
int	getOptimalTileHeight()
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, get16BitLookupTable, 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, 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, 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

NOTE_NAMES

public static final String[] NOTE_NAMES

List of note types.

NOTE_TYPE_LIVE

public static final int NOTE_TYPE_LIVE

See Also:

• Constant Field Values

NOTE_TYPE_FILE1

public static final int NOTE_TYPE_FILE1

See Also:

• Constant Field Values

NOTE_TYPE_NUMBER

public static final int NOTE_TYPE_NUMBER

See Also:

• Constant Field Values

NOTE_TYPE_USER

public static final int NOTE_TYPE_USER

See Also:

• Constant Field Values

NOTE_TYPE_LINE

public static final int NOTE_TYPE_LINE

See Also:

• Constant Field Values

NOTE_TYPE_COLLECT

public static final int NOTE_TYPE_COLLECT

See Also:

• Constant Field Values

NOTE_TYPE_FILE2

public static final int NOTE_TYPE_FILE2

See Also:

• Constant Field Values

NOTE_TYPE_SCALEBAR

public static final int NOTE_TYPE_SCALEBAR

See Also:

• Constant Field Values

NOTE_TYPE_MERGE

public static final int NOTE_TYPE_MERGE

See Also:

• Constant Field Values

NOTE_TYPE_THRUVIEW

public static final int NOTE_TYPE_THRUVIEW

See Also:

• Constant Field Values

NOTE_TYPE_ARROW

public static final int NOTE_TYPE_ARROW

See Also:

• Constant Field Values

NOTE_TYPE_VARIABLE

public static final int NOTE_TYPE_VARIABLE

See Also:

• Constant Field Values

NOTE_TYPE_STRUCTURE

public static final int NOTE_TYPE_STRUCTURE

See Also:

• Constant Field Values

NOTE_TYPE_4D_SERIES

public static final int NOTE_TYPE_4D_SERIES

See Also:

• Constant Field Values

STRUCTURE_LABELS_1

public static final String[] STRUCTURE_LABELS_1

Structure labels.

STRUCTURE_LABELS_2

public static final String[] STRUCTURE_LABELS_2

STRUCTURE_LABELS_3

public static final String[] STRUCTURE_LABELS_3

STRUCTURE_LABELS_4

public static final String[] STRUCTURE_LABELS_4

STRUCTURE_LABELS_5

public static final String[] STRUCTURE_LABELS_5

STRUCTURE_LABELS_6

public static final String[] STRUCTURE_LABELS_6

PIC_SUFFIX

public static final String[] PIC_SUFFIX

LUT_LENGTH

public static final int LUT_LENGTH

See Also:

• Constant Field Values

Constructor Details

BioRadReader

public BioRadReader()

Constructs a new BioRadReader.

Method Details

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

get8BitLookupTable

public byte[][] get8BitLookupTable()

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class FormatReader

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles 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)

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