Package loci.formats.in

Class ZeissCZIReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.ZeissCZIReader

All Implemented Interfaces:

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

public class ZeissCZIReader
extends FormatReader

ZeissCZIReader is the file format reader for Zeiss .czi files.

Field Summary

Fields

Modifier and Type	Field	Description
static final boolean	ALLOW_AUTOSTITCHING_DEFAULT
static final String	ALLOW_AUTOSTITCHING_KEY
static final boolean	INCLUDE_ATTACHMENTS_DEFAULT
static final String	INCLUDE_ATTACHMENTS_KEY
static final boolean	RELATIVE_POSITIONS_DEFAULT
static final String	RELATIVE_POSITIONS_KEY
static final boolean	TRIM_DIMENSIONS_DEFAULT
static final String	TRIM_DIMENSIONS_KEY

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
ZeissCZIReader()	Constructs a new Zeiss .czi reader.

Method Summary

Modifier and Type	Method	Description
boolean	allowAutostitching()
boolean	canReadAttachments()
void	close(boolean fileOnly)
short[][]	get16BitLookupTable()
byte[][]	get8BitLookupTable()
protected ArrayList<String>	getAvailableOptions()
Byte	getFillColor()
int	getOptimalTileHeight()
int	getOptimalTileWidth()
String[]	getSeriesUsedFiles(boolean noPixels)
protected void	initFile(String id)
boolean	isThisType(RandomAccessInputStream stream)
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)
boolean	storeRelativePositions()
boolean	trimDimensions()

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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, 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, 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, isSingleFile, 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

ALLOW_AUTOSTITCHING_KEY

public static final String ALLOW_AUTOSTITCHING_KEY

See Also:

• Constant Field Values

ALLOW_AUTOSTITCHING_DEFAULT

public static final boolean ALLOW_AUTOSTITCHING_DEFAULT

See Also:

• Constant Field Values

INCLUDE_ATTACHMENTS_KEY

public static final String INCLUDE_ATTACHMENTS_KEY

See Also:

• Constant Field Values

INCLUDE_ATTACHMENTS_DEFAULT

public static final boolean INCLUDE_ATTACHMENTS_DEFAULT

See Also:

• Constant Field Values

TRIM_DIMENSIONS_KEY

public static final String TRIM_DIMENSIONS_KEY

See Also:

• Constant Field Values

TRIM_DIMENSIONS_DEFAULT

public static final boolean TRIM_DIMENSIONS_DEFAULT

See Also:

• Constant Field Values

RELATIVE_POSITIONS_KEY

public static final String RELATIVE_POSITIONS_KEY

See Also:

• Constant Field Values

RELATIVE_POSITIONS_DEFAULT

public static final boolean RELATIVE_POSITIONS_DEFAULT

See Also:

• Constant Field Values

Constructor Details

ZeissCZIReader

public ZeissCZIReader()

Constructs a new Zeiss .czi reader.

Method Details

isThisType

public boolean isThisType(RandomAccessInputStream stream)
                   throws IOException

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Throws:

IOException

See Also:

• IFormatReader.isThisType(RandomAccessInputStream)

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

See Also:

• IFormatReader.getSeriesUsedFiles(boolean)

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws FormatException,
IOException

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class FormatReader

Throws:

FormatException

IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
IOException

Specified by:

get16BitLookupTable in interface IFormatReader

Overrides:

get16BitLookupTable in class FormatReader

Throws:

FormatException

IOException

getFillColor

public Byte getFillColor()

Specified by:

getFillColor in interface IFormatReader

Overrides:

getFillColor in class FormatReader

See Also:

• If the fill value was set explicitly, use that. Otherwise, return 255 (white) for RGB data with a pyramid, and 0 in all other cases. RGB data with a pyramid can reasonably be assumed to be a brightfield slide.

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

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

getAvailableOptions

protected ArrayList<String> getAvailableOptions()

Overrides:

getAvailableOptions in class FormatReader

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Overrides:

initFile in class FormatReader

Throws:

FormatException

IOException

allowAutostitching

public boolean allowAutostitching()

canReadAttachments

public boolean canReadAttachments()

trimDimensions

public boolean trimDimensions()

storeRelativePositions

public boolean storeRelativePositions()