Package loci.formats.in

Class ZeissZVIReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.BaseZeissReader

loci.formats.in.ZeissZVIReader

All Implemented Interfaces:

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

public class ZeissZVIReader
extends BaseZeissReader

ZeissZVIReader is the file format reader for Zeiss ZVI files.

Nested Class Summary

Nested classes/interfaces inherited from class loci.formats.in.BaseZeissReader

BaseZeissReader.Context, BaseZeissReader.Tag

Field Summary

Fields

Modifier and Type	Field	Description
protected RandomAccessInputStream	currentPlane
protected int	currentPlaneIndex
protected String[]	files
protected POIService	poi
static final int	ZVI_MAGIC_BYTES

Fields inherited from class loci.formats.in.BaseZeissReader

acquisitionDate, bpp, channelColors, channelIndices, channelName, cIndex, colCount, coordinates, detectorGain, detectorOffset, emWavelength, exposureTime, exWavelength, imageDescription, imageFiles, isJPEG, isZlib, lastPlane, layers, nextChName, nextEmWave, nextExWave, offsets, physicalSizeX, physicalSizeY, physicalSizeZ, rawCount, realHeight, realWidth, roiIDs, rowCount, stageX, stageY, tagsToParse, tileIndices, tiles, timepoint, timepointIndices, timestamps, zIndices

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
ZeissZVIReader()	Constructs a new ZeissZVI reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)
protected void	countImages()
protected void	fillMetadataPass1(MetadataStore store)	Read and store basic dimensions in model
protected void	fillMetadataPass3(MetadataStore store)	Read and store basic dimensions in model
protected void	fillMetadataPass5(MetadataStore store)	Read and store basic dimensions in model
protected void	initFile(String id)
protected void	initVars(String id)
boolean	isThisType(RandomAccessInputStream stream)
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)
protected String	parseROIString(RandomAccessInputStream s)

Methods inherited from class loci.formats.in.BaseZeissReader

fillMetadataPass2, fillMetadataPass4, fillMetadataPass6, fillMetadataPass7, get16BitLookupTable, get8BitLookupTable, getOptimalTileHeight, initFileMain, parseColor, parseInt, parseInt, storeROIs

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, 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, 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

ZVI_MAGIC_BYTES

public static final int ZVI_MAGIC_BYTES

See Also:

• Constant Field Values

poi

protected transient POIService poi

files

protected String[] files

currentPlane

protected transient RandomAccessInputStream currentPlane

currentPlaneIndex

protected transient int currentPlaneIndex

Constructor Details

ZeissZVIReader

public ZeissZVIReader()

Constructs a new ZeissZVI reader.

Method Details

isThisType

public boolean isThisType(RandomAccessInputStream stream)
                   throws IOException

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Throws:

IOException

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 BaseZeissReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Overrides:

initFile in class FormatReader

Throws:

FormatException

IOException

initVars

protected void initVars(String id)
                 throws FormatException,
IOException

Overrides:

initVars in class BaseZeissReader

Throws:

FormatException

IOException

fillMetadataPass1

protected void fillMetadataPass1(MetadataStore store)
                          throws FormatException,
IOException

Description copied from class: BaseZeissReader

Read and store basic dimensions in model

Overrides:

fillMetadataPass1 in class BaseZeissReader

Parameters:

store -

Throws:

FormatException

IOException

fillMetadataPass3

protected void fillMetadataPass3(MetadataStore store)
                          throws FormatException,
IOException

Description copied from class: BaseZeissReader

Read and store basic dimensions in model

Overrides:

fillMetadataPass3 in class BaseZeissReader

Parameters:

store -

Throws:

FormatException

IOException

fillMetadataPass5

protected void fillMetadataPass5(MetadataStore store)
                          throws FormatException,
IOException

Description copied from class: BaseZeissReader

Read and store basic dimensions in model

Overrides:

fillMetadataPass5 in class BaseZeissReader

Parameters:

store -

Throws:

FormatException

IOException

countImages

protected void countImages()

Overrides:

countImages in class BaseZeissReader

parseROIString

protected String parseROIString(RandomAccessInputStream s)
                         throws IOException

Throws:

IOException