Package loci.formats.in

Class ZeissTIFFReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.BaseZeissReader

loci.formats.in.ZeissTIFFReader

All Implemented Interfaces:

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

public class ZeissTIFFReader
extends BaseZeissReader

ZeissTIFFReader is the file format reader for Zeiss AxioVision TIFF files and their companion XML file.

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
static final String[]	TIFF_SUFFIXES
static final String	XML_NAME

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
ZeissTIFFReader()

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)
protected void	countImages()
protected loci.formats.in.ZeissTIFFReader.TIFFInfo	evalFile(String id)	Evaluate the metadata of a TIFF/XML file collection, and return this to the user.
int	fileGroupOption(String id)
protected void	fillMetadataPass1(MetadataStore store)	Read and store basic dimensions in model
protected void	fillMetadataPass2(MetadataStore store)	Read and store basic dimensions in model
protected void	fillMetadataPass5(MetadataStore store)	Read and store basic dimensions in model
protected String	getPrefix(String name)
String[]	getSeriesUsedFiles(boolean noPixels)
protected void	initFile(String id)
protected void	initVars(String id)
boolean	isSingleFile(String id)
boolean	isThisType(String name, boolean open)
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)

Methods inherited from class loci.formats.in.BaseZeissReader

fillMetadataPass3, 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, 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, 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, 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

TIFF_SUFFIXES

public static final String[] TIFF_SUFFIXES

XML_NAME

public static final String XML_NAME

See Also:

• Constant Field Values

Constructor Details

ZeissTIFFReader

public ZeissTIFFReader()

Method Details

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
IOException

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

IOException

getPrefix

protected String getPrefix(String name)

isThisType

public boolean isThisType(String name,
 boolean open)

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
IOException

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Throws:

FormatException

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)

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 BaseZeissReader

Throws:

IOException

evalFile

protected loci.formats.in.ZeissTIFFReader.TIFFInfo evalFile(String id)
                                                     throws FormatException,
IOException

Evaluate the metadata of a TIFF/XML file collection, and return this to the user. This is done by filling a TIFFInfo object containing all of the file and directory paths, plus the parsed metadata.

Parameters:

id - the filename to evaluate. This may be the top-level or per-plane TIFF, or the XML metadata.

Returns:

an TIFFInfo object.

Throws:

FormatException

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

fillMetadataPass2

protected void fillMetadataPass2(MetadataStore store)
                          throws FormatException,
IOException

Description copied from class: BaseZeissReader

Read and store basic dimensions in model

Overrides:

fillMetadataPass2 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