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, IFormatHandler, IFormatReader, IMetadataConfigurable

public class ZeissTIFFReader
extends BaseZeissReader

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

Author:

Melissa Linkert melissa at glencoesoftware.com and Roger Leigh r.leigh at dundee.ac.uk

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	ZeissTIFFReader.Channel
(package private) class	ZeissTIFFReader.Plane
(package private) class	ZeissTIFFReader.Slice
(package private) class	ZeissTIFFReader.TIFFInfo
(package private) class	ZeissTIFFReader.Timepoint

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

BaseZeissReader.Charset, BaseZeissReader.Context, BaseZeissReader.DrawStyle, BaseZeissReader.FeatureType, BaseZeissReader.FillStyle, BaseZeissReader.Layer, BaseZeissReader.LineEndPositions, BaseZeissReader.LineEndStyle, BaseZeissReader.PointStyle, BaseZeissReader.Shape, BaseZeissReader.Tag, BaseZeissReader.TextAlignment

Field Summary

Fields

Modifier and Type	Field and Description
(package private) HashMap<Integer,ZeissTIFFReader.Channel>	channels
(package private) ArrayList<ZeissTIFFReader.Plane>	planes Image planes
(package private) HashMap<Integer,ZeissTIFFReader.Slice>	slices
static String[]	TIFF_SUFFIXES
(package private) ZeissTIFFReader.TIFFInfo	tiffInfo
private MinimalTiffReader	tiffReader Helper reader for TIFF files.
(package private) HashMap<Integer,ZeissTIFFReader.Timepoint>	timepoints
static String	XML_NAME

Fields inherited from class loci.formats.in.BaseZeissReader

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, 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 and Description
ZeissTIFFReader()

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
protected void	countImages()
protected ZeissTIFFReader.TIFFInfo	evalFile(String id) Evaluate the metadata of a TIFF/XML file collection, and return this to the user.
int	fileGroupOption(String id) Returns an int indicating that we cannot, must, or might group the files in a given dataset.
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
(package private) ZeissTIFFReader.Channel	getChannel(int id)
protected String	getPrefix(String name)
String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
(package private) ZeissTIFFReader.Slice	getslice(int id)
(package private) ZeissTIFFReader.Timepoint	getTimepoint(int id)
protected void	initFile(String id) Initializes the given file (parsing header information, etc.).
protected void	initVars(String id)
boolean	isSingleFile(String id) Returns true if this is a single-file format.
boolean	isThisType(String name, boolean open) Checks if a file matches the type of this format reader.
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h) Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Methods inherited from class loci.formats.in.BaseZeissReader

fillMetadataPass3, fillMetadataPass4, fillMetadataPass6, fillMetadataPass7, get16BitLookupTable, get8BitLookupTable, getOptimalTileHeight, initFileMain, parseColor, parseInt, parseInt, parseMainTags, 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, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, 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, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, 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, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Detail

TIFF_SUFFIXES

public static final String[] TIFF_SUFFIXES

XML_NAME

public static final String XML_NAME

See Also:

Constant Field Values

tiffInfo

ZeissTIFFReader.TIFFInfo tiffInfo

planes

ArrayList<ZeissTIFFReader.Plane> planes

Image planes

tiffReader

private MinimalTiffReader tiffReader

Helper reader for TIFF files.

channels

HashMap<Integer,ZeissTIFFReader.Channel> channels

slices

HashMap<Integer,ZeissTIFFReader.Slice> slices

timepoints

HashMap<Integer,ZeissTIFFReader.Timepoint> timepoints

Constructor Detail

ZeissTIFFReader

public ZeissTIFFReader()

Method Detail

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
                            IOException

Description copied from interface: IFormatReader

Returns true if this is a single-file format.

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)

Description copied from class: FormatReader

Checks if a file matches the type of this format reader. Checks filename suffixes against those known for this format. If the suffix check is inconclusive and the open parameter is true, the file is opened and tested with FormatReader.isThisType(RandomAccessInputStream).

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis.

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
                           IOException

Description copied from interface: IFormatReader

Returns an int indicating that we cannot, must, or might group the files in a given dataset.

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

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Parameters:

no - the image index within the file.

buf - a pre-allocated buffer.

x - X coordinate of the upper-left corner of the sub-image

y - Y coordinate of the upper-left corner of the sub-image

w - width of the sub-image

h - height of the sub-image

Returns:

the pre-allocated buffer buf for convenience.

Throws:

FormatException - if there was a problem parsing the metadata of the file.

IOException - if there was a problem reading the file.

See Also:

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

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: IFormatReader

Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().

Specified by:

close in interface IFormatReader

Overrides:

close in class BaseZeissReader

Throws:

IOException

evalFile

protected 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

Description copied from class: FormatReader

Initializes the given file (parsing header information, etc.). Most subclasses should override this method to perform initialization operations such as parsing metadata.

Overrides:

initFile in class FormatReader

Throws:

FormatException - if a parsing error occurs processing the file.

IOException - if an I/O error occurs processing the file

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

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

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

Throws:

FormatException

IOException

countImages

protected void countImages()

Overrides:

countImages in class BaseZeissReader

getChannel

ZeissTIFFReader.Channel getChannel(int id)

getslice

ZeissTIFFReader.Slice getslice(int id)

getTimepoint

ZeissTIFFReader.Timepoint getTimepoint(int id)