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:

java.io.Closeable, java.lang.AutoCloseable, 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.

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.Plane
(package private) class	ZeissTIFFReader.TIFFInfo

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
private java.util.HashMap<java.lang.String,java.lang.String[]>	directoryCache
(package private) java.util.ArrayList<ZeissTIFFReader.Plane>	planes Image planes
static java.lang.String[]	TIFF_SUFFIXES
(package private) ZeissTIFFReader.TIFFInfo	tiffInfo
private MinimalTiffReader	tiffReader Helper reader for TIFF files.
static java.lang.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, 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(java.lang.String id) Evaluate the metadata of a TIFF/XML file collection, and return this to the user.
int	fileGroupOption(java.lang.String id) Returns an indication of whether the files in a multi-file dataset can be handled individually.
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 java.lang.String	getPrefix(java.lang.String name)
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
protected void	initVars(java.lang.String id)
boolean	isSingleFile(java.lang.String id) Returns true if the named file is expected to be the only file in the dataset.
boolean	isThisType(java.lang.String name, boolean open) Checks if a file matches the type of this format reader.
private java.lang.String	lookup(java.lang.String src) Translate a file path from the XML file to an actual path on disk.
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, getAvailableOptions, 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, 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, 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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Detail

TIFF_SUFFIXES

public static final java.lang.String[] TIFF_SUFFIXES

XML_NAME

public static final java.lang.String XML_NAME

See Also:

Constant Field Values

tiffInfo

ZeissTIFFReader.TIFFInfo tiffInfo

planes

java.util.ArrayList<ZeissTIFFReader.Plane> planes

Image planes

tiffReader

private MinimalTiffReader tiffReader

Helper reader for TIFF files.

directoryCache

private transient java.util.HashMap<java.lang.String,java.lang.String[]> directoryCache

Constructor Detail

ZeissTIFFReader

public ZeissTIFFReader()

Method Detail

isSingleFile

public boolean isSingleFile(java.lang.String id)
                     throws FormatException,
                            java.io.IOException

Description copied from interface: IFormatReader

Returns true if the named file is expected to be the only file in the dataset. For single-file formats, always returns true.

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

java.io.IOException

getPrefix

protected java.lang.String getPrefix(java.lang.String name)

isThisType

public boolean isThisType(java.lang.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(java.lang.String id)
                    throws FormatException,
                           java.io.IOException

Description copied from interface: IFormatReader

Returns an indication of whether the files in a multi-file dataset can be handled individually. This method is only useful for formats and datasets which contain multiple files.

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Parameters:

id - a file in the multi-file dataset

Returns:

an int indicating that we cannot, must, or might group the files. A return value of FormatTools.MUST_GROUP indicates that the files cannot be handled separately; the reader will always detect and read all files in the dataset. FormatTools.CAN_GROUP indicates that the files may be handled separately, but file grouping must then be disabled via IFormatReader.setGroupFiles(boolean). FormatTools.CANNOT_GROUP indicates that the files must be handled separately; the reader will not attempt to read all files in the dataset (this is rare).

Throws:

FormatException

java.io.IOException

See Also:

FormatTools.MUST_GROUP, FormatTools.CAN_GROUP, FormatTools.CANNOT_GROUP

openBytes

public byte[] openBytes(int no,
                        byte[] buf,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        java.io.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 plane index within the current series.

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.

java.io.IOException - if there was a problem reading the file.

See Also:

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

getSeriesUsedFiles

public java.lang.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. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

close

public void close(boolean fileOnly)
           throws java.io.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:

java.io.IOException

evalFile

protected ZeissTIFFReader.TIFFInfo evalFile(java.lang.String id)
                                     throws FormatException,
                                            java.io.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

java.io.IOException

initFile

protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.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.

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

initVars

protected void initVars(java.lang.String id)
                 throws FormatException,
                        java.io.IOException

Overrides:

initVars in class BaseZeissReader

Throws:

FormatException

java.io.IOException

fillMetadataPass1

protected void fillMetadataPass1(MetadataStore store)
                          throws FormatException,
                                 java.io.IOException

Description copied from class: BaseZeissReader

Read and store basic dimensions in model

Overrides:

fillMetadataPass1 in class BaseZeissReader

Throws:

FormatException

java.io.IOException

fillMetadataPass2

protected void fillMetadataPass2(MetadataStore store)
                          throws FormatException,
                                 java.io.IOException

Description copied from class: BaseZeissReader

Read and store basic dimensions in model

Overrides:

fillMetadataPass2 in class BaseZeissReader

Throws:

FormatException

java.io.IOException

fillMetadataPass5

protected void fillMetadataPass5(MetadataStore store)
                          throws FormatException,
                                 java.io.IOException

Description copied from class: BaseZeissReader

Read and store basic dimensions in model

Overrides:

fillMetadataPass5 in class BaseZeissReader

Throws:

FormatException

java.io.IOException

countImages

protected void countImages()

Overrides:

countImages in class BaseZeissReader

lookup

private java.lang.String lookup(java.lang.String src)

Translate a file path from the XML file to an actual path on disk. The path stored in the XML file may not have the same case as the path on disk (typically all lower case on disk and possibly mixed case in XML). If a matching file cannot be found, then the path from the XML file is returned. Uses directoryCache so that any given directory is only listed once per initialization, not once per lookup.