Package loci.formats.in

Class OMETiffReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.OMETiffReader

All Implemented Interfaces:

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

public class OMETiffReader
extends SubResolutionFormatReader

OMETiffReader is the file format reader for OME-TIFF files.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	OMETiffReader.OMETiffCoreMetadata
private class	OMETiffReader.OMETiffPlane	Structure containing details on where to find a particular image plane.

Field Summary

Fields

Modifier and Type	Field	Description
static final boolean	FAIL_ON_MISSING_DEFAULT
static final String	FAIL_ON_MISSING_KEY
private boolean	hasSPW
protected OMETiffReader.OMETiffPlane[][]	info	Mapping from series and plane numbers to files and IFD entries.
private int	lastPlane
protected OMEXMLMetadata	meta	Represents OME-XML stored in the current OME-TIFF file(s).
private String	metadataFile
private String	metaFile
static final String[]	OME_TIFF_SUFFIXES
protected OMEXMLService	service	OMEXMLService that can be used to manipulate OME-XML.
protected String[]	used	List of used files.

Fields inherited from class loci.formats.SubResolutionFormatReader

core

Fields inherited from class loci.formats.FormatReader

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
OMETiffReader()	Constructs a new OME-TIFF reader.
OMETiffReader(String name, String[] suffixes)

Method Summary

Modifier and Type	Method	Description
private void	addSubResolutions()
void	close(boolean fileOnly)	Closes the currently open file.
protected void	convertMetadata(OMEXMLMetadata meta, MetadataStore store)	Convert metadata contained within an OMEXMLMetadata object to a separate MetadataStore.
boolean	failOnMissingTIFF()
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
short[][]	get16BitLookupTable()	Gets the 16-bit color lookup table associated with the most recently opened image.
byte[][]	get8BitLookupTable()	Gets the 8-bit color lookup table associated with the most recently opened image.
protected ArrayList<String>	getAvailableOptions()	Returns the list of available metadata options.
String[]	getDomains()	Returns the list of domains represented by the current file.
private static IFD	getFirstIFD(String fname)
MetadataStore	getMetadataStoreForConversion()	Deprecated. Use the general FormatReader.getMetadataStore() method.
MetadataStore	getMetadataStoreForDisplay()	Deprecated. Use the general FormatReader.getMetadataStore() method.
int	getOptimalTileHeight()	Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth()	Returns the optimal sub-image width for use with openBytes.
int	getRequiredDirectories(String[] files)	Returns the number of parent directories that are important when processing the given list of files.
String[]	getSeriesUsedFiles(boolean noPixels)	Returns an array of filenames needed to open the current series.
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
private void	initializeReader(IFormatReader r, String file)
boolean	isSingleFile(String id)	Returns true if the named file is expected to be the only file in the dataset.
boolean	isThisType(String name, boolean open)	Checks if a file matches the type of this format reader.
boolean	isThisType(loci.common.RandomAccessInputStream stream)	Checks if the given stream is a valid stream for this file format.
private String	normalizeFilename(String dir, String name)
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.
private String	readMetadataFile()	Extracts the OME-XML from the current metadataFile.
private void	removeIFDComments(IFormatReader r)
void	reopenFile()	Reopen any files that were closed, and which are expected to be open while the reader is open.
void	setSeries(int series)	Activates the specified series.
private void	setupService()

Methods inherited from class loci.formats.SubResolutionFormatReader

coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution

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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, 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, getPixelType, getPixelType, getPossibleDomains, getPulse, getRGBChannelCount, getRotationTransform, 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, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, 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

OME_TIFF_SUFFIXES

public static final String[] OME_TIFF_SUFFIXES

FAIL_ON_MISSING_KEY

public static final String FAIL_ON_MISSING_KEY

See Also:

• Constant Field Values

FAIL_ON_MISSING_DEFAULT

public static final boolean FAIL_ON_MISSING_DEFAULT

See Also:

• Constant Field Values

info

protected OMETiffReader.OMETiffPlane[][] info

Mapping from series and plane numbers to files and IFD entries.

used

protected String[] used

List of used files.

lastPlane

private int lastPlane

hasSPW

private boolean hasSPW

service

protected OMEXMLService service

OMEXMLService that can be used to manipulate OME-XML.

meta

protected transient OMEXMLMetadata meta

Represents OME-XML stored in the current OME-TIFF file(s).

metaFile

private String metaFile

metadataFile

private String metadataFile

Constructor Details

OMETiffReader

public OMETiffReader()

Constructs a new OME-TIFF reader.

OMETiffReader

public OMETiffReader(String name,
 String[] suffixes)

Method Details

getAvailableOptions

protected ArrayList<String> getAvailableOptions()

Description copied from class: FormatReader

Returns the list of available metadata options.

Overrides:

getAvailableOptions in class FormatReader

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
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

IOException

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

Parameters:

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

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws IOException

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Parameters:

stream - A RandomAccessInputStream representing the file to check. The first byte in the stream is assumed to be the first byte in the file.

Returns:

true if the file represented by the stream can be read by this reader; false otherwise.

Throws:

IOException

getDomains

public String[] getDomains()

Description copied from interface: IFormatReader

Returns the list of domains represented by the current file.

Specified by:

getDomains in interface IFormatReader

Overrides:

getDomains in class FormatReader

setSeries

public void setSeries(int series)

Description copied from interface: IFormatReader

Activates the specified series. This also resets the resolution to 0.

Specified by:

setSeries in interface IFormatReader

Overrides:

setSeries in class SubResolutionFormatReader

See Also:

• Note that the value can change depending upon whether resolutions are flattened, and so reader implementations should use the series and resolutions fields internally.

get8BitLookupTable

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

Description copied from interface: IFormatReader

Gets the 8-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT8 or FormatTools.UINT8, this method will return null.

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class FormatReader

Throws:

FormatException

IOException

get16BitLookupTable

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

Description copied from interface: IFormatReader

Gets the 16-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT16 or FormatTools.UINT16, this method will return null.

Specified by:

get16BitLookupTable in interface IFormatReader

Overrides:

get16BitLookupTable in class FormatReader

Throws:

FormatException

IOException

reopenFile

public void reopenFile()
                throws IOException

Description copied from interface: IFormatReader

Reopen any files that were closed, and which are expected to be open while the reader is open. This assumes that IFormatHandler.setId(java.lang.String) has been called, but close(false) has not been called.

Specified by:

reopenFile in interface IFormatReader

Overrides:

reopenFile in class FormatReader

Throws:

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 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.

IOException - if there was a problem reading the file.

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. 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

fileGroupOption

public int fileGroupOption(String id)

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).

See Also:

• FormatTools.MUST_GROUP
• FormatTools.CAN_GROUP
• FormatTools.CANNOT_GROUP

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 SubResolutionFormatReader

Throws:

IOException

getOptimalTileWidth

public int getOptimalTileWidth()

Description copied from interface: IFormatReader

Returns the optimal sub-image width for use with openBytes.

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class FormatReader

getOptimalTileHeight

public int getOptimalTileHeight()

Description copied from interface: IFormatReader

Returns the optimal sub-image height for use with openBytes.

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight in class FormatReader

getRequiredDirectories

public int getRequiredDirectories(String[] files)
                           throws FormatException,
IOException

Description copied from interface: IFormatReader

Returns the number of parent directories that are important when processing the given list of files. The number of directories is relative to the common parent. For example, given a list with these two files: /path/to/file/foo /path/to/file/that/is/related A return value of 0 indicates that "/path/to/file/" is irrelevant. A return value of 1 indicates that "/path/to/" is irrelevant. Return values less than 0 are invalid. All listed files are assumed to belong to datasets of the same format.

Specified by:

getRequiredDirectories in interface IFormatReader

Overrides:

getRequiredDirectories in class FormatReader

Throws:

FormatException

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Description copied from class: SubResolutionFormatReader

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 SubResolutionFormatReader

Throws:

FormatException - if a parsing error occurs processing the file.

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

getMetadataStoreForDisplay

public MetadataStore getMetadataStoreForDisplay()

Deprecated.

Use the general FormatReader.getMetadataStore() method.

Get a MetadataStore suitable for display. Note: Historically, this method removed certain elements for display purposes and was not be suitable for use with FormatWriter due to not containing required BinData BigEndian attributes. This is no longer the case; the general FormatReader.getMetadataStore() method will always create valid metadata which is suitable for both display and use with FormatWriter, and so should be used instead.

Returns:

the metadata store.

getMetadataStoreForConversion

public MetadataStore getMetadataStoreForConversion()

Deprecated.

Use the general FormatReader.getMetadataStore() method.

Get a MetadataStore suitable for writing. Note: Historically, this method created metadata suitable for use with FormatWriter, but would possibly not generate valid OME-XML if both BinData and TiffData elements were present. This is no longer the case; the general FormatReader.getMetadataStore() method will always create valid metadata which is suitable for use with FormatWriter, and so should be used instead.

Returns:

the metadata store.

convertMetadata

protected void convertMetadata(OMEXMLMetadata meta,
 MetadataStore store)

Convert metadata contained within an OMEXMLMetadata object to a separate MetadataStore. The OMEXMLMetadata object is expected to represent the original OME-XML stored in this OME-TIFF. The MetadataStore is expected to represent the output metadata; if the MetadataStore is of type OMEXMLMetadata, the output is expected to be valid OME-XML. By default, this simply copies everything from the source OMEXMLMetadata to the destination MetadataStore without modification. Classes that extend OMETiffReader may wish to override this method if the OME-XML stored in the OME-TIFF is expected to be invalid or incorrect.

Parameters:

meta - source representing stored OME-XML

store - destination representing valid OME metadata

normalizeFilename

private String normalizeFilename(String dir,
 String name)

setupService

private void setupService()
                   throws FormatException

Throws:

FormatException

addSubResolutions

private void addSubResolutions()
                        throws IOException,
FormatException

Throws:

IOException

FormatException

readMetadataFile

private String readMetadataFile()
                         throws IOException

Extracts the OME-XML from the current metadataFile.

Throws:

IOException

getFirstIFD

private static IFD getFirstIFD(String fname)
                        throws IOException

Throws:

IOException

initializeReader

private void initializeReader(IFormatReader r,
 String file)
                       throws FormatException,
IOException

Throws:

FormatException

IOException

removeIFDComments

private void removeIFDComments(IFormatReader r)

failOnMissingTIFF

public boolean failOnMissingTIFF()