Package loci.formats.in

Class SVSReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.MinimalTiffReader

loci.formats.in.BaseTiffReader

loci.formats.in.SVSReader

All Implemented Interfaces:

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

Direct Known Subclasses:

MikroscanTiffReader

public class SVSReader
extends BaseTiffReader

SVSReader is the file format reader for Aperio SVS TIFF files.

Field Summary

Fields

Modifier and Type	Field	Description
private static final String	APERIO_IMAGE_DESCRIPTION_PREFIX	TIFF image description prefix for Aperio SVS files.
private String[]	comments
private String	date
private static final String	DATE_FORMAT
private ome.xml.model.primitives.Color	displayColor
private ArrayList<String>	dyeNames
private Double	emissionWavelength
private Double	excitationWavelength
private Double	exposureScale
private Double	exposureTime
private int	extraImages
private int	labelIndex
private static final org.slf4j.Logger	LOGGER	Logger for this class.
private int	macroIndex
private Double	magnification
private Double	physicalDistanceFromLeftEdge
private Double	physicalDistanceFromTopEdge
static final boolean	REMOVE_THUMBNAIL_DEFAULT
static final String	REMOVE_THUMBNAIL_KEY
private String	time
private Double[]	zPosition

Fields inherited from class loci.formats.in.BaseTiffReader

DATE_FORMATS

Fields inherited from class loci.formats.in.MinimalTiffReader

canSeparateSeries, equalStrips, ifds, lastPlane, mergeSubIFDs, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit

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, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
SVSReader()	Constructs a new SVS reader.
SVSReader(String name, String[] suffixes)

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
protected ArrayList<String>	getAvailableOptions()	Returns the list of available metadata options.
protected ome.xml.model.primitives.Timestamp	getDatestamp()
protected ome.xml.model.primitives.Color	getDisplayColor()
protected ArrayList<String>	getDyeNames()
protected ome.units.quantity.Length	getEmission()
protected ome.units.quantity.Length	getExcitation()
protected Double	getExposureTime()
protected IFD	getIFD(int no)	Get the IFD corresponding to the given plane in the current series.
private int	getIFDIndex(int coreIndex, int no)
protected double	getMagnification()
int	getOptimalTileHeight()	Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth()	Returns the optimal sub-image width for use with openBytes.
protected ome.units.quantity.Length[]	getPhysicalSizes()
Codec	getTileCodec(int no)	Retrieve a codec that can be used to decompress compressed tiles.
CodecOptions	getTileCodecOptions(int no, int x, int y)	Retrieve codec options that can be used to decompressed the specified tile.
int	getTileColumns(int no)	Get the number of columns of tiles in the specified plane in the current series.
int	getTileRows(int no)	Get the number of rows of tiles in the specified plane in the current series.
protected void	initMetadataStore()	Populates the metadata store using the data parsed in BaseTiffReader.initStandardMetadata() along with some further parsing done in the method itself.
protected void	initStandardMetadata()	Parses standard metadata.
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.
byte[]	openCompressedBytes(int no, byte[] buf, int x, int y)	Retrieve the specified tile without performing any decompression.
byte[]	openCompressedBytes(int no, int x, int y)	Retrieve the specified tile without performing any decompression.
byte[]	openThumbBytes(int no)	Obtains a thumbnail for the specified image plane from the current file, as a byte array.
boolean	removeThumbnail()

Methods inherited from class loci.formats.in.BaseTiffReader

getExifTagName, getImageCreationDate, initFile, initMetadata, put, put, put, put, put, put, put, put, put, put, putDouble, putInt, putString

Methods inherited from class loci.formats.in.MinimalTiffReader

copyTile, get16BitLookupTable, get8BitLookupTable, getCompressedByteCount, getIFDs, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, getTileIndex, initTiffParser, isThisType, reopenFile, setResolutionLevel

Methods inherited from class loci.formats.SubResolutionFormatReader

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

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, 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, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, 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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

REMOVE_THUMBNAIL_KEY

public static final String REMOVE_THUMBNAIL_KEY

See Also:

• Constant Field Values

REMOVE_THUMBNAIL_DEFAULT

public static final boolean REMOVE_THUMBNAIL_DEFAULT

See Also:

• Constant Field Values

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

APERIO_IMAGE_DESCRIPTION_PREFIX

private static final String APERIO_IMAGE_DESCRIPTION_PREFIX

TIFF image description prefix for Aperio SVS files.

See Also:

• Constant Field Values

DATE_FORMAT

private static final String DATE_FORMAT

See Also:

• Constant Field Values

zPosition

private Double[] zPosition

comments

private String[] comments

emissionWavelength

private Double emissionWavelength

excitationWavelength

private Double excitationWavelength

exposureTime

private Double exposureTime

exposureScale

private Double exposureScale

magnification

private Double magnification

date

private String date

time

private String time

dyeNames

private ArrayList<String> dyeNames

displayColor

private transient ome.xml.model.primitives.Color displayColor

labelIndex

private int labelIndex

macroIndex

private int macroIndex

extraImages

private int extraImages

physicalDistanceFromLeftEdge

private transient Double physicalDistanceFromLeftEdge

physicalDistanceFromTopEdge

private transient Double physicalDistanceFromTopEdge

Constructor Details

SVSReader

public SVSReader()

Constructs a new SVS reader.

SVSReader

public SVSReader(String name,
 String[] suffixes)

Method Details

removeThumbnail

public boolean removeThumbnail()

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
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

IOException

See Also:

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

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.

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

Overrides:

openBytes in class MinimalTiffReader

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.

See Also:

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

openThumbBytes

public byte[] openThumbBytes(int no)
                      throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains a thumbnail for the specified image plane from the current file, as a byte array.

Specified by:

openThumbBytes in interface IFormatReader

Overrides:

openThumbBytes in class MinimalTiffReader

Throws:

FormatException

IOException

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 MinimalTiffReader

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 MinimalTiffReader

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 MinimalTiffReader

getTileRows

public int getTileRows(int no)

Description copied from interface: ICompressedTileReader

Get the number of rows of tiles in the specified plane in the current series.

Specified by:

getTileRows in interface ICompressedTileReader

Overrides:

getTileRows in class FormatReader

Parameters:

no - plane index

Returns:

tile row count

getTileColumns

public int getTileColumns(int no)

Description copied from interface: ICompressedTileReader

Get the number of columns of tiles in the specified plane in the current series.

Specified by:

getTileColumns in interface ICompressedTileReader

Overrides:

getTileColumns in class FormatReader

Parameters:

no - plane index

Returns:

tile column count

openCompressedBytes

public byte[] openCompressedBytes(int no,
 int x,
 int y)
                           throws FormatException,
IOException

Description copied from interface: ICompressedTileReader

Retrieve the specified tile without performing any decompression.

Parameters:

no - plane index

x - tile X index (indexed from 0, @see getTileColumns(int))

y - tile Y index (indexed from 0, @see getTileRows(int))

Returns:

compressed tile bytes

Throws:

FormatException

IOException

openCompressedBytes

public byte[] openCompressedBytes(int no,
 byte[] buf,
 int x,
 int y)
                           throws FormatException,
IOException

Description copied from interface: ICompressedTileReader

Retrieve the specified tile without performing any decompression.

Parameters:

no - plane index

buf - pre-allocated buffer in which to store compressed bytes

x - tile X index (indexed from 0, @see getTileColumns(int))

y - tile Y index (indexed from 0, @see getTileRows(int))

Returns:

compressed tile bytes

Throws:

FormatException

IOException

getTileCodec

public Codec getTileCodec(int no)
                   throws FormatException,
IOException

Description copied from interface: ICompressedTileReader

Retrieve a codec that can be used to decompress compressed tiles.

Parameters:

no - plane index

Returns:

codec that can be used for compressed tiles in the specified plane

Throws:

FormatException

IOException

See Also:

• ICompressedTileReader.openCompressedBytes(int,int,int)

getTileCodecOptions

public CodecOptions getTileCodecOptions(int no,
 int x,
 int y)
                                 throws FormatException,
IOException

Description copied from interface: ICompressedTileReader

Retrieve codec options that can be used to decompressed the specified tile.

Parameters:

no - plane index

x - tile X index (indexed from 0, @see getTileColumns(int))

y - tile Y index (indexed from 0, @see getTileRows(int))

Returns:

codec options

Throws:

FormatException

IOException

See Also:

• ICompressedTileReader.getTileCodec(int)

getAvailableOptions

protected ArrayList<String> getAvailableOptions()

Description copied from class: FormatReader

Returns the list of available metadata options.

Overrides:

getAvailableOptions in class FormatReader

initStandardMetadata

protected void initStandardMetadata()
                             throws FormatException,
IOException

Description copied from class: BaseTiffReader

Parses standard metadata. NOTE: Absolutely no calls to the metadata store should be made in this method or methods that override this method. Data will be overwritten if you do so.

Overrides:

initStandardMetadata in class BaseTiffReader

Throws:

FormatException

IOException

initMetadataStore

protected void initMetadataStore()
                          throws FormatException

Description copied from class: BaseTiffReader

Populates the metadata store using the data parsed in BaseTiffReader.initStandardMetadata() along with some further parsing done in the method itself. All calls to the active MetadataStore should be made in this method and only in this method. This is especially important for sub-classes that override the getters for pixel set array size, etc.

Overrides:

initMetadataStore in class BaseTiffReader

Throws:

FormatException

getIFDIndex

private int getIFDIndex(int coreIndex,
 int no)

getEmission

protected ome.units.quantity.Length getEmission()

getExcitation

protected ome.units.quantity.Length getExcitation()

getExposureTime

protected Double getExposureTime()

getDatestamp

protected ome.xml.model.primitives.Timestamp getDatestamp()

getPhysicalSizes

protected ome.units.quantity.Length[] getPhysicalSizes()

getMagnification

protected double getMagnification()

getDyeNames

protected ArrayList<String> getDyeNames()

getDisplayColor

protected ome.xml.model.primitives.Color getDisplayColor()

getIFD

protected IFD getIFD(int no)

Get the IFD corresponding to the given plane in the current series. Initializes the underlying TiffParser if necessary.

Parameters:

no - index

Returns:

corresponding IFD