Package loci.formats.in

Class VentanaReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.MinimalTiffReader

loci.formats.in.BaseTiffReader

loci.formats.in.VentanaReader

All Implemented Interfaces:

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

public class VentanaReader
extends BaseTiffReader

VentanaReader is the file format reader for Ventana .bif files.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	VentanaReader.AreaOfInterest
(package private) class	VentanaReader.Overlap
(package private) class	VentanaReader.TIFFTile

Field Summary

Fields

Modifier and Type	Field	Description
private List<VentanaReader.AreaOfInterest>	areas
private static final int	EXTRA_TAG_1
private static final int	EXTRA_TAG_2
private static final org.slf4j.Logger	LOGGER	Logger for this class.
private Double	magnification
private Double	physicalPixelSize
private int	resolutions
static final boolean	SPLIT_TILES_DEFAULT	Default value of SPLIT_TILES_KEY
static final String	SPLIT_TILES_KEY	MetadataOptions key for determining whether to report each tile as a separate series.
private int	tileHeight
private VentanaReader.TIFFTile[]	tiles
private int	tileWidth
private static final int	XML_TAG
private static final int	Z_TAG

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
VentanaReader()	Constructs a new Ventana reader.

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.
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.
private int	getIFDIndex(int coreIndex)	Note that all planes for a particular resolution or extra image are packed into a single IFD, so the IFD index does not depend upon the plane (e.g.
int	getOptimalTileHeight()	Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth()	Returns the optimal sub-image width for use with openBytes.
private int	getScale(int resolution)
int	getThumbSizeX()	Get the size of the X dimension for the thumbnail.
int	getThumbSizeY()	Get the size of the Y dimension for the thumbnail.
private int	getTileColumn(int index, int rows, int cols)
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[]	openThumbBytes(int no)	Obtains a thumbnail for the specified image plane from the current file, as a byte array.
private void	parseXML(String xml)
private int	scaleCoordinate(int v, int resolution)
private IFD	splitIFD(IFD ifd, int no)	Take the real IFD on disk and reshape it into something that represents only the given plane.
boolean	splitTiles()

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, getCompressedByteCount, getIFDs, getThumbnailIFDs, 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, getTileColumns, getTileRows, 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.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

SPLIT_TILES_KEY

public static final String SPLIT_TILES_KEY

MetadataOptions key for determining whether to report each tile as a separate series.

See Also:

• Constant Field Values

SPLIT_TILES_DEFAULT

public static final boolean SPLIT_TILES_DEFAULT

Default value of SPLIT_TILES_KEY

See Also:

• Constant Field Values

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

XML_TAG

private static final int XML_TAG

See Also:

• Constant Field Values

Z_TAG

private static final int Z_TAG

See Also:

• Constant Field Values

EXTRA_TAG_1

private static final int EXTRA_TAG_1

See Also:

• Constant Field Values

EXTRA_TAG_2

private static final int EXTRA_TAG_2

See Also:

• Constant Field Values

magnification

private Double magnification

areas

private List<VentanaReader.AreaOfInterest> areas

tileWidth

private int tileWidth

tileHeight

private int tileHeight

tiles

private VentanaReader.TIFFTile[] tiles

resolutions

private int resolutions

physicalPixelSize

private Double physicalPixelSize

Constructor Details

VentanaReader

public VentanaReader()

Constructs a new Ventana reader.

Method Details

splitTiles

public boolean splitTiles()

Returns:

true if MetadataOptions are set so that each tile in the full resolution image will be returned as a separate series

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.

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 MinimalTiffReader

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 MinimalTiffReader

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

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

getThumbSizeX

public int getThumbSizeX()

Description copied from interface: IFormatReader

Get the size of the X dimension for the thumbnail.

Specified by:

getThumbSizeX in interface IFormatReader

Overrides:

getThumbSizeX in class MinimalTiffReader

getThumbSizeY

public int getThumbSizeY()

Description copied from interface: IFormatReader

Get the size of the Y dimension for the thumbnail.

Specified by:

getThumbSizeY in interface IFormatReader

Overrides:

getThumbSizeY in class MinimalTiffReader

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

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

getScale

private int getScale(int resolution)

Parameters:

resolution - the resolution for which to calculate a scale factor

Returns:

the scale factor between the full resolution image and the specified resolution

scaleCoordinate

private int scaleCoordinate(int v,
 int resolution)

Parameters:

v - the coordinate in the full resolution

resolution - the resolution for which to calculate a scale factor

Returns:

the scaled coordinate for the target resolution

getTileColumn

private int getTileColumn(int index,
 int rows,
 int cols)

Parameters:

index - the tile index as stored in TileJointInfo nodes

rows - the number of tile rows in an area of interest

cols - the number of tile columns in an area of interest

Returns:

the tile column in grid order (corrects for snake ordering)

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)

Note that all planes for a particular resolution or extra image are packed into a single IFD, so the IFD index does not depend upon the plane (e.g. Z section) needed.

Parameters:

coreIndex - the series or resolution for which to find an IFD

Returns:

the index into MinimalTiffReader.ifds for the given series and plane

splitIFD

private IFD splitIFD(IFD ifd,
 int no)
              throws FormatException,
IOException

Take the real IFD on disk and reshape it into something that represents only the given plane. This should preserve all tags except Z_TAG, and crop the tile byte count and offset arrays to match only the tiles for the given plane. This is necessary because the tile count in the real IFD is X * Y * Z.

Throws:

FormatException

IOException

parseXML

private void parseXML(String xml)
               throws IOException

Throws:

IOException