Package loci.formats

Class FormatReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

All Implemented Interfaces:

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

Direct Known Subclasses:

DelegateReader, SubResolutionFormatReader, WrappedReader

public abstract class FormatReader
extends FormatHandler
implements IFormatReader

Abstract superclass of all biological file format readers.

Field Summary

Fields

Modifier and Type	Field	Description
protected List<CoreMetadata>	core	Core metadata values.
protected int	coreIndex	The number of the current series.
protected String	datasetDescription	Short description of the structure of the dataset.
protected String[]	domains	List of domains in which this format is used.
protected Byte	fillColor	Fill value for undefined pixels.
protected boolean	filterMetadata	Whether or not to filter out invalid metadata.
protected boolean	flattenedResolutions	Whether or not resolutions are flattened.
protected boolean	group	Whether or not to group multi-file formats.
protected boolean	hasCompanionFiles	Whether this format supports multi-file datasets.
protected RandomAccessInputStream	in	Current file.
protected boolean	indexedAsRGB	Whether or not MetadataStore sets C = 3 for indexed color images.
protected Hashtable<String,Object>	metadata	Hashtable containing metadata key/value pairs.
protected MetadataStore	metadataStore	Current metadata store.
protected boolean	normalizeData	Whether or not to normalize float data.
protected int	resolution	The number of the current resolution.
protected boolean	saveOriginalMetadata	Whether or not to save proprietary metadata in the MetadataStore.
protected int	series	The number of the current series (non flat).
protected boolean	suffixNecessary	Whether the file extension matching one of the reader's suffixes is necessary to identify the file as an instance of this format.
protected boolean	suffixSufficient	Whether the file extension matching one of the reader's suffixes is sufficient to identify the file as an instance of this format.
protected static final int	THUMBNAIL_DIMENSION	Default thumbnail width and height.

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
FormatReader(String format, String suffix)	Constructs a format reader with the given name and default suffix.
FormatReader(String format, String[] suffixes)	Constructs a format reader with the given name and default suffixes.

Method Summary

Modifier and Type	Method	Description
protected void	addGlobalMeta(String key, boolean value)	Adds an entry to the global metadata table.
protected void	addGlobalMeta(String key, byte value)	Adds an entry to the global metadata table.
protected void	addGlobalMeta(String key, char value)	Adds an entry to the global metadata table.
protected void	addGlobalMeta(String key, double value)	Adds an entry to the global metadata table.
protected void	addGlobalMeta(String key, float value)	Adds an entry to the global metadata table.
protected void	addGlobalMeta(String key, int value)	Adds an entry to the global metadata table.
protected void	addGlobalMeta(String key, long value)	Adds an entry to the global metadata table.
protected void	addGlobalMeta(String key, short value)	Adds an entry to the global metadata table.
protected void	addGlobalMeta(String key, Object value)	Adds an entry to the global metadata table.
protected void	addGlobalMetaList(String key, Object value)	Add the given key/value pair to the global metadata hashtable.
protected void	addMeta(String key, Object value, Hashtable<String,Object> meta)	Adds an entry to the specified Hashtable.
protected void	addMetaList(String key, Object value, Hashtable<String,Object> meta)	Add the given key/value pair to the given hashtable.
protected void	addSeriesMeta(String key, boolean value)	Adds an entry to the metadata table for the current series.
protected void	addSeriesMeta(String key, byte value)	Adds an entry to the metadata table for the current series.
protected void	addSeriesMeta(String key, char value)	Adds an entry to the metadata table for the current series.
protected void	addSeriesMeta(String key, double value)	Adds an entry to the metadata table for the current series.
protected void	addSeriesMeta(String key, float value)	Adds an entry to the metadata table for the current series.
protected void	addSeriesMeta(String key, int value)	Adds an entry to the metadata table for the current series.
protected void	addSeriesMeta(String key, long value)	Adds an entry to the metadata table for the current series.
protected void	addSeriesMeta(String key, short value)	Adds an entry to the metadata table for the current series.
protected void	addSeriesMeta(String key, Object value)	Adds an entry to the metadata table for the current series.
protected void	addSeriesMetaList(String key, Object value)	Add the given key/value pair to the current series metadata hashtable.
void	close()
void	close(boolean fileOnly)	Closes the currently open file.
int	coreIndexToSeries(int index)	Returns the series corresponding to the specified core index.
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
protected void	flattenHashtables()	Call updateMetadataLists(Hashtable) on all metadata hashtables.
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 AcquisitionMode	getAcquisitionMode(String value)	Deprecated. Use MetadataTools.getAcquisitionMode(String).
FileInfo[]	getAdvancedSeriesUsedFiles(boolean noPixels)	Returns an array of FileInfo objects representing the files needed to open the current series.
FileInfo[]	getAdvancedUsedFiles(boolean noPixels)	Returns an array of FileInfo objects representing the files needed to open this dataset.
protected ArcType	getArcType(String value)	Deprecated. Use MetadataTools.getArcType(String).
protected ArrayList<String>	getAvailableOptions()	Returns the list of available metadata options.
protected Binning	getBinning(String value)	Deprecated. Use MetadataTools.getBinning(String).
int	getBitsPerPixel()	Gets the number of valid bits per pixel.
protected Compression	getCompression(String value)	Deprecated. Use MetadataTools.getCompression(String).
protected ContrastMethod	getContrastMethod(String value)	Deprecated. Use MetadataTools.getContrastMethod(String).
int	getCoreIndex()	Return the index into CoreMetadata of the current resolution/series.
List<CoreMetadata>	getCoreMetadataList()	Obtains the core metadata values for the current file.
protected Correction	getCorrection(String value)	Deprecated. Use MetadataTools.getCorrection(String).
protected CoreMetadata	getCurrentCore()	Get the CoreMetadata corresponding to the current series and resolution
String	getCurrentFile()	Returns the current file.
String	getDatasetStructureDescription()	Returns a short description of the dataset structure.
protected DetectorType	getDetectorType(String value)	Deprecated. Use MetadataTools.getDetectorType(String).
String	getDimensionOrder()	Gets a five-character string representing the dimension order in which planes will be returned.
protected DimensionOrder	getDimensionOrder(String value)	Deprecated. Use MetadataTools.getDimensionOrder(String).
String[]	getDomains()	Returns the list of domains represented by the current file.
int	getEffectiveSizeC()	Gets the effective size of the C dimension, guaranteeing that getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount() regardless of the result of isRGB().
protected ExperimentType	getExperimentType(String value)	Deprecated. Use MetadataTools.getExperimentType(String).
protected FilamentType	getFilamentType(String value)	Deprecated. Use MetadataTools.getFilamentType(String).
Byte	getFillColor()	Return the fill value for undefined pixels.
protected FillRule	getFillRule(String value)	Deprecated. Use MetadataTools.getFillRule(String).
protected FilterType	getFilterType(String value)	Deprecated. Use MetadataTools.getFilterType(String).
protected FontFamily	getFontFamily(String value)	Deprecated. Use MetadataTools.getFontFamily(String).
protected FontStyle	getFontStyle(String value)	Deprecated. Use MetadataTools.getFontStyle(String).
protected Object	getGlobalMeta(String key)	Gets a value from the global metadata table.
Hashtable<String,Object>	getGlobalMetadata()	Obtains the hashtable containing the metadata field/value pairs from the current file.
protected IlluminationType	getIlluminationType(String value)	Deprecated. Use MetadataTools.getIlluminationType(String).
int	getImageCount()	Determines the number of image planes in the current file.
protected Immersion	getImmersion(String value)	Deprecated. Use MetadataTools.getImmersion(String).
int	getIndex(int z, int c, int t)	Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
int	getIndex(int z, int c, int t, int moduloZ, int moduloC, int moduloT)	Gets the rasterized index corresponding to the given Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes).
protected LaserMedium	getLaserMedium(String value)	Deprecated. Use MetadataTools.getLaserMedium(String).
protected LaserType	getLaserType(String value)	Deprecated. Use MetadataTools.getLaserType(String).
protected Marker	getMarker(String value)	Deprecated. Use MetadataTools.getMarker(String).
protected Medium	getMedium(String value)	Deprecated. Use MetadataTools.getMedium(String).
MetadataStore	getMetadataStore()	Retrieves the current metadata store for this reader.
Object	getMetadataStoreRoot()	Retrieves the current metadata store's root object.
Object	getMetadataValue(String field)	Obtains the specified metadata field's value for the current file.
protected MicrobeamManipulationType	getMicrobeamManipulationType(String value)	Deprecated. Use MetadataTools.getMicrobeamManipulationType(String).
protected MicroscopeType	getMicroscopeType(String value)	Deprecated. Use MetadataTools.getMicroscopeType(String).
Modulo	getModuloC()
Modulo	getModuloT()
Modulo	getModuloZ()
protected NamingConvention	getNamingConvention(String value)	Deprecated. Use MetadataTools.getNamingConvention(String).
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	getPixelType()	Gets the pixel type.
protected PixelType	getPixelType(String value)	Deprecated. Use MetadataTools.getPixelType(String).
String[]	getPossibleDomains(String id)	Returns a list of scientific domains in which this format is used.
protected Pulse	getPulse(String value)	Deprecated. Use MetadataTools.getPulse(String).
int	getRequiredDirectories(String[] files)	Returns the number of parent directories that are important when processing the given list of files.
int	getResolution()	Get the current resolution level.
int	getResolutionCount()	Return the number of resolutions for the current series.
int	getRGBChannelCount()	Gets the number of channels returned with each call to openBytes.
protected AffineTransform	getRotationTransform(double theta)	Construct an AffineTransform corresponding to the given angle.
int	getSeries()	Gets the currently active series.
int	getSeriesCount()	Gets the number of series in this file.
protected Object	getSeriesMeta(String key)	Gets an entry from the metadata table for the current series.
Hashtable<String,Object>	getSeriesMetadata()	Obtains the hashtable containing metadata field/value pairs from the current series in the current file.
Object	getSeriesMetadataValue(String field)	Obtains the specified metadata field's value for the current series in the current file.
String[]	getSeriesUsedFiles()	Returns an array of filenames needed to open the current series.
String[]	getSeriesUsedFiles(boolean noPixels)	Returns an array of filenames needed to open the current series.
int	getSizeC()	Gets the size of the C dimension.
int	getSizeT()	Gets the size of the T dimension.
int	getSizeX()	Gets the size of the X dimension.
int	getSizeY()	Gets the size of the Y dimension.
int	getSizeZ()	Gets the size of the Z dimension.
int	getThumbSizeX()	Get the size of the X dimension for the thumbnail.
int	getThumbSizeY()	Get the size of the Y dimension for the thumbnail.
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.
IFormatReader[]	getUnderlyingReaders()	Retrieves all underlying readers.
String[]	getUsedFiles()	Returns an array of filenames needed to open this dataset.
String[]	getUsedFiles(boolean noPixels)	Returns an array of filenames needed to open this dataset.
int[]	getZCTCoords(int index)	Gets the Z, C and T coordinates (real sizes) corresponding to the given rasterized index value.
int[]	getZCTModuloCoords(int index)	Gets the Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes) corresponding to the given rasterized index value.
boolean	hasCompanionFiles()	Returns true if this format supports multi-file datasets.
boolean	hasFlattenedResolutions()	Return whether or not resolution flattening is enabled.
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
boolean	isFalseColor()	Returns false if IFormatReader.isIndexed() is false, or if IFormatReader.isIndexed() is true and the lookup table represents "real" color data.
boolean	isGroupFiles()	Returns true if we should group files in multi-file formats.
boolean	isIndexed()	Gets whether the image planes are indexed color.
boolean	isInterleaved()	Gets whether or not the channels are interleaved.
boolean	isInterleaved(int subC)	Gets whether or not the given sub-channel is interleaved.
boolean	isLittleEndian()	Gets whether the data is in little-endian format.
boolean	isMetadataComplete()	Returns true if this format's metadata is completely parsed.
boolean	isMetadataFiltered()	Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table.
boolean	isNormalized()	Returns true if we should normalize float data.
boolean	isOrderCertain()	Gets whether the dimension order and sizes are known, or merely guesses.
boolean	isOriginalMetadataPopulated()	Returns true if we should save proprietary metadata in the MetadataStore.
boolean	isRGB()	Checks if the image planes in the file have more than one channel per IFormatReader.openBytes(int) call.
boolean	isSingleFile(String id)	Returns true if the named file is expected to be the only file in the dataset.
boolean	isThisType(byte[] block)	Checks if the given block is a valid header for this file format.
boolean	isThisType(String name)	Checks if a file matches the type of this format handler.
boolean	isThisType(String name, boolean open)	Checks if a file matches the type of this format reader.
boolean	isThisType(RandomAccessInputStream stream)	Checks if the given stream is a valid stream for this file format.
boolean	isThumbnailSeries()	Gets whether the current series is a lower resolution copy of a different series.
protected boolean	isUsedFile(String file)	Returns true if the given file name is in the used files list.
protected MetadataStore	makeFilterMetadata()	Return a properly configured loci.formats.meta.FilterMetadata.
byte[]	openBytes(int no)	Obtains the specified image plane from the current file as a byte array.
byte[]	openBytes(int no, byte[] buf)	Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).
abstract 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[]	openBytes(int no, int x, int y, int w, int h)	Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).
Object	openPlane(int no, int x, int y, int w, int h)	Obtains the specified image plane (or sub-image thereof) in the reader's native data structure.
byte[]	openThumbBytes(int no)	Obtains a thumbnail for the specified image plane from the current file, as a byte array.
protected byte[]	readPlane(RandomAccessInputStream s, int x, int y, int w, int h, byte[] buf)	Reads a raw plane from disk.
protected byte[]	readPlane(RandomAccessInputStream s, int x, int y, int w, int h, int scanlinePad, byte[] buf)	Reads a raw plane from disk.
protected byte[]	readPlane(RandomAccessInputStream s, int x, int y, int w, int h, int scanlinePad, int imageWidth, int imageHeight, byte[] buf)
void	reopenFile()	Reopen any files that were closed, and which are expected to be open while the reader is open.
int	seriesToCoreIndex(int series)	Returns the first core index corresponding to the specified series.
void	setCoreIndex(int no)	Set the current resolution/series (ignores subresolutions).
void	setFillColor(Byte color)	Set the fill value for undefined pixels.
void	setFlattenedResolutions(boolean flattened)	Set whether or not to flatten resolutions into individual series.
void	setGroupFiles(boolean groupFiles)	Specifies whether or not to force grouping in multi-file formats.
void	setId(String id)	Initialize a reader from the input file name.
void	setMetadataFiltered(boolean filter)	Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.
void	setMetadataStore(MetadataStore store)	Sets the default metadata store for this reader.
void	setNormalized(boolean normalize)	Specifies whether or not to normalize float data.
void	setOriginalMetadataPopulated(boolean populate)	Specifies whether or not to save proprietary metadata in the MetadataStore.
void	setResolution(int no)	Set the resolution level.
void	setSeries(int no)	Activates the specified series.
protected void	updateMetadataLists(Hashtable<String,Object> meta)	For the given metadata hashtable, replace any value that is a list with one key/value pair per list entry.

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

THUMBNAIL_DIMENSION

protected static final int THUMBNAIL_DIMENSION

Default thumbnail width and height.

See Also:

• Constant Field Values

in

protected transient RandomAccessInputStream in

Current file.

metadata

protected Hashtable<String,Object> metadata

Hashtable containing metadata key/value pairs.

coreIndex

protected int coreIndex

The number of the current series.

series

protected int series

The number of the current series (non flat).

core

protected List<CoreMetadata> core

Core metadata values.

resolution

protected int resolution

The number of the current resolution.

flattenedResolutions

protected boolean flattenedResolutions

Whether or not resolutions are flattened.

suffixNecessary

protected boolean suffixNecessary

Whether the file extension matching one of the reader's suffixes is necessary to identify the file as an instance of this format.

suffixSufficient

protected boolean suffixSufficient

Whether the file extension matching one of the reader's suffixes is sufficient to identify the file as an instance of this format.

hasCompanionFiles

protected boolean hasCompanionFiles

Whether this format supports multi-file datasets.

datasetDescription

protected String datasetDescription

Short description of the structure of the dataset.

normalizeData

protected boolean normalizeData

Whether or not to normalize float data.

filterMetadata

protected boolean filterMetadata

Whether or not to filter out invalid metadata.

saveOriginalMetadata

protected boolean saveOriginalMetadata

Whether or not to save proprietary metadata in the MetadataStore.

indexedAsRGB

protected boolean indexedAsRGB

Whether or not MetadataStore sets C = 3 for indexed color images.

group

protected boolean group

Whether or not to group multi-file formats.

fillColor

protected Byte fillColor

Fill value for undefined pixels.

domains

protected String[] domains

List of domains in which this format is used.

metadataStore

protected MetadataStore metadataStore

Current metadata store. Should never be accessed directly as the semantics of getMetadataStore() prevent "null" access.

Constructor Details

FormatReader

public FormatReader(String format,
 String suffix)

Constructs a format reader with the given name and default suffix.

FormatReader

public FormatReader(String format,
 String[] suffixes)

Constructs a format reader with the given name and default suffixes.

Method Details

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

Throws:

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

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

Throws:

FormatException - if a parsing error occurs processing the file.

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

getAvailableOptions

protected ArrayList<String> getAvailableOptions()

Returns the list of available metadata options.

isUsedFile

protected boolean isUsedFile(String file)

Returns true if the given file name is in the used files list.

addMeta

protected void addMeta(String key,
 Object value,
 Hashtable<String,Object> meta)

Adds an entry to the specified Hashtable.

addGlobalMeta

protected void addGlobalMeta(String key,
 Object value)

Adds an entry to the global metadata table.

addGlobalMeta

protected void addGlobalMeta(String key,
 boolean value)

Adds an entry to the global metadata table.

addGlobalMeta

protected void addGlobalMeta(String key,
 byte value)

Adds an entry to the global metadata table.

addGlobalMeta

protected void addGlobalMeta(String key,
 short value)

Adds an entry to the global metadata table.

addGlobalMeta

protected void addGlobalMeta(String key,
 int value)

Adds an entry to the global metadata table.

addGlobalMeta

protected void addGlobalMeta(String key,
 long value)

Adds an entry to the global metadata table.

addGlobalMeta

protected void addGlobalMeta(String key,
 float value)

Adds an entry to the global metadata table.

addGlobalMeta

protected void addGlobalMeta(String key,
 double value)

Adds an entry to the global metadata table.

addGlobalMeta

protected void addGlobalMeta(String key,
 char value)

Adds an entry to the global metadata table.

getGlobalMeta

protected Object getGlobalMeta(String key)

Gets a value from the global metadata table.

addMetaList

protected void addMetaList(String key,
 Object value,
 Hashtable<String,Object> meta)

Add the given key/value pair to the given hashtable. If the key already exists, a list will be stored in the hashtable and the value will be appended to the list.

Parameters:

key - the key to store in the hashtable

value - the value to store in the hashtable or list

meta - the hashtable in which to store the key/value

addGlobalMetaList

protected void addGlobalMetaList(String key,
 Object value)

Add the given key/value pair to the global metadata hashtable. If the key already exists, a list will be stored in the hashtable and the value will be appended to the list.

Parameters:

key - the key to store in the hashtable

value - the value to store in the hashtable or list

addSeriesMetaList

protected void addSeriesMetaList(String key,
 Object value)

Add the given key/value pair to the current series metadata hashtable. If the key already exists, a list will be stored in the hashtable and the value will be appended to the list.

flattenHashtables

protected void flattenHashtables()

Call updateMetadataLists(Hashtable) on all metadata hashtables.

updateMetadataLists

protected void updateMetadataLists(Hashtable<String,Object> meta)

For the given metadata hashtable, replace any value that is a list with one key/value pair per list entry. The new keys will be the original key with the list index appended.

Parameters:

meta - the hashtable from which to remove lists

addSeriesMeta

protected void addSeriesMeta(String key,
 Object value)

Adds an entry to the metadata table for the current series.

addSeriesMeta

protected void addSeriesMeta(String key,
 boolean value)

Adds an entry to the metadata table for the current series.

addSeriesMeta

protected void addSeriesMeta(String key,
 byte value)

Adds an entry to the metadata table for the current series.

addSeriesMeta

protected void addSeriesMeta(String key,
 short value)

Adds an entry to the metadata table for the current series.

addSeriesMeta

protected void addSeriesMeta(String key,
 int value)

Adds an entry to the metadata table for the current series.

addSeriesMeta

protected void addSeriesMeta(String key,
 long value)

Adds an entry to the metadata table for the current series.

addSeriesMeta

protected void addSeriesMeta(String key,
 float value)

Adds an entry to the metadata table for the current series.

addSeriesMeta

protected void addSeriesMeta(String key,
 double value)

Adds an entry to the metadata table for the current series.

addSeriesMeta

protected void addSeriesMeta(String key,
 char value)

Adds an entry to the metadata table for the current series.

getSeriesMeta

protected Object getSeriesMeta(String key)

Gets an entry from the metadata table for the current series.

readPlane

protected byte[] readPlane(RandomAccessInputStream s,
 int x,
 int y,
 int w,
 int h,
 byte[] buf)
                    throws IOException

Reads a raw plane from disk.

Throws:

IOException

readPlane

protected byte[] readPlane(RandomAccessInputStream s,
 int x,
 int y,
 int w,
 int h,
 int scanlinePad,
 byte[] buf)
                    throws IOException

Reads a raw plane from disk.

Throws:

IOException

readPlane

protected byte[] readPlane(RandomAccessInputStream s,
 int x,
 int y,
 int w,
 int h,
 int scanlinePad,
 int imageWidth,
 int imageHeight,
 byte[] buf)
                    throws IOException

Throws:

IOException

makeFilterMetadata

protected MetadataStore makeFilterMetadata()

Return a properly configured loci.formats.meta.FilterMetadata.

isThisType

public boolean isThisType(String name,
 boolean open)

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 isThisType(RandomAccessInputStream).

Specified by:

isThisType in interface IFormatReader

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(byte[] block)

Description copied from interface: IFormatReader

Checks if the given block is a valid header for this file format.

Specified by:

isThisType in interface IFormatReader

See Also:

• IFormatReader.isThisType(RandomAccessInputStream)

isThisType

public boolean isThisType(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

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

getImageCount

public int getImageCount()

Description copied from interface: IFormatReader

Determines the number of image planes in the current file.

Specified by:

getImageCount in interface IFormatReader

isRGB

public boolean isRGB()

Description copied from interface: IFormatReader

Checks if the image planes in the file have more than one channel per IFormatReader.openBytes(int) call. This method returns true if and only if IFormatReader.getRGBChannelCount() returns a value greater than 1.

Specified by:

isRGB in interface IFormatReader

getSizeX

public int getSizeX()

Description copied from interface: IFormatReader

Gets the size of the X dimension.

Specified by:

getSizeX in interface IFormatReader

getSizeY

public int getSizeY()

Description copied from interface: IFormatReader

Gets the size of the Y dimension.

Specified by:

getSizeY in interface IFormatReader

getSizeZ

public int getSizeZ()

Description copied from interface: IFormatReader

Gets the size of the Z dimension.

Specified by:

getSizeZ in interface IFormatReader

getSizeC

public int getSizeC()

Description copied from interface: IFormatReader

Gets the size of the C dimension.

Specified by:

getSizeC in interface IFormatReader

getSizeT

public int getSizeT()

Description copied from interface: IFormatReader

Gets the size of the T dimension.

Specified by:

getSizeT in interface IFormatReader

getPixelType

public int getPixelType()

Description copied from interface: IFormatReader

Gets the pixel type.

Specified by:

getPixelType in interface IFormatReader

Returns:

the pixel type as an enumeration from FormatTools static pixel types such as FormatTools.INT8.

getBitsPerPixel

public int getBitsPerPixel()

Description copied from interface: IFormatReader

Gets the number of valid bits per pixel. The number of valid bits per pixel is always less than or equal to the number of bits per pixel that correspond to IFormatReader.getPixelType().

Specified by:

getBitsPerPixel in interface IFormatReader

getEffectiveSizeC

public int getEffectiveSizeC()

Description copied from interface: IFormatReader

Gets the effective size of the C dimension, guaranteeing that getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount() regardless of the result of isRGB().

Specified by:

getEffectiveSizeC in interface IFormatReader

getRGBChannelCount

public int getRGBChannelCount()

Description copied from interface: IFormatReader

Gets the number of channels returned with each call to openBytes. The most common case where this value is greater than 1 is for interleaved RGB data, such as a 24-bit color image plane. However, it is possible for this value to be greater than 1 for non-interleaved data, such as an RGB TIFF with Planar rather than Chunky configuration.

Specified by:

getRGBChannelCount in interface IFormatReader

isIndexed

public boolean isIndexed()

Description copied from interface: IFormatReader

Gets whether the image planes are indexed color. This value has no impact on IFormatReader.getSizeC(), IFormatReader.getEffectiveSizeC() or IFormatReader.getRGBChannelCount().

Specified by:

isIndexed in interface IFormatReader

isFalseColor

public boolean isFalseColor()

Description copied from interface: IFormatReader

Returns false if IFormatReader.isIndexed() is false, or if IFormatReader.isIndexed() is true and the lookup table represents "real" color data. Returns true if IFormatReader.isIndexed() is true and the lookup table is only present to aid in visualization.

Specified by:

isFalseColor in interface IFormatReader

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

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

Throws:

FormatException

IOException

getModuloZ

public Modulo getModuloZ()

Specified by:

getModuloZ in interface IFormatReader

getModuloC

public Modulo getModuloC()

Specified by:

getModuloC in interface IFormatReader

getModuloT

public Modulo getModuloT()

Specified by:

getModuloT in interface IFormatReader

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

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

isLittleEndian

public boolean isLittleEndian()

Description copied from interface: IFormatReader

Gets whether the data is in little-endian format.

Specified by:

isLittleEndian in interface IFormatReader

getDimensionOrder

public String getDimensionOrder()

Description copied from interface: IFormatReader

Gets a five-character string representing the dimension order in which planes will be returned. Valid orders are:

• XYCTZ
• XYCZT
• XYTCZ
• XYTZC
• XYZCT
• XYZTC

In cases where the channels are interleaved (e.g., CXYTZ), C will be the first dimension after X and Y (e.g., XYCTZ) and the IFormatReader.isInterleaved() method will return true.

Specified by:

getDimensionOrder in interface IFormatReader

isOrderCertain

public boolean isOrderCertain()

Description copied from interface: IFormatReader

Gets whether the dimension order and sizes are known, or merely guesses.

Specified by:

isOrderCertain in interface IFormatReader

isThumbnailSeries

public boolean isThumbnailSeries()

Description copied from interface: IFormatReader

Gets whether the current series is a lower resolution copy of a different series.

Specified by:

isThumbnailSeries in interface IFormatReader

isInterleaved

public boolean isInterleaved()

Description copied from interface: IFormatReader

Gets whether or not the channels are interleaved. This method exists because X and Y must appear first in the dimension order. For interleaved data, IFormatReader.getDimensionOrder() returns XYCTZ or XYCZT, and this method returns true. Note that this flag returns whether or not the data returned by IFormatReader.openBytes(int) is interleaved. In most cases, this will match the interleaving in the original file, but for some formats (e.g. TIFF) channel re-ordering is done internally and the return value of this method will not match what is in the original file.

Specified by:

isInterleaved in interface IFormatReader

isInterleaved

public boolean isInterleaved(int subC)

Description copied from interface: IFormatReader

Gets whether or not the given sub-channel is interleaved. This method exists because some data with multiple rasterized sub-dimensions within C have one sub-dimension interleaved, and the other not—e.g.,

invalid reference

loci.formats.in.SDTReader

handles spectral-lifetime data with interleaved lifetime bins and non-interleaved spectral channels.

Specified by:

isInterleaved in interface IFormatReader

openBytes

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

Description copied from interface: IFormatReader

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

Specified by:

openBytes in interface IFormatReader

Throws:

FormatException

IOException

See Also:

• IFormatReader.openBytes(int, byte[])

openBytes

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

Description copied from interface: IFormatReader

Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).

Specified by:

openBytes in interface IFormatReader

Parameters:

no - the plane index within the current series.

buf - a pre-allocated buffer.

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.

openBytes

public byte[] openBytes(int no,
 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, whose upper-left corner is given by (x, y).

Specified by:

openBytes in interface IFormatReader

Throws:

FormatException

IOException

openBytes

public abstract 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

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.

openPlane

public Object openPlane(int no,
 int x,
 int y,
 int w,
 int h)
                 throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains the specified image plane (or sub-image thereof) in the reader's native data structure. For most readers this is a byte array; however, some readers call external APIs that work with other types such as BufferedImage. The openPlane method exists to maintain generality and efficiency while avoiding pollution of the API with AWT-specific logic.

Specified by:

openPlane in interface IFormatReader

Throws:

FormatException

IOException

See Also:

• FormatReader
• invalid reference

  loci.formats.gui.BufferedImageReader

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

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

Throws:

IOException

getSeriesCount

public int getSeriesCount()

Description copied from interface: IFormatReader

Gets the number of series in this file.

Specified by:

getSeriesCount in interface IFormatReader

setSeries

public void setSeries(int no)

Description copied from interface: IFormatReader

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

Specified by:

setSeries in interface IFormatReader

getSeries

public int getSeries()

Description copied from interface: IFormatReader

Gets the currently active series.

Specified by:

getSeries in interface IFormatReader

setGroupFiles

public void setGroupFiles(boolean groupFiles)

Description copied from interface: IFormatReader

Specifies whether or not to force grouping in multi-file formats.

Specified by:

setGroupFiles in interface IFormatReader

See Also:

• IFormatReader.fileGroupOption(String)
• IFormatReader.isGroupFiles()

isGroupFiles

public boolean isGroupFiles()

Description copied from interface: IFormatReader

Returns true if we should group files in multi-file formats.

Specified by:

isGroupFiles in interface IFormatReader

See Also:

• IFormatReader.setGroupFiles(boolean)
• IFormatReader.fileGroupOption(String)

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

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

setFillColor

public void setFillColor(Byte color)

Description copied from interface: IFormatReader

Set the fill value for undefined pixels. This can be used to override the default fill value defined in a reader. The default implementation in IFormatReader is a no-op.

Specified by:

setFillColor in interface IFormatReader

Parameters:

color - value that will be used to fill pixel byte arrays

getFillColor

public Byte getFillColor()

Description copied from interface: IFormatReader

Return the fill value for undefined pixels. The default implementation in IFormatReader always returns 0.

Specified by:

getFillColor in interface IFormatReader

See Also:

• If a fill color was not defined by the reader or #setFillColor(Byte), then 0 is returned.

isMetadataComplete

public boolean isMetadataComplete()

Description copied from interface: IFormatReader

Returns true if this format's metadata is completely parsed.

Specified by:

isMetadataComplete in interface IFormatReader

setNormalized

public void setNormalized(boolean normalize)

Description copied from interface: IFormatReader

Specifies whether or not to normalize float data.

Specified by:

setNormalized in interface IFormatReader

isNormalized

public boolean isNormalized()

Description copied from interface: IFormatReader

Returns true if we should normalize float data.

Specified by:

isNormalized in interface IFormatReader

setOriginalMetadataPopulated

public void setOriginalMetadataPopulated(boolean populate)

Description copied from interface: IFormatReader

Specifies whether or not to save proprietary metadata in the MetadataStore.

Specified by:

setOriginalMetadataPopulated in interface IFormatReader

isOriginalMetadataPopulated

public boolean isOriginalMetadataPopulated()

Description copied from interface: IFormatReader

Returns true if we should save proprietary metadata in the MetadataStore.

Specified by:

isOriginalMetadataPopulated in interface IFormatReader

getUsedFiles

public String[] getUsedFiles()

Description copied from interface: IFormatReader

Returns an array of filenames needed to open this dataset. The first element in the array is expected to be the path passed to IFormatHandler.setId(String). 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:

getUsedFiles in interface IFormatReader

getUsedFiles

public String[] getUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open this dataset. 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:

getUsedFiles in interface IFormatReader

getSeriesUsedFiles

public String[] getSeriesUsedFiles()

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. The first element in the array is expected to be the path passed to IFormatHandler.setId(String). 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

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

getAdvancedUsedFiles

public FileInfo[] getAdvancedUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of FileInfo objects representing the files needed to open this dataset. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.

Specified by:

getAdvancedUsedFiles in interface IFormatReader

getAdvancedSeriesUsedFiles

public FileInfo[] getAdvancedSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of FileInfo objects representing the files 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:

getAdvancedSeriesUsedFiles in interface IFormatReader

getCurrentFile

public String getCurrentFile()

Description copied from interface: IFormatReader

Returns the current file.

Specified by:

getCurrentFile in interface IFormatReader

getIndex

public int getIndex(int z,
 int c,
 int t)

Description copied from interface: IFormatReader

Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).

Specified by:

getIndex in interface IFormatReader

getIndex

public int getIndex(int z,
 int c,
 int t,
 int moduloZ,
 int moduloC,
 int moduloT)

Description copied from interface: IFormatReader

Gets the rasterized index corresponding to the given Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes). Note that the Z, C and T coordinates take the modulo dimension sizes into account. The effective size for each of these dimensions is limited to the total size of the dimension divided by the modulo size.

Specified by:

getIndex in interface IFormatReader

getZCTCoords

public int[] getZCTCoords(int index)

Description copied from interface: IFormatReader

Gets the Z, C and T coordinates (real sizes) corresponding to the given rasterized index value.

Specified by:

getZCTCoords in interface IFormatReader

getZCTModuloCoords

public int[] getZCTModuloCoords(int index)

Description copied from interface: IFormatReader

Gets the Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes) corresponding to the given rasterized index value. Note that the Z, C and T coordinates are not the same as those returned by getZCTCoords(int) because the size of the modulo dimensions is taken into account. The effective size for each of these dimensions is limited to the total size of the dimension divided by the modulo size.

Specified by:

getZCTModuloCoords in interface IFormatReader

getMetadataValue

public Object getMetadataValue(String field)

Description copied from interface: IFormatReader

Obtains the specified metadata field's value for the current file.

Specified by:

getMetadataValue in interface IFormatReader

Parameters:

field - the name associated with the metadata field

Returns:

the value, or null if the field doesn't exist

getSeriesMetadataValue

public Object getSeriesMetadataValue(String field)

Description copied from interface: IFormatReader

Obtains the specified metadata field's value for the current series in the current file.

Specified by:

getSeriesMetadataValue in interface IFormatReader

Parameters:

field - the name associated with the metadata field

Returns:

the value, or null if the field doesn't exist

getGlobalMetadata

public Hashtable<String,Object> getGlobalMetadata()

Description copied from interface: IFormatReader

Obtains the hashtable containing the metadata field/value pairs from the current file.

Specified by:

getGlobalMetadata in interface IFormatReader

Returns:

the hashtable containing all non-series-specific metadata from the file

getSeriesMetadata

public Hashtable<String,Object> getSeriesMetadata()

Description copied from interface: IFormatReader

Obtains the hashtable containing metadata field/value pairs from the current series in the current file.

Specified by:

getSeriesMetadata in interface IFormatReader

getCoreMetadataList

public List<CoreMetadata> getCoreMetadataList()

Description copied from interface: IFormatReader

Obtains the core metadata values for the current file.

Specified by:

getCoreMetadataList in interface IFormatReader

setMetadataFiltered

public void setMetadataFiltered(boolean filter)

Description copied from interface: IFormatReader

Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.

Specified by:

setMetadataFiltered in interface IFormatReader

isMetadataFiltered

public boolean isMetadataFiltered()

Description copied from interface: IFormatReader

Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table.

Specified by:

isMetadataFiltered in interface IFormatReader

setMetadataStore

public void setMetadataStore(MetadataStore store)

Description copied from interface: IFormatReader

Sets the default metadata store for this reader.

Specified by:

setMetadataStore in interface IFormatReader

Parameters:

store - a metadata store implementation.

getMetadataStore

public MetadataStore getMetadataStore()

Description copied from interface: IFormatReader

Retrieves the current metadata store for this reader. You can be assured that this method will never return a null metadata store.

Specified by:

getMetadataStore in interface IFormatReader

Returns:

A metadata store implementation.

getMetadataStoreRoot

public Object getMetadataStoreRoot()

Description copied from interface: IFormatReader

Retrieves the current metadata store's root object. It is guaranteed that all file parsing has been performed by the reader prior to retrieval. Requests for a full populated root object should be made using this method.

Specified by:

getMetadataStoreRoot in interface IFormatReader

Returns:

Current metadata store's root object fully populated.

getUnderlyingReaders

public IFormatReader[] getUnderlyingReaders()

Description copied from interface: IFormatReader

Retrieves all underlying readers. Returns null if there are no underlying readers.

Specified by:

getUnderlyingReaders in interface IFormatReader

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

Throws:

FormatException

IOException

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

Throws:

FormatException

IOException

getDatasetStructureDescription

public String getDatasetStructureDescription()

Description copied from interface: IFormatReader

Returns a short description of the dataset structure.

Specified by:

getDatasetStructureDescription in interface IFormatReader

hasCompanionFiles

public boolean hasCompanionFiles()

Description copied from interface: IFormatReader

Returns true if this format supports multi-file datasets.

Specified by:

hasCompanionFiles in interface IFormatReader

getPossibleDomains

public String[] getPossibleDomains(String id)
                            throws FormatException,
IOException

Description copied from interface: IFormatReader

Returns a list of scientific domains in which this format is used.

Specified by:

getPossibleDomains in interface IFormatReader

Throws:

FormatException

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

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

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

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

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

Parameters:

no - plane index

Returns:

tile column count

seriesToCoreIndex

public int seriesToCoreIndex(int series)

Description copied from interface: IFormatReader

Returns the first core index corresponding to the specified series.

Specified by:

seriesToCoreIndex in interface IFormatReader

coreIndexToSeries

public int coreIndexToSeries(int index)

Description copied from interface: IFormatReader

Returns the series corresponding to the specified core index.

Specified by:

coreIndexToSeries in interface IFormatReader

getResolutionCount

public int getResolutionCount()

Description copied from interface: IPyramidHandler

Return the number of resolutions for the current series. Resolutions are stored in descending order, so the largest resolution is first and the smallest resolution is last.

Specified by:

getResolutionCount in interface IPyramidHandler

setResolution

public void setResolution(int no)

Description copied from interface: IPyramidHandler

Set the resolution level.

Specified by:

setResolution in interface IPyramidHandler

See Also:

• IPyramidHandler.getResolutionCount()

getResolution

public int getResolution()

Description copied from interface: IPyramidHandler

Get the current resolution level.

Specified by:

getResolution in interface IPyramidHandler

See Also:

• IPyramidHandler.getResolutionCount()

hasFlattenedResolutions

public boolean hasFlattenedResolutions()

Description copied from interface: IFormatReader

Return whether or not resolution flattening is enabled.

Specified by:

hasFlattenedResolutions in interface IFormatReader

setFlattenedResolutions

public void setFlattenedResolutions(boolean flattened)

Description copied from interface: IFormatReader

Set whether or not to flatten resolutions into individual series.

Specified by:

setFlattenedResolutions in interface IFormatReader

getCoreIndex

public int getCoreIndex()

Description copied from interface: IFormatReader

Return the index into CoreMetadata of the current resolution/series.

Specified by:

getCoreIndex in interface IFormatReader

setCoreIndex

public void setCoreIndex(int no)

Description copied from interface: IFormatReader

Set the current resolution/series (ignores subresolutions). Equivalent to setSeries, but with flattened resolutions always set to false.

Specified by:

setCoreIndex in interface IFormatReader

isThisType

public boolean isThisType(String name)

Description copied from class: FormatHandler

Checks if a file matches the type of this format handler. The default implementation checks filename suffixes against those known for this format.

Specified by:

isThisType in interface IFormatHandler

Overrides:

isThisType in class FormatHandler

setId

public void setId(String id)
           throws FormatException,
IOException

Initialize a reader from the input file name. Call initFile(String id) to initialize the input file, read all of the metadata and set the reader up for reading planes. The performance of this method depends on the format and can be up to several minutes for large file sets.

Specified by:

setId in interface IFormatHandler

Parameters:

id - a String specifying the path to the file

Throws:

FormatException

IOException

close

public void close()
           throws IOException

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Throws:

IOException

getCurrentCore

protected CoreMetadata getCurrentCore()

Get the CoreMetadata corresponding to the current series and resolution

Returns:

the CoreMetadata

getAcquisitionMode

@Deprecated
protected AcquisitionMode getAcquisitionMode(String value)
                                      throws FormatException

Deprecated.

Use MetadataTools.getAcquisitionMode(String).

Retrieves an AcquisitionMode enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getArcType

@Deprecated
protected ArcType getArcType(String value)
                      throws FormatException

Deprecated.

Use MetadataTools.getArcType(String).

Retrieves an ArcType enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getBinning

@Deprecated
protected Binning getBinning(String value)
                      throws FormatException

Deprecated.

Use MetadataTools.getBinning(String).

Retrieves an Binning enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getCompression

@Deprecated
protected Compression getCompression(String value)
                              throws FormatException

Deprecated.

Use MetadataTools.getCompression(String).

Retrieves an Compression enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getContrastMethod

@Deprecated
protected ContrastMethod getContrastMethod(String value)
                                    throws FormatException

Deprecated.

Use MetadataTools.getContrastMethod(String).

Retrieves an ContrastMethod enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getCorrection

@Deprecated
protected Correction getCorrection(String value)
                            throws FormatException

Deprecated.

Use MetadataTools.getCorrection(String).

Retrieves an Correction enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getDetectorType

@Deprecated
protected DetectorType getDetectorType(String value)
                                throws FormatException

Deprecated.

Use MetadataTools.getDetectorType(String).

Retrieves an DetectorType enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getDimensionOrder

@Deprecated
protected DimensionOrder getDimensionOrder(String value)
                                    throws FormatException

Deprecated.

Use MetadataTools.getDimensionOrder(String).

Retrieves an DimensionOrder enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getExperimentType

@Deprecated
protected ExperimentType getExperimentType(String value)
                                    throws FormatException

Deprecated.

Use MetadataTools.getExperimentType(String).

Retrieves an ExperimentType enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getFilamentType

@Deprecated
protected FilamentType getFilamentType(String value)
                                throws FormatException

Deprecated.

Use MetadataTools.getFilamentType(String).

Retrieves an FilamentType enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getFillRule

@Deprecated
protected FillRule getFillRule(String value)
                        throws FormatException

Deprecated.

Use MetadataTools.getFillRule(String).

Retrieves an FillRule enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getFilterType

@Deprecated
protected FilterType getFilterType(String value)
                            throws FormatException

Deprecated.

Use MetadataTools.getFilterType(String).

Retrieves an FilterType enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getFontFamily

@Deprecated
protected FontFamily getFontFamily(String value)
                            throws FormatException

Deprecated.

Use MetadataTools.getFontFamily(String).

Retrieves an FontFamily enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getFontStyle

@Deprecated
protected FontStyle getFontStyle(String value)
                          throws FormatException

Deprecated.

Use MetadataTools.getFontStyle(String).

Retrieves an FontStyle enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getIlluminationType

@Deprecated
protected IlluminationType getIlluminationType(String value)
                                        throws FormatException

Deprecated.

Use MetadataTools.getIlluminationType(String).

Retrieves an IlluminationType enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getImmersion

@Deprecated
protected Immersion getImmersion(String value)
                          throws FormatException

Deprecated.

Use MetadataTools.getImmersion(String).

Retrieves an Immersion enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getLaserMedium

@Deprecated
protected LaserMedium getLaserMedium(String value)
                              throws FormatException

Deprecated.

Use MetadataTools.getLaserMedium(String).

Retrieves an LaserMedium enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getLaserType

@Deprecated
protected LaserType getLaserType(String value)
                          throws FormatException

Deprecated.

Use MetadataTools.getLaserType(String).

Retrieves an LaserType enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getMarker

@Deprecated
protected Marker getMarker(String value)
                    throws FormatException

Deprecated.

Use MetadataTools.getMarker(String).

Retrieves an Marker enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getMedium

@Deprecated
protected Medium getMedium(String value)
                    throws FormatException

Deprecated.

Use MetadataTools.getMedium(String).

Retrieves an Medium enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getMicrobeamManipulationType

@Deprecated
protected MicrobeamManipulationType getMicrobeamManipulationType(String value)
                                                          throws FormatException

Deprecated.

Use MetadataTools.getMicrobeamManipulationType(String).

Retrieves an MicrobeamManipulationType enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getMicroscopeType

@Deprecated
protected MicroscopeType getMicroscopeType(String value)
                                    throws FormatException

Deprecated.

Use MetadataTools.getMicroscopeType(String).

Retrieves an MicroscopeType enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getNamingConvention

@Deprecated
protected NamingConvention getNamingConvention(String value)
                                        throws FormatException

Deprecated.

Use MetadataTools.getNamingConvention(String).

Retrieves an NamingConvention enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getPixelType

@Deprecated
protected PixelType getPixelType(String value)
                          throws FormatException

Deprecated.

Use MetadataTools.getPixelType(String).

Retrieves an PixelType enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getPulse

@Deprecated
protected Pulse getPulse(String value)
                  throws FormatException

Deprecated.

Use MetadataTools.getPulse(String).

Retrieves an Pulse enumeration value for the given String.

Throws:

EnumerationException - if an appropriate enumeration value is not found.

FormatException

getRotationTransform

protected AffineTransform getRotationTransform(double theta)

Construct an AffineTransform corresponding to the given angle.

Parameters:

theta - the angle of rotation in radians