Package loci.formats

Class WrappedReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.WrappedReader

All Implemented Interfaces:

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

Direct Known Subclasses:

FilePatternReader

public abstract class WrappedReader
extends FormatReader

Helper class for readers which wrap other readers. Some methods can only be called before initFile/setId, others can only be called after. This class assumes the helper object is only available after initFile() has been called. Instead the inherited FormatReader and IMetadataConfigurable methods are kept since the properties they set are inherited. These properties can be set on the helper class in initFile() by calling callDeferredSetters(). The following setters and corresponding getters are not passed to the helper. If you initialise the helper in the constructor instead of at runtime during initFile() you may wish to override them. - getSupportedMetadataLevels - setMetadataOptions, getMetadataOptions - setGroupFiles, isGroupFiles - setNormalized, isNormalized - setOriginalMetadataPopulated, isOriginalMetadataPopulated - setMetadataFiltered, isMetadataFiltered - setMetadataStore, getMetadataStore - setFlattenedResolutions, hasFlattenedResolutions Developer note: the list of methods are those in IMetadataConfigurable plus FormatReader methods which contain `FormatTools.assertId(currentId, false, 1)`

Field Summary

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, fillColor, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	WrappedReader(String format, String[] suffixes)	Constructs a new wrapped reader with the given name and suffixes.

Method Summary

Modifier and Type	Method	Description
protected void	callDeferredSetters(ReaderWrapper helper)	A helper may not exist before initFile() is called.
void	close()
void	close(boolean fileOnly)	Closes the currently open file.
int	coreIndexToSeries(int index)	Returns the series corresponding to the specified core index.
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.
int	getBitsPerPixel()	Gets the number of valid bits per pixel.
int	getCoreIndex()	Return the index into CoreMetadata of the current resolution/series.
List<CoreMetadata>	getCoreMetadataList()	Obtains the core metadata values for the current file.
String	getDatasetStructureDescription()	Returns a short description of the dataset structure.
String	getDimensionOrder()	Gets a five-character string representing the dimension order in which planes will be returned.
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().
Hashtable<String,Object>	getGlobalMetadata()	Obtains the hashtable containing the metadata field/value pairs from the current file.
protected abstract ReaderWrapper	getHelper()	Get the helper class that reads images
int	getImageCount()	Determines the number of image planes in the current file.
int	getIndex(int z, int c, int t)	Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
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.
Modulo	getModuloC()
Modulo	getModuloT()
Modulo	getModuloZ()
Class<?>	getNativeDataType()	Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object).
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.
String[]	getPossibleDomains(String id)	Returns a list of scientific domains in which this format is used.
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.
int	getSeries()	Gets the currently active series.
int	getSeriesCount()	Gets the number of series in this file.
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(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.
IFormatReader[]	getUnderlyingReaders()	Retrieves all underlying readers.
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.
boolean	hasCompanionFiles()	Returns true if this format supports multi-file datasets.
boolean	isFalseColor()	Returns false if IFormatReader.isIndexed() is false, or if IFormatReader.isIndexed() is true and the lookup table represents "real" color data.
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	isOrderCertain()	Gets whether the dimension order and sizes are known, or merely guesses.
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	isThumbnailSeries()	Gets whether the current series is a lower resolution copy of a different series.
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).
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.
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	setResolution(int no)	Set the resolution level.
void	setSeries(int no)	Activates the specified series.

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, fileGroupOption, flattenHashtables, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getCompression, getContrastMethod, getCorrection, getCurrentCore, getCurrentFile, getDetectorType, getDimensionOrder, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getIlluminationType, getImmersion, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMicrobeamManipulationType, getMicroscopeType, getNamingConvention, getPixelType, getPulse, getRequiredDirectories, getRotationTransform, getSeriesMeta, getSeriesUsedFiles, getTileColumns, getTileRows, getUsedFiles, getZCTModuloCoords, hasFlattenedResolutions, initFile, isGroupFiles, isMetadataFiltered, isNormalized, isOriginalMetadataPopulated, isThisType, isThisType, isThisType, isThisType, isUsedFile, makeFilterMetadata, readPlane, readPlane, readPlane, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, updateMetadataLists

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, 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, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Constructor Details

WrappedReader

protected WrappedReader(String format,
 String[] suffixes)

Constructs a new wrapped reader with the given name and suffixes.

Method Details

getHelper

protected abstract ReaderWrapper getHelper()

Get the helper class that reads images

reopenFile

public void reopenFile()
                throws IOException

Description copied from interface: IFormatReader

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

Specified by:

reopenFile in interface IFormatReader

Overrides:

reopenFile in class FormatReader

Throws:

IOException

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

Overrides:

getImageCount in class FormatReader

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

Overrides:

isRGB in class FormatReader

getSizeX

public int getSizeX()

Description copied from interface: IFormatReader

Gets the size of the X dimension.

Specified by:

getSizeX in interface IFormatReader

Overrides:

getSizeX in class FormatReader

getSizeY

public int getSizeY()

Description copied from interface: IFormatReader

Gets the size of the Y dimension.

Specified by:

getSizeY in interface IFormatReader

Overrides:

getSizeY in class FormatReader

getSizeZ

public int getSizeZ()

Description copied from interface: IFormatReader

Gets the size of the Z dimension.

Specified by:

getSizeZ in interface IFormatReader

Overrides:

getSizeZ in class FormatReader

getSizeC

public int getSizeC()

Description copied from interface: IFormatReader

Gets the size of the C dimension.

Specified by:

getSizeC in interface IFormatReader

Overrides:

getSizeC in class FormatReader

getSizeT

public int getSizeT()

Description copied from interface: IFormatReader

Gets the size of the T dimension.

Specified by:

getSizeT in interface IFormatReader

Overrides:

getSizeT in class FormatReader

getPixelType

public int getPixelType()

Description copied from interface: IFormatReader

Gets the pixel type.

Specified by:

getPixelType in interface IFormatReader

Overrides:

getPixelType in class FormatReader

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

Overrides:

getBitsPerPixel in class FormatReader

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

Overrides:

getEffectiveSizeC in class FormatReader

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

Overrides:

getRGBChannelCount in class FormatReader

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

Overrides:

isIndexed in class FormatReader

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

Overrides:

isFalseColor in class FormatReader

get8BitLookupTable

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

Description copied from interface: IFormatReader

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

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class FormatReader

Throws:

FormatException

IOException

get16BitLookupTable

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

Description copied from interface: IFormatReader

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

Specified by:

get16BitLookupTable in interface IFormatReader

Overrides:

get16BitLookupTable in class FormatReader

Throws:

FormatException

IOException

getModuloZ

public Modulo getModuloZ()

Specified by:

getModuloZ in interface IFormatReader

Overrides:

getModuloZ in class FormatReader

getModuloC

public Modulo getModuloC()

Specified by:

getModuloC in interface IFormatReader

Overrides:

getModuloC in class FormatReader

getModuloT

public Modulo getModuloT()

Specified by:

getModuloT in interface IFormatReader

Overrides:

getModuloT in class FormatReader

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 FormatReader

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 FormatReader

isLittleEndian

public boolean isLittleEndian()

Description copied from interface: IFormatReader

Gets whether the data is in little-endian format.

Specified by:

isLittleEndian in interface IFormatReader

Overrides:

isLittleEndian in class FormatReader

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

Overrides:

getDimensionOrder in class FormatReader

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

Overrides:

isOrderCertain in class FormatReader

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

Overrides:

isThumbnailSeries in class FormatReader

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

Overrides:

isInterleaved in class FormatReader

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

Specified by:

isInterleaved in interface IFormatReader

Overrides:

isInterleaved in class FormatReader

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

Overrides:

openBytes in class FormatReader

Throws:

FormatException

IOException

See Also:

• IFormatReader.openBytes(int, byte[])

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

Overrides:

openBytes in class FormatReader

Throws:

FormatException

IOException

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

Overrides:

openBytes in class FormatReader

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,
 byte[] buf,
 int x,
 int y,
 int w,
 int h)
                 throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Parameters:

no - the plane index within the current series.

buf - a pre-allocated buffer.

x - X coordinate of the upper-left corner of the sub-image

y - Y coordinate of the upper-left corner of the sub-image

w - width of the sub-image

h - height of the sub-image

Returns:

the pre-allocated buffer buf for convenience.

Throws:

FormatException - if there was a problem parsing the metadata of the file.

IOException - if there was a problem reading the file.

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

Overrides:

openPlane in class FormatReader

Throws:

FormatException

IOException

See Also:

• FormatReader
• 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

Overrides:

openThumbBytes in class FormatReader

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 FormatReader

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

Overrides:

getSeriesCount in class FormatReader

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

Overrides:

setSeries in class FormatReader

getSeries

public int getSeries()

Description copied from interface: IFormatReader

Gets the currently active series.

Specified by:

getSeries in interface IFormatReader

Overrides:

getSeries in class FormatReader

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

Overrides:

isMetadataComplete in class FormatReader

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

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

Overrides:

getUsedFiles in class FormatReader

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

Overrides:

getIndex in class FormatReader

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

Overrides:

getZCTCoords in class FormatReader

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

Overrides:

getMetadataValue in class FormatReader

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

Overrides:

getSeriesMetadataValue in class FormatReader

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

Overrides:

getGlobalMetadata in class FormatReader

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

Overrides:

getSeriesMetadata in class FormatReader

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

Overrides:

getCoreMetadataList in class FormatReader

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

Overrides:

getMetadataStoreRoot in class FormatReader

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

Overrides:

getUnderlyingReaders in class FormatReader

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
IOException

Description copied from interface: IFormatReader

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

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

IOException

getDatasetStructureDescription

public String getDatasetStructureDescription()

Description copied from interface: IFormatReader

Returns a short description of the dataset structure.

Specified by:

getDatasetStructureDescription in interface IFormatReader

Overrides:

getDatasetStructureDescription in class FormatReader

hasCompanionFiles

public boolean hasCompanionFiles()

Description copied from interface: IFormatReader

Returns true if this format supports multi-file datasets.

Specified by:

hasCompanionFiles in interface IFormatReader

Overrides:

hasCompanionFiles in class FormatReader

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

Overrides:

getPossibleDomains in class FormatReader

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

Overrides:

getDomains in class FormatReader

getOptimalTileWidth

public int getOptimalTileWidth()

Description copied from interface: IFormatReader

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

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class FormatReader

getOptimalTileHeight

public int getOptimalTileHeight()

Description copied from interface: IFormatReader

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

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight in class FormatReader

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

Overrides:

getCoreIndex in class FormatReader

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

Overrides:

setCoreIndex in class FormatReader

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

Overrides:

seriesToCoreIndex in class FormatReader

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

Overrides:

coreIndexToSeries in class FormatReader

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

Overrides:

getResolutionCount in class FormatReader

setResolution

public void setResolution(int no)

Description copied from interface: IPyramidHandler

Set the resolution level.

Specified by:

setResolution in interface IPyramidHandler

Overrides:

setResolution in class FormatReader

See Also:

• IPyramidHandler.getResolutionCount()

getResolution

public int getResolution()

Description copied from interface: IPyramidHandler

Get the current resolution level.

Specified by:

getResolution in interface IPyramidHandler

Overrides:

getResolution in class FormatReader

See Also:

• IPyramidHandler.getResolutionCount()

getNativeDataType

public Class<?> getNativeDataType()

Description copied from interface: IFormatHandler

Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object). For most readers this type will be a byte array; however, some readers call external APIs that work with other types such as BufferedImage.

Specified by:

getNativeDataType in interface IFormatHandler

Overrides:

getNativeDataType in class FormatHandler

close

public void close()
           throws IOException

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Overrides:

close in class FormatReader

Throws:

IOException

callDeferredSetters

protected void callDeferredSetters(ReaderWrapper helper)

A helper may not exist before initFile() is called. This mean setters that would otherwise be called on the helper are instead called on this wrapper, and can be passed to the helper by calling this method

Parameters:

helper - The wrapped helper