WrappedReader (Bio-Formats API)

java.lang.Object
- loci.formats.FormatHandler
- - loci.formats.FormatReader
  - - loci.formats.WrappedReader

All Implemented Interfaces:

java.io.Closeable, java.lang.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 and Description
`protected`	`WrappedReader(java.lang.String format, java.lang.String[] suffixes)` Constructs a new wrapped reader with the given name and suffixes.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and 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.
`java.util.List<CoreMetadata>`	`getCoreMetadataList()` Obtains the core metadata values for the current file.
`java.lang.String`	`getDatasetStructureDescription()` Returns a short description of the dataset structure.
`java.lang.String`	`getDimensionOrder()` Gets a five-character string representing the dimension order in which planes will be returned.
`java.lang.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().
`java.util.Hashtable<java.lang.String,java.lang.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).
`java.lang.Object`	`getMetadataStoreRoot()` Retrieves the current metadata store's root object.
`java.lang.Object`	`getMetadataValue(java.lang.String field)` Obtains the specified metadata field's value for the current file.
`Modulo`	`getModuloC()`
`Modulo`	`getModuloT()`
`Modulo`	`getModuloZ()`
`java.lang.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.
`java.lang.String[]`	`getPossibleDomains(java.lang.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.
`java.util.Hashtable<java.lang.String,java.lang.Object>`	`getSeriesMetadata()` Obtains the hashtable containing metadata field/value pairs from the current series in the current file.
`java.lang.Object`	`getSeriesMetadataValue(java.lang.String field)` Obtains the specified metadata field's value for the current series in the current file.
`java.lang.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.
`java.lang.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(java.lang.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).
`java.lang.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.IFormatHandler
getFormat, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable
getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from interface loci.formats.ICompressedTileReader
getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

- Constructor Detail
  - WrappedReader
```
protected WrappedReader(java.lang.String format,
                        java.lang.String[] suffixes)
```
    Constructs a new wrapped reader with the given name and suffixes.
- Method Detail
  - getHelper
```
protected abstract ReaderWrapper getHelper()
```
    Get the helper class that reads images
  - reopenFile
```
public void reopenFile()
                throws java.io.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:
    
    java.io.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,
                                   java.io.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
    
    java.io.IOException
  - get16BitLookupTable
```
public short[][] get16BitLookupTable()
                              throws FormatException,
                                     java.io.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
    
    java.io.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 java.lang.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,
                        java.io.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
    
    java.io.IOException
    
    See Also:
    
    IFormatReader.openBytes(int, byte[])
  - openBytes
```
public byte[] openBytes(int no,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        java.io.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
    
    java.io.IOException
  - openBytes
```
public byte[] openBytes(int no,
                        byte[] buf)
                 throws FormatException,
                        java.io.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.
    
    java.io.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,
                        java.io.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.
    
    java.io.IOException - if there was a problem reading the file.
  - openPlane
```
public java.lang.Object openPlane(int no,
                                  int x,
                                  int y,
                                  int w,
                                  int h)
                           throws FormatException,
                                  java.io.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
    
    java.io.IOException
    
    See Also:
    
    FormatReader, BufferedImageReader
  - openThumbBytes
```
public byte[] openThumbBytes(int no)
                      throws FormatException,
                             java.io.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
    
    java.io.IOException
  - close
```
public void close(boolean fileOnly)
           throws java.io.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:
    
    java.io.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 java.lang.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 java.lang.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 java.lang.Object getMetadataValue(java.lang.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 java.lang.Object getSeriesMetadataValue(java.lang.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 java.util.Hashtable<java.lang.String,java.lang.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 java.util.Hashtable<java.lang.String,java.lang.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 java.util.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 java.lang.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(java.lang.String id)
                     throws FormatException,
                            java.io.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
    
    java.io.IOException
  - getDatasetStructureDescription
```
public java.lang.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 java.lang.String[] getPossibleDomains(java.lang.String id)
                                      throws FormatException,
                                             java.io.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
    
    java.io.IOException
  - getDomains
```
public java.lang.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 java.lang.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 java.io.IOException
```
    Specified by:
    
    close in interface java.io.Closeable
    
    Specified by:
    
    close in interface java.lang.AutoCloseable
    
    Overrides:
    
    close in class FormatReader
    
    Throws:
    
    java.io.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

Class WrappedReader

Field Summary

Fields inherited from class loci.formats.FormatReader

Fields inherited from class loci.formats.FormatHandler

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class loci.formats.FormatReader

Methods inherited from class loci.formats.FormatHandler

Methods inherited from class java.lang.Object

Methods inherited from interface loci.formats.IFormatHandler

Methods inherited from interface loci.formats.IMetadataConfigurable

Methods inherited from interface loci.formats.ICompressedTileReader

Constructor Detail

WrappedReader

Method Detail

getHelper

reopenFile

getImageCount

isRGB

getSizeX

getSizeY

getSizeZ

getSizeC

getSizeT

getPixelType

getBitsPerPixel

getEffectiveSizeC

getRGBChannelCount

isIndexed

isFalseColor

get8BitLookupTable

get16BitLookupTable

getModuloZ

getModuloC

getModuloT

getThumbSizeX

getThumbSizeY

isLittleEndian

getDimensionOrder

isOrderCertain

isThumbnailSeries

isInterleaved

isInterleaved

openBytes

openBytes

openBytes

openBytes

openPlane

openThumbBytes

close

getSeriesCount

setSeries

getSeries

isMetadataComplete

getSeriesUsedFiles

getUsedFiles

getIndex

getZCTCoords

getMetadataValue

getSeriesMetadataValue

getGlobalMetadata

getSeriesMetadata

getCoreMetadataList

getMetadataStoreRoot

getUnderlyingReaders

isSingleFile

getDatasetStructureDescription

hasCompanionFiles

getPossibleDomains

getDomains

getOptimalTileWidth

getOptimalTileHeight

getCoreIndex

setCoreIndex

seriesToCoreIndex

coreIndexToSeries

getResolutionCount

setResolution

getResolution