FormatReader (Bio-Formats API)

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

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

Direct Known Subclasses:

AFIReader, AIMReader, AliconaReader, AmiraReader, AnalyzeReader, APLReader, APNGReader, ARFReader, AVIReader, BaseZeissReader, BDReader, BIFormatReader, BioRadGelReader, BioRadReader, BioRadSCNReader, BMPReader, BrukerReader, BurleighReader, CanonRawReader, CellH5Reader, CellomicsReader, CellSensReader, CellVoyagerReader, CellWorxReader, DelegateReader, DeltavisionReader, DicomReader, Ecat7Reader, EPSReader, FakeReader, FEIReader, FilePatternReader, FitsReader, FlexReader, FlowSightReader, FujiReader, FV1000Reader, GatanDM2Reader, GatanReader, GIFReader, HamamatsuVMSReader, HISReader, HitachiReader, HRDGDFReader, I2IReader, ICSReader, IM3Reader, ImagicReader, ImarisHDFReader, ImarisReader, IMODReader, ImspectorReader, InCell3000Reader, InCellReader, INRReader, InveonReader, IPLabReader, IPWReader, IvisionReader, JEOLReader, JPEG2000Reader, JPXReader, KhorosReader, KodakReader, L2DReader, LegacyND2Reader, LeicaReader, LiFlimReader, LIFReader, LIMReader, MIASReader, MicromanagerReader, MINCReader, MinimalTiffReader, MolecularImagingReader, MRCReader, MRWReader, NAFReader, NativeND2Reader, NativeQTReader, NDPISReader, NiftiReader, NRRDReader, OBFReader, OMETiffReader, OMEXMLReader, OpenlabRawReader, OpenlabReader, OperettaReader, OxfordInstrumentsReader, PCIReader, PCORAWReader, PCXReader, PDSReader, PerkinElmerReader, PGMReader, PictReader, PovrayReader, PQBinReader, PrairieReader, PSDReader, QuesantReader, RHKReader, SBIGReader, ScanrReader, ScreenReader, SDTReader, SeikoReader, SIFReader, SlidebookReader, SMCameraReader, SPCReader, SPEReader, SpiderReader, TargaReader, TCSReader, TextReader, TileJPEGReader, TillVisionReader, TopometrixReader, UBMReader, UnisokuReader, VarianFDFReader, VeecoReader, VGSAMReader, VisitechReader, VolocityClippingReader, VolocityReader, WATOPReader, WlzReader, ZeissCZIReader, ZeissLMSReader, ZeissLSMReader, ZipReader
```
public abstract class FormatReader
extends FormatHandler
implements IFormatReader
```
Abstract superclass of all biological file format readers.

Field Summary

Fields
Modifier and Type	Field and 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.
`private ServiceFactory`	`factory`
`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).
`private OMEXMLService`	`service`
`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 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 and 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

Methods
Modifier and Type	Method and 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, Object 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`	`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, Object 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`	`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 int indicating that we cannot, must, or might group the files in a given dataset.
`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)` Retrieves an `AcquisitionMode` enumeration value for the given 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)` Retrieves an `ArcType` enumeration value for the given String.
`protected Binning`	`getBinning(String value)` Retrieves an `Binning` enumeration value for the given String.
`int`	`getBitsPerPixel()` Gets the number of valid bits per pixel.
`protected Compression`	`getCompression(String value)` Retrieves an `Compression` enumeration value for the given String.
`protected ContrastMethod`	`getContrastMethod(String value)` Retrieves an `ContrastMethod` enumeration value for the given 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)` Retrieves an `Correction` enumeration value for the given String.
`String`	`getCurrentFile()` Returns the current file.
`String`	`getDatasetStructureDescription()` Returns a short description of the dataset structure.
`protected DetectorType`	`getDetectorType(String value)` Retrieves an `DetectorType` enumeration value for the given String.
`String`	`getDimensionOrder()` Gets a five-character string representing the dimension order in which planes will be returned.
`protected DimensionOrder`	`getDimensionOrder(String value)` Retrieves an `DimensionOrder` enumeration value for the given 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)` Retrieves an `ExperimentType` enumeration value for the given String.
`protected FilamentType`	`getFilamentType(String value)` Retrieves an `FilamentType` enumeration value for the given String.
`protected FillRule`	`getFillRule(String value)` Retrieves an `FillRule` enumeration value for the given String.
`protected FilterType`	`getFilterType(String value)` Retrieves an `FilterType` enumeration value for the given String.
`protected FontFamily`	`getFontFamily(String value)` Retrieves an `FontFamily` enumeration value for the given String.
`protected FontStyle`	`getFontStyle(String value)` Retrieves an `FontStyle` enumeration value for the given 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)` Retrieves an `IlluminationType` enumeration value for the given String.
`int`	`getImageCount()` Determines the number of image planes in the current file.
`protected Immersion`	`getImmersion(String value)` Retrieves an `Immersion` enumeration value for the given 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)` Retrieves an `LaserMedium` enumeration value for the given String.
`protected LaserType`	`getLaserType(String value)` Retrieves an `LaserType` enumeration value for the given String.
`protected Marker`	`getMarker(String value)` Retrieves an `Marker` enumeration value for the given String.
`protected Medium`	`getMedium(String value)` Retrieves an `Medium` enumeration value for the given 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)` Retrieves an `MicrobeamManipulationType` enumeration value for the given String.
`protected MicroscopeType`	`getMicroscopeType(String value)` Retrieves an `MicroscopeType` enumeration value for the given String.
`Modulo`	`getModuloC()`
`Modulo`	`getModuloT()`
`Modulo`	`getModuloZ()`
`protected NamingConvention`	`getNamingConvention(String value)` Retrieves an `NamingConvention` enumeration value for the given 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)` Retrieves an `PixelType` enumeration value for the given String.
`String[]`	`getPossibleDomains(String id)` Returns a list of scientific domains in which this format is used.
`protected Pulse`	`getPulse(String value)` Retrieves an `Pulse` enumeration value for the given 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.
`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 this is a single-file format.
`boolean`	`isThisType(byte[] block)` Checks if the given block is a valid header for this file format.
`boolean`	`isThisType(RandomAccessInputStream stream)` Checks if the given stream is a valid stream 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`	`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.
`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`	`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)` Initializes 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.
`private void`	`setupService()` Initialize the OMEXMLService needed by `setId(String)`
`private 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.IFormatHandler
getFormat, getNativeDataType, getSuffixes

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

- Field Detail
  - 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.
  - 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.
  - factory
```
private ServiceFactory factory
```
  - service
```
private OMEXMLService service
```
- Constructor Detail
  - 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 Detail
  - 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
  - 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
```
private 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
  - 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
  - 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.
    
    Specified by:
    
    isThisType in interface IFormatReader
    
    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., 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 image index within the file.
    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 image index within the file.
    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, 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
  - 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
  - fileGroupOption
```
public int fileGroupOption(String id)
                    throws FormatException,
                           IOException
```
    Description copied from interface: IFormatReader
    
    Returns an int indicating that we cannot, must, or might group the files in a given dataset.
    
    Specified by:
    
    fileGroupOption in interface IFormatReader
    
    Throws:
    
    FormatException
    
    IOException
  - 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.
    
    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.
    
    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.
    
    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.
    
    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 this is a single-file format.
    
    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
  - 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: IFormatReader
    
    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 IFormatReader
  - setResolution
```
public void setResolution(int no)
```
    Description copied from interface: IFormatReader
    
    Set the resolution level.
    
    Specified by:
    
    setResolution in interface IFormatReader
    
    See Also:
    IFormatReader.getResolutionCount()
  - getResolution
```
public int getResolution()
```
    Description copied from interface: IFormatReader
    
    Get the current resolution level.
    
    Specified by:
    
    getResolution in interface IFormatReader
    
    See Also:
    IFormatReader.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
```
    Initializes a reader from the input file name. Calls initFile(String id) to initializes the input file, reads all of the metadata and sets 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
  - setupService
```
private void setupService()
```
    Initialize the OMEXMLService needed by setId(String)
  - close
```
public void close()
           throws IOException
```
    Specified by:
    
    close in interface Closeable
    
    Specified by:
    
    close in interface AutoCloseable
    
    Throws:
    
    IOException
  - getAcquisitionMode
```
protected AcquisitionMode getAcquisitionMode(String value)
                                      throws FormatException
```
    Retrieves an AcquisitionMode enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getArcType
```
protected ArcType getArcType(String value)
                      throws FormatException
```
    Retrieves an ArcType enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getBinning
```
protected Binning getBinning(String value)
                      throws FormatException
```
    Retrieves an Binning enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getCompression
```
protected Compression getCompression(String value)
                              throws FormatException
```
    Retrieves an Compression enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getContrastMethod
```
protected ContrastMethod getContrastMethod(String value)
                                    throws FormatException
```
    Retrieves an ContrastMethod enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getCorrection
```
protected Correction getCorrection(String value)
                            throws FormatException
```
    Retrieves an Correction enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getDetectorType
```
protected DetectorType getDetectorType(String value)
                                throws FormatException
```
    Retrieves an DetectorType enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getDimensionOrder
```
protected DimensionOrder getDimensionOrder(String value)
                                    throws FormatException
```
    Retrieves an DimensionOrder enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getExperimentType
```
protected ExperimentType getExperimentType(String value)
                                    throws FormatException
```
    Retrieves an ExperimentType enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getFilamentType
```
protected FilamentType getFilamentType(String value)
                                throws FormatException
```
    Retrieves an FilamentType enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getFillRule
```
protected FillRule getFillRule(String value)
                        throws FormatException
```
    Retrieves an FillRule enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getFilterType
```
protected FilterType getFilterType(String value)
                            throws FormatException
```
    Retrieves an FilterType enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getFontFamily
```
protected FontFamily getFontFamily(String value)
                            throws FormatException
```
    Retrieves an FontFamily enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getFontStyle
```
protected FontStyle getFontStyle(String value)
                          throws FormatException
```
    Retrieves an FontStyle enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getIlluminationType
```
protected IlluminationType getIlluminationType(String value)
                                        throws FormatException
```
    Retrieves an IlluminationType enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getImmersion
```
protected Immersion getImmersion(String value)
                          throws FormatException
```
    Retrieves an Immersion enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getLaserMedium
```
protected LaserMedium getLaserMedium(String value)
                              throws FormatException
```
    Retrieves an LaserMedium enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getLaserType
```
protected LaserType getLaserType(String value)
                          throws FormatException
```
    Retrieves an LaserType enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getMarker
```
protected Marker getMarker(String value)
                    throws FormatException
```
    Retrieves an Marker enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getMedium
```
protected Medium getMedium(String value)
                    throws FormatException
```
    Retrieves an Medium enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getMicrobeamManipulationType
```
protected MicrobeamManipulationType getMicrobeamManipulationType(String value)
                                                          throws FormatException
```
    Retrieves an MicrobeamManipulationType enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getMicroscopeType
```
protected MicroscopeType getMicroscopeType(String value)
                                    throws FormatException
```
    Retrieves an MicroscopeType enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getNamingConvention
```
protected NamingConvention getNamingConvention(String value)
                                        throws FormatException
```
    Retrieves an NamingConvention enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getPixelType
```
protected PixelType getPixelType(String value)
                          throws FormatException
```
    Retrieves an PixelType enumeration value for the given String.
    
    Throws:
    
    EnumerationException - if an appropriate enumeration value is not found.
    
    FormatException
  - getPulse
```
protected Pulse getPulse(String value)
                  throws FormatException
```
    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

Class FormatReader

Field Summary

Fields inherited from class loci.formats.FormatHandler

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

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

Field Detail

THUMBNAIL_DIMENSION

in

metadata

coreIndex

series

core

resolution

flattenedResolutions

suffixNecessary

suffixSufficient

hasCompanionFiles

datasetDescription

normalizeData

filterMetadata

saveOriginalMetadata

indexedAsRGB

group

domains

metadataStore

factory

service

Constructor Detail

FormatReader

FormatReader

Method Detail

reopenFile

initFile

isUsedFile

addMeta

addGlobalMeta

addGlobalMeta

addGlobalMeta

addGlobalMeta

addGlobalMeta

addGlobalMeta

addGlobalMeta

addGlobalMeta

addGlobalMeta

getGlobalMeta

addMetaList

addGlobalMetaList

addSeriesMetaList

flattenHashtables

updateMetadataLists

addSeriesMeta

addSeriesMeta

addSeriesMeta

addSeriesMeta

addSeriesMeta

addSeriesMeta

addSeriesMeta

addSeriesMeta

addSeriesMeta

getSeriesMeta

readPlane

readPlane

makeFilterMetadata

isThisType

isThisType

isThisType

getImageCount

isRGB

getSizeX

getSizeY

getSizeZ

getSizeC

getSizeT

getPixelType

getBitsPerPixel