Index (formats-api 8.2.0 API)

A B C D E F G H I K L M N O P Q R S T U V W Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

AbstractOMEXMLMetadata - Class in loci.formats.ome
AbstractOMEXMLMetadata() - Constructor for class loci.formats.ome.AbstractOMEXMLMetadata
add() - Method in class loci.formats.MetadataList: Add a empty primary array element.
add(int) - Method in class loci.formats.MetadataList: Add a empty primary array element.
add(int, CoreMetadata) - Method in class loci.formats.CoreMetadataList: Add a secondary array element to the specified primary array
add(int, T) - Method in class loci.formats.MetadataList: Add a secondary array element to the specified primary array
add(List<T>) - Method in class loci.formats.MetadataList: Add a new primary element containing the specified values.
add(T) - Method in class loci.formats.MetadataList: Add a new primary element containing a single specified value.
addClass(int, Class<? extends T>) - Method in class loci.formats.ClassList: Adds the given class, which must be assignable to the base class, to the list.
addClass(Class<? extends T>) - Method in class loci.formats.ClassList: Adds the given class, which must be assignable to the base class, to the list.
addFile(String) - Method in class loci.formats.internal.WellContainer
addGlobalMeta(String, boolean) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, byte) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, char) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, double) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, float) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, int) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, long) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, short) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMeta(String, Object) - Method in class loci.formats.FormatReader: Adds an entry to the global metadata table.
addGlobalMetaList(String, Object) - Method in class loci.formats.FormatReader: Add the given key/value pair to the global metadata hashtable.
addMeta(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader: Adds an entry to the specified Hashtable.
addMetadataOnly(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService: Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
addMetadataOnly(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
addMetadataOnly(OMEXMLMetadata, int, boolean) - Method in interface loci.formats.services.OMEXMLService: Insert a MetadataOnly element under the Image specified by 'index' in the given OME-XML metadata object.
addMetadataOnly(OMEXMLMetadata, int, boolean) - Method in class loci.formats.services.OMEXMLServiceImpl
addMetaList(String, Object, Hashtable<String, Object>) - Method in class loci.formats.FormatReader: Add the given key/value pair to the given hashtable.
addModuloAlong(OMEXMLMetadata, CoreMetadata, int) - Method in interface loci.formats.services.OMEXMLService: Adds ModuloAlong* annotations to the given OME-XML metadata object, using the given CoreMetadata object to determine modulo dimensions.
addModuloAlong(OMEXMLMetadata, CoreMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
addOption(String, String) - Method in class loci.formats.ClassList: Add a key/value pair to the list of options.
addSeriesMeta(String, boolean) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, byte) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, char) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, double) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, float) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, int) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, long) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, short) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMeta(String, Object) - Method in class loci.formats.FormatReader: Adds an entry to the metadata table for the current series.
addSeriesMetaList(String, Object) - Method in class loci.formats.FormatReader: Add the given key/value pair to the current series metadata hashtable.
ALL - Enum constant in enum loci.formats.in.MetadataLevel
ALL_DOMAINS - Static variable in class loci.formats.FormatTools: List of all supported domains.
append(List<Class<? extends T>>) - Method in class loci.formats.ClassList: Appends a list of classes which must be assignable to the base class
append(ClassList<T>) - Method in class loci.formats.ClassList: Appends a class list which must be assignable to the base class
asRetrieve(MetadataStore) - Method in interface loci.formats.services.OMEXMLService: Gets the given MetadataStore object as a MetadataRetrieve.
asRetrieve(MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
assertId(String, boolean, int) - Static method in class loci.formats.FormatTools: Asserts that the current file is either null, or not, according to the given flag.
asStore(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService: Gets the given MetadataRetrieve object as a MetadataStore.
asStore(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
ASTRONOMY_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies the astronomy domain.

B

BaseMetadata - Interface in loci.formats.meta
BIT - Static variable in class loci.formats.FormatTools: Identifies the BIT data type used to store pixel values.
bitsPerPixel - Variable in class loci.formats.CoreMetadata: Number of valid bits per pixel.
bitsPerSample - Variable in class loci.formats.codec.CodecOptions: Number of bits per channel.

C

callDeferredSetters(ReaderWrapper) - Method in class loci.formats.WrappedReader: A helper may not exist before initFile() is called.
CAN_GROUP - Static variable in class loci.formats.FormatTools
CAN_GROUP - Static variable in interface loci.formats.IFormatReader
canDoStacks() - Method in class loci.formats.FormatWriter
canDoStacks() - Method in interface loci.formats.IFormatWriter: Reports whether the writer can save multiple images to a single file.
canDoStacks() - Method in class loci.formats.ImageWriter
canDoStacks() - Method in class loci.formats.WriterWrapper
CANNOT_GROUP - Static variable in class loci.formats.FormatTools
CANNOT_GROUP - Static variable in interface loci.formats.IFormatReader
canUsePrecompressedTiles(IFormatReader, IFormatWriter, int, int) - Static method in class loci.formats.FormatTools: Compare the given reader and writer at the specified series and resolution to see if pre-compressed tiles can be transferred directly from the reader to the writer.
changeOutputFile(String) - Method in class loci.formats.FormatWriter
changeOutputFile(String) - Method in interface loci.formats.IFormatWriter: Switch the output file for the current dataset.
changeOutputFile(String) - Method in class loci.formats.ImageWriter
changeOutputFile(String) - Method in class loci.formats.WriterWrapper
CHANNEL - Static variable in class loci.formats.FormatTools: Identifies the Channel dimensional type, representing a generic channel dimension.
CHANNEL_NAME - Static variable in class loci.formats.FormatTools
CHANNEL_NUM - Static variable in class loci.formats.FormatTools
channels - Variable in class loci.formats.codec.CodecOptions: Number of channels.
checkBufferSize(IFormatReader, int) - Static method in class loci.formats.FormatTools
checkBufferSize(IFormatReader, int, int, int) - Static method in class loci.formats.FormatTools: Checks that the given buffer size is large enough to hold a w * h image as returned by the given reader.
checkParams(int, byte[], int, int, int, int) - Method in class loci.formats.FormatWriter: Ensure that the arguments that are being passed to saveBytes(...) are valid.
checkPlaneNumber(IFormatReader, int) - Static method in class loci.formats.FormatTools: Checks that the given plane number is valid for the given reader.
checkPlaneParameters(IFormatReader, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools: Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given reader.
checkSuffix(String, String) - Static method in class loci.formats.FormatHandler: Performs suffix matching for the given filename.
checkSuffix(String, String[]) - Static method in class loci.formats.FormatHandler: Performs suffix matching for the given filename.
checkTileSize(IFormatReader, int, int, int, int) - Static method in class loci.formats.FormatTools: Checks that the given tile size is valid for the given reader.
ClassList<T> - Class in loci.formats: ClassList is a list of classes for use with ImageReader or ImageWriter, parsed from a configuration file such as readers.txt or writers.txt.
ClassList(Class<T>) - Constructor for class loci.formats.ClassList: Constructs a list of classes, initially empty.
ClassList(String, Class<T>) - Constructor for class loci.formats.ClassList: Constructs a list of classes from the given configuration file.
ClassList(String, Class<T>, Class<?>) - Constructor for class loci.formats.ClassList: Constructs a list of classes from the given configuration file.
clear() - Method in class loci.formats.MetadataList: Clear the array.
clear(int) - Method in class loci.formats.MetadataList: Clear the specified primary array element.
clone() - Method in class loci.formats.CoreMetadata
clone(IFormatReader, int) - Method in class loci.formats.CoreMetadata
close() - Method in class loci.formats.FormatReader
close() - Method in class loci.formats.FormatWriter
close() - Method in class loci.formats.ImageReader
close() - Method in class loci.formats.ImageWriter
close() - Method in class loci.formats.ReaderWrapper
close() - Method in class loci.formats.WrappedReader
close() - Method in class loci.formats.WriterWrapper
close(boolean) - Method in class loci.formats.DelegateReader
close(boolean) - Method in class loci.formats.FormatReader
close(boolean) - Method in interface loci.formats.IFormatReader: Closes the currently open file.
close(boolean) - Method in class loci.formats.ImageReader
close(boolean) - Method in class loci.formats.ReaderWrapper
close(boolean) - Method in class loci.formats.SubResolutionFormatReader
close(boolean) - Method in class loci.formats.WrappedReader
cm - Variable in class loci.formats.FormatWriter: Default color model.
Codec - Interface in loci.formats.codec: This class is an interface for any kind of compression or decompression.
CodecOptions - Class in loci.formats.codec: Options for compressing and decompressing data.
CodecOptions() - Constructor for class loci.formats.codec.CodecOptions: Construct a new CodecOptions.
CodecOptions(CodecOptions) - Constructor for class loci.formats.codec.CodecOptions: Construct a new CodecOptions using the given CodecOptions.
colorModel - Variable in class loci.formats.codec.CodecOptions: Color model to use when constructing an image (WRITE).
compareTo(WellContainer) - Method in class loci.formats.internal.WellContainer
compress(byte[][], CodecOptions) - Method in interface loci.formats.codec.Codec: Compresses a block of data.
compress(byte[], CodecOptions) - Method in interface loci.formats.codec.Codec: Compresses a block of data.
compression - Variable in class loci.formats.FormatWriter: Current compression type.
COMPRESSION_SUFFIXES - Static variable in class loci.formats.FormatHandler: Suffixes for supported compression types.
compressionTypes - Variable in class loci.formats.FormatWriter: Available compression types.
convert(String, String) - Static method in class loci.formats.FormatTools: Convenience method for converting the specified input file to the specified output file.
convert(IFormatReader, IFormatWriter, String) - Static method in class loci.formats.FormatTools: Convenience method for writing all of the images and metadata obtained from the specified IFormatReader into the specified IFormatWriter.
convertMetadata(String, MetadataStore) - Method in interface loci.formats.services.OMEXMLService: Converts information from an OME-XML string (source) into a metadata store (destination).
convertMetadata(String, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
convertMetadata(MetadataRetrieve, MetadataStore) - Method in interface loci.formats.services.OMEXMLService: Copies information from a metadata retrieval object (source) into a metadata store (destination).
convertMetadata(MetadataRetrieve, MetadataStore) - Method in class loci.formats.services.OMEXMLServiceImpl
convertMetadata(MetadataRetrieve, MetadataStore) - Static method in class loci.formats.meta.MetadataConverter: Deprecated.

Copies information from a metadata retrieval object (source) into a metadata store (destination).
core - Variable in class loci.formats.FormatReader: Core metadata values.
core - Variable in class loci.formats.SubResolutionFormatReader: List of CoreMetadata objects for each series and resolution.
coreIndex - Variable in class loci.formats.FormatReader: The number of the current series.
coreIndexToSeries(int) - Method in class loci.formats.FormatReader
coreIndexToSeries(int) - Method in interface loci.formats.IFormatReader: Deprecated.
This method is no longer required for sub-resolution support.
coreIndexToSeries(int) - Method in class loci.formats.ImageReader
coreIndexToSeries(int) - Method in class loci.formats.ReaderWrapper
coreIndexToSeries(int) - Method in class loci.formats.SubResolutionFormatReader
coreIndexToSeries(int) - Method in class loci.formats.WrappedReader
CoreMetadata - Class in loci.formats: Encompasses core metadata values.
CoreMetadata() - Constructor for class loci.formats.CoreMetadata
CoreMetadata(CoreMetadata) - Constructor for class loci.formats.CoreMetadata
CoreMetadata(IFormatReader, int) - Constructor for class loci.formats.CoreMetadata
CoreMetadataList - Class in loci.formats
CoreMetadataList() - Constructor for class loci.formats.CoreMetadataList
CoreMetadataList(int) - Constructor for class loci.formats.CoreMetadataList: Construct a list containing a specified number of primary elements.
CoreMetadataList(int[]) - Constructor for class loci.formats.CoreMetadataList: Construct a list containing a specified number of primary and secondary elements.
CoreMetadataList(int, int) - Constructor for class loci.formats.CoreMetadataList: Construct a list containing a specified number of primary elements and a fixed number of secondary elements.
CoreMetadataList(List<CoreMetadata>) - Constructor for class loci.formats.CoreMetadataList
CoreMetadataList(CoreMetadataList) - Constructor for class loci.formats.CoreMetadataList
createAngle(Double, Unit<Angle>) - Static method in class loci.formats.FormatTools
createAngle(Integer, Unit<Angle>) - Static method in class loci.formats.FormatTools
createAngle(T, Unit<Angle>) - Static method in class loci.formats.FormatTools
createElectricPotential(Double, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
createElectricPotential(Integer, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
createElectricPotential(T, Unit<ElectricPotential>) - Static method in class loci.formats.FormatTools
createFrequency(Double, Unit<Frequency>) - Static method in class loci.formats.FormatTools
createFrequency(Integer, Unit<Frequency>) - Static method in class loci.formats.FormatTools
createFrequency(T, Unit<Frequency>) - Static method in class loci.formats.FormatTools
createLength(Double, Unit<Length>) - Static method in class loci.formats.FormatTools
createLength(Integer, Unit<Length>) - Static method in class loci.formats.FormatTools
createLength(T, Unit<Length>) - Static method in class loci.formats.FormatTools
createLSID(String, int...) - Static method in class loci.formats.MetadataTools: Constructs an LSID, given the object type and indices.
createOMEXMLMetadata() - Static method in class loci.formats.MetadataTools: Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package.
createOMEXMLMetadata() - Method in interface loci.formats.services.OMEXMLService: Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package.
createOMEXMLMetadata() - Method in class loci.formats.services.OMEXMLServiceImpl
createOMEXMLMetadata(String) - Method in interface loci.formats.services.OMEXMLService: Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package, wrapping a DOM representation of the given OME-XML string.
createOMEXMLMetadata(String) - Method in class loci.formats.services.OMEXMLServiceImpl
createOMEXMLMetadata(String, String) - Method in interface loci.formats.services.OMEXMLService: Creates an OME-XML metadata object using reflection, to avoid direct dependencies on the optional loci.formats.ome package, wrapping a DOM representation of the given OME-XML string.
createOMEXMLMetadata(String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
createOMEXMLRoot(String) - Method in interface loci.formats.services.OMEXMLService: Constructs an OME root node.
createOMEXMLRoot(String) - Method in class loci.formats.services.OMEXMLServiceImpl
createOutputStream() - Method in class loci.formats.FormatWriter: Create an output stream for the current file path.
createPower(Double, Unit<Power>) - Static method in class loci.formats.FormatTools
createPower(Integer, Unit<Power>) - Static method in class loci.formats.FormatTools
createPower(T, Unit<Power>) - Static method in class loci.formats.FormatTools
createPressure(Double, Unit<Pressure>) - Static method in class loci.formats.FormatTools
createPressure(Integer, Unit<Pressure>) - Static method in class loci.formats.FormatTools
createPressure(T, Unit<Pressure>) - Static method in class loci.formats.FormatTools
createTemperature(Double, Unit<Temperature>) - Static method in class loci.formats.FormatTools
createTemperature(Integer, Unit<Temperature>) - Static method in class loci.formats.FormatTools
createTemperature(T, Unit<Temperature>) - Static method in class loci.formats.FormatTools
createTime(Double, Unit<Time>) - Static method in class loci.formats.FormatTools
createTime(Integer, Unit<Time>) - Static method in class loci.formats.FormatTools
createTime(T, Unit<Time>) - Static method in class loci.formats.FormatTools
CREATOR - Static variable in class loci.formats.FormatTools: Value to use when setting creator/software fields in exported files.
current - Variable in class loci.formats.ImageWriter: Current form index.
currentId - Variable in class loci.formats.FormatHandler: Name of current file.
currentId - Variable in class loci.formats.ImageWriter: Name of current file.

D

data - Variable in class loci.formats.MetadataList
datasetDescription - Variable in class loci.formats.FormatReader: Short description of the structure of the dataset.
DATE - Static variable in class loci.formats.FormatTools: Date on which this release was built.
decompress(byte[]) - Method in interface loci.formats.codec.Codec: Decompresses a block of data.
decompress(byte[][]) - Method in interface loci.formats.codec.Codec: Decompresses a block of data.
decompress(byte[][], CodecOptions) - Method in interface loci.formats.codec.Codec: Decompresses a block of data.
decompress(byte[], CodecOptions) - Method in interface loci.formats.codec.Codec: Decompresses a block of data.
decompress(RandomAccessInputStream, CodecOptions) - Method in interface loci.formats.codec.Codec: Decompresses data from the given RandomAccessInputStream.
DefaultMetadataOptions - Class in loci.formats.in: Default implementation of MetadataOptions.
DefaultMetadataOptions() - Constructor for class loci.formats.in.DefaultMetadataOptions: Construct a new DefaultMetadataOptions.
DefaultMetadataOptions(MetadataLevel) - Constructor for class loci.formats.in.DefaultMetadataOptions: Construct a new DefaultMetadataOptions.
defaultMinMax(int) - Static method in class loci.formats.FormatTools: Get the default range for the specified pixel type.
DelegateReader - Class in loci.formats: DelegateReader is a file format reader that selects which reader to use for a format if there are two readers which handle the same format.
DelegateReader(String, String) - Constructor for class loci.formats.DelegateReader: Constructs a new delegate reader.
DelegateReader(String, String[]) - Constructor for class loci.formats.DelegateReader: Constructs a new delegate reader.
dimensionOrder - Variable in class loci.formats.CoreMetadata: Order in which dimensions are stored.
disableChromaSubsampling - Variable in class loci.formats.codec.CodecOptions: Whether or not to use chroma subsampling.
domains - Variable in class loci.formats.FormatReader: List of domains in which this format is used.
DOUBLE - Static variable in class loci.formats.FormatTools: Identifies the DOUBLE data type used to store pixel values.
DummyMetadata - Class in loci.formats.meta
DummyMetadata() - Constructor for class loci.formats.meta.DummyMetadata
dumpXML() - Method in class loci.formats.ome.OMEPyramidStore
duplicate(Class<? extends IFormatReader>) - Method in class loci.formats.ReaderWrapper: Performs a deep copy of the reader, including nested wrapped readers.
duplicate(Class<? extends IFormatWriter>) - Method in class loci.formats.WriterWrapper: Performs a deep copy of the writer, including nested wrapped writers.
DynamicMetadataOptions - Class in loci.formats.in: Configuration object for readers and writers.
DynamicMetadataOptions() - Constructor for class loci.formats.in.DynamicMetadataOptions: Creates an options object with metadata level set to DynamicMetadataOptions.METADATA_LEVEL_DEFAULT and file validation set to DynamicMetadataOptions.READER_VALIDATE_DEFAULT.
DynamicMetadataOptions(MetadataLevel) - Constructor for class loci.formats.in.DynamicMetadataOptions: Creates an options object with metadata level set to the specified value and file validation set to DynamicMetadataOptions.READER_VALIDATE_DEFAULT

E

EM_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies the electron microscopy domain.
end - Variable in class loci.formats.Modulo
equalReaders(IFormatReader, IFormatReader) - Static method in class loci.formats.FormatTools: Check if the two given readers are equal.
equals(Node, Node) - Method in class loci.formats.services.OMEXMLServiceImpl: Compares two Elements for equality.

F

falseColor - Variable in class loci.formats.CoreMetadata: Indicates whether or not we can ignore the color map (if present).
fileGroupOption(String) - Method in class loci.formats.FormatReader
fileGroupOption(String) - Method in interface loci.formats.IFormatReader: Returns an indication of whether the files in a multi-file dataset can be handled individually.
fileGroupOption(String) - Method in class loci.formats.ImageReader
fileGroupOption(String) - Method in class loci.formats.ReaderWrapper
FileInfo - Class in loci.formats: Encompasses basic metadata about a file.
FileInfo() - Constructor for class loci.formats.FileInfo
filename - Variable in class loci.formats.FileInfo: Absolute path to this file.
fillColor - Variable in class loci.formats.FormatReader: Fill value for undefined pixels.
fillMetadataStore(MetadataStore, int, int, int, int) - Method in class loci.formats.internal.WellContainer
fillMetadataStore(MetadataStore, int, int, int, int, int) - Method in class loci.formats.internal.WellContainer
filterMetadata - Variable in class loci.formats.FormatReader: Whether or not to filter out invalid metadata.
FilterMetadata - Class in loci.formats.meta
FilterMetadata(MetadataStore, boolean) - Constructor for class loci.formats.meta.FilterMetadata
flattenedIndex(int, int) - Method in class loci.formats.CoreMetadataList
flattenedIndexes(int) - Method in class loci.formats.CoreMetadataList
flattenedResolutions - Variable in class loci.formats.FormatReader: Whether or not resolutions are flattened.
flattenedSize() - Method in class loci.formats.CoreMetadataList: Get flattened size (all resolutions in all series)
flattenHashtables() - Method in class loci.formats.FormatReader: Call FormatReader.updateMetadataLists(Hashtable) on all metadata hashtables.
flattenHashtables() - Method in class loci.formats.SubResolutionFormatReader: Call FormatReader.updateMetadataLists(Hashtable) on all metadata hashtables.
FLIM_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies the fluorescence-lifetime domain.
FLOAT - Static variable in class loci.formats.FormatTools: Identifies the FLOAT data type used to store pixel values.
format - Variable in class loci.formats.FormatHandler: Name of this file format.
FormatException - Exception Class in loci.formats: FormatException is the exception thrown when something goes wrong performing a file format operation.
FormatException() - Constructor for exception class loci.formats.FormatException
FormatException(String) - Constructor for exception class loci.formats.FormatException
FormatException(String, Throwable) - Constructor for exception class loci.formats.FormatException
FormatException(Throwable) - Constructor for exception class loci.formats.FormatException
FormatHandler - Class in loci.formats: Abstract superclass of all biological file format readers and writers.
FormatHandler(String, String) - Constructor for class loci.formats.FormatHandler: Constructs a format handler with the given name and default suffix.
FormatHandler(String, String[]) - Constructor for class loci.formats.FormatHandler: Constructs a format handler with the given name and default suffixes.
FormatReader - Class in loci.formats: Abstract superclass of all biological file format readers.
FormatReader(String, String) - Constructor for class loci.formats.FormatReader: Constructs a format reader with the given name and default suffix.
FormatReader(String, String[]) - Constructor for class loci.formats.FormatReader: Constructs a format reader with the given name and default suffixes.
FormatTools - Class in loci.formats: A utility class for format reader and writer implementations.
FormatWriter - Class in loci.formats: Abstract superclass of all biological file format writers.
FormatWriter(String, String) - Constructor for class loci.formats.FormatWriter: Constructs a format writer with the given name and default suffix.
FormatWriter(String, String[]) - Constructor for class loci.formats.FormatWriter: Constructs a format writer with the given name and default suffixes.
fps - Variable in class loci.formats.FormatWriter: Frame rate to use when writing in frames per second, if applicable.
FREQUENCY - Static variable in class loci.formats.FormatTools: Identifies the Frequency dimensional type, representing a dimension consisting of frequencies.

G

GEL_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies the gel and blot imaging domain.
get(int, int) - Method in class loci.formats.MetadataList: Get the array element for the specified indexes.
get(String) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name.
get(String, String) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name.
get16BitLookupTable() - Method in class loci.formats.DelegateReader
get16BitLookupTable() - Method in class loci.formats.FormatReader
get16BitLookupTable() - Method in interface loci.formats.IFormatReader: Gets the 16-bit color lookup table associated with the most recently opened image.
get16BitLookupTable() - Method in class loci.formats.ImageReader
get16BitLookupTable() - Method in class loci.formats.ReaderWrapper
get16BitLookupTable() - Method in class loci.formats.WrappedReader
get8BitLookupTable() - Method in class loci.formats.DelegateReader
get8BitLookupTable() - Method in class loci.formats.FormatReader
get8BitLookupTable() - Method in interface loci.formats.IFormatReader: Gets the 8-bit color lookup table associated with the most recently opened image.
get8BitLookupTable() - Method in class loci.formats.ImageReader
get8BitLookupTable() - Method in class loci.formats.ReaderWrapper
get8BitLookupTable() - Method in class loci.formats.WrappedReader
getAcquisitionMode(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getAcquisitionMode(String).
getAcquisitionMode(String) - Static method in class loci.formats.MetadataTools: Retrieves an AcquisitionMode enumeration value for the given String.
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.FormatReader
getAdvancedSeriesUsedFiles(boolean) - Method in interface loci.formats.IFormatReader: Returns an array of FileInfo objects representing the files needed to open the current series.
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.ImageReader
getAdvancedSeriesUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
getAdvancedUsedFiles(boolean) - Method in class loci.formats.FormatReader
getAdvancedUsedFiles(boolean) - Method in interface loci.formats.IFormatReader: Returns an array of FileInfo objects representing the files needed to open this dataset.
getAdvancedUsedFiles(boolean) - Method in class loci.formats.ImageReader
getAdvancedUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
getAllFiles() - Method in class loci.formats.internal.WellContainer
getArcType(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getArcType(String).
getArcType(String) - Static method in class loci.formats.MetadataTools: Retrieves an ArcType enumeration value for the given String.
getAvailableOptions() - Method in class loci.formats.FormatReader: Returns the list of available metadata options.
getBinning(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getBinning(String).
getBinning(String) - Static method in class loci.formats.MetadataTools: Retrieves an Binning enumeration value for the given String.
getBitsPerPixel() - Method in class loci.formats.FormatReader
getBitsPerPixel() - Method in interface loci.formats.IFormatReader: Gets the number of valid bits per pixel.
getBitsPerPixel() - Method in class loci.formats.ImageReader
getBitsPerPixel() - Method in class loci.formats.ReaderWrapper
getBitsPerPixel() - Method in class loci.formats.WrappedReader
getBoolean(String) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a Boolean.
getBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a Boolean.
getBytesPerPixel(int) - Static method in class loci.formats.FormatTools: Retrieves how many bytes per pixel the current plane or section has.
getBytesPerPixel(String) - Static method in class loci.formats.FormatTools: Retrieves the number of bytes per pixel in the current plane.
getClass(String) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a class.
getClass(String, Class<?>) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a class.
getClasses() - Method in class loci.formats.ClassList: Gets the list of classes as an array.
getCodec() - Method in interface loci.formats.ICompressedTileWriter
getCodec() - Method in class loci.formats.ImageWriter
getCodec() - Method in class loci.formats.WriterWrapper
getCodecOptions() - Method in class loci.formats.FormatWriter
getCodecOptions() - Method in interface loci.formats.ICompressedTileWriter
getCodecOptions() - Method in class loci.formats.ImageWriter
getCodecOptions() - Method in class loci.formats.WriterWrapper
getColorModel() - Method in class loci.formats.FormatWriter
getColorModel() - Method in interface loci.formats.IFormatWriter: Gets the color model.
getColorModel() - Method in class loci.formats.ImageWriter
getColorModel() - Method in class loci.formats.WriterWrapper
getColumnIndex() - Method in class loci.formats.internal.WellContainer
getCompression() - Method in class loci.formats.FormatWriter
getCompression() - Method in interface loci.formats.IFormatWriter: Gets the current compression type.
getCompression() - Method in class loci.formats.ImageWriter
getCompression() - Method in class loci.formats.WriterWrapper
getCompression(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getCompression(String).
getCompression(String) - Static method in class loci.formats.MetadataTools: Retrieves an Compression enumeration value for the given String.
getCompressionTypes() - Method in class loci.formats.FormatWriter
getCompressionTypes() - Method in interface loci.formats.IFormatWriter: Gets the available compression types.
getCompressionTypes() - Method in class loci.formats.ImageWriter
getCompressionTypes() - Method in class loci.formats.WriterWrapper
getContrastMethod(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getContrastMethod(String).
getContrastMethod(String) - Static method in class loci.formats.MetadataTools: Retrieves an ContrastMethod enumeration value for the given String.
getCoreIndex() - Method in class loci.formats.FormatReader
getCoreIndex() - Method in interface loci.formats.IFormatReader: Deprecated.
This method is no longer required for sub-resolution support.
getCoreIndex() - Method in class loci.formats.ImageReader
getCoreIndex() - Method in class loci.formats.ReaderWrapper
getCoreIndex() - Method in class loci.formats.SubResolutionFormatReader
getCoreIndex() - Method in class loci.formats.WrappedReader
getCoreMetadataList() - Method in class loci.formats.FormatReader
getCoreMetadataList() - Method in interface loci.formats.IFormatReader: Deprecated.
Reader internals should not be accessed by reader users
getCoreMetadataList() - Method in class loci.formats.ImageReader
getCoreMetadataList() - Method in class loci.formats.ReaderWrapper
getCoreMetadataList() - Method in class loci.formats.SubResolutionFormatReader
getCoreMetadataList() - Method in class loci.formats.WrappedReader
getCorrection(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getCorrection(String).
getCorrection(String) - Static method in class loci.formats.MetadataTools: Retrieves an Correction enumeration value for the given String.
getCurrentCore() - Method in class loci.formats.FormatReader: Get the CoreMetadata corresponding to the current series and resolution
getCurrentCore() - Method in class loci.formats.SubResolutionFormatReader: Get the CoreMetadata corresponding to the current series and resolution
getCurrentFile() - Method in class loci.formats.FormatReader
getCurrentFile() - Method in interface loci.formats.IFormatReader: Returns the current file.
getCurrentFile() - Method in class loci.formats.ImageReader
getCurrentFile() - Method in class loci.formats.ReaderWrapper
getCutIn(Double) - Static method in class loci.formats.FormatTools
getCutOut(Double) - Static method in class loci.formats.FormatTools
getDatasetStructureDescription() - Method in class loci.formats.FormatReader
getDatasetStructureDescription() - Method in interface loci.formats.IFormatReader: Returns a short description of the dataset structure.
getDatasetStructureDescription() - Method in class loci.formats.ImageReader
getDatasetStructureDescription() - Method in class loci.formats.ReaderWrapper
getDatasetStructureDescription() - Method in class loci.formats.WrappedReader
getDefaultOptions() - Static method in class loci.formats.codec.CodecOptions: Return CodecOptions with reasonable default values.
getDefaultReaderClasses() - Static method in class loci.formats.ImageReader
getDefaultWriterClasses() - Static method in class loci.formats.ImageWriter
getDetectorType(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getDetectorType(String).
getDetectorType(String) - Static method in class loci.formats.MetadataTools: Retrieves an DetectorType enumeration value for the given String.
getDimensionOrder() - Method in class loci.formats.FormatReader
getDimensionOrder() - Method in interface loci.formats.IFormatReader: Gets a five-character string representing the dimension order in which planes will be returned.
getDimensionOrder() - Method in class loci.formats.ImageReader
getDimensionOrder() - Method in class loci.formats.ReaderWrapper
getDimensionOrder() - Method in class loci.formats.WrappedReader
getDimensionOrder(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getDimensionOrder(String).
getDimensionOrder(String) - Static method in class loci.formats.MetadataTools: Retrieves an DimensionOrder enumeration value for the given String.
getDomains() - Method in class loci.formats.FormatReader
getDomains() - Method in interface loci.formats.IFormatReader: Returns the list of domains represented by the current file.
getDomains() - Method in class loci.formats.ImageReader
getDomains() - Method in class loci.formats.ReaderWrapper
getDomains() - Method in class loci.formats.WrappedReader
getDouble(String) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a Double.
getDouble(String, Double) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a Double.
getEffectiveSizeC() - Method in class loci.formats.FormatReader
getEffectiveSizeC() - Method in interface loci.formats.IFormatReader: Gets the effective size of the C dimension, guaranteeing that getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount() regardless of the result of isRGB().
getEffectiveSizeC() - Method in class loci.formats.ImageReader
getEffectiveSizeC() - Method in class loci.formats.ReaderWrapper
getEffectiveSizeC() - Method in class loci.formats.WrappedReader
getEmissionWavelength(Double) - Static method in class loci.formats.FormatTools
getEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as an enumerated type.
getExcitationWavelength(Double) - Static method in class loci.formats.FormatTools
getExperimentType(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getExperimentType(String).
getExperimentType(String) - Static method in class loci.formats.MetadataTools: Retrieves an ExperimentType enumeration value for the given String.
getFieldCount() - Method in class loci.formats.internal.WellContainer
getFilamentType(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getFilamentType(String).
getFilamentType(String) - Static method in class loci.formats.MetadataTools: Retrieves an FilamentType enumeration value for the given String.
getFile(int, int) - Method in class loci.formats.internal.WellContainer
getFile(String) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a file object.
getFile(String, File) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a file object.
getFilename(int, int, IFormatReader, String) - Static method in class loci.formats.FormatTools
getFilename(int, int, IFormatReader, String, boolean) - Static method in class loci.formats.FormatTools
getFilename(int, int, MetadataRetrieve, String, boolean) - Static method in class loci.formats.FormatTools
getFilenames(String, IFormatReader) - Static method in class loci.formats.FormatTools
getFiles(int) - Method in class loci.formats.internal.WellContainer
getFillColor() - Method in class loci.formats.FormatReader
getFillColor() - Method in interface loci.formats.IFormatReader: Return the fill value for undefined pixels.
getFillColor() - Method in class loci.formats.ImageReader
getFillColor() - Method in class loci.formats.ReaderWrapper
getFillRule(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getFillRule(String).
getFillRule(String) - Static method in class loci.formats.MetadataTools: Retrieves an FillRule enumeration value for the given String.
getFilterType(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getFilterType(String).
getFilterType(String) - Static method in class loci.formats.MetadataTools: Retrieves an FilterType enumeration value for the given String.
getFlattenedList() - Method in class loci.formats.CoreMetadataList
getFloat(String) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a Float.
getFloat(String, Float) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a Float.
getFontFamily(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getFontFamily(String).
getFontFamily(String) - Static method in class loci.formats.MetadataTools: Retrieves an FontFamily enumeration value for the given String.
getFontSize(Integer) - Static method in class loci.formats.FormatTools
getFontStyle(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getFontStyle(String).
getFontStyle(String) - Static method in class loci.formats.MetadataTools: Retrieves an FontStyle enumeration value for the given String.
getFormat() - Method in class loci.formats.FormatHandler
getFormat() - Method in interface loci.formats.IFormatHandler: Gets the name of this file format.
getFormat() - Method in class loci.formats.ImageReader
getFormat() - Method in class loci.formats.ImageWriter
getFormat() - Method in class loci.formats.ReaderWrapper
getFormat() - Method in class loci.formats.WriterWrapper
getFormat(String) - Method in class loci.formats.ImageReader: Gets a string describing the file format for the given file.
getFormat(String) - Method in class loci.formats.ImageWriter: Gets a string describing the file format for the given file.
getFramesPerSecond() - Method in class loci.formats.FormatWriter
getFramesPerSecond() - Method in interface loci.formats.IFormatWriter: Gets the frames per second to use when writing.
getFramesPerSecond() - Method in class loci.formats.ImageWriter
getFramesPerSecond() - Method in class loci.formats.WriterWrapper
getGlobalMeta(String) - Method in class loci.formats.FormatReader: Gets a value from the global metadata table.
getGlobalMetadata() - Method in class loci.formats.FormatReader
getGlobalMetadata() - Method in interface loci.formats.IFormatReader: Obtains the hashtable containing the metadata field/value pairs from the current file.
getGlobalMetadata() - Method in class loci.formats.ImageReader
getGlobalMetadata() - Method in class loci.formats.ReaderWrapper
getGlobalMetadata() - Method in class loci.formats.WrappedReader
getHelper() - Method in class loci.formats.WrappedReader: Get the helper class that reads images
getIlluminationType(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getIlluminationType(String).
getIlluminationType(String) - Static method in class loci.formats.MetadataTools: Retrieves an IlluminationType enumeration value for the given String.
getImageCount() - Method in class loci.formats.FormatReader
getImageCount() - Method in interface loci.formats.IFormatReader: Determines the number of image planes in the current file.
getImageCount() - Method in class loci.formats.ImageReader
getImageCount() - Method in class loci.formats.ReaderWrapper
getImageCount() - Method in class loci.formats.WrappedReader
getImagesPerFile(String, IFormatReader) - Static method in class loci.formats.FormatTools
getImmersion(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getImmersion(String).
getImmersion(String) - Static method in class loci.formats.MetadataTools: Retrieves an Immersion enumeration value for the given String.
getIndex(int, int, int) - Method in class loci.formats.FormatReader
getIndex(int, int, int) - Method in interface loci.formats.IFormatReader: Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
getIndex(int, int, int) - Method in class loci.formats.ImageReader
getIndex(int, int, int) - Method in class loci.formats.ReaderWrapper
getIndex(int, int, int) - Method in class loci.formats.WrappedReader
getIndex(int, int, int, int, int, int) - Method in class loci.formats.FormatReader
getIndex(int, int, int, int, int, int) - Method in interface loci.formats.IFormatReader: Gets the rasterized index corresponding to the given Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes).
getIndex(int, int, int, int, int, int) - Method in class loci.formats.ImageReader
getIndex(int, int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
getIndex(String, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools: Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
getIndex(String, int, int, int, int, int, int, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools: Gets the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC, ModuloT coordinates (effective sizes).
getIndex(IFormatReader, int, int, int) - Static method in class loci.formats.FormatTools: Gets the rasterized index corresponding to the given Z, C and T coordinates (real sizes).
getIndex(IFormatReader, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools: Gets the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC and ModuloT coordinates (effective sizes).
getInteger(String) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as an Integer.
getInteger(String, Integer) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as an Integer.
getKey() - Method in class loci.formats.meta.OriginalMetadataAnnotation
getLaserMedium(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getLaserMedium(String).
getLaserMedium(String) - Static method in class loci.formats.MetadataTools: Retrieves an LaserMedium enumeration value for the given String.
getLaserType(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getLaserType(String).
getLaserType(String) - Static method in class loci.formats.MetadataTools: Retrieves an LaserType enumeration value for the given String.
getLatestVersion() - Method in interface loci.formats.services.OMEXMLService: Retrieves the latest supported version of the OME-XML schema.
getLatestVersion() - Method in class loci.formats.services.OMEXMLServiceImpl
getLong(String) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a Long.
getLong(String, Long) - Method in class loci.formats.in.DynamicMetadataOptions: Get the value of property name as a Long.
getMarker(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getMarker(String).
getMarker(String) - Static method in class loci.formats.MetadataTools: Retrieves an Marker enumeration value for the given String.
getMaxFieldCount(Integer) - Static method in class loci.formats.FormatTools
getMedium(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getMedium(String).
getMedium(String) - Static method in class loci.formats.MetadataTools: Retrieves an Medium enumeration value for the given String.
getMetadataLevel() - Method in class loci.formats.in.DefaultMetadataOptions
getMetadataLevel() - Method in class loci.formats.in.DynamicMetadataOptions
getMetadataLevel() - Method in interface loci.formats.in.MetadataOptions: Get the configured metadata level.
getMetadataOptions() - Method in class loci.formats.DelegateReader
getMetadataOptions() - Method in class loci.formats.FormatHandler
getMetadataOptions() - Method in class loci.formats.ImageReader
getMetadataOptions() - Method in class loci.formats.ImageWriter
getMetadataOptions() - Method in interface loci.formats.IMetadataConfigurable
getMetadataOptions() - Method in class loci.formats.ReaderWrapper
getMetadataOptions() - Method in class loci.formats.WriterWrapper
getMetadataOptionsFile(String) - Static method in class loci.formats.in.DynamicMetadataOptions
getMetadataRetrieve() - Method in class loci.formats.FormatWriter
getMetadataRetrieve() - Method in interface loci.formats.IFormatWriter: Retrieves the current metadata retrieval object for this writer.
getMetadataRetrieve() - Method in class loci.formats.ImageWriter
getMetadataRetrieve() - Method in class loci.formats.WriterWrapper
getMetadataStore() - Method in class loci.formats.FormatReader
getMetadataStore() - Method in interface loci.formats.IFormatReader: Retrieves the current metadata store for this reader.
getMetadataStore() - Method in class loci.formats.ImageReader
getMetadataStore() - Method in class loci.formats.ReaderWrapper
getMetadataStoreRoot() - Method in class loci.formats.FormatReader
getMetadataStoreRoot() - Method in interface loci.formats.IFormatReader: Retrieves the current metadata store's root object.
getMetadataStoreRoot() - Method in class loci.formats.ImageReader
getMetadataStoreRoot() - Method in class loci.formats.ReaderWrapper
getMetadataStoreRoot() - Method in class loci.formats.WrappedReader
getMetadataValue(String) - Method in class loci.formats.FormatReader
getMetadataValue(String) - Method in interface loci.formats.IFormatReader: Obtains the specified metadata field's value for the current file.
getMetadataValue(String) - Method in class loci.formats.ImageReader
getMetadataValue(String) - Method in class loci.formats.ReaderWrapper
getMetadataValue(String) - Method in class loci.formats.WrappedReader
getMicrobeamManipulationType(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getMicrobeamManipulationType(String).
getMicrobeamManipulationType(String) - Static method in class loci.formats.MetadataTools: Retrieves an MicrobeamManipulationType enumeration value for the given String.
getMicroscopeType(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getMicroscopeType(String).
getMicroscopeType(String) - Static method in class loci.formats.MetadataTools: Retrieves an MicroscopeType enumeration value for the given String.
getModuloAlongC(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService: Retrieve the ModuloAlongC annotation in the given Image in the given OME-XML metadata object.
getModuloAlongC(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
getModuloAlongT(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService: Retrieve the ModuloAlongT annotation in the given Image in the given OME-XML metadata object.
getModuloAlongT(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
getModuloAlongZ(OMEXMLMetadata, int) - Method in interface loci.formats.services.OMEXMLService: Retrieve the ModuloAlongZ annotation in the given Image in the given OME-XML metadata object.
getModuloAlongZ(OMEXMLMetadata, int) - Method in class loci.formats.services.OMEXMLServiceImpl
getModuloC() - Method in class loci.formats.FormatReader
getModuloC() - Method in interface loci.formats.IFormatReader
getModuloC() - Method in class loci.formats.ImageReader
getModuloC() - Method in class loci.formats.ReaderWrapper
getModuloC() - Method in class loci.formats.WrappedReader
getModuloT() - Method in class loci.formats.FormatReader
getModuloT() - Method in interface loci.formats.IFormatReader
getModuloT() - Method in class loci.formats.ImageReader
getModuloT() - Method in class loci.formats.ReaderWrapper
getModuloT() - Method in class loci.formats.WrappedReader
getModuloZ() - Method in class loci.formats.FormatReader
getModuloZ() - Method in interface loci.formats.IFormatReader
getModuloZ() - Method in class loci.formats.ImageReader
getModuloZ() - Method in class loci.formats.ReaderWrapper
getModuloZ() - Method in class loci.formats.WrappedReader
getNamingConvention(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getNamingConvention(String).
getNamingConvention(String) - Static method in class loci.formats.MetadataTools: Retrieves an NamingConvention enumeration value for the given String.
getNativeDataType() - Method in class loci.formats.FormatHandler
getNativeDataType() - Method in interface loci.formats.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).
getNativeDataType() - Method in class loci.formats.ImageReader
getNativeDataType() - Method in class loci.formats.ImageWriter
getNativeDataType() - Method in class loci.formats.ReaderWrapper
getNativeDataType() - Method in class loci.formats.WrappedReader
getNativeDataType() - Method in class loci.formats.WriterWrapper
getOMEMetadata(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService: Returns a OMEXMLMetadata object with the same contents as the given MetadataRetrieve, converting it if necessary.
getOMEMetadata(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
getOMEXML(MetadataRetrieve) - Method in interface loci.formats.services.OMEXMLService: Extracts an OME-XML metadata string from the given metadata object, by converting to an OME-XML metadata object if necessary.
getOMEXML(MetadataRetrieve) - Method in class loci.formats.services.OMEXMLServiceImpl
getOMEXMLVersion(Object) - Method in interface loci.formats.services.OMEXMLService: Gets the schema version for the given OME-XML metadata or root object (e.g., "2007-06" or "2003-FC").
getOMEXMLVersion(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
getOptimalTileHeight() - Method in class loci.formats.DelegateReader
getOptimalTileHeight() - Method in class loci.formats.FormatReader
getOptimalTileHeight() - Method in interface loci.formats.IFormatReader: Returns the optimal sub-image height for use with openBytes.
getOptimalTileHeight() - Method in class loci.formats.ImageReader
getOptimalTileHeight() - Method in class loci.formats.ReaderWrapper
getOptimalTileHeight() - Method in class loci.formats.WrappedReader
getOptimalTileWidth() - Method in class loci.formats.DelegateReader
getOptimalTileWidth() - Method in class loci.formats.FormatReader
getOptimalTileWidth() - Method in interface loci.formats.IFormatReader: Returns the optimal sub-image width for use with openBytes.
getOptimalTileWidth() - Method in class loci.formats.ImageReader
getOptimalTileWidth() - Method in class loci.formats.ReaderWrapper
getOptimalTileWidth() - Method in class loci.formats.WrappedReader
getOptions() - Method in class loci.formats.ClassList: Gets the list of options as a map.
getOriginalMetadata(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService: Parse any OriginalMetadata annotations from the given OME-XML metadata object and store them in a Hashtable.
getOriginalMetadata(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
getPhysicalSize(Double, String) - Static method in class loci.formats.FormatTools
getPhysicalSizeX(Double) - Static method in class loci.formats.FormatTools: Formats the input value for the physical size in X into a length in microns
getPhysicalSizeX(Double, String) - Static method in class loci.formats.FormatTools: Formats the input value for the physical size in X into a length of the given unit.
getPhysicalSizeX(Double, Unit<Length>) - Static method in class loci.formats.FormatTools: Formats the input value for the physical size in X into a length of the given unit.
getPhysicalSizeY(Double) - Static method in class loci.formats.FormatTools: Formats the input value for the physical size in Y into a length in microns
getPhysicalSizeY(Double, String) - Static method in class loci.formats.FormatTools: Formats the input value for the physical size in Y into a length of the given unit.
getPhysicalSizeY(Double, Unit<Length>) - Static method in class loci.formats.FormatTools: Formats the input value for the physical size in Y into a length of the given unit.
getPhysicalSizeZ(Double) - Static method in class loci.formats.FormatTools: Formats the input value for the physical size in Z into a length in microns.
getPhysicalSizeZ(Double, String) - Static method in class loci.formats.FormatTools: Formats the input value for the physical size in Z into a length of the given unit.
getPhysicalSizeZ(Double, Unit<Length>) - Static method in class loci.formats.FormatTools: Formats the input value for the physical size in Z into a length of the given unit.
getPixelType() - Method in class loci.formats.FormatReader
getPixelType() - Method in interface loci.formats.IFormatReader: Gets the pixel type.
getPixelType() - Method in class loci.formats.ImageReader
getPixelType() - Method in class loci.formats.ReaderWrapper
getPixelType() - Method in class loci.formats.WrappedReader
getPixelType(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getPixelType(String).
getPixelType(String) - Static method in class loci.formats.MetadataTools: Retrieves an PixelType enumeration value for the given String.
getPixelTypes() - Method in class loci.formats.FormatWriter
getPixelTypes() - Method in interface loci.formats.IFormatWriter: Gets the supported pixel types.
getPixelTypes() - Method in class loci.formats.ImageWriter
getPixelTypes() - Method in class loci.formats.WriterWrapper
getPixelTypes(String) - Method in class loci.formats.FormatWriter
getPixelTypes(String) - Method in interface loci.formats.IFormatWriter: Gets the supported pixel types for the given codec.
getPixelTypes(String) - Method in class loci.formats.ImageWriter
getPixelTypes(String) - Method in class loci.formats.WriterWrapper
getPixelTypeString(int) - Static method in class loci.formats.FormatTools: Takes a pixel type value and gets a corresponding string representation.
getPlaneCount() - Method in class loci.formats.FormatWriter: Retrieve the total number of planes in the current series.
getPlaneCount(int) - Method in class loci.formats.FormatWriter: Retrieve the total number of planes in given series.
getPlaneSize(IFormatReader) - Static method in class loci.formats.FormatTools: Returns the size in bytes of a single plane.
getPlaneSize(IFormatReader, int, int) - Static method in class loci.formats.FormatTools: Returns the size in bytes of a w * h tile.
getPlateAcquisition() - Method in class loci.formats.internal.WellContainer
getPossibleDomains(String) - Method in class loci.formats.FormatReader
getPossibleDomains(String) - Method in interface loci.formats.IFormatReader: Returns a list of scientific domains in which this format is used.
getPossibleDomains(String) - Method in class loci.formats.ImageReader
getPossibleDomains(String) - Method in class loci.formats.ReaderWrapper
getPossibleDomains(String) - Method in class loci.formats.WrappedReader
getPulse(String) - Method in class loci.formats.FormatReader: Deprecated.
Use MetadataTools.getPulse(String).
getPulse(String) - Static method in class loci.formats.MetadataTools: Retrieves an Pulse enumeration value for the given String.
getRasterLength(int[]) - Static method in class loci.formats.FormatTools: Computes the number of raster values for a positional array with the given lengths.
getReader() - Method in class loci.formats.ImageReader: Gets the reader used to open the current file.
getReader() - Method in class loci.formats.ReaderWrapper: Gets the wrapped reader.
getReader(Class<? extends IFormatReader>) - Method in class loci.formats.ImageReader: Gets the file format reader instance matching the given class.
getReader(String) - Method in class loci.formats.ImageReader: Gets the reader used to open the given file.
getReader(IFormatReader, Class<? extends IFormatReader>) - Static method in class loci.formats.FormatTools: Recursively look for the first underlying reader that is an instance of the given class.
getReaders() - Method in class loci.formats.ImageReader: Gets all constituent file format readers.
getReorderedIndex(String, String, int, int, int, int, int) - Static method in class loci.formats.FormatTools: Converts index from one dimension order to another.
getReorderedIndex(IFormatReader, String, int) - Static method in class loci.formats.FormatTools: Converts index from the given dimension order to the reader's native one.
getRequiredDirectories(String[]) - Method in class loci.formats.FormatReader
getRequiredDirectories(String[]) - Static method in class loci.formats.FormatTools: Returns the maximum number of directories below the common parent of a list of file paths
getRequiredDirectories(String[]) - Method in interface loci.formats.IFormatReader: Returns the number of parent directories that are important when processing the given list of files.
getRequiredDirectories(String[]) - Method in class loci.formats.ImageReader
getRequiredDirectories(String[]) - Method in class loci.formats.ReaderWrapper
getResolution() - Method in class loci.formats.FormatReader
getResolution() - Method in class loci.formats.FormatWriter
getResolution() - Method in class loci.formats.ImageReader
getResolution() - Method in class loci.formats.ImageWriter
getResolution() - Method in interface loci.formats.IPyramidHandler: Get the current resolution level.
getResolution() - Method in class loci.formats.ReaderWrapper
getResolution() - Method in class loci.formats.SubResolutionFormatReader
getResolution() - Method in class loci.formats.WrappedReader
getResolution() - Method in class loci.formats.WriterWrapper
getResolutionCount() - Method in class loci.formats.FormatReader
getResolutionCount() - Method in class loci.formats.FormatWriter
getResolutionCount() - Method in class loci.formats.ImageReader
getResolutionCount() - Method in class loci.formats.ImageWriter
getResolutionCount() - Method in interface loci.formats.IPyramidHandler: Return the number of resolutions for the current series.
getResolutionCount() - Method in class loci.formats.ReaderWrapper
getResolutionCount() - Method in class loci.formats.SubResolutionFormatReader
getResolutionCount() - Method in class loci.formats.WrappedReader
getResolutionCount() - Method in class loci.formats.WriterWrapper
getResolutionCount(int) - Method in interface loci.formats.meta.IPyramidStore: Retrieve the number of pyramid resolutions defined for the given Image.
getResolutionCount(int) - Method in class loci.formats.ome.OMEPyramidStore
getResolutions() - Method in class loci.formats.FormatWriter
getResolutions() - Method in interface loci.formats.IFormatWriter: Get a list of resolution objects for the current series.
getResolutions() - Method in class loci.formats.ImageWriter
getResolutions() - Method in class loci.formats.WriterWrapper
getResolutionSizeX(int, int) - Method in interface loci.formats.meta.IPyramidStore: Retrieve the image width in pixels of the given pyramid resolution.
getResolutionSizeX(int, int) - Method in class loci.formats.ome.OMEPyramidStore
getResolutionSizeY(int, int) - Method in interface loci.formats.meta.IPyramidStore: Retrieve the image height in pixels of the given pyramid resolution.
getResolutionSizeY(int, int) - Method in class loci.formats.ome.OMEPyramidStore
getRGBChannelCount() - Method in class loci.formats.FormatReader
getRGBChannelCount() - Method in interface loci.formats.IFormatReader: Gets the number of channels returned with each call to openBytes.
getRGBChannelCount() - Method in class loci.formats.ImageReader
getRGBChannelCount() - Method in class loci.formats.ReaderWrapper
getRGBChannelCount() - Method in class loci.formats.WrappedReader
getRotationTransform(double) - Method in class loci.formats.FormatReader: Construct an AffineTransform corresponding to the given angle.
getRowIndex() - Method in class loci.formats.internal.WellContainer
getSamplesPerPixel() - Method in class loci.formats.FormatWriter: Retrieve the number of samples per pixel for the current series.
getSamplesPerPixel(int) - Method in class loci.formats.FormatWriter: Retrieve the number of samples per pixel for given series.
getSeries() - Method in class loci.formats.FormatReader
getSeries() - Method in class loci.formats.FormatWriter
getSeries() - Method in interface loci.formats.IFormatReader: Gets the currently active series.
getSeries() - Method in interface loci.formats.IFormatWriter: Returns the current series.
getSeries() - Method in class loci.formats.ImageReader
getSeries() - Method in class loci.formats.ImageWriter
getSeries() - Method in class loci.formats.ReaderWrapper
getSeries() - Method in class loci.formats.SubResolutionFormatReader
getSeries() - Method in class loci.formats.WrappedReader
getSeries() - Method in class loci.formats.WriterWrapper
getSeriesCount() - Method in class loci.formats.FormatReader
getSeriesCount() - Method in interface loci.formats.IFormatReader: Gets the number of series in this file.
getSeriesCount() - Method in class loci.formats.ImageReader
getSeriesCount() - Method in class loci.formats.ReaderWrapper
getSeriesCount() - Method in class loci.formats.SubResolutionFormatReader
getSeriesCount() - Method in class loci.formats.WrappedReader
getSeriesList() - Method in class loci.formats.CoreMetadataList
getSeriesMeta(String) - Method in class loci.formats.FormatReader: Gets an entry from the metadata table for the current series.
getSeriesMetadata() - Method in class loci.formats.FormatReader
getSeriesMetadata() - Method in interface loci.formats.IFormatReader: Obtains the hashtable containing metadata field/value pairs from the current series in the current file.
getSeriesMetadata() - Method in class loci.formats.ImageReader
getSeriesMetadata() - Method in class loci.formats.ReaderWrapper
getSeriesMetadata() - Method in class loci.formats.WrappedReader
getSeriesMetadataValue(String) - Method in class loci.formats.FormatReader
getSeriesMetadataValue(String) - Method in interface loci.formats.IFormatReader: Obtains the specified metadata field's value for the current series in the current file.
getSeriesMetadataValue(String) - Method in class loci.formats.ImageReader
getSeriesMetadataValue(String) - Method in class loci.formats.ReaderWrapper
getSeriesMetadataValue(String) - Method in class loci.formats.WrappedReader
getSeriesUsedFiles() - Method in class loci.formats.FormatReader
getSeriesUsedFiles() - Method in interface loci.formats.IFormatReader: Returns an array of filenames needed to open the current series.
getSeriesUsedFiles() - Method in class loci.formats.ImageReader
getSeriesUsedFiles() - Method in class loci.formats.ReaderWrapper
getSeriesUsedFiles(boolean) - Method in class loci.formats.DelegateReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.FormatReader
getSeriesUsedFiles(boolean) - Method in interface loci.formats.IFormatReader: Returns an array of filenames needed to open the current series.
getSeriesUsedFiles(boolean) - Method in class loci.formats.ImageReader
getSeriesUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
getSeriesUsedFiles(boolean) - Method in class loci.formats.WrappedReader
getSizeC() - Method in class loci.formats.FormatReader
getSizeC() - Method in interface loci.formats.IFormatReader: Gets the size of the C dimension.
getSizeC() - Method in class loci.formats.ImageReader
getSizeC() - Method in class loci.formats.ReaderWrapper
getSizeC() - Method in class loci.formats.WrappedReader
getSizeT() - Method in class loci.formats.FormatReader
getSizeT() - Method in interface loci.formats.IFormatReader: Gets the size of the T dimension.
getSizeT() - Method in class loci.formats.ImageReader
getSizeT() - Method in class loci.formats.ReaderWrapper
getSizeT() - Method in class loci.formats.WrappedReader
getSizeX() - Method in class loci.formats.FormatReader
getSizeX() - Method in class loci.formats.FormatWriter
getSizeX() - Method in interface loci.formats.IFormatReader: Gets the size of the X dimension.
getSizeX() - Method in class loci.formats.ImageReader
getSizeX() - Method in class loci.formats.ReaderWrapper
getSizeX() - Method in class loci.formats.WrappedReader
getSizeY() - Method in class loci.formats.FormatReader
getSizeY() - Method in class loci.formats.FormatWriter
getSizeY() - Method in interface loci.formats.IFormatReader: Gets the size of the Y dimension.
getSizeY() - Method in class loci.formats.ImageReader
getSizeY() - Method in class loci.formats.ReaderWrapper
getSizeY() - Method in class loci.formats.WrappedReader
getSizeZ() - Method in class loci.formats.FormatReader
getSizeZ() - Method in interface loci.formats.IFormatReader: Gets the size of the Z dimension.
getSizeZ() - Method in class loci.formats.ImageReader
getSizeZ() - Method in class loci.formats.ReaderWrapper
getSizeZ() - Method in class loci.formats.WrappedReader
getStagePosition(Double, String) - Static method in class loci.formats.FormatTools: Formats the input value for the stage position into a length of the given unit.
getStagePosition(Double, Unit<Length>) - Static method in class loci.formats.FormatTools: Formats the input value for the stage position into a length of the given unit.
getSuffixes() - Method in class loci.formats.FormatHandler
getSuffixes() - Method in interface loci.formats.IFormatHandler: Gets the default file suffixes for this file format.
getSuffixes() - Method in class loci.formats.ImageReader
getSuffixes() - Method in class loci.formats.ImageWriter
getSuffixes() - Method in class loci.formats.ReaderWrapper
getSuffixes() - Method in class loci.formats.WriterWrapper
getSupportedMetadataLevels() - Method in class loci.formats.DelegateReader
getSupportedMetadataLevels() - Method in class loci.formats.FormatHandler
getSupportedMetadataLevels() - Method in class loci.formats.ImageReader
getSupportedMetadataLevels() - Method in class loci.formats.ImageWriter
getSupportedMetadataLevels() - Method in interface loci.formats.IMetadataConfigurable
getSupportedMetadataLevels() - Method in class loci.formats.ReaderWrapper
getSupportedMetadataLevels() - Method in class loci.formats.WriterWrapper
getThumbSizeX() - Method in class loci.formats.FormatReader
getThumbSizeX() - Method in interface loci.formats.IFormatReader: Get the size of the X dimension for the thumbnail.
getThumbSizeX() - Method in class loci.formats.ImageReader
getThumbSizeX() - Method in class loci.formats.ReaderWrapper
getThumbSizeX() - Method in class loci.formats.WrappedReader
getThumbSizeY() - Method in class loci.formats.FormatReader
getThumbSizeY() - Method in interface loci.formats.IFormatReader: Get the size of the Y dimension for the thumbnail.
getThumbSizeY() - Method in class loci.formats.ImageReader
getThumbSizeY() - Method in class loci.formats.ReaderWrapper
getThumbSizeY() - Method in class loci.formats.WrappedReader
getTileCodec(int) - Method in interface loci.formats.ICompressedTileReader: Retrieve a codec that can be used to decompress compressed tiles.
getTileCodec(int) - Method in class loci.formats.ImageReader
getTileCodec(int) - Method in class loci.formats.ReaderWrapper
getTileCodecOptions(int, int, int) - Method in interface loci.formats.ICompressedTileReader: Retrieve codec options that can be used to decompressed the specified tile.
getTileCodecOptions(int, int, int) - Method in class loci.formats.ImageReader
getTileCodecOptions(int, int, int) - Method in class loci.formats.ReaderWrapper
getTileColumns(int) - Method in class loci.formats.FormatReader
getTileColumns(int) - Method in interface loci.formats.ICompressedTileReader: Get the number of columns of tiles in the specified plane in the current series.
getTileColumns(int) - Method in class loci.formats.ImageReader
getTileColumns(int) - Method in class loci.formats.ReaderWrapper
getTileFilename(int, int, int, String) - Static method in class loci.formats.FormatTools
getTileRows(int) - Method in class loci.formats.FormatReader
getTileRows(int) - Method in interface loci.formats.ICompressedTileReader: Get the number of rows of tiles in the specified plane in the current series.
getTileRows(int) - Method in class loci.formats.ImageReader
getTileRows(int) - Method in class loci.formats.ReaderWrapper
getTileSizeX() - Method in class loci.formats.FormatWriter
getTileSizeX() - Method in interface loci.formats.IFormatWriter: Retrieves the current tile width Defaults to 0 if not supported
getTileSizeX() - Method in class loci.formats.ImageWriter
getTileSizeX() - Method in class loci.formats.WriterWrapper
getTileSizeY() - Method in class loci.formats.FormatWriter
getTileSizeY() - Method in interface loci.formats.IFormatWriter: Retrieves the current tile height Defaults to 0 if not supported
getTileSizeY() - Method in class loci.formats.ImageWriter
getTileSizeY() - Method in class loci.formats.WriterWrapper
getTime(Double, String) - Static method in class loci.formats.FormatTools: Formats the input value for the time into a length of the given unit.
getUnderlyingReaders() - Method in class loci.formats.FormatReader
getUnderlyingReaders() - Method in interface loci.formats.IFormatReader: Retrieves all underlying readers.
getUnderlyingReaders() - Method in class loci.formats.ImageReader
getUnderlyingReaders() - Method in class loci.formats.ReaderWrapper
getUnderlyingReaders() - Method in class loci.formats.WrappedReader
getUsedFiles() - Method in class loci.formats.FormatReader
getUsedFiles() - Method in interface loci.formats.IFormatReader: Returns an array of filenames needed to open this dataset.
getUsedFiles() - Method in class loci.formats.ImageReader
getUsedFiles() - Method in class loci.formats.ReaderWrapper
getUsedFiles(boolean) - Method in class loci.formats.FormatReader
getUsedFiles(boolean) - Method in interface loci.formats.IFormatReader: Returns an array of filenames needed to open this dataset.
getUsedFiles(boolean) - Method in class loci.formats.ImageReader
getUsedFiles(boolean) - Method in class loci.formats.ReaderWrapper
getUsedFiles(boolean) - Method in class loci.formats.WrappedReader
getValueForKey() - Method in class loci.formats.meta.OriginalMetadataAnnotation: Return just the value (i.e.
getWavelength(Double) - Static method in class loci.formats.FormatTools
getWavelength(Double, String) - Static method in class loci.formats.FormatTools: Formats the input value for the wavelength into a length of the given unit.
getWellIndex() - Method in class loci.formats.internal.WellContainer
getWellName(int, int) - Static method in class loci.formats.FormatTools: Create a simple name for the well at the given row and column.
getWellRowName(int) - Static method in class loci.formats.FormatTools: Create a simple name for the given row of wells.
getWriter() - Method in class loci.formats.ImageWriter: Gets the writer used to save the current file.
getWriter() - Method in class loci.formats.WriterWrapper: Gets the wrapped writer.
getWriter(Class<? extends IFormatWriter>) - Method in class loci.formats.ImageWriter: Gets the file format writer instance matching the given class.
getWriter(String) - Method in class loci.formats.ImageWriter: Gets the writer used to save the given file.
getWriters() - Method in class loci.formats.ImageWriter: Gets all constituent file format writers.
getZCTCoords(int) - Method in class loci.formats.FormatReader
getZCTCoords(int) - Method in interface loci.formats.IFormatReader: Gets the Z, C and T coordinates (real sizes) corresponding to the given rasterized index value.
getZCTCoords(int) - Method in class loci.formats.ImageReader
getZCTCoords(int) - Method in class loci.formats.ReaderWrapper
getZCTCoords(int) - Method in class loci.formats.WrappedReader
getZCTCoords(String, int, int, int, int, int) - Static method in class loci.formats.FormatTools: Gets the Z, C and T coordinates corresponding to the given rasterized index value (real sizes).
getZCTCoords(String, int, int, int, int, int, int, int, int) - Static method in class loci.formats.FormatTools: Gets the Z, C and T coordinates corresponding to the given rasterized index value.
getZCTCoords(IFormatReader, int) - Static method in class loci.formats.FormatTools: Gets the Z, C and T coordinates corresponding to the given rasterized index value (real sizes).
getZCTModuloCoords(int) - Method in class loci.formats.FormatReader
getZCTModuloCoords(int) - Method in interface loci.formats.IFormatReader: Gets the Z, C, T, moduloZ, moduloC and moduloT coordinates (effective sizes) corresponding to the given rasterized index value.
getZCTModuloCoords(int) - Method in class loci.formats.ImageReader
getZCTModuloCoords(int) - Method in class loci.formats.ReaderWrapper
getZCTModuloCoords(IFormatReader, int) - Static method in class loci.formats.FormatTools: Gets the Z, C, T, ModuloZ, ModuloC and ModuloZ coordinates corresponding to the given rasterized index value (effective sizes).
GRAPHICS_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies the graphics domain.
group - Variable in class loci.formats.FormatReader: Whether or not to group multi-file formats.

H

hasCompanionFiles - Variable in class loci.formats.FormatReader: Whether this format supports multi-file datasets.
hasCompanionFiles() - Method in class loci.formats.FormatReader
hasCompanionFiles() - Method in interface loci.formats.IFormatReader: Returns true if this format supports multi-file datasets.
hasCompanionFiles() - Method in class loci.formats.ImageReader
hasCompanionFiles() - Method in class loci.formats.ReaderWrapper
hasCompanionFiles() - Method in class loci.formats.WrappedReader
hasFlattenedResolutions() - Method in class loci.formats.FormatReader
hasFlattenedResolutions() - Method in interface loci.formats.IFormatReader: Return whether or not resolution flattening is enabled.
hasFlattenedResolutions() - Method in class loci.formats.ImageReader
hasFlattenedResolutions() - Method in class loci.formats.ReaderWrapper
hasResolutions() - Method in class loci.formats.FormatWriter
HCS_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies the high content screening domain.
height - Variable in class loci.formats.codec.CodecOptions: Height, in pixels, of the image.
HISTOLOGY_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies the histology domain.

I

ICompressedTileReader - Interface in loci.formats: Interface for reading pre-compressed image tiles.
ICompressedTileWriter - Interface in loci.formats: Interface for writing pre-compressed image tiles.
IFormatHandler - Interface in loci.formats: Interface for all biological file format readers and writers.
IFormatReader - Interface in loci.formats: Interface for all biological file format readers.
IFormatWriter - Interface in loci.formats: Interface for all biological file format writers.
ILLUMINATION - Static variable in class loci.formats.FormatTools: Identifies the Illumination dimensional type, representing a dimension consisting of illuminations.
imageCount - Variable in class loci.formats.CoreMetadata: Total number of images.
ImageReader - Class in loci.formats: ImageReader is the master file format reader for all supported formats.
ImageReader() - Constructor for class loci.formats.ImageReader: Constructs a new ImageReader with the default list of reader classes from readers.txt.
ImageReader(ClassList<IFormatReader>) - Constructor for class loci.formats.ImageReader: Constructs a new ImageReader from the given list of reader classes.
ImageWriter - Class in loci.formats: ImageWriter is the master file format writer for all supported formats.
ImageWriter() - Constructor for class loci.formats.ImageWriter: Constructs a new ImageWriter with the default list of writer classes from writers.txt.
ImageWriter(ClassList<IFormatWriter>) - Constructor for class loci.formats.ImageWriter: Constructs a new ImageWriter from the given list of writer classes.
IMetadata - Interface in loci.formats.meta
IMetadataConfigurable - Interface in loci.formats
IMinMaxStore - Interface in loci.formats.meta: Interface for consumers of minima and maxima pixel intensities across a given wavelength.
in - Variable in class loci.formats.FormatReader: Current file.
index - Variable in class loci.formats.Resolution
indexed - Variable in class loci.formats.CoreMetadata: Indicates whether or not the images are stored as indexed color.
indexedAsRGB - Variable in class loci.formats.FormatReader: Whether or not MetadataStore sets C = 3 for indexed color images.
initFile(String) - Method in class loci.formats.FormatReader: Initializes the given file (parsing header information, etc.).
initFile(String) - Method in class loci.formats.SubResolutionFormatReader: Initializes the given file (parsing header information, etc.).
initialized - Variable in class loci.formats.FormatWriter: Whether each plane in each series of the current file has been prepped for writing.
INT16 - Static variable in class loci.formats.FormatTools: Identifies the INT16 data type used to store pixel values.
INT32 - Static variable in class loci.formats.FormatTools: Identifies the INT32 data type used to store pixel values.
INT8 - Static variable in class loci.formats.FormatTools: Identifies the INT8 data type used to store pixel values.
interleaved - Variable in class loci.formats.codec.CodecOptions: Indicates whether or not channels are interleaved.
interleaved - Variable in class loci.formats.CoreMetadata: True if channels are stored RGBRGBRGB...; false if channels are stored RRR...GGG...BBB...
interleaved - Variable in class loci.formats.FormatWriter: Whether the channels in an RGB image are interleaved.
IPyramidHandler - Interface in loci.formats: Interface for defining image pyramids.
IPyramidStore - Interface in loci.formats.meta: Interface for defining pyramid resolutions.
isAllowedKey(String) - Method in class loci.formats.ClassList: Returns whether a given key is an allowed option.
isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService: Determine whether or not two OMEXMLMetadata objects are equal.
isEqual(OMEXMLMetadata, OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
isFalseColor() - Method in class loci.formats.FormatReader
isFalseColor() - Method in interface loci.formats.IFormatReader: Returns false if IFormatReader.isIndexed() is false, or if IFormatReader.isIndexed() is true and the lookup table represents "real" color data.
isFalseColor() - Method in class loci.formats.ImageReader
isFalseColor() - Method in class loci.formats.ReaderWrapper
isFalseColor() - Method in class loci.formats.WrappedReader
isFloatingPoint(int) - Static method in class loci.formats.FormatTools: Determines whether the given pixel type is floating point or integer.
isFloatingPoint(IFormatReader) - Static method in class loci.formats.FormatTools: Determines whether the given reader represents any floating point data.
isFullPlane(int, int, int, int) - Method in class loci.formats.FormatWriter: Returns true if the given rectangle coordinates correspond to a full image in the given series.
isGroupFiles() - Method in class loci.formats.FormatReader
isGroupFiles() - Method in interface loci.formats.IFormatReader: Returns true if we should group files in multi-file formats.
isGroupFiles() - Method in class loci.formats.ImageReader
isGroupFiles() - Method in class loci.formats.ReaderWrapper
isIndexed() - Method in class loci.formats.FormatReader
isIndexed() - Method in interface loci.formats.IFormatReader: Gets whether the image planes are indexed color.
isIndexed() - Method in class loci.formats.ImageReader
isIndexed() - Method in class loci.formats.ReaderWrapper
isIndexed() - Method in class loci.formats.WrappedReader
isInterleaved() - Method in class loci.formats.FormatReader
isInterleaved() - Method in class loci.formats.FormatWriter
isInterleaved() - Method in interface loci.formats.IFormatReader: Gets whether or not the channels are interleaved.
isInterleaved() - Method in interface loci.formats.IFormatWriter: Gets whether or not the channels in an image are interleaved.
isInterleaved() - Method in class loci.formats.ImageReader
isInterleaved() - Method in class loci.formats.ImageWriter
isInterleaved() - Method in class loci.formats.ReaderWrapper
isInterleaved() - Method in class loci.formats.WrappedReader
isInterleaved() - Method in class loci.formats.WriterWrapper
isInterleaved(int) - Method in class loci.formats.FormatReader
isInterleaved(int) - Method in interface loci.formats.IFormatReader: Gets whether or not the given sub-channel is interleaved.
isInterleaved(int) - Method in class loci.formats.ImageReader
isInterleaved(int) - Method in class loci.formats.ReaderWrapper
isInterleaved(int) - Method in class loci.formats.WrappedReader
isLegacy() - Method in class loci.formats.DelegateReader: Gets whether to use the legacy reader by default.
isLittleEndian() - Method in class loci.formats.FormatReader
isLittleEndian() - Method in interface loci.formats.IFormatReader: Gets whether the data is in little-endian format.
isLittleEndian() - Method in class loci.formats.ImageReader
isLittleEndian() - Method in class loci.formats.ReaderWrapper
isLittleEndian() - Method in class loci.formats.WrappedReader
isMetadataComplete() - Method in class loci.formats.FormatReader
isMetadataComplete() - Method in interface loci.formats.IFormatReader: Returns true if this format's metadata is completely parsed.
isMetadataComplete() - Method in class loci.formats.ImageReader
isMetadataComplete() - Method in class loci.formats.ReaderWrapper
isMetadataComplete() - Method in class loci.formats.WrappedReader
isMetadataFiltered() - Method in class loci.formats.FormatReader
isMetadataFiltered() - Method in interface loci.formats.IFormatReader: Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table.
isMetadataFiltered() - Method in class loci.formats.ImageReader
isMetadataFiltered() - Method in class loci.formats.ReaderWrapper
isNormalized() - Method in class loci.formats.FormatReader
isNormalized() - Method in interface loci.formats.IFormatReader: Returns true if we should normalize float data.
isNormalized() - Method in class loci.formats.ImageReader
isNormalized() - Method in class loci.formats.ReaderWrapper
isOMEXMLMetadata(Object) - Method in interface loci.formats.services.OMEXMLService: Checks whether the given object is an OME-XML metadata object.
isOMEXMLMetadata(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
isOMEXMLRoot(Object) - Method in interface loci.formats.services.OMEXMLService: Checks whether the given object is an OME-XML root object.
isOMEXMLRoot(Object) - Method in class loci.formats.services.OMEXMLServiceImpl
isOrderCertain() - Method in class loci.formats.FormatReader
isOrderCertain() - Method in interface loci.formats.IFormatReader: Gets whether the dimension order and sizes are known, or merely guesses.
isOrderCertain() - Method in class loci.formats.ImageReader
isOrderCertain() - Method in class loci.formats.ReaderWrapper
isOrderCertain() - Method in class loci.formats.WrappedReader
isOriginalMetadataPopulated() - Method in class loci.formats.FormatReader
isOriginalMetadataPopulated() - Method in interface loci.formats.IFormatReader: Returns true if we should save proprietary metadata in the MetadataStore.
isOriginalMetadataPopulated() - Method in class loci.formats.ImageReader
isOriginalMetadataPopulated() - Method in class loci.formats.ReaderWrapper
isPositiveValue(Double) - Static method in class loci.formats.FormatTools
isRGB() - Method in class loci.formats.FormatReader
isRGB() - Method in interface loci.formats.IFormatReader: Checks if the image planes in the file have more than one channel per IFormatReader.openBytes(int) call.
isRGB() - Method in class loci.formats.ImageReader
isRGB() - Method in class loci.formats.ReaderWrapper
isRGB() - Method in class loci.formats.WrappedReader
isSigned(int) - Static method in class loci.formats.FormatTools: Determines whether the given pixel type is signed or unsigned.
isSingleFile(String) - Method in class loci.formats.FormatReader
isSingleFile(String) - Method in interface loci.formats.IFormatReader: Returns true if the named file is expected to be the only file in the dataset.
isSingleFile(String) - Method in class loci.formats.ImageReader
isSingleFile(String) - Method in class loci.formats.ReaderWrapper
isSingleFile(String) - Method in class loci.formats.WrappedReader
isSupportedType(int) - Method in class loci.formats.FormatWriter
isSupportedType(int) - Method in interface loci.formats.IFormatWriter: Checks if the given pixel type is supported.
isSupportedType(int) - Method in class loci.formats.ImageWriter
isSupportedType(int) - Method in class loci.formats.WriterWrapper
isThisType(byte[]) - Method in class loci.formats.FormatReader
isThisType(byte[]) - Method in interface loci.formats.IFormatReader: Checks if the given block is a valid header for this file format.
isThisType(byte[]) - Method in class loci.formats.ImageReader
isThisType(byte[]) - Method in class loci.formats.ReaderWrapper
isThisType(String) - Method in class loci.formats.FormatHandler: Checks if a file matches the type of this format handler.
isThisType(String) - Method in class loci.formats.FormatReader
isThisType(String) - Method in interface loci.formats.IFormatHandler: Checks if the given string is a valid filename for this file format.
isThisType(String) - Method in class loci.formats.ImageReader
isThisType(String) - Method in class loci.formats.ImageWriter
isThisType(String) - Method in class loci.formats.ReaderWrapper
isThisType(String) - Method in class loci.formats.WriterWrapper
isThisType(String, boolean) - Method in class loci.formats.DelegateReader
isThisType(String, boolean) - Method in class loci.formats.FormatReader: Checks if a file matches the type of this format reader.
isThisType(String, boolean) - Method in interface loci.formats.IFormatReader: Checks if the given file is a valid instance of this file format.
isThisType(String, boolean) - Method in class loci.formats.ImageReader
isThisType(String, boolean) - Method in class loci.formats.ReaderWrapper
isThisType(RandomAccessInputStream) - Method in class loci.formats.DelegateReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.FormatReader
isThisType(RandomAccessInputStream) - Method in interface loci.formats.IFormatReader: Checks if the given stream is a valid stream for this file format.
isThisType(RandomAccessInputStream) - Method in class loci.formats.ImageReader
isThisType(RandomAccessInputStream) - Method in class loci.formats.ReaderWrapper
isThumbnailSeries() - Method in class loci.formats.FormatReader
isThumbnailSeries() - Method in interface loci.formats.IFormatReader: Gets whether the current series is a lower resolution copy of a different series.
isThumbnailSeries() - Method in class loci.formats.ImageReader
isThumbnailSeries() - Method in class loci.formats.ReaderWrapper
isThumbnailSeries() - Method in class loci.formats.WrappedReader
isUsedFile(String) - Method in class loci.formats.FormatReader: Returns true if the given file name is in the used files list.
isValidate() - Method in class loci.formats.in.DefaultMetadataOptions
isValidate() - Method in class loci.formats.in.DynamicMetadataOptions
isValidate() - Method in interface loci.formats.in.MetadataOptions: Checks whether file validation has been set.
isWhitelistedKey(String) - Method in class loci.formats.ClassList: Deprecated.
Use ClassList.isAllowedKey(String) instead.

K

keys(Hashtable<String, Object>) - Static method in class loci.formats.MetadataTools: Gets a sorted list of keys from the given hashtable.

L

labels - Variable in class loci.formats.Modulo
LATEST_VERSION - Static variable in class loci.formats.services.OMEXMLServiceImpl: Latest OME-XML version namespace.
legacyReader - Variable in class loci.formats.DelegateReader: Legacy reader.
legacyReaderInitialized - Variable in class loci.formats.DelegateReader: Flag indicating that the legacy reader was successfully initialized.
length() - Method in class loci.formats.Modulo
LIFETIME - Static variable in class loci.formats.FormatTools: Identifies the Lifetime dimensional type, representing a dimension consisting of a lifetime histogram.
littleEndian - Variable in class loci.formats.codec.CodecOptions: Indicates endianness of pixel data.
littleEndian - Variable in class loci.formats.CoreMetadata: Indicates whether or not each pixel's bytes are in little endian order.
LM_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies the light microscopy domain.
loadOptions(String, ArrayList<String>) - Method in class loci.formats.in.DynamicMetadataOptions
loci.formats - package loci.formats
loci.formats.codec - package loci.formats.codec
loci.formats.in - package loci.formats.in
loci.formats.internal - package loci.formats.internal: Package containing common classes for internal use by Bio-Formats readers/writers.
loci.formats.meta - package loci.formats.meta: Package containing core Bio-Formats metadata interfaces for the OME data model.
loci.formats.ome - package loci.formats.ome: Package containing Bio-Formats OME-related logic for OME-XML metadata, and database import, upload and download.
loci.formats.services - package loci.formats.services
LOGGER - Static variable in class loci.formats.FormatHandler
LOGGER - Static variable in class loci.formats.FormatTools
LOGGER - Static variable in class loci.formats.in.DynamicMetadataOptions
lossless - Variable in class loci.formats.codec.CodecOptions: Used with codecs allowing lossy and lossless compression.

M

makeFilterMetadata() - Method in class loci.formats.FormatReader: Return a properly configured loci.formats.meta.FilterMetadata.
makeModuloElement(Document) - Method in class loci.formats.meta.ModuloAnnotation: Construct a DOM element for this annotation using the given Document as the root.
makeOriginalMetadata(Document) - Method in class loci.formats.meta.OriginalMetadataAnnotation: Create a DOM element for this annotation with the given document as the parent.
makeSaneDimensionOrder(String) - Static method in class loci.formats.MetadataTools: Adjusts the given dimension order as needed so that it contains exactly one of each of the following characters: 'X', 'Y', 'Z', 'C', 'T'.
maxBytes - Variable in class loci.formats.codec.CodecOptions: If compressing, this is the maximum number of raw bytes to compress.
MEDICAL_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies the medical imaging domain.
merge(Map<String, Object>, Map<String, Object>, String) - Static method in class loci.formats.MetadataTools: Merges the given lists of metadata, prepending the specified prefix for the destination keys.
metadata - Variable in class loci.formats.FormatReader: Hashtable containing metadata key/value pairs.
METADATA_LEVEL_DEFAULT - Static variable in class loci.formats.in.DynamicMetadataOptions
METADATA_LEVEL_KEY - Static variable in class loci.formats.in.DynamicMetadataOptions
metadataComplete - Variable in class loci.formats.CoreMetadata: Indicates whether or not we are confident that all of the metadata stored within the file has been parsed.
MetadataConverter - Class in loci.formats.meta: Deprecated.
Use ome.xml.meta.MetadataConverter.
MetadataLevel - Enum in loci.formats.in
MetadataList<T> - Class in loci.formats: A container of metadata for FormatReader and other reader implementations.
MetadataList() - Constructor for class loci.formats.MetadataList
MetadataList(int) - Constructor for class loci.formats.MetadataList: Construct a list containing a specified number of primary elements.
MetadataList(int[]) - Constructor for class loci.formats.MetadataList: Construct a list containing a specified number of primary and secondary elements.
MetadataList(int, int) - Constructor for class loci.formats.MetadataList: Construct a list containing a specified number of primary elements and a fixed number of secondary elements.
MetadataList(MetadataList<T>) - Constructor for class loci.formats.MetadataList: Copy a list.
metadataOptions - Variable in class loci.formats.FormatHandler: Metadata parsing options.
MetadataOptions - Interface in loci.formats.in: Holds metadata-related options.
metadataRetrieve - Variable in class loci.formats.FormatWriter: Current metadata retrieval object.
MetadataRetrieve - Interface in loci.formats.meta
metadataStore - Variable in class loci.formats.FormatReader: Current metadata store.
MetadataStore - Interface in loci.formats.meta
MetadataTools - Class in loci.formats: A utility class for working with metadata objects, including MetadataStore, MetadataRetrieve, and OME-XML strings.
MINIMUM - Enum constant in enum loci.formats.in.MetadataLevel
MissingLibraryException - Exception Class in loci.formats: MissingLibraryException is the exception thrown when a particular data stream or filename requires a library that is not present on the system.
MissingLibraryException() - Constructor for exception class loci.formats.MissingLibraryException
MissingLibraryException(String) - Constructor for exception class loci.formats.MissingLibraryException
MissingLibraryException(String, Throwable) - Constructor for exception class loci.formats.MissingLibraryException
MissingLibraryException(Throwable) - Constructor for exception class loci.formats.MissingLibraryException
Modulo - Class in loci.formats: Represents a subdimension of Z, C, or T as needed for supporting Modulo annotations.
Modulo(String) - Constructor for class loci.formats.Modulo
Modulo(Modulo) - Constructor for class loci.formats.Modulo
MODULO_NS - Static variable in class loci.formats.meta.ModuloAnnotation
ModuloAnnotation - Class in loci.formats.meta
ModuloAnnotation() - Constructor for class loci.formats.meta.ModuloAnnotation
moduloC - Variable in class loci.formats.CoreMetadata
moduloT - Variable in class loci.formats.CoreMetadata
moduloZ - Variable in class loci.formats.CoreMetadata
MUST_GROUP - Static variable in class loci.formats.FormatTools: File grouping options.
MUST_GROUP - Static variable in interface loci.formats.IFormatReader: File grouping options.

N

NAMESPACE - Static variable in class loci.formats.ome.OMEPyramidStore
nativeReader - Variable in class loci.formats.DelegateReader: Native reader.
nativeReaderInitialized - Variable in class loci.formats.DelegateReader: Flag indicating that the native reader was successfully initialized.
NO_OME_XML_MSG - Static variable in class loci.formats.services.OMEXMLServiceImpl
NO_OVERLAYS - Enum constant in enum loci.formats.in.MetadataLevel
NON_GRAPHICS_DOMAINS - Static variable in class loci.formats.FormatTools: List of non-graphics domains.
NON_HCS_DOMAINS - Static variable in class loci.formats.FormatTools: List of non-HCS domains.
NON_SPECIAL_DOMAINS - Static variable in class loci.formats.FormatTools: List of domains that do not require special handling.
normalizeData - Variable in class loci.formats.FormatReader: Whether or not to normalize float data.

O

OMEPyramidStore - Class in loci.formats.ome: Extension of OMEXMLMetadataImpl that allows for pyramid resolution storage and retrieval.
OMEPyramidStore() - Constructor for class loci.formats.ome.OMEPyramidStore
OMEXMLMetadata - Interface in loci.formats.ome
OMEXMLMetadataImpl - Class in loci.formats.ome
OMEXMLMetadataImpl() - Constructor for class loci.formats.ome.OMEXMLMetadataImpl
OMEXMLService - Interface in loci.formats.services
OMEXMLServiceImpl - Class in loci.formats.services
OMEXMLServiceImpl() - Constructor for class loci.formats.services.OMEXMLServiceImpl: Default constructor.
openBytes(int) - Method in class loci.formats.FormatReader
openBytes(int) - Method in interface loci.formats.IFormatReader: Obtains the specified image plane from the current file as a byte array.
openBytes(int) - Method in class loci.formats.ImageReader
openBytes(int) - Method in class loci.formats.ReaderWrapper
openBytes(int) - Method in class loci.formats.WrappedReader
openBytes(int, byte[]) - Method in class loci.formats.FormatReader
openBytes(int, byte[]) - Method in interface loci.formats.IFormatReader: Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).
openBytes(int, byte[]) - Method in class loci.formats.ImageReader
openBytes(int, byte[]) - Method in class loci.formats.ReaderWrapper
openBytes(int, byte[]) - Method in class loci.formats.WrappedReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.DelegateReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.FormatReader
openBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.IFormatReader: Obtains a sub-image of the specified image plane into a pre-allocated byte array.
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ImageReader
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ReaderWrapper
openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.WrappedReader
openBytes(int, int, int, int, int) - Method in class loci.formats.FormatReader
openBytes(int, int, int, int, int) - Method in interface loci.formats.IFormatReader: Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).
openBytes(int, int, int, int, int) - Method in class loci.formats.ImageReader
openBytes(int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
openBytes(int, int, int, int, int) - Method in class loci.formats.WrappedReader
openCompressedBytes(int, byte[], int, int) - Method in interface loci.formats.ICompressedTileReader: Retrieve the specified tile without performing any decompression.
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ImageReader
openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.ReaderWrapper
openCompressedBytes(int, int, int) - Method in interface loci.formats.ICompressedTileReader: Retrieve the specified tile without performing any decompression.
openCompressedBytes(int, int, int) - Method in class loci.formats.ImageReader
openCompressedBytes(int, int, int) - Method in class loci.formats.ReaderWrapper
openPlane(int, int, int, int, int) - Method in class loci.formats.FormatReader
openPlane(int, int, int, int, int) - Method in interface loci.formats.IFormatReader: Obtains the specified image plane (or sub-image thereof) in the reader's native data structure.
openPlane(int, int, int, int, int) - Method in class loci.formats.ImageReader
openPlane(int, int, int, int, int) - Method in class loci.formats.ReaderWrapper
openPlane(int, int, int, int, int) - Method in class loci.formats.WrappedReader
openThumbBytes(int) - Method in class loci.formats.FormatReader
openThumbBytes(int) - Method in interface loci.formats.IFormatReader: Obtains a thumbnail for the specified image plane from the current file, as a byte array.
openThumbBytes(int) - Method in class loci.formats.ImageReader
openThumbBytes(int) - Method in class loci.formats.ReaderWrapper
openThumbBytes(int) - Method in class loci.formats.WrappedReader
openThumbBytes(IFormatReader, int) - Static method in class loci.formats.FormatTools: Default implementation for IFormatReader.openThumbBytes(int).
options - Variable in class loci.formats.FormatWriter: The options if required.
orderCertain - Variable in class loci.formats.CoreMetadata: Indicates whether or not we are confident that the dimension order is correct.
ORIGINAL_METADATA_NS - Static variable in class loci.formats.meta.OriginalMetadataAnnotation
OriginalMetadataAnnotation - Class in loci.formats.meta
OriginalMetadataAnnotation() - Constructor for class loci.formats.meta.OriginalMetadataAnnotation
out - Variable in class loci.formats.FormatWriter: Current file.

P

parentDimension - Variable in class loci.formats.Modulo
parentType - Variable in class loci.formats.Modulo
parseFile(String, Class<?>) - Method in class loci.formats.ClassList: Parses a list of classes from a configuration file.
parseLength(String) - Static method in class loci.formats.FormatTools: Parse a length composed of a value and an optional unit
parseLength(String, String) - Static method in class loci.formats.FormatTools: Parse a length composed of a value and an optional unit
parseLine(String) - Method in class loci.formats.ClassList: Parses a class from a string including options and comments.
parseOptions(String) - Method in class loci.formats.ClassList: Parses one or more options from a string.
PHASE - Static variable in class loci.formats.FormatTools: Identifies the Phase dimensional type, representing a dimension consisting of phases.
pixelType - Variable in class loci.formats.CoreMetadata: Describes the number of bytes per pixel.
pixelTypeFromBytes(int, boolean, boolean) - Static method in class loci.formats.FormatTools: Returns an appropriate pixel type given the number of bytes per pixel.
pixelTypeFromString(String) - Static method in class loci.formats.FormatTools: Takes a string value and maps it to one of the pixel type enumerations.
POLARIZATION - Static variable in class loci.formats.FormatTools: Identifies the Polarization dimensional type, representing a dimension consisting of polarization states.
populateMetadata(MetadataStore, int, String, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools: Populates the given MetadataStore, for the specified series, using the provided values.
populateMetadata(MetadataStore, int, String, CoreMetadata) - Static method in class loci.formats.MetadataTools: Populates the given MetadataStore, for the specified series, using the values from the provided CoreMetadata.
populateMetadata(MetadataStore, String, int, String, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools: Populates the given MetadataStore, for the specified series, using the provided values.
populateOriginalMetadata(OMEXMLMetadata, String, String) - Method in interface loci.formats.services.OMEXMLService: Adds the specified key/value pair as a new OriginalMetadata node to the given OME-XML metadata object.
populateOriginalMetadata(OMEXMLMetadata, String, String) - Method in class loci.formats.services.OMEXMLServiceImpl
populateOriginalMetadata(OMEXMLMetadata, Hashtable<String, Object>) - Method in interface loci.formats.services.OMEXMLService: Adds the key/value pairs in the specified Hashtable as new OriginalMetadata annotations in the given OME-XML metadata object.
populateOriginalMetadata(OMEXMLMetadata, Hashtable<String, Object>) - Method in class loci.formats.services.OMEXMLServiceImpl
populatePixels(MetadataStore, IFormatReader) - Static method in class loci.formats.MetadataTools: Populates the Pixels element of the given metadata store, using core metadata from the given reader.
populatePixels(MetadataStore, IFormatReader, boolean) - Static method in class loci.formats.MetadataTools: Populates the Pixels element of the given metadata store, using core metadata from the given reader.
populatePixels(MetadataStore, IFormatReader, boolean, boolean) - Static method in class loci.formats.MetadataTools: Populates the Pixels element of the given metadata store, using core metadata from the given reader.
populatePixelsOnly(MetadataStore, int, boolean, String, String, int, int, int, int, int, int) - Static method in class loci.formats.MetadataTools
populatePixelsOnly(MetadataStore, IFormatReader) - Static method in class loci.formats.MetadataTools
positionToRaster(int[], int[]) - Static method in class loci.formats.FormatTools: Computes a unique 1-D index corresponding to the given multidimensional position.
prepend(List<Class<? extends T>>) - Method in class loci.formats.ClassList: Prepends a list of classes which must be assignable to the base class
prepend(ClassList<T>) - Method in class loci.formats.ClassList: Prepends a class list which must be assignable to the base class
previousImage - Variable in class loci.formats.codec.CodecOptions: Pixels for preceding image (READ/WRITE).
PROPERTY_FILE - Static variable in class loci.formats.FormatTools: Deprecated.
The property file is no longer used.

Q

quality - Variable in class loci.formats.codec.CodecOptions: Compression quality level as it would be provided to: ImageWriteParam.compressionQuality (WRITE).

R

rasterToPosition(int[], int) - Static method in class loci.formats.FormatTools: Computes a unique N-D position corresponding to the given rasterized index value.
rasterToPosition(int[], int, int[]) - Static method in class loci.formats.FormatTools: Computes a unique N-D position corresponding to the given rasterized index value.
reader - Variable in class loci.formats.FileInfo: IFormatReader implementation that would be used to read this file.
reader - Variable in class loci.formats.ReaderWrapper: FormatReader used to read the file.
READER_VALIDATE_DEFAULT - Static variable in class loci.formats.in.DynamicMetadataOptions
READER_VALIDATE_KEY - Static variable in class loci.formats.in.DynamicMetadataOptions
ReaderWrapper - Class in loci.formats: Abstract superclass of reader logic that wraps other readers.
ReaderWrapper() - Constructor for class loci.formats.ReaderWrapper: Constructs a reader wrapper around a new image reader.
ReaderWrapper(IFormatReader) - Constructor for class loci.formats.ReaderWrapper: Constructs a reader wrapper around the given reader.
readPlane(RandomAccessInputStream, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader: Reads a raw plane from disk.
readPlane(RandomAccessInputStream, int, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader: Reads a raw plane from disk.
readPlane(RandomAccessInputStream, int, int, int, int, int, int, int, byte[]) - Method in class loci.formats.FormatReader
remove(int) - Method in class loci.formats.MetadataList: Remove the entire primary array element at the specified index.
remove(int, int) - Method in class loci.formats.MetadataList: Remove the array element at the specified indexes.
removeBinData(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService: Remove all of the BinData elements from the given OME-XML metadata object.
removeBinData(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
removeChannels(OMEXMLMetadata, int, int) - Method in interface loci.formats.services.OMEXMLService: Remove all but the first sizeC valid Channel elements from the given OME-XML metadata object.
removeChannels(OMEXMLMetadata, int, int) - Method in class loci.formats.services.OMEXMLServiceImpl
removeClass(Class<? extends T>) - Method in class loci.formats.ClassList: Removes the given class from the list.
removeTiffData(OMEXMLMetadata) - Method in interface loci.formats.services.OMEXMLService: Remove all of the TiffData elements from the given OME-XML metadata object.
removeTiffData(OMEXMLMetadata) - Method in class loci.formats.services.OMEXMLServiceImpl
reopenFile() - Method in class loci.formats.DelegateReader
reopenFile() - Method in class loci.formats.FormatReader
reopenFile() - Method in interface loci.formats.IFormatReader: Reopen any files that were closed, and which are expected to be open while the reader is open.
reopenFile() - Method in class loci.formats.ImageReader
reopenFile() - Method in class loci.formats.ReaderWrapper
reopenFile() - Method in class loci.formats.WrappedReader
reorder() - Method in class loci.formats.CoreMetadataList
resolution - Variable in class loci.formats.FormatReader: The number of the current resolution.
resolution - Variable in class loci.formats.FormatWriter: Current pyramid resolution.
Resolution - Class in loci.formats: Represents a single subresolution in a pyramid.
Resolution(int, int, int) - Constructor for class loci.formats.Resolution
Resolution(int, int, int, int) - Constructor for class loci.formats.Resolution
resolutionCount - Variable in class loci.formats.CoreMetadata
resolutionData - Variable in class loci.formats.FormatWriter
rgb - Variable in class loci.formats.CoreMetadata: Indicates whether or not the images are stored as RGB (multiple channels per plane).
ROTATION - Static variable in class loci.formats.FormatTools: Identifies the Rotation dimensional type, representing a dimension consisting of rotations.

S

saveBytes(int, byte[]) - Method in class loci.formats.FormatWriter
saveBytes(int, byte[]) - Method in interface loci.formats.IFormatWriter: Saves the given image to the current series in the current file.
saveBytes(int, byte[]) - Method in class loci.formats.ImageWriter
saveBytes(int, byte[]) - Method in class loci.formats.WriterWrapper
saveBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.IFormatWriter: Saves the given image tile to the current series in the current file.
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ImageWriter
saveBytes(int, byte[], int, int, int, int) - Method in class loci.formats.WriterWrapper
saveBytes(int, byte[], Region) - Method in class loci.formats.FormatWriter
saveBytes(int, byte[], Region) - Method in interface loci.formats.IFormatWriter: Saves the given image tile to the current series in the current file.
saveBytes(int, byte[], Region) - Method in class loci.formats.ImageWriter
saveBytes(int, byte[], Region) - Method in class loci.formats.WriterWrapper
saveCompressedBytes(int, byte[], int, int, int, int) - Method in interface loci.formats.ICompressedTileWriter: Save a compressed tile to the current output file.
saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.ImageWriter
saveCompressedBytes(int, byte[], int, int, int, int) - Method in class loci.formats.WriterWrapper
saveOriginalMetadata - Variable in class loci.formats.FormatReader: Whether or not to save proprietary metadata in the MetadataStore.
savePlane(int, Object) - Method in class loci.formats.FormatWriter
savePlane(int, Object) - Method in interface loci.formats.IFormatWriter: Saves the given image plane to the current series in the current file.
savePlane(int, Object) - Method in class loci.formats.ImageWriter
savePlane(int, Object) - Method in class loci.formats.WriterWrapper
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.FormatWriter
savePlane(int, Object, int, int, int, int) - Method in interface loci.formats.IFormatWriter: Saves the given image plane to the current series in the current file.
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.ImageWriter
savePlane(int, Object, int, int, int, int) - Method in class loci.formats.WriterWrapper
savePlane(int, Object, Region) - Method in class loci.formats.FormatWriter
savePlane(int, Object, Region) - Method in interface loci.formats.IFormatWriter: Saves the given image plane to the current series in the current file.
savePlane(int, Object, Region) - Method in class loci.formats.ImageWriter
savePlane(int, Object, Region) - Method in class loci.formats.WriterWrapper
seekToPlaneOffset(long, int, int) - Method in class loci.formats.FormatWriter: Seek to the given (x, y) coordinate of the image that starts at the given offset.
SEM_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies the scanning electron microscopy domain.
sequential - Variable in class loci.formats.FormatWriter: Whether or not we are writing planes sequentially.
series - Variable in class loci.formats.FormatReader: The number of the current series (non flat).
series - Variable in class loci.formats.FormatWriter: Current series.
SERIES_NAME - Static variable in class loci.formats.FormatTools
SERIES_NUM - Static variable in class loci.formats.FormatTools: Patterns to be used when constructing a pattern for output filenames.
seriesMetadata - Variable in class loci.formats.CoreMetadata: Non-core metadata associated with this series.
seriesToCoreIndex(int) - Method in class loci.formats.FormatReader
seriesToCoreIndex(int) - Method in interface loci.formats.IFormatReader: Deprecated.
This method is no longer required for sub-resolution support.
seriesToCoreIndex(int) - Method in class loci.formats.ImageReader
seriesToCoreIndex(int) - Method in class loci.formats.ReaderWrapper
seriesToCoreIndex(int) - Method in class loci.formats.SubResolutionFormatReader
seriesToCoreIndex(int) - Method in class loci.formats.WrappedReader
set(int, int, T) - Method in class loci.formats.MetadataList: Set the array element for the specified indexes.
set(String, String) - Method in class loci.formats.in.DynamicMetadataOptions: Set property name to value.
setAllowOpenFiles(boolean) - Method in class loci.formats.ImageReader: Toggles whether or not file system access is allowed when doing type detection.
setBoolean(String, Boolean) - Method in class loci.formats.in.DynamicMetadataOptions: Set property name to Boolean value.
setChannelGlobalMinMax(int, double, double, int) - Method in interface loci.formats.meta.IMinMaxStore: Populates the channel global minimum and maximum.
setClass(String, Class<?>) - Method in class loci.formats.in.DynamicMetadataOptions: Set property name to Class value.
setCodecOptions(CodecOptions) - Method in class loci.formats.FormatWriter
setCodecOptions(CodecOptions) - Method in interface loci.formats.IFormatWriter: Sets the codec options.
setCodecOptions(CodecOptions) - Method in class loci.formats.ImageWriter
setCodecOptions(CodecOptions) - Method in class loci.formats.WriterWrapper
setColorModel(ColorModel) - Method in class loci.formats.FormatWriter
setColorModel(ColorModel) - Method in interface loci.formats.IFormatWriter: Sets the color model.
setColorModel(ColorModel) - Method in class loci.formats.ImageWriter
setColorModel(ColorModel) - Method in class loci.formats.WriterWrapper
setColumnIndex(int) - Method in class loci.formats.internal.WellContainer
setCompression(String) - Method in class loci.formats.FormatWriter
setCompression(String) - Method in interface loci.formats.IFormatWriter: Sets the current compression type.
setCompression(String) - Method in class loci.formats.ImageWriter
setCompression(String) - Method in class loci.formats.WriterWrapper
setCoreIndex(int) - Method in class loci.formats.DelegateReader
setCoreIndex(int) - Method in class loci.formats.FormatReader
setCoreIndex(int) - Method in interface loci.formats.IFormatReader: Deprecated.
This method is no longer required for sub-resolution support.
setCoreIndex(int) - Method in class loci.formats.ImageReader
setCoreIndex(int) - Method in class loci.formats.ReaderWrapper
setCoreIndex(int) - Method in class loci.formats.SubResolutionFormatReader
setCoreIndex(int) - Method in class loci.formats.WrappedReader
setDefaultCreationDate(MetadataStore, String, int) - Static method in class loci.formats.MetadataTools: Sets a default creation date.
setDefaultDateEnabled(boolean) - Static method in class loci.formats.MetadataTools: Disables the setting of a default creation date.
setDouble(String, Double) - Method in class loci.formats.in.DynamicMetadataOptions: Set property name to Double value.
setEnum(String, T) - Method in class loci.formats.in.DynamicMetadataOptions: Set property name to enumerated type value.
setFieldCount(int) - Method in class loci.formats.internal.WellContainer
setFile(String, File) - Method in class loci.formats.in.DynamicMetadataOptions: Set property name to file object value.
setFillColor(Byte) - Method in class loci.formats.FormatReader
setFillColor(Byte) - Method in interface loci.formats.IFormatReader: Set the fill value for undefined pixels.
setFillColor(Byte) - Method in class loci.formats.ImageReader
setFillColor(Byte) - Method in class loci.formats.ReaderWrapper
setFlattenedList(List<CoreMetadata>) - Method in class loci.formats.CoreMetadataList
setFlattenedResolutions(boolean) - Method in class loci.formats.DelegateReader
setFlattenedResolutions(boolean) - Method in class loci.formats.FormatReader
setFlattenedResolutions(boolean) - Method in interface loci.formats.IFormatReader: Set whether or not to flatten resolutions into individual series.
setFlattenedResolutions(boolean) - Method in class loci.formats.ImageReader
setFlattenedResolutions(boolean) - Method in class loci.formats.ReaderWrapper
setFloat(String, Float) - Method in class loci.formats.in.DynamicMetadataOptions: Set property name to Float value.
setFramesPerSecond(int) - Method in class loci.formats.FormatWriter
setFramesPerSecond(int) - Method in interface loci.formats.IFormatWriter: Sets the frames per second to use when writing.
setFramesPerSecond(int) - Method in class loci.formats.ImageWriter
setFramesPerSecond(int) - Method in class loci.formats.WriterWrapper
setGroupFiles(boolean) - Method in class loci.formats.DelegateReader
setGroupFiles(boolean) - Method in class loci.formats.FormatReader
setGroupFiles(boolean) - Method in interface loci.formats.IFormatReader: Specifies whether or not to force grouping in multi-file formats.
setGroupFiles(boolean) - Method in class loci.formats.ImageReader
setGroupFiles(boolean) - Method in class loci.formats.ReaderWrapper
setId(String) - Method in class loci.formats.DelegateReader
setId(String) - Method in class loci.formats.FormatReader: Initialize a reader from the input file name.
setId(String) - Method in class loci.formats.FormatWriter: Initializes a writer from the input file name.
setId(String) - Method in interface loci.formats.IFormatHandler: Sets the current file name.
setId(String) - Method in class loci.formats.ImageReader
setId(String) - Method in class loci.formats.ImageWriter
setId(String) - Method in class loci.formats.ReaderWrapper
setId(String) - Method in class loci.formats.WriterWrapper
setInteger(String, Integer) - Method in class loci.formats.in.DynamicMetadataOptions: Set property name to Integer value.
setInterleaved(boolean) - Method in class loci.formats.FormatWriter
setInterleaved(boolean) - Method in interface loci.formats.IFormatWriter: Sets whether or not the channels in an image are interleaved.
setInterleaved(boolean) - Method in class loci.formats.ImageWriter
setInterleaved(boolean) - Method in class loci.formats.WriterWrapper
setKeyValue(String, String) - Method in class loci.formats.meta.OriginalMetadataAnnotation: Set the key/value metadata pair for this annotation.
setLegacy(boolean) - Method in class loci.formats.DelegateReader: Sets whether to use the legacy reader by default.
setLong(String, Long) - Method in class loci.formats.in.DynamicMetadataOptions: Set property name to Long value.
setMetadataFiltered(boolean) - Method in class loci.formats.DelegateReader
setMetadataFiltered(boolean) - Method in class loci.formats.FormatReader
setMetadataFiltered(boolean) - Method in interface loci.formats.IFormatReader: Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.
setMetadataFiltered(boolean) - Method in class loci.formats.ImageReader
setMetadataFiltered(boolean) - Method in class loci.formats.ReaderWrapper
setMetadataLevel(MetadataLevel) - Method in class loci.formats.in.DefaultMetadataOptions
setMetadataLevel(MetadataLevel) - Method in class loci.formats.in.DynamicMetadataOptions
setMetadataLevel(MetadataLevel) - Method in interface loci.formats.in.MetadataOptions: Set the metadata level.
setMetadataOptions(MetadataOptions) - Method in class loci.formats.DelegateReader
setMetadataOptions(MetadataOptions) - Method in class loci.formats.FormatHandler
setMetadataOptions(MetadataOptions) - Method in class loci.formats.ImageReader
setMetadataOptions(MetadataOptions) - Method in class loci.formats.ImageWriter
setMetadataOptions(MetadataOptions) - Method in interface loci.formats.IMetadataConfigurable
setMetadataOptions(MetadataOptions) - Method in class loci.formats.ReaderWrapper
setMetadataOptions(MetadataOptions) - Method in class loci.formats.WriterWrapper
setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.FormatWriter
setMetadataRetrieve(MetadataRetrieve) - Method in interface loci.formats.IFormatWriter: Sets the metadata retrieval object from which to retrieve standardized metadata.
setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.ImageWriter
setMetadataRetrieve(MetadataRetrieve) - Method in class loci.formats.WriterWrapper
setMetadataStore(MetadataStore) - Method in class loci.formats.DelegateReader
setMetadataStore(MetadataStore) - Method in class loci.formats.FormatReader
setMetadataStore(MetadataStore) - Method in interface loci.formats.IFormatReader: Sets the default metadata store for this reader.
setMetadataStore(MetadataStore) - Method in class loci.formats.ImageReader
setMetadataStore(MetadataStore) - Method in class loci.formats.ReaderWrapper
setModulo(OMEXMLMetadata, Modulo) - Method in class loci.formats.meta.ModuloAnnotation: Set the value of this annotation using the given Modulo object
setNormalized(boolean) - Method in class loci.formats.DelegateReader
setNormalized(boolean) - Method in class loci.formats.FormatReader
setNormalized(boolean) - Method in interface loci.formats.IFormatReader: Specifies whether or not to normalize float data.
setNormalized(boolean) - Method in class loci.formats.ImageReader
setNormalized(boolean) - Method in class loci.formats.ReaderWrapper
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.DelegateReader
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.FormatReader
setOriginalMetadataPopulated(boolean) - Method in interface loci.formats.IFormatReader: Specifies whether or not to save proprietary metadata in the MetadataStore.
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.ImageReader
setOriginalMetadataPopulated(boolean) - Method in class loci.formats.ReaderWrapper
setPlateAcquisition(int) - Method in class loci.formats.internal.WellContainer
setResolution(int) - Method in class loci.formats.DelegateReader
setResolution(int) - Method in class loci.formats.FormatReader
setResolution(int) - Method in class loci.formats.FormatWriter
setResolution(int) - Method in class loci.formats.ImageReader
setResolution(int) - Method in class loci.formats.ImageWriter
setResolution(int) - Method in interface loci.formats.IPyramidHandler: Set the resolution level.
setResolution(int) - Method in class loci.formats.ReaderWrapper
setResolution(int) - Method in class loci.formats.SubResolutionFormatReader
setResolution(int) - Method in class loci.formats.WrappedReader
setResolution(int) - Method in class loci.formats.WriterWrapper
setResolutions(List<Resolution>) - Method in class loci.formats.FormatWriter
setResolutions(List<Resolution>) - Method in interface loci.formats.IFormatWriter: Specify a list of resolution objects for the current series.
setResolutions(List<Resolution>) - Method in class loci.formats.ImageWriter
setResolutions(List<Resolution>) - Method in class loci.formats.WriterWrapper
setResolutionSizeX(PositiveInteger, int, int) - Method in interface loci.formats.meta.IPyramidStore: Define the image width in pixels of the given pyramid resolution.
setResolutionSizeX(PositiveInteger, int, int) - Method in class loci.formats.ome.OMEPyramidStore
setResolutionSizeY(PositiveInteger, int, int) - Method in interface loci.formats.meta.IPyramidStore: Define the image height in pixels of the given pyramid resolution.
setResolutionSizeY(PositiveInteger, int, int) - Method in class loci.formats.ome.OMEPyramidStore
setRoot(MetadataRoot) - Method in class loci.formats.ome.OMEPyramidStore
setRowIndex(int) - Method in class loci.formats.internal.WellContainer
setSeries(int) - Method in class loci.formats.DelegateReader
setSeries(int) - Method in class loci.formats.FormatReader
setSeries(int) - Method in class loci.formats.FormatWriter
setSeries(int) - Method in interface loci.formats.IFormatReader: Activates the specified series.
setSeries(int) - Method in interface loci.formats.IFormatWriter: Sets the current series.
setSeries(int) - Method in class loci.formats.ImageReader
setSeries(int) - Method in class loci.formats.ImageWriter
setSeries(int) - Method in class loci.formats.ReaderWrapper
setSeries(int) - Method in class loci.formats.SubResolutionFormatReader
setSeries(int) - Method in class loci.formats.WrappedReader
setSeries(int) - Method in class loci.formats.WriterWrapper
setTileSizeX(int) - Method in class loci.formats.FormatWriter
setTileSizeX(int) - Method in interface loci.formats.IFormatWriter: Will attempt to set the tile width to the desired value and return the actual value which will be used
setTileSizeX(int) - Method in class loci.formats.ImageWriter
setTileSizeX(int) - Method in class loci.formats.WriterWrapper
setTileSizeY(int) - Method in class loci.formats.FormatWriter
setTileSizeY(int) - Method in interface loci.formats.IFormatWriter: Will attempt to set the tile height to the desired value and return the actual value which will be used
setTileSizeY(int) - Method in class loci.formats.ImageWriter
setTileSizeY(int) - Method in class loci.formats.WriterWrapper
setValidate(boolean) - Method in class loci.formats.in.DefaultMetadataOptions
setValidate(boolean) - Method in class loci.formats.in.DynamicMetadataOptions
setValidate(boolean) - Method in interface loci.formats.in.MetadataOptions: Specifies whether or not to validate files when reading.
setValidBitsPerPixel(int) - Method in class loci.formats.FormatWriter
setValidBitsPerPixel(int) - Method in interface loci.formats.IFormatWriter: Sets the number of valid bits per pixel.
setValidBitsPerPixel(int) - Method in class loci.formats.ImageWriter
setValidBitsPerPixel(int) - Method in class loci.formats.WriterWrapper
setWellIndex(int) - Method in class loci.formats.internal.WellContainer
setWriteSequentially(boolean) - Method in class loci.formats.FormatWriter
setWriteSequentially(boolean) - Method in interface loci.formats.IFormatWriter: Sets whether or not we know that planes will be written sequentially.
setWriteSequentially(boolean) - Method in class loci.formats.ImageWriter
setWriteSequentially(boolean) - Method in class loci.formats.WriterWrapper
signed - Variable in class loci.formats.codec.CodecOptions: Indicates whether or not the pixel data is signed.
size() - Method in class loci.formats.MetadataList: Get the size of the array (number of primary array elements).
size(int) - Method in class loci.formats.MetadataList: Get the size of the specified primary array element (number of secondary array elements).
sizeC - Variable in class loci.formats.CoreMetadata: Number of channels.
sizes() - Method in class loci.formats.MetadataList: Get the sizes of all primary array elements.
sizeT - Variable in class loci.formats.CoreMetadata: Number of timepoints.
sizeX - Variable in class loci.formats.CoreMetadata: Width (in pixels) of images in this series.
sizeX - Variable in class loci.formats.Resolution
sizeY - Variable in class loci.formats.CoreMetadata: Height (in pixels) of images in this series.
sizeY - Variable in class loci.formats.Resolution
sizeZ - Variable in class loci.formats.CoreMetadata: Number of Z sections.
SPECTRA - Static variable in class loci.formats.FormatTools: Identifies the Spectra dimensional type, representing a dimension consisting of spectral channels.
SPM_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies the scanning probe microscopy domain.
start - Variable in class loci.formats.Modulo
step - Variable in class loci.formats.Modulo
SubResolutionFormatReader - Class in loci.formats: Abstract superclass of all biological file format readers that can handle image pyramids.
SubResolutionFormatReader(String, String) - Constructor for class loci.formats.SubResolutionFormatReader: Constructs a format reader with the given name and default suffix.
SubResolutionFormatReader(String, String[]) - Constructor for class loci.formats.SubResolutionFormatReader: Constructs a format reader with the given name and default suffixes.
suffixes - Variable in class loci.formats.FormatHandler: Valid suffixes for this file format.
suffixNecessary - Variable in class loci.formats.FormatReader: Whether the file extension matching one of the reader's suffixes is necessary to identify the file as an instance of this format.
suffixSufficient - Variable in class loci.formats.FormatReader: Whether the file extension matching one of the reader's suffixes is sufficient to identify the file as an instance of this format.

T

T_NUM - Static variable in class loci.formats.FormatTools
thumbnail - Variable in class loci.formats.CoreMetadata: Indicates whether or not this series is a lower-resolution copy of another series.
THUMBNAIL_DIMENSION - Static variable in class loci.formats.FormatReader: Default thumbnail width and height.
thumbSizeX - Variable in class loci.formats.CoreMetadata: Width (in pixels) of thumbnail images in this series.
thumbSizeY - Variable in class loci.formats.CoreMetadata: Height (in pixels) of thumbnail images in this series.
TILE_NUM - Static variable in class loci.formats.FormatTools
TILE_X - Static variable in class loci.formats.FormatTools
TILE_Y - Static variable in class loci.formats.FormatTools
tileGridXOffset - Variable in class loci.formats.codec.CodecOptions: Horizontal offset of the tile grid as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileGridYOffset - Variable in class loci.formats.codec.CodecOptions: Vertical offset of the tile grid as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileHeight - Variable in class loci.formats.codec.CodecOptions: Tile height as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
tileWidth - Variable in class loci.formats.codec.CodecOptions: Tile width as it would be provided to: ImageWriteParam.setTiling(int, int, int, int) (WRITE).
TIMESTAMP - Static variable in class loci.formats.FormatTools
toString() - Method in class loci.formats.CoreMetadata
toString() - Method in class loci.formats.FileInfo
toXMLAnnotation() - Method in class loci.formats.Modulo
transformToLatestVersion(String) - Method in interface loci.formats.services.OMEXMLService: Transforms the given OME-XML string to the latest supported version of of the OME-XML schema.
transformToLatestVersion(String) - Method in class loci.formats.services.OMEXMLServiceImpl
type - Variable in class loci.formats.Modulo
typeDescription - Variable in class loci.formats.Modulo

U

UINT16 - Static variable in class loci.formats.FormatTools: Identifies the UINT16 data type used to store pixel values.
UINT32 - Static variable in class loci.formats.FormatTools: Identifies the UINT32 data type used to store pixel values.
UINT8 - Static variable in class loci.formats.FormatTools: Identifies the UINT8 data type used to store pixel values.
unit - Variable in class loci.formats.Modulo
UNKNOWN_DOMAIN - Static variable in class loci.formats.FormatTools: Identifies an unknown domain.
UnknownFormatException - Exception Class in loci.formats: UnknownFormatException is the exception thrown when the format of a particular data stream or filename cannot be recognized or is unsupported.
UnknownFormatException() - Constructor for exception class loci.formats.UnknownFormatException
UnknownFormatException(String) - Constructor for exception class loci.formats.UnknownFormatException
UnknownFormatException(String, Throwable) - Constructor for exception class loci.formats.UnknownFormatException
UnknownFormatException(Throwable) - Constructor for exception class loci.formats.UnknownFormatException
UnsupportedCompressionException - Exception Class in loci.formats: UnsupportedCompressionException is the exception thrown when the compression scheme used in a particular file or stream is unsupported.
UnsupportedCompressionException() - Constructor for exception class loci.formats.UnsupportedCompressionException
UnsupportedCompressionException(String) - Constructor for exception class loci.formats.UnsupportedCompressionException
UnsupportedCompressionException(String, Throwable) - Constructor for exception class loci.formats.UnsupportedCompressionException
UnsupportedCompressionException(Throwable) - Constructor for exception class loci.formats.UnsupportedCompressionException
unwrap() - Method in class loci.formats.ReaderWrapper: Unwraps nested wrapped readers until the core reader (i.e., not a ReaderWrapper or ImageReader) is found.
unwrap() - Method in class loci.formats.WriterWrapper: Unwraps nested wrapped writers until the core writer (i.e., not a WriterWrapper or ImageWriter) is found.
unwrap(Class<? extends IFormatReader>, String) - Method in class loci.formats.ReaderWrapper: Unwraps nested wrapped readers until the given reader class is found.
unwrap(Class<? extends IFormatWriter>, String) - Method in class loci.formats.WriterWrapper: Unwraps nested wrapped writers until the given writer class is found.
unwrap(String) - Method in class loci.formats.ReaderWrapper: Unwraps nested wrapped readers until the core reader (i.e., not a ReaderWrapper or ImageReader) is found.
unwrap(String) - Method in class loci.formats.WriterWrapper: Unwraps nested wrapped writers until the core writer (i.e., not a WriterWrapper or ImageWriter) is found.
updateMetadataLists(Hashtable<String, Object>) - Method in class loci.formats.FormatReader: For the given metadata hashtable, replace any value that is a list with one key/value pair per list entry.
URL_BIO_FORMATS - Static variable in class loci.formats.FormatTools: URL of Bio-Formats web page.
URL_BIO_FORMATS_LIBRARIES - Static variable in class loci.formats.FormatTools: URL of 'Bio-Formats as a Java Library' web page.
URL_OME_TIFF - Static variable in class loci.formats.FormatTools: URL of OME-TIFF web page.
usedToInitialize - Variable in class loci.formats.FileInfo: Whether or not this file can be passed to the appropriate reader's setId(String) method.
useLegacy - Variable in class loci.formats.DelegateReader: Flag indicating whether to use legacy reader by default.

V

validateOMEXML(String) - Method in interface loci.formats.services.OMEXMLService: Attempts to validate the given OME-XML string using Java's XML validation facility.
validateOMEXML(String) - Method in class loci.formats.services.OMEXMLServiceImpl
validateOMEXML(String, boolean) - Method in interface loci.formats.services.OMEXMLService: Attempts to validate the given OME-XML string using Java's XML validation facility.
validateOMEXML(String, boolean) - Method in class loci.formats.services.OMEXMLServiceImpl
validBits - Variable in class loci.formats.FormatWriter: The number of valid bits per pixel.
validStream(RandomAccessInputStream, int, boolean) - Static method in class loci.formats.FormatTools: Returns true if the given RandomAccessInputStream conatins at least 'len' bytes.
valueOf(String) - Static method in enum loci.formats.in.MetadataLevel: Returns the enum constant of this type with the specified name.
values() - Static method in enum loci.formats.in.MetadataLevel: Returns an array containing the constants of this enum type, in the order they are declared.
VCS_REVISION - Static variable in class loci.formats.FormatTools: Current VCS revision.
VCS_SHORT_REVISION - Static variable in class loci.formats.FormatTools: Deprecated.
Use the general FormatTools.VCS_REVISION field.
verifyMinimumPopulated(MetadataRetrieve) - Static method in class loci.formats.MetadataTools: Checks whether the given metadata object has the minimum metadata populated to successfully describe an Image.
verifyMinimumPopulated(MetadataRetrieve, int) - Static method in class loci.formats.MetadataTools: Checks whether the given metadata object has the minimum metadata populated to successfully describe the nth Image.
VERSION - Static variable in class loci.formats.FormatTools: Version number of this release.
VERSION_PROPERTIES - Static variable in class loci.formats.FormatTools

W

WellContainer - Class in loci.formats.internal: Represents a well in a plate.
WellContainer() - Constructor for class loci.formats.internal.WellContainer
WellContainer(int, int, int, int) - Constructor for class loci.formats.internal.WellContainer
width - Variable in class loci.formats.codec.CodecOptions: Width, in pixels, of the image.
WrappedReader - Class in loci.formats: Helper class for readers which wrap other readers.
WrappedReader(String, String[]) - Constructor for class loci.formats.WrappedReader: Constructs a new wrapped reader with the given name and suffixes.
writer - Variable in class loci.formats.WriterWrapper: FormatWriter used to write the file.
writers - Variable in class loci.formats.ImageWriter: List of supported file format writers.
WriterWrapper - Class in loci.formats: Abstract superclass of writer logic that wraps other writers.
WriterWrapper() - Constructor for class loci.formats.WriterWrapper: Constructs a writer wrapper around a new image writer.
WriterWrapper(IFormatWriter) - Constructor for class loci.formats.WriterWrapper: Constructs a writer wrapper around the given writer.

Y

ycbcr - Variable in class loci.formats.codec.CodecOptions: Whether or not the decompressed data will be stored as YCbCr.
YEAR - Static variable in class loci.formats.FormatTools: Year in which this release was built.

Z

Z_NUM - Static variable in class loci.formats.FormatTools

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