Package loci.formats

Bio-Formats: a library for reading and writing popular microscopy file formats.

See:
          Description

Interface Summary
IFormatHandler Interface for all biological file format readers and writers.
IFormatReader Interface for all biological file format readers.
IFormatWriter Interface for all biological file format writers.
IRandomAccess Interface for random access into structures (e.g., files or arrays).
MetadataRetrieve TODO - MetadataRetrieve javadoc.
MetadataStore A proxy whose responsibility it is to marshal biological image data into a particular storage medium.
StatusListener A listener for status updates.
StatusReporter Interface for components capable of reporting status updates.
 

Class Summary
AggregateMetadataStore A metadata store which delegates the actual storage to one or more sub metadata stores.
AxisGuesser AxisGuesser guesses which blocks in a file pattern correspond to which dimensional axes (Z, T or C), potentially recommending an adjustment in dimension order within the files, depending on the confidence of each guess.
ChannelFiller Expands indexed color images to RGB.
ChannelMerger Logic to automatically merge channels in a file.
ChannelSeparator Logic to automatically separate the channels in a file.
ClassList ClassList is a list of classes for use with ImageReader or ImageWriter, parsed from a configuration file such as readers.txt or writers.txt.
CoreMetadata Encompasses core metadata values.
DataTools A utility class with convenience methods for reading, writing and decoding words.
DimensionSwapper Handles swapping the dimension order of a file.
DummyMetadata A dummy implementation for MetadataStore and MetadataRetrieve that is used when no other metadata implementations are available.
FilePattern FilePattern is a collection of methods for handling file patterns, a way of succinctly representing a collection of files meant to be part of the same data series.
FileStitcher Logic to stitch together files with similar names.
FormatHandler Abstract superclass of all biological file format readers and writers.
FormatReader Abstract superclass of all biological file format readers.
FormatTools A utility class for format reader and writer implementations.
FormatWriter Abstract superclass of all biological file format writers.
ImageReader ImageReader is the master file format reader for all supported formats.
ImageTools A utility class with convenience methods for manipulating images.
ImageWriter ImageWriter is the master file format writer for all supported formats.
IndexedColorModel TODO - IndexedColorModel javadoc.
LegacyQTTools Utility class for working with QuickTime for Java.
Location Pseudo-extension of java.io.File that supports reading over HTTP.
Log A simple logging class.
LogTools A utility class for logging.
MetadataTools A utility class for working with metadata objects, including MetadataStore, MetadataRetrieve, and OME-XML strings.
MinMaxCalculator Logic to compute minimum and maximum values for each channel.
NumberFilter NumberFilter is a helper filter for FilePattern.findPattern().
RABytes A wrapper for a byte array that implements the IRandomAccess interface.
RAFile A wrapper for RandomAccessFile that implements the IRandomAccess interface.
RandomAccessStream RandomAccessStream provides methods for "intelligent" reading of files and byte arrays.
RAUrl Provides random access to data over HTTP using the IRandomAccess interface.
ReaderWrapper Abstract superclass of reader logic that wraps other readers.
ReflectedUniverse A general-purpose reflection wrapper class.
StatusEvent A event indicating a status update.
TiffIFDEntry This class represents a single raw TIFF IFD entry.
TiffRational A rational number (numerator over denominator).
TiffTools A utility class for manipulating TIFF files.
TwoChannelColorSpace ColorSpace for 2-channel images.
XMLTools A utility class for working with XML (not necessarily OME-XML).
 

Exception Summary
FormatException FormatException is the exception thrown when something goes wrong performing a file format operation.
ReflectException ReflectException is the exception thrown when something goes wrong performing a reflected operation with ReflectedUniverse.
UnknownTagException Thrown when a given entry does not have a particular tag.
 

Package loci.formats Description

Bio-Formats: a library for reading and writing popular microscopy file formats.