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See:
Description
Interface Summary | |
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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 | |
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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 | |
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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. |
Bio-Formats: a library for reading and writing popular microscopy file formats.
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