Skip navigation links
A B C D E F G H I L M N O P R S T U V W X Y Z 

A

AbstractNIOHandle - Class in loci.common
A wrapper for buffered NIO logic that implements the IRandomAccess interface.
AbstractNIOHandle() - Constructor for class loci.common.AbstractNIOHandle
 
AbstractService - Class in loci.common.services
 
AbstractService() - Constructor for class loci.common.services.AbstractService
 
addStatusListener(StatusListener) - Method in interface loci.common.StatusReporter
 
allocate(int...) - Static method in class loci.common.DataTools
Allocates a 1-dimensional byte array matching the product of the given sizes.
allocate(long, int) - Method in class loci.common.NIOByteBufferProvider
Allocates or maps the desired file data into memory.
allocateDirect(long, int) - Method in class loci.common.NIOByteBufferProvider
Allocates memory and copies the desired file data into it.
allocateMappedByteBuffer(long, int) - Method in class loci.common.NIOByteBufferProvider
Memory maps the desired file data into memory.
ALT_ZVI - Static variable in class loci.common.DateTools
 
ALT_ZVI_EPOCH - Static variable in class loci.common.DateTools
 
available() - Method in class loci.common.NIOInputStream
 
available() - Method in class loci.common.RandomAccessInputStream
 
avoidUndeclaredNamespaces(String) - Static method in class loci.common.xml.XMLTools
Replaces NS:tag with NS_tag for undeclared namespaces

B

BaseHandler - Class in loci.common.xml
Top-level SAX handler.
BaseHandler() - Constructor for class loci.common.xml.BaseHandler
 
buffer - Variable in class loci.common.ByteArrayHandle
Backing ByteBuffer.
buffer - Variable in class loci.common.NIOFileHandle
The buffer itself.
bufferSize - Variable in class loci.common.NIOFileHandle
The buffer size.
bufferStartPosition - Variable in class loci.common.NIOFileHandle
The absolute position of the start of the buffer.
ByteArrayHandle - Class in loci.common
A wrapper for a byte array that implements the IRandomAccess interface.
ByteArrayHandle(byte[]) - Constructor for class loci.common.ByteArrayHandle
Creates a random access byte stream to read from, and write to, the bytes specified by the byte[] argument.
ByteArrayHandle(ByteBuffer) - Constructor for class loci.common.ByteArrayHandle
 
ByteArrayHandle(int) - Constructor for class loci.common.ByteArrayHandle
Creates a random access byte stream to read from, and write to.
ByteArrayHandle() - Constructor for class loci.common.ByteArrayHandle
Creates a random access byte stream to write to a byte array.
byteBufferProvider - Variable in class loci.common.NIOFileHandle
Provider class for NIO byte buffers, allocated or memory mapped.
bytesToDouble(byte[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to a double.
bytesToDouble(byte[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array beyond the given offset to a double.
bytesToDouble(byte[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array to a double.
bytesToDouble(short[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to a double.
bytesToDouble(short[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array beyond the given offset to a double.
bytesToDouble(short[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array to a double.
bytesToFloat(byte[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to a float.
bytesToFloat(byte[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array beyond a given offset to a float.
bytesToFloat(byte[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array to a float.
bytesToFloat(short[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond a given offset to a float.
bytesToFloat(short[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array beyond a given offset to a float.
bytesToFloat(short[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array to a float.
bytesToHex(byte[]) - Static method in class loci.common.DataTools
Translates the given byte array into a String of hexadecimal digits.
bytesToInt(byte[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to an int.
bytesToInt(byte[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array beyond the given offset to an int.
bytesToInt(byte[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array to an int.
bytesToInt(short[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to an int.
bytesToInt(short[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array beyond the given offset to an int.
bytesToInt(short[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 4 bytes of a byte array to an int.
bytesToLong(byte[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to a long.
bytesToLong(byte[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array beyond the given offset to a long.
bytesToLong(byte[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array to a long.
bytesToLong(short[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to a long.
bytesToLong(short[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array beyond the given offset to a long.
bytesToLong(short[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 8 bytes of a byte array to a long.
bytesToShort(byte[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array beyond the given offset to a short.
bytesToShort(byte[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 2 bytes of a byte array beyond the given offset to a short.
bytesToShort(byte[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 2 bytes of a byte array to a short.
bytesToShort(short[], int, int, boolean) - Static method in class loci.common.DataTools
Translates up to the first len bytes of a byte array byond the given offset to a short.
bytesToShort(short[], int, boolean) - Static method in class loci.common.DataTools
Translates up to the first 2 bytes of a byte array byond the given offset to a short.
bytesToShort(short[], boolean) - Static method in class loci.common.DataTools
Translates up to the first 2 bytes of a byte array to a short.
BZip2Handle - Class in loci.common
StreamHandle implementation for reading from BZip2-compressed files or byte arrays.
BZip2Handle(String) - Constructor for class loci.common.BZip2Handle
Construct a new BZip2Handle corresponding to the given file.

C

cacheDirectoryListings(boolean) - Static method in class loci.common.Location
Turn cacheing of directory listings on or off.
canRead() - Method in class loci.common.Location
If the underlying location is a URL, this method will return true if the URL exists.
canWrite() - Method in class loci.common.Location
If the underlying location is a URL, this method will always return false.
CaseInsensitiveLocation - Class in loci.common
Case insensitive variant of Location.
CaseInsensitiveLocation(String) - Constructor for class loci.common.CaseInsensitiveLocation
 
CaseInsensitiveLocation(Location) - Constructor for class loci.common.CaseInsensitiveLocation
 
CaseInsensitiveLocation(File) - Constructor for class loci.common.CaseInsensitiveLocation
 
CaseInsensitiveLocation(String, String) - Constructor for class loci.common.CaseInsensitiveLocation
 
CaseInsensitiveLocation(CaseInsensitiveLocation, String) - Constructor for class loci.common.CaseInsensitiveLocation
 
CBZip2InputStream - Class in loci.common
An input stream that decompresses from the BZip2 format (without the file header chars) to be read as any other stream.
CBZip2InputStream(InputStream) - Constructor for class loci.common.CBZip2InputStream
Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.
channel - Variable in class loci.common.NIOFileHandle
The file channel backed by the random access file.
channel - Variable in class loci.common.NIOInputStream
The file channel backed by the random access file.
checkClassDependency(Class<? extends Object>) - Method in class loci.common.services.AbstractService
Checks a given class dependency at runtime to ensure that a given class will be available.
checkValidId(String) - Static method in class loci.common.Location
Checks that the given id points at a valid data stream.
cleanStaleCacheEntries() - Static method in class loci.common.Location
Remove any cached directory listings that have expired.
clearDirectoryListingsCache() - Static method in class loci.common.Location
Clear the directory listings cache.
close() - Method in class loci.common.ByteArrayHandle
 
close() - Method in class loci.common.CBZip2InputStream
 
close() - Method in class loci.common.FileHandle
 
close() - Method in interface loci.common.IRandomAccess
Closes this random access stream and releases any system resources associated with the stream.
close() - Method in class loci.common.NIOFileHandle
 
close() - Method in class loci.common.NIOInputStream
Closes the streams.
close() - Method in class loci.common.RandomAccessInputStream
Closes the streams.
close() - Method in class loci.common.RandomAccessOutputStream
 
close() - Method in class loci.common.StreamHandle
 
close() - Method in class loci.common.ZipHandle
 
COBOL - Static variable in class loci.common.DateTools
 
COBOL_EPOCH - Static variable in class loci.common.DateTools
 
CodedEnum - Interface in loci.common.enumeration
Enumeration which is coded.
Constants - Class in loci.common
Constants that are used within many classes in loci.common.
Constants() - Constructor for class loci.common.Constants
 
containsPoint(int, int) - Method in class loci.common.Region
Returns true if the point specified by the given X and Y coordinates is contained within this region.
containsValue(int[], int) - Static method in class loci.common.DataTools
Returns true if the given value is contained in the given array.
convertDate(long, int) - Static method in class loci.common.DateTools
Converts the given timestamp into an ISO8601 date.
convertDate(long, int, String) - Static method in class loci.common.DateTools
Converts the given timestamp into a date string with the given format.
convertDate(long, int, String, boolean) - Static method in class loci.common.DateTools
Converts the given timestamp into a date string with the given format.
CRC - Class in loci.common
A simple class to hold and calculate the CRC for sanity checking the data.
CRC() - Constructor for class loci.common.CRC
 
CRC_32_TABLE - Static variable in class loci.common.CRC
 
createBuilder() - Static method in class loci.common.xml.XMLTools
Creates a new DocumentBuilder via DocumentBuilderFactory or logs and throws a RuntimeException.
createDocument() - Static method in class loci.common.xml.XMLTools
createNewFile() - Method in class loci.common.Location
Creates a new empty file named by this Location's path name iff a file with this name does not already exist.

D

DataTools - Class in loci.common
A utility class with convenience methods for reading, writing and decoding words.
DateTools - Class in loci.common
A utility class with convenience methods for working with dates.
DebugTools - Class in loci.common
A utility class with convenience methods for debugging.
DEFAULT_BLOCK_SIZE - Static variable in class loci.common.NIOInputStream
Block size to use when searching through the stream.
DEFAULT_BLOCK_SIZE - Static variable in class loci.common.RandomAccessInputStream
Block size to use when searching through the stream.
DEFAULT_HEADER - Static variable in class loci.common.IniTable
Default header name when no header is available.
defaultBufferSize - Static variable in class loci.common.NIOFileHandle
Default NIO buffer size to facilitate buffered I/O.
defaultRWBufferSize - Static variable in class loci.common.NIOFileHandle
Default NIO buffer size to facilitate buffered I/O for read/write streams.
delete() - Method in class loci.common.Location
Deletes this file.
deleteOnExit() - Method in class loci.common.Location
Request that this file be deleted when the JVM terminates.
DependencyException - Exception in loci.common.services
Exception thrown when there is an object instantiation error or error processing dependencies.
DependencyException(String) - Constructor for exception loci.common.services.DependencyException
Default constructor.
DependencyException(String, Class<? extends Service>) - Constructor for exception loci.common.services.DependencyException
Default constructor.
DependencyException(String, Class<? extends Service>, Throwable) - Constructor for exception loci.common.services.DependencyException
Default constructor.
DependencyException(Throwable) - Constructor for exception loci.common.services.DependencyException
Default constructor.
doublesToBytes(double[], boolean) - Static method in class loci.common.DataTools
Translates an array of double values into an array of byte values.
doubleToBytes(double, boolean) - Static method in class loci.common.DataTools
Translates the double value into an array of eight bytes.
dumpXML(String, Document, Element) - Static method in class loci.common.xml.XMLTools
Dumps the given OME-XML DOM tree to a string.
dumpXML(String, Document, Element, boolean) - Static method in class loci.common.xml.XMLTools
Dumps the given OME-XML DOM tree to a string.

E

enableIJLogging(boolean) - Static method in class loci.common.DebugTools
Enable SLF4J logging using logback, in the context of ImageJ.
enableIJLogging(boolean, Appender<ILoggingEvent>) - Static method in class loci.common.LogbackTools
 
enableLogging() - Static method in class loci.common.DebugTools
Attempts to enable SLF4J logging via logback or log4j.
enableLogging(String) - Static method in class loci.common.DebugTools
Attempts to enable SLF4J logging and set the root logger level.
enableLogging() - Static method in class loci.common.Log4jTools
Attempts to enable SLF4J logging via log4j without an external configuration file.
enableLogging() - Static method in class loci.common.LogbackTools
Initializes logback without an external configuration file.
ENCODING - Static variable in class loci.common.Constants
 
encoding - Variable in class loci.common.RandomAccessInputStream
 
EnumException - Exception in loci.common.enumeration
 
EnumException() - Constructor for exception loci.common.enumeration.EnumException
 
EnumException(String) - Constructor for exception loci.common.enumeration.EnumException
 
EnumException(String, Throwable) - Constructor for exception loci.common.enumeration.EnumException
 
EnumException(Throwable) - Constructor for exception loci.common.enumeration.EnumException
 
EOF_ERROR_MSG - Static variable in class loci.common.AbstractNIOHandle
Error message to be used when instantiating an EOFException.
EPSILON - Static variable in class loci.common.Constants
 
equals(Object) - Method in class loci.common.Location
 
equals(Object) - Method in class loci.common.Region
 
error(SAXParseException) - Method in class loci.common.xml.ParserErrorHandler
 
error(SAXParseException) - Method in class loci.common.xml.ValidationErrorHandler
 
escapeXML(String) - Static method in class loci.common.xml.XMLTools
Escape special characters.
exec(String) - Method in class loci.common.ReflectedUniverse
Deprecated.
Executes a command in the universe.
exists() - Method in class loci.common.Location
Returns whether or not the pathname exists.

F

fatalError(SAXParseException) - Method in class loci.common.xml.ParserErrorHandler
 
fatalError(SAXParseException) - Method in class loci.common.xml.ValidationErrorHandler
 
file - Variable in class loci.common.NIOInputStream
The file.
file - Variable in class loci.common.RandomAccessInputStream
The file name.
file - Variable in class loci.common.StreamHandle
Name of the open stream.
FileHandle - Class in loci.common
A wrapper for RandomAccessFile that implements the IRandomAccess interface.
FileHandle(File, String) - Constructor for class loci.common.FileHandle
Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.
FileHandle(String, String) - Constructor for class loci.common.FileHandle
Creates a random access file stream to read from, and optionally to write to, a file with the specified name.
filename - Variable in class loci.common.NIOInputStream
The file name.
FILENAME_FORMAT - Static variable in class loci.common.DateTools
Human readable timestamp filename string
findString(String...) - Method in class loci.common.NIOInputStream
Reads a string ending with one of the given terminating substrings.
findString(boolean, String...) - Method in class loci.common.NIOInputStream
Reads or skips a string ending with one of the given terminating substrings.
findString(int, String...) - Method in class loci.common.NIOInputStream
Reads a string ending with one of the given terminating substrings, using the specified block size for buffering.
findString(boolean, int, String...) - Method in class loci.common.NIOInputStream
Reads or skips a string ending with one of the given terminating substrings, using the specified block size for buffering.
findString(String...) - Method in class loci.common.RandomAccessInputStream
Reads a string ending with one of the given terminating substrings.
findString(boolean, String...) - Method in class loci.common.RandomAccessInputStream
Reads or skips a string ending with one of the given terminating substrings.
findString(int, String...) - Method in class loci.common.RandomAccessInputStream
Reads a string ending with one of the given terminating substrings, using the specified block size for buffering.
findString(boolean, int, String...) - Method in class loci.common.RandomAccessInputStream
Reads or skips a string ending with one of the given terminating substrings, using the specified block size for buffering.
flattenIntoHashMap() - Method in class loci.common.IniList
Flattens all of the INI tables into a single HashMap whose keys are of the format "[table name] table key".
floatsToBytes(float[], boolean) - Static method in class loci.common.DataTools
Translates an array of float values into an array of byte values.
floatToBytes(float, boolean) - Static method in class loci.common.DataTools
Translates the float value into an array of four bytes.
flush() - Method in class loci.common.RandomAccessOutputStream
 
force - Variable in class loci.common.ReflectedUniverse
Deprecated.
Whether to force our way past restrictive access modifiers.
formatDate(String, String) - Static method in class loci.common.DateTools
Formats the given date as an ISO 8601 date.
formatDate(String, String, String) - Static method in class loci.common.DateTools
Formats the given date as an ISO 8601 date.
formatDate(String, String, boolean) - Static method in class loci.common.DateTools
Formats the given date as an ISO 8601 date.
formatDate(String, String, boolean, String) - Static method in class loci.common.DateTools
Formats the given date as an ISO 8601 date.
formatDate(String, String[]) - Static method in class loci.common.DateTools
Formats the given date as an ISO 8601 date.
formatDate(String, String[], boolean) - Static method in class loci.common.DateTools
Formats the given date as an ISO 8601 date.
formatDate(String, String[], String) - Static method in class loci.common.DateTools
Formats the given date as an ISO 8601 date.
formatDate(String, String[], boolean, String) - Static method in class loci.common.DateTools
Formats the given date as an ISO 8601 date.
fp - Variable in class loci.common.StreamHandle
Current position within the stream.

G

getAbsoluteFile() - Method in class loci.common.Location
 
getAbsolutePath() - Method in class loci.common.Location
 
getBaseURI() - Method in class loci.common.xml.LSInputI
 
getBufferSize() - Method in class loci.common.NIOFileHandle
Gets the current buffer size.
getByteBuffer() - Method in class loci.common.ByteArrayHandle
Gets the byte buffer backing this handle.
getBytes() - Method in class loci.common.ByteArrayHandle
Gets the byte array backing this FileHandle.
getByteStream() - Method in class loci.common.xml.LSInputI
 
getCanonicalFile() - Method in class loci.common.Location
 
getCanonicalPath() - Method in class loci.common.Location
Returns the canonical path to this file.
getCertifiedText() - Method in class loci.common.xml.LSInputI
 
getCharacterStream() - Method in class loci.common.xml.LSInputI
 
getCode() - Method in interface loci.common.enumeration.CodedEnum
Retrieves the integer "code" for this enumeration.
getEncoding() - Method in class loci.common.xml.LSInputI
 
getEntryCount() - Method in class loci.common.ZipHandle
Returns the number of entries.
getEntryName() - Method in class loci.common.ZipHandle
Get the name of the backing Zip entry.
getErrorCount() - Method in class loci.common.xml.ValidationErrorHandler
 
getFailureClass() - Method in exception loci.common.services.DependencyException
Returns the class that was used during a failed instantiation.
getFieldName(Class<?>, int) - Static method in class loci.common.DebugTools
This method uses reflection to scan the values of the given class's static fields, returning the first matching field's name.
getFileChannel() - Method in class loci.common.NIOFileHandle
Gets the FileChannel from this FileHandle.
getFilePointer() - Method in class loci.common.ByteArrayHandle
 
getFilePointer() - Method in class loci.common.FileHandle
 
getFilePointer() - Method in interface loci.common.IRandomAccess
Returns the current offset in this stream.
getFilePointer() - Method in class loci.common.NIOFileHandle
 
getFilePointer() - Method in class loci.common.NIOInputStream
Gets the current (absolute) file pointer.
getFilePointer() - Method in class loci.common.RandomAccessInputStream
Gets the current (absolute) file pointer.
getFilePointer() - Method in class loci.common.RandomAccessOutputStream
Returns the current offset within the stream.
getFilePointer() - Method in class loci.common.StreamHandle
 
getFileTimestamp() - Static method in class loci.common.DateTools
Returns a timestamp for the current timezone in a format suitable for a filename in a locale-independent format ("YYYY-MM-DD_HH-MM-SS")
getFinalCRC() - Method in class loci.common.CRC
 
getGlobalCRC() - Method in class loci.common.CRC
 
getHandle(String) - Static method in class loci.common.Location
Gets an IRandomAccess object that can read from the given file.
getHandle(String, boolean) - Static method in class loci.common.Location
Gets an IRandomAccess object that can read from or write to the given file.
getHandle(String, boolean, boolean) - Static method in class loci.common.Location
Gets an IRandomAccess object that can read from or write to the given file.
getHandle(String, boolean, boolean, int) - Static method in class loci.common.Location
 
getHeaders() - Method in class loci.common.IniList
Gets the table names (headers) in the list.
getIdMap() - Static method in class loci.common.Location
Return the id mapping.
getInputStream() - Method in class loci.common.NIOInputStream
Returns the underlying InputStream.
getInputStream() - Method in class loci.common.ZipHandle
Returns the DataInputStream corresponding to the backing Zip entry.
getInstance(Class<T>) - Method in class loci.common.services.ServiceFactory
Retrieves an instance of a given service.
getMappedFile(String) - Static method in class loci.common.Location
Gets the random access handle for the given id.
getMappedId(String) - Static method in class loci.common.Location
Gets the actual filename on disk for the given id.
getMillisFromTicks(long, long) - Static method in class loci.common.DateTools
Converts from two-word tick representation to milliseconds.
getName() - Method in class loci.common.Location
Returns the name of this file, i.e.
getOrder() - Method in class loci.common.ByteArrayHandle
 
getOrder() - Method in class loci.common.FileHandle
 
getOrder() - Method in interface loci.common.IRandomAccess
Returns the current order of the stream.
getOrder() - Method in class loci.common.NIOFileHandle
 
getOrder() - Method in class loci.common.StreamHandle
 
getParent() - Method in class loci.common.Location
Returns the name of this file's parent directory, i.e.
getParentFile() - Method in class loci.common.Location
 
getPath() - Method in class loci.common.Location
 
getProgressMaximum() - Method in class loci.common.StatusEvent
Gets progress maximum.
getProgressValue() - Method in class loci.common.StatusEvent
Gets progress value.
getPublicId() - Method in class loci.common.xml.LSInputI
 
getRandomAccessFile() - Method in class loci.common.FileHandle
Gets the random access file object backing this FileHandle.
getRandomAccessFile() - Method in class loci.common.NIOFileHandle
Gets the random access file object backing this FileHandle.
getSchemaAsStream(String) - Method in interface loci.common.xml.XMLTools.SchemaReader
Get the given XML schema definition as an InputStream.
getStackTrace(Throwable) - Static method in class loci.common.DebugTools
Extracts the given exception's corresponding stack trace to a string.
getStatusMessage() - Method in class loci.common.StatusEvent
Gets status message.
getStringData() - Method in class loci.common.xml.LSInputI
 
getStylesheet(String, Class<?>) - Static method in class loci.common.xml.XMLTools
Gets an XSLT template from the given resource location.
getSystemId() - Method in class loci.common.xml.LSInputI
 
getTable(String) - Method in class loci.common.IniList
Gets the table with the given name (header).
getTime(String, String) - Static method in class loci.common.DateTools
Converts a string date in the given format to a long timestamp (in Unix format: milliseconds since January 1, 1970).
getTime(String, String, String) - Static method in class loci.common.DateTools
Converts a string date in the given format to a long timestamp (in Unix format: milliseconds since January 1, 1970) with special milliseconds handling.
getTimestamp() - Static method in class loci.common.DateTools
Returns a timestamp for the current timezone in a human-readable locale-independent format ("YYYY-MM-DD HH:MM:SS")
getVar(String) - Method in class loci.common.ReflectedUniverse
Deprecated.
Returns the value of a variable or field in the universe.
getXML(Document) - Static method in class loci.common.xml.XMLTools
Converts the given DOM back to a string.
GZipHandle - Class in loci.common
StreamHandle implementation for reading from gzip-compressed files or byte arrays.
GZipHandle(String) - Constructor for class loci.common.GZipHandle
Construct a new GZipHandle for the given file.

H

HandleException - Exception in loci.common
HandleException is the exception thrown when something goes wrong in one of the custom I/O classes.
HandleException() - Constructor for exception loci.common.HandleException
 
HandleException(String) - Constructor for exception loci.common.HandleException
 
HandleException(String, Throwable) - Constructor for exception loci.common.HandleException
 
HandleException(Throwable) - Constructor for exception loci.common.HandleException
 
hashCode() - Method in class loci.common.Location
 
hashCode() - Method in class loci.common.Region
 
HEADER_KEY - Static variable in class loci.common.IniTable
Key to use for storing header value (in brackets).
height - Variable in class loci.common.Region
 

I

indentXML(String) - Static method in class loci.common.xml.XMLTools
Indents XML to be more readable.
indentXML(String, int) - Static method in class loci.common.xml.XMLTools
Indents XML by the given spacing to be more readable.
indentXML(String, boolean) - Static method in class loci.common.xml.XMLTools
Indents XML to be more readable, avoiding any whitespace injection into CDATA if the preserveCData flag is set.
indentXML(String, int, boolean) - Static method in class loci.common.xml.XMLTools
Indents XML by the given spacing to be more readable, avoiding any whitespace injection into CDATA if the preserveCData flag is set.
indexOf(int[], int) - Static method in class loci.common.DataTools
Returns the index of the first occurrence of the given value in the given array.
indexOf(Object[], Object) - Static method in class loci.common.DataTools
Returns the index of the first occurrence of the given value in the given Object array.
IniList - Class in loci.common
A data structure containing a parsed list of INI key/value tables.
IniList() - Constructor for class loci.common.IniList
 
IniParser - Class in loci.common
A simple parser for INI configuration files.
IniParser() - Constructor for class loci.common.IniParser
 
IniTable - Class in loci.common
A data structure containing a parsed list of INI key/value tables.
IniTable() - Constructor for class loci.common.IniTable
 
INITIAL_LENGTH - Static variable in class loci.common.ByteArrayHandle
Initial length of a new file.
initialiseCRC() - Method in class loci.common.CRC
 
IniWriter - Class in loci.common
A simple writer for INI configuration files.
IniWriter() - Constructor for class loci.common.IniWriter
 
intersection(Region) - Method in class loci.common.Region
Returns a Region representing the intersection of this Region with the given Region.
intersects(Region) - Method in class loci.common.Region
Returns true if this region intersects the given region.
intsToBytes(int[], boolean) - Static method in class loci.common.DataTools
Translates an array of int values into an array of byte values.
intToBytes(int, boolean) - Static method in class loci.common.DataTools
Translates the int value into an array of four bytes.
invalidateCache() - Static method in class loci.common.CaseInsensitiveLocation
Remove (invalidate) cached content for all directories.
invalidateCache(File) - Static method in class loci.common.CaseInsensitiveLocation
Remove (invalidate) cached content for the specified directory.
IRandomAccess - Interface in loci.common
Interface for random access into structures (e.g., files or arrays).
isAbsolute() - Method in class loci.common.Location
Tests whether or not this path name is absolute.
isAccessibilityIgnored() - Method in class loci.common.ReflectedUniverse
Deprecated.
Gets whether access modifiers (protected, private, etc.) are ignored.
isBitOnByteBoundary() - Method in class loci.common.RandomAccessInputStream
Checks if the current position is on a byte boundary, that is the next bit in the byte array is the first bit in a byte.
isBZip2File(String) - Static method in class loci.common.BZip2Handle
Returns true if the given filename is a BZip2 file.
isDirectory() - Method in class loci.common.Location
Returns true if this pathname exists and represents a directory.
isEnabled() - Static method in class loci.common.DebugTools
Checks whether SLF4J logging has been enabled via logback or log4j.
isEnabled() - Static method in class loci.common.Log4jTools
Checks whether the log4j framework was successfully enabled
isEnabled() - Static method in class loci.common.LogbackTools
Checks whether logback has been enabled.
isFile() - Method in class loci.common.Location
Returns true if this pathname exists and represents a regular file.
isGZipFile(String) - Static method in class loci.common.GZipHandle
Returns true if the given filename is a gzip file.
isHidden() - Method in class loci.common.Location
Returns true if the pathname is 'hidden'.
isInstance(Class<?>, Object) - Static method in class loci.common.ReflectedUniverse
Deprecated.
Returns whether the given object is compatible with the specified class for the purposes of reflection.
isLittleEndian - Variable in class loci.common.NIOInputStream
Endianness of the stream.
isLittleEndian() - Method in class loci.common.NIOInputStream
Gets the endianness of the stream.
isLittleEndian() - Method in class loci.common.RandomAccessInputStream
Gets the endianness of the stream.
isLittleEndian() - Method in class loci.common.RandomAccessOutputStream
Gets the endianness of the stream.
ISO8601_FORMAT - Static variable in class loci.common.DateTools
ISO 8601 date output formatter without milliseconds.
ISO8601_FORMAT_MS - Static variable in class loci.common.DateTools
ISO 8601 date output formatter with milliseconds.
isReadWrite - Variable in class loci.common.NIOFileHandle
Whether or not the file is opened read/write.
isWarning() - Method in class loci.common.StatusEvent
Returns whether or not this is a warning event.
isZipFile(String) - Static method in class loci.common.ZipHandle
Returns true if the given filename is a Zip file.

L

lastModified() - Method in class loci.common.Location
Return the last modification time of this file, in milliseconds since the UNIX epoch.
length() - Method in class loci.common.ByteArrayHandle
 
length() - Method in class loci.common.FileHandle
 
length() - Method in interface loci.common.IRandomAccess
Returns the length of this stream.
length() - Method in class loci.common.Location
 
length() - Method in class loci.common.NIOFileHandle
 
length() - Method in class loci.common.NIOInputStream
Gets the number of bytes in the file.
length - Variable in class loci.common.RandomAccessInputStream
 
length() - Method in class loci.common.RandomAccessInputStream
Gets the number of bytes in the file.
length() - Method in class loci.common.RandomAccessOutputStream
Returns the length of the file.
length - Variable in class loci.common.StreamHandle
Length of the stream.
length() - Method in class loci.common.StreamHandle
 
list(boolean) - Method in class loci.common.Location
Return a list of all of the files in this directory.
list() - Method in class loci.common.Location
Return a list of file names in this directory.
listFiles() - Method in class loci.common.Location
Return a list of absolute files in this directory.
listing - Variable in class loci.common.Location.ListingsResult
 
loader - Variable in class loci.common.ReflectedUniverse
Deprecated.
Class loader for imported classes.
Location - Class in loci.common
Pseudo-extension of java.io.File that supports reading over HTTP (among other things).
Location(String) - Constructor for class loci.common.Location
 
Location(File) - Constructor for class loci.common.Location
 
Location(String, String) - Constructor for class loci.common.Location
 
Location(Location, String) - Constructor for class loci.common.Location
 
Location.ListingsResult - Class in loci.common
 
loci.common - package loci.common
 
loci.common.enumeration - package loci.common.enumeration
 
loci.common.services - package loci.common.services
 
loci.common.xml - package loci.common.xml
 
Log4jTools - Class in loci.common
A utility class with convenience methods for log4j.
LogbackTools - Class in loci.common
A utility class with convenience methods for logback.
longsToBytes(long[], boolean) - Static method in class loci.common.DataTools
Translates an array of long values into an array of byte values.
longToBytes(long, boolean) - Static method in class loci.common.DataTools
Translates the long value into an array of eight bytes.
LSInputI - Class in loci.common.xml
A simple bean implementation of the LSInput interface.
LSInputI() - Constructor for class loci.common.xml.LSInputI
 

M

main(String[]) - Static method in class loci.common.ReflectedUniverse
Deprecated.
Allows exploration of a reflected universe in an interactive environment.
makeDataArray(byte[], int, boolean, boolean) - Static method in class loci.common.DataTools
Convert a byte array to the appropriate 1D primitive type array.
makeDataArray2D(byte[], int, boolean, boolean, int) - Static method in class loci.common.DataTools
Convert a byte array to the appropriate 2D primitive type array.
makeSigned(byte[]) - Static method in class loci.common.DataTools
 
makeSigned(short[]) - Static method in class loci.common.DataTools
 
makeSigned(int[]) - Static method in class loci.common.DataTools
 
mapFile(String, IRandomAccess) - Static method in class loci.common.Location
Maps the given id to the given IRandomAccess object.
mapId(String, String) - Static method in class loci.common.Location
Maps the given id to an actual filename on disk.
mapMode - Variable in class loci.common.NIOFileHandle
The default map mode for the file.
mark(int) - Method in class loci.common.NIOInputStream
 
mark(int) - Method in class loci.common.RandomAccessInputStream
 
mark - Variable in class loci.common.StreamHandle
Marked position within the stream.
markedPos - Variable in class loci.common.RandomAccessInputStream
 
markSupported() - Method in class loci.common.NIOInputStream
 
markSupported() - Method in class loci.common.RandomAccessInputStream
 
MAX_OVERHEAD - Static variable in class loci.common.RandomAccessInputStream
Maximum size of the buffer used by the DataInputStream.
MAX_SEARCH_SIZE - Static variable in class loci.common.NIOInputStream
Maximum number of bytes to search when searching through the stream.
MAX_SEARCH_SIZE - Static variable in class loci.common.RandomAccessInputStream
Maximum number of bytes to search when searching through the stream.
maximum - Variable in class loci.common.StatusEvent
Current progress maximum.
MICROSOFT - Static variable in class loci.common.DateTools
 
MICROSOFT_EPOCH - Static variable in class loci.common.DateTools
 
MINIMUM_JAVA_VERSION - Static variable in class loci.common.NIOByteBufferProvider
The minimum Java version we know is safe for memory mapped I/O.
mkdirs() - Method in class loci.common.Location
Creates a directory structures described by this Location's internal File instance.

N

NIOByteBufferProvider - Class in loci.common
Provides a facade to byte buffer allocation that enables FileChannel.map() usage on platforms where it's unlikely to give us problems and heap allocation where it is.
NIOByteBufferProvider(FileChannel, FileChannel.MapMode) - Constructor for class loci.common.NIOByteBufferProvider
Default constructor.
NIOFileHandle - Class in loci.common
A wrapper for buffered NIO logic that implements the IRandomAccess interface.
NIOFileHandle(File, String, int) - Constructor for class loci.common.NIOFileHandle
Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.
NIOFileHandle(File, String) - Constructor for class loci.common.NIOFileHandle
Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.
NIOFileHandle(String, String) - Constructor for class loci.common.NIOFileHandle
Creates a random access file stream to read from, and optionally to write to, a file with the specified name.
NIOInputStream - Class in loci.common
NIOInputStream provides methods for "intelligent" reading of files and byte arrays.
NIOInputStream(String) - Constructor for class loci.common.NIOInputStream
Constructs an NIOInputStream around the given file.
NIOInputStream(IRandomAccess) - Constructor for class loci.common.NIOInputStream
Constructs a random access stream around the given handle.
NIOInputStream(byte[]) - Constructor for class loci.common.NIOInputStream
Constructs a random access stream around the given byte array.
normalizeDoubles(double[]) - Static method in class loci.common.DataTools
Normalize the given double array so that the minimum value maps to 0.0 and the maximum value maps to 1.0.
normalizeFloats(float[]) - Static method in class loci.common.DataTools
Normalize the given float array so that the minimum value maps to 0.0 and the maximum value maps to 1.0.
notifyListeners(StatusEvent) - Method in interface loci.common.StatusReporter
 

O

ok() - Method in class loci.common.xml.ValidationErrorHandler
 
openTextResource(String) - Static method in class loci.common.IniParser
Opens a buffered reader for the given resource.
openTextResource(String, Class<?>) - Static method in class loci.common.IniParser
Opens a buffered reader for the given resource.
order - Variable in class loci.common.NIOFileHandle
The buffer's byte ordering.
order(boolean) - Method in class loci.common.NIOInputStream
Sets the endianness of the stream.
order(boolean) - Method in class loci.common.RandomAccessInputStream
Sets the endianness of the stream.
order(boolean) - Method in class loci.common.RandomAccessOutputStream
Sets the endianness of the stream.
order - Variable in class loci.common.StreamHandle
Byte ordering of this stream.
outStream - Variable in class loci.common.StreamHandle
OutputStream to be used for writing.

P

parseByte(String) - Static method in class loci.common.DataTools
Parses the input string into a byte
parseDate(String, String, String) - Static method in class loci.common.DateTools
Parse the given date as a Joda instant
parseDOM(File) - Static method in class loci.common.xml.XMLTools
Parses a DOM from the given XML file on disk.
parseDOM(String) - Static method in class loci.common.xml.XMLTools
Parses a DOM from the given XML string.
parseDOM(InputStream) - Static method in class loci.common.xml.XMLTools
Parses a DOM from the given XML input stream.
parseDouble(String) - Static method in class loci.common.DataTools
Parses the input string into a double accounting for the locale decimal separator
parseFloat(String) - Static method in class loci.common.DataTools
Parses the input string into a float accounting for the locale decimal separator
parseINI(String) - Method in class loci.common.IniParser
Parses the INI-style configuration data from the given resource.
parseINI(String, Class<?>) - Method in class loci.common.IniParser
Parses the INI-style configuration data from the given resource, using the given class to find the resource.
parseINI(File) - Method in class loci.common.IniParser
Parses the INI-style wrapping the given file in a BufferedReader
parseINI(BufferedReader) - Method in class loci.common.IniParser
Parses the INI-style configuration data from the given input stream.
parseInteger(String) - Static method in class loci.common.DataTools
Parses the input string into an integer
parseLong(String) - Static method in class loci.common.DataTools
Parses the input string into a long
ParserErrorHandler - Class in loci.common.xml
Used by various XMLTools methods to handle XML parsing errors.
ParserErrorHandler() - Constructor for class loci.common.xml.ParserErrorHandler
 
parseShort(String) - Static method in class loci.common.DataTools
Parses the input string into a short
parseXML(String) - Static method in class loci.common.xml.XMLTools
Parses the given XML string into a list of key/value pairs.
parseXML(String, DefaultHandler) - Static method in class loci.common.xml.XMLTools
Parses the given XML string using the specified XML handler.
parseXML(RandomAccessInputStream, DefaultHandler) - Static method in class loci.common.xml.XMLTools
Parses the XML contained in the given input stream into using the specified XML handler.
parseXML(byte[], DefaultHandler) - Static method in class loci.common.xml.XMLTools
Parses the XML contained in the given byte array into using the specified XML handler.
parseXML(InputStream, DefaultHandler) - Static method in class loci.common.xml.XMLTools
Parses the XML contained in the given InputStream using the specified XML handler.
position - Variable in class loci.common.NIOFileHandle
The absolute position within the file.
progress - Variable in class loci.common.StatusEvent
Current progress value.

R

raf - Variable in class loci.common.FileHandle
The random access file object backing this FileHandle.
raf - Variable in class loci.common.NIOFileHandle
The random access file object backing this FileHandle.
raf - Variable in class loci.common.NIOInputStream
 
raf - Variable in class loci.common.RandomAccessInputStream
 
RandomAccessInputStream - Class in loci.common
Top-level class for reading from various data sources.
RandomAccessInputStream(String) - Constructor for class loci.common.RandomAccessInputStream
Constructs a hybrid RandomAccessFile/DataInputStream around the given file.
RandomAccessInputStream(String, int) - Constructor for class loci.common.RandomAccessInputStream
Constructs a hybrid RandomAccessFile/DataInputStream around the given file.
RandomAccessInputStream(IRandomAccess) - Constructor for class loci.common.RandomAccessInputStream
Constructs a random access stream around the given handle.
RandomAccessInputStream(IRandomAccess, String) - Constructor for class loci.common.RandomAccessInputStream
Constructs a random access stream around the given handle, and with the associated file path.
RandomAccessInputStream(byte[]) - Constructor for class loci.common.RandomAccessInputStream
Constructs a random access stream around the given byte array.
RandomAccessOutputStream - Class in loci.common
RandomAccessOutputStream provides methods for writing to files and byte arrays.
RandomAccessOutputStream(String) - Constructor for class loci.common.RandomAccessOutputStream
Constructs a random access stream around the given file.
RandomAccessOutputStream(IRandomAccess) - Constructor for class loci.common.RandomAccessOutputStream
Constructs a random access stream around the given handle.
RandomAccessOutputStream(byte[]) - Constructor for class loci.common.RandomAccessOutputStream
Constructs a random access stream around the given byte array.
read(byte[]) - Method in class loci.common.ByteArrayHandle
 
read(byte[], int, int) - Method in class loci.common.ByteArrayHandle
 
read(ByteBuffer) - Method in class loci.common.ByteArrayHandle
 
read(ByteBuffer, int, int) - Method in class loci.common.ByteArrayHandle
 
read() - Method in class loci.common.CBZip2InputStream
 
read(byte[], int, int) - Method in class loci.common.CBZip2InputStream
 
read(byte[]) - Method in class loci.common.FileHandle
 
read(byte[], int, int) - Method in class loci.common.FileHandle
 
read(ByteBuffer) - Method in class loci.common.FileHandle
 
read(ByteBuffer, int, int) - Method in class loci.common.FileHandle
 
read(byte[]) - Method in interface loci.common.IRandomAccess
Reads up to b.length bytes of data from this stream into an array of bytes.
read(byte[], int, int) - Method in interface loci.common.IRandomAccess
Reads up to len bytes of data from this stream into an array of bytes.
read(ByteBuffer) - Method in interface loci.common.IRandomAccess
Reads up to buffer.capacity() bytes of data from this stream into a ByteBuffer.
read(ByteBuffer, int, int) - Method in interface loci.common.IRandomAccess
Reads up to len bytes of data from this stream into a ByteBuffer.
read(byte[]) - Method in class loci.common.NIOFileHandle
 
read(byte[], int, int) - Method in class loci.common.NIOFileHandle
 
read(ByteBuffer) - Method in class loci.common.NIOFileHandle
 
read(ByteBuffer, int, int) - Method in class loci.common.NIOFileHandle
 
read() - Method in class loci.common.NIOInputStream
Alias for readByte().
read(byte[]) - Method in class loci.common.NIOInputStream
Read bytes from the stream into the given array.
read(byte[], int, int) - Method in class loci.common.NIOInputStream
Read n bytes from the stream into the given array at the specified offset.
read(byte[]) - Method in class loci.common.RandomAccessInputStream
Read bytes from the stream into the given array.
read(byte[], int, int) - Method in class loci.common.RandomAccessInputStream
Read n bytes from the stream into the given array at the specified offset.
read(ByteBuffer) - Method in class loci.common.RandomAccessInputStream
Read bytes from the stream into the given buffer.
read(ByteBuffer, int, int) - Method in class loci.common.RandomAccessInputStream
Read n bytes from the stream into the given buffer at the specified offset.
read() - Method in class loci.common.RandomAccessInputStream
 
read(Kryo, Input) - Method in class loci.common.RandomAccessInputStream
 
read(byte[]) - Method in class loci.common.StreamHandle
 
read(byte[], int, int) - Method in class loci.common.StreamHandle
 
read(ByteBuffer) - Method in class loci.common.StreamHandle
 
read(ByteBuffer, int, int) - Method in class loci.common.StreamHandle
 
readBits(int) - Method in class loci.common.RandomAccessInputStream
Returns an int value representing the value of the bits read from the byte array, from the current position.
readBoolean() - Method in class loci.common.ByteArrayHandle
 
readBoolean() - Method in class loci.common.FileHandle
 
readBoolean() - Method in class loci.common.NIOFileHandle
 
readBoolean() - Method in class loci.common.NIOInputStream
Read an input byte and return true if the byte is nonzero.
readBoolean() - Method in class loci.common.RandomAccessInputStream
Read an input byte and return true if the byte is nonzero.
readBoolean() - Method in class loci.common.StreamHandle
 
readByte() - Method in class loci.common.ByteArrayHandle
 
readByte() - Method in class loci.common.FileHandle
 
readByte() - Method in class loci.common.NIOFileHandle
 
readByte() - Method in class loci.common.NIOInputStream
Read one byte and return it.
readByte() - Method in class loci.common.RandomAccessInputStream
Read one byte and return it.
readByte() - Method in class loci.common.StreamHandle
 
readByteToString(int) - Method in class loci.common.RandomAccessInputStream
Reads a byte array of the given length byte by byte.
readChar() - Method in class loci.common.ByteArrayHandle
 
readChar() - Method in class loci.common.FileHandle
 
readChar() - Method in class loci.common.NIOFileHandle
 
readChar() - Method in class loci.common.NIOInputStream
Read an input char.
readChar() - Method in class loci.common.RandomAccessInputStream
Read an input char.
readChar() - Method in class loci.common.StreamHandle
 
readCString() - Method in class loci.common.NIOInputStream
Read a string of arbitrary length, terminated by a null char.
readCString() - Method in class loci.common.RandomAccessInputStream
Read a string of arbitrary length, terminated by a null char.
readDouble() - Method in class loci.common.ByteArrayHandle
 
readDouble() - Method in class loci.common.FileHandle
 
readDouble() - Method in class loci.common.NIOFileHandle
 
readDouble() - Method in class loci.common.NIOInputStream
Read eight bytes and return a double value.
readDouble() - Method in class loci.common.RandomAccessInputStream
Read eight bytes and return a double value.
readDouble() - Method in class loci.common.StreamHandle
 
readFile(String) - Static method in class loci.common.DataTools
Reads the contents of the given file into a string.
readFloat() - Method in class loci.common.ByteArrayHandle
 
readFloat() - Method in class loci.common.FileHandle
 
readFloat() - Method in class loci.common.NIOFileHandle
 
readFloat() - Method in class loci.common.NIOInputStream
Read four bytes and return a float value.
readFloat() - Method in class loci.common.RandomAccessInputStream
Read four bytes and return a float value.
readFloat() - Method in class loci.common.StreamHandle
 
readFully(byte[]) - Method in class loci.common.ByteArrayHandle
 
readFully(byte[], int, int) - Method in class loci.common.ByteArrayHandle
 
readFully(byte[]) - Method in class loci.common.FileHandle
 
readFully(byte[], int, int) - Method in class loci.common.FileHandle
 
readFully(byte[]) - Method in class loci.common.NIOFileHandle
 
readFully(byte[], int, int) - Method in class loci.common.NIOFileHandle
 
readFully(byte[]) - Method in class loci.common.NIOInputStream
Read bytes from the stream into the given array.
readFully(byte[], int, int) - Method in class loci.common.NIOInputStream
Read n bytes from the stream into the given array at the specified offset.
readFully(byte[]) - Method in class loci.common.RandomAccessInputStream
Read bytes from the stream into the given array.
readFully(byte[], int, int) - Method in class loci.common.RandomAccessInputStream
Read n bytes from the stream into the given array at the specified offset.
readFully(byte[]) - Method in class loci.common.StreamHandle
 
readFully(byte[], int, int) - Method in class loci.common.StreamHandle
 
readInt() - Method in class loci.common.ByteArrayHandle
 
readInt() - Method in class loci.common.FileHandle
 
readInt() - Method in class loci.common.NIOFileHandle
 
readInt() - Method in class loci.common.NIOInputStream
Read four input bytes and return an int value.
readInt() - Method in class loci.common.RandomAccessInputStream
Read four input bytes and return an int value.
readInt() - Method in class loci.common.StreamHandle
 
readLine() - Method in class loci.common.ByteArrayHandle
 
readLine() - Method in class loci.common.FileHandle
 
readLine() - Method in class loci.common.NIOFileHandle
 
readLine() - Method in class loci.common.NIOInputStream
Read the next line of text from the input stream.
readLine() - Method in class loci.common.RandomAccessInputStream
Read the next line of text from the input stream.
readLine() - Method in class loci.common.StreamHandle
 
readLong() - Method in class loci.common.ByteArrayHandle
 
readLong() - Method in class loci.common.FileHandle
 
readLong() - Method in class loci.common.NIOFileHandle
 
readLong() - Method in class loci.common.NIOInputStream
Read eight input bytes and return a long value.
readLong() - Method in class loci.common.RandomAccessInputStream
Read eight input bytes and return a long value.
readLong() - Method in class loci.common.StreamHandle
 
readShort() - Method in class loci.common.ByteArrayHandle
 
readShort() - Method in class loci.common.FileHandle
 
readShort() - Method in class loci.common.NIOFileHandle
 
readShort() - Method in class loci.common.NIOInputStream
Read two input bytes and return a short value.
readShort() - Method in class loci.common.RandomAccessInputStream
Read two input bytes and return a short value.
readShort() - Method in class loci.common.StreamHandle
 
readString(String) - Method in class loci.common.NIOInputStream
Reads a string ending with one of the characters in the given string.
readString(int) - Method in class loci.common.NIOInputStream
Read a string of length n.
readString(String) - Method in class loci.common.RandomAccessInputStream
Reads a string ending with one of the characters in the given string.
readString(int) - Method in class loci.common.RandomAccessInputStream
Read a string of up to length n.
readUnsignedByte() - Method in class loci.common.ByteArrayHandle
 
readUnsignedByte() - Method in class loci.common.FileHandle
 
readUnsignedByte() - Method in class loci.common.NIOFileHandle
 
readUnsignedByte() - Method in class loci.common.NIOInputStream
Read an input byte and zero extend it appropriately.
readUnsignedByte() - Method in class loci.common.RandomAccessInputStream
Read an input byte and zero extend it appropriately.
readUnsignedByte() - Method in class loci.common.StreamHandle
 
readUnsignedInt() - Method in class loci.common.RandomAccessInputStream
Read four input bytes and return an unsigned value.
readUnsignedShort() - Method in class loci.common.ByteArrayHandle
 
readUnsignedShort() - Method in class loci.common.FileHandle
 
readUnsignedShort() - Method in class loci.common.NIOFileHandle
 
readUnsignedShort() - Method in class loci.common.NIOInputStream
Read two bytes and return an int in the range 0 through 65535.
readUnsignedShort() - Method in class loci.common.RandomAccessInputStream
Read two bytes and return an int in the range 0 through 65535.
readUnsignedShort() - Method in class loci.common.StreamHandle
 
readUTF() - Method in class loci.common.ByteArrayHandle
 
readUTF() - Method in class loci.common.FileHandle
 
readUTF() - Method in class loci.common.NIOFileHandle
 
readUTF() - Method in class loci.common.NIOInputStream
Read a string that has been encoded using a modified UTF-8 format.
readUTF() - Method in class loci.common.RandomAccessInputStream
Read a string that has been encoded using a modified UTF-8 format.
readUTF() - Method in class loci.common.StreamHandle
 
ReflectedUniverse - Class in loci.common
Deprecated.
ReflectedUniverse() - Constructor for class loci.common.ReflectedUniverse
Deprecated.
Constructs a new reflected universe.
ReflectedUniverse(URL[]) - Constructor for class loci.common.ReflectedUniverse
Deprecated.
Constructs a new reflected universe, with the given URLs representing additional search paths for imported classes (in addition to the CLASSPATH).
ReflectedUniverse(ClassLoader) - Constructor for class loci.common.ReflectedUniverse
Deprecated.
Constructs a new reflected universe that uses the given class loader.
ReflectException - Exception in loci.common
ReflectException is the exception thrown when something goes wrong performing a reflected operation with ReflectedUniverse.
ReflectException() - Constructor for exception loci.common.ReflectException
 
ReflectException(String) - Constructor for exception loci.common.ReflectException
 
ReflectException(String, Throwable) - Constructor for exception loci.common.ReflectException
 
ReflectException(Throwable) - Constructor for exception loci.common.ReflectException
 
Region - Class in loci.common
A class for representing a rectangular region.
Region() - Constructor for class loci.common.Region
 
Region(int, int, int, int) - Constructor for class loci.common.Region
 
removeStatusListener(StatusListener) - Method in interface loci.common.StatusReporter
 
reset() - Static method in class loci.common.Location
Clear all caches and reset cache-related bookkeeping variables to their original values.
reset() - Method in class loci.common.NIOInputStream
 
reset() - Method in class loci.common.RandomAccessInputStream
 
resetStream() - Method in class loci.common.BZip2Handle
 
resetStream() - Method in class loci.common.GZipHandle
 
resetStream() - Method in class loci.common.StreamHandle
Close and reopen the stream; the stream pointer and mark should be reset to 0.
resetStream() - Method in class loci.common.URLHandle
 
resetStream() - Method in class loci.common.ZipHandle
 
resolveEntity(String, String) - Method in class loci.common.xml.BaseHandler
 

S

safeMultiply32(int...) - Static method in class loci.common.DataTools
Checks that the product of the given sizes does not exceed the 32-bit integer limit (i.e., Integer.MAX_VALUE).
safeMultiply64(long...) - Static method in class loci.common.DataTools
Checks that the product of the given sizes does not exceed the 64-bit integer limit (i.e., Long.MAX_VALUE).
samePrefix(String, String) - Static method in class loci.common.DataTools
Check if two filenames have the same prefix.
sanitize(String) - Static method in class loci.common.DataTools
Remove unprintable characters from the given string.
sanitizeDouble(String) - Static method in class loci.common.DataTools
Deprecated.
sanitizeXML(String) - Static method in class loci.common.xml.XMLTools
Remove invalid characters from an XML string.
saveINI(IniList, String) - Method in class loci.common.IniWriter
Saves the given IniList to the given file.
saveINI(IniList, String, boolean, boolean) - Method in class loci.common.IniWriter
Saves the given IniList to the given file.
saveINI(IniList, String, boolean) - Method in class loci.common.IniWriter
Saves the given IniList to the given file.
seek(long) - Method in class loci.common.ByteArrayHandle
 
seek(long) - Method in class loci.common.FileHandle
 
seek(long) - Method in interface loci.common.IRandomAccess
Sets the stream pointer offset, measured from the beginning of this stream, at which the next read or write occurs.
seek(long) - Method in class loci.common.NIOFileHandle
 
seek(long) - Method in class loci.common.NIOInputStream
Seeks to the given offset within the stream.
seek(long) - Method in class loci.common.RandomAccessInputStream
Seeks to the given offset within the stream.
seek(long) - Method in class loci.common.RandomAccessOutputStream
Seeks to the given offset within the stream.
seek(long) - Method in class loci.common.StreamHandle
 
seek(long) - Method in class loci.common.URLHandle
 
Service - Interface in loci.common.services
 
ServiceException - Exception in loci.common.services
Exception thrown when there is an error within a given service.
ServiceException(String) - Constructor for exception loci.common.services.ServiceException
Default constructor.
ServiceException(String, Throwable) - Constructor for exception loci.common.services.ServiceException
Default constructor.
ServiceException(Throwable) - Constructor for exception loci.common.services.ServiceException
Default constructor.
ServiceFactory - Class in loci.common.services
Runtime instantiation of services.
ServiceFactory() - Constructor for class loci.common.services.ServiceFactory
Constructor loading service configuration from the default location.
ServiceFactory(String) - Constructor for class loci.common.services.ServiceFactory
Constructor loading service configuration from a given location.
setAccessibilityIgnored(boolean) - Method in class loci.common.ReflectedUniverse
Deprecated.
Sets whether access modifiers (protected, private, etc.) are ignored.
setBackslashContinuesLine(boolean) - Method in class loci.common.IniParser
Set whether or not a '\' at the end of a line signifies that the line continues on the following line.
setBaseURI(String) - Method in class loci.common.xml.LSInputI
 
setByteStream(InputStream) - Method in class loci.common.xml.LSInputI
 
setCacheDirectoryTimeout(double) - Static method in class loci.common.Location
Cache directory listings for this many seconds before relisting.
setCertifiedText(boolean) - Method in class loci.common.xml.LSInputI
 
setCharacterStream(Reader) - Method in class loci.common.xml.LSInputI
 
setCommentDelimiter(String) - Method in class loci.common.IniParser
Set the String that identifies a comment.
setDefaultBufferSize(int) - Static method in class loci.common.NIOFileHandle
Set the default buffer size for read-only files.
setDefaultReadWriteBufferSize(int) - Static method in class loci.common.NIOFileHandle
Set the default buffer size for read/write files.
setEncoding(String) - Method in class loci.common.RandomAccessInputStream
Sets the native encoding of the stream.
setEncoding(String) - Method in class loci.common.xml.LSInputI
 
setExtend(int) - Method in class loci.common.NIOInputStream
Sets the number of bytes by which to extend the stream.
setGlobalCRC(int) - Method in class loci.common.CRC
 
setIdMap(HashMap<String, Object>) - Static method in class loci.common.Location
Set the id mapping using the given HashMap.
setLength(long) - Method in class loci.common.AbstractNIOHandle
Sets the new length of the handle.
setLength(long) - Method in class loci.common.ByteArrayHandle
 
setLength(long) - Method in class loci.common.NIOFileHandle
 
setLength(long) - Method in class loci.common.RandomAccessInputStream
Sets the length of the stream.
setOrder(ByteOrder) - Method in class loci.common.ByteArrayHandle
 
setOrder(ByteOrder) - Method in class loci.common.FileHandle
 
setOrder(ByteOrder) - Method in interface loci.common.IRandomAccess
Sets the byte order of the stream.
setOrder(ByteOrder) - Method in class loci.common.NIOFileHandle
 
setOrder(ByteOrder) - Method in class loci.common.StreamHandle
 
setPublicId(String) - Method in class loci.common.xml.LSInputI
 
setRootLevel(String) - Static method in class loci.common.DebugTools
Sets the root logger level.
setRootLevel(String) - Static method in class loci.common.Log4jTools
Sets the level of the root logger
setRootLevel(String) - Static method in class loci.common.LogbackTools
Sets the level of the root logger
setStringData(String) - Method in class loci.common.xml.LSInputI
 
setSystemId(String) - Method in class loci.common.xml.LSInputI
 
setVar(String, Object) - Method in class loci.common.ReflectedUniverse
Deprecated.
Registers a variable in the universe.
setVar(String, boolean) - Method in class loci.common.ReflectedUniverse
Deprecated.
Registers a variable of primitive type boolean in the universe.
setVar(String, byte) - Method in class loci.common.ReflectedUniverse
Deprecated.
Registers a variable of primitive type byte in the universe.
setVar(String, char) - Method in class loci.common.ReflectedUniverse
Deprecated.
Registers a variable of primitive type char in the universe.
setVar(String, double) - Method in class loci.common.ReflectedUniverse
Deprecated.
Registers a variable of primitive type double in the universe.
setVar(String, float) - Method in class loci.common.ReflectedUniverse
Deprecated.
Registers a variable of primitive type float in the universe.
setVar(String, int) - Method in class loci.common.ReflectedUniverse
Deprecated.
Registers a variable of primitive type int in the universe.
setVar(String, long) - Method in class loci.common.ReflectedUniverse
Deprecated.
Registers a variable of primitive type long in the universe.
setVar(String, short) - Method in class loci.common.ReflectedUniverse
Deprecated.
Registers a variable of primitive type short in the universe.
shortsToBytes(short[], boolean) - Static method in class loci.common.DataTools
Translates an array of short values into an array of byte values.
shortToBytes(short, boolean) - Static method in class loci.common.DataTools
Translates the short value into an array of two bytes.
skipBits(long) - Method in class loci.common.RandomAccessInputStream
Skips a number of bits in the BitBuffer.
skipBytes(int) - Method in class loci.common.ByteArrayHandle
 
skipBytes(int) - Method in class loci.common.FileHandle
 
skipBytes(int) - Method in class loci.common.NIOFileHandle
 
skipBytes(int) - Method in class loci.common.NIOInputStream
Skip n bytes within the stream.
skipBytes(int) - Method in class loci.common.RandomAccessInputStream
Skip n bytes within the stream.
skipBytes(int) - Method in class loci.common.RandomAccessOutputStream
Advances the current offset by the given number of bytes.
skipBytes(int) - Method in class loci.common.StreamHandle
 
status - Variable in class loci.common.StatusEvent
Current status message.
StatusEvent - Class in loci.common
An event indicating a status update.
StatusEvent(String) - Constructor for class loci.common.StatusEvent
Constructs a status event.
StatusEvent(String, boolean) - Constructor for class loci.common.StatusEvent
Constructs a status event.
StatusEvent(int, int, String) - Constructor for class loci.common.StatusEvent
Constructs a status event.
StatusEvent(int, int, String, boolean) - Constructor for class loci.common.StatusEvent
Constructs a status event.
StatusListener - Interface in loci.common
A listener for status updates.
StatusReporter - Interface in loci.common
A simple interface for objects wishing to report their status to listeners.
statusUpdated(StatusEvent) - Method in interface loci.common.StatusListener
Called when status is updated.
stream - Variable in class loci.common.StreamHandle
InputStream to be used for reading.
StreamHandle - Class in loci.common
Abstract IRandomAccess implementation for reading from InputStreams and writing to OutputStreams.
StreamHandle() - Constructor for class loci.common.StreamHandle
Construct a new StreamHandle.
stripString(String) - Static method in class loci.common.DataTools
Remove null bytes from a string.
swap(short) - Static method in class loci.common.DataTools
 
swap(char) - Static method in class loci.common.DataTools
 
swap(int) - Static method in class loci.common.DataTools
 
swap(long) - Static method in class loci.common.DataTools
 
swap(float) - Static method in class loci.common.DataTools
 
swap(double) - Static method in class loci.common.DataTools
 

T

time - Variable in class loci.common.Location.ListingsResult
 
TIMESTAMP_FORMAT - Static variable in class loci.common.DateTools
Human readable timestamp string
toString() - Method in class loci.common.Location
 
toString() - Method in class loci.common.Region
 
toString() - Method in exception loci.common.services.DependencyException
 
toString() - Method in class loci.common.StatusEvent
 
toURL() - Method in class loci.common.Location
Return the URL corresponding to this pathname.
transformXML(String, Templates) - Static method in class loci.common.xml.XMLTools
Transforms the given XML string using the specified XSLT stylesheet.
transformXML(Source, Templates) - Static method in class loci.common.xml.XMLTools
Transforms the given XML data using the specified XSLT stylesheet.

U

UNIX - Static variable in class loci.common.DateTools
Timestamp formats.
UNIX_EPOCH - Static variable in class loci.common.DateTools
Milliseconds until UNIX epoch.
unpackBytes(long, byte[], int, int, boolean) - Static method in class loci.common.DataTools
Translates nBytes of the given long and places the result in the given byte array.
updateCRC(int) - Method in class loci.common.CRC
 
URLHandle - Class in loci.common
Provides random access to URLs using the IRandomAccess interface.
URLHandle(String) - Constructor for class loci.common.URLHandle
Constructs a new URLHandle using the given URL.

V

validateLength(int) - Method in class loci.common.AbstractNIOHandle
Ensures that the handle has the correct length to be written to and extends it as required.
validateMode(String) - Method in class loci.common.AbstractNIOHandle
Ensures that the file mode is either "r" or "rw".
validateXML(String) - Static method in class loci.common.xml.XMLTools
Attempts to validate the given XML string using Java's XML validation facility.
validateXML(String, String) - Static method in class loci.common.xml.XMLTools
Attempts to validate the given XML string using Java's XML validation facility.
validateXML(String, String, XMLTools.SchemaReader) - Static method in class loci.common.xml.XMLTools
Attempts to validate the given XML string using Java's XML validation facility.
ValidationErrorHandler - Class in loci.common.xml
Used by validateXML to handle XML validation errors.
ValidationErrorHandler() - Constructor for class loci.common.xml.ValidationErrorHandler
 
variables - Variable in class loci.common.ReflectedUniverse
Deprecated.
Hashtable containing all variables present in the universe.

W

warning - Variable in class loci.common.StatusEvent
Whether or not this is a warning event.
warning(SAXParseException) - Method in class loci.common.xml.ParserErrorHandler
 
warning(SAXParseException) - Method in class loci.common.xml.ValidationErrorHandler
 
width - Variable in class loci.common.Region
 
write(byte[]) - Method in class loci.common.ByteArrayHandle
 
write(byte[], int, int) - Method in class loci.common.ByteArrayHandle
 
write(ByteBuffer) - Method in class loci.common.ByteArrayHandle
 
write(ByteBuffer, int, int) - Method in class loci.common.ByteArrayHandle
 
write(int) - Method in class loci.common.ByteArrayHandle
 
write(ByteBuffer) - Method in class loci.common.FileHandle
 
write(ByteBuffer, int, int) - Method in class loci.common.FileHandle
 
write(byte[]) - Method in class loci.common.FileHandle
 
write(byte[], int, int) - Method in class loci.common.FileHandle
 
write(int) - Method in class loci.common.FileHandle
 
write(ByteBuffer) - Method in interface loci.common.IRandomAccess
Writes up to buffer.capacity() bytes of data from the given ByteBuffer to this stream.
write(ByteBuffer, int, int) - Method in interface loci.common.IRandomAccess
Writes up to len bytes of data from the given ByteBuffer to this stream.
write(byte[]) - Method in class loci.common.NIOFileHandle
 
write(byte[], int, int) - Method in class loci.common.NIOFileHandle
 
write(ByteBuffer) - Method in class loci.common.NIOFileHandle
 
write(ByteBuffer, int, int) - Method in class loci.common.NIOFileHandle
 
write(int) - Method in class loci.common.NIOFileHandle
 
write(Kryo, Output) - Method in class loci.common.RandomAccessInputStream
 
write(byte[]) - Method in class loci.common.RandomAccessOutputStream
 
write(byte[], int, int) - Method in class loci.common.RandomAccessOutputStream
 
write(ByteBuffer) - Method in class loci.common.RandomAccessOutputStream
Writes bytes to the stream from the given buffer.
write(ByteBuffer, int, int) - Method in class loci.common.RandomAccessOutputStream
 
write(int) - Method in class loci.common.RandomAccessOutputStream
 
write(ByteBuffer) - Method in class loci.common.StreamHandle
 
write(ByteBuffer, int, int) - Method in class loci.common.StreamHandle
 
write(byte[]) - Method in class loci.common.StreamHandle
 
write(byte[], int, int) - Method in class loci.common.StreamHandle
 
write(int) - Method in class loci.common.StreamHandle
 
writeBits(int, int) - Method in class loci.common.RandomAccessOutputStream
Writes the given value using the given number of bits.
writeBits(String) - Method in class loci.common.RandomAccessOutputStream
Writes the bits represented by a bit string to the buffer.
writeBoolean(boolean) - Method in class loci.common.ByteArrayHandle
 
writeBoolean(boolean) - Method in class loci.common.FileHandle
 
writeBoolean(boolean) - Method in class loci.common.NIOFileHandle
 
writeBoolean(boolean) - Method in class loci.common.RandomAccessOutputStream
 
writeBoolean(boolean) - Method in class loci.common.StreamHandle
 
writeByte(int) - Method in class loci.common.ByteArrayHandle
 
writeByte(int) - Method in class loci.common.FileHandle
 
writeByte(int) - Method in class loci.common.NIOFileHandle
 
writeByte(int) - Method in class loci.common.RandomAccessOutputStream
 
writeByte(int) - Method in class loci.common.StreamHandle
 
writeBytes(String) - Method in class loci.common.ByteArrayHandle
 
writeBytes(String) - Method in class loci.common.FileHandle
 
writeBytes(String) - Method in class loci.common.NIOFileHandle
 
writeBytes(String) - Method in class loci.common.RandomAccessOutputStream
 
writeBytes(String) - Method in class loci.common.StreamHandle
 
writeChar(int) - Method in class loci.common.ByteArrayHandle
 
writeChar(int) - Method in class loci.common.FileHandle
 
writeChar(int) - Method in class loci.common.NIOFileHandle
 
writeChar(int) - Method in class loci.common.RandomAccessOutputStream
 
writeChar(int) - Method in class loci.common.StreamHandle
 
writeChars(String) - Method in class loci.common.ByteArrayHandle
 
writeChars(String) - Method in class loci.common.FileHandle
 
writeChars(String) - Method in class loci.common.NIOFileHandle
 
writeChars(String) - Method in class loci.common.RandomAccessOutputStream
 
writeChars(String) - Method in class loci.common.StreamHandle
 
writeDouble(double) - Method in class loci.common.ByteArrayHandle
 
writeDouble(double) - Method in class loci.common.FileHandle
 
writeDouble(double) - Method in class loci.common.NIOFileHandle
 
writeDouble(double) - Method in class loci.common.RandomAccessOutputStream
 
writeDouble(double) - Method in class loci.common.StreamHandle
 
writeFloat(float) - Method in class loci.common.ByteArrayHandle
 
writeFloat(float) - Method in class loci.common.FileHandle
 
writeFloat(float) - Method in class loci.common.NIOFileHandle
 
writeFloat(float) - Method in class loci.common.RandomAccessOutputStream
 
writeFloat(float) - Method in class loci.common.StreamHandle
 
writeInt(int) - Method in class loci.common.ByteArrayHandle
 
writeInt(int) - Method in class loci.common.FileHandle
 
writeInt(int) - Method in class loci.common.NIOFileHandle
 
writeInt(int) - Method in class loci.common.RandomAccessOutputStream
 
writeInt(int) - Method in class loci.common.StreamHandle
 
writeLine(String) - Method in class loci.common.RandomAccessOutputStream
Writes the given string followed by a newline character.
writeLong(long) - Method in class loci.common.ByteArrayHandle
 
writeLong(long) - Method in class loci.common.FileHandle
 
writeLong(long) - Method in class loci.common.NIOFileHandle
 
writeLong(long) - Method in class loci.common.RandomAccessOutputStream
 
writeLong(long) - Method in class loci.common.StreamHandle
 
writeShort(int) - Method in class loci.common.ByteArrayHandle
 
writeShort(int) - Method in class loci.common.FileHandle
 
writeShort(int) - Method in class loci.common.NIOFileHandle
 
writeShort(int) - Method in class loci.common.RandomAccessOutputStream
 
writeShort(int) - Method in class loci.common.StreamHandle
 
writeUTF(String) - Method in class loci.common.ByteArrayHandle
 
writeUTF(String) - Method in class loci.common.FileHandle
 
writeUTF(String) - Method in class loci.common.NIOFileHandle
 
writeUTF(String) - Method in class loci.common.RandomAccessOutputStream
 
writeUTF(String) - Method in class loci.common.StreamHandle
 
writeXML(OutputStream, Document) - Static method in class loci.common.xml.XMLTools
Writes the specified DOM to the given output stream.
writeXML(OutputStream, Document, boolean) - Static method in class loci.common.xml.XMLTools
Writes the specified DOM to the given output stream.
writeXML(Result, Document, boolean) - Static method in class loci.common.xml.XMLTools
Writes the specified DOM to the given stream.

X

x - Variable in class loci.common.Region
 
XMLTools - Class in loci.common.xml
A utility class for working with XML.
XMLTools.SchemaReader - Interface in loci.common.xml
A schema reader can provide InputStreams for certain XML schemas.

Y

y - Variable in class loci.common.Region
 

Z

ZipHandle - Class in loci.common
StreamHandle implementation for reading from Zip-compressed files or byte arrays.
ZipHandle(String) - Constructor for class loci.common.ZipHandle
 
ZipHandle(String, ZipEntry) - Constructor for class loci.common.ZipHandle
Constructs a new ZipHandle corresponding to the given entry of the specified Zip file.
ZVI - Static variable in class loci.common.DateTools
 
ZVI_EPOCH - Static variable in class loci.common.DateTools
 
A B C D E F G H I L M N O P R S T U V W X Y Z 
Skip navigation links

Copyright © 2005–2016 Open Microscopy Environment. All rights reserved.