- BaseHandler - Class in loci.common.xml
-
Top-level SAX handler.
- BaseHandler() - Constructor for class loci.common.xml.BaseHandler
-
- bucketExists(String) - Method in interface loci.common.services.S3ClientService
-
Check whether a bucket exists
- bucketExists(String) - Method in class loci.common.services.S3ClientServiceImpl
-
- 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
-
Creates a random access byte stream to read from, and
write to, the supplied ByteBuffer.
- 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.
- cacheDirectoryListings(boolean) - Static method in class loci.common.Location
-
Turn cacheing of directory listings on or off.
- cacheObject(String, StreamHandle.Settings) - Static method in class loci.common.S3Handle
-
Download an S3 object to a file system cache if it doesn't already exist
- canHandleScheme(String) - Static method in class loci.common.S3Handle
-
Return true if this is a URL with an s3 scheme
- 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
-
- CaseInsensitiveLocation(String) - Constructor for class loci.common.CaseInsensitiveLocation
-
Deprecated.
- CaseInsensitiveLocation(Location) - Constructor for class loci.common.CaseInsensitiveLocation
-
Deprecated.
- CaseInsensitiveLocation(File) - Constructor for class loci.common.CaseInsensitiveLocation
-
Deprecated.
- CaseInsensitiveLocation(String, String) - Constructor for class loci.common.CaseInsensitiveLocation
-
Deprecated.
- CaseInsensitiveLocation(CaseInsensitiveLocation, String) - Constructor for class loci.common.CaseInsensitiveLocation
-
Deprecated.
- 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.
- connect() - Method in class loci.common.S3Handle
-
Connect to the server
- 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
-
- 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.
- 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.
- DEFAULT_S3_PROTOCOL - Static variable in class loci.common.S3Handle
-
Default protocol for fetching s3://
- 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.
- downloadObject(Path) - Method in class loci.common.S3Handle
-
- downsample(byte[], int, int, double, int, boolean, boolean, int, boolean) - Method in interface loci.common.image.IImageScaler
-
Downsamples the given image.
- downsample(byte[], int, int, double, int, boolean, boolean, int, boolean) - Method in class loci.common.image.SimpleImageScaler
-
- 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.
- 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.
- get(String) - Method in class loci.common.StreamHandle.Settings
-
- getAbsoluteFile() - Method in class loci.common.Location
-
Return the absolute form of this abstract location.
- getAbsolutePath() - Method in class loci.common.Location
-
Return the absolute form of this abstract location.
- getBaseURI() - Method in class loci.common.xml.LSInputI
-
- getBucket() - Method in class loci.common.S3Handle
-
- getBufferSize() - Method in class loci.common.NIOFileHandle
-
- getByteBuffer() - Method in class loci.common.ByteArrayHandle
-
Gets the byte buffer backing this handle.
- getBytes() - Method in class loci.common.ByteArrayHandle
-
Gets a byte array representing the current state of this ByteArrayHandle.
- getByteStream() - Method in class loci.common.xml.LSInputI
-
- getCacheKey() - Method in class loci.common.S3Handle
-
- getCanonicalFile() - Method in class loci.common.Location
-
Returns the canonical path to this file.
- 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
-
- getEntryName() - Method in class loci.common.ZipHandle
-
- 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
-
- 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
-
- getFilePointer() - Method in class loci.common.RandomAccessInputStream
-
- getFilePointer() - Method in class loci.common.RandomAccessOutputStream
-
- getFilePointer() - Method in class loci.common.StreamHandle
-
- getFileTimestamp() - Static method in class loci.common.DateTools
-
- 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
-
Gets an IRandomAccess object that can read from or write to the given file.
- 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
-
- getInputStream() - Method in class loci.common.ZipHandle
-
- 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.
- getObject(String, String, long) - Method in interface loci.common.services.S3ClientService
-
Read an object
- getObject(String, String, String) - Method in interface loci.common.services.S3ClientService
-
Download an object
- getObject(String, String, long) - Method in class loci.common.services.S3ClientServiceImpl
-
- getObject(String, String, String) - Method in class loci.common.services.S3ClientServiceImpl
-
- 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 (endianness) 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 pathname string of this abstract pathname's parent, or null if
this pathname does not have a parent directory.
- getParentFile() - Method in class loci.common.Location
-
Returns the abstract pathname of this abstract pathname's parent, or null
if this pathname does not name a parent directory.
- getPath() - Method in class loci.common.Location
-
Returns the file's path.
- getPath() - Method in class loci.common.S3Handle
-
- getPort() - Method in class loci.common.S3Handle
-
- getProgressMaximum() - Method in class loci.common.StatusEvent
-
- getProgressValue() - Method in class loci.common.StatusEvent
-
- getPublicId() - Method in class loci.common.xml.LSInputI
-
- getRandomAccessFile() - Method in class loci.common.FileHandle
-
- getRandomAccessFile() - Method in class loci.common.NIOFileHandle
-
- getRemoteCacheRootDir() - Method in class loci.common.StreamHandle.Settings
-
- getSchemaAsStream(String) - Method in interface loci.common.xml.XMLTools.SchemaReader
-
- getServer() - Method in class loci.common.S3Handle
-
- 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
-
- 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
-
- 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.
- IImageScaler - Interface in loci.common.image
-
Interface defining image scaling operations.
- 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
-
- initialize() - Method in class loci.common.S3Handle
-
Check bucket or object exists
- initialize(String, int, String, String, String, String) - Method in interface loci.common.services.S3ClientService
-
Initialise the S3 client
- initialize(String, int, String, String, String, String) - Method in class loci.common.services.S3ClientServiceImpl
-
- 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
-
- 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
-
Deprecated.
Remove (invalidate) cached content for all directories.
- invalidateCache(File) - Static method in class loci.common.CaseInsensitiveLocation
-
Deprecated.
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
-
Returns whether or not this file's path 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.
- isBucket() - Method in class loci.common.S3Handle
-
Is this an accessible bucket?
TODO: If this bucket doesn't exist do we return false or thrown an exception?
- 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 whether or not this file is 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 whether or not this file is a regular file (i.e.
- isGZipFile(String) - Static method in class loci.common.GZipHandle
-
- isHidden() - Method in class loci.common.Location
-
Returns whether or not this file is marked hidden by the filesystem.
- 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
-
- 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
-
- isZipFile(String) - Static method in class loci.common.ZipHandle
-
- lastModified() - Method in class loci.common.Location
-
Return the last modification time of the file.
- 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
-
Return the file length in bytes.
- 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
-
- length() - Method in class loci.common.RandomAccessOutputStream
-
- length() - Method in class loci.common.S3Handle
-
- length() - Method in class loci.common.services.S3ClientStat
-
Get length (size) of object
- 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 relative file names in this directory, or null
if this file is not a directory.
- listFiles() - Method in class loci.common.Location
-
Return a list of files in this directory, or null if this file is
not a 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
File that supports reading over HTTP
(among other things).
- Location(String) - Constructor for class loci.common.Location
-
Construct a Location using the given path.
- Location(File) - Constructor for class loci.common.Location
-
Construct a Location using the given file on disk.
- Location(String, String) - Constructor for class loci.common.Location
-
Construct a Location using the given directory and relative path.
- Location(Location, String) - Constructor for class loci.common.Location
-
Construct a Location using the given directory and relative path.
- Location.ListingsResult - Class in loci.common
-
- Location.UrlType - Enum in loci.common
-
- loci.common - package loci.common
-
- loci.common.enumeration - package loci.common.enumeration
-
- loci.common.image - package loci.common.image
-
- 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
-
- 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
-
- 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
-
- 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.
- 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.S3Handle
-
- resetStream(long) - Method in class loci.common.S3Handle
-
Reset the stream to an offset position
- 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
-
- S3_MAX_FORWARD_SEEK - Static variable in class loci.common.S3Handle
-
If seeking more than this distance reset and reopen at offset
- S3ClientService - Interface in loci.common.services
-
An S3 client
- S3ClientServiceException - Exception in loci.common.services
-
Exception thrown when internal error specific to the S3 client is raised
- S3ClientServiceException(String) - Constructor for exception loci.common.services.S3ClientServiceException
-
Constructor.
- S3ClientServiceException(String, Throwable) - Constructor for exception loci.common.services.S3ClientServiceException
-
Constructor.
- S3ClientServiceException(Throwable) - Constructor for exception loci.common.services.S3ClientServiceException
-
Constructor.
- S3ClientServiceImpl - Class in loci.common.services
-
An S3 client
- S3ClientServiceImpl() - Constructor for class loci.common.services.S3ClientServiceImpl
-
Default constructor.
- S3ClientStat - Class in loci.common.services
-
Object stat (attributes) information
- S3Handle - Class in loci.common
-
Provides random access to S3 buckets using the IRandomAccess interface.
- S3Handle(String) - Constructor for class loci.common.S3Handle
-
Open an S3 file
- S3Handle(String, boolean, StreamHandle.Settings) - Constructor for class loci.common.S3Handle
-
Open an S3 file
- 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
-
- 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.
- SCHEME_PARSER - Static variable in class loci.common.S3Handle
-
- 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.S3Handle
-
- 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 (endianness) 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
-
- Settings() - Constructor for class loci.common.StreamHandle.Settings
-
- 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.
- SimpleImageScaler - Class in loci.common.image
-
- SimpleImageScaler() - Constructor for class loci.common.image.SimpleImageScaler
-
- 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(long) - Method in class loci.common.ByteArrayHandle
-
- skipBytes(int) - Method in class loci.common.FileHandle
-
- skipBytes(long) - Method in class loci.common.FileHandle
-
- skipBytes(long) - Method in interface loci.common.IRandomAccess
-
- skipBytes(int) - Method in class loci.common.NIOFileHandle
-
- skipBytes(long) - 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(long) - 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
-
- skipBytes(long) - Method in class loci.common.StreamHandle
-
- statObject(String, String) - Method in interface loci.common.services.S3ClientService
-
Stat the object
- statObject(String, String) - Method in class loci.common.services.S3ClientServiceImpl
-
- 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 non-warning 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 non-warning 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.
- StreamHandle.Settings - Class in loci.common
-
- stripString(String) - Static method in class loci.common.DataTools
-
Remove null bytes from a string.
- swap(short) - Static method in class loci.common.DataTools
-
Reverse the order of bytes in the given short.
- swap(char) - Static method in class loci.common.DataTools
-
Reverse the order of bytes in the given char.
- swap(int) - Static method in class loci.common.DataTools
-
Reverse the order of bytes in the given int.
- swap(long) - Static method in class loci.common.DataTools
-
Reverse the order of bytes in the given long.
- swap(float) - Static method in class loci.common.DataTools
-
Reverse the order of bytes in the given float.
- swap(double) - Static method in class loci.common.DataTools
-
Reverse the order of bytes in the given double.