| Package | Description |
|---|---|
| loci.common.xml | |
| loci.formats |
Bio-Formats: a library for reading and writing popular microscopy file
formats.
|
| loci.formats.codec |
Package containing Bio-Formats compression and decompression logic.
|
| loci.formats.in |
Package containing Bio-Formats file format readers.
|
| loci.formats.out |
Package containing Bio-Formats file format writers.
|
| loci.formats.services | |
| loci.formats.tiff |
Package containing Bio-Formats TIFF code of general utility.
|
| loci.formats.tools |
Package containing utility methods corresponding
to the Bio-Formats command line tools.
|
| loci.ome.io |
OME I/O:
a library for OME database import, upload and download.
|
| loci.poi.hpsf |
|
| loci.poi.hssf.usermodel |
usermodel package maps HSSF low level strutures to familiar workbook/sheet model
|
| loci.poi.poifs.eventfilesystem |
The eventfilesystem is an efficient method for reading OLE 2 CDF files.
|
| loci.poi.poifs.filesystem |
filesystem package maps OLE 2 Compound document files to a more familiar filesystem interface.
|
| loci.poi.poifs.storage |
storage package contains low level binary structures for POIFS's implementation of the OLE 2
Compound Document Format.
|
| ome.metakit |
| Modifier and Type | Method and Description |
|---|---|
static void |
XMLTools.parseXML(RandomAccessInputStream stream,
DefaultHandler handler)
Parses the XML contained in the given input stream into
using the specified XML handler.
|
| Modifier and Type | Field and Description |
|---|---|
protected RandomAccessInputStream |
FormatReader.in
Current file.
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
ReaderWrapper.isThisType(RandomAccessInputStream stream) |
boolean |
IFormatReader.isThisType(RandomAccessInputStream stream)
Checks if the given stream is a valid stream for this file format.
|
boolean |
ImageReader.isThisType(RandomAccessInputStream stream) |
boolean |
FormatReader.isThisType(RandomAccessInputStream stream) |
boolean |
DelegateReader.isThisType(RandomAccessInputStream stream) |
protected byte[] |
FormatReader.readPlane(RandomAccessInputStream s,
int x,
int y,
int w,
int h,
byte[] buf)
Reads a raw plane from disk.
|
protected byte[] |
FormatReader.readPlane(RandomAccessInputStream s,
int x,
int y,
int w,
int h,
int scanlinePad,
byte[] buf)
Reads a raw plane from disk.
|
static boolean |
FormatTools.validStream(RandomAccessInputStream stream,
int len,
boolean littleEndian)
Returns true if the given RandomAccessInputStream conatins at least
'len' bytes.
|
| Modifier and Type | Method and Description |
|---|---|
byte[] |
JPEG2000Codec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
interleaved
littleEndian |
abstract byte[] |
BaseCodec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
LosslessJPEGCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
interleaved
littleEndian |
byte[] |
LZOCodec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
NikonCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter must be an instance of
NikonCodecOptions, and should have the following fields set:
lossy
vPredictor
curve
split
bitsPerSample
maxBytes
width
height |
byte[] |
LZWCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
maxBytes |
byte[] |
MSRLECodec.decompress(RandomAccessInputStream in,
CodecOptions options)
|
byte[] |
Base64Codec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
MJPBCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter must be an instance of
MJPBCodecOptions,
and should have the following fields set:
interlaced
width
height
bitsPerSample
littleEndian
interleaved |
byte[] |
Codec.decompress(RandomAccessInputStream in,
CodecOptions options)
Decompresses data from the given RandomAccessInputStream.
|
byte[] |
JPEGCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
interleaved
littleEndian |
byte[] |
HuffmanCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter must be an instance of
HuffmanCodecOptions, and should have the following fields set:
table
bitsPerSample
maxBytes |
byte[] |
QTRLECodec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
ZlibCodec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
PackbitsCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
maxBytes |
byte[] |
MSVideoCodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
width
height
bitsPerSample
previousImage |
byte[] |
LuraWaveCodec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
PassthroughCodec.decompress(RandomAccessInputStream in,
CodecOptions options) |
byte[] |
RPZACodec.decompress(RandomAccessInputStream in,
CodecOptions options)
|
byte[] |
TargaRLECodec.decompress(RandomAccessInputStream in,
CodecOptions options)
The CodecOptions parameter should have the following fields set:
maxBytes
CodecOptions.bitsPerSample |
void |
JPEGTileDecoder.initialize(RandomAccessInputStream in,
int imageWidth) |
void |
JPEGTileDecoder.initialize(RandomAccessInputStream in,
int y,
int h,
int imageWidth) |
int[] |
JPEGTileDecoder.preprocess(RandomAccessInputStream in)
Pre-process the stream to make sure that the
image width and height are non-zero.
|
| Constructor and Description |
|---|
JPEG2000MetadataParser(RandomAccessInputStream in)
Constructs a new JPEG2000MetadataParser.
|
JPEG2000MetadataParser(RandomAccessInputStream in,
long maximumReadOffset)
Constructs a new JPEG2000MetadataParser.
|
SDTInfo(RandomAccessInputStream in,
Hashtable meta)
Constructs a new SDT header by reading values from the given input source,
populating the given metadata table.
|
| Modifier and Type | Field and Description |
|---|---|
protected RandomAccessInputStream |
TiffWriter.in
Input stream to use when overwriting data.
|
| Modifier and Type | Method and Description |
|---|---|
RandomAccessInputStream |
POIServiceImpl.getDocumentStream(String file) |
RandomAccessInputStream |
POIService.getDocumentStream(String file)
Retrieve a RandomAccessInputStream corresponding to the given file name.
|
| Modifier and Type | Method and Description |
|---|---|
void |
POIServiceImpl.initialize(RandomAccessInputStream s) |
void |
POIService.initialize(RandomAccessInputStream stream)
Construct a new POI filesystem around the given stream.
|
void |
MetakitServiceImpl.initialize(RandomAccessInputStream file) |
void |
MetakitService.initialize(RandomAccessInputStream file) |
void |
JPEGTurboService.initialize(RandomAccessInputStream jpeg,
int width,
int height) |
void |
JPEGTurboServiceImpl.initialize(RandomAccessInputStream jpeg,
int width,
int height) |
| Modifier and Type | Field and Description |
|---|---|
protected RandomAccessInputStream |
TiffParser.in
Input source from which to parse TIFF data.
|
| Modifier and Type | Method and Description |
|---|---|
RandomAccessInputStream |
TiffParser.getStream()
Gets the stream from which TIFF data is being parsed.
|
| Modifier and Type | Method and Description |
|---|---|
void |
TiffSaver.overwriteComment(RandomAccessInputStream in,
Object value)
Convenience method for overwriting a file's first ImageDescription.
|
void |
TiffSaver.overwriteIFDValue(RandomAccessInputStream raf,
int ifd,
int tag,
Object value)
Surgically overwrites an existing IFD value with the given one.
|
void |
TiffSaver.overwriteLastIFDOffset(RandomAccessInputStream raf) |
| Constructor and Description |
|---|
OnDemandLongArray(RandomAccessInputStream in) |
TiffParser(RandomAccessInputStream in)
Constructs a new TIFF parser from the given input source.
|
| Modifier and Type | Field and Description |
|---|---|
protected RandomAccessInputStream |
AmiraParameters.in |
| Modifier and Type | Method and Description |
|---|---|
protected void |
AmiraParameters.readFile(RandomAccessInputStream inputStream) |
| Constructor and Description |
|---|
AmiraParameters(RandomAccessInputStream inputStream) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
OMEReader.isThisType(RandomAccessInputStream stream) |
| Modifier and Type | Method and Description |
|---|---|
RandomAccessInputStream |
SpecialPropertySet.toInputStream() |
RandomAccessInputStream |
MutablePropertySet.toInputStream()
Returns the contents of this property set stream as an input stream.
|
| Constructor and Description |
|---|
HSSFWorkbook(RandomAccessInputStream s) |
HSSFWorkbook(RandomAccessInputStream s,
boolean preserveNodes)
Companion to HSSFWorkbook(POIFSFileSystem), this constructs the POI filesystem around your
inputstream.
|
| Modifier and Type | Method and Description |
|---|---|
void |
POIFSReader.read(RandomAccessInputStream stream,
int size)
Read from an InputStream and process the documents we get
|
| Modifier and Type | Method and Description |
|---|---|
DocumentEntry |
POIFSFileSystem.createDocument(RandomAccessInputStream stream,
String name)
Create a new document to be added to the root directory
|
DocumentEntry |
DirectoryEntry.createDocument(String name,
RandomAccessInputStream stream)
create a new DocumentEntry
|
DocumentEntry |
DirectoryNode.createDocument(String name,
RandomAccessInputStream stream)
create a new DocumentEntry
|
| Constructor and Description |
|---|
DocumentInputStream(DocumentEntry document,
RandomAccessInputStream stream)
Create an InputStream from the specified DocumentEntry
|
DocumentInputStream(POIFSDocument document,
RandomAccessInputStream stream)
Create an InputStream from the specified Document
|
POIFSDocument(String name,
RandomAccessInputStream stream,
int size)
Constructor
|
POIFSFileSystem(RandomAccessInputStream stream,
int size)
Create a POIFSFileSystem from an InputStream
|
| Modifier and Type | Method and Description |
|---|---|
static DocumentBlock[] |
DocumentBlock.convert(long offset,
RandomAccessInputStream stream,
int numBytes,
int size,
int blockSize)
convert a single long array into an array of DocumentBlock
instances
|
static void |
DocumentBlock.read(DocumentBlock[] blocks,
byte[] buffer,
int offset,
int blockSize,
RandomAccessInputStream stream)
read data from an array of DocumentBlocks
|
| Constructor and Description |
|---|
DocumentBlock(RandomAccessInputStream stream,
int size)
Create a single instance initialized with data.
|
RawDataBlock(RandomAccessInputStream stream,
int size,
long pointer)
Constructor RawDataBlock
|
RawDataBlockList(RandomAccessInputStream stream,
int size)
Constructor RawDataBlockList
|
| Modifier and Type | Method and Description |
|---|---|
static int |
MetakitTools.readBpInt(RandomAccessInputStream stream)
Read a byte-packed integer from the given RandomAccessInputStream.
|
static String |
MetakitTools.readPString(RandomAccessInputStream stream)
Read a Pascal-style string from the given RandomAccessInputStream.
|
| Constructor and Description |
|---|
ColumnMap(Column col,
RandomAccessInputStream stream,
int rowCount) |
MetakitReader(RandomAccessInputStream stream) |
Copyright © 2014 Open Microscopy Environment