loci.formats.in
Class OIBReader
java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.in.OIBReader
- All Implemented Interfaces:
- IFormatHandler, IFormatReader, StatusReporter
public class OIBReader
- extends FormatReader
OIBReader is the file format reader for Fluoview FV1000 OIB files.
- Source code:
- Trac,
SVN
- Author:
- Melissa Linkert linkert at wisc.edu
Fields inherited from class loci.formats.FormatReader |
collectMetadata, core, filterMetadata, group, in, metadata, metadataStore, normalizeData, saveOriginalMetadata, series, THUMBNAIL_DIMENSION |
Constructor Summary |
OIBReader()
Constructs a new OIB reader. |
Method Summary |
void |
close()
Closes currently open file(s) and frees allocated memory. |
protected void |
initFile(String id)
Initializes the given file (parsing header information, etc.). |
boolean |
isThisType(byte[] block)
Checks if the given block is a valid header for this file format. |
byte[] |
openBytes(int no,
byte[] buf)
Obtains the specified image from the current file into a pre-allocated byte
array of (sizeX * sizeY * bytesPerPixel). |
protected void |
parseDir(int depth,
Object dir)
|
protected void |
print(int depth,
String s)
Debugging helper method. |
Methods inherited from class loci.formats.FormatReader |
addMeta, checkBytes, close, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getChannelDimLengths, getChannelDimLengths, getChannelDimTypes, getChannelDimTypes, getCoreMetadata, getCoreMetadata, getCurrentFile, getDimensionOrder, getDimensionOrder, getEffectiveSizeC, getEffectiveSizeC, getImageCount, getImageCount, getIndex, getIndex, getMeta, getMetadata, getMetadata, getMetadataStore, getMetadataStore, getMetadataStoreRoot, getMetadataStoreRoot, getMetadataValue, getMetadataValue, getPixelType, getPixelType, getRGBChannelCount, getRGBChannelCount, getSeries, getSeries, getSeriesCount, getSeriesCount, getSizeC, getSizeC, getSizeT, getSizeT, getSizeX, getSizeX, getSizeY, getSizeY, getSizeZ, getSizeZ, getThumbSizeX, getThumbSizeX, getThumbSizeY, getThumbSizeY, getUsedFiles, getUsedFiles, getZCTCoords, getZCTCoords, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isInterleaved, isInterleaved, isLittleEndian, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOrderCertain, isOriginalMetadataPopulated, isRGB, isRGB, isUsedFile, openBytes, openBytes, openBytes, openImage, openImage, openThumbBytes, openThumbBytes, openThumbImage, openThumbImage, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setSeries, setSeries |
Methods inherited from class loci.formats.FormatHandler |
addStatusListener, debug, getFormat, getStatusListeners, getSuffixes, isThisType, isThisType, removeStatusListener, setDebug, setDebugLevel, setId, status, status, status, trace, trace |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
OIBReader
public OIBReader()
- Constructs a new OIB reader.
isThisType
public boolean isThisType(byte[] block)
- Description copied from interface:
IFormatReader
- Checks if the given block is a valid header for this file format.
openBytes
public byte[] openBytes(int no,
byte[] buf)
throws FormatException,
IOException
- Description copied from interface:
IFormatReader
- Obtains the specified image from the current file into a pre-allocated byte
array of (sizeX * sizeY * bytesPerPixel).
- Parameters:
no
- the image index within the file.buf
- a pre-allocated buffer.
- Returns:
- the pre-allocated buffer
buf
for convenience.
- Throws:
FormatException
- if there was a problem parsing the metadata of the
file.
IOException
- if there was a problem reading the file.
close
public void close()
throws IOException
- Description copied from interface:
IFormatHandler
- Closes currently open file(s) and frees allocated memory.
- Specified by:
close
in interface IFormatHandler
- Overrides:
close
in class FormatReader
- Throws:
IOException
initFile
protected void initFile(String id)
throws FormatException,
IOException
- Description copied from class:
FormatReader
- Initializes the given file (parsing header information, etc.).
Most subclasses should override this method to perform
initialization operations such as parsing metadata.
- Overrides:
initFile
in class FormatReader
- Throws:
FormatException
IOException
parseDir
protected void parseDir(int depth,
Object dir)
throws IOException,
FormatException,
ReflectException
- Throws:
IOException
FormatException
ReflectException
print
protected void print(int depth,
String s)
- Debugging helper method.