Package loci.formats.in

Class OBFReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.OBFReader

All Implemented Interfaces:

Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class OBFReader
extends FormatReader

OBFReader is the file format reader for Imspector OBF files.

Author:

Bjoern Thiel bjoern.thiel at mpibpc.mpg.de

See Also:

• The OBF File Format

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	OBFReader.Stack
private class	OBFReader.State

Field Summary

Fields

Modifier and Type	Field	Description
private static final String	FILE_MAGIC_STRING
private int	file_version
private static final boolean	LITTLE_ENDIAN
private static final short	MAGIC_NUMBER
private static final int	MAXIMAL_NUMBER_OF_DIMENSIONS
private OMEXMLMetadata	ome_meta_data
private byte[]	skipBuffer
private static final String	STACK_MAGIC_STRING
private List<OBFReader.Stack>	stacks
private OBFReader.State	state

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, fillColor, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
OBFReader()

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
private int	getBitsPerPixel(int type)
private ArrayList<Element>	getChildNodes(Element root)
private boolean	getCompression(int compression)
private int	getFileVersion(loci.common.RandomAccessInputStream stream)
private long	getLength(long length)
private int	getPixelType(int type)
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
private long	initStack(long current)
private boolean	isFLIMLabel(String label)
boolean	isThisType(loci.common.RandomAccessInputStream stream)	Checks if the given stream is a valid stream for this file format.
byte[]	openBytes(int no, byte[] buffer, int x, int y, int w, int h)	Obtains a sub-image of the specified image plane into a pre-allocated byte array.
private void	readFlimFrame(OBFReader.Stack stack, int no, byte[] buffer, int x, int y, int w, int h)
private void	readFromStack(OBFReader.Stack stack, byte[] buffer, int bufferOffset, int bytes)
private void	readFromStackRaw(OBFReader.Stack stack, byte[] buffer, int bufferOffset, int bytes)
private void	readStackFrame(OBFReader.Stack stack, long sampleOffset, byte[] buffer, int bufferOffset, int w, int h)
private String	readString()
private long	remainingBytesInChunk(OBFReader.Stack stack)
private void	seekToFrameStart(OBFReader.Stack stack, long sampleOffset)
private void	skipBytes(OBFReader.Stack stack, long byteCount)
private void	switchChunk(OBFReader.Stack stack, int chunkIndex)

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, fileGroupOption, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataLists

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

LITTLE_ENDIAN

private static final boolean LITTLE_ENDIAN

See Also:

• Constant Field Values

FILE_MAGIC_STRING

private static final String FILE_MAGIC_STRING

See Also:

• Constant Field Values

STACK_MAGIC_STRING

private static final String STACK_MAGIC_STRING

See Also:

• Constant Field Values

MAGIC_NUMBER

private static final short MAGIC_NUMBER

See Also:

• Constant Field Values

MAXIMAL_NUMBER_OF_DIMENSIONS

private static final int MAXIMAL_NUMBER_OF_DIMENSIONS

See Also:

• Constant Field Values

file_version

private int file_version

ome_meta_data

private transient OMEXMLMetadata ome_meta_data

state

private OBFReader.State state

skipBuffer

private byte[] skipBuffer

stacks

private List<OBFReader.Stack> stacks

Constructor Details

OBFReader

public OBFReader()

Method Details

getFileVersion

private int getFileVersion(loci.common.RandomAccessInputStream stream)
                    throws IOException

Throws:

IOException

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws IOException

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Parameters:

stream - A RandomAccessInputStream representing the file to check. The first byte in the stream is assumed to be the first byte in the file.

Returns:

true if the file represented by the stream can be read by this reader; false otherwise.

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 - if a parsing error occurs processing the file.

IOException - if an I/O error occurs processing the file

initStack

private long initStack(long current)
                throws FormatException,
IOException

Throws:

FormatException

IOException

isFLIMLabel

private boolean isFLIMLabel(String label)

getPixelType

private int getPixelType(int type)
                  throws FormatException

Throws:

FormatException

getBitsPerPixel

private int getBitsPerPixel(int type)
                     throws FormatException

Throws:

FormatException

getLength

private long getLength(long length)
                throws FormatException

Throws:

FormatException

getCompression

private boolean getCompression(int compression)
                        throws FormatException

Throws:

FormatException

readString

private String readString()
                   throws IOException

Throws:

IOException

remainingBytesInChunk

private long remainingBytesInChunk(OBFReader.Stack stack)
                            throws IOException,
FormatException

Throws:

IOException

FormatException

readFromStackRaw

private void readFromStackRaw(OBFReader.Stack stack,
 byte[] buffer,
 int bufferOffset,
 int bytes)
                       throws IOException,
FormatException

Throws:

IOException

FormatException

readFromStack

private void readFromStack(OBFReader.Stack stack,
 byte[] buffer,
 int bufferOffset,
 int bytes)
                    throws IOException,
FormatException

Throws:

IOException

FormatException

switchChunk

private void switchChunk(OBFReader.Stack stack,
 int chunkIndex)
                  throws FormatException

Throws:

FormatException

seekToFrameStart

private void seekToFrameStart(OBFReader.Stack stack,
 long sampleOffset)
                       throws IOException,
FormatException

Throws:

IOException

FormatException

skipBytes

private void skipBytes(OBFReader.Stack stack,
 long byteCount)
                throws IOException,
FormatException

Throws:

IOException

FormatException

readStackFrame

private void readStackFrame(OBFReader.Stack stack,
 long sampleOffset,
 byte[] buffer,
 int bufferOffset,
 int w,
 int h)
                     throws IOException,
FormatException

Throws:

IOException

FormatException

readFlimFrame

private void readFlimFrame(OBFReader.Stack stack,
 int no,
 byte[] buffer,
 int x,
 int y,
 int w,
 int h)
                    throws IOException,
FormatException

Throws:

IOException

FormatException

openBytes

public byte[] openBytes(int no,
 byte[] buffer,
 int x,
 int y,
 int w,
 int h)
                 throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Parameters:

no - the plane index within the current series.

buffer - a pre-allocated buffer.

x - X coordinate of the upper-left corner of the sub-image

y - Y coordinate of the upper-left corner of the sub-image

w - width of the sub-image

h - height of the sub-image

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(boolean fileOnly)
           throws IOException

Description copied from interface: IFormatReader

Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().

Specified by:

close in interface IFormatReader

Overrides:

close in class FormatReader

Throws:

IOException

getChildNodes

private ArrayList<Element> getChildNodes(Element root)