loci.formats.in

Class KLBReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.KLBReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class KLBReader
extends FormatReader

Reader for Keller Lab Block (KLB) files.

Field Summary

Fields

Modifier and Type	Field and Description
private long[]	blockOffsets
private int	blocksPerPlane
static java.lang.String	CHANNEL_PREFIX Prefixes indicating dimensions and projections
private java.util.ArrayList<java.lang.Integer>	channels
private static int	COMPRESSION_BZIP2
private static int	COMPRESSION_NONE
private static int	COMPRESSION_ZLIB
private int	compressionType
private static java.lang.String	DEFAULT_SERIES
private int[]	dims_blockSize
private int[]	dims_xyzct
private java.util.LinkedHashMap<java.lang.String,java.lang.String[][]>	filelist
private static int	FLOAT32_TYPE
private static int	FLOAT64_TYPE
private long	headerSize
private int	headerVersion
private static int	INT16_TYPE
private static int	INT32_TYPE
private static int	INT64_TYPE
private static int	INT8_TYPE
private static int	KLB_DATA_DIMS
private static int	KLB_DEFAULT_HEADER_VERSION
private static int	KLB_METADATA_SIZE
private double	numBlocks
private long	offsetFilePointer
static java.lang.String	PROJECTION_PREFIX
static java.lang.String	PROJECTION_SUFFIX
static java.util.Set<java.lang.String>	SERIES_PREFIXES
private MetadataStore	store
static java.lang.String	TIME_PREFIX
static java.lang.String	TIME_SUFFIX
private static int	UINT16_TYPE
private static int	UINT32_TYPE
private static int	UINT64_TYPE
private static int	UINT8_TYPE

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, 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 and Description
KLBReader() Constructs a new BDV reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
private void	convertPixelType(CoreMetadata ms0, int pixelType)
int	fileGroupOption(java.lang.String id) Returns an indication of whether the files in a multi-file dataset can be handled individually.
java.lang.String[]	getUsedFiles(boolean noPixels) Returns an array of filenames needed to open this dataset.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h) Obtains a sub-image of the specified image plane into a pre-allocated byte array.
private ome.xml.model.primitives.PositiveFloat	readFloat32()
private void	readHeader(CoreMetadata coreMeta)
private int	readUInt32()
private long	readUInt64()
private void	reCalculateBlockOffsets(int no)

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, 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, 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, getUnderlyingReaders, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, 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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Detail

KLB_DATA_DIMS

private static final int KLB_DATA_DIMS

See Also:

Constant Field Values

KLB_METADATA_SIZE

private static final int KLB_METADATA_SIZE

See Also:

Constant Field Values

KLB_DEFAULT_HEADER_VERSION

private static final int KLB_DEFAULT_HEADER_VERSION

See Also:

Constant Field Values

UINT8_TYPE

private static final int UINT8_TYPE

See Also:

Constant Field Values

UINT16_TYPE

private static final int UINT16_TYPE

See Also:

Constant Field Values

UINT32_TYPE

private static final int UINT32_TYPE

See Also:

Constant Field Values

UINT64_TYPE

private static final int UINT64_TYPE

See Also:

Constant Field Values

INT8_TYPE

private static final int INT8_TYPE

See Also:

Constant Field Values

INT16_TYPE

private static final int INT16_TYPE

See Also:

Constant Field Values

INT32_TYPE

private static final int INT32_TYPE

See Also:

Constant Field Values

INT64_TYPE

private static final int INT64_TYPE

See Also:

Constant Field Values

FLOAT32_TYPE

private static final int FLOAT32_TYPE

See Also:

Constant Field Values

FLOAT64_TYPE

private static final int FLOAT64_TYPE

See Also:

Constant Field Values

COMPRESSION_NONE

private static final int COMPRESSION_NONE

See Also:

Constant Field Values

COMPRESSION_BZIP2

private static final int COMPRESSION_BZIP2

See Also:

Constant Field Values

COMPRESSION_ZLIB

private static final int COMPRESSION_ZLIB

See Also:

Constant Field Values

store

private MetadataStore store

compressionType

private int compressionType

numBlocks

private double numBlocks

dims_blockSize

private int[] dims_blockSize

dims_xyzct

private int[] dims_xyzct

blockOffsets

private long[] blockOffsets

headerSize

private long headerSize

blocksPerPlane

private int blocksPerPlane

offsetFilePointer

private long offsetFilePointer

headerVersion

private int headerVersion

filelist

private java.util.LinkedHashMap<java.lang.String,java.lang.String[][]> filelist

channels

private java.util.ArrayList<java.lang.Integer> channels

DEFAULT_SERIES

private static final java.lang.String DEFAULT_SERIES

See Also:

Constant Field Values

CHANNEL_PREFIX

public static final java.lang.String CHANNEL_PREFIX

Prefixes indicating dimensions and projections

See Also:

Constant Field Values

TIME_PREFIX

public static final java.lang.String TIME_PREFIX

See Also:

Constant Field Values

TIME_SUFFIX

public static final java.lang.String TIME_SUFFIX

See Also:

Constant Field Values

PROJECTION_PREFIX

public static final java.lang.String PROJECTION_PREFIX

See Also:

Constant Field Values

PROJECTION_SUFFIX

public static final java.lang.String PROJECTION_SUFFIX

See Also:

Constant Field Values

SERIES_PREFIXES

public static final java.util.Set<java.lang.String> SERIES_PREFIXES

Constructor Detail

KLBReader

public KLBReader()

Constructs a new BDV reader.

Method Detail

openBytes

public byte[] openBytes(int no,
                        byte[] buf,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        java.io.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.

buf - 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.

java.io.IOException - if there was a problem reading the file.

See Also:

IFormatReader.openBytes(int, byte[], int, int, int, int)

initFile

protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.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.

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

readHeader

private void readHeader(CoreMetadata coreMeta)
                 throws java.io.IOException,
                        FormatException

Throws:

java.io.IOException

FormatException

getUsedFiles

public java.lang.String[] getUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open this dataset. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getUsedFiles in interface IFormatReader

Overrides:

getUsedFiles in class FormatReader

reCalculateBlockOffsets

private void reCalculateBlockOffsets(int no)
                              throws java.io.IOException,
                                     FormatException

Throws:

java.io.IOException

FormatException

convertPixelType

private void convertPixelType(CoreMetadata ms0,
                              int pixelType)
                       throws FormatException

Throws:

FormatException

readUInt32

private int readUInt32()
                throws java.io.IOException

Throws:

java.io.IOException

readUInt64

private long readUInt64()
                 throws java.io.IOException

Throws:

java.io.IOException

readFloat32

private ome.xml.model.primitives.PositiveFloat readFloat32()
                                                    throws java.io.IOException

Throws:

java.io.IOException

fileGroupOption

public int fileGroupOption(java.lang.String id)
                    throws FormatException,
                           java.io.IOException

Description copied from interface: IFormatReader

Returns an indication of whether the files in a multi-file dataset can be handled individually. This method is only useful for formats and datasets which contain multiple files.

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Parameters:

id - a file in the multi-file dataset

Returns:

an int indicating that we cannot, must, or might group the files. A return value of FormatTools.MUST_GROUP indicates that the files cannot be handled separately; the reader will always detect and read all files in the dataset. FormatTools.CAN_GROUP indicates that the files may be handled separately, but file grouping must then be disabled via IFormatReader.setGroupFiles(boolean). FormatTools.CANNOT_GROUP indicates that the files must be handled separately; the reader will not attempt to read all files in the dataset (this is rare).

Throws:

FormatException

java.io.IOException

See Also:

FormatTools.MUST_GROUP, FormatTools.CAN_GROUP, FormatTools.CANNOT_GROUP

close

public void close(boolean fileOnly)
           throws java.io.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:

java.io.IOException