loci.formats.in

Class BDVReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.BDVReader

All Implemented Interfaces:

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

public class BDVReader
extends FormatReader

Reader for BDV files.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	BDVReader.BDVXMLHandler
private class	BDVReader.H5Constants
private class	BDVReader.H5Coordinate

Field Summary

Fields

Modifier and Type	Field and Description
private ch.systemsx.cisd.hdf5.HDF5CompoundDataMap[]	bbox
static java.lang.String	BDV_MAGIC_STRING
private java.lang.String	bdvxml
private java.util.List<java.lang.String>	cellObjectNames
private java.util.List<java.lang.Integer>	channelIndexes
private ch.systemsx.cisd.hdf5.HDF5CompoundDataMap[]	classes
private int[][]	COLORS
private java.lang.Integer	firstTimepoint
private java.lang.String	h5Id
private java.util.List<java.lang.String>	H5PathsToImageData
private java.util.List<BDVReader.H5Coordinate>	H5PositionList
static java.lang.String	HDF_MAGIC_STRING
private JHDFService	jhdf
private int	lastChannel
private java.lang.Integer	lastTimepoint
private int	seriesCount
private java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.String,java.lang.String>>	setupAttributeList
private java.util.HashMap<java.lang.Integer,java.lang.Integer>	setupResolutionCounts
private java.util.HashMap<java.lang.Integer,java.util.ArrayList<ome.units.quantity.Length>>	setupVoxelSizes
private int	sizeC
private MetadataStore	store
private java.lang.Integer	timepointIncrement
private boolean	timepointUsePattern
private ch.systemsx.cisd.hdf5.HDF5CompoundDataMap[]	times

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
BDVReader() Constructs a new BDV reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
private java.lang.String	fetchXMLId()
byte[][]	get8BitLookupTable() Gets the 8-bit color lookup table associated with the most recently opened image.
private int	getChannelIndexOfCellObjectName(java.lang.String cellObjectName)
private java.lang.Object	getImageData(int no, int y, int height)
java.lang.String[]	getUsedFiles(boolean noPixels) Returns an array of filenames needed to open this dataset.
private static ome.xml.model.primitives.Color	hex2Rgb(java.lang.String colorStr)
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
private void	initializeJHDFService(java.lang.String id)
boolean	isThisType(loci.common.RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
boolean	isThisType(java.lang.String name, boolean open) Checks if a file matches the type of this format reader.
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 void	parseROIs(int s)
private void	parseStructure()
void	reopenFile() Reopen any files that were closed, and which are expected to be open while the reader is open.

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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, 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, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, 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

HDF_MAGIC_STRING

public static final java.lang.String HDF_MAGIC_STRING

See Also:

Constant Field Values

BDV_MAGIC_STRING

public static final java.lang.String BDV_MAGIC_STRING

See Also:

Constant Field Values

COLORS

private final int[][] COLORS

store

private MetadataStore store

bdvxml

private java.lang.String bdvxml

h5Id

private java.lang.String h5Id

sizeC

private int sizeC

timepointUsePattern

private boolean timepointUsePattern

firstTimepoint

private java.lang.Integer firstTimepoint

lastTimepoint

private java.lang.Integer lastTimepoint

timepointIncrement

private java.lang.Integer timepointIncrement

seriesCount

private int seriesCount

jhdf

private transient JHDFService jhdf

lastChannel

private int lastChannel

H5PositionList

private java.util.List<BDVReader.H5Coordinate> H5PositionList

H5PathsToImageData

private java.util.List<java.lang.String> H5PathsToImageData

cellObjectNames

private java.util.List<java.lang.String> cellObjectNames

channelIndexes

private java.util.List<java.lang.Integer> channelIndexes

setupAttributeList

private java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.String,java.lang.String>> setupAttributeList

setupVoxelSizes

private java.util.HashMap<java.lang.Integer,java.util.ArrayList<ome.units.quantity.Length>> setupVoxelSizes

setupResolutionCounts

private java.util.HashMap<java.lang.Integer,java.lang.Integer> setupResolutionCounts

times

private ch.systemsx.cisd.hdf5.HDF5CompoundDataMap[] times

classes

private ch.systemsx.cisd.hdf5.HDF5CompoundDataMap[] classes

bbox

private ch.systemsx.cisd.hdf5.HDF5CompoundDataMap[] bbox

Constructor Detail

BDVReader

public BDVReader()

Constructs a new BDV reader.

Method Detail

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

fetchXMLId

private java.lang.String fetchXMLId()
                             throws FormatException

Throws:

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

isThisType

public boolean isThisType(java.lang.String name,
                          boolean open)

Description copied from class: FormatReader

Checks if a file matches the type of this format reader. Checks filename suffixes against those known for this format. If the suffix check is inconclusive and the open parameter is true, the file is opened and tested with FormatReader.isThisType(RandomAccessInputStream).

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis.

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws java.io.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:

java.io.IOException

get8BitLookupTable

public byte[][] get8BitLookupTable()

Description copied from interface: IFormatReader

Gets the 8-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT8 or FormatTools.UINT8, this method will return null.

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class FormatReader

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 image index within the file.

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)

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

reopenFile

public void reopenFile()
                throws java.io.IOException

Description copied from interface: IFormatReader

Reopen any files that were closed, and which are expected to be open while the reader is open. This assumes that IFormatHandler.setId(java.lang.String) has been called, but close(false) has not been called.

Specified by:

reopenFile in interface IFormatReader

Overrides:

reopenFile in class FormatReader

Throws:

java.io.IOException

initializeJHDFService

private void initializeJHDFService(java.lang.String id)
                            throws java.io.IOException,
                                   MissingLibraryException

Throws:

java.io.IOException

MissingLibraryException

getImageData

private java.lang.Object getImageData(int no,
                                      int y,
                                      int height)
                               throws FormatException

Throws:

FormatException

parseStructure

private void parseStructure()
                     throws FormatException

Throws:

FormatException

getChannelIndexOfCellObjectName

private int getChannelIndexOfCellObjectName(java.lang.String cellObjectName)

hex2Rgb

private static ome.xml.model.primitives.Color hex2Rgb(java.lang.String colorStr)

parseROIs

private void parseROIs(int s)