loci.formats.in

Class DeltavisionReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.DeltavisionReader

All Implemented Interfaces:

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

public class DeltavisionReader
extends FormatReader

DeltavisionReader is the file format reader for Deltavision files.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private static class	DeltavisionReader.DVExtHdrFields This private class structure holds the details for the extended header.

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	backwardsStage Whether or not the stage moved backwards.
static java.lang.String	DATE_FORMAT Deprecated. Use DATE_FORMATS instead
static java.lang.String[]	DATE_FORMATS
private java.lang.String	deconvolutionLogFile
static int	DV_MAGIC_BYTES_1
static int	DV_MAGIC_BYTES_2
protected DeltavisionReader.DVExtHdrFields[][][]	extHdrFields Initialize an array of Extended Header Field structures.
private int	extSize Size of extended header.
private static int	HEADER_LENGTH
private static java.lang.String[]	IMAGE_TYPES
private int[]	lengths
private static short	LITTLE_ENDIAN
private java.lang.String	logFile
private static int	MAX_CHANNELS
private java.lang.Double[]	ndFilters
private static int	NEW_TYPE
protected int	numFloatsPerSection
protected int	numIntsPerSection The number of ints in each extended header section.
private boolean	truncatedFileFlag
protected int	tSize Size of one time element in the extended header.
protected int	wSize Size of one wave in the extended header.
private int	xTiles Number of tiles in X direction.
private int	yTiles Number of tiles in Y direction.
protected int	zSize Size of one z section in the extended header.

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
DeltavisionReader() Constructs a new Deltavision reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
private void	findLogFiles() Find the log files.
private java.lang.String	getImageSequence(int imageSequence) Get the image sequence string.
private java.lang.String	getPixelString(int filePixelType) Get a descriptive string representing the pixel type.
private int	getPixelType(int filePixelType) Get the OME pixel type from the pixel type stored in the file.
long	getPlaneByteOffset(int currentZ, int currentW, int currentT) Given any specific Z, W, and T of a plane, determine the absolute byte offset of the plane in the file.
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
private int	getTotalOffset(int currentZ, int currentW, int currentT) Given any specific Z, W, and T of a plane, determine the totalOffset from the start of the extended header.
protected void	initExtraMetadata()
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
protected void	initPixels()
boolean	isSingleFile(java.lang.String id) Returns true if the named file is expected to be the only file in the dataset.
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	parseDeconvolutionLog(loci.common.RandomAccessInputStream s, MetadataStore store) Parse deconvolution output, if it exists.
private boolean	parseLogFile(MetadataStore store) Extract metadata from associated log file, if it exists.
private void	populateObjective(MetadataStore store, int lensID) Populate an Objective based upon the lens ID.
private void	readWavelength(int channel, MetadataStore store)
private void	setOffsetInfo(int imgSequence, int numZSections, int numWaves, int numTimes) This method calculates the size of a w, t, z section depending on which sequence is being used (either ZTW, WZT, or ZWT)
void	setTruncatedFileFlag(boolean truncatedFileFlag) This flag indicates if the file is known to be truncated.

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, 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, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, 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

DV_MAGIC_BYTES_1

public static final int DV_MAGIC_BYTES_1

See Also:

Constant Field Values

DV_MAGIC_BYTES_2

public static final int DV_MAGIC_BYTES_2

See Also:

Constant Field Values

DATE_FORMAT

@Deprecated
public static final java.lang.String DATE_FORMAT

Deprecated. Use DATE_FORMATS instead

See Also:

Constant Field Values

DATE_FORMATS

public static final java.lang.String[] DATE_FORMATS

LITTLE_ENDIAN

private static final short LITTLE_ENDIAN

See Also:

Constant Field Values

HEADER_LENGTH

private static final int HEADER_LENGTH

See Also:

Constant Field Values

NEW_TYPE

private static final int NEW_TYPE

See Also:

Constant Field Values

MAX_CHANNELS

private static final int MAX_CHANNELS

See Also:

Constant Field Values

IMAGE_TYPES

private static final java.lang.String[] IMAGE_TYPES

extSize

private int extSize

Size of extended header.

wSize

protected int wSize

Size of one wave in the extended header.

zSize

protected int zSize

Size of one z section in the extended header.

tSize

protected int tSize

Size of one time element in the extended header.

xTiles

private int xTiles

Number of tiles in X direction.

yTiles

private int yTiles

Number of tiles in Y direction.

backwardsStage

private boolean backwardsStage

Whether or not the stage moved backwards.

numIntsPerSection

protected int numIntsPerSection

The number of ints in each extended header section. These fields appear to be all blank but need to be skipped to get to the floats afterwards

numFloatsPerSection

protected int numFloatsPerSection

extHdrFields

protected DeltavisionReader.DVExtHdrFields[][][] extHdrFields

Initialize an array of Extended Header Field structures.

ndFilters

private java.lang.Double[] ndFilters

lengths

private int[] lengths

logFile

private java.lang.String logFile

deconvolutionLogFile

private java.lang.String deconvolutionLogFile

truncatedFileFlag

private boolean truncatedFileFlag

Constructor Detail

DeltavisionReader

public DeltavisionReader()

Constructs a new Deltavision reader.

Method Detail

isSingleFile

public boolean isSingleFile(java.lang.String id)
                     throws FormatException,
                            java.io.IOException

Description copied from interface: IFormatReader

Returns true if the named file is expected to be the only file in the dataset. For single-file formats, always returns true.

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

java.io.IOException

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

getSeriesUsedFiles

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

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. 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:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles 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

setTruncatedFileFlag

public void setTruncatedFileFlag(boolean truncatedFileFlag)

This flag indicates if the file is known to be truncated. If true, the dimension size information is kept as it is specified in the file header, otherwise the length of the file is used to override size information. This flag must be set before FormatReader.setId(String) is called. Default is false.

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

initPixels

protected void initPixels()
                   throws FormatException,
                          java.io.IOException

Throws:

FormatException

java.io.IOException

initExtraMetadata

protected void initExtraMetadata()
                          throws FormatException,
                                 java.io.IOException

Throws:

FormatException

java.io.IOException

getPixelString

private java.lang.String getPixelString(int filePixelType)

Get a descriptive string representing the pixel type.

getPixelType

private int getPixelType(int filePixelType)

Get the OME pixel type from the pixel type stored in the file.

getImageSequence

private java.lang.String getImageSequence(int imageSequence)

Get the image sequence string.

setOffsetInfo

private void setOffsetInfo(int imgSequence,
                           int numZSections,
                           int numWaves,
                           int numTimes)

This method calculates the size of a w, t, z section depending on which sequence is being used (either ZTW, WZT, or ZWT)

Parameters:

imgSequence -

numZSections -

numWaves -

numTimes -

getTotalOffset

private int getTotalOffset(int currentZ,
                           int currentW,
                           int currentT)

Given any specific Z, W, and T of a plane, determine the totalOffset from the start of the extended header.

Parameters:

currentZ -

currentW -

currentT -

getPlaneByteOffset

public long getPlaneByteOffset(int currentZ,
                               int currentW,
                               int currentT)

Given any specific Z, W, and T of a plane, determine the absolute byte offset of the plane in the file.

Parameters:

currentZ -

currentW -

currentT -

findLogFiles

private void findLogFiles()
                   throws java.io.IOException

Find the log files.

Throws:

java.io.IOException

parseLogFile

private boolean parseLogFile(MetadataStore store)
                      throws FormatException,
                             java.io.IOException

Extract metadata from associated log file, if it exists.

Throws:

FormatException

java.io.IOException

parseDeconvolutionLog

private void parseDeconvolutionLog(loci.common.RandomAccessInputStream s,
                                   MetadataStore store)
                            throws java.io.IOException

Parse deconvolution output, if it exists.

Throws:

java.io.IOException

readWavelength

private void readWavelength(int channel,
                            MetadataStore store)
                     throws FormatException,
                            java.io.IOException

Throws:

FormatException

java.io.IOException

populateObjective

private void populateObjective(MetadataStore store,
                               int lensID)
                        throws FormatException

Populate an Objective based upon the lens ID. This is based upon information received from Applied Precision.

Throws:

FormatException