loci.formats.in

Class DCIMGReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.DCIMGReader

All Implemented Interfaces:

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

public class DCIMGReader
extends FormatReader

DCIMGReader reads Hamamatsu DCIMG files. Follows spec/code at https://github.com/python-microscopy/python-microscopy/blob/master/PYME/IO/dcimg.py and https://github.com/lens-biophotonics/dcimg/blob/master/dcimg.py.

Field Summary

Fields

Modifier and Type	Field and Description
private long	bytesPerImage
private long	bytesPerRow
private java.util.List<java.lang.String>	companionFiles
private long	currentStreamPosition
private long	dataOffset
private static long	DCIMG_PIXELTYPE_MONO16
private static long	DCIMG_PIXELTYPE_MONO8
private static long	DCIMG_VERSION_0
private static long	DCIMG_VERSION_1
private boolean	fourPixelCorrectionInFooter
private int	fourPixelCorrectionLine
private long	fourPixelCorrectionOffset
private long	fourPixelOffsetInFrame
private long	frameFooterSize
private long	headerSize
private static boolean	IS_LITTLE
private long	offsetToFooter
private long	offsetToFourPixels
private long	pixelType
private java.lang.String[]	uniqueFiles
private long	version

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 and Description
DCIMGReader()

Method Summary

Modifier and Type	Method and Description
private void	addFileToList(java.lang.String file)
void	close(boolean fileOnly) Closes the currently open file.
int	fileGroupOption(java.lang.String id) Returns an indication of whether the files in a multi-file dataset can be handled individually.
private int	getFourPixelCorrectionLine()
private long	getFourPixelCorrectionOffset()
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
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.
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	parseDCAMVersion0Footer(loci.common.RandomAccessInputStream stream)
private void	parseDCAMVersion0Header(loci.common.RandomAccessInputStream stream)
private void	parseDCAMVersion1Header(loci.common.RandomAccessInputStream stream)
private void	scanDirectory(loci.common.Location dir)

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, 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, 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, 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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Field Detail

IS_LITTLE

private static final boolean IS_LITTLE

See Also:

Constant Field Values

DCIMG_VERSION_0

private static final long DCIMG_VERSION_0

See Also:

Constant Field Values

DCIMG_VERSION_1

private static final long DCIMG_VERSION_1

See Also:

Constant Field Values

DCIMG_PIXELTYPE_MONO8

private static final long DCIMG_PIXELTYPE_MONO8

See Also:

Constant Field Values

DCIMG_PIXELTYPE_MONO16

private static final long DCIMG_PIXELTYPE_MONO16

See Also:

Constant Field Values

version

private long version

headerSize

private long headerSize

dataOffset

private long dataOffset

pixelType

private long pixelType

bytesPerImage

private long bytesPerImage

bytesPerRow

private long bytesPerRow

offsetToFooter

private long offsetToFooter

fourPixelCorrectionInFooter

private boolean fourPixelCorrectionInFooter

offsetToFourPixels

private long offsetToFourPixels

fourPixelOffsetInFrame

private long fourPixelOffsetInFrame

fourPixelCorrectionLine

private int fourPixelCorrectionLine

fourPixelCorrectionOffset

private long fourPixelCorrectionOffset

currentStreamPosition

private long currentStreamPosition

frameFooterSize

private long frameFooterSize

companionFiles

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

uniqueFiles

private java.lang.String[] uniqueFiles

Constructor Detail

DCIMGReader

public DCIMGReader()

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

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

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

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

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.

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

scanDirectory

private void scanDirectory(loci.common.Location dir)
                    throws FormatException,
                           java.io.IOException

Throws:

FormatException

java.io.IOException

addFileToList

private void addFileToList(java.lang.String file)
                    throws FormatException,
                           java.io.IOException

Throws:

FormatException

java.io.IOException

parseDCAMVersion0Header

private void parseDCAMVersion0Header(loci.common.RandomAccessInputStream stream)
                              throws java.io.IOException

Throws:

java.io.IOException

parseDCAMVersion1Header

private void parseDCAMVersion1Header(loci.common.RandomAccessInputStream stream)
                              throws java.io.IOException

Throws:

java.io.IOException

parseDCAMVersion0Footer

private void parseDCAMVersion0Footer(loci.common.RandomAccessInputStream stream)
                              throws java.io.IOException,
                                     FormatException

Throws:

java.io.IOException

FormatException

getFourPixelCorrectionLine

private int getFourPixelCorrectionLine()

getFourPixelCorrectionOffset

private long getFourPixelCorrectionOffset()

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