Package loci.formats.in

Class DicomReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.DicomReader

All Implemented Interfaces:

Closeable, AutoCloseable, loci.formats.ICompressedTileReader, loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler

public class DicomReader
extends loci.formats.SubResolutionFormatReader

DicomReader is the file format reader for DICOM files.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	DICOM_MAGIC_STRING
static final int	HEADER_LENGTH

Fields inherited from class loci.formats.SubResolutionFormatReader

core

Fields inherited from class loci.formats.FormatReader

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
DicomReader()	Constructs a new DICOM reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)
int	fileGroupOption(String id)
short[][]	get16BitLookupTable()
byte[][]	get8BitLookupTable()
List<String>	getChannelNames()
int	getConcatenationIndex()
String	getImageType()
int	getOptimalTileHeight()
int	getOptimalTileWidth()
Length	getPixelSizeX()
Length	getPixelSizeY()
Length	getPixelSizeZ()
List<Double>	getPositionX()
List<Double>	getPositionY()
List<Double>	getPositionZ()
int	getRequiredDirectories(String[] files)
String[]	getSeriesUsedFiles(boolean noPixels)
List<DicomTag>	getTags()	Provide the complete hierarchy of DICOM tags.
loci.formats.codec.Codec	getTileCodec(int no)
loci.formats.codec.CodecOptions	getTileCodecOptions(int no, int x, int y)
int	getTileColumns(int no)
int	getTileRows(int no)
List<DicomTile>	getTiles()
Timestamp	getTimestamp()
List<Double>	getZOffsets()
protected void	initFile(String id)
boolean	isExtendedDepthOfField()
boolean	isThisType(String name, boolean open)
boolean	isThisType(RandomAccessInputStream stream)
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)
byte[]	openCompressedBytes(int no, byte[] buf, int x, int y)
byte[]	openCompressedBytes(int no, int x, int y)
protected Slf4JStopWatch	stopWatch()

Methods inherited from class loci.formats.SubResolutionFormatReader

coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution, setSeries

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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, 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, getPixelType, getPixelType, getPossibleDomains, getPulse, getRGBChannelCount, getRotationTransform, 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, isSingleFile, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, 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 Details

DICOM_MAGIC_STRING

public static final String DICOM_MAGIC_STRING

See Also:

• Constant Field Values

HEADER_LENGTH

public static final int HEADER_LENGTH

See Also:

• Constant Field Values

Constructor Details

DicomReader

public DicomReader()

Constructs a new DICOM reader.

Method Details

getTileRows

public int getTileRows(int no)

Specified by:

getTileRows in interface loci.formats.ICompressedTileReader

Overrides:

getTileRows in class loci.formats.FormatReader

getTileColumns

public int getTileColumns(int no)

Specified by:

getTileColumns in interface loci.formats.ICompressedTileReader

Overrides:

getTileColumns in class loci.formats.FormatReader

openCompressedBytes

public byte[] openCompressedBytes(int no,
 int x,
 int y)
                           throws loci.formats.FormatException,
IOException

Throws:

loci.formats.FormatException

IOException

openCompressedBytes

public byte[] openCompressedBytes(int no,
 byte[] buf,
 int x,
 int y)
                           throws loci.formats.FormatException,
IOException

Throws:

loci.formats.FormatException

IOException

getTileCodec

public loci.formats.codec.Codec getTileCodec(int no)
                                      throws loci.formats.FormatException,
IOException

Throws:

loci.formats.FormatException

IOException

getTileCodecOptions

public loci.formats.codec.CodecOptions getTileCodecOptions(int no,
 int x,
 int y)
                                                    throws loci.formats.FormatException,
IOException

Throws:

loci.formats.FormatException

IOException

isThisType

public boolean isThisType(String name,
 boolean open)

Specified by:

isThisType in interface loci.formats.IFormatReader

Overrides:

isThisType in class loci.formats.FormatReader

isThisType

public boolean isThisType(RandomAccessInputStream stream)
                   throws IOException

Specified by:

isThisType in interface loci.formats.IFormatReader

Overrides:

isThisType in class loci.formats.FormatReader

Throws:

IOException

getRequiredDirectories

public int getRequiredDirectories(String[] files)
                           throws loci.formats.FormatException,
IOException

Specified by:

getRequiredDirectories in interface loci.formats.IFormatReader

Overrides:

getRequiredDirectories in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

get8BitLookupTable

public byte[][] get8BitLookupTable()

Specified by:

get8BitLookupTable in interface loci.formats.IFormatReader

Overrides:

get8BitLookupTable in class loci.formats.FormatReader

get16BitLookupTable

public short[][] get16BitLookupTable()

Specified by:

get16BitLookupTable in interface loci.formats.IFormatReader

Overrides:

get16BitLookupTable in class loci.formats.FormatReader

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Specified by:

getSeriesUsedFiles in interface loci.formats.IFormatReader

Overrides:

getSeriesUsedFiles in class loci.formats.FormatReader

fileGroupOption

public int fileGroupOption(String id)
                    throws loci.formats.FormatException,
IOException

Specified by:

fileGroupOption in interface loci.formats.IFormatReader

Overrides:

fileGroupOption in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

getOptimalTileWidth

public int getOptimalTileWidth()

Specified by:

getOptimalTileWidth in interface loci.formats.IFormatReader

Overrides:

getOptimalTileWidth in class loci.formats.FormatReader

getOptimalTileHeight

public int getOptimalTileHeight()

Specified by:

getOptimalTileHeight in interface loci.formats.IFormatReader

Overrides:

getOptimalTileHeight in class loci.formats.FormatReader

openBytes

public byte[] openBytes(int no,
 byte[] buf,
 int x,
 int y,
 int w,
 int h)
                 throws loci.formats.FormatException,
IOException

Specified by:

openBytes in interface loci.formats.IFormatReader

Specified by:

openBytes in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

See Also:

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

close

public void close(boolean fileOnly)
           throws IOException

Specified by:

close in interface loci.formats.IFormatReader

Overrides:

close in class loci.formats.SubResolutionFormatReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws loci.formats.FormatException,
IOException

Overrides:

initFile in class loci.formats.SubResolutionFormatReader

Throws:

loci.formats.FormatException

IOException

getImageType

public String getImageType()

getTiles

public List<DicomTile> getTiles()

getZOffsets

public List<Double> getZOffsets()

getConcatenationIndex

public int getConcatenationIndex()

getPixelSizeX

public Length getPixelSizeX()

getPixelSizeY

public Length getPixelSizeY()

getPixelSizeZ

public Length getPixelSizeZ()

getPositionX

public List<Double> getPositionX()

getPositionY

public List<Double> getPositionY()

getPositionZ

public List<Double> getPositionZ()

getChannelNames

public List<String> getChannelNames()

isExtendedDepthOfField

public boolean isExtendedDepthOfField()

getTimestamp

public Timestamp getTimestamp()

getTags

public List<DicomTag> getTags()

Provide the complete hierarchy of DICOM tags. Applications that need to query or display the complete tag structure should use this method to retrieve tags instead of relying upon original metadata.

stopWatch

protected Slf4JStopWatch stopWatch()