DicomReader (Bio-Formats API)

java.lang.Object
- loci.formats.FormatHandler
- - loci.formats.FormatReader
  - - loci.formats.in.DicomReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable
```
public class DicomReader
extends FormatReader
```
DicomReader is the file format reader for DICOM files. Much of this code is adapted from ImageJ's DICOM reader; see http://rsb.info.nih.gov/ij/developer/source/ij/plugin/DICOM.java.html

Field Summary

Fields
Modifier and Type	Field and Description
`private static int`	`AE`
`private static int`	`AS`
`private static int`	`AT`
`private boolean`	`bigEndianTransferSyntax`
`private static int`	`BITS_ALLOCATED`
`private int`	`bitsPerPixel` Bits per pixel.
`private static int`	`COLUMNS`
`private List<String>`	`companionFiles`
`private static int`	`CS`
`private static int`	`DA`
`private String`	`date`
`static String`	`DICOM_MAGIC_STRING`
`private static String[]`	`DICOM_SUFFIXES`
`private static int`	`DS`
`private static int`	`DT`
`private int`	`elementLength`
`private static int`	`FD`
`private Map<Integer,List<String>>`	`fileList`
`private static int`	`FL`
`private DicomReader`	`helper`
`private static int`	`ICON_IMAGE_SEQUENCE`
`private int`	`imagesPerFile`
`private String`	`imageType`
`private static int`	`IMPLICIT_VR`
`private boolean`	`inSequence`
`private boolean`	`inverted`
`private static int`	`IS`
`private boolean`	`isDeflate`
`private boolean`	`isJP2K`
`private boolean`	`isJPEG`
`private boolean`	`isRLE`
`private static int`	`ITEM`
`private static int`	`ITEM_DELIMINATION`
`private static int`	`LO`
`private int`	`location`
`private static int`	`LT`
`private byte[][]`	`lut`
`private int`	`maxPixelValue`
`private static int`	`NUMBER_OF_FRAMES`
`private static int`	`OB`
`private boolean`	`oddLocations`
`private long[]`	`offsets`
`private String`	`originalDate`
`private String`	`originalInstance`
`private int`	`originalSeries`
`private String`	`originalTime`
`private static int`	`OW`
`private static int`	`PHOTOMETRIC_INTERPRETATION`
`private static int`	`PIXEL_DATA`
`private static int`	`PIXEL_REPRESENTATION`
`private static int`	`PIXEL_SIGN`
`private static int`	`PIXEL_SPACING`
`private String`	`pixelSizeX`
`private String`	`pixelSizeY`
`private Double`	`pixelSizeZ`
`private static int`	`PLANAR_CONFIGURATION`
`private static int`	`PN`
`private static int`	`QQ`
`private static int`	`RESCALE_INTERCEPT`
`private static int`	`RESCALE_SLOPE`
`private double`	`rescaleIntercept`
`private double`	`rescaleSlope`
`private static int`	`ROWS`
`private static int`	`SAMPLES_PER_PIXEL`
`private static int`	`SEQUENCE_DELIMINATION`
`private static int`	`SH`
`private short[][]`	`shortLut`
`private static int`	`SL`
`private static int`	`SLICE_SPACING`
`private static int`	`SQ`
`private static int`	`SS`
`private static int`	`ST`
`private String`	`time`
`private static int`	`TM`
`private static int`	`TRANSFER_SYNTAX_UID`
`private static com.google.common.collect.ImmutableMap<Integer,String>`	`TYPES`
`private static int`	`UI`
`private static int`	`UL`
`private static int`	`UN`
`private static int`	`US`
`private static int`	`UT`
`private int`	`vr`
`private static int`	`WINDOW_CENTER`
`private static int`	`WINDOW_WIDTH`

Fields inherited from class loci.formats.FormatReader
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler
COMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixes

Fields inherited from interface loci.formats.IFormatReader
CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors
Constructor and Description

DicomReader()
Constructs a new DICOM reader.

Constructors
Constructor and Description
`DicomReader()` Constructs a new DICOM reader.

Method Summary

Methods
Modifier and Type	Method and Description
`private void`	`addFileToList(String file, boolean checkSeries)` Determine if the given file belongs in the same dataset as this file.
`private void`	`addInfo(int tag, int value)`
`private void`	`addInfo(int tag, String value)`
`private void`	`attachCompanionFiles()` DICOM datasets produced by: http://www.ct-imaging.de/index.php/en/ct-systeme-e/mikro-ct-e.html contain a bunch of extra metadata and log files.
`private static com.google.common.collect.ImmutableMap<Integer,String>`	`buildTypes()` Assemble the data dictionary.
`void`	`close(boolean fileOnly)` Closes the currently open file.
`int`	`fileGroupOption(String id)` Returns an int indicating that we cannot, must, or might group the files in a given dataset.
`private String`	`formatTag(int tag)`
`short[][]`	`get16BitLookupTable()` Gets the 16-bit color lookup table associated with the most recently opened image.
`byte[][]`	`get8BitLookupTable()` Gets the 8-bit color lookup table associated with the most recently opened image.
`private String`	`getHeaderInfo(int tag, String value)`
`private int`	`getLength(RandomAccessInputStream stream, int tag)`
`private int`	`getNextTag(RandomAccessInputStream stream)`
`String[]`	`getSeriesUsedFiles(boolean noPixels)` Returns an array of filenames needed to open the current series.
`protected void`	`initFile(String id)` Initializes the given file (parsing header information, etc.).
`boolean`	`isThisType(RandomAccessInputStream stream)` Checks if the given stream is a valid stream for this file format.
`boolean`	`isThisType(String name, boolean open)` Checks if a file matches the type of this format reader.
`private void`	`makeFileList()`
`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`	`scanDirectory(Location dir, boolean checkSeries)` Scan the given directory for files that belong to this dataset.

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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadataOptions, 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, getSupportedMetadataLevels, 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, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

Methods inherited from class loci.formats.FormatHandler
checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes

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

- Field Detail
  - DICOM_MAGIC_STRING
```
public static final String DICOM_MAGIC_STRING
```
    See Also:
    Constant Field Values
  - DICOM_SUFFIXES
```
private static final String[] DICOM_SUFFIXES
```
  - TYPES
```
private static final com.google.common.collect.ImmutableMap<Integer,String> TYPES
```
  - PIXEL_REPRESENTATION
```
private static final int PIXEL_REPRESENTATION
```
    See Also:
    Constant Field Values
  - PIXEL_SIGN
```
private static final int PIXEL_SIGN
```
    See Also:
    Constant Field Values
  - TRANSFER_SYNTAX_UID
```
private static final int TRANSFER_SYNTAX_UID
```
    See Also:
    Constant Field Values
  - SLICE_SPACING
```
private static final int SLICE_SPACING
```
    See Also:
    Constant Field Values
  - SAMPLES_PER_PIXEL
```
private static final int SAMPLES_PER_PIXEL
```
    See Also:
    Constant Field Values
  - PHOTOMETRIC_INTERPRETATION
```
private static final int PHOTOMETRIC_INTERPRETATION
```
    See Also:
    Constant Field Values
  - PLANAR_CONFIGURATION
```
private static final int PLANAR_CONFIGURATION
```
    See Also:
    Constant Field Values
  - NUMBER_OF_FRAMES
```
private static final int NUMBER_OF_FRAMES
```
    See Also:
    Constant Field Values
  - ROWS
```
private static final int ROWS
```
    See Also:
    Constant Field Values
  - COLUMNS
```
private static final int COLUMNS
```
    See Also:
    Constant Field Values
  - PIXEL_SPACING
```
private static final int PIXEL_SPACING
```
    See Also:
    Constant Field Values
  - BITS_ALLOCATED
```
private static final int BITS_ALLOCATED
```
    See Also:
    Constant Field Values
  - WINDOW_CENTER
```
private static final int WINDOW_CENTER
```
    See Also:
    Constant Field Values
  - WINDOW_WIDTH
```
private static final int WINDOW_WIDTH
```
    See Also:
    Constant Field Values
  - RESCALE_INTERCEPT
```
private static final int RESCALE_INTERCEPT
```
    See Also:
    Constant Field Values
  - RESCALE_SLOPE
```
private static final int RESCALE_SLOPE
```
    See Also:
    Constant Field Values
  - ICON_IMAGE_SEQUENCE
```
private static final int ICON_IMAGE_SEQUENCE
```
    See Also:
    Constant Field Values
  - ITEM
```
private static final int ITEM
```
    See Also:
    Constant Field Values
  - ITEM_DELIMINATION
```
private static final int ITEM_DELIMINATION
```
    See Also:
    Constant Field Values
  - SEQUENCE_DELIMINATION
```
private static final int SEQUENCE_DELIMINATION
```
    See Also:
    Constant Field Values
  - PIXEL_DATA
```
private static final int PIXEL_DATA
```
    See Also:
    Constant Field Values
  - AE
```
private static final int AE
```
    See Also:
    Constant Field Values
  - AS
```
private static final int AS
```
    See Also:
    Constant Field Values
  - AT
```
private static final int AT
```
    See Also:
    Constant Field Values
  - CS
```
private static final int CS
```
    See Also:
    Constant Field Values
  - DA
```
private static final int DA
```
    See Also:
    Constant Field Values
  - DS
```
private static final int DS
```
    See Also:
    Constant Field Values
  - DT
```
private static final int DT
```
    See Also:
    Constant Field Values
  - FD
```
private static final int FD
```
    See Also:
    Constant Field Values
  - FL
```
private static final int FL
```
    See Also:
    Constant Field Values
  - IS
```
private static final int IS
```
    See Also:
    Constant Field Values
  - LO
```
private static final int LO
```
    See Also:
    Constant Field Values
  - LT
```
private static final int LT
```
    See Also:
    Constant Field Values
  - PN
```
private static final int PN
```
    See Also:
    Constant Field Values
  - SH
```
private static final int SH
```
    See Also:
    Constant Field Values
  - SL
```
private static final int SL
```
    See Also:
    Constant Field Values
  - SS
```
private static final int SS
```
    See Also:
    Constant Field Values
  - ST
```
private static final int ST
```
    See Also:
    Constant Field Values
  - TM
```
private static final int TM
```
    See Also:
    Constant Field Values
  - UI
```
private static final int UI
```
    See Also:
    Constant Field Values
  - UL
```
private static final int UL
```
    See Also:
    Constant Field Values
  - US
```
private static final int US
```
    See Also:
    Constant Field Values
  - UT
```
private static final int UT
```
    See Also:
    Constant Field Values
  - OB
```
private static final int OB
```
    See Also:
    Constant Field Values
  - OW
```
private static final int OW
```
    See Also:
    Constant Field Values
  - SQ
```
private static final int SQ
```
    See Also:
    Constant Field Values
  - UN
```
private static final int UN
```
    See Also:
    Constant Field Values
  - QQ
```
private static final int QQ
```
    See Also:
    Constant Field Values
  - IMPLICIT_VR
```
private static final int IMPLICIT_VR
```
    See Also:
    Constant Field Values
  - bitsPerPixel
```
private int bitsPerPixel
```
    Bits per pixel.
  - location
```
private int location
```
  - elementLength
```
private int elementLength
```
  - vr
```
private int vr
```
  - oddLocations
```
private boolean oddLocations
```
  - inSequence
```
private boolean inSequence
```
  - bigEndianTransferSyntax
```
private boolean bigEndianTransferSyntax
```
  - lut
```
private byte[][] lut
```
  - shortLut
```
private short[][] shortLut
```
  - offsets
```
private long[] offsets
```
  - maxPixelValue
```
private int maxPixelValue
```
  - rescaleSlope
```
private double rescaleSlope
```
  - rescaleIntercept
```
private double rescaleIntercept
```
  - isJP2K
```
private boolean isJP2K
```
  - isJPEG
```
private boolean isJPEG
```
  - isRLE
```
private boolean isRLE
```
  - isDeflate
```
private boolean isDeflate
```
  - inverted
```
private boolean inverted
```
  - date
```
private String date
```
  - time
```
private String time
```
  - imageType
```
private String imageType
```
  - pixelSizeX
```
private String pixelSizeX
```
  - pixelSizeY
```
private String pixelSizeY
```
  - pixelSizeZ
```
private Double pixelSizeZ
```
  - fileList
```
private Map<Integer,List<String>> fileList
```
  - imagesPerFile
```
private int imagesPerFile
```
  - originalDate
```
private String originalDate
```
  - originalTime
```
private String originalTime
```
  - originalInstance
```
private String originalInstance
```
  - originalSeries
```
private int originalSeries
```
  - helper
```
private DicomReader helper
```
  - companionFiles
```
private List<String> companionFiles
```
- Constructor Detail
  - DicomReader
```
public DicomReader()
```
    Constructs a new DICOM reader.
- Method Detail
  - isThisType
```
public boolean isThisType(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(RandomAccessInputStream stream)
                   throws IOException
```
    Description copied from interface: IFormatReader
    
    Checks if the given stream is a valid stream for this file format.
    
    Specified by:
    
    isThisType in interface IFormatReader
    
    Overrides:
    
    isThisType in class FormatReader
    
    Throws:
    
    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
  - get16BitLookupTable
```
public short[][] get16BitLookupTable()
```
    Description copied from interface: IFormatReader
    
    Gets the 16-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.INT16 or FormatTools.UINT16, this method will return null.
    
    Specified by:
    
    get16BitLookupTable in interface IFormatReader
    
    Overrides:
    
    get16BitLookupTable in class FormatReader
  - getSeriesUsedFiles
```
public 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.
    
    Specified by:
    
    getSeriesUsedFiles in interface IFormatReader
    
    Overrides:
    
    getSeriesUsedFiles in class FormatReader
  - fileGroupOption
```
public int fileGroupOption(String id)
                    throws FormatException,
                           IOException
```
    Description copied from interface: IFormatReader
    
    Returns an int indicating that we cannot, must, or might group the files in a given dataset.
    
    Specified by:
    
    fileGroupOption in interface IFormatReader
    
    Overrides:
    
    fileGroupOption in class FormatReader
    
    Throws:
    
    FormatException
    
    IOException
  - openBytes
```
public byte[] openBytes(int no,
               byte[] buf,
               int x,
               int y,
               int w,
               int h)
                 throws FormatException,
                        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.
    
    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 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:
    
    IOException
  - initFile
```
protected void initFile(String id)
                 throws FormatException,
                        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.
    
    IOException - if an I/O error occurs processing the file
  - addInfo
```
private void addInfo(int tag,
           String value)
              throws IOException
```
    Throws:
    
    IOException
  - addInfo
```
private void addInfo(int tag,
           int value)
              throws IOException
```
    Throws:
    
    IOException
  - getHeaderInfo
```
private String getHeaderInfo(int tag,
                   String value)
                      throws IOException
```
    Throws:
    
    IOException
  - getLength
```
private int getLength(RandomAccessInputStream stream,
            int tag)
               throws IOException
```
    Throws:
    
    IOException
  - getNextTag
```
private int getNextTag(RandomAccessInputStream stream)
                throws FormatException,
                       IOException
```
    Throws:
    
    FormatException
    
    IOException
  - makeFileList
```
private void makeFileList()
                   throws FormatException,
                          IOException
```
    Throws:
    
    FormatException
    
    IOException
  - scanDirectory
```
private void scanDirectory(Location dir,
                 boolean checkSeries)
                    throws FormatException,
                           IOException
```
    Scan the given directory for files that belong to this dataset.
    
    Throws:
    
    FormatException
    
    IOException
  - addFileToList
```
private void addFileToList(String file,
                 boolean checkSeries)
                    throws FormatException,
                           IOException
```
    Determine if the given file belongs in the same dataset as this file.
    
    Throws:
    
    FormatException
    
    IOException
  - formatTag
```
private String formatTag(int tag)
```
  - attachCompanionFiles
```
private void attachCompanionFiles()
                           throws IOException
```
    DICOM datasets produced by: http://www.ct-imaging.de/index.php/en/ct-systeme-e/mikro-ct-e.html contain a bunch of extra metadata and log files. We do not parse these extra files, but do locate and attach them to the DICOM file(s).
    
    Throws:
    
    IOException
  - buildTypes
```
private static com.google.common.collect.ImmutableMap<Integer,String> buildTypes()
```
    Assemble the data dictionary. This is incomplete at best, since there are literally thousands of fields defined by the DICOM specifications.

Class DicomReader

Field Summary

Fields inherited from class loci.formats.FormatReader

Fields inherited from class loci.formats.FormatHandler

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class loci.formats.FormatReader

Methods inherited from class loci.formats.FormatHandler

Methods inherited from class java.lang.Object

Methods inherited from interface loci.formats.IFormatHandler

Field Detail

DICOM_MAGIC_STRING

DICOM_SUFFIXES

TYPES

PIXEL_REPRESENTATION

PIXEL_SIGN

TRANSFER_SYNTAX_UID

SLICE_SPACING

SAMPLES_PER_PIXEL

PHOTOMETRIC_INTERPRETATION

PLANAR_CONFIGURATION

NUMBER_OF_FRAMES

ROWS

COLUMNS

PIXEL_SPACING

BITS_ALLOCATED

WINDOW_CENTER

WINDOW_WIDTH

RESCALE_INTERCEPT

RESCALE_SLOPE

ICON_IMAGE_SEQUENCE

ITEM

ITEM_DELIMINATION

SEQUENCE_DELIMINATION

PIXEL_DATA

AE

AS

AT

CS

DA

DS

DT

FD

FL

IS

LO

LT

PN

SH

SL

SS

ST

TM

UI

UL

US

UT

OB

OW

SQ

UN

QQ

IMPLICIT_VR

bitsPerPixel

location

elementLength

vr

oddLocations

inSequence

bigEndianTransferSyntax

lut

shortLut

offsets

maxPixelValue

rescaleSlope

rescaleIntercept

isJP2K

isJPEG

isRLE