com.pixelmed.dicom
Class AttributeList

java.lang.Object
  java.util.AbstractMap<K,V>
      java.util.TreeMap<AttributeTag,Attribute>
          com.pixelmed.dicom.AttributeList

All Implemented Interfaces:

Serializable, Cloneable, Map<AttributeTag,Attribute>, NavigableMap<AttributeTag,Attribute>, SortedMap<AttributeTag,Attribute>

public class AttributeList
extends TreeMap<AttributeTag,Attribute>

The AttributeList class maintains a list of individual DICOM attributes.

Instances of the class may be used for entire composite storage SOP instances, or fragments of such instances such as meta information headers, or simply as lists of attributes to be passed to other methods (e.g. lists of attributes to add or remove from another list).

The class is actually implemented by extending java.util.TreeMap as a map of AttributeTag keys to Attribute values. Consequently, all the methods of the underlying collection are available, including adding key-value pairs and extracting values by key. Iteration through the list of key-value pairs in the map is also supported, and the iterator returns values in the ascending numerical order of the AttributeTag keys, since that is how AttributeTag implements Comparable.

Note that large attribute values such as Pixel Data may be left on disk rather than actually read in when the list is created, and loaded on demand; extreme caution should be taken if the underlying file from which an AttributeList has been read is moved or renamed; a specific method, setFileUsedByOnDiskAttributes(), is provided to address this concern.

The class provides methods for reading entire objects as a list of attributes, from files or streams. For example, the following fragment will read an entire object from the specified file and dump the contents of the attribute list:

        AttributeList list = new AttributeList();
        list.read(arg[0]);
        System.err.print(list);
 

Similarly, methods are provided for writing entire objects. For example, the previous fragment could be extended to write the list to a file unchanged as follows:

        list.write(arg[1],TransferSyntax.ExplicitVRLittleEndian,true,true);
 

Note that in general, one would want to perform significantly more cleaning up before writing an object that has just been read, and a number of such methods are provided either in this class or on related classes as illustrated in this example:

        AttributeList list = new AttributeList();
        list.read(arg[0]);
        //list.removePrivateAttributes();
        list.removeGroupLengthAttributes();
        list.removeMetaInformationHeaderAttributes();
        list.remove(TagFromName.DataSetTrailingPadding);
        list.correctDecompressedImagePixelModule();
        list.insertLossyImageCompressionHistoryIfDecompressed();
        FileMetaInformation.addFileMetaInformation(list,TransferSyntax.ExplicitVRLittleEndian,"OURAETITLE");
        list.write(arg[1],TransferSyntax.ExplicitVRLittleEndian,true,true);
 

Note that this example is essentially the functionality of the main() method of this class, which may be used as a copying utility when invoked with input and output file arguments.

Correction of the PhotometricInterpretation and related attributes by an explicit call to the correctDecompressedImagePixelModule() method is necessary if the color space of a compressed input transfer syntax was changed during decompression (e.g., from YBR_FULL_422 for JPEG lossy to RGB), since the PixelData is always decompressed during reading by the read() method and its ilk; the call does nothing (is harmless) if the input was not compressed or not multi-component.

Individual attributes can be added or deleted as desired, either using a newly created list or one which has been read in from an existing object. For example, to zero out the patient's name one might do something like the following:

        list.replaceWithZeroLengthIfPresent(TagFromName.PatientName);
 

or to replace it with a particular value one might do the following:

        Attribute a = new PersonNameAttribute(TagFromName.PatientName);
        a.addValue(value);
        list.put(TagFromName.PatientName,a);            // one could list.remove(TagFromName.PatientName) first, but this is implicit in the put
 

A more compact shorthand method for adding new (or replacing existing) attributes (if they are in the dictionary so that the VR can be determined) is also supplied:

        list.putNewAttribute(TagFromName.PatientName);
 

and if a specific character set other than the default is in use:

        list.putNewAttribute(TagFromName.PatientName,specificCharacterSet);
 

and since this method returns the generated attribute, values can easily be added as:

        list.putNewAttribute(TagFromName.PatientName,specificCharacterSet).addValue("Blo^Joe");
 

Note also that the Attribute class provides some useful static methods for extracting and manipulating individual attributes within a list. For example:

        String patientName=Attribute.getSingleStringValueOrNull(list,TagFromName.PatientName);
 

Ideally one should take care when adding or manipulating lists of attributes to handle the specific character set correctly and consistently when there is a possibility that it may be other than the default. The previous example of replacing the patient's name could be more properly rewritten as:

        SpecificCharacterSet specificCharacterSet = new SpecificCharacterSet(Attribute.getStringValues(list,TagFromName.SpecificCharacterSet));
        Attribute a = new PersonNameAttribute(TagFromName.PatientName,specificCharacterSet);
        a.addValue(value);
        list.put(TagFromName.PatientName,a);
 

Note that in this example if the SpecificCharacterSet attribute were not found or was present but empty the various intervening methods would return null and the SpecificCharacterSet() constructor would use the default (ascii) character set.

When an attribute list is read in, the SpecificCharacterSet attribute is automatically detected and set and applied to all string attributes as they are read in and converted to the internal string form which is used by Java (Unicode).

The same applies when they are written, with some limitations on which character sets are supported. However, if new attributes have been added to the list with a different SpecificCharacterSet, it is necessary to call insertSuitableSpecificCharacterSetForAllStringValues() before writing, which will check all string values of all attributes affected by SpecificCharacterSet, choose a suitable new SpecificCharacterSet, and insert or replace the existing SpecificCharacterSet attribute. By the time that the list is written out, all of the Attributes must have the same SpecificCharacterSet.

See Also:

Attribute, AttributeTag, FileMetaInformation, SpecificCharacterSet, TagFromName, TransferSyntax, Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class java.util.AbstractMap

AbstractMap.SimpleEntry<K,V>, AbstractMap.SimpleImmutableEntry<K,V>

Field Summary

protected double	compressionRatio
protected static DicomDictionary	dictionary
protected String	lossyMethod
protected boolean	pixelDataWasDecompressed
protected boolean	pixelDataWasLossy

Constructor Summary

AttributeList()

Method Summary

String	buildInstanceTitleFromAttributeList() Construct a text title to describe this list.
static String	buildInstanceTitleFromAttributeList(AttributeList list) Construct a text title to describe the specified list.
protected void	checkSanityOfValueLength(long vl, byte[] vr, AttributeTag tag, boolean encounteredIncorrectImplicitVRElementEncodinginExplicitVR) Check that the value length is reasonable under the circumstances.
void	correctDecompressedImagePixelModule() Correct the PhotometricInterpretation and Planar Configuration iff the color space if a compressed input transfer syntax was decompressed during reading.
protected static void	createDictionaryifNecessary()
boolean	equals(Object o)
Set<String>	findAllNestedReferencedSOPInstanceUIDs() Find all referenced SOP Instance UIDs that are nested within Sequences in this list.
static Set<String>	findAllNestedReferencedSOPInstanceUIDs(AttributeList list) Find all referenced SOP Instance UIDs that are nested within Sequences in the specified list.
static Set<String>	findAllNestedReferencedSOPInstanceUIDs(AttributeList list, Set<String> setOfReferencedSOPInstanceUIDs) Find all referenced SOP Instance UIDs that are nested within Sequences in the specified list and add them to the supplied set.
Set<String>	findAllNestedReferencedSOPInstanceUIDs(Set<String> setOfReferencedSOPInstanceUIDs) Find all referenced SOP Instance UIDs that are nested within Sequences in this list and add them to the supplied set.
Attribute	get(AttributeTag t) Returns the value (attribute) to which this map maps the specified key (tag).
String	getDecompressedPhotometricInterpretation() Get the corrected PhotometricInterpretation iff the color space was a compressed input transfer syntax that was decompressed during reading.
String	getDecompressedPhotometricInterpretation(String vPhotometricInterpretation) Get the corrected PhotometricInterpretation iff the color space was a compressed input transfer syntax that was decompressed during reading.
String	getDelimitedStringValuesOrDefault(String dflt, NumberFormat format, String delimiter) Get all the string values for the attribute list, separated by the specified delimiter.
static DicomDictionary	getDictionary() Get the dictionary in use for this list.
String	getPrivateCreatorString(AttributeTag tag) Get the private creator of a private tag.
AttributeTag	getPrivateCreatorTag(AttributeTag tag) Get the private creator of a private tag.
SpecificCharacterSet	getSuitableSpecificCharacterSetForAllStringValues() Get a new SpecificCharacterSet suitable for encoding all of the values of the string attributes of a dataset.
int	hashCode()
void	insertLossyImageCompressionHistoryIfDecompressed() Update the lossy image compression history attributes if a lossy compressed input transfer syntax was decompress during reading.
void	insertSuitableSpecificCharacterSetForAllStringValues() Insert a new SpecificCharacterSet suitable for encoding all of the values of the string attributes of a dataset into the AttributeList.
boolean	isEnhanced() Determine whether or not this list is an enhanced instance.
boolean	isImage() Determine whether or not this list is an image.
boolean	isSRDocument() Determine whether or not this list is an SR Document.
static void	main(String[] arg) Read the DICOM input file as a list of attributes and write it to the specified output file or dump it.
Attribute	put(Attribute a) Associates the specified value (attribute) with the key that is the existing tag of the attribute.
Attribute	put(AttributeTag t, Attribute a) Associates the specified value (attribute) with the specified key (tag).
Attribute	putNewAttribute(AttributeTag t) Create a new attribute with the specified tag and insert it in the map associating the generated attribute with the specified tag as the key.
Attribute	putNewAttribute(AttributeTag t, SpecificCharacterSet specificCharacterSet) Create a new attribute with the specified tag and insert it in the map associating the generated attribute with the specified tag as the key.
long	read(DicomInputStream i) Read all the DICOM attributes in the stream until there are no more.
long	read(DicomInputStream i, AttributeTag stopAtTag) Read all the DICOM attributes in the stream until the specified tag is encountered.
long	read(File file) Read an entire DICOM object in the specified file.
long	read(File file, AttributeTag stopAtTag) Read an entire DICOM object in the specified file.
long	read(String name) Read an entire DICOM object in the specified file.
long	read(String name, AttributeTag stopAtTag) Read an entire DICOM object in the specified file.
long	read(String name, String transferSyntaxUID, boolean hasMeta, boolean useBufferedStream) Read an entire DICOM object in the specified file.
long	read(String name, String transferSyntaxUID, boolean hasMeta, boolean useBufferedStream, AttributeTag stopAtTag) Read an entire DICOM object in the specified file.
long	readOnlyMetaInformationHeader(DicomInputStream i) Read the meta information header (if present) and then stop.
long	readOnlyMetaInformationHeader(File file) Read the meta information header (if present) for the specified file and then close it.
long	readOnlyMetaInformationHeader(String name) Read the meta information header (if present) for the specified file and then close it.
Attribute	remove(AttributeTag tag) Removes the mapping for this key (tag), if present.
void	removeCurveAttributes() Remove any curve attributes present in the list.
void	removeGroupLengthAttributes() Remove any group length attributes present in the list, except the meta information header length, as well as LengthToEnd.
void	removeMetaInformationHeaderAttributes() Remove any meta information header attributes present in the list.
void	removeOverlayAttributes() Remove any overlay attributes present in the list.
void	removePrivateAttributes() Remove any private attributes present in the list.
void	removeUnsafePrivateAttributes() Remove unsafe private attributes present in the list.
void	replaceWithDummyValueIfPresent(AttributeTag tag, String dummyValue) Replaces an attribute with a dummy value, if present in the list.
void	replaceWithZeroLengthIfPresent(AttributeTag tag) Replaces an attribute with a zero length attribute, if present in the list.
void	setFileUsedByOnDiskAttributes(File file) Change the file containing the data used by any attribute whose values are left on disk, for example if the file has been renamed.
void	setSpecificCharacterSet(SpecificCharacterSet specificCharacterSet) Set the SpecificCharacterSet suitable for all of the string attributes of a dataset in an AttributeList.
String	toString() Dump the contents of the attribute list as a human-readable string.
String	toString(DicomDictionary dictionary) Dump the contents of the attribute list as a human-readable string.
void	write(DicomOutputStream dout) Write the entire attribute list to the specified stream.
void	write(DicomOutputStream dout, boolean useMeta) Write the entire attribute list to the specified stream.
void	write(File file) Write the entire attribute list to the specified file in explicit VR little endian transfer syntax with a meta information header.
void	write(File file, String transferSyntaxUID, boolean useMeta, boolean useBufferedStream) Write the entire attribute list to the specified file.
void	write(OutputStream o, String transferSyntaxUID, boolean useMeta, boolean useBufferedStream) Write the entire attribute list to the specified stream.
void	write(OutputStream o, String transferSyntaxUID, boolean useMeta, boolean useBufferedStream, boolean closeAfterWrite) Write the entire attribute list to the specified stream.
void	write(String name) Write the entire attribute list to the named file in explicit VR little endian transfer syntax with a meta information header.
void	write(String name, String transferSyntaxUID, boolean useMeta, boolean useBufferedStream) Write the entire attribute list to the named file.
protected void	writeFragment(DicomOutputStream dout) Write the entire attribute list (which may be part of a larger enclosing dataset) to the specified stream.

Methods inherited from class java.util.TreeMap

ceilingEntry, ceilingKey, clear, clone, comparator, containsKey, containsValue, descendingKeySet, descendingMap, entrySet, firstEntry, firstKey, floorEntry, floorKey, get, headMap, headMap, higherEntry, higherKey, keySet, lastEntry, lastKey, lowerEntry, lowerKey, navigableKeySet, pollFirstEntry, pollLastEntry, putAll, remove, size, subMap, subMap, tailMap, tailMap, values

Methods inherited from class java.util.AbstractMap

isEmpty

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Map

isEmpty

Field Detail

dictionary

protected static DicomDictionary dictionary

pixelDataWasDecompressed

protected boolean pixelDataWasDecompressed

pixelDataWasLossy

protected boolean pixelDataWasLossy

lossyMethod

protected String lossyMethod

compressionRatio

protected double compressionRatio

Constructor Detail

AttributeList

public AttributeList()

Method Detail

checkSanityOfValueLength

protected void checkSanityOfValueLength(long vl,
                                        byte[] vr,
                                        AttributeTag tag,
                                        boolean encounteredIncorrectImplicitVRElementEncodinginExplicitVR)
                                 throws DicomException

Check that the value length is reasonable under the circumstances.

Used to avoid trying to allocate insanely large attribute values when parsing corrupt or non-DICOM datasets.

Protected so that this can be overridden in sub-classes if necessary for a particular application.

Parameters:

vl -

vr -

tag -

encounteredIncorrectImplicitVRElementEncodinginExplicitVR - which increases the likelihood of an insane value

Throws:

DicomException - if the value lenght is not reasonable

createDictionaryifNecessary

protected static void createDictionaryifNecessary()

equals

public boolean equals(Object o)

Specified by:

equals in interface Map<AttributeTag,Attribute>

Overrides:

equals in class AbstractMap<AttributeTag,Attribute>

hashCode

public int hashCode()

Specified by:

hashCode in interface Map<AttributeTag,Attribute>

Overrides:

hashCode in class AbstractMap<AttributeTag,Attribute>

readOnlyMetaInformationHeader

public long readOnlyMetaInformationHeader(DicomInputStream i)
                                   throws IOException,
                                          DicomException

Read the meta information header (if present) and then stop.

Leaves the stream opened and positioned at the start of the data set.

Parameters:

i - the stream to read from

Returns:

the byte offset at which the read stopped

Throws:

IOException

DicomException

read

public long read(DicomInputStream i,
                 AttributeTag stopAtTag)
          throws IOException,
                 DicomException

Read all the DICOM attributes in the stream until the specified tag is encountered.

Does not read beyond the group element pair of the specified stop tag.

Leaves the stream open.

Parameters:

i - the stream to read from

stopAtTag - the tag (in the top level data set) at which to stop

Returns:

the byte offset at which the read stopped (which will be just past the stopAtTag, if stopped)

Throws:

IOException

DicomException

read

public long read(DicomInputStream i)
          throws IOException,
                 DicomException

Read all the DICOM attributes in the stream until there are no more.

Leaves the stream open.

Parameters:

i - the stream to read from

Returns:

the byte offset at which the read stopped

Throws:

IOException

DicomException

read

public long read(String name,
                 String transferSyntaxUID,
                 boolean hasMeta,
                 boolean useBufferedStream)
          throws IOException,
                 DicomException

Read an entire DICOM object in the specified file.

Reads the attributes of both the meta information header (if present) and data set.

Parameters:

name - the input file name

transferSyntaxUID - the transfer syntax to use for the data set (leave null for autodetection)

hasMeta - look for a meta information header

useBufferedStream - buffer the input for better performance

Returns:

the byte offset at which the read stopped

Throws:

IOException

DicomException

read

public long read(String name,
                 String transferSyntaxUID,
                 boolean hasMeta,
                 boolean useBufferedStream,
                 AttributeTag stopAtTag)
          throws IOException,
                 DicomException

Read an entire DICOM object in the specified file.

Reads the attributes of both the meta information header (if present) and data set.

Parameters:

name - the input file name

transferSyntaxUID - the transfer syntax to use for the data set (leave null for autodetection)

hasMeta - look for a meta information header

useBufferedStream - buffer the input for better performance

stopAtTag - the tag (in the top level data set) at which to stop

Returns:

the byte offset at which the read stopped (which will be just past the stopAtTag, if stopped)

Throws:

IOException

DicomException

readOnlyMetaInformationHeader

public long readOnlyMetaInformationHeader(String name)
                                   throws IOException,
                                          DicomException

Read the meta information header (if present) for the specified file and then close it.

Parameters:

name - the input file name

Returns:

the byte offset at which the read stopped

Throws:

IOException

DicomException

read

public long read(String name)
          throws IOException,
                 DicomException

Read an entire DICOM object in the specified file.

Reads the attributes of both the meta information header (if present) and data set.

Always tries to automatically detect the meta information header or transfer syntax if no meta information header and buffers the input for better performance.

Parameters:

name - the input file name

Returns:

the byte offset at which the read stopped

Throws:

IOException

DicomException

read

public long read(String name,
                 AttributeTag stopAtTag)
          throws IOException,
                 DicomException

Read an entire DICOM object in the specified file.

Reads the attributes of both the meta information header (if present) and data set.

Always tries to automatically detect the meta information header or transfer syntax if no meta information header and buffers the input for better performance.

Parameters:

name - the input file name

stopAtTag - the tag (in the top level data set) at which to stop

Returns:

the byte offset at which the read stopped (which will be just past the stopAtTag, if stopped)

Throws:

IOException

DicomException

read

public long read(File file)
          throws IOException,
                 DicomException

Read an entire DICOM object in the specified file.

Reads the attributes of both the meta information header (if present) and data set.

Always tries to automatically detect the meta information header or transfer syntax if no meta information header and buffers the input for better performance.

Parameters:

file - the input file

Returns:

the byte offset at which the read stopped

Throws:

IOException

DicomException

read

public long read(File file,
                 AttributeTag stopAtTag)
          throws IOException,
                 DicomException

Read an entire DICOM object in the specified file.

Reads the attributes of both the meta information header (if present) and data set.

Always tries to automatically detect the meta information header or transfer syntax if no meta information header and buffers the input for better performance.

Parameters:

file - the input file

stopAtTag - the tag (in the top level data set) at which to stop

Returns:

the byte offset at which the read stopped (which will be just past the stopAtTag, if stopped)

Throws:

IOException

DicomException

readOnlyMetaInformationHeader

public long readOnlyMetaInformationHeader(File file)
                                   throws IOException,
                                          DicomException

Read the meta information header (if present) for the specified file and then close it.

Parameters:

file - the input file

Returns:

the byte offset at which the read stopped

Throws:

IOException

DicomException

writeFragment

protected void writeFragment(DicomOutputStream dout)
                      throws IOException,
                             DicomException

Write the entire attribute list (which may be part of a larger enclosing dataset) to the specified stream.

Does not close the output stream, assumes any meta header vs. dataset ransition has occurred and further assumes that any additional codecs (like deflate) have already been pushed onto the stream.

Intended for use only for write datasets that are within sequence items (hence is not public).

Parameters:

dout - the stream to write to

Throws:

IOException

DicomException

write

public void write(DicomOutputStream dout,
                  boolean useMeta)
           throws IOException,
                  DicomException

Write the entire attribute list to the specified stream.

Leaves the stream open.

Parameters:

dout - the stream to write to

useMeta - true if the meta information header attributes are to be written, false if they are to be ommitted

Throws:

IOException

DicomException

write

public void write(DicomOutputStream dout)
           throws IOException,
                  DicomException

Write the entire attribute list to the specified stream.

Leaves the stream open.

Parameters:

dout - the stream to write to

Throws:

IOException

DicomException

write

public void write(OutputStream o,
                  String transferSyntaxUID,
                  boolean useMeta,
                  boolean useBufferedStream)
           throws IOException,
                  DicomException

Write the entire attribute list to the specified stream.

Closes the stream after writing.

Parameters:

o - the stream to write to

transferSyntaxUID - the transfer syntax to use to write the data set

useMeta - write the meta information header attributes (if true they must be present in the list with appropriate values already)

useBufferedStream - buffer the output for better performance (set this true only if the supplied stream is not already buffered)

Throws:

IOException

DicomException

write

public void write(OutputStream o,
                  String transferSyntaxUID,
                  boolean useMeta,
                  boolean useBufferedStream,
                  boolean closeAfterWrite)
           throws IOException,
                  DicomException

Write the entire attribute list to the specified stream.

Parameters:

o - the stream to write to

transferSyntaxUID - the transfer syntax to use to write the data set

useMeta - write the meta information header attributes (if true they must be present in the list with appropriate values already)

useBufferedStream - buffer the output for better performance (set this true only if the supplied stream is not already buffered)

closeAfterWrite - requests that the supplied stream be closed after writing

Throws:

IOException

DicomException

write

public void write(String name,
                  String transferSyntaxUID,
                  boolean useMeta,
                  boolean useBufferedStream)
           throws IOException,
                  DicomException

Write the entire attribute list to the named file.

Parameters:

name - the file name to write to

transferSyntaxUID - the transfer syntax to use to write the data set

useMeta - write the meta information header attributes (if true they must be present in the list with appropriate values already)

useBufferedStream - buffer the output for better performance

Throws:

IOException

DicomException

write

public void write(String name)
           throws IOException,
                  DicomException

Write the entire attribute list to the named file in explicit VR little endian transfer syntax with a meta information header.

Parameters:

name - the file name to write to

Throws:

IOException

DicomException

write

public void write(File file,
                  String transferSyntaxUID,
                  boolean useMeta,
                  boolean useBufferedStream)
           throws IOException,
                  DicomException

Write the entire attribute list to the specified file.

Parameters:

file - the file to write to

transferSyntaxUID - the transfer syntax to use to write the data set

useMeta - write the meta information header attributes (if true they must be present in the list with appropriate values already)

useBufferedStream - buffer the output for better performance

Throws:

IOException

DicomException

write

public void write(File file)
           throws IOException,
                  DicomException

Write the entire attribute list to the specified file in explicit VR little endian transfer syntax with a meta information header.

Parameters:

file - the file to write to

Throws:

IOException

DicomException

put

public Attribute put(AttributeTag t,
                     Attribute a)
              throws NullPointerException,
                     ClassCastException

Associates the specified value (attribute) with the specified key (tag).

If the map previously contained a mapping for this key, the old value is replaced.

No untyped Object put(Object key, Object value) method is required to over ride the super class method since the parent TreeMap class of AttributeList is now typed, and the untyped method would have the same erasure.

Specified by:

put in interface Map<AttributeTag,Attribute>

Overrides:

put in class TreeMap<AttributeTag,Attribute>

Parameters:

t - key (tag) with which the specified value (attribute) is to be associated

a - value (attribute) to be associated with the specified key (tag)

Returns:

previous value (attribute) associated with specified key (tag), or null if there was no mapping for key (tag)

Throws:

NullPointerException - thrown if a or t is null

ClassCastException - thrown if a or t is not the correct class

See Also:

TreeMap.put(Object,Object)

put

public Attribute put(Attribute a)

Associates the specified value (attribute) with the key that is the existing tag of the attribute.

If the map previously contained a mapping for this key, the old value is replaced.

Parameters:

a - value (attribute) to be associated with the specified key (tag)

Returns:

previous value (attribute) associated with specified key (tag), or null if there was no mapping for key (tag)

Throws:

NullPointerException - thrown if a or t is null

See Also:

put(AttributeTag,Attribute)

get

public Attribute get(AttributeTag t)

Returns the value (attribute) to which this map maps the specified key (tag).

Returns null if the map contains no mapping for this key. A return value of null does indicate that the map contains no mapping for the key, unlike java.util.get(Object) since the put operation checks for and disallows null insertions. This contract will hold true unless one goes to great effort to insert a key that maps to a null value by using one of the other insertion methods of the super class, in which case other operations (like writing) may fail later with a NullPointerException.

Parameters:

t - key (tag) whose associated value (attribute) is to be returned

isImage

public boolean isImage()

Determine whether or not this list is an image.

An image is defined to be something with a PixelData attribute at the top level.

Returns:

true if an image

isEnhanced

public boolean isEnhanced()

Determine whether or not this list is an enhanced instance.

An enhanced instance is defined to be something with a Shared or Per-Frame Functional Groups Sequence attribute at the top level.

Returns:

true if an enhanced instance

isSRDocument

public boolean isSRDocument()

Determine whether or not this list is an SR Document.

An SR Document is defined to be something with a ContentSequence attribute at the top level.

Returns:

true if an SR Document

See Also:

SOPClass.isStructuredReport(String)

getDictionary

public static DicomDictionary getDictionary()

Get the dictionary in use for this list.

Creates one if necessary.

Returns:

the dictionary

remove

public Attribute remove(AttributeTag tag)

Removes the mapping for this key (tag), if present.

Parameters:

tag - key (tag) for which mapping should be removed

Returns:

previous value (attribute) associated with specified key (tag), or null if there was no mapping for key (tag)

replaceWithZeroLengthIfPresent

public void replaceWithZeroLengthIfPresent(AttributeTag tag)
                                    throws DicomException

Replaces an attribute with a zero length attribute, if present in the list.

Does nothing if the attribute was not already present.

Parameters:

tag - key (tag) for which the attribute should be replaced

Throws:

DicomException - thrown if there is any difficulty creating the new zero length attribute

replaceWithDummyValueIfPresent

public void replaceWithDummyValueIfPresent(AttributeTag tag,
                                           String dummyValue)
                                    throws DicomException

Replaces an attribute with a dummy value, if present in the list.

Does nothing if the attribute was not already present.

Parameters:

tag - key (tag) for which the attribute should be replaced

dummyValue - the dummy value to use

Throws:

DicomException - thrown if there is any difficulty creating the new zero length attribute

removePrivateAttributes

public void removePrivateAttributes()

Remove any private attributes present in the list.

Private attributes are all those with an odd group number.

Also recurses into standard sequences and removes any private attributes therein.

removeUnsafePrivateAttributes

public void removeUnsafePrivateAttributes()

Remove unsafe private attributes present in the list.

Unsafe private attributes are all those with an odd group number that are not known to be safe, in the sense that they do not contain individually identifiable information.

Will not remove private creators of potentially safe private tags, even if there are no such safe tags found.

Also recurses into standard sequences and removes any unsafe private attributes therein.

See Also:

ClinicalTrialsAttributes

getPrivateCreatorTag

public AttributeTag getPrivateCreatorTag(AttributeTag tag)

Get the private creator of a private tag.

Parameters:

tag - the private tag

Returns:

the private creator tag

getPrivateCreatorString

public String getPrivateCreatorString(AttributeTag tag)

Get the private creator of a private tag.

Parameters:

tag - the private tag

Returns:

the private creator, or an empty String if not found

removeMetaInformationHeaderAttributes

public void removeMetaInformationHeaderAttributes()

Remove any meta information header attributes present in the list.

Meta information header attributes are all those in group 0x0002.

Note that this should always be done when modifying the SOP Class or Instance UID of an attribute list what has been read before writing, since it is vital that the corresponding meta information header attributes match those in the data set.

See Also:

FileMetaInformation

removeGroupLengthAttributes

public void removeGroupLengthAttributes()

Remove any group length attributes present in the list, except the meta information header length, as well as LengthToEnd.

Group length attributes are all those with an element of 0x0000.

LengthToEnd (0x0008,0x0001) is always removed if present as well.

These have never been required in DICOM and are a holdover from the old ACR-NEMA days, and are a source of constant problems, so should always be removed.

The meta information header length is left alone, since it is mandatory.

Also recurses into sequences and removes any contained group lengths.

See Also:

FileMetaInformation

removeOverlayAttributes

public void removeOverlayAttributes()

Remove any overlay attributes present in the list.

Overlay attributes are those for which com.pixelmed.dicom.AttributeTag.isOverlayGroup() returns true.

Note that any overlay data in the high bits of the PixelData are NOT removed by this method but can be removed by reading the PixelData into a com.pixelmed.display.SourceImage and creating a new PixelData attribute from it.

removeCurveAttributes

public void removeCurveAttributes()

Remove any curve attributes present in the list.

Curve attributes are those for which com.pixelmed.dicom.AttributeTag.isCurveGroup() returns true.

toString

public String toString()

Dump the contents of the attribute list as a human-readable string.

Each attribute is written to a separate line, in the form defined for com.pixelmed.dicom.Attribute.toString().

Overrides:

toString in class AbstractMap<AttributeTag,Attribute>

Returns:

the string

toString

public String toString(DicomDictionary dictionary)

Dump the contents of the attribute list as a human-readable string.

Each attribute is written to a separate line, in the form defined for com.pixelmed.dicom.Attribute.toString(DicomDictionary dictionary).

Parameters:

dictionary - the dictionary to use to look up the name

Returns:

the string

getDelimitedStringValuesOrDefault

public String getDelimitedStringValuesOrDefault(String dflt,
                                                NumberFormat format,
                                                String delimiter)

Get all the string values for the attribute list, separated by the specified delimiter.

If there is no string value for an individual value or an exception trying to fetch it, the supplied default is returned for each Attribute.

A canonicalized (unpadded) form is returned for each Attribute value, not the original string.

Parameters:

dflt - what to return if there are no (valid) string values

format - the format to use for each numerical or decimal value (null if none)

delimiter - the delimiter to use between each value

Returns:

the values as a delimited String

setFileUsedByOnDiskAttributes

public void setFileUsedByOnDiskAttributes(File file)

Change the file containing the data used by any attribute whose values are left on disk, for example if the file has been renamed.

Parameters:

file - the new file containing the data

putNewAttribute

public Attribute putNewAttribute(AttributeTag t,
                                 SpecificCharacterSet specificCharacterSet)
                          throws DicomException

Create a new attribute with the specified tag and insert it in the map associating the generated attribute with the specified tag as the key.

If the map previously contained a mapping for the tag (key), the old value is replaced.

Parameters:

t - key (AttributeTag tag) with which the generated attribute is to be associated

specificCharacterSet - the SpecificCharacterSet to be used text values

Returns:

the newly created attribute

Throws:

DicomException - if cannot create attribute, such as if cannot find tag in dictionary

putNewAttribute

public Attribute putNewAttribute(AttributeTag t)
                          throws DicomException

Create a new attribute with the specified tag and insert it in the map associating the generated attribute with the specified tag as the key.

If the map previously contained a mapping for the tag (key), the old value is replaced.

Parameters:

t - key (AttributeTag tag) with which the generated attribute is to be associated

Returns:

the newly created attribute

Throws:

DicomException - if cannot create attribute, such as if cannot find tag in dictionary

setSpecificCharacterSet

public void setSpecificCharacterSet(SpecificCharacterSet specificCharacterSet)

Set the SpecificCharacterSet suitable for all of the string attributes of a dataset in an AttributeList.

Any existing SpecificCharacterSet for Attributes (whether read or created de novo) is replaced.

Recurses into SequenceAttributes.

getSuitableSpecificCharacterSetForAllStringValues

public SpecificCharacterSet getSuitableSpecificCharacterSetForAllStringValues()

Get a new SpecificCharacterSet suitable for encoding all of the values of the string attributes of a dataset.

Any existing SpecificCharacterSet within the AttributeList or any SpecificCharacterSet established for specific Attributes (e.g., when read or created de novo) is ignored.

Only a single value is ever used (i.e., ISO 2022 escapes are not created).

Returns:

a new SpecificCharacterSet sufficient to encode all values

insertSuitableSpecificCharacterSetForAllStringValues

public void insertSuitableSpecificCharacterSetForAllStringValues()
                                                          throws DicomException

Insert a new SpecificCharacterSet suitable for encoding all of the values of the string attributes of a dataset into the AttributeList.

Any existing SpecificCharacterSet within the AttributeList or any SpecificCharacterSet established for specific Attributes (e.g., when read or created de novo) is ignored.

Only a single value is ever used (i.e., ISO 2022 escapes are not created).

If the encoding is ASCII, which is the default, the SpecificCharacterSet is removed (since it is Type 1C).

Throws:

DicomException - if cannot create attribute

insertLossyImageCompressionHistoryIfDecompressed

public void insertLossyImageCompressionHistoryIfDecompressed()
                                                      throws DicomException

Update the lossy image compression history attributes if a lossy compressed input transfer syntax was decompress during reading.

E.g., from YBR_FULL_422 for JPEG lossy to RGB.

Does nothing (is harmless) if the input was not compressed or not multi-component.

Recurses into sequences in case there is icon pixel data that was also decompressed.

Throws:

DicomException - if cannot create replacement attribute

getDecompressedPhotometricInterpretation

public String getDecompressedPhotometricInterpretation()
                                                throws DicomException

Get the corrected PhotometricInterpretation iff the color space was a compressed input transfer syntax that was decompressed during reading.

E.g., from YBR_FULL_422 for JPEG lossy to RGB.

Returns:

the corrected PhotometricInterpretation, or original PhotometricInterpretation if it does not need correction

Throws:

DicomException - if cannot create replacement attribute

getDecompressedPhotometricInterpretation

public String getDecompressedPhotometricInterpretation(String vPhotometricInterpretation)
                                                throws DicomException

Get the corrected PhotometricInterpretation iff the color space was a compressed input transfer syntax that was decompressed during reading.

E.g., from YBR_FULL_422 for JPEG lossy to RGB.

param vPhotometricInterpretation the PhotometricInterpretation supplied in the AttributeList

Returns:

the corrected PhotometricInterpretation, or original PhotometricInterpretation if it does not need correction

Throws:

DicomException

correctDecompressedImagePixelModule

public void correctDecompressedImagePixelModule()
                                         throws DicomException

Correct the PhotometricInterpretation and Planar Configuration iff the color space if a compressed input transfer syntax was decompressed during reading.

E.g., from YBR_FULL_422 for JPEG lossy to RGB.

Does nothing (is harmless) if the input was not compressed or not multi-component.

Recurses into sequences in case there is icon pixel data that was also decompressed.

Throws:

DicomException - if cannot create replacement attribute

buildInstanceTitleFromAttributeList

public String buildInstanceTitleFromAttributeList()

Construct a text title to describe this list.

Returns:

a single line constructed from patient, study, series and instance attribute values

buildInstanceTitleFromAttributeList

public static String buildInstanceTitleFromAttributeList(AttributeList list)

Construct a text title to describe the specified list.

Parameters:

list -

Returns:

a single line constructed from patient, study, series and instance attribute values (or empty string if list is null)

findAllNestedReferencedSOPInstanceUIDs

public static Set<String> findAllNestedReferencedSOPInstanceUIDs(AttributeList list,
                                                                 Set<String> setOfReferencedSOPInstanceUIDs)

Find all referenced SOP Instance UIDs that are nested within Sequences in the specified list and add them to the supplied set.

Parameters:

list -

setOfReferencedSOPInstanceUIDs - may be empty or null

Returns:

the supplied set or a new set if null, with all referenced SOP Instance UIDs found added

findAllNestedReferencedSOPInstanceUIDs

public static Set<String> findAllNestedReferencedSOPInstanceUIDs(AttributeList list)

Find all referenced SOP Instance UIDs that are nested within Sequences in the specified list.

Parameters:

list -

Returns:

a set of all referenced SOP Instance UIDs

findAllNestedReferencedSOPInstanceUIDs

public Set<String> findAllNestedReferencedSOPInstanceUIDs(Set<String> setOfReferencedSOPInstanceUIDs)

Find all referenced SOP Instance UIDs that are nested within Sequences in this list and add them to the supplied set.

Parameters:

setOfReferencedSOPInstanceUIDs - may be empty or null

Returns:

the supplied set or a new set if null, with all referenced SOP Instance UIDs found added

findAllNestedReferencedSOPInstanceUIDs

public Set<String> findAllNestedReferencedSOPInstanceUIDs()

Find all referenced SOP Instance UIDs that are nested within Sequences in this list.

Returns:

a set of all referenced SOP Instance UIDs

main

public static void main(String[] arg)

Read the DICOM input file as a list of attributes and write it to the specified output file or dump it.

When copying, removes any group lengths and creates a new meta information header.

Parameters:

arg - array of one string (the filename to read and dump), two strings (the filename to read and the filename to write), three strings (the filename to read, the transfer syntax to write, the filename to write), or four strings (the transfer syntax to read (must be zero length if metaheader present), the filename to read, the transfer syntax to write, the filename to write) five strings (the transfer syntax to read (must be zero length if metaheader present), the filename to read, the transfer syntax to write, the filename to write, and whether or not to write a metaheader)