com.pixelmed.dicom

Class ClinicalTrialsAttributes

java.lang.Object

com.pixelmed.dicom.ClinicalTrialsAttributes

public abstract class ClinicalTrialsAttributes
extends java.lang.Object

An abstract class of static methods to support removing identifying attributes and adding Clinical Trials Patient, Study and Series Modules attributes.

UID attributes are handled specially, in that they may be kept, removed or remapped. Remapping means that any UID that is not standard (e.g., not a SOP Class, etc.) will be replaced consistently with another generated UID, such that when that UID is encountered again, the same replacement value will be used. The replacement mapping persists within the invocation of the JVM until it is explciitly flushed. A different JVM invocation will replace the UIDs with different values. Therefore, multiple instances that need to be remapped consistently must be cleaned within the same invocation.

Note that this map could grow quite large and consumes resources in memory, and hence in a server application should be flushed at appropriate intervals using the appropriate method.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	ClinicalTrialsAttributes.HandleDates
class	ClinicalTrialsAttributes.HandleStructuredContent
class	ClinicalTrialsAttributes.HandleUIDs

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	defaultValueForMissingNonZeroLengthStrings
static java.lang.String	defaultValueForMissingPossiblyZeroLengthStrings
protected static DicomDictionary	dictionary
protected static java.util.Map	mapOfOriginalToReplacementUIDs
static java.lang.String	replacementForAgeString
static java.lang.String	replacementForContainerIdentifier
static java.lang.String	replacementForContentCreatorName
static java.lang.String	replacementForDateInStructuredContent
static java.lang.String	replacementForDateTimeInStructuredContent
static java.lang.String	replacementForDescriptionOrLabel
static java.lang.String	replacementForDetectorID
static java.lang.String	replacementForDeviceSerialNumber
static java.lang.String	replacementForPersonNameInStructuredContent
static java.lang.String	replacementForSpecimenIdentifier
static java.lang.String	replacementForTextInStructuredContent
static java.lang.String	replacementForTimeInStructuredContent
static java.lang.String	replacementForVerifyingObserverName
static java.lang.String	replacementForVerifyingOrganization
protected static UIDGenerator	uidGenerator

Method Summary

Modifier and Type	Method and Description
static void	addAgeDerivedFromBirthDateAndStudyRelatedDate(AttributeList list) Add the Patient's Age derived from the Patient's Birth Date and study-related date.
static void	addClinicalTrialsAttributes(AttributeList list, boolean replaceConventionalAttributes, java.lang.String clinicalTrialSponsorName, java.lang.String clinicalTrialProtocolID, java.lang.String clinicalTrialProtocolName, java.lang.String clinicalTrialSiteID, java.lang.String clinicalTrialSiteName, java.lang.String clinicalTrialSubjectID, java.lang.String clinicalTrialSubjectReadingID, java.lang.String clinicalTrialTimePointID, java.lang.String clinicalTrialTimePointDescription, java.lang.String clinicalTrialCoordinatingCenterName) Add the attributes of the Clinical Trials Patient, Study and Series Modules, to a list of attributes.
static void	addContributingEquipmentSequence(AttributeList list, boolean retainExistingItems, CodedSequenceItem purposeOfReferenceCodeSequence, java.lang.String manufacturer, java.lang.String institutionName, java.lang.String institutionalDepartmentName, CodedSequenceItem institutionalDepartmentTypeCodeSequence, java.lang.String institutionAddress, java.lang.String stationName, java.lang.String manufacturerModelName, java.lang.String deviceSerialNumber, java.lang.String softwareVersion, java.lang.String contributionDescription, java.lang.String contributionDateTime, java.lang.String[] operatorNames, PersonIdentification[] operatorIdentifications) Add the attributes of the Contributing Equipment Sequence to a list of attributes.
static void	addContributingEquipmentSequence(AttributeList list, boolean retainExistingItems, CodedSequenceItem purposeOfReferenceCodeSequence, java.lang.String manufacturer, java.lang.String institutionName, java.lang.String institutionalDepartmentName, java.lang.String institutionAddress, java.lang.String stationName, java.lang.String manufacturerModelName, java.lang.String deviceSerialNumber, java.lang.String softwareVersion, java.lang.String contributionDescription) Add the attributes of the Contributing Equipment Sequence to a list of attributes.
static void	addContributingEquipmentSequence(AttributeList list, boolean retainExistingItems, CodedSequenceItem purposeOfReferenceCodeSequence, java.lang.String manufacturer, java.lang.String institutionName, java.lang.String institutionalDepartmentName, java.lang.String institutionAddress, java.lang.String stationName, java.lang.String manufacturerModelName, java.lang.String deviceSerialNumber, java.lang.String softwareVersion, java.lang.String contributionDescription, java.lang.String contributionDateTime) Add the attributes of the Contributing Equipment Sequence to a list of attributes.
static void	addContributingEquipmentSequence(AttributeList list, boolean retainExistingItems, CodedSequenceItem purposeOfReferenceCodeSequence, java.lang.String manufacturer, java.lang.String institutionName, java.lang.String institutionalDepartmentName, java.lang.String institutionAddress, java.lang.String stationName, java.lang.String manufacturerModelName, java.lang.String deviceSerialNumber, java.lang.String softwareVersion, java.lang.String contributionDescription, java.lang.String contributionDateTime, java.lang.String[] operatorNames, PersonIdentification[] operatorIdentifications) Add the attributes of the Contributing Equipment Sequence to a list of attributes.
static void	addContributingEquipmentSequence(AttributeList list, java.lang.String manufacturer, java.lang.String institutionName, java.lang.String institutionalDepartmentName, java.lang.String institutionAddress, java.lang.String stationName, java.lang.String manufacturerModelName, java.lang.String deviceSerialNumber, java.lang.String softwareVersion) Add the attributes of the Contributing Equipment Sequence to a list of attributes.
protected static void	addType1LongStringAttribute(AttributeList list, AttributeTag t, java.lang.String value, SpecificCharacterSet specificCharacterSet)
protected static void	addType2LongStringAttribute(AttributeList list, AttributeTag t, java.lang.String value, SpecificCharacterSet specificCharacterSet)
protected static void	addType3DateTimeAttribute(AttributeList list, AttributeTag t, java.lang.String value)
protected static void	addType3LongStringAttribute(AttributeList list, AttributeTag t, java.lang.String value, SpecificCharacterSet specificCharacterSet)
protected static void	addType3ShortStringAttribute(AttributeList list, AttributeTag t, java.lang.String value, SpecificCharacterSet specificCharacterSet)
protected static void	addType3ShortTextAttribute(AttributeList list, AttributeTag t, java.lang.String value, SpecificCharacterSet specificCharacterSet)
static java.util.Date	findEarliestDateTime(AttributeList list) Get the earliest patient event related date and time.
protected static java.util.Date	findEarliestDateTime(AttributeList list, java.util.Date earliestSoFar, java.lang.String dateToUseForUnaccompaniedTimes) Get the earliest patient event related date and time.
static void	flushMapOfUIDs() Flush (remove all entries in) the map of original UIDs to replacement UIDs.
static java.util.Date	getDateOffsetByEarliestMovedToEpoch(java.util.Date existingDate, java.util.Date epochForDateModification, java.util.Date earliest) Move the date and time by the offset from the earliest date to the epoch.
static java.lang.String	getDateToUseForUnaccompaniedTimes(AttributeList list) Get the date to use for time attributes that don't have a date sibling and which may be nested in sequences.
static java.util.Map<java.lang.String,java.lang.String>	getMapOfOriginalToReplacementUIDs() Get the map of original UIDs to replacement UIDs.
static AttributeTag	getTagOfTimeAttributeCorrespondingToDateAttribute(AttributeTag dateTag) Get the Time Attribute corresponding to the Date Attribute.
static boolean	isSafePrivateAttribute(AttributeTag tag, AttributeList list) Is a private tag safe?
static boolean	isSafePrivateAttribute(java.lang.String creator, AttributeTag tag) Is a private tag safe?
static boolean	isSafePrivateSequenceAttribute(java.lang.String creator, AttributeTag tag) Is a private tag a safe sequence VR that needs to be read as SQ if UN.
protected static boolean	isValidCandidateForEarliestDateTime(java.util.Date candidate)
static void	main(java.lang.String[] arg) For testing.
static void	remapUIDAttributes(AttributeList list) Remap UID attributes in a list of attributes, recursively iterating through nested sequences.
static void	removeClinicalTrialsAttributes(AttributeList list) Remove the attributes of the Clinical Trials Patient, Study and Series Modules, from a list of attributes.
protected static void	removeOrCleanStructuredContent(AttributeList list, int handleStructuredContent, boolean keepDescriptors, boolean keepSeriesDescriptors, boolean keepProtocolName, boolean keepPatientCharacteristics, boolean keepDeviceIdentity, boolean keepInstitutionIdentity, int handleUIDs, int handleDates) Remove or clean structured content including the SR content tree (whether an SR object or not) in a list of attributes, recursively iterating through nested sequences.
static void	removeOrNullIdentifyingAttributes(AttributeList list, boolean keepUIDs, boolean keepDescriptors, boolean keepPatientCharacteristics) De-identify a list of attributes.
static void	removeOrNullIdentifyingAttributes(AttributeList list, int handleUIDs, boolean keepDescriptors, boolean keepPatientCharacteristics) De-identify a list of attributes.
static void	removeOrNullIdentifyingAttributes(AttributeList list, int handleUIDs, boolean keepDescriptors, boolean keepSeriesDescriptors, boolean keepPatientCharacteristics, boolean keepDeviceIdentity, boolean keepInstitutionIdentity) De-identify a list of attributes.
static void	removeOrNullIdentifyingAttributes(AttributeList list, int handleUIDs, boolean keepDescriptors, boolean keepSeriesDescriptors, boolean keepProtocolName, boolean keepPatientCharacteristics, boolean keepDeviceIdentity, boolean keepInstitutionIdentity, int handleDates, java.util.Date epochForDateModification, java.util.Date earliestDateInSet) De-identify a list of attributes.
static void	removeOrNullIdentifyingAttributes(AttributeList list, int handleUIDs, boolean keepDescriptors, boolean keepSeriesDescriptors, boolean keepProtocolName, boolean keepPatientCharacteristics, boolean keepDeviceIdentity, boolean keepInstitutionIdentity, int handleDates, java.util.Date epochForDateModification, java.util.Date earliestDateInSet, int handleStructuredContent) De-identify a list of attributes.
static void	removeOrNullIdentifyingAttributes(AttributeList list, int handleUIDs, boolean keepDescriptors, boolean keepSeriesDescriptors, boolean keepProtocolName, boolean keepPatientCharacteristics, boolean keepDeviceIdentity, boolean keepInstitutionIdentity, int handleDates, java.util.Date epochForDateModification, java.util.Date earliestDateInSet, int handleStructuredContent, boolean aggregateAgesOver89) De-identify a list of attributes.
static void	removeOrNullIdentifyingAttributes(AttributeList list, int handleUIDs, boolean keepDescriptors, boolean keepSeriesDescriptors, boolean keepPatientCharacteristics, boolean keepDeviceIdentity, boolean keepInstitutionIdentity, int handleDates, java.util.Date epochForDateModification, java.util.Date earliestDateInSet) De-identify a list of attributes.
protected static void	removeOrNullIdentifyingAttributesRecursively(AttributeList list, int handleUIDs, boolean keepDescriptors, boolean keepSeriesDescriptors, boolean keepProtocolName, boolean keepPatientCharacteristics, boolean keepDeviceIdentity, boolean keepInstitutionIdentity, boolean aggregateAgesOver89) De-identify a list of attributes, recursively iterating through nested sequences.
protected static void	removeOrRemapDateAndTimeAttributes(AttributeList list, int handleDates, java.util.Date epochForDateModification, java.util.Date earliest, java.lang.String dateToUseForUnaccompaniedTimes) Remove or remap Date, Time and DateTime attributes (other than Patient Birth) in a list of attributes, recursively iterating through nested sequences.
protected static void	removeOrRemapUIDAttributes(AttributeList list, int handleUIDs) Remove or remap UID attributes in a list of attributes, recursively iterating through nested sequences.
protected static void	removeStructuredContent(AttributeList list)
static void	removeUIDAttributes(AttributeList list) Remove UID attributes in a list of attributes, recursively iterating through nested sequences.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

defaultValueForMissingNonZeroLengthStrings

public static final java.lang.String defaultValueForMissingNonZeroLengthStrings

See Also:

Constant Field Values

defaultValueForMissingPossiblyZeroLengthStrings

public static final java.lang.String defaultValueForMissingPossiblyZeroLengthStrings

See Also:

Constant Field Values

dictionary

protected static final DicomDictionary dictionary

mapOfOriginalToReplacementUIDs

protected static java.util.Map mapOfOriginalToReplacementUIDs

replacementForAgeString

public static final java.lang.String replacementForAgeString

See Also:

Constant Field Values

replacementForContainerIdentifier

public static final java.lang.String replacementForContainerIdentifier

See Also:

Constant Field Values

replacementForContentCreatorName

public static final java.lang.String replacementForContentCreatorName

See Also:

Constant Field Values

replacementForDateInStructuredContent

public static final java.lang.String replacementForDateInStructuredContent

See Also:

Constant Field Values

replacementForDateTimeInStructuredContent

public static final java.lang.String replacementForDateTimeInStructuredContent

See Also:

Constant Field Values

replacementForDescriptionOrLabel

public static final java.lang.String replacementForDescriptionOrLabel

See Also:

Constant Field Values

replacementForDetectorID

public static final java.lang.String replacementForDetectorID

See Also:

Constant Field Values

replacementForDeviceSerialNumber

public static final java.lang.String replacementForDeviceSerialNumber

See Also:

Constant Field Values

replacementForPersonNameInStructuredContent

public static final java.lang.String replacementForPersonNameInStructuredContent

See Also:

Constant Field Values

replacementForSpecimenIdentifier

public static final java.lang.String replacementForSpecimenIdentifier

See Also:

Constant Field Values

replacementForTextInStructuredContent

public static final java.lang.String replacementForTextInStructuredContent

See Also:

Constant Field Values

replacementForTimeInStructuredContent

public static final java.lang.String replacementForTimeInStructuredContent

See Also:

Constant Field Values

replacementForVerifyingObserverName

public static final java.lang.String replacementForVerifyingObserverName

See Also:

Constant Field Values

replacementForVerifyingOrganization

public static final java.lang.String replacementForVerifyingOrganization

See Also:

Constant Field Values

uidGenerator

protected static UIDGenerator uidGenerator

Method Detail

addAgeDerivedFromBirthDateAndStudyRelatedDate

public static void addAgeDerivedFromBirthDateAndStudyRelatedDate(AttributeList list)

Add the Patient's Age derived from the Patient's Birth Date and study-related date.

Does nothing if no value for Patient's Birth Date.

Uses the Study, Series, Acquisition or Content Date in that order if present, else does nothing.

Parameters:

list - the list of attributes in which to find the dob and date and to which to add the age

addClinicalTrialsAttributes

public static void addClinicalTrialsAttributes(AttributeList list,
                                               boolean replaceConventionalAttributes,
                                               java.lang.String clinicalTrialSponsorName,
                                               java.lang.String clinicalTrialProtocolID,
                                               java.lang.String clinicalTrialProtocolName,
                                               java.lang.String clinicalTrialSiteID,
                                               java.lang.String clinicalTrialSiteName,
                                               java.lang.String clinicalTrialSubjectID,
                                               java.lang.String clinicalTrialSubjectReadingID,
                                               java.lang.String clinicalTrialTimePointID,
                                               java.lang.String clinicalTrialTimePointDescription,
                                               java.lang.String clinicalTrialCoordinatingCenterName)
                                        throws DicomException

Add the attributes of the Clinical Trials Patient, Study and Series Modules, to a list of attributes.

Parameters:

list - the list of attributes to which to add the attributes

replaceConventionalAttributes - if true, use the supplied clinical trials attributes in place of the conventional ID attributes as well

clinicalTrialSponsorName - the sponsor name

clinicalTrialProtocolID - the protocol ID

clinicalTrialProtocolName - the protocol name

clinicalTrialSiteID - the site ID

clinicalTrialSiteName - the site name

clinicalTrialSubjectID - the subject ID

clinicalTrialSubjectReadingID - the subject reading ID

clinicalTrialTimePointID - the time point ID

clinicalTrialTimePointDescription - the time point description

clinicalTrialCoordinatingCenterName - the coordinating center name

Throws:

DicomException - if error in DICOM encoding

addContributingEquipmentSequence

public static void addContributingEquipmentSequence(AttributeList list,
                                                    boolean retainExistingItems,
                                                    CodedSequenceItem purposeOfReferenceCodeSequence,
                                                    java.lang.String manufacturer,
                                                    java.lang.String institutionName,
                                                    java.lang.String institutionalDepartmentName,
                                                    CodedSequenceItem institutionalDepartmentTypeCodeSequence,
                                                    java.lang.String institutionAddress,
                                                    java.lang.String stationName,
                                                    java.lang.String manufacturerModelName,
                                                    java.lang.String deviceSerialNumber,
                                                    java.lang.String softwareVersion,
                                                    java.lang.String contributionDescription,
                                                    java.lang.String contributionDateTime,
                                                    java.lang.String[] operatorNames,
                                                    PersonIdentification[] operatorIdentifications)
                                             throws DicomException

Add the attributes of the Contributing Equipment Sequence to a list of attributes.

Attributes are added if supplied string value are added if not null. May be zero length.

Parameters:

list - the list of attributes to which to add the Contributing Equipment Sequence

retainExistingItems - if true, retain any existing items in Contributing Equipment Sequence, otherwise remove them

purposeOfReferenceCodeSequence - the purpose of reference

manufacturer - the manufacturer

institutionName - the institution name

institutionalDepartmentName - the institution department name

institutionalDepartmentTypeCodeSequence - the institution department type

institutionAddress - the institution address

stationName - the station name

manufacturerModelName - the manufacturer model name

deviceSerialNumber - the device serial number

softwareVersion - the software version

contributionDescription - the contribution description

contributionDateTime - the contribution datetime

operatorNames - an array of Strings of one or more operator's names, or null if not to be added

operatorIdentifications - an array of PersonIdentification, or null if not to be added

Throws:

DicomException - if error in DICOM encoding

addContributingEquipmentSequence

public static void addContributingEquipmentSequence(AttributeList list,
                                                    boolean retainExistingItems,
                                                    CodedSequenceItem purposeOfReferenceCodeSequence,
                                                    java.lang.String manufacturer,
                                                    java.lang.String institutionName,
                                                    java.lang.String institutionalDepartmentName,
                                                    java.lang.String institutionAddress,
                                                    java.lang.String stationName,
                                                    java.lang.String manufacturerModelName,
                                                    java.lang.String deviceSerialNumber,
                                                    java.lang.String softwareVersion,
                                                    java.lang.String contributionDescription)
                                             throws DicomException

Add the attributes of the Contributing Equipment Sequence to a list of attributes.

Attributes are added if supplied string value are added if not null. May be zero length.

Parameters:

list - the list of attributes to which to add the Contributing Equipment Sequence

retainExistingItems - if true, retain any existing items in Contributing Equipment Sequence, otherwise remove them

purposeOfReferenceCodeSequence - the purpose of reference

manufacturer - the manufacturer

institutionName - the institution name

institutionalDepartmentName - the institution department name

institutionAddress - the institution address

stationName - the station name

manufacturerModelName - the manufacturer model name

deviceSerialNumber - the device serial number

softwareVersion - the software version

contributionDescription - the contribution description

Throws:

DicomException - if error in DICOM encoding

addContributingEquipmentSequence

public static void addContributingEquipmentSequence(AttributeList list,
                                                    boolean retainExistingItems,
                                                    CodedSequenceItem purposeOfReferenceCodeSequence,
                                                    java.lang.String manufacturer,
                                                    java.lang.String institutionName,
                                                    java.lang.String institutionalDepartmentName,
                                                    java.lang.String institutionAddress,
                                                    java.lang.String stationName,
                                                    java.lang.String manufacturerModelName,
                                                    java.lang.String deviceSerialNumber,
                                                    java.lang.String softwareVersion,
                                                    java.lang.String contributionDescription,
                                                    java.lang.String contributionDateTime)
                                             throws DicomException

Add the attributes of the Contributing Equipment Sequence to a list of attributes.

Attributes are added if supplied string value are added if not null. May be zero length.

Parameters:

list - the list of attributes to which to add the Contributing Equipment Sequence

retainExistingItems - if true, retain any existing items in Contributing Equipment Sequence, otherwise remove them

purposeOfReferenceCodeSequence - the purpose of reference

manufacturer - the manufacturer

institutionName - the institution name

institutionalDepartmentName - the institution department name

institutionAddress - the institution address

stationName - the station name

manufacturerModelName - the manufacturer model name

deviceSerialNumber - the device serial number

softwareVersion - the software version

contributionDescription - the contribution description

contributionDateTime - the contribution datetime

Throws:

DicomException - if error in DICOM encoding

addContributingEquipmentSequence

public static void addContributingEquipmentSequence(AttributeList list,
                                                    boolean retainExistingItems,
                                                    CodedSequenceItem purposeOfReferenceCodeSequence,
                                                    java.lang.String manufacturer,
                                                    java.lang.String institutionName,
                                                    java.lang.String institutionalDepartmentName,
                                                    java.lang.String institutionAddress,
                                                    java.lang.String stationName,
                                                    java.lang.String manufacturerModelName,
                                                    java.lang.String deviceSerialNumber,
                                                    java.lang.String softwareVersion,
                                                    java.lang.String contributionDescription,
                                                    java.lang.String contributionDateTime,
                                                    java.lang.String[] operatorNames,
                                                    PersonIdentification[] operatorIdentifications)
                                             throws DicomException

Add the attributes of the Contributing Equipment Sequence to a list of attributes.

Attributes are added if supplied string value are added if not null. May be zero length.

Parameters:

list - the list of attributes to which to add the Contributing Equipment Sequence

retainExistingItems - if true, retain any existing items in Contributing Equipment Sequence, otherwise remove them

purposeOfReferenceCodeSequence - the purpose of reference

manufacturer - the manufacturer

institutionName - the institution name

institutionalDepartmentName - the institution department name

institutionAddress - the institution address

stationName - the station name

manufacturerModelName - the manufacturer model name

deviceSerialNumber - the device serial number

softwareVersion - the software version

contributionDescription - the contribution description

contributionDateTime - the contribution datetime

operatorNames - an array of Strings of one or more operator's names, or null if not to be added

operatorIdentifications - an array of PersonIdentification, or null if not to be added

Throws:

DicomException - if error in DICOM encoding

addContributingEquipmentSequence

public static void addContributingEquipmentSequence(AttributeList list,
                                                    java.lang.String manufacturer,
                                                    java.lang.String institutionName,
                                                    java.lang.String institutionalDepartmentName,
                                                    java.lang.String institutionAddress,
                                                    java.lang.String stationName,
                                                    java.lang.String manufacturerModelName,
                                                    java.lang.String deviceSerialNumber,
                                                    java.lang.String softwareVersion)
                                             throws DicomException

Add the attributes of the Contributing Equipment Sequence to a list of attributes.

Attributes are added if supplied string value are added if not null. May be zero length.

Retains any existing items in Contributing Equipment Sequence.

Uses ("109104","DCM","De-identifying Equipment") for the Purpose of Reference.

Uses "Deidentified" for the Contribution Description.

Uses the current date and time for the Contribution DateTime.

Parameters:

list - the list of attributes to which to add the Contributing Equipment Sequence

manufacturer - the manufacturer

institutionName - the institution name

institutionalDepartmentName - the institution department name

institutionAddress - the institution address

stationName - the station name

manufacturerModelName - the manufacturer model name

deviceSerialNumber - the device serial number

softwareVersion - the software version

Throws:

DicomException - if error in DICOM encoding

addType1LongStringAttribute

protected static void addType1LongStringAttribute(AttributeList list,
                                                  AttributeTag t,
                                                  java.lang.String value,
                                                  SpecificCharacterSet specificCharacterSet)
                                           throws DicomException

Throws:

DicomException

addType2LongStringAttribute

protected static void addType2LongStringAttribute(AttributeList list,
                                                  AttributeTag t,
                                                  java.lang.String value,
                                                  SpecificCharacterSet specificCharacterSet)
                                           throws DicomException

Throws:

DicomException

addType3DateTimeAttribute

protected static void addType3DateTimeAttribute(AttributeList list,
                                                AttributeTag t,
                                                java.lang.String value)
                                         throws DicomException

Throws:

DicomException

addType3LongStringAttribute

protected static void addType3LongStringAttribute(AttributeList list,
                                                  AttributeTag t,
                                                  java.lang.String value,
                                                  SpecificCharacterSet specificCharacterSet)
                                           throws DicomException

Throws:

DicomException

addType3ShortStringAttribute

protected static void addType3ShortStringAttribute(AttributeList list,
                                                   AttributeTag t,
                                                   java.lang.String value,
                                                   SpecificCharacterSet specificCharacterSet)
                                            throws DicomException

Throws:

DicomException

addType3ShortTextAttribute

protected static void addType3ShortTextAttribute(AttributeList list,
                                                 AttributeTag t,
                                                 java.lang.String value,
                                                 SpecificCharacterSet specificCharacterSet)
                                          throws DicomException

Throws:

DicomException

findEarliestDateTime

public static java.util.Date findEarliestDateTime(AttributeList list)

Get the earliest patient event related date and time.

Ignores equipment related dates like calibration, patient related dates like birth date, and non-patient instance related dates like effective and information issue.

Parameters:

list - the list of attributes from the top level data set

Returns:

the earliest date and time

findEarliestDateTime

protected static java.util.Date findEarliestDateTime(AttributeList list,
                                                     java.util.Date earliestSoFar,
                                                     java.lang.String dateToUseForUnaccompaniedTimes)

Get the earliest patient event related date and time.

Ignores equipment related dates like calibration, patient related dates like birth date, and non-patient instance related dates like effective and information issue.

Parameters:

list - the list of attributes from the top level data set

earliestSoFar - for recursion

dateToUseForUnaccompaniedTimes - the date to use for time attributes that don't have a date sibling

Returns:

the earliest date and time

flushMapOfUIDs

public static void flushMapOfUIDs()

Flush (remove all entries in) the map of original UIDs to replacement UIDs.

getDateOffsetByEarliestMovedToEpoch

public static java.util.Date getDateOffsetByEarliestMovedToEpoch(java.util.Date existingDate,
                                                                 java.util.Date epochForDateModification,
                                                                 java.util.Date earliest)

Move the date and time by the offset from the earliest date to the epoch.

Parameters:

existingDate -

epochForDateModification -

earliest -

Returns:

the updated date and time

getDateToUseForUnaccompaniedTimes

public static java.lang.String getDateToUseForUnaccompaniedTimes(AttributeList list)

Get the date to use for time attributes that don't have a date sibling and which may be nested in sequences.

E.g., to use with RadiopharmaceuticalStartTime.

Parameters:

list - the list of attributes from the top level data set

Returns:

a date to use, or an empty string if none

getMapOfOriginalToReplacementUIDs

public static java.util.Map<java.lang.String,java.lang.String> getMapOfOriginalToReplacementUIDs()

Get the map of original UIDs to replacement UIDs.

getTagOfTimeAttributeCorrespondingToDateAttribute

public static AttributeTag getTagOfTimeAttributeCorrespondingToDateAttribute(AttributeTag dateTag)

Get the Time Attribute corresponding to the Date Attribute.

Parameters:

dateTag -

Returns:

the AttributeTag of the corresponding Time Attribute, if any, otherwise null

isSafePrivateAttribute

public static boolean isSafePrivateAttribute(AttributeTag tag,
                                             AttributeList list)

Is a private tag safe?

Safe private attributes are all those that are known not to contain individually identifiable information.

Private creators are always considered safe.

Private transient UIDs are also considered "safe", since they can then be removed/remapped based in a subsequent step.

Parameters:

tag - the tag in question

list - the list in which the tag is contained from which the private creator can be extracted

Returns:

true if safe

isSafePrivateAttribute

public static boolean isSafePrivateAttribute(java.lang.String creator,
                                             AttributeTag tag)

Is a private tag safe?

Safe private attributes are all those that are known not to contain individually identifiable informationR.

Private creators are always considered safe, though there is no point in calling this method for private creator tags ... use AttributeTag.isPrivateCreator() instead.

Private transient UIDs are also considered "safe", since they can then be removed/remapped based in a subsequent step.

Parameters:

creator - the private creator of the block containing the tag

tag - the tag in question

Returns:

true if safe

isSafePrivateSequenceAttribute

public static boolean isSafePrivateSequenceAttribute(java.lang.String creator,
                                                     AttributeTag tag)

Is a private tag a safe sequence VR that needs to be read as SQ if UN.

Parameters:

creator - the private creator of the block containing the tag

tag - the tag in question

Returns:

true if a safe SQ private tag

isValidCandidateForEarliestDateTime

protected static boolean isValidCandidateForEarliestDateTime(java.util.Date candidate)

main

public static void main(java.lang.String[] arg)

For testing.

Read a DICOM object from the file specified on the command line, and remove identifying attributes, and add sample clinical trials attributes.

Parameters:

arg - two arguments, a DICOM input file and a DICOM output file

remapUIDAttributes

public static void remapUIDAttributes(AttributeList list)
                               throws DicomException

Remap UID attributes in a list of attributes, recursively iterating through nested sequences.

Parameters:

list - the list of attributes to be cleaned up

Throws:

DicomException - if error in DICOM encoding

removeClinicalTrialsAttributes

public static void removeClinicalTrialsAttributes(AttributeList list)

Remove the attributes of the Clinical Trials Patient, Study and Series Modules, from a list of attributes.

Parameters:

list - the list of attributes from which to remove the attributes

removeOrCleanStructuredContent

protected static void removeOrCleanStructuredContent(AttributeList list,
                                                     int handleStructuredContent,
                                                     boolean keepDescriptors,
                                                     boolean keepSeriesDescriptors,
                                                     boolean keepProtocolName,
                                                     boolean keepPatientCharacteristics,
                                                     boolean keepDeviceIdentity,
                                                     boolean keepInstitutionIdentity,
                                                     int handleUIDs,
                                                     int handleDates)
                                              throws DicomException

Remove or clean structured content including the SR content tree (whether an SR object or not) in a list of attributes, recursively iterating through nested sequences.

Parameters:

list - the list of attributes to be cleaned up

handleStructuredContent - keep, remove or modify structured content

keepDescriptors - if true, keep the text description and comment attributes

keepSeriesDescriptors - if true, keep the series description even if all other descriptors are removed

keepProtocolName - if true, keep protocol name even if all other descriptors are removed

keepPatientCharacteristics - if true, keep patient characteristics (such as might be needed for PET SUV calculations)

keepDeviceIdentity - if true, keep device identity

keepInstitutionIdentity - if true, keep institution identity

handleUIDs - remove or remap the UIDs

handleDates - keep, remove or modify dates and times

Throws:

DicomException - if error in DICOM encoding

removeOrNullIdentifyingAttributes

public static void removeOrNullIdentifyingAttributes(AttributeList list,
                                                     boolean keepUIDs,
                                                     boolean keepDescriptors,
                                                     boolean keepPatientCharacteristics)
                                              throws DicomException

De-identify a list of attributes.

De-identifies attributes within nested sequences, other than Context Sequence.

Handles UIDs as requested, including within nested sequences, including Context Sequence.

Leaves dates and times alone (other than Patient Birth).

Does not de-identify any specific content items in structured content, e.g., within Content Sequence.

Also adds record that de-identification has been performed.

Parameters:

list - the list of attributes to be cleaned up

keepUIDs - if true, keep the UIDs

keepDescriptors - if true, keep the text description and comment attributes

keepPatientCharacteristics - if true, keep patient characteristics (such as might be needed for PET SUV calculations)

Throws:

DicomException - if error in DICOM encoding

removeOrNullIdentifyingAttributes

public static void removeOrNullIdentifyingAttributes(AttributeList list,
                                                     int handleUIDs,
                                                     boolean keepDescriptors,
                                                     boolean keepPatientCharacteristics)
                                              throws DicomException

De-identify a list of attributes.

De-identifies attributes within nested sequences, other than Context Sequence.

Handles UIDs as requested, including within nested sequences, including Context Sequence.

Leaves dates and times alone (other than Patient Birth).

Does not de-identify any specific content items in structured content, e.g., within Content Sequence.

Also adds record that de-identification has been performed.

Parameters:

list - the list of attributes to be cleaned up

handleUIDs - keep, remove or remap the UIDs

keepDescriptors - if true, keep the text description and comment attributes

keepPatientCharacteristics - if true, keep patient characteristics (such as might be needed for PET SUV calculations)

Throws:

DicomException - if error in DICOM encoding

removeOrNullIdentifyingAttributes

public static void removeOrNullIdentifyingAttributes(AttributeList list,
                                                     int handleUIDs,
                                                     boolean keepDescriptors,
                                                     boolean keepSeriesDescriptors,
                                                     boolean keepPatientCharacteristics,
                                                     boolean keepDeviceIdentity,
                                                     boolean keepInstitutionIdentity)
                                              throws DicomException

De-identify a list of attributes.

De-identifies attributes within nested sequences, other than Context Sequence.

Handles UIDs as requested, including within nested sequences, including Context Sequence.

Leaves dates and times alone (other than Patient Birth).

Does not de-identify any specific content items in structured content, e.g., within Content Sequence.

Also adds record that de-identification has been performed.

Parameters:

list - the list of attributes to be cleaned up

handleUIDs - keep, remove or remap the UIDs

keepDescriptors - if true, keep the text description and comment attributes

keepSeriesDescriptors - if true, keep the series description even if all other descriptors are removed

keepPatientCharacteristics - if true, keep patient characteristics (such as might be needed for PET SUV calculations)

keepDeviceIdentity - if true, keep device identity

keepInstitutionIdentity - if true, keep institution identity

Throws:

DicomException - if error in DICOM encoding

removeOrNullIdentifyingAttributes

public static void removeOrNullIdentifyingAttributes(AttributeList list,
                                                     int handleUIDs,
                                                     boolean keepDescriptors,
                                                     boolean keepSeriesDescriptors,
                                                     boolean keepProtocolName,
                                                     boolean keepPatientCharacteristics,
                                                     boolean keepDeviceIdentity,
                                                     boolean keepInstitutionIdentity,
                                                     int handleDates,
                                                     java.util.Date epochForDateModification,
                                                     java.util.Date earliestDateInSet)
                                              throws DicomException

De-identify a list of attributes.

De-identifies attributes within nested sequences.

Handles UIDs as requested, including within nested sequences, including Content Sequence.

Handles dates and times as requested (other than Patient Birth), including within nested sequences, including Content Sequence.

Does not de-identify any specific content items in structured content, e.g., within Content Sequence.

Also adds record that de-identification has been performed.

Parameters:

list - the list of attributes to be cleaned up

handleUIDs - keep, remove or remap the UIDs

keepDescriptors - if true, keep the text description and comment attributes

keepSeriesDescriptors - if true, keep the series description even if all other descriptors are removed

keepProtocolName - if true, keep protocol name even if all other descriptors are removed

keepPatientCharacteristics - if true, keep patient characteristics (such as might be needed for PET SUV calculations)

keepDeviceIdentity - if true, keep device identity

keepInstitutionIdentity - if true, keep institution identity

handleDates - keep, remove or modify dates and times

epochForDateModification - the epoch to which to move the earliest date, used if handleDates is modify dates, otherwise null

earliestDateInSet - the known earliest date to move to the specified epoch, used if handleDates is modify dates, otherwise null; if null, the earliest in the supplied list is used; MUST be the earliest date and time else unaccompanied time attributes may cross midnight

Throws:

DicomException - if error in DICOM encoding

removeOrNullIdentifyingAttributes

public static void removeOrNullIdentifyingAttributes(AttributeList list,
                                                     int handleUIDs,
                                                     boolean keepDescriptors,
                                                     boolean keepSeriesDescriptors,
                                                     boolean keepProtocolName,
                                                     boolean keepPatientCharacteristics,
                                                     boolean keepDeviceIdentity,
                                                     boolean keepInstitutionIdentity,
                                                     int handleDates,
                                                     java.util.Date epochForDateModification,
                                                     java.util.Date earliestDateInSet,
                                                     int handleStructuredContent)
                                              throws DicomException

De-identify a list of attributes.

De-identifies attributes within nested sequences.

Handles UIDs as requested, including within nested sequences, including Content Sequence.

Handles dates and times as requested (other than Patient Birth), including within nested sequences, including Content Sequence.

Handles structured content as requested, including within nested sequences, including (and not just confined to) Content Sequence.

Also adds record that de-identification has been performed.

Parameters:

list - the list of attributes to be cleaned up

handleUIDs - keep, remove or remap the UIDs

keepDescriptors - if true, keep the text description and comment attributes

keepSeriesDescriptors - if true, keep the series description even if all other descriptors are removed

keepProtocolName - if true, keep protocol name even if all other descriptors are removed

keepPatientCharacteristics - if true, keep patient characteristics (such as might be needed for PET SUV calculations)

keepDeviceIdentity - if true, keep device identity

keepInstitutionIdentity - if true, keep institution identity

handleDates - keep, remove or modify dates and times

epochForDateModification - the epoch to which to move the earliest date, used if handleDates is modify dates, otherwise null

earliestDateInSet - the known earliest date to move to the specified epoch, used if handleDates is modify dates, otherwise null; if null, the earliest in the supplied list is used; MUST be the earliest date and time else unaccompanied time attributes may cross midnight

handleStructuredContent - keep, remove or modify structured content

Throws:

DicomException - if error in DICOM encoding

removeOrNullIdentifyingAttributes

public static void removeOrNullIdentifyingAttributes(AttributeList list,
                                                     int handleUIDs,
                                                     boolean keepDescriptors,
                                                     boolean keepSeriesDescriptors,
                                                     boolean keepProtocolName,
                                                     boolean keepPatientCharacteristics,
                                                     boolean keepDeviceIdentity,
                                                     boolean keepInstitutionIdentity,
                                                     int handleDates,
                                                     java.util.Date epochForDateModification,
                                                     java.util.Date earliestDateInSet,
                                                     int handleStructuredContent,
                                                     boolean aggregateAgesOver89)
                                              throws DicomException

De-identify a list of attributes.

De-identifies attributes within nested sequences.

Handles UIDs as requested, including within nested sequences, including Content Sequence.

Handles dates and times as requested (other than Patient Birth), including within nested sequences, including Content Sequence.

Can optionally group ages over 89 years into single age of 90 as per HIPAA PR §164.514(b)(2)(i)(C).

Handles structured content as requested, including within nested sequences, including (and not just confined to) Content Sequence.

Also adds record that de-identification has been performed.

Parameters:

list - the list of attributes to be cleaned up

handleUIDs - keep, remove or remap the UIDs

keepDescriptors - if true, keep the text description and comment attributes

keepSeriesDescriptors - if true, keep the series description even if all other descriptors are removed

keepProtocolName - if true, keep protocol name even if all other descriptors are removed

keepPatientCharacteristics - if true, keep patient characteristics (such as might be needed for PET SUV calculations)

keepDeviceIdentity - if true, keep device identity

keepInstitutionIdentity - if true, keep institution identity

handleDates - keep, remove or modify dates and times

epochForDateModification - the epoch to which to move the earliest date, used if handleDates is modify dates, otherwise null

earliestDateInSet - the known earliest date to move to the specified epoch, used if handleDates is modify dates, otherwise null; if null, the earliest in the supplied list is used; MUST be the earliest date and time else unaccompanied time attributes may cross midnight

handleStructuredContent - keep, remove or modify structured content

aggregateAgesOver89 - if true, and keepPatientCharacteristics true, combine patient ages over 89 years into single 90 year category

Throws:

DicomException - if error in DICOM encoding

removeOrNullIdentifyingAttributes

public static void removeOrNullIdentifyingAttributes(AttributeList list,
                                                     int handleUIDs,
                                                     boolean keepDescriptors,
                                                     boolean keepSeriesDescriptors,
                                                     boolean keepPatientCharacteristics,
                                                     boolean keepDeviceIdentity,
                                                     boolean keepInstitutionIdentity,
                                                     int handleDates,
                                                     java.util.Date epochForDateModification,
                                                     java.util.Date earliestDateInSet)
                                              throws DicomException

De-identify a list of attributes.

De-identifies attributes within nested sequences, other than Context Sequence.

Handles UIDs as requested, including within nested sequences, including Context Sequence.

Handles dates and times as requested (other than Patient Birth), including within nested sequences, including Context Sequence.

Does not de-identify any specific content items in structured content, e.g., within Content Sequence.

Also adds record that de-identification has been performed.

Parameters:

list - the list of attributes to be cleaned up

handleUIDs - keep, remove or remap the UIDs

keepDescriptors - if true, keep the text description and comment attributes

keepSeriesDescriptors - if true, keep the series description even if all other descriptors are removed

keepPatientCharacteristics - if true, keep patient characteristics (such as might be needed for PET SUV calculations)

keepDeviceIdentity - if true, keep device identity

keepInstitutionIdentity - if true, keep institution identity

handleDates - keep, remove or modify dates and times

epochForDateModification - the epoch to which to move the earliest date, used if handleDates is modify dates, otherwise null

earliestDateInSet - the known earliest date to move to the specified epoch, used if handleDates is modify dates, otherwise null; if null, the earliest in the supplied list is used; MUST be the earliest date and time else unaccompanied time attributes may cross midnight

Throws:

DicomException - if error in DICOM encoding

removeOrNullIdentifyingAttributesRecursively

protected static void removeOrNullIdentifyingAttributesRecursively(AttributeList list,
                                                                   int handleUIDs,
                                                                   boolean keepDescriptors,
                                                                   boolean keepSeriesDescriptors,
                                                                   boolean keepProtocolName,
                                                                   boolean keepPatientCharacteristics,
                                                                   boolean keepDeviceIdentity,
                                                                   boolean keepInstitutionIdentity,
                                                                   boolean aggregateAgesOver89)
                                                            throws DicomException

De-identify a list of attributes, recursively iterating through nested sequences.

Does not process UIDs, but does remove sequences that would be invalidated by removing UIDs, e.g., Source Image Sequence and Referenced Image Sequence. If necessary caller should use removeOrRemapUIDAttributes().

Does not process dates and times (other than Patient Birth). If necessary caller should use removeOrRemapDateAndTimeAttributes().

Parameters:

list - the list of attributes to be cleaned up

handleUIDs - keep, remove or remap the UIDs

keepDescriptors - if true, keep the text description and comment attributes

keepSeriesDescriptors - if true, keep the series description even if all other descriptors are removed

keepProtocolName - if true, keep protocol name even if all other descriptors are removed

keepPatientCharacteristics - if true, keep patient characteristics (such as might be needed for PET SUV calculations)

keepDeviceIdentity - if true, keep device identity

keepInstitutionIdentity - if true, keep device identity

aggregateAgesOver89 - if true, and keepPatientCharacteristics true, combine patient ages over 89 years into single 90 year category

Throws:

DicomException - if error in DICOM encoding

removeOrRemapDateAndTimeAttributes

protected static void removeOrRemapDateAndTimeAttributes(AttributeList list,
                                                         int handleDates,
                                                         java.util.Date epochForDateModification,
                                                         java.util.Date earliest,
                                                         java.lang.String dateToUseForUnaccompaniedTimes)
                                                  throws DicomException

Remove or remap Date, Time and DateTime attributes (other than Patient Birth) in a list of attributes, recursively iterating through nested sequences.

Parameters:

list - the list of attributes to be cleaned up

handleDates - keep, remove or modify dates and times

epochForDateModification - used if handleDates is modify dates, otherwise null

earliest - used to determine the offset from the epoch to remove from all dates and times - MUST be the earliest date and time else unaccompanied time attributes may cross midnight

dateToUseForUnaccompaniedTimes - used for time attributes that don't have a date sibling and which may be nested in sequences, e.g., RadiopharmaceuticalStartTime

Throws:

DicomException - if error in DICOM encoding

removeOrRemapUIDAttributes

protected static void removeOrRemapUIDAttributes(AttributeList list,
                                                 int handleUIDs)
                                          throws DicomException

Remove or remap UID attributes in a list of attributes, recursively iterating through nested sequences.

Parameters:

list - the list of attributes to be cleaned up

handleUIDs - remove or remap the UIDs

Throws:

DicomException - if error in DICOM encoding

removeStructuredContent

protected static void removeStructuredContent(AttributeList list)

removeUIDAttributes

public static void removeUIDAttributes(AttributeList list)
                                throws DicomException

Remove UID attributes in a list of attributes, recursively iterating through nested sequences.

Parameters:

list - the list of attributes to be cleaned up

Throws:

DicomException - if error in DICOM encoding