orthanc: OrthancFramework/Sources/DicomParsing/DicomModification.cpp comparison

comparison OrthancFramework/Sources/DicomParsing/DicomModification.cpp @ 4678:2e850edf03d6

Full support for the anonymization of subsequences containing tags whose VR is UI

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Fri, 04 Jun 2021 17:38:43 +0200
parents	521e39b3f2c0
children	e3810750dc9d

comparison

equal deleted inserted replaced

-:521e39b3f2c0
+:2e850edf03d6
 static const std::string ORTHANC_DEIDENTIFICATION_METHOD_2021b =
 "Orthanc " ORTHANC_VERSION " - PS 3.15-2021b Table E.1-1 Basic Profile";
 namespace Orthanc
 {
+DicomModification::DicomTagRange::DicomTagRange(uint16_t groupFrom,
+uint16_t groupTo,
+uint16_t elementFrom,
+uint16_t elementTo) :
+groupFrom_(groupFrom),
+groupTo_(groupTo),
+elementFrom_(elementFrom),
+elementTo_(elementTo)
+{
+}
+bool DicomModification::DicomTagRange::Contains(const DicomTag& tag) const
+{
+return (tag.GetGroup() >= groupFrom_ &&
+tag.GetGroup() <= groupTo_ &&
+tag.GetElement() >= elementFrom_ &&
+tag.GetElement() <= elementTo_);
+}
 class DicomModification::RelationshipsVisitor : public ITagVisitor
 {
 private:
 DicomModification&  that_;
 const std::vector<size_t>& parentIndexes,
 const DicomTag& tag,
 ValueRepresentation vr,
 const std::string& value)
 {
+// Note that all the tags in "uids_" have the VR UI (unique
+// identifier), and are considered as strings
 if (!IsEnabled(tag))
 {
 return Action_None;
 }
-else if (parentTags.size() == 2 &&
+else if (!parentTags.empty() &&  // Don't anonymize twice the anonymization done by "MapDicomTags()"
-parentTags[0] == DICOM_TAG_REFERENCED_FRAME_OF_REFERENCE_SEQUENCE &&
+tag == DICOM_TAG_STUDY_INSTANCE_UID)
-parentTags[1] == DICOM_TAG_RT_REFERENCED_STUDY_SEQUENCE &&
+{
-tag == DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)
+newValue = that_.MapDicomIdentifier(value, ResourceType_Study);
-{
-// in RT-STRUCT, this ReferencedSOPInstanceUID is actually referencing a StudyInstanceUID !!
-// (observed in many data sets including: https://wiki.cancerimagingarchive.net/display/Public/Lung+CT+Segmentation+Challenge+2017)
-// tested in test_anonymize_relationships_5
-newValue = that_.MapDicomIdentifier(Toolbox::StripSpaces(value), ResourceType_Study);
 return Action_Replace;
 }
-else if (tag == DICOM_TAG_FRAME_OF_REFERENCE_UID ||
+else if (!parentTags.empty() &&  // Don't anonymize twice the anonymization done by "MapDicomTags()"
-tag == DICOM_TAG_REFERENCED_FRAME_OF_REFERENCE_UID ||
+tag == DICOM_TAG_SERIES_INSTANCE_UID)
-tag == DICOM_TAG_REFERENCED_SOP_INSTANCE_UID ||
+{
-tag == DICOM_TAG_RELATED_FRAME_OF_REFERENCE_UID)
+newValue = that_.MapDicomIdentifier(value, ResourceType_Series);
-{
-newValue = that_.MapDicomIdentifier(Toolbox::StripSpaces(value), ResourceType_Instance);
 return Action_Replace;
 }
-else if (parentTags.size() == 1 &&
+else if (!parentTags.empty() &&  // Don't anonymize twice the anonymization done by "MapDicomTags()"
-parentTags[0] == DICOM_TAG_CURRENT_REQUESTED_PROCEDURE_EVIDENCE_SEQUENCE &&
+tag == DICOM_TAG_SOP_INSTANCE_UID)
-tag == DICOM_TAG_STUDY_INSTANCE_UID)
+{
-{
+newValue = that_.MapDicomIdentifier(value, ResourceType_Instance);
-newValue = that_.MapDicomIdentifier(Toolbox::StripSpaces(value), ResourceType_Study);
 return Action_Replace;
 }
-else if (parentTags.size() == 2 &&
+else if (that_.uids_.find(tag) != that_.uids_.end())
-parentTags[0] == DICOM_TAG_CURRENT_REQUESTED_PROCEDURE_EVIDENCE_SEQUENCE &&
+{
-parentTags[1] == DICOM_TAG_REFERENCED_SERIES_SEQUENCE &&
+assert(vr == ValueRepresentation_UniqueIdentifier ||
-tag == DICOM_TAG_SERIES_INSTANCE_UID)
+vr == ValueRepresentation_NotSupported /* for older versions of DCMTK */);
-{
-newValue = that_.MapDicomIdentifier(Toolbox::StripSpaces(value), ResourceType_Series);
+if (parentTags.size() == 2 &&
+parentTags[0] == DICOM_TAG_REFERENCED_FRAME_OF_REFERENCE_SEQUENCE &&
+parentTags[1] == DICOM_TAG_RT_REFERENCED_STUDY_SEQUENCE &&
+tag == DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)
+{
+// in RT-STRUCT, this ReferencedSOPInstanceUID is actually referencing a StudyInstanceUID !!
+// (observed in many data sets including: https://wiki.cancerimagingarchive.net/display/Public/Lung+CT+Segmentation+Challenge+2017)
+// tested in test_anonymize_relationships_5
+newValue = that_.MapDicomIdentifier(value, ResourceType_Study);
+}
+else
+{
+newValue = that_.MapDicomIdentifier(value, ResourceType_Instance);
+}
 return Action_Replace;
 }
-else if (parentTags.size() == 3 &&
-parentTags[0] == DICOM_TAG_REFERENCED_FRAME_OF_REFERENCE_SEQUENCE &&
-parentTags[1] == DICOM_TAG_RT_REFERENCED_STUDY_SEQUENCE &&
-parentTags[2] == DICOM_TAG_RT_REFERENCED_SERIES_SEQUENCE &&
-tag == DICOM_TAG_SERIES_INSTANCE_UID)
-{
-newValue = that_.MapDicomIdentifier(Toolbox::StripSpaces(value), ResourceType_Series);
-return Action_Replace;
-}
-else if (parentTags.size() == 1 &&
-parentTags[0] == DICOM_TAG_REFERENCED_SERIES_SEQUENCE &&
-tag == DICOM_TAG_SERIES_INSTANCE_UID)
-{
-newValue = that_.MapDicomIdentifier(Toolbox::StripSpaces(value), ResourceType_Series);
-return Action_Replace;
-}
 else
 {
 return Action_None;
 }
 }
 void RemoveRelationships(ParsedDicomFile& dicom) const
 {
-// Sequences containing the UID relationships
+for (SetOfTags::const_iterator it = that_.uids_.begin(); it != that_.uids_.end(); ++it)
+{
+if (*it != DICOM_TAG_STUDY_INSTANCE_UID &&
+*it != DICOM_TAG_SERIES_INSTANCE_UID &&
+*it != DICOM_TAG_SOP_INSTANCE_UID)
+{
+RemoveIfEnabled(dicom, *it);
+}
+}
+// The only two sequences with to the "X/Z/U*" rule in the
+// basic profile. They were already present in Orthanc 1.9.3.
 RemoveIfEnabled(dicom, DICOM_TAG_REFERENCED_IMAGE_SEQUENCE);
 RemoveIfEnabled(dicom, DICOM_TAG_SOURCE_IMAGE_SEQUENCE);
-// Individual tags
-RemoveIfEnabled(dicom, DICOM_TAG_FRAME_OF_REFERENCE_UID);
-// The tags below should never occur at the first level of the
-// hierarchy, but remove them anyway
-RemoveIfEnabled(dicom, DICOM_TAG_REFERENCED_FRAME_OF_REFERENCE_UID);
-RemoveIfEnabled(dicom, DICOM_TAG_REFERENCED_SOP_INSTANCE_UID);
-RemoveIfEnabled(dicom, DICOM_TAG_RELATED_FRAME_OF_REFERENCE_UID);
 }
 };
 bool DicomModification::CancelReplacement(const DicomTag& tag)
 }
 std::string DicomModification::MapDicomIdentifier(const std::string& original,
 ResourceType level)
 {
+const std::string stripped = Toolbox::StripSpaces(original);
 std::string mapped;
-UidMap::const_iterator previous = uidMap_.find(std::make_pair(level, original));
+UidMap::const_iterator previous = uidMap_.find(std::make_pair(level, stripped));
 if (previous == uidMap_.end())
 {
 if (identifierGenerator_ == NULL)
 {
 mapped = FromDcmtkBridge::GenerateUniqueIdentifier(level);
 }
 else
 {
-if (!identifierGenerator_->Apply(mapped, original, level, currentSource_))
+if (!identifierGenerator_->Apply(mapped, stripped, level, currentSource_))
 {
 throw OrthancException(ErrorCode_InternalError,
 "Unable to generate an anonymized ID");
 }
 }
-uidMap_.insert(std::make_pair(std::make_pair(level, original), mapped));
+uidMap_.insert(std::make_pair(std::make_pair(level, stripped), mapped));
 }
 else
 {
 mapped = previous->second;
 }
 if (!const_cast<const ParsedDicomFile&>(dicom).GetTagValue(original, *tag))
 {
 original = "";
 }
-std::string mapped = MapDicomIdentifier(Toolbox::StripSpaces(original), level);
+std::string mapped = MapDicomIdentifier(original, level);
 dicom.Replace(*tag, mapped,
 false /* don't try and decode data URI scheme for UIDs */,
 DicomReplaceMode_InsertIfAbsent, privateCreator_);
 }
 bool wasRemoved = IsRemoved(tag);
 bool wasCleared = IsCleared(tag);
 removals_.erase(tag);
 clearings_.erase(tag);
+uids_.erase(tag);
 bool wasReplaced = CancelReplacement(tag);
 if (tag == DICOM_TAG_STUDY_INSTANCE_UID)
 {
 void DicomModification::Remove(const DicomTag& tag)
 {
 removals_.insert(tag);
 clearings_.erase(tag);
+uids_.erase(tag);
 CancelReplacement(tag);
 privateTagsToKeep_.erase(tag);
 MarkNotOrthancAnonymization();
 }
 void DicomModification::Clear(const DicomTag& tag)
 {
 removals_.erase(tag);
 clearings_.insert(tag);
+uids_.erase(tag);
 CancelReplacement(tag);
 privateTagsToKeep_.erase(tag);
 MarkNotOrthancAnonymization();
 }
 bool DicomModification::IsRemoved(const DicomTag& tag) const
 {
-return removals_.find(tag) != removals_.end();
+if (removals_.find(tag) != removals_.end())
+{
+return true;
+}
+else
+{
+for (RemovedRanges::const_iterator it = removedRanges_.begin();
+it != removedRanges_.end(); it++)
+{
+if (it->Contains(tag))
+{
+return true;
+}
+}
+return false;
+}
 }
 bool DicomModification::IsCleared(const DicomTag& tag) const
 {
 return clearings_.find(tag) != clearings_.end();
 const Json::Value& value,
 bool safeForAnonymization)
 {
 clearings_.erase(tag);
 removals_.erase(tag);
+uids_.erase(tag);
 privateTagsToKeep_.erase(tag);
 ReplaceInternal(tag, value);
 if (!safeForAnonymization)
 {
 {
 return level_;
 }
+static void SetupUidsFromOrthancInternal(std::set<DicomTag>& uids,
+std::set<DicomTag>& removals,
+const DicomTag& tag)
+{
+uids.insert(tag);
+removals.erase(tag);  // Necessary if unserializing a job from 1.9.3
+}
+void DicomModification::SetupUidsFromOrthanc_1_9_3()
+{
+/**
+* Values below come from the hardcoded UID of Orthanc 1.9.3
+* in DicomModification::RelationshipsVisitor::VisitString() and
+* DicomModification::RelationshipsVisitor::RemoveRelationships()
+* https://hg.orthanc-server.com/orthanc/file/Orthanc-1.9.3/OrthancFramework/Sources/DicomParsing/DicomModification.cpp#l117
+**/
+uids_.clear();
+SetupUidsFromOrthancInternal(uids_, removals_, DicomTag(0x0008, 0x0014));  // Instance Creator UID                   <= from SetupAnonymization2008()
+SetupUidsFromOrthancInternal(uids_, removals_, DicomTag(0x0008, 0x1155));  // Referenced SOP Instance UID            <= from VisitString() + RemoveRelationships()
+SetupUidsFromOrthancInternal(uids_, removals_, DicomTag(0x0020, 0x0052));  // Frame of Reference UID                 <= from VisitString() + RemoveRelationships()
+SetupUidsFromOrthancInternal(uids_, removals_, DicomTag(0x0020, 0x0200));  // Synchronization Frame of Reference UID <= from SetupAnonymization2008()
+SetupUidsFromOrthancInternal(uids_, removals_, DicomTag(0x0040, 0xa124));  // UID                                    <= from SetupAnonymization2008()
+SetupUidsFromOrthancInternal(uids_, removals_, DicomTag(0x0088, 0x0140));  // Storage Media File-set UID             <= from SetupAnonymization2008()
+SetupUidsFromOrthancInternal(uids_, removals_, DicomTag(0x3006, 0x0024));  // Referenced Frame of Reference UID      <= from VisitString() + RemoveRelationships()
+SetupUidsFromOrthancInternal(uids_, removals_, DicomTag(0x3006, 0x00c2));  // Related Frame of Reference UID         <= from VisitString() + RemoveRelationships()
+}
 void DicomModification::SetupAnonymization2008()
 {
 // This is Table E.1-1 from PS 3.15-2008 - DICOM Part 15: Security and System Management Profiles
 // https://raw.githubusercontent.com/jodogne/dicom-specification/master/2008/08_15pu.pdf
+SetupUidsFromOrthanc_1_9_3();
-removals_.insert(DicomTag(0x0008, 0x0014));  // Instance Creator UID
+//uids_.insert(DicomTag(0x0008, 0x0014));  // Instance Creator UID => set in SetupUidsFromOrthanc_1_9_3()
 //removals_.insert(DicomTag(0x0008, 0x0018));  // SOP Instance UID => set in Apply()
 removals_.insert(DicomTag(0x0008, 0x0050));  // Accession Number
 removals_.insert(DicomTag(0x0008, 0x0080));  // Institution Name
 removals_.insert(DicomTag(0x0008, 0x0081));  // Institution Address
 removals_.insert(DicomTag(0x0008, 0x0090));  // Referring Physician's Name
 removals_.insert(DicomTag(0x0008, 0x1048));  // Physician(s) of Record
 removals_.insert(DicomTag(0x0008, 0x1050));  // Performing Physicians' Name
 removals_.insert(DicomTag(0x0008, 0x1060));  // Name of Physician(s) Reading Study
 removals_.insert(DicomTag(0x0008, 0x1070));  // Operators' Name
 removals_.insert(DicomTag(0x0008, 0x1080));  // Admitting Diagnoses Description
-//removals_.insert(DicomTag(0x0008, 0x1155));  // Referenced SOP Instance UID => RelationshipsVisitor
+//uids_.insert(DicomTag(0x0008, 0x1155));      // Referenced SOP Instance UID => set in SetupUidsFromOrthanc_1_9_3()
 removals_.insert(DicomTag(0x0008, 0x2111));  // Derivation Description
 //removals_.insert(DicomTag(0x0010, 0x0010));  // Patient's Name => cf. below (*)
 //removals_.insert(DicomTag(0x0010, 0x0020));  // Patient ID => cf. below (*)
 removals_.insert(DicomTag(0x0010, 0x0030));  // Patient's Birth Date
 removals_.insert(DicomTag(0x0010, 0x0032));  // Patient's Birth Time
 removals_.insert(DicomTag(0x0018, 0x1000));  // Device Serial Number
 removals_.insert(DicomTag(0x0018, 0x1030));  // Protocol Name
 //removals_.insert(DicomTag(0x0020, 0x000d));  // Study Instance UID => set in Apply()
 //removals_.insert(DicomTag(0x0020, 0x000e));  // Series Instance UID => set in Apply()
 removals_.insert(DicomTag(0x0020, 0x0010));  // Study ID
-//removals_.insert(DicomTag(0x0020, 0x0052));  // Frame of Reference UID => cf. RelationshipsVisitor
+//uids_.insert(DicomTag(0x0020, 0x0052));      // Frame of Reference UID => set in SetupUidsFromOrthanc_1_9_3()
-removals_.insert(DicomTag(0x0020, 0x0200));  // Synchronization Frame of Reference UID
+//uids_.insert(DicomTag(0x0020, 0x0200));      // Synchronization Frame of Reference UID => set in SetupUidsFromOrthanc_1_9_3()
 removals_.insert(DicomTag(0x0020, 0x4000));  // Image Comments
 removals_.insert(DicomTag(0x0040, 0x0275));  // Request Attributes Sequence
-removals_.insert(DicomTag(0x0040, 0xa124));  // UID
+//uids_.insert(DicomTag(0x0040, 0xa124));      // UID => set in SetupUidsFromOrthanc_1_9_3()
 removals_.insert(DicomTag(0x0040, 0xa730));  // Content Sequence
-removals_.insert(DicomTag(0x0088, 0x0140));  // Storage Media File-set UID
+//uids_.insert(DicomTag(0x0088, 0x0140));      // Storage Media File-set UID => set in SetupUidsFromOrthanc_1_9_3()
-//removals_.insert(DicomTag(0x3006, 0x0024));  // Referenced Frame of Reference UID => RelationshipsVisitor
+//uids_.insert(DicomTag(0x3006, 0x0024));      // Referenced Frame of Reference UID => set in SetupUidsFromOrthanc_1_9_3()
-//removals_.insert(DicomTag(0x3006, 0x00c2));  // Related Frame of Reference UID => RelationshipsVisitor
+//uids_.insert(DicomTag(0x3006, 0x00c2));      // Related Frame of Reference UID => set in SetupUidsFromOrthanc_1_9_3()
 // Some more removals (from the experience of DICOM files at the CHU of Liege)
 removals_.insert(DicomTag(0x0010, 0x1040));  // Patient's Address
 removals_.insert(DicomTag(0x0032, 0x1032));  // Requesting Physician
 removals_.insert(DicomTag(0x0010, 0x2154));  // PatientTelephoneNumbers
 {
 isAnonymization_ = true;
 removals_.clear();
 clearings_.clear();
+removedRanges_.clear();
+uids_.clear();
 ClearReplacements();
 removePrivateTags_ = true;
 level_ = ResourceType_Patient;
 uidMap_.clear();
 privateTagsToKeep_.clear();
 // (*) Choose a random patient name and ID
 std::string patientId = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient);
 ReplaceInternal(DICOM_TAG_PATIENT_ID, patientId);
 ReplaceInternal(DICOM_TAG_PATIENT_NAME, patientId);
+// Sanity check
+for (SetOfTags::const_iterator it = uids_.begin(); it != uids_.end(); ++it)
+{
+ValueRepresentation vr = FromDcmtkBridge::LookupValueRepresentation(*it);
+if (vr != ValueRepresentation_UniqueIdentifier &&
+vr != ValueRepresentation_NotSupported /* for older versions of DCMTK */)
+{
+throw OrthancException(ErrorCode_InternalError);
+}
+}
 }
 void DicomModification::Apply(ParsedDicomFile& toModify)
 {
 // Check the request
 static const char* MAP_PATIENTS = "MapPatients";
 static const char* MAP_STUDIES = "MapStudies";
 static const char* MAP_SERIES = "MapSeries";
 static const char* MAP_INSTANCES = "MapInstances";
 static const char* PRIVATE_CREATOR = "PrivateCreator";  // New in Orthanc 1.6.0
+static const char* UIDS = "Uids";                       // New in Orthanc 1.9.4
+static const char* REMOVED_RANGES = "RemovedRanges";    // New in Orthanc 1.9.4
 void DicomModification::Serialize(Json::Value& value) const
 {
 if (identifierGenerator_ != NULL)
 {
 }
 assert(tmp2 != NULL);
 (*tmp2) [it->first.second] = it->second;
 }
+// New in Orthanc 1.9.4
+SerializationToolbox::WriteSetOfTags(value, uids_, UIDS);
+// New in Orthanc 1.9.4
+Json::Value ranges = Json::arrayValue;
+for (RemovedRanges::const_iterator it = removedRanges_.begin(); it != removedRanges_.end(); ++it)
+{
+Json::Value item = Json::arrayValue;
+item.append(it->GetGroupFrom());
+item.append(it->GetGroupTo());
+item.append(it->GetElementFrom());
+item.append(it->GetElementTo());
+ranges.append(item);
+}
+value[REMOVED_RANGES] = ranges;
 }
 void DicomModification::UnserializeUidMap(ResourceType level,
 const Json::Value& serialized,
 const char* field)
 UnserializeUidMap(ResourceType_Patient, serialized, MAP_PATIENTS);
 UnserializeUidMap(ResourceType_Study, serialized, MAP_STUDIES);
 UnserializeUidMap(ResourceType_Series, serialized, MAP_SERIES);
 UnserializeUidMap(ResourceType_Instance, serialized, MAP_INSTANCES);
+// New in Orthanc 1.9.4
+if (serialized.isMember(UIDS))  // Backward compatibility with Orthanc <= 1.9.3
+{
+SerializationToolbox::ReadSetOfTags(uids_, serialized, UIDS);
+}
+else
+{
+SetupUidsFromOrthanc_1_9_3();
+}
+// New in Orthanc 1.9.4
+removedRanges_.clear();
+if (serialized.isMember(REMOVED_RANGES))  // Backward compatibility with Orthanc <= 1.9.3
+{
+const Json::Value& ranges = serialized[REMOVED_RANGES];
+if (ranges.type() != Json::arrayValue)
+{
+throw OrthancException(ErrorCode_BadFileFormat);
+}
+else
+{
+for (Json::Value::ArrayIndex i = 0; i < ranges.size(); i++)
+{
+if (ranges[i].type() != Json::arrayValue ||
+ranges[i].size() != 4 ||
+!ranges[i][0].isUInt() ||
+!ranges[i][1].isUInt() ||
+!ranges[i][2].isUInt() ||
+!ranges[i][3].isUInt())
+{
+throw OrthancException(ErrorCode_BadFileFormat);
+}
+else
+{
+Json::LargestUInt groupFrom = ranges[i][0].asUInt();
+Json::LargestUInt groupTo = ranges[i][1].asUInt();
+Json::LargestUInt elementFrom = ranges[i][2].asUInt();
+Json::LargestUInt elementTo = ranges[i][3].asUInt();
+if (groupFrom > groupTo ||
+elementFrom > elementTo ||
+groupTo > 0xffffu ||
+elementTo > 0xffffu)
+{
+throw OrthancException(ErrorCode_BadFileFormat);
+}
+else
+{
+removedRanges_.push_back(DicomTagRange(groupFrom, groupTo, elementFrom, elementTo));
+}
+}
+}
+}
+}
 }
 void DicomModification::SetPrivateCreator(const std::string &privateCreator)
 {

Mercurial > hg > orthanc

comparison OrthancFramework/Sources/DicomParsing/DicomModification.cpp @ 4678:2e850edf03d6