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comparison OrthancServer/Sources/ServerContext.cpp @ 5044:6fed78e13233

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Refactored DicomMap to handle sequences when needed
author Alain Mazy <am@osimis.io>
date Tue, 28 Jun 2022 17:45:09 +0200
parents ec5c203a97ea
children 22966345eaba
comparison
equal deleted inserted replaced
5043:ec5c203a97ea 5044:6fed78e13233
524 524
525 DicomTransferSyntax transferSyntax; 525 DicomTransferSyntax transferSyntax;
526 bool hasTransferSyntax = dicom.LookupTransferSyntax(transferSyntax); 526 bool hasTransferSyntax = dicom.LookupTransferSyntax(transferSyntax);
527 527
528 DicomMap summary; 528 DicomMap summary;
529 dicom.GetSummary(summary); // -> this includes only the leaf nodes 529 dicom.GetSummary(summary); // -> from Orthanc 1.11.1, this includes the leaf nodes and sequences
530 530
531 std::set<DicomTag> allMainDicomTags = DicomMap::GetAllMainDicomTags(); 531 std::set<DicomTag> allMainDicomTags = DicomMap::GetAllMainDicomTags();
532 std::set<DicomTag> mainDicomSequences;
533 DicomMap::ExtractSequences(mainDicomSequences, allMainDicomTags);
534 DicomSequencesMap sequencesToStore;
535 532
536 try 533 try
537 { 534 {
538 MetricsRegistry::Timer timer(GetMetricsRegistry(), "orthanc_store_dicom_duration_ms"); 535 MetricsRegistry::Timer timer(GetMetricsRegistry(), "orthanc_store_dicom_duration_ms");
539 StorageAccessor accessor(area_, storageCache_, GetMetricsRegistry()); 536 StorageAccessor accessor(area_, storageCache_, GetMetricsRegistry());
540 537
541 DicomInstanceHasher hasher(summary); 538 DicomInstanceHasher hasher(summary);
542 resultPublicId = hasher.HashInstance(); 539 resultPublicId = hasher.HashInstance();
543 540
544 Json::Value dicomAsJson; // -> this includes the sequences 541 Json::Value dicomAsJson;
545 542 dicom.GetDicomAsJson(dicomAsJson, allMainDicomTags); // don't crop any main dicom tags
546 dicom.GetDicomAsJson(dicomAsJson, mainDicomSequences /*ignoreTagLength*/); // make sure that sequences that we wish to store in DB are not 'cropped'
547 sequencesToStore.FromDicomAsJson(dicomAsJson, mainDicomSequences);
548 543
549 Json::Value simplifiedTags; 544 Json::Value simplifiedTags;
550 Toolbox::SimplifyDicomAsJson(simplifiedTags, dicomAsJson, DicomToJsonFormat_Human); 545 Toolbox::SimplifyDicomAsJson(simplifiedTags, dicomAsJson, DicomToJsonFormat_Human);
551 546
552 // Test if the instance must be filtered out 547 // Test if the instance must be filtered out
621 } 616 }
622 617
623 typedef std::map<MetadataType, std::string> InstanceMetadata; 618 typedef std::map<MetadataType, std::string> InstanceMetadata;
624 InstanceMetadata instanceMetadata; 619 InstanceMetadata instanceMetadata;
625 result.SetStatus(index_.Store( 620 result.SetStatus(index_.Store(
626 instanceMetadata, summary, sequencesToStore, attachments, dicom.GetMetadata(), dicom.GetOrigin(), overwrite, 621 instanceMetadata, summary, attachments, dicom.GetMetadata(), dicom.GetOrigin(), overwrite,
627 hasTransferSyntax, transferSyntax, hasPixelDataOffset, pixelDataOffset, isReconstruct)); 622 hasTransferSyntax, transferSyntax, hasPixelDataOffset, pixelDataOffset, isReconstruct));
628 623
629 // Only keep the metadata for the "instance" level 624 // Only keep the metadata for the "instance" level
630 dicom.ClearMetadata(); 625 dicom.ClearMetadata();
631 626
1899 } 1894 }
1900 1895
1901 const std::string& ServerContext::GetDeidentifiedContent(const DicomElement &element) const 1896 const std::string& ServerContext::GetDeidentifiedContent(const DicomElement &element) const
1902 { 1897 {
1903 static const std::string redactedContent = "*** POTENTIAL PHI ***"; 1898 static const std::string redactedContent = "*** POTENTIAL PHI ***";
1899 static const std::string emptyContent = "";
1904 1900
1905 const DicomTag& tag = element.GetTag(); 1901 const DicomTag& tag = element.GetTag();
1902 if (element.GetValue().IsSequence())
1903 {
1904 return emptyContent;
1905 }
1906
1906 if (deidentifyLogs_ && 1907 if (deidentifyLogs_ &&
1907 !element.GetValue().GetContent().empty() && 1908 !element.GetValue().GetContent().empty() &&
1908 logsDeidentifierRules_.IsAlteredTag(tag)) 1909 logsDeidentifierRules_.IsAlteredTag(tag))
1909 { 1910 {
1910 return redactedContent; 1911 return redactedContent;
2081 resource.tags_.ExtractResourceInformation(mainDicomTags, resource.type_); 2082 resource.tags_.ExtractResourceInformation(mainDicomTags, resource.type_);
2082 2083
2083 target[MAIN_DICOM_TAGS] = Json::objectValue; 2084 target[MAIN_DICOM_TAGS] = Json::objectValue;
2084 FromDcmtkBridge::ToJson(target[MAIN_DICOM_TAGS], mainDicomTags, format); 2085 FromDcmtkBridge::ToJson(target[MAIN_DICOM_TAGS], mainDicomTags, format);
2085 2086
2086 {// add the main DICOM sequences to the main dicom tags
2087 const std::set<DicomTag>& mainDicomTags = DicomMap::GetMainDicomTags(resource.type_);
2088 std::set<DicomTag> mainDicomSequences;
2089 DicomMap::ExtractSequences(mainDicomSequences, mainDicomTags);
2090 resource.sequences_.ToJson(target[MAIN_DICOM_TAGS], format, mainDicomSequences);
2091 }
2092
2093 if (resource.type_ == ResourceType_Study) 2087 if (resource.type_ == ResourceType_Study)
2094 { 2088 {
2095 DicomMap patientMainDicomTags; 2089 DicomMap patientMainDicomTags;
2096 resource.tags_.ExtractPatientInformation(patientMainDicomTags); 2090 resource.tags_.ExtractPatientInformation(patientMainDicomTags);
2097 2091
2106 DicomMap tags; 2100 DicomMap tags;
2107 resource.tags_.ExtractTags(tags, requestedTags); 2101 resource.tags_.ExtractTags(tags, requestedTags);
2108 2102
2109 target[REQUESTED_TAGS] = Json::objectValue; 2103 target[REQUESTED_TAGS] = Json::objectValue;
2110 FromDcmtkBridge::ToJson(target[REQUESTED_TAGS], tags, format); 2104 FromDcmtkBridge::ToJson(target[REQUESTED_TAGS], tags, format);
2111
2112 {// add the requested sequences to the requested tags
2113 std::set<DicomTag> requestedDicomSequences;
2114 DicomMap::ExtractSequences(requestedDicomSequences, requestedTags);
2115 resource.sequences_.ToJson(target[REQUESTED_TAGS], format, requestedDicomSequences);
2116 }
2117 2105
2118 } 2106 }
2119 2107
2120 } 2108 }
2121 2109
2424 } 2412 }
2425 2413
2426 // possibly merge missing requested tags from dicom-as-json 2414 // possibly merge missing requested tags from dicom-as-json
2427 if (!resource.missingRequestedTags_.empty() && !DicomMap::HasOnlyComputedTags(resource.missingRequestedTags_)) 2415 if (!resource.missingRequestedTags_.empty() && !DicomMap::HasOnlyComputedTags(resource.missingRequestedTags_))
2428 { 2416 {
2429 std::set<DicomTag> missingSequences;
2430 DicomMap::ExtractSequences(missingSequences, resource.missingRequestedTags_);
2431
2432 OrthancConfiguration::ReaderLock lock; 2417 OrthancConfiguration::ReaderLock lock;
2433 if (lock.GetConfiguration().IsWarningEnabled(Warnings_001_TagsBeingReadFromStorage)) 2418 if (lock.GetConfiguration().IsWarningEnabled(Warnings_001_TagsBeingReadFromStorage))
2434 { 2419 {
2435 std::set<DicomTag> missingTags; 2420 std::set<DicomTag> missingTags;
2436 Toolbox::AppendSets(missingTags, resource.missingRequestedTags_); 2421 Toolbox::AppendSets(missingTags, resource.missingRequestedTags_);
2472 } 2457 }
2473 } 2458 }
2474 2459
2475 Json::Value tmpDicomAsJson; 2460 Json::Value tmpDicomAsJson;
2476 ReadDicomAsJson(tmpDicomAsJson, instanceId_, resource.missingRequestedTags_ /* ignoreTagLength */); // read all tags from DICOM and avoid cropping requested tags 2461 ReadDicomAsJson(tmpDicomAsJson, instanceId_, resource.missingRequestedTags_ /* ignoreTagLength */); // read all tags from DICOM and avoid cropping requested tags
2477 tagsFromJson.FromDicomAsJson(tmpDicomAsJson); 2462 tagsFromJson.FromDicomAsJson(tmpDicomAsJson, false /* append */, true /* parseSequences*/);
2478 resource.sequences_.FromDicomAsJson(tmpDicomAsJson, missingSequences);
2479 } 2463 }
2480 else 2464 else
2481 { 2465 {
2482 tagsFromJson.FromDicomAsJson(*dicomAsJson); 2466 tagsFromJson.FromDicomAsJson(*dicomAsJson, false /* append */, true /* parseSequences*/);
2483 resource.sequences_.FromDicomAsJson(*dicomAsJson, missingSequences);
2484 } 2467 }
2485 2468
2486 resource.tags_.Merge(tagsFromJson); 2469 resource.tags_.Merge(tagsFromJson);
2487 } 2470 }
2488 2471