Mercurial > hg > orthanc
view OrthancServer/ServerToolbox.cpp @ 2162:d738945c25cd
migrating TODO from Trello
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 22 Nov 2016 11:29:03 +0100 |
parents | 0c09d1af22f3 |
children | e3fd5bc429a2 |
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/** * Orthanc - A Lightweight, RESTful DICOM Store * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * * This program is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. * * In addition, as a special exception, the copyright holders of this * program give permission to link the code of its release with the * OpenSSL project's "OpenSSL" library (or with modified versions of it * that use the same license as the "OpenSSL" library), and distribute * the linked executables. You must obey the GNU General Public License * in all respects for all of the code used other than "OpenSSL". If you * modify file(s) with this exception, you may extend this exception to * your version of the file(s), but you are not obligated to do so. If * you do not wish to do so, delete this exception statement from your * version. If you delete this exception statement from all source files * in the program, then also delete it here. * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. **/ #include "PrecompiledHeadersServer.h" #include "ServerToolbox.h" #include "../Core/DicomFormat/DicomArray.h" #include "../Core/FileStorage/StorageAccessor.h" #include "../Core/Logging.h" #include "../Core/OrthancException.h" #include "ParsedDicomFile.h" #include <cassert> namespace Orthanc { namespace ServerToolbox { static const DicomTag patientIdentifiers[] = { DICOM_TAG_PATIENT_ID, DICOM_TAG_PATIENT_NAME, DICOM_TAG_PATIENT_BIRTH_DATE }; static const DicomTag studyIdentifiers[] = { DICOM_TAG_PATIENT_ID, DICOM_TAG_PATIENT_NAME, DICOM_TAG_PATIENT_BIRTH_DATE, DICOM_TAG_STUDY_INSTANCE_UID, DICOM_TAG_ACCESSION_NUMBER, DICOM_TAG_STUDY_DESCRIPTION, DICOM_TAG_STUDY_DATE }; static const DicomTag seriesIdentifiers[] = { DICOM_TAG_SERIES_INSTANCE_UID }; static const DicomTag instanceIdentifiers[] = { DICOM_TAG_SOP_INSTANCE_UID }; void SimplifyTags(Json::Value& target, const Json::Value& source, DicomToJsonFormat format) { assert(source.isObject()); target = Json::objectValue; Json::Value::Members members = source.getMemberNames(); for (size_t i = 0; i < members.size(); i++) { const Json::Value& v = source[members[i]]; const std::string& type = v["Type"].asString(); std::string name; switch (format) { case DicomToJsonFormat_Human: name = v["Name"].asString(); break; case DicomToJsonFormat_Short: name = members[i]; break; default: throw OrthancException(ErrorCode_ParameterOutOfRange); } if (type == "String") { target[name] = v["Value"].asString(); } else if (type == "TooLong" || type == "Null") { target[name] = Json::nullValue; } else if (type == "Sequence") { const Json::Value& array = v["Value"]; assert(array.isArray()); Json::Value children = Json::arrayValue; for (Json::Value::ArrayIndex i = 0; i < array.size(); i++) { Json::Value c; SimplifyTags(c, array[i], format); children.append(c); } target[name] = children; } else { assert(0); } } } static std::string ValueAsString(const DicomMap& summary, const DicomTag& tag) { const DicomValue& value = summary.GetValue(tag); if (value.IsNull()) { return "(null)"; } else { return value.GetContent(); } } void LogMissingRequiredTag(const DicomMap& summary) { std::string s, t; if (summary.HasTag(DICOM_TAG_PATIENT_ID)) { if (t.size() > 0) t += ", "; t += "PatientID=" + ValueAsString(summary, DICOM_TAG_PATIENT_ID); } else { if (s.size() > 0) s += ", "; s += "PatientID"; } if (summary.HasTag(DICOM_TAG_STUDY_INSTANCE_UID)) { if (t.size() > 0) t += ", "; t += "StudyInstanceUID=" + ValueAsString(summary, DICOM_TAG_STUDY_INSTANCE_UID); } else { if (s.size() > 0) s += ", "; s += "StudyInstanceUID"; } if (summary.HasTag(DICOM_TAG_SERIES_INSTANCE_UID)) { if (t.size() > 0) t += ", "; t += "SeriesInstanceUID=" + ValueAsString(summary, DICOM_TAG_SERIES_INSTANCE_UID); } else { if (s.size() > 0) s += ", "; s += "SeriesInstanceUID"; } if (summary.HasTag(DICOM_TAG_SOP_INSTANCE_UID)) { if (t.size() > 0) t += ", "; t += "SOPInstanceUID=" + ValueAsString(summary, DICOM_TAG_SOP_INSTANCE_UID); } else { if (s.size() > 0) s += ", "; s += "SOPInstanceUID"; } if (t.size() == 0) { LOG(ERROR) << "Store has failed because all the required tags (" << s << ") are missing (is it a DICOMDIR file?)"; } else { LOG(ERROR) << "Store has failed because required tags (" << s << ") are missing for the following instance: " << t; } } static void StoreMainDicomTagsInternal(IDatabaseWrapper& database, int64_t resource, const DicomMap& tags) { DicomArray flattened(tags); for (size_t i = 0; i < flattened.GetSize(); i++) { const DicomElement& element = flattened.GetElement(i); const DicomTag& tag = element.GetTag(); const DicomValue& value = element.GetValue(); if (!value.IsNull() && !value.IsBinary()) { database.SetMainDicomTag(resource, tag, element.GetValue().GetContent()); } } } static void StoreIdentifiers(IDatabaseWrapper& database, int64_t resource, ResourceType level, const DicomMap& map) { const DicomTag* tags; size_t size; LoadIdentifiers(tags, size, level); for (size_t i = 0; i < size; i++) { const DicomValue* value = map.TestAndGetValue(tags[i]); if (value != NULL && !value->IsNull() && !value->IsBinary()) { std::string s = NormalizeIdentifier(value->GetContent()); database.SetIdentifierTag(resource, tags[i], s); } } } void StoreMainDicomTags(IDatabaseWrapper& database, int64_t resource, ResourceType level, const DicomMap& dicomSummary) { // WARNING: The database should be locked with a transaction! StoreIdentifiers(database, resource, level, dicomSummary); DicomMap tags; switch (level) { case ResourceType_Patient: dicomSummary.ExtractPatientInformation(tags); break; case ResourceType_Study: // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6) dicomSummary.ExtractPatientInformation(tags); StoreMainDicomTagsInternal(database, resource, tags); dicomSummary.ExtractStudyInformation(tags); break; case ResourceType_Series: dicomSummary.ExtractSeriesInformation(tags); break; case ResourceType_Instance: dicomSummary.ExtractInstanceInformation(tags); break; default: throw OrthancException(ErrorCode_InternalError); } StoreMainDicomTagsInternal(database, resource, tags); } bool FindOneChildInstance(int64_t& result, IDatabaseWrapper& database, int64_t resource, ResourceType type) { for (;;) { if (type == ResourceType_Instance) { result = resource; return true; } std::list<int64_t> children; database.GetChildrenInternalId(children, resource); if (children.empty()) { return false; } resource = children.front(); type = GetChildResourceType(type); } } void ReconstructMainDicomTags(IDatabaseWrapper& database, IStorageArea& storageArea, ResourceType level) { // WARNING: The database should be locked with a transaction! // TODO: This function might consume much memory if level == // ResourceType_Instance. To improve this, first download the // list of studies, then remove the instances for each single // study (check out OrthancRestApi::InvalidateTags for an // example). Take this improvement into consideration for the // next upgrade of the database schema. const char* plural = NULL; switch (level) { case ResourceType_Patient: plural = "patients"; break; case ResourceType_Study: plural = "studies"; break; case ResourceType_Series: plural = "series"; break; case ResourceType_Instance: plural = "instances"; break; default: throw OrthancException(ErrorCode_InternalError); } LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; std::list<std::string> resources; database.GetAllPublicIds(resources, level); for (std::list<std::string>::const_iterator it = resources.begin(); it != resources.end(); ++it) { // Locate the resource and one of its child instances int64_t resource, instance; ResourceType tmp; if (!database.LookupResource(resource, tmp, *it) || tmp != level || !FindOneChildInstance(instance, database, resource, level)) { LOG(ERROR) << "Cannot find an instance for " << EnumerationToString(level) << " with identifier " << *it; throw OrthancException(ErrorCode_InternalError); } // Get the DICOM file attached to some instances in the resource FileInfo attachment; if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom)) { LOG(ERROR) << "Cannot retrieve the DICOM file associated with instance " << database.GetPublicId(instance); throw OrthancException(ErrorCode_InternalError); } try { // Read and parse the content of the DICOM file StorageAccessor accessor(storageArea); std::string content; accessor.Read(content, attachment); ParsedDicomFile dicom(content); // Update the tags of this resource DicomMap dicomSummary; dicom.Convert(dicomSummary); database.ClearMainDicomTags(resource); StoreMainDicomTags(database, resource, level, dicomSummary); } catch (OrthancException&) { LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid() << " associated with instance " << database.GetPublicId(instance); throw; } } } void LoadIdentifiers(const DicomTag*& tags, size_t& size, ResourceType level) { switch (level) { case ResourceType_Patient: tags = patientIdentifiers; size = sizeof(patientIdentifiers) / sizeof(DicomTag); break; case ResourceType_Study: tags = studyIdentifiers; size = sizeof(studyIdentifiers) / sizeof(DicomTag); break; case ResourceType_Series: tags = seriesIdentifiers; size = sizeof(seriesIdentifiers) / sizeof(DicomTag); break; case ResourceType_Instance: tags = instanceIdentifiers; size = sizeof(instanceIdentifiers) / sizeof(DicomTag); break; default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } std::string NormalizeIdentifier(const std::string& value) { std::string t; t.reserve(value.size()); for (size_t i = 0; i < value.size(); i++) { if (value[i] == '%' || value[i] == '_') { t.push_back(' '); // These characters might break wildcard queries in SQL } else if (isascii(value[i]) && !iscntrl(value[i]) && (!isspace(value[i]) || value[i] == ' ')) { t.push_back(value[i]); } } Toolbox::ToUpperCase(t); return Toolbox::StripSpaces(t); } bool IsIdentifier(const DicomTag& tag, ResourceType level) { const DicomTag* tags; size_t size; LoadIdentifiers(tags, size, level); for (size_t i = 0; i < size; i++) { if (tag == tags[i]) { return true; } } return false; } } }