Mercurial > hg > orthanc
view Core/DicomFormat/DicomMap.cpp @ 3965:7f296ae25039
reviewed CommandDispatcher.cpp
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 22 May 2020 08:33:26 +0200 |
parents | e7003b2203a7 |
children |
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/** * Orthanc - A Lightweight, RESTful DICOM Store * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * Copyright (C) 2017-2020 Osimis S.A., 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 "../PrecompiledHeaders.h" #include "DicomMap.h" #include <stdio.h> #include <memory> #include "../Compatibility.h" #include "../Endianness.h" #include "../Logging.h" #include "../OrthancException.h" #include "../Toolbox.h" #include "DicomArray.h" namespace Orthanc { namespace { struct MainDicomTag { const DicomTag tag_; const char* name_; }; } static const MainDicomTag PATIENT_MAIN_DICOM_TAGS[] = { // { DicomTag(0x0010, 0x1010), "PatientAge" }, // { DicomTag(0x0010, 0x1040), "PatientAddress" }, { DicomTag(0x0010, 0x0010), "PatientName" }, { DicomTag(0x0010, 0x0030), "PatientBirthDate" }, { DicomTag(0x0010, 0x0040), "PatientSex" }, { DicomTag(0x0010, 0x1000), "OtherPatientIDs" }, { DICOM_TAG_PATIENT_ID, "PatientID" } }; static const MainDicomTag STUDY_MAIN_DICOM_TAGS[] = { // { DicomTag(0x0010, 0x1020), "PatientSize" }, // { DicomTag(0x0010, 0x1030), "PatientWeight" }, { DICOM_TAG_STUDY_DATE, "StudyDate" }, { DicomTag(0x0008, 0x0030), "StudyTime" }, { DicomTag(0x0020, 0x0010), "StudyID" }, { DICOM_TAG_STUDY_DESCRIPTION, "StudyDescription" }, { DICOM_TAG_ACCESSION_NUMBER, "AccessionNumber" }, { DICOM_TAG_STUDY_INSTANCE_UID, "StudyInstanceUID" }, // New in db v6 { DICOM_TAG_REQUESTED_PROCEDURE_DESCRIPTION, "RequestedProcedureDescription" }, { DICOM_TAG_INSTITUTION_NAME, "InstitutionName" }, { DICOM_TAG_REQUESTING_PHYSICIAN, "RequestingPhysician" }, { DICOM_TAG_REFERRING_PHYSICIAN_NAME, "ReferringPhysicianName" } }; static const MainDicomTag SERIES_MAIN_DICOM_TAGS[] = { // { DicomTag(0x0010, 0x1080), "MilitaryRank" }, { DicomTag(0x0008, 0x0021), "SeriesDate" }, { DicomTag(0x0008, 0x0031), "SeriesTime" }, { DICOM_TAG_MODALITY, "Modality" }, { DicomTag(0x0008, 0x0070), "Manufacturer" }, { DicomTag(0x0008, 0x1010), "StationName" }, { DICOM_TAG_SERIES_DESCRIPTION, "SeriesDescription" }, { DicomTag(0x0018, 0x0015), "BodyPartExamined" }, { DicomTag(0x0018, 0x0024), "SequenceName" }, { DicomTag(0x0018, 0x1030), "ProtocolName" }, { DicomTag(0x0020, 0x0011), "SeriesNumber" }, { DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES, "CardiacNumberOfImages" }, { DICOM_TAG_IMAGES_IN_ACQUISITION, "ImagesInAcquisition" }, { DICOM_TAG_NUMBER_OF_TEMPORAL_POSITIONS, "NumberOfTemporalPositions" }, { DICOM_TAG_NUMBER_OF_SLICES, "NumberOfSlices" }, { DICOM_TAG_NUMBER_OF_TIME_SLICES, "NumberOfTimeSlices" }, { DICOM_TAG_SERIES_INSTANCE_UID, "SeriesInstanceUID" }, // New in db v6 { DICOM_TAG_IMAGE_ORIENTATION_PATIENT, "ImageOrientationPatient" }, { DICOM_TAG_SERIES_TYPE, "SeriesType" }, { DICOM_TAG_OPERATOR_NAME, "OperatorsName" }, { DICOM_TAG_PERFORMED_PROCEDURE_STEP_DESCRIPTION, "PerformedProcedureStepDescription" }, { DICOM_TAG_ACQUISITION_DEVICE_PROCESSING_DESCRIPTION, "AcquisitionDeviceProcessingDescription" }, { DICOM_TAG_CONTRAST_BOLUS_AGENT, "ContrastBolusAgent" } }; static const MainDicomTag INSTANCE_MAIN_DICOM_TAGS[] = { { DicomTag(0x0008, 0x0012), "InstanceCreationDate" }, { DicomTag(0x0008, 0x0013), "InstanceCreationTime" }, { DicomTag(0x0020, 0x0012), "AcquisitionNumber" }, { DICOM_TAG_IMAGE_INDEX, "ImageIndex" }, { DICOM_TAG_INSTANCE_NUMBER, "InstanceNumber" }, { DICOM_TAG_NUMBER_OF_FRAMES, "NumberOfFrames" }, { DICOM_TAG_TEMPORAL_POSITION_IDENTIFIER, "TemporalPositionIdentifier" }, { DICOM_TAG_SOP_INSTANCE_UID, "SOPInstanceUID" }, // New in db v6 { DICOM_TAG_IMAGE_POSITION_PATIENT, "ImagePositionPatient" }, { DICOM_TAG_IMAGE_COMMENTS, "ImageComments" }, /** * Main DICOM tags that are not part of any release of the * database schema yet, and that will be part of future db v7. In * the meantime, the user must call "/tools/reconstruct" once to * access these tags if the corresponding DICOM files where * indexed in the database by an older version of Orthanc. **/ { DICOM_TAG_IMAGE_ORIENTATION_PATIENT, "ImageOrientationPatient" } // New in Orthanc 1.4.2 }; static void LoadMainDicomTags(const MainDicomTag*& tags, size_t& size, ResourceType level) { switch (level) { case ResourceType_Patient: tags = PATIENT_MAIN_DICOM_TAGS; size = sizeof(PATIENT_MAIN_DICOM_TAGS) / sizeof(MainDicomTag); break; case ResourceType_Study: tags = STUDY_MAIN_DICOM_TAGS; size = sizeof(STUDY_MAIN_DICOM_TAGS) / sizeof(MainDicomTag); break; case ResourceType_Series: tags = SERIES_MAIN_DICOM_TAGS; size = sizeof(SERIES_MAIN_DICOM_TAGS) / sizeof(MainDicomTag); break; case ResourceType_Instance: tags = INSTANCE_MAIN_DICOM_TAGS; size = sizeof(INSTANCE_MAIN_DICOM_TAGS) / sizeof(MainDicomTag); break; default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } static void LoadMainDicomTags(std::map<DicomTag, std::string>& target, ResourceType level) { const MainDicomTag* tags = NULL; size_t size; LoadMainDicomTags(tags, size, level); assert(tags != NULL && size != 0); for (size_t i = 0; i < size; i++) { assert(target.find(tags[i].tag_) == target.end()); target[tags[i].tag_] = tags[i].name_; } } namespace { class DicomTag2 : public DicomTag { public: DicomTag2() : DicomTag(0, 0) // To make std::map<> happy { } DicomTag2(const DicomTag& tag) : DicomTag(tag) { } }; } static void LoadMainDicomTags(std::map<std::string, DicomTag2>& target, ResourceType level) { const MainDicomTag* tags = NULL; size_t size; LoadMainDicomTags(tags, size, level); assert(tags != NULL && size != 0); for (size_t i = 0; i < size; i++) { assert(target.find(tags[i].name_) == target.end()); target[tags[i].name_] = tags[i].tag_; } } void DicomMap::SetValueInternal(uint16_t group, uint16_t element, DicomValue* value) { DicomTag tag(group, element); Content::iterator it = content_.find(tag); if (it != content_.end()) { delete it->second; it->second = value; } else { content_.insert(std::make_pair(tag, value)); } } void DicomMap::Clear() { for (Content::iterator it = content_.begin(); it != content_.end(); ++it) { assert(it->second != NULL); delete it->second; } content_.clear(); } static void ExtractTags(DicomMap& result, const DicomMap::Content& source, const MainDicomTag* tags, size_t count) { result.Clear(); for (unsigned int i = 0; i < count; i++) { DicomMap::Content::const_iterator it = source.find(tags[i].tag_); if (it != source.end()) { result.SetValue(it->first, *it->second /* value will be cloned */); } } } void DicomMap::ExtractPatientInformation(DicomMap& result) const { ExtractTags(result, content_, PATIENT_MAIN_DICOM_TAGS, sizeof(PATIENT_MAIN_DICOM_TAGS) / sizeof(MainDicomTag)); } void DicomMap::ExtractStudyInformation(DicomMap& result) const { ExtractTags(result, content_, STUDY_MAIN_DICOM_TAGS, sizeof(STUDY_MAIN_DICOM_TAGS) / sizeof(MainDicomTag)); } void DicomMap::ExtractSeriesInformation(DicomMap& result) const { ExtractTags(result, content_, SERIES_MAIN_DICOM_TAGS, sizeof(SERIES_MAIN_DICOM_TAGS) / sizeof(MainDicomTag)); } void DicomMap::ExtractInstanceInformation(DicomMap& result) const { ExtractTags(result, content_, INSTANCE_MAIN_DICOM_TAGS, sizeof(INSTANCE_MAIN_DICOM_TAGS) / sizeof(MainDicomTag)); } DicomMap* DicomMap::Clone() const { std::unique_ptr<DicomMap> result(new DicomMap); for (Content::const_iterator it = content_.begin(); it != content_.end(); ++it) { result->content_.insert(std::make_pair(it->first, it->second->Clone())); } return result.release(); } void DicomMap::Assign(const DicomMap& other) { Clear(); for (Content::const_iterator it = other.content_.begin(); it != other.content_.end(); ++it) { content_.insert(std::make_pair(it->first, it->second->Clone())); } } const DicomValue& DicomMap::GetValue(const DicomTag& tag) const { const DicomValue* value = TestAndGetValue(tag); if (value) { return *value; } else { throw OrthancException(ErrorCode_InexistentTag); } } const DicomValue* DicomMap::TestAndGetValue(const DicomTag& tag) const { Content::const_iterator it = content_.find(tag); if (it == content_.end()) { return NULL; } else { return it->second; } } void DicomMap::Remove(const DicomTag& tag) { Content::iterator it = content_.find(tag); if (it != content_.end()) { delete it->second; content_.erase(it); } } static void SetupFindTemplate(DicomMap& result, const MainDicomTag* tags, size_t count) { result.Clear(); for (size_t i = 0; i < count; i++) { result.SetValue(tags[i].tag_, "", false); } } void DicomMap::SetupFindPatientTemplate(DicomMap& result) { SetupFindTemplate(result, PATIENT_MAIN_DICOM_TAGS, sizeof(PATIENT_MAIN_DICOM_TAGS) / sizeof(MainDicomTag)); } void DicomMap::SetupFindStudyTemplate(DicomMap& result) { SetupFindTemplate(result, STUDY_MAIN_DICOM_TAGS, sizeof(STUDY_MAIN_DICOM_TAGS) / sizeof(MainDicomTag)); result.SetValue(DICOM_TAG_ACCESSION_NUMBER, "", false); result.SetValue(DICOM_TAG_PATIENT_ID, "", false); // These main DICOM tags are only indirectly related to the // General Study Module, remove them result.Remove(DICOM_TAG_INSTITUTION_NAME); result.Remove(DICOM_TAG_REQUESTING_PHYSICIAN); result.Remove(DICOM_TAG_REQUESTED_PROCEDURE_DESCRIPTION); } void DicomMap::SetupFindSeriesTemplate(DicomMap& result) { SetupFindTemplate(result, SERIES_MAIN_DICOM_TAGS, sizeof(SERIES_MAIN_DICOM_TAGS) / sizeof(MainDicomTag)); result.SetValue(DICOM_TAG_ACCESSION_NUMBER, "", false); result.SetValue(DICOM_TAG_PATIENT_ID, "", false); result.SetValue(DICOM_TAG_STUDY_INSTANCE_UID, "", false); // These tags are considered as "main" by Orthanc, but are not in the Series module result.Remove(DicomTag(0x0008, 0x0070)); // Manufacturer result.Remove(DicomTag(0x0008, 0x1010)); // Station name result.Remove(DicomTag(0x0018, 0x0024)); // Sequence name result.Remove(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES); result.Remove(DICOM_TAG_IMAGES_IN_ACQUISITION); result.Remove(DICOM_TAG_NUMBER_OF_SLICES); result.Remove(DICOM_TAG_NUMBER_OF_TEMPORAL_POSITIONS); result.Remove(DICOM_TAG_NUMBER_OF_TIME_SLICES); result.Remove(DICOM_TAG_IMAGE_ORIENTATION_PATIENT); result.Remove(DICOM_TAG_SERIES_TYPE); result.Remove(DICOM_TAG_ACQUISITION_DEVICE_PROCESSING_DESCRIPTION); result.Remove(DICOM_TAG_CONTRAST_BOLUS_AGENT); } void DicomMap::SetupFindInstanceTemplate(DicomMap& result) { SetupFindTemplate(result, INSTANCE_MAIN_DICOM_TAGS, sizeof(INSTANCE_MAIN_DICOM_TAGS) / sizeof(MainDicomTag)); result.SetValue(DICOM_TAG_ACCESSION_NUMBER, "", false); result.SetValue(DICOM_TAG_PATIENT_ID, "", false); result.SetValue(DICOM_TAG_STUDY_INSTANCE_UID, "", false); result.SetValue(DICOM_TAG_SERIES_INSTANCE_UID, "", false); } void DicomMap::CopyTagIfExists(const DicomMap& source, const DicomTag& tag) { if (source.HasTag(tag)) { SetValue(tag, source.GetValue(tag)); } } bool DicomMap::IsMainDicomTag(const DicomTag& tag, ResourceType level) { const MainDicomTag *tags = NULL; size_t size; LoadMainDicomTags(tags, size, level); for (size_t i = 0; i < size; i++) { if (tags[i].tag_ == tag) { return true; } } return false; } bool DicomMap::IsMainDicomTag(const DicomTag& tag) { return (IsMainDicomTag(tag, ResourceType_Patient) || IsMainDicomTag(tag, ResourceType_Study) || IsMainDicomTag(tag, ResourceType_Series) || IsMainDicomTag(tag, ResourceType_Instance)); } void DicomMap::GetMainDicomTagsInternal(std::set<DicomTag>& result, ResourceType level) { const MainDicomTag *tags = NULL; size_t size; LoadMainDicomTags(tags, size, level); for (size_t i = 0; i < size; i++) { result.insert(tags[i].tag_); } } void DicomMap::GetMainDicomTags(std::set<DicomTag>& result, ResourceType level) { result.clear(); GetMainDicomTagsInternal(result, level); } void DicomMap::GetMainDicomTags(std::set<DicomTag>& result) { result.clear(); GetMainDicomTagsInternal(result, ResourceType_Patient); GetMainDicomTagsInternal(result, ResourceType_Study); GetMainDicomTagsInternal(result, ResourceType_Series); GetMainDicomTagsInternal(result, ResourceType_Instance); } void DicomMap::GetTags(std::set<DicomTag>& tags) const { tags.clear(); for (Content::const_iterator it = content_.begin(); it != content_.end(); ++it) { tags.insert(it->first); } } static uint16_t ReadUnsignedInteger16(const char* dicom) { return le16toh(*reinterpret_cast<const uint16_t*>(dicom)); } static uint32_t ReadUnsignedInteger32(const char* dicom) { return le32toh(*reinterpret_cast<const uint32_t*>(dicom)); } static bool ValidateTag(const ValueRepresentation& vr, const std::string& value) { switch (vr) { case ValueRepresentation_ApplicationEntity: return value.size() <= 16; case ValueRepresentation_AgeString: return (value.size() == 4 && isdigit(value[0]) && isdigit(value[1]) && isdigit(value[2]) && (value[3] == 'D' || value[3] == 'W' || value[3] == 'M' || value[3] == 'Y')); case ValueRepresentation_AttributeTag: return value.size() == 4; case ValueRepresentation_CodeString: return value.size() <= 16; case ValueRepresentation_Date: return value.size() <= 18; case ValueRepresentation_DecimalString: return value.size() <= 16; case ValueRepresentation_DateTime: return value.size() <= 54; case ValueRepresentation_FloatingPointSingle: return value.size() == 4; case ValueRepresentation_FloatingPointDouble: return value.size() == 8; case ValueRepresentation_IntegerString: return value.size() <= 12; case ValueRepresentation_LongString: return value.size() <= 64; case ValueRepresentation_LongText: return value.size() <= 10240; case ValueRepresentation_OtherByte: return true; case ValueRepresentation_OtherDouble: return value.size() <= (static_cast<uint64_t>(1) << 32) - 8; case ValueRepresentation_OtherFloat: return value.size() <= (static_cast<uint64_t>(1) << 32) - 4; case ValueRepresentation_OtherLong: return true; case ValueRepresentation_OtherWord: return true; case ValueRepresentation_PersonName: return true; case ValueRepresentation_ShortString: return value.size() <= 16; case ValueRepresentation_SignedLong: return value.size() == 4; case ValueRepresentation_Sequence: return true; case ValueRepresentation_SignedShort: return value.size() == 2; case ValueRepresentation_ShortText: return value.size() <= 1024; case ValueRepresentation_Time: return value.size() <= 28; case ValueRepresentation_UnlimitedCharacters: return value.size() <= (static_cast<uint64_t>(1) << 32) - 2; case ValueRepresentation_UniqueIdentifier: return value.size() <= 64; case ValueRepresentation_UnsignedLong: return value.size() == 4; case ValueRepresentation_Unknown: return true; case ValueRepresentation_UniversalResource: return value.size() <= (static_cast<uint64_t>(1) << 32) - 2; case ValueRepresentation_UnsignedShort: return value.size() == 2; case ValueRepresentation_UnlimitedText: return value.size() <= (static_cast<uint64_t>(1) << 32) - 2; default: // Assume unsupported tags are OK return true; } } static void RemoveTagPadding(std::string& value, const ValueRepresentation& vr) { /** * Remove padding from character strings, if need be. For the time * being, only the UI VR is supported. * http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_6.2.html **/ switch (vr) { case ValueRepresentation_UniqueIdentifier: { /** * "Values with a VR of UI shall be padded with a single * trailing NULL (00H) character when necessary to achieve even * length." **/ if (!value.empty() && value[value.size() - 1] == '\0') { value.resize(value.size() - 1); } break; } /** * TODO implement other VR **/ default: // No padding is applicable to this VR break; } } static bool ReadNextTag(DicomTag& tag, ValueRepresentation& vr, std::string& value, const char* dicom, size_t size, size_t& position) { /** * http://dicom.nema.org/medical/dicom/current/output/chtml/part05/chapter_7.html#sect_7.1.2 * This function reads a data element with Explicit VR encoded using Little-Endian. **/ if (position + 6 > size) { return false; } tag = DicomTag(ReadUnsignedInteger16(dicom + position), ReadUnsignedInteger16(dicom + position + 2)); vr = StringToValueRepresentation(std::string(dicom + position + 4, 2), true); if (vr == ValueRepresentation_NotSupported) { return false; } if (vr == ValueRepresentation_OtherByte || vr == ValueRepresentation_OtherDouble || vr == ValueRepresentation_OtherFloat || vr == ValueRepresentation_OtherLong || vr == ValueRepresentation_OtherWord || vr == ValueRepresentation_Sequence || vr == ValueRepresentation_UnlimitedCharacters || vr == ValueRepresentation_UniversalResource || vr == ValueRepresentation_UnlimitedText || vr == ValueRepresentation_Unknown) // Note that "UN" should never appear in the Meta Information { if (position + 12 > size) { return false; } uint32_t length = ReadUnsignedInteger32(dicom + position + 8); if (position + 12 + length > size) { return false; } value.assign(dicom + position + 12, length); position += (12 + length); } else { if (position + 8 > size) { return false; } uint16_t length = ReadUnsignedInteger16(dicom + position + 6); if (position + 8 + length > size) { return false; } value.assign(dicom + position + 8, length); position += (8 + length); } if (!ValidateTag(vr, value)) { return false; } RemoveTagPadding(value, vr); return true; } bool DicomMap::IsDicomFile(const void* dicom, size_t size) { /** * http://dicom.nema.org/medical/dicom/current/output/chtml/part10/chapter_7.html * According to Table 7.1-1, besides the "DICM" DICOM prefix, the * file preamble (i.e. dicom[0..127]) should not be taken into * account to determine whether the file is or is not a DICOM file. **/ const uint8_t* p = reinterpret_cast<const uint8_t*>(dicom); return (size >= 132 && p[128] == 'D' && p[129] == 'I' && p[130] == 'C' && p[131] == 'M'); } bool DicomMap::ParseDicomMetaInformation(DicomMap& result, const void* dicom, size_t size) { if (!IsDicomFile(dicom, size)) { return false; } /** * The DICOM File Meta Information must be encoded using the * Explicit VR Little Endian Transfer Syntax * (UID=1.2.840.10008.1.2.1). **/ result.Clear(); // First, we read the "File Meta Information Group Length" tag // (0002,0000) to know where to stop reading the meta header size_t position = 132; DicomTag tag(0x0000, 0x0000); // Dummy initialization ValueRepresentation vr; std::string value; if (!ReadNextTag(tag, vr, value, reinterpret_cast<const char*>(dicom), size, position) || tag.GetGroup() != 0x0002 || tag.GetElement() != 0x0000 || vr != ValueRepresentation_UnsignedLong || value.size() != 4) { return false; } size_t stopPosition = position + ReadUnsignedInteger32(value.c_str()); if (stopPosition > size) { return false; } while (position < stopPosition) { if (ReadNextTag(tag, vr, value, reinterpret_cast<const char*>(dicom), size, position)) { result.SetValue(tag, value, IsBinaryValueRepresentation(vr)); } else { return false; } } return true; } 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 DicomMap::LogMissingTagsForStore() const { std::string s, t; if (HasTag(DICOM_TAG_PATIENT_ID)) { if (t.size() > 0) t += ", "; t += "PatientID=" + ValueAsString(*this, DICOM_TAG_PATIENT_ID); } else { if (s.size() > 0) s += ", "; s += "PatientID"; } if (HasTag(DICOM_TAG_STUDY_INSTANCE_UID)) { if (t.size() > 0) t += ", "; t += "StudyInstanceUID=" + ValueAsString(*this, DICOM_TAG_STUDY_INSTANCE_UID); } else { if (s.size() > 0) s += ", "; s += "StudyInstanceUID"; } if (HasTag(DICOM_TAG_SERIES_INSTANCE_UID)) { if (t.size() > 0) t += ", "; t += "SeriesInstanceUID=" + ValueAsString(*this, DICOM_TAG_SERIES_INSTANCE_UID); } else { if (s.size() > 0) s += ", "; s += "SeriesInstanceUID"; } if (HasTag(DICOM_TAG_SOP_INSTANCE_UID)) { if (t.size() > 0) t += ", "; t += "SOPInstanceUID=" + ValueAsString(*this, 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; } } bool DicomMap::LookupStringValue(std::string& result, const DicomTag& tag, bool allowBinary) const { const DicomValue* value = TestAndGetValue(tag); if (value == NULL) { return false; } else { return value->CopyToString(result, allowBinary); } } bool DicomMap::ParseInteger32(int32_t& result, const DicomTag& tag) const { const DicomValue* value = TestAndGetValue(tag); if (value == NULL) { return false; } else { return value->ParseInteger32(result); } } bool DicomMap::ParseInteger64(int64_t& result, const DicomTag& tag) const { const DicomValue* value = TestAndGetValue(tag); if (value == NULL) { return false; } else { return value->ParseInteger64(result); } } bool DicomMap::ParseUnsignedInteger32(uint32_t& result, const DicomTag& tag) const { const DicomValue* value = TestAndGetValue(tag); if (value == NULL) { return false; } else { return value->ParseUnsignedInteger32(result); } } bool DicomMap::ParseUnsignedInteger64(uint64_t& result, const DicomTag& tag) const { const DicomValue* value = TestAndGetValue(tag); if (value == NULL) { return false; } else { return value->ParseUnsignedInteger64(result); } } bool DicomMap::ParseFloat(float& result, const DicomTag& tag) const { const DicomValue* value = TestAndGetValue(tag); if (value == NULL) { return false; } else { return value->ParseFloat(result); } } bool DicomMap::ParseFirstFloat(float& result, const DicomTag& tag) const { const DicomValue* value = TestAndGetValue(tag); if (value == NULL) { return false; } else { return value->ParseFirstFloat(result); } } bool DicomMap::ParseDouble(double& result, const DicomTag& tag) const { const DicomValue* value = TestAndGetValue(tag); if (value == NULL) { return false; } else { return value->ParseDouble(result); } } void DicomMap::FromDicomAsJson(const Json::Value& dicomAsJson) { if (dicomAsJson.type() != Json::objectValue) { throw OrthancException(ErrorCode_BadFileFormat); } Clear(); Json::Value::Members tags = dicomAsJson.getMemberNames(); for (Json::Value::Members::const_iterator it = tags.begin(); it != tags.end(); ++it) { DicomTag tag(0, 0); if (!DicomTag::ParseHexadecimal(tag, it->c_str())) { throw OrthancException(ErrorCode_CorruptedFile); } const Json::Value& value = dicomAsJson[*it]; if (value.type() != Json::objectValue || !value.isMember("Type") || !value.isMember("Value") || value["Type"].type() != Json::stringValue) { throw OrthancException(ErrorCode_CorruptedFile); } if (value["Type"] == "String") { if (value["Value"].type() != Json::stringValue) { throw OrthancException(ErrorCode_CorruptedFile); } else { SetValue(tag, value["Value"].asString(), false /* not binary */); } } } } void DicomMap::Merge(const DicomMap& other) { for (Content::const_iterator it = other.content_.begin(); it != other.content_.end(); ++it) { assert(it->second != NULL); if (content_.find(it->first) == content_.end()) { content_[it->first] = it->second->Clone(); } } } void DicomMap::MergeMainDicomTags(const DicomMap& other, ResourceType level) { const MainDicomTag* tags = NULL; size_t size = 0; LoadMainDicomTags(tags, size, level); assert(tags != NULL && size > 0); for (size_t i = 0; i < size; i++) { Content::const_iterator found = other.content_.find(tags[i].tag_); if (found != other.content_.end() && content_.find(tags[i].tag_) == content_.end()) { assert(found->second != NULL); content_[tags[i].tag_] = found->second->Clone(); } } } void DicomMap::ExtractMainDicomTags(const DicomMap& other) { Clear(); MergeMainDicomTags(other, ResourceType_Patient); MergeMainDicomTags(other, ResourceType_Study); MergeMainDicomTags(other, ResourceType_Series); MergeMainDicomTags(other, ResourceType_Instance); } bool DicomMap::HasOnlyMainDicomTags() const { // TODO - Speed up possible by making this std::set a global variable std::set<DicomTag> mainDicomTags; GetMainDicomTags(mainDicomTags); for (Content::const_iterator it = content_.begin(); it != content_.end(); ++it) { if (mainDicomTags.find(it->first) == mainDicomTags.end()) { return false; } } return true; } void DicomMap::Serialize(Json::Value& target) const { target = Json::objectValue; for (Content::const_iterator it = content_.begin(); it != content_.end(); ++it) { assert(it->second != NULL); std::string tag = it->first.Format(); Json::Value value; it->second->Serialize(value); target[tag] = value; } } void DicomMap::Unserialize(const Json::Value& source) { Clear(); if (source.type() != Json::objectValue) { throw OrthancException(ErrorCode_BadFileFormat); } Json::Value::Members tags = source.getMemberNames(); for (size_t i = 0; i < tags.size(); i++) { DicomTag tag(0, 0); if (!DicomTag::ParseHexadecimal(tag, tags[i].c_str()) || content_.find(tag) != content_.end()) { throw OrthancException(ErrorCode_BadFileFormat); } std::unique_ptr<DicomValue> value(new DicomValue); value->Unserialize(source[tags[i]]); content_[tag] = value.release(); } } void DicomMap::FromDicomWeb(const Json::Value& source) { static const char* const ALPHABETIC = "Alphabetic"; static const char* const IDEOGRAPHIC = "Ideographic"; static const char* const INLINE_BINARY = "InlineBinary"; static const char* const PHONETIC = "Phonetic"; static const char* const VALUE = "Value"; static const char* const VR = "vr"; Clear(); if (source.type() != Json::objectValue) { throw OrthancException(ErrorCode_BadFileFormat); } Json::Value::Members tags = source.getMemberNames(); for (size_t i = 0; i < tags.size(); i++) { const Json::Value& item = source[tags[i]]; DicomTag tag(0, 0); if (item.type() != Json::objectValue || !item.isMember(VR) || item[VR].type() != Json::stringValue || !DicomTag::ParseHexadecimal(tag, tags[i].c_str())) { throw OrthancException(ErrorCode_BadFileFormat); } ValueRepresentation vr = StringToValueRepresentation(item[VR].asString(), false); if (item.isMember(INLINE_BINARY)) { const Json::Value& value = item[INLINE_BINARY]; if (value.type() == Json::stringValue) { std::string decoded; Toolbox::DecodeBase64(decoded, value.asString()); SetValue(tag, decoded, true /* binary data */); } } else if (!item.isMember(VALUE)) { // Tag is present, but it has a null value SetValue(tag, "", false /* not binary */); } else { const Json::Value& value = item[VALUE]; if (value.type() == Json::arrayValue) { bool supported = true; std::string s; for (Json::Value::ArrayIndex i = 0; i < value.size() && supported; i++) { if (!s.empty()) { s += '\\'; } switch (value[i].type()) { case Json::objectValue: if (vr == ValueRepresentation_PersonName && value[i].type() == Json::objectValue) { if (value[i].isMember(ALPHABETIC) && value[i][ALPHABETIC].type() == Json::stringValue) { s += value[i][ALPHABETIC].asString(); } bool hasIdeographic = false; if (value[i].isMember(IDEOGRAPHIC) && value[i][IDEOGRAPHIC].type() == Json::stringValue) { s += '=' + value[i][IDEOGRAPHIC].asString(); hasIdeographic = true; } if (value[i].isMember(PHONETIC) && value[i][PHONETIC].type() == Json::stringValue) { if (!hasIdeographic) { s += '='; } s += '=' + value[i][PHONETIC].asString(); } } else { // This is the case of sequences supported = false; } break; case Json::stringValue: s += value[i].asString(); break; case Json::intValue: s += boost::lexical_cast<std::string>(value[i].asInt()); break; case Json::uintValue: s += boost::lexical_cast<std::string>(value[i].asUInt()); break; case Json::realValue: s += boost::lexical_cast<std::string>(value[i].asDouble()); break; default: break; } } if (supported) { SetValue(tag, s, false /* not binary */); } } } } } std::string DicomMap::GetStringValue(const DicomTag& tag, const std::string& defaultValue, bool allowBinary) const { std::string s; if (LookupStringValue(s, tag, allowBinary)) { return s; } else { return defaultValue; } } void DicomMap::RemoveBinaryTags() { Content kept; for (Content::iterator it = content_.begin(); it != content_.end(); ++it) { assert(it->second != NULL); if (!it->second->IsBinary() && !it->second->IsNull()) { kept[it->first] = it->second; } else { delete it->second; } } content_ = kept; } void DicomMap::DumpMainDicomTags(Json::Value& target, ResourceType level) const { std::map<DicomTag, std::string> mainTags; // TODO - Create a singleton to hold this map LoadMainDicomTags(mainTags, level); target = Json::objectValue; for (Content::const_iterator it = content_.begin(); it != content_.end(); ++it) { assert(it->second != NULL); if (!it->second->IsBinary() && !it->second->IsNull()) { std::map<DicomTag, std::string>::const_iterator found = mainTags.find(it->first); if (found != mainTags.end()) { target[found->second] = it->second->GetContent(); } } } } void DicomMap::ParseMainDicomTags(const Json::Value& source, ResourceType level) { if (source.type() != Json::objectValue) { throw OrthancException(ErrorCode_BadFileFormat); } std::map<std::string, DicomTag2> mainTags; // TODO - Create a singleton to hold this map LoadMainDicomTags(mainTags, level); Json::Value::Members members = source.getMemberNames(); for (size_t i = 0; i < members.size(); i++) { std::map<std::string, DicomTag2>::const_iterator found = mainTags.find(members[i]); if (found != mainTags.end()) { const Json::Value& value = source[members[i]]; if (value.type() != Json::stringValue) { throw OrthancException(ErrorCode_BadFileFormat); } else { SetValue(found->second, value.asString(), false); } } } } void DicomMap::Print(FILE* fp) const { DicomArray a(*this); a.Print(fp); } }