Mercurial > hg > orthanc
view Core/DicomFormat/DicomMap.cpp @ 2643:56bee263645f jobs
fix for msvc
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 29 May 2018 09:12:33 +0200 |
parents | 878b59270859 |
children | d88970f1ffbf |
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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) 2017-2018 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 "../Endianness.h" #include "../Logging.h" #include "../OrthancException.h" namespace Orthanc { static DicomTag patientTags[] = { //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 }; static DicomTag studyTags[] = { //DicomTag(0x0010, 0x1020), // PatientSize //DicomTag(0x0010, 0x1030) // PatientWeight DICOM_TAG_STUDY_DATE, DicomTag(0x0008, 0x0030), // StudyTime DicomTag(0x0020, 0x0010), // StudyID DICOM_TAG_STUDY_DESCRIPTION, DICOM_TAG_ACCESSION_NUMBER, DICOM_TAG_STUDY_INSTANCE_UID, DICOM_TAG_REQUESTED_PROCEDURE_DESCRIPTION, // New in db v6 DICOM_TAG_INSTITUTION_NAME, // New in db v6 DICOM_TAG_REQUESTING_PHYSICIAN, // New in db v6 DICOM_TAG_REFERRING_PHYSICIAN_NAME // New in db v6 }; static DicomTag seriesTags[] = { //DicomTag(0x0010, 0x1080), // MilitaryRank DicomTag(0x0008, 0x0021), // SeriesDate DicomTag(0x0008, 0x0031), // SeriesTime DICOM_TAG_MODALITY, DicomTag(0x0008, 0x0070), // Manufacturer DicomTag(0x0008, 0x1010), // StationName DICOM_TAG_SERIES_DESCRIPTION, DicomTag(0x0018, 0x0015), // BodyPartExamined DicomTag(0x0018, 0x0024), // SequenceName DicomTag(0x0018, 0x1030), // ProtocolName DicomTag(0x0020, 0x0011), // SeriesNumber DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES, DICOM_TAG_IMAGES_IN_ACQUISITION, DICOM_TAG_NUMBER_OF_TEMPORAL_POSITIONS, DICOM_TAG_NUMBER_OF_SLICES, DICOM_TAG_NUMBER_OF_TIME_SLICES, DICOM_TAG_SERIES_INSTANCE_UID, DICOM_TAG_IMAGE_ORIENTATION_PATIENT, // New in db v6 DICOM_TAG_SERIES_TYPE, // New in db v6 DICOM_TAG_OPERATOR_NAME, // New in db v6 DICOM_TAG_PERFORMED_PROCEDURE_STEP_DESCRIPTION, // New in db v6 DICOM_TAG_ACQUISITION_DEVICE_PROCESSING_DESCRIPTION, // New in db v6 DICOM_TAG_CONTRAST_BOLUS_AGENT // New in db v6 }; static DicomTag instanceTags[] = { DicomTag(0x0008, 0x0012), // InstanceCreationDate DicomTag(0x0008, 0x0013), // InstanceCreationTime DicomTag(0x0020, 0x0012), // AcquisitionNumber DICOM_TAG_IMAGE_INDEX, DICOM_TAG_INSTANCE_NUMBER, DICOM_TAG_NUMBER_OF_FRAMES, DICOM_TAG_TEMPORAL_POSITION_IDENTIFIER, DICOM_TAG_SOP_INSTANCE_UID, DICOM_TAG_IMAGE_POSITION_PATIENT, // New in db v6 DICOM_TAG_IMAGE_COMMENTS // New in db v6 }; void DicomMap::LoadMainDicomTags(const DicomTag*& tags, size_t& size, ResourceType level) { switch (level) { case ResourceType_Patient: tags = patientTags; size = sizeof(patientTags) / sizeof(DicomTag); break; case ResourceType_Study: tags = studyTags; size = sizeof(studyTags) / sizeof(DicomTag); break; case ResourceType_Series: tags = seriesTags; size = sizeof(seriesTags) / sizeof(DicomTag); break; case ResourceType_Instance: tags = instanceTags; size = sizeof(instanceTags) / sizeof(DicomTag); break; default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } void DicomMap::SetValue(uint16_t group, uint16_t element, DicomValue* value) { DicomTag tag(group, element); Map::iterator it = map_.find(tag); if (it != map_.end()) { delete it->second; it->second = value; } else { map_.insert(std::make_pair(tag, value)); } } void DicomMap::SetValue(DicomTag tag, DicomValue* value) { SetValue(tag.GetGroup(), tag.GetElement(), value); } void DicomMap::Clear() { for (Map::iterator it = map_.begin(); it != map_.end(); ++it) { delete it->second; } map_.clear(); } void DicomMap::ExtractTags(DicomMap& result, const DicomTag* tags, size_t count) const { result.Clear(); for (unsigned int i = 0; i < count; i++) { Map::const_iterator it = map_.find(tags[i]); if (it != map_.end()) { result.SetValue(it->first, it->second->Clone()); } } } void DicomMap::ExtractPatientInformation(DicomMap& result) const { ExtractTags(result, patientTags, sizeof(patientTags) / sizeof(DicomTag)); } void DicomMap::ExtractStudyInformation(DicomMap& result) const { ExtractTags(result, studyTags, sizeof(studyTags) / sizeof(DicomTag)); } void DicomMap::ExtractSeriesInformation(DicomMap& result) const { ExtractTags(result, seriesTags, sizeof(seriesTags) / sizeof(DicomTag)); } void DicomMap::ExtractInstanceInformation(DicomMap& result) const { ExtractTags(result, instanceTags, sizeof(instanceTags) / sizeof(DicomTag)); } DicomMap* DicomMap::Clone() const { std::auto_ptr<DicomMap> result(new DicomMap); for (Map::const_iterator it = map_.begin(); it != map_.end(); ++it) { result->map_.insert(std::make_pair(it->first, it->second->Clone())); } return result.release(); } void DicomMap::Assign(const DicomMap& other) { Clear(); for (Map::const_iterator it = other.map_.begin(); it != other.map_.end(); ++it) { map_.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 { Map::const_iterator it = map_.find(tag); if (it == map_.end()) { return NULL; } else { return it->second; } } void DicomMap::Remove(const DicomTag& tag) { Map::iterator it = map_.find(tag); if (it != map_.end()) { delete it->second; map_.erase(it); } } static void SetupFindTemplate(DicomMap& result, const DicomTag* tags, size_t count) { result.Clear(); for (size_t i = 0; i < count; i++) { result.SetValue(tags[i], "", false); } } void DicomMap::SetupFindPatientTemplate(DicomMap& result) { SetupFindTemplate(result, patientTags, sizeof(patientTags) / sizeof(DicomTag)); } void DicomMap::SetupFindStudyTemplate(DicomMap& result) { SetupFindTemplate(result, studyTags, sizeof(studyTags) / sizeof(DicomTag)); 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, seriesTags, sizeof(seriesTags) / sizeof(DicomTag)); 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, instanceTags, sizeof(instanceTags) / sizeof(DicomTag)); 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) { DicomTag *tags = NULL; size_t size; switch (level) { case ResourceType_Patient: tags = patientTags; size = sizeof(patientTags) / sizeof(DicomTag); break; case ResourceType_Study: tags = studyTags; size = sizeof(studyTags) / sizeof(DicomTag); break; case ResourceType_Series: tags = seriesTags; size = sizeof(seriesTags) / sizeof(DicomTag); break; case ResourceType_Instance: tags = instanceTags; size = sizeof(instanceTags) / sizeof(DicomTag); break; default: throw OrthancException(ErrorCode_ParameterOutOfRange); } for (size_t i = 0; i < size; i++) { if (tags[i] == 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) { DicomTag *tags = NULL; size_t size; switch (level) { case ResourceType_Patient: tags = patientTags; size = sizeof(patientTags) / sizeof(DicomTag); break; case ResourceType_Study: tags = studyTags; size = sizeof(studyTags) / sizeof(DicomTag); break; case ResourceType_Series: tags = seriesTags; size = sizeof(seriesTags) / sizeof(DicomTag); break; case ResourceType_Instance: tags = instanceTags; size = sizeof(instanceTags) / sizeof(DicomTag); break; default: throw OrthancException(ErrorCode_ParameterOutOfRange); } for (size_t i = 0; i < size; i++) { result.insert(tags[i]); } } 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 (Map::const_iterator it = map_.begin(); it != map_.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::ParseDicomMetaInformation(DicomMap& result, const char* 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. **/ if (size < 132 || dicom[128] != 'D' || dicom[129] != 'I' || dicom[130] != 'C' || dicom[131] != 'M') { 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, 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, 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::CopyToString(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::ParseDouble(double& result, const DicomTag& tag) const { const DicomValue* value = TestAndGetValue(tag); if (value == NULL) { return false; } else { return value->ParseDouble(result); } } }