Mercurial > hg > orthanc-wsi
diff Resources/Orthanc/Core/DicomFormat/DicomMap.cpp @ 59:7a3853d51c45
Move "Framework/Orthanc/" as "Resources/Orthanc/"
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 25 Nov 2016 16:34:34 +0100 |
parents | Framework/Orthanc/Core/DicomFormat/DicomMap.cpp@dc730d11b101 |
children | ff0ef01c332c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Resources/Orthanc/Core/DicomFormat/DicomMap.cpp Fri Nov 25 16:34:34 2016 +0100 @@ -0,0 +1,783 @@ +/** + * 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 "../PrecompiledHeaders.h" +#include "DicomMap.h" + +#include <stdio.h> +#include <memory> +#include "../Endianness.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; + } +}