orthanc: OrthancFramework/Sources/DicomFormat/DicomMap.cpp comparison

comparison OrthancFramework/Sources/DicomFormat/DicomMap.cpp @ 4044:d25f4c0fa160 framework

splitting code into OrthancFramework and OrthancServer

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Wed, 10 Jun 2020 20:30:34 +0200
parents	Core/DicomFormat/DicomMap.cpp@e7003b2203a7
children	bf7b9edf6b81

comparison

equal deleted inserted replaced

-:6c6239aec462
+:d25f4c0fa160
+/**
+* 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);
+}
+}

Mercurial > hg > orthanc

comparison OrthancFramework/Sources/DicomFormat/DicomMap.cpp @ 4044:d25f4c0fa160 framework