Mercurial > hg > orthanc
diff OrthancServer/FromDcmtkBridge.cpp @ 790:331eaf9d9d69
ParsedDicomFile
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Mon, 05 May 2014 18:55:10 +0200 |
parents | 55dae8c5a6ab |
children | 777b6b694da6 |
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--- a/OrthancServer/FromDcmtkBridge.cpp Mon May 05 18:43:34 2014 +0200 +++ b/OrthancServer/FromDcmtkBridge.cpp Mon May 05 18:55:10 2014 +0200 @@ -131,51 +131,8 @@ #include <dcmtk/dcmdata/dcostrmb.h> -static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; - - - namespace Orthanc { - void ParsedDicomFile::Setup(const char* buffer, size_t size) - { - DcmInputBufferStream is; - if (size > 0) - { - is.setBuffer(buffer, size); - } - is.setEos(); - - file_.reset(new DcmFileFormat); - file_->transferInit(); - if (!file_->read(is).good()) - { - throw OrthancException(ErrorCode_BadFileFormat); - } - file_->loadAllDataIntoMemory(); - file_->transferEnd(); - } - - - static void SendPathValueForDictionary(RestApiOutput& output, - DcmItem& dicom) - { - Json::Value v = Json::arrayValue; - - for (unsigned long i = 0; i < dicom.card(); i++) - { - DcmElement* element = dicom.getElement(i); - if (element) - { - char buf[16]; - sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); - v.append(buf); - } - } - - output.AnswerJson(v); - } - static inline uint16_t GetCharValue(char c) { if (c >= '0' && c <= '9') @@ -196,698 +153,6 @@ GetCharValue(c[3])); } - static void ParseTagAndGroup(DcmTagKey& key, - const std::string& tag) - { - DicomTag t = FromDcmtkBridge::ParseTag(tag); - key = DcmTagKey(t.GetGroup(), t.GetElement()); - } - - - static void SendSequence(RestApiOutput& output, - DcmSequenceOfItems& sequence) - { - // This element is a sequence - Json::Value v = Json::arrayValue; - - for (unsigned long i = 0; i < sequence.card(); i++) - { - v.append(boost::lexical_cast<std::string>(i)); - } - - output.AnswerJson(v); - } - - - static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, - E_TransferSyntax transferSyntax) - { - DcmPixelSequence* pixelSequence = NULL; - if (pixelData.getEncapsulatedRepresentation - (transferSyntax, NULL, pixelSequence).good() && pixelSequence) - { - return pixelSequence->card(); - } - else - { - return 1; - } - } - - - static void AnswerDicomField(RestApiOutput& output, - DcmElement& element, - E_TransferSyntax transferSyntax) - { - // This element is nor a sequence, neither a pixel-data - std::string buffer; - buffer.resize(65536); - Uint32 length = element.getLength(transferSyntax); - Uint32 offset = 0; - - output.GetLowLevelOutput().SendOkHeader(CONTENT_TYPE_OCTET_STREAM, true, length, NULL); - - while (offset < length) - { - Uint32 nbytes; - if (length - offset < buffer.size()) - { - nbytes = length - offset; - } - else - { - nbytes = buffer.size(); - } - - OFCondition cond = element.getPartialValue(&buffer[0], offset, nbytes); - - if (cond.good()) - { - output.GetLowLevelOutput().Send(&buffer[0], nbytes); - offset += nbytes; - } - else - { - LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); - return; - } - } - - output.MarkLowLevelOutputDone(); - } - - - static bool AnswerPixelData(RestApiOutput& output, - DcmItem& dicom, - E_TransferSyntax transferSyntax, - const std::string* blockUri) - { - DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), - DICOM_TAG_PIXEL_DATA.GetElement()); - - DcmElement *element = NULL; - if (!dicom.findAndGetElement(k, element).good() || - element == NULL) - { - return false; - } - - try - { - DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); - if (blockUri == NULL) - { - // The user asks how many blocks are presents in this pixel data - unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); - - Json::Value result(Json::arrayValue); - for (unsigned int i = 0; i < blocks; i++) - { - result.append(boost::lexical_cast<std::string>(i)); - } - - output.AnswerJson(result); - return true; - } - - - unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); - - if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) - { - DcmPixelSequence* pixelSequence = NULL; - if (pixelData.getEncapsulatedRepresentation - (transferSyntax, NULL, pixelSequence).good() && pixelSequence) - { - // This is the case for JPEG transfer syntaxes - if (block < pixelSequence->card()) - { - DcmPixelItem* pixelItem = NULL; - if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) - { - if (pixelItem->getLength() == 0) - { - output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); - return true; - } - - Uint8* buffer = NULL; - if (pixelItem->getUint8Array(buffer).good() && buffer) - { - output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); - return true; - } - } - } - } - else - { - // This is the case for raw, uncompressed image buffers - assert(*blockUri == "0"); - AnswerDicomField(output, *element, transferSyntax); - } - } - } - catch (boost::bad_lexical_cast&) - { - // The URI entered by the user is not a number - } - catch (std::bad_cast&) - { - // This should never happen - } - - return false; - } - - - - static void SendPathValueForLeaf(RestApiOutput& output, - const std::string& tag, - DcmItem& dicom, - E_TransferSyntax transferSyntax) - { - DcmTagKey k; - ParseTagAndGroup(k, tag); - - DcmSequenceOfItems* sequence = NULL; - if (dicom.findAndGetSequence(k, sequence).good() && - sequence != NULL && - sequence->getVR() == EVR_SQ) - { - SendSequence(output, *sequence); - return; - } - - DcmElement* element = NULL; - if (dicom.findAndGetElement(k, element).good() && - element != NULL && - //element->getVR() != EVR_UNKNOWN && // This would forbid private tags - element->getVR() != EVR_SQ) - { - AnswerDicomField(output, *element, transferSyntax); - } - } - - void ParsedDicomFile::SendPathValue(RestApiOutput& output, - const UriComponents& uri) - { - DcmItem* dicom = file_->getDataset(); - E_TransferSyntax transferSyntax = file_->getDataset()->getOriginalXfer(); - - // Special case: Accessing the pixel data - if (uri.size() == 1 || - uri.size() == 2) - { - DcmTagKey tag; - ParseTagAndGroup(tag, uri[0]); - - if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && - tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) - { - AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); - return; - } - } - - // Go down in the tag hierarchy according to the URI - for (size_t pos = 0; pos < uri.size() / 2; pos++) - { - size_t index; - try - { - index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); - } - catch (boost::bad_lexical_cast&) - { - return; - } - - DcmTagKey k; - DcmItem *child = NULL; - ParseTagAndGroup(k, uri[2 * pos]); - if (!dicom->findAndGetSequenceItem(k, child, index).good() || - child == NULL) - { - return; - } - - dicom = child; - } - - // We have reached the end of the URI - if (uri.size() % 2 == 0) - { - SendPathValueForDictionary(output, *dicom); - } - else - { - SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); - } - } - - - - - - static DcmElement* CreateElementForTag(const DicomTag& tag) - { - DcmTag key(tag.GetGroup(), tag.GetElement()); - - switch (key.getEVR()) - { - // http://support.dcmtk.org/docs/dcvr_8h-source.html - - /** - * TODO. - **/ - - case EVR_OB: // other byte - case EVR_OF: // other float - case EVR_OW: // other word - case EVR_AT: // attribute tag - throw OrthancException(ErrorCode_NotImplemented); - - case EVR_UN: // unknown value representation - throw OrthancException(ErrorCode_ParameterOutOfRange); - - - /** - * String types. - * http://support.dcmtk.org/docs/classDcmByteString.html - **/ - - case EVR_AS: // age string - return new DcmAgeString(key); - - case EVR_AE: // application entity title - return new DcmApplicationEntity(key); - - case EVR_CS: // code string - return new DcmCodeString(key); - - case EVR_DA: // date string - return new DcmDate(key); - - case EVR_DT: // date time string - return new DcmDateTime(key); - - case EVR_DS: // decimal string - return new DcmDecimalString(key); - - case EVR_IS: // integer string - return new DcmIntegerString(key); - - case EVR_TM: // time string - return new DcmTime(key); - - case EVR_UI: // unique identifier - return new DcmUniqueIdentifier(key); - - case EVR_ST: // short text - return new DcmShortText(key); - - case EVR_LO: // long string - return new DcmLongString(key); - - case EVR_LT: // long text - return new DcmLongText(key); - - case EVR_UT: // unlimited text - return new DcmUnlimitedText(key); - - case EVR_SH: // short string - return new DcmShortString(key); - - case EVR_PN: // person name - return new DcmPersonName(key); - - - /** - * Numerical types - **/ - - case EVR_SL: // signed long - return new DcmSignedLong(key); - - case EVR_SS: // signed short - return new DcmSignedShort(key); - - case EVR_UL: // unsigned long - return new DcmUnsignedLong(key); - - case EVR_US: // unsigned short - return new DcmUnsignedShort(key); - - case EVR_FL: // float single-precision - return new DcmFloatingPointSingle(key); - - case EVR_FD: // float double-precision - return new DcmFloatingPointDouble(key); - - - /** - * Sequence types, should never occur at this point. - **/ - - case EVR_SQ: // sequence of items - throw OrthancException(ErrorCode_ParameterOutOfRange); - - - /** - * Internal to DCMTK. - **/ - - case EVR_ox: // OB or OW depending on context - case EVR_xs: // SS or US depending on context - case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) - case EVR_na: // na="not applicable", for data which has no VR - case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor - case EVR_item: // used internally for items - case EVR_metainfo: // used internally for meta info datasets - case EVR_dataset: // used internally for datasets - case EVR_fileFormat: // used internally for DICOM files - case EVR_dicomDir: // used internally for DICOMDIR objects - case EVR_dirRecord: // used internally for DICOMDIR records - case EVR_pixelSQ: // used internally for pixel sequences in a compressed image - case EVR_pixelItem: // used internally for pixel items in a compressed image - case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) - case EVR_PixelData: // used internally for uncompressed pixeld data - case EVR_OverlayData: // used internally for overlay data - case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR - default: - break; - } - - throw OrthancException(ErrorCode_InternalError); - } - - - - static void FillElementWithString(DcmElement& element, - const DicomTag& tag, - const std::string& value) - { - DcmTag key(tag.GetGroup(), tag.GetElement()); - bool ok = false; - - try - { - switch (key.getEVR()) - { - // http://support.dcmtk.org/docs/dcvr_8h-source.html - - /** - * TODO. - **/ - - case EVR_OB: // other byte - case EVR_OF: // other float - case EVR_OW: // other word - case EVR_AT: // attribute tag - throw OrthancException(ErrorCode_NotImplemented); - - case EVR_UN: // unknown value representation - throw OrthancException(ErrorCode_ParameterOutOfRange); - - - /** - * String types. - **/ - - case EVR_DS: // decimal string - case EVR_IS: // integer string - case EVR_AS: // age string - case EVR_DA: // date string - case EVR_DT: // date time string - case EVR_TM: // time string - case EVR_AE: // application entity title - case EVR_CS: // code string - case EVR_SH: // short string - case EVR_LO: // long string - case EVR_ST: // short text - case EVR_LT: // long text - case EVR_UT: // unlimited text - case EVR_PN: // person name - case EVR_UI: // unique identifier - { - ok = element.putString(value.c_str()).good(); - break; - } - - - /** - * Numerical types - **/ - - case EVR_SL: // signed long - { - ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good(); - break; - } - - case EVR_SS: // signed short - { - ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good(); - break; - } - - case EVR_UL: // unsigned long - { - ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good(); - break; - } - - case EVR_US: // unsigned short - { - ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good(); - break; - } - - case EVR_FL: // float single-precision - { - ok = element.putFloat32(boost::lexical_cast<float>(value)).good(); - break; - } - - case EVR_FD: // float double-precision - { - ok = element.putFloat64(boost::lexical_cast<double>(value)).good(); - break; - } - - - /** - * Sequence types, should never occur at this point. - **/ - - case EVR_SQ: // sequence of items - { - ok = false; - break; - } - - - /** - * Internal to DCMTK. - **/ - - case EVR_ox: // OB or OW depending on context - case EVR_xs: // SS or US depending on context - case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) - case EVR_na: // na="not applicable", for data which has no VR - case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor - case EVR_item: // used internally for items - case EVR_metainfo: // used internally for meta info datasets - case EVR_dataset: // used internally for datasets - case EVR_fileFormat: // used internally for DICOM files - case EVR_dicomDir: // used internally for DICOMDIR objects - case EVR_dirRecord: // used internally for DICOMDIR records - case EVR_pixelSQ: // used internally for pixel sequences in a compressed image - case EVR_pixelItem: // used internally for pixel items in a compressed image - case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) - case EVR_PixelData: // used internally for uncompressed pixeld data - case EVR_OverlayData: // used internally for overlay data - case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR - default: - break; - } - } - catch (boost::bad_lexical_cast&) - { - ok = false; - } - - if (!ok) - { - throw OrthancException(ErrorCode_InternalError); - } - } - - - void ParsedDicomFile::Remove(const DicomTag& tag) - { - DcmTagKey key(tag.GetGroup(), tag.GetElement()); - DcmElement* element = file_->getDataset()->remove(key); - if (element != NULL) - { - delete element; - } - } - - - - void ParsedDicomFile::RemovePrivateTags() - { - typedef std::list<DcmElement*> Tags; - - Tags privateTags; - - DcmDataset& dataset = *file_->getDataset(); - for (unsigned long i = 0; i < dataset.card(); i++) - { - DcmElement* element = dataset.getElement(i); - DcmTag tag(element->getTag()); - if (!strcmp("PrivateCreator", tag.getTagName()) || // TODO - This may change with future versions of DCMTK - tag.getPrivateCreator() != NULL) - { - privateTags.push_back(element); - } - } - - for (Tags::iterator it = privateTags.begin(); - it != privateTags.end(); ++it) - { - DcmElement* tmp = dataset.remove(*it); - if (tmp != NULL) - { - delete tmp; - } - } - } - - - - void ParsedDicomFile::Insert(const DicomTag& tag, - const std::string& value) - { - std::auto_ptr<DcmElement> element(CreateElementForTag(tag)); - FillElementWithString(*element, tag, value); - - if (!file_->getDataset()->insert(element.release(), false, false).good()) - { - // This field already exists - throw OrthancException(ErrorCode_InternalError); - } - } - - - void ParsedDicomFile::Replace(const DicomTag& tag, - const std::string& value, - DicomReplaceMode mode) - { - DcmTagKey key(tag.GetGroup(), tag.GetElement()); - DcmElement* element = NULL; - - if (!file_->getDataset()->findAndGetElement(key, element).good() || - element == NULL) - { - // This field does not exist, act wrt. the specified "mode" - switch (mode) - { - case DicomReplaceMode_InsertIfAbsent: - Insert(tag, value); - break; - - case DicomReplaceMode_ThrowIfAbsent: - throw OrthancException(ErrorCode_InexistentItem); - - case DicomReplaceMode_IgnoreIfAbsent: - return; - } - } - else - { - FillElementWithString(*element, tag, value); - } - - - /** - * dcmodify will automatically correct 'Media Storage SOP Class - * UID' and 'Media Storage SOP Instance UID' in the metaheader, if - * you make changes to the related tags in the dataset ('SOP Class - * UID' and 'SOP Instance UID') via insert or modify mode - * options. You can disable this behaviour by using the -nmu - * option. - **/ - - if (tag == DICOM_TAG_SOP_CLASS_UID) - { - Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); - } - - if (tag == DICOM_TAG_SOP_INSTANCE_UID) - { - Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); - } - } - - - void ParsedDicomFile::Answer(RestApiOutput& output) - { - std::string serialized; - if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, file_->getDataset())) - { - output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); - } - } - - - - bool ParsedDicomFile::GetTagValue(std::string& value, - const DicomTag& tag) - { - DcmTagKey k(tag.GetGroup(), tag.GetElement()); - DcmDataset& dataset = *file_->getDataset(); - DcmElement* element = NULL; - if (!dataset.findAndGetElement(k, element).good() || - element == NULL) - { - return false; - } - - std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element)); - - if (v.get() == NULL) - { - value = ""; - } - else - { - value = v->AsString(); - } - - return true; - } - - - - DicomInstanceHasher ParsedDicomFile::GetHasher() - { - std::string patientId, studyUid, seriesUid, instanceUid; - - if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || - !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || - !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || - !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) - { - throw OrthancException(ErrorCode_BadFileFormat); - } - - return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); - } - - void FromDcmtkBridge::Convert(DicomMap& target, DcmDataset& dataset) { target.Clear(); @@ -1737,24 +1002,4 @@ return false; } } - - - void ParsedDicomFile::SaveToFile(const std::string& path) - { - // TODO Avoid using a temporary memory buffer, write directly on disk - std::string content; - SaveToMemoryBuffer(content); - Toolbox::WriteFile(content, path); - } - - - ParsedDicomFile::ParsedDicomFile() - { - file_.reset(new DcmFileFormat); - Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); - Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); - Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); - Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); - } - }