Mercurial > hg > orthanc
diff OrthancServer/ParsedDicomFile.cpp @ 948:e57e08ed510f dicom-rt
integration mainline -> dicom-rt
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Wed, 25 Jun 2014 13:57:05 +0200 |
parents | 87791ebc1f50 |
children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/ParsedDicomFile.cpp Wed Jun 25 13:57:05 2014 +0200 @@ -0,0 +1,1332 @@ +/** + * Orthanc - A Lightweight, RESTful DICOM Store + * Copyright (C) 2012-2014 Medical Physics Department, CHU 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/>. + **/ + + + +/*========================================================================= + + This file is based on portions of the following project: + + Program: GDCM (Grassroots DICOM). A DICOM library + Module: http://gdcm.sourceforge.net/Copyright.html + +Copyright (c) 2006-2011 Mathieu Malaterre +Copyright (c) 1993-2005 CREATIS +(CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image) +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + + * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any + contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to + endorse or promote products derived from this software without specific + prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +=========================================================================*/ + + +#include "PrecompiledHeadersServer.h" + +#ifndef NOMINMAX +#define NOMINMAX +#endif + +#include "ParsedDicomFile.h" + +#include "FromDcmtkBridge.h" +#include "ToDcmtkBridge.h" +#include "Internals/DicomImageDecoder.h" +#include "../Core/Toolbox.h" +#include "../Core/OrthancException.h" +#include "../Core/ImageFormats/ImageBuffer.h" +#include "../Core/ImageFormats/PngWriter.h" +#include "../Core/Uuid.h" +#include "../Core/DicomFormat/DicomString.h" +#include "../Core/DicomFormat/DicomNullValue.h" +#include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" +#include "../Core/ImageFormats/PngReader.h" + +#include <list> +#include <limits> + +#include <boost/lexical_cast.hpp> + +#include <dcmtk/dcmdata/dcchrstr.h> +#include <dcmtk/dcmdata/dcdicent.h> +#include <dcmtk/dcmdata/dcdict.h> +#include <dcmtk/dcmdata/dcfilefo.h> +#include <dcmtk/dcmdata/dcistrmb.h> +#include <dcmtk/dcmdata/dcuid.h> +#include <dcmtk/dcmdata/dcmetinf.h> + +#include <dcmtk/dcmdata/dcvrae.h> +#include <dcmtk/dcmdata/dcvras.h> +#include <dcmtk/dcmdata/dcvrcs.h> +#include <dcmtk/dcmdata/dcvrda.h> +#include <dcmtk/dcmdata/dcvrds.h> +#include <dcmtk/dcmdata/dcvrdt.h> +#include <dcmtk/dcmdata/dcvrfd.h> +#include <dcmtk/dcmdata/dcvrfl.h> +#include <dcmtk/dcmdata/dcvris.h> +#include <dcmtk/dcmdata/dcvrlo.h> +#include <dcmtk/dcmdata/dcvrlt.h> +#include <dcmtk/dcmdata/dcvrpn.h> +#include <dcmtk/dcmdata/dcvrsh.h> +#include <dcmtk/dcmdata/dcvrsl.h> +#include <dcmtk/dcmdata/dcvrss.h> +#include <dcmtk/dcmdata/dcvrst.h> +#include <dcmtk/dcmdata/dcvrtm.h> +#include <dcmtk/dcmdata/dcvrui.h> +#include <dcmtk/dcmdata/dcvrul.h> +#include <dcmtk/dcmdata/dcvrus.h> +#include <dcmtk/dcmdata/dcvrut.h> +#include <dcmtk/dcmdata/dcpixel.h> +#include <dcmtk/dcmdata/dcpixseq.h> +#include <dcmtk/dcmdata/dcpxitem.h> + + +#include <boost/math/special_functions/round.hpp> +#include <glog/logging.h> +#include <dcmtk/dcmdata/dcostrmb.h> + + +static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; + + + +namespace Orthanc +{ + struct ParsedDicomFile::PImpl + { + std::auto_ptr<DcmFileFormat> file_; + }; + + + // This method can only be called from the constructors! + void ParsedDicomFile::Setup(const char* buffer, size_t size) + { + DcmInputBufferStream is; + if (size > 0) + { + is.setBuffer(buffer, size); + } + is.setEos(); + + pimpl_->file_.reset(new DcmFileFormat); + pimpl_->file_->transferInit(); + if (!pimpl_->file_->read(is).good()) + { + delete pimpl_; // Avoid a memory leak due to exception + // throwing, as we are in the constructor + + throw OrthancException(ErrorCode_BadFileFormat); + } + pimpl_->file_->loadAllDataIntoMemory(); + pimpl_->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') + return c - '0'; + else if (c >= 'a' && c <= 'f') + return c - 'a' + 10; + else if (c >= 'A' && c <= 'F') + return c - 'A' + 10; + else + return 0; + } + + static inline uint16_t GetTagValue(const char* c) + { + return ((GetCharValue(c[0]) << 12) + + (GetCharValue(c[1]) << 8) + + (GetCharValue(c[2]) << 4) + + 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 = pimpl_->file_->getDataset(); + E_TransferSyntax transferSyntax = pimpl_->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 = pimpl_->file_->getDataset()->remove(key); + if (element != NULL) + { + delete element; + } + } + + + + void ParsedDicomFile::RemovePrivateTags() + { + typedef std::list<DcmElement*> Tags; + + Tags privateTags; + + DcmDataset& dataset = *pimpl_->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 (!pimpl_->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 (!pimpl_->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, pimpl_->file_->getDataset())) + { + output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); + } + } + + + + + static bool GetTagValueInternal(std::string& value, + DcmItem& item, + const DicomTag& tag) + { + DcmTagKey k(tag.GetGroup(), tag.GetElement()); + DcmElement* element = NULL; + if (!item.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; + } + + + bool ParsedDicomFile::GetTagValue(std::string& value, + const DicomTag& tag) + { + DcmDataset& dataset = *pimpl_->file_->getDataset(); + return GetTagValueInternal(value, dataset, tag); + } + + + + 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); + } + + + static void StoreElement(Json::Value& target, + DcmElement& element, + unsigned int maxStringLength); + + static void StoreItem(Json::Value& target, + DcmItem& item, + unsigned int maxStringLength) + { + target = Json::Value(Json::objectValue); + + for (unsigned long i = 0; i < item.card(); i++) + { + DcmElement* element = item.getElement(i); + StoreElement(target, *element, maxStringLength); + } + } + + + static void StoreElement(Json::Value& target, + DcmElement& element, + unsigned int maxStringLength) + { + assert(target.type() == Json::objectValue); + + DicomTag tag(FromDcmtkBridge::GetTag(element)); + const std::string formattedTag = tag.Format(); + +#if 0 + const std::string tagName = FromDcmtkBridge::GetName(tag); +#else + // This version of the code gives access to the name of the private tags + DcmTag tagbis(element.getTag()); + const std::string tagName(tagbis.getTagName()); +#endif + + if (element.isLeaf()) + { + Json::Value value(Json::objectValue); + value["Name"] = tagName; + + if (tagbis.getPrivateCreator() != NULL) + { + value["PrivateCreator"] = tagbis.getPrivateCreator(); + } + + std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); + if (v->IsNull()) + { + value["Type"] = "Null"; + value["Value"] = Json::nullValue; + } + else + { + std::string s = v->AsString(); + if (maxStringLength == 0 || + s.size() <= maxStringLength) + { + value["Type"] = "String"; + value["Value"] = s; + } + else + { + value["Type"] = "TooLong"; + value["Value"] = Json::nullValue; + } + } + + target[formattedTag] = value; + } + else + { + Json::Value children(Json::arrayValue); + + // "All subclasses of DcmElement except for DcmSequenceOfItems + // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset + // etc. are not." The following cast is thus OK. + DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); + + for (unsigned long i = 0; i < sequence.card(); i++) + { + DcmItem* child = sequence.getItem(i); + Json::Value& v = children.append(Json::objectValue); + StoreItem(v, *child, maxStringLength); + } + + target[formattedTag]["Name"] = tagName; + target[formattedTag]["Type"] = "Sequence"; + target[formattedTag]["Value"] = children; + } + } + + + template <typename T> + static void ExtractPngImageTruncate(std::string& result, + DicomIntegerPixelAccessor& accessor, + PixelFormat format) + { + assert(accessor.GetInformation().GetChannelCount() == 1); + + PngWriter w; + + std::vector<T> image(accessor.GetInformation().GetWidth() * accessor.GetInformation().GetHeight(), 0); + T* pixel = &image[0]; + for (unsigned int y = 0; y < accessor.GetInformation().GetHeight(); y++) + { + for (unsigned int x = 0; x < accessor.GetInformation().GetWidth(); x++, pixel++) + { + int32_t v = accessor.GetValue(x, y); + if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) + *pixel = std::numeric_limits<T>::min(); + else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) + *pixel = std::numeric_limits<T>::max(); + else + *pixel = static_cast<T>(v); + } + } + + w.WriteToMemory(result, accessor.GetInformation().GetWidth(), accessor.GetInformation().GetHeight(), + accessor.GetInformation().GetWidth() * sizeof(T), format, &image[0]); + } + + + void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) + { + FromDcmtkBridge::SaveToMemoryBuffer(buffer, pimpl_->file_->getDataset()); + } + + + 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() : pimpl_(new PImpl) + { + pimpl_->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)); + } + + + ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) + { + Setup(content, size); + } + + ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) + { + if (content.size() == 0) + { + Setup(NULL, 0); + } + else + { + Setup(&content[0], content.size()); + } + } + + + ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : + pimpl_(new PImpl) + { + pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); + } + + + ParsedDicomFile::~ParsedDicomFile() + { + delete pimpl_; + } + + + void* ParsedDicomFile::GetDcmtkObject() + { + return pimpl_->file_.get(); + } + + + ParsedDicomFile* ParsedDicomFile::Clone() + { + return new ParsedDicomFile(*this); + } + + + void ParsedDicomFile::EmbedImage(const std::string& dataUriScheme) + { + std::string mime, content; + Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); + + std::string decoded; + Toolbox::DecodeBase64(decoded, content); + + if (mime == "image/png") + { + PngReader reader; + reader.ReadFromMemory(decoded); + EmbedImage(reader); + } + else + { + throw OrthancException(ErrorCode_NotImplemented); + } + } + + + void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) + { + if (accessor.GetFormat() != PixelFormat_Grayscale8 && + accessor.GetFormat() != PixelFormat_Grayscale16 && + accessor.GetFormat() != PixelFormat_RGB24 && + accessor.GetFormat() != PixelFormat_RGBA32) + { + throw OrthancException(ErrorCode_NotImplemented); + } + + if (accessor.GetFormat() == PixelFormat_RGBA32) + { + LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; + } + + // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html + + Remove(DICOM_TAG_PIXEL_DATA); + Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); + Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); + Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); + Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); + Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels + Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved + Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); + Replace(DICOM_TAG_BITS_ALLOCATED, "8"); + Replace(DICOM_TAG_BITS_STORED, "8"); + Replace(DICOM_TAG_HIGH_BIT, "7"); + + unsigned int bytesPerPixel = 1; + + switch (accessor.GetFormat()) + { + case PixelFormat_RGB24: + case PixelFormat_RGBA32: + Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); + Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); + bytesPerPixel = 3; + break; + + case PixelFormat_Grayscale8: + break; + + case PixelFormat_Grayscale16: + Replace(DICOM_TAG_BITS_ALLOCATED, "16"); + Replace(DICOM_TAG_BITS_STORED, "16"); + Replace(DICOM_TAG_HIGH_BIT, "15"); + bytesPerPixel = 2; + break; + + default: + throw OrthancException(ErrorCode_NotImplemented); + } + + DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), + DICOM_TAG_PIXEL_DATA.GetElement()); + + std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); + + unsigned int pitch = accessor.GetWidth() * bytesPerPixel; + Uint8* target = NULL; + pixels->createUint8Array(accessor.GetHeight() * pitch, target); + + for (unsigned int y = 0; y < accessor.GetHeight(); y++) + { + switch (accessor.GetFormat()) + { + case PixelFormat_RGB24: + case PixelFormat_Grayscale8: + case PixelFormat_Grayscale16: + case PixelFormat_SignedGrayscale16: + { + memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); + target += pitch; + break; + } + + case PixelFormat_RGBA32: + { + // The alpha channel is not supported by the DICOM standard + const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)); + for (unsigned int x = 0; x < accessor.GetWidth(); x++, target += 3, source += 4) + { + target[0] = source[0]; + target[1] = source[1]; + target[2] = source[2]; + } + + break; + } + + default: + throw OrthancException(ErrorCode_NotImplemented); + } + } + + if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) + { + throw OrthancException(ErrorCode_InternalError); + } + } + + + void ParsedDicomFile::ExtractImage(ImageBuffer& result, + unsigned int frame) + { + DcmDataset& dataset = *pimpl_->file_->getDataset(); + + if (!DicomImageDecoder::Decode(result, dataset, frame)) + { + throw OrthancException(ErrorCode_BadFileFormat); + } + } + + + void ParsedDicomFile::ExtractImage(ImageBuffer& result, + unsigned int frame, + ImageExtractionMode mode) + { + DcmDataset& dataset = *pimpl_->file_->getDataset(); + + bool ok = false; + + switch (mode) + { + case ImageExtractionMode_UInt8: + ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale8); + break; + + case ImageExtractionMode_UInt16: + ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale16); + break; + + case ImageExtractionMode_Int16: + ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_SignedGrayscale16); + break; + + case ImageExtractionMode_Preview: + ok = DicomImageDecoder::DecodePreview(result, dataset, frame); + break; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + + if (!ok) + { + throw OrthancException(ErrorCode_BadFileFormat); + } + } + + + void ParsedDicomFile::ExtractPngImage(std::string& result, + unsigned int frame, + ImageExtractionMode mode) + { + ImageBuffer buffer; + ExtractImage(buffer, frame, mode); + + ImageAccessor accessor(buffer.GetConstAccessor()); + PngWriter writer; + writer.WriteToMemory(result, accessor); + } + + + bool ParsedDicomFile::GetTagValue(std::string& value, + const SequencePath& path, + const DicomTag& tag) + { + if (path.size() == 0) + { + return GetTagValue(value, tag); + } + + DcmItem* current = pimpl_->file_->getDataset(); + assert(current != NULL); + + for (SequencePath::const_iterator it = path.begin(); it != path.end(); it++) + { + DcmTagKey k(it->first.GetGroup(), it->first.GetElement()); + + DcmSequenceOfItems* sequence = NULL; + if (!current->findAndGetSequence(k, sequence).good() || + sequence == NULL || + sequence->getVR() != EVR_SQ) + { + return false; + } + + if (it->second < 0 || it->second > sequence->card()) + { + return false; + } + + current = sequence->getItem(it->second); + + if (current == NULL) + { + return false; + } + } + + return GetTagValueInternal(value, *current, tag); + } + +}