orthanc: Core/DicomParsing/ParsedDicomFile.cpp comparison

comparison Core/DicomParsing/ParsedDicomFile.cpp @ 2382:7284093111b0

big reorganization to cleanly separate framework vs. server

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Tue, 29 Aug 2017 21:17:35 +0200
parents	OrthancServer/ParsedDicomFile.cpp@b8969010b534
children	75c779ca948c

comparison

equal deleted inserted replaced

-:b8969010b534
+:7284093111b0
+/**
+* Orthanc - A Lightweight, RESTful DICOM Store
+* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+* Department, University Hospital of Liege, Belgium
+* Copyright (C) 2017 Osimis, 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 "../PrecompiledHeaders.h"
+#ifndef NOMINMAX
+#define NOMINMAX
+#endif
+#include "ParsedDicomFile.h"
+#include "FromDcmtkBridge.h"
+#include "ToDcmtkBridge.h"
+#include "Internals/DicomFrameIndex.h"
+#include "../Logging.h"
+#include "../OrthancException.h"
+#include "../Toolbox.h"
+#include "../SystemToolbox.h"
+#if ORTHANC_ENABLE_JPEG == 1
+#  include "../Images/JpegReader.h"
+#endif
+#if ORTHANC_ENABLE_PNG == 1
+#  include "../Images/PngReader.h"
+#endif
+#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/dcuid.h>
+#include <dcmtk/dcmdata/dcmetinf.h>
+#include <dcmtk/dcmdata/dcdeftag.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 <dcmtk/dcmdata/dcostrmb.h>
+#include <boost/algorithm/string/predicate.hpp>
+#if DCMTK_VERSION_NUMBER <= 360
+#  define EXS_JPEGProcess1      EXS_JPEGProcess1TransferSyntax
+#endif
+static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream";
+namespace Orthanc
+{
+struct ParsedDicomFile::PImpl
+{
+std::auto_ptr<DcmFileFormat> file_;
+std::auto_ptr<DicomFrameIndex>  frameIndex_;
+};
+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;
+}
+}
+namespace
+{
+class DicomFieldStream : public IHttpStreamAnswer
+{
+private:
+DcmElement&  element_;
+uint32_t     length_;
+uint32_t     offset_;
+std::string  chunk_;
+size_t       chunkSize_;
+public:
+DicomFieldStream(DcmElement& element,
+E_TransferSyntax transferSyntax) :
+element_(element),
+length_(element.getLength(transferSyntax)),
+offset_(0),
+chunkSize_(0)
+{
+static const size_t CHUNK_SIZE = 64 * 1024;  // Use chunks of max 64KB
+chunk_.resize(CHUNK_SIZE);
+}
+virtual HttpCompression SetupHttpCompression(bool /*gzipAllowed*/,
+bool /*deflateAllowed*/)
+{
+// No support for compression
+return HttpCompression_None;
+}
+virtual bool HasContentFilename(std::string& filename)
+{
+return false;
+}
+virtual std::string GetContentType()
+{
+return "";
+}
+virtual uint64_t  GetContentLength()
+{
+return length_;
+}
+virtual bool ReadNextChunk()
+{
+assert(offset_ <= length_);
+if (offset_ == length_)
+{
+return false;
+}
+else
+{
+if (length_ - offset_ < chunk_.size())
+{
+chunkSize_ = length_ - offset_;
+}
+else
+{
+chunkSize_ = chunk_.size();
+}
+OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_);
+offset_ += chunkSize_;
+if (!cond.good())
+{
+LOG(ERROR) << "Error while sending a DICOM field: " << cond.text();
+throw OrthancException(ErrorCode_InternalError);
+}
+return true;
+}
+}
+virtual const char *GetChunkContent()
+{
+return chunk_.c_str();
+}
+virtual size_t GetChunkSize()
+{
+return chunkSize_;
+}
+};
+}
+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 present 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");
+DicomFieldStream stream(*element, transferSyntax);
+output.AnswerStream(stream);
+}
+}
+}
+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)
+{
+DicomFieldStream stream(*element, transferSyntax);
+output.AnswerStream(stream);
+}
+}
+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);
+}
+}
+void ParsedDicomFile::Remove(const DicomTag& tag)
+{
+InvalidateCache();
+DcmTagKey key(tag.GetGroup(), tag.GetElement());
+DcmElement* element = pimpl_->file_->getDataset()->remove(key);
+if (element != NULL)
+{
+delete element;
+}
+}
+void ParsedDicomFile::Clear(const DicomTag& tag,
+bool onlyIfExists)
+{
+InvalidateCache();
+DcmItem* dicom = pimpl_->file_->getDataset();
+DcmTagKey key(tag.GetGroup(), tag.GetElement());
+if (onlyIfExists &&
+!dicom->tagExists(key))
+{
+// The tag is non-existing, do not clear it
+}
+else
+{
+if (!dicom->insertEmptyElement(key, OFTrue /* replace old value */).good())
+{
+throw OrthancException(ErrorCode_InternalError);
+}
+}
+}
+void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep)
+{
+InvalidateCache();
+DcmDataset& dataset = *pimpl_->file_->getDataset();
+// Loop over the dataset to detect its private tags
+typedef std::list<DcmElement*> Tags;
+Tags privateTags;
+for (unsigned long i = 0; i < dataset.card(); i++)
+{
+DcmElement* element = dataset.getElement(i);
+DcmTag tag(element->getTag());
+// Is this a private tag?
+if (tag.isPrivate())
+{
+bool remove = true;
+// Check whether this private tag is to be kept
+if (toKeep != NULL)
+{
+DicomTag tmp = FromDcmtkBridge::Convert(tag);
+if (toKeep->find(tmp) != toKeep->end())
+{
+remove = false;  // Keep it
+}
+}
+if (remove)
+{
+privateTags.push_back(element);
+}
+}
+}
+// Loop over the detected private tags to remove them
+for (Tags::iterator it = privateTags.begin();
+it != privateTags.end(); ++it)
+{
+DcmElement* tmp = dataset.remove(*it);
+if (tmp != NULL)
+{
+delete tmp;
+}
+}
+}
+static void InsertInternal(DcmDataset& dicom,
+DcmElement* element)
+{
+OFCondition cond = dicom.insert(element, false, false);
+if (!cond.good())
+{
+// This field already exists
+delete element;
+throw OrthancException(ErrorCode_InternalError);
+}
+}
+void ParsedDicomFile::Insert(const DicomTag& tag,
+const Json::Value& value,
+bool decodeDataUriScheme)
+{
+if (pimpl_->file_->getDataset()->tagExists(ToDcmtkBridge::Convert(tag)))
+{
+throw OrthancException(ErrorCode_AlreadyExistingTag);
+}
+if (decodeDataUriScheme &&
+value.type() == Json::stringValue &&
+(tag == DICOM_TAG_ENCAPSULATED_DOCUMENT ||
+tag == DICOM_TAG_PIXEL_DATA))
+{
+if (EmbedContentInternal(value.asString()))
+{
+return;
+}
+}
+InvalidateCache();
+std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, GetEncoding()));
+InsertInternal(*pimpl_->file_->getDataset(), element.release());
+}
+static bool CanReplaceProceed(DcmDataset& dicom,
+const DcmTagKey& tag,
+DicomReplaceMode mode)
+{
+if (dicom.findAndDeleteElement(tag).good())
+{
+// This tag was existing, it has been deleted
+return true;
+}
+else
+{
+// This tag was absent, act wrt. the specified "mode"
+switch (mode)
+{
+case DicomReplaceMode_InsertIfAbsent:
+return true;
+case DicomReplaceMode_ThrowIfAbsent:
+throw OrthancException(ErrorCode_InexistentItem);
+case DicomReplaceMode_IgnoreIfAbsent:
+return false;
+default:
+throw OrthancException(ErrorCode_ParameterOutOfRange);
+}
+}
+}
+void ParsedDicomFile::UpdateStorageUid(const DicomTag& tag,
+const std::string& utf8Value,
+bool decodeDataUriScheme)
+{
+if (tag != DICOM_TAG_SOP_CLASS_UID &&
+tag != DICOM_TAG_SOP_INSTANCE_UID)
+{
+return;
+}
+std::string binary;
+const std::string* decoded = &utf8Value;
+if (decodeDataUriScheme &&
+boost::starts_with(utf8Value, "data:application/octet-stream;base64,"))
+{
+std::string mime;
+if (!Toolbox::DecodeDataUriScheme(mime, binary, utf8Value))
+{
+throw OrthancException(ErrorCode_BadFileFormat);
+}
+decoded = &binary;
+}
+else
+{
+Encoding encoding = GetEncoding();
+if (GetEncoding() != Encoding_Utf8)
+{
+binary = Toolbox::ConvertFromUtf8(utf8Value, encoding);
+decoded = &binary;
+}
+}
+/**
+* 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)
+{
+ReplacePlainString(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, *decoded);
+}
+if (tag == DICOM_TAG_SOP_INSTANCE_UID)
+{
+ReplacePlainString(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, *decoded);
+}
+}
+void ParsedDicomFile::Replace(const DicomTag& tag,
+const std::string& utf8Value,
+bool decodeDataUriScheme,
+DicomReplaceMode mode)
+{
+InvalidateCache();
+DcmDataset& dicom = *pimpl_->file_->getDataset();
+if (CanReplaceProceed(dicom, ToDcmtkBridge::Convert(tag), mode))
+{
+// Either the tag was previously existing (and now removed), or
+// the replace mode was set to "InsertIfAbsent"
+if (decodeDataUriScheme &&
+(tag == DICOM_TAG_ENCAPSULATED_DOCUMENT ||
+tag == DICOM_TAG_PIXEL_DATA))
+{
+if (EmbedContentInternal(utf8Value))
+{
+return;
+}
+}
+std::auto_ptr<DcmElement> element(FromDcmtkBridge::CreateElementForTag(tag));
+FromDcmtkBridge::FillElementWithString(*element, tag, utf8Value, decodeDataUriScheme, GetEncoding());
+InsertInternal(dicom, element.release());
+UpdateStorageUid(tag, utf8Value, false);
+}
+}
+void ParsedDicomFile::Replace(const DicomTag& tag,
+const Json::Value& value,
+bool decodeDataUriScheme,
+DicomReplaceMode mode)
+{
+InvalidateCache();
+DcmDataset& dicom = *pimpl_->file_->getDataset();
+if (CanReplaceProceed(dicom, ToDcmtkBridge::Convert(tag), mode))
+{
+// Either the tag was previously existing (and now removed), or
+// the replace mode was set to "InsertIfAbsent"
+if (decodeDataUriScheme &&
+value.type() == Json::stringValue &&
+(tag == DICOM_TAG_ENCAPSULATED_DOCUMENT ||
+tag == DICOM_TAG_PIXEL_DATA))
+{
+if (EmbedContentInternal(value.asString()))
+{
+return;
+}
+}
+InsertInternal(dicom, FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, GetEncoding()));
+if (tag == DICOM_TAG_SOP_CLASS_UID ||
+tag == DICOM_TAG_SOP_INSTANCE_UID)
+{
+if (value.type() != Json::stringValue)
+{
+throw OrthancException(ErrorCode_BadParameterType);
+}
+UpdateStorageUid(tag, value.asString(), decodeDataUriScheme);
+}
+}
+}
+void ParsedDicomFile::Answer(RestApiOutput& output)
+{
+std::string serialized;
+if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->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 = *pimpl_->file_->getDataset();
+if (tag.IsPrivate() ||
+FromDcmtkBridge::IsUnknownTag(tag) ||
+tag == DICOM_TAG_PIXEL_DATA ||
+tag == DICOM_TAG_ENCAPSULATED_DOCUMENT)
+{
+const Uint8* data = NULL;   // This is freed in the destructor of the dataset
+long unsigned int count = 0;
+if (dataset.findAndGetUint8Array(k, data, &count).good())
+{
+if (count > 0)
+{
+assert(data != NULL);
+value.assign(reinterpret_cast<const char*>(data), count);
+}
+else
+{
+value.clear();
+}
+return true;
+}
+else
+{
+return false;
+}
+}
+else
+{
+DcmElement* element = NULL;
+if (!dataset.findAndGetElement(k, element).good() ||
+element == NULL)
+{
+return false;
+}
+std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement
+(*element, DicomToJsonFlags_Default,
+ORTHANC_MAXIMUM_TAG_LENGTH, GetEncoding()));
+if (v.get() == NULL ||
+v->IsNull())
+{
+value = "";
+}
+else
+{
+// TODO v->IsBinary()
+value = v->GetContent();
+}
+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 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);
+SystemToolbox::WriteFile(content, path);
+}
+ParsedDicomFile::ParsedDicomFile(bool createIdentifiers) : pimpl_(new PImpl)
+{
+pimpl_->file_.reset(new DcmFileFormat);
+if (createIdentifiers)
+{
+ReplacePlainString(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient));
+ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study));
+ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series));
+ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
+}
+}
+void ParsedDicomFile::CreateFromDicomMap(const DicomMap& source,
+Encoding defaultEncoding)
+{
+pimpl_->file_.reset(new DcmFileFormat);
+const DicomValue* tmp = source.TestAndGetValue(DICOM_TAG_SPECIFIC_CHARACTER_SET);
+if (tmp != NULL)
+{
+Encoding encoding;
+if (tmp->IsNull() ||
+tmp->IsBinary() ||
+!GetDicomEncoding(encoding, tmp->GetContent().c_str()))
+{
+throw OrthancException(ErrorCode_ParameterOutOfRange);
+}
+else
+{
+SetEncoding(encoding);
+}
+}
+else
+{
+SetEncoding(defaultEncoding);
+}
+for (DicomMap::Map::const_iterator
+it = source.map_.begin(); it != source.map_.end(); ++it)
+{
+if (it->first != DICOM_TAG_SPECIFIC_CHARACTER_SET &&
+!it->second->IsNull())
+{
+ReplacePlainString(it->first, it->second->GetContent());
+}
+}
+}
+ParsedDicomFile::ParsedDicomFile(const DicomMap& map,
+Encoding defaultEncoding) :
+pimpl_(new PImpl)
+{
+CreateFromDicomMap(map, defaultEncoding);
+}
+ParsedDicomFile::ParsedDicomFile(const DicomMap& map) :
+pimpl_(new PImpl)
+{
+CreateFromDicomMap(map, GetDefaultDicomEncoding());
+}
+ParsedDicomFile::ParsedDicomFile(const void* content,
+size_t size) : pimpl_(new PImpl)
+{
+pimpl_->file_.reset(FromDcmtkBridge::LoadFromMemoryBuffer(content, size));
+}
+ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl)
+{
+if (content.size() == 0)
+{
+pimpl_->file_.reset(FromDcmtkBridge::LoadFromMemoryBuffer(NULL, 0));
+}
+else
+{
+pimpl_->file_.reset(FromDcmtkBridge::LoadFromMemoryBuffer(&content[0], content.size()));
+}
+}
+ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) :
+pimpl_(new PImpl)
+{
+pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone()));
+// Create a new instance-level identifier
+ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
+}
+ParsedDicomFile::ParsedDicomFile(DcmDataset& dicom) : pimpl_(new PImpl)
+{
+pimpl_->file_.reset(new DcmFileFormat(&dicom));
+}
+ParsedDicomFile::ParsedDicomFile(DcmFileFormat& dicom) : pimpl_(new PImpl)
+{
+pimpl_->file_.reset(new DcmFileFormat(dicom));
+}
+ParsedDicomFile::~ParsedDicomFile()
+{
+delete pimpl_;
+}
+DcmFileFormat& ParsedDicomFile::GetDcmtkObject() const
+{
+return *pimpl_->file_.get();
+}
+ParsedDicomFile* ParsedDicomFile::Clone()
+{
+return new ParsedDicomFile(*this);
+}
+bool ParsedDicomFile::EmbedContentInternal(const std::string& dataUriScheme)
+{
+std::string mime, content;
+if (!Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme))
+{
+return false;
+}
+Toolbox::ToLowerCase(mime);
+if (mime == "image/png")
+{
+#if ORTHANC_ENABLE_PNG == 1
+EmbedImage(mime, content);
+#else
+LOG(ERROR) << "Orthanc was compiled without support of PNG";
+throw OrthancException(ErrorCode_NotImplemented);
+#endif
+}
+else if (mime == "image/jpeg")
+{
+#if ORTHANC_ENABLE_JPEG == 1
+EmbedImage(mime, content);
+#else
+LOG(ERROR) << "Orthanc was compiled without support of JPEG";
+throw OrthancException(ErrorCode_NotImplemented);
+#endif
+}
+else if (mime == "application/pdf")
+{
+EmbedPdf(content);
+}
+else
+{
+LOG(ERROR) << "Unsupported MIME type for the content of a new DICOM file: " << mime;
+throw OrthancException(ErrorCode_NotImplemented);
+}
+return true;
+}
+void ParsedDicomFile::EmbedContent(const std::string& dataUriScheme)
+{
+if (!EmbedContentInternal(dataUriScheme))
+{
+throw OrthancException(ErrorCode_BadFileFormat);
+}
+}
+#if (ORTHANC_ENABLE_JPEG == 1 &&  \
+ORTHANC_ENABLE_PNG == 1)
+void ParsedDicomFile::EmbedImage(const std::string& mime,
+const std::string& content)
+{
+if (mime == "image/png")
+{
+PngReader reader;
+reader.ReadFromMemory(content);
+EmbedImage(reader);
+}
+else if (mime == "image/jpeg")
+{
+JpegReader reader;
+reader.ReadFromMemory(content);
+EmbedImage(reader);
+}
+else
+{
+throw OrthancException(ErrorCode_NotImplemented);
+}
+}
+#endif
+void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor)
+{
+if (accessor.GetFormat() != PixelFormat_Grayscale8 &&
+accessor.GetFormat() != PixelFormat_Grayscale16 &&
+accessor.GetFormat() != PixelFormat_SignedGrayscale16 &&
+accessor.GetFormat() != PixelFormat_RGB24 &&
+accessor.GetFormat() != PixelFormat_RGBA32)
+{
+throw OrthancException(ErrorCode_NotImplemented);
+}
+InvalidateCache();
+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);
+ReplacePlainString(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth()));
+ReplacePlainString(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight()));
+ReplacePlainString(DICOM_TAG_SAMPLES_PER_PIXEL, "1");
+ReplacePlainString(DICOM_TAG_NUMBER_OF_FRAMES, "1");
+if (accessor.GetFormat() == PixelFormat_SignedGrayscale16)
+{
+ReplacePlainString(DICOM_TAG_PIXEL_REPRESENTATION, "1");
+}
+else
+{
+ReplacePlainString(DICOM_TAG_PIXEL_REPRESENTATION, "0");  // Unsigned pixels
+}
+ReplacePlainString(DICOM_TAG_PLANAR_CONFIGURATION, "0");  // Color channels are interleaved
+ReplacePlainString(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2");
+unsigned int bytesPerPixel = 0;
+switch (accessor.GetFormat())
+{
+case PixelFormat_Grayscale8:
+ReplacePlainString(DICOM_TAG_BITS_ALLOCATED, "8");
+ReplacePlainString(DICOM_TAG_BITS_STORED, "8");
+ReplacePlainString(DICOM_TAG_HIGH_BIT, "7");
+bytesPerPixel = 1;
+break;
+case PixelFormat_RGB24:
+case PixelFormat_RGBA32:
+ReplacePlainString(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB");
+ReplacePlainString(DICOM_TAG_SAMPLES_PER_PIXEL, "3");
+ReplacePlainString(DICOM_TAG_BITS_ALLOCATED, "8");
+ReplacePlainString(DICOM_TAG_BITS_STORED, "8");
+ReplacePlainString(DICOM_TAG_HIGH_BIT, "7");
+bytesPerPixel = 3;
+break;
+case PixelFormat_Grayscale16:
+case PixelFormat_SignedGrayscale16:
+ReplacePlainString(DICOM_TAG_BITS_ALLOCATED, "16");
+ReplacePlainString(DICOM_TAG_BITS_STORED, "16");
+ReplacePlainString(DICOM_TAG_HIGH_BIT, "15");
+bytesPerPixel = 2;
+break;
+default:
+throw OrthancException(ErrorCode_NotImplemented);
+}
+assert(bytesPerPixel != 0);
+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);
+}
+}
+Encoding ParsedDicomFile::GetEncoding() const
+{
+return FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset(),
+GetDefaultDicomEncoding());
+}
+void ParsedDicomFile::SetEncoding(Encoding encoding)
+{
+if (encoding == Encoding_Windows1251)
+{
+// This Cyrillic codepage is not officially supported by the
+// DICOM standard. Do not set the SpecificCharacterSet tag.
+return;
+}
+std::string s = GetDicomSpecificCharacterSet(encoding);
+ReplacePlainString(DICOM_TAG_SPECIFIC_CHARACTER_SET, s);
+}
+void ParsedDicomFile::DatasetToJson(Json::Value& target,
+DicomToJsonFormat format,
+DicomToJsonFlags flags,
+unsigned int maxStringLength)
+{
+FromDcmtkBridge::ExtractDicomAsJson(target, *pimpl_->file_->getDataset(),
+format, flags, maxStringLength, GetDefaultDicomEncoding());
+}
+void ParsedDicomFile::DatasetToJson(Json::Value& target)
+{
+FromDcmtkBridge::ExtractDicomAsJson(target, *pimpl_->file_->getDataset());
+}
+void ParsedDicomFile::HeaderToJson(Json::Value& target,
+DicomToJsonFormat format)
+{
+FromDcmtkBridge::ExtractHeaderAsJson(target, *pimpl_->file_->getMetaInfo(), format, DicomToJsonFlags_None, 0);
+}
+bool ParsedDicomFile::HasTag(const DicomTag& tag) const
+{
+DcmTag key(tag.GetGroup(), tag.GetElement());
+return pimpl_->file_->getDataset()->tagExists(key);
+}
+void ParsedDicomFile::EmbedPdf(const std::string& pdf)
+{
+if (pdf.size() < 5 ||  // (*)
+strncmp("%PDF-", pdf.c_str(), 5) != 0)
+{
+LOG(ERROR) << "Not a PDF file";
+throw OrthancException(ErrorCode_BadFileFormat);
+}
+InvalidateCache();
+ReplacePlainString(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage);
+ReplacePlainString(FromDcmtkBridge::Convert(DCM_Modality), "OT");
+ReplacePlainString(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD");
+ReplacePlainString(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf");
+//ReplacePlainString(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1");
+std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument));
+size_t s = pdf.size();
+if (s & 1)
+{
+// The size of the buffer must be even
+s += 1;
+}
+Uint8* bytes = NULL;
+OFCondition result = element->createUint8Array(s, bytes);
+if (!result.good() || bytes == NULL)
+{
+throw OrthancException(ErrorCode_NotEnoughMemory);
+}
+// Blank pad byte (no access violation, as "pdf.size() >= 5" because of (*) )
+bytes[s - 1] = 0;
+memcpy(bytes, pdf.c_str(), pdf.size());
+DcmPolymorphOBOW* obj = element.release();
+result = pimpl_->file_->getDataset()->insert(obj);
+if (!result.good())
+{
+delete obj;
+throw OrthancException(ErrorCode_NotEnoughMemory);
+}
+}
+bool ParsedDicomFile::ExtractPdf(std::string& pdf)
+{
+std::string sop, mime;
+if (!GetTagValue(sop, DICOM_TAG_SOP_CLASS_UID) ||
+!GetTagValue(mime, FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument)) ||
+sop != UID_EncapsulatedPDFStorage ||
+mime != "application/pdf")
+{
+return false;
+}
+if (!GetTagValue(pdf, DICOM_TAG_ENCAPSULATED_DOCUMENT))
+{
+return false;
+}
+// Strip the possible pad byte at the end of file, because the
+// encapsulated documents must always have an even length. The PDF
+// format expects files to end with %%EOF followed by CR/LF. If
+// the last character of the file is not a CR or LF, we assume it
+// is a pad byte and remove it.
+if (pdf.size() > 0)
+{
+char last = *pdf.rbegin();
+if (last != 10 && last != 13)
+{
+pdf.resize(pdf.size() - 1);
+}
+}
+return true;
+}
+ParsedDicomFile* ParsedDicomFile::CreateFromJson(const Json::Value& json,
+DicomFromJsonFlags flags)
+{
+	const bool generateIdentifiers = (flags & DicomFromJsonFlags_GenerateIdentifiers) ? true : false;
+	const bool decodeDataUriScheme = (flags & DicomFromJsonFlags_DecodeDataUriScheme) ? true : false;
+std::auto_ptr<ParsedDicomFile> result(new ParsedDicomFile(generateIdentifiers));
+result->SetEncoding(FromDcmtkBridge::ExtractEncoding(json, GetDefaultDicomEncoding()));
+const Json::Value::Members tags = json.getMemberNames();
+for (size_t i = 0; i < tags.size(); i++)
+{
+DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]);
+const Json::Value& value = json[tags[i]];
+if (tag == DICOM_TAG_PIXEL_DATA ||
+tag == DICOM_TAG_ENCAPSULATED_DOCUMENT)
+{
+if (value.type() != Json::stringValue)
+{
+throw OrthancException(ErrorCode_BadRequest);
+}
+else
+{
+result->EmbedContent(value.asString());
+}
+}
+else if (tag != DICOM_TAG_SPECIFIC_CHARACTER_SET)
+{
+result->Replace(tag, value, decodeDataUriScheme, DicomReplaceMode_InsertIfAbsent);
+}
+}
+return result.release();
+}
+void ParsedDicomFile::GetRawFrame(std::string& target,
+std::string& mime,
+unsigned int frameId)
+{
+if (pimpl_->frameIndex_.get() == NULL)
+{
+pimpl_->frameIndex_.reset(new DicomFrameIndex(*pimpl_->file_));
+}
+pimpl_->frameIndex_->GetRawFrame(target, frameId);
+E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer();
+switch (transferSyntax)
+{
+case EXS_JPEGProcess1:
+mime = "image/jpeg";
+break;
+case EXS_JPEG2000LosslessOnly:
+case EXS_JPEG2000:
+mime = "image/jp2";
+break;
+default:
+mime = "application/octet-stream";
+break;
+}
+}
+void ParsedDicomFile::InvalidateCache()
+{
+pimpl_->frameIndex_.reset(NULL);
+}
+unsigned int ParsedDicomFile::GetFramesCount() const
+{
+return DicomFrameIndex::GetFramesCount(*pimpl_->file_);
+}
+void ParsedDicomFile::ChangeEncoding(Encoding target)
+{
+Encoding source = GetEncoding();
+if (source != target)  // Avoid unnecessary conversion
+{
+ReplacePlainString(DICOM_TAG_SPECIFIC_CHARACTER_SET, GetDicomSpecificCharacterSet(target));
+FromDcmtkBridge::ChangeStringEncoding(*pimpl_->file_->getDataset(), source, target);
+}
+}
+void ParsedDicomFile::ExtractDicomSummary(DicomMap& target) const
+{
+FromDcmtkBridge::ExtractDicomSummary(target, *pimpl_->file_->getDataset());
+}
+void ParsedDicomFile::ExtractDicomAsJson(Json::Value& target) const
+{
+FromDcmtkBridge::ExtractDicomAsJson(target, *pimpl_->file_->getDataset());
+}
+bool ParsedDicomFile::LookupTransferSyntax(std::string& result)
+{
+return FromDcmtkBridge::LookupTransferSyntax(result, *pimpl_->file_);
+}
+bool ParsedDicomFile::LookupPhotometricInterpretation(PhotometricInterpretation& result) const
+{
+DcmTagKey k(DICOM_TAG_PHOTOMETRIC_INTERPRETATION.GetGroup(),
+DICOM_TAG_PHOTOMETRIC_INTERPRETATION.GetElement());
+DcmDataset& dataset = *pimpl_->file_->getDataset();
+const char *c = NULL;
+if (dataset.findAndGetString(k, c).good() &&
+c != NULL)
+{
+result = StringToPhotometricInterpretation(c);
+return true;
+}
+else
+{
+return false;
+}
+}
+}

Mercurial > hg > orthanc

comparison Core/DicomParsing/ParsedDicomFile.cpp @ 2382:7284093111b0