orthanc: OrthancServer/ParsedDicomFile.cpp comparison

comparison 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

comparison

equal deleted inserted replaced

-:c19552f604d5
+:e57e08ed510f
+/**
+* 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);
+}
+}

Mercurial > hg > orthanc

comparison OrthancServer/ParsedDicomFile.cpp @ 948:e57e08ed510f dicom-rt