orthanc-stone: Framework/Loaders/SeriesOrderedFrames.cpp comparison

comparison Framework/Loaders/SeriesOrderedFrames.cpp @ 1228:c471a0aa137b broker

adding the next generation of loaders

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Mon, 09 Dec 2019 13:58:37 +0100
parents
children	0ca50d275b9a

comparison

equal deleted inserted replaced

-:a1c0c9c9f9af
+:c471a0aa137b
+/**
+* Stone of Orthanc
+* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+* Department, University Hospital of Liege, Belgium
+* Copyright (C) 2017-2019 Osimis S.A., Belgium
+*
+* This program is free software: you can redistribute it and/or
+* modify it under the terms of the GNU Affero General Public License
+* as published by the Free Software Foundation, either version 3 of
+* the License, or (at your option) any later version.
+*
+* 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
+* Affero General Public License for more details.
+*
+* You should have received a copy of the GNU Affero General Public License
+* along with this program. If not, see <http://www.gnu.org/licenses/>.
+**/
+#include "../Toolbox/SlicesSorter.h"
+#include "SeriesOrderedFrames.h"
+#include <Core/OrthancException.h>
+namespace OrthancStone
+{
+class SeriesOrderedFrames::Instance : public boost::noncopyable
+{
+private:
+std::auto_ptr<Orthanc::DicomMap>  dicom_;
+DicomInstanceParameters           parameters_;
+public:
+Instance(const Orthanc::DicomMap& dicom) :
+dicom_(dicom.Clone()),
+parameters_(dicom)
+{
+}
+const Orthanc::DicomMap& GetInstance() const
+{
+return *dicom_;
+}
+const DicomInstanceParameters& GetInstanceParameters() const
+{
+return parameters_;
+}
+bool Lookup3DGeometry(CoordinateSystem3D& target) const
+{
+try
+{
+std::string imagePositionPatient, imageOrientationPatient;
+if (dicom_->LookupStringValue(imagePositionPatient, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
+dicom_->LookupStringValue(imageOrientationPatient, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
+{
+target = CoordinateSystem3D(imagePositionPatient, imageOrientationPatient);
+return true;
+}
+}
+catch (Orthanc::OrthancException&)
+{
+}
+return false;
+}
+bool LookupIndexInSeries(int& target) const
+{
+std::string value;
+if (dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_INSTANCE_NUMBER, false) ||
+dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_IMAGE_INDEX, false))
+{
+try
+{
+target = boost::lexical_cast<int>(value);
+return true;
+}
+catch (boost::bad_lexical_cast&)
+{
+}
+}
+return false;
+}
+};
+class SeriesOrderedFrames::Frame : public boost::noncopyable
+{
+private:
+const Instance*  instance_;
+unsigned int     frameIndex_;
+public:
+Frame(const Instance& instance,
+unsigned int frameIndex) :
+instance_(&instance),
+frameIndex_(frameIndex)
+{
+if (frameIndex_ >= instance.GetInstanceParameters().GetImageInformation().GetNumberOfFrames())
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+}
+}
+const Orthanc::DicomMap& GetInstance() const
+{
+assert(instance_ != NULL);
+return instance_->GetInstance();
+}
+const DicomInstanceParameters& GetInstanceParameters() const
+{
+assert(instance_ != NULL);
+return instance_->GetInstanceParameters();
+}
+unsigned int GetFrameIndex() const
+{
+return frameIndex_;
+}
+};
+class SeriesOrderedFrames::InstanceWithIndexInSeries
+{
+private:
+const Instance* instance_;  // Don't use a reference to make "std::sort()" happy
+int             index_;
+public:
+InstanceWithIndexInSeries(const Instance& instance) :
+instance_(&instance)
+{
+if (!instance_->LookupIndexInSeries(index_))
+{
+index_ = std::numeric_limits<int>::max();
+}
+}
+const Instance& GetInstance() const
+{
+return *instance_;
+}
+int GetIndexInSeries() const
+{
+return index_;
+}
+bool operator< (const InstanceWithIndexInSeries& other) const
+{
+return (index_ < other.index_);
+}
+};
+void SeriesOrderedFrames::Clear()
+{
+for (size_t i = 0; i < instances_.size(); i++)
+{
+assert(instances_[i] != NULL);
+delete instances_[i];
+}
+for (size_t i = 0; i < orderedFrames_.size(); i++)
+{
+assert(orderedFrames_[i] != NULL);
+delete orderedFrames_[i];
+}
+instances_.clear();
+orderedFrames_.clear();
+}
+bool SeriesOrderedFrames::Sort3DVolume()
+{
+SlicesSorter sorter;
+sorter.Reserve(instances_.size());
+for (size_t i = 0; i < instances_.size(); i++)
+{
+CoordinateSystem3D geometry;
+if (instances_[i]->Lookup3DGeometry(geometry))
+{
+sorter.AddSlice(geometry, new Orthanc::SingleValueObject<Instance*>(instances_[i]));
+}
+else
+{
+return false;   // Not a 3D volume
+}
+}
+if (!sorter.Sort() ||
+sorter.GetSlicesCount() != instances_.size() ||
+!sorter.AreAllSlicesDistinct())
+{
+return false;
+}
+else
+{
+for (size_t i = 0; i < sorter.GetSlicesCount(); i++)
+{
+assert(sorter.HasSlicePayload(i));
+const Orthanc::SingleValueObject<Instance*>& payload =
+dynamic_cast<const Orthanc::SingleValueObject<Instance*>&>(sorter.GetSlicePayload(i));
+assert(payload.GetValue() != NULL);
+for (size_t j = 0; j < payload.GetValue()->GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++)
+{
+orderedFrames_.push_back(new Frame(*payload.GetValue(), j));
+}
+}
+isRegular_ = sorter.ComputeSpacingBetweenSlices(spacingBetweenSlices_);
+return true;
+}
+}
+void SeriesOrderedFrames::SortIndexInSeries()
+{
+std::vector<InstanceWithIndexInSeries> tmp;
+tmp.reserve(instances_.size());
+for (size_t i = 0; i < instances_.size(); i++)
+{
+assert(instances_[i] != NULL);
+tmp.push_back(InstanceWithIndexInSeries(*instances_[i]));
+}
+std::sort(tmp.begin(), tmp.end());
+for (size_t i = 0; i < tmp.size(); i++)
+{
+for (size_t j = 0; j < tmp[i].GetInstance().GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++)
+{
+orderedFrames_.push_back(new Frame(tmp[i].GetInstance(), j));
+}
+}
+}
+const SeriesOrderedFrames::Frame& SeriesOrderedFrames::GetFrame(size_t seriesIndex) const
+{
+if (seriesIndex >= orderedFrames_.size())
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+}
+else
+{
+assert(orderedFrames_[seriesIndex] != NULL);
+return *(orderedFrames_[seriesIndex]);
+}
+}
+SeriesOrderedFrames::SeriesOrderedFrames(LoadedDicomResources& instances) :
+isVolume_(false),
+isRegular_(false),
+spacingBetweenSlices_(0)
+{
+instances_.reserve(instances.GetSize());
+size_t numberOfFrames = 0;
+for (size_t i = 0; i < instances.GetSize(); i++)
+{
+try
+{
+std::auto_ptr<Instance> instance(new Instance(instances.GetResource(i)));
+numberOfFrames += instance->GetInstanceParameters().GetImageInformation().GetNumberOfFrames();
+instances_.push_back(instance.release());
+}
+catch (Orthanc::OrthancException&)
+{
+// The instance has not all the required DICOM tags, skip it
+}
+}
+orderedFrames_.reserve(numberOfFrames);
+if (Sort3DVolume())
+{
+isVolume_ = true;
+if (isRegular_)
+{
+LOG(INFO) << "Regular 3D volume detected";
+}
+else
+{
+LOG(INFO) << "Non-regular 3D volume detected";
+}
+}
+else
+{
+LOG(INFO) << "Series is not a 3D volume, sorting by index";
+SortIndexInSeries();
+}
+LOG(INFO) << "Number of frames: " << orderedFrames_.size();
+}
+unsigned int SeriesOrderedFrames::GetFrameIndex(size_t seriesIndex) const
+{
+return GetFrame(seriesIndex).GetFrameIndex();
+}
+const Orthanc::DicomMap& SeriesOrderedFrames::GetInstance(size_t seriesIndex) const
+{
+return GetFrame(seriesIndex).GetInstance();
+}
+const DicomInstanceParameters& SeriesOrderedFrames::GetInstanceParameters(size_t seriesIndex) const
+{
+return GetFrame(seriesIndex).GetInstanceParameters();
+}
+double SeriesOrderedFrames::GetSpacingBetweenSlices() const
+{
+if (IsRegular3DVolume())
+{
+return spacingBetweenSlices_;
+}
+else
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+}
+}
+}

Mercurial > hg > orthanc-stone

comparison Framework/Loaders/SeriesOrderedFrames.cpp @ 1228:c471a0aa137b broker