Mercurial > hg > orthanc-stone
view OrthancStone/Sources/Loaders/SeriesOrderedFrames.cpp @ 2174:2410a171ebfb
refactoring using DicomWebDataset and OrthancNativeDataset
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 22 Oct 2024 21:52:34 +0200 |
parents | 16c01cc201e7 |
children |
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/** * Stone of Orthanc * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * Copyright (C) 2017-2023 Osimis S.A., Belgium * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium * * This program is free software: you can redistribute it and/or * modify it under the terms of the GNU Lesser 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 * Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this program. If not, see * <http://www.gnu.org/licenses/>. **/ #include "../Toolbox/SlicesSorter.h" #include "SeriesOrderedFrames.h" #include <Logging.h> #include <OrthancException.h> namespace OrthancStone { class SeriesOrderedFrames::Instance : public boost::noncopyable { private: std::unique_ptr<Orthanc::DicomMap> dicom_; DicomInstanceParameters parameters_; public: explicit 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: explicit 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(), static_cast<unsigned int>(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(), static_cast<unsigned int>(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::unique_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); } } }