Mercurial > hg > orthanc
view OrthancServer/SliceOrdering.cpp @ 3664:85acfcc15829 storage-commitment
sample storage commitment plugin, C++ wrapper
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 12 Feb 2020 16:06:58 +0100 |
parents | 94f4a18a79cc |
children | 104e27133ebd |
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/** * Orthanc - A Lightweight, RESTful DICOM Store * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * Copyright (C) 2017-2020 Osimis S.A., 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/>. **/ #include "PrecompiledHeadersServer.h" #include "SliceOrdering.h" #include "../Core/Logging.h" #include "../Core/Toolbox.h" #include "ServerEnumerations.h" #include "ServerIndex.h" #include <algorithm> #include <boost/lexical_cast.hpp> #include <boost/noncopyable.hpp> namespace Orthanc { static bool TokenizeVector(std::vector<float>& result, const std::string& value, unsigned int expectedSize) { std::vector<std::string> tokens; Toolbox::TokenizeString(tokens, value, '\\'); if (tokens.size() != expectedSize) { return false; } result.resize(tokens.size()); for (size_t i = 0; i < tokens.size(); i++) { try { result[i] = boost::lexical_cast<float>(tokens[i]); } catch (boost::bad_lexical_cast&) { return false; } } return true; } static bool TokenizeVector(std::vector<float>& result, const DicomMap& map, const DicomTag& tag, unsigned int expectedSize) { const DicomValue* value = map.TestAndGetValue(tag); if (value == NULL || value->IsNull() || value->IsBinary()) { return false; } else { return TokenizeVector(result, value->GetContent(), expectedSize); } } static bool IsCloseToZero(double x) { return fabs(x) < 10.0 * std::numeric_limits<float>::epsilon(); } bool SliceOrdering::ComputeNormal(Vector& normal, const DicomMap& dicom) { std::vector<float> cosines; if (TokenizeVector(cosines, dicom, DICOM_TAG_IMAGE_ORIENTATION_PATIENT, 6)) { assert(cosines.size() == 6); normal[0] = cosines[1] * cosines[5] - cosines[2] * cosines[4]; normal[1] = cosines[2] * cosines[3] - cosines[0] * cosines[5]; normal[2] = cosines[0] * cosines[4] - cosines[1] * cosines[3]; return true; } else { return false; } } bool SliceOrdering::IsParallelOrOpposite(const Vector& u, const Vector& v) { // Check out "GeometryToolbox::IsParallelOrOpposite()" in Stone of // Orthanc for explanations const double u1 = u[0]; const double u2 = u[1]; const double u3 = u[2]; const double normU = sqrt(u1 * u1 + u2 * u2 + u3 * u3); const double v1 = v[0]; const double v2 = v[1]; const double v3 = v[2]; const double normV = sqrt(v1 * v1 + v2 * v2 + v3 * v3); if (IsCloseToZero(normU * normV)) { return false; } else { const double cosAngle = (u1 * v1 + u2 * v2 + u3 * v3) / (normU * normV); return (IsCloseToZero(cosAngle - 1.0) || // Close to +1: Parallel, non-opposite IsCloseToZero(fabs(cosAngle) - 1.0)); // Close to -1: Parallel, opposite } } struct SliceOrdering::Instance : public boost::noncopyable { private: std::string instanceId_; bool hasPosition_; Vector position_; bool hasNormal_; Vector normal_; bool hasIndexInSeries_; size_t indexInSeries_; unsigned int framesCount_; public: Instance(ServerIndex& index, const std::string& instanceId) : instanceId_(instanceId), framesCount_(1) { DicomMap instance; if (!index.GetMainDicomTags(instance, instanceId, ResourceType_Instance, ResourceType_Instance)) { throw OrthancException(ErrorCode_UnknownResource); } const DicomValue* frames = instance.TestAndGetValue(DICOM_TAG_NUMBER_OF_FRAMES); if (frames != NULL && !frames->IsNull() && !frames->IsBinary()) { try { framesCount_ = boost::lexical_cast<unsigned int>(frames->GetContent()); } catch (boost::bad_lexical_cast&) { } } std::vector<float> tmp; hasPosition_ = TokenizeVector(tmp, instance, DICOM_TAG_IMAGE_POSITION_PATIENT, 3); if (hasPosition_) { position_[0] = tmp[0]; position_[1] = tmp[1]; position_[2] = tmp[2]; } hasNormal_ = ComputeNormal(normal_, instance); std::string s; hasIndexInSeries_ = false; try { if (index.LookupMetadata(s, instanceId, MetadataType_Instance_IndexInSeries)) { indexInSeries_ = boost::lexical_cast<size_t>(s); hasIndexInSeries_ = true; } } catch (boost::bad_lexical_cast&) { } } const std::string& GetIdentifier() const { return instanceId_; } bool HasPosition() const { return hasPosition_; } float ComputeRelativePosition(const Vector& normal) const { assert(HasPosition()); return (normal[0] * position_[0] + normal[1] * position_[1] + normal[2] * position_[2]); } bool HasIndexInSeries() const { return hasIndexInSeries_; } size_t GetIndexInSeries() const { assert(HasIndexInSeries()); return indexInSeries_; } unsigned int GetFramesCount() const { return framesCount_; } bool HasNormal() const { return hasNormal_; } const Vector& GetNormal() const { assert(hasNormal_); return normal_; } }; class SliceOrdering::PositionComparator { private: const Vector& normal_; public: PositionComparator(const Vector& normal) : normal_(normal) { } int operator() (const Instance* a, const Instance* b) const { return a->ComputeRelativePosition(normal_) < b->ComputeRelativePosition(normal_); } }; bool SliceOrdering::IndexInSeriesComparator(const SliceOrdering::Instance* a, const SliceOrdering::Instance* b) { return a->GetIndexInSeries() < b->GetIndexInSeries(); } void SliceOrdering::ComputeNormal() { DicomMap series; if (!index_.GetMainDicomTags(series, seriesId_, ResourceType_Series, ResourceType_Series)) { throw OrthancException(ErrorCode_UnknownResource); } hasNormal_ = ComputeNormal(normal_, series); } void SliceOrdering::CreateInstances() { std::list<std::string> instancesId; index_.GetChildren(instancesId, seriesId_); instances_.reserve(instancesId.size()); for (std::list<std::string>::const_iterator it = instancesId.begin(); it != instancesId.end(); ++it) { instances_.push_back(new Instance(index_, *it)); } } bool SliceOrdering::SortUsingPositions() { if (instances_.size() <= 1) { // One single instance: It is sorted by default sortedInstances_ = instances_; return true; } if (!hasNormal_) { return false; } sortedInstances_.clear(); // consider only the instances with a position and correctly oriented (if they have a normal) for (size_t i = 0; i < instances_.size(); i++) { assert(instances_[i] != NULL); if (instances_[i]->HasPosition() && (!instances_[i]->HasNormal() || IsParallelOrOpposite(instances_[i]->GetNormal(), normal_))) { sortedInstances_.push_back(instances_[i]); } } if (sortedInstances_.size() == 0) { return false; } PositionComparator comparator(normal_); std::sort(sortedInstances_.begin(), sortedInstances_.end(), comparator); float a = sortedInstances_[0]->ComputeRelativePosition(normal_); for (size_t i = 1; i < sortedInstances_.size(); i++) { float b = sortedInstances_[i]->ComputeRelativePosition(normal_); if (std::fabs(b - a) <= 10.0f * std::numeric_limits<float>::epsilon()) { // Not enough space between two slices along the normal of the volume return false; } a = b; } // This is a 3D volume isVolume_ = true; return true; } bool SliceOrdering::SortUsingIndexInSeries() { if (instances_.size() <= 1) { // One single instance: It is sorted by default sortedInstances_ = instances_; return true; } sortedInstances_.clear(); // consider only the instances with an index for (size_t i = 0; i < instances_.size(); i++) { assert(instances_[i] != NULL); if (instances_[i]->HasIndexInSeries()) { sortedInstances_.push_back(instances_[i]); } } if (sortedInstances_.size() == 0) // if we were not able to sort instances because none of them had an index, return all instances in a "random" order { sortedInstances_ = instances_; } else { std::sort(sortedInstances_.begin(), sortedInstances_.end(), IndexInSeriesComparator); for (size_t i = 1; i < sortedInstances_.size(); i++) { if (sortedInstances_[i - 1]->GetIndexInSeries() == sortedInstances_[i]->GetIndexInSeries()) { // The current "IndexInSeries" occurs 2 times: Not a proper ordering LOG(WARNING) << "This series contains 2 slices with the same index, trying to display it anyway"; break; } } } return true; } SliceOrdering::SliceOrdering(ServerIndex& index, const std::string& seriesId) : index_(index), seriesId_(seriesId), isVolume_(false) { ComputeNormal(); CreateInstances(); if (!SortUsingPositions() && !SortUsingIndexInSeries()) { throw OrthancException(ErrorCode_CannotOrderSlices, "Unable to order the slices of series " + seriesId); } } SliceOrdering::~SliceOrdering() { for (std::vector<Instance*>::iterator it = instances_.begin(); it != instances_.end(); ++it) { if (*it != NULL) { delete *it; } } } const std::string& SliceOrdering::GetSortedInstanceId(size_t index) const { if (index >= sortedInstances_.size()) { throw OrthancException(ErrorCode_ParameterOutOfRange); } else { return sortedInstances_[index]->GetIdentifier(); } } unsigned int SliceOrdering::GetSortedInstanceFramesCount(size_t index) const { if (index >= sortedInstances_.size()) { throw OrthancException(ErrorCode_ParameterOutOfRange); } else { return sortedInstances_[index]->GetFramesCount(); } } void SliceOrdering::Format(Json::Value& result) const { result = Json::objectValue; result["Type"] = (isVolume_ ? "Volume" : "Sequence"); Json::Value tmp = Json::arrayValue; for (size_t i = 0; i < GetSortedInstancesCount(); i++) { tmp.append(GetBasePath(ResourceType_Instance, GetSortedInstanceId(i)) + "/file"); } result["Dicom"] = tmp; Json::Value slicesShort = Json::arrayValue; tmp.clear(); for (size_t i = 0; i < GetSortedInstancesCount(); i++) { std::string base = GetBasePath(ResourceType_Instance, GetSortedInstanceId(i)); for (size_t j = 0; j < GetSortedInstanceFramesCount(i); j++) { tmp.append(base + "/frames/" + boost::lexical_cast<std::string>(j)); } Json::Value tmp2 = Json::arrayValue; tmp2.append(GetSortedInstanceId(i)); tmp2.append(0); tmp2.append(GetSortedInstanceFramesCount(i)); slicesShort.append(tmp2); } result["Slices"] = tmp; result["SlicesShort"] = slicesShort; } }