orthanc-stone: OrthancStone/Sources/Toolbox/SortedFrames.cpp comparison

comparison OrthancStone/Sources/Toolbox/SortedFrames.cpp @ 1512:244ad1e4e76a

reorganization of folders

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Tue, 07 Jul 2020 16:21:02 +0200
parents	Framework/Toolbox/SortedFrames.cpp@5d892f5dd9c4
children	85e117739eca

comparison

equal deleted inserted replaced

-:9dfeee74c1e6
+:244ad1e4e76a
+/**
+* Stone of Orthanc
+* 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 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 "SortedFrames.h"
+#include "GeometryToolbox.h"
+#include <OrthancException.h>
+#include <Toolbox.h>
+namespace OrthancStone
+{
+SortedFrames::Instance::Instance(const Orthanc::DicomMap& tags)
+{
+tags_.Assign(tags);
+if (!tags.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false))
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+}
+uint32_t tmp;
+if (tags.ParseUnsignedInteger32(tmp, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))
+{
+numberOfFrames_ = tmp;
+}
+else
+{
+numberOfFrames_ = 1;
+}
+std::string photometric;
+if (tags.LookupStringValue(photometric, Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION, false))
+{
+Orthanc::Toolbox::StripSpaces(photometric);
+monochrome1_ = (photometric == "MONOCHROME1");
+}
+else
+{
+monochrome1_ = false;
+}
+hasPosition_ = (
+LinearAlgebra::ParseVector(position_, tags, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT) &&
+position_.size() == 3 &&
+GeometryToolbox::ComputeNormal(normal_, tags));
+}
+const Vector& SortedFrames::Instance::GetNormal() const
+{
+if (hasPosition_)
+{
+return normal_;
+}
+else
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+}
+}
+const Vector& SortedFrames::Instance::GetPosition() const
+{
+if (hasPosition_)
+{
+return position_;
+}
+else
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+}
+}
+SortedFrames::Frame::Frame(const Instance& instance,
+unsigned int frameIndex) :
+instance_(&instance),
+frameIndex_(frameIndex)
+{
+if (frameIndex >= instance.GetNumberOfFrames())
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+}
+}
+const SortedFrames::Instance& SortedFrames::GetInstance(size_t index) const
+{
+if (index >= instances_.size())
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+}
+else
+{
+assert(instances_[index] != NULL);
+return *instances_[index];
+}
+}
+const SortedFrames::Frame& SortedFrames::GetFrame(size_t index) const
+{
+if (!sorted_)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls,
+"Sort() has not been called");
+}
+if (index >= frames_.size())
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+}
+else
+{
+return frames_[index];
+}
+}
+void SortedFrames::Clear()
+{
+for (size_t i = 0; i < instances_.size(); i++)
+{
+assert(instances_[i] != NULL);
+delete instances_[i];
+}
+studyInstanceUid_.clear();
+seriesInstanceUid_.clear();
+frames_.clear();
+sorted_ = true;
+}
+void SortedFrames::AddInstance(const Orthanc::DicomMap& tags)
+{
+std::unique_ptr<Instance> instance(new Instance(tags));
+std::string studyInstanceUid, seriesInstanceUid;
+if (!tags.LookupStringValue(studyInstanceUid, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) ||
+!tags.LookupStringValue(seriesInstanceUid, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false))
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+}
+if (instances_.empty())
+{
+studyInstanceUid_ = studyInstanceUid;
+seriesInstanceUid_ = seriesInstanceUid;
+}
+else
+{
+if (studyInstanceUid_ != studyInstanceUid ||
+seriesInstanceUid_ != seriesInstanceUid)
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange,
+"Mixing instances from different series");
+}
+}
+instances_.push_back(instance.release());
+sorted_ = false;
+frames_.clear();
+}
+void SortedFrames::AddFramesOfInstance(std::set<size_t>& remainingInstances,
+size_t index)
+{
+assert(instances_[index] != NULL);
+const Instance& instance = *instances_[index];
+for (unsigned int i = 0; i < instance.GetNumberOfFrames(); i++)
+{
+frames_.push_back(Frame(instance, i));
+}
+assert(remainingInstances.find(index) != remainingInstances.end());
+remainingInstances.erase(index);
+}
+namespace
+{
+template<typename T>
+class SortableItem
+{
+private:
+T            value_;
+size_t       instance_;
+std::string  sopInstanceUid_;
+public:
+SortableItem(const T& value,
+size_t instance,
+const std::string& sopInstanceUid) :
+value_(value),
+instance_(instance),
+sopInstanceUid_(sopInstanceUid)
+{
+}
+size_t GetInstanceIndex() const
+{
+return instance_;
+}
+bool operator< (const SortableItem& other) const
+{
+return (value_ < other.value_ ||
+(value_ == other.value_ &&
+sopInstanceUid_ < other.sopInstanceUid_));
+}
+};
+}
+void SortedFrames::SortUsingIntegerTag(std::set<size_t>& remainingInstances,
+const Orthanc::DicomTag& tag)
+{
+std::vector< SortableItem<int32_t> > items;
+items.reserve(remainingInstances.size());
+for (std::set<size_t>::const_iterator it = remainingInstances.begin();
+it != remainingInstances.end(); ++it)
+{
+assert(instances_[*it] != NULL);
+const Instance& instance = *instances_[*it];
+int32_t value;
+std::string sopInstanceUid;
+if (instance.GetTags().ParseInteger32(value, tag) &&
+instance.GetTags().LookupStringValue(
+sopInstanceUid, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false))
+{
+items.push_back(SortableItem<int32_t>(value, *it, sopInstanceUid));
+}
+}
+std::sort(items.begin(), items.end());
+for (size_t i = 0; i < items.size(); i++)
+{
+AddFramesOfInstance(remainingInstances, items[i].GetInstanceIndex());
+}
+}
+void SortedFrames::SortUsingSopInstanceUid(std::set<size_t>& remainingInstances)
+{
+std::vector<SortableItem<int32_t> > items;
+items.reserve(remainingInstances.size());
+for (std::set<size_t>::const_iterator it = remainingInstances.begin();
+it != remainingInstances.end(); ++it)
+{
+assert(instances_[*it] != NULL);
+const Instance& instance = *instances_[*it];
+std::string sopInstanceUid;
+if (instance.GetTags().LookupStringValue(
+sopInstanceUid, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false))
+{
+items.push_back(SortableItem<int32_t>(0 /* arbitrary value */, *it, sopInstanceUid));
+}
+}
+std::sort(items.begin(), items.end());
+for (size_t i = 0; i < items.size(); i++)
+{
+AddFramesOfInstance(remainingInstances, items[i].GetInstanceIndex());
+}
+}
+void SortedFrames::SortUsing3DLocation(std::set<size_t>& remainingInstances)
+{
+/**
+* Compute the mean of the normal vectors, using the recursive
+* formula for arithmetic means for numerical stability.
+* https://diego.assencio.com/?index=c34d06f4f4de2375658ed41f70177d59
+**/
+Vector meanNormal;
+LinearAlgebra::AssignVector(meanNormal, 0, 0, 0);
+unsigned int n = 0;
+for (std::set<size_t>::const_iterator it = remainingInstances.begin();
+it != remainingInstances.end(); ++it)
+{
+assert(instances_[*it] != NULL);
+const Instance& instance = *instances_[*it];
+if (instance.HasPosition())
+{
+n += 1;
+meanNormal += (instance.GetNormal() - meanNormal) / static_cast<float>(n);
+}
+}
+std::vector<SortableItem<float> > items;
+items.reserve(n);
+for (std::set<size_t>::const_iterator it = remainingInstances.begin();
+it != remainingInstances.end(); ++it)
+{
+assert(instances_[*it] != NULL);
+const Instance& instance = *instances_[*it];
+std::string sopInstanceUid;
+if (instance.HasPosition() &&
+instance.GetTags().LookupStringValue(
+sopInstanceUid, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false))
+{
+double p = LinearAlgebra::DotProduct(meanNormal, instance.GetPosition());
+items.push_back(SortableItem<float>(p, *it, sopInstanceUid));
+}
+}
+assert(items.size() <= n);
+std::sort(items.begin(), items.end());
+for (size_t i = 0; i < items.size(); i++)
+{
+AddFramesOfInstance(remainingInstances, items[i].GetInstanceIndex());
+}
+}
+size_t SortedFrames::GetFramesCount() const
+{
+if (sorted_)
+{
+return frames_.size();
+}
+else
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls,
+"Sort() has not been called");
+}
+}
+void SortedFrames::Sort()
+{
+if (!sorted_)
+{
+size_t totalFrames = 0;
+std::set<size_t> remainingInstances;
+for (size_t i = 0; i < instances_.size(); i++)
+{
+assert(instances_[i] != NULL);
+totalFrames += instances_[i]->GetNumberOfFrames();
+remainingInstances.insert(i);
+}
+frames_.clear();
+frames_.reserve(totalFrames);
+SortUsingIntegerTag(remainingInstances, Orthanc::DICOM_TAG_INSTANCE_NUMBER);  // VR is "IS"
+SortUsingIntegerTag(remainingInstances, Orthanc::DICOM_TAG_IMAGE_INDEX);  // VR is "US"
+SortUsing3DLocation(remainingInstances);
+SortUsingSopInstanceUid(remainingInstances);
+// The following could in theory happen if several instances
+// have the same SOPInstanceUID, no ordering is available
+for (std::set<size_t>::const_iterator it = remainingInstances.begin();
+it != remainingInstances.end(); it++)
+{
+AddFramesOfInstance(remainingInstances, *it);
+}
+if (frames_.size() != totalFrames ||
+!remainingInstances.empty())
+{
+throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+}
+sorted_ = true;
+}
+}
+}

Mercurial > hg > orthanc-stone

comparison OrthancStone/Sources/Toolbox/SortedFrames.cpp @ 1512:244ad1e4e76a