diff --git a/Modules/SemanticRelations/src/mitkSemanticRelationsInference.cpp b/Modules/SemanticRelations/src/mitkSemanticRelationsInference.cpp index a974ed4571..ef3610ceb7 100644 --- a/Modules/SemanticRelations/src/mitkSemanticRelationsInference.cpp +++ b/Modules/SemanticRelations/src/mitkSemanticRelationsInference.cpp @@ -1,591 +1,586 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkSemanticRelationsInference.h" // semantic relations module #include "mitkControlPointManager.h" #include "mitkDICOMHelper.h" #include "mitkNodePredicates.h" #include "mitkRelationStorage.h" #include "mitkSemanticRelationException.h" /************************************************************************/ /* functions to get instances / attributes */ /************************************************************************/ mitk::SemanticTypes::LesionClassVector mitk::SemanticRelationsInference::GetAllLesionClassesOfCase(const SemanticTypes::CaseID& caseID) { SemanticTypes::LesionVector allLesionsOfCase = RelationStorage::GetAllLesionsOfCase(caseID); SemanticTypes::LesionClassVector allLesionClassesOfCase; for (const auto& lesion : allLesionsOfCase) { allLesionClassesOfCase.push_back(lesion.lesionClass); } // remove duplicate entries auto lessThan = [](const SemanticTypes::LesionClass& lesionClassLeft, const SemanticTypes::LesionClass& lesionClassRight) { return lesionClassLeft.UID < lesionClassRight.UID; }; auto equal = [](const SemanticTypes::LesionClass& lesionClassLeft, const SemanticTypes::LesionClass& lesionClassRight) { return lesionClassLeft.UID == lesionClassRight.UID; }; std::sort(allLesionClassesOfCase.begin(), allLesionClassesOfCase.end(), lessThan); allLesionClassesOfCase.erase(std::unique(allLesionClassesOfCase.begin(), allLesionClassesOfCase.end(), equal), allLesionClassesOfCase.end()); return allLesionClassesOfCase; } mitk::SemanticTypes::Lesion mitk::SemanticRelationsInference::GetLesionOfSegmentation(const DataNode* segmentationNode) { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } SemanticTypes::CaseID caseID = ""; SemanticTypes::ID segmentationID = ""; try { caseID = GetCaseIDFromDataNode(segmentationNode); segmentationID = GetIDFromDataNode(segmentationNode); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get the lesion of the given segmentation data node."; } return RelationStorage::GetLesionOfSegmentation(caseID, segmentationID); } mitk::SemanticTypes::LesionVector mitk::SemanticRelationsInference::GetAllLesionsOfImage(const DataNode* imageNode) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid image data node."; } SemanticTypes::CaseID caseID = ""; SemanticTypes::ID imageID = ""; try { caseID = GetCaseIDFromDataNode(imageNode); imageID = GetIDFromDataNode(imageNode); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get all lesions of the given image data node."; } SemanticTypes::LesionVector allLesionsOfImage; // 1. get all segmentations that are connected to the given image // 2. get the lesion of each segmentation // 3. guarantee uniqueness of lesions SemanticTypes::IDVector allSegmentationIDsOfImage = RelationStorage::GetAllSegmentationIDsOfImage(caseID, imageID); for (const auto& segmentationID : allSegmentationIDsOfImage) { // get represented lesion of the current segmentation SemanticTypes::Lesion representedLesion = RelationStorage::GetLesionOfSegmentation(caseID, segmentationID); if (!representedLesion.UID.empty()) { allLesionsOfImage.push_back(representedLesion); } } // remove duplicate entries auto lessThan = [](const SemanticTypes::Lesion& lesionLeft, const SemanticTypes::Lesion& lesionRight) { return lesionLeft.UID < lesionRight.UID; }; auto equal = [](const SemanticTypes::Lesion& lesionLeft, const SemanticTypes::Lesion& lesionRight) { return lesionLeft.UID == lesionRight.UID; }; std::sort(allLesionsOfImage.begin(), allLesionsOfImage.end(), lessThan); allLesionsOfImage.erase(std::unique(allLesionsOfImage.begin(), allLesionsOfImage.end(), equal), allLesionsOfImage.end()); return allLesionsOfImage; } mitk::SemanticTypes::LesionVector mitk::SemanticRelationsInference::GetAllLesionsOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::LesionVector allLesions = RelationStorage::GetAllLesionsOfCase(caseID); // filter the lesions: use only those, where the associated data is connected to image data that refers to the given control point using a lambda function auto lambda = [&caseID, &controlPoint](const SemanticTypes::Lesion& lesion) { return !SpecificImageExists(caseID, lesion, controlPoint); }; allLesions.erase(std::remove_if(allLesions.begin(), allLesions.end(), lambda), allLesions.end()); return allLesions; } mitk::SemanticTypes::LesionVector mitk::SemanticRelationsInference::GetAllLesionsOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) { SemanticTypes::LesionVector allLesions = RelationStorage::GetAllLesionsOfCase(caseID); // filter the lesions: use only those, where the associated data is connected to image data that refers to the given information type using a lambda function auto lambda = [&caseID, &informationType](const SemanticTypes::Lesion& lesion) { return !SpecificImageExists(caseID, lesion, informationType); }; allLesions.erase(std::remove_if(allLesions.begin(), allLesions.end(), lambda), allLesions.end()); return allLesions; } mitk::SemanticTypes::LesionVector mitk::SemanticRelationsInference::GetAllSpecificLesions(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) { auto allLesionsOfControlPoint = GetAllLesionsOfControlPoint(caseID, controlPoint); auto allLesionsOfInformationType = GetAllLesionsOfInformationType(caseID, informationType); SemanticTypes::LesionVector allLesionsIntersection; auto lessThan = [](const SemanticTypes::Lesion& lesionLeft, const SemanticTypes::Lesion& lesionRight) { return lesionLeft.UID < lesionRight.UID; }; - auto equal = [](const SemanticTypes::Lesion& lesionLeft, const SemanticTypes::Lesion& lesionRight) - { - return lesionLeft.UID == lesionRight.UID; - }; - std::sort(allLesionsOfControlPoint.begin(), allLesionsOfControlPoint.end(), lessThan); std::sort(allLesionsOfInformationType.begin(), allLesionsOfInformationType.end(), lessThan); SemanticTypes::IDVector allImageIDsIntersection; // set_intersection removes duplicated nodes std::set_intersection(allLesionsOfControlPoint.begin(), allLesionsOfControlPoint.end(), allLesionsOfInformationType.begin(), allLesionsOfInformationType.end(), - std::back_inserter(allLesionsIntersection), equal); + std::back_inserter(allLesionsIntersection), lessThan); return allLesionsIntersection; } bool mitk::SemanticRelationsInference::IsRepresentingALesion(const DataNode* segmentationNode) { SemanticTypes::Lesion representedLesion; try { representedLesion = GetLesionOfSegmentation(segmentationNode); } catch (const SemanticRelationException&) { return false; } return !representedLesion.UID.empty(); } bool mitk::SemanticRelationsInference::IsRepresentingALesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID) { SemanticTypes::Lesion representedLesion = RelationStorage::GetLesionOfSegmentation(caseID, segmentationID); return !representedLesion.UID.empty(); } bool mitk::SemanticRelationsInference::IsLesionPresent(const SemanticTypes::Lesion& lesion, const DataNode* dataNode) { SemanticTypes::CaseID caseID = ""; SemanticTypes::ID dataNodeID = ""; try { caseID = GetCaseIDFromDataNode(dataNode); dataNodeID = GetIDFromDataNode(dataNode); } catch (const SemanticRelationException&) { return false; } if (NodePredicates::GetImagePredicate()->CheckNode(dataNode)) { return IsLesionPresentOnImage(caseID, lesion, dataNodeID); } if (NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode)) { return IsLesionPresentOnSegmentation(caseID, lesion, dataNodeID); } return false; } bool mitk::SemanticRelationsInference::IsLesionPresentOnImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ID& imageID) { SemanticTypes::IDVector allImageIDsOfLesion; try { allImageIDsOfLesion = GetAllImageIDsOfLesion(caseID, lesion); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get all image IDs of the given lesion to determine the lesion presence."; } for (const auto& imageIDOfLesion : allImageIDsOfLesion) { if (imageIDOfLesion == imageID) { return true; } } return false; } bool mitk::SemanticRelationsInference::IsLesionPresentOnSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ID& segmentationID) { const auto representedLesion = RelationStorage::GetLesionOfSegmentation(caseID, segmentationID); return lesion.UID == representedLesion.UID; } bool mitk::SemanticRelationsInference::IsLesionPresentAtControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::IDVector allImageIDsOfLesion; try { allImageIDsOfLesion = GetAllImageIDsOfLesion(caseID, lesion); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get all image IDs of the given lesion to determine the lesion presence."; } for (const auto& imageIDOfLesion : allImageIDsOfLesion) { auto imageControlPoint = RelationStorage::GetControlPointOfImage(caseID, imageIDOfLesion); if (imageControlPoint.date == controlPoint.date) { return true; } } return false; } bool mitk::SemanticRelationsInference::InstanceExists(const DataNode* dataNode) { SemanticTypes::CaseID caseID = ""; SemanticTypes::ID dataNodeID = ""; try { caseID = GetCaseIDFromDataNode(dataNode); dataNodeID = GetIDFromDataNode(dataNode); } catch (const SemanticRelationException&) { return false; } if (NodePredicates::GetImagePredicate()->CheckNode(dataNode)) { SemanticTypes::IDVector allImageIDsOfCase = RelationStorage::GetAllImageIDsOfCase(caseID); return std::find(allImageIDsOfCase.begin(), allImageIDsOfCase.end(), dataNodeID) != allImageIDsOfCase.end(); } if (NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode)) { SemanticTypes::IDVector allSegmentationIDsOfCase = RelationStorage::GetAllSegmentationIDsOfCase(caseID); return std::find(allSegmentationIDsOfCase.begin(), allSegmentationIDsOfCase.end(), dataNodeID) != allSegmentationIDsOfCase.end(); } return false; } bool mitk::SemanticRelationsInference::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { SemanticTypes::LesionVector allLesions = RelationStorage::GetAllLesionsOfCase(caseID); // filter all lesions: check for equality with the given lesion using a lambda function auto lambda = [&lesion](const SemanticTypes::Lesion& currentLesion) { return currentLesion.UID == lesion.UID; }; const auto existingLesion = std::find_if(allLesions.begin(), allLesions.end(), lambda); return existingLesion != allLesions.end(); } mitk::SemanticTypes::IDVector mitk::SemanticRelationsInference::GetAllImageIDsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { if (!InstanceExists(caseID, lesion)) { mitkThrowException(SemanticRelationException) << "Could not find an existing lesion instance for the given caseID " << caseID << " and lesion " << lesion.UID << "."; } SemanticTypes::IDVector allImageIDsOfLesion; // 1. get all segmentations that define the lesion // 2. get the parentID (imageID) of each segmentation // 3. guarantee uniqueness of image IDs SemanticTypes::IDVector allSegmentationIDsOfLesion = RelationStorage::GetAllSegmentationIDsOfLesion(caseID, lesion); for (const auto& segmentationID : allSegmentationIDsOfLesion) { // get parent ID of the current segmentation ID SemanticTypes::ID imageID = RelationStorage::GetImageIDOfSegmentation(caseID, segmentationID); if(!imageID.empty()) { allImageIDsOfLesion.push_back(imageID); } } std::sort(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end()); allImageIDsOfLesion.erase(std::unique(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end()), allImageIDsOfLesion.end()); return allImageIDsOfLesion; } mitk::SemanticTypes::IDVector mitk::SemanticRelationsInference::GetAllImageIDsOfExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod) { if (!InstanceExists(caseID, examinationPeriod)) { mitkThrowException(SemanticRelationException) << "Could not find an existing examination period for the given caseID " << caseID << " and examination period " << examinationPeriod.name << "."; } SemanticTypes::IDVector allImageIDsOfExaminationPeriod; // 1. get all control point UIDs of the examination period // 2. get all images of each control points to find all images of the examination period SemanticTypes::ControlPoint controlPoint; for (const auto& controlPointUID : examinationPeriod.controlPointUIDs) { controlPoint = GetControlPointByUID(caseID, controlPointUID); auto allImageIDsOfControlPoint = RelationStorage::GetAllImageIDsOfControlPoint(caseID, controlPoint); allImageIDsOfExaminationPeriod.insert(allImageIDsOfExaminationPeriod.end(), allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end()); } return allImageIDsOfExaminationPeriod; } mitk::SemanticTypes::ControlPoint mitk::SemanticRelationsInference::GetControlPointOfImage(const DataNode* imageNode) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = ""; SemanticTypes::ID imageID = ""; try { caseID = GetCaseIDFromDataNode(imageNode); imageID = GetIDFromDataNode(imageNode); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get the control point of the given image data node."; } return RelationStorage::GetControlPointOfImage(caseID, imageID); } mitk::SemanticTypes::ControlPointVector mitk::SemanticRelationsInference::GetAllControlPointsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID); // filter the control points: use only those, where the associated image data has a segmentation that refers to the given lesion using a lambda function auto lambda = [&caseID, &lesion](const SemanticTypes::ControlPoint& controlPoint) { return !SpecificImageExists(caseID, lesion, controlPoint); }; allControlPoints.erase(std::remove_if(allControlPoints.begin(), allControlPoints.end(), lambda), allControlPoints.end()); return allControlPoints; } mitk::SemanticTypes::ControlPointVector mitk::SemanticRelationsInference::GetAllControlPointsOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) { SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID); // filter the control points: use only those, where the associated image data refers to the given information type using a lambda function auto lambda = [&caseID, &informationType](const SemanticTypes::ControlPoint& controlPoint) { return !SpecificImageExists(caseID, informationType, controlPoint); }; allControlPoints.erase(std::remove_if(allControlPoints.begin(), allControlPoints.end(), lambda), allControlPoints.end()); return allControlPoints; } bool mitk::SemanticRelationsInference::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID); // filter all control points: check for equality with the given control point using a lambda function auto lambda = [&controlPoint](const SemanticTypes::ControlPoint& currentControlPoint) { return currentControlPoint.UID == controlPoint.UID; }; const auto existingControlPoint = std::find_if(allControlPoints.begin(), allControlPoints.end(), lambda); if (existingControlPoint != allControlPoints.end()) { return true; } else { return false; } } bool mitk::SemanticRelationsInference::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod) { SemanticTypes::ExaminationPeriodVector allExaminationPeriods = RelationStorage::GetAllExaminationPeriodsOfCase(caseID); // filter all examination periods: check for equality with the given examination period using a lambda function auto lambda = [&examinationPeriod](const SemanticTypes::ExaminationPeriod& currentExaminationPeriod) { return currentExaminationPeriod.UID == examinationPeriod.UID; }; const auto existingExaminationPeriod = std::find_if(allExaminationPeriods.begin(), allExaminationPeriods.end(), lambda); if (existingExaminationPeriod != allExaminationPeriods.end()) { return true; } else { return false; } } mitk::SemanticTypes::InformationType mitk::SemanticRelationsInference::GetInformationTypeOfImage(const DataNode* imageNode) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid image data node."; } SemanticTypes::CaseID caseID = ""; SemanticTypes::ID imageID = ""; try { caseID = GetCaseIDFromDataNode(imageNode); imageID = GetIDFromDataNode(imageNode); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get the information type of the given image data node."; } return RelationStorage::GetInformationTypeOfImage(caseID, imageID); } mitk::SemanticTypes::InformationTypeVector mitk::SemanticRelationsInference::GetAllInformationTypesOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::InformationTypeVector allInformationTypes = RelationStorage::GetAllInformationTypesOfCase(caseID); // filter the information types: use only those, where the associated data refers to the given control point using a lambda function auto lambda = [&caseID, &controlPoint](const SemanticTypes::InformationType& informationType) { return !SpecificImageExists(caseID, informationType, controlPoint); }; allInformationTypes.erase(std::remove_if(allInformationTypes.begin(), allInformationTypes.end(), lambda), allInformationTypes.end()); return allInformationTypes; } bool mitk::SemanticRelationsInference::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) { SemanticTypes::InformationTypeVector allInformationTypes = RelationStorage::GetAllInformationTypesOfCase(caseID); // filter all information types: check for equality with the given information type using a lambda function auto lambda = [&informationType](const SemanticTypes::InformationType& currentInformationType) { return currentInformationType == informationType; }; const auto existingInformationType = std::find_if(allInformationTypes.begin(), allInformationTypes.end(), lambda); if (existingInformationType != allInformationTypes.end()) { return true; } else { return false; } } bool mitk::SemanticRelationsInference::SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::InformationType& informationType) { SemanticTypes::IDVector allImageIDsOfLesion; try { allImageIDsOfLesion = GetAllImageIDsOfLesion(caseID, lesion); } catch (const SemanticRelationException&) { return false; } SemanticTypes::IDVector allImageIDsOfInformationType = RelationStorage::GetAllImageIDsOfInformationType(caseID, informationType); std::sort(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end()); std::sort(allImageIDsOfInformationType.begin(), allImageIDsOfInformationType.end()); SemanticTypes::IDVector allImageIDsIntersection; // set_intersection removes duplicated nodes, since 'GetAllImageIDsOfInformationType' only contains at most one of each node std::set_intersection(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end(), allImageIDsOfInformationType.begin(), allImageIDsOfInformationType.end(), std::back_inserter(allImageIDsIntersection)); // if the vector of intersecting image IDs is empty, the information type does not contain the lesion return !allImageIDsIntersection.empty(); } bool mitk::SemanticRelationsInference::SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::IDVector allImageIDsOfLesion; try { allImageIDsOfLesion = GetAllImageIDsOfLesion(caseID, lesion); } catch (const SemanticRelationException&) { return false; } SemanticTypes::IDVector allImageIDsOfControlPoint = RelationStorage::GetAllImageIDsOfControlPoint(caseID, controlPoint); std::sort(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end()); std::sort(allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end()); SemanticTypes::IDVector allImageIDsIntersection; // set_intersection removes duplicated nodes, since 'GetAllImageIDsOfControlPoint' only contains at most one of each node std::set_intersection(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end(), allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end(), std::back_inserter(allImageIDsIntersection)); // if the vector of intersecting image IDs is empty, the control point does not contain the lesion return !allImageIDsIntersection.empty(); } bool mitk::SemanticRelationsInference::SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::IDVector allImageIDsOfInformationType = RelationStorage::GetAllImageIDsOfInformationType(caseID, informationType); SemanticTypes::IDVector allImageIDsOfControlPoint = RelationStorage::GetAllImageIDsOfControlPoint(caseID, controlPoint); std::sort(allImageIDsOfInformationType.begin(), allImageIDsOfInformationType.end()); std::sort(allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end()); SemanticTypes::IDVector allImageIDsIntersection; // set_intersection removes duplicated nodes std::set_intersection(allImageIDsOfInformationType.begin(), allImageIDsOfInformationType.end(), allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end(), std::back_inserter(allImageIDsIntersection)); // if the vector of intersecting image IDs is empty no image exists for the given information type and control point return !allImageIDsIntersection.empty(); }