diff --git a/Modules/SemanticRelations/include/mitkControlPointManager.h b/Modules/SemanticRelations/include/mitkControlPointManager.h index a9bd1f33bb..ced8bd1e44 100644 --- a/Modules/SemanticRelations/include/mitkControlPointManager.h +++ b/Modules/SemanticRelations/include/mitkControlPointManager.h @@ -1,61 +1,80 @@ /*=================================================================== 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. ===================================================================*/ #ifndef MITKCONTROLPOINTMANAGER_H #define MITKCONTROLPOINTMANAGER_H // semantic relations module #include "mitkSemanticTypes.h" #include // mitk core #include namespace mitk { /* * @brief Provides helper functions that are needed to work with control points. * * These functions help to generate new control points, check for overlapping / containing control points or provide functionality * to find a fitting control point or even extend an already existing control point. */ /* * @brief Generates a control point from a given data node. * The date is extracted from the data node by using the 'DICOMHelper::GetDICOMDateFromDataNode'-function. * 'GenerateControlPoint(const SemanticTypes::TimePoint&)' is used to generate a new control point from this extracted date. * * @par datanode A data node pointer, whose date should be included in the newly generated control point. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint GenerateControlPoint(const mitk::DataNode* datanode); /* * @brief Returns a string that displays the given control point in the format "YYYY-MM-DD". * This function is used in the GUI to display the control point as header in the "information-type - control-point"-matrix. * * @par controlPoint The control point to convert into a string. */ MITKSEMANTICRELATIONS_EXPORT std::string GetControlPointAsString(const SemanticTypes::ControlPoint& controlPoint); /** * @brief Returns an already existing control point from the given vector of control points. This existing control point has the * the same date (year, month, day) as the given single control point. * If no existing control point can be found an empty control point is returned. * * @par controlPoint The control point to check for existence. * @par allControlPoints The vector of already existing control points. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint FindExistingControlPoint(const SemanticTypes::ControlPoint& controlPoint, std::vector& allControlPoints); + /** + * @brief Returns an already existing close control point from the given vector of control points. This closest control point has a date + * date that is within a certain distance-in-days to the given control point. + * If no closest control point can be found within the distance threshold an empty control point is returned. + * + * @par controlPoint The control point to check for distance. + * @par allControlPoints The vector of already existing control points. + */ + MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint FindClosestControlPoint(const SemanticTypes::ControlPoint& controlPoint, std::vector& allControlPoints); + /** + * @brief Returns the examination period to which the given control point belongs. + * Each examination point holds a vector of control point UIDs so that the UID of the given control point can be compared against the UIDs of the vector. + * An empty examination period is returned if, + * - the given vector of examination periods is empty + * - the examination periods do not contain any control point UIDs + * - the UID of the given control point is not contained in any examination period + */ + MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ExaminationPeriod FindExaminationPeriod(const SemanticTypes::ControlPoint& controlPoint, std::vector& allExaminationPeriods); + } // namespace mitk #endif // MITKCONTROLPOINTMANAGER_H diff --git a/Modules/SemanticRelations/include/mitkRelationStorage.h b/Modules/SemanticRelations/include/mitkRelationStorage.h index 499702ff5c..90630cc4b9 100644 --- a/Modules/SemanticRelations/include/mitkRelationStorage.h +++ b/Modules/SemanticRelations/include/mitkRelationStorage.h @@ -1,87 +1,94 @@ /*=================================================================== 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. ===================================================================*/ #ifndef MITKRELATIONSTORAGE_H #define MITKRELATIONSTORAGE_H // semantic relations module #include "mitkDICOMHelper.h" #include "mitkSemanticTypes.h" // mitk core #include #include namespace mitk { class RelationStorage { public: void SetDataStorage(DataStorage::Pointer dataStorage); std::vector GetAllLesionsOfCase(const SemanticTypes::CaseID& caseID); SemanticTypes::Lesion GetRepresentedLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID); std::vector GetAllSegmentationsOfCase(const SemanticTypes::CaseID& caseID); std::vector mitk::RelationStorage::GetAllSegmentationIDsOfCase(const SemanticTypes::CaseID& caseID); SemanticTypes::ControlPoint GetControlPointOfData(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& dataNodeID); std::vector GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID); + std::vector GetAllExaminationPeriodsOfCase(const SemanticTypes::CaseID& caseID); + SemanticTypes::InformationType GetInformationTypeOfImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID); std::vector GetAllInformationTypesOfCase(const SemanticTypes::CaseID& caseID); std::vector GetAllImagesOfCase(const SemanticTypes::CaseID& caseID); std::vector GetAllImageIDsOfCase(const SemanticTypes::CaseID& caseID); std::vector GetAllCaseIDs(); void AddCase(const SemanticTypes::CaseID& caseID); void AddImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageNodeID); void RemoveImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageNodeID); void AddSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationNodeID, const SemanticTypes::ID& parentDataNodeID); void RemoveSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationNodeID); void AddLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion); void OverwriteLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion); void LinkSegmentationToLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID, const SemanticTypes::Lesion& lesion); void UnlinkSegmentationFromLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID); void RemoveLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion); void RemoveLesionClass(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& lesionClassID); void AddControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint); void LinkDataToControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& dataNodeID, const SemanticTypes::ControlPoint& controlPoint); void UnlinkDataFromControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& dataNodeID); void RemoveControlPointFromCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint); + void AddExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod); + void AddControlPointToExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriod examinationPeriod); + void RemoveControlPointFromExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriod examinationPeriod); + void RemoveExaminationPeriodFromCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod examinationPeriod); + void AddInformationTypeToImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID, const SemanticTypes::InformationType informationType); void RemoveInformationTypeFromImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID); void RemoveInformationTypeFromCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType informationType); private: // access the storage and retrieve the case data, stored under the given case ID mitk::PropertyList::Pointer GetStorageData(const SemanticTypes::CaseID& caseID); mitk::SemanticTypes::Lesion GenerateLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& lesionID); DataStorage::Pointer m_DataStorage; }; } // namespace mitk #endif // MITKRELATIONSTORAGE_H diff --git a/Modules/SemanticRelations/include/mitkSemanticRelations.h b/Modules/SemanticRelations/include/mitkSemanticRelations.h index 516b0989d8..b2924156c6 100644 --- a/Modules/SemanticRelations/include/mitkSemanticRelations.h +++ b/Modules/SemanticRelations/include/mitkSemanticRelations.h @@ -1,595 +1,635 @@ /*=================================================================== 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. ===================================================================*/ #ifndef MITKSEMANTICRELATIONS_H #define MITKSEMANTICRELATIONS_H #include // semantic relations module #include "mitkControlPointManager.h" #include "mitkDICOMHelper.h" #include "mitkISemanticRelationsObservable.h" #include "mitkISemanticRelationsObserver.h" #include "mitkRelationStorage.h" #include "mitkSemanticTypes.h" // mitk core #include #include namespace mitk { - /* + /** * @brief The API provides functions to query and manipulate image relations and instances, * that are helpful during follow-up examination, like control-points (time period), * types of the images or lesions that may be visible on multiple images. * * The class is able to generate IDs from given data nodes using DICOM information. * These IDs are used to identify the corresponding instances of a specific case. * The case can also be directly identified by the given case ID. * * In the BlackSwan context the case is identified with the DICOM PatientID. * * In order for most functions to work the case ID has to be defined in the model. If not, * the functions do nothing. */ class MITKSEMANTICRELATIONS_EXPORT SemanticRelations : public ISemanticRelationsObservable { public: SemanticRelations(mitk::DataStorage::Pointer dataStorage); ~SemanticRelations(); using LesionVector = std::vector; using LesionClassVector = std::vector; using ControlPointVector = std::vector; + using ExaminationPeriodVector = std::vector; using InformationTypeVector = std::vector; using DataNodeVector = std::vector ; /************************************************************************/ /* functions to implement the observer pattern */ /************************************************************************/ - /* + /** * @brief Adds the given concrete observer to the vector that holds all currently registered observer. * If the observer is already registered, it will not be added to the observer vector. * * @param observer The concrete observer to register. */ virtual void AddObserver(ISemanticRelationsObserver* observer) override; - /* + /** * @brief Removes the given concrete observer from the vector that holds all currently registered observer. * * @param observer The concrete observer to unregister. */ virtual void RemoveObserver(ISemanticRelationsObserver* observer) override; /************************************************************************/ /* functions to get instances / attributes */ /************************************************************************/ - /* + /** * @brief Returns a vector of all lesions that are currently available for the given case. * The lesions may be marked by a segmentation or may be empty - with no connection to a specific image / segmentation of the case data. * If no lesions are stored for the current case, an empty vector is returned. * * @param caseID The current case identifier is defined by the given string. * @return A vector of lesions. */ LesionVector GetAllLesionsOfCase(const SemanticTypes::CaseID& caseID) const; /** * @brief * * */ LesionClassVector GetAllLesionClassesOfCase(const SemanticTypes::CaseID& caseID) const; - /* + /** * @brief Returns a vector of all lesions that are valid for the given case, given a specific control point. * * @param caseID The current case identifier is defined by the given string. * @param controlPoint A specific control point which has to be available at a returned (found) lesion: * Only those lesions are returned for which the image of the associated segmentation is linked to the given control point. * If the control point instance does not exist, an empty vector is returned. * @return A vector of control points. */ LesionVector GetAllLesionsOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const; - /* + /** * @brief Returns a vector of all lesions that are currently available for the current case and are connected to the given image (via a segmentation). * If no lesions are stored for the current case, an empty vector is returned. If no segmentation nodes are * connected with the image node, no lesions for the specific image will be found and an empty vector is returned. * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * @pre The image node has to have associated segmentation nodes (child nodes) in order to reference a lesion. * * @param imageNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. * @return A vector of lesions. */ LesionVector GetAllLesionsInImage(const DataNode* imageNode) const; - /* + /** * @brief Returns the lesion that is defined by the given segmentation data. * * @pre The given segmentation data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr). * @pre The segmentation data node has to represent a lesion. If not, the retrieved lesion will be empty, which leads to an exception. * @throw SemanticRelationException, if the segmentation does not represent an existing lesion (this can be checked via 'IsRepresentingALesion'). * * @param segmentationNode The segmentation identifier is extracted from the given data node. * @return The represented lesion. */ SemanticTypes::Lesion GetRepresentedLesion(const DataNode* segmentationNode) const; - /* + /** * @brief Check if the given segmentation refers to an existing lesion instance. * This function can be used before calling 'GetRepresentedLesion' in order to avoid a possible exception. * * @param segmentationNode The segmentation identifier is extracted from the given data node. * @return True, if the segmentation refers to an existing lesion; false otherwise. */ bool IsRepresentingALesion(const DataNode* segmentationNode) const; /** * @brief * * */ bool InstanceExists(const DataNode* dataNode) const; - /* + /** * @brief Return a vector of all segmentations that are currently available for the given case. * The segmentations may be connected / not connected to a lesion of the case. * If no segmentations are stored for the current case, an empty vector is returned. * * @pre The data storage member has to be valid (!nullptr). * @throw SemanticRelationException, if the data storage member is invalid (==nullptr). * * @param caseID The current case identifier is defined by the given string. * @return A vector of data nodes representing segmentations. */ mitk::SemanticRelations::DataNodeVector GetAllSegmentationsOfCase(const SemanticTypes::CaseID& caseID) const; - /* + /** * @brief Return a vector of all segmentations that define the given lesion. These segmentations don't have to be linked to the same image. * If the lesion is not referred to by any segmentation, an empty vector is returned. * * @pre The data storage member has to be valid (!nullptr). * @throw SemanticRelationException, if the data storage member is invalid (==nullptr). * @pre The UID of the lesion has to exist for a lesion instance. * @throw SemanticRelationException, if UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param lesion A Lesion with a UID that identifies the corresponding lesion instance. * @return A vector of data nodes representing segmentations that define the given lesion. */ DataNodeVector GetAllSegmentationsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const; - /* + /** * @brief Return a vector of all images that are currently available for the given case. * * @pre The data storage member has to be valid (!nullptr). * @throw SemanticRelationException, if the data storage member is invalid (==nullptr). * * @param caseID The current case identifier is defined by the given string. * @return A vector of data nodes representing images. */ DataNodeVector GetAllImagesOfCase(const SemanticTypes::CaseID& caseID) const; - /* + /** * @brief Return a vector of all images that are connected to those segmentations that are linked to the given lesion. * If the lesion is not referred to by any segmentation, an empty vector is returned. * * @pre The UID of the lesion has to exist for a lesion instance. * @throw SemanticRelationException, if UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param lesion A Lesion with a UID that identifies the corresponding lesion instance. * @return A vector of data nodes representing images on which the lesions are visible. */ DataNodeVector GetAllImagesOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const; - /* + /** * @brief Check if the given lesion instance exists. * This function can be used before calling 'GetAllSegmentationsOfLesion' in order to avoid a possible exception. * This function can be used before calling 'AddLesionInstance' in order to avoid a possible exception. * * @param caseID The current case identifier is defined by the given string. * @param lesion A Lesion with a UID that identifies the corresponding lesion instance. * @return True, if the lesion instance exists; false otherwise. */ bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const; - /* + /** * @brief Return a vector of all control points that are valid for the given case. * * @param caseID The current case identifier is defined by the given string. * @return A vector of control points. */ ControlPointVector GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID) const; - /* + /** * @brief Return a vector of all control points that are valid for the given case, given a specific lesion * * @param caseID The current case identifier is defined by the given string. * @param lesion A specific lesion which has to be available at a returned (found) control point: * Only those control points are returned for which an associated data has a segmentation that references the given lesion. * If the lesion does not exists, an empty vector is returned. * @return A vector of control points. */ ControlPointVector GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const; - /* + /** * @brief Return a vector of all control points that are valid for the given case, given a specific information type. * * @param caseID The current case identifier is defined by the given string. * @param informationType A specific information type which has to be available at a returned (found) control point: * Only those control points are returned for which an associated data has the given information type. * If the information type instance does not exists, an empty vector is returned. * @return A vector of control points. */ ControlPointVector GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) const; - /* + /** * @brief Return the control point of a data node. * If the data node is not linked to a control point or the data node refers to a non-existing control point, * a control point with an empty UID is returned. * * @pre The given data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given data node is invalid (==nullptr). * * @param dataNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. - * @return The control point of the given data node. + * @return The control point of the given data node. */ SemanticTypes::ControlPoint GetControlPointOfData(const DataNode* dataNode) const; - /* + /** * @brief Return a vector of all image nodes that link to the given control point. * If the control point is not referred to by any data node, an empty vector is returned. * * @pre The UID of the control point has to exist for a control point instance. * @throw SemanticRelationException, if the UID of the control point does not exist for a control point instance (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param controlPoint A control point with a UID that identifies the corresponding control point instance. - * @return A vector of image nodes that link to the given control point. + * @return A vector of image nodes that link to the given control point. */ DataNodeVector GetAllImagesOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const; - /* + /** * @brief Check if the given control point instance exists. * This function can be used before calling 'GetAllDataOfControlPoint' in order to avoid a possible exception. * This function can be used before adding, linking and unlinking control points to avoid a possible exception. * * @param caseID The current case identifier is defined by the given string. * @param controlPoint A control point with a UID that identifies the corresponding control point instance. - * @return True, if the control point instance exists; false otherwise. + * @return True, if the control point instance exists; false otherwise. */ bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const; - /* + /** + * @brief Return a vector of all examination periods nodes that are valid for the given case. + * + * @param caseID The current case identifier is defined by the given string. + * @return A vector of examination periods. + */ + ExaminationPeriodVector GetAllExaminationPeriodsOfCase(const SemanticTypes::CaseID& caseID) const; + /** + * @brief Check if the given examination period instance exists. + * This function can be used before calling 'AddExaminationPeriod' in order to avoid a possible exception. + * + * @param caseID The current case identifier is defined by the given string. + * @param examinationPeriod An examination period with a UID that identifies the corresponding examination period instance. + * @return True, if the examination period instance exists; false otherwise. + */ + bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod) const; + /** * @brief Return a vector of all information types that are valid for the given case. * * @param caseID The current case identifier is defined by the given string. * @return A vector of information types. */ InformationTypeVector GetAllInformationTypesOfCase(const SemanticTypes::CaseID& caseID) const; - /* + /** * @brief Return a vector of all information types that are valid for the given case, given a specific control point. * * @param caseID The current case identifier is defined by the given string. * @param controlPoint A specific control point which has to be available at a returned (found) information type: * Only those information types are returned for which an associated data is linked to the given control point. * If the control point instance does not exist, an empty vector is returned. * @return A vector of information types. */ InformationTypeVector GetAllInformationTypesOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const; - /* + /** * @brief Return the information type of the given image. * If the image does not contain any information type, an empty information type is returned. * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * * @param imageNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. * @return The information type of the given data node. */ SemanticTypes::InformationType GetInformationTypeOfImage(const DataNode* imageNode) const; - /* + /** * @brief Return a vector of all image nodes that are defined with the given information type. * * @pre The information type has to exist for the given case (and is therefore used by at least one data node). * @throw SemanticRelationException, if the information type is not used by any data node (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param informationType An information type that identifies the corresponding information type instance. * @return A vector of image nodes that are defined with the given information type. */ DataNodeVector GetAllImagesOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) const; - /* + /** * @brief Return a vector of all image nodes that are defined with the given information type and with the given control point. * * @pre The UID of the control point has to exist for a control point instance. * The information type has to exist for the given case (and is therefore used by at least one data node). * @throw SemanticRelationException, if the UID of the control point does not exist for a control point instance (this can be checked via 'InstanceExists') or * if the information type is not used by any data node (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param controlPoint A control point with a UID that identifies the corresponding control point instance. * @param informationType An information type that identifies the corresponding information type instance. * @return A vector of image nodes that are defined with the given information type with the given control point. */ DataNodeVector GetAllSpecificImages(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const; /** * @brief Return a vector of all segmentation nodes that are defined with the given information type and with the given control point. * The function uses the 'GetAllSpecificImages'-function to retrieve the specific images and then searches for the derived nodes (segmentation child nodes). * * @pre The UID of the control point has to exist for a control point instance. * The information type has to exist for the given case (and is therefore used by at least one data node). * @throw SemanticRelationException, if the UID of the control point does not exist for a control point instance (this can be checked via 'InstanceExists') or * if the information type is not used by any data node (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param controlPoint A control point with a UID that identifies the corresponding control point instance. * @param informationType An information type that identifies the corresponding information type instance. * @return A vector of segmentation nodes that are defined with the given information type with the given control point. */ DataNodeVector GetAllSpecificSegmentations(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const; - /* + /** * @brief Check if the given information type exists. * This function can be used before calling 'GetAllDataOfInformationType' in order to avoid a possible exception. * * @param caseID The current case identifier is defined by the given string. * @param informationType An information type * @return True, if the information type exists; false otherwise. */ bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) const; - /* + /** * @brief Return a vector of all CaseIDs that are currently available. * * @return A vector of CaseIDs as strings. */ std::vector GetAllCaseIDs() const; /************************************************************************/ /* functions to add / remove instances / attributes */ /************************************************************************/ - /* + /** * @brief Add the given image to the set of already existing images. * The date is extracted from the DICOM data of the image node and is compared to already existing control points in the semantic relations model. * The function tries to find a fitting control point or to extend an already existing control point, if the extracted control point is close to * any other, already existing control point. * Finally, the image is linked to the correct control point. * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * * @param imageNode The current case identifier and node identifier is extracted from the given image data node, which contains DICOM information about the case and the node. */ void AddImage(const DataNode* imageNode); - /* + /** * @brief Remove the given image from the set of already existing images. * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * * @param imageNode The current case identifier and node identifier is extracted from the given image data node, which contains DICOM information about the case and the node. */ void RemoveImage(const DataNode* imageNode); - /* + /** * @brief Add a newly created lesion to the set of already existing lesions - with no connection to a specific image / segmentation of the case data. * * @pre The UID of the lesion must not already exist for a lesion instance. * @throw SemanticRelationException, it the UID of the lesion already exists for a lesion instance (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param lesion The lesion instance to add. */ void AddLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion); - /* + /** * @brief Overwrite an already existing lesion instance (this may be useful to overwrite the lesion with a different lesion class). * * @pre The UID of the lesion has to exist for a lesion instance. * @throw SemanticRelationException, if the UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param lesion The lesion instance that overwrites an existing lesion. */ void OverwriteLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion); - /* + /** * @brief Add a newly created lesion to the set of already existing lesions. The lesion is added and a reference to * the lesion is added to the segmentation data. If the segmentation is already linked to a lesion, the * old linkage is overwritten (this can be checked via 'IsRepresentingALesion'). * * @pre The given segmentation data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr). * @pre The UID of the lesion must not already exist for a lesion instance. * @throw SemanticRelationException, if the UID of the lesion already exists for a lesion instance (this can be checked via 'InstanceExists'). * * @param segmentationNode The segmentation identifier is extracted from the given data node. The segmentation node has DICOM information from its parent node. * @param lesion The lesion instance to add and link. */ void AddLesionAndLinkSegmentation(const DataNode* segmentationNode, const SemanticTypes::Lesion& lesion); - /* + /** * @brief Remove the given lesion from the set of already existing lesions. * * @pre The UID of the lesion has to exist for a lesion instance. * @throw SemanticRelationException, if the UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists'). * @pre The function needs to assure that no segmentation is still representing (linked to) this lesion. * @throw SemanticRelationException, if the lesion instance to remove is still linked to by any segmentation (this can be checked via 'GetAllSegmentationsOfLesion'). * * @param caseID The current case identifier is defined by the given string. * @param lesion The lesion instance to remove. */ void RemoveLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion); - /* + /** * @brief Add a segmentation instance to the set of already existing segmentations - with no connection to a specific lesion. * * @param segmentationNode The segmentation identifier is extracted from the given data node. The segmentation node has DICOM information from its parent node. * @param parentNode The node identifier of the parent node is extracted from the given parent data node. */ void AddSegmentation(const DataNode* segmentationNode, const DataNode* parentNode); - /* + /** * @brief Link the given segmentation instance to an an already existing lesion instance. If the segmentation is already linked to a lesion instance, the * old linkage is overwritten (this can be checked via 'IsRepresentingALesion'). * * @pre The given segmentation data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr). * @pre The UID of the lesion has to exist for a lesion instance. * @throw SemanticRelationException, if the UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists'). * * @param segmentationNode The segmentation identifier is extracted from the given data node. The segmentation node has DICOM information from its parent node. * @param lesion The lesion instance to link. */ void LinkSegmentationToLesion(const DataNode* segmentationNode, const SemanticTypes::Lesion& lesion); - /* + /** * @brief Unlink the given segmentation instance from the linked lesion instance. * The lesion may stay unlinked to any segmentation. * * @pre The given segmentation data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr). * * @param segmentationNode The segmentation identifier is extracted from the given data node. The segmentation node has DICOM information from its parent node. */ void UnlinkSegmentationFromLesion(const DataNode* segmentationNode); - /* + /** * @brief Remove the given segmentation from the set of already existing segmentations. * * @pre The given segmentation data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr). * * @param segmentationNode The segmentation identifier is extracted from the given data node. The segmentation node has DICOM information from its parent node. */ void RemoveSegmentation(const DataNode* segmentationNode); /** * @brief Set the control point for the given data node. * * @pre The given data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given data node is invalid (==nullptr). */ void SetControlPointOfData(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint); - /* + /** * @brief Add a newly created control point to the set of already existing control points. A reference to the control point is added to the given data. * This function combines adding a control point and linking it, since a control point with no associated data is not allowed. * * @pre The given data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given data node is invalid (==nullptr). * @pre The UID of the control point must not already exist for a control point instance. * @throw SemanticRelationException, if the UID of the control point already exists for a control point instance (this can be checked via 'InstanceExists'). * @pre The given control point must not already be contained in an existing control point interval. * @throw SemanticRelationException, if the given control point is already contained in an existing control point interval (this can be checked via 'CheckContainingControlPoint'). * @pre The given control point must contain the date of the given data node (if parameter 'checkConsistence = true'). * @throw SemanticRelationException, if the given control point does not contain the date of the given data node and 'checkConsistence = true' (this can be checked via 'ControlPointManager::InsideControlPoint'). * * @param dataNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. * @param controlPoint The control point instance to add. For a newly added control point always has "startDate = endDate". * @param checkConsistence If true, the function checks, whether the date of the data node actually lies inside the control point to link. */ void AddControlPointAndLinkData(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence = true); - /* + /** * @brief Link the given data to an already existing control point. * * @pre The given data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given data node is invalid (==nullptr). * @pre The UID of the control point has to exist for a control point instance. * @throw SemanticRelationException, if the UID of the control point does not exists for a control point instance (this can be checked via 'InstanceExists'). * @pre The given control point must contain the date of the given data node (if parameter 'checkConsistence = true'). * @throw SemanticRelationException, if the given control point does not contain the date of the given data node and 'checkConsistence = true' (this can be checked via 'ControlPointManager::InsideControlPoint'). * * @param dataNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. - * @param controlPoint The control point instance to add link. + * @param controlPoint The control point instance to link. * @param checkConsistence If true, the function checks, whether the date of the data node actually lies inside the control point to link. */ void LinkDataToControlPoint(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence = true); - /* + /** * @brief Unlink the given image from the linked control point. * If data is unlinked from a control point, the function needs to check whether the control point is still linked to any other data: * - if not, the control point instance will be removed (has to be removed since a control point with no associated data is not allowed). * - if so, the function has to make sure that the control point instance is shortened to its minimum time period (e.g. moving the end point to an earlier date). * * @param dataNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. */ void UnlinkDataFromControlPoint(const DataNode* dataNode); /** + * @brief Add an examination period instance to the set of already existing examination periods - with no connection to a specific control point. + * + * @pre The UID of the examination period must not already exist for an examination period instance. + * @throw SemanticRelationException, if the UID of the examination period already exists for a examination period instance (this can be checked via 'InstanceExists'). + * + * @param caseID The current case identifier is defined by the given string. + * @param examinationPeriod The examination period to add. + */ + void AddExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod); + /** + * @brief Add a control point to the vector of control point UIDs of an existing examination period. + * + * @pre The UID of the control point has to exist for a control point instance. + * @throw SemanticRelationException, if the UID of the control point does not exists for a control point instance (this can be checked via 'InstanceExists'). + * @pre The UID of the examination period must not already exist for an examination period instance. + * @throw SemanticRelationException, if the UID of the examination period already exists for a examination period instance (this can be checked via 'InstanceExists'). + * + * @param caseID The current case identifier is defined by the given string. + * @param controlPoint The control point instance to add to the examination period. + * @param examinationPeriod The examination period to which the control point should be added. + */ + void AddControlPointToExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriod& examinationPeriod); + /** * @brief Set (and possibly overwrite) the information type of the given image. * An already associated information type might be removed if is not referenced by any other image: * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * @post If the information type instance did not exist before, it is now added. * * @param imageNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. * @param informationType An information type that identifies the corresponding information type instance. */ void SetInformationType(const DataNode* imageNode, const SemanticTypes::InformationType& informationType); - /* + /** * @brief Set the information type of the given image. * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * @post If the information type instance did not exist before, it is now added. * * @param imageNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. * @param informationType An information type that identifies the corresponding information type instance. */ void AddInformationTypeToImage(const DataNode* imageNode, const SemanticTypes::InformationType& informationType); - /* + /** * @brief Remove the information type of the given image. * If the information type is removed, the function needs to check whether the information type is referenced by any other image: * - if not, the information type instance can be removed (has to be removed since an information type with no associated image is not allowed). * - if so, the information type is just removed from the given image. * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * * @param imageNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. */ void RemoveInformationTypeFromImage(const DataNode* imageNode); private: // the relation storage serves as a storage accessor and can be sub-classed for custom demands std::shared_ptr m_RelationStorage; DataStorage::Pointer m_DataStorage; - /* + /** * @brief A vector that stores the currently registered observer of this observable subject. */ static std::vector m_ObserverVector; - /* + /** * @brief The SemanticRelations, as an example of an observable subject, notifies (updates) the observer with a given case ID. * The view's caseID was set before in the GUI. The parts of the view that observe changes in the semantic relations are only updated, * if the given case ID is equal to the observer's current caseID and thus the observer currently shows the semantic information of the given case. * * @param caseID The caseID that identifies the currently active patient / case. */ virtual void NotifyObserver(const mitk::SemanticTypes::CaseID& caseID) const override; - /* + /** * @brief Determine if the given control point contains images, which are connected to segmentations that represent the given lesion. * If the lesion or the control point are not correctly stored, the function returns false. * * @param caseID The current case identifier is defined by the given string. * @param lesion A Lesion with a UID that identifies the corresponding lesion instance. * @param controlPoint A control point with a UID that identifies the corresponding control point instance. * * @return True, if the given control point contains data that is related to the given lesion; false otherwise. */ bool ControlPointContainsLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint) const; - /* + /** * @brief Determine if the given control point contains images, which refer to the given information type. * If the information type or the control point are not correctly stored, the function returns false. * * @param caseID The current case identifier is defined by the given string. * @param informationType An information type that identifies the corresponding information type instance. * @param controlPoint A control point with a UID that identifies the corresponding control point instance. * * @return True, if the given control point contains data that is related to the given information type; false otherwise. */ bool ControlPointContainsInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType, const SemanticTypes::ControlPoint& controlPoint) const; /** * @brief Remove all control points from the storage that are not referenced by any image anymore. * This might happen if an image has been removed (and unlinked from the corresponding control point) * or if the user sets a new control point for an image manually in the GUI. * * @param caseID The current case identifier is defined by the given string. */ void ClearControlPoints(const SemanticTypes::CaseID& caseID); }; } // namespace mitk #endif // MITKSEMANTICRELATIONS_H diff --git a/Modules/SemanticRelations/include/mitkSemanticTypes.h b/Modules/SemanticRelations/include/mitkSemanticTypes.h index cdb7128860..c043e10bdc 100644 --- a/Modules/SemanticRelations/include/mitkSemanticTypes.h +++ b/Modules/SemanticRelations/include/mitkSemanticTypes.h @@ -1,90 +1,100 @@ /*=================================================================== 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. ===================================================================*/ #ifndef MITKSEMANTICTYPES_H #define MITKSEMANTICTYPES_H // c++ #include #include +#include namespace mitk { namespace SemanticTypes { using ID = std::string; using CaseID = std::string; // an ID of the current case (e.g. the DICOM PatientID) using InformationType = std::string; /* * @brief The concept of a control point. */ struct ControlPoint { ID UID; int year = 0; int month = 0; int day = 0; bool operator<(const ControlPoint& other) const { return std::tie(year, month, day) < std::tie(other.year, other.month, other.day); } bool operator>(const ControlPoint& other) const { return std::tie(year, month, day) > std::tie(other.year, other.month, other.day); } bool operator==(const ControlPoint& other) const { return (!operator<(other) && !operator>(other)); } bool operator!=(const ControlPoint& other) const { return (operator<(other) || operator>(other)); } bool operator<=(const ControlPoint& other) const { return (operator<(other) || operator==(other)); } bool operator>=(const ControlPoint& other) const { return (operator>(other) || operator==(other)); } }; + /** + * @brief The concept of an examination period. + */ + struct ExaminationPeriod + { + ID UID; + std::vector controlPointIDs; + }; + /* * @brief The concept of a lesion class. */ struct LesionClass { ID UID; std::string classType = ""; }; /* * @brief The concept of a lesion. */ struct Lesion { ID UID; std::string name = ""; LesionClass lesionClass; }; } // namespace SemanticTypes } // namespace mitk #endif // MITKSEMANTICTYPES_H diff --git a/Modules/SemanticRelations/src/mitkControlPointManager.cpp b/Modules/SemanticRelations/src/mitkControlPointManager.cpp index e37e061fbb..36ed1af607 100644 --- a/Modules/SemanticRelations/src/mitkControlPointManager.cpp +++ b/Modules/SemanticRelations/src/mitkControlPointManager.cpp @@ -1,77 +1,161 @@ /*=================================================================== 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. ===================================================================*/ // semantic relations module #include "mitkControlPointManager.h" #include "mitkDICOMHelper.h" #include "mitkUIDGeneratorBoost.h" // mitk core #include -double CalculateDistanceInDays(mitk::SemanticTypes::ControlPoint leftControlPoint, mitk::SemanticTypes::ControlPoint rightControlPoint); +double CalculateDistanceInDays(const mitk::SemanticTypes::ControlPoint& leftControlPoint, const mitk::SemanticTypes::ControlPoint& rightControlPoint); mitk::SemanticTypes::ControlPoint mitk::GenerateControlPoint(const mitk::DataNode* datanode) { SemanticTypes::ControlPoint controlPoint = GetDICOMDateFromDataNode(datanode); controlPoint.UID = UIDGeneratorBoost::GenerateUID(); return controlPoint; } std::string mitk::GetControlPointAsString(const SemanticTypes::ControlPoint& controlPoint) { std::stringstream controlPointAsString; controlPointAsString << std::to_string(controlPoint.year) << "-" << std::setfill('0') << std::setw(2) << std::to_string(controlPoint.month) << "-" << std::setfill('0') << std::setw(2) << std::to_string(controlPoint.day); return controlPointAsString.str(); } mitk::SemanticTypes::ControlPoint mitk::FindExistingControlPoint(const SemanticTypes::ControlPoint& controlPoint, std::vector& allControlPoints) { for (const auto& currentControlPoint : allControlPoints) { if (controlPoint == currentControlPoint) { return currentControlPoint; } } return SemanticTypes::ControlPoint(); } -double CalculateDistanceInDays(mitk::SemanticTypes::ControlPoint leftControlPoint, mitk::SemanticTypes::ControlPoint rightControlPoint) +mitk::SemanticTypes::ControlPoint mitk::FindClosestControlPoint(const SemanticTypes::ControlPoint& controlPoint, std::vector& allControlPoints) +{ + if (allControlPoints.empty()) + { + return SemanticTypes::ControlPoint(); + } + + // sort the vector of control points for easier lookup + std::sort(allControlPoints.begin(), allControlPoints.end()); + // new control point does not match an existing control point + // check if the control point is close to an already existing control point + std::vector::const_iterator it; + for (it = allControlPoints.begin(); it != allControlPoints.end(); ++it) + { + if (controlPoint < *it) + { + break; + } + } + + SemanticTypes::ControlPoint nextControlPoint; + SemanticTypes::ControlPoint previousControlPoint; + if (it == allControlPoints.begin()) + { + // new date is smaller ("older") than the smallest already existing control point + nextControlPoint = *it; + } + else if (it != allControlPoints.end()) + { + // new date is greater ("newer") than an already existing control point, + // but smaller ("older") than another already existing control point + nextControlPoint = *it; + previousControlPoint = *(--it); + } + else + { + // new date is greater ("newer") than the greatest already existing control point + previousControlPoint = *(--it); + } + + // test distance to next and previous time period + double distanceToNextExaminationPeriod = CalculateDistanceInDays(nextControlPoint, controlPoint); + double distanceToPreviousExaminationPeriod = CalculateDistanceInDays(previousControlPoint, controlPoint); + + SemanticTypes::ControlPoint closestControlPoint; + double closestDistanceInDays = 0.0; + if (distanceToNextExaminationPeriod < distanceToPreviousExaminationPeriod) + { + // control point is closer to the next control point + closestControlPoint = nextControlPoint; + closestDistanceInDays = distanceToNextExaminationPeriod; + } + else + { + // control point is closer to the previous control point + closestControlPoint = previousControlPoint; + closestDistanceInDays = distanceToPreviousExaminationPeriod; + } + + double THRESHOLD_DISTANCE_IN_DAYS = 30.0; + if (std::abs(closestDistanceInDays) < THRESHOLD_DISTANCE_IN_DAYS) + { + return closestControlPoint; + } + + return SemanticTypes::ControlPoint(); +} + +mitk::SemanticTypes::ExaminationPeriod mitk::FindExaminationPeriod(const SemanticTypes::ControlPoint& controlPoint, std::vector& allExaminationPeriods) +{ + for (const auto& examinationPeriod : allExaminationPeriods) + { + for (const auto& UID : examinationPeriod.controlPointIDs) + { + if (controlPoint.UID == UID) + { + return examinationPeriod; + } + } + } + + return SemanticTypes::ExaminationPeriod(); +} + +double CalculateDistanceInDays(const mitk::SemanticTypes::ControlPoint& leftControlPoint, const mitk::SemanticTypes::ControlPoint& rightControlPoint) { std::tm leftTimeStructure = { 0, 0, 0, leftControlPoint.day, leftControlPoint.month - 1, leftControlPoint.year - 1900 }; std::tm rightTimeStructure = { 0, 0, 0, rightControlPoint.day, rightControlPoint.month - 1, rightControlPoint.year - 1900 }; time_t leftTime = mktime(&leftTimeStructure); time_t rightTime = mktime(&rightTimeStructure); if (leftTime == -1 || rightTime == -1) { // date is not initialized, no difference can be computed return std::numeric_limits::max(); } // compute distance here double secondsPerDay = 60 * 60 * 24; double timeDifferenceInDays = std::difftime(leftTime, rightTime) / secondsPerDay; return timeDifferenceInDays; } diff --git a/Modules/SemanticRelations/src/mitkRelationStorage.cpp b/Modules/SemanticRelations/src/mitkRelationStorage.cpp index ebd0a502fa..bdc4dc9fb5 100644 --- a/Modules/SemanticRelations/src/mitkRelationStorage.cpp +++ b/Modules/SemanticRelations/src/mitkRelationStorage.cpp @@ -1,1188 +1,1359 @@ /*=================================================================== 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. ===================================================================*/ // semantic relations module #include "mitkRelationStorage.h" #include "mitkNodePredicates.h" // multi label module #include // mitk core #include #include // c++ #include #include void mitk::RelationStorage::SetDataStorage(DataStorage::Pointer dataStorage) { if (m_DataStorage != dataStorage) { // set the new data storage m_DataStorage = dataStorage; } } std::vector mitk::RelationStorage::GetAllLesionsOfCase(const SemanticTypes::CaseID& caseID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return std::vector(); } // retrieve a vector property that contains the valid lesion-IDs for the current case mitk::VectorProperty* vectorProperty = dynamic_cast*>(propertyList->GetProperty("lesions")); if (nullptr == vectorProperty) { MITK_INFO << "Could not find any lesion in the storage."; return std::vector(); } std::vector vectorValue = vectorProperty->GetValue(); std::vector allLesionsOfCase; for (const auto& lesionID : vectorValue) { SemanticTypes::Lesion generatedLesion = GenerateLesion(caseID, lesionID); if (!generatedLesion.UID.empty()) { allLesionsOfCase.push_back(generatedLesion); } } return allLesionsOfCase; } mitk::SemanticTypes::Lesion mitk::RelationStorage::GetRepresentedLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return SemanticTypes::Lesion(); } // retrieve a vector property that contains the referenced ID of a segmentation (0. image ID 1. lesion ID) mitk::VectorProperty* segmentationVectorProperty = dynamic_cast*>(propertyList->GetProperty(segmentationID)); if (nullptr == segmentationVectorProperty) { MITK_INFO << "Could not find the segmentation node " << segmentationID << " in the storage."; return SemanticTypes::Lesion(); } std::vector segmentationVectorValue = segmentationVectorProperty->GetValue(); // the lesion ID of a segmentation is the second value in the vector if (segmentationVectorValue.size() != 2) { MITK_INFO << "Incorrect segmentation storage. Not two (2) IDs stored."; return SemanticTypes::Lesion(); } else { std::string lesionID = segmentationVectorValue[1]; return GenerateLesion(caseID, lesionID); } } std::vector mitk::RelationStorage::GetAllSegmentationsOfCase(const SemanticTypes::CaseID& caseID) { if (m_DataStorage.IsNull()) { MITK_INFO << "No valid data storage found in the mitkPersistenceService-class. Segmentations of the current case can not be retrieved."; return std::vector(); } std::vector allSegmentationIDsOfCase = GetAllSegmentationIDsOfCase(caseID); std::vector allSegmentationsOfCase; // get all segmentation nodes of the current data storage // only those nodes are respected, that are currently held in the data storage DataStorage::SetOfObjects::ConstPointer segmentationNodes = m_DataStorage->GetSubset(NodePredicates::GetSegmentationPredicate()); for (auto it = segmentationNodes->Begin(); it != segmentationNodes->End(); ++it) { DataNode* segmentationNode = it->Value(); try { // find the corresponding segmentation node for the given segmentation ID std::string nodeCaseID = GetCaseIDFromDataNode(segmentationNode); std::string nodeSegmentationID = GetIDFromDataNode(segmentationNode); if (nodeCaseID == caseID && (std::find(allSegmentationIDsOfCase.begin(), allSegmentationIDsOfCase.end(), nodeSegmentationID) != allSegmentationIDsOfCase.end())) { // found current image node in the storage, add it to the return vector allSegmentationsOfCase.push_back(segmentationNode); } } catch (const std::exception&) { // found a segmentation node that is not stored in the semantic relations // this segmentation node does not have any DICOM information --> exception thrown // continue with the next segmentation to compare IDs continue; } } return allSegmentationsOfCase; } std::vector mitk::RelationStorage::GetAllSegmentationIDsOfCase(const SemanticTypes::CaseID& caseID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return std::vector(); } // retrieve a vector property that contains the valid segmentation-IDs for the current case mitk::VectorProperty* allSegmentationsVectorProperty = dynamic_cast*>(propertyList->GetProperty("segmentations")); if (nullptr == allSegmentationsVectorProperty) { MITK_INFO << "Could not find any segmentation in the storage."; return std::vector(); } return allSegmentationsVectorProperty->GetValue(); } mitk::SemanticTypes::ControlPoint mitk::RelationStorage::GetControlPointOfData(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& dataNodeID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return SemanticTypes::ControlPoint(); } // retrieve a vector property that contains the information type and the referenced ID of a data node (0. information type 1. control point ID) mitk::VectorProperty* dataNodeVectorProperty = dynamic_cast*>(propertyList->GetProperty(dataNodeID)); if (nullptr == dataNodeVectorProperty) { MITK_INFO << "Could not find the data node " << dataNodeID << " in the storage."; return SemanticTypes::ControlPoint(); } std::vector dataNodeVectorValue = dataNodeVectorProperty->GetValue(); SemanticTypes::ControlPoint controlPoint; // an image node has to have exactly two values (the information type and the ID of the control point) if (dataNodeVectorValue.size() != 2) { MITK_INFO << "Incorrect data storage. Not two (2) values stored."; return SemanticTypes::ControlPoint(); } else { // the second value of the data node vector is the ID of the referenced control point std::string controlPointID = dataNodeVectorValue[1]; // retrieve a vector property that contains the integer values of the date of a control point (0. year 1. month 2. day) mitk::VectorProperty* controlPointVectorProperty = dynamic_cast*>(propertyList->GetProperty(controlPointID)); if (nullptr == controlPointVectorProperty) { MITK_INFO << "Could not find the control point " << controlPointID << " in the storage."; return SemanticTypes::ControlPoint(); } std::vector controlPointVectorValue = controlPointVectorProperty->GetValue(); // a control point has to have exactly three integer values (year, month and day) if (controlPointVectorValue.size() != 3) { MITK_INFO << "Incorrect control point storage. Not three (3) values of the date are stored."; return SemanticTypes::ControlPoint(); } else { // set the values of the control point controlPoint.UID = controlPointID; controlPoint.year = controlPointVectorValue[0]; controlPoint.month = controlPointVectorValue[1]; controlPoint.day = controlPointVectorValue[2]; } } return controlPoint; } std::vector mitk::RelationStorage::GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return std::vector(); } // retrieve a vector property that contains the valid control point-IDs for the current case mitk::VectorProperty* vectorProperty = dynamic_cast*>(propertyList->GetProperty("controlpoints")); if (nullptr == vectorProperty) { MITK_INFO << "Could not find any control points in the storage."; return std::vector(); } std::vector vectorValue = vectorProperty->GetValue(); std::vector allControlPoints; for (const auto& controlPointID : vectorValue) { // retrieve a vector property that contains the integer values of the date of a control point (0. year 1. month 2. day) mitk::VectorProperty* controlPointVectorProperty = dynamic_cast*>(propertyList->GetProperty(controlPointID)); if (nullptr == controlPointVectorProperty) { MITK_INFO << "Could not find the control point " << controlPointID << " in the storage."; continue; } std::vector controlPointVectorValue = controlPointVectorProperty->GetValue(); // a control point has to have exactly three integer values (year, month and day) if (controlPointVectorValue.size() != 3) { MITK_INFO << "Incorrect control point storage. Not three (3) values of the date are stored."; continue; } else { // set the values of the control point SemanticTypes::ControlPoint generatedControlPoint; generatedControlPoint.UID = controlPointID; generatedControlPoint.year = controlPointVectorValue[0]; generatedControlPoint.month = controlPointVectorValue[1]; generatedControlPoint.day = controlPointVectorValue[2]; allControlPoints.push_back(generatedControlPoint); } } return allControlPoints; } +std::vector mitk::RelationStorage::GetAllExaminationPeriodsOfCase(const SemanticTypes::CaseID& caseID) +{ + mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); + if (nullptr == propertyList) + { + MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; + return std::vector(); + } + + // retrieve a vector property that contains the valid examination period UIDs for the current case + mitk::VectorProperty::Pointer vectorProperty = dynamic_cast*>(propertyList->GetProperty("examinationperiods")); + if (nullptr == vectorProperty) + { + MITK_INFO << "Could not find any examination periods in the storage."; + return std::vector(); + } + + std::vector vectorValue = vectorProperty->GetValue(); + std::vector allExaminationPeriods; + for (const auto& examinationPeriodID : vectorValue) + { + // retrieve a vector property that contains the represented control point-IDs + mitk::VectorProperty::Pointer examinationPeriodVectorProperty = dynamic_cast*>(propertyList->GetProperty(examinationPeriodID)); + if (nullptr == examinationPeriodVectorProperty) + { + MITK_INFO << "Could not find the examination period " << examinationPeriodID << " in the storage."; + continue; + } + + std::vector examinationPeriodVectorValue = examinationPeriodVectorProperty->GetValue(); + /* + // an examination period has an arbitrary number of control points (at least one) + if (examinationPeriodVectorValue.size() < 1) + { + MITK_INFO << "Incorrect examination period storage. At least one (1) control point ID has to be stored."; + continue; + } + else + { + */ + // set the values of the control point + SemanticTypes::ExaminationPeriod generatedExaminationPeriod; + generatedExaminationPeriod.UID = examinationPeriodID; + for (const auto& controlpointID : examinationPeriodVectorValue) + { + generatedExaminationPeriod.controlPointIDs.push_back(controlpointID); + } + + allExaminationPeriods.push_back(generatedExaminationPeriod); + //} + } + return allExaminationPeriods; +} + mitk::SemanticTypes::InformationType mitk::RelationStorage::GetInformationTypeOfImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return SemanticTypes::InformationType(); } // retrieve a vector property that contains the information type and the referenced ID of an image data node (0. information type 1. control point ID) mitk::VectorProperty* dataNodeVectorProperty = dynamic_cast*>(propertyList->GetProperty(imageID)); if (nullptr == dataNodeVectorProperty) { MITK_INFO << "Could not find the image " << imageID << " in the storage."; return SemanticTypes::InformationType(); } std::vector dataNodeVectorValue = dataNodeVectorProperty->GetValue(); // an image node has to have exactly two values (the information type and the ID of the control point) if (dataNodeVectorValue.size() != 2) { MITK_INFO << "Incorrect data storage. Not two (2) values stored."; return SemanticTypes::InformationType(); } else { // the first value of the data node vector is the information type return dataNodeVectorValue[0]; } } std::vector mitk::RelationStorage::GetAllInformationTypesOfCase(const SemanticTypes::CaseID& caseID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return std::vector(); } // retrieve a vector property that contains the valid information types of the current case mitk::VectorProperty* informationTypeVectorProperty = dynamic_cast*>(propertyList->GetProperty("informationtypes")); if (nullptr == informationTypeVectorProperty) { MITK_INFO << "Could not find any information types in the storage."; return std::vector(); } return informationTypeVectorProperty->GetValue(); } std::vector mitk::RelationStorage::GetAllImagesOfCase(const SemanticTypes::CaseID& caseID) { if (m_DataStorage.IsNull()) { MITK_INFO << "No valid data storage found in the mitkPersistenceService-class. Images of the current case can not be retrieved."; return std::vector(); } std::vector allImageIDsOfCase = GetAllImageIDsOfCase(caseID); std::vector allImagesOfCase; // get all image nodes of the current data storage // only those nodes are respected, that are currently held in the data storage DataStorage::SetOfObjects::ConstPointer imageNodes = m_DataStorage->GetSubset(NodePredicates::GetImagePredicate()); for (auto it = imageNodes->Begin(); it != imageNodes->End(); ++it) { DataNode* imageNode = it->Value(); // find the corresponding image node for the given segmentation ID std::string nodeCaseID = GetCaseIDFromDataNode(imageNode); std::string nodeImageID = GetIDFromDataNode(imageNode); if (nodeCaseID == caseID && (std::find(allImageIDsOfCase.begin(), allImageIDsOfCase.end(), nodeImageID) != allImageIDsOfCase.end())) { // found current image node in the storage, add it to the return vector allImagesOfCase.push_back(imageNode); } } return allImagesOfCase; } std::vector mitk::RelationStorage::GetAllImageIDsOfCase(const SemanticTypes::CaseID& caseID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return std::vector(); } // retrieve a vector property that contains the valid image-IDs of the current case mitk::VectorProperty* allImagesVectorProperty = dynamic_cast*>(propertyList->GetProperty("images")); if (nullptr == allImagesVectorProperty) { MITK_INFO << "Could not find any image in the storage."; return std::vector(); } return allImagesVectorProperty->GetValue(); } std::vector mitk::RelationStorage::GetAllCaseIDs() { PERSISTENCE_GET_SERVICE_MACRO if (nullptr == persistenceService) { MITK_INFO << "Persistence service could not be loaded"; return std::vector(); } // the property list is valid for a certain scenario and contains all the case IDs of the radiological user's MITK session std::string listIdentifier = "caseIDs"; mitk::PropertyList::Pointer propertyList = persistenceService->GetPropertyList(listIdentifier); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << listIdentifier << " for the current MITK workbench / session."; return std::vector(); } // retrieve a vector property that contains all case IDs mitk::VectorProperty* caseIDsVectorProperty = dynamic_cast*>(propertyList->GetProperty(listIdentifier)); if (nullptr == caseIDsVectorProperty) { MITK_INFO << "Could not find the property " << listIdentifier << " for the " << listIdentifier << " property list."; return std::vector(); } return caseIDsVectorProperty->GetValue(); } void mitk::RelationStorage::AddCase(const SemanticTypes::CaseID& caseID) { PERSISTENCE_GET_SERVICE_MACRO if (nullptr == persistenceService) { MITK_INFO << "Persistence service could not be loaded"; return; } // the property list is valid for a certain scenario and contains all the case IDs of the radiological user's MITK session std::string listIdentifier = "caseIDs"; mitk::PropertyList::Pointer propertyList = persistenceService->GetPropertyList(listIdentifier); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << listIdentifier << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains all case IDs mitk::VectorProperty::Pointer caseIDsVectorProperty = dynamic_cast*>(propertyList->GetProperty(listIdentifier)); std::vector caseIDsVectorValue; if (nullptr == caseIDsVectorProperty) { caseIDsVectorProperty = mitk::VectorProperty::New(); } else { caseIDsVectorValue = caseIDsVectorProperty->GetValue(); } auto existingCase = std::find(caseIDsVectorValue.begin(), caseIDsVectorValue.end(), caseID); if (existingCase != caseIDsVectorValue.end()) { return; } else { // add case to the "caseIDs" property list caseIDsVectorValue.push_back(caseID); caseIDsVectorProperty->SetValue(caseIDsVectorValue); propertyList->SetProperty(listIdentifier, caseIDsVectorProperty); } } void mitk::RelationStorage::AddImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageNodeID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid image-IDs for the current case mitk::VectorProperty::Pointer allImagesVectorProperty = dynamic_cast*>(propertyList->GetProperty("images")); std::vector allImagesIDs; if (nullptr == allImagesVectorProperty) { allImagesVectorProperty = mitk::VectorProperty::New(); } else { allImagesIDs = allImagesVectorProperty->GetValue(); } auto existingImage = std::find(allImagesIDs.begin(), allImagesIDs.end(), imageNodeID); if (existingImage != allImagesIDs.end()) { return; } else { // add image to the "images" property list allImagesIDs.push_back(imageNodeID); allImagesVectorProperty->SetValue(allImagesIDs); propertyList->SetProperty("images", allImagesVectorProperty); // add the image itself mitk::VectorProperty::Pointer imageNodeVectorProperty = mitk::VectorProperty::New(); // an image node has to have exactly two values (the information type and the ID of the control point) std::vector imageNodeVectorValue(2); imageNodeVectorProperty->SetValue(imageNodeVectorValue); propertyList->SetProperty(imageNodeID, imageNodeVectorProperty); } } void mitk::RelationStorage::RemoveImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageNodeID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid image-IDs for the current case mitk::VectorProperty::Pointer allImagesVectorProperty = dynamic_cast*>(propertyList->GetProperty("images")); if (nullptr == allImagesVectorProperty) { MITK_INFO << "Could not find any images in the storage."; return; } // remove the image reference from the list of all images of the current case std::vector allImagesIDs = allImagesVectorProperty->GetValue(); allImagesIDs.erase(std::remove(allImagesIDs.begin(), allImagesIDs.end(), imageNodeID), allImagesIDs.end()); if (allImagesIDs.size() == 0) { // no more images stored -> remove the images property list propertyList->DeleteProperty("images"); } else { // or store the modified vector value allImagesVectorProperty->SetValue(allImagesIDs); } // remove the image instance itself propertyList->DeleteProperty(imageNodeID); } void mitk::RelationStorage::AddSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationNodeID, const SemanticTypes::ID& parentNodeID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid segmentation-IDs for the current case mitk::VectorProperty::Pointer allSegmentationsVectorProperty = dynamic_cast*>(propertyList->GetProperty("segmentations")); std::vector allSegmentationsIDs; if (nullptr == allSegmentationsVectorProperty) { allSegmentationsVectorProperty = mitk::VectorProperty::New(); } else { allSegmentationsIDs = allSegmentationsVectorProperty->GetValue(); } auto existingImage = std::find(allSegmentationsIDs.begin(), allSegmentationsIDs.end(), segmentationNodeID); if (existingImage != allSegmentationsIDs.end()) { return; } else { // add segmentation to the "segmentations" property list allSegmentationsIDs.push_back(segmentationNodeID); allSegmentationsVectorProperty->SetValue(allSegmentationsIDs); propertyList->SetProperty("segmentations", allSegmentationsVectorProperty); // add the segmentation itself mitk::VectorProperty::Pointer segmentationNodeVectorProperty = mitk::VectorProperty::New(); // a segmentation node has to have exactly two values (the ID of the referenced image and the ID of the referenced lesion) std::vector segmentationNodeVectorValue(2); segmentationNodeVectorValue[0] = parentNodeID; segmentationNodeVectorProperty->SetValue(segmentationNodeVectorValue); propertyList->SetProperty(segmentationNodeID, segmentationNodeVectorProperty); } } void mitk::RelationStorage::RemoveSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationNodeID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid segmentation-IDs for the current case mitk::VectorProperty::Pointer allSegmentationsVectorProperty = dynamic_cast*>(propertyList->GetProperty("segmentations")); if (nullptr == allSegmentationsVectorProperty) { MITK_INFO << "Could not find any segmentation in the storage."; return; } // remove the lesion reference from the list of all lesions of the current case std::vector allSegmentationsIDs = allSegmentationsVectorProperty->GetValue(); allSegmentationsIDs.erase(std::remove(allSegmentationsIDs.begin(), allSegmentationsIDs.end(), segmentationNodeID), allSegmentationsIDs.end()); if (allSegmentationsIDs.size() == 0) { // no more segmentations stored -> remove the segmentations property list propertyList->DeleteProperty("segmentations"); } else { // or store the modified vector value allSegmentationsVectorProperty->SetValue(allSegmentationsIDs); } // remove the lesion instance itself propertyList->DeleteProperty(segmentationNodeID); } void mitk::RelationStorage::AddLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid lesion-IDs for the current case mitk::VectorProperty::Pointer lesionsVectorProperty = dynamic_cast*>(propertyList->GetProperty("lesions")); std::vector lesionsVectorValue; if (nullptr == lesionsVectorProperty) { lesionsVectorProperty = mitk::VectorProperty::New(); } else { lesionsVectorValue = lesionsVectorProperty->GetValue(); } const auto& existingIndex = std::find(lesionsVectorValue.begin(), lesionsVectorValue.end(), lesion.UID); if (existingIndex != lesionsVectorValue.end()) { return; } else { // add the new lesion id from the given lesion to the vector of all current lesion IDs lesionsVectorValue.push_back(lesion.UID); // overwrite the current vector property with the new, extended string vector lesionsVectorProperty->SetValue(lesionsVectorValue); propertyList->SetProperty("lesions", lesionsVectorProperty); // add the lesion with the lesion UID as the key and the lesion information as value std::vector lesionData; lesionData.push_back(lesion.name); lesionData.push_back(lesion.lesionClass.UID); mitk::VectorProperty::Pointer newLesionVectorProperty = mitk::VectorProperty::New(); newLesionVectorProperty->SetValue(lesionData); propertyList->SetProperty(lesion.UID, newLesionVectorProperty); // add the lesion class with the lesion class UID as key and the class type as value std::string lesionClassType = lesion.lesionClass.classType; propertyList->SetStringProperty(lesion.lesionClass.UID.c_str(), lesionClassType.c_str()); } } void mitk::RelationStorage::OverwriteLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid lesion-IDs for the current case mitk::VectorProperty* lesionVectorProperty = dynamic_cast*>(propertyList->GetProperty("lesions")); if (nullptr == lesionVectorProperty) { MITK_INFO << "Could not find any lesion in the storage."; return; } std::vector lesionVectorValue = lesionVectorProperty->GetValue(); const auto existingLesion = std::find(lesionVectorValue.begin(), lesionVectorValue.end(), lesion.UID); if (existingLesion != lesionVectorValue.end()) { // overwrite the referenced lesion class UID with the new, given lesion class data std::vector lesionData; lesionData.push_back(lesion.name); lesionData.push_back(lesion.lesionClass.UID); mitk::VectorProperty::Pointer newLesionVectorProperty = mitk::VectorProperty::New(); newLesionVectorProperty->SetValue(lesionData); propertyList->SetProperty(lesion.UID, newLesionVectorProperty); // overwrite the lesion class with the lesion class UID as key and the new, given class type as value std::string lesionClassType = lesion.lesionClass.classType; propertyList->SetStringProperty(lesion.lesionClass.UID.c_str(), lesionClassType.c_str()); } else { MITK_INFO << "Could not find lesion " << lesion.UID << " in the storage. Cannot overwrite the lesion."; } } void mitk::RelationStorage::LinkSegmentationToLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID, const SemanticTypes::Lesion& lesion) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid lesion-IDs for the current case mitk::VectorProperty* lesionVectorProperty = dynamic_cast*>(propertyList->GetProperty("lesions")); if (nullptr == lesionVectorProperty) { MITK_INFO << "Could not find any lesion property in the storage."; return; } std::vector lesionVectorValue = lesionVectorProperty->GetValue(); const auto existingLesion = std::find(lesionVectorValue.begin(), lesionVectorValue.end(), lesion.UID); if (existingLesion != lesionVectorValue.end()) { // set / overwrite the lesion reference of the given segmentation // retrieve a vector property that contains the referenced ID of a segmentation (0. image ID 1. lesion ID) mitk::VectorProperty* segmentationVectorProperty = dynamic_cast*>(propertyList->GetProperty(segmentationID)); if (nullptr == segmentationVectorProperty) { MITK_INFO << "Could not find the segmentation node " << segmentationID << " in the storage. Cannot link segmentation to lesion."; return; } std::vector segmentationVectorValue = segmentationVectorProperty->GetValue(); if (segmentationVectorValue.size() != 2) { MITK_INFO << "Incorrect segmentation storage. Not two (2) IDs stored."; return; } else { // the lesion ID of a segmentation is the second value in the vector segmentationVectorValue[1] = lesion.UID; segmentationVectorProperty->SetValue(segmentationVectorValue); } } else { MITK_INFO << "Could not find lesion " << lesion.UID << " in the storage. Cannot link segmentation to lesion."; } } void mitk::RelationStorage::UnlinkSegmentationFromLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the referenced ID of a segmentation (0. image ID 1. lesion ID) mitk::VectorProperty* segmentationVectorProperty = dynamic_cast*>(propertyList->GetProperty(segmentationID)); if (nullptr == segmentationVectorProperty) { MITK_INFO << "Could not find the segmentation node " << segmentationID << " in the storage. Cannot unlink lesion from segmentation."; return; } std::vector segmentationVectorValue = segmentationVectorProperty->GetValue(); // a segmentation has to have exactly two values (the ID of the linked image and the ID of the lesion) if (segmentationVectorValue.size() != 2) { MITK_INFO << "Incorrect data storage. Not two (2) values stored."; return; } else { // the second value of the data node vector is the ID of the referenced lesion // set the lesion reference to an empty string for removal segmentationVectorValue[1] = ""; segmentationVectorProperty->SetValue(segmentationVectorValue); } } void mitk::RelationStorage::RemoveLesion(const mitk::SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid lesions of the current case mitk::VectorProperty* lesionVectorProperty = dynamic_cast*>(propertyList->GetProperty("lesions")); if (nullptr == lesionVectorProperty) { MITK_INFO << "Could not find any lesion property in the storage."; return; } // remove the lesion reference from the list of all lesions of the current case std::vector lesionVectorValue = lesionVectorProperty->GetValue(); lesionVectorValue.erase(std::remove(lesionVectorValue.begin(), lesionVectorValue.end(), lesion.UID), lesionVectorValue.end()); if (lesionVectorValue.size() == 0) { // no more lesions stored -> remove the lesions property list propertyList->DeleteProperty("lesions"); } else { // or store the modified vector value lesionVectorProperty->SetValue(lesionVectorValue); } // remove the lesion instance itself // the lesion data is stored under the lesion ID mitk::VectorProperty* lesionDataProperty = dynamic_cast*>(propertyList->GetProperty(lesion.UID)); if (nullptr == lesionDataProperty) { MITK_INFO << "Lesion " << lesion.UID << " not found (already removed?). Cannot remove the lesion."; return; } std::vector lesionData = lesionDataProperty->GetValue(); // a lesion date has to have exactly two values (the name of the lesion and the UID of the lesion class) if (lesionData.size() != 2) { MITK_INFO << "Incorrect lesion data storage. Not two (2) strings of the lesion UID and the lesion name are stored."; } else { std::string lesionClassID = lesionData[1]; RemoveLesionClass(caseID, lesionClassID); } propertyList->DeleteProperty(lesion.UID); } void mitk::RelationStorage::RemoveLesionClass(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& lesionClassID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the lesion class mitk::StringProperty* lesionClassProperty = dynamic_cast(propertyList->GetProperty(lesionClassID)); if (nullptr == lesionClassProperty) { MITK_INFO << "Lesion class " << lesionClassID << " not found (already removed?). Cannot remove the lesion class."; return; } // retrieve a vector property that contains the valid lesions of the current case mitk::VectorProperty* lesionVectorProperty = dynamic_cast*>(propertyList->GetProperty("lesions")); if (nullptr == lesionVectorProperty) { return; } // check if the lesion class ID is referenced by any other lesion std::vector lesionVectorValue = lesionVectorProperty->GetValue(); const auto existingLesionClass = std::find_if(lesionVectorValue.begin(), lesionVectorValue.end(), [&propertyList, &lesionClassID](const std::string& lesionID) { mitk::VectorProperty* lesionDataProperty = dynamic_cast*>(propertyList->GetProperty(lesionID)); if (nullptr == lesionDataProperty) { return false; } else { std::vector lesionData = lesionDataProperty->GetValue(); // a lesion date has to have exactly two values (the name of the lesion and the UID of the lesion class) if (lesionData.size() != 2) { return false; } else { return lesionData[1] == lesionClassID; } } }); if (existingLesionClass == lesionVectorValue.end()) { // lesion class ID not referenced; remove lesion class propertyList->DeleteProperty(lesionClassID); } } void mitk::RelationStorage::AddControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid controlPoint UIDs for the current case mitk::VectorProperty::Pointer controlPointVectorProperty = dynamic_cast*>(propertyList->GetProperty("controlpoints")); std::vector controlPointVectorValue; if (nullptr == controlPointVectorProperty) { controlPointVectorProperty = mitk::VectorProperty::New(); } else { controlPointVectorValue = controlPointVectorProperty->GetValue(); } const auto existingControlPoint = std::find(controlPointVectorValue.begin(), controlPointVectorValue.end(), controlPoint.UID); if (existingControlPoint != controlPointVectorValue.end()) { return; } else { // add the new control point UID from the given control point to the vector of all current control point UIDs controlPointVectorValue.push_back(controlPoint.UID); // overwrite the current vector property with the new, extended string vector controlPointVectorProperty->SetValue(controlPointVectorValue); propertyList->SetProperty("controlpoints", controlPointVectorProperty); // store the control point values (the three integer values of a date) std::vector controlPointDate; controlPointDate.push_back(controlPoint.year); controlPointDate.push_back(controlPoint.month); controlPointDate.push_back(controlPoint.day); mitk::VectorProperty::Pointer newControlPointVectorProperty = mitk::VectorProperty::New(); newControlPointVectorProperty->SetValue(controlPointDate); propertyList->SetProperty(controlPoint.UID, newControlPointVectorProperty); } } void mitk::RelationStorage::LinkDataToControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& dataNodeID, const SemanticTypes::ControlPoint& controlPoint) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid controlPoint UIDs for the current case mitk::VectorProperty* controlPointVectorProperty = dynamic_cast*>(propertyList->GetProperty("controlpoints")); if (nullptr == controlPointVectorProperty) { MITK_INFO << "Could not find any control point property in the storage."; return; } std::vector controlPointVectorValue = controlPointVectorProperty->GetValue(); const auto existingControlPoint = std::find(controlPointVectorValue.begin(), controlPointVectorValue.end(), controlPoint.UID); if (existingControlPoint != controlPointVectorValue.end()) { // set / overwrite the control point reference of the given data // retrieve a vector property that contains the referenced ID of a data node (0. information type 1. control point ID) mitk::VectorProperty* dataNodeVectorProperty = dynamic_cast*>(propertyList->GetProperty(dataNodeID)); if (nullptr == dataNodeVectorProperty) { MITK_INFO << "Could not find the data node " << dataNodeID << " in the storage. Cannot link data to control point."; return; } std::vector dataNodeVectorValue = dataNodeVectorProperty->GetValue(); // an image node has to have exactly two values (the information type and the ID of the control point) if (dataNodeVectorValue.size() != 2) { MITK_INFO << "Incorrect data storage. Not two (2) values stored."; return; } else { // the second value of the data node vector is the ID of the referenced control point dataNodeVectorValue[1] = controlPoint.UID; dataNodeVectorProperty->SetValue(dataNodeVectorValue); } } else { MITK_INFO << "Could not find control point " << controlPoint.UID << " in the storage. Cannot link data to control point."; } } void mitk::RelationStorage::UnlinkDataFromControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& dataNodeID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the referenced ID of a date (0. information type 1. control point ID) mitk::VectorProperty* dataNodeVectorProperty = dynamic_cast*>(propertyList->GetProperty(dataNodeID)); if (nullptr == dataNodeVectorProperty) { MITK_INFO << "Could not find the date " << dataNodeID << " in the storage. Cannot unlink control point from date."; return; } std::vector dataNodeVectorValue = dataNodeVectorProperty->GetValue(); // a data node has to have exactly two values (the information type and the ID of the control point) if (dataNodeVectorValue.size() != 2) { MITK_INFO << "Incorrect data storage. Not two (2) values stored."; return; } else { // the second value of the data node vector is the ID of the referenced control point // set the control point reference to an empty string for removal dataNodeVectorValue[1] = ""; dataNodeVectorProperty->SetValue(dataNodeVectorValue); } } void mitk::RelationStorage::RemoveControlPointFromCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid controlPoint UIDs for the current case mitk::VectorProperty* allControlPointsVectorProperty = dynamic_cast*>(propertyList->GetProperty("controlpoints")); if (nullptr == allControlPointsVectorProperty) { MITK_INFO << "Could not find any control point property in the storage."; return; } // remove the control point reference from the list of all control points of the current case std::vector currentControlPointVectorValue = allControlPointsVectorProperty->GetValue(); currentControlPointVectorValue.erase(std::remove(currentControlPointVectorValue.begin(), currentControlPointVectorValue.end(), controlPoint.UID), currentControlPointVectorValue.end()); allControlPointsVectorProperty->SetValue(currentControlPointVectorValue); // remove the control point instance itself propertyList->DeleteProperty(controlPoint.UID); } +void mitk::RelationStorage::AddExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod) +{ + mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); + if (nullptr == propertyList) + { + MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; + return; + } + // retrieve a vector property that contains the valid examination period UIDs for the current case + mitk::VectorProperty::Pointer vectorProperty = dynamic_cast*>(propertyList->GetProperty("examinationperiods")); + std::vector examinationPeriodsVectorValue; + if (nullptr == vectorProperty) + { + vectorProperty = mitk::VectorProperty::New(); + } + else + { + examinationPeriodsVectorValue = vectorProperty->GetValue(); + } + + const auto& existingIndex = std::find(examinationPeriodsVectorValue.begin(), examinationPeriodsVectorValue.end(), examinationPeriod.UID); + if (existingIndex != examinationPeriodsVectorValue.end()) + { + return; + } + else + { + // add the new examination period id from the given examination period to the vector of all current examination period IDs + examinationPeriodsVectorValue.push_back(examinationPeriod.UID); + // overwrite the current vector property with the new, extended string vector + vectorProperty->SetValue(examinationPeriodsVectorValue); + propertyList->SetProperty("examinationperiods", vectorProperty); + + // add the examination period with the UID as the key and an empty control point UIDs vector as value + std::vector controlPointUIDs; + mitk::VectorProperty::Pointer newExaminationPeriodVectorProperty = mitk::VectorProperty::New(); + newExaminationPeriodVectorProperty->SetValue(controlPointUIDs); + propertyList->SetProperty(examinationPeriod.UID, newExaminationPeriodVectorProperty); + } +} + +void mitk::RelationStorage::AddControlPointToExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriod examinationPeriod) +{ + mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); + if (nullptr == propertyList) + { + MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; + return; + } + + // retrieve a vector property that contains the represented control point UIDs of the given examination period + mitk::VectorProperty* controlPointUIDsVectorProperty = dynamic_cast*>(propertyList->GetProperty(examinationPeriod.UID)); + if (nullptr == controlPointUIDsVectorProperty) + { + MITK_INFO << "Could not find examination period " << examinationPeriod.UID << " in the storage. Cannot add the control point to the examination period."; + return; + } + + std::vector controlPointUIDsVectorValue = controlPointUIDsVectorProperty->GetValue(); + // store the control point UID + controlPointUIDsVectorValue.push_back(controlPoint.UID); + controlPointUIDsVectorProperty->SetValue(controlPointUIDsVectorValue); +} + +void mitk::RelationStorage::RemoveControlPointFromExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriod examinationPeriod) +{ + mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); + if (nullptr == propertyList) + { + MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; + return; + } + + // retrieve a vector property that contains the represented control point UIDs of the given examination period + mitk::VectorProperty* controlPointUIDsVectorProperty = dynamic_cast*>(propertyList->GetProperty(examinationPeriod.UID)); + if (nullptr == controlPointUIDsVectorProperty) + { + MITK_INFO << "Could not find examination period " << examinationPeriod.UID << " in the storage. Cannot add the control point to the examination period."; + return; + } + + std::vector controlPointUIDsVectorValue = controlPointUIDsVectorProperty->GetValue(); + controlPointUIDsVectorValue.erase(std::remove(controlPointUIDsVectorValue.begin(), controlPointUIDsVectorValue.end(), controlPoint.UID), controlPointUIDsVectorValue.end()); + // store the modified vector value + controlPointUIDsVectorProperty->SetValue(controlPointUIDsVectorValue); +} + +void mitk::RelationStorage::RemoveExaminationPeriodFromCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod examinationPeriod) +{ + mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); + if (nullptr == propertyList) + { + MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; + return; + } + // retrieve a vector property that contains the valid examination period UIDs for the current case + mitk::VectorProperty::Pointer vectorProperty = dynamic_cast*>(propertyList->GetProperty("examinationperiods")); + if (nullptr == vectorProperty) + { + MITK_INFO << "Could not find any examination periods in the storage."; + return; + } + + std::vector examinationPeriodVectorValue = vectorProperty->GetValue(); + examinationPeriodVectorValue.erase(std::remove(examinationPeriodVectorValue.begin(), examinationPeriodVectorValue.end(), examinationPeriod.UID), examinationPeriodVectorValue.end()); + if (examinationPeriodVectorValue.size() == 0) + { + // no more examination periods stored -> remove the examination period property list + propertyList->DeleteProperty("examinationperiods"); + } + else + { + // or store the modified vector value + vectorProperty->SetValue(examinationPeriodVectorValue); + } +} + void mitk::RelationStorage::AddInformationTypeToImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID, const SemanticTypes::InformationType informationType) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid information types of the current case mitk::VectorProperty::Pointer informationTypeVectorProperty = dynamic_cast*>(propertyList->GetProperty("informationtypes")); std::vector informationTypeVectorValue; if (nullptr == informationTypeVectorProperty) { informationTypeVectorProperty = mitk::VectorProperty::New(); } else { informationTypeVectorValue = informationTypeVectorProperty->GetValue(); } const auto existingInformationType = std::find(informationTypeVectorValue.begin(), informationTypeVectorValue.end(), informationType); if (existingInformationType == informationTypeVectorValue.end()) { // at first: add the information type to the storage informationTypeVectorValue.push_back(informationType); informationTypeVectorProperty->SetValue(informationTypeVectorValue); propertyList->SetProperty("informationtypes", informationTypeVectorProperty); } // set / overwrite the information type of the given data // retrieve a vector property that contains the referenced ID of an image (0. information type 1. control point ID) mitk::VectorProperty* imageNodeVectorProperty = dynamic_cast*>(propertyList->GetProperty(imageID)); if (nullptr == imageNodeVectorProperty) { MITK_INFO << "Could not find the image " << imageID << " in the storage. Cannot add information type to image."; return; } std::vector imageNodeVectorValue = imageNodeVectorProperty->GetValue(); // an image node has to have exactly two values (the information type and the ID of the control point) if (imageNodeVectorValue.size() != 2) { MITK_INFO << "Incorrect data storage. Not two (2) values stored."; return; } else { // the first value of the data node vector is the information type imageNodeVectorValue[0] = informationType; imageNodeVectorProperty->SetValue(imageNodeVectorValue); } } void mitk::RelationStorage::RemoveInformationTypeFromImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the referenced ID of an image (0. information type 1. control point ID) mitk::VectorProperty* imageNodeVectorProperty = dynamic_cast*>(propertyList->GetProperty(imageID)); if (nullptr == imageNodeVectorProperty) { MITK_INFO << "Could not find the image " << imageID << " in the storage. Cannot remove information type from image."; return; } std::vector imageNodeVectorValue = imageNodeVectorProperty->GetValue(); // an image node has to have exactly two values (the information type and the ID of the control point) if (imageNodeVectorValue.size() != 2) { MITK_INFO << "Incorrect data storage. Not two (2) values stored."; return; } else { // the first value of the data node vector is the information type // set the information type to an empty string for removal imageNodeVectorValue[0] = ""; imageNodeVectorProperty->SetValue(imageNodeVectorValue); } } void mitk::RelationStorage::RemoveInformationTypeFromCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType informationType) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return; } // retrieve a vector property that contains the valid information types of the current case mitk::VectorProperty* informationTypeVectorProperty = dynamic_cast*>(propertyList->GetProperty("informationtypes")); if (nullptr == informationTypeVectorProperty) { MITK_INFO << "Could not find any information type property in the storage."; return; } std::vector informationTypeVectorValue = informationTypeVectorProperty->GetValue(); informationTypeVectorValue.erase(std::remove(informationTypeVectorValue.begin(), informationTypeVectorValue.end(), informationType), informationTypeVectorValue.end()); if (informationTypeVectorValue.size() == 0) { // no more information types stored -> remove the information types property list propertyList->DeleteProperty("informationtypes"); } else { // or store the modified vector value informationTypeVectorProperty->SetValue(informationTypeVectorValue); } } mitk::PropertyList::Pointer mitk::RelationStorage::GetStorageData(const SemanticTypes::CaseID& caseID) { // access the storage PERSISTENCE_GET_SERVICE_MACRO if (nullptr == persistenceService) { MITK_INFO << "Persistence service could not be loaded"; return nullptr; } // the property list is valid for a whole case and contains all the properties for the current case // the persistence service may create a new property list with the given ID, if no property list is found return persistenceService->GetPropertyList(const_cast(caseID)); } mitk::SemanticTypes::Lesion mitk::RelationStorage::GenerateLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& lesionID) { mitk::PropertyList::Pointer propertyList = GetStorageData(caseID); if (nullptr == propertyList) { MITK_INFO << "Could not find the property list " << caseID << " for the current MITK workbench / session."; return SemanticTypes::Lesion(); } mitk::VectorProperty* lesionDataProperty = dynamic_cast*>(propertyList->GetProperty(lesionID)); if (nullptr == lesionDataProperty) { MITK_INFO << "Lesion " << lesionID << " not found. Lesion can not be retrieved."; return SemanticTypes::Lesion(); } std::vector lesionData = lesionDataProperty->GetValue(); // a lesion date has to have exactly two values (the name of the lesion and the UID of the lesion class) if (lesionData.size() != 2) { MITK_INFO << "Incorrect lesion data storage. Not two (2) strings of the lesion name and the lesion UID are stored."; return SemanticTypes::Lesion(); } // the lesion class ID is stored as the second property std::string lesionClassID = lesionData[1]; mitk::StringProperty* lesionClassProperty = dynamic_cast(propertyList->GetProperty(lesionClassID)); if (nullptr != lesionClassProperty) { SemanticTypes::LesionClass generatedLesionClass; generatedLesionClass.UID = lesionClassID; generatedLesionClass.classType = lesionClassProperty->GetValue(); SemanticTypes::Lesion generatedLesion; generatedLesion.UID = lesionID; generatedLesion.name = lesionData[0]; generatedLesion.lesionClass = generatedLesionClass; return generatedLesion; } else { MITK_INFO << "Incorrect lesion class storage. Lesion " << lesionID << " can not be retrieved."; return SemanticTypes::Lesion(); } } diff --git a/Modules/SemanticRelations/src/mitkSemanticRelations.cpp b/Modules/SemanticRelations/src/mitkSemanticRelations.cpp index d17d962025..f5489a6095 100644 --- a/Modules/SemanticRelations/src/mitkSemanticRelations.cpp +++ b/Modules/SemanticRelations/src/mitkSemanticRelations.cpp @@ -1,934 +1,1002 @@ /*=================================================================== 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. ===================================================================*/ // semantic relations module #include "mitkSemanticRelations.h" #include "mitkSemanticRelationException.h" #include "mitkNodePredicates.h" #include "mitkUIDGeneratorBoost.h" // multi label module #include // c++ #include #include std::vector mitk::SemanticRelations::m_ObserverVector; mitk::SemanticRelations::SemanticRelations(DataStorage::Pointer dataStorage) : m_DataStorage(dataStorage) { m_RelationStorage = std::make_shared(); m_RelationStorage->SetDataStorage(m_DataStorage); } mitk::SemanticRelations::~SemanticRelations() { // nothing here } void mitk::SemanticRelations::AddObserver(ISemanticRelationsObserver* observer) { std::vector::iterator existingObserver = std::find(m_ObserverVector.begin(), m_ObserverVector.end(), observer); if (existingObserver != m_ObserverVector.end()) { // no need to add the already existing observer return; } m_ObserverVector.push_back(observer); } void mitk::SemanticRelations::RemoveObserver(ISemanticRelationsObserver* observer) { m_ObserverVector.erase(std::remove(m_ObserverVector.begin(), m_ObserverVector.end(), observer), m_ObserverVector.end()); } /************************************************************************/ /* functions to get instances / attributes */ /************************************************************************/ mitk::SemanticRelations::LesionVector mitk::SemanticRelations::GetAllLesionsOfCase(const SemanticTypes::CaseID& caseID) const { return m_RelationStorage->GetAllLesionsOfCase(caseID); } mitk::SemanticRelations::LesionVector mitk::SemanticRelations::GetAllLesionsOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const { LesionVector allLesions = 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, this](const SemanticTypes::Lesion& lesion) { return !ControlPointContainsLesion(caseID, lesion, controlPoint); }; allLesions.erase(std::remove_if(allLesions.begin(), allLesions.end(), lambda), allLesions.end()); return allLesions; } mitk::SemanticRelations::LesionClassVector mitk::SemanticRelations::GetAllLesionClassesOfCase(const SemanticTypes::CaseID& caseID) const { LesionVector allLesionsOfCase = GetAllLesionsOfCase(caseID); LesionClassVector allLesionClassesOfCase; for (const auto& lesion : allLesionsOfCase) { allLesionClassesOfCase.push_back(lesion.lesionClass); } // remove duplicate entries auto lessThan = [](const SemanticTypes::LesionClass& lesionClassL, const SemanticTypes::LesionClass& lesionClassR) { return lesionClassL.UID < lesionClassR.UID; }; auto equal = [](const SemanticTypes::LesionClass& lesionClassL, const SemanticTypes::LesionClass& lesionClassR) { return lesionClassL.UID == lesionClassR.UID; }; std::sort(allLesionClassesOfCase.begin(), allLesionClassesOfCase.end(), lessThan); allLesionClassesOfCase.erase(std::unique(allLesionClassesOfCase.begin(), allLesionClassesOfCase.end(), equal), allLesionClassesOfCase.end()); return allLesionClassesOfCase; } mitk::SemanticRelations::LesionVector mitk::SemanticRelations::GetAllLesionsInImage(const DataNode* imageNode) const { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid image data node."; } if (m_DataStorage.IsNull()) { mitkThrowException(SemanticRelationException) << "Not a valid data storage."; } LesionVector allLesionsInImage; // get child nodes of the current node with the segmentation predicate DataStorage::SetOfObjects::ConstPointer segmentationNodes = m_DataStorage->GetDerivations(imageNode, NodePredicates::GetSegmentationPredicate(), false); for (auto it = segmentationNodes->Begin(); it != segmentationNodes->End(); ++it) { DataNode* segmentationNode = it->Value(); try { SemanticTypes::Lesion representedLesion = GetRepresentedLesion(segmentationNode); allLesionsInImage.push_back(representedLesion); } catch (const SemanticRelationException&) { continue; } } return allLesionsInImage; } mitk::SemanticTypes::Lesion mitk::SemanticRelations::GetRepresentedLesion(const DataNode* segmentationNode) const { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(segmentationNode); SemanticTypes::ID segmentationID = GetIDFromDataNode(segmentationNode); SemanticTypes::Lesion representedLesion = m_RelationStorage->GetRepresentedLesion(caseID, segmentationID); if (representedLesion.UID.empty()) { mitkThrowException(SemanticRelationException) << "Could not find a represented lesion instance for the given segmentation node " << segmentationNode->GetName(); } else { return representedLesion; } } bool mitk::SemanticRelations::IsRepresentingALesion(const DataNode* segmentationNode) const { try { SemanticTypes::Lesion representedLesion = GetRepresentedLesion(segmentationNode); return true; } catch (const Exception&) { return false; } } bool mitk::SemanticRelations::InstanceExists(const DataNode* dataNode) const { try { SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(dataNode); SemanticTypes::ID dataNodeID = GetIDFromDataNode(dataNode); if (mitk::NodePredicates::GetImagePredicate()->CheckNode(dataNode)) { std::vector allImageIDsOfCase = m_RelationStorage->GetAllImageIDsOfCase(caseID); return std::find(allImageIDsOfCase.begin(), allImageIDsOfCase.end(), dataNodeID) != allImageIDsOfCase.end(); } else if (mitk::NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode)) { std::vector allSegmentationIDsOfCase = m_RelationStorage->GetAllSegmentationIDsOfCase(caseID); return std::find(allSegmentationIDsOfCase.begin(), allSegmentationIDsOfCase.end(), dataNodeID) != allSegmentationIDsOfCase.end(); } else { return false; } } catch (const SemanticRelationException&) { return false; } } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllSegmentationsOfCase(const SemanticTypes::CaseID& caseID) const { if (m_DataStorage.IsNull()) { mitkThrowException(SemanticRelationException) << "Not a valid data storage."; } return m_RelationStorage->GetAllSegmentationsOfCase(caseID); } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllSegmentationsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const { if (m_DataStorage.IsNull()) { mitkThrowException(SemanticRelationException) << "Not a valid data storage."; } if (InstanceExists(caseID, lesion)) { // lesion exists, retrieve all case segmentations from the storage DataNodeVector allSegmentationsOfLesion = GetAllSegmentationsOfCase(caseID); // filter all segmentations: check for semantic relation with the given lesion using a lambda function auto lambda = [&lesion, this](DataNode::Pointer segmentation) { try { SemanticTypes::Lesion representedLesion = GetRepresentedLesion(segmentation); return lesion.UID != representedLesion.UID; } catch (const SemanticRelationException&) { return true; } }; allSegmentationsOfLesion.erase(std::remove_if(allSegmentationsOfLesion.begin(), allSegmentationsOfLesion.end(), lambda), allSegmentationsOfLesion.end()); return allSegmentationsOfLesion; } else { mitkThrowException(SemanticRelationException) << "Could not find an existing lesion instance for the given caseID " << caseID << " and lesion " << lesion.UID << "."; } } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllImagesOfCase(const SemanticTypes::CaseID& caseID) const { if (m_DataStorage.IsNull()) { mitkThrowException(SemanticRelationException) << "Not a valid data storage."; } return m_RelationStorage->GetAllImagesOfCase(caseID); } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllImagesOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const { if (m_DataStorage.IsNull()) { mitkThrowException(SemanticRelationException) << "Not a valid data storage."; } DataNodeVector allImagesOfLesion; // 1. get all segmentations that define the lesion // 2. retrieve the parent node (source) of the found segmentation node DataNodeVector allSegmentationsOfLesion = GetAllSegmentationsOfLesion(caseID, lesion); for (const auto& segmentationNode : allSegmentationsOfLesion) { // get parent node of the current segmentation node with the node predicate DataStorage::SetOfObjects::ConstPointer parentNodes = m_DataStorage->GetSources(segmentationNode, NodePredicates::GetImagePredicate(), false); for (auto it = parentNodes->Begin(); it != parentNodes->End(); ++it) { DataNode::Pointer dataNode = it->Value(); allImagesOfLesion.push_back(it->Value()); } } std::sort(allImagesOfLesion.begin(), allImagesOfLesion.end()); allImagesOfLesion.erase(std::unique(allImagesOfLesion.begin(), allImagesOfLesion.end()), allImagesOfLesion.end()); return allImagesOfLesion; } bool mitk::SemanticRelations::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const { LesionVector allLesions = 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); if (existingLesion != allLesions.end()) { return true; } else { return false; } } mitk::SemanticRelations::ControlPointVector mitk::SemanticRelations::GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID) const { return m_RelationStorage->GetAllControlPointsOfCase(caseID); } mitk::SemanticRelations::ControlPointVector mitk::SemanticRelations::GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const { ControlPointVector allControlPoints = 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, this](const SemanticTypes::ControlPoint& controlPoint) { return !ControlPointContainsLesion(caseID, lesion, controlPoint); }; allControlPoints.erase(std::remove_if(allControlPoints.begin(), allControlPoints.end(), lambda), allControlPoints.end()); return allControlPoints; } mitk::SemanticRelations::ControlPointVector mitk::SemanticRelations::GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) const { ControlPointVector allControlPoints = 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, this](const SemanticTypes::ControlPoint& controlPoint) { return !ControlPointContainsInformationType(caseID, informationType, controlPoint); }; allControlPoints.erase(std::remove_if(allControlPoints.begin(), allControlPoints.end(), lambda), allControlPoints.end()); return allControlPoints; } mitk::SemanticTypes::ControlPoint mitk::SemanticRelations::GetControlPointOfData(const DataNode* dataNode) const { if (nullptr == dataNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(dataNode); SemanticTypes::ID dataNodeID = GetIDFromDataNode(dataNode); return m_RelationStorage->GetControlPointOfData(caseID, dataNodeID); } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllImagesOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const { if (m_DataStorage.IsNull()) { mitkThrow() << "Not a valid data storage."; } if (InstanceExists(caseID, controlPoint)) { // control point exists, retrieve all images from the storage DataNodeVector allImagesOfControlPoint = GetAllImagesOfCase(caseID); // filter all images to remove the ones with a different control point using a lambda function auto lambda = [&controlPoint, this](DataNode::Pointer imageNode) { return controlPoint.UID != GetControlPointOfData(imageNode).UID; }; allImagesOfControlPoint.erase(std::remove_if(allImagesOfControlPoint.begin(), allImagesOfControlPoint.end(), lambda), allImagesOfControlPoint.end()); return allImagesOfControlPoint; } else { mitkThrowException(SemanticRelationException) << "Could not find an existing control point instance for the given caseID " << caseID << " and control point " << controlPoint.UID << "."; } } bool mitk::SemanticRelations::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const { ControlPointVector allControlPoints = 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; } } +mitk::SemanticRelations::ExaminationPeriodVector mitk::SemanticRelations::GetAllExaminationPeriodsOfCase(const SemanticTypes::CaseID& caseID) const +{ + return m_RelationStorage->GetAllExaminationPeriodsOfCase(caseID); +} + +bool mitk::SemanticRelations::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod) const +{ + ExaminationPeriodVector allExaminationPeriods = 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::SemanticRelations::InformationTypeVector mitk::SemanticRelations::GetAllInformationTypesOfCase(const SemanticTypes::CaseID& caseID) const { return m_RelationStorage->GetAllInformationTypesOfCase(caseID); } mitk::SemanticRelations::InformationTypeVector mitk::SemanticRelations::GetAllInformationTypesOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const { InformationTypeVector allInformationTypes = 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, this](const SemanticTypes::InformationType& informationType) { return !ControlPointContainsInformationType(caseID, informationType, controlPoint); }; allInformationTypes.erase(std::remove_if(allInformationTypes.begin(), allInformationTypes.end(), lambda), allInformationTypes.end()); return allInformationTypes; } mitk::SemanticTypes::InformationType mitk::SemanticRelations::GetInformationTypeOfImage(const DataNode* imageNode) const { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid image data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); SemanticTypes::ID imageID = GetIDFromDataNode(imageNode); return m_RelationStorage->GetInformationTypeOfImage(caseID, imageID); } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllImagesOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) const { if (m_DataStorage.IsNull()) { mitkThrow() << "Not a valid data storage."; } if (InstanceExists(caseID, informationType)) { // information type exists, retrieve all images from the storage DataNodeVector allImagesOfInformationType = GetAllImagesOfCase(caseID); // filter all images to remove the ones with a different information type using a lambda function auto lambda = [&informationType, this](DataNode::Pointer imageNode) { return informationType != GetInformationTypeOfImage(imageNode); }; allImagesOfInformationType.erase(std::remove_if(allImagesOfInformationType.begin(), allImagesOfInformationType.end(), lambda), allImagesOfInformationType.end()); return allImagesOfInformationType; } else { mitkThrowException(SemanticRelationException) << "Could not find an existing information type for the given caseID " << caseID << " and information type " << informationType; } } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllSpecificImages(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const { if (m_DataStorage.IsNull()) { mitkThrow() << "Not a valid data storage."; } if (InstanceExists(caseID, controlPoint)) { if (InstanceExists(caseID, informationType)) { // control point exists, information type exists, retrieve all images from the storage DataNodeVector allImagesOfCase = GetAllImagesOfCase(caseID); // filter all images to remove the ones with a different control point and information type using a lambda function auto lambda = [&controlPoint, &informationType, this](DataNode::Pointer imageNode) { return (informationType != GetInformationTypeOfImage(imageNode)) || (controlPoint != GetControlPointOfData(imageNode)); }; allImagesOfCase.erase(std::remove_if(allImagesOfCase.begin(), allImagesOfCase.end(), lambda), allImagesOfCase.end()); return allImagesOfCase; } else { mitkThrowException(SemanticRelationException) << "Could not find an existing information type for the given caseID " << caseID << " and information type " << informationType; } } else { mitkThrowException(SemanticRelationException) << "Could not find an existing control point for the given caseID " << caseID << " and control point " << controlPoint.UID; } } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllSpecificSegmentations(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const { if (m_DataStorage.IsNull()) { mitkThrow() << "Not a valid data storage."; } DataNodeVector allSpecificImages = GetAllSpecificImages(caseID, controlPoint, informationType); DataNodeVector allSpecificSegmentations; for (const auto& imageNode : allSpecificImages) { DataStorage::SetOfObjects::ConstPointer segmentationNodes = m_DataStorage->GetDerivations(imageNode, NodePredicates::GetSegmentationPredicate(), false); for (auto it = segmentationNodes->Begin(); it != segmentationNodes->End(); ++it) { allSpecificSegmentations.push_back(it->Value()); } } return allSpecificSegmentations; } bool mitk::SemanticRelations::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) const { InformationTypeVector allInformationTypes = 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; } } std::vector mitk::SemanticRelations::GetAllCaseIDs() const { return m_RelationStorage->GetAllCaseIDs(); } /************************************************************************/ /* functions to add / remove instances / attributes */ /************************************************************************/ void mitk::SemanticRelations::AddImage(const DataNode* imageNode) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } // continue with a valid data node SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); SemanticTypes::ID nodeID = GetIDFromDataNode(imageNode); m_RelationStorage->AddCase(caseID); m_RelationStorage->AddImage(caseID, nodeID); SemanticTypes::InformationType informationType = GetDICOMModalityFromDataNode(imageNode); AddInformationTypeToImage(imageNode, informationType); // set the correct control point for this image SemanticTypes::ControlPoint controlPoint = GenerateControlPoint(imageNode); SetControlPointOfData(imageNode, controlPoint); } void mitk::SemanticRelations::RemoveImage(const DataNode* imageNode) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } // continue with a valid data node SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); SemanticTypes::ID nodeID = GetIDFromDataNode(imageNode); RemoveInformationTypeFromImage(imageNode); UnlinkDataFromControlPoint(imageNode); m_RelationStorage->RemoveImage(caseID, nodeID); NotifyObserver(caseID); } void mitk::SemanticRelations::AddLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { if (InstanceExists(caseID, lesion)) { mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to add already exists for the given case."; } else { m_RelationStorage->AddLesion(caseID, lesion); NotifyObserver(caseID); } } void mitk::SemanticRelations::OverwriteLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { if (InstanceExists(caseID, lesion)) { m_RelationStorage->OverwriteLesion(caseID, lesion); NotifyObserver(caseID); } else { mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to overwrite does not exist for the given case."; } } void mitk::SemanticRelations::AddLesionAndLinkSegmentation(const DataNode* segmentationNode, const SemanticTypes::Lesion& lesion) { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(segmentationNode); AddLesion(caseID, lesion); LinkSegmentationToLesion(segmentationNode, lesion); NotifyObserver(caseID); } void mitk::SemanticRelations::RemoveLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { if (InstanceExists(caseID, lesion)) { DataNodeVector allSegmentationsOfLesion = GetAllSegmentationsOfLesion(caseID, lesion); if (allSegmentationsOfLesion.empty()) { // no more segmentations are linked to the specific lesion // the lesion can be removed from the storage m_RelationStorage->RemoveLesion(caseID, lesion); NotifyObserver(caseID); } else { mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to remove is still referred to by a segmentation node. Lesion will not be removed."; } } else { mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to remove does not exist for the given case."; } } void mitk::SemanticRelations::AddSegmentation(const DataNode* segmentationNode, const DataNode* parentNode) { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } if (nullptr == parentNode) { mitkThrowException(SemanticRelationException) << "Not a valid parent data node."; } // continue with a valid data node SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(segmentationNode); SemanticTypes::ID segmentationNodeID = GetIDFromDataNode(segmentationNode); SemanticTypes::ID parentNodeID = GetIDFromDataNode(parentNode); m_RelationStorage->AddSegmentation(caseID, segmentationNodeID, parentNodeID); NotifyObserver(caseID); } void mitk::SemanticRelations::LinkSegmentationToLesion(const DataNode* segmentationNode, const SemanticTypes::Lesion& lesion) { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(segmentationNode); if (InstanceExists(caseID, lesion)) { SemanticTypes::ID segmentationID = GetIDFromDataNode(segmentationNode); m_RelationStorage->LinkSegmentationToLesion(caseID, segmentationID, lesion); NotifyObserver(caseID); } else { mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to link does not exist for the given case."; } } void mitk::SemanticRelations::UnlinkSegmentationFromLesion(const DataNode* segmentationNode) { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(segmentationNode); SemanticTypes::ID segmentationID = GetIDFromDataNode(segmentationNode); m_RelationStorage->UnlinkSegmentationFromLesion(caseID, segmentationID); NotifyObserver(caseID); } void mitk::SemanticRelations::RemoveSegmentation(const DataNode* segmentationNode) { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } // continue with a valid data node SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(segmentationNode); SemanticTypes::ID segmentationNodeID = GetIDFromDataNode(segmentationNode); m_RelationStorage->RemoveSegmentation(caseID, segmentationNodeID); NotifyObserver(caseID); } void mitk::SemanticRelations::SetControlPointOfData(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint) { if (nullptr == dataNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(dataNode); ControlPointVector allControlPoints = GetAllControlPointsOfCase(caseID); // need to check if an already existing control point fits/contains the user control point SemanticTypes::ControlPoint existingControlPoint = FindExistingControlPoint(controlPoint, allControlPoints); if (!existingControlPoint.UID.empty()) { try { - // found a fitting control point + // found an already existing control point LinkDataToControlPoint(dataNode, existingControlPoint, false); } catch (const SemanticRelationException&) { mitkThrowException(SemanticRelationException) << "The data can not be linked. Inconsistency in the semantic relations storage assumed."; } } else { try { AddControlPointAndLinkData(dataNode, controlPoint, false); + // added a new control point + // find closest control point to add the new control point to the correct examination period + SemanticTypes::ControlPoint closestControlPoint = FindClosestControlPoint(controlPoint, allControlPoints); + ExaminationPeriodVector allExaminationPeriods = GetAllExaminationPeriodsOfCase(caseID); + SemanticTypes::ExaminationPeriod examinationPeriod = FindExaminationPeriod(closestControlPoint, allExaminationPeriods); + if (examinationPeriod.UID.empty()) + { + // no closest control point (exceed threshold) or no examination period found + // create a new examination period for this control point and add it to the storage + examinationPeriod.UID = UIDGeneratorBoost::GenerateUID(); + AddExaminationPeriod(caseID, examinationPeriod); + } + + // add the control point to the (newly created or found / close) examination period + AddControlPointToExaminationPeriod(caseID, controlPoint, examinationPeriod); } catch (const SemanticRelationException&) { mitkThrowException(SemanticRelationException) << "The data can not be linked. Inconsistency in the semantic relations storage assumed."; } } ClearControlPoints(caseID); NotifyObserver(caseID); } void mitk::SemanticRelations::AddControlPointAndLinkData(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence) { if (nullptr == dataNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(dataNode); if (InstanceExists(caseID, controlPoint)) { mitkThrowException(SemanticRelationException) << "The control point " << controlPoint.UID << " to add already exists for the given case. \n Use 'LinkDataToControlPoint' instead."; } m_RelationStorage->AddControlPoint(caseID, controlPoint); LinkDataToControlPoint(dataNode, controlPoint, checkConsistence); } void mitk::SemanticRelations::LinkDataToControlPoint(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence) { if (nullptr == dataNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(dataNode); if (InstanceExists(caseID, controlPoint)) { SemanticTypes::ID dataID = GetIDFromDataNode(dataNode); m_RelationStorage->LinkDataToControlPoint(caseID, dataID, controlPoint); } else { mitkThrowException(SemanticRelationException) << "The control point " << controlPoint.UID << " to link does not exist for the given case."; } } void mitk::SemanticRelations::UnlinkDataFromControlPoint(const DataNode* dataNode) { if (nullptr == dataNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(dataNode); SemanticTypes::ID dataID = GetIDFromDataNode(dataNode); SemanticTypes::ControlPoint controlPoint = m_RelationStorage->GetControlPointOfData(caseID, dataID); m_RelationStorage->UnlinkDataFromControlPoint(caseID, dataID); ClearControlPoints(caseID); } +void mitk::SemanticRelations::AddExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod) +{ + if (InstanceExists(caseID, examinationPeriod)) + { + mitkThrowException(SemanticRelationException) << "The examination period " << examinationPeriod.UID << " to add already exists for the given case."; + } + else + { + m_RelationStorage->AddExaminationPeriod(caseID, examinationPeriod); + } +} + +void mitk::SemanticRelations::AddControlPointToExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriod& examinationPeriod) +{ + if (!InstanceExists(caseID, controlPoint)) + { + mitkThrowException(SemanticRelationException) << "The control point " << controlPoint.UID << " to add does not exist for the given case."; + } + + if (!InstanceExists(caseID, examinationPeriod)) + { + mitkThrowException(SemanticRelationException) << "The examination period " << examinationPeriod.UID << " does not exist for the given case. \n Use 'AddExaminationPeriod' before."; + } + + m_RelationStorage->AddControlPointToExaminationPeriod(caseID, controlPoint, examinationPeriod); +} + void mitk::SemanticRelations::SetInformationType(const DataNode* imageNode, const SemanticTypes::InformationType& informationType) { RemoveInformationTypeFromImage(imageNode); AddInformationTypeToImage(imageNode, informationType); SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); NotifyObserver(caseID); } void mitk::SemanticRelations::AddInformationTypeToImage(const DataNode* imageNode, const SemanticTypes::InformationType& informationType) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid image data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); SemanticTypes::ID imageID = GetIDFromDataNode(imageNode); m_RelationStorage->AddInformationTypeToImage(caseID, imageID, informationType); } void mitk::SemanticRelations::RemoveInformationTypeFromImage(const DataNode* imageNode) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid image data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); SemanticTypes::ID imageID = GetIDFromDataNode(imageNode); SemanticTypes::InformationType originalInformationType = m_RelationStorage->GetInformationTypeOfImage(caseID, imageID); m_RelationStorage->RemoveInformationTypeFromImage(caseID, imageID); // check for further references to the removed information type std::vector allImageIDsVectorValue = m_RelationStorage->GetAllImageIDsOfCase(caseID); for (const auto otherImageID : allImageIDsVectorValue) { SemanticTypes::InformationType otherInformationType = m_RelationStorage->GetInformationTypeOfImage(caseID, otherImageID); if (otherInformationType == originalInformationType) { // found the information type in another image -> cannot remove the information type from the case return; } } // given information type was not referred by any other image of the case -> the information type can be removed from the case m_RelationStorage->RemoveInformationTypeFromCase(caseID, originalInformationType); } /************************************************************************/ /* private functions */ /************************************************************************/ void mitk::SemanticRelations::NotifyObserver(const SemanticTypes::CaseID& caseID) const { for (auto& observer : m_ObserverVector) { observer->Update(caseID); } } bool mitk::SemanticRelations::ControlPointContainsLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint) const { DataNodeVector allImagesOfLesion; try { allImagesOfLesion = GetAllImagesOfLesion(caseID, lesion); } catch (const SemanticRelationException&) { // error retrieving image data; lesion has to be outside the control point return false; } DataNodeVector allImagesOfControlPoint; try { allImagesOfControlPoint = GetAllImagesOfControlPoint(caseID, controlPoint); } catch (const SemanticRelationException&) { // error retrieving control point data; lesion has to be outside the control point return false; } std::sort(allImagesOfLesion.begin(), allImagesOfLesion.end()); std::sort(allImagesOfControlPoint.begin(), allImagesOfControlPoint.end()); DataNodeVector allImagesIntersection; // set intersection removes duplicated nodes, since 'GetAllImagesOfControlPoint' only contains at most one of each node std::set_intersection(allImagesOfLesion.begin(), allImagesOfLesion.end(), allImagesOfControlPoint.begin(), allImagesOfControlPoint.end(), std::back_inserter(allImagesIntersection)); // if the vector of intersecting data is empty, the control point does not contain the lesion return !allImagesIntersection.empty(); } bool mitk::SemanticRelations::ControlPointContainsInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType, const SemanticTypes::ControlPoint& controlPoint) const { DataNodeVector allImagesIntersection = GetAllSpecificImages(caseID, controlPoint, informationType); return !allImagesIntersection.empty(); } void mitk::SemanticRelations::ClearControlPoints(const SemanticTypes::CaseID& caseID) { ControlPointVector allControlPointsOfCase; try { allControlPointsOfCase = GetAllControlPointsOfCase(caseID); } catch (const SemanticRelationException&) { // error retrieving control point data return; } DataNodeVector allImagesOfCase; try { allImagesOfCase = GetAllImagesOfCase(caseID); } catch (const SemanticRelationException&) { // error retrieving image data return; } ControlPointVector allControlPoints; for (const auto& image : allImagesOfCase) { try { allControlPoints.push_back(GetControlPointOfData(image)); } catch (const SemanticRelationException&) { // error retrieving control point of data continue; } } std::sort(allControlPointsOfCase.begin(), allControlPointsOfCase.end()); std::sort(allControlPoints.begin(), allControlPoints.end()); ControlPointVector allControlPointsDifference; std::set_difference(allControlPointsOfCase.begin(), allControlPointsOfCase.end(), allControlPoints.begin(), allControlPoints.end(), std::inserter(allControlPointsDifference, allControlPointsDifference.begin())); + auto allExaminationPeriods = GetAllExaminationPeriodsOfCase(caseID); for (const auto& controlPoint : allControlPointsDifference) { + const auto& examinationPeriod = FindExaminationPeriod(controlPoint, allExaminationPeriods); + m_RelationStorage->RemoveControlPointFromExaminationPeriod(caseID, controlPoint, examinationPeriod); m_RelationStorage->RemoveControlPointFromCase(caseID, controlPoint); } }