diff --git a/Modules/SemanticRelations/include/mitkControlPointManager.h b/Modules/SemanticRelations/include/mitkControlPointManager.h index c1343ebd8f..89d3895344 100644 --- a/Modules/SemanticRelations/include/mitkControlPointManager.h +++ b/Modules/SemanticRelations/include/mitkControlPointManager.h @@ -1,93 +1,104 @@ /*=================================================================== 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 #include // semantic relations module #include "mitkSemanticTypes.h" // 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. * * @param 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 Find and return a whole control point including its date given a specific control point UID. * * @param controlPointUID The control point UID as string. * @param allControlPoints All currently known control points of a specific case. * * @return The control point with its UID and the date. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint GetControlPointByUID(const SemanticTypes::ID& controlPointUID, const SemanticTypes::ControlPointVector& allControlPoints); /** * @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. * * @param controlPoint The control point to check for existence. * @param allControlPoints The vector of already existing control points. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint FindExistingControlPoint(const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ControlPointVector& 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. * * @param controlPoint The control point to check for distance. * @param allControlPoints The vector of already existing control points. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint FindClosestControlPoint(const SemanticTypes::ControlPoint& controlPoint, SemanticTypes::ControlPointVector& 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 * * @param controlPoint The control point of which the examination period should be found. * @param allExaminationPeriods All currently known examination periods of a specific case. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ExaminationPeriod FindExaminationPeriod(const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriodVector& allExaminationPeriods); /** + * @brief Return the examination period to which the given data node belongs. + * The DICOM date of the data node is used to find an already existing or the closest control point in the semantic relations storage. + * If such a control point is found, the 'FindExaminationPeriod'-function with this control point as an argument is used + * to actually find the corresponding examination period. + * + * @param datanode A data node pointer, whose date should be included in the newly generated control point. + * + * @return The examination period that contains the given data node. + */ + MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ExaminationPeriod FindExaminationPeriod(const DataNode* dataNode); + /** * @brief Sort the given vector of examination periods. * Each examination period has a vector of control point UIDs (stored in chronological order). * The examination periods can be sorted by comparing the first control points of the examination periods. * * @param allExaminationPeriods All currently known examination periods of a specific case. * @param allControlPoints All currently known control points of a specific case. */ MITKSEMANTICRELATIONS_EXPORT void SortExaminationPeriods(SemanticTypes::ExaminationPeriodVector& allExaminationPeriods, const SemanticTypes::ControlPointVector& allControlPoints); } // namespace mitk #endif // MITKCONTROLPOINTMANAGER_H diff --git a/Modules/SemanticRelations/include/mitkSemanticRelationsDataStorageAccess.h b/Modules/SemanticRelations/include/mitkSemanticRelationsDataStorageAccess.h index 4aaec86e9c..65f8f321e7 100644 --- a/Modules/SemanticRelations/include/mitkSemanticRelationsDataStorageAccess.h +++ b/Modules/SemanticRelations/include/mitkSemanticRelationsDataStorageAccess.h @@ -1,158 +1,178 @@ /*=================================================================== 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 MITKSEMANTICRELATIONSDATASTORAGEACCESS_H #define MITKSEMANTICRELATIONSDATASTORAGEACCESS_H #include // semantic relations module #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 order for most functions to work the case ID has to be used as a parameter. * If not, these functions do nothing. */ class MITKSEMANTICRELATIONS_EXPORT SemanticRelationsDataStorageAccess { public: using DataNodeVector = std::vector; SemanticRelationsDataStorageAccess(DataStorage* dataStorage); /************************************************************************/ /* functions to get instances / attributes */ /************************************************************************/ /** * @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. */ 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 specified by the given vector of image IDs. + * + * @pre The data storage member has to be valid (!nullptr). + * @throw SemanticRelationException, if the data storage member is invalid (==nullptr). + * + * @param imageIDs A vector of image IDs that represent the images in the data storage. + * @return A vector of data nodes representing images. + */ + DataNodeVector GetAllImagesByID(const SemanticTypes::IDVector& imageIDs) 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 Return a vector of all image nodes that are defined with the given information type and with the given control point. + * @brief Return a vector of all image nodes that are defined with the given control point and the given information type. * * @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. + * @return A vector of image nodes that are defined with the given control point and the given information type. */ 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. + * @brief Return a vector of all image nodes that are defined with the given information type and the given examination period. + * The function uses the 'SemanticRelationsInference::GetAllImageIDsOfExaminationPeriod'-function to retrieve the imageIDs of the examination period and + * then compares the information type of all these images against the given information type. + * + * @param informationType An information type that identifies the corresponding information type instance. + * @param examinationPeriod An examination period that identifies the corresponding examination period 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::InformationType& informationType, const SemanticTypes::ExaminationPeriod& examinationPeriod) const; + /** + * @brief Return a vector of all segmentation nodes that are defined with the given control point and the given information type. * 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. + * @return A vector of segmentation nodes that are defined with the given control point and the given information type. */ DataNodeVector GetAllSpecificSegmentations(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const; /** * @brief Return the single segmentation node that is defined with the given information type, the given control point and is representing the given lesion. * The function uses the 'GetAllSpecificSegmentations'-function to retrieve the specific segmentations and then checks for the represented lesion. * * @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). * The lesion has to exist for the given case. * @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') or * if the lesion does not exist for the given case (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. * @param lesion A lesion with a UID that identifies the corresponding lesion instance. * @return A single segmentation node that is defined with the given information type, the given control point and is representing the given lesion. */ DataNode::Pointer GetSpecificSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType, const SemanticTypes::Lesion& lesion) const; private: WeakPointer m_DataStorage; }; } // namespace mitk #endif // MITKSEMANTICRELATIONSDATASTORAGEACCESS_H diff --git a/Modules/SemanticRelations/include/mitkSemanticRelationsInference.h b/Modules/SemanticRelations/include/mitkSemanticRelationsInference.h index a323f62748..d4e06f310d 100644 --- a/Modules/SemanticRelations/include/mitkSemanticRelationsInference.h +++ b/Modules/SemanticRelations/include/mitkSemanticRelationsInference.h @@ -1,315 +1,327 @@ /*=================================================================== 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 MITKSEMANTICRELATIONSINFERENCE_H #define MITKSEMANTICRELATIONSINFERENCE_H #include // semantic relations module #include "mitkSemanticTypes.h" // mitk core #include namespace mitk { /** * @brief The API provides functions to query 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 order for most functions to work the case ID has to be used as a parameter. * If not, these functions do nothing. */ namespace SemanticRelationsInference { /************************************************************************/ /* functions to get instances / attributes */ /************************************************************************/ /** * @brief Return a vector of lesion classes that are currently available for the given case. * * @param caseID The current case identifier is defined by the given string. * @return A vector of lesion classes. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionClassVector GetAllLesionClassesOfCase(const SemanticTypes::CaseID& caseID); /** * @brief Return the lesion that is defined by the given segmentation. * * @pre The given segmentation data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given segmentation 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. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::Lesion GetLesionOfSegmentation(const DataNode* segmentationNode); /** * @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 segmentations 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). * * @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. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionVector GetAllLesionsOfImage(const DataNode* imageNode); /** * @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 lesions. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionVector GetAllLesionsOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint); /** * @brief Returns a vector of all lesions 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) lesion: * Only those lesions are returned for which the image of the associated segmentation is of the given information type. * If the information type instance does not exist, an empty vector is returned. * @return A vector of lesions. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionVector GetAllLesionsOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType); /** * @brief Returns a vector of all lesions that are valid for the given case, given a specific control point and a specific information type. * * @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. * @param informationType A specific information type which has to be available at a returned (found) lesion: * Only those lesions are returned for which the image of the associated segmentation is of the given information type. * If the information type instance does not exist, an empty vector is returned. * @return A vector of lesions. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionVector GetAllSpecificLesions(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType); /** * @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. */ MITKSEMANTICRELATIONS_EXPORT bool IsRepresentingALesion(const DataNode* segmentationNode); /** * @brief Check if the segmentation identified by the given segmentation ID refers to an existing lesion instance. * This function can be used before calling 'GetRepresentedLesion' in order to avoid a possible exception. * * @param caseID The current case identifier is defined by the given string. * @param segmentationID The segmentation node identifier is defined by the given string. * @return True, if the segmentation refers to an existing lesion; false otherwise. */ MITKSEMANTICRELATIONS_EXPORT bool IsRepresentingALesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID); /** * @brief Check if the given lesion is present on the given data node. * The function receives the case- and the node-ID from the DICOM tags of the node itself. * It uses node predicates to decide if the node is an image or a segmentation node. * * @param lesion A lesion with a UID that identifies the corresponding lesion instance. * @param dataNode A data node to check. * @return True, if the lesion is present on the data node; false otherwise. */ MITKSEMANTICRELATIONS_EXPORT bool IsLesionPresent(const SemanticTypes::Lesion& lesion, const DataNode* dataNode); /** * @brief Check if the given lesion is related to the image identified by the given image ID. * Each lesion is represented by a segmentation which is connected to its parent image. * * @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 imageID The image node identifier is defined by the given string. * @return True, if the lesion is related to image identified by the given image ID; false otherwise. */ MITKSEMANTICRELATIONS_EXPORT bool IsLesionPresentOnImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ID& imageID); /** * @brief Check if the given lesion is present on the segmentation identified by the given segmentation ID. * * @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 segmentationID The segmentation node identifier is defined by the given string. * @return True, if the lesion is present on the segmentation identified by the given segmentation ID; false otherwise. */ MITKSEMANTICRELATIONS_EXPORT bool IsLesionPresentOnSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ID& segmentationID); /** * @brief Check if the given lesion is present at the given control point. * * @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 lesion is present at the given control point; false otherwise. */ MITKSEMANTICRELATIONS_EXPORT bool IsLesionPresentAtControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint); /** * @brief Check if the given data node exists in the relation storage. * The function receives the case- and the node-ID from the DICOM tags of the node itself. * It uses node predicates to decide if the node is an image or a segmentation node and searches * through the corresponding relations. * * @param dataNode A data node to check. * @return True, if the data node exists; false otherwise. */ MITKSEMANTICRELATIONS_EXPORT bool InstanceExists(const DataNode* dataNode); /** * @brief Check if the given lesion instance exists. * 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. */ MITKSEMANTICRELATIONS_EXPORT bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion); /** * @brief Return a vector of all image IDs that identify images that are related to the given lesion. * Each lesion is represented by a segmentation which is connected to its parent image. * If the lesion is not represented 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 IDs identifying images that identify images that are related to the given lesion. + * @return A vector of IDs identifying images that are related to the given lesion. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::IDVector GetAllImageIDsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion); /** + * @brief Return a vector of all image IDs that identify images that are related to the given examination period. + * If the examination period is not used by and image, an empty vector is returned. + * + * @pre The UID of the examination period has to exist for an examination period instance. + * @throw SemanticRelationException, if UID of the examination period does not exist for an examination period instance (this can be checked via 'InstanceExists'). + * + * @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 A vector of IDs identifying images that are related to the given examination period. + */ + MITKSEMANTICRELATIONS_EXPORT SemanticTypes::IDVector GetAllImageIDsOfExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod); + /** * @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 image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image 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. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint GetControlPointOfImage(const DataNode* dataNode); /** * @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. + * @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. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPointVector GetAllControlPointsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion); /** * @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. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPointVector GetAllControlPointsOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType); /** * @brief Check if the given control point instance exists. * 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. */ MITKSEMANTICRELATIONS_EXPORT bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint); /** * @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. */ MITKSEMANTICRELATIONS_EXPORT bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod); /** * @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. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::InformationType GetInformationTypeOfImage(const DataNode* imageNode); /** * @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. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::InformationTypeVector GetAllInformationTypesOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint); /** * @brief Check if the given information type exists. * * @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. */ MITKSEMANTICRELATIONS_EXPORT bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType); /** * @brief Determine if the given information type contains images, which are connected to segmentations that represent the given lesion. * If the lesion or the information type 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 informationType An information type that identifies the corresponding information type instance. * * @return True, if the given information type contains data that is related to the given lesion; false otherwise. */ MITKSEMANTICRELATIONS_EXPORT bool SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::InformationType& informationType); /** * @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. */ MITKSEMANTICRELATIONS_EXPORT bool SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint); /** * @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. */ MITKSEMANTICRELATIONS_EXPORT bool SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType, const SemanticTypes::ControlPoint& controlPoint); } // namespace SemanticRelationsInference } // namespace mitk #endif // MITKSEMANTICRELATIONSINFERENCE_H diff --git a/Modules/SemanticRelations/src/mitkControlPointManager.cpp b/Modules/SemanticRelations/src/mitkControlPointManager.cpp index 98f1486379..5f56a67eef 100644 --- a/Modules/SemanticRelations/src/mitkControlPointManager.cpp +++ b/Modules/SemanticRelations/src/mitkControlPointManager.cpp @@ -1,179 +1,219 @@ /*=================================================================== 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 "mitkRelationStorage.h" #include "mitkSemanticRelationException.h" #include "mitkUIDGeneratorBoost.h" // mitk core #include mitk::SemanticTypes::ControlPoint mitk::GenerateControlPoint(const DataNode* datanode) { SemanticTypes::ControlPoint controlPoint; try { controlPoint = GetDICOMDateFromDataNode(datanode); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot generate a control point from the DICOM tag of the given data node"; } controlPoint.UID = UIDGeneratorBoost::GenerateUID(); return controlPoint; } mitk::SemanticTypes::ControlPoint mitk::GetControlPointByUID(const SemanticTypes::ID& controlPointUID, const std::vector& allControlPoints) { auto lambda = [&controlPointUID](const SemanticTypes::ControlPoint& currentControlPoint) { return currentControlPoint.UID == controlPointUID; }; const auto existingControlPoint = std::find_if(allControlPoints.begin(), allControlPoints.end(), lambda); mitk::SemanticTypes::ControlPoint controlPoint; if (existingControlPoint != allControlPoints.end()) { controlPoint = *existingControlPoint; } return controlPoint; } mitk::SemanticTypes::ControlPoint mitk::FindExistingControlPoint(const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ControlPointVector& allControlPoints) { for (const auto& currentControlPoint : allControlPoints) { if (controlPoint.date == currentControlPoint.date) { return currentControlPoint; } } return SemanticTypes::ControlPoint(); } mitk::SemanticTypes::ControlPoint mitk::FindClosestControlPoint(const SemanticTypes::ControlPoint& controlPoint, SemanticTypes::ControlPointVector& 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.date < it->date) { 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 = nextControlPoint.DistanceInDays(controlPoint); double distanceToPreviousExaminationPeriod = previousControlPoint.DistanceInDays(controlPoint); SemanticTypes::ControlPoint closestControlPoint; int closestDistanceInDays = 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; } int THRESHOLD_DISTANCE_IN_DAYS = 30; if (closestDistanceInDays <= THRESHOLD_DISTANCE_IN_DAYS) { return closestControlPoint; } return SemanticTypes::ControlPoint(); } mitk::SemanticTypes::ExaminationPeriod mitk::FindExaminationPeriod(const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriodVector& allExaminationPeriods) { for (const auto& examinationPeriod : allExaminationPeriods) { for (const auto& UID : examinationPeriod.controlPointUIDs) { if (controlPoint.UID == UID) { return examinationPeriod; } } } return SemanticTypes::ExaminationPeriod(); } +mitk::SemanticTypes::ExaminationPeriod mitk::FindExaminationPeriod(const DataNode* dataNode) +{ + SemanticTypes::CaseID caseID = ""; + SemanticTypes::InformationType informationType; + SemanticTypes::ControlPoint controlPoint; + try + { + caseID = GetCaseIDFromDataNode(dataNode); + informationType = GetDICOMModalityFromDataNode(dataNode); + controlPoint = GetDICOMDateFromDataNode(dataNode); + } + catch (SemanticRelationException& e) + { + mitkReThrow(e) << "Cannot find an examination period. "; + } + + SemanticTypes::ExaminationPeriod specificExaminationPeriod; + SemanticTypes::ControlPoint specificControlPoint; + // find the closest control point + auto allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID); + auto existingControlPoint = FindExistingControlPoint(controlPoint, allControlPoints); + if (!existingControlPoint.UID.empty()) + { + specificControlPoint = existingControlPoint; + } + else + { + auto closestControlPoint = FindClosestControlPoint(controlPoint, allControlPoints); + if (!closestControlPoint.UID.empty()) + { + specificControlPoint = closestControlPoint; + } + } + + // find the containing examination period + auto allExaminationPeriods = RelationStorage::GetAllExaminationPeriodsOfCase(caseID); + return FindExaminationPeriod(specificControlPoint, allExaminationPeriods); +} + void mitk::SortExaminationPeriods(SemanticTypes::ExaminationPeriodVector& allExaminationPeriods, const SemanticTypes::ControlPointVector& allControlPoints) { auto lambda = [allControlPoints](const SemanticTypes::ExaminationPeriod& leftExaminationPeriod, const SemanticTypes::ExaminationPeriod& rightExaminationPeriod) { if (leftExaminationPeriod.controlPointUIDs.empty()) { return true; } if (rightExaminationPeriod.controlPointUIDs.empty()) { return false; } const auto leftUID = leftExaminationPeriod.controlPointUIDs.front(); const auto rightUID = rightExaminationPeriod.controlPointUIDs.front(); const auto& leftControlPoint = GetControlPointByUID(leftUID, allControlPoints); const auto& rightControlPoint = GetControlPointByUID(rightUID, allControlPoints); return leftControlPoint.date < rightControlPoint.date; }; std::sort(allExaminationPeriods.begin(), allExaminationPeriods.end(), lambda); } diff --git a/Modules/SemanticRelations/src/mitkSemanticRelationsDataStorageAccess.cpp b/Modules/SemanticRelations/src/mitkSemanticRelationsDataStorageAccess.cpp index 25fd91513c..decd9c8593 100644 --- a/Modules/SemanticRelations/src/mitkSemanticRelationsDataStorageAccess.cpp +++ b/Modules/SemanticRelations/src/mitkSemanticRelationsDataStorageAccess.cpp @@ -1,272 +1,342 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkSemanticRelationsDataStorageAccess.h" // semantic relations module #include "mitkControlPointManager.h" #include "mitkDICOMHelper.h" #include "mitkNodePredicates.h" #include "mitkRelationStorage.h" #include "mitkSemanticRelationException.h" #include "mitkSemanticRelationsInference.h" // c++ #include #include mitk::SemanticRelationsDataStorageAccess::SemanticRelationsDataStorageAccess(DataStorage* dataStorage) : m_DataStorage(dataStorage) { // nothing here } /************************************************************************/ /* functions to get instances / attributes */ /************************************************************************/ mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSegmentationsOfCase(const SemanticTypes::CaseID& caseID) const { if (m_DataStorage.IsExpired()) { mitkThrowException(SemanticRelationException) << "Not a valid data storage."; } std::vector allSegmentationIDsOfCase = RelationStorage::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.Lock()->GetSubset(NodePredicates::GetSegmentationPredicate()); for (auto it = segmentationNodes->Begin(); it != segmentationNodes->End(); ++it) { DataNode* segmentationNode = it->Value(); std::string caseID; std::string segmentationID; try { // find the corresponding segmentation node for the given segmentation ID caseID = GetCaseIDFromDataNode(segmentationNode); segmentationID = GetIDFromDataNode(segmentationNode); } catch (SemanticRelationException&) { // 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; } if (caseID == caseID && (std::find(allSegmentationIDsOfCase.begin(), allSegmentationIDsOfCase.end(), segmentationID) != allSegmentationIDsOfCase.end())) { // found current image node in the storage, add it to the return vector allSegmentationsOfCase.push_back(segmentationNode); } } return allSegmentationsOfCase; } mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSegmentationsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const { if (SemanticRelationsInference::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 = SemanticRelationsInference::GetLesionOfSegmentation(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::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllImagesOfCase(const SemanticTypes::CaseID& caseID) const { if (m_DataStorage.IsExpired()) { mitkThrowException(SemanticRelationException) << "Not a valid data storage."; } std::vector allImageIDsOfCase = RelationStorage::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.Lock()->GetSubset(NodePredicates::GetImagePredicate()); for (auto it = imageNodes->Begin(); it != imageNodes->End(); ++it) { DataNode* imageNode = it->Value(); std::string caseID; std::string imageID; try { // find the corresponding image node for the given segmentation ID caseID = GetCaseIDFromDataNode(imageNode); imageID = GetIDFromDataNode(imageNode); } catch (SemanticRelationException&) { // found an image node that is not stored in the semantic relations // this image node does not have any DICOM information --> exception thrown // continue with the next image to compare IDs continue; } if (caseID == caseID && (std::find(allImageIDsOfCase.begin(), allImageIDsOfCase.end(), imageID) != allImageIDsOfCase.end())) { // found current image node in the storage, add it to the return vector allImagesOfCase.push_back(imageNode); } } return allImagesOfCase; } +mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllImagesByID(const SemanticTypes::IDVector& imageIDs) const +{ + if (m_DataStorage.IsExpired()) + { + mitkThrowException(SemanticRelationException) << "Not a valid data storage."; + } + + DataNodeVector 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.Lock()->GetSubset(NodePredicates::GetImagePredicate()); + for (auto it = imageNodes->Begin(); it != imageNodes->End(); ++it) + { + DataNode* imageNode = it->Value(); + + SemanticTypes::CaseID currentCaseID; + SemanticTypes::ID imageID; + try + { + // find the corresponding image node for the given segmentation ID + imageID = GetIDFromDataNode(imageNode); + } + catch (SemanticRelationException&) + { + // found an image node that is not stored in the semantic relations + // this image node does not have any DICOM information --> exception thrown + // continue with the next image to compare IDs + continue; + } + + if (std::find(imageIDs.begin(), imageIDs.end(), imageID) != imageIDs.end()) + { + // found current image node in the storage, add it to the return vector + allImagesOfCase.push_back(imageNode); + } + } + + return allImagesOfCase; +} + mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllImagesOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const { if (m_DataStorage.IsExpired()) { 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.Lock()->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; } mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSpecificImages(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const { if (SemanticRelationsInference::InstanceExists(caseID, controlPoint)) { if (SemanticRelationsInference::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 != SemanticRelationsInference::GetInformationTypeOfImage(imageNode)) || (controlPoint.date != SemanticRelationsInference::GetControlPointOfImage(imageNode).date); }; 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::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSpecificImages(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType, const SemanticTypes::ExaminationPeriod& examinationPeriod) const +{ + if (SemanticRelationsInference::InstanceExists(caseID, informationType)) + { + if (SemanticRelationsInference::InstanceExists(caseID, examinationPeriod)) + { + // examination period exists, information type exists, retrieve all imageIDs from the storage + auto allImageIDsOfExaminationPeriod = SemanticRelationsInference::GetAllImageIDsOfExaminationPeriod(caseID, examinationPeriod); + // filter all images to remove the ones with a different information type using a lambda function + auto lambda = [&caseID, &informationType, this](SemanticTypes::ID imageID) + { + return (informationType != RelationStorage::GetInformationTypeOfImage(caseID, imageID)); + }; + + allImageIDsOfExaminationPeriod.erase(std::remove_if(allImageIDsOfExaminationPeriod.begin(), allImageIDsOfExaminationPeriod.end(), lambda), allImageIDsOfExaminationPeriod.end()); + + auto allImagesOfExaminationPeriod = GetAllImagesByID(allImageIDsOfExaminationPeriod); + return allImagesOfExaminationPeriod; + } + else + { + mitkThrowException(SemanticRelationException) << "Could not find an existing examination period for the given caseID " << caseID << " and examination period " << examinationPeriod.name; + } + } + else + { + mitkThrowException(SemanticRelationException) << "Could not find an existing information type for the given caseID " << caseID << " and information type " << informationType; + } +} + mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSpecificSegmentations(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const { if (m_DataStorage.IsExpired()) { mitkThrow() << "Not a valid data storage."; } DataNodeVector allSpecificImages; try { allSpecificImages = GetAllSpecificImages(caseID, controlPoint, informationType); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get the specific segmentation"; } DataNodeVector allSpecificSegmentations; for (const auto& imageNode : allSpecificImages) { DataStorage::SetOfObjects::ConstPointer segmentationNodes = m_DataStorage.Lock()->GetDerivations(imageNode, NodePredicates::GetSegmentationPredicate(), false); for (auto it = segmentationNodes->Begin(); it != segmentationNodes->End(); ++it) { allSpecificSegmentations.push_back(it->Value()); } } return allSpecificSegmentations; } mitk::DataNode::Pointer mitk::SemanticRelationsDataStorageAccess::GetSpecificSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType, const SemanticTypes::Lesion& lesion) const { if (m_DataStorage.IsExpired()) { mitkThrow() << "Not a valid data storage."; } DataNodeVector allSpecificSegmentations; try { allSpecificSegmentations = GetAllSpecificSegmentations(caseID, controlPoint, informationType); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get the specific segmentation"; } for (const auto& segmentationNode : allSpecificSegmentations) { SemanticTypes::Lesion representedLesion = SemanticRelationsInference::GetLesionOfSegmentation(segmentationNode); if (representedLesion.UID == lesion.UID) { return segmentationNode; } } return mitk::DataNode::Pointer(); } diff --git a/Modules/SemanticRelations/src/mitkSemanticRelationsInference.cpp b/Modules/SemanticRelations/src/mitkSemanticRelationsInference.cpp index ad1ca571a5..3cd01a1b11 100644 --- a/Modules/SemanticRelations/src/mitkSemanticRelationsInference.cpp +++ b/Modules/SemanticRelations/src/mitkSemanticRelationsInference.cpp @@ -1,570 +1,592 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkSemanticRelationsInference.h" // semantic relations module #include "mitkControlPointManager.h" #include "mitkDICOMHelper.h" #include "mitkNodePredicates.h" #include "mitkRelationStorage.h" #include "mitkSemanticRelationException.h" /************************************************************************/ /* functions to get instances / attributes */ /************************************************************************/ mitk::SemanticTypes::LesionClassVector mitk::SemanticRelationsInference::GetAllLesionClassesOfCase(const SemanticTypes::CaseID& caseID) { SemanticTypes::LesionVector allLesionsOfCase = RelationStorage::GetAllLesionsOfCase(caseID); SemanticTypes::LesionClassVector allLesionClassesOfCase; for (const auto& lesion : allLesionsOfCase) { allLesionClassesOfCase.push_back(lesion.lesionClass); } // remove duplicate entries auto lessThan = [](const SemanticTypes::LesionClass& lesionClassLeft, const SemanticTypes::LesionClass& lesionClassRight) { return lesionClassLeft.UID < lesionClassRight.UID; }; auto equal = [](const SemanticTypes::LesionClass& lesionClassLeft, const SemanticTypes::LesionClass& lesionClassRight) { return lesionClassLeft.UID == lesionClassRight.UID; }; std::sort(allLesionClassesOfCase.begin(), allLesionClassesOfCase.end(), lessThan); allLesionClassesOfCase.erase(std::unique(allLesionClassesOfCase.begin(), allLesionClassesOfCase.end(), equal), allLesionClassesOfCase.end()); return allLesionClassesOfCase; } mitk::SemanticTypes::Lesion mitk::SemanticRelationsInference::GetLesionOfSegmentation(const DataNode* segmentationNode) { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } SemanticTypes::CaseID caseID = ""; SemanticTypes::ID segmentationID = ""; try { caseID = GetCaseIDFromDataNode(segmentationNode); segmentationID = GetIDFromDataNode(segmentationNode); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get the lesion of the given segmentation data node."; } return RelationStorage::GetLesionOfSegmentation(caseID, segmentationID); } mitk::SemanticTypes::LesionVector mitk::SemanticRelationsInference::GetAllLesionsOfImage(const DataNode* imageNode) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid image data node."; } SemanticTypes::CaseID caseID = ""; SemanticTypes::ID imageID = ""; try { caseID = GetCaseIDFromDataNode(imageNode); imageID = GetIDFromDataNode(imageNode); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get all lesions of the given image data node."; } SemanticTypes::LesionVector allLesionsOfImage; // 1. get all segmentations that are connected to the given image // 2. get the lesion of each segmentation // 3. guarantee uniqueness of lesions SemanticTypes::IDVector allSegmentationIDsOfImage = RelationStorage::GetAllSegmentationIDsOfImage(caseID, imageID); for (const auto& segmentationID : allSegmentationIDsOfImage) { // get represented lesion of the current segmentation SemanticTypes::Lesion representedLesion = RelationStorage::GetLesionOfSegmentation(caseID, segmentationID); if (!representedLesion.UID.empty()) { allLesionsOfImage.push_back(representedLesion); } } // remove duplicate entries auto lessThan = [](const SemanticTypes::Lesion& lesionLeft, const SemanticTypes::Lesion& lesionRight) { return lesionLeft.UID < lesionRight.UID; }; auto equal = [](const SemanticTypes::Lesion& lesionLeft, const SemanticTypes::Lesion& lesionRight) { return lesionLeft.UID == lesionRight.UID; }; std::sort(allLesionsOfImage.begin(), allLesionsOfImage.end(), lessThan); allLesionsOfImage.erase(std::unique(allLesionsOfImage.begin(), allLesionsOfImage.end(), equal), allLesionsOfImage.end()); return allLesionsOfImage; } mitk::SemanticTypes::LesionVector mitk::SemanticRelationsInference::GetAllLesionsOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::LesionVector allLesions = RelationStorage::GetAllLesionsOfCase(caseID); // filter the lesions: use only those, where the associated data is connected to image data that refers to the given control point using a lambda function auto lambda = [&caseID, &controlPoint](const SemanticTypes::Lesion& lesion) { return !SpecificImageExists(caseID, lesion, controlPoint); }; allLesions.erase(std::remove_if(allLesions.begin(), allLesions.end(), lambda), allLesions.end()); return allLesions; } mitk::SemanticTypes::LesionVector mitk::SemanticRelationsInference::GetAllLesionsOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) { SemanticTypes::LesionVector allLesions = RelationStorage::GetAllLesionsOfCase(caseID); // filter the lesions: use only those, where the associated data is connected to image data that refers to the given information type using a lambda function auto lambda = [&caseID, &informationType](const SemanticTypes::Lesion& lesion) { return !SpecificImageExists(caseID, lesion, informationType); }; allLesions.erase(std::remove_if(allLesions.begin(), allLesions.end(), lambda), allLesions.end()); return allLesions; } mitk::SemanticTypes::LesionVector mitk::SemanticRelationsInference::GetAllSpecificLesions(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) { auto allLesionsOfControlPoint = GetAllLesionsOfControlPoint(caseID, controlPoint); auto allLesionsOfInformationType = GetAllLesionsOfInformationType(caseID, informationType); SemanticTypes::LesionVector allLesionsIntersection; auto lessThan = [](const SemanticTypes::Lesion& lesionLeft, const SemanticTypes::Lesion& lesionRight) { return lesionLeft.UID < lesionRight.UID; }; auto equal = [](const SemanticTypes::Lesion& lesionLeft, const SemanticTypes::Lesion& lesionRight) { return lesionLeft.UID == lesionRight.UID; }; std::sort(allLesionsOfControlPoint.begin(), allLesionsOfControlPoint.end(), lessThan); std::sort(allLesionsOfInformationType.begin(), allLesionsOfInformationType.end(), lessThan); SemanticTypes::IDVector allImageIDsIntersection; // set_intersection removes duplicated nodes std::set_intersection(allLesionsOfControlPoint.begin(), allLesionsOfControlPoint.end(), allLesionsOfInformationType.begin(), allLesionsOfInformationType.end(), std::back_inserter(allLesionsIntersection), equal); return allLesionsIntersection; } bool mitk::SemanticRelationsInference::IsRepresentingALesion(const DataNode* segmentationNode) { SemanticTypes::Lesion representedLesion; try { representedLesion = GetLesionOfSegmentation(segmentationNode); } catch (const SemanticRelationException&) { return false; } return !representedLesion.UID.empty(); } bool mitk::SemanticRelationsInference::IsRepresentingALesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID) { SemanticTypes::Lesion representedLesion = RelationStorage::GetLesionOfSegmentation(caseID, segmentationID); return !representedLesion.UID.empty(); } bool mitk::SemanticRelationsInference::IsLesionPresent(const SemanticTypes::Lesion& lesion, const DataNode* dataNode) { SemanticTypes::CaseID caseID = ""; SemanticTypes::ID dataNodeID = ""; try { caseID = GetCaseIDFromDataNode(dataNode); dataNodeID = GetIDFromDataNode(dataNode); } catch (const SemanticRelationException&) { return false; } if (NodePredicates::GetImagePredicate()->CheckNode(dataNode)) { return IsLesionPresentOnImage(caseID, lesion, dataNodeID); } if (NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode)) { return IsLesionPresentOnSegmentation(caseID, lesion, dataNodeID); } return false; } bool mitk::SemanticRelationsInference::IsLesionPresentOnImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ID& imageID) { SemanticTypes::IDVector allImageIDsOfLesion; try { allImageIDsOfLesion = GetAllImageIDsOfLesion(caseID, lesion); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get all image IDs of the given lesion to determine the lesion presence."; } for (const auto& imageIDOfLesion : allImageIDsOfLesion) { if (imageIDOfLesion == imageID) { return true; } } return false; } bool mitk::SemanticRelationsInference::IsLesionPresentOnSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ID& segmentationID) { const auto representedLesion = RelationStorage::GetLesionOfSegmentation(caseID, segmentationID); return lesion.UID == representedLesion.UID; } bool mitk::SemanticRelationsInference::IsLesionPresentAtControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::IDVector allImageIDsOfLesion; try { allImageIDsOfLesion = GetAllImageIDsOfLesion(caseID, lesion); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get all image IDs of the given lesion to determine the lesion presence."; } for (const auto& imageIDOfLesion : allImageIDsOfLesion) { auto imageControlPoint = mitk::RelationStorage::GetControlPointOfImage(caseID, imageIDOfLesion); if (imageControlPoint.date == controlPoint.date) { return true; } } return false; } bool mitk::SemanticRelationsInference::InstanceExists(const DataNode* dataNode) { SemanticTypes::CaseID caseID = ""; SemanticTypes::ID dataNodeID = ""; try { caseID = GetCaseIDFromDataNode(dataNode); dataNodeID = GetIDFromDataNode(dataNode); } catch (const SemanticRelationException&) { return false; } if (NodePredicates::GetImagePredicate()->CheckNode(dataNode)) { std::vector allImageIDsOfCase = RelationStorage::GetAllImageIDsOfCase(caseID); return std::find(allImageIDsOfCase.begin(), allImageIDsOfCase.end(), dataNodeID) != allImageIDsOfCase.end(); } if (NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode)) { std::vector allSegmentationIDsOfCase = RelationStorage::GetAllSegmentationIDsOfCase(caseID); return std::find(allSegmentationIDsOfCase.begin(), allSegmentationIDsOfCase.end(), dataNodeID) != allSegmentationIDsOfCase.end(); } return false; } bool mitk::SemanticRelationsInference::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { SemanticTypes::LesionVector allLesions = RelationStorage::GetAllLesionsOfCase(caseID); // filter all lesions: check for equality with the given lesion using a lambda function auto lambda = [&lesion](const SemanticTypes::Lesion& currentLesion) { return currentLesion.UID == lesion.UID; }; const auto existingLesion = std::find_if(allLesions.begin(), allLesions.end(), lambda); return existingLesion != allLesions.end(); } mitk::SemanticTypes::IDVector mitk::SemanticRelationsInference::GetAllImageIDsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { if (!InstanceExists(caseID, lesion)) { mitkThrowException(SemanticRelationException) << "Could not find an existing lesion instance for the given caseID " << caseID << " and lesion " << lesion.UID << "."; } SemanticTypes::IDVector allImageIDsOfLesion; // 1. get all segmentations that define the lesion // 2. get the parentID (imageID) of each segmentation // 3. guarantee uniqueness of image IDs SemanticTypes::IDVector allSegmentationIDsOfLesion = RelationStorage::GetAllSegmentationIDsOfLesion(caseID, lesion); for (const auto& segmentationID : allSegmentationIDsOfLesion) { // get parent ID of the current segmentation ID SemanticTypes::ID imageID = RelationStorage::GetImageIDOfSegmentation(caseID, segmentationID); if(!imageID.empty()) { allImageIDsOfLesion.push_back(imageID); } } std::sort(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end()); allImageIDsOfLesion.erase(std::unique(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end()), allImageIDsOfLesion.end()); return allImageIDsOfLesion; } +mitk::SemanticTypes::IDVector mitk::SemanticRelationsInference::GetAllImageIDsOfExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod) +{ + if (!InstanceExists(caseID, examinationPeriod)) + { + mitkThrowException(SemanticRelationException) << "Could not find an existing examination period for the given caseID " << caseID << " and examination period " << examinationPeriod.name << "."; + } + + SemanticTypes::IDVector allImageIDsOfExaminationPeriod; + // 1. get all control point UIDs of the examination period + // 2. get all images of each control points to find all images of the examination period + auto allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID); + SemanticTypes::ControlPoint controlPoint; + for (const auto& controlPointUID : examinationPeriod.controlPointUIDs) + { + controlPoint = GetControlPointByUID(controlPointUID, allControlPoints); + auto allImageIDsOfControlPoint = RelationStorage::GetAllImageIDsOfControlPoint(caseID, controlPoint); + allImageIDsOfExaminationPeriod.insert(allImageIDsOfExaminationPeriod.end(), allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end()); + } + + return allImageIDsOfExaminationPeriod; +} + mitk::SemanticTypes::ControlPoint mitk::SemanticRelationsInference::GetControlPointOfImage(const DataNode* imageNode) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = ""; SemanticTypes::ID imageID = ""; try { caseID = GetCaseIDFromDataNode(imageNode); imageID = GetIDFromDataNode(imageNode); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get the control point of the given image data node."; } return RelationStorage::GetControlPointOfImage(caseID, imageID); } mitk::SemanticTypes::ControlPointVector mitk::SemanticRelationsInference::GetAllControlPointsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID); // filter the control points: use only those, where the associated image data has a segmentation that refers to the given lesion using a lambda function auto lambda = [&caseID, &lesion](const SemanticTypes::ControlPoint& controlPoint) { return !SpecificImageExists(caseID, lesion, controlPoint); }; allControlPoints.erase(std::remove_if(allControlPoints.begin(), allControlPoints.end(), lambda), allControlPoints.end()); return allControlPoints; } mitk::SemanticTypes::ControlPointVector mitk::SemanticRelationsInference::GetAllControlPointsOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) { SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID); // filter the control points: use only those, where the associated image data refers to the given information type using a lambda function auto lambda = [&caseID, &informationType](const SemanticTypes::ControlPoint& controlPoint) { return !SpecificImageExists(caseID, informationType, controlPoint); }; allControlPoints.erase(std::remove_if(allControlPoints.begin(), allControlPoints.end(), lambda), allControlPoints.end()); return allControlPoints; } bool mitk::SemanticRelationsInference::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID); // filter all control points: check for equality with the given control point using a lambda function auto lambda = [&controlPoint](const SemanticTypes::ControlPoint& currentControlPoint) { return currentControlPoint.UID == controlPoint.UID; }; const auto existingControlPoint = std::find_if(allControlPoints.begin(), allControlPoints.end(), lambda); if (existingControlPoint != allControlPoints.end()) { return true; } else { return false; } } bool mitk::SemanticRelationsInference::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod) { SemanticTypes::ExaminationPeriodVector allExaminationPeriods = RelationStorage::GetAllExaminationPeriodsOfCase(caseID); // filter all examination periods: check for equality with the given examination period using a lambda function auto lambda = [&examinationPeriod](const SemanticTypes::ExaminationPeriod& currentExaminationPeriod) { return currentExaminationPeriod.UID == examinationPeriod.UID; }; const auto existingExaminationPeriod = std::find_if(allExaminationPeriods.begin(), allExaminationPeriods.end(), lambda); if (existingExaminationPeriod != allExaminationPeriods.end()) { return true; } else { return false; } } mitk::SemanticTypes::InformationType mitk::SemanticRelationsInference::GetInformationTypeOfImage(const DataNode* imageNode) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid image data node."; } SemanticTypes::CaseID caseID = ""; SemanticTypes::ID imageID = ""; try { caseID = GetCaseIDFromDataNode(imageNode); imageID = GetIDFromDataNode(imageNode); } catch (SemanticRelationException& e) { mitkReThrow(e) << "Cannot get the information type of the given image data node."; } return RelationStorage::GetInformationTypeOfImage(caseID, imageID); } mitk::SemanticTypes::InformationTypeVector mitk::SemanticRelationsInference::GetAllInformationTypesOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::InformationTypeVector allInformationTypes = RelationStorage::GetAllInformationTypesOfCase(caseID); // filter the information types: use only those, where the associated data refers to the given control point using a lambda function auto lambda = [&caseID, &controlPoint](const SemanticTypes::InformationType& informationType) { return !SpecificImageExists(caseID, informationType, controlPoint); }; allInformationTypes.erase(std::remove_if(allInformationTypes.begin(), allInformationTypes.end(), lambda), allInformationTypes.end()); return allInformationTypes; } bool mitk::SemanticRelationsInference::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) { SemanticTypes::InformationTypeVector allInformationTypes = RelationStorage::GetAllInformationTypesOfCase(caseID); // filter all information types: check for equality with the given information type using a lambda function auto lambda = [&informationType](const SemanticTypes::InformationType& currentInformationType) { return currentInformationType == informationType; }; const auto existingInformationType = std::find_if(allInformationTypes.begin(), allInformationTypes.end(), lambda); if (existingInformationType != allInformationTypes.end()) { return true; } else { return false; } } bool mitk::SemanticRelationsInference::SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::InformationType& informationType) { SemanticTypes::IDVector allImageIDsOfLesion; try { allImageIDsOfLesion = GetAllImageIDsOfLesion(caseID, lesion); } catch (const SemanticRelationException&) { return false; } SemanticTypes::IDVector allImageIDsOfInformationType = RelationStorage::GetAllImageIDsOfInformationType(caseID, informationType); std::sort(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end()); std::sort(allImageIDsOfInformationType.begin(), allImageIDsOfInformationType.end()); SemanticTypes::IDVector allImageIDsIntersection; // set_intersection removes duplicated nodes, since 'GetAllImageIDsOfInformationType' only contains at most one of each node std::set_intersection(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end(), allImageIDsOfInformationType.begin(), allImageIDsOfInformationType.end(), std::back_inserter(allImageIDsIntersection)); // if the vector of intersecting image IDs is empty, the information type does not contain the lesion return !allImageIDsIntersection.empty(); } bool mitk::SemanticRelationsInference::SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::IDVector allImageIDsOfLesion; try { allImageIDsOfLesion = GetAllImageIDsOfLesion(caseID, lesion); } catch (const SemanticRelationException&) { return false; } SemanticTypes::IDVector allImageIDsOfControlPoint = RelationStorage::GetAllImageIDsOfControlPoint(caseID, controlPoint); std::sort(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end()); std::sort(allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end()); SemanticTypes::IDVector allImageIDsIntersection; // set_intersection removes duplicated nodes, since 'GetAllImageIDsOfControlPoint' only contains at most one of each node std::set_intersection(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end(), allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end(), std::back_inserter(allImageIDsIntersection)); // if the vector of intersecting image IDs is empty, the control point does not contain the lesion return !allImageIDsIntersection.empty(); } bool mitk::SemanticRelationsInference::SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::IDVector allImageIDsOfInformationType = RelationStorage::GetAllImageIDsOfInformationType(caseID, informationType); SemanticTypes::IDVector allImageIDsOfControlPoint = RelationStorage::GetAllImageIDsOfControlPoint(caseID, controlPoint); std::sort(allImageIDsOfInformationType.begin(), allImageIDsOfInformationType.end()); std::sort(allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end()); SemanticTypes::IDVector allImageIDsIntersection; // set_intersection removes duplicated nodes std::set_intersection(allImageIDsOfInformationType.begin(), allImageIDsOfInformationType.end(), allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end(), std::back_inserter(allImageIDsIntersection)); // if the vector of intersecting image IDs is empty no image exists for the given information type and control point return !allImageIDsIntersection.empty(); } diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.cpp index 31c17047e8..163299ed1b 100644 --- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.cpp +++ b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.cpp @@ -1,207 +1,275 @@ /*=================================================================== 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 plugin #include "QmitkDataNodeAddToSemanticRelationsAction.h" +#include "QmitkDataNodeRemoveFromSemanticRelationsAction.h" // semantic relations module +#include #include #include +#include #include #include +#include #include // mitk gui common plugin #include // mitk core #include // qt #include // namespace that contains the concrete action namespace AddToSemanticRelationsAction { - void Run(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, const mitk::DataStorage* dataStorage, const mitk::DataNode* dataNode) + void Run(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, mitk::DataStorage* dataStorage, const mitk::DataNode* dataNode) { if (nullptr == dataNode) { return; } if (mitk::NodePredicates::GetImagePredicate()->CheckNode(dataNode)) { - AddImage(semanticRelationsIntegration, dataNode); + AddImage(semanticRelationsIntegration, dataStorage, dataNode); } else if (mitk::NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode)) { AddSegmentation(semanticRelationsIntegration, dataStorage, dataNode); } } - void AddImage(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, const mitk::DataNode* image) + void AddImage(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, mitk::DataStorage* dataStorage, const mitk::DataNode* image) { if (nullptr == image) { return; } + mitk::SemanticTypes::InformationType informationType; + mitk::SemanticTypes::ExaminationPeriod examinationPeriod; + mitk::SemanticRelationsDataStorageAccess::DataNodeVector allSpecificImages; + try + { + mitk::SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(image); + informationType = GetDICOMModalityFromDataNode(image); + // see if the examination period - information type cell is already taken + examinationPeriod = FindExaminationPeriod(image); + auto semanticRelationsDataStorageAccess = mitk::SemanticRelationsDataStorageAccess(dataStorage); + try + { + allSpecificImages = semanticRelationsDataStorageAccess.GetAllSpecificImages(caseID, informationType, examinationPeriod); + } + catch (const mitk::SemanticRelationException&) + { + // just continue since an exception means that there is no specific image + } + } + catch (const mitk::SemanticRelationException& e) + { + std::stringstream exceptionMessage; exceptionMessage << e; + QMessageBox msgBox(QMessageBox::Warning, + "Could not add the selected image.", + "The program wasn't able to correctly add the selected images.\n" + "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n")); + msgBox.exec(); + } + + if (!allSpecificImages.empty()) + { + // examination period - information type cell is already taken + // ask if cell should be overwritten + QMessageBox::StandardButton answerButton = + QMessageBox::question(nullptr, + "Specific image already exists.", + QString::fromStdString("Force overwriting existing image " + informationType + " at " + examinationPeriod.name + "?"), + QMessageBox::Yes | QMessageBox::No, QMessageBox::Yes); + + if (answerButton == QMessageBox::Yes) + { + try + { + // remove already existent images at specific cell + for (const auto& specificImage : allSpecificImages) + { + RemoveFromSemanticRelationsAction::Run(semanticRelationsIntegration, dataStorage, specificImage); + } + } + catch (const mitk::SemanticRelationException& e) + { + std::stringstream exceptionMessage; exceptionMessage << e; + QMessageBox msgBox(QMessageBox::Warning, + "Could not add the selected image.", + "The program wasn't able to correctly add the selected images.\n" + "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n")); + msgBox.exec(); + } + } + else + { + // else case is: no overwriting + return; + } + } + + // specific image does not exists or has been removed; adding the image should work try { - // add the image to the semantic relations storage semanticRelationsIntegration->AddImage(image); } catch (const mitk::SemanticRelationException& e) { std::stringstream exceptionMessage; exceptionMessage << e; QMessageBox msgBox(QMessageBox::Warning, "Could not add the selected image.", "The program wasn't able to correctly add the selected images.\n" - "Reason:\n" + QString::fromStdString(exceptionMessage.str())); + "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n")); msgBox.exec(); - return; } } - void AddSegmentation(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, const mitk::DataStorage* dataStorage, const mitk::DataNode* segmentation) + void AddSegmentation(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, mitk::DataStorage* dataStorage, const mitk::DataNode* segmentation) { if (nullptr == segmentation) { return; } mitk::BaseData* baseData = segmentation->GetData(); if (nullptr == baseData) { return; } // continue with valid segmentation data // get parent node of the current segmentation node with the node predicate mitk::DataStorage::SetOfObjects::ConstPointer parentNodes = dataStorage->GetSources(segmentation, mitk::NodePredicates::GetImagePredicate(), false); if (parentNodes->empty()) { // segmentation without corresponding image will not be added - std::stringstream exceptionMessage; exceptionMessage << "No parent image found"; QMessageBox msgBox(QMessageBox::Warning, "Could not add the selected segmentation.", "The program wasn't able to correctly add the selected segmentation.\n" - "Reason:\n" + QString::fromStdString(exceptionMessage.str())); + "Reason: No parent image found"); msgBox.exec(); return; } // check for already existing, identifying base properties auto caseIDPropertyName = mitk::GetCaseIDDICOMProperty(); auto nodeIDPropertyName = mitk::GetNodeIDDICOMProperty(); mitk::BaseProperty* caseIDProperty = baseData->GetProperty(caseIDPropertyName.c_str()); mitk::BaseProperty* nodeIDProperty = baseData->GetProperty(nodeIDPropertyName.c_str()); if (nullptr == caseIDProperty || nullptr == nodeIDProperty) { MITK_INFO << "No DICOM tags for case and node identification found. Transferring DICOM tags from the parent node to the selected segmentation node."; mitk::SemanticTypes::CaseID caseID; mitk::SemanticTypes::ID nodeID; try { caseID = mitk::GetCaseIDFromDataNode(parentNodes->front()); nodeID = mitk::GetIDFromDataNode(parentNodes->front()); } catch (const mitk::SemanticRelationException& e) { std::stringstream exceptionMessage; exceptionMessage << e; QMessageBox msgBox(QMessageBox::Warning, "Could not add the selected segmentation.", "The program wasn't able to correctly add the selected segmentation.\n" "Reason:\n" + QString::fromStdString(exceptionMessage.str())); msgBox.exec(); return; } // transfer DICOM tags to the segmentation node baseData->SetProperty(caseIDPropertyName, mitk::TemporoSpatialStringProperty::New(caseID)); // add UID to distinguish between different segmentations of the same parent node baseData->SetProperty(nodeIDPropertyName, mitk::TemporoSpatialStringProperty::New(nodeID + mitk::UIDGeneratorBoost::GenerateUID())); } // add the parent node if not already existent if (!mitk::SemanticRelationsInference::InstanceExists(parentNodes->front())) { - AddImage(semanticRelationsIntegration, parentNodes->front()); + AddImage(semanticRelationsIntegration, dataStorage, parentNodes->front()); } try { // add the segmentation with its parent image to the semantic relations storage semanticRelationsIntegration->AddSegmentation(segmentation, parentNodes->front()); } catch (const mitk::SemanticRelationException& e) { std::stringstream exceptionMessage; exceptionMessage << e; QMessageBox msgBox(QMessageBox::Warning, "Could not add the selected segmentation.", "The program wasn't able to correctly add the selected segmentation.\n" "Reason:\n" + QString::fromStdString(exceptionMessage.str())); msgBox.exec(); return; } } } QmitkDataNodeAddToSemanticRelationsAction::QmitkDataNodeAddToSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite) : QAction(parent) , QmitkAbstractSemanticRelationsAction(workbenchPartSite) { setText(tr("Add to semantic relations")); InitializeAction(); } QmitkDataNodeAddToSemanticRelationsAction::QmitkDataNodeAddToSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite) : QAction(parent) , QmitkAbstractSemanticRelationsAction(berry::IWorkbenchPartSite::Pointer(workbenchPartSite)) { setText(tr("Add to semantic relations")); InitializeAction(); } QmitkDataNodeAddToSemanticRelationsAction::~QmitkDataNodeAddToSemanticRelationsAction() { // nothing here } void QmitkDataNodeAddToSemanticRelationsAction::InitializeAction() { connect(this, &QAction::triggered, this, &QmitkDataNodeAddToSemanticRelationsAction::OnActionTriggered); } void QmitkDataNodeAddToSemanticRelationsAction::OnActionTriggered(bool /*checked*/) { if (nullptr == m_SemanticRelationsIntegration) { return; } if (m_DataStorage.IsExpired()) { return; } auto dataNode = GetSelectedNode(); AddToSemanticRelationsAction::Run(m_SemanticRelationsIntegration.get(), m_DataStorage.Lock(), dataNode); } diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.h index 2a61c5d1fe..4f75c566a9 100644 --- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.h +++ b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.h @@ -1,57 +1,57 @@ /*=================================================================== 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 QMITKDATANODEADDTOSEMANTICRELATIONSACTION_H #define QMITKDATANODEADDTOSEMANTICRELATIONSACTION_H #include // mitk gui qt application plugin #include "QmitkAbstractSemanticRelationsAction.h" // qt #include namespace AddToSemanticRelationsAction { - MITK_GUI_SEMANTICRELATIONS_EXPORT void Run(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, const mitk::DataStorage* dataStorage, const mitk::DataNode* image); + MITK_GUI_SEMANTICRELATIONS_EXPORT void Run(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, mitk::DataStorage* dataStorage, const mitk::DataNode* image); - void AddImage(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, const mitk::DataNode* image); - void AddSegmentation(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, const mitk::DataStorage* dataStorage, const mitk::DataNode* segmentation); + void AddImage(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, mitk::DataStorage* dataStorage, const mitk::DataNode* image); + void AddSegmentation(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, mitk::DataStorage* dataStorage, const mitk::DataNode* segmentation); } class MITK_GUI_SEMANTICRELATIONS_EXPORT QmitkDataNodeAddToSemanticRelationsAction : public QAction, public QmitkAbstractSemanticRelationsAction { Q_OBJECT public: QmitkDataNodeAddToSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite); QmitkDataNodeAddToSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite); virtual ~QmitkDataNodeAddToSemanticRelationsAction() override; private Q_SLOTS: void OnActionTriggered(bool); protected: virtual void InitializeAction() override; }; #endif // QMITKDATANODEADDTOSEMANTICRELATIONSACTION_H diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.cpp index 5f2b2ca4dc..86ae166272 100644 --- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.cpp +++ b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.cpp @@ -1,147 +1,147 @@ /*=================================================================== 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 plugin #include "QmitkDataNodeRemoveFromSemanticRelationsAction.h" // semantic relations module #include #include // mitk gui common plugin #include // qt #include // namespace that contains the concrete action namespace RemoveFromSemanticRelationsAction { - void Run(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, const mitk::DataStorage* dataStorage, const mitk::DataNode* dataNode) + void Run(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, mitk::DataStorage* dataStorage, const mitk::DataNode* dataNode) { if (nullptr == dataNode) { return; } if (mitk::NodePredicates::GetImagePredicate()->CheckNode(dataNode)) { RemoveImage(semanticRelationsIntegration, dataStorage, dataNode); } else if (mitk::NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode)) { RemoveSegmentation(semanticRelationsIntegration, dataNode); } } - void RemoveImage(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, const mitk::DataStorage* dataStorage, const mitk::DataNode* image) + void RemoveImage(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, mitk::DataStorage* dataStorage, const mitk::DataNode* image) { if (nullptr == image) { return; } try { // remove each corresponding segmentation from the semantic relations storage mitk::DataStorage::SetOfObjects::ConstPointer childNodes = dataStorage->GetDerivations(image, mitk::NodePredicates::GetSegmentationPredicate(), false); for (auto it = childNodes->Begin(); it != childNodes->End(); ++it) { RemoveSegmentation(semanticRelationsIntegration, it->Value()); } // remove the image from the semantic relations storage semanticRelationsIntegration->RemoveImage(image); } catch (const mitk::SemanticRelationException& e) { std::stringstream exceptionMessage; exceptionMessage << e; QMessageBox msgBox; msgBox.setWindowTitle("Could not remove the selected image."); msgBox.setText("The program wasn't able to correctly remove the selected image.\n" "Reason:\n" + QString::fromStdString(exceptionMessage.str())); msgBox.setIcon(QMessageBox::Warning); msgBox.exec(); return; } } void RemoveSegmentation(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, const mitk::DataNode* segmentation) { if (nullptr == segmentation) { return; } try { // remove the segmentation from the semantic relations storage semanticRelationsIntegration->RemoveSegmentation(segmentation); } catch (const mitk::SemanticRelationException& e) { std::stringstream exceptionMessage; exceptionMessage << e; QMessageBox msgBox; msgBox.setWindowTitle("Could not remove the selected segmentation."); msgBox.setText("The program wasn't able to correctly remove the selected segmentation.\n" "Reason:\n" + QString::fromStdString(exceptionMessage.str())); msgBox.setIcon(QMessageBox::Warning); msgBox.exec(); return; } } } QmitkDataNodeRemoveFromSemanticRelationsAction::QmitkDataNodeRemoveFromSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite) : QAction(parent) , QmitkAbstractSemanticRelationsAction(workbenchPartSite) { setText(tr("Remove from semantic relations")); InitializeAction(); } QmitkDataNodeRemoveFromSemanticRelationsAction::QmitkDataNodeRemoveFromSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite) : QAction(parent) , QmitkAbstractSemanticRelationsAction(berry::IWorkbenchPartSite::Pointer(workbenchPartSite)) { setText(tr("Remove from semantic relations")); InitializeAction(); } QmitkDataNodeRemoveFromSemanticRelationsAction::~QmitkDataNodeRemoveFromSemanticRelationsAction() { // nothing here } void QmitkDataNodeRemoveFromSemanticRelationsAction::InitializeAction() { connect(this, &QAction::triggered, this, &QmitkDataNodeRemoveFromSemanticRelationsAction::OnActionTriggered); } void QmitkDataNodeRemoveFromSemanticRelationsAction::OnActionTriggered(bool /*checked*/) { if (nullptr == m_SemanticRelationsIntegration) { return; } if (m_DataStorage.IsExpired()) { return; } auto dataNode = GetSelectedNode(); RemoveFromSemanticRelationsAction::Run(m_SemanticRelationsIntegration.get(), m_DataStorage.Lock(),dataNode); } diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.h index 7b2fbd75fd..4aebf291f7 100644 --- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.h +++ b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.h @@ -1,57 +1,57 @@ /*=================================================================== 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 QMITKDATANODEREMOVEFROMSEMANTICRELATIONSACTION_H #define QMITKDATANODEREMOVEFROMSEMANTICRELATIONSACTION_H #include // mitk gui qt application plugin #include "QmitkAbstractSemanticRelationsAction.h" // qt #include namespace RemoveFromSemanticRelationsAction { - MITK_GUI_SEMANTICRELATIONS_EXPORT void Run(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, const mitk::DataStorage* dataStorage, const mitk::DataNode* dataNode); + MITK_GUI_SEMANTICRELATIONS_EXPORT void Run(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, mitk::DataStorage* dataStorage, const mitk::DataNode* dataNode); - void RemoveImage(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, const mitk::DataStorage* dataStorage, const mitk::DataNode* image); + void RemoveImage(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, mitk::DataStorage* dataStorage, const mitk::DataNode* image); void RemoveSegmentation(mitk::SemanticRelationsIntegration* semanticRelationsIntegration, const mitk::DataNode* segmentation); } class MITK_GUI_SEMANTICRELATIONS_EXPORT QmitkDataNodeRemoveFromSemanticRelationsAction : public QAction, public QmitkAbstractSemanticRelationsAction { Q_OBJECT public: QmitkDataNodeRemoveFromSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite); QmitkDataNodeRemoveFromSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite); virtual ~QmitkDataNodeRemoveFromSemanticRelationsAction() override; private Q_SLOTS: void OnActionTriggered(bool); protected: virtual void InitializeAction() override; }; #endif // QMITKDATANODEREMOVEFROMSEMANTICRELATIONSACTION_H