diff --git a/Modules/SemanticRelations/include/mitkControlPointManager.h b/Modules/SemanticRelations/include/mitkControlPointManager.h index c1fcce9ec8..026fac8333 100644 --- a/Modules/SemanticRelations/include/mitkControlPointManager.h +++ b/Modules/SemanticRelations/include/mitkControlPointManager.h @@ -1,166 +1,166 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef MITKCONTROLPOINTMANAGER_H #define MITKCONTROLPOINTMANAGER_H // semantic relations module #include "mitkSemanticTypes.h" #include // mitk core #include namespace mitk { /* * @brief Provides helper functions that are needed to work with control points. * * These functions help to generate new control points, check for overlapping / containing control points or provide functionality * to find a fitting control point or even extend an already existing control point. */ /* * @brief Generates a control point from a given vector of data nodes. * The start point and the end point for the newly generated control point are determined by the * earliest and the latest date of all the given data nodes, using 'GetStartPoint' and 'GetEndPoint'. * * @par dataNodes A vector of data node pointers that contain all the dates, that should be included in the newly generated control point. */ - MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint GenerateControlPoint(const std::vector& dataNodes); + MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint GenerateControlPoint(const std::vector& dataNodes); /* * @brief Generates a control point from a given data node. * The date is extracted from the data node by using the 'DICOMHelper::GetDateFromDataNode'-function. Inside the helper-function * the randomly generated UID is assigned to the UID of the date. * 'GenerateControlPoint(const SemanticTypes::Date&)' is used to generate a new control point from this extracted date. * * @par datanode A data node pointer, whose date should be included in the newly generated control point. */ - MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint GenerateControlPoint(const mitk::DataNode* datanode); + MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint GenerateControlPoint(const DataNode* datanode); /* * @brief Generates a control point from a given date. * Providing a single date, this date is assigned to both the start point and the end point of the newly created control point. * In order to reference both dates as individual instances, a new randomly generated UID is assigned to the UID of the end point. * * @par date A single date that is used to define both the start point and the end point of the newly created control point. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint GenerateControlPoint(const SemanticTypes::Date& date); /* * @brief Returns a string that displays the start point and the end point of the given control point in the format "YYYY-MM-DD to YYYY-MM-DD". * If the end point is the same as the start point, only one date is returned in the format "YYYY-MM-DD". * This function is used in the GUI to display the dates of a control point as header in the "information-type - control-point"-matrix. * * @par controlPoint The control point to convert into a string. */ MITKSEMANTICRELATIONS_EXPORT std::string GetControlPointAsString(const SemanticTypes::ControlPoint& controlPoint); /* * @brief Checks if the date that is extracted from the given data node lies inside the given control point. * To lie inside the given control point, * - the extracted date has to be greater or equal to the start point of the control point * AND * - the date has to be smaller or equal to the end point of the control point * * @par dataNode The data node whose extracted date has to be checked. * @par controlPoint The control point in which the extracted date of the data node may lie. * * @return True, if the extracted date lies inside the given control point; false otherwise. */ - MITKSEMANTICRELATIONS_EXPORT bool InsideControlPoint(const mitk::DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint); + MITKSEMANTICRELATIONS_EXPORT bool InsideControlPoint(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint); /* * @brief Checks if the given date lies inside the given control point. * To lie inside the given control point, * - the date has to be greater or equal to the start point of the control point * AND * - the date has to be smaller or equal to the end point of the control point * * @par date The date to be checked. * @par controlPoint The control point in which the date may lie. * * @return True, if the date lies inside the given control point; false otherwise. */ MITKSEMANTICRELATIONS_EXPORT bool InsideControlPoint(const SemanticTypes::Date& date, const SemanticTypes::ControlPoint& controlPoint); /* * @brief Checks if a given control point lies inside another given control point. * To lie inside another control point, * - the start point of the first control point has to be greater or equal to the start point of the second control point * AND * - the end point of the first control point has to be smaller or equal to the end point of the second control point * * @par containedControlPoint The control point that may be contained in the second control point. * @par containingControlPoint The control point in which the first control point may lie. * * @return True, if the first control point lies inside the second control point; false otherwise. */ MITKSEMANTICRELATIONS_EXPORT bool InsideControlPoint(const SemanticTypes::ControlPoint& containedControlPoint, const SemanticTypes::ControlPoint& containingControlPoint); /* * @brief Checks if a given control point overlaps with a neighboring control point. * To overlap, * - the start point of the first control point has to be smaller than the end point of the second control point * AND * - the end point of the first control point has to be greater than the start point of the second control point * * @par controlPoint The control point to be checked. * @par neighboringControlPoint The neighboring control point to be checked. * * @return True, if both the control points overlap with eatch other; false otherwise. */ MITKSEMANTICRELATIONS_EXPORT bool CheckForOverlap(const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ControlPoint& neighboringControlPoint); /* * @brief Extracts a date from the given data node using the 'DICOMHelper::GetDateFromDataNode'-function. * If a real date can be extracted, the second 'FindFittingControlPoint'-function is used to find a control point that contains the given date. * If no date can be extracted from the data node, the function prints an info and returns an empty control point. * * @par dataNode A data node pointer, whose extracted date may be found in the given control points. * @par allControlPoints A vector of control points that may contain the extracted date. * * @return The return value of the second 'FindFittingControlPoint'-function. * An empty control point, if no date can be extracted from the data node. */ - MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint FindFittingControlPoint(const mitk::DataNode* dataNode, std::vector& allControlPoints); + MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint FindFittingControlPoint(const DataNode* dataNode, std::vector& allControlPoints); /* * @brief Tries to find a control point in all the given control points that contains the given date. * The correct control point may be found by using the 'InsideControlPoint' function with the date, evaluated on each control point. * * @par date The date that may be found in the given control points. * @par allControlPoints A vector of control points that may contain the given date. * * @return The control point that contains the given date. An empty control point, if the date is not contained in any of the given control points. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint FindFittingControlPoint(const SemanticTypes::Date& date, std::vector& allControlPoints); /* * @brief Extracts a date from the given data node using the 'DICOMHelper::GetDateFromDataNode'-function. * If a real date can be extracted, the second 'ExtendClosestControlPoint'-function is used to try to extend a close control point. * If no date can be extracted from the data node, the function prints an info and returns an empty control point. * * @par dataNode A data node pointer, whose extracted date may be used to extend a close control points. * @par allControlPoints A vector of control points of which the closest control point may be extended by the extracted date. * * @return The return value of the second 'ExtendClosestControlPoint'-function. * An empty control point, if no date can be extracted from the data node. */ - MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint ExtendClosestControlPoint(const mitk::DataNode* dataNode, std::vector& allControlPoints); + MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint ExtendClosestControlPoint(const DataNode* dataNode, std::vector& allControlPoints); /* * @brief Tries to find the closest control point to the given date in all the given control points. This is done by sorting the given vector of all control points and * finding the first control point that is newer than the given date. Then the distances to the neighboring control points (older and newer, if existent) is calculated, * using 'CalculateDistanceInDays'. If the smaller distance is smaller than a certain threshold, the corresponding control point is extended and returned, using the * 'ExtendControlPoint'-function. If not, an empty control point is returned. * * @return The return value of the 'ExtendControlPoint'-function. * An empty control point, if the distance between the date and the closest control point exceeds a certain threshold. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint ExtendClosestControlPoint(const SemanticTypes::Date& date, std::vector& allControlPoints); } // namespace mitk #endif // MITKCONTROLPOINTMANAGER_H diff --git a/Modules/SemanticRelations/include/mitkLesionManager.h b/Modules/SemanticRelations/include/mitkLesionManager.h index f775f86f34..3983edfbb2 100644 --- a/Modules/SemanticRelations/include/mitkLesionManager.h +++ b/Modules/SemanticRelations/include/mitkLesionManager.h @@ -1,82 +1,81 @@ /*=================================================================== 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 MITKLESIONMANAGER_H #define MITKLESIONMANAGER_H #include // semantic relations module #include "mitkSemanticRelations.h" #include "mitkSemanticTypes.h" #include "mitkLesionData.h" // mitk core #include /* * @brief Provides helper functions that are needed to work with lesions. * * These functions help to generate new lesions, check for existing lesions or provide functionality * to find existing lesion class types. */ namespace mitk { typedef std::vector LesionClassVector; /** * @brief Generate a new lesion and lesion class with UIDs and the given string as lesion class type. * * @param lesionClassType The lesion class type as string. Default parameter is "". */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::Lesion GenerateNewLesion(const std::string& lesionClassType = ""); /** * @brief Generate a new lesion class with UID and the given string as lesion class type. * * @param lesionClassType The lesion class type as string. Default parameter is "". */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionClass GenerateNewLesionClass(const std::string& lesionClassType = ""); /** * @brief Find and return a whole lesion including its lesion class given a specific lesion UID. * * @param lesionUID The lesion UID as string. * @param allLesions All currently known lesions of a specific case. * * @return The lesion with its UID and the lesion class. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::Lesion GetLesionByUID(const SemanticTypes::ID& lesionUID, const std::vector& allLesions); /** * @brief Find and return the whole lesion class including its UID given a specific lesion class type. * * @param lesionClassType The lesion class type as string. * @param allLesionClasses All currently known lesion classes of a specific case. * * @return The lesion class with its UID and the class type. */ MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionClass FindExistingLesionClass(const std::string& lesionClassType, const std::vector& allLesionClasses); /** * @brief Generate and store additional lesion data such as lesion presence and lesion volume for each control point. * * @param lesionData The lesion data that holds the lesion and will hold the additional lesion data. * @param caseID The current case ID. * @param semanticRelations An instance of the semantic relations to retrieve the additional data. */ - MITKSEMANTICRELATIONS_EXPORT void GenerateAdditionalLesionData(mitk::LesionData& lesionData, const SemanticTypes::CaseID& caseID, std::shared_ptr semanticRelations); - + MITKSEMANTICRELATIONS_EXPORT void GenerateAdditionalLesionData(LesionData& lesionData, const SemanticTypes::CaseID& caseID, std::shared_ptr semanticRelations); } // namespace mitk #endif // MITKLESIONMANAGER_H diff --git a/Modules/SemanticRelations/include/mitkSemanticRelations.h b/Modules/SemanticRelations/include/mitkSemanticRelations.h index cf60f26f9c..f3c18003d1 100644 --- a/Modules/SemanticRelations/include/mitkSemanticRelations.h +++ b/Modules/SemanticRelations/include/mitkSemanticRelations.h @@ -1,654 +1,635 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef MITKSEMANTICRELATIONS_H #define MITKSEMANTICRELATIONS_H #include // semantic relations module -#include "mitkControlPointManager.h" #include "mitkDICOMHelper.h" #include "mitkISemanticRelationsObservable.h" #include "mitkISemanticRelationsObserver.h" #include "mitkRelationStorage.h" #include "mitkSemanticTypes.h" // mitk core #include #include namespace mitk { /* * @brief The API provides functions to query and manipulate image relations and instances, * that are helpful during follow-up examination, like control-points (time period), * types of the images or lesions that may be visible on multiple images. * * The class is able to generate IDs from given data nodes using DICOM information. * These IDs are used to identify the corresponding instances of a specific case. * The case can also be directly identified by the given case ID. * * In the BlackSwan context the case is identified with the DICOM PatientID. * * In order for most functions to work the case ID has to be defined in the model. If not, * the functions do nothing. */ class MITKSEMANTICRELATIONS_EXPORT SemanticRelations : public ISemanticRelationsObservable { public: SemanticRelations(mitk::DataStorage::Pointer dataStorage); ~SemanticRelations(); typedef std::vector LesionVector; typedef std::vector LesionClassVector; typedef std::vector ControlpointVector; typedef std::vector InformationTypeVector; typedef std::vector DataNodeVector; /************************************************************************/ /* functions to implement the observer pattern */ /************************************************************************/ /* * @brief Adds the given concrete observer to the vector that holds all currently registered observer. * If the observer is already registered, it will not be added to the observer vector. * * @param observer The concrete observer to register. */ virtual void AddObserver(ISemanticRelationsObserver* observer) override; /* * @brief Removes the given concrete observer from the vector that holds all currently registered observer. * * @param observer The concrete observer to unregister. */ virtual void RemoveObserver(ISemanticRelationsObserver* observer) override; /************************************************************************/ /* functions to get instances / attributes */ /************************************************************************/ /* * @brief Returns a vector of all lesions that are currently available for the given case. * The lesions may be marked by a segmentation or may be empty - with no connection to a specific image / segmentation of the case data. * If no lesions are stored for the current case, an empty vector is returned. * * @param caseID The current case identifier is defined by the given string. * @return A vector of lesions. */ LesionVector GetAllLesionsOfCase(const SemanticTypes::CaseID& caseID) const; /** * @brief * * */ LesionClassVector GetAllLesionClassesOfCase(const SemanticTypes::CaseID& caseID) const; /* * @brief Returns a vector of all lesions that are valid for the given case, given a specific control point. * * @param caseID The current case identifier is defined by the given string. * @param controlPoint A specific control point which has to be available at a returned (found) lesion: * Only those lesions are returned for which the image of the associated segmentation is linked to the given control point. * If the control point instance does not exist, an empty vector is returned. * @return A vector of control points. */ LesionVector GetAllLesionsOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const; /* * @brief Returns a vector of all lesions that are currently available for the current case and are connected to the given image (via a segmentation). * If no lesions are stored for the current case, an empty vector is returned. If no segmentation nodes are * connected with the image node, no lesions for the specific image will be found and an empty vector is returned. * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * @pre The image node has to have associated segmentation nodes (child nodes) in order to reference a lesion. * * @param imageNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. * @return A vector of lesions. */ LesionVector GetAllLesionsInImage(const DataNode* imageNode) const; /* * @brief Returns the lesion that is defined by the given segmentation data. * * @pre The given segmentation data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr). * @pre The segmentation data node has to represent a lesion. If not, the retrieved lesion will be empty, which leads to an exception. * @throw SemanticRelationException, if the segmentation does not represent an existing lesion (this can be checked via 'IsRepresentingALesion'). * * @param segmentationNode The segmentation identifier is extracted from the given data node. * @return The represented lesion. */ SemanticTypes::Lesion GetRepresentedLesion(const DataNode* segmentationNode) const; - /** - * @brief Return the lesion presence of a given lesion at a 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. - */ - bool GetLesionPresence(const SemanticTypes::CaseID& caseID, const mitk::SemanticTypes::Lesion& lesion, const mitk::SemanticTypes::ControlPoint& controllPoint) const; - /** - * @brief Return the lesion volume of a given lesion at a 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 A value indicating the lesion volume. - */ - double GetLesionVolume(const SemanticTypes::CaseID& caseID, const mitk::SemanticTypes::Lesion& lesion, const mitk::SemanticTypes::ControlPoint& controllPoint) const; /* * @brief Check if the given segmentation refers to an existing lesion instance. * This function can be used before calling 'GetRepresentedLesion' in order to avoid a possible exception. * * @param segmentationNode The segmentation identifier is extracted from the given data node. * @return True, if the segmentation refers to an existing lesion; false otherwise. */ bool IsRepresentingALesion(const DataNode* segmentationNode) const; /** * @brief 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. */ bool InstanceExists(const DataNode* dataNode) const; /* * @brief Return a vector of all segmentations that are currently available for the given case. * The segmentations may be connected / not connected to a lesion of the case. * If no segmentations are stored for the current case, an empty vector is returned. * * @pre The data storage member has to be valid (!nullptr). * @throw SemanticRelationException, if the data storage member is invalid (==nullptr). * * @param caseID The current case identifier is defined by the given string. * @return A vector of data nodes representing segmentations. */ mitk::SemanticRelations::DataNodeVector GetAllSegmentationsOfCase(const SemanticTypes::CaseID& caseID) const; /* * @brief Return a vector of all segmentations that define the given lesion. These segmentations don't have to be linked to the same image. * If the lesion is not referred to by any segmentation, an empty vector is returned. * * @pre The data storage member has to be valid (!nullptr). * @throw SemanticRelationException, if the data storage member is invalid (==nullptr). * @pre The UID of the lesion has to exist for a lesion instance. * @throw SemanticRelationException, if UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param lesion A Lesion with a UID that identifies the corresponding lesion instance. * @return A vector of data nodes representing segmentations that define the given lesion. */ DataNodeVector GetAllSegmentationsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const; /* * @brief Return a vector of all images that are currently available for the given case. * * @pre The data storage member has to be valid (!nullptr). * @throw SemanticRelationException, if the data storage member is invalid (==nullptr). * * @param caseID The current case identifier is defined by the given string. * @return A vector of data nodes representing images. */ DataNodeVector GetAllImagesOfCase(const SemanticTypes::CaseID& caseID) const; /* * @brief Return a vector of all images that are connected to those segmentations that are linked to the given lesion. * If the lesion is not referred to by any segmentation, an empty vector is returned. * * @pre The UID of the lesion has to exist for a lesion instance. * @throw SemanticRelationException, if UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param lesion A Lesion with a UID that identifies the corresponding lesion instance. * @return A vector of data nodes representing images on which the lesions are visible. */ DataNodeVector GetAllImagesOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const; /* * @brief Check if the given lesion instance exists. * This function can be used before calling 'GetAllSegmentationsOfLesion' in order to avoid a possible exception. * This function can be used before calling 'AddLesionInstance' in order to avoid a possible exception. * * @param caseID The current case identifier is defined by the given string. * @param lesion A Lesion with a UID that identifies the corresponding lesion instance. * @return True, if the lesion instance exists; false otherwise. */ bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const; /* * @brief Return a vector of all control points that are valid for the given case. * * @param caseID The current case identifier is defined by the given string. * @return A vector of control points. */ ControlpointVector GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID) const; /* * @brief Return a vector of all control points that are valid for the given case, given a specific lesion * * @param caseID The current case identifier is defined by the given string. * @param lesion A specific lesion which has to be available at a returned (found) control point: * Only those control points are returned for which an associated data has a segmentation that references the given lesion. * If the lesion does not exists, an empty vector is returned. * @return A vector of control points. */ ControlpointVector GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const; /* * @brief Return a vector of all control points that are valid for the given case, given a specific information type. * * @param caseID The current case identifier is defined by the given string. * @param informationType A specific information type which has to be available at a returned (found) control point: * Only those control points are returned for which an associated data has the given information type. * If the information type instance does not exists, an empty vector is returned. * @return A vector of control points. */ ControlpointVector GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) const; /* * @brief Return the control point of a data node. * If the data node is not linked to a control point or the data node refers to a non-existing control point, * a control point with an empty UID is returned. * * @pre The given 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 control point of the given data node. */ SemanticTypes::ControlPoint GetControlPointOfImage(const DataNode* imageNode) const; /* * @brief Return a vector of all image nodes that link to the given control point. * If the control point is not referred to by any data node, an empty vector is returned. * * @pre The UID of the control point has to exist for a control point instance. * @throw SemanticRelationException, if the UID of the control point does not exist for a control point instance (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param controlPoint A control point with a UID that identifies the corresponding control point instance. * @return A vector of image nodes that link to the given control point. */ DataNodeVector GetAllImagesOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const; /* * @brief Check if the given control point instance exists. * This function can be used before calling 'GetAllDataOfControlPoint' in order to avoid a possible exception. * This function can be used before adding, linking and unlinking control points to avoid a possible exception. * * @param caseID The current case identifier is defined by the given string. * @param controlPoint A control point with a UID that identifies the corresponding control point instance. * @return True, if the control point instance exists; false otherwise. */ bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const; /* * @brief Return a vector of all information types that are valid for the given case. * * @param caseID The current case identifier is defined by the given string. * @return A vector of information types. */ InformationTypeVector GetAllInformationTypesOfCase(const SemanticTypes::CaseID& caseID) const; /* * @brief Return a vector of all information types that are valid for the given case, given a specific control point. * * @param caseID The current case identifier is defined by the given string. * @param controlPoint A specific control point which has to be available at a returned (found) information type: * Only those information types are returned for which an associated data is linked to the given control point. * If the control point instance does not exist, an empty vector is returned. * @return A vector of information types. */ InformationTypeVector GetAllInformationTypesOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const; /* * @brief Return the information type of the given image. * If the image does not contain any information type, an empty information type is returned. * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * * @param imageNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. * @return The information type of the given data node. */ SemanticTypes::InformationType GetInformationTypeOfImage(const DataNode* imageNode) const; /* * @brief Return a vector of all image nodes that are defined with the given information type. * * @pre The information type has to exist for the given case (and is therefore used by at least one data node). * @throw SemanticRelationException, if the information type is not used by any data node (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param informationType An information type that identifies the corresponding information type instance. * @return A vector of image nodes that are defined with the given information type. */ DataNodeVector GetAllImagesOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) const; /* * @brief Return a vector of all image nodes that are defined with the given information type and with the given control point. * * @pre The UID of the control point has to exist for a control point instance. * The information type has to exist for the given case (and is therefore used by at least one data node). * @throw SemanticRelationException, if the UID of the control point does not exist for a control point instance (this can be checked via 'InstanceExists') or * if the information type is not used by any data node (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param controlPoint A control point with a UID that identifies the corresponding control point instance. * @param informationType An information type that identifies the corresponding information type instance. * @return A vector of image nodes that are defined with the given information type with the given control point. */ DataNodeVector GetAllSpecificImages(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const; /** * @brief Return a vector of all segmentation nodes that are defined with the given information type and with the given control point. * The function uses the 'GetAllSpecificImages'-function to retrieve the specific images and then searches for the derived nodes (segmentation child nodes). * * @pre The UID of the control point has to exist for a control point instance. * The information type has to exist for the given case (and is therefore used by at least one data node). * @throw SemanticRelationException, if the UID of the control point does not exist for a control point instance (this can be checked via 'InstanceExists') or * if the information type is not used by any data node (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param controlPoint A control point with a UID that identifies the corresponding control point instance. * @param informationType An information type that identifies the corresponding information type instance. * @return A vector of segmentation nodes that are defined with the given information type with the given control point. */ DataNodeVector GetAllSpecificSegmentations(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const; /* * @brief Check if the given information type exists. * This function can be used before calling 'GetAllDataOfInformationType' in order to avoid a possible exception. * * @param caseID The current case identifier is defined by the given string. * @param informationType An information type * @return True, if the information type exists; false otherwise. */ bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) const; /* * @brief Return a vector of all CaseIDs that are currently available. * * @return A vector of CaseIDs as strings. */ std::vector GetAllCaseIDs() const; /************************************************************************/ /* functions to add / remove instances / attributes */ /************************************************************************/ /* * @brief Add the given image to the set of already existing images. * The date is extracted from the DICOM data of the image node and is compared to already existing control points in the semantic relations model. * The function tries to find a fitting control point or to extend an already existing control point, if the extracted control point is close to * any other, already existing control point. * Finally, the image is linked to the correct control point. * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * * @param imageNode The current case identifier and node identifier is extracted from the given image data node, which contains DICOM information about the case and the node. */ void AddImage(const DataNode* imageNode); /* * @brief Remove the given image from the set of already existing images. * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * * @param imageNode The current case identifier and node identifier is extracted from the given image data node, which contains DICOM information about the case and the node. */ void RemoveImage(const DataNode* imageNode); /* * @brief Add a newly created lesion to the set of already existing lesions - with no connection to a specific image / segmentation of the case data. * * @pre The UID of the lesion must not already exist for a lesion instance. * @throw SemanticRelationException, it the UID of the lesion already exists for a lesion instance (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param lesion The lesion instance to add. */ void AddLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion); /* * @brief Overwrite an already existing lesion instance (this may be useful to overwrite the lesion with a different lesion class). * * @pre The UID of the lesion has to exist for a lesion instance. * @throw SemanticRelationException, if the UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists'). * * @param caseID The current case identifier is defined by the given string. * @param lesion The lesion instance that overwrites an existing lesion. */ void OverwriteLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion); /* * @brief Add a newly created lesion to the set of already existing lesions. The lesion is added and a reference to * the lesion is added to the segmentation data. If the segmentation is already linked to a lesion, the * old linkage is overwritten (this can be checked via 'IsRepresentingALesion'). * * @pre The given segmentation data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr). * @pre The UID of the lesion must not already exist for a lesion instance. * @throw SemanticRelationException, if the UID of the lesion already exists for a lesion instance (this can be checked via 'InstanceExists'). * * @param segmentationNode The segmentation identifier is extracted from the given data node. The segmentation node has DICOM information from its parent node. * @param lesion The lesion instance to add and link. */ void AddLesionAndLinkSegmentation(const DataNode* segmentationNode, const SemanticTypes::Lesion& lesion); /* * @brief Remove the given lesion from the set of already existing lesions. * * @pre The UID of the lesion has to exist for a lesion instance. * @throw SemanticRelationException, if the UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists'). * @pre The function needs to assure that no segmentation is still representing (linked to) this lesion. * @throw SemanticRelationException, if the lesion instance to remove is still linked to by any segmentation (this can be checked via 'GetAllSegmentationsOfLesion'). * * @param caseID The current case identifier is defined by the given string. * @param lesion The lesion instance to remove. */ void RemoveLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion); /* * @brief Add a segmentation instance to the set of already existing segmentations - with no connection to a specific lesion. * * @param segmentationNode The segmentation identifier is extracted from the given data node. The segmentation node has DICOM information from its parent node. * @param parentNode The node identifier of the parent node is extracted from the given parent data node. */ void AddSegmentation(const DataNode* segmentationNode, const DataNode* parentNode); /* * @brief Link the given segmentation instance to an an already existing lesion instance. If the segmentation is already linked to a lesion instance, the * old linkage is overwritten (this can be checked via 'IsRepresentingALesion'). * * @pre The given segmentation data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr). * @pre The UID of the lesion has to exist for a lesion instance. * @throw SemanticRelationException, if the UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists'). * * @param segmentationNode The segmentation identifier is extracted from the given data node. The segmentation node has DICOM information from its parent node. * @param lesion The lesion instance to link. */ void LinkSegmentationToLesion(const DataNode* segmentationNode, const SemanticTypes::Lesion& lesion); /* * @brief Unlink the given segmentation instance from the linked lesion instance. * The lesion may stay unlinked to any segmentation. * * @pre The given segmentation data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr). * * @param segmentationNode The segmentation identifier is extracted from the given data node. The segmentation node has DICOM information from its parent node. */ void UnlinkSegmentationFromLesion(const DataNode* segmentationNode); /* * @brief Remove the given segmentation from the set of already existing segmentations. * * @pre The given segmentation data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr). * * @param segmentationNode The segmentation identifier is extracted from the given data node. The segmentation node has DICOM information from its parent node. */ void RemoveSegmentation(const DataNode* segmentationNode); /** * @brief Use the given date to set the control point for the given data node. * The function tries to find a fitting control point for the given data and link to this control point or extend it. * If no fitting (or any) control point is found a new control point is generated from the date and added to the semantic relations storage. * * @pre The given data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given data node is invalid (==nullptr). */ void SetControlPointFromDate(const DataNode* dataNode, const SemanticTypes::Date& date); /* * @brief Add a newly created control point to the set of already existing control points. A reference to the control point is added to the given data. * This function combines adding a control point and linking it, since a control point with no associated data is not allowed. * * @pre The given data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given data node is invalid (==nullptr). * @pre The UID of the control point must not already exist for a control point instance. * @throw SemanticRelationException, if the UID of the control point already exists for a control point instance (this can be checked via 'InstanceExists'). * @pre The given control point must not already be contained in an existing control point interval. * @throw SemanticRelationException, if the given control point is already contained in an existing control point interval (this can be checked via 'CheckContainingControlPoint'). * @pre The given control point must contain the date of the given data node (if parameter 'checkConsistence = true'). * @throw SemanticRelationException, if the given control point does not contain the date of the given data node and 'checkConsistence = true' (this can be checked via 'ControlPointManager::InsideControlPoint'). * * @param dataNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. * @param controlPoint The control point instance to add. For a newly added control point always has "startDate = endDate". * @param checkConsistence If true, the function checks, whether the date of the data node actually lies inside the control point to link. */ void AddControlPointAndLinkData(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence = true); /* * @brief Link the given data to an already existing control point and overwrite the start or end point of the control point. * * @pre The given data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given data node is invalid (==nullptr). * @pre The UID of the control point has to exist for a control point instance. * @throw SemanticRelationException, if the UID of the control point does not exists for a control point instance (this can be checked via 'InstanceExists'). * @pre The given control point must contain the date of the given data node (if parameter 'checkConsistence = true'). * @throw SemanticRelationException, if the given control point does not contain the date of the given data node and 'checkConsistence = true' (this can be checked via 'ControlPointManager::InsideControlPoint'). * @pre The given control point must differ from the overwritten control point, but only either in the start point or in the end point. * It is not possible to overwrite a single control point from a single date and simultaneously changing both ends of the time period. * @throw SemanticRelationException, if the given control point does not differ from the overwritten control point or if the given control point differs in the start date and the end date from the overwritten control point. * @pre The given control point must not overlap with an already existing control point. * @throw SemanticRelationException, if the given control point overlaps with an already existing control point interval (this can be checked via 'CheckOverlappingControlPoint'). * * @param dataNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. * @param controlPoint The control point instance that overwrites an existing control point. * @param checkConsistence If true, the function checks, whether the date of the data node actually lies inside the control point to link. */ void OverwriteControlPointAndLinkData(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence = true); /* * @brief Link the given data to an already existing control point. * * @pre The given data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given data node is invalid (==nullptr). * @pre The UID of the control point has to exist for a control point instance. * @throw SemanticRelationException, if the UID of the control point does not exists for a control point instance (this can be checked via 'InstanceExists'). * @pre The given control point must contain the date of the given data node (if parameter 'checkConsistence = true'). * @throw SemanticRelationException, if the given control point does not contain the date of the given data node and 'checkConsistence = true' (this can be checked via 'ControlPointManager::InsideControlPoint'). * * @param dataNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. * @param controlPoint The control point instance to add link. * @param checkConsistence If true, the function checks, whether the date of the data node actually lies inside the control point to link. */ void LinkDataToControlPoint(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence = true); /* * @brief Unlink the given image from the linked control point. * If data is unlinked from a control point, the function needs to check whether the control point is still linked to any other data: * - if not, the control point instance will be removed (has to be removed since a control point with no associated data is not allowed). * - if so, the function has to make sure that the control point instance is shortened to its minimum time period (e.g. moving the end point to an earlier date). * * @param dataNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. */ void UnlinkDataFromControlPoint(const DataNode* dataNode); /** * @brief Set (and possibly overwrite) the information type of the given image. * An already associated information type might be removed if is not referenced by any other image: * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * @post If the information type instance did not exist before, it is now added. * * @param imageNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. * @param informationType An information type that identifies the corresponding information type instance. */ void SetInformationType(const DataNode* imageNode, const SemanticTypes::InformationType& informationType); /* * @brief Set the information type of the given image. * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * @post If the information type instance did not exist before, it is now added. * * @param imageNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. * @param informationType An information type that identifies the corresponding information type instance. */ void AddInformationTypeToImage(const DataNode* imageNode, const SemanticTypes::InformationType& informationType); /* * @brief Remove the information type of the given image. * If the information type is removed, the function needs to check whether the information type is referenced by any other image: * - if not, the information type instance can be removed (has to be removed since an information type with no associated image is not allowed). * - if so, the information type is just removed from the given image. * * @pre The given image data node has to be valid (!nullptr). * @throw SemanticRelationException, if the given image data node is invalid (==nullptr). * * @param imageNode The current case identifier is extracted from the given data node, which contains DICOM information about the case. */ void RemoveInformationTypeFromImage(const DataNode* imageNode); private: // the relation storage serves as a storage accessor and can be sub-classed for custom demands std::shared_ptr m_RelationStorage; DataStorage::Pointer m_DataStorage; /* * @brief A vector that stores the currently registered observer of this observable subject. */ static std::vector m_ObserverVector; /* * @brief The SemanticRelations, as an example of an observable subject, notifies (updates) the observer with a given case ID. * The view's caseID was set before in the GUI. The parts of the view that observe changes in the semantic relations are only updated, * if the given case ID is equal to the observer's current caseID and thus the observer currently shows the semantic information of the given case. * * @param caseID The caseID that identifies the currently active patient / case. */ virtual void NotifyObserver(const mitk::SemanticTypes::CaseID& caseID) const override; /* * @brief Determine if the given control point contains images, which are connected to segmentations that represent the given lesion. * If the lesion or the control point are not correctly stored, the function returns false. * * @param caseID The current case identifier is defined by the given string. * @param lesion A Lesion with a UID that identifies the corresponding lesion instance. * @param controlPoint A control point with a UID that identifies the corresponding control point instance. * * @return True, if the given control point contains data that is related to the given lesion; false otherwise. */ bool ControlPointContainsLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint) const; /* * @brief Determine if the given control point contains images, which refer to the given information type. * If the information type or the control point are not correctly stored, the function returns false. * * @param caseID The current case identifier is defined by the given string. * @param informationType An information type that identifies the corresponding information type instance. * @param controlPoint A control point with a UID that identifies the corresponding control point instance. * * @return True, if the given control point contains data that is related to the given information type; false otherwise. */ bool ControlPointContainsInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType, const SemanticTypes::ControlPoint& controlPoint) const; /* * @brief Check if the given control point overlaps with an already existing control point. * If the UID already exists, then the given control point may overlap with the previous or next control point, * because the start point or the end point of the given control point might be modified (different to the same control point * that is stored at the moment). * If the UID does not already exists, the previous and next control point are found by comparing the dates of the already * existing control points and the given control point. * * @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. */ bool CheckOverlappingControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint); /* * @brief Check if the given control point is contained within an already existing control point. * If the UID already exists, then the given control point is contained in this same control point. * However, the function does not check if the given control point is really contained (just compares UID) in this case. * If the UID does not already exist, the already existing control points are tested to see if they contain the * given control point. * * @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. */ bool CheckContainingControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint); }; } // namespace mitk #endif // MITKSEMANTICRELATIONS_H diff --git a/Modules/SemanticRelations/src/mitkControlPointManager.cpp b/Modules/SemanticRelations/src/mitkControlPointManager.cpp index 20626fc866..bc6c908a9e 100644 --- a/Modules/SemanticRelations/src/mitkControlPointManager.cpp +++ b/Modules/SemanticRelations/src/mitkControlPointManager.cpp @@ -1,304 +1,304 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // semantic relations module #include "mitkControlPointManager.h" #include "mitkDICOMHelper.h" #include "mitkUIDGeneratorBoost.h" // mitk core #include // c++ #include mitk::SemanticTypes::Date GetStartPoint(const std::vector& dataNodes); mitk::SemanticTypes::Date GetEndPoint(const std::vector& dataNodes); void ExtendControlPoint(mitk::SemanticTypes::ControlPoint& controlPoint, mitk::SemanticTypes::Date date); double CalculateDistanceInDays(mitk::SemanticTypes::Date leftDate, mitk::SemanticTypes::Date rightDate); -mitk::SemanticTypes::ControlPoint mitk::GenerateControlPoint(const std::vector& dataNodes) +mitk::SemanticTypes::ControlPoint mitk::GenerateControlPoint(const std::vector& dataNodes) { SemanticTypes::ControlPoint controlPoint; SemanticTypes::Date startPoint = GetStartPoint(dataNodes); SemanticTypes::Date endPoint = GetEndPoint(dataNodes); // set the values of the control point controlPoint.UID = UIDGeneratorBoost::GenerateUID(); controlPoint.startPoint = startPoint; controlPoint.endPoint = endPoint; return controlPoint; } -mitk::SemanticTypes::ControlPoint mitk::GenerateControlPoint(const mitk::DataNode* datanode) +mitk::SemanticTypes::ControlPoint mitk::GenerateControlPoint(const DataNode* datanode) { SemanticTypes::ControlPoint controlPoint; SemanticTypes::Date date = GetDICOMDateFromDataNode(datanode); return GenerateControlPoint(date); } mitk::SemanticTypes::ControlPoint mitk::GenerateControlPoint(const SemanticTypes::Date& date) { SemanticTypes::ControlPoint controlPoint; // set the values of the control point controlPoint.UID = UIDGeneratorBoost::GenerateUID(); controlPoint.startPoint = date; controlPoint.endPoint = date; // create new UID so that the start point and the end point have a different UID controlPoint.endPoint.UID = UIDGeneratorBoost::GenerateUID(); return controlPoint; } std::string mitk::GetControlPointAsString(const SemanticTypes::ControlPoint& controlPoint) { std::stringstream dateAsString; SemanticTypes::Date startPoint = controlPoint.startPoint; SemanticTypes::Date endPoint = controlPoint.endPoint; dateAsString << std::to_string(controlPoint.startPoint.year) << "-" << std::setfill('0') << std::setw(2) << std::to_string(startPoint.month) << "-" << std::setfill('0') << std::setw(2) << std::to_string(startPoint.day); if (startPoint != endPoint) { dateAsString << " to \n " << std::to_string(endPoint.year) << "-" << std::setfill('0') << std::setw(2) << std::to_string(endPoint.month) << "-" << std::setfill('0') << std::setw(2) << std::to_string(endPoint.day); } return dateAsString.str(); } -bool mitk::InsideControlPoint(const mitk::DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint) +bool mitk::InsideControlPoint(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint) { SemanticTypes::Date date = GetDICOMDateFromDataNode(dataNode); if (date >= controlPoint.startPoint && date <= controlPoint.endPoint && !controlPoint.UID.empty()) { return true; } return false; } bool mitk::InsideControlPoint(const SemanticTypes::Date& date, const SemanticTypes::ControlPoint& controlPoint) { if (date >= controlPoint.startPoint && date <= controlPoint.endPoint) { return true; } return false; } bool mitk::InsideControlPoint(const SemanticTypes::ControlPoint& containedControlPoint, const SemanticTypes::ControlPoint& containingControlPoint) { if (containedControlPoint.startPoint >= containingControlPoint.startPoint && containedControlPoint.endPoint <= containingControlPoint.endPoint) { return true; } return false; } bool mitk::CheckForOverlap(const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ControlPoint& neighboringControlPoint) { if (controlPoint.startPoint >= neighboringControlPoint.endPoint || controlPoint.endPoint <= neighboringControlPoint.startPoint) { return false; } return true; } -mitk::SemanticTypes::ControlPoint mitk::FindFittingControlPoint(const mitk::DataNode* dataNode, std::vector& allControlPoints) +mitk::SemanticTypes::ControlPoint mitk::FindFittingControlPoint(const DataNode* dataNode, std::vector& allControlPoints) { SemanticTypes::Date dateFromDataNode = GetDICOMDateFromDataNode(dataNode); if (0 == dateFromDataNode.year) { MITK_INFO << "Could not deduce a valid date from the given data node."; return SemanticTypes::ControlPoint(); } return FindFittingControlPoint(dateFromDataNode, allControlPoints); } mitk::SemanticTypes::ControlPoint mitk::FindFittingControlPoint(const SemanticTypes::Date& date, std::vector& allControlPoints) { // check if the date of the data node fits into an existing control point interval for (const auto& controlPoint : allControlPoints) { if (InsideControlPoint(date, controlPoint)) { // return the fitting control point that contains the date from the given data node return controlPoint; } } return SemanticTypes::ControlPoint(); } -mitk::SemanticTypes::ControlPoint mitk::ExtendClosestControlPoint(const mitk::DataNode* dataNode, std::vector& allControlPoints) +mitk::SemanticTypes::ControlPoint mitk::ExtendClosestControlPoint(const DataNode* dataNode, std::vector& allControlPoints) { SemanticTypes::Date dateFromDataNode = GetDICOMDateFromDataNode(dataNode); if (0 == dateFromDataNode.year) { MITK_INFO << "Could not deduce a valid date from the given data node."; return SemanticTypes::ControlPoint(); } return ExtendClosestControlPoint(dateFromDataNode, allControlPoints); } mitk::SemanticTypes::ControlPoint mitk::ExtendClosestControlPoint(const SemanticTypes::Date& date, std::vector& allControlPoints) { // sort the vector of control points for easier lookup std::sort(allControlPoints.begin(), allControlPoints.end()); // new date does not fit into an existing control point // check if the date of the data node is close to an already existing control point std::vector::const_iterator it; for (it = allControlPoints.begin(); it != allControlPoints.end(); ++it) { if (date < it->startPoint) { break; // cannot be inside this control point; therefore has to be greater ("newer") than 'it->endPoint' } } SemanticTypes::ControlPoint nextControlPoint; SemanticTypes::ControlPoint previousControlPoint; SemanticTypes::Date nextDate; SemanticTypes::Date previousDate; if (it == allControlPoints.begin()) { // new date is smaller ("older") than the smallest already existing control point nextControlPoint = *it; nextDate = it->startPoint; } else if (it != allControlPoints.end()) { // new date is greater ("newer") than the smallest already existing control point, // but smaller ("older") than the greatest already existing control point nextControlPoint = *it; nextDate = nextControlPoint.startPoint; previousControlPoint = *(--it); previousDate = previousControlPoint.endPoint; } else { // new date is greater ("newer") than the greatest already existing control point previousControlPoint = *(--it); previousDate = previousControlPoint.endPoint; } // test distance to next and previous time period double distanceToNextTimePeriod = CalculateDistanceInDays(nextDate, date); double distanceToPreviousTimePeriod = CalculateDistanceInDays(previousDate, date); SemanticTypes::ControlPoint closestControlPoint; double closestDistanceInDays = 0.0; if (distanceToNextTimePeriod < distanceToPreviousTimePeriod) { // date is closer to the next control point closestControlPoint = nextControlPoint; closestDistanceInDays = distanceToNextTimePeriod; } else { // date is closer to the previous control point closestControlPoint = previousControlPoint; closestDistanceInDays = distanceToPreviousTimePeriod; } // extend the control point or create a control point double THRESHOLD_DISTANCE_IN_DAYS = 30.0; if (std::abs(closestDistanceInDays) < THRESHOLD_DISTANCE_IN_DAYS) { // extend the closest control point ExtendControlPoint(closestControlPoint, date); return closestControlPoint; } return SemanticTypes::ControlPoint(); } mitk::SemanticTypes::Date GetStartPoint(const std::vector& dataNodes) { // lambda function for "less than" comparison of two dates of two data nodes auto minLambda = [](const mitk::DataNode::Pointer& left, const mitk::DataNode::Pointer& right) { return GetDICOMDateFromDataNode(left) < GetDICOMDateFromDataNode(right); }; // find the data node with the smallest date value and return this earliest date as the start point auto minElement = std::min_element(dataNodes.begin(), dataNodes.end(), minLambda); return GetDICOMDateFromDataNode(*minElement); } mitk::SemanticTypes::Date GetEndPoint(const std::vector& dataNodes) { // lambda function for "greater than" comparison of two dates of two data nodes auto maxLambda = [](const mitk::DataNode::Pointer& left, const mitk::DataNode::Pointer& right) { return GetDICOMDateFromDataNode(left) > GetDICOMDateFromDataNode(right); }; // find the data node with the largest date value and return this latest date as the end point auto maxElement = std::max_element(dataNodes.begin(), dataNodes.end(), maxLambda); return GetDICOMDateFromDataNode(*maxElement); } void ExtendControlPoint(mitk::SemanticTypes::ControlPoint& controlPoint, mitk::SemanticTypes::Date date) { if (controlPoint.startPoint > date) { // date has to extend the older start point of the control point (move start point to the earlier date) controlPoint.startPoint.year = date.year; controlPoint.startPoint.month = date.month; controlPoint.startPoint.day = date.day; } else if (controlPoint.endPoint < date) { // date has to extend the newer end point of the control point (move end point to the later date) controlPoint.endPoint.year = date.year; controlPoint.endPoint.month = date.month; controlPoint.endPoint.day = date.day; } // else: date is inside the control point } double CalculateDistanceInDays(mitk::SemanticTypes::Date leftDate, mitk::SemanticTypes::Date rightDate) { // compute distance here std::tm leftTimeStructure = { 0, 0, 0, leftDate.day, leftDate.month - 1, leftDate.year - 1900 }; std::tm rightTimeStructure = { 0, 0, 0, rightDate.day, rightDate.month - 1, rightDate.year - 1900 }; time_t leftTime = mktime(&leftTimeStructure); time_t rightTime = mktime(&rightTimeStructure); if (leftTime == -1 || rightTime == -1) { // date is not initialized, no difference can be computed return std::numeric_limits::max(); } double secondsPerDay = 60 * 60 * 24; double timeDifferenceInDays = std::difftime(leftTime, rightTime) / secondsPerDay; return timeDifferenceInDays; } diff --git a/Modules/SemanticRelations/src/mitkLesionManager.cpp b/Modules/SemanticRelations/src/mitkLesionManager.cpp index c887c275bf..c15c54b016 100644 --- a/Modules/SemanticRelations/src/mitkLesionManager.cpp +++ b/Modules/SemanticRelations/src/mitkLesionManager.cpp @@ -1,95 +1,144 @@ /*=================================================================== 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 "mitkLesionManager.h" +#include "mitkSemanticRelationException.h" #include "mitkUIDGeneratorBoost.h" +bool GetLesionPresence(const mitk::SemanticTypes::CaseID& caseID, std::shared_ptr semanticRelations, const mitk::SemanticTypes::Lesion& lesion, const mitk::SemanticTypes::ControlPoint& controlPoint); + +double GetLesionVolume(const mitk::SemanticTypes::CaseID& caseID, std::shared_ptr semanticRelations, const mitk::SemanticTypes::Lesion& lesion, const mitk::SemanticTypes::ControlPoint& controlPoint); + mitk::SemanticTypes::Lesion mitk::GenerateNewLesion(const std::string& lesionClassType/* = ""*/) { mitk::SemanticTypes::Lesion lesion; lesion.UID = mitk::UIDGeneratorBoost::GenerateUID(); lesion.name = lesion.UID; lesion.lesionClass = mitk::SemanticTypes::LesionClass(); lesion.lesionClass.UID = mitk::UIDGeneratorBoost::GenerateUID(); lesion.lesionClass.classType = lesionClassType; return lesion; } mitk::SemanticTypes::LesionClass mitk::GenerateNewLesionClass(const std::string& lesionClassType/* = ""*/) { mitk::SemanticTypes::LesionClass lesionClass; lesionClass.UID = mitk::UIDGeneratorBoost::GenerateUID(); lesionClass.classType = lesionClassType; return lesionClass; } mitk::SemanticTypes::Lesion mitk::GetLesionByUID(const SemanticTypes::ID& lesionUID, const std::vector& allLesions) { auto lambda = [&lesionUID](const SemanticTypes::Lesion& currentLesion) { return currentLesion.UID == lesionUID; }; const auto existingLesion = std::find_if(allLesions.begin(), allLesions.end(), lambda); mitk::SemanticTypes::Lesion lesion; if (existingLesion != allLesions.end()) { lesion = *existingLesion; } return lesion; } mitk::SemanticTypes::LesionClass mitk::FindExistingLesionClass(const std::string& lesionClassType, const std::vector& allLesionClasses) { auto lambda = [&lesionClassType](const SemanticTypes::LesionClass& currentLesionClass) { return currentLesionClass.classType == lesionClassType; }; const auto existingLesionClass = std::find_if(allLesionClasses.begin(), allLesionClasses.end(), lambda); mitk::SemanticTypes::LesionClass lesionClass; if (existingLesionClass != allLesionClasses.end()) { lesionClass = *existingLesionClass; } return lesionClass; } -void mitk::GenerateAdditionalLesionData(mitk::LesionData& lesionData, const SemanticTypes::CaseID& caseID, std::shared_ptr semanticRelations) +void mitk::GenerateAdditionalLesionData(LesionData& lesionData, const SemanticTypes::CaseID& caseID, std::shared_ptr semanticRelations) { std::vector lesionPresence; std::vector lesionVolume; - mitk::SemanticTypes::Lesion lesion = lesionData.GetLesion(); - std::vector controlPoints = semanticRelations->GetAllControlPointsOfCase(caseID); - for (const auto& controlPoint : controlPoints) + SemanticTypes::Lesion lesion = lesionData.GetLesion(); + bool presence = false; + double volume = 0.0; + try { - bool presence = semanticRelations->GetLesionPresence(caseID, lesion, controlPoint); - lesionPresence.push_back(presence); - - double volume = semanticRelations->GetLesionVolume(caseID, lesion, controlPoint); - lesionVolume.push_back(volume); + std::vector controlPoints = semanticRelations->GetAllControlPointsOfCase(caseID); + for (const auto& controlPoint : controlPoints) + { + presence = GetLesionPresence(caseID, semanticRelations, lesion, controlPoint); + lesionPresence.push_back(presence); + + volume = GetLesionVolume(caseID, semanticRelations, lesion, controlPoint); + lesionVolume.push_back(volume); + } + } + catch (const mitk::SemanticRelationException&) + { + return; } lesionData.SetLesionPresence(lesionPresence); lesionData.SetLesionVolume(lesionVolume); } + +bool GetLesionPresence(const mitk::SemanticTypes::CaseID& caseID, std::shared_ptr semanticRelations, const mitk::SemanticTypes::Lesion& lesion, const mitk::SemanticTypes::ControlPoint& controllPoint) +{ + try + { + mitk::SemanticRelations::DataNodeVector allImagesOfLesion = semanticRelations->GetAllImagesOfLesion(caseID, lesion); + for (const auto& image : allImagesOfLesion) + { + auto imageControlPoint = semanticRelations->GetControlPointOfImage(image); + if (imageControlPoint == controllPoint) + { + return true; + } + } + } + catch (const mitk::SemanticRelationException&) + { + return false; + } + + return false; +} + +double GetLesionVolume(const mitk::SemanticTypes::CaseID& caseID, std::shared_ptr semanticRelations, const mitk::SemanticTypes::Lesion& lesion, const mitk::SemanticTypes::ControlPoint& controlPoint) +{ + bool presence = GetLesionPresence(caseID, semanticRelations, lesion, controlPoint); + if (presence) + { + return 1.0; + } + else + { + return 0.0; + } +} diff --git a/Modules/SemanticRelations/src/mitkSemanticRelations.cpp b/Modules/SemanticRelations/src/mitkSemanticRelations.cpp index a593c169d7..b9f79eac31 100644 --- a/Modules/SemanticRelations/src/mitkSemanticRelations.cpp +++ b/Modules/SemanticRelations/src/mitkSemanticRelations.cpp @@ -1,1189 +1,1146 @@ /*=================================================================== 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 "mitkNodePredicates.h" #include "mitkSemanticRelations.h" #include "mitkSemanticRelationException.h" -#include "mitkNodePredicates.h" #include "mitkUIDGeneratorBoost.h" // multi label module #include // c++ #include std::vector mitk::SemanticRelations::m_ObserverVector; mitk::SemanticRelations::SemanticRelations(DataStorage::Pointer dataStorage) : m_DataStorage(dataStorage) { m_RelationStorage = std::make_shared(); m_RelationStorage->SetDataStorage(m_DataStorage); } mitk::SemanticRelations::~SemanticRelations() { // nothing here } void mitk::SemanticRelations::AddObserver(ISemanticRelationsObserver* observer) { std::vector::iterator existingObserver = std::find(m_ObserverVector.begin(), m_ObserverVector.end(), observer); if (existingObserver != m_ObserverVector.end()) { // no need to add the already existing observer return; } m_ObserverVector.push_back(observer); } void mitk::SemanticRelations::RemoveObserver(ISemanticRelationsObserver* observer) { m_ObserverVector.erase(std::remove(m_ObserverVector.begin(), m_ObserverVector.end(), observer), m_ObserverVector.end()); } /************************************************************************/ /* functions to get instances / attributes */ /************************************************************************/ mitk::SemanticRelations::LesionVector mitk::SemanticRelations::GetAllLesionsOfCase(const SemanticTypes::CaseID& caseID) const { return m_RelationStorage->GetAllLesionsOfCase(caseID); } mitk::SemanticRelations::LesionVector mitk::SemanticRelations::GetAllLesionsOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const { LesionVector allLesions = GetAllLesionsOfCase(caseID); // filter the lesions: use only those, where the associated data is connected to image data that refers to the given control point using a lambda function auto lambda = [&caseID, &controlPoint, this](const SemanticTypes::Lesion& lesion) { return !ControlPointContainsLesion(caseID, lesion, controlPoint); }; allLesions.erase(std::remove_if(allLesions.begin(), allLesions.end(), lambda), allLesions.end()); return allLesions; } mitk::SemanticRelations::LesionClassVector mitk::SemanticRelations::GetAllLesionClassesOfCase(const SemanticTypes::CaseID& caseID) const { LesionVector allLesionsOfCase = GetAllLesionsOfCase(caseID); LesionClassVector allLesionClassesOfCase; for (const auto& lesion : allLesionsOfCase) { allLesionClassesOfCase.push_back(lesion.lesionClass); } // remove duplicate entries auto lessThan = [](const SemanticTypes::LesionClass& lesionClassL, const SemanticTypes::LesionClass& lesionClassR) { return lesionClassL.UID < lesionClassR.UID; }; auto equal = [](const SemanticTypes::LesionClass& lesionClassL, const SemanticTypes::LesionClass& lesionClassR) { return lesionClassL.UID == lesionClassR.UID; }; std::sort(allLesionClassesOfCase.begin(), allLesionClassesOfCase.end(), lessThan); allLesionClassesOfCase.erase(std::unique(allLesionClassesOfCase.begin(), allLesionClassesOfCase.end(), equal), allLesionClassesOfCase.end()); return allLesionClassesOfCase; } mitk::SemanticRelations::LesionVector mitk::SemanticRelations::GetAllLesionsInImage(const DataNode* imageNode) const { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid image data node."; } if (m_DataStorage.IsNull()) { mitkThrowException(SemanticRelationException) << "Not a valid data storage."; } LesionVector allLesionsInImage; // get child nodes of the current node with the segmentation predicate DataStorage::SetOfObjects::ConstPointer segmentationNodes = m_DataStorage->GetDerivations(imageNode, NodePredicates::GetSegmentationPredicate(), false); for (auto it = segmentationNodes->Begin(); it != segmentationNodes->End(); ++it) { DataNode* segmentationNode = it->Value(); try { SemanticTypes::Lesion representedLesion = GetRepresentedLesion(segmentationNode); allLesionsInImage.push_back(representedLesion); } catch (const SemanticRelationException&) { continue; } } return allLesionsInImage; } mitk::SemanticTypes::Lesion mitk::SemanticRelations::GetRepresentedLesion(const DataNode* segmentationNode) const { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(segmentationNode); SemanticTypes::ID segmentationID = GetIDFromDataNode(segmentationNode); SemanticTypes::Lesion representedLesion = m_RelationStorage->GetRepresentedLesion(caseID, segmentationID); if (representedLesion.UID.empty()) { mitkThrowException(SemanticRelationException) << "Could not find a represented lesion instance for the given segmentation node " << segmentationNode->GetName(); } else { return representedLesion; } } -bool mitk::SemanticRelations::GetLesionPresence(const SemanticTypes::CaseID& caseID, const mitk::SemanticTypes::Lesion& lesion, const mitk::SemanticTypes::ControlPoint& controllPoint) const -{ - try - { - mitk::SemanticRelations::DataNodeVector allImagesOfLesion = GetAllImagesOfLesion(caseID, lesion); - for (const auto& image : allImagesOfLesion) - { - auto imageControlPoint = GetControlPointOfImage(image); - if (imageControlPoint == controllPoint) - { - return true; - } - } - } - catch (const mitk::SemanticRelationException&) - { - return false; - } - - return false; -} - -double mitk::SemanticRelations::GetLesionVolume(const SemanticTypes::CaseID& caseID, const mitk::SemanticTypes::Lesion& lesion, const mitk::SemanticTypes::ControlPoint& controllPoint) const -{ - try - { - mitk::SemanticRelations::DataNodeVector allImagesOfLesion = GetAllImagesOfLesion(caseID, lesion); - for (const auto& image : allImagesOfLesion) - { - auto imageControlPoint = GetControlPointOfImage(image); - if (imageControlPoint == controllPoint) - { - return 1.0; - } - } - } - catch (const mitk::SemanticRelationException&) - { - return 0.0; - } - - return 0.0; -} - bool mitk::SemanticRelations::IsRepresentingALesion(const DataNode* segmentationNode) const { try { SemanticTypes::Lesion representedLesion = GetRepresentedLesion(segmentationNode); return true; } catch (const Exception&) { return false; } } bool mitk::SemanticRelations::InstanceExists(const DataNode* dataNode) const { try { SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(dataNode); SemanticTypes::ID dataNodeID = GetIDFromDataNode(dataNode); if (mitk::NodePredicates::GetImagePredicate()->CheckNode(dataNode)) { std::vector allImageIDsOfCase = m_RelationStorage->GetAllImageIDsOfCase(caseID); return std::find(allImageIDsOfCase.begin(), allImageIDsOfCase.end(), dataNodeID) != allImageIDsOfCase.end(); } else if (mitk::NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode)) { std::vector allSegmentationIDsOfCase = m_RelationStorage->GetAllSegmentationIDsOfCase(caseID); return std::find(allSegmentationIDsOfCase.begin(), allSegmentationIDsOfCase.end(), dataNodeID) != allSegmentationIDsOfCase.end(); } else { return false; } } catch (const SemanticRelationException&) { return false; } } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllSegmentationsOfCase(const SemanticTypes::CaseID& caseID) const { if (m_DataStorage.IsNull()) { mitkThrowException(SemanticRelationException) << "Not a valid data storage."; } return m_RelationStorage->GetAllSegmentationsOfCase(caseID); } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllSegmentationsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const { if (m_DataStorage.IsNull()) { mitkThrowException(SemanticRelationException) << "Not a valid data storage."; } if (InstanceExists(caseID, lesion)) { // lesion exists, retrieve all case segmentations from the storage DataNodeVector allSegmentationsOfLesion = GetAllSegmentationsOfCase(caseID); // filter all segmentations: check for semantic relation with the given lesion using a lambda function auto lambda = [&lesion, this](DataNode::Pointer segmentation) { try { SemanticTypes::Lesion representedLesion = GetRepresentedLesion(segmentation); return lesion.UID != representedLesion.UID; } catch (const SemanticRelationException&) { return true; } }; allSegmentationsOfLesion.erase(std::remove_if(allSegmentationsOfLesion.begin(), allSegmentationsOfLesion.end(), lambda), allSegmentationsOfLesion.end()); return allSegmentationsOfLesion; } else { mitkThrowException(SemanticRelationException) << "Could not find an existing lesion instance for the given caseID " << caseID << " and lesion " << lesion.UID << "."; } } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllImagesOfCase(const SemanticTypes::CaseID& caseID) const { if (m_DataStorage.IsNull()) { mitkThrowException(SemanticRelationException) << "Not a valid data storage."; } return m_RelationStorage->GetAllImagesOfCase(caseID); } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllImagesOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const { if (m_DataStorage.IsNull()) { mitkThrowException(SemanticRelationException) << "Not a valid data storage."; } DataNodeVector allImagesOfLesion; // 1. get all segmentations that define the lesion // 2. retrieve the parent node (source) of the found segmentation node DataNodeVector allSegmentationsOfLesion = GetAllSegmentationsOfLesion(caseID, lesion); for (const auto& segmentationNode : allSegmentationsOfLesion) { // get parent node of the current segmentation node with the node predicate DataStorage::SetOfObjects::ConstPointer parentNodes = m_DataStorage->GetSources(segmentationNode, NodePredicates::GetImagePredicate(), false); for (auto it = parentNodes->Begin(); it != parentNodes->End(); ++it) { DataNode::Pointer dataNode = it->Value(); allImagesOfLesion.push_back(it->Value()); } } std::sort(allImagesOfLesion.begin(), allImagesOfLesion.end()); allImagesOfLesion.erase(std::unique(allImagesOfLesion.begin(), allImagesOfLesion.end()), allImagesOfLesion.end()); return allImagesOfLesion; } bool mitk::SemanticRelations::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const { LesionVector allLesions = GetAllLesionsOfCase(caseID); // filter all lesions: check for equality with the given lesion using a lambda function auto lambda = [&lesion](const SemanticTypes::Lesion& currentLesion) { return currentLesion.UID == lesion.UID; }; const auto existingLesion = std::find_if(allLesions.begin(), allLesions.end(), lambda); if (existingLesion != allLesions.end()) { return true; } else { return false; } } mitk::SemanticRelations::ControlpointVector mitk::SemanticRelations::GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID) const { return m_RelationStorage->GetAllControlPointsOfCase(caseID); } mitk::SemanticRelations::ControlpointVector mitk::SemanticRelations::GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const { ControlpointVector allControlPoints = GetAllControlPointsOfCase(caseID); // filter the control points: use only those, where the associated image data has a segmentation that refers to the given lesion using a lambda function auto lambda = [&caseID, &lesion, this](const SemanticTypes::ControlPoint& controlPoint) { return !ControlPointContainsLesion(caseID, lesion, controlPoint); }; allControlPoints.erase(std::remove_if(allControlPoints.begin(), allControlPoints.end(), lambda), allControlPoints.end()); return allControlPoints; } mitk::SemanticRelations::ControlpointVector mitk::SemanticRelations::GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) const { ControlpointVector allControlPoints = GetAllControlPointsOfCase(caseID); // filter the control points: use only those, where the associated image data refers to the given information type using a lambda function auto lambda = [&caseID, &informationType, this](const SemanticTypes::ControlPoint& controlPoint) { return !ControlPointContainsInformationType(caseID, informationType, controlPoint); }; allControlPoints.erase(std::remove_if(allControlPoints.begin(), allControlPoints.end(), lambda), allControlPoints.end()); return allControlPoints; } mitk::SemanticTypes::ControlPoint mitk::SemanticRelations::GetControlPointOfImage(const DataNode* imageNode) const { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); SemanticTypes::ID dataNodeID = GetIDFromDataNode(imageNode); return m_RelationStorage->GetControlPointOfImage(caseID, dataNodeID); } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllImagesOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const { if (m_DataStorage.IsNull()) { mitkThrow() << "Not a valid data storage."; } if (InstanceExists(caseID, controlPoint)) { // control point exists, retrieve all images from the storage DataNodeVector allImagesOfControlPoint = GetAllImagesOfCase(caseID); // filter all images to remove the ones with a different control point using a lambda function auto lambda = [&controlPoint, this](DataNode::Pointer imageNode) { return controlPoint.UID != GetControlPointOfImage(imageNode).UID; }; allImagesOfControlPoint.erase(std::remove_if(allImagesOfControlPoint.begin(), allImagesOfControlPoint.end(), lambda), allImagesOfControlPoint.end()); return allImagesOfControlPoint; } else { mitkThrowException(SemanticRelationException) << "Could not find an existing control point instance for the given caseID " << caseID << " and control point " << controlPoint.UID << "."; } } bool mitk::SemanticRelations::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const { ControlpointVector allControlPoints = GetAllControlPointsOfCase(caseID); // filter all control points: check for equality with the given control point using a lambda function auto lambda = [&controlPoint](const SemanticTypes::ControlPoint& currentControlPoint) { return currentControlPoint.UID == controlPoint.UID; }; const auto existingControlPoint = std::find_if(allControlPoints.begin(), allControlPoints.end(), lambda); if (existingControlPoint != allControlPoints.end()) { return true; } else { return false; } } mitk::SemanticRelations::InformationTypeVector mitk::SemanticRelations::GetAllInformationTypesOfCase(const SemanticTypes::CaseID& caseID) const { return m_RelationStorage->GetAllInformationTypesOfCase(caseID); } mitk::SemanticRelations::InformationTypeVector mitk::SemanticRelations::GetAllInformationTypesOfCase(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) const { InformationTypeVector allInformationTypes = GetAllInformationTypesOfCase(caseID); // filter the information types: use only those, where the associated data refers to the given control point using a lambda function auto lambda = [&caseID, &controlPoint, this](const SemanticTypes::InformationType& informationType) { return !ControlPointContainsInformationType(caseID, informationType, controlPoint); }; allInformationTypes.erase(std::remove_if(allInformationTypes.begin(), allInformationTypes.end(), lambda), allInformationTypes.end()); return allInformationTypes; } mitk::SemanticTypes::InformationType mitk::SemanticRelations::GetInformationTypeOfImage(const DataNode* imageNode) const { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid image data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); SemanticTypes::ID imageID = GetIDFromDataNode(imageNode); return m_RelationStorage->GetInformationTypeOfImage(caseID, imageID); } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllImagesOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) const { if (m_DataStorage.IsNull()) { mitkThrow() << "Not a valid data storage."; } if (InstanceExists(caseID, informationType)) { // information type exists, retrieve all images from the storage DataNodeVector allImagesOfInformationType = GetAllImagesOfCase(caseID); // filter all images to remove the ones with a different information type using a lambda function auto lambda = [&informationType, this](DataNode::Pointer imageNode) { return informationType != GetInformationTypeOfImage(imageNode); }; allImagesOfInformationType.erase(std::remove_if(allImagesOfInformationType.begin(), allImagesOfInformationType.end(), lambda), allImagesOfInformationType.end()); return allImagesOfInformationType; } else { mitkThrowException(SemanticRelationException) << "Could not find an existing information type for the given caseID " << caseID << " and information type " << informationType; } } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllSpecificImages(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const { if (m_DataStorage.IsNull()) { mitkThrow() << "Not a valid data storage."; } if (InstanceExists(caseID, controlPoint)) { if (InstanceExists(caseID, informationType)) { // control point exists, information type exists, retrieve all images from the storage DataNodeVector allImagesOfCase = GetAllImagesOfCase(caseID); // filter all images to remove the ones with a different control point and information type using a lambda function auto lambda = [&controlPoint, &informationType, this](DataNode::Pointer imageNode) { return (informationType != GetInformationTypeOfImage(imageNode)) || (controlPoint != GetControlPointOfImage(imageNode)); }; allImagesOfCase.erase(std::remove_if(allImagesOfCase.begin(), allImagesOfCase.end(), lambda), allImagesOfCase.end()); return allImagesOfCase; } else { mitkThrowException(SemanticRelationException) << "Could not find an existing information type for the given caseID " << caseID << " and information type " << informationType; } } else { mitkThrowException(SemanticRelationException) << "Could not find an existing control point for the given caseID " << caseID << " and control point " << controlPoint.UID; } } mitk::SemanticRelations::DataNodeVector mitk::SemanticRelations::GetAllSpecificSegmentations(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const { if (m_DataStorage.IsNull()) { mitkThrow() << "Not a valid data storage."; } DataNodeVector allSpecificImages = GetAllSpecificImages(caseID, controlPoint, informationType); DataNodeVector allSpecificSegmentations; for (const auto& imageNode : allSpecificImages) { DataStorage::SetOfObjects::ConstPointer segmentationNodes = m_DataStorage->GetDerivations(imageNode, NodePredicates::GetSegmentationPredicate(), false); for (auto it = segmentationNodes->Begin(); it != segmentationNodes->End(); ++it) { allSpecificSegmentations.push_back(it->Value()); } } return allSpecificSegmentations; } bool mitk::SemanticRelations::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType) const { InformationTypeVector allInformationTypes = GetAllInformationTypesOfCase(caseID); // filter all information types: check for equality with the given information type using a lambda function auto lambda = [&informationType](const SemanticTypes::InformationType& currentInformationType) { return currentInformationType == informationType; }; const auto existingInformationType = std::find_if(allInformationTypes.begin(), allInformationTypes.end(), lambda); if (existingInformationType != allInformationTypes.end()) { return true; } else { return false; } } std::vector mitk::SemanticRelations::GetAllCaseIDs() const { return m_RelationStorage->GetAllCaseIDs(); } /************************************************************************/ /* functions to add / remove instances / attributes */ /************************************************************************/ void mitk::SemanticRelations::AddImage(const DataNode* imageNode) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } // continue with a valid data node SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); SemanticTypes::ID nodeID = GetIDFromDataNode(imageNode); m_RelationStorage->AddCase(caseID); m_RelationStorage->AddImage(caseID, nodeID); SemanticTypes::InformationType informationType = GetDICOMModalityFromDataNode(imageNode); AddInformationTypeToImage(imageNode, informationType); // find the correct control point for this image std::vector allControlPoints = GetAllControlPointsOfCase(caseID); if (allControlPoints.empty()) { // no stored control point // create a new control point for the image data SemanticTypes::ControlPoint newControlPoint = GenerateControlPoint(imageNode); AddControlPointAndLinkData(imageNode, newControlPoint); NotifyObserver(caseID); return; } // some control points already exist - find a control point where the date of the data node fits in SemanticTypes::ControlPoint fittingControlPoint = FindFittingControlPoint(imageNode, allControlPoints); if (fittingControlPoint.UID.empty()) { // did not find a fitting control point, although some control points already exist // need to see if a close control point can be extended SemanticTypes::ControlPoint extendedControlPoint = ExtendClosestControlPoint(imageNode, allControlPoints); if (extendedControlPoint.UID.empty()) { // closest control point can not be extended // create a new control point for the image data SemanticTypes::ControlPoint newControlPoint = GenerateControlPoint(imageNode); AddControlPointAndLinkData(imageNode, newControlPoint); } else { // found a control point that was extended OverwriteControlPointAndLinkData(imageNode, extendedControlPoint); } } else { // found a fitting control point LinkDataToControlPoint(imageNode, fittingControlPoint); } NotifyObserver(caseID); } void mitk::SemanticRelations::RemoveImage(const DataNode* imageNode) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } // continue with a valid data node SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); SemanticTypes::ID nodeID = GetIDFromDataNode(imageNode); RemoveInformationTypeFromImage(imageNode); UnlinkDataFromControlPoint(imageNode); m_RelationStorage->RemoveImage(caseID, nodeID); NotifyObserver(caseID); } void mitk::SemanticRelations::AddLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { if (InstanceExists(caseID, lesion)) { mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to add already exists for the given case."; } else { m_RelationStorage->AddLesion(caseID, lesion); NotifyObserver(caseID); } } void mitk::SemanticRelations::OverwriteLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { if (InstanceExists(caseID, lesion)) { m_RelationStorage->OverwriteLesion(caseID, lesion); NotifyObserver(caseID); } else { mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to overwrite does not exist for the given case."; } } void mitk::SemanticRelations::AddLesionAndLinkSegmentation(const DataNode* segmentationNode, const SemanticTypes::Lesion& lesion) { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(segmentationNode); AddLesion(caseID, lesion); LinkSegmentationToLesion(segmentationNode, lesion); NotifyObserver(caseID); } void mitk::SemanticRelations::RemoveLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) { if (InstanceExists(caseID, lesion)) { DataNodeVector allSegmentationsOfLesion = GetAllSegmentationsOfLesion(caseID, lesion); if (allSegmentationsOfLesion.empty()) { // no more segmentations are linked to the specific lesion // the lesion can be removed from the storage m_RelationStorage->RemoveLesion(caseID, lesion); NotifyObserver(caseID); } else { mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to remove is still referred to by a segmentation node. Lesion will not be removed."; } } else { mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to remove does not exist for the given case."; } } void mitk::SemanticRelations::AddSegmentation(const DataNode* segmentationNode, const DataNode* parentNode) { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } if (nullptr == parentNode) { mitkThrowException(SemanticRelationException) << "Not a valid parent data node."; } // continue with a valid data node SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(segmentationNode); SemanticTypes::ID segmentationNodeID = GetIDFromDataNode(segmentationNode); SemanticTypes::ID parentNodeID = GetIDFromDataNode(parentNode); m_RelationStorage->AddSegmentation(caseID, segmentationNodeID, parentNodeID); NotifyObserver(caseID); } void mitk::SemanticRelations::LinkSegmentationToLesion(const DataNode* segmentationNode, const SemanticTypes::Lesion& lesion) { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(segmentationNode); if (InstanceExists(caseID, lesion)) { SemanticTypes::ID segmentationID = GetIDFromDataNode(segmentationNode); m_RelationStorage->LinkSegmentationToLesion(caseID, segmentationID, lesion); NotifyObserver(caseID); } else { mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to link does not exist for the given case."; } } void mitk::SemanticRelations::UnlinkSegmentationFromLesion(const DataNode* segmentationNode) { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(segmentationNode); SemanticTypes::ID segmentationID = GetIDFromDataNode(segmentationNode); m_RelationStorage->UnlinkSegmentationFromLesion(caseID, segmentationID); NotifyObserver(caseID); } void mitk::SemanticRelations::RemoveSegmentation(const DataNode* segmentationNode) { if (nullptr == segmentationNode) { mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node."; } // continue with a valid data node SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(segmentationNode); SemanticTypes::ID segmentationNodeID = GetIDFromDataNode(segmentationNode); m_RelationStorage->RemoveSegmentation(caseID, segmentationNodeID); NotifyObserver(caseID); } void mitk::SemanticRelations::SetControlPointFromDate(const DataNode* dataNode, const SemanticTypes::Date& date) { if (nullptr == dataNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(dataNode); // store the current control point to relink it, if anything goes wrong mitk::SemanticTypes::ControlPoint originalControlPoint = GetControlPointOfImage(dataNode); // unlink the data, that is about to receive a new date // this is needed in order to not extend a single control point, to which the selected node is currently linked UnlinkDataFromControlPoint(dataNode); ControlpointVector allControlPoints = GetAllControlPointsOfCase(caseID); if (!allControlPoints.empty()) { // need to check if an already existing control point fits/contains the user control point SemanticTypes::ControlPoint fittingControlPoint = FindFittingControlPoint(date, allControlPoints); if (!fittingControlPoint.UID.empty()) { try { // found a fitting control point LinkDataToControlPoint(dataNode, fittingControlPoint, false); } catch (const SemanticRelationException&) { try { // link to the original control point LinkDataToControlPoint(dataNode, originalControlPoint, false); } catch (const SemanticRelationException&) { mitkThrowException(SemanticRelationException) << "The data can not be linked. Inconsistency in the semantic relations storage assumed."; } } return; } // did not find a fitting control point, although some control points already exist // need to check if a close control point can be found and extended SemanticTypes::ControlPoint extendedControlPoint = ExtendClosestControlPoint(date, allControlPoints); if (!extendedControlPoint.UID.empty()) { try { // found and extended a close control point OverwriteControlPointAndLinkData(dataNode, extendedControlPoint, false); } catch (const SemanticRelationException&) { try { // link to the original control point LinkDataToControlPoint(dataNode, originalControlPoint, false); } catch (const SemanticRelationException&) { mitkThrowException(SemanticRelationException) << "The data can not be linked Inconsistency in the semantic relations storage assumed."; } } return; } } // generate a control point from the user-given date SemanticTypes::ControlPoint controlPointFromUserDate = GenerateControlPoint(date); try { AddControlPointAndLinkData(dataNode, controlPointFromUserDate, false); } catch (const SemanticRelationException&) { try { // link to the original control point LinkDataToControlPoint(dataNode, originalControlPoint, false); } catch (const SemanticRelationException&) { mitkThrowException(SemanticRelationException) << "The data can not be linked. Inconsistency in the semantic relations storage assumed."; } } NotifyObserver(caseID); } void mitk::SemanticRelations::AddControlPointAndLinkData(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence) { if (nullptr == dataNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(dataNode); if (InstanceExists(caseID, controlPoint)) { mitkThrowException(SemanticRelationException) << "The control point " << controlPoint.UID << " to add already exists for the given case. \n Use 'LinkDataToControlPoint' instead."; } // control point does not already exist bool contained = CheckContainingControlPoint(caseID, controlPoint); if (contained) { mitkThrowException(SemanticRelationException) << "The control point " << controlPoint.UID << " to add is already contained in an existing control point."; } // control point is not already contained in an existing control point if (checkConsistence) { // to check the consistency, the control point manager checks, if the date extracted from the data node is inside the given control point bool insideControlPoint = InsideControlPoint(dataNode, controlPoint); if (!insideControlPoint) { mitkThrowException(SemanticRelationException) << "The control point " << controlPoint.UID << " to add does not contain the date of the given data node."; } } m_RelationStorage->AddControlPoint(caseID, controlPoint); LinkDataToControlPoint(dataNode, controlPoint, checkConsistence); } void mitk::SemanticRelations::OverwriteControlPointAndLinkData(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence) { if (nullptr == dataNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(dataNode); ControlpointVector allControlPoints = GetAllControlPointsOfCase(caseID); const auto existingControlPoint = std::find_if(allControlPoints.begin(), allControlPoints.end(), [&controlPoint](const SemanticTypes::ControlPoint& currentControlPoint) { return currentControlPoint.UID == controlPoint.UID; }); if (existingControlPoint != allControlPoints.end()) { // control point does already exist if (checkConsistence) { // to check the consistency, the control point manager checks, if the date extracted from the data node is inside the given control point bool insideControlPoint = InsideControlPoint(dataNode, controlPoint); if (!insideControlPoint) { mitkThrowException(SemanticRelationException) << "The overwriting control point " << controlPoint.UID << " does not contain the date of the given data node."; } } bool sameStartPoint = controlPoint.startPoint == (*existingControlPoint).startPoint; bool sameEndPoint = controlPoint.endPoint == (*existingControlPoint).endPoint; if (!sameStartPoint && !sameEndPoint) { mitkThrowException(SemanticRelationException) << "The overwriting control point " << controlPoint.UID << " differs in the start date and in the end date from the original control point."; } if (sameStartPoint && sameEndPoint) { mitkThrowException(SemanticRelationException) << "The overwriting control point " << controlPoint.UID << " does not differ from the original control point."; } bool overlapping = CheckOverlappingControlPoint(caseID, controlPoint); if (overlapping) { mitkThrowException(SemanticRelationException) << "The overwriting control point " << controlPoint.UID << " overlaps with an already existing control point"; } else { m_RelationStorage->OverwriteControlPoint(caseID, controlPoint); LinkDataToControlPoint(dataNode, controlPoint, checkConsistence); } } else { mitkThrowException(SemanticRelationException) << "The control point " << controlPoint.UID << " to overwrite does not exist for the given case. \n Use 'AddControlPointAndLinkData' instead."; } } void mitk::SemanticRelations::LinkDataToControlPoint(const DataNode* dataNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence) { if (nullptr == dataNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(dataNode); if (InstanceExists(caseID, controlPoint)) { SemanticTypes::ID dataID = GetIDFromDataNode(dataNode); // control point does already exist if (checkConsistence) { // to check the consistency, the control point manager checks, if the date extracted from the data node is inside the given control point bool insideControlPoint = InsideControlPoint(dataNode, controlPoint); if (!insideControlPoint) { mitkThrowException(SemanticRelationException) << "The data to link does not lie inside the given control point " << controlPoint.UID << " ."; } } m_RelationStorage->LinkDataToControlPoint(caseID, dataID, controlPoint); } else { mitkThrowException(SemanticRelationException) << "The control point " << controlPoint.UID << " to link does not exist for the given case."; } } void mitk::SemanticRelations::UnlinkDataFromControlPoint(const DataNode* dataNode) { if (nullptr == dataNode) { mitkThrowException(SemanticRelationException) << "Not a valid data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(dataNode); SemanticTypes::ID dataID = GetIDFromDataNode(dataNode); SemanticTypes::ControlPoint controlPoint = m_RelationStorage->GetControlPointOfImage(caseID, dataID); m_RelationStorage->UnlinkDataFromControlPoint(caseID, dataID); DataNodeVector allImagesOfControlPoint = GetAllImagesOfControlPoint(caseID, controlPoint); if (allImagesOfControlPoint.empty()) { // no more data is linked to the specific control point // the control point can be removed from the storage m_RelationStorage->RemoveControlPointFromCase(caseID, controlPoint); } else { // some data is still linked to this control point // the control point can not be removed, but has to be adjusted to fit the remaining data SemanticTypes::ControlPoint adjustedControlPoint = GenerateControlPoint(allImagesOfControlPoint); // set the UIDs to be the same, so that all references still work adjustedControlPoint.UID = controlPoint.UID; adjustedControlPoint.startPoint.UID = controlPoint.startPoint.UID; adjustedControlPoint.endPoint.UID = controlPoint.endPoint.UID; m_RelationStorage->OverwriteControlPoint(caseID, adjustedControlPoint); } } void mitk::SemanticRelations::SetInformationType(const DataNode* imageNode, const SemanticTypes::InformationType& informationType) { RemoveInformationTypeFromImage(imageNode); AddInformationTypeToImage(imageNode, informationType); SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); NotifyObserver(caseID); } void mitk::SemanticRelations::AddInformationTypeToImage(const DataNode* imageNode, const SemanticTypes::InformationType& informationType) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid image data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); SemanticTypes::ID imageID = GetIDFromDataNode(imageNode); m_RelationStorage->AddInformationTypeToImage(caseID, imageID, informationType); } void mitk::SemanticRelations::RemoveInformationTypeFromImage(const DataNode* imageNode) { if (nullptr == imageNode) { mitkThrowException(SemanticRelationException) << "Not a valid image data node."; } SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(imageNode); SemanticTypes::ID imageID = GetIDFromDataNode(imageNode); SemanticTypes::InformationType originalInformationType = m_RelationStorage->GetInformationTypeOfImage(caseID, imageID); m_RelationStorage->RemoveInformationTypeFromImage(caseID, imageID); // check for further references to the removed information type std::vector allImageIDsVectorValue = m_RelationStorage->GetAllImageIDsOfCase(caseID); for (const auto otherImageID : allImageIDsVectorValue) { SemanticTypes::InformationType otherInformationType = m_RelationStorage->GetInformationTypeOfImage(caseID, otherImageID); if (otherInformationType == originalInformationType) { // found the information type in another image -> cannot remove the information type from the case return; } } // given information type was not referred by any other image of the case -> the information type can be removed from the case m_RelationStorage->RemoveInformationTypeFromCase(caseID, originalInformationType); } /************************************************************************/ /* private functions */ /************************************************************************/ void mitk::SemanticRelations::NotifyObserver(const SemanticTypes::CaseID& caseID) const { for (auto& observer : m_ObserverVector) { observer->Update(caseID); } } bool mitk::SemanticRelations::ControlPointContainsLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint) const { DataNodeVector allImagesOfLesion; try { allImagesOfLesion = GetAllImagesOfLesion(caseID, lesion); } catch (const SemanticRelationException&) { // error retrieving image data; lesion has to be outside the control point return false; } DataNodeVector allImagesOfControlPoint; try { allImagesOfControlPoint = GetAllImagesOfControlPoint(caseID, controlPoint); } catch (const SemanticRelationException&) { // error retrieving control point data; lesion has to be outside the control point return false; } std::sort(allImagesOfLesion.begin(), allImagesOfLesion.end()); std::sort(allImagesOfControlPoint.begin(), allImagesOfControlPoint.end()); DataNodeVector allImagesIntersection; // set intersection removes duplicated nodes, since 'GetAllImagesOfControlPoint' only contains at most one of each node std::set_intersection(allImagesOfLesion.begin(), allImagesOfLesion.end(), allImagesOfControlPoint.begin(), allImagesOfControlPoint.end(), std::back_inserter(allImagesIntersection)); // if the vector of intersecting data is empty, the control point does not contain the lesion return !allImagesIntersection.empty(); } bool mitk::SemanticRelations::ControlPointContainsInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType, const SemanticTypes::ControlPoint& controlPoint) const { DataNodeVector allImagesIntersection = GetAllSpecificImages(caseID, controlPoint, informationType); return !allImagesIntersection.empty(); } bool mitk::SemanticRelations::CheckOverlappingControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) { ControlpointVector allControlPoints = GetAllControlPointsOfCase(caseID); if (allControlPoints.empty()) { return false; } std::sort(allControlPoints.begin(), allControlPoints.end()); const auto existingControlPoint = std::find_if(allControlPoints.begin(), allControlPoints.end(), [&controlPoint](const SemanticTypes::ControlPoint& currentControlPoint) { return currentControlPoint.UID == controlPoint.UID; }); auto nextControlPoint = allControlPoints.end(); auto previousControlPoint = allControlPoints.begin(); if (existingControlPoint != allControlPoints.end()) { // case overwriting: control point already contained in the list of all existing control points nextControlPoint = std::next(existingControlPoint, 1); if (existingControlPoint != allControlPoints.begin()) { previousControlPoint = std::prev(existingControlPoint, 1); } } else { // case adding: control point not contained in the list of all existing control points nextControlPoint = std::find_if(allControlPoints.begin(), allControlPoints.end(), [&controlPoint](const SemanticTypes::ControlPoint& currentControlPoint) { return currentControlPoint.startPoint >= controlPoint.endPoint; }); if (nextControlPoint != allControlPoints.begin()) { previousControlPoint = std::prev(existingControlPoint, 1); } } // check the neighboring control points for overlap bool overlapWithNext = false; bool overlapWithPrevious = CheckForOverlap(controlPoint, *previousControlPoint); if (nextControlPoint != allControlPoints.end()) { overlapWithNext = CheckForOverlap(controlPoint, *nextControlPoint); } return overlapWithNext || overlapWithPrevious; // return true if at least one overlap is detected } bool mitk::SemanticRelations::CheckContainingControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint) { ControlpointVector allControlPoints = GetAllControlPointsOfCase(caseID); if (allControlPoints.empty()) { return false; } const auto existingControlPoint = std::find_if(allControlPoints.begin(), allControlPoints.end(), [&controlPoint](const SemanticTypes::ControlPoint& currentControlPoint) { return currentControlPoint.UID == controlPoint.UID; }); if (existingControlPoint != allControlPoints.end()) { // case overwriting: control point already contained in the list of all existing control points // -> duplicated control point found (regardless of the actual start point and end point) return true; } else { // case adding: control point not contained in the list of all existing control points for (const auto& existingControlPoint : allControlPoints) { bool contained = InsideControlPoint(controlPoint, existingControlPoint); if (contained) { return true; } } } return false; } diff --git a/Modules/SemanticRelationsUI/src/QmitkLesionTreeModel.cpp b/Modules/SemanticRelationsUI/src/QmitkLesionTreeModel.cpp index d91b9c77c8..19005030f1 100644 --- a/Modules/SemanticRelationsUI/src/QmitkLesionTreeModel.cpp +++ b/Modules/SemanticRelationsUI/src/QmitkLesionTreeModel.cpp @@ -1,254 +1,258 @@ /*=================================================================== 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 UI module #include "QmitkLesionTreeModel.h" // semantic relations module #include #include #include QmitkLesionTreeModel::QmitkLesionTreeModel(QObject* parent/* = nullptr*/) : QmitkAbstractSemanticRelationsStorageModel(parent) , m_RootItem(std::make_shared(mitk::LesionData())) { // nothing here } QmitkLesionTreeModel::~QmitkLesionTreeModel() { // nothing here } ////////////////////////////////////////////////////////////////////////// // overridden virtual functions from QAbstractItemModel ////////////////////////////////////////////////////////////////////////// QModelIndex QmitkLesionTreeModel::index(int row, int column, const QModelIndex& itemIndex) const { if (!hasIndex(row, column, itemIndex)) { return QModelIndex(); } auto childItem = GetItemByIndex(itemIndex)->GetChildInRow(row); if (nullptr == childItem) { return QModelIndex(); } return createIndex(row, column, childItem.get()); } QModelIndex QmitkLesionTreeModel::parent(const QModelIndex& itemIndex) const { if (!itemIndex.isValid()) { return QModelIndex(); } auto parentItem = GetItemByIndex(itemIndex)->GetParent(); if (parentItem.expired()) { return QModelIndex(); } auto sharedParent = parentItem.lock(); if (sharedParent == m_RootItem) { return QModelIndex(); } return createIndex(sharedParent->GetRow(), 0, sharedParent.get()); } int QmitkLesionTreeModel::rowCount(const QModelIndex& itemIndex/* = QModelIndex()*/) const { return GetItemByIndex(itemIndex)->ChildCount(); } int QmitkLesionTreeModel::columnCount(const QModelIndex&/* itemIndex = QModelIndex() */) const { return m_ControlPoints.size() + 1; } QVariant QmitkLesionTreeModel::data(const QModelIndex& index, int role) const { if (!index.isValid()) { return QVariant(); } if (index.column() < 0 || index.column() > static_cast(m_ControlPoints.size())) { return QVariant(); } QmitkLesionTreeItem* currentItem = GetItemByIndex(index); - if (currentItem->GetParent().expired()) + if (Qt::DisplayRole == role) { - return QVariant(); - } - - auto parentItem = currentItem->GetParent().lock(); - // parent exists and is the root item -> 1. item of a lesion entry - if (m_RootItem == parentItem) - { - if (Qt::DisplayRole == role) + if (currentItem->GetParent().expired()) { - // display role fills the first columns with the property name "Volume" - if (0 == index.column()) - { - return "Volume"; - } - else - { - // display role fills other columns with the lesion volume info - return QVariant(currentItem->GetData().GetLesionVolume().at(index.column() - 1)); - } - - return ""; + return QVariant(); } - } - // parent is not the root item -> 2. item of a lesion entry - else - { - if (Qt::DisplayRole == role) + + auto parentItem = currentItem->GetParent().lock(); + // parent exists and is the root item -> 1. item of a lesion entry + if (m_RootItem == parentItem) { // display role fills the first columns with the lesion UID / name if (0 == index.column()) { std::string itemString = currentItem->GetData().GetLesionName(); if (itemString.empty()) { itemString = currentItem->GetData().GetLesionUID(); } return QString::fromStdString(itemString); } else { // display role fills other columns with the lesion presence info - return QVariant(currentItem->GetData().GetLesionPresence().at(index.column() - 1)); - } + const auto lesionPresence = currentItem->GetData().GetLesionPresence(); + if (index.column() - 1 > static_cast(lesionPresence.size())) + { + return ""; + } - return ""; + return QVariant(lesionPresence.at(index.column() - 1)); + } + } + // parent is not the root item -> 2. item of a lesion entry + else + { + // display role fills the first columns with the property name "Volume" + if (0 == index.column()) + { + return "Volume"; + } + else + { + // display role fills other columns with the lesion volume info + const auto lesionVolume= currentItem->GetData().GetLesionVolume(); + if (index.column() - 1 > static_cast(lesionVolume.size())) + { + return ""; + } + return QVariant(lesionVolume.at(index.column() - 1)); + } } } if (Qt::UserRole == role) { return QVariant::fromValue(currentItem); } return QVariant(); } QVariant QmitkLesionTreeModel::headerData(int section, Qt::Orientation orientation, int role) const { if (Qt::Horizontal == orientation && Qt::DisplayRole == role) { if (0 == section) { return QVariant("Lesion"); } if (m_ControlPoints.size() >= section) { mitk::SemanticTypes::ControlPoint currentControlPoint = m_ControlPoints.at(section-1); // generate a string from the control point std::string currentControlPointAsString = mitk::GetControlPointAsString(currentControlPoint); return QVariant(QString::fromStdString(currentControlPointAsString)); } } return QVariant(); } void QmitkLesionTreeModel::NodePredicateChanged() { // does not react to node predicate changes } void QmitkLesionTreeModel::NodeAdded(const mitk::DataNode* node) { // does not react to data storage changes } void QmitkLesionTreeModel::NodeChanged(const mitk::DataNode* node) { // does not react to data storage changes } void QmitkLesionTreeModel::NodeRemoved(const mitk::DataNode* node) { // does not react to data storage changes } void QmitkLesionTreeModel::SetData() { m_RootItem = std::make_shared(mitk::LesionData()); // get all control points of current case m_ControlPoints = m_SemanticRelations->GetAllControlPointsOfCase(m_CaseID); // sort the vector of control points for the timeline std::sort(m_ControlPoints.begin(), m_ControlPoints.end()); SetLesionData(); } void QmitkLesionTreeModel::SetLesionData() { std::vector allLesions = m_SemanticRelations->GetAllLesionsOfCase(m_CaseID); for (auto& lesion : allLesions) { AddLesion(lesion); } } void QmitkLesionTreeModel::AddLesion(const mitk::SemanticTypes::Lesion& lesion) { if (nullptr == m_SemanticRelations) { return; } // create new lesion tree item data and modify it according to the control point data mitk::LesionData lesionData(lesion); mitk::GenerateAdditionalLesionData(lesionData, m_CaseID, m_SemanticRelations); // add the 1. level lesion item to the root item std::shared_ptr newLesionTreeItem = std::make_shared(lesionData); m_RootItem->AddChild(newLesionTreeItem); // add the 2. level lesion item to the 1. level lesion item std::shared_ptr newChildItem = std::make_shared(lesionData); newLesionTreeItem->AddChild(newChildItem); } QmitkLesionTreeItem* QmitkLesionTreeModel::GetItemByIndex(const QModelIndex& index) const { if (index.isValid()) { auto item = static_cast(index.internalPointer()); if (nullptr != item) { return item; } } return m_RootItem.get(); } diff --git a/Modules/SemanticRelationsUI/src/QmitkPatientTableModel.cpp b/Modules/SemanticRelationsUI/src/QmitkPatientTableModel.cpp index 595655f1b6..95137b61dd 100644 --- a/Modules/SemanticRelationsUI/src/QmitkPatientTableModel.cpp +++ b/Modules/SemanticRelationsUI/src/QmitkPatientTableModel.cpp @@ -1,353 +1,354 @@ /*=================================================================== 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 UI module #include "QmitkPatientTableModel.h" #include "QmitkSemanticRelationsUIHelper.h" // semantic relations module +#include #include #include #include #include // qt #include QmitkPatientTableModel::QmitkPatientTableModel(QObject* parent /*= nullptr*/) : QmitkAbstractSemanticRelationsStorageModel(parent) , m_SelectedNodeType("Image") { // nothing here } QmitkPatientTableModel::~QmitkPatientTableModel() { // nothing here } QModelIndex QmitkPatientTableModel::index(int row, int column, const QModelIndex& parent/* = QModelIndex()*/) const { if (hasIndex(row, column, parent)) { return createIndex(row, column); } return QModelIndex(); } QModelIndex QmitkPatientTableModel::parent(const QModelIndex& child) const { return QModelIndex(); } int QmitkPatientTableModel::rowCount(const QModelIndex& parent/* = QModelIndex()*/) const { if (parent.isValid()) { return 0; } return m_InformationTypes.size(); } int QmitkPatientTableModel::columnCount(const QModelIndex& parent/* = QModelIndex()*/) const { if (parent.isValid()) { return 0; } return m_ControlPoints.size(); } QVariant QmitkPatientTableModel::data(const QModelIndex& index, int role/* = Qt::DisplayRole*/) const { if (!index.isValid()) { return QVariant(); } if (index.row() < 0 || index.row() >= static_cast(m_InformationTypes.size()) || index.column() < 0 || index.column() >= static_cast(m_ControlPoints.size())) { return QVariant(); } mitk::DataNode* dataNode = GetCurrentDataNode(index); if (nullptr == dataNode) { return QVariant(); } if (Qt::DecorationRole == role) { auto it = m_PixmapMap.find(dataNode); if (it != m_PixmapMap.end()) { return QVariant(it->second); } } else if (QmitkDataNodeRole == role) { return QVariant::fromValue(mitk::DataNode::Pointer(dataNode)); } else if (QmitkDataNodeRawPointerRole == role) { return QVariant::fromValue(dataNode); } else if (Qt::BackgroundColorRole == role) { auto it = m_LesionPresence.find(dataNode); if (it != m_LesionPresence.end()) { return it->second ? QVariant(QColor(Qt::green)) : QVariant(QColor(Qt::transparent)); } return QVariant(QColor(Qt::transparent)); } return QVariant(); } QVariant QmitkPatientTableModel::headerData(int section, Qt::Orientation orientation, int role) const { if (Qt::Horizontal == orientation && Qt::DisplayRole == role) { if (m_ControlPoints.size() > section) { mitk::SemanticTypes::ControlPoint currentControlPoint = m_ControlPoints.at(section); // generate a string from the control point std::string currentControlPointAsString = mitk::GetControlPointAsString(currentControlPoint); return QVariant(QString::fromStdString(currentControlPointAsString)); } } if (Qt::Vertical == orientation && Qt::DisplayRole == role) { if (m_InformationTypes.size() > section) { mitk::SemanticTypes::InformationType currentInformationType = m_InformationTypes.at(section); return QVariant(QString::fromStdString(currentInformationType)); } } return QVariant(); } Qt::ItemFlags QmitkPatientTableModel::flags(const QModelIndex& index) const { Qt::ItemFlags flags; mitk::DataNode* dataNode = GetCurrentDataNode(index); if (nullptr != dataNode) { flags = Qt::ItemIsEnabled | Qt::ItemIsSelectable; } return flags; } void QmitkPatientTableModel::SetNodeType(const std::string& nodeType) { m_SelectedNodeType = nodeType; UpdateModelData(); } void QmitkPatientTableModel::NodePredicateChanged() { UpdateModelData(); } void QmitkPatientTableModel::NodeAdded(const mitk::DataNode* node) { // does not react to data storage changes } void QmitkPatientTableModel::NodeChanged(const mitk::DataNode* node) { // nothing here, since the "'NodeChanged'-event is currently sent far too often //UpdateModelData(); } void QmitkPatientTableModel::NodeRemoved(const mitk::DataNode* node) { // does not react to data storage changes } void QmitkPatientTableModel::SetPixmapOfNode(const mitk::DataNode* dataNode, QPixmap* pixmapFromImage) { if (nullptr == dataNode) { return; } std::map::iterator iter = m_PixmapMap.find(dataNode); if (iter != m_PixmapMap.end()) { // key already existing if (nullptr != pixmapFromImage) { // overwrite already stored pixmap iter->second = pixmapFromImage->scaled(120, 120, Qt::IgnoreAspectRatio); } else { // remove key if no pixmap is given m_PixmapMap.erase(iter); } } else { m_PixmapMap.insert(std::make_pair(dataNode, pixmapFromImage->scaled(120, 120, Qt::IgnoreAspectRatio))); } } void QmitkPatientTableModel::SetLesionPresence(const mitk::DataNode* dataNode, bool lesionPresence) { if (nullptr == dataNode) { return; } std::map::iterator iter = m_LesionPresence.find(dataNode); if (iter != m_LesionPresence.end()) { // key already existing, overwrite already stored bool value iter->second = lesionPresence; } else { m_LesionPresence.insert(std::make_pair(dataNode, lesionPresence)); } } void QmitkPatientTableModel::SetData() { // get all control points of current case m_ControlPoints = m_SemanticRelations->GetAllControlPointsOfCase(m_CaseID); // sort the vector of control points for the timeline std::sort(m_ControlPoints.begin(), m_ControlPoints.end()); // get all information types points of current case m_InformationTypes = m_SemanticRelations->GetAllInformationTypesOfCase(m_CaseID); m_PixmapMap.clear(); m_LesionPresence.clear(); SetDataNodes(); } void QmitkPatientTableModel::SetDataNodes() { std::vector allDataNodes; if("Image" == m_SelectedNodeType) { allDataNodes = m_SemanticRelations->GetAllImagesOfCase(m_CaseID); } else if("Segmentation" == m_SelectedNodeType) { allDataNodes = m_SemanticRelations->GetAllSegmentationsOfCase(m_CaseID); } for (const auto& dataNode : allDataNodes) { // set the pixmap for the current node QPixmap pixmapFromImage = QmitkSemanticRelationsUIHelper::GetPixmapFromImageNode(dataNode); SetPixmapOfNode(dataNode, &pixmapFromImage); // set the lesion presence for the current node if (m_SemanticRelations->InstanceExists(m_CaseID, m_Lesion)) { bool lesionPresence = lesionPresence = IsLesionPresentOnDataNode(dataNode); SetLesionPresence(dataNode, lesionPresence); } else { m_LesionPresence.clear(); } } } bool QmitkPatientTableModel::IsLesionPresentOnDataNode(const mitk::DataNode* dataNode) const { if (m_DataStorage.IsExpired()) { return false; } auto dataStorage = m_DataStorage.Lock(); try { mitk::SemanticRelations::DataNodeVector allSegmentationsOfLesion = m_SemanticRelations->GetAllSegmentationsOfLesion(m_CaseID, m_Lesion); for (const auto& segmentation : allSegmentationsOfLesion) { if ("Segmentation" == m_SelectedNodeType) { if (dataNode == segmentation) { // found a segmentation of the node that is represented by the selected lesion return true; } } else if ("Image" == m_SelectedNodeType) { // get parent node of the current segmentation node with the node predicate mitk::DataStorage::SetOfObjects::ConstPointer parentNodes = dataStorage->GetSources(segmentation, mitk::NodePredicates::GetImagePredicate(), false); for (auto it = parentNodes->Begin(); it != parentNodes->End(); ++it) { if (dataNode == it.Value()) { // found a segmentation of the node that is represented by the selected lesion return true; } } } } } catch (const mitk::SemanticRelationException&) { return false; } return false; } mitk::DataNode* QmitkPatientTableModel::GetCurrentDataNode(const QModelIndex& index) const { mitk::SemanticTypes::ControlPoint currentControlPoint = m_ControlPoints.at(index.column()); mitk::SemanticTypes::InformationType currentInformationType = m_InformationTypes.at(index.row()); try { std::vector filteredDataNodes; if ("Image" == m_SelectedNodeType) { filteredDataNodes = m_SemanticRelations->GetAllSpecificImages(m_CaseID, currentControlPoint, currentInformationType); } else if ("Segmentation" == m_SelectedNodeType) { filteredDataNodes = m_SemanticRelations->GetAllSpecificSegmentations(m_CaseID, currentControlPoint, currentInformationType); } if (filteredDataNodes.empty()) { return nullptr; } return filteredDataNodes.front(); } catch (const mitk::SemanticRelationException&) { return nullptr; } }