diff --git a/code/masks/boost/rttbBoostMaskRedesign.cpp b/code/masks/boost/rttbBoostMaskRedesign.cpp index 39c9ee8..58b4cdc 100644 --- a/code/masks/boost/rttbBoostMaskRedesign.cpp +++ b/code/masks/boost/rttbBoostMaskRedesign.cpp @@ -1,287 +1,303 @@ #include #include #include #include #include #include #include #include #include "rttbBoostMaskRedesign.h" #include "rttbNullPointerException.h" #include "rttbInvalidParameterException.h" namespace rttb { namespace masks { namespace boostRedesign { BoostMask::BoostMask(BoostMask::GeometricInfoPointer aDoseGeoInfo, BoostMask::StructPointer aStructure, bool strict) - :_geometricInfo(aDoseGeoInfo), _structure(aStructure), _strict(strict), _voxelInStructure(::boost::make_shared()){ + :_geometricInfo(aDoseGeoInfo), _structure(aStructure), _strict(strict), _voxelInStructure(::boost::make_shared()) + { _isUpToDate = false; if (!_geometricInfo){ throw rttb::core::NullPointerException("Error: Geometric info is NULL!"); } else if (!_structure){ throw rttb::core::NullPointerException("Error: Structure is NULL!"); } } - BoostMask::MaskVoxelListPointer BoostMask::getRelevantVoxelVector(){ + BoostMask::MaskVoxelListPointer BoostMask::getRelevantVoxelVector() + { if (!_isUpToDate){ calcMask(); } return _voxelInStructure; } - void BoostMask::calcMask(){ + void BoostMask::calcMask() + { preprocessing(); _isUpToDate = true; } - void BoostMask::preprocessing(){ - + void BoostMask::preprocessing() + { rttb::PolygonSequenceType polygonSequence = _structure->getStructureVector(); //Convert world coordinate polygons to the polygons with geometry coordinate rttb::PolygonSequenceType geometryCoordinatePolygonVector; rttb::PolygonSequenceType::iterator it; - for (it = polygonSequence.begin(); it != polygonSequence.end(); ++it){ - PolygonType rttbPolygon = *it; - PolygonType geometryCoordinatePolygon = worldCoordinateToGeometryCoordinatePolygon(rttbPolygon); - geometryCoordinatePolygonVector.push_back(geometryCoordinatePolygon); - - } - - //Get global bounding box rttb::DoubleVoxelGridIndex3D globalMaxGridIndex(0.0, 0.0, 0); rttb::DoubleVoxelGridIndex3D globalMinGridIndex(_geometricInfo->getNumColumns(), _geometricInfo->getNumRows(), 0); - for (it = geometryCoordinatePolygonVector.begin(); it != geometryCoordinatePolygonVector.end(); ++it){ - PolygonType geometryCoordinatePolygon = *it; - rttb::DoubleVoxelGridIndex3D maxGridIndex; - rttb::DoubleVoxelGridIndex3D minGridIndex; - - //get min/max for x/y/z of the contour - calcMinMax(geometryCoordinatePolygon, minGridIndex, maxGridIndex); + for (it = polygonSequence.begin(); it != polygonSequence.end(); ++it){ + PolygonType rttbPolygon = *it; + PolygonType geometryCoordinatePolygon; - //check tilt, if more than the error constant throw exception - if (checkTilt(minGridIndex, maxGridIndex, errorConstant)){ + //1. convert polygon to geometry coordinate polygons + //2. calculate global min/max + //3. check if polygon is planar + if (!preprocessingPolygon(rttbPolygon, geometryCoordinatePolygon, globalMinGridIndex, globalMaxGridIndex, errorConstant)) + { throw rttb::core::Exception("TiltedMaskPlaneException"); } - - //get global min/max for x/y/z of all contours - //min and max for x - if (minGridIndex(0) < globalMinGridIndex(0)){ - globalMinGridIndex(0) = minGridIndex(0); - } - if (maxGridIndex(0) > globalMaxGridIndex(0)){ - globalMaxGridIndex(0) = maxGridIndex(0); - } - //min and max for y - if (minGridIndex(1) < globalMinGridIndex(1)){ - globalMinGridIndex(1) = minGridIndex(1); - } - if (maxGridIndex(1) > globalMaxGridIndex(1)){ - globalMaxGridIndex(1) = maxGridIndex(1); - } - //min and max for z - if (minGridIndex(2) < globalMinGridIndex(2)){ - globalMinGridIndex(2) = minGridIndex(2); - } - if (maxGridIndex(2) > globalMaxGridIndex(2)){ - globalMaxGridIndex(2) = maxGridIndex(2); - } - + geometryCoordinatePolygonVector.push_back(geometryCoordinatePolygon); } _globalBoundingBox.push_back(globalMinGridIndex); _globalBoundingBox.push_back(globalMaxGridIndex); //convert rttb polygon sequence to a map of z index and a vector of boost ring 2d (without holes) BoostRingMap ringMap = convertRTTBPolygonSequenceToBoostRingMap(geometryCoordinatePolygonVector); //check donut and convert to a map of z index and a vector of boost polygon 2d (with or without holes) _geometryCoordinateBoostPolygonMap.clear(); BoostRingMap::iterator itMap; for (itMap = ringMap.begin(); itMap != ringMap.end(); ++itMap){ BoostPolygonVector polygonVector = checkDonutAndConvert((*itMap).second); _geometryCoordinateBoostPolygonMap.insert(std::pair((*itMap).first, polygonVector)); } } - rttb::PolygonType BoostMask::worldCoordinateToGeometryCoordinatePolygon(const rttb::PolygonType& aRTTBPolygon){ - rttb::PolygonType geometryCoordinatePolygon; + bool BoostMask::preprocessingPolygon(const rttb::PolygonType& aRTTBPolygon, rttb::PolygonType& geometryCoordinatePolygon, rttb::DoubleVoxelGridIndex3D& minimum, rttb::DoubleVoxelGridIndex3D& maximum, double aErrorConstant) + { + + double minZ = _geometricInfo->getNumSlices(); + double maxZ = 0.0; for (unsigned int i = 0; i < aRTTBPolygon.size(); i++){ rttb::WorldCoordinate3D worldCoordinatePoint = aRTTBPolygon.at(i); + //convert to geometry coordinate polygon rttb::DoubleVoxelGridIndex3D geometryCoordinatePoint; _geometricInfo->worldCoordinateToGeometryCoordinate(worldCoordinatePoint, geometryCoordinatePoint); geometryCoordinatePolygon.push_back(geometryCoordinatePoint); - } - return geometryCoordinatePolygon; - } - - bool BoostMask::checkTilt(const rttb::DoubleVoxelGridIndex3D& minimum, const rttb::DoubleVoxelGridIndex3D& maximum, double aErrorConstant){ - return (abs(maximum(2) - minimum(2)) > aErrorConstant); - } - - void BoostMask::calcMinMax(const rttb::PolygonType& aRTTBPolygon, rttb::DoubleVoxelGridIndex3D minimum, rttb::DoubleVoxelGridIndex3D maximum){ - maximum(0) = 0.0; - maximum(1) = 0.0; - maximum(2) = 0.0; - minimum(0) = _geometricInfo->getNumColumns(); - minimum(1) = _geometricInfo->getNumRows(); - minimum(2) = _geometricInfo->getNumSlices(); - - //get min and max for x/y/z of a contour - PolygonType::const_iterator polygonIt; - for (polygonIt = aRTTBPolygon.begin(); polygonIt < aRTTBPolygon.end(); ++polygonIt){ - rttb::DoubleVoxelGridIndex3D geometryCoordinatePoint = *polygonIt; + //calculate the current global min/max //min and max for x if (geometryCoordinatePoint(0) < minimum(0)){ minimum(0) = geometryCoordinatePoint(0); } if (geometryCoordinatePoint(0) > maximum(0)){ maximum(0) = geometryCoordinatePoint(0); } //min and max for y if (geometryCoordinatePoint(1) < minimum(1)){ minimum(1) = geometryCoordinatePoint(1); } if (geometryCoordinatePoint(1) > maximum(1)){ maximum(1) = geometryCoordinatePoint(1); } //min and max for z if (geometryCoordinatePoint(2) < minimum(2)){ minimum(2) = geometryCoordinatePoint(2); } if (geometryCoordinatePoint(2) > maximum(2)){ maximum(2) = geometryCoordinatePoint(2); } + + //check planar + if (geometryCoordinatePoint(2) < minZ){ + minZ = geometryCoordinatePoint(2); + } + if (geometryCoordinatePoint(2) > maxZ){ + maxZ = geometryCoordinatePoint(2); + } + } + + return (abs(maxZ - minZ) <= aErrorConstant); } - BoostMask::BoostRing2D BoostMask::convertRTTBPolygonToBoostRing(const rttb::PolygonType& aRTTBPolygon){ + BoostMask::BoostRing2D BoostMask::convertRTTBPolygonToBoostRing(const rttb::PolygonType& aRTTBPolygon) + { BoostMask::BoostRing2D polygon2D; BoostPoint2D firstPoint; for (unsigned int i = 0; i < aRTTBPolygon.size(); i++){ rttb::WorldCoordinate3D rttbPoint = aRTTBPolygon.at(i); BoostPoint2D boostPoint(rttbPoint[0], rttbPoint[1]); if (i == 0){ firstPoint = boostPoint; } ::boost::geometry::append(polygon2D, boostPoint); } ::boost::geometry::append(polygon2D, firstPoint); return polygon2D; } - BoostMask::BoostRingMap BoostMask::convertRTTBPolygonSequenceToBoostRingMap(const rttb::PolygonSequenceType& aRTTBPolygonVector){ + BoostMask::BoostRingMap BoostMask::convertRTTBPolygonSequenceToBoostRingMap(const rttb::PolygonSequenceType& aRTTBPolygonVector) + { rttb::PolygonSequenceType::const_iterator it; BoostMask::BoostRingMap aRingMap; for (it = aRTTBPolygonVector.begin(); it != aRTTBPolygonVector.end(); ++it){ rttb::PolygonType rttbPolygon = *it; double zIndex = rttbPolygon.at(0)[2];//get the first z index of the polygon - BoostMask::BoostRingMap::iterator findIt = aRingMap.find(zIndex); - //if the z index is found (same slice), add the polygon to vector - if (findIt != aRingMap.end()){ - BoostRingVector ringVector = (*findIt).second; - ringVector.push_back(convertRTTBPolygonToBoostRing(rttbPolygon)); + if (!aRingMap.empty()) + { + BoostMask::BoostRingMap::const_iterator findIt = findNearestKey(aRingMap, zIndex, errorConstant); + + //if the z index is found (same slice), add the polygon to vector + if (findIt != aRingMap.end()){ + BoostRingVector ringVector = (*findIt).second; + ringVector.push_back(convertRTTBPolygonToBoostRing(rttbPolygon)); + } } + //if it is the first z index in the map, insert vector with the polygon - else{ - BoostRingVector ringVector; - ringVector.push_back(convertRTTBPolygonToBoostRing(rttbPolygon)); - aRingMap.insert(std::pair(zIndex, ringVector)); - } + BoostRingVector ringVector; + ringVector.push_back(convertRTTBPolygonToBoostRing(rttbPolygon)); + aRingMap.insert(std::pair(zIndex, ringVector)); + } return aRingMap; } - BoostMask::BoostPolygonVector BoostMask::checkDonutAndConvert(const BoostMask::BoostRingVector& aRingVector){ + BoostMask::BoostRingMap::const_iterator BoostMask::findNearestKey(const BoostMask::BoostRingMap& aBoostRingMap, double aIndex, double aErrorConstant) + { + BoostMask::BoostRingMap::const_iterator find = aBoostRingMap.find(aIndex); + //if find a key equivalent to aIndex, found + if (find != aBoostRingMap.end()) + { + return find; + } + else + { + BoostMask::BoostRingMap::const_iterator lowerBound = aBoostRingMap.lower_bound(aIndex); + //if the lower bound very close to aIndex, found + if (abs((*lowerBound).first - aIndex) <= aErrorConstant) + { + return lowerBound; + } + else + { + //if the lower bound is the beginning, not found + if (lowerBound == aBoostRingMap.begin()) + { + return aBoostRingMap.end(); + } + else + { + BoostMask::BoostRingMap::const_iterator lowerBound1 = --lowerBound;//the key before the lower bound + //if the key before the lower bound very close to a Index, found + if (abs((*lowerBound1).first - aIndex) <= aErrorConstant) + { + return lowerBound1; + } + //else, not found + else + { + return aBoostRingMap.end(); + } + } + } + + } + } + + BoostMask::BoostPolygonVector BoostMask::checkDonutAndConvert(const BoostMask::BoostRingVector& aRingVector) + { //check donut BoostMask::BoostRingVector::const_iterator it1; BoostMask::BoostRingVector::const_iterator it2; BoostMask::BoostPolygonVector boostPolygonVector; std::vector donutIndexVector;//store the outer and inner ring index BoostMask::BoostPolygonVector donutVector;//store new generated donut polygon //Get donut index and donut polygon unsigned int index1 = 0; for (it1 = aRingVector.begin(); it1 != aRingVector.end(); it1++, index1++){ bool it1IsDonut = false; //check if the ring is already determined as a donut for (unsigned int i = 0; i < donutIndexVector.size(); i++){ if (donutIndexVector.at(i) == index1){ it1IsDonut = true; break; } } //if not jet, check now if (!it1IsDonut){ bool it2IsDonut = false; unsigned int index2 = 0; for (it2 = aRingVector.begin(); it2 != aRingVector.end(); it2++, index2++){ if (it2 != it1){ BoostMask::BoostPolygon2D polygon2D; if (::boost::geometry::within(*it1, *it2)){ ::boost::geometry::append(polygon2D, *it2);//append an outer ring to the polygon ::boost::geometry::interior_rings(polygon2D).resize(1);//create an interior ring ::boost::geometry::append(polygon2D, *it1, 0);//append a ring to the interior ring it2IsDonut = true; } //if donut else if (::boost::geometry::within(*it2, *it1)){ ::boost::geometry::append(polygon2D, *it1);//append an outer ring to the polygon ::boost::geometry::interior_rings(polygon2D).resize(1);//create an interior ring ::boost::geometry::append(polygon2D, *it2, 0);//append a ring to the interior ring it2IsDonut = true; } if (it2IsDonut){ donutIndexVector.push_back(index1); donutIndexVector.push_back(index2); donutVector.push_back(polygon2D);//store donut polygon break;//Only store the first donut! } } } } } //Store no donut polygon to boostPolygonVector index1 = 0; for (it1 = aRingVector.begin(); it1 != aRingVector.end(); it1++, index1++){ bool it1IsDonut = false; //check if the ring is the outer or inner of a donut for (unsigned int i = 0; i < donutIndexVector.size(); i++){ if (donutIndexVector.at(i) == index1){ it1IsDonut = true; break; } } if (!it1IsDonut){ BoostMask::BoostPolygon2D polygon2D; ::boost::geometry::append(polygon2D, *it1); boostPolygonVector.push_back(polygon2D);//insert the ring, which is not a part of donut } } //Append donut polygon to boostPolygonVector BoostMask::BoostPolygonVector::iterator itDonut; for (itDonut = donutVector.begin(); itDonut != donutVector.end(); itDonut++){ boostPolygonVector.push_back(*itDonut);//append donuts } return boostPolygonVector; } } } } \ No newline at end of file diff --git a/code/masks/boost/rttbBoostMaskRedesign.h b/code/masks/boost/rttbBoostMaskRedesign.h index 967d5db..99655ad 100644 --- a/code/masks/boost/rttbBoostMaskRedesign.h +++ b/code/masks/boost/rttbBoostMaskRedesign.h @@ -1,155 +1,153 @@ // ----------------------------------------------------------------------- // RTToolbox - DKFZ radiotherapy quantitative evaluation library // // Copyright (c) German Cancer Research Center (DKFZ), // Software development for Integrated Diagnostics and Therapy (SIDT). // ALL RIGHTS RESERVED. // See rttbCopyright.txt or // http://www.dkfz.de/en/sidt/projects/rttb/copyright.html // // This software is distributed WITHOUT ANY WARRANTY; without even // the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR // PURPOSE. See the above copyright notices for more information. // //------------------------------------------------------------------------ /*! // @file // @version $Revision: 1127 $ (last changed revision) // @date $Date: 2015-10-01 13:33:33 +0200 (Do, 01 Okt 2015) $ (last change date) // @author $Author: hentsch $ (last changed by) */ #ifndef __BOOST_MASK_H #define __BOOST_MASK_H #include "rttbBaseType.h" #include "rttbStructure.h" #include "rttbGeometricInfo.h" #include "rttbMaskVoxel.h" #include "rttbMaskAccessorInterface.h" #include #include #include #include #include namespace rttb { namespace masks { namespace boostRedesign { /*! @class BoostMask * @brief Implementation of voxelization using boost::geometry. * @attention If "strict" is set to true, an exception will be thrown when the given structure has self intersection. * (A structure without self interseciton means all contours of the structure have no self intersection, and * the polygons on the same slice have no intersection between each other, unless the case of a donut. A donut is accepted.) * If "strict" is set to false, debug information will be displayed when the given structure has self intersection. Self intersections will be ignored * and the mask will be calculated, however, it may cause errors in the mask results. */ class BoostMask { public: typedef ::boost::shared_ptr GeometricInfoPointer; typedef core::Structure::StructTypePointer StructPointer; typedef core::MaskAccessorInterface::MaskVoxelList MaskVoxelList; typedef core::MaskAccessorInterface::MaskVoxelListPointer MaskVoxelListPointer; /*! @brief Constructor * @exception rttb::core::NullPointerException thrown if aDoseGeoInfo or aStructure is NULL * @param strict indicates whether to allow self intersection in the structure. If it is set to true, an exception will be thrown when the given structure has self intersection. * @exception InvalidParameterException thrown if strict is true and the structure has self intersections */ BoostMask(GeometricInfoPointer aDoseGeoInfo, StructPointer aStructure, bool strict = true); /*! @brief Generate mask and return the voxels in the mask * @exception rttb::core::InvalidParameterException thrown if the structure has self intersections */ MaskVoxelListPointer getRelevantVoxelVector(); private: typedef ::boost::geometry::model::d2::point_xy BoostPoint2D; typedef ::boost::geometry::model::polygon< ::boost::geometry::model::d2::point_xy > BoostPolygon2D; typedef ::boost::geometry::model::ring< ::boost::geometry::model::d2::point_xy > BoostRing2D; typedef std::deque BoostPolygonDeque; typedef std::vector BoostRingVector;//polygon without holes typedef std::vector BoostPolygonVector;//polygon with or without holes typedef std::vector VoxelIndexVector; typedef std::map BoostPolygonMap;//map of the z index with the vector of boost 2d polygon typedef std::map BoostRingMap;//map of the z index with the vector of boost 2d ring GeometricInfoPointer _geometricInfo; StructPointer _structure; /*! @brief The map of z index and a vector of all boost polygons with the same z index. This will be used to calculate the mask. * Key: the double z grid index * Value: the vector of all boost 2d polygons with the same z grid index (donut polygon is accepted). */ BoostPolygonMap _geometryCoordinateBoostPolygonMap; /*! @brief The min and max index of the global bounding box. * The first index has the minimum for x/y/z of the global bounding box. * The second index has the maximum for x/y/z of the global bounding index. */ std::vector _globalBoundingBox; bool _strict; //vector of the MaskVoxel inside the structure MaskVoxelListPointer _voxelInStructure; /*! @brief If the mask is up to date */ bool _isUpToDate; /*! @brief Voxelization and generate mask */ void calcMask(); /*! @brief The preprocessing step, wich consists of the following logic and Sub setps: - *For all contours in a struct: - *1) Transfer the contour polygons into boost::geometry structures - *1a) Convert the contur points from world coordinates into geometry coordinates. - *1b) get min and max for x/y/z of a contour - *2) Tilt check: if difference of z_min and z_max is larger then a tolerance value -> there is a tilt. Throw rttb::TiltedMaskPlaneException. - *3) Get struct-bounding-box: get x_min_struct, y_min_struct, x_max_struct, y_max_struct to define the bounding box that containes all contours of a struct in x-y-dimensions. + * For all contours in a struct: + * 1) Transfer the contour polygons into boost::geometry structures + * 1a) Convert the contur points from world coordinates into geometry coordinates. + * 1b) get min and max for x/y/z of a contour + * 2) Tilt check: if difference of z_min and z_max is larger then a tolerance value -> there is a tilt. Throw rttb::TiltedMaskPlaneException. + * 3) Get struct-bounding-box: get x_min_struct, y_min_struct, x_max_struct, y_max_struct to define the bounding box that containes all contours of a struct in x-y-dimensions. */ void preprocessing(); - /*! @brief Convert the rttb polygon with world corrdinate to the rttb polygon with double geometry coordinate + /*! @brief Convert the rttb polygon with world corrdinate to the rttb polygon with double geometry coordinate, calculate the current min/max + * and check if the polygon is planar + * @param minimum the current global minimum + * @param maximum the current global maximum + * @return Return true if the polygon is planar, which means that the minminal and maximal z-coordinate of the polygon is not larger than a error constant */ - rttb::PolygonType worldCoordinateToGeometryCoordinatePolygon(const rttb::PolygonType& aRTTBPolygon); - - /*! @brief Check if the polygon with the minimum and maximum is tilted more than a error constant - @return Return true if tilted > aErrorConstant - */ - bool checkTilt(const rttb::DoubleVoxelGridIndex3D& minimum, const rttb::DoubleVoxelGridIndex3D& maximum, double aErrorConstant); - - /*! @brief Calculate minimum and maximum for x/y/z of the polygon - */ - void calcMinMax(const rttb::PolygonType& aRTTBPolygon, rttb::DoubleVoxelGridIndex3D minimum, rttb::DoubleVoxelGridIndex3D maximum); - - /*! @brief If 2 rttb polygons in the vector build a donut, convert the 2 rttb polygons to a donut boost polygon, other rttb polygons unchanged convert to boost ring*/ - + bool preprocessingPolygon(const rttb::PolygonType& aRTTBPolygon, rttb::PolygonType& geometryCoordinatePolygon, rttb::DoubleVoxelGridIndex3D& minimum, rttb::DoubleVoxelGridIndex3D& maximum, double aErrorConstant); /*! @brief Convert a rttb 3d polygon to a 2d boost ring*/ BoostRing2D convertRTTBPolygonToBoostRing(const rttb::PolygonType& aRTTBPolygon); /*! @brief Convert a rttb 3d polygon to a map of z index with a vector of boost 2d ring, because of tilt check use the first z index of the polygon as the map key*/ BoostRingMap convertRTTBPolygonSequenceToBoostRingMap(const rttb::PolygonSequenceType& aRTTBPolygonVector); + + /*! @brief Find the key with error constant to aIndex + * @pre aBoostRingMap should not be empty + * @return Return aBoostRingMap.end() if the key is not found + */ + BoostMask::BoostRingMap::const_iterator findNearestKey(const BoostMask::BoostRingMap& aBoostRingMap, double aIndex, double aErrorConstant); /*! @brief If 2 rings in the vector build a donut, convert the 2 rings to a donut polygon, other rings unchanged*/ BoostPolygonVector checkDonutAndConvert(const BoostRingVector& aRingVector); }; } } } #endif \ No newline at end of file