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cxBranchList.h
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1 /*=========================================================================
2 This file is part of CustusX, an Image Guided Therapy Application.
3 
4 Copyright (c) 2008-2014, SINTEF Department of Medical Technology
5 All rights reserved.
6 
7 Redistribution and use in source and binary forms, with or without
8 modification, are permitted provided that the following conditions are met:
9 
10 1. Redistributions of source code must retain the above copyright notice,
11  this list of conditions and the following disclaimer.
12 
13 2. Redistributions in binary form must reproduce the above copyright notice,
14  this list of conditions and the following disclaimer in the documentation
15  and/or other materials provided with the distribution.
16 
17 3. Neither the name of the copyright holder nor the names of its contributors
18  may be used to endorse or promote products derived from this software
19  without specific prior written permission.
20 
21 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
22 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
23 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
24 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
25 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
26 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
27 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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29 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
30 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
31 =========================================================================*/
32 #ifndef BRANCHLIST_H_
33 #define BRANCHLIST_H_
34 
35 #include "cxBranch.h"
36 #include "cxMesh.h"
37 #include "cxVector3D.h"
38 #include <vtkPolyData.h>
39 #include "org_custusx_registration_method_bronchoscopy_Export.h"
40 
41 
42 namespace cx
43 {
44 
45 typedef std::vector< Eigen::Matrix4d > M4Vector;
46 typedef boost::shared_ptr<class BranchList> BranchListPtr;
47 
48 class org_custusx_registration_method_bronchoscopy_EXPORT BranchList
49 {
50  std::vector<BranchPtr> mBranches;
51 public:
52  BranchList();
53  virtual ~BranchList();
54  void addBranch(BranchPtr b);
55  void deleteBranch(BranchPtr b);
56  void deleteAllBranches();
57  std::vector<BranchPtr> getBranches();
58  void findBranchesInCenterline(Eigen::MatrixXd positions);
59  void selectGenerations(int maxGeneration);
60  void calculateOrientations();
61  void smoothOrientations();
62  void interpolateBranchPositions(int interpolationFactor);
63  void smoothBranchPositions();
64  BranchListPtr removePositionsForLocalRegistration(Eigen::MatrixXd trackingPositions, double maxDistance);
65 
66 };
67 
68 std::pair<Eigen::MatrixXd,Eigen::MatrixXd > findConnectedPointsInCT(int startIndex , Eigen::MatrixXd positionsNotUsed);
69 Eigen::MatrixXd sortMatrix(int rowNumber, Eigen::MatrixXd matrix);
70 Eigen::MatrixXd eraseCol(int removeIndex, Eigen::MatrixXd positions);
71 std::pair<Eigen::MatrixXd::Index, double> dsearch(Eigen::Vector3d p, Eigen::MatrixXd positions);
72 std::pair<std::vector<Eigen::MatrixXd::Index>, Eigen::VectorXd > dsearchn(Eigen::MatrixXd p1, Eigen::MatrixXd p2);
73 
74 }//namespace cx
75 
76 #endif /* BRANCHLIST_H_ */
std::pair< Eigen::MatrixXd, Eigen::MatrixXd > findConnectedPointsInCT(int startIndex, Eigen::MatrixXd positionsNotUsed)
boost::shared_ptr< class BranchList > BranchListPtr
boost::shared_ptr< class Branch > BranchPtr
std::pair< Eigen::MatrixXd::Index, double > dsearch(Eigen::Vector3d p, Eigen::MatrixXd positions)
std::pair< std::vector< Eigen::MatrixXd::Index >, Eigen::VectorXd > dsearchn(Eigen::MatrixXd p1, Eigen::MatrixXd p2)
Eigen::MatrixXd eraseCol(int removeIndex, Eigen::MatrixXd positions)
Eigen::MatrixXd sortMatrix(int rowNumber, Eigen::MatrixXd matrix)
std::vector< Eigen::Matrix4d > M4Vector