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cxBronchoscopyRegistration.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
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30 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
31 =========================================================================*/
32 #ifndef BRONCHOSCOPYREGISTRATION_H_
33 #define BRONCHOSCOPYREGISTRATION_H_
34 
35 //#include "PositionData.h"
36 #include "cxBranchList.h"
37 #include <vector>
38 #include "vtkForwardDeclarations.h"
39 
40 
41 typedef std::vector< Eigen::Matrix4d > M4Vector;
42 
43 
44 namespace cx
45 {
46 
47 typedef std::map<double, Transform3D> TimedTransformMap;
48 typedef boost::shared_ptr<class BranchList> BranchListPtr;
49 
51 {
52  BranchListPtr mBranchListPtr;
53  bool mCenterlineProcessed;
54 
55 public:
57  vtkPolyDataPtr processCenterline(vtkPolyDataPtr centerline, Transform3D rMd, int numberOfGenerations = 0);
58  Eigen::Matrix4d runBronchoscopyRegistration(TimedTransformMap trackingData_prMt, Transform3D old_rMpr, double maxDistanceForLocalRegistration);
59  bool isCenterlineProcessed();
60  virtual ~BronchoscopyRegistration();
61 };
62 
64 Eigen::Matrix4d registrationAlgorithm(BranchListPtr branches, M4Vector Tnavigation);
65 std::vector<Eigen::MatrixXd::Index> dsearch2n(Eigen::MatrixXd pos1, Eigen::MatrixXd pos2, Eigen::MatrixXd ori1, Eigen::MatrixXd ori2);
66 vtkPointsPtr convertTovtkPoints(Eigen::MatrixXd positions);
67 Eigen::Matrix4d performLandmarkRegistration(vtkPointsPtr source, vtkPointsPtr target, bool* ok);
68 std::pair<Eigen::MatrixXd , Eigen::MatrixXd> RemoveInvalidData(Eigen::MatrixXd positionData, Eigen::MatrixXd orientationData);
70 }//namespace cx
71 
72 #endif /* BRONCHOSCOPYREGISTRATION_H_ */
Transform3D Transform3D
Transform3D is a representation of an affine 3D transform.
boost::shared_ptr< class BranchList > BranchListPtr
std::pair< Eigen::MatrixXd, Eigen::MatrixXd > RemoveInvalidData(Eigen::MatrixXd positionData, Eigen::MatrixXd orientationData)
vtkPointsPtr convertTovtkPoints(Eigen::MatrixXd positions)
vtkSmartPointer< class vtkPolyData > vtkPolyDataPtr
std::vector< Eigen::MatrixXd::Index > dsearch2n(Eigen::MatrixXd pos1, Eigen::MatrixXd pos2, Eigen::MatrixXd ori1, Eigen::MatrixXd ori2)
M4Vector excludeClosePositions(M4Vector Tnavigation)
Eigen::Matrix4d runBronchoscopyRegistration(TimedTransformMap trackingData_prMt, Transform3D old_rMpr, double maxDistanceForLocalRegistration)
vtkPolyDataPtr processCenterline(vtkPolyDataPtr centerline, Transform3D rMd, int numberOfGenerations=0)
Eigen::Matrix4d performLandmarkRegistration(vtkPointsPtr source, vtkPointsPtr target)
std::vector< Eigen::Matrix4d > M4Vector
std::vector< Eigen::Matrix4d > M4Vector
Eigen::Matrix4d registrationAlgorithm(BranchListPtr branches, M4Vector Tnavigation, Transform3D old_rMpr)
std::map< double, Transform3D > TimedTransformMap
vtkSmartPointer< class vtkPoints > vtkPointsPtr