Chaste  Release::3.4
HeartGeometryInformation.hpp
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35 #ifndef HEARTGEOMETRYINFORMATION_HPP_
36 #define HEARTGEOMETRYINFORMATION_HPP_
37 
38 #include <vector>
39 #include <string>
40 #include <set>
41 #include "DistanceMapCalculator.hpp"
42 #include "AbstractTetrahedralMesh.hpp"
43 #include "ChasteCuboid.hpp"
44 
46 typedef enum HeartLayerType_
47 {
48  ENDO = 0,
49  MID,
50  EPI
51 } HeartLayerType;
52 
54 typedef unsigned HeartRegionType;
55 
56 
61 template<unsigned SPACE_DIM>
63 {
64 private:
65 
67  static const double LEFT_SEPTUM_SIZE;
69  static const double RIGHT_SEPTUM_SIZE;
70 
72  std::vector<unsigned> mEpiSurface;
73 
75  std::vector<unsigned> mEndoSurface;
76 
78  std::vector<unsigned> mLVSurface;
79 
81  std::vector<unsigned> mRVSurface;
82 
96  void GetNodesAtSurface(const std::string& rSurfaceFileName,
97  std::vector<unsigned>& rSurfaceNodes,
98  bool indexFromZero=true) const;
99 
106  void ProcessLine(const std::string& rLineFromFile,
107  std::set<unsigned>& rSurfaceNodeIndexSet,
108  unsigned offset) const;
109 
117  double GetDistanceToEndo(unsigned nodeIndex);
118 
125  double GetDistanceToEpi(unsigned nodeIndex);
126 
129 
131  std::vector<double> mDistMapEpicardium;
132 
134  std::vector<double> mDistMapEndocardium;
135 
137  std::vector<double> mDistMapRightVentricle;
138 
140  std::vector<double> mDistMapLeftVentricle;
141 
144 
146  std::vector<HeartLayerType> mLayerForEachNode;
147 
153  ChasteCuboid<SPACE_DIM> CalculateBoundingBoxOfSurface(const std::vector<unsigned>& rSurfaceNodes);
154 
155 public:
157 
162  static const HeartRegionType LEFT_SEPTUM=1003;
164  static const HeartRegionType RIGHT_SEPTUM=1004;
170  static const HeartRegionType UNKNOWN=1007;
171 
182  const std::string& rEpiFile,
183  const std::string& rEndoFile,
184  bool indexFromZero);
185 
186 
202  const std::string& rEpiFile,
203  const std::string& rLVFile,
204  const std::string& rRVFile,
205  bool indexFromZero);
206 
216  HeartGeometryInformation (std::string nodeHeterogeneityFileName);
217 
222  HeartRegionType GetHeartRegion (unsigned nodeIndex) const;
223 
228  std::vector<double>& rGetDistanceMapEpicardium()
229  {
230  return mDistMapEpicardium;
231  }
232 
237  std::vector<double>& rGetDistanceMapEndocardium()
238  {
239  assert(mNumberOfSurfacesProvided==2);
240  return mDistMapEndocardium;
241  }
242 
247  std::vector<double>& rGetDistanceMapRightVentricle()
248  {
249  assert(mNumberOfSurfacesProvided==3);
250  return mDistMapRightVentricle;
251  }
252 
257  std::vector<double>& rGetDistanceMapLeftVentricle()
258  {
259  assert(mNumberOfSurfacesProvided==3);
260  return mDistMapLeftVentricle;
261  }
262 
264  const std::vector<unsigned>& rGetNodesOnEpiSurface()
265  {
266  return mEpiSurface;
267  }
268 
269 
271  const std::vector<unsigned>& rGetNodesOnEndoSurface()
272  {
273  assert(mNumberOfSurfacesProvided==2);
274  return mEndoSurface;
275  }
276 
278  const std::vector<unsigned>& rGetNodesOnLVSurface()
279  {
280  assert(mNumberOfSurfacesProvided==3);
281  return mLVSurface;
282  }
283 
285  const std::vector<unsigned>& rGetNodesOnRVSurface()
286  {
287  assert(mNumberOfSurfacesProvided==3);
288  return mRVSurface;
289  }
290 
294  const std::vector<HeartLayerType>& rGetLayerForEachNode()
295  {
296  assert(mLayerForEachNode.size()>0);
297  return mLayerForEachNode;
298  }
299 
305  double CalculateRelativeWallPosition(unsigned nodeIndex);
306 
312  void DetermineLayerForEachNode(double epiFraction, double endoFraction);
313 
321  void WriteLayerForEachNode(std::string outputDir, std::string file);
322 
331  {
333  }
342  {
344  }
353  {
355  }
364  {
366  }
367 };
368 #endif //HEARTGEOMETRYINFORMATION_HPP_
369 
std::vector< unsigned > mEndoSurface
ChasteCuboid< SPACE_DIM > CalculateBoundingBoxOfEpi()
const std::vector< HeartLayerType > & rGetLayerForEachNode()
static const HeartRegionType RIGHT_VENTRICLE_SURFACE
void DetermineLayerForEachNode(double epiFraction, double endoFraction)
std::vector< double > mDistMapEpicardium
std::vector< double > & rGetDistanceMapEndocardium()
const std::vector< unsigned > & rGetNodesOnEndoSurface()
std::vector< double > mDistMapRightVentricle
std::vector< HeartLayerType > mLayerForEachNode
static const HeartRegionType LEFT_SEPTUM
void WriteLayerForEachNode(std::string outputDir, std::string file)
void GetNodesAtSurface(const std::string &rSurfaceFileName, std::vector< unsigned > &rSurfaceNodes, bool indexFromZero=true) const
std::vector< unsigned > mRVSurface
static const HeartRegionType RIGHT_SEPTUM
static const HeartRegionType UNKNOWN
const std::vector< unsigned > & rGetNodesOnEpiSurface()
std::vector< double > & rGetDistanceMapEpicardium()
ChasteCuboid< SPACE_DIM > CalculateBoundingBoxOfLV()
double CalculateRelativeWallPosition(unsigned nodeIndex)
ChasteCuboid< SPACE_DIM > CalculateBoundingBoxOfSurface(const std::vector< unsigned > &rSurfaceNodes)
double GetDistanceToEpi(unsigned nodeIndex)
std::vector< double > & rGetDistanceMapLeftVentricle()
ChasteCuboid< SPACE_DIM > CalculateBoundingBoxOfRV()
std::vector< double > & rGetDistanceMapRightVentricle()
const std::vector< unsigned > & rGetNodesOnRVSurface()
HeartGeometryInformation(AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > &rMesh, const std::string &rEpiFile, const std::string &rEndoFile, bool indexFromZero)
const std::vector< unsigned > & rGetNodesOnLVSurface()
ChasteCuboid< SPACE_DIM > CalculateBoundingBoxOfEndo()
void ProcessLine(const std::string &rLineFromFile, std::set< unsigned > &rSurfaceNodeIndexSet, unsigned offset) const
static const HeartRegionType LEFT_VENTRICLE_SURFACE
std::vector< double > mDistMapLeftVentricle
static const HeartRegionType RIGHT_VENTRICLE_WALL
HeartRegionType GetHeartRegion(unsigned nodeIndex) const
static const HeartRegionType LEFT_VENTRICLE_WALL
double GetDistanceToEndo(unsigned nodeIndex)
AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > * mpMesh
std::vector< double > mDistMapEndocardium
std::vector< unsigned > mLVSurface
std::vector< unsigned > mEpiSurface