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Commit 71cb3b50 authored by Kirill Terekhov's avatar Kirill Terekhov
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Fixes for kdtree used in mesh adaptation

parent 14da724f
Pipeline #173 failed with stages
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      Source/Headers/inmost_mesh.h
      View file @ 71cb3b50
      ......@@ -3399,20 +3399,9 @@ namespace INMOST
      {
      public:
      inline static bool cell_point(const Cell & c, const Storage::real p[3])
      {
      return c.Inside(p);
      }
      inline static bool cell_point(const Cell & c, const Storage::real p[3]) {return c.Inside(p);}
      template<typename bbox_type>
      inline static int bbox_point(const Storage::real p[3], const bbox_type bbox[6])
      {
      for(int i = 0; i < 3; i++)
      {
      if( p[i] < bbox[i*2]-1.0e-4 || p[i] > bbox[i*2+1]+1.0e-4 )
      return 0;
      }
      return 1;
      }
      inline static int bbox_point(const Storage::real p[3], const bbox_type bbox[6], bool print = false);
      private:
      struct entry
      {
      ......@@ -3431,250 +3420,21 @@ namespace INMOST
      INMOST_DATA_ENUM_TYPE size;
      float bbox[6];
      SearchKDTree * children;
      static int cmpElements0(const void * a,const void * b)
      {
      const entry * ea = ((const entry *)a);
      const entry * eb = ((const entry *)b);
      float ad = ea->xyz[0];
      float bd = eb->xyz[0];
      return (ad > bd) - (ad < bd);
      }
      static int cmpElements1(const void * a,const void * b)
      {
      const entry * ea = ((const entry *)a);
      const entry * eb = ((const entry *)b);
      float ad = ea->xyz[1];
      float bd = eb->xyz[1];
      return (ad > bd) - (ad < bd);
      }
      static int cmpElements2(const void * a,const void * b)
      {
      const entry * ea = ((const entry *)a);
      const entry * eb = ((const entry *)b);
      float ad = ea->xyz[2];
      float bd = eb->xyz[2];
      return (ad > bd) - (ad < bd);
      }
      inline static unsigned int flip(const unsigned int * fp)
      {
      unsigned int mask = -((int)(*fp >> 31)) | 0x80000000;
      return *fp ^ mask;
      }
      #define _m0(x) (x & 0x7FF)
      #define _m1(x) (x >> 11 & 0x7FF)
      #define _m2(x) (x >> 22 )
      void radix_sort(int dim, struct entry * temp)
      {
      unsigned int i;
      const unsigned int kHist = 2048;
      unsigned int b0[kHist * 3];
      unsigned int *b1 = b0 + kHist;
      unsigned int *b2 = b1 + kHist;
      memset(b0,0,sizeof(unsigned int)*kHist*3);
      for (i = 0; i < size; i++)
      {
      unsigned int fi = flip((unsigned int *)&set[i].xyz[dim]);
      ++b0[_m0(fi)]; ++b1[_m1(fi)]; ++b2[_m2(fi)];
      }
      {
      unsigned int sum0 = 0, sum1 = 0, sum2 = 0;
      for (i = 0; i < kHist; i++)
      {
      b0[kHist-1] = b0[i] + sum0; b0[i] = sum0 - 1; sum0 = b0[kHist-1];
      b1[kHist-1] = b1[i] + sum1; b1[i] = sum1 - 1; sum1 = b1[kHist-1];
      b2[kHist-1] = b2[i] + sum2; b2[i] = sum2 - 1; sum2 = b2[kHist-1];
      }
      }
      for (i = 0; i < size; i++) temp[++b0[_m0(flip((unsigned int *)&set[i].xyz[dim]))]] = set[i];
      for (i = 0; i < size; i++) set[++b1[_m1(flip((unsigned int *)&temp[i].xyz[dim]))]] = temp[i];
      for (i = 0; i < size; i++) temp[++b2[_m2(flip((unsigned int *)&set[i].xyz[dim]))]] = set[i];
      for (i = 0; i < size; i++) set[i] = temp[i];
      }
      void kdtree_build(int dim, int & done, int total, struct entry * temp)
      {
      if( size > 1 )
      {
      if( size > 128 ) radix_sort(dim,temp); else
      switch(dim)
      {
      case 0: qsort(set,size,sizeof(entry),cmpElements0);break;
      case 1: qsort(set,size,sizeof(entry),cmpElements1);break;
      case 2: qsort(set,size,sizeof(entry),cmpElements2);break;
      }
      children = static_cast<SearchKDTree *>(malloc(sizeof(SearchKDTree)*2));//new kdtree[2];
      children[0].children = NULL;
      children[0].set = set;
      children[0].size = size/2;
      children[0].m = m;
      children[1].children = NULL;
      children[1].set = set+size/2;
      children[1].size = size - size/2;
      children[1].m = m;
      children[0].kdtree_build((dim+1)%3,done,total,temp);
      children[1].kdtree_build((dim+1)%3,done,total,temp);
      for(int k = 0; k < 3; k++)
      {
      bbox[0+2*k] = std::min<float>(children[0].bbox[0+2*k],children[1].bbox[0+2*k]);
      bbox[1+2*k] = std::max<float>(children[0].bbox[1+2*k],children[1].bbox[1+2*k]);
      }
      }
      else
      {
      assert(size == 1);
      {
      ElementArray<Node> nodes = Element(m,set[0].e)->getNodes();
      bbox[0] = bbox[2] = bbox[4] = 1.0e20f;
      bbox[1] = bbox[3] = bbox[5] = -1.0e20f;
      for(ElementArray<Node>::size_type k = 0; k < nodes.size(); ++k)
      {
      Storage::real_array coords = nodes[k].Coords();
      for(Storage::real_array::size_type q = 0; q < coords.size(); q++)
      {
      bbox[q*2+0] = std::min<float>(bbox[q*2+0],(float)coords[q]);
      bbox[q*2+1] = std::max<float>(bbox[q*2+1],(float)coords[q]);
      }
      }
      for(int k = m->GetDimensions(); k < 3; ++k)
      {
      bbox[k*2+0] = -1.0e20f;
      bbox[k*2+1] = 1.0e20f;
      }
      }
      }
      }
      static int cmpElements0(const void * a,const void * b);
      static int cmpElements1(const void * a,const void * b);
      static int cmpElements2(const void * a,const void * b);
      inline static unsigned int flip(const unsigned int * fp);
      void radix_sort(int dim, struct entry * temp);
      void kdtree_build(int dim, int & done, int total, struct entry * temp);
      SearchKDTree() : set(NULL), size(0), children(NULL) {}
      Cell SubSearchCell(const Storage::real p[3], bool print)
      {
      Cell ret = InvalidCell();
      if( size == 1 )
      {
      if( print ) std::cout << "test cell " << GetHandleID(set[0].e) << std::endl;
      if( m->HideMarker() )
      {
      m->SwapModification(false);
      if( cell_point(Cell(m,set[0].e),p) )
      ret = Cell(m,set[0].e);
      m->SwapModification(false);
      }
      else
      {
      if( cell_point(Cell(m,set[0].e),p) )
      ret = Cell(m,set[0].e);
      }
      }
      else
      {
      assert(size > 1);
      if( bbox_point(p,bbox) )
      {
      if( print )
      {
      std::cout << "point " << p[0] << " " << p[1] << " " << p[2] << " is in bbox ";
      std::cout << " x " << bbox[0] << ":" << bbox[1];
      std::cout << " y " << bbox[2] << ":" << bbox[3];
      std::cout << " z " << bbox[4] << ":" << bbox[5];
      std::cout << std::endl;
      }
      if( print ) std::cout << "try left child" << std::endl;
      ret = children[0].SubSearchCell(p,print);
      if( print ) std::cout << "ret " << (ret.isValid() ? ret.LocalID() : -1) << std::endl;
      if( !ret.isValid() )
      {
      if( print ) std::cout << "try right child" << std::endl;
      ret = children[1].SubSearchCell(p,print);
      if( print ) std::cout << "ret " << (ret.isValid() ? ret.LocalID() : -1) << std::endl;
      }
      }
      else if( print )
      {
      std::cout << "point " << p[0] << " " << p[1] << " " << p[2] << " is not in bbox ";
      std::cout << " x " << bbox[0] << ":" << bbox[1];
      std::cout << " y " << bbox[2] << ":" << bbox[3];
      std::cout << " z " << bbox[4] << ":" << bbox[5];
      std::cout << std::endl;
      }
      }
      return ret;
      }
      void clear_children() { if( children ) {children[0].clear_children(); children[1].clear_children(); free(children);}}
      Cell SubSearchCell(const Storage::real p[3], bool print);
      void clear_children();
      public:
      SearchKDTree(Mesh * m) : m(m), children(NULL)
      {
      size = m->NumberOfCells();
      if( size )
      {
      set = new entry[size];
      INMOST_DATA_ENUM_TYPE k = 0;
      for(Mesh::iteratorCell it = m->BeginCell(); it != m->EndCell(); ++it)
      {
      set[k].e = it->GetHandle();
      Storage::real cnt[3] = {0,0,0};
      m->GetGeometricData(set[k].e,CENTROID,cnt);
      set[k].xyz[0] = (float)cnt[0];
      set[k].xyz[1] = (float)cnt[1];
      set[k].xyz[2] = (float)cnt[2];
      ++k;
      }
      int done = 0, total = size;
      struct entry * temp = new entry[size];
      kdtree_build(0,done,total,temp);
      delete [] temp;
      if( size > 1 )
      {
      for(int k = 0; k < 3; k++)
      {
      bbox[0+2*k] = std::min<float>(children[0].bbox[0+2*k],children[1].bbox[0+2*k]);
      bbox[1+2*k] = std::max<float>(children[0].bbox[1+2*k],children[1].bbox[1+2*k]);
      }
      }
      }
      }
      SearchKDTree(Mesh * m, HandleType * _set, unsigned set_size) : m(m), children(NULL)
      {
      size = set_size;
      if( size )
      {
      set = new entry[size];
      for(unsigned k = 0; k < set_size; ++k)
      {
      set[k].e = _set[k];
      Storage::real cnt[3] = {0,0,0};
      m->GetGeometricData(set[k].e,CENTROID,cnt);
      set[k].xyz[0] = (float)cnt[0];
      set[k].xyz[1] = (float)cnt[1];
      set[k].xyz[2] = (float)cnt[2];
      }
      int done = 0, total = size;
      struct entry * temp = new entry[size];
      kdtree_build(0,done,total,temp);
      delete [] temp;
      if( size > 1 )
      {
      for(int k = 0; k < 3; k++)
      {
      bbox[0+2*k] = std::min<float>(children[0].bbox[0+2*k],children[1].bbox[0+2*k]);
      bbox[1+2*k] = std::max<float>(children[0].bbox[1+2*k],children[1].bbox[1+2*k]);
      }
      }
      }
      else set = NULL;
      }
      ~SearchKDTree()
      {
      if( size )
      {
      delete [] set;
      clear_children();
      }
      }
      Cell SearchCell(const Storage::real * point, bool print = false)
      {
      return SubSearchCell(point, print);
      }
      SearchKDTree(Mesh * m);
      SearchKDTree(Mesh * m, HandleType * _set, unsigned set_size);
      ~SearchKDTree();
      Cell SearchCell(const Storage::real * point, bool print = false);
      };
      ......
      Source/Mesh/CMakeLists.txt
      View file @ 71cb3b50
      ......@@ -13,6 +13,7 @@ set(SOURCE
      ${CMAKE_CURRENT_SOURCE_DIR}/iterator.cpp
      ${CMAKE_CURRENT_SOURCE_DIR}/modify.cpp
      ${CMAKE_CURRENT_SOURCE_DIR}/parallel.cpp
      ${CMAKE_CURRENT_SOURCE_DIR}/kdtree.cpp
      PARENT_SCOPE
      )
      ......@@ -20,4 +21,4 @@ set(HEADER
      ${HEADER}
      ${CMAKE_CURRENT_SOURCE_DIR}/incident_matrix.hpp
      PARENT_SCOPE
      )
      \ No newline at end of file
      )
      Source/Mesh/kdtree.cpp 0 → 100644
      View file @ 71cb3b50
      #include "inmost_mesh.h"
      #if defined(USE_MESH)
      #define _m0(x) (x & 0x7FF)
      #define _m1(x) (x >> 11 & 0x7FF)
      #define _m2(x) (x >> 22 )
      namespace INMOST
      {
      template<typename bbox_type>
      inline int SearchKDTree::bbox_point(const Storage::real p[3], const bbox_type bbox[6], bool print)
      {
      for(int i = 0; i < 3; i++)
      {
      if( p[i] < bbox[i*2]-1.0e-3 || p[i] > bbox[i*2+1]+1.0e-3 )
      {
      if( print )
      {
      std::cout << "fail on " << i << " ";
      if( p[i] < bbox[i*2]-1.0e-3 ) std::cout << p[i] << " is less then " << bbox[i*2]-1.0e-3 << "(" << bbox[i*2] << ")";
      if( p[i] > bbox[i*2+1]+1.0e-3 ) std::cout << p[i] << " is greater then " << bbox[i*2+1]+1.0e-3 << "(" << bbox[i*2+1] << ")";
      std::cout << std::endl;
      }
      return 0;
      }
      }
      if( print ) std::cout << "all ok!" << std::endl;
      return 1;
      }
      int SearchKDTree::cmpElements0(const void * a,const void * b)
      {
      const entry * ea = ((const entry *)a);
      const entry * eb = ((const entry *)b);
      float ad = ea->xyz[0];
      float bd = eb->xyz[0];
      return (ad > bd) - (ad < bd);
      }
      int SearchKDTree::cmpElements1(const void * a,const void * b)
      {
      const entry * ea = ((const entry *)a);
      const entry * eb = ((const entry *)b);
      float ad = ea->xyz[1];
      float bd = eb->xyz[1];
      return (ad > bd) - (ad < bd);
      }
      int SearchKDTree::cmpElements2(const void * a,const void * b)
      {
      const entry * ea = ((const entry *)a);
      const entry * eb = ((const entry *)b);
      float ad = ea->xyz[2];
      float bd = eb->xyz[2];
      return (ad > bd) - (ad < bd);
      }
      inline unsigned int SearchKDTree::flip(const unsigned int * fp)
      {
      unsigned int mask = -((int)(*fp >> 31)) | 0x80000000;
      return *fp ^ mask;
      }
      void SearchKDTree::radix_sort(int dim, struct entry * temp)
      {
      unsigned int i;
      const unsigned int kHist = 2048;
      unsigned int b0[kHist * 3];
      unsigned int *b1 = b0 + kHist;
      unsigned int *b2 = b1 + kHist;
      memset(b0,0,sizeof(unsigned int)*kHist*3);
      for (i = 0; i < size; i++)
      {
      unsigned int fi = flip((unsigned int *)&set[i].xyz[dim]);
      ++b0[_m0(fi)]; ++b1[_m1(fi)]; ++b2[_m2(fi)];
      }
      {
      unsigned int sum0 = 0, sum1 = 0, sum2 = 0;
      for (i = 0; i < kHist; i++)
      {
      b0[kHist-1] = b0[i] + sum0; b0[i] = sum0 - 1; sum0 = b0[kHist-1];
      b1[kHist-1] = b1[i] + sum1; b1[i] = sum1 - 1; sum1 = b1[kHist-1];
      b2[kHist-1] = b2[i] + sum2; b2[i] = sum2 - 1; sum2 = b2[kHist-1];
      }
      }
      for (i = 0; i < size; i++) temp[++b0[_m0(flip((unsigned int *)&set[i].xyz[dim]))]] = set[i];
      for (i = 0; i < size; i++) set[++b1[_m1(flip((unsigned int *)&temp[i].xyz[dim]))]] = temp[i];
      for (i = 0; i < size; i++) temp[++b2[_m2(flip((unsigned int *)&set[i].xyz[dim]))]] = set[i];
      for (i = 0; i < size; i++) set[i] = temp[i];
      }
      void SearchKDTree::kdtree_build(int dim, int & done, int total, struct entry * temp)
      {
      if( size > 1 )
      {
      if( size > 128 ) radix_sort(dim,temp); else
      switch(dim)
      {
      case 0: qsort(set,size,sizeof(entry),cmpElements0);break;
      case 1: qsort(set,size,sizeof(entry),cmpElements1);break;
      case 2: qsort(set,size,sizeof(entry),cmpElements2);break;
      }
      children = static_cast<SearchKDTree *>(malloc(sizeof(SearchKDTree)*2));//new kdtree[2];
      children[0].children = NULL;
      children[0].set = set;
      children[0].size = size/2;
      children[0].m = m;
      children[1].children = NULL;
      children[1].set = set+size/2;
      children[1].size = size - size/2;
      children[1].m = m;
      children[0].kdtree_build((dim+1)%3,done,total,temp);
      children[1].kdtree_build((dim+1)%3,done,total,temp);
      for(int k = 0; k < 3; k++)
      {
      bbox[0+2*k] = std::min<float>(children[0].bbox[0+2*k],children[1].bbox[0+2*k]);
      bbox[1+2*k] = std::max<float>(children[0].bbox[1+2*k],children[1].bbox[1+2*k]);
      }
      }
      else
      {
      assert(size == 1);
      {
      bool checkm = false, invm = false;
      if( m->HideMarker() )
      {
      checkm = true;
      if( m->GetMarker(set[0].e,m->HideMarker()) ) invm = true;
      }
      Element::adj_type & nodes = m->HighConn(set[0].e);
      bbox[0] = bbox[2] = bbox[4] = 1.0e20f;
      bbox[1] = bbox[3] = bbox[5] = -1.0e20f;
      if( checkm )
      {
      for(unsigned k = 0; k < nodes.size(); ++k)
      {
      bool hidn = m->GetMarker(nodes[k],m->HideMarker());
      bool newn = m->GetMarker(nodes[k],m->NewMarker());
      if( invm && newn ) continue;
      if( !invm && hidn ) continue;
      Storage::real_array coords = m->RealArrayDF(nodes[k],m->CoordsTag());;
      for(unsigned q = 0; q < coords.size(); q++)
      {
      bbox[q*2+0] = std::min<float>(bbox[q*2+0],(float)coords[q]);
      bbox[q*2+1] = std::max<float>(bbox[q*2+1],(float)coords[q]);
      }
      }
      }
      else for(unsigned k = 0; k < nodes.size(); ++k)
      {
      Storage::real_array coords = m->RealArrayDF(set[0].e,m->CoordsTag());;
      for(unsigned q = 0; q < coords.size(); q++)
      {
      bbox[q*2+0] = std::min<float>(bbox[q*2+0],(float)coords[q]);
      bbox[q*2+1] = std::max<float>(bbox[q*2+1],(float)coords[q]);
      }
      }
      for(int k = m->GetDimensions(); k < 3; ++k)
      {
      bbox[k*2+0] = -1.0e20f;
      bbox[k*2+1] = 1.0e20f;
      }
      }
      }
      }
      Cell SearchKDTree::SubSearchCell(const Storage::real p[3], bool print)
      {
      Cell ret = InvalidCell();
      if( size == 1 )
      {
      if( print ) std::cout << "test cell " << GetHandleID(set[0].e) << std::endl;
      if( m->HideMarker() && m->GetMarker(set[0].e,m->HideMarker()) )
      {
      m->SwapModification(false);
      if( cell_point(Cell(m,set[0].e),p) )
      ret = Cell(m,set[0].e);
      m->SwapModification(false);
      }
      else
      {
      if( cell_point(Cell(m,set[0].e),p) )
      ret = Cell(m,set[0].e);
      }
      }
      else
      {
      assert(size > 1);
      if( bbox_point(p,bbox) )
      {
      if( print )
      {
      std::cout << "point " << p[0] << " " << p[1] << " " << p[2] << " is in bbox ";
      std::cout << " x " << bbox[0] << ":" << bbox[1];
      std::cout << " y " << bbox[2] << ":" << bbox[3];
      std::cout << " z " << bbox[4] << ":" << bbox[5];
      std::cout << std::endl;
      }
      if( print ) std::cout << "try left child" << std::endl;
      ret = children[0].SubSearchCell(p,print);
      if( print ) std::cout << "ret " << (ret.isValid() ? ret.LocalID() : -1) << std::endl;
      if( !ret.isValid() )
      {
      if( print ) std::cout << "try right child" << std::endl;
      ret = children[1].SubSearchCell(p,print);
      if( print ) std::cout << "ret " << (ret.isValid() ? ret.LocalID() : -1) << std::endl;
      }
      }
      else if( print )
      {
      std::cout << "point " << p[0] << " " << p[1] << " " << p[2] << " is not in bbox ";
      std::cout << " x " << bbox[0] << ":" << bbox[1];
      std::cout << " y " << bbox[2] << ":" << bbox[3];
      std::cout << " z " << bbox[4] << ":" << bbox[5];
      std::cout << std::endl;
      bbox_point(p,bbox,true);
      }
      }
      return ret;
      }
      void SearchKDTree::clear_children()
      {
      if( children )
      {
      children[0].clear_children();
      children[1].clear_children();
      free(children);
      }
      }
      SearchKDTree::SearchKDTree(Mesh * m) : m(m), children(NULL)
      {
      size = m->NumberOfCells();
      if( size )
      {
      set = new entry[size];
      INMOST_DATA_ENUM_TYPE k = 0;
      for(Mesh::iteratorCell it = m->BeginCell(); it != m->EndCell(); ++it)
      {
      set[k].e = it->GetHandle();
      Storage::real cnt[3] = {0,0,0};
      m->GetGeometricData(set[k].e,CENTROID,cnt);
      set[k].xyz[0] = (float)cnt[0];
      set[k].xyz[1] = (float)cnt[1];
      set[k].xyz[2] = (float)cnt[2];
      ++k;
      }
      int done = 0, total = size;
      struct entry * temp = new entry[size];
      kdtree_build(0,done,total,temp);
      delete [] temp;
      if( size > 1 )
      {
      for(int k = 0; k < 3; k++)
      {
      bbox[0+2*k] = std::min<float>(children[0].bbox[0+2*k],children[1].bbox[0+2*k]);
      bbox[1+2*k] = std::max<float>(children[0].bbox[1+2*k],children[1].bbox[1+2*k]);
      }
      }
      }
      }
      SearchKDTree::SearchKDTree(Mesh * m, HandleType * _set, unsigned set_size) : m(m), children(NULL)
      {
      size = set_size;
      if( size )
      {
      set = new entry[size];
      for(unsigned k = 0; k < set_size; ++k)
      {
      set[k].e = _set[k];
      Storage::real cnt[3] = {0,0,0};
      m->GetGeometricData(set[k].e,CENTROID,cnt);
      set[k].xyz[0] = (float)cnt[0];
      set[k].xyz[1] = (float)cnt[1];
      set[k].xyz[2] = (float)cnt[2];
      }
      int done = 0, total = size;
      struct entry * temp = new entry[size];
      kdtree_build(0,done,total,temp);
      delete [] temp;
      if( size > 1 )
      {
      for(int k = 0; k < 3; k++)
      {
      bbox[0+2*k] = std::min<float>(children[0].bbox[0+2*k],children[1].bbox[0+2*k]);
      bbox[1+2*k] = std::max<float>(children[0].bbox[1+2*k],children[1].bbox[1+2*k]);
      }
      }
      }
      else set = NULL;
      }
      SearchKDTree::~SearchKDTree()
      {
      if( size )
      {
      delete [] set;
      clear_children();
      }
      }
      Cell SearchKDTree::SearchCell(const Storage::real * point, bool print)
      {
      return SubSearchCell(point, print);
      }
      }
      #endif
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