Clipper
xmap.h
1 
4 //C Copyright (C) 2000-2006 Kevin Cowtan and University of York
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43 
44 
45 #ifndef CLIPPER_XMAP
46 #define CLIPPER_XMAP
47 
48 
49 #include "fftmap.h"
50 #include "fftmap_sparse.h"
51 #include "derivs.h"
52 
53 
54 namespace clipper
55 {
56 
58  {
59  public:
60  class Key
61  {
62  public:
63  Key( const Spgr_descr& spgr_descr, const Grid_sampling& grid ) :
64  spgr_descr_(spgr_descr), grid_sampling_(grid) {}
65  const Spgr_descr& spgr_descr() const { return spgr_descr_; }
66  const Grid_sampling& grid_sampling() const { return grid_sampling_; }
67  private:
68  Spgr_descr spgr_descr_;
69  Grid_sampling grid_sampling_;
70  };
71 
72  Xmap_cacheobj( const Key& xmap_cachekey );
73  bool matches( const Key& xmap_cachekey ) const;
74  String format() const;
75  // data
76  Key key;
80  int nsym; // number of symops
81  std::vector<unsigned char> asu;
82  std::vector<Isymop> isymop;
83  std::vector<int> du, dv, dw;
86  static Mutex mutex;
87  };
88 
89 
91 
100  class Xmap_base
101  {
102  public:
103  enum FFTtype { Default, Normal, Sparse };
104 
106  bool is_null() const;
107 
109  const Cell& cell() const { return cell_; }
111  const Spacegroup& spacegroup() const { return spacegroup_; }
113  const Grid_sampling& grid_sampling() const { return grid_sam_; }
115  const Grid_range& grid_asu() const { return cacheref.data().asu_grid; }
117 
118  inline Coord_grid coord_of( const int& index ) const
119  { return cacheref.data().map_grid.deindex( index ); }
121 
123  inline int index_of( const Coord_grid& coord ) const {
124  if ( cacheref.data().asu_grid.in_grid( coord ) ) {
125  const int i = cacheref.data().map_grid.index( coord );
126  if ( asu[ i ] == 0 ) return i;
127  }
128  return -1;
129  }
131  Coord_grid to_map_unit( const Coord_grid& pos ) const
132  { return pos.unit( grid_sam_ ); }
133 
135  const RTop<>& operator_orth_grid() const { return rt_orth_grid; }
137  const RTop<>& operator_grid_orth() const { return rt_grid_orth; }
139 
141  inline Coord_orth coord_orth( const Coord_map& cm ) const
142  { return Coord_orth( rt_grid_orth.rot()*cm ); }
144 
146  inline Coord_map coord_map( const Coord_orth& co ) const
147  { return Coord_map ( rt_orth_grid.rot()*co ); }
148 
150  bool in_map( const Coord_grid& ) const { return true; }
152  template<class I> bool in_map( const Coord_map& cm ) const { return true; }
153 
155  int multiplicity( const Coord_grid& pos ) const;
156 
158 
163  {
164  public:
166  inline const Xmap_base& base_xmap() const { return *map_; }
168  inline const int& index() const { return index_; }
170  bool last() const { return ( index_ >= map_->map_grid.size() ); }
171  protected:
173  const Xmap_base* map_;
175  int index_;
176  };
177 
179 
191  {
192  public:
196  explicit Map_reference_index( const Xmap_base& map )
197  { map_ = &map; index_=0; next(); }
199  Map_reference_index( const Xmap_base& map, const Coord_grid& pos ) { map_ = &map; int sym; map_->find_sym( pos, index_, sym ); }
201  inline Coord_grid coord() const
202  { return map_->map_grid.deindex(index_); }
204  inline const Coord_orth coord_orth() const
205  { return Coord_orth( map_->rt_grid_orth.rot() * coord().coord_map() ); }
208  { int sym; map_->find_sym( pos, index_, sym ); return *this; }
211  do {
212  index_++; if ( last() ) break;
213  } while ( map_->asu[index_] != 0 );
214  return *this;
215  }
217  /* Use for e.g. peak search. Valid for -1 <= du/dv/dw <= 1 only.
218  \param du/dv/dw Coordinate offset. \return Map index. */
219  inline int index_offset(const int& du,const int& dv,const int& dw) const {
220  int i = index_ + du*map_->du[0] + dv*map_->dv[0] + dw*map_->dw[0];
221  if ( map_->asu[i] != 0 ) { i = map_->map_grid.index( map_->to_map_unit( map_->map_grid.deindex(i).transform( map_->isymop[map_->asu[i]-1] ) ) ); }
222  return i;
223  }
224  // inherited functions listed for documentation purposes
225  //-- const Xmap_base& base_xmap() const;
226  //-- const int& index() const;
227  //-- bool last() const;
228  };
229 
231 
243  {
244  public:
248  explicit Map_reference_coord( const Xmap_base& map )
249  { map_ = &map; index_ = 0; next(); }
251  Map_reference_coord( const Xmap_base& map, const Coord_grid& pos ) {
252  map_ = &map;
253  pos_ = pos;
254  map_->find_sym( pos_, index_, sym_ );
255  }
257  inline const Coord_grid& coord() const { return pos_; }
259  inline const Coord_orth coord_orth() const
260  { return Coord_orth( map_->rt_grid_orth.rot() * coord().coord_map() ); }
262  inline const int& sym() const { return sym_; }
266 
268  sym_ = 0;
269  do {
270  index_++; if ( last() ) break;
271  } while ( map_->asu[index_] != 0 );
273  return *this;
274  }
275  // Increment u,v,w
276  inline Map_reference_coord& next_u() { pos_.u()++; index_ += map_->du[sym_]; if (map_->asu[index_] != 0) edge(); return *this; }
277  inline Map_reference_coord& next_v() { pos_.v()++; index_ += map_->dv[sym_]; if (map_->asu[index_] != 0) edge(); return *this; }
278  inline Map_reference_coord& next_w() { pos_.w()++; index_ += map_->dw[sym_]; if (map_->asu[index_] != 0) edge(); return *this; }
279  inline Map_reference_coord& prev_u() { pos_.u()--; index_ -= map_->du[sym_]; if (map_->asu[index_] != 0) edge(); return *this; }
280  inline Map_reference_coord& prev_v() { pos_.v()--; index_ -= map_->dv[sym_]; if (map_->asu[index_] != 0) edge(); return *this; }
281  inline Map_reference_coord& prev_w() { pos_.w()--; index_ -= map_->dw[sym_]; if (map_->asu[index_] != 0) edge(); return *this; }
282  inline Map_reference_coord& operator =( const Coord_grid& pos )
284  { return set_coord( pos ); }
285  // inherited functions listed for documentation purposes
286  //-- const Xmap_base& base_xmap() const;
287  //-- const int& index() const;
288  //-- bool last() const;
289 
290  protected:
292  int sym_;
295 
297  void edge();
298  };
299 
301  Map_reference_index first() const { return Map_reference_index( *this ); }
305  static FFTtype& default_type() { return default_type_; }
306  protected:
308  const unsigned char* asu;
309  const Isymop* isymop;
310  const int* du;
311  const int* dv;
312  const int* dw;
315  int nsym;
316 
320 
323 
325  Xmap_base();
327  void init( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling& grid_sam );
328  inline void find_sym( const Coord_grid& base, int& index, int& sym ) const;
329  void asu_error( const Coord_grid& pos ) const;
330 
331  static FFTtype default_type_;
332 
333  friend class Xmap_base::Map_reference_base;
334  friend class Xmap_base::Map_reference_index;
335  friend class Xmap_base::Map_reference_coord;
336  };
337 
338 
339 
340 
342 
356  template<class T> class Xmap : public Xmap_base
357  {
358  public:
360  Xmap() {}
362  Xmap( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling& grid_sam ) { init( spacegroup, cell, grid_sam ); }
364  void init( const Spacegroup& spacegroup, const Cell& cell, const Grid_sampling& grid_sam ) { Xmap_base::init( spacegroup, cell, grid_sam ); list.resize( cacheref.data().asu.size() ); }
365 
367  inline const T& operator[] (const Xmap_base::Map_reference_index& ix) const
368  { return list[ix.index()]; }
371  { return list[ix.index()]; }
372 
374  inline const T& operator[] (const Xmap_base::Map_reference_coord& ix) const
375  { return list[ix.index()]; }
378  { return list[ix.index()]; }
379 
381  const T& get_data( const Coord_grid& pos ) const;
383  void set_data( const Coord_grid& pos, const T& val );
385  inline const T& get_data( const int& index ) const;
387  bool set_data( const int& index, const T& val );
388 
390  template<class I> T interp( const Coord_frac& pos ) const;
392  template<class I> void interp_grad( const Coord_frac& pos, T& val, Grad_frac<T>& grad ) const;
394  template<class I> void interp_curv( const Coord_frac& pos, T& val, Grad_frac<T>& grad, Curv_frac<T>& curv ) const;
396  template<class I> T interp( const Coord_map& pos ) const;
398  template<class I> void interp_grad( const Coord_map& pos, T& val, Grad_map<T>& grad ) const;
400  template<class I> void interp_curv( const Coord_map& pos, T& val, Grad_map<T>& grad, Curv_map<T>& curv ) const;
401 
403  template<class H> void fft_from( const H& fphidata, const FFTtype type = Default );
405  template<class H> void fft_to ( H& fphidata, const FFTtype type = Default ) const;
406 
407  // inherited functions listed for documentation purposes
408  //-- const Cell& cell() const;
409  //-- const Spacegroup& spacegroup() const;
410  //-- const Grid_sampling& grid_sampling() const;
411  //-- const Grid_range& grid_asu() const;
412  //-- inline Coord_grid coord_of( const int& index ) const;
413  //-- inline int index_of( const Coord_grid& coord ) const;
414  //-- const int multiplicity( const Coord_grid& pos ) const;
415  //-- const Coord_grid to_map_unit( const Coord_grid& pos ) const;
416  //-- const Map_reference_index first() const;
417  //-- const Map_reference_coord first_coord() const;
418 
420  const T& operator =( const T& value );
422  const Xmap<T>& operator +=( const Xmap<T>& other );
424  const Xmap<T>& operator -=( const Xmap<T>& other );
425 
426  private:
427  std::vector<T> list;
428  };
429 
430 
431 
432  // implementations
433 
434  void Xmap_base::find_sym( const Coord_grid& base, int& index, int& sym ) const
435  {
436  // first deal with first symop, and cache for highest performance
437  Coord_grid rot = to_map_unit( base );
438  if ( asu_grid.in_grid( rot ) ) {
439  index = map_grid.index( rot );
440  if ( asu[ index ] == 0 ) {
441  sym = 0;
442  } else {
443  sym = asu[ index ] - 1;
444  index = map_grid.index( to_map_unit( base.transform(isymop[sym]) ) );
445  }
446  } else {
447  // now deal with other symops
448  for ( sym = 1; sym < nsym; sym++ ) {
449  rot = to_map_unit( base.transform( isymop[sym] ) );
450  if ( asu_grid.in_grid( rot ) ) {
451  index = map_grid.index( rot );
452  if ( asu[ index ] == 0 ) return;
453  }
454  }
455  index = 0; // redundent, to avoid compiler warnings
456  asu_error( base );
457  }
458  return;
459  }
460 
461 
466  template<class T> const T& Xmap<T>::get_data( const Coord_grid& pos ) const
467  {
468  int index, sym;
469  find_sym( pos, index, sym );
470  return list[ index ];
471  }
472 
477  template<class T> void Xmap<T>::set_data( const Coord_grid& pos, const T& val )
478  {
479  int index, sym;
480  find_sym( pos, index, sym );
481  list[ index ] = val;
482  }
483 
490  template<class T> const T& Xmap<T>::get_data( const int& index ) const
491  { return list[index]; }
492 
500  template<class T> bool Xmap<T>::set_data( const int& index, const T& val )
501  {
502  if ( index >= 0 && index < list.size() )
503  if ( asu[index] == 0 ) {
504  list[index] = val;
505  return true;
506  }
507  return false;
508  }
509 
518  template<class T> template<class I> T Xmap<T>::interp( const Coord_frac& pos ) const
519  {
520  T val;
521  I::interp( *this, pos.coord_map( grid_sam_ ), val );
522  return val;
523  }
524 
525 
533  template<class T> template<class I> void Xmap<T>::interp_grad( const Coord_frac& pos, T& val, Grad_frac<T>& grad ) const
534  {
535  Grad_map<T> g;
536  I::interp_grad( *this, pos.coord_map( grid_sam_ ), val, g );
537  grad = g.grad_frac( grid_sam_ );
538  }
539 
540 
550  template<class T> template<class I> void Xmap<T>::interp_curv( const Coord_frac& pos, T& val, Grad_frac<T>& grad, Curv_frac<T>& curv ) const
551  {
552  Grad_map<T> g;
553  Curv_map<T> c;
554  I::interp_curv( *this, pos.coord_map( grid_sam_ ), val, g, c );
555  grad = g.grad_frac( grid_sam_ );
556  curv = c.curv_frac( grid_sam_ );
557  }
558 
559 
568  template<class T> template<class I> T Xmap<T>::interp( const Coord_map& pos ) const
569  {
570  T val;
571  I::interp( *this, pos, val );
572  return val;
573  }
574 
575 
583  template<class T> template<class I> void Xmap<T>::interp_grad( const Coord_map& pos, T& val, Grad_map<T>& grad ) const
584  { I::interp_grad( *this, pos, val, grad ); }
585 
586 
596  template<class T> template<class I> void Xmap<T>::interp_curv( const Coord_map& pos, T& val, Grad_map<T>& grad, Curv_map<T>& curv ) const
597  { I::interp_curv( *this, pos, val, grad, curv ); }
598 
599 
604  template<class T> template<class H> void Xmap<T>::fft_from( const H& fphidata, const FFTtype type )
605  {
606  if ( type == Sparse || ( type == Default && default_type() == Sparse ) ) {
607  // make a sparse fftmap
608  FFTmap_sparse_p1_hx fftmap( grid_sampling() );
609  // copy from reflection data
610  typename H::HKL_reference_index ih;
611  ffttype f, phi0, phi1;
612  int sym;
613  for ( ih = fphidata.first_data(); !ih.last(); fphidata.next_data( ih ) ) {
614  f = fphidata[ih].f();
615  if ( f != 0.0 ) {
616  phi0 = fphidata[ih].phi();
617  const HKL& hkl = ih.hkl();
618  fftmap.set_hkl( hkl,
619  std::complex<ffttype>( f*cos(phi0), f*sin(phi0) ) );
620  for ( sym = 1; sym < spacegroup_.num_primops(); sym++ ) {
621  phi1 = phi0 + hkl.sym_phase_shift( spacegroup_.symop(sym) );
622  fftmap.set_hkl( hkl.transform( isymop[sym] ),
623  std::complex<ffttype>( f*cos(phi1), f*sin(phi1) ) );
624  }
625  }
626  }
627  // require output ASU coords
628  for ( Map_reference_index ix = first(); !ix.last(); ix.next() )
629  fftmap.require_real_data( ix.coord() );
630  // do fft
631  fftmap.fft_h_to_x(1.0/cell().volume());
632  // fill map ASU
633  for ( Map_reference_index ix = first(); !ix.last(); ix.next() )
634  (*this)[ix] = fftmap.real_data( ix.coord() );
635  } else {
636  // make a normal fftmap
637  FFTmap_p1 fftmap( grid_sampling() );
638  // copy from reflection data
639  typename H::HKL_reference_index ih;
640  ffttype f, phi0, phi1;
641  int sym;
642  for ( ih = fphidata.first_data(); !ih.last(); fphidata.next_data( ih ) ) {
643  f = fphidata[ih].f();
644  if ( f != 0.0 ) {
645  phi0 = fphidata[ih].phi();
646  const HKL& hkl = ih.hkl();
647  fftmap.set_hkl( hkl,
648  std::complex<ffttype>( f*cos(phi0), f*sin(phi0) ) );
649  for ( sym = 1; sym < spacegroup_.num_primops(); sym++ ) {
650  phi1 = phi0 + hkl.sym_phase_shift( spacegroup_.symop(sym) );
651  fftmap.set_hkl( hkl.transform( isymop[sym] ),
652  std::complex<ffttype>( f*cos(phi1), f*sin(phi1) ) );
653  }
654  }
655  }
656  // do fft
657  fftmap.fft_h_to_x(1.0/cell().volume());
658  // fill map ASU
659  for ( Map_reference_index ix = first(); !ix.last(); ix.next() )
660  (*this)[ix] = fftmap.real_data( ix.coord() );
661  }
662  }
663 
664 
673  template<class T> template<class H> void Xmap<T>::fft_to ( H& fphidata, const FFTtype type ) const
674  {
675  if ( type == Sparse || ( type == Default && default_type() == Sparse ) ) {
676  // make a sparse fftmap
677  FFTmap_sparse_p1_xh fftmap( grid_sampling() );
678  // copy from map data
679  ffttype f;
680  int sym;
681  for ( Map_reference_index ix = first(); !ix.last(); ix.next() ) {
682  f = (*this)[ix];
683  if ( f != 0.0 ) {
684  fftmap.real_data( ix.coord() ) = f;
685  for ( sym = 1; sym < cacheref.data().nsym; sym++ )
686  fftmap.real_data(
687  ix.coord().transform( isymop[sym] ).unit( grid_sam_ ) ) = f;
688  }
689  }
690  // require output ASU coords
691  typename H::HKL_reference_index ih;
692  for ( ih = fphidata.first(); !ih.last(); ih.next() )
693  fftmap.require_hkl( ih.hkl() );
694  // do fft
695  fftmap.fft_x_to_h(cell().volume());
696  // fill data ASU
697  for ( ih = fphidata.first(); !ih.last(); ih.next() ) {
698  std::complex<ffttype> c = fftmap.get_hkl( ih.hkl() );
699  fphidata[ih].f() = std::abs(c);
700  fphidata[ih].phi() = std::arg(c);
701  }
702  } else {
703  // make a normal fftmap
704  FFTmap_p1 fftmap( grid_sampling() );
705  // copy from map data
706  ffttype f;
707  int sym;
708  for ( Map_reference_index ix = first(); !ix.last(); ix.next() ) {
709  f = (*this)[ix];
710  if ( f != 0.0 ) {
711  fftmap.real_data( ix.coord() ) = f;
712  for ( sym = 1; sym < cacheref.data().nsym; sym++ )
713  fftmap.real_data(
714  ix.coord().transform( isymop[sym] ).unit( grid_sam_ ) ) = f;
715  }
716  }
717  // do fft
718  fftmap.fft_x_to_h(cell().volume());
719  // fill data ASU
720  typename H::HKL_reference_index ih;
721  for ( ih = fphidata.first(); !ih.last(); ih.next() ) {
722  std::complex<ffttype> c = fftmap.get_hkl( ih.hkl() );
723  fphidata[ih].f() = std::abs(c);
724  fphidata[ih].phi() = std::arg(c);
725  }
726  }
727  }
728 
729 
732  template<class T> const T& Xmap<T>::operator =( const T& value )
733  {
734  // copy value into map
735  for ( Map_reference_index im = first(); !im.last(); im.next() )
736  list[im.index()] = value;
737  return value;
738  }
739 
740 
742  template<class T> const Xmap<T>& Xmap<T>::operator +=( const Xmap<T>& other )
743  {
744  if ( spacegroup().hash() != other.spacegroup().hash() ||
745  grid_sampling() != other.grid_sampling() )
746  Message::message( Message_fatal( "Xmap: map mismatch in +=" ) );
747  for ( Map_reference_index im = first(); !im.last(); im.next() )
748  list[im.index()] += other[im];
749  return (*this);
750  }
751 
753  template<class T> const Xmap<T>& Xmap<T>::operator -=( const Xmap<T>& other )
754  {
755  if ( spacegroup().hash() != other.spacegroup().hash() ||
756  grid_sampling() != other.grid_sampling() )
757  Message::message( Message_fatal( "Xmap: map mismatch in -=" ) );
758  for ( Map_reference_index im = first(); !im.last(); im.next() )
759  list[im.index()] -= other[im];
760  return (*this);
761  }
762 
763 
764 } // namespace clipper
765 
766 #endif
clipper::Xmap_base::coord_map
Coord_map coord_map(const Coord_orth &co) const
convert orthogonal coordinate to map
Definition: xmap.h:146
clipper::Coord_grid
Grid coordinate.
Definition: coords.h:237
clipper::Xmap_base::grid_sampling
const Grid_sampling & grid_sampling() const
get the cell grid
Definition: xmap.h:113
clipper::FFTmap_sparse_p1_hx::set_hkl
void set_hkl(const HKL &hkl, const std::complex< ffttype > &f)
set reciprocal space data by hkl
Definition: fftmap_sparse.cpp:143
clipper::Xmap
Xmap<T>: actual crystallographic map class.
Definition: xmap.h:357
clipper::Xmap_cacheobj::symperm
Array2d< unsigned char > symperm
Perumtation matrix of symops.
Definition: xmap.h:84
clipper::Xmap_base::coord_of
Coord_grid coord_of(const int &index) const
map coordinate from index
Definition: xmap.h:118
clipper::Xmap_cacheobj::mat_grid_orth
Mat33 mat_grid_orth
for backward compatibility
Definition: xmap.h:85
clipper::Xmap_base::du
const int * du
fast access ptr
Definition: xmap.h:310
clipper
clipper::Xmap_cacheobj
Definition: xmap.h:58
clipper::Mat33
3x3-matrix class
Definition: clipper_types.h:183
clipper::Xmap::init
void init(const Spacegroup &spacegroup, const Cell &cell, const Grid_sampling &grid_sam)
initialiser: from spacegroup, cell, and grid
Definition: xmap.h:364
clipper::Xmap_base::cell_
Cell cell_
unit cell
Definition: xmap.h:317
clipper::Xmap_cacheobj::asu
std::vector< unsigned char > asu
ASU flag array.
Definition: xmap.h:81
clipper::Xmap_base::index_of
int index_of(const Coord_grid &coord) const
map index from coordinate
Definition: xmap.h:123
clipper::FFTmap_p1::get_hkl
std::complex< ffttype > get_hkl(const HKL &hkl) const
get reciprocal space data: slow form with hemisphere check
Definition: fftmap.cpp:213
clipper::Xmap_base::isymop
const Isymop * isymop
fast access ptr
Definition: xmap.h:309
clipper::Xmap_base::Map_reference_base::base_xmap
const Xmap_base & base_xmap() const
return the parent Xmap
Definition: xmap.h:166
clipper::RTop::rot
const Mat33< T > & rot() const
get rotation
Definition: clipper_types.h:337
clipper::Grid_range::deindex
Coord_grid deindex(const int &index) const
grid deindexing operator
Definition: coords.h:607
clipper::Coord_grid::unit
Coord_grid unit(const Grid_sampling &g) const
reduce to unit box: (0..nu-1, 0..nv-1, 0..nw-1)
Definition: coords.h:744
clipper::FFTmap_p1::real_data
const ffttype & real_data(const Coord_grid &c) const
get real space data
Definition: fftmap.h:119
clipper::Xmap::operator-=
const Xmap< T > & operator-=(const Xmap< T > &other)
subtract another map from this one
Definition: xmap.h:753
clipper::Xmap_base::Map_reference_coord::next_u
Map_reference_coord & next_u()
increment u
Definition: xmap.h:276
clipper::Xmap::interp_curv
void interp_curv(const Coord_frac &pos, T &val, Grad_frac< T > &grad, Curv_frac< T > &curv) const
get map value and curv for fractional coord using supplied interpolator
Definition: xmap.h:550
clipper::Xmap_base::default_type_
static FFTtype default_type_
default backend type
Definition: xmap.h:331
clipper::Xmap_base::grid_sam_
Grid_sampling grid_sam_
grid for the whole cell
Definition: xmap.h:319
clipper::Xmap_base::operator_grid_orth
const RTop & operator_grid_orth() const
return the grid-to-orthogonal coordinate operator (translation is zero)
Definition: xmap.h:137
clipper::Curv_map
map coordinate curvatures, with respect to grid u,v,w
Definition: derivs.h:146
clipper::Xmap_base::first_coord
Map_reference_coord first_coord() const
return a Map_reference_coord for this map
Definition: xmap.h:303
clipper::Xmap_base::Xmap_base
Xmap_base()
Null constructor, for later initialisation.
Definition: xmap.cpp:131
clipper::FFTmap_p1::fft_h_to_x
void fft_h_to_x(const ftype &scale)
Transform to real space.
Definition: fftmap.cpp:149
clipper::Xmap_base::dv
const int * dv
fast access ptr
Definition: xmap.h:311
clipper::Xmap_base::dw
const int * dw
fast access ptr
Definition: xmap.h:312
clipper::Xmap_base::coord_orth
Coord_orth coord_orth(const Coord_map &cm) const
convert map coordinate to orthogonal
Definition: xmap.h:141
clipper::Isymop
Integerised symmetry matrix.
Definition: symop.h:109
clipper::Xmap_base::Map_reference_coord::next_w
Map_reference_coord & next_w()
increment w
Definition: xmap.h:278
clipper::Coord_frac
fractional (cell) coordinates
Definition: coords.h:343
clipper::Message_fatal
Fatal message (level = 9)
Definition: clipper_message.h:129
clipper::Coord_grid::v
const int & v() const
get v
Definition: coords.h:249
clipper::Spacegroup
Spacegroup object.
Definition: spacegroup.h:173
clipper::Xmap_base::default_type
static FFTtype & default_type()
set/get default backend type
Definition: xmap.h:305
clipper::Xmap_base::Map_reference_base::index
const int & index() const
Get the index into the map data array.
Definition: xmap.h:168
clipper::Xmap_base::Map_reference_coord::prev_w
Map_reference_coord & prev_w()
decrement w
Definition: xmap.h:281
clipper::Xmap_cacheobj::format
String format() const
string description
Definition: xmap.cpp:121
clipper::Xmap_base::Map_reference_coord::next_v
Map_reference_coord & next_v()
increment v
Definition: xmap.h:277
clipper::Cell
Cell object.
Definition: cell.h:122
clipper::FFTmap_p1
FFTmap_p1: low level P1 map used for calculating FFTs.
Definition: fftmap.h:81
clipper::HKL::sym_phase_shift
ftype sym_phase_shift(const Symop &op) const
return symmetry phase shift for this HKL under op
Definition: coords.h:707
clipper::Xmap::Xmap
Xmap(const Spacegroup &spacegroup, const Cell &cell, const Grid_sampling &grid_sam)
constructor: from spacegroup, cell, and grid
Definition: xmap.h:362
clipper::Grad_map::grad_frac
Grad_frac< T > grad_frac(const Grid &g) const
grid-fractional derivative conversion
Definition: derivs.h:189
clipper::Xmap_base::Map_reference_coord::sym
const int & sym() const
Get current symmetry operator.
Definition: xmap.h:262
clipper::Message::message
static void message(const T &message)
pass a message
Definition: clipper_message.h:93
clipper::Xmap_cacheobj::asu_grid
Grid_range asu_grid
grid for the ASU
Definition: xmap.h:78
clipper::Coord_grid::w
const int & w() const
get w
Definition: coords.h:250
clipper::Curv_map::curv_frac
Curv_frac< T > curv_frac(const Grid &g) const
grid-fractional derivative conversion
Definition: derivs.h:226
clipper::Xmap_base::Map_reference_index::Map_reference_index
Map_reference_index(const Xmap_base &map)
Constructor: takes parent map.
Definition: xmap.h:196
clipper::Xmap_base::Map_reference_coord::prev_u
Map_reference_coord & prev_u()
increment u
Definition: xmap.h:279
clipper::Xmap_base::asu_grid
Grid_range asu_grid
fast access copy
Definition: xmap.h:313
clipper::Coord_map
map coordinate: this is like Coord_grid, but non-integer
Definition: coords.h:388
clipper::FFTmap_sparse_p1_xh::fft_x_to_h
void fft_x_to_h(const ftype &scale)
Transform to real space.
Definition: fftmap_sparse.cpp:294
clipper::Xmap_base::Map_reference_coord::operator=
Map_reference_coord & operator=(const Coord_grid &pos)
Assignment operator from a coord.
Definition: xmap.h:283
clipper::Xmap_base::Map_reference_coord
Map reference with coordinate-like behaviour.
Definition: xmap.h:243
clipper::HKL
reflection 'Miller' index
Definition: coords.h:146
clipper::FFTmap_sparse_p1_xh
FFTmap_sparse_p1_xh: low level sparse P1 map used for calculating FFTs.
Definition: fftmap_sparse.h:125
clipper::Xmap_base::Map_reference_coord::Map_reference_coord
Map_reference_coord()
Null constructor.
Definition: xmap.h:246
clipper::Xmap_base::Map_reference_index::Map_reference_index
Map_reference_index(const Xmap_base &map, const Coord_grid &pos)
Constructor: takes parent map and coord.
Definition: xmap.h:199
clipper::Xmap::operator[]
const T & operator[](const Xmap_base::Map_reference_index &ix) const
get data by Map_reference_index
Definition: xmap.h:367
clipper::Spgr_descr::hash
const unsigned int & hash() const
return the hash code for the spacegroup
Definition: spacegroup.h:133
clipper::Grid_range::in_grid
bool in_grid(Coord_grid g) const
determine if a point is in the grid
Definition: coords.h:602
clipper::Xmap_base::in_map
bool in_map(const Coord_map &cm) const
(This method is for compatibility with NXmap - it always returns true)
Definition: xmap.h:152
clipper::Xmap_base::nsym
int nsym
fast access copy
Definition: xmap.h:315
clipper::Grid::size
int size() const
return size of grid array
Definition: coords.h:489
clipper::Grad_map
map coordinate gradient, with respect to grid u,v,w
Definition: derivs.h:102
clipper::Xmap_base::map_grid
Grid_range map_grid
fast access copy
Definition: xmap.h:314
clipper::Coord_grid::u
const int & u() const
get u
Definition: coords.h:248
clipper::FFTmap_sparse_p1_hx::fft_h_to_x
void fft_h_to_x(const ftype &scale)
Transform to real space.
Definition: fftmap_sparse.cpp:157
clipper::Xmap_base
Xmap_base: base for crystallographic map class.
Definition: xmap.h:101
clipper::Grid_sampling
Grid sampling of a unit cell.
Definition: coords.h:516
clipper::Grad_frac
fractional (cell) gradient, with respect to fractional u,v,w
Definition: derivs.h:82
clipper::Xmap_base::grid_asu
const Grid_range & grid_asu() const
get the ASU grid
Definition: xmap.h:115
clipper::Xmap_cacheobj::matches
bool matches(const Key &xmap_cachekey) const
compare entry
Definition: xmap.cpp:112
clipper::Xmap_base::to_map_unit
Coord_grid to_map_unit(const Coord_grid &pos) const
function to pick right cell repeat for any grid coord
Definition: xmap.h:131
clipper::Xmap_base::in_map
bool in_map(const Coord_grid &) const
(This method is for compatibility with NXmap - it always returns true)
Definition: xmap.h:150
clipper::Xmap_cacheobj::mutex
static Mutex mutex
thread safety
Definition: xmap.h:86
clipper::Xmap::get_data
const T & get_data(const Coord_grid &pos) const
get a density value for an arbitrary position
Definition: xmap.h:466
clipper::Xmap_base::rt_grid_orth
RTop rt_grid_orth
grid->orth operator
Definition: xmap.h:322
clipper::Xmap_base::rt_orth_grid
RTop rt_orth_grid
orth->grid operator
Definition: xmap.h:321
clipper::Xmap_base::Map_reference_coord::coord_orth
const Coord_orth coord_orth() const
Get current value of orthogonal coordinate.
Definition: xmap.h:259
clipper::Xmap_base::is_null
bool is_null() const
test if object has been initialised
Definition: xmap.cpp:200
clipper::Xmap::Xmap
Xmap()
Null constructor, for later initialisation.
Definition: xmap.h:360
clipper::Xmap_cacheobj::key
Key key
key
Definition: xmap.h:76
clipper::Xmap_cacheobj::Xmap_cacheobj
Xmap_cacheobj(const Key &xmap_cachekey)
construct entry
Definition: xmap.cpp:55
clipper::Spgr_descr
spacegroup description
Definition: spacegroup.h:74
clipper::Coord_frac::coord_map
Coord_map coord_map(const Grid &g) const
fractional-grid coordinate conversion
Definition: coords.h:791
clipper::String
String extension with simple parsing methods.
Definition: clipper_types.h:65
clipper::Xmap_base::Map_reference_coord::next
Map_reference_coord & next()
Simple increment.
Definition: xmap.h:267
clipper::ObjectCache::Reference
ObjectCache reference class.
Definition: clipper_memory.h:155
clipper::Xmap_base::Map_reference_base
Map reference base class.
Definition: xmap.h:163
clipper::Xmap_cacheobj::isymop
std::vector< Isymop > isymop
Integerised symops.
Definition: xmap.h:82
clipper::Mutex
Mutex class: used for locking and unlocking shared resources.
Definition: clipper_thread.h:64
clipper::Xmap_cacheobj::xtl_grid
Grid_sampling xtl_grid
grid for the cell
Definition: xmap.h:77
clipper::Xmap_base::Map_reference_index
Map reference with index-like behaviour.
Definition: xmap.h:191
clipper::Xmap::fft_to
void fft_to(H &fphidata, const FFTtype type=Default) const
FFT from map to reflection list.
Definition: xmap.h:673
clipper::Xmap_base::Map_reference_index::set_coord
Map_reference_index & set_coord(const Coord_grid &pos)
Set current value of coordinate - optimised for nearby coords.
Definition: xmap.h:207
clipper::Xmap_base::spacegroup
const Spacegroup & spacegroup() const
get the spacegroup
Definition: xmap.h:111
clipper::Xmap::interp_grad
void interp_grad(const Coord_frac &pos, T &val, Grad_frac< T > &grad) const
get map value and grad for fractional coord using supplied interpolator
Definition: xmap.h:533
clipper::Xmap_cacheobj::dw
std::vector< int > dw
symmetry grid shifts to index
Definition: xmap.h:83
clipper::FFTmap_p1::fft_x_to_h
void fft_x_to_h(const ftype &scale)
Transform to reciprocal space.
Definition: fftmap.cpp:181
clipper::Xmap_base::init
void init(const Spacegroup &spacegroup, const Cell &cell, const Grid_sampling &grid_sam)
initialiser
Definition: xmap.cpp:171
clipper::FFTmap_sparse_p1_hx::real_data
const ffttype & real_data(const Coord_grid &uvw) const
get real space data ( uvw must be in grid_real() )
Definition: fftmap_sparse.h:111
clipper::FFTmap_sparse_p1_hx::require_real_data
void require_real_data(const Coord_grid &uvw)
express need for real space data
Definition: fftmap_sparse.h:108
clipper::FFTmap_p1::set_hkl
void set_hkl(const HKL &hkl, const std::complex< ffttype > &f)
set reciprocal space data: slow form with hemisphere check
Definition: fftmap.cpp:229
clipper::Xmap_base::Map_reference_coord::set_coord
Map_reference_coord & set_coord(const Coord_grid &pos)
Set current value of coordinate - optimised for nearby coords.
Definition: xmap.cpp:136
clipper::Grid_range
Grid range class: defines array limits for a grid.
Definition: coords.h:585
clipper::Xmap_base::Map_reference_coord::Map_reference_coord
Map_reference_coord(const Xmap_base &map)
Constructor: takes parent map.
Definition: xmap.h:248
clipper::Xmap_base::first
Map_reference_index first() const
return a Map_reference_index for this map
Definition: xmap.h:301
clipper::Xmap_base::Map_reference_base::last
bool last() const
Check for end of map.
Definition: xmap.h:170
clipper::RTop<>
clipper::Xmap_base::spacegroup_
Spacegroup spacegroup_
spacegroup
Definition: xmap.h:318
clipper::Xmap_base::cell
const Cell & cell() const
get the cell
Definition: xmap.h:109
clipper::Xmap_base::Map_reference_index::coord_orth
const Coord_orth coord_orth() const
Get current value of orthogonal coordinate.
Definition: xmap.h:204
clipper::Array2d< unsigned char >
clipper::Xmap_base::cacheref
ObjectCache< Xmap_cacheobj >::Reference cacheref
object cache reference
Definition: xmap.h:307
clipper::Xmap_cacheobj::map_grid
Grid_range map_grid
grid for the ASU, plus border
Definition: xmap.h:79
clipper::FFTmap_sparse_p1_xh::real_data
ffttype & real_data(const Coord_grid &uvw)
set real space data ( uvw must be in grid_real() )
Definition: fftmap_sparse.h:136
clipper::Xmap::interp
T interp(const Coord_frac &pos) const
get map value for fractional coord using supplied interpolator
Definition: xmap.h:518
clipper::Xmap_base::Map_reference_index::index_offset
int index_offset(const int &du, const int &dv, const int &dw) const
Index of neighbouring point.
Definition: xmap.h:219
clipper::FFTmap_sparse_p1_xh::get_hkl
const std::complex< ffttype > get_hkl(const HKL &hkl) const
get reciprocal space data by hkl
Definition: fftmap_sparse.cpp:267
clipper::Xmap_base::Map_reference_coord::edge
void edge()
Reset index for a different symop when we hit the map border.
Definition: xmap.cpp:152
clipper::Grid_range::index
int index(const Coord_grid &c) const
grid indexing operator
Definition: coords.h:605
clipper::Xmap_base::Map_reference_coord::pos_
Coord_grid pos_
Current coord.
Definition: xmap.h:294
clipper::Coord_grid::transform
Coord_grid transform(const Isymop &op) const
return transformed coordinate
Definition: coords.h:260
clipper::Xmap_base::asu
const unsigned char * asu
fast access ptr
Definition: xmap.h:308
clipper::FFTmap_sparse_p1_hx
FFTmap_sparse_p1_hx: low level sparse P1 map used for calculating FFTs.
Definition: fftmap_sparse.h:92
clipper::FFTmap_sparse_p1_xh::require_hkl
void require_hkl(const HKL &hkl)
express need for reciprocal space data by hkl
Definition: fftmap_sparse.cpp:255
clipper::HKL::transform
HKL transform(const Symop &op) const
return transformed hkl
Definition: coords.h:696
clipper::Xmap::set_data
void set_data(const Coord_grid &pos, const T &val)
set a density value for an arbitrary position
Definition: xmap.h:477
clipper::Xmap_base::Map_reference_coord::coord
const Coord_grid & coord() const
Get current value of coordinate.
Definition: xmap.h:257
clipper::Xmap::fft_from
void fft_from(const H &fphidata, const FFTtype type=Default)
FFT from reflection list to map.
Definition: xmap.h:604
clipper::Curv_frac
fractional (cell) curvatures, with respect to fractional u,v,w
Definition: derivs.h:132
clipper::Xmap::operator+=
const Xmap< T > & operator+=(const Xmap< T > &other)
add another map to this one
Definition: xmap.h:742
clipper::Xmap_base::Map_reference_coord::Map_reference_coord
Map_reference_coord(const Xmap_base &map, const Coord_grid &pos)
Constructor: takes parent map and coord.
Definition: xmap.h:251
clipper::Xmap_base::Map_reference_coord::sym_
int sym_
Current symop.
Definition: xmap.h:292
clipper::Xmap_base::Map_reference_index::Map_reference_index
Map_reference_index()
Null constructor.
Definition: xmap.h:194
clipper::Xmap_base::Map_reference_index::next
Map_reference_index & next()
Simple increment.
Definition: xmap.h:210
clipper::Xmap_base::Map_reference_index::coord
Coord_grid coord() const
Get current grid coordinate.
Definition: xmap.h:201
clipper::Xmap_base::Map_reference_coord::prev_v
Map_reference_coord & prev_v()
decrement v
Definition: xmap.h:280
clipper::Xmap::operator=
const T & operator=(const T &value)
assignment operator: assigns a single value to the whole map
Definition: xmap.h:732
clipper::Xmap_base::multiplicity
int multiplicity(const Coord_grid &pos) const
get multiplicity of a map grid point
Definition: xmap.cpp:211
clipper::Xmap_base::Map_reference_base::map_
const Xmap_base * map_
pointer to map for which this Map_reference_index is defined
Definition: xmap.h:173
clipper::Xmap_base::Map_reference_base::index_
int index_
integer index_ into map data array
Definition: xmap.h:175
clipper::Xmap_cacheobj::Key
Definition: xmap.h:61
clipper::Xmap_base::operator_orth_grid
const RTop & operator_orth_grid() const
return the orthogonal-to-grid coordinate operator (translation is zero)
Definition: xmap.h:135
clipper::Coord_orth
orthogonal (Angstrom) coordinates
Definition: coords.h:303