ObjCryst::CellExplorer Class Reference
Algorithm class to find the correct indexing from observed peak positions. More...
Inheritance diagram for ObjCryst::CellExplorer:
Collaboration diagram for ObjCryst::CellExplorer:
Public Member Functions | |
| CellExplorer (const PeakList &dhkl, const CrystalSystem lattice, const unsigned int nbSpurious) | |
| void | Evolution (unsigned int ng, const bool randomize=true, const float f=0.7, const float cr=0.5, unsigned int np=100) |
| void | SetLengthMinMax (const float min, const float max) |
| void | SetAngleMinMax (const float min, const float max) |
| void | SetVolumeMinMax (const float min, const float max) |
| void | SetNbSpurious (const unsigned int nb) |
| void | SetD2Error (const float err) |
| Allowed error on 1/d (squared!), used for dicvol. | |
| void | SetMinMaxZeroShift (const float min, const float max) |
| void | SetCrystalSystem (const CrystalSystem system) |
| void | SetCrystalCentering (const CrystalCentering cent) |
| virtual const string & | GetClassName () const |
| Name for this class ("RefinableObj", "Crystal",...). This is only useful to distinguish different classes when picking up objects from the RefinableObj Global Registry. | |
| virtual const string & | GetName () const |
| Name of the object. | |
| virtual void | Print () const |
| virtual unsigned int | GetNbLSQFunction () const |
| Number of LSQ functions. | |
| virtual const CrystVector_REAL & | GetLSQCalc (const unsigned int) const |
| Get the current calculated value for the LSQ function. | |
| virtual const CrystVector_REAL & | GetLSQObs (const unsigned int) const |
| Get the observed values for the LSQ function. | |
| virtual const CrystVector_REAL & | GetLSQWeight (const unsigned int) const |
| Get the weight values for the LSQ function. | |
| virtual const CrystVector_REAL & | GetLSQDeriv (const unsigned int, RefinablePar &) |
| Get the first derivative values for the LSQ function, for a given parameter. | |
| virtual void | BeginOptimization (const bool allowApproximations=false, const bool enableRestraints=false) |
| This should be called by any optimization class at the begining of an optimization. | |
| void | LSQRefine (int nbCycle=1, bool useLevenbergMarquardt=true, const bool silent=false) |
| void | DicVol (const float minScore=10, const unsigned int minDepth=3, const float stopOnScore=50.0, const unsigned int stopOnDepth=6) |
| Run DicVOl algorithm, store only solutions with score >minScore or depth>=minDepth, stop at the end of one volume interval (~400 A^3) if best score>stopOnScore, or if one solution was found at depth>=stopOnDepth. | |
| void | ReduceSolutions (const bool updateReportThreshold=false) |
| Sort all solutions by score, remove duplicates. | |
| float | GetBestScore () const |
|
const std::list< std::pair < RecUnitCell, float > > & | GetSolutions () const |
|
std::list< std::pair < RecUnitCell, float > > & | GetSolutions () |
Private Member Functions | |
| unsigned int | RDicVol (RecUnitCell uc0, RecUnitCell uc1, unsigned int depth, unsigned long &nbCalc, const float minV, const float maxV, vector< unsigned int > vdepth=vector< unsigned int >()) |
| void | Init () |
Private Attributes | |
|
std::list< std::pair < RecUnitCell, float > > | mvSolution |
| Max number of obs reflections to use. | |
| unsigned int | mnpar |
| const PeakList * | mpPeakList |
| float | mLengthMin |
| float | mLengthMax |
| float | mAngleMin |
| float | mAngleMax |
| float | mVolumeMin |
| float | mVolumeMax |
| float | mZeroShiftMin |
| float | mZeroShiftMax |
| float | mMin [7] |
| Min values for all parameters (7=unit cell +zero). | |
| float | mAmp [7] |
| Max amplitude (max=min+amplitude) for all parameters All parameters are treated as periodic for DE (??). | |
| CrystalSystem | mlattice |
| Lattice type for which we search. | |
| CrystalCentering | mCentering |
| Centering type. | |
| unsigned int | mNbSpurious |
| float | mD2Error |
| LSQNumObj | mLSQObj |
| CrystVector_REAL | mObs |
| CrystVector_REAL | mCalc |
| CrystVector_REAL | mWeight |
| CrystVector_REAL | mDeriv |
| RecUnitCell | mRecUnitCell |
| Reciprocal unit cell used for least squares refinement. | |
| float | mBestScore |
| Current best score. | |
| std::vector< unsigned int > | mvNbSolutionDepth |
| Number of solutions found during dicvol search, at each depth. | |
| float | mMinScoreReport |
| unsigned int | mMaxDicVolDepth |
| unsigned int | mDicVolDepthReport |
| float | mCosAngMax |
| Stored value of cos(max ang) for tricilinic search - we do not want to recompute the cos at every dicvol iteration. | |
| unsigned int | mNbLSQExcept |
| Number of exceptions caught during LSQ, in a given search - above 20 LSQ is disabled. | |
Detailed Description
Algorithm class to find the correct indexing from observed peak positions.
Definition at line 212 of file Indexing.h.
Member Function Documentation
| void ObjCryst::CellExplorer::BeginOptimization | ( | const bool | allowApproximations = false, |
|
| const bool | enableRestraints = false | |||
| ) | [virtual] |
This should be called by any optimization class at the begining of an optimization.
This will also check that everything is ready, eg call the RefinableObj::Prepare() function. This also affects all sub-objects.
- Note:
- this may be called several time for some objects which are used by several other objects, or for nested optimizations (e.g. least-squares optimizations inside a global one).
- EndOptimization() must be called at the end of the optimization, the same number of time BeginOptimization() was called !
- Parameters:
-
allowApproximations,: if true, then the object can use faster but less precise functions during the optimization. This is useful for global optimization not using derivatives. enableRestraints,:
- Deprecated:
- if true, then restrained parameters will be allowed to go beyond theur hard limits. This implies that the algorithm will take into account the cost (penalty) related to the restraints. Objects which do not use restraints will simply ignore this. WARNING: this parameter may be removed with the new likelihood scheme.
Reimplemented from ObjCryst::RefinableObj.
Definition at line 1473 of file Indexing.cpp.
| void ObjCryst::CellExplorer::DicVol | ( | const float | minScore = 10, |
|
| const unsigned int | minDepth = 3, |
|||
| const float | stopOnScore = 50.0, |
|||
| const unsigned int | stopOnDepth = 6 | |||
| ) |
Run DicVOl algorithm, store only solutions with score >minScore or depth>=minDepth, stop at the end of one volume interval (~400 A^3) if best score>stopOnScore, or if one solution was found at depth>=stopOnDepth.
If stopOnDepth==0, do not stop for any depth
Definition at line 2113 of file Indexing.cpp.
| const CrystVector_REAL & ObjCryst::CellExplorer::GetLSQDeriv | ( | const unsigned int | n, | |
| RefinablePar & | par | |||
| ) | [virtual] |
Get the first derivative values for the LSQ function, for a given parameter.
Note that the default method in the base RefinableObj class is to use numerical derivatives, so it should be overridden for better precision.
- Todo:
- This should be a const method, and the given RefPar should be const too...
Reimplemented from ObjCryst::RefinableObj.
Definition at line 1443 of file Indexing.cpp.
| void ObjCryst::CellExplorer::ReduceSolutions | ( | const bool | updateReportThreshold = false |
) |
Sort all solutions by score, remove duplicates.
- Parameters:
-
updateReportThreshold,: if true, when too many solutions are produced, the threshold above which solutions are reported will be updated to get less solutions.
Definition at line 2615 of file Indexing.cpp.
The documentation for this class was generated from the following files:
