Main Page   Namespace List   Class Hierarchy   Alphabetical List   Compound List   Namespace Members   Compound Members   Related Pages  

ObjCryst::RefinableObj Class Reference

Generic Refinable Object. More...

#include <RefinableObj.h>

Inheritance diagram for ObjCryst::RefinableObj::

ObjCryst::Crystal ObjCryst::PowderPattern ObjCryst::PowderPatternComponent ObjCryst::Radiation ObjCryst::Scatterer ObjCryst::ScatteringData ObjCryst::ScatteringPower ObjCryst::ZMoveMinimizer List of all members.

Public Methods

 RefinableObj ()
 Constructor.

 RefinableObj (const bool internalUseOnly)
 Constructor. Using internalUseOnly=true will avoid registering the the object to any registry, and thus (for example) no display will be created, nor will this object be automatically be saved.

 RefinableObj (const RefinableObj &old)
 Defined not implemented... Should never be called (copying the refinable parameters would allow you to modify the input object). Use the default constructor and RefinableObj::AddPar(RefinableObj&) instead.

virtual ~RefinableObj ()
 Destructor.

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 SetName (const string &name)
 Name of the object.

void operator= (const RefinableObj &old)
 Defined not implemented... More...

void PrepareForRefinement () const
 Find which parameters are used and not fixed, for a refinement /optimization. This must be called before any refinement...

void FixAllPar ()
 Fix All parameters.

void UnFixAllPar ()
 UnFix All parameters.

void SetParIsFixed (const long parIndex, const bool fix)
 Fix/un-fix one parameter from its #.

void SetParIsFixed (const string &parName, const bool fix)
 Fix/un-fix one parameter from its name.

void SetParIsFixed (const RefParType *type, const bool fix)
 Fix/un-fix one family of parameters.

void SetParIsUsed (const string &parName, const bool use)
 Set whether a parameter is used.

void SetParIsUsed (const RefParType *type, const bool use)
 Set whether a family of parameters is used.

long GetNbPar () const
 Total number of refinable parameter in the object. Note that some may be actually fixed or even not used !! For refinement use PrepareForRefinement(), NbRefParNotFixed(), and ParNotFixed(i).

long GetNbParNotFixed () const
 Total number of non-fixed parameters. Is initialized by PrepareForRefinement().

RefinableParGetPar (const long i)
 Access all parameters in the order they were inputted.

const RefinableParGetPar (const long i) const
 Access all parameters in the order they were inputted.

RefinableParGetPar (const string &name)
 Access all parameters from their name.

const RefinableParGetPar (const string &name) const
 Access all parameters from their name.

RefinableParGetPar (const REAL *)
 Access parameter from its adress.

const RefinableParGetPar (const REAL *) const
 Access parameter from its adress.

RefinableParGetParNotFixed (const long i)
 Access all parameters in the order they were inputted, skipping fixed parameters. Must call PrepareForRefinement() before !

const RefinableParGetParNotFixed (const long i) const
 Access all parameters in the order they were inputed, skipping fixed parameters. Must call PrepareForRefinement() before !

void AddPar (const RefinablePar &newRefPar)
 Add a refinable parameter. More...

void AddPar (RefinablePar *newRefPar)
 Add a refinable parameter. More...

void AddPar (RefinableObj &newRefParList)
 Add all the parameters in another RefinableObj. More...

virtual void Print () const
long CreateParamSet (const string name="") const
 Save the current set of refined values in a new set. More...

void SaveParamSet (const long id) const
 Save the current set of refined values over a previously-created set of saved values. More...

void RestoreParamSet (const long id)
 Restore a saved set of values. More...

const CrystVector_REAL & GetParamSet (const long setId) const
 Access one save refpar set. More...

CrystVector_REAL & GetParamSet (const long setId)
 Access one save refpar set. More...

REAL GetParamSet_ParNotFixedHumanValue (const long setId, const long parNumber) const
 Access the (human) value of one refined parameter in a saved set of parameters. More...

const void EraseAllParamSet ()
 Erase all saved refpar sets.

void SetLimitsAbsolute (const string &parName, const REAL min, const REAL max)
 Change the limits for a given parameter, giving absolute new limits.

void SetLimitsAbsolute (const RefParType *type, const REAL min, const REAL max)
 Change the limits for a category of parameters, giving absolute new limits.

void SetLimitsRelative (const string &parName, const REAL min, const REAL max)
 Change the limits for a given parameter, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max) Thus min should logically be <0 and max >0.

void SetLimitsRelative (const RefParType *type, const REAL min, const REAL max)
 Change the limits for a category of parameters, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max). Thus min should logically be <0 and max >0.

void SetLimitsProportional (const string &parName, const REAL min, const REAL max)
 Change the limits for a given parameter, proportionnaly to the current value. min should be < 1. and max > 1.

void SetLimitsProportional (const RefParType *type, const REAL min, const REAL max)
 Change the limits for a category of parameters, proportionnaly to their current value. min should be < 1. and max > 1.

void SetGlobalOptimStep (const RefParType *type, const REAL step)
 Change the maximum step to use during Global Optimization algorithms.

ObjRegistry< RefinableObj > & GetSubObjRegistry ()
 Access to the registry of RefinableObj used by this object.

const ObjRegistry< RefinableObj > & GetSubObjRegistry () const
 Access to the registry of RefinableObj used by this object.

virtual void RegisterClient (RefinableObj &) const
 Register a new object using this object. More...

virtual void DeRegisterClient (RefinableObj &) const
 Deregister an object (which not any more) using this object.

bool IsBeingRefined () const
 Is the object being refined ? (Can be refined by one algorithm at a time only.).

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. More...

virtual void EndOptimization ()
 This should be called by any optimization class at the end of an optimization. More...

virtual void RandomizeConfiguration ()
 Randomize Configuration (before a global optimization). This Affects only parameters which are limited and not fixed. The randomization also affects all sub-objects (recursive).

virtual void GlobalOptRandomMove (const REAL mutationAmplitude)
 Make a random move of the current configuration. More...

void BeginGlobalOptRandomMove ()
 Raise a flag, to be sure not to make a random change more than once in each RefinableObj. More...

virtual unsigned int GetNbCostFunction () const
 Number of Cost functions.

virtual const string & GetCostFunctionName (const unsigned int) const
 Get a Cost function name from its id#.

virtual const string & GetCostFunctionDescription (const unsigned int) const
 Get the (short) description of a cost function.

virtual REAL GetCostFunctionValue (const unsigned int)
 Get the current value of a cost function this should be 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.

void ResetParList ()
 Re-init the list of refinable parameters, removing all parameters. This does not delete the RefinablePar if RefinableObj::mDeleteRefParInDestructor is false.

virtual void XMLOutput (ostream &os, int indent=0) const
 Output to stream in well-formed XML. More...

virtual void XMLInput (istream &is, const XMLCrystTag &tag)
 Input From stream. More...

virtual void UpdateDisplay () const
 If there is an interface, this should be automatically be called each time there is a 'new, significant' configuration to report.

unsigned int GetNbOption () const
 Number of Options for this object.

RefObjOptGetOption (const unsigned int i)
 Access to the options.

const RefObjOptGetOption (const unsigned int i) const
 const access to the options.

virtual void GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
 Get the gene group assigned to each parameter. More...

void SetDeleteRefParInDestructor (const bool b)
 Set this object not to delete its list of parameters when destroyed. More...

const RefinableObjClockGetRefParListClock () const
 What was the last time a RefinablePar was added/removed ?

virtual REAL GetRestraintCost () const
 Get the restraint cost (penalty). More...

void AddRestraint (Restraint *pNewRestraint)
 Add a new restraint.


Protected Methods

long FindPar (const string &name) const
 Find a refinable parameter with a given name.

long FindPar (const REAL *) const
 Find a refinable parameter from the adress of its value.

void AddSubRefObj (RefinableObj &)
 Add an object in the registry of used objects. More...

void RemoveSubRefObj (RefinableObj &)
 Remove an object in the registry of used objects. More...

void InitRandomSeedFromTime () const
 Init the seed for random number generation from current time. More...

void AddOption (RefObjOpt *opt)
 Add an option for this parameter. More...

virtual void Prepare ()
 Prepare everything (if necessary) for an optimization/calculation. More...


Protected Attributes

string mName
 Name for this RefinableObject. Should be unique, at least in the same scope.+.

RefinablePar ** mpRefPar
 Array of pointers to the refinable parameters.

long mNbRefPar
 Number of refinable parameters.

long mMaxNbRefPar
 Maximum number of refinable parameters (array size-dynamically allocated).

Restraint ** mpRestraint
 Array of pointers to the restraints for this object. This excludes all RefinableP.ar declared in RefinableObj::mpRefPar, which can also be restrained.

long mNbRestraint
 Number of refinable parameters (not including possible RefinablePar which are also restrained).

long mMaxNbRestraint
 Maximum number of restraints (dynamically allocated).

CrystVector_REAL ** mpSavedValuesSet
 Array of pointers to arrays used to save sets of values for all parameters.

string ** mpSavedValuesSetName
 Names associated to the saved values sets.

CrystVector_bool mSavedValuesSetIsUsed
 Is the set associated with (id) currently used ?

long mNbRefParNotFixed
 Total of not-fixed parameters.

CrystVector_long mRefparNotFixedIndex
 Index of not-fixed parameters.

bool mIsbeingRefined
 Is the object being refined ?

ObjRegistry< RefinableObj > mSubObjRegistry
 Registry of RefinableObject needed for this object (owned by this object or not).

ObjRegistry< RefinableObj > mClientObjRegistry
 Registry of RefinableObject using this object. This is mutable so that client can modify it (kludge?).

ObjRegistry< RefObjOptmOptionRegistry
 List of options for this object. Note that these are just references, to options allocated by the object, to have a simple global access to all options.

bool mDeleteRefParInDestructor
 If true (the default), then all RefinablePar will be deleted when the the object is deleted. The opposite option (false) should only be used in RefinableObj holding 'copies' of other objects, such as in algorithms.

RefinableObjClock mRefParListClock
 Last time the RefinableParList was modified (a parameter added or removed).

bool mRandomMoveIsDone
 This true is false if RefinableObj::GlobalOptRandomMove() has been called since RefinableObj::BeginGlobalOptRandomMove() was called. More...


Static Protected Attributes

const int mMaxNbSavedSets = 1000
 Max number of saved sets (memory is dynamically allocated...).


Detailed Description

Generic Refinable Object.

This is basically a list of refinable parameters, with other basic common properties such as a name,. etc... This allows optimization/refinement algorithms to access the parameters without knowing what the object really is.

Todo:
Define more clearly which operations are recursive (ie also modify sub-objects).


Member Function Documentation

void ObjCryst::RefinableObj::AddOption RefObjOpt   opt [protected]
 

Add an option for this parameter.

For internal use only.

void ObjCryst::RefinableObj::AddPar RefinableObj &    newRefParList
 

Add all the parameters in another RefinableObj.

Parameters are \not copied, so they should be allocated in the heap.

Warning:
If a copy of another RefinableObj parameter list is made, such as in the OptimizationObj class, make sure that upon deletion of this object the parameters will not be destroyed. To do this use RefinableObj::SetDeleteRefParInDestructor(false).

void ObjCryst::RefinableObj::AddPar RefinablePar   newRefPar
 

Add a refinable parameter.

The parameter is not copied, so it should be allocated in the heap.

void ObjCryst::RefinableObj::AddPar const RefinablePar   newRefPar
 

Add a refinable parameter.

The parameter is copied, so it need only be allocated temporarily.

Deprecated:
Use the next function, which supplies the parameter as a pointer, and avoids a useless copy.

void ObjCryst::RefinableObj::AddSubRefObj RefinableObj &    [protected]
 

Add an object in the registry of used objects.

For internal use only.

void ObjCryst::RefinableObj::BeginGlobalOptRandomMove  
 

Raise a flag, to be sure not to make a random change more than once in each RefinableObj.

This calls recursively all sub-objects.

This is necessary since one object may be included in several others. This must be called before making a random configuration change on a list of objects.

virtual void ObjCryst::RefinableObj::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.
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:  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.

Reimplemented in ObjCryst::Crystal, ObjCryst::PowderPatternDiffraction, and ObjCryst::ScatteringData.

long ObjCryst::RefinableObj::CreateParamSet const string    name = "" const
 

Save the current set of refined values in a new set.

Parameters:
name  : the name associated to this set of values. Names should be unique.
Returns:
an number identifying the set of saved values.

virtual void ObjCryst::RefinableObj::EndOptimization   [virtual]
 

This should be called by any optimization class at the end of an optimization.

This also affects all sub-objects.

Note:
this may be called several time for some objects which are used by several other objects.

Reimplemented in ObjCryst::PowderPatternDiffraction, ObjCryst::ScatteringData, and ObjCryst::ZScatterer.

virtual void ObjCryst::RefinableObj::GetGeneGroup const RefinableObj &    obj,
CrystVector_uint &    groupIndex,
unsigned int &    firstGroup
const [virtual]
 

Get the gene group assigned to each parameter.

Each parameter (a gene in terms of genetic algorithms) can be assigned to a gene group. Thus when mating two configurations, genes will be exchanged by groups. By default (in the base RefinabeObj class), each parameter is alone in its group. Derived classes can group genes for a better s** life.

The number identifying a gene group only has a meaning in a given object. It can also change on subsequent calls, and thus is not unique.

Parameters:
obj  the \RefinableObj, supplied by an algorithm class (OptimizationObj,..), which contains a list of parameters, some of which (but possibly all or none) are parameters belonging to this object.
groupIndex  a vector of unsigned integers, one for each parameter in the input object, giving an unsigned integer value as gene group index. At the beginning this vector should contain only zeros (no group assigned).
firstGroup  this is the number of groups which have already been assigned, plus one. The gene groups returned by this object will start from this value, and increment firstGroup for each gene group used, so that different RefinableObj cannot share a gene group.
Note:
this function is not optimized, and should only be called at the beginning of a refinement.

Reimplemented in ObjCryst::Atom, ObjCryst::Crystal, ObjCryst::PowderPatternBackground, ObjCryst::PowderPatternDiffraction, ObjCryst::PowderPattern, ObjCryst::ScatteringPower, and ObjCryst::ZScatterer.

CrystVector_REAL& ObjCryst::RefinableObj::GetParamSet const long    setId
 

Access one save refpar set.

Parameters:
setId  : the number identifying the set.

const CrystVector_REAL& ObjCryst::RefinableObj::GetParamSet const long    setId const
 

Access one save refpar set.

Parameters:
setId  : the number identifying the set.

REAL ObjCryst::RefinableObj::GetParamSet_ParNotFixedHumanValue const long    setId,
const long    parNumber
const
 

Access the (human) value of one refined parameter in a saved set of parameters.

For internal use only.

Parameters:
setId  : the number identifying the set.
parNumber  : the number identifying the parameter in the list of refined parameters
Returns:
if parNumber=5 and setId=37, then the returned value will be the value (scaled if it is an angle) value of the 5th not-fixed parameter in the saved set #37.

virtual REAL ObjCryst::RefinableObj::GetRestraintCost   const [virtual]
 

Get the restraint cost (penalty).

Note:
by default this returns 0, so this must be overloaded by any object which actually uses retsraint.
Todo:
Instead, we could return by default the sum of the restraints, but this is dangerous since we need to have objects using restraints fully responsible for them.

virtual void ObjCryst::RefinableObj::GlobalOptRandomMove const REAL    mutationAmplitude [virtual]
 

Make a random move of the current configuration.

This is for global optimization algorithms. the moves for each parameter are less than their global optimization step, multiplied by the mutation amplitude.

\warning: this makes a random move for the parameter declared for this object, and it is the duty of the object to decide whether the included objects should be moved and how. (eg an algorithm should only call for a move with the top object, and this object decides how he and his sub-objects moves). By default (RefinableObj implementation) all included objects are moved recursively.

RefinableObj::

Parameters:
mutationAmplitude:  multiplier for the maximum move amplitude, for all parameters

Reimplemented in ObjCryst::Crystal, and ObjCryst::ZScatterer.

void ObjCryst::RefinableObj::InitRandomSeedFromTime   const [protected]
 

Init the seed for random number generation from current time.

For internal use only.

void ObjCryst::RefinableObj::operator= const RefinableObj &    old
 

Defined not implemented...

Should never be called

virtual void ObjCryst::RefinableObj::Prepare   [protected, virtual]
 

Prepare everything (if necessary) for an optimization/calculation.

For internal use only.

Reimplemented in ObjCryst::PowderPatternComponent, ObjCryst::PowderPatternBackground, ObjCryst::PowderPatternDiffraction, and ObjCryst::PowderPattern.

virtual void ObjCryst::RefinableObj::RegisterClient RefinableObj &    const [virtual]
 

Register a new object using this object.

Todo:
: the clients should be const, but are not... This need to be fixed...

void ObjCryst::RefinableObj::RemoveSubRefObj RefinableObj &    [protected]
 

Remove an object in the registry of used objects.

For internal use only.

void ObjCryst::RefinableObj::RestoreParamSet const long    id
 

Restore a saved set of values.

Parameters:
id  : the number identifying the set.
Warning:
this only affects parameters which are used and not fixed. Others remain unchanged.

void ObjCryst::RefinableObj::SaveParamSet const long    id const
 

Save the current set of refined values over a previously-created set of saved values.

Parameters:
id  the number identifying the set of saved values.

void ObjCryst::RefinableObj::SetDeleteRefParInDestructor const bool    b
 

Set this object not to delete its list of parameters when destroyed.

This is used for the RefinableObj in algorithms objects (OptimizationObj), which only hold copies of parameters from the refined objects.

virtual void ObjCryst::RefinableObj::XMLInput istream &    is,
const XMLCrystTag   tag
[virtual]
 

Input From stream.

Todo:
Add an bool XMLInputTag(is,tag) function to recognize all the tags from the stream. So that each inherited class can use the XMLInputTag function from its parent (ie take advantage of inheritance). The children class would first try to interpret the tag, then if unsuccessful would pass it to its parent (thus allowing overloading), etc...

Reimplemented in ObjCryst::Atom, ObjCryst::Crystal, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::PowderPatternBackground, ObjCryst::PowderPatternDiffraction, ObjCryst::PowderPattern, ObjCryst::Radiation, ObjCryst::ScatteringPowerAtom, and ObjCryst::ZScatterer.

virtual void ObjCryst::RefinableObj::XMLOutput ostream &    os,
int    indent = 0
const [virtual]
 

Output to stream in well-formed XML.

Todo:
Use inheritance.. as for XMLInputTag()...

Reimplemented in ObjCryst::Atom, ObjCryst::Crystal, ObjCryst::DiffractionDataSingleCrystal, ObjCryst::PowderPatternBackground, ObjCryst::PowderPatternDiffraction, ObjCryst::PowderPattern, ObjCryst::Radiation, ObjCryst::ScatteringPowerAtom, and ObjCryst::ZScatterer.


Member Data Documentation

bool ObjCryst::RefinableObj::mRandomMoveIsDone [protected]
 

This true is false if RefinableObj::GlobalOptRandomMove() has been called since RefinableObj::BeginGlobalOptRandomMove() was called.

For internal use only.


The documentation for this class was generated from the following file:
Generated on Tue Feb 5 17:37:24 2002 for ObjCryst++ by doxygen1.2.13.1 written by Dimitri van Heesch, © 1997-2001