Changeset 766

Timestamp:

01/11/10 22:55:57 (14 years ago)

Author:

mido

Message:

abstract methods restored wherever they are meaningful
macros NOT_IMPLEMENTED and NOT_IMPLEMENTED_VOID defined to make sources shorter
emix::set_parameters and mmix::set_parameters removed, corresponding acces methods created and the corresponding validate methods improved appropriately
some compilator warnings were avoided
and also a few other things cleaned up

Location:

library

Files:

• bdm/base/bdmbase.cpp (modified) (4 diffs)
• bdm/base/bdmbase.h (modified) (15 diffs)
• bdm/base/datasources.h (modified) (3 diffs)
• bdm/base/loggers.cpp (modified) (2 diffs)
• bdm/base/loggers.h (modified) (3 diffs)
• bdm/bdmerror.h (modified) (1 diff)
• bdm/bdmroot.h (modified) (2 diffs)
• bdm/estim/arx.cpp (modified) (1 diff)
• bdm/estim/arx.h (modified) (2 diffs)
• bdm/estim/ekf_template.h (modified) (1 diff)
• bdm/estim/kalman.h (modified) (5 diffs)
• bdm/estim/mixtures.cpp (modified) (4 diffs)
• bdm/estim/mixtures.h (modified) (3 diffs)
• bdm/estim/particles.cpp (modified) (1 diff)
• bdm/estim/particles.h (modified) (8 diffs)
• bdm/itpp_ext.cpp (modified) (3 diffs)
• bdm/math/chmat.h (modified) (1 diff)
• bdm/math/square_mat.h (modified) (6 diffs)
• bdm/mex/mex_BM.h (modified) (2 diffs)
• bdm/mex/mex_datasource.h (modified) (1 diff)
• bdm/stat/discrete.cpp (modified) (1 diff)
• bdm/stat/emix.cpp (modified) (4 diffs)
• bdm/stat/emix.h (modified) (10 diffs)
• bdm/stat/exp_family.h (modified) (9 diffs)
• bdm/stat/merger.h (modified) (1 diff)
• tests/stresssuite/arx_stress.cpp (modified) (1 diff)
• tests/stresssuite/mixtures_stress.cpp (modified) (1 diff)
• tests/stresssuite/square_mat_stress.cpp (modified) (9 diffs)
• tests/testsuite/emix_test.cpp (modified) (2 diffs)
• tests/testsuite/square_mat_test.cpp (modified) (1 diff)

library/bdm/base/bdmbase.cpp

@@ -27 +27 @@
 };
 
-int RV::init ( const string &name, int size ) {
+int RV::assign_id( const string &name, int size ) {
         //Refer
         int id;
@@ -86 +86 @@
         int id;
         for ( int i = 0; i < len; i++ ) {
-                id = init ( in_names ( i ), in_sizes ( i ) );
+                id = assign_id ( in_names ( i ), in_sizes ( i ) );
                 ids ( i ) = id;
         }
@@ -100 +100 @@
 
 bool RV::add ( const RV &rv2 ) {
-        // TODO
         if ( rv2.len > 0 ) { //rv2 is nonempty
                 ivec ind = rv2.findself ( *this ); //should be -1 all the time
@@ -146 +145 @@
 }
 
-shared_ptr<pdf> epdf::condition ( const RV &rv ) const {
-        bdm_warning ( "Not implemented" );
-        return shared_ptr<pdf>();
-}
-
-shared_ptr<epdf> epdf::marginal ( const RV &rv ) const {
-        bdm_warning ( "Not implemented" );
-        return shared_ptr<epdf>();
-}
+shared_ptr<pdf> epdf::condition ( const RV &rv ) const NOT_IMPLEMENTED( shared_ptr<pdf>() );
+
+
+shared_ptr<epdf> epdf::marginal ( const RV &rv ) const NOT_IMPLEMENTED( shared_ptr<epdf>() );
 
 mat epdf::sample_mat ( int N ) const {

library/bdm/base/bdmbase.h

@@ -108 +108 @@
 
         //! auxiliary function used in constructor
-        void init ( const Array<std::string> &in_names, const ivec &in_sizes, const ivec &in_times );
-        int init ( const string &name, int size );
+        void init( const Array<std::string> &in_names, const ivec &in_sizes, const ivec &in_times );
+
+        //! auxiliary function assigning unique integer index related to the passed name and size of the random variable
+        int assign_id( const string &name, int size );
+
         //! Private constructor from IDs, potentially dangerous since all ids must be valid!
         //! dummy is there to prevent confusion with RV(" string");
@@ -319 +322 @@
 
         //! log this vector
-        virtual void log_vector ( int id, const vec &v ) {
-                bdm_error ( "Not implemented" );
-        };
+        virtual void log_vector ( int id, const vec &v ) = 0;
 
         virtual Setting & log_to_setting ( int id ) {
                 return settings ( id )->add ( Setting::TypeGroup );
         }
-
         //! log this double
-        virtual void logit ( int id, const double &d ) {
-                bdm_error ( "Not implemented" );
-        };
+        virtual void logit ( int id, const double &d ) = 0;
 
         //! Shifts storage position for another time step.
-        virtual void step() {
-                bdm_error ( "Not implemneted" );
-        };
+        virtual void step() = 0;
 
         //! Finalize storing information
@@ -385 +381 @@
         //!dimension of the condition
         int dimc;
+
         //! random variable in condition
         RV rvc;
@@ -402 +399 @@
         pdf ( const pdf &m ) : dimc ( m.dimc ), rvc ( m.rvc ), dim ( m.dim ), rv ( m.rv ) { }
 
-        //! copy of the current object - make sure to implement
-        virtual pdf* _copy_() const {
-                return new pdf ( *this );
-        }
         //!@}
 
@@ -412 +405 @@
 
         //! Returns a sample from the density conditioned on \c cond, \f$x \sim epdf(rv|cond)\f$. \param cond is numeric value of \c rv
-        virtual vec samplecond ( const vec &cond ) {
-                bdm_error ( "Not implemented" );
-                return vec();
-        }
+        virtual vec samplecond ( const vec &cond ) = 0;
 
         //! Returns \param N samples from the density conditioned on \c cond, \f$x \sim epdf(rv|cond)\f$. \param cond is numeric value of \c rv
@@ -421 +411 @@
 
         //! Shortcut for conditioning and evaluation of the internal epdf. In some cases,  this operation can be implemented efficiently.
-        virtual double evallogcond ( const vec &yt, const vec &cond ) {
-                bdm_error ( "Not implemented" );
-                return 0.0;
-        }
+        virtual double evallogcond ( const vec &yt, const vec &cond ) = 0;
 
         //! Matrix version of evallogcond
@@ -521 +508 @@
         }
         
-        epdf* _copy_() const {
-                return new epdf ( *this );
-        }
         //!@}
 
@@ -530 +514 @@
 
         //! Returns a sample, \f$ x \f$ from density \f$ f_x()\f$
-        virtual vec sample() const {
-                bdm_error ( "not implemented" );
-                return vec();
-        }
+        virtual vec sample() const = 0;
 
         //! Returns N samples, \f$ [x_1 , x_2 , \ldots \ \f$  from density \f$ f_x(rv)\f$
@@ -540 +521 @@
         //! Compute log-probability of argument \c val
         //! In case the argument is out of suport return -Infinity
-        virtual double evallog ( const vec &val ) const {
-                bdm_error ( "not implemented" );
-                return 0.0;
-        }
-
+        virtual double evallog ( const vec &val ) const = 0;
+        
         //! Compute log-probability of multiple values argument \c val
         virtual vec evallog_mat ( const mat &Val ) const;
@@ -557 +535 @@
         virtual shared_ptr<epdf> marginal ( const RV &rv ) const;
 
-        //! return expected value
-        virtual vec mean() const {
-                bdm_error ( "not implemneted" );
-                return vec();
-        }
+        virtual vec mean() const = 0;
 
         //! return expected variance (not covariance!)
-        virtual vec variance() const {
-                bdm_error ( "not implemneted" );
-                return vec();
-        }
+        virtual vec variance() const = 0;
 
         //! Lower and upper bounds of \c percentage % quantile, returns mean-2*sigma as default
@@ -639 +610 @@
         //! Update \c iepdf so that it represents this pdf conditioned on \c rvc = cond
         //! This function provides convenient reimplementation in offsprings
-        virtual void condition ( const vec &cond ) {
-                bdm_error ( "Not implemented" );
-        }
+        virtual void condition ( const vec &cond ) = 0;
 
         //!access function to iepdf
@@ -942 +911 @@
         }
         //! Returns full vector of observed data=[output, input]
-        virtual void getdata ( vec &dt ) const {
-                bdm_error ( "abstract class" );
-        }
+        virtual void getdata ( vec &dt ) const = 0;
+
         //! Returns data records at indeces.
-        virtual void getdata ( vec &dt, const ivec &indeces ) {
-                bdm_error ( "abstract class" );
-        }
-
-        //! Accepts action variable and schedule it for application.
-        virtual void write ( const vec &ut ) {
-                bdm_error ( "abstract class" );
-        }
+        virtual void getdata ( vec &dt, const ivec &indeces ) = 0;
+
+        //! Accepts action variable and schedule it for application.    
+        virtual void write ( const vec &ut ) = 0;
 
         //! Accepts action variables at specific indeces
-        virtual void write ( const vec &ut, const ivec &indeces ) {
-                bdm_error ( "abstract class" );
-        }
+        virtual void write ( const vec &ut, const ivec &indeces ) = 0;
 
         //! Moves from \f$ t \f$ to \f$ t+1 \f$, i.e. perfroms the actions and reads response of the system.
-        virtual void step() {
-                bdm_error ( "abstract class" );
-        }
+        virtual void step() = 0;
 
         //! Register DS for logging into logger L
@@ -1033 +993 @@
 //      BM ( const BM &B ) :  yrv ( B.yrv ), dimy(B.dimy), rvc ( B.rvc ),dimc(B.dimc), ll ( B.ll ), evalll ( B.evalll ) {}
         //! \brief Copy function required in vectors, Arrays of BM etc. Have to be DELETED manually!
-        //! Prototype: \code BM* _copy_() const {return new BM(*this);} \endcode
-        virtual BM* _copy_() const {
-                return NULL;
-        };
+        //! Prototype: \code BM* _copy() const {return new BM(*this);} \endcode
+        virtual BM* _copy() const {             return NULL;    }; // TODO NEBUDE TU TAKY LEPSI BDM_ERROR??!
         //!@}
 
@@ -1054 +1012 @@
         //! This function evaluates only \f$ y_t \f$, condition is assumed to be the last used in bayes().
         //! See bdm::BM::predictor for conditional version.
-        virtual double logpred ( const vec &yt ) const {
-                bdm_error ( "Not implemented" );
-                return 0.0;
-        }
+        virtual double logpred ( const vec &yt ) const = 0;
 
         //! Matrix version of logpred
@@ -1069 +1024 @@
 
         //!Constructs a predictive density \f$ f(d_{t+1} |d_{t}, \ldots d_{0}) \f$
-        virtual epdf* epredictor() const {
-                bdm_error ( "Not implemented" );
-                return NULL;
-        };
+        virtual epdf* epredictor() const = 0;
+
         //!Constructs conditional density of 1-step ahead predictor \f$ f(d_{t+1} |d_{t+h-1}, \ldots d_{t}) \f$
-        virtual pdf* predictor() const {
-                bdm_error ( "Not implemented" );
-                return NULL;
-        };
+        virtual pdf* predictor() const = 0;
+
         //!@}
 

library/bdm/base/datasources.h

@@ -129 +129 @@
         }
 
+        //! Accepts action variable and schedule it for application.    
+        virtual void write ( const vec &ut ) NOT_IMPLEMENTED_VOID;
+                
+        //! Accepts action variables at specific indeces
+        virtual void write ( const vec &ut, const ivec &indeces ) NOT_IMPLEMENTED_VOID;
+
         /*!
         \code
@@ -182 +188 @@
         }
 
+
+        //! Returns data records at indeces.
+        virtual void getdata ( vec &dt, const ivec &indeces ) NOT_IMPLEMENTED_VOID;
+
+
         /*!
         \code
@@ -353 +364 @@
         }
 
+        virtual void write ( const vec &ut, const ivec &indeces ) NOT_IMPLEMENTED_VOID;
+
         /*! UI for stateDS
 

library/bdm/base/loggers.cpp

@@ -48 +48 @@
 
 void memlog::from_setting ( const Setting &set ) {
-        // TODO tady se natvrdo ocekava existence stringu, nejsou zadne defaulty.. je to tak OK?
         UI::get ( maxlen,  set, "maxlen", UI::compulsory );
         UI::get ( filename, set, "filename" );
@@ -174 +173 @@
 
 void dirfilelog::from_setting ( const Setting &set ) {
-        // TODO tady se natvrdo ocekava existence stringu, nejsou zadne defaulty.. je to tak OK?
         dirname = ( const char* ) set["dirname"];
         maxlen = set["maxlen"];

library/bdm/base/loggers.h

@@ -78 +78 @@
         /*! \brief UI for memlog
 
-        TODO dat tam kam patri, a to celej blok
-
         \code
         logger = {
@@ -130 +128 @@
         /*! \brief UI for stdlog
 
-        TODO dat tam kam patri, a to celej blok
-
         \code
         logger = {
@@ -140 +136 @@
         void from_setting ( const Setting &set ) {
         }
-
 };
 UIREGISTER ( stdlog );

library/bdm/bdmerror.h

@@ -64 +64 @@
         } else ((void) 0)
 
+#define NOT_IMPLEMENTED(RESULT) { bdm_error( "Not implemented" ); return RESULT; }
+
+#define NOT_IMPLEMENTED_VOID { bdm_error( "Not implemented" ); }
+
 #endif
-

library/bdm/bdmroot.h

@@ -19 +19 @@
 #include "itpp_ext.h"
 #include "base/libconfig/lib/libconfig.h++"
+#include "bdmerror.h"
 
 using namespace libconfig;
@@ -94 +95 @@
         virtual void validate() {
         }
+
+        //! Virtual method providing deep copy of instances
+        virtual root* _copy() const NOT_IMPLEMENTED(NULL);
+        
+
         //! access function
         int _log_level() const {

library/bdm/estim/arx.cpp

@@ -78 +78 @@
 }
 
-ARX* ARX::_copy_ ( ) const {
+ARX* ARX::_copy ( ) const {
         ARX* Tmp = new ARX ( *this );
         return Tmp;

library/bdm/estim/arx.h

@@ -56 +56 @@
         ARX ( const double frg0 = 1.0 ) : BMEF ( frg0 ),  have_constant ( true ), dyad(), est(), alter_est() {};
         ARX ( const ARX &A0 ) : BMEF ( A0 ),  have_constant ( A0.have_constant ), dyad ( A0.dyad ), est ( A0.est ), alter_est ( A0.alter_est ) { };
-        ARX* _copy_() const;
+
+        ARX* _copy() const;
+
         void set_parameters ( double frg0 ) {
                 frg = frg0;
@@ -174 +176 @@
         //! copy constructor
         ARXfrg ( const ARXfrg &A0 ) : ARX ( A0 ) {};
-        ARXfrg* _copy_() const {
+        virtual ARXfrg* _copy() const {
                 ARXfrg *A = new ARXfrg ( *this );
                 return A;

library/bdm/estim/ekf_template.h

@@ -30 +30 @@
 class EKFCh_dQ : public EKFCh {
 public:
-        BM* _copy_() const {return new EKFCh_dQ(*this);}
+        root* _copy_() const {
+                return new EKFCh_dQ(*this);
+        }
+
         //! new bayes, expects cond = [ut, Qt]
         void bayes( const vec &yt , const vec &cond) {

library/bdm/estim/kalman.h

@@ -154 +154 @@
                 bdm_assert ( est.dimension(), "Statistics and model parameters mismatch" );
         }
+
+        virtual double logpred ( const vec &yt ) const NOT_IMPLEMENTED(0);
+
+        virtual epdf* epredictor() const NOT_IMPLEMENTED(NULL);
+        
+        virtual pdf* predictor() const NOT_IMPLEMENTED(NULL);
 };
 /*!
@@ -165 +171 @@
         //! Here dt = [yt;ut] of appropriate dimensions
         void bayes ( const vec &yt, const vec &cond = empty_vec );
-        BM* _copy_() const {
+
+        virtual KalmanFull* _copy() const {
                 KalmanFull* K = new KalmanFull;
                 K->set_parameters ( A, B, C, D, Q, R );
@@ -192 +199 @@
 public:
         //! copy constructor
-        BM* _copy_() const {
+        virtual KalmanCh* _copy() const {
                 KalmanCh* K = new KalmanCh;
                 K->set_parameters ( A, B, C, D, Q, R );
@@ -335 +342 @@
 public:
         //! copy constructor duplicated - calls different set_parameters
-        BM* _copy_() const {
+        EKFCh* _copy() const {
                 return new EKFCh(*this);
         }
@@ -422 +429 @@
         // TODO dodelat void to_setting( Setting &set ) const;
 
+        virtual double logpred ( const vec &yt ) const NOT_IMPLEMENTED(0); 
+
+        virtual epdf* epredictor() const NOT_IMPLEMENTED(NULL); 
+
+        virtual pdf* predictor() const NOT_IMPLEMENTED(NULL); 
 };
 

library/bdm/estim/mixtures.cpp

@@ -15 +15 @@
         int ndat = Data.cols();
         //Estimate  Com0 from all data
-        Coms ( 0 ) = Com0->_copy_();
+        Coms ( 0 ) = (BMEF*) Com0->_copy();
 //      Coms(0)->set_evalll(false);
         Coms ( 0 )->bayes_batch ( Data );
@@ -24 +24 @@
         for ( i = 1; i < n; i++ ) {
                 //copy Com0 and create new rvs for them
-                Coms ( i ) =  Coms ( 0 )->_copy_ ( );
+                Coms ( i ) =  (BMEF*) Coms ( 0 )->_copy ( );
         }
         //Pick some data for each component and update it
         for ( i = 0; i < n; i++ ) {
                 //pick one datum
-                int ind = floor ( ndat * UniRNG.sample() );
+                int ind = (int) floor ( ndat * UniRNG.sample() );
                 Coms ( i )->bayes ( Data.get_col ( ind ), empty_vec );
                 //flatten back to oringinal
@@ -49 +49 @@
         Array<BMEF*> Coms0 ( n );
         for ( i = 0; i < n; i++ ) {
-                Coms0 ( i ) = ( BMEF* ) Coms ( i )->_copy_();
+                Coms0 ( i ) = ( BMEF* ) Coms ( i )->_copy();
         }
 
@@ -147 +147 @@
         emix* tmp;
         tmp = new emix( );
-        tmp->set_parameters ( weights.posterior().mean(), pC );
+        tmp->_w() = weights.posterior().mean();
+        tmp->_Coms() = pC;
         tmp->validate();
         return tmp;

library/bdm/estim/mixtures.h

@@ -75 +75 @@
                         weights (), method ( QB ) {
                 for ( int i = 0; i < n; i++ ) {
-                        Coms ( i ) = ( BMEF* ) Coms0 ( i )->_copy_();
+                        Coms ( i ) = ( BMEF* ) Coms0 ( i )->_copy();
                 }
                 weights.set_parameters(alpha0);
@@ -92 +92 @@
                         weights ( M2.weights ), method ( M2.method ) {
                 for ( int i = 0; i < n; i++ ) {
-                        Coms ( i ) = M2.Coms ( i )->_copy_();
+                        Coms ( i ) = (BMEF*) M2.Coms ( i )->_copy();
                 }
                 build_est();
@@ -144 +144 @@
 }
 #endif // MIXTURES_H
-
-

library/bdm/estim/particles.cpp

@@ -168 +168 @@
                         if ( ind ( i ) != i ) {//replace the current Bm by a new one
                                 delete BMs ( i );
-                                BMs ( i ) = BMs ( ind ( i ) )->_copy_(); //copy constructor
+                                BMs ( i ) = (BM*) BMs ( ind ( i ) )->_copy(); //copy constructor
                         }
                 };

library/bdm/estim/particles.h

@@ -203 +203 @@
                 return _samples;
         }
+
+        virtual double logpred ( const vec &yt ) const NOT_IMPLEMENTED(0);
+
+        virtual epdf* epredictor() const NOT_IMPLEMENTED(NULL);
+        
+        virtual pdf* predictor() const NOT_IMPLEMENTED(NULL);
 };
 UIREGISTER ( PF );
@@ -242 +248 @@
                 void qbounds ( vec &lb, vec &ub, double perc = 0.95 ) const;
 
-                vec sample() const {
-                        bdm_error ( "Not implemented" );
-                        return vec();
-                }
-
-                double evallog ( const vec &val ) const {
-                        bdm_error ( "not implemented" );
-                        return 0.0;
-                }
+                vec sample() const NOT_IMPLEMENTED(0);
+
+                double evallog ( const vec &val ) const NOT_IMPLEMENTED(0);             
         };
 
@@ -282 +282 @@
                 //BMcond0 .condition ( pf->posterior()._sample ( 0 ) );
                 for ( int i = 0; i < n; i++ ) {
-                        BMs ( i ) = BMcond0._copy_();
+                        BMs ( i ) = (BM*) BMcond0._copy();
                 }
         };
 
         void bayes ( const vec &yt, const vec &cond );
+
         const epdf& posterior() const {
                 return jest;
@@ -301 +302 @@
         }
         PF& _pf() {return *pf;}
+
+
+        virtual double logpred ( const vec &yt ) const NOT_IMPLEMENTED(0); 
+                
+        virtual epdf* epredictor() const NOT_IMPLEMENTED(NULL); 
+        
+        virtual pdf* predictor() const NOT_IMPLEMENTED(NULL); 
+
 
         /*! configuration structure for basic PF
@@ -315 +324 @@
         void from_setting ( const Setting &set ) {
                 shared_ptr<pdf> par = UI::build<pdf> ( set, "parameter_pdf", UI::compulsory );
-                shared_ptr<pdf> obs = new pdf(); // not used!!
 
                 pf = new PF;
@@ -321 +329 @@
                 pf->prior_from_set ( set );
                 pf->resmethod_from_set ( set );
-                pf->set_model ( par, obs );
+                pf->set_model ( par, par ); // too hackish!
 
                 shared_ptr<BM> BM0 = UI::build<BM> ( set, "BM", UI::compulsory );
@@ -340 +348 @@
                 validate();
         }
+
         void validate() {
                 try {
                         pf->validate();
-                } catch ( std::exception &e ) {
+                } catch ( std::exception ) {
                         throw UIException ( "Error in PF part of MPF:" );
                 }
@@ -351 +360 @@
                 pf2bm.set_connection ( BMs ( 0 )->_rvc(), pf->posterior()._rv() );
         }
-
 };
 UIREGISTER ( MPF );

library/bdm/itpp_ext.cpp

@@ -359 +359 @@
         }
         if ( xa == ( int ) xa ) {
-                n = xa;
+                n = (int) xa;
                 for ( k = 1; k < n; k++ ) {
                         s += 1.0 / k;
@@ -365 +365 @@
                 ps =  s - el;
         } else if ( ( xa + 0.5 ) == ( ( int ) ( xa + 0.5 ) ) ) {
-                n = xa - 0.5;
+                n = (int) (xa - 0.5);
                 for ( k = 1; k <= n; k++ ) {
                         s += 1.0 / ( 2.0 * k - 1.0 );
@@ -410 +410 @@
         //! generate randun() sample
         double get() {
-                long long tmp = A * seed;
+                long tmp = (long) (A * seed);
                 tmp = tmp % M;
                 seed = tmp;

library/bdm/math/chmat.h

@@ -77 +77 @@
           it shouldn't actually be called.
         */
-        chmat ( const chmat &M, const ivec &perm ) {
-                bdm_error ( "not implemented" );
-        }
+        chmat ( const chmat &M, const ivec &perm ) NOT_IMPLEMENTED_VOID;
 
         //! Access function

library/bdm/math/square_mat.h

@@ -42 +42 @@
          BLAS-2b operation.
          */
-        virtual void opupdt ( const vec &v, double w ) {
-                bdm_error ( "not implemented" );
-        };
+        virtual void opupdt ( const vec &v, double w ) = 0;
 
         /*! \brief Conversion to full matrix.
         */
-
-        virtual mat to_mat() const {
-                bdm_error ( "not implemented" );
-                return mat ( 0, 0 );
-        }
+        virtual mat to_mat() const = 0;
 
         /*! \brief Inplace symmetric multiplication by a SQUARE matrix \f$C\f$, i.e. \f$V = C*V*C'\f$
         @param C multiplying matrix,
         */
-        virtual void mult_sym ( const mat &C ) {
-                bdm_error ( "not implemented" );
-        };
+        virtual void mult_sym ( const mat &C ) = 0;
 
         /*! \brief Inplace symmetric multiplication by a SQUARE transpose of matrix \f$C\f$, i.e. \f$V = C'*V*C\f$
         @param C multiplying matrix,
         */
-        virtual void mult_sym_t ( const mat &C ) {
-                bdm_error ( "not implemented" );
-        }
-
+        virtual void mult_sym_t ( const mat &C ) = 0;
 
         /*!
@@ -73 +62 @@
 
         */
-        virtual double logdet() const {
-                bdm_error ( "not implemented" );
-                return 0;
-        };
+        virtual double logdet() const = 0;
 
         /*!
@@ -83 +69 @@
         Used e.g. in generating normal samples.
         */
-        virtual vec sqrt_mult ( const vec &v )  const {
-                bdm_error ( "not implemented" );
-                return vec ( 0 );
-        };
+        virtual vec sqrt_mult ( const vec &v )  const = 0;
 
         /*!
@@ -92 +75 @@
 
         */
-        virtual double qform ( const vec &v ) const {
-                bdm_error ( "not implemented" );
-                return 0;
-        };
+        virtual double qform ( const vec &v ) const = 0;
 
         /*!
@@ -101 +81 @@
 
         */
-        virtual double invqform ( const vec &v ) const {
-                bdm_error ( "not implemented" );
-                return 0;
-        };
+        virtual double invqform ( const vec &v ) const = 0;
 
 //      //! easy version of the
@@ -110 +87 @@
 
         //! Clearing matrix so that it corresponds to zeros.
-        virtual void clear() {
-                bdm_error ( "not implemented" );
-        };
+        virtual void clear() = 0;
 
         //! Reimplementing common functions of mat: cols().

library/bdm/mex/mex_BM.h

@@ -38 +38 @@
                 return mxArray2vec ( tmp );
         }
+
+        virtual vec sample() const NOT_IMPLEMENTED(0);
+
+        virtual double evallog ( const vec &val ) const NOT_IMPLEMENTED(0);
+        
+        virtual vec variance() const NOT_IMPLEMENTED(0);
 };
 UIREGISTER ( mexEpdf );
@@ -92 +98 @@
                 return est;
         } //tohle by melo zustat!!
+
+        virtual double logpred ( const vec &yt ) const  NOT_IMPLEMENTED(0);
+
+        virtual epdf* epredictor() const NOT_IMPLEMENTED(NULL);
+
+        virtual pdf* predictor() const NOT_IMPLEMENTED(NULL);
 };
 UIREGISTER ( mexBM );

library/bdm/mex/mex_datasource.h

@@ -117 +117 @@
         }
 
+        virtual void getdata ( vec &dt, const ivec &indeces ) NOT_IMPLEMENTED_VOID;
+
+        virtual void write ( const vec &ut, const ivec &indeces ) NOT_IMPLEMENTED_VOID;
+
+
         void step() {
                 mxArray* tmp;

library/bdm/stat/discrete.cpp

@@ -81 +81 @@
                                 inds ( j ) = gridsizes ( j ) - 1;
                         else {
-                                inds ( j ) = ::round ( val ( j ) - ranges ( j ) ( 0 ) / steps ( j ) );
+                                inds ( j ) = (int) ::round ( val ( j ) - ranges ( j ) ( 0 ) / steps ( j ) );
                         }
                 }

library/bdm/stat/emix.cpp

@@ -3 +3 @@
 namespace bdm {
 
-void emix::set_parameters ( const vec &w0, const Array<shared_ptr<epdf> > &Coms0 ) {
-        w = w0 / sum ( w0 );
-        
-        bool isnamed = Coms0 ( 0 )->isnamed();
-        RV tmp_rv;
-        if ( isnamed ) tmp_rv = Coms0 ( 0 )->_rv();
-        Coms = Coms0;
-
-        if ( isnamed ) epdf::set_rv ( tmp_rv ); //coms aer already OK, no need for set_rv
-}
-
 void emix::validate (){
-        dim = Coms ( 0 )->dimension();
-        bool isnamed = Coms ( 0 )->isnamed();
-        int i;
-        RV tmp_rv;
-        if ( isnamed ) tmp_rv = Coms ( 0 )->_rv();
-        for ( i = 0; i < w.length(); i++ ) {
+        bdm_assert ( Coms.length() > 0, "There has to be at least one component." );
+
+        bdm_assert ( Coms.length() == w.length(), "It is obligatory to define weights of all the components." );
+
+        double sum_w = sum ( w );
+        bdm_assert ( sum_w != 0, "There has to be a component with non-zero weight." );
+        w = w / sum_w;
+
+        int dim = Coms ( 0 )->dimension();
+        for ( int i = 1; i < Coms.length(); i++ ) {
                 bdm_assert ( dim == ( Coms ( i )->dimension() ), "Component sizes do not match!" );
-                bdm_assert ( !isnamed || tmp_rv.equal ( Coms ( i )->_rv() ), "Component RVs do not match!" );
-        }
-
-}
-
-
+                bdm_assert ( Coms(i)->isnamed() , "An unnamed component is forbidden here!" );
+        }
+
+        set_rv ( Coms ( 0 )->_rv() ); 
+}
+
+void emix::from_setting ( const Setting &set ) {
+        UI::get ( Coms, set, "pdfs", UI::compulsory );
+
+        if ( !UI::get ( w, set, "weights", UI::optional ) ) {
+                int len = Coms.length();
+                w.set_length ( len );
+                w = 1.0 / len;
+        }
+
+        validate();
+}
 
 
@@ -109 +113 @@
         }
 
-        target.set_parameters ( w, Cn );
+        target._w() = w;
+        target._Coms() = Cn;
         target.validate();
 }
@@ -190 +195 @@
         }
 
-        target.set_parameters ( w, Cn );
+        target._w() = w;
+        target._Coms() = Cn;
         target.validate();
 }
@@ -313 +319 @@
                 dls ( i ) = new datalink_m2m;
                 dls ( i )->set_connection ( pdfs ( i )->_rv(), pdfs ( i )->_rvc(), _rv(), _rvc() );
+        }
+}
+
+void mmix::validate()
+{       
+        bdm_assert ( Coms.length() > 0, "There has to be at least one component." );
+
+        bdm_assert ( Coms.length() == w.length(), "It is obligatory to define weights of all the components." );
+
+        double sum_w = sum ( w );
+        bdm_assert ( sum_w != 0, "There has to be a component with non-zero weight." );
+        w = w / sum_w;
+
+        int dim = Coms ( 0 )->dimension();
+        int dimc = Coms ( 0 )->dimensionc();
+        for ( int i = 1; i < Coms.length(); i++ ) {
+                bdm_assert ( dim == ( Coms ( i )->dimension() ), "Component sizes do not match!" );
+                bdm_assert ( dimc == ( Coms ( i )->dimensionc() ), "Component sizes do not match!" );
+                bdm_assert ( Coms(i)->isnamed() , "An unnamed component is forbidden here!" );
+        }
+
+        set_rv ( Coms ( 0 )->_rv() );
+        set_rvc ( Coms ( 0 )->_rvc() );
+}
+
+void mmix::from_setting ( const Setting &set ) {
+        UI::get ( Coms, set, "pdfs", UI::compulsory );
+
+        if ( !UI::get ( w, set, "weights", UI::optional ) ) {
+                int len = Coms.length();
+                w.set_length ( len );
+                w = 1.0 / len;
         }
 }

library/bdm/stat/emix.h

@@ -53 +53 @@
                 // adjust rv and rvc
 
-                set_rv ( rv ); // TODO co kdyby tohle samo uz nastavovalo dimension?!?!
+                set_rv ( rv ); 
                 dim = rv._dsize();
 
@@ -81 +81 @@
                 return tmp;
         }
+
+        //! Returns a sample from the density conditioned on \c cond, \f$x \sim epdf(rv|cond)\f$. \param cond is numeric value of \c rv
+        virtual vec samplecond ( const vec &cond ) NOT_IMPLEMENTED(0);
+
         //! Object takes ownership of nom and will destroy it
         void ownnom() {
@@ -91 +95 @@
                 }
         }
+
+
+
 
 private:
@@ -120 +127 @@
         emix ( ) : epdf ( ) { }
 
-        /*!
-          \brief Set weights \c w and components \c Coms
-
-          Shared pointers in Coms are kept inside this instance and
-          shouldn't be modified after being passed to this method.
-        */
-        void set_parameters ( const vec &w, const Array<shared_ptr<epdf> > &Coms );
-    
         virtual void validate ();
 
@@ -148 +147 @@
         shared_ptr<pdf> condition ( const RV &rv ) const;
 
-        //Access methods
-        //! returns a pointer to the internal mean value. Use with Care!
+        //Access methods        
+        //! returns a reference to the internal weights. Use with Care!
         vec& _w() {
                 return w;
         }
 
-        //!access function
+        /*!
+          \brief returns a reference to the internal array of components. Use with Care! Set components \c Coms
+
+          Shared pointers in Coms are kept inside this instance and
+          shouldn't be modified after being passed to this method.
+        */
+        Array<shared_ptr<epdf>>& _Coms ( ) {
+                return Coms;
+        }
+
+        //! returns a reference to the internal components specified by index i. Use with Care!
         shared_ptr<epdf> _Coms ( int i ) {
                 return Coms ( i );
@@ -174 +183 @@
         //! \endcode
         //!@}
-        void from_setting ( const Setting &set ) {
-
-                vec w0;
-                Array<shared_ptr<epdf> > Coms0;
-
-                UI::get ( Coms0, set, "pdfs", UI::compulsory );
-
-                if ( !UI::get ( w0, set, "weights", UI::optional ) ) {
-                        int len = Coms.length();
-                        w0.set_length ( len );
-                        w0 = 1.0 / len;
-                }
-
-                // TODO asi lze nacitat primocare do w a coms, jen co bude hotovy validate()
-                set_parameters ( w0, Coms0 );
-                validate();
-        }
+        void from_setting ( const Setting &set );
 };
 SHAREDPTR ( emix );
@@ -284 +277 @@
         //! Data link for each pdfs
         Array<shared_ptr<datalink_m2m> > dls;
-
-protected:
-        //! dummy epdf used only as storage for RV and dim
-        epdf iepdf;
 
 public:
@@ -330 +319 @@
         //!@}
         void from_setting ( const Setting &set ) {
-                Array<shared_ptr<pdf> > atmp; //temporary Array
-                UI::get ( atmp, set, "pdfs", UI::compulsory );
-                set_elements ( atmp );
+                Array<shared_ptr<pdf> > temp_array; 
+                UI::get ( temp_array, set, "pdfs", UI::compulsory );
+                set_elements ( temp_array );
         }
 };
@@ -418 +407 @@
         mmix() : Coms ( 0 ) { }
 
-        //! Set weights \c w and components \c R
-        void set_parameters ( const vec &w0, const Array<shared_ptr<pdf> > &Coms0 ) {
-                //!\todo check if all components are OK
-                Coms = Coms0;
-                w = w0;
-
-                if ( Coms0.length() > 0 ) {
-                        set_rv ( Coms ( 0 )->_rv() );
-                        dim = rv._dsize();
-                        set_rvc ( Coms ( 0 )->_rvc() );
-                        dimc = rvc._dsize();
-                }
-        }
         double evallogcond ( const vec &dt, const vec &cond ) {
                 double ll = 0.0;
@@ -449 +425 @@
         //! \endcode
         //!@}
-        void from_setting ( const Setting &set ) {
-                UI::get ( Coms, set, "pdfs", UI::compulsory );
-
-                // TODO ma byt zde, ci ve validate()?
-                if ( Coms.length() > 0 ) {
-                        set_rv ( Coms ( 0 )->_rv() );
-                        dim = rv._dsize();
-                        set_rvc ( Coms ( 0 )->_rvc() );
-                        dimc = rvc._dsize();
-                }
-
-                if ( !UI::get ( w, set, "weights", UI::optional ) ) {
-                        int len = Coms.length();
-                        w.set_length ( len );
-                        w = 1.0 / len;
-                }
-        }
+        void from_setting ( const Setting &set );
+
+        virtual void validate();
 };
 SHAREDPTR ( mmix );

library/bdm/stat/exp_family.h

@@ -44 +44 @@
 
         //!Evaluate normalized log-probability
-        virtual double evallog_nn ( const vec &val ) const {
-                bdm_error ( "Not implemented" );
-                return 0.0;
-        }
+        virtual double evallog_nn ( const vec &val ) const NOT_IMPLEMENTED(0);
 
         //!Evaluate normalized log-probability
@@ -73 +70 @@
 
         //!Power of the density, used e.g. to flatten the density
-        virtual void pow ( double p ) {
-                bdm_error ( "Not implemented" );
-        }
+        virtual void pow ( double p ) NOT_IMPLEMENTED_VOID;
 };
 
@@ -92 +87 @@
         BMEF ( const BMEF &B ) : BM ( B ), frg ( B.frg ), last_lognc ( B.last_lognc ) {}
         //!get statistics from another model
-        virtual void set_statistics ( const BMEF* BM0 ) {
-                bdm_error ( "Not implemented" );
-        }
+        virtual void set_statistics ( const BMEF* BM0 ) NOT_IMPLEMENTED_VOID;
 
         //! Weighted update of sufficient statistics (Bayes rule)
@@ -102 +95 @@
 
         //!Flatten the posterior according to the given BMEF (of the same type!)
-        virtual void flatten ( const BMEF * B ) {
-                bdm_error ( "Not implemented" );
-        }
-
-        BMEF* _copy_ () const {
-                bdm_error ( "function _copy_ not implemented for this BM" );
-                return NULL;
-        }
+        virtual void flatten ( const BMEF * B ) NOT_IMPLEMENTED_VOID;
+
+        double logpred ( const vec &yt ) const NOT_IMPLEMENTED(0);
+        
+        virtual epdf* epredictor() const NOT_IMPLEMENTED(NULL);
+
+        virtual pdf* predictor() const NOT_IMPLEMENTED(NULL);
 
         void to_setting ( Setting &set ) const
         {                       
                 BM::to_setting( set );
-                // TODO DOPLNIT? CHYBI FROM_SETTING PRO INSPIRACI
+                // TODO DOPLNIT? ALE MOMENTALNE CHYBI FROM_SETTING PRO INSPIRACI
         } 
 };
@@ -1112 +1104 @@
         //! Constructor
         migamma_ref () : migamma (), refl () {};
+        
         //! Set value of \c k
         void set_parameters ( double k0 , vec ref0, double l0 ) {
@@ -1266 +1259 @@
                 return X*Y._Ch();// return upper triangular part of the decomposition
         }
+
         vec sample () const {
                 return vec ( sample_mat()._data(), p*p );
         }
+
+        virtual vec mean() const NOT_IMPLEMENTED(0);
+
+        //! return expected variance (not covariance!)
+        virtual vec variance() const NOT_IMPLEMENTED(0);
+
+        virtual double evallog ( const vec &val ) const NOT_IMPLEMENTED(0);
+
         //! fast access function y0 will be copied into Y.Ch.
         void setY ( const mat &Ch0 ) {
                 copy_vector ( dim, Ch0._data(), Y._Ch()._data() );
         }
+
         //! fast access function y0 will be copied into Y.Ch.
         void _setY ( const vec &ch0 ) {
                 copy_vector ( dim, ch0._data(), Y._Ch()._data() );
         }
+
         //! access function
         const chmat& getY() const {
@@ -1321 +1325 @@
                 W.setY ( iCh );
         }
+
         virtual double evallog ( const vec &val ) const {
                 chmat X ( p );
@@ -1345 +1350 @@
         };
 
+        virtual vec mean() const NOT_IMPLEMENTED(0);
+
+        //! return expected variance (not covariance!)
+        virtual vec variance() const NOT_IMPLEMENTED(0);
 };
 
@@ -1464 +1473 @@
 
         //! inherited operation : NOT implemented
-        vec sample() const {
-                bdm_error ( "Not implemented" );
-                return vec();
-        }
+        vec sample() const NOT_IMPLEMENTED(0);
 
         //! inherited operation : NOT implemented
-        double evallog ( const vec &val ) const {
-                bdm_error ( "Not implemented" );
-                return 0.0;
-        }
+        double evallog ( const vec &val ) const NOT_IMPLEMENTED(0);
 
         vec mean() const {

library/bdm/stat/merger.h

@@ -148 +148 @@
 
         vec variance() const;
+
+        //! Compute log-probability of argument \c val
+        virtual double evallog ( const vec &val ) const NOT_IMPLEMENTED(0);
+
+        //! Returns a sample, \f$ x \f$ from density \f$ f_x()\f$
+        virtual vec sample() const NOT_IMPLEMENTED(0);
 
         //!@}

library/tests/stresssuite/arx_stress.cpp

@@ -24 +24 @@
         //Test constructor
         mat V0 = 0.00001 * eye ( ord + 1 );
-        V0 ( 0.0 ) = 1; //
+        V0 ( 0 ) = 1; //
         double nu0 = ord + 5.0;
 

library/tests/stresssuite/mixtures_stress.cpp

@@ -67 +67 @@
         emix Simul;
         Simul.set_rv ( x );
-        Simul.set_parameters ( "0.5 0.6", Sim );
+        Simul._w() = "0.5 0.6";
+        Simul._Coms() = Sim;
         Simul.validate();
 

library/tests/stresssuite/square_mat_stress.cpp

@@ -60 +60 @@
 
         tt.tic();
-        TMatrix sqmat ( A );
+        TMatrix sq_mat ( A );
         double elapsed = tt.toc();
         cout << "ctor(" << sz << " x " << sz << "): " << elapsed << " s" << endl;
 
         tt.tic();
-        mat res = sqmat.to_mat();
+        mat res = sq_mat.to_mat();
         elapsed = tt.toc();
 
@@ -76 +76 @@
         vec v = point->get_vector();
         double w = point->get_scalar();
-        TMatrix sqmat2 = sqmat;
-
-        tt.tic();
-        sqmat2.opupdt ( v, w );
+        TMatrix sq_mat2 = sq_mat;
+
+        tt.tic();
+        sq_mat2.opupdt ( v, w );
         elapsed = tt.toc();
 
         if ( !fast ) {
                 mat expA = A + w * outer_product ( v, v );
-                CHECK_CLOSE ( expA, sqmat2.to_mat(), epsilon );
+                CHECK_CLOSE ( expA, sq_mat2.to_mat(), epsilon );
         }
 
@@ -92 +92 @@
 
         tt.tic();
-        sqmat.inv ( invmat );
+        sq_mat.inv ( invmat );
         elapsed = tt.toc();
 
@@ -104 +104 @@
 
         tt.tic();
-        double ld = sqmat.logdet();
+        double ld = sq_mat.logdet();
         elapsed = tt.toc();
 
@@ -115 +115 @@
 
         tt.tic();
-        double q = sqmat.qform ( ones ( sz ) );
+        double q = sq_mat.qform ( ones ( sz ) );
         elapsed = tt.toc();
 
@@ -125 +125 @@
 
         tt.tic();
-        q = sqmat.qform ( v );
+        q = sq_mat.qform ( v );
         elapsed = tt.toc();
 
@@ -136 +136 @@
 
         tt.tic();
-        q = sqmat.invqform ( v );
+        q = sq_mat.invqform ( v );
         elapsed = tt.toc();
 
@@ -146 +146 @@
         cout << "invqform: " << elapsed << " s" << endl;
 
-        TMatrix twice = sqmat;
-
-        tt.tic();
-        twice += sqmat;
+        TMatrix twice = sq_mat;
+
+        tt.tic();
+        twice += sq_mat;
         elapsed = tt.toc();
 
@@ -159 +159 @@
         cout << "+=: " << elapsed << " s" << endl;
 
-        sqmat2 = sqmat;
-
-        tt.tic();
-        sqmat2.mult_sym ( A );
+        sq_mat2 = sq_mat;
+
+        tt.tic();
+        sq_mat2.mult_sym ( A );
         elapsed = tt.toc();
 
         if ( !fast ) {
                 res = ( A * A ) * A.T();
-                CHECK_CLOSE ( res, sqmat2.to_mat(), epsilon );
+                CHECK_CLOSE ( res, sq_mat2.to_mat(), epsilon );
         }
 

library/tests/testsuite/emix_test.cpp

@@ -38 +38 @@
         emix M1;
         M1.set_rv ( xy );
-        M1.set_parameters ( vec ( "1" ), A1 );
+        M1._Coms() = A1;
+        M1._w() = 1;
         M1.validate();
 
@@ -68 +69 @@
         emix M2;
         M2.set_rv ( xy );
-        M2.set_parameters ( vec ( "1" ), A2 );
+        M2._Coms() = A2;
+        M2._w() = 1;
         M2.validate();
 

library/tests/testsuite/square_mat_test.cpp

@@ -20 +20 @@
         mat A = A0 * A0.T();
 
-        TMatrix sqmat ( A );
-        CHECK_EQUAL ( sz, sqmat.rows() );
-        CHECK_EQUAL ( sz, sqmat.cols() );
+        TMatrix sq_mat ( A );
+        CHECK_EQUAL ( sz, sq_mat.rows() );
+        CHECK_EQUAL ( sz, sq_mat.cols() );
 
-        mat res = sqmat.to_mat();
+        mat res = sq_mat.to_mat();
         CHECK_CLOSE ( A, res, epsilon );
 
         vec v = randu ( sz );
         double w = randu();
-        TMatrix sqmat2 = sqmat;
-        sqmat2.opupdt ( v, w );
+        TMatrix sq_mat2 = sq_mat;
+        sq_mat2.opupdt ( v, w );
 
         res = A + w * outer_product ( v, v );
-        CHECK_CLOSE ( res, sqmat2.to_mat(), epsilon );
+        CHECK_CLOSE ( res, sq_mat2.to_mat(), epsilon );
 
         TMatrix invmat ( sz );
-        sqmat.inv ( invmat );
+        sq_mat.inv ( invmat );
         mat invA = inv ( A );
         CHECK_CLOSE ( invA, invmat.to_mat(), epsilon );
 
         double d = det ( A );
-        CHECK_CLOSE ( log ( d ), sqmat.logdet(), epsilon );
+        CHECK_CLOSE ( log ( d ), sq_mat.logdet(), epsilon );
 
-        double q = sqmat.qform ( ones ( sz ) );
+        double q = sq_mat.qform ( ones ( sz ) );
         CHECK_CLOSE ( sumsum ( A ), q, epsilon );
 
-        q = sqmat.qform ( v );
+        q = sq_mat.qform ( v );
         double r = ( A * v ) * v;
         CHECK_CLOSE ( r, q, epsilon );
 
-        q = sqmat.invqform ( v );
+        q = sq_mat.invqform ( v );
         r = ( invA * v ) * v;
         CHECK_CLOSE ( r, q, epsilon );
 
-        sqmat2 = sqmat;
-        sqmat2.clear();
-        CHECK_EQUAL ( 0, sqmat2.qform ( ones ( sz ) ) );
+        sq_mat2 = sq_mat;
+        sq_mat2.clear();
+        CHECK_EQUAL ( 0, sq_mat2.qform ( ones ( sz ) ) );
 
-        TMatrix twice = sqmat;
-        twice += sqmat;
+        TMatrix twice = sq_mat;
+        twice += sq_mat;
         res = 2 * A;
         CHECK_CLOSE ( res, twice.to_mat(), epsilon );
 
-        twice = sqmat;
+        twice = sq_mat;
         twice *= 2;
         CHECK_CLOSE ( res, twice.to_mat(), epsilon );
 
-        sqmat2 = sqmat;
+        sq_mat2 = sq_mat;
         mat B = randu ( sz, sz );
-        sqmat2.mult_sym ( B );
+        sq_mat2.mult_sym ( B );
         res = ( B * A ) * B.T();
-        CHECK_CLOSE ( res, sqmat2.to_mat(), epsilon );
+        CHECK_CLOSE ( res, sq_mat2.to_mat(), epsilon );
 
         mat C = randu ( sz, sz - 1 );
         TMatrix CAC ( sz - 1 );
-        sqmat.mult_sym_t ( C, CAC );
+        sq_mat.mult_sym_t ( C, CAC );
         res = ( C.T() * A ) * C;
         CHECK_CLOSE ( res, CAC.to_mat(), epsilon );
 
-        sqmat2 = sqmat;
-        sqmat2.mult_sym_t ( B );
+        sq_mat2 = sq_mat;
+        sq_mat2.mult_sym_t ( B );
         res = ( B.T() * A ) * B;
-        CHECK_CLOSE ( res, sqmat2.to_mat(), epsilon );
+        CHECK_CLOSE ( res, sq_mat2.to_mat(), epsilon );
 }