Changeset 162 for bdm/stat

Timestamp:

09/04/08 20:27:01 (16 years ago)

Author:

smidl

Message:

opravy a dokumentace

Location:

bdm/stat

Files:

• emix.h (modified) (3 diffs)
• libBM.cpp (modified) (4 diffs)
• libBM.h (modified) (3 diffs)
• libEF.cpp (modified) (1 diff)
• libEF.h (modified) (1 diff)
• loggers.cpp (modified) (7 diffs)
• loggers.h (modified) (4 diffs)

bdm/stat/emix.h

@@ -31 +31 @@
 */
 class emix : public epdf {
-        protected:
-                //! weights of the components
-                vec w;
-                //! Component (epdfs)
-                Array<epdf*> Coms;
-        public:
-                //!Default constructor
-                emix(RV &rv) : epdf(rv) {};
-                //! Set weights \c w and components \c R
-                void set_parameters(const vec &w, const Array<epdf*> &Coms);
+protected:
+        //! weights of the components
+        vec w;
+        //! Component (epdfs)
+        Array<epdf*> Coms;
+public:
+        //!Default constructor
+        emix ( RV &rv ) : epdf ( rv ) {};
+        //! Set weights \c w and components \c R
+        void set_parameters ( const vec &w, const Array<epdf*> &Coms );
 
-                vec sample() const;
-                vec mean() const {
-                        int i; vec mu = zeros(rv.count());
-                        for (i = 0;i < w.length();i++) {mu += w(i) * Coms(i)->mean(); }
-                        return mu;
-                }
-                double evalpdflog(const vec &val) const {
-                        int i;
-                        double sum = 0.0;
-                        for (i = 0;i < w.length();i++) {sum += w(i) * Coms(i)->evalpdflog(val);}
-                        return log(sum);
-                };
+        vec sample() const;
+        vec mean() const {
+                int i; vec mu = zeros ( rv.count() );
+                for ( i = 0;i < w.length();i++ ) {mu += w ( i ) * Coms ( i )->mean(); }
+                return mu;
+        }
+        double evalpdflog ( const vec &val ) const {
+                int i;
+                double sum = 0.0;
+                for ( i = 0;i < w.length();i++ ) {sum += w ( i ) * Coms ( i )->evalpdflog ( val );}
+                return log ( sum );
+        };
 
 //Access methods
-                //! returns a pointer to the internal mean value. Use with Care!
-                vec& _w() {return w;}
+        //! returns a pointer to the internal mean value. Use with Care!
+        vec& _w() {return w;}
 };
 
@@ -68 +68 @@
 Note that
 */
-class eprod: public epdf {
-        protected:
-                //
-                int n;
-                // pointers to epdfs
-                Array<epdf*> epdfs;
-                Array<mpdf*> mpdfs;
-                //
-                Array<ivec> rvinds;
-                Array<ivec> rvcinds;
-                //! Indicate independence of its factors
-                bool independent;
-                //! Indicate internal creation of mpdfs which must be destroyed
-                bool intermpdfs;
-        public:
-                //!Constructor from list of eFacs or list of mFacs
-                eprod(Array<mpdf*> mFacs): epdf(RV()), n(mFacs.length()), epdfs(n), mpdfs(mFacs), rvinds(n), rvcinds(n) {
-                        int i;
-                        intermpdfs = false;
-                        for (i = 0;i < n;i++) {
-                                rv.add(mpdfs(i)->_rv()); //add rv to common rvs.
-                                epdfs(i) = &(mpdfs(i)->_epdf()); // add pointer to epdf
-                        };
-                        independent = true;
-                        //test rvc of mpdfs and fill rvinds
-                        for (i = 0;i < n;i++) {
-                                // find ith rv in common rv
-                                rvinds(i) = mpdfs(i)->_rv().dataind(rv);
-                                // find ith rvc in common rv
-                                rvcinds(i) = mpdfs(i)->_rvc().dataind(rv);
-                                if (rvcinds(i).length()>0) {independent = false;}
-                        }
-
+class mprod: public mpdf {
+protected:
+        //
+        int n;
+        // pointers to epdfs
+        Array<epdf*> epdfs;
+        Array<mpdf*> mpdfs;
+        //
+        //! Indeces of rvs in common rv
+        Array<ivec> rvinds;
+        //! Indeces of rvc in common rv
+        Array<ivec> rvcinrv;
+        //! Indeces of rvc in common rvc
+        Array<ivec> rvcinds;
+        //! Indicate independence of its factors
+        bool independent;
+//      //! Indicate internal creation of mpdfs which must be destroyed
+//      bool intermpdfs;
+public:
+        //!Constructor from list of eFacs or list of mFacs
+        mprod ( Array<mpdf*> mFacs ) : mpdf ( RV(), RV() ), n ( mFacs.length() ), epdfs ( n ), mpdfs ( mFacs ), rvinds ( n ), rvcinrv ( n ), rvcinds ( n ) {
+                int i;
+                // Create rv
+                for ( i = 0;i < n;i++ ) {
+                        rv.add ( mpdfs ( i )->_rv() ); //add rv to common rvs.
+                        epdfs ( i ) = & ( mpdfs ( i )->_epdf() ); // add pointer to epdf
                 };
-                eprod(Array<epdf*> eFacs): epdf(RV()), n(eFacs.length()), epdfs(eFacs), mpdfs(n), rvinds(n), rvcinds(n) {
-                        int i;
-                        intermpdfs = true;
-                        for (i = 0;i < n;i++) {
-                                if (rv.add(eFacs(i)->_rv())) {it_error("Incompatible eFacs.rv!");} //add rv to common rvs.
-                                mpdfs(i) = new mepdf(*(epdfs(i)));
-                                epdfs(i) = &(mpdfs(i)->_epdf()); // add pointer to epdf
-                        };
-                        independent = true;
-                        //test rvc of mpdfs and fill rvinds
-                        for (i = 0;i < n;i++) {
-                                // find ith rv in common rv
-                                rvinds(i) = mpdfs(i)->_rv().dataind(rv);
-                        }
+                // Create rvc
+                for ( i = 0;i < n;i++ ) {
+                        rvc.add ( mpdfs ( i )->_rv().subt ( rv ) ); //add rv to common rvs.
                 };
 
-                double evalpdflog(const vec &val) const {
-                        int i;
-                        double res = 0.0;
-                        for (i = n - 1;i > 0;i++) {
-                                if (rvcinds(i).length() > 0)
-                                        {mpdfs(i)->condition(val(rvcinds(i)));}
-                                // add logarithms
-                                res += epdfs(i)->evalpdflog(val(rvinds(i)));
+                independent = true;
+                //test rvc of mpdfs and fill rvinds
+                for ( i = 0;i < n;i++ ) {
+                        // find ith rv in common rv
+                        rvinds ( i ) = mpdfs ( i )->_rv().dataind ( rv );
+                        // find ith rvc in common rv
+                        rvcinrv ( i ) = mpdfs ( i )->_rvc().dataind ( rv );
+                        // find ith rvc in common rv
+                        rvcinds ( i ) = mpdfs ( i )->_rvc().dataind ( rvc );
+                        //
+                        if ( rvcinds ( i ).length() >0 ) {independent = false;}
+                        if ( rvcinds ( i ).length() >0 ) {independent = false;}
+                }
+        };
+
+        double evalpdflog ( const vec &val ) const {
+                int i;
+                double res = 0.0;
+                for ( i = n - 1;i > 0;i++ ) {
+                        if ( rvcinds ( i ).length() > 0 )
+                                {mpdfs ( i )->condition ( val ( rvcinds ( i ) ) );}
+                        // add logarithms
+                        res += epdfs ( i )->evalpdflog ( val ( rvinds ( i ) ) );
+                }
+                return res;
+        }
+        vec samplecond ( const vec &cond, double &ll ) {
+                vec smp=zeros ( rv.count() );
+                vec condi;
+                for ( int i = ( n - 1 );i >= 0;i-- ) {
+                        if ( rvcinds ( i ).length() > 0 ) {
+                                condi = zeros ( rvcinrv.length() + rvcinds.length() );
+                                // copy data in condition
+                                set_subvector ( condi,rvcinds ( i ), cond );
+                                // copy data in already generated sample
+                                set_subvector ( condi,rvcinrv ( i ), smp );
+
+                                mpdfs ( i )->condition ( condi );
                         }
-                        return res;
+                        // copy contribution of this pdf into smp
+                        set_subvector ( smp,rvinds ( i ), epdfs ( i )->sample() );
                 }
-                vec sample () const{
-                        vec smp=zeros(rv.count());
-                        for (int i = (n - 1);i >= 0;i--) {
-                                if (rvcinds(i).length() > 0)
-                                        {mpdfs(i)->condition(smp(rvcinds(i)));}
-                                set_subvector(smp,rvinds(i), epdfs(i)->sample());
-                        }                       
-                        return smp;
-                }
-                vec mean() const{
-                        vec tmp(rv.count());
-                        if (independent) {
-                                for (int i=0;i<n;i++) {
-                                        vec pom = epdfs(i)->mean();
-                                        set_subvector(tmp,rvinds(i), pom);
-                                }
-                        }
-                        else {
-                                int N=50*rv.count();
-                                it_warning("eprod.mean() computed by sampling");
-                                tmp = zeros(rv.count());
-                                for (int i=0;i<N;i++){ tmp += sample();}
-                                tmp /=N;
-                        }
-                        return tmp;
-                }
-                ~eprod(){if (intermpdfs) {for (int i=0;i<n;i++){delete mpdfs(i);}}};
+                return smp;
+        }
+        mat samplecond ( const vec &cond, vec &ll, int N ) {
+                mat Smp(rv.count(),N);
+                for(int i=0;i<N;i++){Smp.set_col(i,samplecond(cond,ll(i)));}
+                return Smp;
+        }
+//      vec mean() const {
+//              vec tmp ( rv.count() );
+//              if ( independent ) {
+//                      for ( int i=0;i<n;i++ ) {
+//                              vec pom = epdfs ( i )->mean();
+//                              set_subvector ( tmp,rvinds ( i ), pom );
+//                      }
+//              }
+//              else {
+//                      int N=50*rv.count();
+//                      it_warning ( "eprod.mean() computed by sampling" );
+//                      tmp = zeros ( rv.count() );
+//                      for ( int i=0;i<N;i++ ) { tmp += sample();}
+//                      tmp /=N;
+//              }
+//              return tmp;
+//      }
+
+        ~mprod() {};
 };
 
@@ -162 +174 @@
 */
 class mmix : public mpdf {
-        protected:
-                //! Component (epdfs)
-                Array<mpdf*> Coms;
-                //!Internal epdf
-                emix Epdf;
-        public:
-                //!Default constructor
-                mmix(RV &rv, RV &rvc) : mpdf(rv, rvc), Epdf(rv) {ep = &Epdf;};
-                //! Set weights \c w and components \c R
-                void set_parameters(const vec &w, const Array<mpdf*> &Coms) {
-                        Array<epdf*> Eps(Coms.length());
+protected:
+        //! Component (epdfs)
+        Array<mpdf*> Coms;
+        //!Internal epdf
+        emix Epdf;
+public:
+        //!Default constructor
+        mmix ( RV &rv, RV &rvc ) : mpdf ( rv, rvc ), Epdf ( rv ) {ep = &Epdf;};
+        //! Set weights \c w and components \c R
+        void set_parameters ( const vec &w, const Array<mpdf*> &Coms ) {
+                Array<epdf*> Eps ( Coms.length() );
 
-                        for (int i = 0;i < Coms.length();i++) {
-                                Eps(i) = & (Coms(i)->_epdf());
-                        }
-                        Epdf.set_parameters(w, Eps);
-                };
+                for ( int i = 0;i < Coms.length();i++ ) {
+                        Eps ( i ) = & ( Coms ( i )->_epdf() );
+                }
+                Epdf.set_parameters ( w, Eps );
+        };
 
-                void condition(const vec &cond) {
-                        for (int i = 0;i < Coms.length();i++) {Coms(i)->condition(cond);}
-                };
+        void condition ( const vec &cond ) {
+                for ( int i = 0;i < Coms.length();i++ ) {Coms ( i )->condition ( cond );}
+        };
 };
 #endif //MX_H

bdm/stat/libBM.cpp

@@ -7 +7 @@
 using std::cout;
 
+static int RVcounter=0;
+
 void RV::init ( ivec in_ids, Array<std::string> in_names, ivec in_sizes, ivec in_times ) {
-        //
+        //Refer
         int i;
         len = in_ids.length();
         //PRUDENT_MODE
         // All vetors should be of same length
-        if ( ( len != in_ids.length() ) || \
-                ( len != in_names.length() ) || \
+        if ( ( len != in_names.length() ) || \
                 ( len != in_sizes.length() ) || \
                 ( len != in_times.length() ) ) {
@@ -28 +29 @@
 };
 
-RV::RV ( ivec in_ids, Array<std::string> in_names, ivec in_sizes, ivec in_times ) {
-        init ( in_ids, in_names, in_sizes, in_times );
+RV::RV ( Array<std::string> in_names, ivec in_sizes, ivec in_times ) {
+        int len = in_names.length();
+        init ( linspace ( RVcounter+1, RVcounter+len ), in_names, in_sizes, in_times );
+        RVcounter+=len;
 }
 
-RV::RV() : tsize ( 0 ), len ( 0 ) {};
+RV::RV ( Array<std::string> in_names, ivec in_sizes ) {
+        int len = in_names.length();
+        init ( linspace ( RVcounter+1, RVcounter+len ), in_names, in_sizes, zeros_i ( in_names.length() ) );
+        RVcounter+=len;
+}
+
+RV::RV ( Array<std::string> in_names ) {
+        int len = in_names.length();
+        init ( linspace ( RVcounter+1, RVcounter+len ), in_names, ones_i ( in_names.length() ), zeros_i ( in_names.length() ) );
+        RVcounter+=len;
+}
+
+RV::RV() : tsize ( 0 ), len ( 0 ), ids ( 0 ), names ( 0 ), sizes ( 0 ), times ( 0 ) {};
 
 bool RV::add ( const RV &rv2 ) {
         // TODO
-        ivec ind = rv2.findself ( *this ); //should be -1 all the time
-        ivec index = itpp::find(ind==-1); 
-        
-        if ( index.length() < rv2.len ) { //conflict
-                ids = concat ( ids, rv2.ids(index) );
-                sizes = concat ( sizes, rv2.sizes(index) );
-                times = concat ( times, rv2.times(index) );
-                names = concat ( names, rv2.names(to_Arr(index)) );
+        if ( rv2.len>0 ) { //rv2 is nonempty
+                ivec ind = rv2.findself ( *this ); //should be -1 all the time
+                ivec index = itpp::find ( ind==-1 );
+
+
+                if ( index.length() < rv2.len ) { //conflict
+                        ids = concat ( ids, rv2.ids ( index ) );
+                        sizes = concat ( sizes, rv2.sizes ( index ) );
+                        times = concat ( times, rv2.times ( index ) );
+                        names = concat ( names, rv2.names ( to_Arr ( index ) ) );
+                }
+                else {
+                        ids = concat ( ids, rv2.ids );
+                        sizes = concat ( sizes, rv2.sizes );
+                        times = concat ( times, rv2.times );
+                        names = concat ( names, rv2.names );
+                }
+                tsize = sum ( sizes );
+                len = ids.length();
+                return ( index.length() <rv2.len );
         }
-        else {
-                ids = concat ( ids, rv2.ids );
-                sizes = concat ( sizes, rv2.sizes );
-                times = concat ( times, rv2.times );
-                names = concat ( names, rv2.names );
+        else { //rv2 is empty
+                return true;
         }
-        tsize = sum(sizes);
-        len = ids.length();
-        return (index.length()<rv2.len);
-
 //      return *this;
 };
 
-RV::RV ( ivec in_ids ) {
-
-        len = in_ids.length();
-        Array<std::string> A ( len );
-        std::string rvstr = "rv";
-
-        for ( int i = 0; i < len;i++ ) {
-                A ( i ) = rvstr + to_str ( i );
-        }
-
-        init ( in_ids, A, ones_i ( len ), zeros_i ( len ) );
-}
+// RV::RV ( ivec in_ids ) {
+//
+//      len = in_ids.length();
+//      Array<std::string> A ( len );
+//      std::string rvstr = "rv";
+//
+//      for ( int i = 0; i < len;i++ ) {
+//              A ( i ) = rvstr + to_str ( i );
+//      }
+//
+//      init ( in_ids, A, ones_i ( len ), zeros_i ( len ) );
+// }
 
 RV RV::subselect ( ivec ind ) const {
-        return RV ( ids ( ind ), names ( to_Arr ( ind ) ), sizes ( ind ), times ( ind ) );
+        RV ret;
+        ret.init ( ids ( ind ), names ( to_Arr ( ind ) ), sizes ( ind ), times ( ind ) );
+        return ret;
 }
 
@@ -78 +100 @@
 
 RV RV::operator() ( ivec ind ) const {
-        return RV ( ids ( ind ), names ( to_Arr ( ind ) ), sizes ( ind ), times ( ind ) );
+        RV ret;
+        if ( ind.length() >0 ) {
+                ret.init ( ids ( ind ), names ( to_Arr ( ind ) ), sizes ( ind ), times ( ind ) );
+        }
+        return ret;
 }
 
@@ -127 +153 @@
 
 RV RV::subt ( const RV rv2 ) const {
+        cout << *this <<endl;
+        cout << rv2 <<endl;
+
         ivec res = this->findself ( rv2 ); // nonzeros
         ivec valid = itpp::find ( res == -1 ); //-1 => value not found => it remains

bdm/stat/libBM.h

@@ -52 +52 @@
 private:
         //! auxiliary function used in constructor
-        void init ( ivec in_ids, Array<std::string> in_names, ivec in_sizes, ivec in_times );
-public:
-        //! Full constructor which is called by the others
-        RV ( ivec in_ids, Array<std::string> in_names, ivec in_sizes, ivec in_times );
-        //! default constructor
-        RV ( ivec ids );
-        //! Empty constructor will be set later
+        void init (ivec in_ids, Array<std::string> in_names, ivec in_sizes, ivec in_times );
+public:
+        //! Full constructor 
+        RV ( Array<std::string> in_names, ivec in_sizes, ivec in_times );
+        //! Constructor with times=0
+        RV ( Array<std::string> in_names, ivec in_sizes );
+        //! Constructor with sizes=1, times=0
+        RV ( Array<std::string> in_names );
+        //! Constructor of empty RV
         RV ();
 
@@ -137 +139 @@
 public:
         //!default constructor
-        epdf() :rv ( ivec ( 0 ) ) {};
+        epdf() :rv ( ) {};
 
         //!default constructor
@@ -180 +182 @@
 //      virtual fnc moment ( const int order = 1 );
         //! 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 \param ll is a return value of log-likelihood of the sample.
-        virtual vec samplecond ( vec &cond, double &ll ) {this->condition ( cond );
+        virtual vec samplecond (const vec &cond, double &ll ) {this->condition ( cond );
         vec temp= ep->sample();
         ll=ep->evalpdflog ( temp );return temp;};
         //! 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 \param ll is a return value of log-likelihood of the sample.
-        virtual mat samplecond ( vec &cond, vec &ll, int N ) {
+        virtual mat samplecond (const vec &cond, vec &ll, int N ) {
                 this->condition ( cond );
                 mat temp ( rv.count(),N ); vec smp ( rv.count() ); 

bdm/stat/libEF.cpp

@@ -112 +112 @@
 };
 
-vec mgamma::samplecond ( vec &cond, double &ll ) {
-        this->condition(cond );
-        vec smp = epdf.sample();
-        ll = epdf.evalpdflog ( smp );
-        return smp;
-};
-
-//Fixme repetition of mlnorm.samplecond.
-mat mgamma::samplecond ( vec &cond, vec &lik, int n ) {
-        int i;
-        int dim = rv.count();
-        mat Smp ( dim,n );
-        vec smp ( dim );
-        this->condition ( cond );
-
-        for ( i=0; i<n; i++ ) {
-                smp = epdf.sample();
-                lik ( i ) = epdf.eval ( smp );
-                Smp.set_col ( i ,smp );
-        }
-
-        return Smp;
-};
-
 ivec eEmp::resample ( RESAMPLING_METHOD method ) {
         ivec ind=zeros_i ( n );

bdm/stat/libEF.h

@@ -270 +270 @@
         //! Set value of \c k
         void set_parameters ( double k );
-        //!Generate one sample of the posterior
-        vec samplecond ( vec &cond, double &lik );
-        //!Generate matrix of samples of the posterior
-        mat samplecond ( vec &cond, vec &lik, int n );
         void condition ( const vec &val ) {*_beta=k/val;};
 };

bdm/stat/loggers.cpp

@@ -8 +8 @@
 #endif
 
-void memlog::itsave(const char* fname){
-        it_file itf(fname);
+void memlog::itsave ( const char* fname ) {
+        it_file itf ( fname );
         int i;
-        for (i=0; i<entries.length();i++){
-         itf << Name(names(i)) << vectors(i);
+        for ( i=0; i<entries.length();i++ ) {
+                if ( names ( i ).length() <1 ) {
+                        std::ostringstream o;
+                        o<<"Variable"<<i;
+                        itf << Name ( o.str() ) << vectors ( i );
+                }
+                else {
+                        itf << Name ( names ( i ) ) << vectors ( i );
+                }
         }
 }
@@ -26 +33 @@
 
 // Initialize directory
-        makedir(dirname); // 
+        makedir ( dirname ); //
 
 // directory OK, or it can be overwritten
@@ -40 +47 @@
                                 scalarnames ( ii ) = names ( i ) + "_" + entries ( i ).name ( j );
                                 ii++;
-                        } else {
+                        }
+                        else {
                                 for ( k=0;k<rvsize;k++ ) { //for all scalars in given RV
                                         sprintf ( num,"%d",k );
@@ -62 +70 @@
         memlog::init();
 
+        //Delete old data
         write_buffers ( 0 );
 }
@@ -81 +90 @@
         for ( i=0;i<nen;i++ ) { //for entries
                 Dt = vectors ( i )._data();
-                DtRows = vectors(i).rows();
-                
+                DtRows = vectors ( i ).rows();
+
                 jj=0;
                 for ( j=0;j<entries ( i ).length();j++ ) { //for RVs in entries
@@ -93 +102 @@
                                                 fp = open ( filename, O_CREAT | O_WRONLY | O_APPEND, 00644 );
 
-                                        write ( fp,&Dt[jj*(DtRows)],(Len)*sizeof ( double ) );
+                                        write ( fp,&Dt[jj* ( DtRows ) ], ( Len ) *sizeof ( double ) );
                                         close ( fp );
 
@@ -106 +115 @@
 }
 
-void dirfilelog::step ( bool final ) {
+void dirfilelog::step ( ) {
 
-        if ( final ) {
-                if ( ind>0 )
-                        write_buffers ( ind ); //assuming here that i+1 was not filled
-        } else
-                if ( ind== ( maxlen -1 ) ) {
-                        write_buffers ( ind+1 );
-                        ind = 0;
-                } else
-                        ind++;
+        if ( ind== ( maxlen -1 ) ) {
+                write_buffers ( ind+1 );
+                ind = 0;
+        }
+        else
+                ind++;
 
 }
+
+void dirfilelog::finalize ( ) {
+        if ( ind>0 )
+                write_buffers ( ind ); //assuming here that i+1 was not filled
+}

bdm/stat/loggers.h

@@ -37 +37 @@
 
 //! returns an identifier which will be later needed for calling the log() function
-        virtual int add ( RV rv, string name="" ) {
+        virtual int add (const RV &rv, string name="" ) {
                 int id=entries.length();
                 names=concat ( names, name ); // diff
@@ -48 +48 @@
         virtual void logit ( int id, vec v ) =0;
 
-//! consider this record to be complete
-        virtual void step(bool final=false) =0;
+//! Shifts storage position for another time step.
+        virtual void step() =0;
+
+        //! Finalize storing information
+        virtual void finalize() {};
 
         //! for future use
@@ -82 +85 @@
                 ;
         }
-        void step(bool final=false) {if ( ind<maxlen ) ind++; else it_error ( "memlog::ind is too high;" );}
-        void logit ( int id, vec v ) {vectors ( id ).set_row ( ind,v );}
+        void step() {if ( ind<maxlen ) ind++; else it_error ( "memlog::ind is too high;" );}
+        void logit ( int id, vec v ) {
+                it_assert_debug(id<vectors.length(),"Logger was not initialized, run init().");
+                vectors ( id ).set_row ( ind,v );}
         //! Save values into an itfile named after \c fname.
         void itsave(const char* fname);
@@ -110 +115 @@
         //! Initialize storage
         void init();
-        void step(bool final=false);
+        void step();
+        void finalize();
         /*! \brief Write memory storage to disk. 
         @param Len length of buffer to be written, if 0 the file is truncated at 0.