Changeset 377

Timestamp:

06/15/09 18:27:16 (16 years ago)

Author:

mido

Message:

1) globalni prejmenovani Setting &root na Setting &set
2) smazani par zastaralych adresaru
3) oprava warningu v doc\local
4) prejmenovani SettingsResolver? na SettingResolver? a drobne vylepseni funkcnosti
5) odstranena duplikace kodu v user_info.cpp

Files:

• applications/pmsm/pmsm.h (modified) (1 diff)
• applications/pmsm/pmsmDS.h (modified) (1 diff)
• bdm/bdmroot.h (modified) (2 diffs)
• bdm/config (deleted)
• bdm/estim/arx.cpp (modified) (4 diffs)
• bdm/estim/arx.h (modified) (1 diff)
• bdm/estim/libKF.cpp (modified) (3 diffs)
• bdm/estim/libKF.h (modified) (2 diffs)
• bdm/stat/libBM.cpp (modified) (2 diffs)
• bdm/stat/libBM.h (modified) (12 diffs)
• bdm/stat/libDS.cpp (modified) (5 diffs)
• bdm/stat/libDS.h (modified) (3 diffs)
• bdm/stat/libEF.cpp (modified) (1 diff)
• bdm/stat/libEF.h (modified) (3 diffs)
• bdm/stat/loggers.cpp (modified) (2 diffs)
• bdm/stat/loggers.h (modified) (2 diffs)
• bdm/user_info.cpp (modified) (13 diffs)
• bdm/user_info.h (modified) (6 diffs)
• doc/local/codingrules.dox (modified) (1 diff)
• doc/local/install.dox (modified) (2 diffs)
• library/mex/mexds.h (modified) (1 diff)
• tests/testUI.cpp (modified) (5 diffs)

applications/pmsm/pmsm.h

@@ -98 +98 @@
         void from_setting( const Setting &root )
         {       
-                UI::SettingsResolver params_exp(root["params"]);
-                const Setting& params=params_exp.root();
+                UI::SettingResolver params_exp(root["params"]);
+                const Setting& params=params_exp.result;
 
                 set_parameters ( params["Rs"], params["Ls"], 125e-6, params["Fmag"], \

applications/pmsm/pmsmDS.h

@@ -167 +167 @@
     void from_setting( const Setting &root )
     {
-                UI::SettingsResolver params_exp(root["params"]);
-                const Setting& params=params_exp.root();
+                UI::SettingResolver params_exp(root["params"]);
+                const Setting& params=params_exp.result;
 
         set_parameters ( params["Rs"], params["Ls"], params["Fmag"], \

bdm/bdmroot.h

@@ -40 +40 @@
 
         //! This method arrange instance properties according the data stored in the Setting structure
-        virtual void from_setting( const Setting &root )
+        virtual void from_setting( const Setting &set )
         {
         }
 
         //! This method save all the instance properties into the Setting structure 
-        virtual void to_setting( Setting &root ) const
+        virtual void to_setting( Setting &set ) const
         {       
         }
@@ -53 +53 @@
         {
         }
-
 };
 

bdm/estim/arx.cpp

@@ -194 +194 @@
 }
 
-void ARX::from_setting( const Setting &root ) 
+void ARX::from_setting( const Setting &set ) 
 {       
-        RV *yrv = UI::build<RV>(root,"y");
-        RV *rrv = UI::build<RV>(root,"rgr");
+        RV *yrv = UI::build<RV>(set,"y");
+        RV *rrv = UI::build<RV>(set,"rgr");
         int ylen = yrv->_dsize();
         int rgrlen = rrv->_dsize();
@@ -203 +203 @@
         //init
         mat V0;
-        if( root.exists("dV0") )
+        if( set.exists("dV0") )
         {
                 vec dV0;
-                UI::get( dV0, root, "dV0" );
+                UI::get( dV0, set, "dV0" );
                 V0=diag ( dV0 );
         }
@@ -213 +213 @@
         
         double nu0;
-        if ( !root.lookupValue( "nu0", nu0 ) ) 
+        if ( !set.lookupValue( "nu0", nu0 ) ) 
                 nu0 = rgrlen+ylen+2;
 
         double frg;
-        if ( !root.lookupValue( "frg", frg ) ) 
+        if ( !set.lookupValue( "frg", frg ) ) 
                 frg = 1.0;
 
@@ -231 +231 @@
 }
 
-/*void ARX::to_setting( Setting &root ) const
+/*void ARX::to_setting( Setting &set ) const
 {       
-        Transport::to_setting( root );
-
-        Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt );
+        Transport::to_setting( set );
+
+        Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt );
         kilometers_setting = kilometers;
 
-        UI::save( passengers, root, "passengers" );
+        UI::save( passengers, set, "passengers" );
 }*/
 

bdm/estim/arx.h

@@ -139 +139 @@
         The estimator will assign names of the posterior in the form ["theta_i" and "r_i"]
         */
-        void from_setting( const Setting &root );
+        void from_setting( const Setting &set );
 
-        // TODO dodelat void to_setting( Setting &root ) const;
+        // TODO dodelat void to_setting( Setting &set ) const;
 };
 

bdm/estim/libKF.cpp

@@ -250 +250 @@
 }
 
-void EKFCh::from_setting( const Setting &root ) 
+void EKFCh::from_setting( const Setting &set ) 
 {       
-        diffbifn* IM = UI::build<diffbifn>(root, "IM");
-        diffbifn* OM = UI::build<diffbifn>(root, "OM");
+        diffbifn* IM = UI::build<diffbifn>(set, "IM");
+        diffbifn* OM = UI::build<diffbifn>(set, "OM");
         
         //statistics
         int dim=IM->dimension();
         vec mu0;
-        if(root.exists("mu0"))
-                UI::get( mu0, root, "mu0");
+        if(set.exists("mu0"))
+                UI::get( mu0, set, "mu0");
         else
                 mu0=zeros(dim);
 
         mat P0;
-        if(root.exists("dP0"))
+        if(set.exists("dP0"))
         {
                 vec dP0;
-                UI::get( dP0, root, "dP0");
+                UI::get( dP0, set, "dP0");
                 P0=diag(dP0);
         }
-        else if ( root.exists( "P0" ) )
-                UI::get(P0, root, "P0");
+        else if ( set.exists( "P0" ) )
+                UI::get(P0, set, "P0");
         else
                 P0=eye(dim);
@@ -279 +279 @@
         //parameters
         vec dQ, dR;
-        UI::get( dQ, root, "dQ");
-        UI::get( dR, root, "dR");
+        UI::get( dQ, set, "dQ");
+        UI::get( dR, set, "dR");
         set_parameters(IM, OM, diag(dQ), diag(dR));
 
         //connect
-        RV* drv = UI::build<RV>(root, "drv");
+        RV* drv = UI::build<RV>(set, "drv");
         set_drv(*drv);
-        RV* rv = UI::build<RV>(root, "rv");
+        RV* rv = UI::build<RV>(set, "rv");
         set_rv(*rv);
         
         string options;
-        if(root.lookupValue( "options", options ))
+        if(set.lookupValue( "options", options ))
                 set_options(options);   
 }
 
-/*void EKFCh::to_setting( Setting &root ) const
+/*void EKFCh::to_setting( Setting &set ) const
 {       
-        Transport::to_setting( root );
-
-        Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt );
+        Transport::to_setting( set );
+
+        Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt );
         kilometers_setting = kilometers;
 
-        UI::save( passengers, root, "passengers" );
+        UI::save( passengers, set, "passengers" );
 }*/
 
-void MultiModel::from_setting( const Setting &root ) 
+void MultiModel::from_setting( const Setting &set ) 
 {       
         Array<EKFCh*> A;
-        UI::get( A, root, "models");
+        UI::get( A, set, "models");
         
         set_parameters(A);
@@ -314 +314 @@
 
         string options;
-        if(root.lookupValue( "options", options ))
+        if(set.lookupValue( "options", options ))
                 set_options(options);   
 }
 
-/*void MultiModel::to_setting( Setting &root ) const
+/*void MultiModel::to_setting( Setting &set ) const
 {       
-        Transport::to_setting( root );
-
-        Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt );
+        Transport::to_setting( set );
+
+        Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt );
         kilometers_setting = kilometers;
 
-        UI::save( passengers, root, "passengers" );
+        UI::save( passengers, set, "passengers" );
 }*/
 

bdm/estim/libKF.h

@@ -260 +260 @@
                         void bayes ( const vec &dt );
 
-                        void from_setting( const Setting &root );
-
-                        // TODO dodelat void to_setting( Setting &root ) const;
+                        void from_setting( const Setting &set );
+
+                        // TODO dodelat void to_setting( Setting &set ) const;
 
         };
@@ -457 +457 @@
                         const enorm<chmat>& posterior() const {return est;}
 
-                        void from_setting( const Setting &root );
-
-                        // TODO dodelat void to_setting( Setting &root ) const;
+                        void from_setting( const Setting &set );
+
+                        // TODO dodelat void to_setting( Setting &set ) const;
 
         };

bdm/stat/libBM.cpp

@@ -212 +212 @@
 }
 
-void RV::from_setting( const Setting &root ) 
+void RV::from_setting( const Setting &set ) 
 {       
         Array<string> A;
-        if( root.exists("names"))
-                UI::get( A, root, "names" );
+        if( set.exists("names"))
+                UI::get( A, set, "names" );
         else
                 A.set_length(0);
         
         ivec szs;
-        if( root.exists("sizes"))
-                UI::get(szs,root,"sizes");
+        if( set.exists("sizes"))
+                UI::get(szs,set,"sizes");
         else
                 szs = ones_i(A.length());
         
         ivec tms;
-        if( root.exists( "times") )
-                UI::get(tms,root,"times");
+        if( set.exists( "times") )
+                UI::get(tms,set,"times");
         else
                 tms = zeros_i(A.length());
@@ -236 +236 @@
 }
 
-/*void RV::to_setting( Setting &root ) const
+/*void RV::to_setting( Setting &set ) const
 {       
-        Transport::to_setting( root );
-
-        Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt );
+        Transport::to_setting( set );
+
+        Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt );
         kilometers_setting = kilometers;
 
-        UI::save( passengers, root, "passengers" );
+        UI::save( passengers, set, "passengers" );
 }*/
-
-
 
 RV concat ( const RV &rv1, const RV &rv2 ) {

bdm/stat/libBM.h

@@ -25 +25 @@
 using namespace std;
 
-namespace bdm {
+namespace bdm
+{
 
 typedef std::map<string, int> RVmap;
@@ -32 +33 @@
 
 //! Structure of RV (used internally), i.e. expanded RVs - TODO tak proc je ve verejnem prostoru jmen? upravit
-class str {
-public:
-        //! vector id ids (non-unique!)
-        ivec ids;
-        //! vector of times
-        ivec times;
-        //!Default constructor
-        str ( ivec ids0, ivec times0 ) :ids ( ids0 ),times ( times0 ) {
-                it_assert_debug ( times0.length() ==ids0.length(),"Incompatible input" );
-        };
+class str
+{
+public:
+  //! vector id ids (non-unique!)
+  ivec ids;
+  //! vector of times
+  ivec times;
+  //!Default constructor
+  str(ivec ids0, ivec times0) : ids(ids0), times(times0) {
+    it_assert_debug(times0.length() == ids0.length(), "Incompatible input");
+  };
 };
 
@@ -82 +84 @@
 */
 
-class RV :public bdmroot {
-protected:
-        //! size of the data vector
-        int dsize;
-        //! number of individual rvs
-        int len;
-        //! Vector of unique IDs
-        ivec ids;
-        //! Vector of shifts from current time
-        ivec times;
+class RV : public bdmroot
+{
+protected:
+  //! size of the data vector
+  int dsize;
+  //! number of individual rvs
+  int len;
+  //! Vector of unique IDs
+  ivec ids;
+  //! Vector of shifts from current time
+  ivec times;
 
 private:
-        //! auxiliary function used in constructor
-        void init ( Array<std::string> in_names, ivec in_sizes, ivec in_times );
-        int init ( const  string &name, int size );
-public:
-        //! \name Constructors
-        //!@{
-
-        //! Full constructor
-        RV ( Array<std::string> in_names, ivec in_sizes, ivec in_times ) {init ( in_names,in_sizes,in_times );};
-        //! Constructor with times=0
-        RV ( Array<std::string> in_names, ivec in_sizes ) {init ( in_names,in_sizes,zeros_i ( in_names.length() ) );};
-        //! Constructor with sizes=1, times=0
-        RV ( Array<std::string> in_names ) {init ( in_names,ones_i ( in_names.length() ),zeros_i ( in_names.length() ) );}
-        //! Constructor of empty RV
-        RV () :dsize ( 0 ),len ( 0 ),ids ( 0 ),times ( 0 ) {};
-        //! Constructor of a single RV with given id
-        RV ( string name, int sz, int tm=0 );
-        //!@}
-
-        //! \name Access functions
-        //!@{
-
-        //! Printing output e.g. for debugging.
-        friend std::ostream &operator<< ( std::ostream &os, const RV &rv );
-        int _dsize() const {return dsize;} ;
-        //! Recount size of the corresponding data vector
-        int countsize() const;
-        ivec cumsizes() const;
-        int length() const {return len;} ;
-        int id ( int at ) const{return ids ( at );};
-        int size ( int at ) const {return RV_SIZES ( ids ( at ) );};
-        int time ( int at ) const{return times ( at );};
-        std::string name ( int at ) const {return RV_NAMES ( ids ( at ) );};
-        void set_time ( int at, int time0 ) {times ( at ) =time0;};
-        //!@}
-
-        //TODO why not inline and later??
-
-        //! \name Algebra on Random Variables
-        //!@{
-
-        //! Find indices of self in another rv, \return ivec of the same size as self.
-        ivec findself ( const RV &rv2 ) const;
-        //! Compare if \c rv2 is identical to this \c RV
-        bool equal ( const RV &rv2 ) const;
-        //! Add (concat) another variable to the current one, \return true if all rv2 were added, false if rv2 is in conflict
-        bool add ( const RV &rv2 );
-        //! Subtract  another variable from the current one
-        RV subt ( const RV &rv2 ) const;
-        //! Select only variables at indeces ind
-        RV subselect ( const ivec &ind ) const;
-        //! Select only variables at indeces ind
-        RV operator() ( const ivec &ind ) const {return subselect ( ind );};
-        //! Select from data vector starting at di1 to di2
-        RV operator() ( int di1, int di2 ) const {
-                ivec sz=cumsizes();
-                int i1=0;
-                while ( sz ( i1 ) <di1 ) i1++;
-                int i2=i1;
-                while ( sz ( i2 ) <di2 ) i2++;
-                return subselect ( linspace ( i1,i2 ) );
-        };
-        //! Shift \c time shifted by delta.
-        void t ( int delta );
-        //!@}
-
-        //!\name Relation to vectors
-        //!@{
-
-        //! generate \c str from rv, by expanding sizes TODO to_string.. 
-        str tostr() const;
-        //! when this rv is a part of bigger rv, this function returns indeces of self in the data vector of the bigger crv.
-        //! Then, data can be copied via: data_of_this = cdata(ind);
-        ivec dataind ( const RV &crv ) const;
-        //! generate mutual indeces when copying data betwenn self and crv.
-        //! Data are copied via: data_of_this(selfi) = data_of_rv2(rv2i)
-        void dataind ( const RV &rv2, ivec &selfi, ivec &rv2i ) const;
-        //! Minimum time-offset
-        int mint () const {return min ( times );};
-        //!@}
-
-        // TODO aktualizovat dle soucasneho UI
-        /*! \brief UI for class RV (description of data vectors)
-
-        \code
-        rv = {
-                type = "rv"; //identifier of the description
-                // UNIQUE IDENTIFIER same names = same variable
-                names = ["a", "b", "c", ...];   // which will be used e.g. in loggers 
-
-                //optional arguments
-                sizes = [1, 2, 3, ...];         // (optional) default = ones()
-                times = [-1, -2, 0, ...];       // time shifts with respect to current time (optional) default = zeros()
-        }
-        \endcode
-        */
-        void from_setting( const Setting &root );
-
-        // TODO dodelat void to_setting( Setting &root ) const;
+  //! auxiliary function used in constructor
+  void init(Array<std::string> in_names, ivec in_sizes, ivec in_times);
+  int init(const  string &name, int size);
+public:
+  //! \name Constructors
+  //!@{
+
+  //! Full constructor
+  RV(Array<std::string> in_names, ivec in_sizes, ivec in_times) {init(in_names, in_sizes, in_times);};
+  //! Constructor with times=0
+  RV(Array<std::string> in_names, ivec in_sizes) {init(in_names, in_sizes, zeros_i(in_names.length()));};
+  //! Constructor with sizes=1, times=0
+  RV(Array<std::string> in_names) {init(in_names, ones_i(in_names.length()), zeros_i(in_names.length()));}
+  //! Constructor of empty RV
+  RV() : dsize(0), len(0), ids(0), times(0) {};
+  //! Constructor of a single RV with given id
+  RV(string name, int sz, int tm = 0);
+  //!@}
+
+  //! \name Access functions
+  //!@{
+
+  //! Printing output e.g. for debugging.
+  friend std::ostream &operator<< (std::ostream &os, const RV &rv);
+  int _dsize() const {return dsize;} ;
+  //! Recount size of the corresponding data vector
+  int countsize() const;
+  ivec cumsizes() const;
+  int length() const {return len;} ;
+  int id(int at) const {return ids(at);};
+  int size(int at) const {return RV_SIZES(ids(at));};
+  int time(int at) const {return times(at);};
+  std::string name(int at) const {return RV_NAMES(ids(at));};
+  void set_time(int at, int time0) {times(at) = time0;};
+  //!@}
+
+  //TODO why not inline and later??
+
+  //! \name Algebra on Random Variables
+  //!@{
+
+  //! Find indices of self in another rv, \return ivec of the same size as self.
+  ivec findself(const RV &rv2) const;
+  //! Compare if \c rv2 is identical to this \c RV
+  bool equal(const RV &rv2) const;
+  //! Add (concat) another variable to the current one, \return true if all rv2 were added, false if rv2 is in conflict
+  bool add(const RV &rv2);
+  //! Subtract  another variable from the current one
+  RV subt(const RV &rv2) const;
+  //! Select only variables at indeces ind
+  RV subselect(const ivec &ind) const;
+  //! Select only variables at indeces ind
+  RV operator()(const ivec &ind) const {return subselect(ind);};
+  //! Select from data vector starting at di1 to di2
+  RV operator()(int di1, int di2) const {
+    ivec sz = cumsizes();
+    int i1 = 0;
+    while (sz(i1) < di1) i1++;
+    int i2 = i1;
+    while (sz(i2) < di2) i2++;
+    return subselect(linspace(i1, i2));
+  };
+  //! Shift \c time shifted by delta.
+  void t(int delta);
+  //!@}
+
+  //!\name Relation to vectors
+  //!@{
+
+  //! generate \c str from rv, by expanding sizes TODO to_string..
+  str tostr() const;
+  //! when this rv is a part of bigger rv, this function returns indeces of self in the data vector of the bigger crv.
+  //! Then, data can be copied via: data_of_this = cdata(ind);
+  ivec dataind(const RV &crv) const;
+  //! generate mutual indeces when copying data betwenn self and crv.
+  //! Data are copied via: data_of_this(selfi) = data_of_rv2(rv2i)
+  void dataind(const RV &rv2, ivec &selfi, ivec &rv2i) const;
+  //! Minimum time-offset
+  int mint() const {return min(times);};
+  //!@}
+
+  // TODO aktualizovat dle soucasneho UI
+  /*! \brief UI for class RV (description of data vectors)
+
+  \code
+  rv = {
+    type = "rv"; //identifier of the description
+    // UNIQUE IDENTIFIER same names = same variable
+    names = ["a", "b", "c", ...];   // which will be used e.g. in loggers
+
+    //optional arguments
+    sizes = [1, 2, 3, ...];         // (optional) default = ones()
+    times = [-1, -2, 0, ...];       // time shifts with respect to current time (optional) default = zeros()
+  }
+  \endcode
+  */
+  void from_setting(const Setting &set);
+
+  // TODO dodelat void to_setting( Setting &set ) const;
 };
 UIREGISTER(RV);
 
 //! Concat two random variables
-RV concat ( const RV &rv1, const RV &rv2 );
+RV concat(const RV &rv1, const RV &rv2);
 
 //!Default empty RV that can be used as default argument
@@ -204 +207 @@
 //! Class representing function \f$f(x)\f$ of variable \f$x\f$ represented by \c rv
 
-class fnc :public bdmroot {
-protected:
-        //! Length of the output vector
-        int dimy;
-public:
-        //!default constructor
-        fnc ( ) {};
-        //! function evaluates numerical value of \f$f(x)\f$ at \f$x=\f$ \c cond
-        virtual vec eval ( const vec &cond ) {
-                return vec ( 0 );
-        };
-
-        //! function substitutes given value into an appropriate position
-        virtual void condition ( const vec &val ) {};
-
-        //! access function
-        int dimension() const{return dimy;}
+class fnc : public bdmroot
+{
+protected:
+  //! Length of the output vector
+  int dimy;
+public:
+  //!default constructor
+  fnc() {};
+  //! function evaluates numerical value of \f$f(x)\f$ at \f$x=\f$ \c cond
+  virtual vec eval(const vec &cond) {
+    return vec(0);
+  };
+
+  //! function substitutes given value into an appropriate position
+  virtual void condition(const vec &val) {};
+
+  //! access function
+  int dimension() const {return dimy;}
 };
 
@@ -227 +231 @@
 //! Probability density function with numerical statistics, e.g. posterior density.
 
-class epdf : public bdmroot {
-protected:
-        //! dimension of the random variable
-        int dim;
-        //! Description of the random variable
-        RV rv;
-
-public:
-        /*! \name Constructors
-         Construction of each epdf should support two types of constructors:
-        \li empty constructor,
-        \li copy constructor,
-
-        The following constructors should be supported for convenience:
-        \li constructor followed by calling \c set_parameters()
-        \li constructor accepting random variables calling \c set_rv()
-
-         All internal data structures are constructed as empty. Their values (including sizes) will be set by method \c set_parameters(). This way references can be initialized in constructors.
-        @{*/
-        epdf() :dim ( 0 ),rv ( ) {};
-        epdf ( const epdf &e ) :dim ( e.dim ),rv ( e.rv ) {};
-        epdf ( const RV &rv0 ) {set_rv ( rv0 );};
-        void set_parameters ( int dim0 ) {dim=dim0;}
-        //!@}
-
-        //! \name Matematical Operations
-        //!@{
-
-        //! Returns a sample, \f$ x \f$ from density \f$ f_x()\f$
-        virtual vec sample () const {it_error ( "not implemneted" );return vec ( 0 );};
-        //! Returns N samples, \f$ [x_1 , x_2 , \ldots \ \f$  from density \f$ f_x(rv)\f$
-        virtual mat sample_m ( int N ) const;
-        //! Compute log-probability of argument \c val
-        virtual double evallog ( const vec &val ) const {it_error ( "not implemneted" );return 0.0;};
-        //! Compute log-probability of multiple values argument \c val
-        virtual vec evallog_m ( const mat &Val ) const {
-                vec x ( Val.cols() );
-                for ( int i=0;i<Val.cols();i++ ) {x ( i ) =evallog ( Val.get_col ( i ) ) ;}
-                return x;
-        }
-        //! Return conditional density on the given RV, the remaining rvs will be in conditioning
-        virtual mpdf* condition ( const RV &rv ) const  {it_warning ( "Not implemented" ); return NULL;}
-        //! Return marginal density on the given RV, the remainig rvs are intergrated out
-        virtual epdf* marginal ( const RV &rv ) const {it_warning ( "Not implemented" ); return NULL;}
-        //! return expected value
-        virtual vec mean() const {it_error ( "not implemneted" );return vec ( 0 );};
-        //! return expected variance (not covariance!)
-        virtual vec variance() const {it_error ( "not implemneted" );return vec ( 0 );};
-        //! Lower and upper bounds of \c percentage % quantile, returns mean-2*sigma as default
-        virtual void qbounds ( vec &lb, vec &ub, double percentage=0.95 ) const {
-                vec mea=mean(); vec std=sqrt ( variance() );
-                lb = mea-2*std; ub=mea+2*std;
-        };
-        //!@}
-
-        //! \name Connection to other classes
-        //! Description of the random quantity via attribute \c rv is optional.
-        //! For operations such as sampling \c rv does not need to be set. However, for \c marginalization
-        //! and \c conditioning \c rv has to be set. NB:
-        //! @{
-
-        //!Name its rv
-        void set_rv ( const RV &rv0 ) {rv = rv0; }//it_assert_debug(isnamed(),""); };
-        //! True if rv is assigned
-        bool isnamed() const {bool b= ( dim==rv._dsize() );return b;}
-        //! Return name (fails when isnamed is false)
-        const RV& _rv() const {it_assert_debug ( isnamed(),"" ); return rv;}
-        //!@}
-
-        //! \name Access to attributes
-        //! @{
-
-        //! Size of the random variable
-        int dimension() const {return dim;}
-        //!@}
+class epdf : public bdmroot
+{
+protected:
+  //! dimension of the random variable
+  int dim;
+  //! Description of the random variable
+  RV rv;
+
+public:
+  /*! \name Constructors
+   Construction of each epdf should support two types of constructors:
+  \li empty constructor,
+  \li copy constructor,
+
+  The following constructors should be supported for convenience:
+  \li constructor followed by calling \c set_parameters()
+  \li constructor accepting random variables calling \c set_rv()
+
+   All internal data structures are constructed as empty. Their values (including sizes) will be set by method \c set_parameters(). This way references can be initialized in constructors.
+  @{*/
+  epdf() : dim(0), rv() {};
+  epdf(const epdf &e) : dim(e.dim), rv(e.rv) {};
+  epdf(const RV &rv0) {set_rv(rv0);};
+  void set_parameters(int dim0) {dim = dim0;}
+  //!@}
+
+  //! \name Matematical Operations
+  //!@{
+
+  //! Returns a sample, \f$ x \f$ from density \f$ f_x()\f$
+  virtual vec sample() const {it_error("not implemneted"); return vec(0);};
+  //! Returns N samples, \f$ [x_1 , x_2 , \ldots \ \f$  from density \f$ f_x(rv)\f$
+  virtual mat sample_m(int N) const;
+  //! Compute log-probability of argument \c val
+  virtual double evallog(const vec &val) const {it_error("not implemneted"); return 0.0;};
+  //! Compute log-probability of multiple values argument \c val
+  virtual vec evallog_m(const mat &Val) const {
+    vec x(Val.cols());
+    for (int i = 0; i < Val.cols(); i++) {x(i) = evallog(Val.get_col(i)) ;}
+    return x;
+  }
+  //! Return conditional density on the given RV, the remaining rvs will be in conditioning
+  virtual mpdf* condition(const RV &rv) const  {it_warning("Not implemented"); return NULL;}
+
+  //! Return marginal density on the given RV, the remainig rvs are intergrated out
+  virtual epdf* marginal(const RV &rv) const {it_warning("Not implemented"); return NULL;}
+
+  //! return expected value
+  virtual vec mean() const {it_error("not implemneted"); return vec(0);};
+
+  //! return expected variance (not covariance!)
+  virtual vec variance() const {it_error("not implemneted"); return vec(0);};
+  //! Lower and upper bounds of \c percentage % quantile, returns mean-2*sigma as default
+  virtual void qbounds(vec &lb, vec &ub, double percentage = 0.95) const {
+    vec mea = mean();
+    vec std = sqrt(variance());
+    lb = mea - 2 * std;
+    ub = mea + 2 * std;
+  };
+  //!@}
+
+  //! \name Connection to other classes
+  //! Description of the random quantity via attribute \c rv is optional.
+  //! For operations such as sampling \c rv does not need to be set. However, for \c marginalization
+  //! and \c conditioning \c rv has to be set. NB:
+  //! @{
+
+  //!Name its rv
+  void set_rv(const RV &rv0) {rv = rv0; }   //it_assert_debug(isnamed(),""); };
+  //! True if rv is assigned
+  bool isnamed() const {bool b = (dim == rv._dsize()); return b;}
+  //! Return name (fails when isnamed is false)
+  const RV& _rv() const {it_assert_debug(isnamed(), ""); return rv;}
+  //!@}
+
+  //! \name Access to attributes
+  //! @{
+
+  //! Size of the random variable
+  int dimension() const {return dim;}
+  //!@}
 
 };
@@ -309 +319 @@
 //TODO Samplecond can be generalized
 
-class mpdf : public bdmroot {
-protected:
-        //!dimension of the condition
-        int dimc;
-        //! random variable in condition
-        RV rvc;
-        //! pointer to internal epdf
-        epdf* ep;
-public:
-        //! \name Constructors
-        //! @{
-
-        mpdf ( ) :dimc ( 0 ),rvc ( ) {};
-        //! copy constructor does not set pointer \c ep - has to be done in offsprings!
-        mpdf ( const mpdf &m ) :dimc ( m.dimc ),rvc ( m.rvc ) {};
-        //!@}
-
-        //! \name Matematical operations
-        //!@{
-
-        //! 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 ) {
-                this->condition ( cond );
-                vec temp= ep->sample();
-                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 
-        virtual mat samplecond_m ( const vec &cond, int N ) {
-                this->condition ( cond );
-                mat temp ( ep->dimension(),N ); vec smp ( ep->dimension() );
-                for ( int i=0;i<N;i++ ) {smp=ep->sample() ;temp.set_col ( i, smp );}
-                return temp;
-        };
-        //! Update \c ep so that it represents this mpdf conditioned on \c rvc = cond
-        virtual void condition ( const vec &cond ) {it_error ( "Not implemented" );};
-
-        //! Shortcut for conditioning and evaluation of the internal epdf. In some cases,  this operation can be implemented efficiently.
-        virtual double evallogcond ( const vec &dt, const vec &cond ) {
-                double tmp; this->condition ( cond );tmp = ep->evallog ( dt );          it_assert_debug ( std::isfinite ( tmp ),"Infinite value" ); return tmp;
-        };
-
-        //! Matrix version of evallogcond
-        virtual vec evallogcond_m ( const mat &Dt, const vec &cond ) {this->condition ( cond );return ep->evallog_m ( Dt );};
-
-        //! \name Access to attributes
-        //! @{
-
-        RV _rv() {return ep->_rv();}
-        RV _rvc() {it_assert_debug ( isnamed(),"" ); return rvc;}
-        int dimension() {return ep->dimension();}
-        int dimensionc() {return dimc;}
-        epdf& _epdf() {return *ep;}
-        epdf* _e() {return ep;}
-        //!@}
-
-        //! \name Connection to other objects
-        //!@{
-        void set_rvc ( const RV &rvc0 ) {rvc=rvc0;}
-        void set_rv ( const RV &rv0 ) {ep->set_rv ( rv0 );}
-        bool isnamed() {return ( ep->isnamed() ) && ( dimc==rvc._dsize() );}
-        //!@}
+class mpdf : public bdmroot
+{
+protected:
+  //!dimension of the condition
+  int dimc;
+  //! random variable in condition
+  RV rvc;
+  //! pointer to internal epdf
+  epdf* ep;
+public:
+  //! \name Constructors
+  //! @{
+
+  mpdf() : dimc(0), rvc() {};
+  //! copy constructor does not set pointer \c ep - has to be done in offsprings!
+  mpdf(const mpdf &m) : dimc(m.dimc), rvc(m.rvc) {};
+  //!@}
+
+  //! \name Matematical operations
+  //!@{
+
+  //! 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) {
+    this->condition(cond);
+    vec temp = ep->sample();
+    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
+  virtual mat samplecond_m(const vec &cond, int N) {
+    this->condition(cond);
+    mat temp(ep->dimension(), N);
+    vec smp(ep->dimension());
+    for (int i = 0; i < N; i++) {smp = ep->sample() ; temp.set_col(i, smp);}
+    return temp;
+  };
+  //! Update \c ep so that it represents this mpdf conditioned on \c rvc = cond
+  virtual void condition(const vec &cond) {it_error("Not implemented");};
+
+  //! Shortcut for conditioning and evaluation of the internal epdf. In some cases,  this operation can be implemented efficiently.
+  virtual double evallogcond(const vec &dt, const vec &cond) {
+    double tmp;
+    this->condition(cond);
+    tmp = ep->evallog(dt);
+    it_assert_debug(std::isfinite(tmp), "Infinite value");
+    return tmp;
+  };
+
+  //! Matrix version of evallogcond
+  virtual vec evallogcond_m(const mat &Dt, const vec &cond) {this->condition(cond); return ep->evallog_m(Dt);};
+
+  //! \name Access to attributes
+  //! @{
+
+  RV _rv() {return ep->_rv();}
+  RV _rvc() {it_assert_debug(isnamed(), ""); return rvc;}
+  int dimension() {return ep->dimension();}
+  int dimensionc() {return dimc;}
+  epdf& _epdf() {return *ep;}
+  epdf* _e() {return ep;}
+  //!@}
+
+  //! \name Connection to other objects
+  //!@{
+  void set_rvc(const RV &rvc0) {rvc = rvc0;}
+  void set_rv(const RV &rv0) {ep->set_rv(rv0);}
+  bool isnamed() {return (ep->isnamed()) && (dimc == rvc._dsize());}
+  //!@}
 };
 
@@ -378 +394 @@
 \dot
 digraph datalink {
-        node [shape=record];
-        subgraph cluster0 {
-                label = "Up";
-        up [label="<1>|<2>|<3>|<4>|<5>"];
-                color = "white"
+  node [shape=record];
+  subgraph cluster0 {
+    label = "Up";
+      up [label="<1>|<2>|<3>|<4>|<5>"];
+    color = "white"
 }
-        subgraph cluster1{
-                label = "Down";
-                labelloc = b;
-        down [label="<1>|<2>|<3>"];
-                color = "white"
+  subgraph cluster1{
+    label = "Down";
+    labelloc = b;
+      down [label="<1>|<2>|<3>"];
+    color = "white"
 }
     up:1 -> down:1;
@@ -397 +413 @@
 
 */
-class datalink {
-protected:
-        //! Remember how long val should be
-        int downsize;
-        //! Remember how long val of "Up" should be
-        int upsize;
-        //! val-to-val link, indeces of the upper val
-        ivec v2v_up;
-public:
-        //! Constructor
-        datalink () {};
-        datalink ( const RV &rv, const RV &rv_up ) {set_connection ( rv,rv_up );};
-        //! set connection, rv must be fully present in rv_up
-        void set_connection ( const RV &rv, const RV &rv_up ) {
-                downsize = rv._dsize();
-                upsize = rv_up._dsize();
-                v2v_up= ( rv.dataind ( rv_up ) );
-
-                it_assert_debug ( v2v_up.length() ==downsize,"rv is not fully in rv_up" );
-        }
-        //! set connection using indeces
-        void set_connection ( int ds, int us, const ivec &upind ) {
-                downsize = ds;
-                upsize = us;
-                v2v_up= upind;
-
-                it_assert_debug ( v2v_up.length() ==downsize,"rv is not fully in rv_up" );
-        }
-        //! Get val for myself from val of "Up"
-        vec pushdown ( const vec &val_up ) {
-                it_assert_debug ( upsize==val_up.length(),"Wrong val_up" );
-                return get_vec ( val_up,v2v_up );
-        }
-        //! Fill val of "Up" by my pieces
-        void pushup ( vec &val_up, const vec &val ) {
-                it_assert_debug ( downsize==val.length(),"Wrong val" );
-                it_assert_debug ( upsize==val_up.length(),"Wrong val_up" );
-                set_subvector ( val_up, v2v_up, val );
-        }
+class datalink
+{
+protected:
+  //! Remember how long val should be
+  int downsize;
+  //! Remember how long val of "Up" should be
+  int upsize;
+  //! val-to-val link, indeces of the upper val
+  ivec v2v_up;
+public:
+  //! Constructor
+  datalink() {};
+  datalink(const RV &rv, const RV &rv_up) {set_connection(rv, rv_up);};
+  //! set connection, rv must be fully present in rv_up
+  void set_connection(const RV &rv, const RV &rv_up) {
+    downsize = rv._dsize();
+    upsize = rv_up._dsize();
+    v2v_up = (rv.dataind(rv_up));
+
+    it_assert_debug(v2v_up.length() == downsize, "rv is not fully in rv_up");
+  }
+  //! set connection using indeces
+  void set_connection(int ds, int us, const ivec &upind) {
+    downsize = ds;
+    upsize = us;
+    v2v_up = upind;
+
+    it_assert_debug(v2v_up.length() == downsize, "rv is not fully in rv_up");
+  }
+  //! Get val for myself from val of "Up"
+  vec pushdown(const vec &val_up) {
+    it_assert_debug(upsize == val_up.length(), "Wrong val_up");
+    return get_vec(val_up, v2v_up);
+  }
+  //! Fill val of "Up" by my pieces
+  void pushup(vec &val_up, const vec &val) {
+    it_assert_debug(downsize == val.length(), "Wrong val");
+    it_assert_debug(upsize == val_up.length(), "Wrong val_up");
+    set_subvector(val_up, v2v_up, val);
+  }
 };
 
 //! data link between
-class datalink_m2e: public datalink {
-protected:
-        //! Remember how long cond should be
-        int condsize;
-        //!upper_val-to-local_cond link, indeces of the upper val
-        ivec v2c_up;
-        //!upper_val-to-local_cond link, ideces of the local cond
-        ivec v2c_lo;
-
-public:
-        datalink_m2e() {};
-        //! Constructor
-        void set_connection ( const RV &rv,  const RV &rvc, const RV &rv_up ) {
-                datalink::set_connection ( rv,rv_up );
-                condsize=  rvc._dsize();
-                //establish v2c connection
-                rvc.dataind ( rv_up, v2c_lo, v2c_up );
-        }
-        //!Construct condition
-        vec get_cond ( const vec &val_up ) {
-                vec tmp ( condsize );
-                set_subvector ( tmp,v2c_lo,val_up ( v2c_up ) );
-                return tmp;
-        }
-        void pushup_cond ( vec &val_up, const vec &val, const vec &cond ) {
-                it_assert_debug ( downsize==val.length(),"Wrong val" );
-                it_assert_debug ( upsize==val_up.length(),"Wrong val_up" );
-                set_subvector ( val_up, v2v_up, val );
-                set_subvector ( val_up, v2c_up, cond );
-        }
+class datalink_m2e: public datalink
+{
+protected:
+  //! Remember how long cond should be
+  int condsize;
+  //!upper_val-to-local_cond link, indeces of the upper val
+  ivec v2c_up;
+  //!upper_val-to-local_cond link, ideces of the local cond
+  ivec v2c_lo;
+
+public:
+  datalink_m2e() {};
+  //! Constructor
+  void set_connection(const RV &rv,  const RV &rvc, const RV &rv_up) {
+    datalink::set_connection(rv, rv_up);
+    condsize =  rvc._dsize();
+    //establish v2c connection
+    rvc.dataind(rv_up, v2c_lo, v2c_up);
+  }
+  //!Construct condition
+  vec get_cond(const vec &val_up) {
+    vec tmp(condsize);
+    set_subvector(tmp, v2c_lo, val_up(v2c_up));
+    return tmp;
+  }
+  void pushup_cond(vec &val_up, const vec &val, const vec &cond) {
+    it_assert_debug(downsize == val.length(), "Wrong val");
+    it_assert_debug(upsize == val_up.length(), "Wrong val_up");
+    set_subvector(val_up, v2v_up, val);
+    set_subvector(val_up, v2c_up, cond);
+  }
 };
 //!DataLink is a connection between mpdf and its superordinate (Up)
 //! This class links
-class datalink_m2m: public datalink_m2e {
-protected:
-        //!cond-to-cond link, indeces of the upper cond
-        ivec c2c_up;
-        //!cond-to-cond link, indeces of the local cond
-        ivec c2c_lo;
-public:
-        //! Constructor
-        datalink_m2m() {};
-        void set_connection ( const RV &rv, const RV &rvc, const RV &rv_up, const RV &rvc_up ) {
-                datalink_m2e::set_connection ( rv, rvc, rv_up );
-                //establish c2c connection
-                rvc.dataind ( rvc_up, c2c_lo, c2c_up );
-                it_assert_debug ( c2c_lo.length() +v2c_lo.length() ==condsize, "cond is not fully given" );
-        }
-        //! Get cond for myself from val and cond of "Up"
-        vec get_cond ( const vec &val_up, const vec &cond_up ) {
-                vec tmp ( condsize );
-                set_subvector ( tmp,v2c_lo,val_up ( v2c_up ) );
-                set_subvector ( tmp,c2c_lo,cond_up ( c2c_up ) );
-                return tmp;
-        }
-        //! Fill
+class datalink_m2m: public datalink_m2e
+{
+protected:
+  //!cond-to-cond link, indeces of the upper cond
+  ivec c2c_up;
+  //!cond-to-cond link, indeces of the local cond
+  ivec c2c_lo;
+public:
+  //! Constructor
+  datalink_m2m() {};
+  void set_connection(const RV &rv, const RV &rvc, const RV &rv_up, const RV &rvc_up) {
+    datalink_m2e::set_connection(rv, rvc, rv_up);
+    //establish c2c connection
+    rvc.dataind(rvc_up, c2c_lo, c2c_up);
+    it_assert_debug(c2c_lo.length() + v2c_lo.length() == condsize, "cond is not fully given");
+  }
+  //! Get cond for myself from val and cond of "Up"
+  vec get_cond(const vec &val_up, const vec &cond_up) {
+    vec tmp(condsize);
+    set_subvector(tmp, v2c_lo, val_up(v2c_up));
+    set_subvector(tmp, c2c_lo, cond_up(c2c_up));
+    return tmp;
+  }
+  //! Fill
 
 };
@@ -503 +522 @@
 This class abstracts logging of results from implementation. This class replaces direct logging of results (e.g. to files or to global variables) by calling methods of a logger. Specializations of this abstract class for specific storage method are designed.
  */
-class logger : public bdmroot {
-protected:
-        //! RVs of all logged variables.
-        Array<RV> entries;
-        //! Names of logged quantities, e.g. names of algorithm variants
-        Array<string> names;
-public:
-        //!Default constructor
-        logger ( ) : entries ( 0 ),names ( 0 ) {}
-
-        //! returns an identifier which will be later needed for calling the \c logit() function
-        //! For empty RV it returns -1, this entry will be ignored by \c logit().
-        virtual int add ( const RV &rv, string prefix="" ) {
-                int id;
-                if ( rv._dsize() >0 ) {
-                        id=entries.length();
-                        names=concat ( names, prefix); // diff
-                        entries.set_length ( id+1,true );
-                        entries ( id ) = rv;
-                }
-                else { id =-1;}
-                return id; // identifier of the last entry
-        }
-
-        //! log this vector
-        virtual void logit ( int id, const vec &v ) =0;
-        //! log this double
-        virtual void logit ( int id, const double &d ) =0;
-
-        //! Shifts storage position for another time step.
-        virtual void step() =0;
-
-        //! Finalize storing information
-        virtual void finalize() {};
-
-        //! Initialize the storage
-        virtual void init() {};
+class logger : public bdmroot
+{
+protected:
+  //! RVs of all logged variables.
+  Array<RV> entries;
+  //! Names of logged quantities, e.g. names of algorithm variants
+  Array<string> names;
+public:
+  //!Default constructor
+  logger() : entries(0), names(0) {}
+
+  //! returns an identifier which will be later needed for calling the \c logit() function
+  //! For empty RV it returns -1, this entry will be ignored by \c logit().
+  virtual int add(const RV &rv, string prefix = "") {
+    int id;
+    if (rv._dsize() > 0) {
+      id = entries.length();
+      names = concat(names, prefix); // diff
+      entries.set_length(id + 1, true);
+      entries(id) = rv;
+    }
+    else { id = -1;}
+    return id; // identifier of the last entry
+  }
+
+  //! log this vector
+  virtual void logit(int id, const vec &v) = 0;
+  //! log this double
+  virtual void logit(int id, const double &d) = 0;
+
+  //! Shifts storage position for another time step.
+  virtual void step() = 0;
+
+  //! Finalize storing information
+  virtual void finalize() {};
+
+  //! Initialize the storage
+  virtual void init() {};
 
 };
@@ -546 +566 @@
 
 */
-class mepdf : public mpdf {
-public:
-        //!Default constructor
-        mepdf ( epdf* em ) :mpdf ( ) {ep= em ;};
-        mepdf (const epdf* em ) :mpdf ( ) {ep=const_cast<epdf*>( em );};
-        void condition ( const vec &cond ) {}
+class mepdf : public mpdf
+{
+public:
+  //!Default constructor
+  mepdf(epdf* em) : mpdf() {ep = em ;};
+  mepdf(const epdf* em) : mpdf() {ep = const_cast<epdf*>(em);};
+  void condition(const vec &cond) {}
 };
 
 //!\brief Abstract composition of pdfs, will be used for specific classes
 //!this abstract class is common to epdf and mpdf
-class compositepdf {
-protected:
-        //!Number of mpdfs in the composite
-        int n;
-        //! Elements of composition
-        Array<mpdf*> mpdfs;
-public:
-        compositepdf ( Array<mpdf*> A0 ) : n ( A0.length() ), mpdfs ( A0 ) {};
-        //! find common rv, flag \param checkoverlap modifies whether overlaps are acceptable
-        RV getrv ( bool checkoverlap=false );
-        //! common rvc of all mpdfs is written to rvc
-        void setrvc ( const RV &rv, RV &rvc );
+class compositepdf
+{
+protected:
+  //!Number of mpdfs in the composite
+  int n;
+  //! Elements of composition
+  Array<mpdf*> mpdfs;
+public:
+  compositepdf(Array<mpdf*> A0) : n(A0.length()), mpdfs(A0) {};
+  //! find common rv, flag \param checkoverlap modifies whether overlaps are acceptable
+  RV getrv(bool checkoverlap = false);
+  //! common rvc of all mpdfs is written to rvc
+  void setrvc(const RV &rv, RV &rvc);
 };
 
@@ -577 +599 @@
 */
 
-class DS : public bdmroot {
-protected:
-        int dtsize;
-        int utsize;
-        //!Description of data returned by \c getdata().
-        RV Drv;
-        //!Description of data witten by by \c write().
-        RV Urv; //
-        //! Remember its own index in Logger L
-        int L_dt, L_ut;
-public:
-        //! default constructors
-        DS() :Drv ( ),Urv ( ) {};
-        //! Returns full vector of observed data=[output, input]
-        virtual void getdata ( vec &dt ) {it_error ( "abstract class" );};
-        //! Returns data records at indeces.
-        virtual void getdata ( vec &dt, const ivec &indeces ) {it_error ( "abstract class" );};
-        //! Accepts action variable and schedule it for application.
-        virtual void write ( vec &ut ) {it_error ( "abstract class" );};
-        //! Accepts action variables at specific indeces
-        virtual void write ( vec &ut, const ivec &indeces ) {it_error ( "abstract class" );};
-
-        //! Moves from \f$ t \f$ to \f$ t+1 \f$, i.e. perfroms the actions and reads response of the system.
-        virtual void step() =0;
-
-        //! Register DS for logging into logger L
-        virtual void log_add ( logger &L ) {
-                it_assert_debug ( dtsize==Drv._dsize(),"" );
-                it_assert_debug ( utsize==Urv._dsize(),"" );
-
-                L_dt=L.add ( Drv,"" );
-                L_ut=L.add ( Urv,"" );
-        }
-        //! Register DS for logging into logger L
-        virtual void logit ( logger &L ) {
-                vec tmp ( Drv._dsize() +Urv._dsize() );
-                getdata ( tmp );
-                // d is first in getdata
-                L.logit ( L_dt,tmp.left ( Drv._dsize() ) );
-                // u follows after d in getdata
-                L.logit ( L_ut,tmp.mid ( Drv._dsize(), Urv._dsize() ) );
-        }
-        //!access function
-        virtual RV _drv() const {return concat ( Drv,Urv );}
-        //!access function
-        const RV& _urv() const {return Urv;}
-        //! set random rvariables
-        virtual void set_drv (const  RV &drv, const RV &urv) { Drv=drv;Urv=urv;}
+class DS : public bdmroot
+{
+protected:
+  int dtsize;
+  int utsize;
+  //!Description of data returned by \c getdata().
+  RV Drv;
+  //!Description of data witten by by \c write().
+  RV Urv; //
+  //! Remember its own index in Logger L
+  int L_dt, L_ut;
+public:
+  //! default constructors
+  DS() : Drv(), Urv() {};
+  //! Returns full vector of observed data=[output, input]
+  virtual void getdata(vec &dt) {it_error("abstract class");};
+  //! Returns data records at indeces.
+  virtual void getdata(vec &dt, const ivec &indeces) {it_error("abstract class");};
+  //! Accepts action variable and schedule it for application.
+  virtual void write(vec &ut) {it_error("abstract class");};
+  //! Accepts action variables at specific indeces
+  virtual void write(vec &ut, const ivec &indeces) {it_error("abstract class");};
+
+  //! Moves from \f$ t \f$ to \f$ t+1 \f$, i.e. perfroms the actions and reads response of the system.
+  virtual void step() = 0;
+
+  //! Register DS for logging into logger L
+  virtual void log_add(logger &L) {
+    it_assert_debug(dtsize == Drv._dsize(), "");
+    it_assert_debug(utsize == Urv._dsize(), "");
+
+    L_dt = L.add(Drv, "");
+    L_ut = L.add(Urv, "");
+  }
+  //! Register DS for logging into logger L
+  virtual void logit(logger &L) {
+    vec tmp(Drv._dsize() + Urv._dsize());
+    getdata(tmp);
+    // d is first in getdata
+    L.logit(L_dt, tmp.left(Drv._dsize()));
+    // u follows after d in getdata
+    L.logit(L_ut, tmp.mid(Drv._dsize(), Urv._dsize()));
+  }
+  //!access function
+  virtual RV _drv() const {return concat(Drv, Urv);}
+  //!access function
+  const RV& _urv() const {return Urv;}
+  //! set random rvariables
+  virtual void set_drv(const  RV &drv, const RV &urv) { Drv = drv; Urv = urv;}
 };
 
@@ -648 +671 @@
 */
 
-class BM :public bdmroot {
-protected:
-        //! Random variable of the data (optional)
-        RV drv;
-        //!Logarithm of marginalized data likelihood.
-        double ll;
-        //!  If true, the filter will compute likelihood of the data record and store it in \c ll . Set to false if you want to save computational time.
-        bool evalll;
-public:
-        //! \name Constructors
-        //! @{
-
-        BM () :ll ( 0 ),evalll ( true ), LIDs ( 4 ), LFlags(4) {
-                LIDs=-1;/*empty IDs*/ LFlags=0; LFlags(0)=1;/*log only mean*/};
-        BM ( const BM &B ) :  drv ( B.drv ), ll ( B.ll ), evalll ( B.evalll ) {}
-        //! 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;};
-        //!@}
-
-        //! \name Mathematical operations
-        //!@{
-
-        /*! \brief Incremental Bayes rule
-        @param dt vector of input data
-        */
-        virtual void bayes ( const vec &dt ) = 0;
-        //! Batch Bayes rule (columns of Dt are observations)
-        virtual void bayesB ( const mat &Dt );
-        //! Evaluates predictive log-likelihood of the given data record
-        //! I.e. marginal likelihood of the data with the posterior integrated out.
-        virtual double logpred ( const vec &dt ) const{it_error ( "Not implemented" );return 0.0;}
-        //! Matrix version of logpred
-        vec logpred_m ( const mat &dt ) const{vec tmp ( dt.cols() );for ( int i=0;i<dt.cols();i++ ) {tmp ( i ) =logpred ( dt.get_col ( i ) );}return tmp;}
-
-        //!Constructs a predictive density \f$ f(d_{t+1} |d_{t}, \ldots d_{0}) \f$
-        virtual epdf* epredictor ( ) const {it_error ( "Not implemented" );return NULL;};
-        //!Constructs a conditional density 1-step ahead predictor \f$ f(d_{t+1} |d_{t+h-1}, \ldots d_{t})
-        virtual mpdf* predictor ( ) const {it_error ( "Not implemented" );return NULL;};
-        //!@}
-
-        //! \name Extension to conditional BM
-        //! This extension is useful e.g. in Marginalized Particle Filter (\ref bdm::MPF).
-        //! Alternatively, it can be used for automated connection to DS when the condition is observed
-        //!@{
-
-        //! Name of extension variable
-        RV rvc;
-        //! access function
-        const RV& _rvc() const {return rvc;}
-
-        //! Substitute \c val for \c rvc.
-        virtual void condition ( const vec &val ) {it_error ( "Not implemented!" );};
-
-        //!@}
-
-
-        //! \name Access to attributes
-        //!@{
-
-        const RV& _drv() const {return drv;}
-        void set_drv ( const RV &rv ) {drv=rv;}
-        void set_rv ( const RV &rv ) {const_cast<epdf&> ( posterior() ).set_rv ( rv );}
-        double _ll() const {return ll;}
-        void set_evalll ( bool evl0 ) {evalll=evl0;}
-        virtual const epdf& posterior() const =0;
-        virtual const epdf* _e() const =0;
-        //!@}
-
-        //! \name Logging of results
-        //!@{
-
-        //! Set boolean options from a string recognized are: "logbounds,logll"
-        virtual void set_options ( const string &opt ) {
-                LFlags(0)=1;
-                if ( opt.find ( "logbounds" ) !=string::npos ) {LFlags(1)=1; LFlags(2)=1;}
-                if ( opt.find ( "logll" ) !=string::npos ) {LFlags(3)=1;}
-        }
-        //! IDs of storages in loggers 4:[1=mean,2=lb,3=ub,4=ll]
-        ivec LIDs;
-
-        //! Flags for logging - same size as LIDs, each entry correspond to the same in LIDs
-        ivec LFlags;
-        //! Add all logged variables to a logger
-        virtual void log_add ( logger &L, const string &name="" ) {
-                // internal
-                RV r;
-                if ( posterior().isnamed() ) {r=posterior()._rv();}
-                else{r=RV ( "est", posterior().dimension() );};
-
-                // Add mean value
-                if (LFlags(0)) LIDs ( 0 ) =L.add ( r,name+"mean_" );
-                if (LFlags(1)) LIDs ( 1 ) =L.add ( r,name+"lb_" );
-                if (LFlags(2)) LIDs ( 2 ) =L.add ( r,name+"ub_" );
-                if (LFlags(3)) LIDs ( 3 ) =L.add ( RV("ll",1),name ); //TODO: "local" RV 
-        }
-        virtual void logit ( logger &L ) {
-                L.logit ( LIDs ( 0 ), posterior().mean() );
-                if ( LFlags(1) || LFlags(2)) { //if one of them is off, its LID==-1 and will not be stored
-                        vec ub,lb;
-                        posterior().qbounds ( lb,ub );
-                        L.logit ( LIDs ( 1 ), lb ); 
-                        L.logit ( LIDs ( 2 ), ub );
-                }
-                if (LFlags(3)) L.logit ( LIDs ( 3 ), ll );
-        }
-        //!@}
+class BM : public bdmroot
+{
+protected:
+  //! Random variable of the data (optional)
+  RV drv;
+  //!Logarithm of marginalized data likelihood.
+  double ll;
+  //!  If true, the filter will compute likelihood of the data record and store it in \c ll . Set to false if you want to save computational time.
+  bool evalll;
+public:
+  //! \name Constructors
+  //! @{
+
+  BM() : ll(0), evalll(true), LIDs(4), LFlags(4) {
+    LIDs = -1;/*empty IDs*/
+    LFlags = 0;
+    LFlags(0) = 1;/*log only mean*/
+  };
+  BM(const BM &B) :  drv(B.drv), ll(B.ll), evalll(B.evalll) {}
+  //! 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;};
+  //!@}
+
+  //! \name Mathematical operations
+  //!@{
+
+  /*! \brief Incremental Bayes rule
+  @param dt vector of input data
+  */
+  virtual void bayes(const vec &dt) = 0;
+  //! Batch Bayes rule (columns of Dt are observations)
+  virtual void bayesB(const mat &Dt);
+  //! Evaluates predictive log-likelihood of the given data record
+  //! I.e. marginal likelihood of the data with the posterior integrated out.
+  virtual double logpred(const vec &dt) const {it_error("Not implemented"); return 0.0;}
+  //! Matrix version of logpred
+  vec logpred_m(const mat &dt) const {vec tmp(dt.cols()); for (int i = 0; i < dt.cols(); i++) {tmp(i) = logpred(dt.get_col(i));} return tmp;}
+
+  //!Constructs a predictive density \f$ f(d_{t+1} |d_{t}, \ldots d_{0}) \f$
+  virtual epdf* epredictor() const {it_error("Not implemented"); return NULL;};
+  //!Constructs a conditional density 1-step ahead predictor \f$ f(d_{t+1} |d_{t+h-1}, \ldots d_{t})
+  virtual mpdf* predictor() const {it_error("Not implemented"); return NULL;};
+  //!@}
+
+  //! \name Extension to conditional BM
+  //! This extension is useful e.g. in Marginalized Particle Filter (\ref bdm::MPF).
+  //! Alternatively, it can be used for automated connection to DS when the condition is observed
+  //!@{
+
+  //! Name of extension variable
+  RV rvc;
+  //! access function
+  const RV& _rvc() const {return rvc;}
+
+  //! Substitute \c val for \c rvc.
+  virtual void condition(const vec &val) {it_error("Not implemented!");};
+
+  //!@}
+
+
+  //! \name Access to attributes
+  //!@{
+
+  const RV& _drv() const {return drv;}
+  void set_drv(const RV &rv) {drv = rv;}
+  void set_rv(const RV &rv) {const_cast<epdf&>(posterior()).set_rv(rv);}
+  double _ll() const {return ll;}
+  void set_evalll(bool evl0) {evalll = evl0;}
+  virtual const epdf& posterior() const = 0;
+  virtual const epdf* _e() const = 0;
+  //!@}
+
+  //! \name Logging of results
+  //!@{
+
+  //! Set boolean options from a string recognized are: "logbounds,logll"
+  virtual void set_options(const string &opt) {
+    LFlags(0) = 1;
+    if (opt.find("logbounds") != string::npos) {LFlags(1) = 1; LFlags(2) = 1;}
+    if (opt.find("logll") != string::npos) {LFlags(3) = 1;}
+  }
+  //! IDs of storages in loggers 4:[1=mean,2=lb,3=ub,4=ll]
+  ivec LIDs;
+
+  //! Flags for logging - same size as LIDs, each entry correspond to the same in LIDs
+  ivec LFlags;
+  //! Add all logged variables to a logger
+  virtual void log_add(logger &L, const string &name = "") {
+    // internal
+    RV r;
+    if (posterior().isnamed()) {r = posterior()._rv();}
+    else {r = RV("est", posterior().dimension());};
+
+    // Add mean value
+    if (LFlags(0)) LIDs(0) = L.add(r, name + "mean_");
+    if (LFlags(1)) LIDs(1) = L.add(r, name + "lb_");
+    if (LFlags(2)) LIDs(2) = L.add(r, name + "ub_");
+    if (LFlags(3)) LIDs(3) = L.add(RV("ll", 1), name);    //TODO: "local" RV
+  }
+  virtual void logit(logger &L) {
+    L.logit(LIDs(0), posterior().mean());
+    if (LFlags(1) || LFlags(2)) {  //if one of them is off, its LID==-1 and will not be stored
+      vec ub, lb;
+      posterior().qbounds(lb, ub);
+      L.logit(LIDs(1), lb);
+      L.logit(LIDs(2), ub);
+    }
+    if (LFlags(3)) L.logit(LIDs(3), ll);
+  }
+  //!@}
 };
 

bdm/stat/libDS.cpp

@@ -1 +1 @@
 
 #include "libDS.h"
-//#include "..\user_info.h"
 
 using namespace bdm;
@@ -55 +54 @@
 }
 
-void ArxDS::from_setting( const Setting &root ) 
+void ArxDS::from_setting( const Setting &set ) 
 {       
-        RV *yrv = UI::build<RV>( root, "y" );
-        RV *urv = UI::build<RV>( root, "u" );
-        RV *rrv = UI::build<RV>( root, "rgr" ); 
+        RV *yrv = UI::build<RV>( set, "y" );
+        RV *urv = UI::build<RV>( set, "u" );
+        RV *rrv = UI::build<RV>( set, "rgr" ); 
                                 
         mat Th;
-        UI::get( Th, root, "theta" );
+        UI::get( Th, set, "theta" );
 
         vec mu0;
-        if( root.exists( "offset" ))
-                UI::get( mu0, root, "offset" );
+        if( set.exists( "offset" ))
+                UI::get( mu0, set, "offset" );
         else
                 mu0= zeros( yrv->_dsize() );
 
         mat sqR;
-        UI::get( sqR, root, "r" );
+        UI::get( sqR, set, "r" );
         set_parameters(Th,mu0,sqR);
         set_drv(*yrv,*urv,*rrv);
 
-        if(root.exists("opt"))
-                set_options(root["opt"]);
+        if(set.exists("opt"))
+                set_options(set["opt"]);
 }
 
-/*void ArxDS::to_setting( Setting &root ) const
+/*void ArxDS::to_setting( Setting &set ) const
 {       
-        Transport::to_setting( root );
+        Transport::to_setting( set );
 
-        Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt );
+        Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt );
         kilometers_setting = kilometers;
 
-        UI::save( passengers, root, "passengers" );
+        UI::save( passengers, set, "passengers" );
 }*/
 
@@ -124 +123 @@
 }
 
-void ITppFileDS::from_setting( const Setting &root ) 
+void ITppFileDS::from_setting( const Setting &set ) 
 {       
-        RV* rvtmp = UI::build<RV>(root, "rv" );
+        RV* rvtmp = UI::build<RV>(set, "rv" );
 
-        it_file it ( root["filename"] );
-        it << Name ( root["varname"] ); 
+        it_file it ( set["filename"] );
+        it << Name ( set["varname"] ); 
         it >> Data;
         time = 0;
@@ -137 +136 @@
 }
 
-/*void ITppFileDS::to_setting( Setting &root ) const
+/*void ITppFileDS::to_setting( Setting &set ) const
 {       
-        Transport::to_setting( root );
+        Transport::to_setting( set );
 
-        Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt );
+        Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt );
         kilometers_setting = kilometers;
 
-        UI::save( passengers, root, "passengers" );
+        UI::save( passengers, set, "passengers" );
 }*/
 
-void stateDS::from_setting( const Setting &root ) 
+void stateDS::from_setting( const Setting &set ) 
 {       
-        IM = UI::build<mpdf>(root, "IM");
-        OM = UI::build<mpdf>(root, "OM");
+        IM = UI::build<mpdf>(set, "IM");
+        OM = UI::build<mpdf>(set, "OM");
 
         dt.set_length( OM->dimension() );
@@ -156 +155 @@
         ut.set_length(0);
         
-        RV* rvtmp = UI::build<RV>(root["IM"], "rvu");                   
+        RV* rvtmp = UI::build<RV>(set["IM"], "rvu");                    
         //set_drv(rvtmp);
 }
 
-/*void stateDS::to_setting( Setting &root ) const
+/*void stateDS::to_setting( Setting &set ) const
 {       
-        Transport::to_setting( root );
+        Transport::to_setting( set );
 
-        Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt );
+        Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt );
         kilometers_setting = kilometers;
 
-        UI::save( passengers, root, "passengers" );
+        UI::save( passengers, set, "passengers" );
 }*/
 

bdm/stat/libDS.h

@@ -94 +94 @@
         };
 
-        void from_setting( const Setting &root );
-
-        // TODO dodelat void to_setting( Setting &root ) const;
+        void from_setting( const Setting &set );
+
+        // TODO dodelat void to_setting( Setting &set ) const;
 
 };
@@ -242 +242 @@
         Result is ARX data source offering with full history as Drv.
         */
-        void from_setting( const Setting &root );
-
-        // TODO dodelat void to_setting( Setting &root ) const;
+        void from_setting( const Setting &set );
+
+        // TODO dodelat void to_setting( Setting &set ) const;
 };
 
@@ -316 +316 @@
         \endcode
         */
-        void from_setting( const Setting &root );
-
-        // TODO dodelat void to_setting( Setting &root ) const;
+        void from_setting( const Setting &set );
+
+        // TODO dodelat void to_setting( Setting &set ) const;
 
 };

bdm/stat/libEF.cpp

@@ -319 +319 @@
 }
 
-void migamma_ref::from_setting( const Setting &root ) 
+void migamma_ref::from_setting( const Setting &set ) 
 {                               
         vec ref;
-        UI::get( ref, root, "ref" );
-        set_parameters(root["k"],ref,root["l"]);
-}
-
-/*void migamma_ref::to_setting( Setting &root ) const
+        UI::get( ref, set, "ref" );
+        set_parameters(set["k"],ref,set["l"]);
+}
+
+/*void migamma_ref::to_setting( Setting &set ) const
 {       
-        Transport::to_setting( root );
-
-        Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt );
+        Transport::to_setting( set );
+
+        Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt );
         kilometers_setting = kilometers;
 
-        UI::save( passengers, root, "passengers" );
+        UI::save( passengers, set, "passengers" );
 }*/
 
 
-void mlognorm::from_setting( const Setting &root ) 
+void mlognorm::from_setting( const Setting &set ) 
 {       
         vec mu0;
-        UI::get( mu0, root, "mu0");
-        set_parameters(mu0.length(),root["k"]);
+        UI::get( mu0, set, "mu0");
+        set_parameters(mu0.length(),set["k"]);
         condition(mu0);
 }
 
-/*void mlognorm::to_setting( Setting &root ) const
+/*void mlognorm::to_setting( Setting &set ) const
 {       
-        Transport::to_setting( root );
-
-        Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt );
+        Transport::to_setting( set );
+
+        Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt );
         kilometers_setting = kilometers;
 
-        UI::save( passengers, root, "passengers" );
+        UI::save( passengers, set, "passengers" );
 }*/
 

bdm/stat/libEF.h

@@ -544 +544 @@
                         */
 
-                        void from_setting( const Setting &root ) 
+                        void from_setting( const Setting &set ) 
                         {       
-                                fnc* g = UI::build<fnc>( root, "g" );
+                                fnc* g = UI::build<fnc>( set, "g" );
 
                                 mat R;
-                                if ( root.exists( "dR" ) )
+                                if ( set.exists( "dR" ) )
                                 {
                                         vec dR;
-                                        UI::get( dR, root, "dR" );
+                                        UI::get( dR, set, "dR" );
                                         R=diag(dR);
                                 }
                                 else 
-                                        UI::get( R, root, "R");                                 
+                                        UI::get( R, set, "R");                                  
                 
                                 set_parameters(g,R);
                         }
 
-                        /*void mgnorm::to_setting( Setting &root ) const
+                        /*void mgnorm::to_setting( Setting &set ) const
                         {       
-                                Transport::to_setting( root );
-
-                                Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt );
+                                Transport::to_setting( set );
+
+                                Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt );
                                 kilometers_setting = kilometers;
 
-                                UI::save( passengers, root, "passengers" );
+                                UI::save( passengers, set, "passengers" );
                         }*/
 
@@ -780 +780 @@
                         Result if
                          */
-                        void from_setting( const Setting &root );
-
-                        // TODO dodelat void to_setting( Setting &root ) const;
+                        void from_setting( const Setting &set );
+
+                        // TODO dodelat void to_setting( Setting &set ) const;
         };
 
@@ -859 +859 @@
 
                          */
-                        void from_setting( const Setting &root );
-
-                        // TODO dodelat void to_setting( Setting &root ) const;
+                        void from_setting( const Setting &set );
+
+                        // TODO dodelat void to_setting( Setting &set ) const;
 
         };

bdm/stat/loggers.cpp

@@ -27 +27 @@
 }
 
-void memlog::from_setting( const Setting &root ) 
+void memlog::from_setting( const Setting &set ) 
 {       
         // TODO tady se natvrdo ocekava existence stringu, nejsou zadne defaulty.. je to tak OK?
-        string itfilename = (const char*)root["filename"];
-        maxlen = root["maxlen"];
+        string itfilename = (const char*)set["filename"];
+        maxlen = set["maxlen"];
 }
 
-/*void memlog::to_setting( Setting &root ) const
+/*void memlog::to_setting( Setting &set ) const
 {       
-        Transport::to_setting( root );
+        Transport::to_setting( set );
 
-        Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt );
+        Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt );
         kilometers_setting = kilometers;
 
-        UI::save( passengers, root, "passengers" );
+        UI::save( passengers, set, "passengers" );
 }*/
 
@@ -159 +159 @@
 
 
-void dirfilelog::from_setting( const Setting &root ) 
+void dirfilelog::from_setting( const Setting &set ) 
 {       
         // TODO tady se natvrdo ocekava existence stringu, nejsou zadne defaulty.. je to tak OK?
-        dirname = (const char*)root["dirname"];
-        maxlen = root["maxlen"];
+        dirname = (const char*)set["dirname"];
+        maxlen = set["maxlen"];
         scalarnames.set_length(0);
 }
 
-/*void dirfilelog::to_setting( Setting &root ) const
+/*void dirfilelog::to_setting( Setting &set ) const
 {       
-        Transport::to_setting( root );
+        Transport::to_setting( set );
 
-        Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt );
+        Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt );
         kilometers_setting = kilometers;
 
-        UI::save( passengers, root, "passengers" );
+        UI::save( passengers, set, "passengers" );
 }*/
 

bdm/stat/loggers.h

@@ -77 +77 @@
         \endcode
          */
-        void from_setting( const Setting &root );
+        void from_setting( const Setting &set );
 
-        // TODO dodelat void to_setting( Setting &root ) const;
+        // TODO dodelat void to_setting( Setting &set ) const;
 };
 
@@ -125 +125 @@
         \endcode
         */
-        void from_setting( const Setting &root );
+        void from_setting( const Setting &set );
 
-        // TODO dodelat void to_setting( Setting &root ) const;
+        // TODO dodelat void to_setting( Setting &set ) const;
 };
 

bdm/user_info.cpp

@@ -15 +15 @@
 namespace bdm
 {
-
-
 ///////////////////////// UI FILE /////////////////////////////////////////////
-
 
 UI_File::UI_File ()
@@ -88 +85 @@
     String_To_UI_Map::const_iterator iter = mapped_strings().find( class_name );
     if ( iter == mapped_strings().end())
+                // TODO dat sem vypis seznamu registrovanych trid
         it_error ( "UI error: class " + class_name + " was not properly registered. Use the macro ""UIREGISTER([class name]);"" within your code." );
     return *iter->second;
@@ -102 +100 @@
 ///////////////////////// INTERNAL LINK EXPANDER /////////////////////////////////////////////
 
-UI::SettingsResolver::SettingsResolver( const Setting &potential_link )
-{
-    file = NULL;
-    result = &potential_link;
-
+UI::SettingResolver::SettingResolver( const Setting &potential_link ): result( initialize_reference( file, potential_link ) )
+{
+}
+
+const Setting& UI::SettingResolver::initialize_reference(UI_File *&file, const Setting &potential_link)
+{
     if ( potential_link.getType() !=  Setting::TypeString )
-        return;
-
-    string link = (const char*) potential_link;
+            return potential_link;
+        
+        string link = (const char*) potential_link;
     size_t aerobase = link.find('@');
+
+        const Setting *result;
     if ( aerobase != string::npos )
     {
@@ -120 +121 @@
     }
     else
+        {
+                file = NULL;
+                result = &potential_link;
         while ( !result->isRoot() )
             result = &result->getParent();
+        }
 
     if ( !result->exists( link ) )
         ui_error( "linked Setting was not found", potential_link );
 
-    result = &(*result)[link];
-}
-
-UI::SettingsResolver::~SettingsResolver()
+    return (*result)[link];
+}
+
+UI::SettingResolver::~SettingResolver()
 {
     if ( file ) delete file;
-}
-
-const Setting& UI::SettingsResolver::root() const
-{
-    return *result;
 }
 
@@ -151 +151 @@
 void UI::save( const string &str, Setting &element )
 {
-    Setting &root = element.add( Setting::TypeString );
-    root = str;
+    Setting &set = element.add( Setting::TypeString );
+    set = str;
 }
 
@@ -158 +158 @@
 {
 
-    Setting &root = (name == "") ? element.add( Setting::TypeList )
+    Setting &set = (name == "") ? element.add( Setting::TypeList )
                     : element.add( name, Setting::TypeList );
 
-    Setting &cols = root.add( Setting::TypeInt );
+    Setting &cols = set.add( Setting::TypeInt );
     cols = matrix.cols();
 
-    Setting &rows = root.add( Setting::TypeInt );
+    Setting &rows = set.add( Setting::TypeInt );
     rows = matrix.rows();
 
-    Setting &elements = root.add( Setting::TypeArray );
+    Setting &elements = set.add( Setting::TypeArray );
 
     // build matrix row-wise
@@ -183 +183 @@
 {
 
-    Setting &root = (name == "") ? element.add( Setting::TypeArray )
+    Setting &set = (name == "") ? element.add( Setting::TypeArray )
                     : element.add( name, Setting::TypeArray );
     for ( int i=0; i<vector.length(); i++ )
     {
-        Setting &new_field = root.add(Setting::TypeInt);
+        Setting &new_field = set.add(Setting::TypeInt);
         new_field = vector(i);
     }
@@ -196 +196 @@
 void UI::save( const vec &vector, Setting &element, const string &name)
 {
-
-    Setting &root = (name == "") ? element.add( Setting::TypeArray )
+    Setting &set = (name == "") ? element.add( Setting::TypeArray )
                     : element.add( name, Setting::TypeArray );
     for ( int i=0; i<vector.length(); i++ )
     {
-                Setting &new_field = root.add(Setting::TypeFloat);
+                Setting &new_field = set.add(Setting::TypeFloat);
         new_field = vector(i);
     }
@@ -211 +210 @@
 void UI::from_setting( mat& matrix, const Setting &element )
 {
-    const SettingsResolver link_expander( element );
-    const Setting &root = link_expander.root();
-
-    if ( root.isNumber() )
+    const SettingResolver link( element );
+
+    if ( link.result.isNumber() )
     {
         matrix.set_size( 1, 1 );
-        matrix(0,0) = root;
-        return;
-    }
-
-    if ( root.isList() )
-    {
-        if ( root.getLength() != 3 )
-            ui_error( "the setting supposed to represent a matrix element has wrong syntax", root );
-
-        Setting &rows_setting = root[0];
-        Setting &cols_setting = root[1];
-        Setting &elements = root[2];
+        matrix(0,0) = link.result;
+        return;
+    }
+
+    if ( link.result.isList() )
+    {
+        if ( link.result.getLength() != 3 )
+            ui_error( "the setting supposed to represent a matrix element has wrong syntax", link.result );
+
+        Setting &rows_setting = link.result[0];
+        Setting &cols_setting = link.result[1];
+        Setting &elements = link.result[2];
 
         ASSERT_UITYPE(cols_setting,TypeInt);
@@ -238 +236 @@
 
         if ( cols < 0 | rows < 0 )
-            ui_error( "the dimensions of a matrix has to be non-negative", root );
+            ui_error( "the dimensions of a matrix has to be non-negative", link.result );
 
         if ( elements.getLength() != cols * rows )
@@ -259 +257 @@
     }
 
-    ui_error( "only numeric types or TypeList are supported as matrix values", root );
+    ui_error( "only numeric types or TypeList are supported as matrix values", link.result );
 }
 
@@ -265 +263 @@
 void UI::from_setting( ivec &vector, const Setting &element )
 {
-    const SettingsResolver link_expander( element );
-    const Setting &root = link_expander.root();
-
-    if ( root.isNumber() )
-    {
-        ASSERT_UITYPE(root,TypeInt);
+    const SettingResolver link( element );
+
+    if ( link.result.isNumber() )
+    {
+        ASSERT_UITYPE(link.result,TypeInt);
         vector.set_length( 1 );
-        vector(0) = root;
-        return;
-    }
-
-    if ( root.isList() )
-    {
-        if ( root.getLength() != 3 )
-            ui_error( "the setting supposed to represent a matrix element has wrong syntax", root );
-
-        Setting &cols_setting = root[0];
-        Setting &rows_setting = root[1];
-        Setting &elements = root[2];
-
-        ASSERT_UITYPE(cols_setting,TypeInt);
-        ASSERT_UITYPE(rows_setting,TypeInt);
-        ASSERT_UITYPE(elements,TypeArray);
-
-        int cols = cols_setting;
-        int rows = rows_setting;
-
-        if ( cols < 0 | rows < 0)
-            ui_error( "the dimensions of a matrix has to be non-negative", root );
-
-        if ( elements.getLength() != cols * rows )
-            ui_error( "the count of the matrix elements is incompatible with matrix dimension", elements );
-
-        if ( cols != 1 & rows !=1)
-            ui_error( "the vector length is invalid, it seems to be rather a matrix", elements );
-
-        int len = rows * cols;
+        vector(0) = link.result;
+        return;
+    }
+
+    if ( link.result.isList() )
+    {
+                mat matrix;
+                from_setting( matrix, link.result );
+
+        if ( matrix.cols() != 1 & matrix.rows() !=1)
+                        ui_error( "the vector length is invalid, it seems to be rather a matrix", link.result );
+
+        int len = matrix.rows() * matrix.cols();
         vector.set_length ( len );
         if ( len == 0 ) return;
 
+                Setting &elements = link.result[2];
         ASSERT_UITYPE(elements[0],TypeInt);
-        for ( int i=0; i<len; i++ )
-            vector(i) = elements[i];
-        return;
-    }
-
-    if ( root.isArray() )
-    {
-        int len = root.getLength();
+
+
+        if ( matrix.cols() == 1 )
+                        for ( int i=0; i<len; i++ )
+                                vector(i) = matrix(i,1);
+                else
+                        for ( int i=0; i<len; i++ )
+                                vector(i) = matrix(1,i);
+        return;
+
+    }
+
+    if ( link.result.isArray() )
+    {
+        int len = link.result.getLength();
         vector.set_length( len );
         if ( len == 0 ) return;
 
-        ASSERT_UITYPE(root[0],TypeInt);
+        ASSERT_UITYPE(link.result[0],TypeInt);
         for ( int i=0; i < len; i++ )
-            vector(i) = root[i];
-        return;
-    }
-
-    ui_error( "only numeric types, TypeArray or TypeList are supported as vector values", root );
+            vector(i) = link.result[i];
+        return;
+    }
+
+    ui_error( "only numeric types, TypeArray or TypeList are supported as vector values", link.result );
 }
 
@@ -329 +317 @@
 void UI::from_setting( vec &vector, const Setting &element )
 {
-    const SettingsResolver link_expander( element );
-    const Setting &root = link_expander.root();
-
-    if ( root.isNumber() )
+    const SettingResolver link( element );
+
+    if ( link.result.isNumber() )
     {
         vector.set_length( 1 );
-        vector(0) = root;
-        return;
-    }
-
-    if ( root.isList() )
-    {
-        if ( root.getLength() != 3 )
-            ui_error( "the setting supposed to represent a matrix element has wrong syntax", root );
-
-        Setting &cols_setting = root[0];
-        Setting &rows_setting = root[1];
-        Setting &elements = root[2];
-
-        ASSERT_UITYPE(cols_setting,TypeInt);
-        ASSERT_UITYPE(rows_setting,TypeInt);
-        ASSERT_UITYPE(elements,TypeArray);
-
-        int cols = cols_setting;
-        int rows = rows_setting;
-
-        if ( cols < 0 | rows < 0)
-            ui_error( "the dimensions of a matrix has to be non-negative", root );
-
-        if ( elements.getLength() != cols * rows )
-            ui_error( "the count of the matrix elements is incompatible with matrix dimension", elements );
-
-        if ( cols != 1 & rows !=1)
-            ui_error( "the vector length is invalid, it seems to be rather a matrix", elements );
-
-        int len = rows * cols;
+        vector(0) = link.result;
+        return;
+    }
+
+    if ( link.result.isList() )
+    {
+                mat matrix;
+                from_setting( matrix, link.result );
+
+        if ( matrix.cols() != 1 & matrix.rows() !=1)
+                        ui_error( "the vector length is invalid, it seems to be rather a matrix", link.result );
+
+        int len = matrix.rows() * matrix.cols();
         vector.set_length ( len );
         if ( len == 0 ) return;
 
-        if ( !elements[0].isNumber())
-            ui_error("a vector element has to be a number", elements[0]);
-
-        for ( int i=0; i<len; i++ )
-            vector(i) = elements[i];
-        return;
-    }
-
-    if ( root.isArray() )
-    {
-        int len = root.getLength();
+        if ( matrix.cols() == 1 )
+                        for ( int i=0; i<len; i++ )
+                                vector(i) = matrix(i,1);
+                else
+                        for ( int i=0; i<len; i++ )
+                                vector(i) = matrix(1,i);
+        return;
+    }
+
+    if ( link.result.isArray() )
+    {
+        int len = link.result.getLength();
         vector.set_length( len );
         if ( len == 0 ) return;
 
-        if ( !root[0].isNumber())
-            ui_error("a vector element has to be a number", root[0]);
-
-        for ( int i=0; i < len; i++ ) {
-        double tmp= (root[i]);
-            vector(i) = tmp;
-}
-        return;
-    }
-
-    ui_error( "only numeric types, TypeArray or TypeList are supported as vector values", root );
+        if ( !link.result[0].isNumber())
+            ui_error("a vector element has to be a number", link.result[0]);
+
+        for ( int i=0; i < len; i++ ) 
+            vector(i) = link.result[i];
+
+                return;
+    }
+
+    ui_error( "only numeric types, TypeArray or TypeList are supported as vector values", link.result );
 }
 

bdm/user_info.h

@@ -137 +137 @@
         template<class T> static void from_setting( T* &instance, const Setting &element )
         {                       
-                const SettingsResolver link_expander( element );
-                const Setting &root = link_expander.root();
-
-                ASSERT_UITYPE(root,TypeGroup);
+                const SettingResolver link( element );
+
+                ASSERT_UITYPE(link.result,TypeGroup);
 
                 // we get a velue stored in the "class" attribute 
                 string class_name;
-                if( !root.lookupValue( "class", class_name ) )
-                        ui_error( "the obligatory ""class"" identifier is missing", root );
+                if( !link.result.lookupValue( "class", class_name ) )
+                        ui_error( "the obligatory ""class"" identifier is missing", link.result );
         
                 // and finally we find a UserInfo related to this type
@@ -164 +163 @@
                 try
                 {
-                        instance->from_setting( root );
+                        instance->from_setting( link.result );
                 }
                 catch(SettingException xcptn)
@@ -177 +176 @@
         template<class T> static void from_setting( Array<T> &array_to_load, const Setting &element )
         {
-                const SettingsResolver link_expander( element );
-                const Setting &root = link_expander.root();
-
-                ASSERT_UITYPE(root,TypeList);
-
-                int len = root.getLength();
+                const SettingResolver link( element );
+
+                ASSERT_UITYPE(link.result,TypeList);
+
+                int len = link.result.getLength();
                 array_to_load.set_length( len );
                 if( len == 0 ) return;
                 
                 for( int i=0; i < len; i++ ) 
-                        from_setting( array_to_load(i), root[i] ); 
+                        from_setting( array_to_load(i), link.result[i] ); 
         }
 
@@ -212 +210 @@
         // vraci true, kdyz to byl platny link, jinak false.. v pripade chyby konci it_errorem..
         // do elementu vrati setting prislusny po rozbaleni linku, jinak ponecha beze zmeny
-        class SettingsResolver  
+        class SettingResolver   
         {
         private:
                 UI_File *file;
-                const Setting *result;
+
+                const Setting &initialize_reference( UI_File* &file, const Setting &potential_link);
 
         public:
-
-                SettingsResolver( const Setting &potential_link );
+                const Setting &result;
+
+                SettingResolver( const Setting &potential_link );
                 
-                ~SettingsResolver();
-                
-                const Setting& root() const;
+                ~SettingResolver();             
         };
 
@@ -270 +268 @@
         template< class T> static void save( const T * const instance, Setting &element, const string &name = "")
         {
-                Setting &root = (name == "") ? element.add( Setting::TypeGroup )                                                        
+                Setting &set = (name == "") ? element.add( Setting::TypeGroup )                                                 
                                                                          : element.add( name, Setting::TypeGroup );             
 
@@ -276 +274 @@
                         
                 // add attribute "class" 
-                Setting &type = root.add( "class", Setting::TypeString );
+                Setting &type = set.add( "class", Setting::TypeString );
                 type = class_name;
 
                 try
                 {
-                        instance->to_setting( root );
+                        instance->to_setting( set );
                 }
                 catch(SettingException xcptn)

doc/local/codingrules.dox

@@ -40 +40 @@
 <ul>
 
-<li> if possible, each `#inline ... ' dircetive should be located within the `.h'
-file, one obvious exception is the case of `#inline [filename].h' written in 
+<li> if possible, each `\#include ... ' dircetive should be located within the `.h'
+file, one obvious exception is the case of `\#include "[filename].h"' written in 
 `[filename].cpp' </li>
 
 <li> firstly, system headers should be included (i.e. those with brackets 
-`#include <header_name>'), other headers (like `#include my_header_name.h') 
+`\#include \<system_header_name\>'), other headers (like `\#include "my_header_name.h"') 
 should follow (this rule leads to the faster search of an error on some 
 compilators) </li>

doc/local/install.dox

@@ -18 +18 @@
 For download use an appropriate SVN client http://subversion.tigris.org/links.html#clients
 
-Download the source files to any directory of your choise, this directoory will be refered to as <bdm_dir>.
+Download the source files to any directory of your choise, this directoory will be refered to as \<bdm_dir\>.
 
 \subsection pre Prerequisities
@@ -57 +57 @@
 For convenience of the beginners, DLLS of the ACML and lib+include files for ITPP and ACML are
 provided at: http://staff.utia.cas.cz/smidl/Public/mixpp_win32lib.zip
-If you want to use them copy the content of the zip file to <bdm_dir>\system\win32\ directory and
+If you want to use them copy the content of the zip file to \<bdm_dir\>/system/win32/ directory and
 make sure to set your PATH environment variable:
 \code

library/mex/mexds.h

@@ -1 @@
-//#include "../bdm/stat/libDS_ui.h"
+#include "../bdm/stat/libDS.h"
+#include "mexparse.h"
 
-/*! \brief Create memory data source from mxArray
+namespace bdm {
+/*!
+* \brief Memory storage of off-line data column-wise
 
-\code
-system={
-        type="mexDS";
-        varname="";            // name of workspace variable
-        rids=[1 1 1];          // numbers of data rows
-        tds =[0 1 2];          // time delays
-        };
-\endcode
+The data are stored in an internal matrix \c Data . Each column of Data corresponds to one discrete time observation \f$t\f$. Access to this matrix is via indices \c rowid and \c delays.
 
-MemDS with the above fields will be created;
+The data can be loaded from a file.
+*/
+class MexDS : public MemDS {
+                //!Default constructor
+        MexDS () {};
 
-\todo Very memory inefficient implementation. The data file is copied 2 times! 
-For better implementatin we would need MemDS with pointer to the raw data. Then it could operate directly inside mxArray.
+        /*! \brief Create memory data source from mxArray
 
-*/
-class UImexDS: public UIbuilder{
-        public:
-                UImexDS():UIbuilder("mexDS"){};
-                bdmroot* build(Setting &S) const{
-                        mat Data;
-                        ivec rids;
-                        ivec tds;
-                        try{
-                                Data = mxArray2mat(mexGetVariable("base",S["varname"]));
-                                rids=getivec(S["rids"]);
-                                tds = getivec(S["tds"]);
-                        }
-                        catch UICATCH ;
-                        
-                        MemDS* M=new MemDS(Data,rids,tds);
-                        RV* r; UIbuild(S["rv"],r);
-                        RV ru=RV();
-                        M->set_rvs(*r,ru);
-                        return M;
+        \code
+        system={
+                type="mexDS";
+                varname="";            // name of workspace variable
+                rids=[1 1 1];          // numbers of data rows
+                tds =[0 1 2];          // time delays
                 };
+        \endcode
+
+        MemDS with the above fields will be created;
+
+        \todo Very memory inefficient implementation. The data file is copied 2 times! 
+        For better implementatin we would need MemDS with pointer to the raw data. Then it could operate directly inside mxArray.
+
+        */
+        void from_setting( const Setting &set )
+        {       
+                Data = mxArray2mat(mexGetVariable("base",set["varname"]));
+                UI::get( rowid, set, "rids" );
+                it_assert_debug ( max ( rowid ) <=Data.rows(),"MemDS rowid is too high for given Dat." );
+
+                UI::get( delays, set, "tds" );
+                time = max ( delays );
+                it_assert_debug ( time < Data.cols(),"MemDS delays are too high." );
+
+                RV* r = UI::build<RV>(set,"rv");
+                RV ru=RV();
+                set_rvs(*r,ru);
+        }
+
+
+        // TODO dodelat void to_setting( Setting &set ) const;
 };
-UIREGISTER(UImexDS);
+
+UIREGISTER(MexDS);
+
+}

tests/testUI.cpp

@@ -24 +24 @@
   }
 
-  virtual void from_setting(const Setting &root) {
-    root.lookupValue("name", name);
-  }
-
-  virtual void to_setting(Setting &root) const {
-    Setting &name_setting = root.add("name", Setting::TypeString);
+  virtual void from_setting(const Setting &set) {
+    set.lookupValue("name", name);
+  }
+
+  virtual void to_setting(Setting &set) const {
+    Setting &name_setting = set.add("name", Setting::TypeString);
     name_setting = name;
   }
@@ -50 +50 @@
   }
 
-  virtual void from_setting(const Setting &root) {
-    root.lookupValue("number", number);
-        if( root.exists( "software" ) )
-                UI::get(software, root, "software");
-  }
-
-  virtual void to_setting(Setting &root) const {
-    Setting &number_setting = root.add("number", Setting::TypeInt);
+  virtual void from_setting(const Setting &set) {
+    set.lookupValue("number", number);
+        if( set.exists( "software" ) )
+                UI::get(software, set, "software");
+  }
+
+  virtual void to_setting(Setting &set) const {
+    Setting &number_setting = set.add("number", Setting::TypeInt);
     number_setting = number;
 
-    UI::save(software, root, "software");
+    UI::save(software, set, "software");
   }
 
@@ -89 +89 @@
   }
 
-  virtual void from_setting(const Setting &root) {
-    root.lookupValue("year", year);
-    root.lookupValue("manufacturer", manufacturer);
-  }
-
-  virtual void to_setting(Setting &root) const {
-    Setting &year_setting = root.add("year", Setting::TypeInt);
+  virtual void from_setting(const Setting &set) {
+    set.lookupValue("year", year);
+    set.lookupValue("manufacturer", manufacturer);
+  }
+
+  virtual void to_setting(Setting &set) const {
+    Setting &year_setting = set.add("year", Setting::TypeInt);
     year_setting = year;
 
-    Setting &manufacturer_setting = root.add("manufacturer", Setting::TypeString);
+    Setting &manufacturer_setting = set.add("manufacturer", Setting::TypeString);
     manufacturer_setting = manufacturer;
   }
@@ -118 +118 @@
   }
 
-  virtual void from_setting(const Setting &root) {
-    Transport::from_setting(root);
-
-    root.lookupValue("kilometers", kilometers);
-
-        if( root.exists( "passengers" ) )
-            UI::get(passengers, root, "passengers");
-  }
-
-  virtual void to_setting(Setting &root) const {
-    Transport::to_setting(root);
-
-    Setting &kilometers_setting = root.add("kilometers", Setting::TypeInt);
+  virtual void from_setting(const Setting &set) {
+    Transport::from_setting(set);
+
+    set.lookupValue("kilometers", kilometers);
+
+        if( set.exists( "passengers" ) )
+            UI::get(passengers, set, "passengers");
+  }
+
+  virtual void to_setting(Setting &set) const {
+    Transport::to_setting(set);
+
+    Setting &kilometers_setting = set.add("kilometers", Setting::TypeInt);
     kilometers_setting = kilometers;
 
-    UI::save(passengers, root, "passengers");
+    UI::save(passengers, set, "passengers");
   }
 
@@ -167 +167 @@
   }
 
-  void from_setting(const Setting &root) {
-    Transport::from_setting(root);
-
-    root.lookupValue("electricLights", electricLights);
-
-        UI::get(matr, root, "matr");
-  }
-
-  void to_setting(Setting &root) const {
-    Transport::to_setting(root);
-
-    Setting &electricLights_setting = root.add("electricLights", Setting::TypeBoolean);
+  void from_setting(const Setting &set) {
+    Transport::from_setting(set);
+
+    set.lookupValue("electricLights", electricLights);
+
+        UI::get(matr, set, "matr");
+  }
+
+  void to_setting(Setting &set) const {
+    Transport::to_setting(set);
+
+    Setting &electricLights_setting = set.add("electricLights", Setting::TypeBoolean);
     electricLights_setting = electricLights;
 
-    UI::save(matr, root, "matr");
+    UI::save(matr, set, "matr");
   }