Changeset 1058

Timestamp:

06/07/10 22:36:56 (15 years ago)

Author:

smidl

Message:

doc + DS cleanup

Files:

• applications/bdmtoolbox/tutorial/userguide/memds_example.m (modified) (1 diff)
• library/bdm/base/bdmbase.cpp (modified) (2 diffs)
• library/bdm/base/bdmbase.h (modified) (2 diffs)
• library/bdm/base/datasources.cpp (modified) (2 diffs)
• library/bdm/base/datasources.h (modified) (9 diffs)
• library/bdm/mex/mex_datasource.h (modified) (1 diff)
• library/bdm/stat/exp_family.h (modified) (1 diff)

applications/bdmtoolbox/tutorial/userguide/memds_example.m

@@ -12 +12 @@
 %M=simulator(DS2);
 
-M.ch0
+M.DS_dt_
 %M.DS_dt_Data

library/bdm/base/bdmbase.cpp

@@ -530 +530 @@
 
 void DS::from_setting ( const Setting &set ) {
-        RV rv;
-        if( UI::get( rv, set, "drv", UI::optional ) )
-                set_drv ( rv, RV() );
+        UI::get( Drv, set, "drv", UI::optional );
+        UI::get(log_level, set, "log_level",UI::optional);
 }
 
@@ -538 +537 @@
         if( !Drv._dsize() && dtsize > 0 )
         {
-                RV *r = new RV();
+                Drv = RV();
                 for ( int i = 0; i < dtsize; i++ ) {
-                        r->add ( RV ( "ch" + num2str ( i ), 1, 0 ) );
-                }
-                set_drv ( *r, RV() );
-                delete r;
+                        Drv.add ( RV("", dtsize ));
+                }
         }
 }

library/bdm/base/bdmbase.h

@@ -1162 +1162 @@
 
 The DataSource has three main data interaction structures:
-\li input, \f$ u_t \f$,
-\li output \f$ d_t \f$,
-In simulators, d_t may contain "hidden" variables as well.
+\li input, \f$ u_t \f$, which are described via RVs in attribute \c urv
+\li observations \f$ d_t \f$, which are described in \c drv
+In simulators, dt may contain "hidden" variables as well.
+
 */
 
@@ -1234 +1235 @@
         }
 
-        //! set random variables
-        virtual void set_drv ( const  RV &drv, const RV &urv) {
-                Drv = drv;
-                Urv = urv;
-        }
-
+        /*! 
+        \code
+        drv  = bdm::RV::from_setting             // decription of observed data 
+        urv  = bdm::RV::from_setting             // decription of input data
+        log_level = "logdt,logut"                // when set, both the simulated data and the inputs are stored to the logger
+                                                 // By default both are on. It makes sense to switch them off for MemDS where the data are already stored.
+        \endcode
+        */
         void from_setting ( const Setting &set );
 

library/bdm/base/datasources.cpp

@@ -23 +23 @@
 }
 
-void MemDS::set_drv ( const RV &drv ) {
-        bdm_assert_debug ( drv._dsize() == Data.rows(), "MemDS::set_rvs incompatible drv" );
-        DS::set_drv ( drv, RV() );
-}
-
 void MemDS::from_setting ( const Setting &set ) {
         DS::from_setting ( set );
@@ -40 +35 @@
 void MemDS::validate()
 {
+        if (Urv._dsize()>0){
+                bdm_error ( "MemDS::urv is not supported" );
+        }
         dtsize = Data.rows();
         utsize = 0;

library/bdm/base/datasources.h

@@ -20 +20 @@
 namespace bdm {
 /*!
-* \brief Memory storage of off-line data column-wise
-
-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.
-
-The data can be loaded from a file.
+* \brief Memory storage of off-line data column-wise (used mostly in C++)
+
+The data are stored in an internal matrix \c Data . E
+ach column of Data corresponds to one discrete time observation \f$t\f$. 
+
 */
 class MemDS : public DS {
@@ -49 +49 @@
         void getdata ( vec &dt, const ivec &indices );
 
-        void set_drv ( const RV &drv );
-
-        void set_drv ( const RV &drv, const RV &urv )
-        {
-                if (urv._dsize()>0){
-                bdm_error ( "MemDS::urv is not supported" );
-                } else {
-                        DS::set_drv(drv,urv);
-                }
-                        
-        }
-
         void write ( const vec &ut ) {
                 if (ut.size()>0){
@@ -77 +65 @@
         /*! Create object from the following structure
         \code
-        DS.class = "MemDS";
-        DS.Data = (...);               % Data matrix or data vector
+        class = "MemDS";
+        Data = (...);               % Data matrix or data vector
            --- optional ---
-        DS.drv = {class="RV"; ...}     % Identification how rows of the matrix Data will be known to others
-        DS.time = 0;                   % Index of the first column to user_info,
-        DS.log_level = "logdt,logut";  % switches to log (or not log) dt or ut
-        }
+        time = 0;                   % Index of the first column to user_info,
+        ...                         % fields from  bdm::DS::from_setting
         \endcode
 
@@ -104 +90 @@
 UIREGISTER ( MemDS );
 
-/*! Pseudovirtual class for reading data from files
+/*! \brief Pseudovirtual class for reading data from files
 
 */
@@ -111 +97 @@
         string filename;
 public:
+        /*! reads what DS::from_setting 
+        \code
+        filename = 'data_file.ext';           // name of the file where the data sare stored
+        the same as #bdm::DS
+        \endcode
+        */
         void from_setting ( const Setting & set );
 };
@@ -144 +136 @@
 /*!
 * \brief CSV file data storage
+
 The constructor creates \c Data matrix from the records in a CSV file \c fname. The orientation can be of two types:
 1. \c BY_COL which is default - the data are stored in columns; one column per time \f$t\f$, one row per data item.
@@ -201 +194 @@
                 dt =  zeros ( iepdf->dimension() );
                 dtsize = dt.length();
-                set_drv ( iepdf->_rv(), RV() );
+                Drv = iepdf->_rv();
                 utsize = 0;
         }
@@ -251 +244 @@
         \code
         class = "PdfDS";
-        pdf = {class="pdf_offspring", ...};  // pdf to simulate
+        pdf = bdm::pdf::from_setting;          // pdf to simulate, any offspring of pdf
         --- optional ---
-        init_rv = {class="RV",names=...};      // define what rv to initialize - typically delayed values!
+        init_rv = bdm::RV::from_setting;       // define what rv to initialize - typically delayed values!
         init_values = [...];                   // vector of initial values corresponding to init_rv
         \endcode
@@ -267 +260 @@
                 // input is what in not in Yrv
                 Urv = rgrv0.subt ( Yrv );
-                set_drv ( concat(Yrv,Urv), Urv );
+                Drv=  concat(Yrv,Urv);
                 // connect input and output to rvc
                 ut2rgr.set_connection ( ipdf->_rvc(), Urv );

library/bdm/mex/mex_datasource.h

@@ -52 +52 @@
                 
                 if (Drv._dsize()!=dtsize){
-                        RV def ( ( const char* ) set["varname"], dtsize );
-                        set_drv ( def, Urv );
+                        Drv=RV( ( const char* ) set["varname"], dtsize );
                 }
                 column = 0;

library/bdm/stat/exp_family.h

@@ -682 +682 @@
 /*! \brief Random Walk with vector Beta distribution
 Using simple assignment
-\f{align} 
-\alpha &= rvc / k + \beta_c \\
-\beta &= (1-rvc) / k + \beta_c \\
-\f{align}
+\f{eqnarray} 
+\alpha &=& rvc / k + \beta_c \\
+\beta &= &(1-rvc) / k + \beta_c \\
+\f{eqnarray}
 for each element of alpha and beta, mean value = rvc, variance = (k+1)*mean*mean;