Changeset 1056

Timestamp:

06/07/10 22:00:36 (15 years ago)

Author:

smidl

Message:

Cleanup in datasources

Location:

library/bdm

Files:

• base/datasources.h (modified) (1 diff)
• mex/mex_datasource.h (modified) (2 diffs)

library/bdm/base/datasources.h

@@ -304 +304 @@
 UIREGISTER ( PdfDS );
 
-//! State-space data source simulating two densities
-class StateDS : public DS {
-protected:
-        //!conditional pdf of the state evolution \f$ f(x_t|x_{t-1}) \f$
-        shared_ptr<pdf> IM;
-
-        //!conditional pdf of the observations \f$ f(d_t|x_t) \f$
-        shared_ptr<pdf> OM;
-
-        //! result storage
-        vec dt;
-        //! state storage
-        vec xt;
-        //! input storage
-        vec ut;
-
-        //! datalink from ut to IM.rvc
-        datalink_part u2imc;
-        //! datalink from ut to OM.rvc
-        datalink_part u2omc;
-public:
-        void getdata ( vec &dt0 ) const {
-                dt0 = dt;
-        }
-        void write ( const vec &ut0 ) {
-                ut = ut0;
-        }
-
-        void getdata ( vec &dt0, const ivec &indices ) {
-                dt0 = dt ( indices );
-        }
-
-        virtual void step();
-
-        //! set parameters
-        void set_parameters ( shared_ptr<pdf> IM0, shared_ptr<pdf> OM0 ) {
-                IM = IM0;
-                OM = OM0;
-        }
-        void set_initx ( const vec &x0 ) {
-                xt = x0;
-        }
-
-        virtual void write ( const vec &ut, const ivec &indices ) NOT_IMPLEMENTED_VOID;
-
-        /*! UI for stateDS
-
-        The DS is constructed from a structure with fields:
-        \code
-        class = "stateDS";
-        //Internal model
-        IM = { type = "pdf-offspring"; };
-        //Observation model
-        OM = { type = "pdf-offspring"; }
-        //initial state
-        x0 = [...]; //vector of data
-        \endcode
-        Both models must have defined \c rv. and \c rvc
-        Random variables not found in any rv are considered to be inputs.
-        */
-        void from_setting ( const Setting &set );
-
-        // TODO dodelat void to_setting( Setting &set ) const;
-
-        void validate();
-};
-
-UIREGISTER ( StateDS );
-SHAREDPTR ( StateDS );
-
 }; //namespace
 

library/bdm/mex/mex_datasource.h

@@ -9 +9 @@
 namespace bdm {
 /*!
-* \brief Memory storage of off-line data column-wise
+* \brief DataSource reading data columns from a Matlab matrix 
 
-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.
+The data are stored in a arbitrary Matlab matrix. Each column of the matrix corresponds to one discrete time observation \f$t\f$. 
+The DataSource needs to know the name of the matrix and possibly decription of its contents (via RV)_
 
-The data can be loaded from a file.
 */
-class mxArrayDS : public MemDS {
+class mxArrayDS : public DS {
+        protected:
+                //! raw pointer to data
+                double *data;
+                //! maximum length of data
+                int max_len;
+                //! active column 
+                int column;
 public:
+        
         //!Default constructor
-        mxArrayDS () : MemDS() {};
+        mxArrayDS () : DS() {};
 
-        /*! \brief Create memory data source from mxArray
+        /*! \brief Create data source from mxArray
 
         \code
-        system={
-                type="mexDS";
-                varname="";                // name of workspace variable
-                row_rv = {class='RV',...}  // definition of
-                };
+        class   = 'mxArrayDS';
+        varname = 'data_matrix';         // name of a workspace variable
+        drv     = {class='RV',...}       // names of data in columns
         \endcode
-
-        MemDS with the above fields will be created;
-
+        
         */
         void from_setting ( const Setting &set ) {
-                Data = mxArray2mat ( mexGetVariable ( "base", set["varname"] ) );
-                /*              UI::get ( rowid, set, "rids" , UI::compulsory );
-                                bdm_assert_debug ( max ( rowid ) <= Data.rows(), "MemDS rowid is too high for given Dat." );
-
-                                UI::get ( delays, set, "tds", UI::compulsory );
-                                time = max ( delays );
-                                bdm_assert_debug ( time < Data.cols(), "MemDS delays are too high." );
-                */
-                //set MemDS
-                dtsize = Data.rows();
+                string name;
+                UI::get(name, set, "varname", UI::compulsory);
+                mxArray *mxAr = mexGetVariable ( "base", name.c_str() );
+                
+                bdm_assert(mxIsNumeric(mxAr),"Matlab variable: "+name +" is not a matrix");
+                
+                dtsize = mxGetM(mxAr);
+                max_len= mxGetN(mxAr);
+                data = (double*)mxGetPr(mxAr);
                 utsize = 0;
 
-                shared_ptr<RV> r = UI::build<RV> ( set, "rv", UI::optional );
-                RV ru = RV();
-                if ( r ) {
-                        set_drv ( *r, ru );
-                } else {
-                        RV def ( ( const char* ) set["varname"], Data.rows() );
-                        set_drv ( def, ru );
+                DS::from_setting(set); //read drv
+                
+                if (Drv._dsize()!=dtsize){
+                        RV def ( ( const char* ) set["varname"], dtsize );
+                        set_drv ( def, Urv );
+                }
+                column = 0;
+        
+                if (max_length()>0){
+                        dt = vec(&data[column*dtsize],dtsize);
                 }
         }
 
-
-        // TODO dodelat void to_setting( Setting &set ) const;
+        int max_length() {return max_len;}
+        
+        void step(){
+                if (column<max_length()){
+                        column++;
+                
+                        dt = vec(&data[column*dtsize],dtsize);
+                } else {
+                        bdm_error("DS: trying to read after max_length()");
+                }
+        }
 };
 
@@ -63 +78 @@
 SHAREDPTR ( mxArrayDS );
 
-/*!
-* \brief Matlab wrapper for DS mapping functions step() to a matlab function
-
-The identifier of matlab function is stored in attribute \c name.
-This identifier defines:
-\li function to call to do a step(): name_step.m
-\li workspace variable to write input to: name_input
-*/
-class mexDS : public DS {
-protected:
-        //! identifier of matlab function
-        string step_name;
-        //! identifier of matlab input variabel
-        string input_name;
-        //! cache of results from name_step
-        vec dt;
-        //! cache of inputs
-        vec ut;
-public:
-        //!Default constructor
-        mexDS () : DS() {};
-
-        /*! \brief Data source computed by matlab function
-
-        \code
-        system={
-                class="mexDS";
-                step_name="";              // name of function to call
-                input_name="";             // name of workspace variable where inputs are written
-                drv = {class='RV',...}  // identification of outputs
-                urv = {class='RV',...}   // identification of inputs
-                };
-        \endcode
-
-        MemDS with the above fields will be created;
-
-        */
-        void from_setting ( const Setting &set ) {
-                UI::get ( step_name, set, "step_name", UI::compulsory );
-                UI::get ( input_name, set, "input_name", UI::compulsory );
-
-                shared_ptr<RV> rd = UI::build<RV> ( set, "drv", UI::compulsory );
-                shared_ptr<RV> ru = UI::build<RV> ( set, "urv", UI::compulsory );
-
-                dtsize = rd->_dsize();
-                utsize = ru->_dsize();
-
-                set_drv ( *rd, *ru );
-                validate();
-        }
-
-        virtual void getdata ( vec &dt, const ivec &indices ) NOT_IMPLEMENTED_VOID;
-
-        virtual void write ( const vec &ut, const ivec &indices ) NOT_IMPLEMENTED_VOID;
-
-
-        void step() {
-                mxArray* tmp;
-                mxArray* dummy = NULL;
-                // write inputs to variable input_name
-                mxArray* mxinp = mexGetVariable ( "global", input_name.c_str() ) ;
-                if ( mxinp ) {
-                        if ( ( int ) mxGetM ( mxinp ) != utsize || ( int ) mxGetN ( mxinp ) != utsize ) {
-                                // mxinp is invalid - create new one
-                                mxDestroyArray ( mxinp );
-                                mxinp = mxCreateDoubleMatrix ( utsize, 1, mxREAL );
-                        }
-
-                } else {
-                        mxinp = mxCreateDoubleMatrix ( utsize, 1, mxREAL );
-                }
-                vec2mxArray ( ut, mxinp );
-                mexPutVariable ( "global", input_name.c_str(), mxinp );
-                // call function step_name
-                mexCallMATLAB ( 1, &tmp, 0, ( mxArray ** ) &dummy, step_name.c_str() );
-                // save its results
-                bdm_assert_debug ( ( int ) mxGetM ( tmp ) == dtsize || ( int ) mxGetN ( tmp ) == dtsize, "mexDS.step() expected return vector of length " + num2str ( dtsize ) +
-                                   "got vector " + num2str ( ( int ) mxGetM ( tmp ) ) + "x" + num2str ( ( int ) mxGetN ( tmp ) ) );
-                //write  y
-                dt.set_subvector ( 0, mxArray2vec ( tmp ) );
-                //write u
-        }
-        void write ( const vec &ut0 ) {
-                bdm_assert_debug ( ut0.length() == ut.length(), "mexDS: Incompatible input vector" );
-                ut = ut0;
-        }
-        void getdata ( vec &dt_out ) const {
-                bdm_assert_debug ( dt_out.length() == dt.length(), "mexDS: Incompatible output vector" );
-                dt_out = dt;
-        }
-
-        void validate() {
-                dt = zeros ( dtsize );
-                ut = zeros ( utsize );
-        }
-
-        // TODO dodelat void to_setting( Setting &set ) const;
-};
-
-UIREGISTER ( mexDS );
-SHAREDPTR ( mexDS );
-
 }
 #endif //MXDS_H