Changeset 907

Timestamp:

04/19/10 12:44:57 (15 years ago)

Author:

mido

Message:

LOG LEVEL improved and hopefully finished

Location:

library

Files:

• bdm/base/bdmbase.cpp (modified) (7 diffs)
• bdm/base/bdmbase.h (modified) (11 diffs)
• bdm/base/datasources.cpp (modified) (4 diffs)
• bdm/base/datasources.h (modified) (3 diffs)
• bdm/base/loggers.cpp (modified) (1 diff)
• bdm/base/loggers.h (modified) (3 diffs)
• bdm/base/user_info.cpp (modified) (2 diffs)
• bdm/base/user_info.h (modified) (12 diffs)
• bdm/bdmroot.cpp (modified) (1 diff)
• bdm/bdmroot.h (modified) (5 diffs)
• bdm/design/ctrlbase.h (modified) (1 diff)
• bdm/estim/kalman.cpp (modified) (1 diff)
• bdm/estim/kalman.h (modified) (1 diff)
• bdm/estim/particles.h (modified) (2 diffs)
• bdm/stat/exp_family.cpp (modified) (2 diffs)
• bdm/stat/exp_family.h (modified) (2 diffs)
• tests/CMakeLists.txt (modified) (1 diff)
• tests/testsuite/datasource_test.cpp (modified) (1 diff)
• tests/testsuite/logger_test.cpp (modified) (4 diffs)

library/bdm/base/bdmbase.cpp

@@ -99 +99 @@
 }
 
+RV::RV ( int sz, int tm ) {
+        Array<string> A ( 1 );
+        A ( 0 ) = "";
+        init ( A, vec_1 ( sz ), vec_1 ( tm ) );
+}
+
 bool RV::add ( const RV &rv2 ) {
         if ( rv2.len > 0 ) { //rv2 is nonempty
@@ -426 +432 @@
 }
 
-int logger::add_vector ( const RV &rv, const string &prefix, const string &name ) {
-        int id;
-        if ( rv._dsize() > 0 ) {
-                id = entries.length();
-                if( name.length() > 0 ) {
-                        names = concat ( names, prefix + separator + name); // diff
-                } else {
-                        names = concat ( names, prefix ); // diff
-                }
-                entries.set_length ( id + 1, true );
-                entries ( id ) = rv;
-        } else {
-                id = -1;
-        }
-        return id; // identifier of the last entry
-}
-
-int logger::add_setting ( const string &prefix ) {
-        Setting &root = setting_conf.getRoot();
-        int id = root.getLength(); //root must be group!!
-        if ( prefix.length() > 0 ) {
-                settings.set_length ( id + 1, true );
-                settings ( id ) = &root.add ( prefix, Setting::TypeList );
-        } else {
-                id = -1;
-        }
-        return id;
+
+string logger::remove_log_prefix_if_possible( string name_with_prefix )
+{
+        string possible_log_prefix = name_with_prefix.substr(0,3);
+        if( possible_log_prefix == "log" )
+                return name_with_prefix.substr(3,name_with_prefix.length()-3);
+        else return name_with_prefix;
 }
 
 void epdf::log_register ( logger &L, const string &prefix ) {
+        root::log_register ( L, prefix );
+
         RV r;
         if ( isnamed() ) {
                 r = _rv();
         } else {
-                r = RV ( "", dimension() );
+                r = RV (  dimension() );
         };
-        root::log_register ( L, prefix );
-
-        // log full data
+
         if ( log_level[logfull] ) {
-                logrec->ids.set_size ( 1 );
-                logrec->ids ( 0 ) = logrec->L.add_setting ( prefix );
+                // log full data
+                registered_logger->add_setting ( log_level, logfull, prefix );
         } else {
                 // log only
-                logrec->ids.set_size ( 3 );
-                if ( log_level[logmean] ) {
-                        logrec->ids ( 0 ) = logrec->L.add_vector ( r, prefix, "mean" );
-                }
-                if ( log_level[loglbound]  ) {
-                        logrec->ids ( 1 ) = logrec->L.add_vector ( r, prefix, "lb" );
-                }       
-                if ( log_level[logubound]  ) {
-                        logrec->ids ( 2 ) = logrec->L.add_vector ( r, prefix, "ub" );
-                }
-        
+
+                if ( log_level[logmean] )
+                        registered_logger->add_vector ( log_level, logmean, r, prefix );                        
+                if ( log_level[loglbound] )
+                        registered_logger->add_vector ( log_level, loglbound, r, prefix );
+                if ( log_level[logubound] )
+                        registered_logger->add_vector ( log_level, logubound, r, prefix );
         }
 }
@@ -486 +468 @@
 void epdf::log_write() const {
         if ( log_level[logfull] ) {
-                UI::save(this,  logrec->L.log_to_setting ( logrec->ids ( 0 ) ) );
+                log_level.store( logfull, this );
         } else {
                 if ( log_level[logmean] ) {
-                        logrec->L.log_vector ( logrec->ids ( 0 ), mean() );
+                        log_level.store( logmean, mean() );
                 }
                 if ( log_level[loglbound] || log_level[logubound] ) {
@@ -496 +478 @@
                                 qbounds ( lb, ub );
                                 if (log_level[loglbound])
-                                        logrec->L.log_vector ( logrec->ids ( 1 ), lb );
+                                        log_level.store( loglbound, lb );
                                 if (log_level[logubound])
-                                        logrec->L.log_vector ( logrec->ids ( 2 ), ub );
+                                        log_level.store( logubound, ub );
                         }
                 }
@@ -543 +525 @@
 
         root::log_register ( L, prefix );
-        //we know that
-        if ( log_level.any() ) {
-                logrec->ids.set_size ( 1 );
-                logrec->ids ( 0 ) = logrec->L.add_vector ( Drv, prefix );
-        //      logrec->ids ( 1 ) = logrec->L.add_vector ( Urv, prefix );
-        }
+
+
+        if ( log_level[logdt] )
+                registered_logger->add_vector ( log_level, logdt, Drv, prefix );        
+        if ( log_level[logut] )
+                registered_logger->add_vector ( log_level, logut, Urv, prefix );
 }
 
 void DS::log_write ( ) const {
-        if ( log_level.any() ) {
+        if( log_level[logdt] ) {
                 vec tmp ( Drv._dsize());
                 getdata ( tmp );
                 // d is first in getdata
-                logrec->L.log_vector ( logrec->ids ( 0 ), tmp );
+                log_level.store( logdt, tmp );
+        }
+        if( log_level[logut] ) { 
+                bdm_warning("We are sorry, but DS::log_write() is not able to log \"ut\" at the moment, would you be so kind and code this functionality?");
+        }
+}
+
+
+void DS::from_setting ( const Setting &set ) {
+        shared_ptr<RV> r = UI::build<RV> ( set, "drv", UI::optional );
+        if ( r )        
+                set_drv ( *r, RV() );
+}
+
+void DS::validate() {
+        if( !Drv._dsize() && dtsize > 0 )
+        {
+                RV *r = new RV();
+                for ( int i = 0; i < dtsize; i++ ) {
+                        r->add ( RV ( "ch" + num2str ( i ), 1, 0 ) );
+                }
+                set_drv ( *r, RV() );
+                delete r;
         }
 }
@@ -563 +567 @@
         root::log_register ( L, prefix );
 
-        if ( log_level.any() ) {
-                logrec->ids.set_size ( 1 );
-                logrec->ids ( 0) = L.add_vector ( RV ( "", 1 ), prefix, "ll" );
-        }
-        
+        if ( log_level[logevidence] )
+                registered_logger->add_vector ( log_level, logevidence, RV ( 1 ), prefix );     
+
         if (log_level[logbounds]){
                 prior().log_level[epdf::loglbound]=true;
@@ -580 +582 @@
 void BM::log_write ( ) const {
         posterior().log_write();
-        if ( log_level.any() ) {
-                logrec->L.logit ( logrec->ids ( 0 ), ll );
-        }
+
+        if( log_level[logevidence] ) 
+                log_level.store( logevidence, ll );
 }
 

library/bdm/base/bdmbase.h

@@ -86 +86 @@
         //! Internal global variable storing names of RVs
         static Array<string> NAMES;
-
         //! TODO
         const static int BUFFER_STEP;
-
         //! TODO
         static str2int_map MAP;
@@ -141 +139 @@
         RV() : dsize ( 0 ), len ( 0 ), ids ( 0 ), times ( 0 ) {}
 
-        //! Constructor of a single RV with given id
+        //! Constructor of a single RV 
         RV ( string name, int sz, int tm = 0 );
+
+        //! Constructor of a single nameless RV 
+        RV ( int sz, int tm = 0 );
 
         // compiler-generated copy constructor is used
@@ -295 +296 @@
 RV concat ( const RV &rv1, const RV &rv2 );
 
+
+//! This class stores a details that will be logged to a logger
+template<class T> class log_level_template : public log_level_base {
+        //! this is necessary to allow logger to set ids vector appropriately and also to set registered_logger
+        friend class logger; 
+
+        //! vector of log IDs - one element for each entry
+        ivec ids;
+
+        //! internal pointer to the logger to which this log_level is registered
+        //! 
+        //! it is set to NULL at the beginning
+        logger * registered_logger;
+
+public:
+        //! default constructor
+        log_level_template() {
+                registered_logger = NULL;
+                ids.set_size(  T::log_level_names().length() );
+                ids = -1;
+        }
+
+        //! This method stores a vector to the proper place in registered logger 
+        void store( const enum T::log_level_enums log_level_enum, const vec &vect ) const
+        {
+                bdm_assert_debug( registered_logger != NULL, "You have to register instance to a logger first! Use root::log_register(...) method.");
+                bdm_assert_debug( ids( log_level_enum ) >= 0, "This particular vector was not added to logger! Use logger::add_vector(...) method.");
+                registered_logger->log_vector( ids( log_level_enum ), vect );
+        }
+
+        //! This method stores a double to the proper place in registered logger 
+        void store( const enum T::log_level_enums log_level_enum, const double &dbl ) const
+        {
+                bdm_assert_debug( registered_logger != NULL, "You have to register instance to a logger first! See root::log_register(...) method.");
+                bdm_assert_debug( ids( log_level_enum ) >= 0, "This particular double was not added to logger! Use logger::add_vector(...) method.");
+                registered_logger->log_double( ids( log_level_enum ), dbl );
+        }
+
+        //! This method stores a Setting obtained by call of UI::save( data, .. ) to the proper place in registered logger 
+        template<class U> void store( const enum T::log_level_enums log_level_enum, const U data ) const
+        {                       
+                bdm_assert_debug( registered_logger != NULL, "You have to register instance to a logger first! See root::log_register(...) method.");
+                bdm_assert_debug( ids( log_level_enum ) >= 0, "This particular vector was not added to logger! Use logger::add_setting(...) method.");
+                registered_logger->log_setting( ids( log_level_enum ), data);
+        }
+
+
+        //! string equivalents of the used enumerations which are filled with a help of #LOG_LEVEL macro within class T
+        const Array<string> &names() const
+        {
+                return T::log_level_names();
+        }
+
+        //! read only operator for testing  individual fields of log_level
+        //!
+        //! it is necessary to acces it with a proper enumeration type, thus this approach is type-safe
+        bool operator [] (const enum T::log_level_enums &log_level_enum ) const
+        {
+                return values[log_level_enum];
+        }
+
+        //! operator for setting an individual field of log_level 
+        //!
+        //! it is necessary to acces it with a proper enumeration type, thus this approach is type-safe
+        bitset<32>::reference operator [] (const enum T::log_level_enums &log_level_enum )
+        {
+                return values[log_level_enum];
+        }
+};
+
+/*!
+  \def LOG_LEVEL(classname,...)
+  \brief Macro for defining a log_level attribute with a specific set of enumerations related to a specific class 
+
+  This macro has to be called within a class declaration. Its argument \a classname has to correspond to that wrapping class.
+  This macro defines a log_level instance which can be modified either directly or by the means of #UI class.
+
+  One of the main purposes of this macro is to allow variability in using enumerations. By relating them to their names through
+  an array of strings, we are no more dependant on their precise ordering. What is more, we can add or remove any without harming 
+  any applications which are using this library.
+
+  \todo Write a more detailed explanation including also examples
+
+  \ref ui
+*/
+#define LOG_LEVEL(classname,...) public: enum log_level_enums { __VA_ARGS__ }; log_level_template<classname> log_level; private: friend class log_level_template<classname>; static const Array<string> &log_level_names() { static const Array<string> log_level_names = log_level_base::string2Array( #__VA_ARGS__ ); return log_level_names; }
+
+
 /*!
 @brief Class for storing results (and semi-results) of an experiment
@@ -301 +390 @@
 */
 class logger : public root {
+private:
+        //! this method removes a "log" prefix from a string, i.e., it transforms "logevidence" to "evidence"
+        //!
+        //! for other cases, it keeps string unchanged
+        static string remove_log_prefix_if_possible( string name_with_prefix );
 protected:
         //! RVs of all logged variables.
@@ -310 +404 @@
         //! list of Settings for specific ids
         Array<Setting*> settings;
-public:
-        //!Default constructor
-        logger ( const string separator0 ) : entries ( 0 ), names ( 0 ), separator ( separator0 ) {}
-
+
+        //! log this instance to Setting
+        //!
+        //! this method has to be called only through \c log_level class to assure the validity of the passed id
+        template<class U> void log_setting ( int id, const U data ) {
+                UI::save(data, *settings ( id ) );
+        }
+
+        //! log this vector 
+        //!
+        //! this method has to be called only through \c log_level class to assure the validity of the passed id
+        virtual void log_vector ( int id, const vec &v ) NOT_IMPLEMENTED_VOID;
+
+        //! log this double
+        //!
+        //! this method has to be called only through \c log_level class to assure the validity of the passed id
+        virtual void log_double ( int id, const double &d ) NOT_IMPLEMENTED_VOID;
+
+        //! it is necessary to allow log_levels to call log_setting, log_vector and log_double methods
+        template<class T> friend class log_level_template;
+public:
         //!separator of prefixes of entries
         //!
@@ -319 +430 @@
         const string separator;
 
-
-        //! 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_vector ( const RV &rv, const string &prefix, const string &name = "" );
-
-        virtual int add_setting ( const string &prefix );
-
-        //! log this vector
-        virtual void log_vector ( int id, const vec &v ) = 0;
-
-        virtual Setting & log_to_setting ( int id ) {
-                return settings ( id )->add ( Setting::TypeGroup );
-        }
-        //! log this double
-        virtual void logit ( int id, const double &d ) = 0;
+        //!Default constructor
+        logger ( const string separator ) : entries ( 0 ), names ( 0 ), separator ( separator ) {}
+
+        //!Destructor calls the finalize method
+        ~logger() {
+                finalize(); 
+        }
+
+        //! sets up the ids identifier in the passed log_level instance to permit future calls of the log_level_template<T>::store(...) method
+        //!
+        //! It also sets a pointer to logger or justify it is correctly assigned from previous call to this procedure 
+        //! Entries with empty RV will be ignored 
+        template<class T> void add_vector ( log_level_template<T> &log_level, enum T::log_level_enums const log_level_enum, const RV &rv, const string &prefix )
+        {
+                if( !log_level.registered_logger )
+                        log_level.registered_logger = this;
+                else
+                        bdm_assert_debug ( log_level.registered_logger == this, "This log_level is already registered to another logger!");
+
+
+                if ( rv._dsize() == 0 ) 
+                        return;
+                
+                int id = entries.length();
+                string adjusted_name = remove_log_prefix_if_possible( log_level.names()(log_level_enum) );
+                names = concat ( names, prefix + separator + adjusted_name ); // diff
+                entries.set_length ( id + 1, true );
+                entries ( id ) = rv;
+                log_level.ids(log_level_enum) = id; 
+        }
+
+        //! sets up the ids identifier in the passed log_level instance to permit future calls of the log_level_template<T>::store(...) method
+        //!
+        //! It also sets a pointer to logger or justify it is correctly assigned from previous call to this procedure 
+        template<class T> void add_setting ( log_level_template<T> &log_level, enum T::log_level_enums const log_level_enum,  const string &prefix ) {
+                if( !log_level.registered_logger )
+                        log_level.registered_logger = this;
+                else
+                        bdm_assert_debug ( log_level.registered_logger == this, "This log_level is already registered to another logger!");
+
+                Setting &root = setting_conf.getRoot(); 
+                int id = root.getLength(); //root must be group!!
+                settings.set_length ( id + 1, true );                   
+                string adjusted_name = remove_log_prefix_if_possible( log_level.names()(log_level_enum) );
+                settings ( id ) = &root.add ( prefix + separator + adjusted_name, Setting::TypeList );          
+                log_level.ids(log_level_enum) = id; 
+        }
 
         //! Shifts storage position for another time step.
@@ -339 +482 @@
 
         //! Finalize storing information
+        //!
+        //! This method is called either directly or via destructor ~logger(), therefore it has to permit repetitive calls for the case it is called twice
         virtual void finalize() {};
 
@@ -344 +489 @@
         virtual void init() {};
 };
-
-
 
 //! Class representing function \f$f(x)\f$ of variable \f$x\f$ represented by \c rv
@@ -907 +1050 @@
 
 class DS : public root {
-        //! \var log_level_enums dt
+        //! \var log_level_enums logdt
         //! TODO DOPLNIT
-        LOG_LEVEL(DS, dt);
+
+        //! \var log_level_enums logut 
+        //! TODO DOPLNIT
+        LOG_LEVEL(DS,logdt,logut);
 
 protected:
@@ -923 +1069 @@
         //! default constructors
         DS() : dtsize ( 0 ), utsize ( 0 ), Drv(), Urv(){
-                log_level[dt] = true;
+                log_level[logdt] = true;
+                log_level[logut] = true;
         };
 
@@ -967 +1114 @@
                 Urv = urv;
         }
+
+        void from_setting ( const Setting &set );
+
+        void validate();
 };
 

library/bdm/base/datasources.cpp

@@ -36 +36 @@
                 time = 0;
         }
-        
-        shared_ptr<RV> r = UI::build<RV> ( set, "drv", UI::optional );
-        if ( !r ) {
-                r = new RV();
-                for ( int i = 0; i < Data.rows(); i++ ) {
-                        r->add ( RV ( "ch" + num2str ( i ), 1, 0 ) );
-                }
-        }
-        
-        set_drv ( *r );
-        dtsize = r->_dsize();
+}
+
+void MemDS::validate()
+{
+        dtsize = Data.rows();
         utsize = 0;
+        DS::validate();
 }
+
 
 void FileDS::from_setting ( const Setting & set ) {
@@ -58 +54 @@
 
         time = 0;
-
-        shared_ptr<RV> r = UI::build<RV> ( set, "drv", UI::optional );
-        if ( !r ) {
-                r = new RV();
-                for ( int i = 0; i < Data.rows(); i++ ) {
-                        r->add ( RV ( "ch" + num2str ( i ), 1, 0 ) );
-                }
-        }
-        
-        set_drv ( *r );
-        dtsize = r->_dsize();
-        utsize = 0;
 }
 
@@ -92 +76 @@
 }
 
+void CsvFileDS::validate() {
+        // TODO NASTASVIT DSIZE, OKOMENTOVAT PRO VOLAM DS::VALIDATE AZ PAK
+}
+
 void ITppFileDS::from_setting ( const Setting & set ) {
         FileDS::from_setting ( set );
@@ -101 +89 @@
         it << Name ( varname );
         it >> Data;
+}
+
+void ITppFileDS::validate() {
+        // TODO NASTASVIT DSIZE, OKOMENTOVAT PRO VOLAM DS::VALIDATE AZ PAK
 }
 

library/bdm/base/datasources.h

@@ -89 +89 @@
         */
         void from_setting ( const Setting &set );
+
+        void validate();
 };
 UIREGISTER ( MemDS );
@@ -127 +129 @@
         // TODO dodelat void to_setting( Setting &set ) const;
 
+        void validate(); 
 };
 
@@ -142 +145 @@
 public:
         void from_setting ( const Setting & set );
+
+        void validate();
 };
 

library/bdm/base/loggers.cpp

@@ -167 +167 @@
 
 void dirfilelog::finalize ( ) {
-        if ( ind > 0 )
+        if ( ind > 0 && !buffers_written) {
                 write_buffers ( ind ); //assuming here that i+1 was not filled
+                buffers_written = true;
+        }
 }
 

library/bdm/base/loggers.h

@@ -34 +34 @@
         //! name of  file to save results (IT file for vectors and cfg for settings)
         string filename;
+
+        //! this flag is only to assure reentrance of the finalize() method 
+        bool file_saved;
 public:
         //! convenience constructor
-        memlog ( int maxlen0, string fn = "" ) : logger ( "_" ), maxlen ( maxlen0 ), ind ( 0 ), vectors ( 0 ), filename ( fn ) {}
+        memlog ( int maxlen0, string fn = "" ) : logger ( "_" ), maxlen ( maxlen0 ), ind ( 0 ), vectors ( 0 ), filename ( fn ), file_saved(false) {}
 
         //!Default constructor
-        memlog() : logger ( "_" ), maxlen ( 0 ), ind ( 0 ), vectors ( 0 ) {}
+        memlog() : logger ( "_" ), maxlen ( 0 ), ind ( 0 ), vectors ( 0 ), file_saved(false) {}
 
         //! Initialize storage
@@ -66 +69 @@
         //!
         void finalize() {
-                if ( filename.length() > 0 ) {
+                if ( filename.length() > 0 && !file_saved ) {
                         itsave ( ( filename + ".it" ).c_str() );
                         if ( settings.length() > 0 ) {
                                 setting_conf.writeFile ( ( filename + ".cfg" ).c_str() );
                         }
+                        file_saved = true;
                 }
 
@@ -153 +157 @@
         //! Automatically generated
         Array<string> scalarnames;
+
+        //! this flag is only to assure reentrance of the finalize() method 
+        bool buffers_written;
 public:
         /*!\brief Default constructor
         @param dirname0 name of the directory in which to store the results
         @param maxlen0 length of the memory buffers, when full the buffers will be dumped to HDD and returned to the beginning. */
-        dirfilelog ( string dirname0, int maxlen0 ) : memlog ( maxlen0 ), dirname ( dirname0 ), scalarnames ( 0 ) {}
+        dirfilelog ( string dirname0, int maxlen0 ) : memlog ( maxlen0 ), dirname ( dirname0 ), scalarnames ( 0 ), buffers_written(false) {}
 
-        dirfilelog() {}
+        dirfilelog() : buffers_written(false) {}
 
         //! Initialize storage

library/bdm/base/user_info.cpp

@@ -235 +235 @@
 }
 
+void UI::save ( const log_level_base &log_level, Setting &element, const string &name ) {
+        assert_type ( element, Setting::TypeGroup );
+
+        string string_to_write;
+
+        Setting *list;
+        if( element.exists( name ) ) 
+        {
+                list = &element[name];
+                assert_type ( *list, Setting::TypeString );
+                string_to_write = ( const char* ) *list;
+        }
+        else
+                list = &element.add ( name, Setting::TypeString ); 
+
+        for( unsigned int i = 0; i < log_level.values.size(); i++ )
+                if( log_level.values[i] ) // a jeste zkontrolovat zda to jmeno uz neni obsazeno? 
+                {
+                        if( string_to_write.length() > 0 )
+                                string_to_write = string_to_write + ',';
+                        string_to_write = string_to_write + log_level.names()(i);
+                }
+                        
+        *list = string_to_write;
+}
+
 void UI::from_setting ( mat& matrix, const Setting &element ) {
         const SettingResolver link ( element );
@@ -367 +393 @@
 }
 
+void UI::from_setting ( log_level_base &log_level, const Setting &element )
+{
+        string raw_log_level;
+        UI::get( raw_log_level, element );
+        Array<string> loaded_log_level = log_level_base::string2Array( raw_log_level );
+        
+        log_level.values.reset();
+
+        for( int i = 0; i < loaded_log_level.length(); i++ )
+                for( int j = 0; j < log_level.names().length(); j++ ){
+                        if( loaded_log_level(i) == log_level.names()(j)  ) 
+                        {
+                                log_level.values[j] = true;
+                                break;
+                        } 
+                }
+}
+
 }//namespace

library/bdm/base/user_info.h

@@ -304 +304 @@
         //! This method converts a Setting into a real scalar   
         static void from_setting ( double &real, const Setting &element );
-
-        //! This method converts a Setting into a specific log_level_template<T> variant and initialize options properly
-        template< class T> static void from_setting ( log_level_template<T> &log_level, const Setting &element )
-        {
-                string raw_log_level;
-                UI::get( raw_log_level, element );
-                Array<string> loaded_log_level = log_level_template<T>::string2Array( raw_log_level );
-                
-                log_level.values.reset();
-
-                for( int i = 0; i < loaded_log_level.length(); i++ )
-                        for( int j = 0; j < log_level.names().length(); j++ ){
-                                if( loaded_log_level(i) == log_level.names()(j)  ) 
-                                {
-                                        log_level.values[j] = true;
-                                        break;
-                                } 
-                        }
-        }
+        //! This method converts a Setting into a log_level variant and initialize options properly
+        static void from_setting ( log_level_base &log_level, const Setting &element );
 
         //! This method converts a Setting into a class T descendant
@@ -374 +357 @@
 
         //! This method converts a Setting into a descendant of class
-        //! T, wrapped in an instance of shared_ptr<T> .
+        //! T, wrapped in an instance of bdm::shared_ptr<T> .
         template<class T>
-        static void from_setting ( shared_ptr<T> &instance, const Setting &element ) {
+        static void from_setting ( bdm::shared_ptr<T> &instance, const Setting &element ) {
                 T *tmp_inst = 0;
                 from_setting ( tmp_inst, element );
@@ -398 +381 @@
         }
 
-
         //! This is dummy version of the from_setting method for other, unsupported types. It just throws an exception.
         //!
         //! At the moment, this is the only way how to compile the library without obtaining the compiler error c2665.
         //! The exception can help to find the place where the template is misused and also to correct it.
-        template<class T> static void from_setting ( T &variable_to_load, const Setting &element ) {
-                std::string msg = "UIException: from_setting is not implemented for type ";
+//      template<class T> static void from_setting ( T &variable_to_load, const Setting &element ) {
+//              std::string msg = "UIException: from_setting is not implemented for type ";
 //              try{
-                        variable_to_load.from_setting(element);
+//                      variable_to_load.from_setting(element);
 /*              } catch (...){
                 msg += typeid ( T ).name();
@@ -412 +394 @@
                 throw UISettingException ( msg, element );
                 }*/
-        }
+//      }
 
 
@@ -432 +414 @@
         //! The new instance of type T* is constructed and initialized with values stored in the Setting element[name]
         //!
-        //! If there is not any sub-element named #name and settingPresence is #optional, an empty shared_ptr<T> is returned. When settingPresence is #compulsory, the returned shared_ptr<T> is never empty (an exception is thrown when the object isn't found).
+        //! If there is not any sub-element named #name and settingPresence is #optional, an empty bdm::shared_ptr<T> is returned. When settingPresence is #compulsory, the returned bdm::shared_ptr<T> is never empty (an exception is thrown when the object isn't found).
         template<class T>
-        static shared_ptr<T> build ( const Setting &element, const string &name, SettingPresence settingPresence = optional ) {
+        static bdm::shared_ptr<T> build ( const Setting &element, const string &name, SettingPresence settingPresence = optional ) {
                 if ( !element.exists ( name ) ) {
                         if ( settingPresence == optional )
-                                return shared_ptr<T>();
+                                return bdm::shared_ptr<T>();
                         else
                                 throw UISettingException ( "UIException: the compulsory Setting named \"" + name + "\" is missing.", element );
                 }
 
-                shared_ptr<T> instance;
+                bdm::shared_ptr<T> instance;
                 from_setting<T> ( instance, to_child_setting ( element, name ) );
                 return instance;
@@ -449 +431 @@
         //! The new instance of type T* is constructed and initialized with values stored in the Setting element[index]
         //!
-        //! If there is not any sub-element indexed by #index, and settingPresence is #optional, an empty shared_ptr<T> is returned. When settingPresence is #compulsory, the returned shared_ptr<T> is never empty (an exception is thrown when the object isn't found).
+        //! If there is not any sub-element indexed by #index, and settingPresence is #optional, an empty bdm::shared_ptr<T> is returned. When settingPresence is #compulsory, the returned bdm::shared_ptr<T> is never empty (an exception is thrown when the object isn't found).
         template<class T>
-        static shared_ptr<T> build ( const Setting &element, const int index, SettingPresence settingPresence = optional ) {
+        static bdm::shared_ptr<T> build ( const Setting &element, const int index, SettingPresence settingPresence = optional ) {
                 if ( element.getLength() <= index ) {
                         if ( settingPresence == optional )
-                                return shared_ptr<T>();
+                                return bdm::shared_ptr<T>();
                         else {
                                 stringstream stream;
@@ -462 +444 @@
                 }
 
-                shared_ptr<T> instance;
+                bdm::shared_ptr<T> instance;
                 from_setting<T> ( instance, to_child_setting ( element, index ) );
                 return instance;
@@ -471 +453 @@
 //! Handy in mex files. Use with care.
         template<class T>
-        static shared_ptr<T> build ( const Setting &element, SettingPresence settingPresence = optional ) {
-                shared_ptr<T> instance;
+        static bdm::shared_ptr<T> build ( const Setting &element, SettingPresence settingPresence = optional ) {
+                bdm::shared_ptr<T> instance;
                 from_setting<T> ( instance,  element );
                 return instance;
@@ -545 +527 @@
                 if ( element.getLength() <= index ) {
                         if ( settingPresence == optional )
-                                return shared_ptr<T>();
+                                return bdm::shared_ptr<T>();
                         else {
                                 stringstream stream;
@@ -590 +572 @@
         }
 
-        template< class T> static void save ( const shared_ptr<T> &instance, Setting &element, const string &name = "" ) {
+        template< class T> static void save ( const bdm::shared_ptr<T> &instance, Setting &element, const string &name = "" ) {
                 save<T> ( instance.get(), element, name );
         }
@@ -603 +585 @@
         }
 
-        // The only difference from classical UserInfo approach to log_level_template is the fact
+        //! A matrix(of type mat) is stored in the new child Setting appended to the passed element
+        static void save ( const mat &matrix, Setting &element, const string &name = "" );
+
+        //! An integer vector (of type ivec) is stored in the new child Setting appended to the passed element
+        static void save ( const ivec &vec, Setting &element, const string &name = "" );
+
+        //! A double vector (of type vec) is stored in the new child Setting appended to the passed element
+        static void save ( const vec &vector, Setting &element, const string &name = "" );
+
+        //! A string is stored in the new child Setting appended to the passed element
+        static void save ( const string &str, Setting &element, const string &name = "" );
+
+        //! An integer is stored in the new child Setting appended to the passed element
+        static void save ( const int &integer, Setting &element, const string &name = "" );
+
+        //! A double is stored in the new child Setting appended to the passed element
+        static void save ( const double &real, Setting &element, const string &name = "" );
+
+// The only difference from classical UserInfo approach to log_level_template is the fact
         // that the actual UI element related to log_level_template could possibly exists yet. In this case, 
         // we do not want to throw an exception like in the case of any other type being loaded
@@ -609 +609 @@
         // possible that more instances of log_level_template class (templated with different classes)
         // can be stored in only one line in a configuration file
-        template< class T> static void save ( const log_level_template<T> &log_level, Setting &element, const string &name = "log_level"  ) {
-                assert_type ( element, Setting::TypeGroup );
-
-                string string_to_write;
-
-                Setting *list;
-                if( element.exists( name ) ) 
-                {
-                        list = &element[name];
-                        assert_type ( *list, Setting::TypeString );
-                        string_to_write = ( const char* ) *list;
-                }
-                else
-                        list = &element.add ( name, Setting::TypeString ); 
-
-                for( unsigned int i = 0; i < log_level.values.size(); i++ )
-                        if( log_level.values[i] ) // a jeste zkontrolovat zda to jmeno uz neni obsazeno? 
-                        {
-                                if( string_to_write.length() > 0 )
-                                        string_to_write = string_to_write + ',';
-                                string_to_write = string_to_write + log_level.names()(i);
-                        }
-                        
-                *list = string_to_write;
-        }
-
-
-        //! A matrix(of type mat) is stored in the new child Setting appended to the passed element
-        static void save ( const mat &matrix, Setting &element, const string &name = "" );
-
-        //! An integer vector (of type ivec) is stored in the new child Setting appended to the passed element
-        static void save ( const ivec &vec, Setting &element, const string &name = "" );
-
-        //! A double vector (of type vec) is stored in the new child Setting appended to the passed element
-        static void save ( const vec &vector, Setting &element, const string &name = "" );
-
-        //! A string is stored in the new child Setting appended to the passed element
-        static void save ( const string &str, Setting &element, const string &name = "" );
-
-        //! An integer is stored in the new child Setting appended to the passed element
-        static void save ( const int &integer, Setting &element, const string &name = "" );
-
-        //! A double is stored in the new child Setting appended to the passed element
-        static void save ( const double &real, Setting &element, const string &name = "" );
+        static void save ( const log_level_base &log_level, Setting &element, const string &name = "log_level"  );
+
         //!@}
 

library/bdm/bdmroot.cpp

@@ -4 +4 @@
 namespace bdm {
         
+        //! a general utility transforming a comma-separated sequence of strings into an instance of Array<strings>
+        Array<string> log_level_base::string2Array( const string &input )
+        {
+                string result = input;
+                string::size_type loc;
+                while( loc = result.find( ',' ), loc != string::npos )
+                        result[loc] = ' ';
+                return Array<string>("{ " + result + " }" );
+        }
+
         void UI_DBG (const  Setting &S, const string &spc, ostream &out =cout){
                 const char *Name=S.getName();

library/bdm/bdmroot.h

@@ -37 +37 @@
 //! auxiliary function for debugging
 void UI_DBG (const Setting &S, const string &spc, ostream &out );
-        
-//! This class stores a details that will be logged to a logger
-template<class T> class log_level_template {
+
+//forward declaration
+class logger;
+
+//! base class for all log_levels
+//!
+//! the existence of this class is forced by the necessity of passing log_levels to user_info methods, however, the main functionality
+//! is located in \c log_level_template class
+class log_level_base
+{
 private:
         // UserInfo class have to be able to read all the internal 
@@ -45 +52 @@
         friend class UI;
 
+protected:
         //! boolean flags related indicating which details will be logged to a logger
         bitset<32> values;
+        
+public:
+
+        //! a general utility transforming a comma-separated sequence of strings into an instance of Array<strings>
+        static Array<string> string2Array( const string &input );
 
         //! string equivalents of the used enumerations which are filled with a help of #LOG_LEVEL macro within class T
-        const Array<string> &names() const
-        {
-                return T::log_level_names();
-        }
-
-public:
-        
-        //! a general utility transforming a comma-separated sequence of strings into an instance of Array<strings>
-        static Array<string> string2Array( const string &input )
-        {
-                string result = input;
-                string::size_type loc;
-                while( loc = result.find( ',' ), loc != string::npos )
-                        result[loc] = ' ';
-                return Array<string>("{ " + result + " }" );
-        }
-
-        //! is any field of log_level active?
-        bool any() const
-        {
-                return values.any();
-        }
-
-        //! read only operator for testing  individual fields of log_level
-        //!
-        //! it is necessary to acces it with a proper enumeration type, thus this approach is type-safe
-        bool operator [] (const enum T::log_level_enums &log_level ) const
-        {
-                return values[log_level];
-        }
-
-        //! operator for setting an individual field of log_level 
-        //!
-        //! it is necessary to acces it with a proper enumeration type, thus this approach is type-safe
-        bitset<32>::reference operator [] (const enum T::log_level_enums &log_level )
-        {
-                return values[log_level];
-        }
+        virtual const Array<string> &names() const = 0;
 };
 
-/*!
-  \def LOG_LEVEL(classname,...)
-  \brief Macro for defining a log_level attribute with a specific set of enumerations related to a specific class 
-
-  This macro has to be called within a class declaration. Its argument \a classname has to correspond to that wrapping class.
-  This macro defines a log_level instance which can be modified either directly or by the means of #UI class.
-
-  One of the main purposes of this macro is to allow variability in using enumerations. By relating them to their names through
-  an array of strings, we are no more dependant on their precise ordering. What is more, we can add or remove any without harming 
-  any applications which are using this library.
-
-  \todo Write a more detailed explanation including also examples
-
-  \ref ui
-*/
-#define LOG_LEVEL(classname,...) public: enum log_level_enums { __VA_ARGS__ }; log_level_template<classname> log_level; private: friend class log_level_template<classname>; static const Array<string> &log_level_names() { static const Array<string> log_level_names = log_level_template<classname>::string2Array( #__VA_ARGS__ ); return log_level_names; }
-
-//forward declaration
-class logger;
-
-//! information about connection to a logger
-class log_record {
-public:
-        //!remember which logger is registered
-        logger &L;
-        //! vector of log IDs - one element for each entry
-        ivec ids;
-
-        //!default constructor
-        log_record ( logger &L0 ) : L ( L0 ), ids ( 0 ) {}
-};
 
 //! Root class of BDM objects
@@ -127 +72 @@
         friend class UI;
 
-        //! This method is a dummy method closely related to to the #LOG_LEVEL macro, do not remove it
-        static const string &log_level_names() 
-        { 
-                static const string log_level_names; 
-                return log_level_names; 
-        }; 
-
 protected:
-        //! record of connections to the logger
-        log_record* logrec;
+        //!remember which logger is registered
+        logger * registered_logger;
 
         /*!     
@@ -217 +155 @@
 
 public:
-        //! This enumeration defines all possible options specifing the level of details logged by a logger about this specific class 
-        //! 
-        //! It has to be reimplemented in descendant classes using the #LOG_LEVEL macro
-        enum log_level_enums { };
-
+        
         //!default constructor
-        root() : logrec ( NULL ) {};
+        root() : registered_logger ( NULL ) {};
 
         //! make sure this is a virtual object
         virtual ~root() {
-                if ( logrec ) delete logrec;
         }
 
@@ -242 +175 @@
         //! The level of details (parameter \c level ) is individual for each class.
         virtual void log_register ( logger &L, const string &prefix ) {
-                logrec = new log_record ( L );
+                registered_logger = &L;
         }
 
         //! Write current information into the given logger
         virtual void log_write() const {
-        }
+        } 
 
         /*!     

library/bdm/design/ctrlbase.h

@@ -36 +36 @@
 
         void from_setting ( const Setting &set ) {
-                UI::get ( rv, set, "rv", UI::optional );
-                UI::get ( rvc, set, "rvc", UI::optional );
+                shared_ptr<RV> rv_ptr = UI::build<RV>( set, "rv", UI::optional );
+                if( rv_ptr ) rv = *rv_ptr;
+                shared_ptr<RV> rvc_ptr = UI::build<RV>( set, "rvc", UI::optional );
+                if( rvc_ptr ) rvc = *rvc_ptr;
         }
         //! access function

library/bdm/estim/kalman.cpp

@@ -120 +120 @@
         vec &_yp = fy._mu();
         //TODO get rid of Q in qr()!
-//      mat Q;
+        //      mat Q;
 
         //R and Q are already set in set_parameters()

library/bdm/estim/kalman.h

@@ -139 +139 @@
                 set_statistics ( mu0, P0 );
                 // Initial values
-                UI::get ( yrv, set, "yrv", UI::optional );
-                UI::get ( rvc, set, "urv", UI::optional );
-                set_yrv ( concat ( yrv, rvc ) );
-
-                validate();
+                shared_ptr<RV> yrv_ptr = UI::build<RV>( set, "yrv", UI::optional );
+                if( !yrv_ptr ) yrv_ptr = new RV();
+                shared_ptr<RV> rvc_ptr = UI::build<RV>( set, "urv", UI::optional );
+                if( !rvc_ptr ) rvc_ptr = new RV();
+                set_yrv ( concat ( *yrv_ptr, *rvc_ptr ) );
         }
         //! validate object

library/bdm/estim/particles.h

@@ -579 +579 @@
 //              void log_register( logger &L, const string &prefix ){
 //                      BM::log_register(L,prefix);
-//                      logrec->ids.set_size ( 3 );
-//                      logrec->ids(1)= L.add_vector(RV("Q",dimension()*dimension()), prefix+L.prefix_sep()+"Q");
-//                      logrec->ids(2)= L.add_vector(RV("R",dimensiony()*dimensiony()), prefix+L.prefix_sep()+"R");
+//                      registered_logger->ids.set_size ( 3 );
+//                      registered_logger->ids(1)= L.add_vector(RV("Q",dimension()*dimension()), prefix+L.prefix_sep()+"Q");
+//                      registered_logger->ids(2)= L.add_vector(RV("R",dimensiony()*dimensiony()), prefix+L.prefix_sep()+"R");
 //                      
 //              };
@@ -599 +599 @@
 //                              
 //                      }
-//                      logrec->L.log_vector ( logrec->ids ( 1 ), cvectorize(mQ) );
-//                      logrec->L.log_vector ( logrec->ids ( 2 ), cvectorize(mR) );
+//                      registered_logger->L.log_vector ( registered_logger->ids ( 1 ), cvectorize(mQ) );
+//                      registered_logger->L.log_vector ( registered_logger->ids ( 2 ), cvectorize(mR) );
 //                      
 //              }

library/bdm/stat/exp_family.cpp

@@ -298 +298 @@
 
 void egiw::log_register ( bdm::logger& L, const string& prefix ) {
-        if ( log_level[tri] ) {
+        if ( log_level[logmean] || log_level[logvariance] ) { 
                 root::log_register ( L, prefix );
-                logrec->ids.set_length ( 2 );
                 int th_dim = dimension() - dimx * ( dimx + 1 ) / 2;
-                logrec->ids ( 0 ) = L.add_vector ( RV ( "", th_dim ), prefix, "mean" );
-                logrec->ids ( 1 ) = L.add_vector ( RV ( "", th_dim * th_dim ), prefix, "variance" );
+
+                if ( log_level[logmean] )
+                        registered_logger->add_vector( log_level, logmean, RV ( th_dim ), prefix ); 
+                if ( log_level[logvariance] )
+                        registered_logger->add_vector( log_level, logvariance, RV ( th_dim * th_dim ), prefix );
         } else {
                 epdf::log_register ( L, prefix );
@@ -310 +312 @@
 
 void egiw::log_write() const {
-        if ( log_level[tri] ) {
+        if ( log_level[logmean] || log_level[logvariance] ) { 
                 mat M;
                 ldmat Lam;
                 ldmat Vz;
                 factorize ( M, Vz, Lam );
-                logrec->L.log_vector ( logrec->ids ( 0 ), est_theta() );
-                logrec->L.log_vector ( logrec->ids ( 1 ), cvectorize ( est_theta_cov().to_mat() ) );
+                if( log_level[logmean] )
+                        log_level.store( logmean, est_theta() );
+                if( log_level[logvariance] )
+                        log_level.store( logvariance, cvectorize ( est_theta_cov().to_mat() ) );
         } else {
                 epdf::log_write();
         }
-
 }
 

library/bdm/stat/exp_family.h

@@ -102 +102 @@
                 BM::to_setting( set );
                 UI::save(frg, set, "frg");
-                // TODO DOPLNIT? ALE MOMENTALNE CHYBI FROM_SETTING PRO INSPIRACI
         } 
+
         void from_setting( const Setting &set) {
                 BM::from_setting(set);
                 if ( !UI::get ( frg, set, "frg" ) )
                         frg = 1.0;
-        
         }
 
@@ -349 +348 @@
 */
 class egiw : public eEF {
-        //! \var log_level_enums tri
+        //! \var log_level_enums logvariance
         //! TODO DOPLNIT
-        LOG_LEVEL(egiw,tri);
+
+        //! \var log_level_enums logmean
+        //! TODO DOPLNIT
+        LOG_LEVEL(egiw,logmean, logvariance);
 
 protected:

library/tests/CMakeLists.txt

@@ -1 +1 @@
 # Make sure the compiler can find include files from our Bdm library.
 include_directories (${BDM_SOURCE_DIR}/bdm)
-include_directories (./unittest-cpp)
+include_directories (${BDM_SOURCE_DIR}/tests/unittest-cpp)
 
 # Make sure the linker can find the Hello library once it is built.
 link_directories (${BDM_BINARY_DIR}/bdm)
-link_directories (./unittest-cpp)
+link_directories (${BDM_BINARY_DIR}/tests/unittest-cpp)
 
 SET(testutil_src general_suite.cpp general_suite.h epdf_harness.cpp epdf_harness.h mat_checks.cpp mat_checks.h 

library/tests/testsuite/datasource_test.cpp

@@ -8 +8 @@
 TEST ( EpdfDS_test ) {
         UIFile uif ( "epdfds.cfg" );
-
         shared_ptr<EpdfDS> ds = UI::build<EpdfDS> ( uif, "ds" );
 

library/tests/testsuite/logger_test.cpp

@@ -32 +32 @@
 }
 
+class log_tester : public root
+{
+        LOG_LEVEL(log_tester,logr,logth,logpol);
+public:
+        RV th, r;
+        int pol, i;
+
+        log_tester() {
+                th = RV ( "{alog blog }" );
+                r = RV ( "{r }", "2" );
+                pol = 11;
+
+                log_level[logr] = true;
+                log_level[logth] = true;
+                log_level[logpol] = true;
+        }
+
+        void log_register( logger &L, const string prefix ) {
+                root::log_register( L, prefix );
+                L.add_vector( log_level, logr, r, prefix );
+                L.add_vector( log_level, logth, th, prefix );
+                L.add_setting( log_level, logpol, prefix );
+        }
+
+        void log_write() const {
+                root::log_write();
+                log_level.store( logr, vec_2 ( ( double ) i, ( double ) ( i + 1 ) ) );
+                log_level.store( logth, vec_2 ( ( double ) ( 100 - i ), ( double ) ( i - 50 ) ) );
+                log_level.store( logpol, pol );
+        }
+
+};
+
 TEST ( memlog_test ) {
-        RV th = RV ( "{alog blog }" );
-        RV r = RV ( "{r }", "2" );
-
         string ls ( "memlog_test" );
         remove_all ( ls.c_str() );
@@ -41 +71 @@
         memlog logger ( 100, ls );
 
-        int pol = 11;
 
-        int rid = logger.add_vector ( r, "" );
-        int thid = logger.add_vector ( th, "th" );
-        int polid = logger.add_setting ( "pols" );
-
+        log_tester tester;
+        tester.log_register( logger, "memlog" );
+        
         logger.init();
 
-        for ( int i = 0; i < 10; i++ ) {
-                logger.log_vector ( rid, vec_2 ( ( double ) i, ( double ) ( i + 1 ) ) );
-                logger.log_vector ( thid, vec_2 ( ( double ) ( 100 - i ), ( double ) ( i - 50 ) ) );
-                UI::save ( pol, logger.log_to_setting ( polid ), "polozka" );
+        for ( tester.i = 0; tester.i < 10; tester.i++ ) {
+                tester.log_write();
                 logger.step();
         }
@@ -63 +89 @@
 
 TEST ( dirfilelog_test ) {
-        RV th = RV ( "{alog blog }" );
-        RV r = RV ( "{r }", "2" );
+
 
         string ls ( "exp" );
@@ -71 +96 @@
         remove_all ( "dirfilelog_files" );
 
-        dirfilelog L ( "dirfilelog_files", 10 );
+        dirfilelog logger ( "dirfilelog_files", 10 );
 
-        int rid = L.add_vector ( r, "" );
-        int thid = L.add_vector ( th, "th" );
+        log_tester tester;
+        tester.log_register( logger, "dirfilelog" );    
 
-        L.init();
+        logger.init();
 
-        for ( int i = 0; i < 150; i++ ) {
-                L.log_vector ( rid, vec_2 ( ( double ) i, ( double ) ( i + 1 ) ) );
-                L.log_vector ( thid, vec_2 ( ( double ) ( 100 - i ), ( double ) ( i - 50 ) ) );
-                L.step();
+        for ( tester.i = 0; tester.i < 150; tester.i++ ) {
+                tester.log_write();
+                logger.step();
         }
 
-        L.finalize();
+        logger.finalize();
 
         std::string expected ( load_test_file ( "logger_test_dirfile_format.matrix" ) );