[1.3.22] 2024-11-01

*Context*
- Methods Context::sumPrimitiveSurfaceArea(), Context::calculatePrimitiveDataAreaWeightedMean(), and Context::calculatePrimitiveDataAreaWeightedSum() to check if primitive area is NaN, and if so exclude it from calculations.
- Added parse_int2(), parse_int3, and parse_RGBcolor functions to global.cpp.
- Added open_xml_file() function to global.cpp that opens an XML file and checks for basic validity.
- Added 'Location' type to helios_vector_types.h to store latitude, longitude, and UTC offset.
- Added Context::listTimeseriesVariables() to return a list of all existing timeseries variables.

*Plant Architecture*
- Some updates to soybean model parameters.
- Added methods to query UUIDs and Object IDs for all plants in the model to avoid having to loop over each plant instance.
- Some additional checks were needed to make sure the tube internode object actually exists in the Context, otherwise there could be an out-of-bounds error.
- Removed the Shoot Parameter 'internode_radius_max', as it is not needed anymore after the pipe-model-based internode girth scaling was added.
- Corrected some issues with reading/writing plants using strings or XML. Namely, some parameters like the phyllotactic angle were not being applied correctly across shoots.
- Added PlantArchitecture::getCurrentPytomerParameters() to make it easy to get all the phytomer parameters structures to pass to PlantArchitecture::generatePlantFromString().

*Radiation*
- Split spectral_data/surface_spectral_library.xml into separate files for soil, leaves, bark, and fruit, and added many new species. Credit to Kyle Rizzo for these additions.
- Some default values were set in RadiationModel.cpp while others were set in RadiationModel.h. Everything was moved to be set in the RadiationModel constructor, which is in RadiationModel.cpp.

*Solar Position*
- Default constructor changed to load the location based on the location set in the Context.
- UTC offset variable changed from int to float type.

*Visualizer*
- Visualizer::printWindow() now creates the output directory if it does not already exist.

core/include/Context.h

@@ -2012,6 +2012,9 @@ class Context{
      \sa setTime(), getTime()
      */
     helios::Time sim_time;
+
+    //! Simulation location (latitude, longitude, UTC offset)
+    helios::Location sim_location;
 
     //! Random number generation engine
     std::minstd_rand0 generator;
@@ -5660,6 +5663,9 @@ class Context{
      */
     bool doesTimeseriesVariableExist( const char* label ) const;
 
+    //! List all existing timeseries variables
+    std::vector<std::string> listTimeseriesVariables() const;
+
     //! Load tabular weather data from text file into timeseries
     void loadTabularTimeseriesData( const std::string &data_file, const std::vector<std::string> &column_labels, const std::string &delimiter, const std::string &date_string_format="YYYYMMDD", uint headerlines=0 );
 
@@ -6024,6 +6030,18 @@ class Context{
      * \sa setTime()
      */
     helios::Time getTime() const;
+
+    //! Set the location of the simulation (latitude, longitude, and UTC offset)
+    /**
+     * \param[in] location Location vector
+     */
+    void setLocation( const helios::Location &location );
+
+    //! Get the location of the simulation (latitude, longitude, and UTC offset)
+    /**
+     * \return Location vector
+     */
+    helios::Location getLocation() const;
 
     //! Draw a random number from a uniform distribution between 0 and 1
     /**

core/include/global.h

@@ -253,6 +253,22 @@ namespace helios{
  */
     bool parse_int( const std::string &input_string, int &converted_int );
 
+//! Convert a string into an int2 with error checking
+/**
+ * \param[in] input_string String to be converted to numerical value
+ * \param[out] converted_int2 Output numerical value converted from input string
+ * \return True if conversion was successful, false if unsuccessful
+ */
+    bool parse_int2( const std::string &input_string, int2 &converted_int2 );
+
+//! Convert a string into an int3 with error checking
+/**
+ * \param[in] input_string String to be converted to numerical value
+ * \param[out] converted_int3 Output numerical value converted from input string
+ * \return True if conversion was successful, false if unsuccessful
+ */
+    bool parse_int3( const std::string &input_string, int3 &converted_int3 );
+
 //! Convert a string into an unsigned integer with error checking
 /**
  * \param[in] input_string String to be converted to numerical value
@@ -277,6 +293,16 @@ namespace helios{
      */
     bool parse_vec3( const std::string &input_string, vec3 &converted_vec3 );
 
+    //! Convert a string into an RGBcolor with error checking
+    /**
+     * \param[in] input_string String to be converted to numerical value
+     * \param[out] converted_rgb Output numerical value converted from input string
+     * \return True if conversion was successful, false if unsuccessful
+     */
+    bool parse_RGBcolor( const std::string &input_string, RGBcolor &converted_rgb );
+
+    bool open_xml_file( const std::string &xml_file, pugi::xml_document &xmldoc, std::string &error_string );
+
     //! Parse an XML tag containing an integer value
     /**
      * \param[in] node XML node containing the tag

core/include/helios_vector_types.h

@@ -1463,6 +1463,69 @@ inline bool Time::operator!=( const Time &c ) const{
    return c.hour!=hour || c.minute!=minute || c.second!=second;
 }
 
+//! Location vector
+/**
+ * \ingroup vectors
+*/
+    struct Location{
+
+        //! Latitude in degrees (+northern hemisphere, -southern hemisphere)
+        float latitude_deg;
+        //! Longitude in degrees (+western hemisphere, -eastern hemisphere)
+        float longitude_deg;
+        //! Offset from UTC in hours (+moving West)
+        float UTC_offset;
+
+        //! Default constructor
+        Location(){
+            latitude_deg = 38.55f;
+            longitude_deg = 121.76f;
+            UTC_offset = 8;
+        }
+
+        //! latitude/longitude/UTC constructor
+        /**
+         * \param[in] hour Hour of day (0-23)
+         * \param[in] minute Minute of hour (0-59)
+        */
+        Location( float latitude_deg, float longitude_deg, float UTC_offset ){
+
+            this->latitude_deg = latitude_deg;
+            this->longitude_deg = longitude_deg;
+            this->UTC_offset = UTC_offset;
+
+        }
+
+        //! check for equality of two locations
+        bool operator==( const helios::Location &c ) const;
+        //! check for inequality of two locations
+        bool operator!=( const helios::Location &c ) const;
+
+        //! Write Location to output stream
+        friend std::ostream &operator<<(std::ostream &os, helios::Location const &t) {
+            return os << "<" << t.latitude_deg << "," << t.longitude_deg << "," << t.UTC_offset << ">";
+        }
+
+    };
+
+//! Make a Location vector
+/**
+ * \param[in] latitude_deg Latitude in degrees (+northern hemisphere, -southern hemisphere)
+ * \param[in] longitude_deg Longitude in degrees (+western hemisphere, -eastern hemisphere)
+ * \param[in] UTC_offset Offset from UTC in hours (+moving West)
+ * \ingroup vectors
+*/
+    inline Location make_Location( float latitude_deg, float longitude_deg, float UTC_offset ){
+        return {latitude_deg,longitude_deg,UTC_offset};
+    }
+
+    inline bool Location::operator==( const Location &c ) const{
+        return c.latitude_deg==latitude_deg && c.longitude_deg==longitude_deg && c.UTC_offset==UTC_offset;
+    }
+
+    inline bool Location::operator!=( const Location &c ) const{
+        return c.latitude_deg!=latitude_deg || c.longitude_deg!=longitude_deg || c.UTC_offset!=UTC_offset;
+    }
 
 //! Vector of spherical coordinates (elevation,azimuth)
 /**

core/src/Context.cpp

@@ -25,6 +25,8 @@ Context::Context(){
 
     sim_time = make_Time(12,0);
 
+    sim_location = make_Location(38.55, 121.76, 8);
+
     // --- Initialize random number generator ---- //
 
     unsigned seed = std::chrono::system_clock::now().time_since_epoch().count();
@@ -1165,6 +1167,14 @@ Time Context::getTime() const{
     return sim_time;
 }
 
+void Context::setLocation( const helios::Location &location ){
+    sim_location = location;
+}
+
+helios::Location Context::getLocation() const{
+    return sim_location;
+}
+
 float Context::randu(){
     return unif_distribution(generator);
 }
@@ -2023,6 +2033,16 @@ bool Context::doesTimeseriesVariableExist( const char* label ) const{
 
 }
 
+std::vector<std::string> Context::listTimeseriesVariables() const{
+    std::vector<std::string> labels;
+    labels.reserve( timeseries_data.size() );
+    for( const auto& it : timeseries_data ){
+        labels.push_back(it.first);
+    }
+    return labels;
+}
+
+
 void Context::getDomainBoundingBox( vec2& xbounds, vec2& ybounds, vec2& zbounds ) const{
 
     xbounds.x = 1e8;