WIP : output_management

src/walter/output_manager.py

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+"""
+this is output_manager.
+"""
+### Importation de libraries
+import pandas as pd
+from math import pi
+import os
+import os.path
+
+# which_output_files = pd.read_csv(pj(data_dir, "which_output_files.csv"), sep="\t")
+# write_output_file = {"GAI": which_output_files.GAIp[0], "Peraxes": which_output_files.Peraxes[0],
+#                      "Proba": which_output_files.Proba[0], "Apex_Sirius": which_output_files.Apex_sirius[0],
+#                      "Apex": which_output_files.Apex[0], "Apex_R": which_output_files.Apex_R[0],
+#                      "Blade": which_output_files.Blade[0], "Internode": which_output_files.Internode[0],
+#                      "Sheath": which_output_files.Sheath[0], "Ear": which_output_files.Ear[0],
+#                      "Peduncle": which_output_files.Peduncle[0], "PAR_per_axes": which_output_files.PAR_per_axes[0],
+#                      "Lstring": which_output_files.Lstring[0], "Lscene": which_output_files.Lscene[0]}
+# print "ce qu'on ecrit:", write_output_file["Lscene"]
+
+
+### --- Initialisation --- ###
+
+# initialise all the variables at the same time.
+
+class Logger(object):
+    """ Composite class to log the different elements through time during the simulation
+
+    This class has the same interface than Log and contains the set of sub-Log class instances.
+    """
+    loggers = None
+
+    def get_global_loggers(self):
+        if self.loggers is None:
+            Logger()
+        else:
+            return self.loggers
+
+
+    def __init__(self):
+        """ Create all the children classes based on the csv config file"""
+        if self.loggers is None:
+            subclass = [ApexSiriusLog,
+                        ApexRLog,
+                        ApexLog,
+                        BladeLog,
+                        InternodeLog,
+                        SheathLog,
+                        EarLog,
+                        PeduncleLog,
+                        GAILog,
+                        PeraxesLog,
+                        ProbaLog,
+                        DebugLog]
+
+            #Do not check the condition of config_file
+            self.loggers = dict((klass.name, klass()) for klass in subclass)
+
+    def add_ParPerAxesLog(self):
+        """ Add children class in Logger if there isn't defined in the init"""
+        self.loggers[ParPerAxesLog.name] = ParPerAxesLog()
+
+    def write(self, dirname):
+        """Write each logger into a file"""
+        if self.loggers is not None:
+            for subclass in self.loggers.values():
+                subclass.write(dirname)
+
+
+    def log(self, name, **kwds):
+        """log each logger """
+        self.get_global_loggers()
+        self.loggers[name].log(**kwds)
+
+
+
+# ABSTRACT Class
+class Log(object):
+    """
+    Abstract class used to implements the differents subclass
+    """
+    def __init__(self):
+        """
+        Initialize the dictionnary
+        """
+        self.df = dict()
+        for var in self.fields:
+            self.df[var] = []
+
+    def write(self, dirname):
+        """
+        Write the csv file
+        """
+        _df = pd.DataFrame(self.df)
+        df = _df.reindex(self.fields, axis="columns", copy=False)
+        # create or check if the directory exist and create it if not
+
+        if not os.path.exists(dirname):
+            os.makedirs(dirname)
+
+        df.to_csv(os.path.join(dirname, self.name + ".csv"), sep="\t",
+                  header=True, index=False)
+
+    def log(self, **kwargs):
+        for var in self.df:
+            self.df[var].append(kwargs.get(var, None))
+
+
+
+### SUBCLASS - LEGACY OF LOG ###
+
+class GAILog(Log):
+    """
+    Log GAI through time.
+
+    """
+    fields = ["Init_flag", "Elapsed_time", "Temp_cum", "DOY", "Genotype",
+              "Num_plante", "Surface_plante", "Surface_visible", "Surface_sol",
+              "GAI_tot", "GAI_center", "GAI_ind", "GAI_prox", "Position"]
+
+    name = 'GAI'
+
+    def activate(self):
+        """
+        Caribu is enabled
+        """
+        self.fields.append(("Weakest_axis", "PAR_weakest_axis"))
+        self.__init__()
+
+    def __init__(self):
+        """
+        Initialize the GAI output file.
+        """
+        super(GAILog, self).__init__()
+
+
+class ApexSiriusLog(Log):
+    """
+    Log Apex_Sirius throught time
+
+    """
+    fields = ["Elapsed_time","Temperature","Temp_cum","Daylength","Num_plante",
+              "Genotype","PN","LN","Sumtemp","Vern_rate","Vern_prog",
+              "Vern_flag","Debut_ppd_flag","Fin_ppd_flag","Ln_pot","Var_L_min",
+              "Ln_app","Ln_final"]
+
+    name = 'ApexSirius'
+
+    def __init__(self):
+        """
+        Initialize the Apex_Sirius output file
+        """
+        super(ApexSiriusLog, self).__init__()
+
+
+class ApexLog(Log):
+    """
+    Log Apex throught time
+
+    """
+    fields = ["Elapsed_time","Temperature","Temp_cum","Time_count","Sum_temp",
+              "Current_PAR","Num_plante", "Genotype","Num_talle","Num_cohorte",
+              "Nb_phyto_emi","Nb_emerged_leaf","Transiflo_flag",
+              "STOP_init_flag","Transiflo_DOY","Ln_final"]
+    name = 'Apex'
+
+    def __init__(self):
+        """
+        Initialize the Apex_Sirius output file
+        """
+        super(ApexLog, self).__init__()
+
+
+class ApexRLog(Log):
+    """
+    Log Apex throught time
+
+    """
+    fields = ["Elapsed_time","DOY","Temperature","Temp_cum","Sum_temp",
+              "Num_plante","Genotype","Num_cohorte","Ln_final","Num_talle",
+              "Date_epiaison","Epi_DOY","Date_de_flo","Mont_flag","Mont_DOY",
+              "Flo_flag","Flo_DOY","Death_flag","Date_de_maturite", "Mat_DOY"]
+
+    name = 'ApexR'
+
+    def __init__(self):
+        """
+        Initialize the ApexR output file
+        """
+        super(ApexRLog, self).__init__()
+
+
+class BladeLog(Log):
+    """
+    Log Blade throught time
+
+    """
+    fields = ["Elapsed_time","Temp_cum","Temperature","Num_plante","Genotype",
+              "Num_talle","Num_cohorte","Num_rang","Blade_sumtemp","Blade_width",
+              "Blade_length","Blade_visible_length","Blade_final_length",
+              "Blade_visible_surface","Blade_surface","Blade_PAR","Senesc_flag",
+              "Photosynthetic"]
+    name = 'Blade'
+
+    def __init__(self):
+        """
+        Initialize the Blade output file
+        """
+        super(BladeLog, self).__init__()
+
+
+class InternodeLog(Log):
+    """
+    Log Internode throught time
+    """
+    fields = ["Elapsed_time","Temp_cum","Temperature","Num_plante","Genotype",
+              "Num_talle","Num_cohorte","Num_rang","Internode_length",
+              "Internode_final_length","Internode_surface","Internode_PAR",
+              "Photosynthetic"]
+    name = 'Internode'
+
+    def __init__(self):
+        """
+        Initialize the Internode output file
+        """
+        super(InternodeLog, self).__init__()
+
+
+class PeduncleLog(Log):
+    """
+    Log Peduncle throught time
+    """
+    fields = ["Elapsed_time","Temp_cum","Temperature","Num_plante","Genotype",
+              "Num_talle","Num_cohorte","Num_rang", "Sum_temp",
+              "Peduncle_length","Peduncle_final_length","Peduncle_surface",
+              "Peduncle_PAR","Photosynthetic"]
+    name = 'Peduncle'
+
+    def __init__(self):
+        """
+        Initialize the Peduncle output file
+        """
+        super(PeduncleLog, self).__init__()
+
+
+class SheathLog(Log):
+    """
+    Log Sheath throught time
+    """
+    fields = ["Elapsed_time","Temp_cum","Temperature","Num_plante","Genotype",
+              "Num_talle","Num_cohorte","Num_rang","Sheath_sumtemp",
+              "Sheath_diameter","Sheath_length","Sheath_final_length",
+              "Sheath_surface","Sheath_PAR","Photosynthetic"]
+    name = 'Sheath'
+
+    def __init__(self):
+        """
+        Initialize the Sheath output file
+        """
+        super(SheathLog,self).__init__()
+
+
+class EarLog(Log):
+    """
+    Log Ear throught time
+    """
+    fields = ["Elapsed_time","Temp_cum","Temperature","Num_plante","Genotype",
+              "Num_talle","Ear_sumtemp","Ear_length","Ear_surface","Ear_PAR",
+              "Photosynthetic","Emerged"]
+
+    name = 'Ear'
+
+    def __init__(self):
+        """
+        Initialize the Ear output file
+        """
+        super(EarLog, self).__init__()
+
+
+class ProbaLog(Log):
+    """
+    Log Proba throught time
+    """
+    fields = ["Elapsed_time","Temp_cum","Temperature","Num_plante","Genotype",
+              "Num_talle","Ear_sumtemp","Ear_length","Ear_surface","Ear_PAR",
+              "Photosynthetic","Emerged"]
+
+    name = 'Proba'
+
+    def __init__(self):
+        """
+        Initialize the Proba output file
+        """
+        super(ProbaLog, self).__init__()
+
+
+class PeraxesLog(Log):
+    """
+    Log Peraxes throught time
+    """
+    fields = ["Init_flag", "Elapsed_time", "DOY", "Temperature", "Temp_cum", "Num_plante", "Num_talle", "Sheath_max",
+                 "Collar_height", "Dead_collar_height", "Delta_H", "Visible_leaves_surface", "Visible_surface",
+                 "Leaf_contrib_to_GAI", "Stem_contrib_to_GAI", "Ear_contrib_to_GAI", "Peduncle_contrib_to_GAI",
+                 "Stop_growth_flag"]
+
+    name = 'Peraxes'
+
+    def __init__(self):
+        """
+        Initialize the Peraxes output file
+        """
+        super(PeraxesLog, self).__init__()
+
+
+class DebugLog(Log):
+        """
+        Log Debug throught time
+        """
+        fields = ["Elapsed_time", "Temp_cum", "Num_plante", "Num_talle",
+                  "Organ_PAR",
+                  "Organ_type", "Num_organe", "Organ_surface", "Ei"]
+
+        name = 'Debug'
+
+        def __init__(self):
+            """
+            Initialize the Debug output file
+            """
+            super(DebugLog, self).__init__()
+
+
+class ParPerAxesLog(Log):
+    """
+    Log ParPerAxes throught time
+    """
+    fields = ["Elapsed_time", "Temp_cum", "Num_plante", "Num_talle",
+              "Sum_PAR", "Inc_PAR", "Abs_int_PAR"]
+    name = 'ParPerAxes'
+
+    def __init__(self):
+        """
+        Initialize the ParPerAxes output file
+        """
+        super(ParPerAxesLog, self).__init__()
+
+### --- Log