Fspm wheat tillers

src/alinea/adel/adel_dynamic.py

@@ -1,7 +1,9 @@
 """ Prototype adel model that uses mtg edition functions"""
+import pandas
+
 from openalea.mtg import MTG
 from alinea.adel.astk_interface import AdelWheat
-from alinea.adel.mtg_editions import find_metamers, add_plant, add_vegetative_metamer, new_mtg_factory, update_organ_elements
+from alinea.adel.mtg_editions import find_metamers, add_axe, add_plant, add_vegetative_metamer, new_mtg_factory, update_organ_elements
 from alinea.adel.AdelR import plantSample
 from alinea.adel.mtg_interpreter import mtg_interpreter, transform_geom
 
@@ -26,13 +28,29 @@ def build_stand(self):
                       axis_properties=ms_properties)
         return g
 
+    def add_tiller(self, g, label='T1', plant_number=1):
+       add_axe(g, label, plant_number)
+       return g
+
+
     def add_metamer(self, g, plant=1, axe='MS'):
         vid_plant, vid_axe, metamers = find_metamers(g, plant, axe)
         nff = g.property('nff')[vid_axe]
         num_metamer = len(metamers)
         df = self.phytoT(axe)
         m = df.loc[df['n'] == num_metamer, :].to_dict('list')
         metamer_properties = {'L_shape': m['Ll'][0]}
+        if 'index_relative_to_MS_phytomer' in self.devT['dimT']:
+            dfd = pandas.DataFrame(self.devT['axeT']).merge(
+                pandas.DataFrame(self.devT['dimT'])).loc[:, (
+                      'id_plt', 'id_axis', 'index_phytomer',
+                      'index_relative_to_MS_phytomer')]
+            metamer_properties.update({'index_relative_to_MS_phytomer':
+                                           dfd.set_index(['id_plt', 'id_axis',
+                                                          'index_phytomer']).loc[
+                                               (plant, axe,
+                                                num_metamer), 'index_relative_to_MS_phytomer']})
+
         ntop = nff - num_metamer + 1
         shape_key = None
         lctype = int(m['Lindex'][0])

src/alinea/adel/astk_interface.py

@@ -1,6 +1,7 @@
 """ Class instanciating a wheat canopy and complying to astk canopy interface
 """
 
+import pandas
 
 from alinea.adel.AdelR import setAdel, RunAdel, genGeoAxe, checkAxeDyn, getAxeT, \
     getPhenT, getPhytoT, saveRData
@@ -104,12 +105,40 @@ def timing(delay, steps, weather, start_date):
                                dt=delay) if not i % delay  else TimeControlSet(
             dt=0) for i in range(steps))
 
-    def setup_canopy(self, age=10):
+    def setup_canopy(self, age=None):
+        """ Create a canopy of a given age
+
+        Args:
+            age: thermal time age of the canopy (simce emergence 1).
+            If None (default) a full grown canopy is returned (TT = last
+            ligulation + 300)
+
+        Returns:
+
+        """
+
+        if age is None:
+            axT = pandas.DataFrame(self.devT['axeT'])
+            phenT = pandas.DataFrame(self.devT['phenT'])
+            axT = axT.loc[axT['TT_stop_axis'] == 'NA']
+            axT = axT.merge(phenT)
+            TT_last_col = (axT['TT_col_phytomer1'] + axT['dTT_col_phytomer']).max()
+            age = TT_last_col + 300
+
 
         self.new_stand(age=age)
 
         if self.duplicate is None:
             canopy = RunAdel(age, self.pars, adelpars=self.run_adel_pars)
+            # add index_relative_to_MS_phytomer to parameters
+            if 'index_relative_to_MS_phytomer' in self.devT['dimT']:
+                dfd = pandas.DataFrame(self.devT['axeT']).merge(
+                    pandas.DataFrame(self.devT['dimT'])).loc[:, (
+                      'id_plt', 'id_axis', 'index_phytomer',
+                      'index_relative_to_MS_phytomer')]
+                canopy = pandas.DataFrame(canopy).merge(dfd.rename(
+                    columns={'id_plt': 'plant', 'id_axis': 'axe_id',
+                             'index_phytomer': 'numphy'})).to_dict('list')
             stand = zip(self.positions, self.plant_azimuths)
             g = self.build_mtg(canopy, stand,
                                aborting_tiller_reduction=self.aborting_tiller_reduction)

src/alinea/adel/mtg_editions.py

@@ -10,6 +10,7 @@
 #
 # ==============================================================================
 """ new mtg edition function (should be integrated in new mtg"""
+# TODO add to adel dressdyn
 from openalea.mtg.traversal import iter_mtg
 from alinea.adel.newmtg import internode_elements, sheath_elements, blade_elements, convert, properties_from_dict, adel_metamer
 from openalea.mtg import MTG, fat_mtg
@@ -523,7 +524,9 @@ def new_mtg_factory(parameters, metamer_factory=adel_metamer, leaf_sectors=1,
             components = metamer_factory(Lsect=leaf_sectors, shape_key=xysr_key,
                                          elongation=elongation, leaves=leaves[species],
                                          **args)
-            args = {'L_shape': args.get('L_shape')}
+            args = {'L_shape': args.get('L_shape'),
+                    'index_relative_to_MS_phytomer': args.get(
+                        'index_relative_to_MS_phytomer')}
         #
         metamer_properties = args
         internode, sheath, blade = None, None, None

src/alinea/adel/newmtg.py

@@ -537,7 +537,9 @@ def mtg_factory(parameters, metamer_factory=adel_metamer, leaf_sectors=1,
             components = metamer_factory(Lsect=leaf_sectors, shape_key=xysr_key,
                                          elongation=elongation,
                                          leaves=leaves[species], **args)
-            args = {'L_shape': args.get('L_shape')}
+            args = {'L_shape': args.get('L_shape'),
+                    'index_relative_to_MS_phytomer': args.get(
+                        'index_relative_to_MS_phytomer')}
         #
         label = 'metamer' + str(num_metamer)
         new_metamer = g.add_component(vid_axe, edge_type='/', label=label,