From cd563c7d2529958847b735589739468ae9853044 Mon Sep 17 00:00:00 2001
From: Christian Fournier <Christian.Fournier@supagro.inra.fr>
Date: Wed, 7 Mar 2018 10:43:02 +0100
Subject: [PATCH 1/7] add todo

---
 src/alinea/adel/mtg_editions.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/alinea/adel/mtg_editions.py b/src/alinea/adel/mtg_editions.py
index 49162fa6..793b5a98 100644
--- a/src/alinea/adel/mtg_editions.py
+++ b/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

From 8b6d9e201cc55c49ffb489fef26fb161d461f5ba Mon Sep 17 00:00:00 2001
From: RomainB <romain.barillot@inra.fr>
Date: Wed, 7 Mar 2018 10:45:15 +0100
Subject: [PATCH 2/7] Add new function add_tiller

---
 src/alinea/adel/adel_dynamic.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/alinea/adel/adel_dynamic.py b/src/alinea/adel/adel_dynamic.py
index bc33c893..3c19e8c3 100644
--- a/src/alinea/adel/adel_dynamic.py
+++ b/src/alinea/adel/adel_dynamic.py
@@ -1,7 +1,7 @@
 """ Prototype adel model that uses mtg edition functions"""
 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
 
@@ -26,6 +26,11 @@ 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]

From 232e1c7c19be32da6617a864fc5c3278f56dc27d Mon Sep 17 00:00:00 2001
From: mngauthier <gauth.marion@gmail.com>
Date: Thu, 8 Mar 2018 11:09:35 +0100
Subject: [PATCH 3/7] CR coding Sprint 180307

---
 CR coding sprint 07-03-18.docx | Bin 0 -> 15608 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 CR coding sprint 07-03-18.docx

diff --git a/CR coding sprint 07-03-18.docx b/CR coding sprint 07-03-18.docx
new file mode 100644
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HcmV?d00001


From b2d541d76c9fd4c1dd39a3c2681f32e18b1c0dfb Mon Sep 17 00:00:00 2001
From: Christian Fournier <Christian.Fournier@supagro.inra.fr>
Date: Thu, 8 Mar 2018 13:49:06 +0100
Subject: [PATCH 4/7] add index_relative_to_MS_phytomer to metamer properties

---
 src/alinea/adel/adel_dynamic.py   | 13 +++++++++++++
 src/alinea/adel/astk_interface.py | 10 ++++++++++
 src/alinea/adel/mtg_editions.py   |  4 +++-
 src/alinea/adel/newmtg.py         |  4 +++-
 4 files changed, 29 insertions(+), 2 deletions(-)

diff --git a/src/alinea/adel/adel_dynamic.py b/src/alinea/adel/adel_dynamic.py
index bc33c893..e9d56dd7 100644
--- a/src/alinea/adel/adel_dynamic.py
+++ b/src/alinea/adel/adel_dynamic.py
@@ -1,4 +1,6 @@
 """ 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
@@ -33,6 +35,17 @@ def add_metamer(self, g, plant=1, axe='MS'):
         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])
diff --git a/src/alinea/adel/astk_interface.py b/src/alinea/adel/astk_interface.py
index abd5cd52..61f6661d 100644
--- a/src/alinea/adel/astk_interface.py
+++ b/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
@@ -101,6 +102,15 @@ def setup_canopy(self, age=10):
 
         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)
diff --git a/src/alinea/adel/mtg_editions.py b/src/alinea/adel/mtg_editions.py
index 793b5a98..9a32e2a9 100644
--- a/src/alinea/adel/mtg_editions.py
+++ b/src/alinea/adel/mtg_editions.py
@@ -514,7 +514,9 @@ 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
diff --git a/src/alinea/adel/newmtg.py b/src/alinea/adel/newmtg.py
index c7029dd8..046f8c6c 100644
--- a/src/alinea/adel/newmtg.py
+++ b/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,

From dc4ea080362f3bfab6c7512e5b075461537d5058 Mon Sep 17 00:00:00 2001
From: Christian Fournier <Christian.Fournier@supagro.inra.fr>
Date: Thu, 8 Mar 2018 14:16:20 +0100
Subject: [PATCH 5/7] use age = last col + 300 as default in setup_canopy

---
 src/alinea/adel/astk_interface.py | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/src/alinea/adel/astk_interface.py b/src/alinea/adel/astk_interface.py
index 61f6661d..0c28d5c3 100644
--- a/src/alinea/adel/astk_interface.py
+++ b/src/alinea/adel/astk_interface.py
@@ -96,7 +96,26 @@ 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)
 

From 6d9c029bfd4fbe0510b8884301b6b6e2c855291f Mon Sep 17 00:00:00 2001
From: Christian Fournier <Christian.Fournier@supagro.inra.fr>
Date: Thu, 8 Mar 2018 15:49:06 +0100
Subject: [PATCH 6/7] add arg to indicate devT units

---
 src/alinea/adel/astk_interface.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/alinea/adel/astk_interface.py b/src/alinea/adel/astk_interface.py
index 0c28d5c3..c39f89ce 100644
--- a/src/alinea/adel/astk_interface.py
+++ b/src/alinea/adel/astk_interface.py
@@ -21,7 +21,7 @@ def __init__(self, devT=None, sample='random', thermal_time_model=None,
                  aborting_tiller_reduction=1.0, ssipars=None,
                  nplants=1, duplicate=None, species=None, nsect=1, leaves=None, stand=None,
                  aspect='smart', split=False,
-                 face_up=False, classic=False, scene_unit='cm',
+                 face_up=False, classic=False, devT_unit='cm', scene_unit='cm',
                  age=None, seed=None,
                  leaf_db=None,
                  positions=None,
@@ -32,6 +32,14 @@ def __init__(self, devT=None, sample='random', thermal_time_model=None,
 
         if devT is None:
             devT = adel_data.devT()
+            devT_unit = 'cm'
+
+        if devT_unit != scene_unit:
+            convert = self.conv_units[devT_unit] / self.conv_units[scene_unit]
+            for x in ('L_internode', 'W_internode', 'W_sheath', 'W_blade', 'L_sheath',
+                      'L_blade'):
+                devT['dimT'][x] *= convert
+
         self.devT = devT
 
         self.ref_plants = list(set(self.devT['axeT']['id_plt']))

From bff7e88de5b4c207bdc1e6a52085d503ecaafb77 Mon Sep 17 00:00:00 2001
From: Christian Fournier <Christian.Fournier@supagro.inra.fr>
Date: Wed, 21 Mar 2018 15:35:14 +0100
Subject: [PATCH 7/7] remove docx (content has been added to Dynamic tillering
 project on GitHub)

---
 CR coding sprint 07-03-18.docx | Bin 15608 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 CR coding sprint 07-03-18.docx

diff --git a/CR coding sprint 07-03-18.docx b/CR coding sprint 07-03-18.docx
deleted file mode 100644
index 007443d51d9556b270674281b1cfa3195538f6a3..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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