Merge pull request #1 from ggarin/master

Refacto of Septo3D_v2

example/comparison_mildew_septoria.py

@@ -21,7 +21,7 @@
 
 # Imports for septoria
 from alinea.alep.protocol import *
-from alinea.alep.septoria import plugin_septoria
+from alinea.alep.septo3d_v2 import plugin_septoria
 from alinea.alep.disease_operation import generate_stock_du
 from alinea.alep.disease_outputs import LeafInspector
 from alinea.alep.inoculation import RandomInoculation

example/dispersal_units_functioning.py

@@ -24,7 +24,7 @@
 
 # Imports for septoria
 from alinea.alep.protocol import *
-from alinea.alep.septoria import plugin_septoria
+from alinea.alep.septo3d_v2 import plugin_septoria
 from alinea.alep.disease_operation import generate_stock_du
 from alinea.alep.disease_outputs import LeafInspector, save_image
 from alinea.alep.inoculation import RandomInoculation

example/draw_outputs.py

@@ -6,7 +6,7 @@
     import pickle
 import pandas
 import numpy
-from alinea.alep.septoria import is_iterable
+from alinea.alep.septo3d_v2 import is_iterable
 from collections import OrderedDict
 import matplotlib.pyplot as plt
 from matplotlib import cm

example/example_brown_rust.py

@@ -3,7 +3,7 @@
 """
 from alinea.echap.weather_data import read_weather_year
 from alinea.alep.brown_rust import BrownRustFungus
-from alinea.alep.septoria_age_physio import SeptoriaFungus
+from alinea.alep.septo3d_v2 import SeptoriaFungus
 from alinea.alep.disease_outputs import BrownRustRecorder, plot_by_leaf, conf_int
 from alinea.alep.growth_control import (NoPriorityGrowthControl,
                                         GeometricPoissonCompetition,

example/example_septo_pesticide.py

@@ -14,7 +14,7 @@
 
 # Imports for septoria
 from alinea.alep.protocol import *
-from alinea.alep.septoria import plugin_septoria
+from alinea.alep.septo3d_v2 import plugin_septoria
 from alinea.popdrops.alep_interface import PopDropsEmission, PopDropsTransport
 from alinea.alep.growth_control import PriorityGrowthControl
 from alinea.alep.infection_control import BiotrophDUPositionModel

example/example_septoria.py

@@ -1,7 +1,7 @@
 """ Examples to test consistency of septoria model.
 """
 from alinea.echap.weather_data import read_weather_year
-from alinea.alep.septoria import plugin_septoria
+from alinea.alep.septo3d_v2 import plugin_septoria
 from alinea.alep.disease_outputs import AdelSeptoRecorder, plot_by_leaf, conf_int
 from alinea.alep.growth_control import SeptoRustCompetition
 from alinea.alep.inoculation import AirborneContamination
@@ -55,6 +55,7 @@ def example_surface(nb_steps = 4500, density_lesions = 1, with_compet = False,
     df = weather.data
     df = df.reset_index()
     df = df[df['degree_days']>0]
+    df['date'] = df['datetime']
     g, leaf = get_g_and_one_leaf()
     leaf.area = leaf_area
     leaf.green_area = leaf_area
@@ -251,4 +252,8 @@ def rmse_logi(params = (300., 0.05)):
     x0, k = res.x
     plot(x, linear_growth_list(x))
     plot(x, logistic(x, x0=x0, k=k, Kmax=0.3))
-    return x0, k
+    return x0, k
+
+if __name__ == '__main__':
+    example_surface()
+    plt.show()

example/mem_test.py

@@ -1,10 +1,7 @@
 from alinea.adel.data_samples import adel_two_metamers_stand
-from alinea.alep.fungal_objects import Fungus
 from memory_profiler import profile
 from alinea.alep.septoria_age_physio import *
-import numpy as np
-from septo_decomposed import run_disease
-from variable_septoria import *
+from alinea.alep.simulation_tools.variable_septoria import *
 
 def create_g(leaf_sectors = 1, density = 350, interleaf = 10, 
             leaf_length = 20, leaf_width = 1, Einc = 0):

example/movie_septoria.py

@@ -24,7 +24,7 @@
 
 # Imports for septoria
 from alinea.alep.protocol import *
-from alinea.alep.septoria import plugin_septoria
+from alinea.alep.septo3d_v2 import plugin_septoria
 from alinea.alep.disease_operation import generate_stock_du
 from alinea.alep.inoculation import RandomInoculation
 from alinea.alep.dispersal_emission import SeptoriaRainEmission

example/one_leaf_septo.py

@@ -22,7 +22,7 @@
 
 # Imports for septoria
 from alinea.alep.protocol import *
-from alinea.alep.septoria import plugin_septoria
+from alinea.alep.septo3d_v2 import plugin_septoria
 from alinea.alep.growth_control import NoPriorityGrowthControl
 from alinea.alep.dispersal_emission import SeptoriaRainEmission
 from alinea.alep.disease_outputs import LeafInspector