Refactor parameterisation

src/walter/crop_conception.py

@@ -0,0 +1,205 @@
+"""compute crop_schemes for different configurations"""
+from __future__ import division
+from math import floor, ceil, sqrt
+
+
+def design_crop_classical(nb_plt_temp=1, nb_rang=1, densite=150, dist_inter_rang = 0.135):
+    crop_scheme = {"dist_inter_rang": dist_inter_rang, "density": densite}
+    area = nb_plt_temp / crop_scheme["density"]
+    dy = nb_rang * dist_inter_rang
+    dx = area / dy
+    nb_plante_par_rang = int(nb_plt_temp / nb_rang)
+    dist_intra = dx / nb_plante_par_rang
+    nplant_peupl = int(nb_rang * nb_plante_par_rang)
+    crop_scheme["nplant_peupl"] = nplant_peupl
+    crop_scheme["dx"] = dx
+    crop_scheme["dy"] = dy
+    crop_scheme["surface_sol"] = dx * dy
+    crop_scheme["nb_rang"] = nb_rang
+    crop_scheme["nb_plante_par_rang"] = nb_plante_par_rang
+    crop_scheme["dist_intra_rang"] = dist_intra
+    crop_scheme["real_density"] = nplant_peupl / crop_scheme["surface_sol"]
+    crop_scheme["map_middle_y"] = ((crop_scheme["nb_rang"] * (
+    crop_scheme["dist_inter_rang"]) * 100) + (
+                                   crop_scheme["dist_inter_rang"]) * 100) / 2
+    crop_scheme["map_middle_x"] = ((crop_scheme["nb_plante_par_rang"] * (
+    crop_scheme["dist_intra_rang"]) * 100) + (
+                                   crop_scheme["dist_intra_rang"]) * 100) / 2
+    return crop_scheme
+
+def design_crop_mesh_for_nplants (densite=150, nb_plt_utiles=1, dist_border_x=0, dist_border_y=0):
+    crop_scheme = {"density": densite}
+    nb_rang_utiles = floor(sqrt(nb_plt_utiles))
+    nb_plant_par_rang_utiles = ceil(sqrt(nb_plt_utiles))
+    d_intra = sqrt(1/densite)
+    d_inter = d_intra
+    nb_rang = nb_rang_utiles + ceil((dist_border_x/100)/d_inter) + ceil((dist_border_x/100)/d_inter)
+    nb_plant_par_rang = nb_plant_par_rang_utiles + ceil((dist_border_y/100)/d_intra) + ceil((dist_border_y/100)/d_intra)
+    dx = nb_rang*d_inter
+    dy = nb_plant_par_rang*d_intra
+    nplant_peupl = nb_rang*nb_plant_par_rang
+    crop_scheme["area"] = dx*dy
+    crop_scheme["nb_rang"] = int(nb_rang)
+    crop_scheme["nb_plante_par_rang"] = int(nb_plant_par_rang)
+    crop_scheme["dist_inter_rang"] = d_intra
+    crop_scheme["dist_intra_rang"] = d_intra
+    crop_scheme["dx"] = dx
+    crop_scheme["dy"] = dy
+    crop_scheme["nplant_peupl"] = int(nplant_peupl)
+    crop_scheme["real_density"] = nplant_peupl/crop_scheme["area"]
+    crop_scheme["surface_sol"] = dx*dy
+    crop_scheme["map_middle_y"] = ((crop_scheme["nb_rang"] * (crop_scheme["dist_inter_rang"])*100) + (crop_scheme["dist_inter_rang"])*100)/2
+    crop_scheme["map_middle_x"] = ((crop_scheme["nb_plante_par_rang"] * (crop_scheme["dist_intra_rang"])*100) + (crop_scheme["dist_intra_rang"])*100)/2
+    return crop_scheme
+
+
+def adapting_crop_area(density=150, area_min=1, area_max=13, dist_inter=0.135, opt_plt_nb=10):
+    crop_scheme = {"dist_inter_rang": dist_inter, "density": density}
+    #print "density : ",density, "opt : ",opt_plt_nb, "area_max", area_max
+    if density < (opt_plt_nb/area_max):
+        area_temp = area_max
+        plt_nb_temp = density*area_temp
+    #elif (opt_plt_nb/area_max) < density < 55:
+    #  area_temp = (50/density)
+    #  plt_nb_temp = density*area_temp
+    elif density > (opt_plt_nb/area_min):
+        area_temp = area_min
+        plt_nb_temp = density*area_temp
+    else:
+        #a = (area_max - area_min)/((opt_plt_nb/area_max) - (opt_plt_nb/area_min))
+        #b = area_min - a*(opt_plt_nb/area_min)
+        #area = a * density + b
+        area_temp = (opt_plt_nb/density)
+        plt_nb_temp = density*area_temp
+    nb_rang = int(ceil(sqrt(area_temp)/dist_inter))
+    dy = nb_rang * dist_inter
+    dx = (area_temp/dy)
+    nb_plante_par_rang = int(plt_nb_temp/nb_rang)
+    dist_intra = dx/nb_plante_par_rang
+    nplant_peupl = int(nb_rang*nb_plante_par_rang)
+    crop_scheme["dx"] = dx
+    crop_scheme["dy"] = dy
+    crop_scheme["surface_sol"] = dx*dy
+    crop_scheme["nb_rang"] = nb_rang
+    crop_scheme["nb_plante_par_rang"] = nb_plante_par_rang
+    crop_scheme["dist_intra_rang"] = dist_intra
+    crop_scheme["nplant_peupl"] = nplant_peupl
+    crop_scheme["real_density"] = nplant_peupl/crop_scheme["surface_sol"]
+    crop_scheme["map_middle_y"] = ((crop_scheme["nb_rang"] * (crop_scheme["dist_inter_rang"])*100) + (crop_scheme["dist_inter_rang"])*100)/2
+    crop_scheme["map_middle_x"] = ((crop_scheme["nb_plante_par_rang"] * (crop_scheme["dist_intra_rang"])*100) + (crop_scheme["dist_intra_rang"])*100)/2
+    return crop_scheme
+
+
+def design_crop_Darwinkel(area=1, density=150):
+    crop_scheme = {"area": area, "density": density}
+    nb_rang = floor(sqrt(area * density))
+    nb_plant_par_rang = ceil(sqrt(area * density))
+    d_intra = sqrt(area/(nb_rang*nb_plant_par_rang))
+    dx = nb_rang*d_intra
+    dy = nb_plant_par_rang*d_intra
+    nplant_peupl = nb_rang*nb_plant_par_rang
+    crop_scheme["nb_rang"] = int(nb_rang)
+    crop_scheme["nb_plante_par_rang"] = int(nb_plant_par_rang)
+    crop_scheme["dist_inter_rang"] = d_intra
+    crop_scheme["dist_intra_rang"] = d_intra
+    crop_scheme["dx"] = dx
+    crop_scheme["dy"] = dy
+    crop_scheme["nplant_peupl"] = int(nplant_peupl)
+    crop_scheme["real_density"] = nplant_peupl/area
+    crop_scheme["surface_sol"] = dx*dy
+    crop_scheme["map_middle_y"] = ((crop_scheme["nb_rang"] * (crop_scheme["dist_inter_rang"])*100) + (crop_scheme["dist_inter_rang"])*100)/2
+    crop_scheme["map_middle_x"] = ((crop_scheme["nb_plante_par_rang"] * (crop_scheme["dist_intra_rang"])*100) + (crop_scheme["dist_intra_rang"])*100)/2
+    return crop_scheme
+
+
+def crop_conception(crop_ccptn='Mesh_for_n_plants', densite=150, nb_rang=1,
+                    dist_inter_rang=.135, nb_plt_utiles=1, dist_border_x=0.,
+                    dist_border_y=0, area_targeted=1, area_min=1, area_max=13,
+                    opt_plt_nb=10, nb_plt_temp=1):
+    if crop_ccptn == 'classical':
+        crop_scheme = design_crop_classical(nb_plt_temp, nb_rang, densite,
+                                            dist_inter_rang)
+    elif crop_ccptn == 'Mesh_for_nplants':
+        crop_scheme = design_crop_mesh_for_nplants(densite, nb_plt_utiles,
+                                                   dist_border_x, dist_border_y)
+    elif crop_ccptn == 'Darwinkel_original':
+        crop_scheme = design_crop_Darwinkel(area_targeted, densite)
+    elif crop_ccptn == 'neo_Darwinkel':
+        crop_scheme = adapting_crop_area(densite, area_min, area_max,
+                                         dist_inter_rang, opt_plt_nb)
+    else:
+        raise ValueError('unknown crop_ccptn: ' + crop_ccptn)
+    return crop_scheme
+
+
+#def crop_conception2(densite, dx, dy, dist_inter_rang, area_max):
+#  if dx*dy > area_max:
+#    print "ATTENTION LES DIMENSIONS DE LA PARCELLE SONT TROP GRANDES!"
+#    dx, dy = sqrt(area_max)-0.01, sqrt(area_max)-0.01
+#  nb_rang_m2 = 1/dist_inter_rang
+#  nb_plante_par_rang_m2 = densite/nb_rang_m2
+#  crop_scheme["nb_rang"] = int(floor(dx*nb_rang_m2))
+#  crop_scheme["nb_plante_par_rang"] = int(floor(dy*nb_plante_par_rang_m2))
+#  crop_scheme["dist_intra_rang"] = dy/crop_scheme["nb_plante_par_rang"]
+#  crop_scheme["nplant_peupl"] = crop_scheme["nb_plante_par_rang"]*crop_scheme["nb_rang"]
+#  print crop_scheme
+#  return crop_scheme
+
+# def crop_conception(densite, nb_rang, dist_inter_rang, nb_plante_min,
+#                     nb_plante_max):
+#     crop_scheme = {"dist_inter_rang": dist_inter_rang, "density": densite}
+#     crop_scheme["nb_rang"] = int(nb_rang)
+#     dx = nb_rang * dist_inter_rang
+#     nb_rang_m2 = 1 / dist_inter_rang
+#     nb_plante_par_rang_m2 = densite / nb_rang_m2
+#     dist_intra_rang = 1 / nb_plante_par_rang_m2
+#     nb_plt_p_rang_min = nb_plante_min / nb_rang
+#     nb_plt_p_rang_max = nb_plante_max / nb_rang
+#     crop_scheme["dx"], crop_scheme["dist_intra_rang"] = dx, dist_intra_rang
+#     resultats = {}
+#     if nb_plante_min == nb_plante_max == 1:
+#         nb_plante_par_rang = 1
+#         nb_rang = 1
+#         dx, dy = dist_inter_rang, 1 / nb_plante_par_rang_m2
+#         nplant_peupl = 1
+#         crop_scheme["dy"] = dy
+#         crop_scheme["nb_plante_par_rang"], crop_scheme["nplant_peupl"] = int(
+#             nb_plante_par_rang), int(nplant_peupl)
+#     else:
+#         if round(nb_plt_p_rang_max * dist_intra_rang, 2) - round(
+#                         nb_plt_p_rang_min * dist_intra_rang, 2) < 0.01:
+#             dy = round(nb_plt_p_rang_min * dist_intra_rang, 2)
+#             nb_plante_par_rang = floor(dy * nb_plante_par_rang_m2)
+#             nplant_peupl = nb_rang * nb_plante_par_rang
+#             surface_sol = dx * dy
+#             virtual_density = nplant_peupl / surface_sol
+#             ecart_de_densite = abs(densite - virtual_density) / densite
+#             resultats[ecart_de_densite] = (dx, dy)
+#             crop_scheme["nb_plante_par_rang"], crop_scheme[
+#                 "nplant_peupl"] = int(nb_plante_par_rang), int(nplant_peupl)
+#         else:
+#             for dy in np.arange(round(nb_plt_p_rang_min * dist_intra_rang, 2),
+#                                 round(nb_plt_p_rang_max * dist_intra_rang, 2),
+#                                 0.01):
+#                 nb_plante_par_rang = floor(dy * nb_plante_par_rang_m2)
+#                 nplant_peupl = nb_rang * nb_plante_par_rang
+#                 surface_sol = dx * dy
+#                 virtual_density = nplant_peupl / surface_sol
+#                 ecart_de_densite = abs(densite - virtual_density) / densite
+#                 resultats[ecart_de_densite] = (round(dx, 2), round(dy, 2))
+#             dy = round(resultats[min(resultats.keys())][1], 2)
+#             nb_plante_par_rang = floor(dy * nb_plante_par_rang_m2)
+#             nplant_peupl = nb_rang * nb_plante_par_rang
+#             crop_scheme["nb_plante_par_rang"], crop_scheme[
+#                 "nplant_peupl"] = int(nb_plante_par_rang), int(nplant_peupl)
+#         crop_scheme["dy"] = dy
+#         if min(resultats.keys()) * 100 > 5:
+#             print "ATTENTION ERREUR CONSEQUENTE DE PREDICTION DE LA DENSITE"
+#     crop_scheme["surface_sol"] = dx * dy
+#     crop_scheme["map_middle_y"] = ((crop_scheme["nb_rang"] * (
+#     crop_scheme["dist_inter_rang"]) * 100) + (
+#                                    crop_scheme["dist_inter_rang"]) * 100) / 2
+#     crop_scheme["map_middle_x"] = ((crop_scheme["nb_plante_par_rang"] * (
+#     crop_scheme["dist_intra_rang"]) * 100) + (
+#                                    crop_scheme["dist_intra_rang"]) * 100) / 2
+#     return crop_scheme

src/walter/experimental_conditions.py

@@ -0,0 +1,129 @@
+import datetime
+
+dico_latitudes = {'Gif_sur_Yvette': 48.5, 'Le_Pin_aux_Haras': 48.7,
+                  'Lelystad': 52.5, 'Le_Rheu': 48.1,
+                  'Alenya': 42.6, 'Grignon': 48.8,
+                  'Colmar': 48.1, 'Fagniere': 49, 'Clermont': 45.7,
+                  "Nottingham": 52.9}
+
+experiments = {
+    "Sreten": {"sowing_date": datetime.date(1998, 10, 15),
+               "year": "1999",
+               "meteo": "Grignon",
+               "location": "Grignon",
+               "dist_inter_rang": 0.175,
+               "genotype": ["Soissons"],
+               "Ln_final": {"Soissons": 11}},
+    "Rim1-1": {"sowing_date": datetime.date(2007, 9, 25), "year": "2008",
+               "location": "Grignon", "meteo": "Grignon",
+               "dist_inter_rang": 0.175,
+               "genotype": ["Soissons"], "Ln_final": {"Soissons": 11}},
+    "Rim1-2": {"sowing_date": datetime.date(2007, 11, 12), "year": "2008",
+               "location": "Grignon", "meteo": "Grignon",
+               "dist_inter_rang": 0.175,
+               "genotype": ["Soissons"], "Ln_final": {"Soissons": 11}},
+    "Rim2-1": {"sowing_date": datetime.date(2008, 9, 30), "year": "2009",
+               "location": "Grignon", "meteo": "Grignon",
+               "dist_inter_rang": 0.175,
+               "genotype": ["Soissons"], "Ln_final": {"Soissons": 11}},
+    "Rim2-2": {"sowing_date": datetime.date(2008, 11, 17), "year": "2009",
+               "location": "Grignon", "meteo": "Grignon",
+               "dist_inter_rang": 0.175,
+               "genotype": ["Soissons"], "Ln_final": {"Soissons": 11}},
+    "Jillian": {"sowing_date": datetime.date(2003, 10, 16), "year": "2004",
+                "location": "Grignon", "meteo": "Grignon",
+                "dist_inter_rang": 0.175,
+                "genotype": ["Soissons"], "Ln_final": {"Soissons": 11}},
+    "Jessica": {"sowing_date": datetime.date(2005, 10, 27), "year": "2006",
+                "meteo": "Grignon", "location": "Grignon",
+                "dist_inter_rang": 0.175,
+                "genotype": ["Soissons"], "Ln_final": {"Soissons": 11.3}},
+    "Mariem": {"sowing_date": datetime.date(2010, 10, 26), "year": "1901",
+               "location": "Grignon", "meteo": "Grignon",
+               "dist_inter_rang": 0.175,
+               "genotype": ["Maxwell"], "Ln_final": {"Maxwell": 11.3}},
+    "Darwinkel": {"sowing_date": datetime.date(1976, 10, 19),
+                  "year": "1977", "location": "Lelystad", "meteo": "Lelystad",
+                  "dist_inter_rang": 0.175, "genotype": ["Lely"],
+                  "Ln_final": {"Lely": 11}},
+    "Darwinkel_temp": {"sowing_date": datetime.date(2013, 10, 19),
+                       "year": "1901", "location": "Grignon",
+                       "meteo": "Grignon",
+                       "dist_inter_rang": 0.175, "genotype": ["Maxwell"],
+                       "Ln_final": {"Maxwell": 11}},
+    "Wheatamix-2014": {"sowing_date": datetime.date(2013, 10, 31),
+                       "year": "2014", "location": "Grignon",
+                       "meteo": "Grignon",
+                       "dist_inter_rang": 0.175, "genotype": ["Soissons"],
+                       "Ln_final": {"Soissons": 11}},
+    "Ouitamics-2014": {"sowing_date": datetime.date(2013, 10, 30),
+                       "year": "2014", "location": "Gif_sur_Yvette",
+                       "meteo": "Gif_sur_Yvette",
+                       "dist_inter_rang": 0.15,
+                       "genotype": ["Soissons", "Apache", "Renan",
+                                    "Caphorn", "A208", "A210", "F236",
+                                    "A398"],
+                       "Ln_final": {"Soissons": 11, "Apache": 11, "Renan": 11,
+                                    "Caphorn": 11, "A208": 11, "A210": 11,
+                                    "F236": 11, "A398": 11}},
+    "None": {"sowing_date": datetime.date(2013, 10, 15), "year": "2014",
+             "location": "Gif_sur_Yvette", "meteo": "Gif_sur_Yvette",
+             "dist_inter_rang": 0.1,
+             "genotype": ["Soissons", "Maxwell"],
+             "Ln_final": {"Soissons": 11,"Maxwell": 11}},
+    "Mariem_mean": {"sowing_date": datetime.date(1900, 10, 26),
+                    "year": "1901", "meteo": "Grignon_mean10",
+                    "location": "Grignon",
+                    "dist_inter_rang": 0.175, "genotype": ["Maxwell"],
+                    "Ln_final": {"Maxwell": 11}},
+    "Darwinkel_Grignon_mean": {"sowing_date": datetime.date(1900, 10, 19),
+                               "year": "1901", "meteo": "Grignon_mean10",
+                               "location": "Grignon",
+                               "genotype": ["Maxwell"],
+                               "Ln_final": {"Maxwell": 11}},
+    "Darwinkel_mean": {"sowing_date": datetime.date(1900, 10, 19),
+                       "year": "1901", "meteo": "Lelystad_mean10",
+                       "location": "Lelystad",
+                       "dist_inter_rang": 0.175, "genotype": ["Maxwell"],
+                       "Ln_final": {"Maxwell": 11.3}
+                       },
+    "Sparkes_2001": {"sowing_date": datetime.date(2000, 10, 17),
+                     "year": "2001", "location": "Nottingham",
+                     "meteo": "Nottingham",
+                     "dist_inter_rang": 0.135, "genotype": ["Maxwell"],
+                     "Ln_final": {"Maxwell": 11}},
+    "Sparkes_2002": {"sowing_date": datetime.date(2001, 10, 4),
+                     "year": "2002", "location": "Nottingham",
+                     "meteo": "Nottingham",
+                     "dist_inter_rang": 0.135, "genotype": ["Maxwell"],
+                     "Ln_final": {"Maxwell": 11}},
+    "Sparkes_2003": {"sowing_date": datetime.date(2002, 9, 20),
+                     "year": "2003", "location": "Nottingham",
+                     "meteo": "Nottingham",
+                     "dist_inter_rang": 0.135, "genotype": ["Maxwell"],
+                     "Ln_final": {"Maxwell": 11}},
+    "Association": {"sowing_date": datetime.date(2013, 10, 30),
+                    "year": "2014", "location": "Gif_sur_Yvette",
+                    "meteo": "Gif_sur_Yvette",
+                    "dist_inter_rang": 0.175,
+                    "genotype": ["Gigant_Maxwell", "Darwinkel_Maxwell"],
+                    "Ln_final": {"Gigant_Maxwell": 11, "Darwinkel_Maxwell": 11}},
+    "Sensitivity_Analysis": {"sowing_date": datetime.date(1900, 10, 15),
+                             "year": "1901", "meteo": "Climat_moy_AS",
+                             "location": "Grignon",
+                             "dist_inter_rang": 0.175,
+                             "genotype": ["Maxwell"],
+                             "Ln_final": {"Maxwell": 11.3}},
+}
+
+
+def experimental_conditions(expe_related='Sensitivity_Analysis'):
+    return experiments[expe_related]
+
+
+def liste_expe():
+    return experiments.keys()
+
+
+def get_latitude(location):
+    return dico_latitudes[location]