def main():
ofname = "fitting_results_%s.csv" % ("Mercado")
results_dir = "results"
data_dir = "data"
plot_dir = "plots"
# Normal way
model = FarquharC3(peaked_Jmax=True, peaked_Vcmax=True, model_Q10=True)
F = FitJmaxVcmaxRd(model, ofname, results_dir, data_dir, plot_dir)
F.main(print_to_screen=True)
# Using Rdark measurement, assuming Rd = Rdark * 0.6
ofname = "fitting_results_%s.csv" % ("Mercado_Rdark")
model = FarquharC3(peaked_Jmax=True, peaked_Vcmax=True)
F = FitJmaxVcmaxKnownRdark(model, ofname, results_dir, data_dir, plot_dir)
F.main(print_to_screen=True)
def main():
#
## Generate some data to estimate V_hat_cmax from
#
deg2kelvin = 273.15
model = FarquharC3(peaked_Jmax=True, peaked_Vcmax=True, model_Q10=True)
Ci = np.arange(0, 1500, 150)
curve = 1
Tleaf = 25.0
Tleaf += deg2kelvin
Jmax25 = 150.0
Vcmax25 = Jmax25 / 1.6
Rd25 = 2.0
Eaj = 30000.0
Eav = 60000.0
deltaSj = 650.0
deltaSv = 650.0
Hdv = 200000.0
Hdj = 200000.0
Q10 = 2.0
(An, Acn, Ajn) = model.calc_photosynthesis(Ci=Ci,
Tleaf=Tleaf,
Par=None,
Jmax=None,
Vcmax=None,
Jmax25=Jmax25,
Vcmax25=Vcmax25,
Rd=None,
Q10=Q10,
Eaj=Eaj,
Eav=Eav,
deltaSj=deltaSj,
deltaSv=deltaSv,
Rd25=Rd25,
Hdv=Hdv,
Hdj=Hdj)
Rd = model.calc_resp(Tleaf, Q10, Rd25, Tref=25.0)
#
## Use Ci at 300
#
V = OnePointVcmax()
Vcmax_est = V.est_vcmax(model, An[2], Rd, Ci[2], Tleaf)
print(Vcmax25, Vcmax_est)
print(fname)
data = np.recfromcsv(fname,
delimiter=delimiter,
names=True,
case_sensitive=True)
return data
##############################
# Fit Eaj, Eav, delSj + delSv
##############################
infname = "results/normalised_results.csv"
ofname = "ea_results.csv"
results_dir = "results"
data_dir = "data"
model = FarquharC3()
peaked = True
############################
# Need to add the groupby column...(JUST FOR THE EXAMPLE!)
data = read_data(infname)
header = ["Jmax", "Vcmax", "Jnorm", "Vnorm", "Rd", "Tav", \
"Tarrh", "R2", "n", "Species", "Leaf", "Curve", \
"Filename", "Season", "fitgroup"]
if os.path.isfile(infname):
os.remove(infname)
fp = open(infname, 'w')
wr = csv.writer(fp, delimiter=',', quoting=csv.QUOTE_NONE, escapechar=' ')
wr.writerow(header)
for row in data:
new_row = []
import os
import sys
import glob
import numpy as np
import matplotlib.pyplot as plt
import csv
from fit_farquhar_model.farquhar_model import FarquharC3
fname = "data2/example2.csv"
fp = open(fname, "wb")
wr = csv.writer(fp, delimiter=',', quoting=csv.QUOTE_NONE, escapechar=' ')
wr.writerow(
["Curve", "Tleaf", "Ci", "Photo", "Par", "Species", "Season", "Leaf"])
deg2kelvin = 273.15
model = FarquharC3(peaked_Jmax=True, peaked_Vcmax=True)
Ci = np.arange(0, 1500, 150)
Par = np.ones(len(Ci)) * 1500.
curve = 1
for Tleaf in np.arange(15.0, 40.0, 5.0):
Tleaf += deg2kelvin
Jmax25 = 150.0
Vcmax25 = Jmax25 / 1.6
r25 = 0.5
Eaj = 30000.0
Eav = 60000.0
deltaSj = 650.0
deltaSv = 650.0
Hdv = 200000.0
Hdj = 200000.0
f = open("/Users/mdekauwe/Desktop/synthetic_data.csv", "w")
print >> f, "Species,Leaf,Curve,Photo,Ci,Tleaf,Season,fitgroup"
for curve_num in np.unique(df["Curve"]):
curve_df = df[df["Curve"] == curve_num]
curve_df = curve_df.sort(['Ci'], ascending=True)
curve_df.index = range(len(curve_df)) # need to reindex slice
#print curve_df["Leaf"][0]
leaf_index = curve_df["Leaf"][0] - 1
Vcmax25 = Vvals[leaf_index]
Jmax25 = Vvals[leaf_index] * Jfac
Rd25 = Vvals[leaf_index] * Rdfac
model = FarquharC3(peaked_Jmax=True, peaked_Vcmax=True, model_Q10=False)
(An, Anc, Anj) = model.calc_photosynthesis(Ci=curve_df["Ci"],
Tleaf=curve_df["Tleaf"],
Par=None,
Jmax=None,
Vcmax=None,
Jmax25=Jmax25,
Vcmax25=Vcmax25,
Rd=None,
Q10=None,
Eaj=Eaj,
Eav=Eav,
deltaSj=delSj,
deltaSv=delSv,
Rd25=Rd25,
Ear=Ear,
Example fit to some synthetic data... That's all folks. """ __author__ = "Martin De Kauwe" __version__ = "1.0 (13.08.2012)" __email__ = "*****@*****.**" import os import sys import glob import numpy as np from fit_farquhar_model.farquhar_model import FarquharC3 from fit_farquhar_model.fit_model import FitJmaxVcmaxRd ############################## # Fit Jmax, Vcmax + Rd ############################## ofname = "fitting_results.csv" results_dir = "results" data_dir = "data2" plot_dir = "plots" Egamma = 37830.0 model = FarquharC3(peaked_Jmax=True, peaked_Vcmax=True, Egamma=Egamma) ############################## F = FitJmaxVcmaxRd(model, ofname, results_dir, data_dir, plot_dir) F.main(print_to_screen=False)
