In [1]:
%matplotlib inline
import os
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import pyemu
instaniate pyemu object and drop prior info. Then reorder the jacobian and save as binary. This is needed because the pest utilities require strict order between the control file and jacobian
In [2]:
la = pyemu.Schur("freyberg.jcb",verbose=False)
la.drop_prior_information()
jco_ord = la.jco.get(la.pst.obs_names,la.pst.par_names)
ord_base = "freyberg_ord"
jco_ord.to_binary(ord_base + ".jco")
la.pst.write(ord_base+".pst")
extract and save the forecast sensitivity vectors
In [3]:
pv_names = []
predictions = ["travel_time", "sw_gw_0","sw_gw_1","sw_gw_2"]
for pred in predictions:
pv = jco_ord.extract(pred).T
pv_name = pred + ".vec"
pv.to_ascii(pv_name)
pv_names.append(pv_name)
save the prior parameter covariance matrix as an uncertainty file
In [4]:
prior_uncfile = "pest.unc"
la.parcov.to_uncfile(prior_uncfile,covmat_file=None)
In [6]:
post_mat = "post.cov"
post_unc = "post.unc"
args = [ord_base + ".pst","1.0",prior_uncfile,
post_mat,post_unc,"1"]
pd7_in = "predunc7.in"
f = open(pd7_in,'w')
f.write('\n'.join(args)+'\n')
f.close()
out = "pd7.out"
pd7 = os.path.join("exe","i64predunc7.exe")
os.system(pd7 + " <" + pd7_in + " >"+out)
for line in open(out).readlines():
print line,
load the posterior matrix written by predunc7
In [8]:
post_pd7 = pyemu.Cov()
post_pd7.from_ascii(post_mat)
la_ord = pyemu.Schur(jco=ord_base+".jco",predictions=predictions)
post_pyemu = la_ord.posterior_parameter
#post_pyemu = post_pyemu.get(post_pd7.row_names)
The cumulative difference between the two posterior matrices:
In [9]:
delta = (post_pd7 - post_pyemu).x
(post_pd7 - post_pyemu).to_ascii("delta.cov")
print delta.sum()
print delta.max(),delta.min()
In [10]:
args = [ord_base + ".pst", "1.0", prior_uncfile, None, "1"]
pd1_in = "predunc1.in"
pd1 = os.path.join("exe", "i64predunc1.exe")
pd1_results = {}
for pv_name in pv_names:
args[3] = pv_name
f = open(pd1_in, 'w')
f.write('\n'.join(args) + '\n')
f.close()
out = "predunc1" + pv_name + ".out"
os.system(pd1 + " <" + pd1_in + ">" + out)
f = open(out,'r')
for line in f:
if "pre-cal " in line.lower():
pre_cal = float(line.strip().split()[-2])
elif "post-cal " in line.lower():
post_cal = float(line.strip().split()[-2])
f.close()
pd1_results[pv_name.split('.')[0].lower()] = [pre_cal, post_cal]
organize the pyemu results into a structure for comparison
In [11]:
pyemu_results = {}
for pname in la_ord.prior_prediction.keys():
pyemu_results[pname] = [np.sqrt(la_ord.prior_prediction[pname]),
np.sqrt(la_ord.posterior_prediction[pname])]
compare the results:
In [12]:
f = open("predunc1_textable.dat",'w')
for pname in pd1_results.keys():
print pname
f.write(pname+"&{0:6.5f}&{1:6.5}&{2:6.5f}&{3:6.5f}\\\n"\
.format(pd1_results[pname][0],pyemu_results[pname][0],
pd1_results[pname][1],pyemu_results[pname][1]))
print "prior",pname,pd1_results[pname][0],pyemu_results[pname][0]
print "post",pname,pd1_results[pname][1],pyemu_results[pname][1]
f.close()
In [18]:
f = open("pred_list.dat",'w')
out_files = []
for pv in pv_names:
out_name = pv+".predvar1b.out"
out_files.append(out_name)
f.write(pv+" "+out_name+"\n")
f.close()
args = [ord_base+".pst","1.0","pest.unc","pred_list.dat"]
for i in xrange(36):
args.append(str(i))
args.append('')
args.append("n")
args.append("n")
args.append("y")
args.append("n")
args.append("n")
f = open("predvar1b.in", 'w')
f.write('\n'.join(args) + '\n')
f.close()
os.system("exe\\predvar1b.exe <predvar1b.in")
Out[18]:
In [19]:
pv1b_results = {}
for out_file in out_files:
pred_name = out_file.split('.')[0]
f = open(out_file,'r')
for _ in xrange(3):
f.readline()
arr = np.loadtxt(f)
pv1b_results[pred_name] = arr
now for pyemu
In [22]:
omitted_parameters = [pname for pname in la.pst.parameter_data.parnme if pname.startswith("wf")]
la_ord_errvar = pyemu.ErrVar(jco=ord_base+".jco",
predictions=predictions,
omitted_parameters=omitted_parameters,
verbose=False)
df = la_ord_errvar.get_errvar_dataframe(np.arange(36))
df
Out[22]:
generate some plots to verify
In [23]:
fig = plt.figure(figsize=(6,6))
max_idx = 15
idx = np.arange(max_idx)
for ipred,pred in enumerate(predictions):
arr = pv1b_results[pred][:max_idx,:]
first = df[("first", pred)][:max_idx]
second = df[("second", pred)][:max_idx]
third = df[("third", pred)][:max_idx]
ax = plt.subplot(len(predictions),1,ipred+1)
#ax.plot(arr[:,1],color='b',dashes=(6,6),lw=4,alpha=0.5)
#ax.plot(first,color='b')
#ax.plot(arr[:,2],color='g',dashes=(6,4),lw=4,alpha=0.5)
#ax.plot(second,color='g')
#ax.plot(arr[:,3],color='r',dashes=(6,4),lw=4,alpha=0.5)
#ax.plot(third,color='r')
ax.scatter(idx,arr[:,1],marker='x',s=40,color='g',
label="PREDVAR1B - first term")
ax.scatter(idx,arr[:,2],marker='x',s=40,color='b',
label="PREDVAR1B - second term")
ax.scatter(idx,arr[:,3],marker='x',s=40,color='r',
label="PREVAR1B - third term")
ax.scatter(idx,first,marker='o',facecolor='none',
s=50,color='g',label='pyEMU - first term')
ax.scatter(idx,second,marker='o',facecolor='none',
s=50,color='b',label="pyEMU - second term")
ax.scatter(idx,third,marker='o',facecolor='none',
s=50,color='r',label="pyEMU - third term")
ax.set_ylabel("forecast variance")
ax.set_title("forecast: " + pred)
if ipred == len(predictions) -1:
ax.legend(loc="lower center",bbox_to_anchor=(0.5,-0.75),
scatterpoints=1,ncol=2)
ax.set_xlabel("singular values")
#break
plt.savefig("predvar1b_ver.eps")
In [24]:
cmd_args = [os.path.join("exe","i64identpar.exe"),ord_base,"5",
"null","null","ident.out","/s"]
cmd_line = ' '.join(cmd_args)+'\n'
print(cmd_line)
print(os.getcwd())
os.system(cmd_line)
Out[24]:
In [25]:
identpar_df = pd.read_csv("ident.out",delim_whitespace=True)
In [28]:
la_ord_errvar = pyemu.ErrVar(jco=ord_base+".jco",
predictions=predictions,
verbose=False)
df = la_ord_errvar.get_identifiability_dataframe(5)
df
Out[28]:
cheap plot to verify
In [29]:
fig = plt.figure()
ax = plt.subplot(111)
axt = plt.twinx()
ax.plot(identpar_df["identifiability"])
ax.plot(df["ident"])
ax.set_xlim(-10,600)
diff = identpar_df["identifiability"].values - df["ident"].values
#print(diff)
axt.plot(diff)
axt.set_ylim(-1,1)
ax.set_xlabel("parmaeter")
ax.set_ylabel("identifiability")
axt.set_ylabel("difference")
Out[29]:
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