def draw(self, cov, num_reals=1, names=None):
""" draw random realizations from a multivariate
Gaussian distribution
Parameters:
----------
cov: a Cov instance
covariance structure to draw from
num_reals: int
number of realizations to generate
names : list of names to draw for. If None, values all names
are drawn
Returns:
-------
None
"""
# set up some realization names
#real_names = ["{0:d}".format(i)
# for i in range(num_reals)]
real_names = np.arange(num_reals, dtype=np.int64)
# make sure everything is cool WRT ordering
if names is not None:
vals = self.mean_values.loc[names]
cov = cov.get(names)
elif self.names != cov.row_names:
names = get_common_elements(self.names, cov.row_names)
vals = self.mean_values.loc[names]
cov = cov.get(names)
pass
else:
vals = self.mean_values
names = self.names
# generate random numbers
if cov.isdiagonal: #much faster
val_array = np.array([np.random.normal(mu,std,size=num_reals) for\
mu,std in zip(vals,np.sqrt(cov.x))]).transpose()
#for mu,std in zip(vals,np.sqrt(cov.x)):
# val_array.append(np.random.normal(mu,std,size=num_reals))
#val_array = np.array(val_array).transpose()
else:
val_array = np.random.multivariate_normal(vals, cov.as_2d,
num_reals)
self.loc[:, :] = np.NaN
self.dropna(inplace=True)
# this sucks - can only set by enlargement one row at a time
for rname, vals in zip(real_names, val_array):
self.loc[rname, names] = vals
# set NaNs to mean_values
idx = pd.isnull(self.loc[rname, :])
self.loc[rname, idx] = self.mean_values[idx]
def draw(self,cov,num_reals=1):
""" draw random realizations from a multivariate
Gaussian distribution
Parameters:
----------
cov: a Cov instance
covariance structure to draw from
num_reals: int
number of realizations to generate
Returns:
-------
None
"""
# set up some column names
real_names = ["{0:d}".format(i)
for i in range(num_reals)]
# make sure everything is cool WRT ordering
if self.names != cov.row_names:
common_names = get_common_elements(self.names,
cov.row_names)
vals = self.mean_values.loc[common_names]
cov = cov.get(common_names)
pass
else:
vals = self.mean_values
common_names = self.names
# generate random numbers
val_array = np.random.multivariate_normal(vals, cov.as_2d,num_reals)
self.loc[:,:] = np.NaN
self.dropna(inplace=True)
# this sucks - can only set by enlargement one row at a time
for rname,vals in zip(real_names,val_array):
self.loc[rname,common_names] = vals
# set NaNs to mean_values
idx = pd.isnull(self.loc[rname,:])
self.loc[rname,idx] = self.mean_values[idx]
def from_gaussian_draw(cls, pe, cov, num_reals=1):
""" this is an experiemental method to help speed up draws
for a really large (>1E6) ensemble sizes. gets around the
dataframe expansion-by-loc that is one col at a time. WARNING:
this constructor transforms the pe argument!
:param pe: ParameterEnsemble instance
"param cov: Covariance instance
:param num_reals: number of realizations to generate
:return: ParameterEnsemble
"""
# set up some column names
real_names = ["{0:d}".format(i) for i in range(num_reals)]
if not pe.istransformed:
pe._transform()
# make sure everything is cool WRT ordering
if pe.names != cov.row_names:
common_names = get_common_elements(pe.names, cov.row_names)
vals = pe.mean_values.loc[common_names]
cov = cov.get(common_names)
pass
else:
vals = pe.mean_values
common_names = pe.names
vals = pe.mean_values
df = pd.DataFrame(data=np.random.multivariate_normal(
vals, cov.as_2d, num_reals),
columns=common_names,
index=real_names)
# replace the realizations for fixed parameters with the original
# parval1 in the control file
pe.pst.parameter_data.index = pe.pst.parameter_data.parnme
fixed_vals = pe.pst.parameter_data.loc[pe.fixed_indexer, "parval1"]
for fname, fval in zip(fixed_vals.index, fixed_vals.values):
df.loc[:, fname] = fval
istransformed = pe.pst.parameter_data.loc[:, "partrans"] == "log"
df.loc[:, istransformed] = 10.0**df.loc[:, istransformed]
return cls.from_dataframe(pst=pe.pst, df=df)
def draw(self, cov, num_reals=1):
""" draw random realizations from a multivariate
Gaussian distribution
Parameters:
----------
cov: a Cov instance
covariance structure to draw from
num_reals: int
number of realizations to generate
Returns:
-------
None
"""
# set up some column names
real_names = ["{0:d}".format(i) for i in range(num_reals)]
# make sure everything is cool WRT ordering
if self.names != cov.row_names:
common_names = get_common_elements(self.names, cov.row_names)
vals = self.mean_values.loc[common_names]
cov = cov.get(common_names)
pass
else:
vals = self.mean_values
common_names = self.names
# generate random numbers
val_array = np.random.multivariate_normal(vals, cov.as_2d, num_reals)
self.loc[:, :] = np.NaN
self.dropna(inplace=True)
# this sucks - can only set by enlargement one row at a time
for rname, vals in zip(real_names, val_array):
self.loc[rname, common_names] = vals
# set NaNs to mean_values
idx = pd.isnull(self.loc[rname, :])
self.loc[rname, idx] = self.mean_values[idx]
def project(self, projection_matrix, inplace=True, log=None, enforce=True):
""" project the ensemble
Parameters:
----------
projection_matrix: (pyemu.Matrix) projection operator - must already respect log transform
inplace: (boolean) project self or return a new ParameterEnsemble instance
log: (pyemu.la.logger instance) for logging progress
enforce: (bool) parameter bound enforcement flag (True)
Returns:
-------
if not inplace, ParameterEnsemble, otherwise None
"""
if not self.istransformed:
self._transform()
#make sure everything is cool WRT ordering
common_names = get_common_elements(self.adj_names,
projection_matrix.row_names)
base = self.mean_values.loc[common_names]
projection_matrix = projection_matrix.get(common_names, common_names)
if not inplace:
new_en = ParameterEnsemble(pst=self.pst.get(),
data=self.loc[:, :].copy(),
columns=self.columns,
mean_values=self.mean_values.copy(),
istransformed=self.istransformed)
for real in self.index:
if log is not None:
log("projecting realization {0}".format(real))
# null space projection of difference vector
pdiff = np.dot(projection_matrix.x,
(self.loc[real,common_names] - base)\
.as_matrix())
# lb_fac = np.abs(pdiff)/((base+pdiff)-self.lbnd)
# lb_fac[pdiff>0.0] = 1.0
#
# ub_fac = np.abs(pdiff)/(self.ubnd-(base+pdiff))
# ub_fac[pdiff<=0.0] = 1.0
#
# factor = max(lb_fac.max(),
# ub_fac.max())
if inplace:
self.loc[real, common_names] = base + pdiff
else:
new_en.loc[real, common_names] = base + pdiff
if log is not None:
log("projecting realization {0}".format(real))
if not inplace:
if enforce:
new_en.enforce()
new_en._back_transform()
return new_en
if enforce:
self.enforce()
self._back_transform()
def project(self,projection_matrix,inplace=True,log=None,enforce=True):
""" project the ensemble
Parameters:
----------
projection_matrix: (pyemu.Matrix) projection operator - must already respect log transform
inplace: (boolean) project self or return a new ParameterEnsemble instance
log: (pyemu.la.logger instance) for logging progress
enforce: (bool) parameter bound enforcement flag (True)
Returns:
-------
if not inplace, ParameterEnsemble, otherwise None
"""
if not self.istransformed:
self._transform()
#make sure everything is cool WRT ordering
common_names = get_common_elements(self.adj_names,
projection_matrix.row_names)
base = self.mean_values.loc[common_names]
projection_matrix = projection_matrix.get(common_names,common_names)
if not inplace:
new_en = ParameterEnsemble(pst=self.pst.get(),data=self.loc[:,:].copy(),
columns=self.columns,
mean_values=self.mean_values.copy(),istransformed=self.istransformed)
for real in self.index:
if log is not None:
log("projecting realization {0}".format(real))
# null space projection of difference vector
pdiff = np.dot(projection_matrix.x,
(self.loc[real,common_names] - base)\
.as_matrix())
# lb_fac = np.abs(pdiff)/((base+pdiff)-self.lbnd)
# lb_fac[pdiff>0.0] = 1.0
#
# ub_fac = np.abs(pdiff)/(self.ubnd-(base+pdiff))
# ub_fac[pdiff<=0.0] = 1.0
#
# factor = max(lb_fac.max(),
# ub_fac.max())
if inplace:
self.loc[real,common_names] = base + pdiff
else:
new_en.loc[real,common_names] = base + pdiff
if log is not None:
log("projecting realization {0}".format(real))
if not inplace:
if enforce:
new_en.enforce()
new_en._back_transform()
return new_en
if enforce:
self.enforce()
self._back_transform()
def project(self,
projection_matrix,
inplace=True,
log=None,
enforce_bounds="reset"):
""" project the ensemble
Parameters:
----------
projection_matrix: (pyemu.Matrix) projection operator - must already respect log transform
inplace: (boolean) project self or return a new ParameterEnsemble instance
log: (pyemu.la.logger instance) for logging progress
enforce_bounds: (str) parameter bound enforcement flag. 'drop' removes
offending realizations, 'reset' resets offending values)
Returns:
-------
if not inplace, ParameterEnsemble, otherwise None
"""
if self.istransformed:
self._back_transform()
istransformed = self.pst.parameter_data.loc[:, "partrans"] == "log"
self.loc[:, istransformed] = self.loc[:, istransformed].applymap(
lambda x: math.log10(x))
self.__istransformed = True
#make sure everything is cool WRT ordering
common_names = get_common_elements(self.adj_names,
projection_matrix.row_names)
base = self.mean_values.loc[common_names]
projection_matrix = projection_matrix.get(common_names, common_names)
if not inplace:
new_en = ParameterEnsemble(pst=self.pst.get(),
data=self.loc[:, :].copy(),
columns=self.columns,
mean_values=self.mean_values.copy(),
istransformed=self.istransformed)
for real in self.index:
if log is not None:
log("projecting realization {0}".format(real))
# null space projection of difference vector
pdiff = self.loc[real, common_names] - base
pdiff = np.dot(projection_matrix.x,
(self.loc[real,common_names] - base)\
.as_matrix())
# lb_fac = np.abs(pdiff)/((base+pdiff)-self.lbnd)
# lb_fac[pdiff>0.0] = 1.0
#
# ub_fac = np.abs(pdiff)/(self.ubnd-(base+pdiff))
# ub_fac[pdiff<=0.0] = 1.0
#
# factor = max(lb_fac.max(),
# ub_fac.max())
if inplace:
self.loc[real, common_names] = base + pdiff
else:
new_en.loc[real, common_names] = base + pdiff
if log is not None:
log("projecting realization {0}".format(real))
if not inplace:
new_en.enforce(enforce_bounds)
new_en.loc[:, istransformed] = 10.0**new_en.loc[:, istransformed]
new_en.__istransformed = False
#new_en._back_transform()
return new_en
self.enforce(enforce_bounds)
self.loc[:, istransformed] = 10.0**self.loc[:, istransformed]
self.__istransformed = False
def from_gaussian_draw(cls, pe, cov, num_reals=1):
""" this is an experiemental method to help speed up draws
for a really large (>1E6) ensemble sizes. gets around the
dataframe expansion-by-loc that is one col at a time. WARNING:
this constructor transforms the pe argument!
:param pe: ParameterEnsemble instance
"param cov: Covariance instance
:param num_reals: number of realizations to generate
:return: ParameterEnsemble
"""
# set up some column names
#real_names = ["{0:d}".format(i)
# for i in range(num_reals)]
real_names = np.arange(num_reals, dtype=np.int64)
if not pe.istransformed:
pe._transform()
# make sure everything is cool WRT ordering
if pe.names != cov.row_names:
common_names = get_common_elements(pe.names, cov.row_names)
vals = pe.mean_values.loc[common_names]
cov = cov.get(common_names)
pass
else:
vals = pe.mean_values
common_names = pe.names
if cov.isdiagonal:
print("making diagonal cov draws")
arr = np.zeros((num_reals, len(pe.names)))
stds = {
pname: std
for pname, std in zip(common_names, np.sqrt(cov.x.flatten()))
}
means = {pname: val for pname, val in zip(common_names, vals)}
for i, pname in enumerate(pe.names):
if pname in pe.pst.adj_par_names:
s = stds[pname]
v = means[pname]
arr[:, i] = np.random.normal(means[pname],
stds[pname],
size=num_reals)
else:
arr[:, i] = means[pname]
df = pd.DataFrame(data=arr, columns=common_names, index=real_names)
else:
#vals = pe.mean_values
print("making full cov draws")
df = pd.DataFrame(data=np.random.multivariate_normal(
vals, cov.as_2d, num_reals),
columns=common_names,
index=real_names)
#print(df.shape,cov.shape)
istransformed = pe.pst.parameter_data.loc[common_names,
"partrans"] == "log"
print("back transforming")
df.loc[:, istransformed] = 10.0**df.loc[:, istransformed]
# replace the realizations for fixed parameters with the original
# parval1 in the control file
print("handling fixed pars")
pe.pst.parameter_data.index = pe.pst.parameter_data.parnme
fixed_vals = pe.pst.parameter_data.loc[pe.fixed_indexer, "parval1"]
for fname, fval in zip(fixed_vals.index, fixed_vals.values):
#if fname not in df.columns:
# continue
print(fname)
df.loc[:, fname] = fval
#print("apply tied")
new_pe = cls.from_dataframe(pst=pe.pst, df=df)
#ParameterEnsemble.apply_tied(new_pe)
return new_pe
def from_gaussian_draw_homegrown(cls, pe, cov, num_reals=1):
""" this is an experiemental method to help speed up draws
for a really large (>1E6) ensemble sizes. gets around the
dataframe expansion-by-loc that is one col at a time. Implements
multivariate normal draws to get around the 32-bit lapack limitations
in scipy/numpy
Parameters
----------
pe : ParameterEnsemble
existing ParameterEnsemble used to get information
needed to call ParameterEnsemble constructor
cov : (pyemu.Cov)
covariance matrix to use for drawing
num_reals : int
number of realizations to generate
Returns
-------
ParameterEnsemble : ParameterEnsemble
Note
----
this constructor transforms the pe argument!
"""
s = datetime.now()
print("{0} - starting home-grown multivariate draws".format(s))
# set up some column names
# real_names = ["{0:d}".format(i)
# for i in range(num_reals)]
real_names = np.arange(num_reals, dtype=np.int64)
if not pe.istransformed:
pe._transform()
# make sure everything is cool WRT ordering
if pe.names != cov.row_names:
common_names = get_common_elements(pe.names, cov.row_names)
vals = pe.mean_values.loc[common_names]
cov = cov.get(common_names)
pass
else:
vals = pe.mean_values
common_names = pe.names
#generate standard normal vectors
snv = np.random.randn(num_reals, cov.shape[0])
#jwhite - 18-dec-17: the cholesky version is giving significantly diff
#results compared to eigen solve, so turning this off for now - need to
#learn more about this...
use_chol = False
if use_chol:
a = np.linalg.cholesky(cov.as_2d)
else:
#decompose...
v, w = np.linalg.eigh(cov.as_2d)
#form projection matrix
a = np.dot(w, np.diag(np.sqrt(v)))
#project...
reals = []
for vec in snv:
real = vals + np.dot(a, vec)
reals.append(real)
df = pd.DataFrame(reals, columns=common_names, index=real_names)
istransformed = pe.pst.parameter_data.loc[common_names,
"partrans"] == "log"
#print("back transforming")
df.loc[:, istransformed] = 10.0**df.loc[:, istransformed]
# replace the realizations for fixed parameters with the original
# parval1 in the control file
#print("handling fixed pars")
pe.pst.parameter_data.index = pe.pst.parameter_data.parnme
fixed_vals = pe.pst.parameter_data.loc[pe.fixed_indexer, "parval1"]
for fname, fval in zip(fixed_vals.index, fixed_vals.values):
# if fname not in df.columns:
# continue
#print(fname)
df.loc[:, fname] = fval
# print("apply tied")
new_pe = cls.from_dataframe(pst=pe.pst, df=df)
# ParameterEnsemble.apply_tied(new_pe)
e = datetime.now()
print("{0} - done...took {1}".format(e, (e - s).total_seconds()))
return new_pe
def project(self,
projection_matrix,
inplace=True,
log=None,
enforce_bounds="reset"):
""" project the ensemble using the null-space Monte Carlo method
Parameters
----------
projection_matrix : pyemu.Matrix
projection operator - must already respect log transform
inplace : bool
project self or return a new ParameterEnsemble instance
log: pyemu.Logger
for logging progress
enforce_bounds : str
parameter bound enforcement flag. 'drop' removes
offending realizations, 'reset' resets offending values
Returns
-------
ParameterEnsemble : ParameterEnsemble
if inplace is False
"""
if self.istransformed:
self._back_transform()
istransformed = self.pst.parameter_data.loc[:, "partrans"] == "log"
self.loc[:, istransformed] = self.loc[:, istransformed].applymap(
lambda x: math.log10(x))
self.__istransformed = True
#make sure everything is cool WRT ordering
common_names = get_common_elements(self.adj_names,
projection_matrix.row_names)
base = self.mean_values.loc[common_names]
projection_matrix = projection_matrix.get(common_names, common_names)
if not inplace:
new_en = ParameterEnsemble(pst=self.pst.get(),
data=self.loc[:, :].copy(),
columns=self.columns,
mean_values=self.mean_values.copy(),
istransformed=self.istransformed)
for real in self.index:
if log is not None:
log("projecting realization {0}".format(real))
# null space projection of difference vector
pdiff = self.loc[real, common_names] - base
pdiff = np.dot(projection_matrix.x,
(self.loc[real,common_names] - base)\
.as_matrix())
if inplace:
self.loc[real, common_names] = base + pdiff
else:
new_en.loc[real, common_names] = base + pdiff
if log is not None:
log("projecting realization {0}".format(real))
if not inplace:
new_en.enforce(enforce_bounds)
new_en.loc[:, istransformed] = 10.0**new_en.loc[:, istransformed]
new_en.__istransformed = False
#new_en._back_transform()
return new_en
self.enforce(enforce_bounds)
self.loc[:, istransformed] = 10.0**self.loc[:, istransformed]
self.__istransformed = False