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Commit 74237b2f authored by Marco Selig's avatar Marco Selig
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several minor fixes; version updated.

parent 2395b49a
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Showing with 121 additions and 48 deletions
nifty_core.py
View file @ 74237b2f
......@@ -484,7 +484,7 @@ class _about(object): ## nifty support class for global settings
"""
## version
self._version = "0.5.0"
self._version = "0.5.5"
## switches and notifications
self._errors = notification(default=True,ccode=notification._code)
......@@ -730,9 +730,9 @@ class random(object):
spec = domain.enforce_power(kwargs.get("spec",1),size=len(kindex),kindex=kindex,codomain=codomain)
kpack = [codomain.power_indices.get("pindex"),kindex]
else:
kindex = domain.power_indixes.get("kindex")
kindex = domain.power_indices.get("kindex")
spec = domain.enforce_power(kwargs.get("spec",1),size=len(kindex),kindex=kindex)
kpack = [domain.power_indixes.get("pindex"),kindex]
kpack = [domain.power_indices.get("pindex"),kindex]
return [key,spec,kpack]
elif(key=="uni"):
......@@ -1126,7 +1126,7 @@ class space(object):
Indexing with the unindexing array undoes the indexing with the
indexing array; i.e., ``power == power[pindex].flatten()[pundex]``.
See also
See Also
--------
get_power_index
......@@ -1161,7 +1161,7 @@ class space(object):
-------
None
See also
See Also
--------
get_power_indices
......@@ -1213,7 +1213,7 @@ class space(object):
Indexing with the unindexing array undoes the indexing with the
indexing array; i.e., ``power == power[pindex].flatten()[pundex]``.
See also
See Also
--------
set_power_indices
......@@ -1489,13 +1489,17 @@ class space(object):
Returns
-------
dot : float
dot : scalar
Inner product of the two arrays.
"""
x = self.enforce_shape(np.array(x,dtype=self.datatype))
y = self.enforce_shape(np.array(y,dtype=self.datatype))
## inner product
return np.dot(np.conjugate(x),y,out=None)
dot = np.dot(np.conjugate(x),y,out=None)
if(np.isreal(dot)):
return np.real(dot)
else:
return dot
##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
......@@ -2130,6 +2134,8 @@ class point_space(space):
if(bool(kwargs.get("save",False))):
fig.savefig(str(kwargs.get("save")),dpi=None,facecolor=None,edgecolor=None,orientation='portrait',papertype=None,format=None,transparent=False,bbox_inches=None,pad_inches=0.1)
pl.close(fig)
else:
fig.canvas.draw()
##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
......@@ -2530,7 +2536,7 @@ class rg_space(space):
-------
None
See also
See Also
--------
get_power_indices
......@@ -2894,13 +2900,17 @@ class rg_space(space):
Returns
-------
dot : float
dot : scalar
Inner product of the two arrays.
"""
x = self.enforce_shape(np.array(x,dtype=self.datatype))
y = self.enforce_shape(np.array(y,dtype=self.datatype))
## inner product
return np.dot(np.conjugate(x.flatten(order='C')),y.flatten(order='C'),out=None)
dot = np.dot(np.conjugate(x.flatten(order='C')),y.flatten(order='C'),out=None)
if(np.isreal(dot)):
return np.real(dot)
else:
return dot
##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
......@@ -3311,6 +3321,8 @@ class rg_space(space):
if(bool(kwargs.get("save",False))):
fig.savefig(str(kwargs.get("save")),dpi=None,facecolor=None,edgecolor=None,orientation='portrait',papertype=None,format=None,transparent=False,bbox_inches=None,pad_inches=0.1)
pl.close(fig)
else:
fig.canvas.draw()
##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
......@@ -3613,7 +3625,7 @@ class lm_space(space):
-------
None
See also
See Also
--------
get_power_indices
......@@ -3895,12 +3907,11 @@ class lm_space(space):
Returns
-------
dot : float
dot : scalar
Inner product of the two arrays.
"""
x = self.enforce_shape(np.array(x,dtype=self.datatype))
y = self.enforce_shape(np.array(y,dtype=self.datatype))
## inner product
if(self.datatype==np.complex64):
return gl.dotlm_f(x,y,lmax=self.para[0],mmax=self.para[1])
......@@ -4167,6 +4178,8 @@ class lm_space(space):
if(bool(kwargs.get("save",False))):
fig.savefig(str(kwargs.get("save")),dpi=None,facecolor=None,edgecolor=None,orientation='portrait',papertype=None,format=None,transparent=False,bbox_inches=None,pad_inches=0.1)
pl.close(fig)
else:
fig.canvas.draw()
##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
......@@ -4836,6 +4849,8 @@ class gl_space(space):
if(bool(kwargs.get("save",False))):
fig.savefig(str(kwargs.get("save")),dpi=None,facecolor=None,edgecolor=None,orientation='portrait',papertype=None,format=None,transparent=False,bbox_inches=None,pad_inches=0.1)
pl.close(fig)
else:
fig.canvas.draw()
##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
......@@ -5432,6 +5447,8 @@ class hp_space(space):
if(bool(kwargs.get("save",False))):
fig.savefig(str(kwargs.get("save")),dpi=None,facecolor=None,edgecolor=None,orientation='portrait',papertype=None,format=None,transparent=False,bbox_inches=None,pad_inches=0.1)
pl.close(fig)
else:
fig.canvas.draw()
##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
......@@ -5900,13 +5917,17 @@ class nested_space(space):
Returns
-------
dot : float
dot : scalar
Inner product of the two arrays.
"""
x = self.enforce_shape(np.array(x,dtype=self.datatype))
y = self.enforce_shape(np.array(y,dtype=self.datatype))
## inner product
return np.sum(np.conjugate(x)*y,axis=None,dtype=None,out=None)
dot = np.sum(np.conjugate(x)*y,axis=None,dtype=None,out=None)
if(np.isreal(dot)):
return np.real(dot)
else:
return dot
def calc_pseudo_dot(self,x,y,**kwargs):
"""
......@@ -7074,7 +7095,7 @@ def cos(x):
cosx : {scalar, array, field}
Cosine of `x` to the specified base.
See also
See Also
--------
sin
tan
......@@ -7105,7 +7126,7 @@ def sin(x):
sinx : {scalar, array, field}
Sine of `x` to the specified base.
See also
See Also
--------
cos
tan
......@@ -7137,7 +7158,7 @@ def cosh(x):
coshx : {scalar, array, field}
cosh of `x` to the specified base.
See also
See Also
--------
sinh
tanh
......@@ -7169,7 +7190,7 @@ def sinh(x):
sinhx : {scalar, array, field}
sinh of `x` to the specified base.
See also
See Also
--------
cosh
tanh
......@@ -7201,7 +7222,7 @@ def tan(x):
tanx : {scalar, array, field}
Tangent of `x` to the specified base.
See also
See Also
--------
cos
sin
......@@ -7233,7 +7254,7 @@ def tanh(x):
tanhx : {scalar, array, field}
tanh of `x` to the specified base.
See also
See Also
--------
cosh
sinh
......@@ -7264,7 +7285,7 @@ def arccos(x):
arccosx : {scalar, array, field}
arccos of `x` to the specified base.
See also
See Also
--------
arcsin
arctan
......@@ -7296,7 +7317,7 @@ def arcsin(x):
arcsinx : {scalar, array, field}
Logarithm of `x` to the specified base.
See also
See Also
--------
arccos
arctan
......@@ -7328,7 +7349,7 @@ def arccosh(x):
arccoshx : {scalar, array, field}
arccos of `x` to the specified base.
See also
See Also
--------
arcsinh
arctanh
......@@ -7359,7 +7380,7 @@ def arcsinh(x):
arcsinhx : {scalar, array, field}
arcsinh of `x` to the specified base.
See also
See Also
--------
arccosh
arctanh
......@@ -7390,7 +7411,7 @@ def arctan(x):
arctanx : {scalar, array, field}
arctan of `x` to the specified base.
See also
See Also
--------
arccos
arcsin
......@@ -7421,7 +7442,7 @@ def arctanh(x):
arctanhx : {scalar, array, field}
arctanh of `x` to the specified base.
See also
See Also
--------
arccosh
arcsinh
......@@ -7479,7 +7500,7 @@ def exp(x):
expx : {scalar, array, field}
Exponential of `x` to the specified base.
See also
See Also
--------
log
......@@ -7511,7 +7532,7 @@ def log(x,base=None):
logx : {scalar, array, field}
Logarithm of `x` to the specified base.
See also
See Also
--------
exp
......@@ -8116,8 +8137,11 @@ class operator(object):
if(domain is None):
domain = self.domain
diag = diagonal_probing(self,function=self.times,domain=domain,target=target,random=random,ncpu=ncpu,nrun=nrun,nper=nper,var=var,save=save,path=path,prefix=prefix,**kwargs)(loop=loop)
if(diag is None):
about.warnings.cprint("WARNING: 'NoneType' forwarded.")
return None
## weight if ...
if(not domain.discrete)and(bare):
elif(not domain.discrete)and(bare):
if(isinstance(diag,tuple)): ## diag == (diag,variance)
return domain.calc_weight(diag[0],power=-1),domain.calc_weight(diag[1],power=-1)
else:
......@@ -8193,8 +8217,11 @@ class operator(object):
if(domain is None):
domain = self.target
diag = diagonal_probing(self,function=self.inverse_times,domain=domain,target=target,random=random,ncpu=ncpu,nrun=nrun,nper=nper,var=var,save=save,path=path,prefix=prefix,**kwargs)(loop=loop)
if(diag is None):
about.warnings.cprint("WARNING: 'NoneType' forwarded.")
return None
## weight if ...
if(not domain.discrete)and(bare):
elif(not domain.discrete)and(bare):
if(isinstance(diag,tuple)): ## diag == (diag,variance)
return domain.calc_weight(diag[0],power=-1),domain.calc_weight(diag[1],power=-1)
else:
......@@ -8290,7 +8317,10 @@ class operator(object):
"""
if(domain is None):
domain = self.domain
return field(domain,val=self.diag(bare=bare,domain=domain,target=target,var=False,**kwargs),target=target)
diag = self.diag(bare=bare,domain=domain,target=target,var=False,**kwargs)
if(diag is None):
return None
return field(domain,val=diag,target=target)
def inverse_hat(self,bare=False,domain=None,target=None,**kwargs):
"""
......@@ -8354,7 +8384,10 @@ class operator(object):
"""
if(domain is None):
domain = self.target
return field(domain,val=self.inverse_diag(bare=bare,domain=domain,target=target,var=False,**kwargs),target=target)
diag = self.inverse_diag(bare=bare,domain=domain,target=target,var=False,**kwargs)
if(diag is None):
return None
return field(domain,val=diag,target=target)
def hathat(self,domain=None,**kwargs):
"""
......@@ -8413,7 +8446,10 @@ class operator(object):
"""
if(domain is None):
domain = self.domain
return diagonal_operator(domain=domain,diag=self.diag(bare=False,domain=domain,var=False,**kwargs),bare=False)
diag = self.diag(bare=False,domain=domain,var=False,**kwargs)
if(diag is None):
return None
return diagonal_operator(domain=domain,diag=diag,bare=False)
def inverse_hathat(self,domain=None,**kwargs):
"""
......@@ -8473,7 +8509,10 @@ class operator(object):
"""
if(domain is None):
domain = self.target
return diagonal_operator(domain=domain,diag=self.inverse_diag(bare=False,domain=domain,var=False,**kwargs),bare=False)
diag = self.inverse_diag(bare=False,domain=domain,var=False,**kwargs)
if(diag is None):
return None
return diagonal_operator(domain=domain,diag=diag,bare=False)
##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
......@@ -9740,6 +9779,8 @@ class projection_operator(operator):
if(isinstance(x,operator)):
## compute non-bare diagonal of the operator x
x = x.diag(bare=False,domain=self.domain,target=x.domain,var=False,**kwargs)
if(x is None):
raise TypeError(about._error.cstring("ERROR: 'NoneType' encountered."))
elif(isinstance(x,field)):
## check domain
......@@ -10573,6 +10614,7 @@ class probing(object):
"""
if(len(results)==0):
about.warnings.cprint("WARNING: probing failed.")
return None
elif(self.var):
return np.mean(np.array(results),axis=0,dtype=None,out=None),np.var(np.array(results),axis=0,dtype=None,out=None,ddof=0)/(len(results)-1)
......@@ -11279,6 +11321,7 @@ class diagonal_probing(probing):
"""
num = len(results)
if(num==0):
about.warnings.cprint("WARNING: probing failed.")
return None
elif(self.save is None):
if(self.var):
......
nifty_power.py
View file @ 74237b2f
......@@ -401,7 +401,7 @@ def infer_power(m,domain=None,Sk=None,D=None,pindex=None,pundex=None,kindex=None
derived, and the implications of a certain choise of the perception
tuple (delta,epsilon) are discussed.
The further incorporation of a smoothness prior as detailed in [#]_,
where the underlying formula(s), Eq.(27), of this implementation are
where the underlying formula(s), Eq.(26), of this implementation are
derived and discussed in terms of their applicability.
References
......
nifty_tools.py
View file @ 74237b2f
......@@ -185,13 +185,14 @@ class invertible_operator(operator):
"""
x_,convergence = conjugate_gradient(self.inverse_times,x,W=W,spam=spam,reset=reset,note=note)(x0=x0,tol=tol,clevel=clevel,limii=limii)
if(not self.imp): ## continiuos domain/target
x_.weight(power=-1,overwrite=True)
## check convergence
if(not convergence):
if(not force):
if(not force)or(x_ is None):
return None
about.warnings.cprint("WARNING: conjugate gradient failed.")
## weight if ...
if(not self.imp): ## continiuos domain/target
x_.weight(power=-1,overwrite=True)
return x_
def _inverse_multiply(self,x,force=False,W=None,spam=None,reset=None,note=False,x0=None,tol=1E-4,clevel=1,limii=None,**kwargs):
......@@ -242,13 +243,14 @@ class invertible_operator(operator):
"""
x_,convergence = conjugate_gradient(self.times,x,W=W,spam=spam,reset=reset,note=note)(x0=x0,tol=tol,clevel=clevel,limii=limii)
if(not self.imp): ## continiuos domain/target
x_.weight(power=1,overwrite=True)
## check convergence
if(not convergence):
if(not force):
if(not force)or(x_ is None):
return None
about.warnings.cprint("WARNING: conjugate gradient failed.")
## weight if ...
if(not self.imp): ## continiuos domain/target
x_.weight(power=1,overwrite=True)
return x_
##-----------------------------------------------------------------------------
......@@ -578,6 +580,10 @@ class conjugate_gradient(object):
note : bool, *optional*
Indicates whether notes are printed or not (default: False).
See Also
--------
scipy.sparse.linalg.cg
Notes
-----
After initialization by `__init__`, the minimizer is started by calling
......@@ -585,10 +591,11 @@ class conjugate_gradient(object):
if enabled, will state the iteration number, current step widths
`alpha` and `beta`, the current relative residual `delta` that is
compared to the tolerance, and the convergence level if changed.
The minimizer will exit in two states: QUIT if the maximum number of
iterations is reached, or DONE if convergence is achieved. Returned
will be the latest `x` and the latest convergence level, which can
evaluate ``True`` for all exit states.
The minimizer will exit in three states: DEAD if alpha becomes
infinite, QUIT if the maximum number of iterations is reached, or DONE
if convergence is achieved. Returned will be the latest `x` and the
latest convergence level, which can evaluate ``True`` for the exit
states QUIT and DONE.
References
----------
......@@ -714,12 +721,17 @@ class conjugate_gradient(object):
def _calc_without(self,tol=1E-4,clevel=1,limii=None): ## > runs cg without preconditioner
clevel = int(clevel)
if(limii is None):
limii = 10*self.b.domain.dim(split=False)
else:
limii = int(limii)
r = self.b-self.A(self.x)
d = field(self.b.domain,val=np.copy(r.val),target=self.b.target)
gamma = r.dot(d)
if(gamma==0):
return self.x,clevel+1
delta_ = np.absolute(gamma)**(-0.5)
convergence = 0
......@@ -727,6 +739,9 @@ class conjugate_gradient(object):
while(True):
q = self.A(d)
alpha = gamma/d.dot(q) ## positive definite
if(not np.isfinite(alpha)):
self.note.cprint("\niteration : %08u alpha = NAN\n... dead."%ii)
return self.x,0
self.x += alpha*d
if(ii%self.reset==0)or(np.signbit(np.real(alpha))):
r = self.b-self.A(self.x)
......@@ -769,8 +784,11 @@ class conjugate_gradient(object):
def _calc_with(self,tol=1E-4,clevel=1,limii=None): ## > runs cg with preconditioner
clevel = int(clevel)
if(limii is None):
limii = 10*self.b.domain.dim(split=False)
else:
limii = int(limii)
r = self.b-self.A(self.x)
d = self.W(r)
......@@ -782,6 +800,9 @@ class conjugate_gradient(object):
while(True):
q = self.A(d)
alpha = gamma/d.dot(q) ## positive definite
if(not np.isfinite(alpha)):
self.note.cprint("\niteration : %08u alpha = NAN\n... dead."%ii)
return self.x,0
self.x += alpha*d ## update
if(ii%self.reset==0)or(np.signbit(np.real(alpha))):
r = self.b-self.A(self.x)
......@@ -861,6 +882,11 @@ class steepest_descent(object):
note : bool, *optional*
Indicates whether notes are printed or not (default: False).
See Also
--------
scipy.optimize.fmin_cg, scipy.optimize.fmin_ncg,
scipy.optimize.fmin_l_bfgs_b
Notes
-----
After initialization by `__init__`, the minimizer is started by calling
......@@ -982,6 +1008,10 @@ class steepest_descent(object):
if(not isinstance(x0,field)):
raise TypeError(about._errors.cstring("ERROR: invalid input."))
self.x = x0
clevel = int(clevel)
limii = int(limii)
E,g = self.eggs(self.x) ## energy and gradient
norm = g.norm() ## gradient norm
......
setup.py
View file @ 74237b2f
......@@ -23,7 +23,7 @@ from distutils.core import setup
import os
setup(name="nifty",
version="0.5.0",
version="0.5.5",
description="Numerical Information Field Theory",
author="Marco Selig",
author_email="mselig@mpa-garching.mpg.de",
......
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