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NIFTy
Commit de59bf62 authored by Marco Selig's avatar Marco Selig
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version update.

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README.rst
View file @ de59bf62
......@@ -63,6 +63,7 @@ apply to fields.
vector
* ``response_operator`` - exemplary responses that include a convolution,
masking and projection
* ``propagator_operator`` - information propagator in Wiener filter theory
* (and more)
* (and more)
......@@ -96,7 +97,7 @@ Requirements
Download
........
The latest release is tagged **v0.4.2** and is available as a source package
The latest release is tagged **v0.6.0** and is available as a source package
at `<https://github.com/mselig/nifty/tags>`_. The current version can be
obtained by cloning the repository::
......@@ -122,7 +123,7 @@ Please, acknowledge the use of NIFTY in your publication(s) by using a phrase
such as the following:
*"Some of the results in this publication have been derived using the NIFTY
[Selig et al., 2013] package."*
package [Selig et al., 2013]."*
References
..........
......
demos/demo_wf1.py
View file @ de59bf62
......@@ -33,8 +33,6 @@
"""
from __future__ import division
from nifty import * # version 0.6.0
from nifty.nifty_tools import *
# some signal space; e.g., a two-dimensional regular grid
......@@ -57,15 +55,11 @@ n = N.get_random_field(domain=d_space) # generate
d = R(s) + n # compute data
j = R.adjoint_times(N.inverse_times(d)) # define information source
D = propagator_operator(S=S,N=N,R=R) # define information propagator
D = propagator_operator(S=S, N=N, R=R) # define information propagator
m = D(j, tol=1E-4, note=True) # reconstruct map
s.plot(title="signal") # plot signal
d_ = field(x_space, val=d.val, target=k_space)
d_.plot(title="data", vmin=s.val.min(), vmax=s.val.max()) # plot data
......
demos/demo_wf2.py
View file @ de59bf62
......@@ -33,8 +33,6 @@
"""
from __future__ import division
from nifty import * # version 0.6.0
from nifty.nifty_tools import *
# some signal space; e.g., a two-dimensional regular grid
......@@ -57,10 +55,8 @@ n = N.get_random_field(domain=d_space) # generate
d = R(s) + n # compute data
j = R.adjoint_times(N.inverse_times(d)) # define information source
D = propagator_operator(S=S,N=N,R=R) # define information propagator
D = propagator_operator(S=S, N=N, R=R) # define information propagator
def eggs(x):
......@@ -68,17 +64,15 @@ def eggs(x):
Calculation of the information Hamiltonian and its gradient.
"""
Dx = D.inverse_times(x)
H = 0.5 * Dx.dot(x) - j.dot(x) # compute information Hamiltonian
g = Dx - j # compute its gradient
return H,g
DIx = D.inverse_times(x)
H = 0.5 * DIx.dot(x) - j.dot(x) # compute information Hamiltonian
g = DIx - j # compute its gradient
return H, g
m = field(x_space, target=k_space) # reconstruct map
m,convergence = steepest_descent(eggs=eggs, note=True)(m, tol=1E-4, clevel=3)
s.plot(title="signal") # plot signal
d_ = field(x_space, val=d.val, target=k_space)
d_.plot(title="data", vmin=s.val.min(), vmax=s.val.max()) # plot data
......
nifty_core.py
View file @ de59bf62
......@@ -486,7 +486,7 @@ class _about(object): ## nifty support class for global settings
"""
## version
self._version = "0.5.9"
self._version = "0.6.0"
## switches and notifications
self._errors = notification(default=True,ccode=notification._code)
......@@ -11703,17 +11703,17 @@ class probing(object):
##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
def evaluate(self,sum_,num_,var_):
def evaluate(self,summa,num,var):
"""
Evaluates the probing results.
Parameters
----------
sum_ : numpy.array
summa : numpy.array
Sum of all probing results.
num_ : int
num : int
Number of successful probings (not returning ``None``).
var_ : numpy.array
var : numpy.array
Sum of all squared probing results
Returns
......@@ -11727,27 +11727,27 @@ class probing(object):
(`final`,`var`).
"""
if(num_<self.nrun):
about.infos.cflush(" ( %u probe(s) failed, effectiveness == %.1f%% )\n"%(self.nrun-num_,100*num_/self.nrun))
if(num_==0):
if(num<self.nrun):
about.infos.cflush(" ( %u probe(s) failed, effectiveness == %.1f%% )\n"%(self.nrun-num,100*num/self.nrun))
if(num==0):
about.warnings.cprint("WARNING: probing failed.")
return None
else:
about.infos.cflush("\n")
if(sum_.size==1):
sum_ = sum_.flatten(order='C')[0]
var_ = var_.flatten(order='C')[0]
if(np.iscomplexobj(sum_))and(np.all(np.imag(sum_)==0)):
sum_ = np.real(sum_)
if(summa.size==1):
summa = summa.flatten(order='C')[0]
var = var.flatten(order='C')[0]
if(np.iscomplexobj(summa))and(np.all(np.imag(summa)==0)):
summa = np.real(summa)
final = sum_*(1/num_)
final = summa*(1/num)
if(self.var):
if(num_==1):
if(num==1):
about.warnings.cprint("WARNING: infinite variance.")
return final,None
else:
var = var_*(1/(num_*(num_-1)))-np.real(np.conjugate(final)*final)*(1/(num_-1))
var = var*(1/(num*(num-1)))-np.real(np.conjugate(final)*final)*(1/(num-1))
return final,var
else:
return final
......@@ -11858,7 +11858,7 @@ class probing(object):
## evaluate
return self.evaluate(_sum,_num,_var)
def __call__(self,loop=False,**kwargs): ## FIXME: doc
def __call__(self,loop=False,**kwargs):
"""
Starts the probing process.
......@@ -12129,17 +12129,17 @@ class trace_probing(probing):
##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
def evaluate(self,sum_,num_,var_):
def evaluate(self,summa,num,var):
"""
Evaluates the probing results.
Parameters
----------
sum_ : scalar
summa : scalar
Sum of all probing results.
num_ : int
num : int
Number of successful probings (not returning ``None``).
var_ : scalar
var : scalar
Sum of all squared probing results
Returns
......@@ -12153,24 +12153,24 @@ class trace_probing(probing):
(`final`,`var`).
"""
if(num_<self.nrun):
about.infos.cflush(" ( %u probe(s) failed, effectiveness == %.1f%% )\n"%(self.nrun-num_,100*num_/self.nrun))
if(num_==0):
if(num<self.nrun):
about.infos.cflush(" ( %u probe(s) failed, effectiveness == %.1f%% )\n"%(self.nrun-num,100*num/self.nrun))
if(num==0):
about.warnings.cprint("WARNING: probing failed.")
return None
else:
about.infos.cflush("\n")
if(self.domain.datatype in [np.complex64,np.complex128]):
sum_ = np.real(sum_)
summa = np.real(summa)
final = sum_/num_
final = summa/num
if(self.var):
if(num_==1):
if(num==1):
about.warnings.cprint("WARNING: infinite variance.")
return final,None
else:
var = var_/(num_*(num_-1))-np.real(np.conjugate(final)*final)/(num_-1)
var = var/(num*(num-1))-np.real(np.conjugate(final)*final)/(num-1)
return final,var
else:
return final
......
nifty_power.py
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......@@ -28,11 +28,11 @@
.. /__/ /__/ /__/ /__/ \___/ \___ / power
.. /______/
NIFTy offers a number of automatized routines for handling
NIFTY offers a number of automatized routines for handling
power spectra. It is possible to draw a field from a random distribution
with a certain autocorrelation or, equivalently, with a certain
power spectrum in its conjugate space (see :py:func:`field.random`). In
NIFTy, it is usually assumed that such a field follows statistical
NIFTY, it is usually assumed that such a field follows statistical
homogeneity and isotropy. Fields which are only statistically homogeneous
can also be created using the diagonal operator routine.
......
nifty_tools.py
View file @ de59bf62
......@@ -28,9 +28,12 @@
.. /__/ /__/ /__/ /__/ \___/ \___ / tools
.. /______/
A nifty set of tools.
## TODO: *DESCRIPTION*
This module extends NIFTY with a nifty set of tools including further
operators, namely the :py:class:`invertible_operator` and the
:py:class:`propagator_operator`, and minimization schemes, namely
:py:class:`steepest_descent` and :py:class:`conjugate_gradient`. Those
tools are supposed to support the user in solving information field
theoretical problems (almost) without numerical pain.
"""
from __future__ import division
......@@ -51,9 +54,10 @@ class invertible_operator(operator):
NIFTY subclass for invertible, self-adjoint (linear) operators
The base NIFTY operator class is an abstract class from which other
specific operator subclasses, including those preimplemented in NIFTY
(e.g. the diagonal operator class) must be derived.
The invertible operator class is an abstract class for self-adjoint or
symmetric (linear) operators from which other more specific operator
subclassescan be derived. Such operators inherit an automated inversion
routine, namely conjugate gradient.
Parameters
----------
......@@ -76,9 +80,9 @@ class invertible_operator(operator):
Notes
-----
Operator classes derived from this one only need a `_multiply` or
`_inverse_multiply` instance method to perform the other. However, one
of them needs to be defined.
This class is not meant to be instantiated. Operator classes derived
from this one only need a `_multiply` or `_inverse_multiply` instance
method to perform the other. However, one of them needs to be defined.
Attributes
----------
......@@ -275,8 +279,8 @@ class propagator_operator(operator):
NIFTY subclass for propagator operators (of a certain family)
The propagator operators :math:`D` implemented here have an inverse
formulation like :math:`S^{-1} + M`, :math:`S^{-1} + N^{-1}`, or
:math:`S^{-1} + R^\dagger N^{-1} R` as appearing in Wiener filter
formulation like :math:`(S^{-1} + M)`, :math:`(S^{-1} + N^{-1})`, or
:math:`(S^{-1} + R^\dagger N^{-1} R)` as appearing in Wiener filter
theory.
Parameters
......@@ -296,7 +300,7 @@ class propagator_operator(operator):
Notes
-----
The propagator will puzzle the operators `S` and `M` or `R`,`N` or
The propagator will puzzle the operators `S` and `M` or `R`, `N` or
only `N` together in the predefined from, a domain is set
automatically. The application of the inverse is done by invoking a
conjugate gradient.
......@@ -610,8 +614,8 @@ class conjugate_gradient(object):
References
----------
.. [#] J. R. Shewchuk, 1994, `"An Introduction to the Conjugate
Gradient Method Without the Agonizing Pain"
`<http://www.cs.cmu.edu/~quake-papers/painless-conjugate-gradient.pdf>`_
Gradient Method Without the Agonizing Pain"
<http://www.cs.cmu.edu/~quake-papers/painless-conjugate-gradient.pdf>`_
Examples
--------
......
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