Commit 27e4cc32 authored by Martin Reinecke's avatar Martin Reinecke
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more doc work; in progress...

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NIFTy Code
.. currentmodule:: nifty4
The NIFTy code is divided in the concepts Domains, Fields, Operators and Minimization
Code Overview
The fundamental building blocks required for IFT computations are best
recognized from a large distance, ignoring all technical details.
.. toctree::
:maxdepth: 2
:caption: Concepts
From such a perspective,
- IFT problems largely consist of *minimization* problems involving a large
number of equations.
- The equations are built mostly from the application of *linear operators*, but
there may also be nonlinear functions involved.
- The unknowns in the equations represent either continuous physical *fields*,
or they are simply individual measured *data* points.
- The locations and volume elements attached to discretized *field* values are
supplied by *domain* objects. There are many variants of such discretized
*domains* supported by NIFTy4, including Cartesian and spherical geometries
and their harmonic counterparts. *Fields* can live on arbitrary products of
such *domains*.
In the following sections, the concepts briefly presented here will be
discussed in more detail; this is done in reversed order of their introduction,
to avoid forward references.
Abstract base class
One of the fundamental building blocks of the NIFTy4 framework is the *domain*.
Its required capabilities are expressed by the abstract :class:`Domain` class.
A domain must be able to answer the following queries:
- its total number of data entries (pixels), which is accessible via the
:attr:`~Domain.size` property
- the shape of the array that is supposed to hold these data entries
(obtainable by means of the :attr:`~Domain.shape` property)
- equality comparison to another :class:`Domain` instance
Unstructured domains
Domains can be either *structured* (i.e. there is geometrical information
associated with them, like position in space and volume factors),
or *unstructured* (meaning that the data points have no associated manifold).
Unstructured domains can be described by instances of NIFTy's
:class:`UnstructuredDomain` class.
Structured domains
In contrast to unstructured domains, these domains have an assigned geometry.
NIFTy requires them to provide the volume elements of their grid cells.
The additional methods are specified in the abstract class
- The attributes :attr:`~StructuredDomain.scalar_dvol`,
:attr:`~StructuredDomain.dvol`, and :attr:`~StructuredDomain.total_volume`
provide information about the domain's pixel volume(s) and its total volume.
- The property :attr:`~StructuredDomain.harmonic` specifies whether a domain
is harmonic (i.e. describes a frequency space) or not
- Iff the domain is harmonic, the methods
:meth:`~StructuredDomain.get_unique_k_lengths`, and
:meth:`~StructuredDomain.get_fft_smoothing_kernel_function` provide absolute
distances of the individual grid cells from the origin and assist with
Gaussian convolution.
NIFTy comes with several concrete subclasses of :class:`StructuredDomain`:
- :class:`RGSpace` represents a regular Cartesian grid with an arbitrary
number of dimensions, which is supposed to be periodic in each dimension.
- :class:`HPSpace` and :class:`GLSpace` describe pixelisations of the
2-sphere; their counterpart in harmonic space is :class:`LMSpace`, which
contains spherical harmonic coefficients.
- :class:`PowerSpace` is used to describe one-dimensional power spectra.
Among these, :class:`RGSpace` can be harmonic or not (depending on constructor arguments), :class:`GLSpace`, :class:`HPSpace`, and :class:`PowerSpace` are
pure position domains (i.e. nonharmonic), and :class:`LMSpace` is always
Combinations of domains
The fundamental classes described above are often sufficient to specify the
domain of a field. In some cases, however, it will be necessary to have the
field live on a product of elementary domains instead of a single one.
Some examples are:
- sky emission depending on location and energy. This could be represented by
a product of an :class:`HPSpace` (for location) with an :class:`RGSpace`
(for energy).
- a polarised field, which could be modeled as a product of any structured
domain representing location with a four-element :class:`UnstructuredDomain`
holding Stokes I, Q, U and V components.
Consequently, NIFTy defines a class called :class:`DomainTuple` holding
a sequence of :class:`Domain` objects, which is used to specify full field
domains. In principle, a :class:`DomainTuple` can even be empty, which implies
that the field living on it is a scalar.
A :class:`Field` object consists of the following components:
- a domain in form of a :class:`DomainTuple` object
- a data type (e.g. numpy.float64)
- an array containing the actual values
Fields support arithmetic operations, contractions, etc.
Linear Operators
A linear operator (represented by NIFTy4's abstract :class:`LinearOperator`
class) can be interpreted as an (implicitly defined) matrix.
It can be applied to :class:`Field` instances, resulting in other :class:`Field`
instances that potentially live on other domains.
There are four basic ways of applying an operator :math:`A` to a field :math:`f`:
- direct multiplication: :math:`A\cdot f`
- adjoint multiplication: :math:`A^\dagger \cdot f`
- inverse multiplication: :math:`A^{-1}\cdot f`
- adjoint inverse multiplication: :math:`(A^\dagger)^{-1}\cdot f`
(For linear operators, inverse adjoint multiplication and adjoint inverse
multiplication are equivalent.)
These different actions of an operator ``Op`` on a field ``f`` can be invoked
in various ways:
- direct multiplication: ``Op(f)`` or ``Op.times(f)`` or ``Op.apply(f, Op.TIMES)``
- adjoint multiplication: ``Op.adjoint_times(f)`` or ``Op.apply(f, Op.ADJOINT_TIMES)``
- inverse multiplication: ``Op.inverse_times(f)`` or ``Op.apply(f, Op.INVERSE_TIMES)``
- adjoint inverse multiplication: ``Op.adjoint_inverse_times(f)`` or ``Op.apply(f, Op.ADJOINT_INVERSE_TIMES)``
Operator classes defined in NIFTy may implement an arbitrary subset of these
four operations. This subset can be queried using the
:attr:`~LinearOperator.capability` property.
If needed, the set of supported operations can be enhanced by iterative
inversion methods;
for example, an operator defining direct and adjoint multiplication could be
enhanced to support the complete set by this method. This functionality is
provided by NIFTy's :class:`InversionEnabler` class, which is itself a linear
There are two :class:`DomainTuple` objects associated with a
:class:`LinearOperator`: a :attr:`~LinearOperator.domain` and a
Direct multiplication and adjoint inverse multiplication transform a field
living on the operator's :attr:`~LinearOperator.domain` to one living on the operator's :attr:``, whereas adjoint multiplication
and inverse multiplication transform from :attr:`` to :attr:`~LinearOperator.domain`.
Operators with identical domain and target can be derived from
:class:`EndomorphicOperator`; typical examples for this category are the :class:`ScalingOperator`, which simply multiplies its input by a scalar
value, and :class:`DiagonalOperator`, which multiplies every value of its input
field with potentially different values.
Further operator classes provided by NIFTy are
- :class:`HarmonicTransformOperator` for transforms from harmonic domain to
their counterparts in position space, and their adjoint
- :class:`PowerDistributor` for transforms from a :class:`PowerSpace` to
the associated harmonic domain, and their adjoint
- :class:`GeometryRemover`, which transforms from structured domains to
unstructured ones. This is typically needed when building instrument response
Nifty4 allows simple and intuitive construction of altered and combined
As an example, if ``A``, ``B`` and ``C`` are of type :class:`LinearOperator`
and ``f1`` and ``f2`` are :class:`Field` s, writing::
X = A*B.inverse*A.adjoint + C
f2 = X(f1)
will perform the operation suggested intuitively by the notation, checking
domain compatibility while building the composed operator.
The combined operator infers its domain and target from its constituents,
as well as the set of operations it can support.
The properties :attr:`~LinearOperator.adjoint` and
:attr:`~LinearOperator.inverse` return a new operator which behaves as if it
were the original operator's adjoint or inverse, respectively.
.. _minimization:
Most problems in IFT are solved by (possibly nested) minimizations of high-dimensional functions, which are often nonlinear.
In NIFTy4 such functions are represented by objects of type :class:`Energy`.
These hold the prescription how to calculate the function's value, gradient and (optionally) curvature at any given position.
Function values are floating-point scalars, gradients have the form of fields living on the energy's position domain, and curvatures are represented by linear operator objects.
Some examples of concrete energy classes delivered with NIFTy4 are :class:`QuadraticEnergy` (with position-independent curvature, mainly used with conjugate gradient minimization) and :class:`WienerFilterEnergy`.
Energies are classes that typically have to be provided by the user when tackling new IFT problems.
The minimization procedure can be carried out by one of several algorithms; NIFTy4 currently ships solvers based on
- the conjugate gradient method (for quadratic energies)
- the steepest descent method
- the VL-BFGS method
- the relaxed Newton method, and
- a nonlinear conjugate gradient method
Domains <concepts/domains>
Fields <concepts/field>
Operators <concepts/operators>
Minimization <concepts/minimization>
......@@ -37,8 +37,8 @@ NIFTy requires them to provide the volume elements of their grid cells.
The additional methods are specified in the abstract class
- Methods :meth:`~StructuredDomain.scalar_dvol`,
:meth:`~StructuredDomain.dvol`, and :meth:`~StructuredDomain.total_volume`
- The attributes :attr:`~StructuredDomain.scalar_dvol`,
:attr:`~StructuredDomain.dvol`, and :attr:`~StructuredDomain.total_volume`
provide information about the domain's pixel volume(s) and its total volume.
- The property :attr:`~StructuredDomain.harmonic` specifies whether a domain
is harmonic (i.e. describes a frequency space) or not
......@@ -24,7 +24,6 @@ Contents
Gallery <>
Indices and tables
......@@ -25,6 +25,20 @@ from .linear_operator import LinearOperator
class InversionEnabler(LinearOperator):
"""Class which augments the capability of another operator object via
numerical inversion.
op : :class:`EndomorphicOperator`
The operator to be enhanced.
The InversionEnabler object will support the same operation modes as
`op`, and additionally the inverse set. The newly-added modes will
be computed by iterative inversion.
inverter : :class:`Minimizer`
The minimizer to use for the iterative numerical inversion.
Typically, this is a :class:`ConjugateGradient` object.
preconditioner : :class:`LinearOperator`, optional
if not None, this operator is used as a preconditioner during the
iterative inversion, to accelerate convergence.
def __init__(self, op, inverter, preconditioner=None):
......@@ -29,6 +29,25 @@ class LinearOperator(with_metaclass(
The base NIFTY operator class is an abstract class from which
other specific operator subclasses are derived.
TIMES : int
Symbolic constant representing normal operator application
Symbolic constant representing adjoint operator application
Symbolic constant representing inverse operator application
Symbolic constant representing adjoint inverse operator application
The symbolic constants for the operation modes can be combined by the
"bitwise-or" operator "|", for expressing the capability of the operator
by means of a single integer number.
_validMode = (False, True, True, False, True, False, False, False, True)
......@@ -131,7 +150,7 @@ class LinearOperator(with_metaclass(
def capability(self):
"""int : the supported operation modes
Returns the suppoerted subset of :attr:`TIMES`, :attr:`ADJOINT_TIMES`,
Returns the supported subset of :attr:`TIMES`, :attr:`ADJOINT_TIMES`,
joined together by the "|" operator.
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