README.md 4.76 KB
Newer Older
1
2
3
4
5
6
7
8
9
WARNING:
========

The code on this branch is not meant to be an official version of NIFTy.
As a consequence, it does not install as package "nifty", but rather as
"nifty2go", to allow parallel installation alongside the official NIFTy and
avoid any conflicts.


Martin Reinecke's avatar
Martin Reinecke committed
10
NIFTy - Numerical Information Field Theory
Jait Dixit's avatar
Jait Dixit committed
11
==========================================
Martin Reinecke's avatar
Martin Reinecke committed
12
13
[![build status](https://gitlab.mpcdf.mpg.de/ift/NIFTy/badges/nifty2go/build.svg)](https://gitlab.mpcdf.mpg.de/ift/NIFTy/commits/nifty2go)
[![coverage report](https://gitlab.mpcdf.mpg.de/ift/NIFTy/badges/nifty2go/coverage.svg)](https://gitlab.mpcdf.mpg.de/ift/NIFTy/commits/nifty2go)
Jait Dixit's avatar
Jait Dixit committed
14

Martin Reinecke's avatar
Martin Reinecke committed
15
**NIFTy** project homepage:
Jait Dixit's avatar
Jait Dixit committed
16
17
18
19
20
21
22
[http://www.mpa-garching.mpg.de/ift/nifty/](http://www.mpa-garching.mpg.de/ift/nifty/)

Summary
-------

### Description

Martin Reinecke's avatar
Martin Reinecke committed
23
**NIFTy**, "**N**umerical **I**nformation **F**ield **T**heor<strong>y</strong>", is
Jait Dixit's avatar
Jait Dixit committed
24
25
26
a versatile library designed to enable the development of signal
inference algorithms that operate regardless of the underlying spatial
grid and its resolution. Its object-oriented framework is written in
Martin Reinecke's avatar
updates  
Martin Reinecke committed
27
Python, although it accesses libraries written in C++ and C for
Jait Dixit's avatar
Jait Dixit committed
28
29
efficiency.

Martin Reinecke's avatar
Martin Reinecke committed
30
NIFTy offers a toolkit that abstracts discretized representations of
Jait Dixit's avatar
Jait Dixit committed
31
32
33
34
35
continuous spaces, fields in these spaces, and operators acting on
fields into classes. Thereby, the correct normalization of operations on
fields is taken care of automatically without concerning the user. This
allows for an abstract formulation and programming of inference
algorithms, including those derived within information field theory.
Martin Reinecke's avatar
Martin Reinecke committed
36
Thus, NIFTy permits its user to rapidly prototype algorithms in 1D, and
Jait Dixit's avatar
Jait Dixit committed
37
then apply the developed code in higher-dimensional settings of real
Martin Reinecke's avatar
Martin Reinecke committed
38
world problems. The set of spaces on which NIFTy operates comprises
Jait Dixit's avatar
Jait Dixit committed
39
40
41
42
43
44
point sets, *n*-dimensional regular grids, spherical spaces, their
harmonic counterparts, and product spaces constructed as combinations of
those.

### Class & Feature Overview

Martin Reinecke's avatar
Martin Reinecke committed
45
The NIFTy library features three main classes: **spaces** that represent
Jait Dixit's avatar
Jait Dixit committed
46
47
48
49
certain grids, **fields** that are defined on spaces, and **operators**
that apply to fields.

-   [Spaces](http://www.mpa-garching.mpg.de/ift/nifty/space.html)
Martin Reinecke's avatar
updates  
Martin Reinecke committed
50
51
52
53
    -   `RGSpace` - *n*-dimensional regular Euclidean grid
    -   `LMSpace` - spherical harmonics
    -   `GLSpace` - Gauss-Legendre grid on the 2-sphere
    -   `HPSpace` - [HEALPix](http://sourceforge.net/projects/healpix/)
Jait Dixit's avatar
Jait Dixit committed
54
55
        grid on the 2-sphere
-   [Fields](http://www.mpa-garching.mpg.de/ift/nifty/field.html)
Martin Reinecke's avatar
updates  
Martin Reinecke committed
56
    -   `Field` - generic class for (discretized) fields
Jait Dixit's avatar
Jait Dixit committed
57
58
59

<!-- -->

Martin Reinecke's avatar
updates  
Martin Reinecke committed
60
    Field.conjugate     Field.dim          Field.norm
Martin Reinecke's avatar
Martin Reinecke committed
61
    Field.vdot          Field.weight
Jait Dixit's avatar
Jait Dixit committed
62
63

-   [Operators](http://www.mpa-garching.mpg.de/ift/nifty/operator.html)
Martin Reinecke's avatar
updates  
Martin Reinecke committed
64
    -   `DiagonalOperator` - purely diagonal matrices in a specified
Jait Dixit's avatar
Jait Dixit committed
65
        basis
Martin Reinecke's avatar
Martin Reinecke committed
66
67
    -   `FFTOperator` - conversion between spaces and their harmonic
                        counterparts
Jait Dixit's avatar
Jait Dixit committed
68
69
70
71
72
73
74
75
76
77
78
    -   (and more)
-   (and more)

*Parts of this summary are taken from* [1] *without marking them
explicitly as quotations.*

Installation
------------

### Requirements

Martin Reinecke's avatar
update  
Martin Reinecke committed
79
-   [Python](http://www.python.org/) (v2.7.x or 3.5.x)
Jait Dixit's avatar
Jait Dixit committed
80
81
    -   [NumPy](http://www.numpy.org/)

Martin Reinecke's avatar
Martin Reinecke committed
82
### Sources
Jait Dixit's avatar
Jait Dixit committed
83

Martin Reinecke's avatar
updates  
Martin Reinecke committed
84
The current version of Nifty3 can be obtained by cloning the repository:
Jait Dixit's avatar
Jait Dixit committed
85
86
87
88

    git clone https://gitlab.mpcdf.mpg.de/ift/NIFTy.git


Martin Reinecke's avatar
Martin Reinecke committed
89
### Installation via pip
Jait Dixit's avatar
Jait Dixit committed
90

Martin Reinecke's avatar
Martin Reinecke committed
91
It is possible to simply install NIFTy with all its dependencies via the command
Jait Dixit's avatar
Jait Dixit committed
92

Martin Reinecke's avatar
Martin Reinecke committed
93
pip install --user --process-dependency-links --egg git+https://gitlab.mpcdf.mpg.de/ift/NIFTy.git@nifty2go
Jait Dixit's avatar
Jait Dixit committed
94

Theo Steininger's avatar
Theo Steininger committed
95
96
97
98
### Running the tests

In oder to run the tests one needs two additional packages:

Martin Reinecke's avatar
Martin Reinecke committed
99
    pip install nose parameterized
100
101

Afterwards the tests (including a coverage report) are run using the following
Theo Steininger's avatar
Theo Steininger committed
102
command in the repository root:
103

104
    nosetests -x --with-coverage --cover-html --cover-package=nifty2go
Theo Steininger's avatar
Theo Steininger committed
105
106


Jait Dixit's avatar
Jait Dixit committed
107
108
### First Steps

Martin Reinecke's avatar
Martin Reinecke committed
109
For a quick start, you can browse through the [informal
Jait Dixit's avatar
Jait Dixit committed
110
introduction](http://www.mpa-garching.mpg.de/ift/nifty/start.html) or
Martin Reinecke's avatar
Martin Reinecke committed
111
dive into NIFTy by running one of the demonstrations, e.g.:
Jait Dixit's avatar
Jait Dixit committed
112

Martin Reinecke's avatar
Martin Reinecke committed
113
    python demos/wiener_filter_via_curvature.py
Jait Dixit's avatar
Jait Dixit committed
114
115
116
117

Acknowledgement
---------------

Martin Reinecke's avatar
Martin Reinecke committed
118
Please acknowledge the use of NIFTy in your publication(s) by using a
Jait Dixit's avatar
Jait Dixit committed
119
120
121
phrase such as the following:

> *"Some of the results in this publication have been derived using the
Martin Reinecke's avatar
Martin Reinecke committed
122
> NIFTy package [Selig et al., 2013]."*
Jait Dixit's avatar
Jait Dixit committed
123
124
125
126
127
128

### References

Release Notes
-------------

Martin Reinecke's avatar
Martin Reinecke committed
129
The NIFTy package is licensed under the
Jait Dixit's avatar
Jait Dixit committed
130
131
132
133
134
[GPLv3](http://www.gnu.org/licenses/gpl.html) and is distributed
*without any warranty*.

* * * * *

Martin Reinecke's avatar
Martin Reinecke committed
135
**NIFTy** project homepage:
Jait Dixit's avatar
Jait Dixit committed
136
137
[](http://www.mpa-garching.mpg.de/ift/nifty/)

Martin Reinecke's avatar
Martin Reinecke committed
138
[1] Selig et al., "NIFTy - Numerical Information Field Theory - a
Jait Dixit's avatar
Jait Dixit committed
139
140
versatile Python library for signal inference", [A&A, vol. 554, id.
A26](http://dx.doi.org/10.1051/0004-6361/201321236), 2013;
141
[arXiv:1301.4499](http://www.arxiv.org/abs/1301.4499)