Commit 102c1aad authored by Theo Steininger's avatar Theo Steininger

Merge branch 'master' into fftw_for_the_masses

# Conflicts:
#	test/test_spaces/test_power_space.py
parents 693d7194 05d1d092
Pipeline #13333 failed with stage
in 5 minutes and 19 seconds
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = build
# User-friendly check for sphinx-build
ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
endif
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
.PHONY: help
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html to make standalone HTML files"
@echo " dirhtml to make HTML files named index.html in directories"
@echo " singlehtml to make a single large HTML file"
@echo " pickle to make pickle files"
@echo " json to make JSON files"
@echo " htmlhelp to make HTML files and a HTML help project"
@echo " qthelp to make HTML files and a qthelp project"
@echo " applehelp to make an Apple Help Book"
@echo " devhelp to make HTML files and a Devhelp project"
@echo " epub to make an epub"
@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
@echo " latexpdf to make LaTeX files and run them through pdflatex"
@echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
@echo " text to make text files"
@echo " man to make manual pages"
@echo " texinfo to make Texinfo files"
@echo " info to make Texinfo files and run them through makeinfo"
@echo " gettext to make PO message catalogs"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " xml to make Docutils-native XML files"
@echo " pseudoxml to make pseudoxml-XML files for display purposes"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
@echo " coverage to run coverage check of the documentation (if enabled)"
.PHONY: clean
clean:
rm -rf $(BUILDDIR)/*
.PHONY: html
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
.PHONY: dirhtml
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
.PHONY: singlehtml
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
.PHONY: pickle
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
.PHONY: json
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
.PHONY: htmlhelp
htmlhelp:
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
@echo
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in $(BUILDDIR)/htmlhelp."
.PHONY: qthelp
qthelp:
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
@echo
@echo "Build finished; now you can run "qcollectiongenerator" with the" \
".qhcp project file in $(BUILDDIR)/qthelp, like this:"
@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/NIFTY.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/NIFTY.qhc"
.PHONY: applehelp
applehelp:
$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
@echo
@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
@echo "N.B. You won't be able to view it unless you put it in" \
"~/Library/Documentation/Help or install it in your application" \
"bundle."
.PHONY: devhelp
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/NIFTY"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/NIFTY"
@echo "# devhelp"
.PHONY: epub
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
.PHONY: latex
latex:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo
@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
@echo "Run \`make' in that directory to run these through (pdf)latex" \
"(use \`make latexpdf' here to do that automatically)."
.PHONY: latexpdf
latexpdf:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through pdflatex..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
.PHONY: latexpdfja
latexpdfja:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through platex and dvipdfmx..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
.PHONY: text
text:
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
@echo "Build finished. The text files are in $(BUILDDIR)/text."
.PHONY: man
man:
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
@echo
@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
.PHONY: texinfo
texinfo:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo
@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
.PHONY: info
info:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)/texinfo info
@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
.PHONY: gettext
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
.PHONY: changes
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
.PHONY: linkcheck
linkcheck:
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
@echo
@echo "Link check complete; look for any errors in the above output " \
"or in $(BUILDDIR)/linkcheck/output.txt."
.PHONY: doctest
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
.PHONY: coverage
coverage:
$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
@echo "Testing of coverage in the sources finished, look at the " \
"results in $(BUILDDIR)/coverage/python.txt."
.PHONY: xml
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
.PHONY: pseudoxml
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
.. currentmodule:: nifty
The ``ComposedOperator`` class -- A possibility to combine several operators
............................................................................
.. autoclass:: ComposedOperator
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``ConjugateGradient`` class -- Minimization routine
.......................................................
.. autoclass:: ConjugateGradient
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``DescentMinimizer`` class -- The Base class for minimizers
...............................................................
.. autoclass:: DescentMinimizer
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``DiagonalOperator`` class -- ...
.....................................
.. autoclass:: DiagonalOperator
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``EndomorphicOperator`` class -- ...
........................................
.. autoclass:: EndomorphicOperator
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``FFTOperator`` class -- Fourier Transformations
....................................................
.. autoclass:: FFTOperator
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``GLSpace`` class -- Gauss-Legendre pixelization of the sphere
..................................................................
.. autoclass:: GLSpace
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``GLLMTransformation`` class -- A transformation routine
............................................................
.. autoclass:: GLLMTransformation
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``HPSpace`` class -- HEALPix discretization of the sphere
.............................................................
.. autoclass:: HPSpace
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``HPLMTransformation`` class -- A transformation routine
............................................................
.. autoclass:: HPLMTransformation
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``InvertibleOperatorMixin`` class -- ...
............................................
.. autoclass:: InvertibleOperatorMixin
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``LMSpace`` class -- Spherical Harmonics components
.......................................................
.. autoclass:: LMSpace
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``LMGLTransformation`` class -- A transformation routine
............................................................
.. autoclass:: LMGLTransformation
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``LMHPTransformation`` class -- A transformation routine
............................................................
.. autoclass:: LMHPTransformation
:show-inheritance:
:members:
Minimization
------------
NIFTY provides several minimization routines.
.. toctree::
:maxdepth: 1
conjugate_gradient
descent_minimizer
Operators
=========
Operators perform some operation on a given field. In practice an operator can
take the form of an explicit matrix (e.g. stored in a Numpy array) or it may be
implicitly defined as a function (e.g. an FFT operation would not be encoded in
a matrix, but performed using an FFT routine). NIFTY includes a framework for
handling arbitrary operators, and basic methods for manipulating these
operators. Common functions like taking traces and extracting diagonals are
provided.
In order to have a blueprint for operators capable of handling fields, any
application of operators is split into a general and a concrete part. The
general part comprises the correct involvement of normalizations and
transformations, necessary for any operator type, while the concrete part is
unique for each operator subclass. In analogy to the field class, any operator
instance has a set of properties that specify its domain and target as well as
some additional flags.
Operator classes
----------------
NIFTY provides a base class for defining operators, as well as several pre-implemented operator types that are very often needed for signal inference
algorithms.
.. toctree::
:maxdepth: 1
diagonal_operator
fft_operator
composed_operator
response_operator
smoothing_operator
projection_operator
propagator_operator
endomorphic_operator
invertible_operator_mixin
transformations
.. currentmodule:: nifty
The ``LinearOperator`` class -- The base Operator Object
--------------------------------------------------------
.. autoclass:: LinearOperator
:show-inheritance:
:members:
......@@ -33,7 +33,6 @@ algorithms.
propagator_operator
endomorphic_operator
invertible_operator_mixin
transformations
.. currentmodule:: nifty
......
.. currentmodule:: nifty
The ``PowerSpace`` class -- The natural space underlying power-spectra
.......................................................................
.. autoclass:: PowerSpace
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``ProjectionOperator`` class -- ...
.......................................
.. autoclass:: ProjectionOperator
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``PropagatorOperator`` class -- ...
.......................................
.. autoclass:: PropagatorOperator
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``ResponseOperator`` class -- A possible response implementation
....................................................................
.. autoclass:: ResponseOperator
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``RGSpace`` class -- Regular Cartesian grids
................................................
.. autoclass:: RGSpace
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``RGRGTransformation`` class -- A transformation routine
............................................................
.. autoclass:: RGRGTransformation
:show-inheritance:
:members:
.. currentmodule:: nifty
The ``SmoothingOperator`` class -- Smoothing fields
...................................................
.. autoclass:: SmoothingOperator
:show-inheritance:
:members:
Spaces
======
The :py:class:`Space` classes of NIFTY represent geometrical spaces approximated by grids in the computer environment. Each subclass of the base class corresponds to a specific grid type and replaces some of the inherited methods with its own methods that are unique to the respective grid. This framework ensures an abstract handling of spaces independent of the underlying geometrical grid and the grid's resolution.
Each instance of a :py:class:`Space` needs to capture all structural and dimensional specifics of the grid and all computationally relevant quantities such as the data type of associated field values. These parameters are stored as properties of an instance of the class at its initialization, and they do not need to be accessed explicitly by the user thereafter. This prevents the writing of grid or resolution dependent code.
Spatial symmetries of a system can be exploited by corresponding coordinate transformations. Often, transformations from one basis to its harmonic counterpart can greatly reduce the computational complexity of algorithms. The harmonic basis is defined by the eigenbasis of the Laplace operator; e.g., for a flat position space it is the Fourier basis. This conjugation of bases is implemented in NIFTY by distinguishing conjugate space classes, which can be obtained by the instance method *get_codomain* (and checked for by *check_codomain*). Moreover, transformations between conjugate spaces are performed automatically if required.
Space classes
-------------
Next to the generic :py:class:`Space` class, NIFTY has implementations of five subclasses, representing specific geometrical spaces and their discretizations.
.. toctree::
:maxdepth: 1
rg_space
hp_space
gl_space
lm_space
power_space
.. currentmodule:: nifty
The ``Space`` class -- The base Space object
--------------------------------------------
.. autoclass:: Space
:show-inheritance:
:members:
Transformations
---------------
NIFTY provides transformations
.. toctree::
:maxdepth: 1
rgrg_transformation
gllm_transformation
hplm_transformation
lmgl_transformation
lmhp_transformation
This diff is collapsed.
......@@ -23,29 +23,29 @@ from .line_search import LineSearch
class LineSearchStrongWolfe(LineSearch):
"""Class for finding a step size that satisfies the strong Wolfe conditions.
Algorithm contains two stages. It begins whit a trial step length and it
Algorithm contains two stages. It begins whit a trial step length and it
keeps increasing the it until it finds an acceptable step length or an
interval. If it does not satisfy the Wolfe conditions it performs the Zoom
algorithm (second stage). By interpolating it decreases the size of the
interval until an acceptable step length is found.
interval. If it does not satisfy the Wolfe conditions it performs the Zoom
algorithm (second stage). By interpolating it decreases the size of the
interval until an acceptable step length is found.
Parameters
----------
c1 : float
c1 : float
Parameter for Armijo condition rule. (Default: 1e-4)
c2 : float
Parameter for curvature condition rule. (Default: 0.9)
max_step_size : float
Maximum step allowed in to be made in the descent direction.
Maximum step allowed in to be made in the descent direction.
(Default: 50)
max_iterations : integer
Maximum number of iterations performed by the line search algorithm.
(Default: 10)
max_zoom_iterations : integer
Maximum number of iterations performed by the zoom algorithm.
Maximum number of iterations performed by the zoom algorithm.
(Default: 10)
Attributes
----------
c1 : float
......@@ -53,19 +53,18 @@ class LineSearchStrongWolfe(LineSearch):
c2 : float
Parameter for curvature condition rule.
max_step_size : float
Maximum step allowed in to be made in the descent direction.
Maximum step allowed in to be made in the descent direction.
max_iterations : integer
Maximum number of iterations performed by the line search algorithm.
max_zoom_iterations : integer
Maximum number of iterations performed by the zoom algorithm.
"""
def __init__(self, c1=1e-4, c2=0.9,
max_step_size=50, max_iterations=10,
max_zoom_iterations=10):
super(LineSearchStrongWolfe, self).__init__()
self.c1 = np.float(c1)
......@@ -76,11 +75,11 @@ class LineSearchStrongWolfe(LineSearch):
def perform_line_search(self, energy, pk, f_k_minus_1=None):
"""Performs the first stage of the algorithm.
It starts with a trial step size and it keeps increasing it until it
satisfy the strong Wolf conditions. It also performs the descent and
It starts with a trial step size and it keeps increasing it until it
satisfy the strong Wolf conditions. It also performs the descent and
returns the optimal step length and the new enrgy.
Parameters
----------
energy : Energy object
......@@ -89,9 +88,9 @@ class LineSearchStrongWolfe(LineSearch):
pk : Field
Unit vector pointing into the search direction.
f_k_minus_1 : float
Value of the fuction (which is being minimized) at the k-1
Value of the fuction (which is being minimized) at the k-1
iteration of the line search procedure. (Default: None)
Returns
-------
alpha_star : float
......@@ -100,9 +99,9 @@ class LineSearchStrongWolfe(LineSearch):
Value of the energy after the performed descent.
energy_star : Energy object
The new Energy object on the new position.
"""
"""
self._set_line_energy(energy, pk, f_k_minus_1=f_k_minus_1)
c1 = self.c1
c2 = self.c2
......@@ -195,11 +194,11 @@ class LineSearchStrongWolfe(LineSearch):
def _zoom(self, alpha_lo, alpha_hi, phi_0, phiprime_0,
phi_lo, phiprime_lo, phi_hi, c1, c2):
"""Performs the second stage of the line search algorithm.
If the first stage was not successful then the Zoom algorithm tries to
find a suitable step length by using bisection, quadratic, cubic
If the first stage was not successful then the Zoom algorithm tries to
find a suitable step length by using bisection, quadratic, cubic
interpolation.
Parameters
----------
alpha_lo : float
......@@ -207,24 +206,24 @@ class LineSearchStrongWolfe(LineSearch):
alph_hi : float
The upper boundary for the step length interval.
phi_0 : float
Value of the energy at the starting point of the line search
Value of the energy at the starting point of the line search
algorithm.
phiprime_0 : Field