Merge branch 'master' into 'sphinx_docs'

# Conflicts:
#   docs/source/conf.py
#   docs/source/field.rst
#   docs/source/index.rst

README.md

@@ -11,7 +11,7 @@ Summary
 
 ### Description
 
-**NIFTY**, "**N**umerical **I**nformation **F**ield **T**heor**y**", is
+**NIFTY**, "**N**umerical **I**nformation **F**ield **T**heor<strong>y</strong>", is
 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
@@ -87,21 +87,17 @@ Starting with a fresh Ubuntu installation move to a folder like
 
 -   Install basic packages like python, python-dev, gsl and others:
 
-        sudo apt-get install curl git autoconf python-dev python-pip python-numpy
+        sudo apt-get install curl git autoconf libtool python-dev python-pip python-numpy
 
 -   Install pyHealpix:
 
         git clone https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
-        cd pyHealpix
-        autoreconf -i && ./configure --prefix=$HOME/.local --enable-openmp --enable-native-optimizations && make -j4 && make install
-        cd ..
+        (cd pyHealpix && autoreconf -i && ./configure --prefix=$HOME/.local --enable-openmp --enable-native-optimizations && make -j4 install)
 
 -   Finally, NIFTy:
 
         git clone https://gitlab.mpcdf.mpg.de/ift/NIFTy.git
-        cd NIFTy
-        python setup.py install --user
-        cd ..
+        (cd NIFTy && python setup.py install --user)
 
 ### Installation on Linux systems in general
 
@@ -139,16 +135,13 @@ may cause trouble.
 -   Install NIFTy:
 
         git clone https://gitlab.mpcdf.mpg.de/ift/NIFTy.git
-        cd NIFTy
-        python setup.py install --user
-        cd ..
+        (cd NIFTy && python setup.py install --user)
 
 ### Running the tests
 
 In oder to run the tests one needs two additional packages:
 
-    pip install nose
-    pip install parameterized
+    pip install nose parameterized
 
 Afterwards the tests (including a coverage report) are run using the following
 command in the repository root:

ci/install_basics.sh

 #!/bin/bash
 
-apt-get install -y build-essential python python-pip python-dev git autoconf gsl-bin libgsl-dev wget 
+apt-get install -y build-essential python python-pip python-dev git autoconf libtool gsl-bin libgsl-dev wget

ci/install_h5py.sh

 #!/bin/bash
 
 apt-get install -y libhdf5-10 libhdf5-dev libhdf5-openmpi-10 libhdf5-openmpi-dev hdf5-tools
-
-export CC=mpicc
-export HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi
-export HDF5_MPI="ON"
-
-pip install --no-binary=h5py h5py
+CC=mpicc HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi HDF5_MPI="ON" pip install --no-binary=h5py h5py

ci/install_mpi4py.sh

 #!/bin/bash
 
 apt-get install -y openmpi-bin libopenmpi-dev
-pip install mpi4py
\ No newline at end of file
+pip install mpi4py

ci/install_pyHealpix.sh

 #!/bin/bash
 
 git clone https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
-cd pyHealpix
-autoreconf -i && ./configure && make -j4 install
-cd ..
+(cd pyHealpix && autoreconf -i && ./configure --enable-openmp --enable-native-optimizations && make -j4 install)
 rm -rf pyHealpix

ci/install_pyfftw.sh

@@ -3,7 +3,5 @@
 apt-get install -y libatlas-base-dev libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-mpi-dev libfftw3-mpi3 libfftw3-quad3 libfftw3-single3
 
 git clone -b mpi https://github.com/fredros/pyFFTW.git
-cd pyFFTW/
-CC=mpicc python setup.py build_ext install
-cd ..
-rm -r pyFFTW
+(cd pyFFTW && CC=mpicc python setup.py build_ext install)
+rm -rf pyFFTW

docs/Makefile

+# 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."

docs/source/composed_operator.rst

+.. currentmodule:: nifty
+
+The ``ComposedOperator`` class -- A possibility to combine several operators
+............................................................................
+
+.. autoclass:: ComposedOperator
+    :show-inheritance:
+    :members:

docs/source/conf.py

@@ -325,4 +325,4 @@ texinfo_documents = [
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-#intersphinx_mapping = {'https://docs.python.org/': None}
+#intersphinx_mapping = {'https://docs.python.org/': None}
\ No newline at end of file

docs/source/conjugate_gradient.rst

+.. currentmodule:: nifty
+
+The ``ConjugateGradient`` class -- Minimization routine
+.......................................................
+
+.. autoclass:: ConjugateGradient
+    :show-inheritance:
+    :members:

docs/source/descent_minimizer.rst

+.. currentmodule:: nifty
+
+The ``DescentMinimizer`` class -- The Base class for minimizers
+...............................................................
+
+.. autoclass:: DescentMinimizer
+    :show-inheritance:
+    :members:

docs/source/diagonal_operator.rst

+.. currentmodule:: nifty
+
+The ``DiagonalOperator`` class -- ...
+.....................................
+
+.. autoclass:: DiagonalOperator
+    :show-inheritance:
+    :members:

docs/source/endomorphic_operator.rst

+.. currentmodule:: nifty
+
+The ``EndomorphicOperator`` class -- ...
+........................................
+
+.. autoclass:: EndomorphicOperator
+    :show-inheritance:
+    :members:

docs/source/fft_operator.rst

+.. currentmodule:: nifty
+
+The ``FFTOperator`` class -- Fourier Transformations
+....................................................
+
+.. autoclass:: FFTOperator
+    :show-inheritance:
+    :members:

docs/source/field.rst

@@ -10,4 +10,3 @@ In NIFTY, Fields are used to store data arrays and carry all the needed metainfo
 .. autoclass:: Field
     :show-inheritance:
     :members:
-

docs/source/gl_space.rst

+.. currentmodule:: nifty
+
+The ``GLSpace`` class -- Gauss-Legendre pixelization of the sphere
+..................................................................
+
+.. autoclass:: GLSpace
+    :show-inheritance:
+    :members:

docs/source/gllm_transformation.rst

+.. currentmodule:: nifty
+
+The ``GLLMTransformation`` class -- A transformation routine
+............................................................
+
+
+.. autoclass:: GLLMTransformation
+    :show-inheritance:
+    :members:

docs/source/hp_space.rst

+.. currentmodule:: nifty
+
+The ``HPSpace`` class -- HEALPix discretization of the sphere
+.............................................................
+
+
+.. autoclass:: HPSpace
+    :show-inheritance:
+    :members:

docs/source/hplm_transformation.rst

+.. currentmodule:: nifty
+
+The ``HPLMTransformation`` class -- A transformation routine
+............................................................
+
+
+.. autoclass:: HPLMTransformation
+    :show-inheritance:
+    :members:

docs/source/index.rst

@@ -38,4 +38,3 @@ Indices and tables
 * :ref:`genindex`
 * :any:`Module Index <mod/modules>`
 * :ref:`search`
-

docs/source/invertible_operator_mixin.rst

+.. currentmodule:: nifty
+
+The ``InvertibleOperatorMixin`` class -- ...
+............................................
+
+.. autoclass:: InvertibleOperatorMixin
+    :show-inheritance:
+    :members:

docs/source/lm_space.rst

+.. currentmodule:: nifty
+
+The ``LMSpace`` class -- Spherical Harmonics components
+.......................................................
+
+.. autoclass:: LMSpace
+    :show-inheritance:
+    :members:

docs/source/lmgl_transformation.rst

+.. currentmodule:: nifty
+
+The ``LMGLTransformation`` class -- A transformation routine
+............................................................
+
+
+.. autoclass:: LMGLTransformation
+    :show-inheritance:
+    :members:

docs/source/lmhp_transformation.rst

+.. currentmodule:: nifty
+
+The ``LMHPTransformation`` class -- A transformation routine
+............................................................
+
+.. autoclass:: LMHPTransformation
+    :show-inheritance:
+    :members:

docs/source/minimization.rst

+Minimization
+------------
+NIFTY provides several minimization routines.
+
+
+.. toctree:: 
+    :maxdepth: 1
+
+    conjugate_gradient
+    descent_minimizer
+

docs/source/operator.rst

+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:

docs/source/power_space.rst

+.. currentmodule:: nifty
+
+The ``PowerSpace`` class --  The natural space underlying power-spectra
+.......................................................................
+
+.. autoclass:: PowerSpace
+    :show-inheritance:
+    :members:

docs/source/projection_operator.rst

+.. currentmodule:: nifty
+
+The ``ProjectionOperator`` class -- ...
+.......................................
+
+.. autoclass:: ProjectionOperator
+    :show-inheritance:
+    :members:

docs/source/propagator_operator.rst

+.. currentmodule:: nifty
+
+The ``PropagatorOperator`` class -- ...
+.......................................
+
+.. autoclass:: PropagatorOperator
+    :show-inheritance:
+    :members:

docs/source/response_operator.rst

+.. currentmodule:: nifty
+
+The ``ResponseOperator`` class -- A possible response implementation
+....................................................................
+
+.. autoclass:: ResponseOperator
+    :show-inheritance:
+    :members:

docs/source/rg_space.rst

+.. currentmodule:: nifty
+
+The ``RGSpace`` class -- Regular Cartesian grids
+................................................
+
+.. autoclass:: RGSpace
+    :show-inheritance:
+    :members:

docs/source/rgrg_transformation.rst

+.. currentmodule:: nifty
+
+The ``RGRGTransformation`` class -- A transformation routine
+............................................................
+
+
+.. autoclass:: RGRGTransformation
+    :show-inheritance:
+    :members:

docs/source/smoothing_operator.rst

+.. currentmodule:: nifty
+
+The ``SmoothingOperator`` class -- Smoothing fields
+...................................................
+
+.. autoclass:: SmoothingOperator
+    :show-inheritance:
+    :members:

docs/source/spaces.rst

+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
+