[pynfft] 01/03: Imported Upstream version 1.2
Ghislain Vaillant
ghisvail-guest at moszumanska.debian.org
Sat Jan 18 17:55:35 UTC 2014
This is an automated email from the git hooks/post-receive script.
ghisvail-guest pushed a commit to branch master
in repository pynfft.
commit 850688fb06e7ebb5a9a78270cdd1164121da9f9b
Author: Ghislain Vaillant <ghisvail at gmail.com>
Date: Sat Jan 18 17:46:58 2014 +0000
Imported Upstream version 1.2
---
CHANGELOG.txt | 119 ++++++
CONTRIBUTING.rst | 19 +
COPYING.txt | 675 +++++++++++++++++++++++++++++++++
PKG-INFO | 34 ++
README.rst | 100 +++++
doc/Makefile | 153 ++++++++
doc/source/api.rst | 7 +
doc/source/api/nfft.rst | 59 +++
doc/source/api/util.rst | 24 ++
doc/source/conf.py | 242 ++++++++++++
doc/source/index.rst | 54 +++
doc/source/tutorial.rst | 216 +++++++++++
pyNFFT.egg-info/PKG-INFO | 34 ++
pyNFFT.egg-info/SOURCES.txt | 28 ++
pyNFFT.egg-info/dependency_links.txt | 1 +
pyNFFT.egg-info/requires.txt | 2 +
pyNFFT.egg-info/top_level.txt | 1 +
pynfft/__init__.py | 20 +
pynfft/cnfft3.pxd | 154 ++++++++
pynfft/cnfft3util.pxd | 34 ++
pynfft/nfft.pyx | 707 +++++++++++++++++++++++++++++++++++
pynfft/util.pyx | 83 ++++
requirements.txt | 3 +
setup.cfg | 13 +
setup.py | 154 ++++++++
tests/__init__.py | 0
tests/test_nfft.py | 209 +++++++++++
27 files changed, 3145 insertions(+)
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
new file mode 100644
index 0000000..b7d6292
--- /dev/null
+++ b/CHANGELOG.txt
@@ -0,0 +1,119 @@
+Changelog
+=========
+
+Changes in version 1.2
+----------------------
+
+ * code refactoring, prepare for move to multi-precision version of NFFT
+ * break support for old 1.0.x API
+ * add option to precompute at construct time
+
+Changes in version 1.1.1
+------------------------
+
+ * simplify build system
+ * add support for pip dependencies
+ * simplify documentation tree
+ * add option for generating documentation in build system
+ * source distribution is now embedding the documentation
+
+Changes in version 1.1
+----------------------
+
+ * PEP 440 compliant version string
+ * more pythonic API, breaks compatibility with 1.0.x
+ * documentation update
+
+
+Changes in version 1.0.1
+------------------------
+
+ * update installation instructions
+ * change registration of cleanup routine to use Py_AtExit
+
+
+Changes in version 1.0
+----------------------
+
+ * simplify code base
+ * pynfft.nfft and pynfft.solver moved to pynfft
+ * revert support for multiple floating precision
+ * fix missing documentation for the solver
+
+
+Changes in version 0.6
+----------------------
+
+ * pynfft.nfft: enable openmp support
+
+Changes in version 0.5
+----------------------
+
+ * pynfft.nfft: rewrite NFFT class internals to support multiple floating
+ point precision, coming in a future version of libnfft3
+ * Documentation: first draft of the tutorial section
+
+Changes in version 0.4.1
+------------------------
+
+ * New simplified test suite.
+
+Changes in version 0.4
+----------------------
+
+ * Improved flag management: NFFT now only accepts the list of supported
+ flags listed in its documentaton.
+ * pynfft.util: utility functions listed in nfft3util.h. Only, the random
+ initializers and Voronoi weights computation functions have been wrapped.
+ * Changelog is no longer part of the sphinx tree.
+
+Changes in version 0.3.1
+------------------------
+
+ * Fixed issue #1: crash in test_nfft due to use of MALLOC flags
+
+Changes in version 0.3
+----------------------
+
+ * Improve precomputation flag management in NFFT and Solver classes
+ * Various code improvements
+ * Update documentation for all modules
+
+Changes in version 0.2.4
+------------------------
+
+ * Add sphinx documentation
+
+Changes in version 0.2.3
+------------------------
+
+ * Level-up Solver class with the improvement made on NFFT
+ * Update test suite for pynfft.nfft
+
+Changes in version 0.2.2
+------------------------
+
+ * Completed switch to non-malloc'd arrays for x, f and f_hat. These are now managed by internal or external numpy arrays
+ * Remove management of obsolete MALLOC flags
+ * Fix broken test for non-contiguousness for external arrays
+
+Changes in version 0.2.1
+------------------------
+
+ * Added experimental support for external python arrays, which can replace the internal malloc'd x, f and f_hat
+
+Changes in version 0.2
+------------------------
+
+ * Added support for the solver component of the NFFT library
+
+Changes in version 0.1.1
+------------------------
+
+ * Added non-complete test coverage for pynfft.nfft
+
+Version 0.1
+-----------
+
+ * Initial release. Experimental support for the nfft component of the NFFT library
+
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
new file mode 100644
index 0000000..74601fe
--- /dev/null
+++ b/CONTRIBUTING.rst
@@ -0,0 +1,19 @@
+How to contribute to pyNFFT
+===========================
+
+Please feel free to [open issues][] and send pull requests on GitHub. When sending a pull request, please create a new feature branch, and send your pull
+request from that branch. Please do *not* send pull requests from your `master`
+branch because to avoid potential merge conflicts.
+
+Improving features
+-----------------
+
+The NFFT library contains a lot more features than the pyNFFT wrapper supports
+at the moment. If you are interested in developping one of these features, feel
+free to get coding and send me your contribution for inclusion to the project.
+
+Coding style
+------------
+
+This project follows the PEP8 coding guidelines. Please make sure your code has been tested with a code analysis tool such as `pyflakes <https://pypi.python.org/pypi/pyflakes>`_ and `pep8 <https://pypi.python.org/pypi/pep8>`_ before submitting it.
+
diff --git a/COPYING.txt b/COPYING.txt
new file mode 100644
index 0000000..10926e8
--- /dev/null
+++ b/COPYING.txt
@@ -0,0 +1,675 @@
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+Also add information on how to contact you by electronic and paper mail.
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+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+
diff --git a/PKG-INFO b/PKG-INFO
new file mode 100644
index 0000000..2985b06
--- /dev/null
+++ b/PKG-INFO
@@ -0,0 +1,34 @@
+Metadata-Version: 1.1
+Name: pyNFFT
+Version: 1.2
+Summary: A pythonic wrapper around NFFT
+Home-page: https://github.com/ghisvail/pyNFFT.git
+Author: Ghislain Vaillant
+Author-email: ghisvail at gmail.com
+License: UNKNOWN
+Description: "The NFFT is a C subroutine library for computing the
+ nonequispaced discrete Fourier transform (NDFT) in one or more dimensions, of
+ arbitrary input size, and of complex data."
+
+ The NFFT library is licensed under GPLv2 and available at:
+ http://www-user.tu-chemnitz.de/~potts/nfft/index.php
+
+ This wrapper provides a somewhat Pythonic access to some of the core NFFT
+ library functionalities and is largely inspired from the pyFFTW project
+ developped by Henry Gomersall (http://hgomersall.github.io/pyFFTW/).
+
+ This project is still work in progress and is still considered beta quality. In
+ particular, the API is not yet frozen and is likely to change as the
+ development continues. Please consult the documentation and changelog for more
+ information.
+Platform: UNKNOWN
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Multimedia :: Sound/Audio :: Analysis
diff --git a/README.rst b/README.rst
new file mode 100644
index 0000000..b5e3010
--- /dev/null
+++ b/README.rst
@@ -0,0 +1,100 @@
+pyNFFT - a Pythonic wrapper around the NFFT library
+===================================================
+
+"The NFFT is a C subroutine library for computing the nonequispaced discrete
+Fourier transform (NDFT) in one or more dimensions, of arbitrary input size,
+and of complex data."
+
+The `NFFT library <http://www-user.tu-chemnitz.de/~potts/nfft/index.php>`_
+is licensed under GPLv2.
+
+This wrapper provides a somewhat Pythonic access to some of the core NFFT
+library functionalities and is largely inspired from the pyFFTW project
+developped by Henry Gomersall (http://hgomersall.github.io/pyFFTW/).
+
+The documentation is hosted on
+`pythonhosted <http://pythonhosted.org/pyNFFT/>`_, the source code is
+available on `github <https://github.com/ghisvail/pyNFFT>`_ and the
+Python package index page is
+`here <https://pypi.python.org/pypi/pyNFFT>`_.
+
+Usage
+-----
+
+See the `tutorial <http://pythonhosted.org/pyNFFT/tutorial.html>`_
+section of the documentation.
+
+Installation
+------------
+
+Support for pip/easy_install has been added via the `Python Package Index
+<http://pypi.python.org/pypi/>`_. The pyNFFT package can be installed via::
+
+ pip install pynfft
+
+or::
+
+ easy_install pynfft
+
+Installation will fail if the NFFT library is not installed in a system-aware
+location. A workaround for this is to first call pip with::
+
+ pip install --no-install pynfft
+
+cd to where pip downloaded the package, then build with `setup.py`::
+
+ python setup.py build_ext -I <path_to_include> -L <path_to_lib>
+ -R <path_to_lib>
+
+and do a final call to pip::
+
+ pip install --no-download pynfft
+
+Building
+--------
+
+The pyNFFT package can be built from the cloned git repository by calling::
+
+ python setup.py build
+
+and then installed with::
+
+ python setup.py install
+
+The build process requires Cython in order to generate the cythonized
+c-files and use them for creating the shared object.::
+
+ python setup.py build_ext --inplace
+
+If you installed the NFFT library in a non system-aware location, use
+the `-I`, `-L` and `-R` flags. For instance, if your NFFT library is
+installed in $HOME/local::
+
+ $python setup.py build_ext --inplace -I <path_to_include>
+ -L <path_to_lib> -R <path_to_lib>
+
+Build info
+----------
+
+The NFFT library has to be compiled with the --enable-openmp flag to
+allow for the generation of the threaded version of the library.
+Without it, any attempt to building the project will fail.
+
+Requirements
+------------
+
+- Python 2.7 or greater
+- Numpy 1.6 or greater
+- NFFT library 3.2 or greater, compiled with openMP support
+- Cython 0.12 or greater
+
+Contributing
+------------
+
+See the CONTRIBUTING file.
+
+License
+-------
+
+The pyNFFT project is licensed under the GPLv3.
+See the bundled COPYING file for more details.
diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 0000000..dda5b4a
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,153 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+BUILDDIR = build
+
+# 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 clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+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 " 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 " 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 " linkcheck to check all external links for integrity"
+ @echo " doctest to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+ -rm -rf $(BUILDDIR)/*
+
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+ $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+ @echo
+ @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+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."
+
+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/pyNFFT.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pyNFFT.qhc"
+
+devhelp:
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+ @echo
+ @echo "Build finished."
+ @echo "To view the help file:"
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/pyNFFT"
+ @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyNFFT"
+ @echo "# devhelp"
+
+epub:
+ $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+ @echo
+ @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+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)."
+
+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."
+
+text:
+ $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+ @echo
+ @echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+ $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+ @echo
+ @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+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)."
+
+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."
+
+gettext:
+ $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+ @echo
+ @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+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."
+
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+ "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/doc/source/api.rst b/doc/source/api.rst
new file mode 100644
index 0000000..3b53eb2
--- /dev/null
+++ b/doc/source/api.rst
@@ -0,0 +1,7 @@
+API Reference
+*************
+
+.. toctree::
+
+ /api/nfft
+ /api/util
diff --git a/doc/source/api/nfft.rst b/doc/source/api/nfft.rst
new file mode 100644
index 0000000..d58a5d1
--- /dev/null
+++ b/doc/source/api/nfft.rst
@@ -0,0 +1,59 @@
+``pynfft`` - The core NFFT functionalities
+==========================================
+
+.. automodule:: pynfft
+
+NFFT Class
+----------
+
+.. autoclass:: pynfft.NFFT(f, f_hat, x=None, n=None, m=12, flags=None, *args, **kwargs)
+
+ .. autoattribute:: pynfft.NFFT.f
+
+ .. autoattribute:: pynfft.NFFT.f_hat
+
+ .. autoattribute:: pynfft.NFFT.x
+
+ .. autoattribute:: pynfft.NFFT.M
+
+ .. autoattribute:: pynfft.NFFT.d
+
+ .. autoattribute:: pynfft.NFFT.N
+
+ .. autoattribute:: pynfft.NFFT.N_total
+
+ .. autoattribute:: pynfft.NFFT.n
+
+ .. autoattribute:: pynfft.NFFT.m
+
+ .. autoattribute:: pynfft.NFFT.dtype
+
+ .. autoattribute:: pynfft.NFFT.flags
+
+ .. automethod:: pynfft.NFFT.precompute
+
+ .. automethod:: pynfft.NFFT.forward
+
+ .. automethod:: pynfft.NFFT.adjoint
+
+
+Solver Class
+------------
+
+.. autoclass:: pynfft.Solver(nfft_plan, flags=None)
+
+ .. autoattribute:: pynfft.Solver.w
+
+ .. autoattribute:: pynfft.Solver.w_hat
+
+ .. autoattribute:: pynfft.Solver.y
+
+ .. autoattribute:: pynfft.Solver.f_hat_iter
+
+ .. autoattribute:: pynfft.Solver.r_iter
+
+ .. autoattribute:: pynfft.Solver.flags
+
+ .. automethod:: pynfft.Solver.before_loop
+
+ .. automethod:: pynfft.Solver.loop_one_step
diff --git a/doc/source/api/util.rst b/doc/source/api/util.rst
new file mode 100644
index 0000000..b27326d
--- /dev/null
+++ b/doc/source/api/util.rst
@@ -0,0 +1,24 @@
+``pynfft.util`` - Utility functions
+===================================
+
+.. automodule:: pynfft.util
+
+Functions used for initialization of :class:`pynfft.NFFT` attributes in test
+scripts. For instance::
+
+ >>> from pynfft.util import vrand_unit_complex, vrand_shifted_unit_double
+ >>> x = np.empty(20, dtype=np.float64)
+ >>> vrand_shifted_unit_double(x)
+ >>> f_hat = np.empty(16, dtype=np.complex128)
+ >>> vrand_unit_complex(f_hat)
+
+.. autofunction:: pynfft.util.vrand_unit_complex(x)
+
+.. autofunction:: pynfft.util.vrand_shifted_unit_double(x)
+
+Functions used for computing the density compensation weights necessary for the
+iterative solver and adjoint NFFT.
+
+.. autofunction:: pynfft.util.voronoi_weights_1d(w, x)
+
+.. autofunction:: pynfft.util.voronoi_weights_S2(w, xi)
diff --git a/doc/source/conf.py b/doc/source/conf.py
new file mode 100644
index 0000000..8000861
--- /dev/null
+++ b/doc/source/conf.py
@@ -0,0 +1,242 @@
+# -*- coding: utf-8 -*-
+#
+# pyNFFT documentation build configuration file, created by
+# sphinx-quickstart on Fri Nov 8 19:44:07 2013.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+sys.path.insert(0, os.path.abspath('../..'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'pyNFFT'
+copyright = u'2013, Ghislain Vaillant'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '1.2'
+# The full version, including alpha/beta/rc tags.
+release = '1.2'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+#html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'pyNFFTdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+ ('index', 'pyNFFT.tex', u'pyNFFT Documentation',
+ u'Ghislain Vaillant', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ ('index', 'pynfft', u'pyNFFT Documentation',
+ [u'Ghislain Vaillant'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output ------------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ ('index', 'pyNFFT', u'pyNFFT Documentation',
+ u'Ghislain Vaillant', 'pyNFFT', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
diff --git a/doc/source/index.rst b/doc/source/index.rst
new file mode 100644
index 0000000..d4a63e4
--- /dev/null
+++ b/doc/source/index.rst
@@ -0,0 +1,54 @@
+.. pyNFFT documentation master file, created by
+ sphinx-quickstart on Thu May 30 19:37:18 2013.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to pyNFFT's documentation!
+==================================
+
+Introduction
+------------
+
+**pyNFFT** is a set of Pythonic wrapper classes around the `NFFT library
+<http://www-user.tu-chemnitz.de/~potts/nfft/>`_. The aim is to provide access
+to the core functionalities of the library using a more straightforward
+instantiation through Python classes, while keeping similar naming
+conventions to the C-library structures and routines.
+
+Right now, only the NFFT and solver components of the library are supported.
+Support for other components `may` come in the future, but is conditionned
+by the author's need for them. If you're interested in getting these components
+wrapped as well, please feel free to contribute.
+
+The design of the pyNFFT package assumes that the NFFT has been **compiled with
+OpenMP support**.
+
+The core interface of the NFFT is provided by the unified class,
+:class:`pynfft.NFFT`. The solver interface is in
+:class:`pynfft.Solver`.
+
+A comprehensive unittest suite is included with the source on the repository.
+The suite will be updated as more functionalities get introducted.
+
+Content
+-------
+
+.. toctree::
+ :maxdepth: 2
+
+ tutorial.rst
+ api.rst
+
+About this documentation
+------------------------
+
+This documentation is generated using the `Sphinx
+<http://sphinx.pocoo.org/>`_ documentation generator.
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/doc/source/tutorial.rst b/doc/source/tutorial.rst
new file mode 100644
index 0000000..a523865
--- /dev/null
+++ b/doc/source/tutorial.rst
@@ -0,0 +1,216 @@
+Using the NFFT
+==============
+
+In this tutorial, we assume that you are already familiar with the
+`non-uniform discrete Fourier transform
+<http://en.wikipedia.org/wiki/Non-uniform_discrete_Fourier_transform>`_
+and the `NFFT library <http://www-user.tu-chemnitz.de/~potts/nfft/>`_
+used for fast computation of NDFTs.
+
+Like the `FFTW library <http://www.fftw.org/>`_, the NFFT library relies
+on a specific data structure, called a plan, which stores all the data
+required for efficient computation and re-use of the NDFT. Each plan is
+tailored for a specific transform, depending on the geometry, level of
+precomputation and design parameters. The `NFFT manual
+<http://www-user.tu-chemnitz.de/~potts/nfft/guide3/html/index.html>`_
+contains comprehensive explanation on the NFFT implementation.
+
+The pyNFFT package provides a set of Pythonic wrappers around the main
+data structures of the NFFT library. Use of Python wrappers allows to
+simplify the manipulation of the library, whilst benefiting from the
+significant speedup provided by its C-implementation. Although the NFFT
+library supports many more applications, only the NFFT and iterative
+solver components have been wrapped so far.
+
+This tutorial is split into three main sections. In the first one, the
+general workflow for using the core of the
+:class:`pynfft.NFFT` class will be explained. Then, the
+:class:`pynfft.NFFT` class API will be detailed and illustrated with
+examples for the univariate and multivariate cases. Finally, the
+:class:`pynfft.Solver` iterative solver class will be briefly presented.
+
+.. _workflow:
+
+Workflow
+--------
+
+For users already familiar with the NFFT C-library, the workflow is
+basically the same. It consists in the following three steps:
+
+ #. instantiation
+
+ #. precomputation
+
+ #. execution
+
+In step 1, information such as the geometry of the transform or the
+desired level of precomputation is provided to the constructor, which
+takes care of allocating the internal arrays of the plan.
+
+Precomputation (step 2) can be started once the location of the
+non-uniform nodes have been set to the plan. Depending on the size of
+the transform and level of precomputation, this step may take some time.
+
+Finally (step 3), the forward or adjoint NFFT is computed by first
+setting the input data in either `f_hat` (forward) or `f` (adjoint),
+calling the corresponding function, and reading the output in `f`
+(forward) or `f_hat` (adjoint).
+
+.. _using_nfft:
+
+Using the NFFT
+--------------
+
+The core of this library is provided through the
+:class:`pyfftw.NFFT class`. All nfft components provided by the NFFT
+library are fully encapsulated within this class.
+
+In its simplest form, a pyfftw.NFFT object is created with a pair of
+complementary numpy arrays: the `f` and `f_hat` arrays, which can both
+act as input or output depending on the chosen transform, forward or
+adjoint.
+
+These arrays must be C-contiguous and of `numpy.complex128` type.
+Support for other floating precision could be coming later, when the
+NFFT library starts supporting multiple floating precision builds,
+like the FFTW does.
+
+**instantiation**
+
+The bare minimum to instantiate a new :class:`pynfft.NFFT` object is to
+specify the data arrays `f` and `f_hat`. The constructor will attempt to
+guess the geometry parameters from these arrays: `M`, the number of
+non-uniform nodes, and `N`, the shape of the uniform data.
+
+ >>> from pynfft import NFFT
+ >>> f = np.empty(96, dtype=np.complex128)
+ >>> f_hat = np.empty([16, 16], dtype=np.complex128)
+ >>> this_nfft = NFFT(f=f, f_hat=f_hat)
+ >>> print this_nfft.M
+ 96
+ >>> print this_nfft.N
+ (16, 16)
+
+More control over the precision, storage and speed of the NFFT can be
+gained by overriding the default design parameters `m`, `n` and
+`flags`. For more information, please consult the `NFFT manual
+<http://www-user.tu-chemnitz.de/~potts/nfft/guide3/html/index.html>`_.
+
+**precomputation**
+
+Precomputation *must* be performed before calling any of the
+transforms. The user can manually set the nodes of the NFFT object
+using the :attr:`pynfft.NFFT.x` property before calling the
+:meth:`pynfft.NFFT.precompute` method.
+
+ >>> this_nfft = NFFT(f=f, f_hat=f_hat)
+ >>> this_nfft.x = some_x
+ >>> this_nfft.precompute()
+
+Alternatively, precomputation can be performed at construct time:
+
+ >>> this_nfft = NFFT(f=f, f_hat=f_hat, x=x, precompute=True)
+
+**execution**
+
+The actual forward and adjoint NFFT are performed by calling the
+:meth:`pynfft.NFFT.forward` and :meth:`pynfft.NFFT.adjoint` methods.
+
+ >>> # forward transform
+ >>> ret = this_nfft.forward()
+ >>> # adjoint transform
+ >>> ret = this_nfft.adjoint()
+
+.. _using_solver:
+
+Using the iterative solver
+--------------------------
+
+**instantiation**
+
+The instantiation of a :class:`pynfft.Solver` object requires an
+instance of :class:`pynfft.NFFT`. The following code shows you a
+simple example:
+
+ >>> from pynfft import NFFT, Solver
+ >>> this_nfft = NFFT(f=some_f, f_hat=some_F, x=some_x, precompute=True)
+ >>> this_solver = Solver(this_nfft)
+
+It is strongly recommended to use an already *precomputed*
+:class:`pynfft.NFFT` object to instantiate a :class:`pynfft.Solver`
+object, or at the very least, make sure to call its precompute method
+before carrying on with the solver.
+
+Since the solver will typically run several iterations before
+converging to a stable solution, it is also strongly encourage to use
+the maximum level of precomputation to speed-up each call to the NFFT.
+Please check the paragraph regarding the choice of precomputation flags
+for the :class:`pynfft.NFFT`.
+
+By default, the :class:`pynfft.Solver` class uses the Conjugate
+Gradient of the first kind method (CGNR flag). This may be overriden in
+the constructor:
+
+ >>> this_solver = Solver(this_nfft, flags='CGNE')
+
+Convergence to a stable solution can be significantly speed-up using the
+right pre-conditioning weights. These can be specified by the flags
+'PRECOMPUTE_WEIGHT' and 'PRECOMPUTE_DAMP' and accessed by the
+:attr:`pynfft.Solver.w` and :attr:`pynfft.Solver.w_hat` attributes. By
+default, these weights are set to 1.
+
+ >>> this_solver = Solver(this_nfft, flags=('PRECOMPUTE_WEIGHT'))
+ >>> this_solver.w = some_w
+
+**using the solver**
+
+Before iterating, the solver has to be intialized. As a reminder, make
+sure the :class:`pynfft.NFFT` object used to instantiate the solver has
+been *precomputed*. Otherwise, the solver will be in an undefined state
+and will not behave properly.
+
+Initialization of the solver is performed first setting the non-uniform
+samples :attr:`pynfft.Solver.y` and initial guess of the solution
+:attr:`pynfft.Solver.f_hat_iter` and then calling the
+:meth:`pynfft.Solver.before_loop` method.
+
+ >>> this_solver.y = some_y
+ >>> this_solver.f_hat_iter = some_f_hat_iter
+ >>> this_solver.before_loop()
+
+By default, the initial guess of the solution is set to 0, which makes
+the first iteration of the solver essentially behave like a standard
+call to the adjoint NFFT.
+
+After initialization of the solver, a single iteration can be performed
+by calling the :meth:`pynfft.Solver.loop_one_step` method. With each
+iteration, the current solution is written in the
+:attr:`pynfft.Solver.f_hat_iter` attribute.
+
+ >>> this_solver.loop_one_step()
+ >>> print this_solver.f_hat_iter
+ >>> this_solver.loop_one_step()
+ >>> print this_solver.f_hat_iter
+
+The :class:`pynfft.Solver` class only supports one iteration at a time.
+It is at the discretion to implement the desired stopping condition,
+based for instance on a maximum iteration count or a threshold value on
+the residuals. The residuals can be read in the
+:attr:`pynfft.Solver.r_iter` attribute. Below are two simple examples:
+
+ - with a maximum number of iterations:
+
+ >>> niter = 10 # set number of iterations to 10
+ >>> for iiter in range(niter):
+ >>> this_solver.loop_one_step()
+
+ - with a threshold value:
+
+ >>> threshold = 1e-3
+ >>> try:
+ >>> while True:
+ >>> this_solver.loop_one_step()
+ >>> if(np.all(this_solver.r_iter < threshold)):
+ >>> raise StopCondition
+ >>> except StopCondition:
+ >>> # rest of the algorithm
diff --git a/pyNFFT.egg-info/PKG-INFO b/pyNFFT.egg-info/PKG-INFO
new file mode 100644
index 0000000..2985b06
--- /dev/null
+++ b/pyNFFT.egg-info/PKG-INFO
@@ -0,0 +1,34 @@
+Metadata-Version: 1.1
+Name: pyNFFT
+Version: 1.2
+Summary: A pythonic wrapper around NFFT
+Home-page: https://github.com/ghisvail/pyNFFT.git
+Author: Ghislain Vaillant
+Author-email: ghisvail at gmail.com
+License: UNKNOWN
+Description: "The NFFT is a C subroutine library for computing the
+ nonequispaced discrete Fourier transform (NDFT) in one or more dimensions, of
+ arbitrary input size, and of complex data."
+
+ The NFFT library is licensed under GPLv2 and available at:
+ http://www-user.tu-chemnitz.de/~potts/nfft/index.php
+
+ This wrapper provides a somewhat Pythonic access to some of the core NFFT
+ library functionalities and is largely inspired from the pyFFTW project
+ developped by Henry Gomersall (http://hgomersall.github.io/pyFFTW/).
+
+ This project is still work in progress and is still considered beta quality. In
+ particular, the API is not yet frozen and is likely to change as the
+ development continues. Please consult the documentation and changelog for more
+ information.
+Platform: UNKNOWN
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Multimedia :: Sound/Audio :: Analysis
diff --git a/pyNFFT.egg-info/SOURCES.txt b/pyNFFT.egg-info/SOURCES.txt
new file mode 100644
index 0000000..64629ee
--- /dev/null
+++ b/pyNFFT.egg-info/SOURCES.txt
@@ -0,0 +1,28 @@
+CHANGELOG.txt
+CONTRIBUTING.rst
+COPYING.txt
+README.rst
+requirements.txt
+setup.cfg
+setup.py
+/home/gv10-jessie/workspace/pyNFFT/pynfft/nfft.pyx
+/home/gv10-jessie/workspace/pyNFFT/pynfft/util.pyx
+doc/Makefile
+doc/source/api.rst
+doc/source/conf.py
+doc/source/index.rst
+doc/source/tutorial.rst
+doc/source/api/nfft.rst
+doc/source/api/util.rst
+pyNFFT.egg-info/PKG-INFO
+pyNFFT.egg-info/SOURCES.txt
+pyNFFT.egg-info/dependency_links.txt
+pyNFFT.egg-info/requires.txt
+pyNFFT.egg-info/top_level.txt
+pynfft/__init__.py
+pynfft/cnfft3.pxd
+pynfft/cnfft3util.pxd
+pynfft/nfft.pyx
+pynfft/util.pyx
+tests/__init__.py
+tests/test_nfft.py
\ No newline at end of file
diff --git a/pyNFFT.egg-info/dependency_links.txt b/pyNFFT.egg-info/dependency_links.txt
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/pyNFFT.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
diff --git a/pyNFFT.egg-info/requires.txt b/pyNFFT.egg-info/requires.txt
new file mode 100644
index 0000000..513352a
--- /dev/null
+++ b/pyNFFT.egg-info/requires.txt
@@ -0,0 +1,2 @@
+numpy
+cython
\ No newline at end of file
diff --git a/pyNFFT.egg-info/top_level.txt b/pyNFFT.egg-info/top_level.txt
new file mode 100644
index 0000000..bf62d41
--- /dev/null
+++ b/pyNFFT.egg-info/top_level.txt
@@ -0,0 +1 @@
+pynfft
diff --git a/pynfft/__init__.py b/pynfft/__init__.py
new file mode 100644
index 0000000..7711a72
--- /dev/null
+++ b/pynfft/__init__.py
@@ -0,0 +1,20 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2013 Ghislain Vaillant
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+from .nfft import NFFT, Solver
+import util
diff --git a/pynfft/cnfft3.pxd b/pynfft/cnfft3.pxd
new file mode 100644
index 0000000..3e2424d
--- /dev/null
+++ b/pynfft/cnfft3.pxd
@@ -0,0 +1,154 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2013 Ghislain Vaillant
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+cdef extern from "nfft3.h":
+
+ # precomputation flags for the NFFT component
+ ctypedef enum:
+ PRE_PHI_HUT #(1U<< 0)
+ FG_PSI #(1U<< 1)
+ PRE_LIN_PSI #(1U<< 2)
+ PRE_FG_PSI #(1U<< 3)
+ PRE_PSI #(1U<< 4)
+ PRE_FULL_PSI #(1U<< 5)
+ MALLOC_X #(1U<< 6)
+ MALLOC_F_HAT #(1U<< 7)
+ MALLOC_F #(1U<< 8)
+ FFT_OUT_OF_PLACE #(1U<< 9)
+ FFTW_INIT #(1U<< 10)
+ NFFT_SORT_NODES #(1U<< 11)
+ NFFT_OMP_BLOCKWISE_ADJOINT #(1U<<12)
+ PRE_ONE_PSI #(PRE_LIN_PSI| PRE_FG_PSI| PRE_PSI| PRE_FULL_PSI)
+
+ # precomputation flags for the FFTW component
+ ctypedef enum:
+ FFTW_ESTIMATE
+ FFTW_DESTROY_INPUT
+
+ # double precision complex type
+ ctypedef double fftw_complex[2]
+
+ # double precision NFFT plan
+ ctypedef struct nfft_plan:
+ fftw_complex *f_hat
+ # Vector of Fourier coefficients, size is N_total float_types.
+ fftw_complex *f
+ # Vector of samples, size is M_total float types.
+ double *x
+ # Nodes in time/spatial domain, size is $dM$ doubles.
+
+ void nfft_trafo_direct (nfft_plan *ths) nogil
+ # Computes a NDFT.
+
+ void nfft_adjoint_direct (nfft_plan *ths) nogil
+ # Computes an adjoint NDFT.
+
+ void nfft_trafo (nfft_plan *ths) nogil
+ # Computes a NFFT, see the definition.
+
+ void nfft_adjoint (nfft_plan *ths) nogil
+ # Computes an adjoint NFFT, see the definition.
+
+ void nfft_init_guru (nfft_plan *ths, int d, int *N, int M, int *n, int m,
+ unsigned nfft_flags, unsigned fftw_flags)
+ # Initialisation of a transform plan, guru.
+
+ void nfft_precompute_one_psi (nfft_plan *ths) nogil
+ # Precomputation for a transform plan.
+
+ void nfft_finalize (nfft_plan *ths)
+ # Destroys a transform plan.
+
+
+ ctypedef enum:
+ # precomputation flags for solver
+ LANDWEBER #(1U<< 0)
+ STEEPEST_DESCENT #(1U<< 1)
+ CGNR #(1U<< 2)
+ CGNE #(1U<< 3)
+ NORMS_FOR_LANDWEBER #(1U<< 4)
+ PRECOMPUTE_WEIGHT #(1U<< 5)
+ PRECOMPUTE_DAMP #(1U<< 6)
+
+ # stripped down alias of a NFFT plan used by solver
+ ctypedef struct nfft_mv_plan_complex:
+ pass
+
+ # complex solver plan
+ ctypedef struct solver_plan_complex:
+ nfft_mv_plan_complex *mv
+ # matrix vector multiplication.
+ unsigned flags
+ # iteration type
+ double *w
+ # weighting factors
+ double *w_hat
+ # damping factors
+ fftw_complex *y
+ # right hand side, samples
+ fftw_complex *f_hat_iter
+ # iterative solution
+ fftw_complex *r_iter
+ # iterated residual vector
+ fftw_complex *z_hat_iter
+ # residual of normal equation of \ first kind
+ fftw_complex *p_hat_iter
+ # search direction.
+ fftw_complex *v_iter
+ # residual vector update
+ double alpha_iter
+ # step size for search direction
+ double beta_iter
+ # step size for search correction
+ double dot_r_iter
+ # weighted dotproduct of r_iter
+ double dot_r_iter_old
+ # previous dot_r_iter
+ double dot_z_hat_iter
+ # weighted dotproduct of \ z_hat_iter
+ double dot_z_hat_iter_old
+ # previous dot_z_hat_iter
+ double dot_p_hat_iter
+ # weighted dotproduct of \ p_hat_iter
+ double dot_v_iter
+ # weighted dotproduct of v_iter
+
+ void solver_init_advanced_complex(solver_plan_complex *ths,
+ nfft_mv_plan_complex *mv,
+ unsigned flags)
+ # Advanced initialisation.
+
+ void solver_before_loop_complex(solver_plan_complex *ths) nogil
+ # Setting up residuals before the actual iteration.
+
+ void solver_loop_one_step_complex(solver_plan_complex *ths) nogil
+ # Doing one step in the iteration.
+
+ void solver_finalize_complex(solver_plan_complex *ths)
+ # Destroys the plan for the inverse transform.
+
+
+cdef extern from "fftw3.h":
+
+ void fftw_cleanup()
+ # cleanup routines
+
+ void fftw_init_threads()
+ # threading routines
+
+ void fftw_cleanup_threads()
+ # cleanup routines
diff --git a/pynfft/cnfft3util.pxd b/pynfft/cnfft3util.pxd
new file mode 100644
index 0000000..5dbdd18
--- /dev/null
+++ b/pynfft/cnfft3util.pxd
@@ -0,0 +1,34 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2013 Ghislain Vaillant
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+from cnfft3 cimport fftw_complex
+
+cdef extern from "nfft3util.h":
+
+ void nfft_vrand_unit_complex (fftw_complex *x, int n)
+ # Inits a vector of random complex numbers in \
+ # $[0,1]\times[0,1]{\rm i}$ .
+
+ void nfft_vrand_shifted_unit_double (double *x, int n)
+ # Inits a vector of random double numbers in $[-1/2,1/2]$ .
+
+ void nfft_voronoi_weights_1d (double *w, double *x, int M)
+ # Computes non periodic voronoi weights, \
+ # assumes ordered nodes $x_j$.
+
+ void nfft_voronoi_weights_S2(double *w, double *xi, int M)
+ # Computes voronoi weights for nodes on the sphere S^2. */
diff --git a/pynfft/nfft.pyx b/pynfft/nfft.pyx
new file mode 100644
index 0000000..2a131bf
--- /dev/null
+++ b/pynfft/nfft.pyx
@@ -0,0 +1,707 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2013 Ghislain Vaillant
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+import numpy as np
+cimport numpy as np
+from libc.stdlib cimport malloc, free
+from libc cimport limits
+from cnfft3 cimport *
+
+cdef extern from *:
+ int Py_AtExit(void (*callback)())
+
+# Initialize module
+# Numpy must be initialized. When using numpy from C or Cython you must
+# _always_ do that, or you will have segfaults
+np.import_array()
+
+# initialize FFTW threads
+fftw_init_threads()
+
+# register cleanup callbacks
+cdef void _cleanup():
+ fftw_cleanup()
+ fftw_cleanup_threads()
+
+Py_AtExit(_cleanup)
+
+
+########
+# NFFT #
+########
+
+cdef object nfft_supported_flags_tuple
+nfft_supported_flags_tuple = (
+ 'PRE_PHI_HUT',
+ 'FG_PSI',
+ 'PRE_LIN_PSI',
+ 'PRE_FG_PSI',
+ 'PRE_PSI',
+ 'PRE_FULL_PSI',
+ )
+nfft_supported_flags = nfft_supported_flags_tuple
+
+cdef object nfft_flags_dict
+nfft_flags_dict = {
+ 'PRE_PHI_HUT':PRE_PHI_HUT,
+ 'FG_PSI':FG_PSI,
+ 'PRE_LIN_PSI':PRE_LIN_PSI,
+ 'PRE_FG_PSI':PRE_FG_PSI,
+ 'PRE_PSI':PRE_PSI,
+ 'PRE_FULL_PSI':PRE_FULL_PSI,
+ 'MALLOC_X':MALLOC_X,
+ 'MALLOC_F_HAT':MALLOC_F_HAT,
+ 'MALLOC_F':MALLOC_F,
+ 'FFT_OUT_OF_PLACE':FFT_OUT_OF_PLACE,
+ 'FFTW_INIT':FFTW_INIT,
+ 'NFFT_SORT_NODES':NFFT_SORT_NODES,
+ 'NFFT_OMP_BLOCKWISE_ADJOINT':NFFT_OMP_BLOCKWISE_ADJOINT,
+ 'PRE_ONE_PSI':PRE_ONE_PSI,
+ }
+nfft_flags = nfft_flags_dict.copy()
+
+cdef object fftw_flags_dict
+fftw_flags_dict = {
+ 'FFTW_ESTIMATE':FFTW_ESTIMATE,
+ 'FFTW_DESTROY_INPUT':FFTW_DESTROY_INPUT,
+ }
+fftw_flags = fftw_flags_dict.copy()
+
+
+cdef class NFFT(object):
+ '''
+ NFFT is a class for computing the multivariate Non-uniform Discrete
+ Fourier (NDFT) transform using the NFFT library. The interface is
+ designed to be somewhat pythonic, whilst preserving the workflow of the
+ original C-library. Computation of the NFFT is achieved in 3 steps :
+ instantiation, precomputation and execution.
+
+ On instantiation, the geometry of the transform is guessed from the shape
+ of the input arrays :attr:`f` and :attr:`f_hat`. The node array :attr:`x`
+ can be optionally provided, otherwise it will be created internally.
+
+ Precomputation initializes the internals of the transform prior to
+ execution, and is called with the :meth:`precompute` method.
+
+ The forward and adjoint NFFT can be called with :meth:`forward` and
+ :meth:`adjoint` respectively. Each of these methods support internal array
+ update and coercion to the right internal dtype.
+ '''
+ cdef nfft_plan _plan
+ cdef int _d
+ cdef int _M
+ cdef int _m
+ cdef object _N
+ cdef object _n
+ cdef object _dtype
+ cdef object _flags
+ cdef object __f
+ cdef object __f_hat
+ cdef object __x
+
+ # where the C-related content of the class is being initialized
+ def __cinit__(self, f, f_hat, x=None, n=None, m=12, flags=None,
+ precompute=False, *args, **kwargs):
+
+ # support only double / double complex NFFT
+ # TODO: if support for multiple floating precision lands in the
+ # NFFT library, adapt this section to dynamically figure the
+ # real and complex dtypes
+ dtype_real = np.dtype('float64')
+ dtype_complex = np.dtype('complex128')
+
+ # precompute at construct time possible if x is provided
+ precompute = precompute and (x is not None)
+
+ # sanity checks on input arrays
+ if not isinstance(f, np.ndarray):
+ raise ValueError('f must be an instance of numpy.ndarray')
+
+ if not f.flags.c_contiguous:
+ raise ValueError('f must be C-contiguous')
+
+ if f.dtype != dtype_complex:
+ raise ValueError('f must be of type %s'%(dtype_complex))
+
+ if not isinstance(f_hat, np.ndarray):
+ raise ValueError('f_hat: must be an instance of numpy.ndarray')
+
+ if not f_hat.flags.c_contiguous:
+ raise ValueError('f_hat must be C-contiguous')
+
+ if f_hat.dtype != dtype_complex:
+ raise ValueError('f_hat must be of type %s'%(dtype_complex))
+
+ # guess geometry from input array if missing from optional inputs
+ M = f.size
+ N = f_hat.shape
+ d = f_hat.ndim
+ n = n if n is not None else [2 * Nt for Nt in N]
+ if len(n) != d:
+ raise ValueError('n should be of same length as N')
+ N_total = np.prod(N)
+ n_total = np.prod(n)
+
+ # check geometry is compatible with C-class internals
+ int_max = <Py_ssize_t>limits.INT_MAX
+ if not all([Nt > 0 for Nt in N]):
+ raise ValueError('N must be strictly positive')
+ if not all([Nt < int_max for Nt in N]):
+ raise ValueError('N exceeds integer limit value')
+ if not N_total < int_max:
+ raise ValueError('product of N exceeds integer limit value')
+ if not all([nt > 0 for nt in n]):
+ raise ValueError('n must be strictly positive')
+ if not all([nt < int_max for nt in n]):
+ raise ValueError('n exceeds integer limit value')
+ if not n_total < int_max:
+ raise ValueError('product of n exceeds integer limit value')
+ if not M > 0:
+ raise ValueError('M must be strictly positive')
+ if not M < int_max:
+ raise ValueError('M exceeds integer limit value')
+ if not m > 0:
+ raise ValueError('m must be strictly positive')
+ if not m < int_max:
+ raise ValueError('m exceeds integer limit value')
+
+ # sanity check on optional x array
+ if x is not None:
+ if not isinstance(x, np.ndarray):
+ raise ValueError('x must be an instance of numpy.ndarray')
+
+ if not x.flags.c_contiguous:
+ raise ValueError('x must be C-contiguous')
+
+ if x.dtype != dtype_real:
+ raise ValueError('x must be of type %s'%(dtype_real))
+
+ try:
+ x = x.reshape([M, d])
+ except ValueError:
+ raise ValueError('x is incompatible with geometry')
+ else:
+ x = np.empty([M, d], dtype=dtype_real)
+
+ # convert tuple of litteral precomputation flags to its expected
+ # C-compatible value. Each flag is a power of 2, which allows to compute
+ # this value using BITOR operations.
+ cdef unsigned int _nfft_flags = 0
+ cdef unsigned int _fftw_flags = 0
+ flags_used = ()
+
+ # sanity checks on user specified flags if any,
+ # else use default ones:
+ if flags is not None:
+ try:
+ flags = tuple(flags)
+ except:
+ flags = (flags,)
+ finally:
+ for each_flag in flags:
+ if each_flag not in nfft_supported_flags_tuple:
+ raise ValueError('Unsupported flag: %s'%(each_flag))
+ flags_used += flags
+ else:
+ flags_used += ('PRE_PHI_HUT', 'PRE_PSI',)
+
+ # set specific flags, for which we don't want the user to have a say
+ # on:
+ # FFTW specific flags
+ flags_used += ('FFTW_INIT', 'FFT_OUT_OF_PLACE', 'FFTW_ESTIMATE',
+ 'FFTW_DESTROY_INPUT',)
+
+ # Parallel computation flag
+ flags_used += ('NFFT_SORT_NODES',)
+
+ # Parallel computation flag, set only if multivariate transform
+ if d > 1:
+ flags_used += ('NFFT_OMP_BLOCKWISE_ADJOINT',)
+
+ # Calculate the flag code for the guru interface used for
+ # initialization
+ for each_flag in flags_used:
+ try:
+ _nfft_flags |= nfft_flags_dict[each_flag]
+ except KeyError:
+ try:
+ _fftw_flags |= fftw_flags_dict[each_flag]
+ except KeyError:
+ raise ValueError('Invalid flag: ' + '\'' +
+ each_flag + '\' is not a valid flag.')
+
+ # initialize plan
+ cdef int *p_N = <int *>malloc(sizeof(int) * d)
+ if p_N == NULL:
+ raise MemoryError
+ for t in range(d):
+ p_N[t] = N[t]
+
+ cdef int *p_n = <int *>malloc(sizeof(int) * d)
+ if p_n == NULL:
+ raise MemoryError
+ for t in range(d):
+ p_n[t] = n[t]
+
+ try:
+ nfft_init_guru(&self._plan, d, p_N, M, p_n, m,
+ _nfft_flags, _fftw_flags)
+ except:
+ raise MemoryError
+ finally:
+ free(p_N)
+ free(p_n)
+
+ self.__x = x
+ self.__f = f
+ self.__f_hat = f_hat
+ self._d = d
+ self._M = M
+ self._m = m
+ self._N = N
+ self._n = n
+ self._dtype = dtype_complex
+ self._flags = flags_used
+
+ # connect Python arrays to plan internals
+ self._update_f()
+ self._update_f_hat()
+ self._update_x()
+
+ # optional precomputation
+ if precompute:
+ self.execute_precomputation()
+
+ # here, just holds the documentation of the class constructor
+ def __init__(self, f, f_hat, x=None, n=None, m=12, flags=None,
+ *args, **kwargs):
+ '''
+ :param f: external array holding the non-uniform samples.
+ :type f: ndarray
+ :param f_hat: external array holding the Fourier coefficients.
+ :type f_hat: ndarray
+ :param x: optional array holding the nodes.
+ :type x: ndarray
+ :param n: oversampled multi-bandwith, default to 2 * N.
+ :type n: tuple of int
+ :param m: Cut-off parameter of the window function.
+ :type m: int
+ :param flags: list of precomputation flags, see note below.
+ :type flags: tuple
+
+ **Precomputation flags**
+
+ This table lists the supported precomputation flags for the NFFT.
+
+ +----------------------------+--------------------------------------------------+
+ | Flag | Description |
+ +============================+==================================================+
+ | PRE_PHI_HUT | Precompute the roll-off correction coefficients. |
+ +----------------------------+--------------------------------------------------+
+ | FG_PSI | Convolution uses Fast Gaussian properties. |
+ +----------------------------+--------------------------------------------------+
+ | PRE_LIN_PSI | Convolution uses a precomputed look-up table. |
+ +----------------------------+--------------------------------------------------+
+ | PRE_FG_PSI | Precompute Fast Gaussian. |
+ +----------------------------+--------------------------------------------------+
+ | PRE_PSI | Standard precomputation, uses M*(2m+2)*d values. |
+ +----------------------------+--------------------------------------------------+
+ | PRE_FULL_PSI | Full precomputation, uses M*(2m+2)^d values. |
+ +----------------------------+--------------------------------------------------+
+
+ Default value is ``flags = ('PRE_PHI_HUT', 'PRE_PSI')``.
+ '''
+ pass
+
+ def __dealloc__(self):
+ nfft_finalize(&self._plan)
+
+ def forward(self, use_dft=False):
+ '''Performs the forward NFFT.
+
+ :param use_dft: whether to use the DFT instead of the fast algorithm.
+ :type use_dft: boolean
+ :returns: the updated f array.
+ :rtype: ndarray
+
+ '''
+ if use_dft:
+ self.execute_trafo_direct()
+ else:
+ self.execute_trafo()
+ return self.f
+
+ def adjoint(self, use_dft=False):
+ '''Performs the adjoint NFFT.
+
+ :param use_dft: whether to use the DFT instead of the fast algorithm.
+ :type use_dft: boolean
+ :returns: the updated f_hat array.
+ :rtype: ndarray
+
+ '''
+ if use_dft:
+ self.execute_adjoint_direct()
+ else:
+ self.execute_adjoint()
+ return self.f_hat
+
+ def precompute(self):
+ '''Precomputes the NFFT plan internals.'''
+ self.execute_precomputation()
+
+ cdef execute_precomputation(self):
+ with nogil:
+ nfft_precompute_one_psi(&self._plan)
+
+ cdef execute_trafo(self):
+ with nogil:
+ nfft_trafo(&self._plan)
+
+ cdef execute_trafo_direct(self):
+ with nogil:
+ nfft_trafo_direct(&self._plan)
+
+ cpdef execute_adjoint(self):
+ with nogil:
+ nfft_adjoint(&self._plan)
+
+ cpdef execute_adjoint_direct(self):
+ with nogil:
+ nfft_adjoint_direct(&self._plan)
+
+ @property
+ def f(self):
+ '''The vector of non-uniform samples.'''
+ return self.__f
+
+ @f.setter
+ def f(self, new_f):
+ if not isinstance(new_f, np.ndarray):
+ raise ValueError('array is not an instance of numpy.ndarray')
+ if not new_f.flags.c_contiguous:
+ raise ValueError('array is not C-contiguous')
+ if new_f.dtype != self.__f.dtype:
+ raise ValueError('array dtype is not compatible')
+ try:
+ new_f = new_f.reshape(self.M)
+ except ValueError:
+ raise ValueError('array shape is not compatible')
+ self.__f = new_f
+ self._update_f()
+
+ cdef _update_f(self):
+ '''C-level array updater.'''
+ self._plan.f = <fftw_complex *>np.PyArray_DATA(self.__f)
+
+ @property
+ def f_hat(self):
+ '''The vector of Fourier coefficients.'''
+ return self.__f_hat
+
+ @f_hat.setter
+ def f_hat(self, new_f_hat):
+ if not isinstance(new_f_hat, np.ndarray):
+ raise ValueError('array is not an instance of numpy.ndarray')
+ if not new_f_hat.flags.c_contiguous:
+ raise ValueError('array is not C-contiguous')
+ if new_f_hat.dtype != self.__f_hat.dtype:
+ raise ValueError('array dtype is not compatible')
+ try:
+ new_f_hat = new_f_hat.reshape(self.N)
+ except ValueError:
+ raise ValueError('array shape is not compatible')
+ self.__f_hat = new_f_hat
+ self._update_f_hat()
+
+ cdef _update_f_hat(self):
+ '''C-level array updater.'''
+ self._plan.f_hat = <fftw_complex *>np.PyArray_DATA(self.__f_hat)
+
+ @property
+ def x(self):
+ '''The nodes in time/spatial domain.'''
+ return self.__x
+
+ @x.setter
+ def x(self, new_x):
+ if not isinstance(new_x, np.ndarray):
+ raise ValueError('array is not an instance of numpy.ndarray')
+ if not new_x.flags.c_contiguous:
+ raise ValueError('array is not C-contiguous')
+ if new_x.dtype != self.__x.dtype:
+ raise ValueError('array dtype is not compatible')
+ try:
+ new_x = new_x.reshape([self.M, self.d])
+ except ValueError:
+ raise ValueError('array shape is not compatible')
+ self.__x = new_x
+ self._update_x()
+
+ cdef _update_x(self):
+ '''C-level array updater.'''
+ self._plan.x = <double *>np.PyArray_DATA(self.__x)
+
+ @property
+ def d(self):
+ '''The dimensionality of the NFFT.'''
+ return self._d
+
+ @property
+ def m(self):
+ '''The cut-off parameter of the window function.'''
+ return self._m
+
+ @property
+ def M(self):
+ '''The total number of samples.'''
+ return self._M
+
+ @property
+ def N_total(self):
+ '''The total number of Fourier coefficients.'''
+ return np.prod(self.N)
+
+ @property
+ def N(self):
+ '''The multi-bandwith size.'''
+ return self._N
+
+ @property
+ def n(self):
+ '''The oversampled multi-bandwith size.'''
+ return self._n
+
+ @property
+ def dtype(self):
+ '''The dtype of the NFFT.'''
+ return self._dtype
+
+ @property
+ def flags(self):
+ '''The precomputation flags.'''
+ return self._flags
+
+
+##########
+# Solver #
+##########
+
+cdef object solver_flags_dict
+solver_flags_dict = {
+ 'LANDWEBER':LANDWEBER,
+ 'STEEPEST_DESCENT':STEEPEST_DESCENT,
+ 'CGNR':CGNR,
+ 'CGNE':CGNE,
+ 'NORMS_FOR_LANDWEBER':NORMS_FOR_LANDWEBER,
+ 'PRECOMPUTE_WEIGHT':PRECOMPUTE_WEIGHT,
+ 'PRECOMPUTE_DAMP':PRECOMPUTE_DAMP,
+ }
+solver_flags = solver_flags_dict.copy()
+
+cdef class Solver:
+ '''
+ Solver is a class for computing the adjoint NFFT iteratively..
+
+ The instantiation requires a NFFT object used internally for the multiple
+ forward and adjoint NFFT performed. The class uses conjugate-gradient as
+ the default solver but alternative solvers can be specified.
+
+ Because the stopping conidition of the iterative computation may change
+ from one application to another, the implementation only let you carry
+ one iteration at a time with a call to :meth:`loop_one_step`.
+ Initialization of the solver is done by calling the :meth:`before_loop`
+ method.
+
+ The class exposes the internals of the solver through call to their
+ respective properties.
+ '''
+ cdef solver_plan_complex _plan
+ cdef NFFT _nfft_plan
+ cdef object _w
+ cdef object _w_hat
+ cdef object _y
+ cdef object _f_hat_iter
+ cdef object _r_iter
+ cdef object _dtype
+ cdef object _flags
+
+ def __cinit__(self, NFFT nfft_plan, flags=None):
+
+ # support only double / double complex NFFT
+ # TODO: if support for multiple floating precision lands in the
+ # NFFT library, adapt this section to dynamically figure the
+ # real and complex dtypes
+ dtype_real = np.dtype('float64')
+ dtype_complex = np.dtype('complex128')
+
+ # convert tuple of litteral precomputation flags to its expected
+ # C-compatible value. Each flag is a power of 2, which allows to compute
+ # this value using BITOR operations.
+ cdef unsigned int _flags = 0
+ flags_used = ()
+
+ # sanity checks on user specified flags if any,
+ # else use default ones:
+ if flags is not None:
+ try:
+ flags = tuple(flags)
+ except:
+ flags = (flags,)
+ finally:
+ flags_used += flags
+ else:
+ flags_used += ('CGNR',)
+
+ for each_flag in flags_used:
+ try:
+ _flags |= solver_flags_dict[each_flag]
+ except KeyError:
+ raise ValueError('Invalid flag: ' + '\'' +
+ each_flag + '\' is not a valid flag.')
+
+ # initialize plan
+ try:
+ solver_init_advanced_complex(&self._plan,
+ <nfft_mv_plan_complex*>&(nfft_plan._plan), _flags)
+ except:
+ raise MemoryError
+
+ self._nfft_plan = nfft_plan
+ d = nfft_plan.d
+ M = nfft_plan.M
+ N = nfft_plan.N
+
+ cdef np.npy_intp shape_M[1]
+ shape_M[0] = M
+
+ self._r_iter = np.PyArray_SimpleNewFromData(1, shape_M,
+ np.NPY_COMPLEX128, <void *>(self._plan.r_iter))
+
+ self._y = np.PyArray_SimpleNewFromData(1, shape_M,
+ np.NPY_COMPLEX128, <void *>(self._plan.y))
+
+ if 'PRECOMPUTE_WEIGHT' in flags_used:
+ self._w = np.PyArray_SimpleNewFromData(1, shape_M,
+ np.NPY_FLOAT64, <void *>(self._plan.w))
+ self._w[:] = 1 # make sure weights are initialized
+ else:
+ self._w = None
+
+ cdef np.npy_intp *shape_N
+ try:
+ shape_N = <np.npy_intp*>malloc(d*sizeof(np.npy_intp))
+ except:
+ raise MemoryError
+ for dt in range(d):
+ shape_N[dt] = N[dt]
+
+ self._f_hat_iter = np.PyArray_SimpleNewFromData(d, shape_N,
+ np.NPY_COMPLEX128, <void *>(self._plan.f_hat_iter))
+ self._f_hat_iter[:] = 0 # default initial guess
+
+ if 'PRECOMPUTE_DAMP' in flags_used:
+ self._w_hat = np.PyArray_SimpleNewFromData(d, shape_N,
+ np.NPY_FLOAT64, <void *>(self._plan.w_hat))
+ self._w_hat[:] = 1 # make sure weights are initialized
+ else:
+ self._w_hat = None
+
+ free(shape_N)
+
+ self._dtype = dtype_complex
+ self._flags = flags_used
+
+
+ def __init__(self, nfft_plan, flags=None):
+ '''
+ :param plan: instance of NFFT.
+ :type plan: :class:`NFFT`
+ :param flags: list of instantiation flags, see below.
+ :type flags: tuple
+
+ **Instantiation flags**
+
+ +---------------------+-----------------------------------------------------------------------------+
+ | Flag | Description |
+ +=====================+=============================================================================+
+ | LANDWEBER | Use Landweber (Richardson) iteration. |
+ +---------------------+-----------------------------------------------------------------------------+
+ | STEEPEST_DESCENT | Use steepest descent iteration. |
+ +---------------------+-----------------------------------------------------------------------------+
+ | CGNR | Use conjugate gradient (normal equation of the 1st kind). |
+ +---------------------+-----------------------------------------------------------------------------+
+ | CGNE | Use conjugate gradient (normal equation of the 2nd kind). |
+ +---------------------+-----------------------------------------------------------------------------+
+ | NORMS_FOR_LANDWEBER | Use Landweber iteration to compute the residual norm. |
+ +---------------------+-----------------------------------------------------------------------------+
+ | PRECOMPUTE_WEIGHT | Weight the samples, e.g. to cope with varying sampling density. |
+ +---------------------+-----------------------------------------------------------------------------+
+ | PRECOMPUTE_DAMP | Weight the Fourier coefficients, e.g. to favour fast decaying coefficients. |
+ +---------------------+-----------------------------------------------------------------------------+
+
+ Default value is ``flags = ('CGNR',)``.
+ '''
+ pass
+
+ def __dealloc__(self):
+ solver_finalize_complex(&self._plan)
+
+ cpdef before_loop(self):
+ '''Initialize solver internals.'''
+ with nogil:
+ solver_before_loop_complex(&self._plan)
+
+ cpdef loop_one_step(self):
+ '''Perform one iteration.'''
+ with nogil:
+ solver_loop_one_step_complex(&self._plan)
+
+ @property
+ def w(self):
+ '''Weighting factors.'''
+ return self._w
+
+ @property
+ def w_hat(self):
+ '''Damping factors.'''
+ return self._w_hat
+
+ @property
+ def y(self):
+ '''Right hand side, samples.'''
+ return self._y
+
+ @property
+ def f_hat_iter(self):
+ '''Iterative solution.'''
+ return self._f_hat_iter
+
+ @property
+ def r_iter(self):
+ '''Residual vector.'''
+ return self._r_iter
+
+ @property
+ def dtype(self):
+ '''The dtype of the solver.'''
+ return self._dtype
+
+ @property
+ def flags(self):
+ '''The precomputation flags.'''
+ return self._flags
diff --git a/pynfft/util.pyx b/pynfft/util.pyx
new file mode 100644
index 0000000..e03cf56
--- /dev/null
+++ b/pynfft/util.pyx
@@ -0,0 +1,83 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2013 Ghislain Vaillant
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+import numpy as np
+cimport numpy as np
+from cnfft3util cimport *
+
+
+# Numpy must be initialized. When using numpy from C or Cython you must
+# _always_ do that, or you will have segfaults
+np.import_array()
+
+def vrand_unit_complex (object[np.complex128_t, mode='c'] x not None):
+ '''
+ Utilitary function for initializing a vector of knots to random
+ values within the range [-0.5, 0.5).
+
+ Used for testing :attr:`pynfft.NFFT.x`.
+
+ :param x: pre-allocated array
+ :type x: ndarray <complex128>
+ '''
+ nfft_vrand_unit_complex(<fftw_complex *>&x[0], x.size)
+
+def vrand_shifted_unit_double (object[np.float64_t, mode='c'] x not None):
+ '''
+ Utilitary function for initializing a vector of data to random
+ complex values within the range [0, 1).
+
+ Used for testing :attr:`pynfft.NFFT.f` and
+ :attr:`pynfft.NFFT.f_hat`.
+
+ :param x: pre-allocated array
+ :type x: ndarray <float64>
+ '''
+ nfft_vrand_shifted_unit_double(<double *>&x[0], x.size)
+
+def voronoi_weights_1d (object[np.float64_t, mode='c'] w not None,
+ object[np.float64_t, mode='c'] x not None):
+ '''
+ Utilitary function for computing density compensation weights from 1D knots.
+
+ :param w: pre-allocated array
+ :type w: ndarray <float64>
+ :param x: ordered 1D knots
+ :type x: ndarray <float64>
+ '''
+ if x.size != w.size:
+ raise ValueError('Incompatible size between weights and nodes \
+ (%d, %d)'%(w.size, x.size))
+ nfft_voronoi_weights_1d(<double *>&w[0], <double *>&x[0], w.size)
+
+def voronoi_weights_S2 (object[np.float64_t, mode='c'] w not None,
+ object[np.float64_t, mode='c'] xi not None):
+ '''
+ Utilitary function for computing density compensation weights from knots
+ located on the surface of a sphere.
+
+ Useful for reconstruction of 3D radial data.
+
+ :param w: pre-allocated array
+ :type w: ndarray <float64>
+ :param xi: angular locations (2D) on the unit sphere
+ :type xi: ndarray <float64>
+ '''
+ if xi.size != 2 * w.size:
+ raise ValueError('Incompatible size between weights and nodes \
+ (%d, %d)'%(w.size, xi.size))
+ nfft_voronoi_weights_S2(<double *>&w[0], <double *>&xi[0], w.size)
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..2cf777e
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,3 @@
+cython>=0.12
+numpy>=1.6
+
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..811f979
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,13 @@
+[build_sphinx]
+source-dir = doc/source
+build-dir = doc/build
+all_files = 1
+
+[upload_sphinx]
+upload-dir = doc/build/html
+
+[egg_info]
+tag_build =
+tag_date = 0
+tag_svn_revision = 0
+
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..673b34b
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,154 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2013 Ghislain Vaillant
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+try:
+ from setuptools import setup, Command, Extension
+except ImportError:
+ from distutils.core import setup, Command, Extension
+from Cython.Distutils import build_ext as build_ext
+
+import os
+import os.path
+import numpy
+import shutil
+
+setup_dir = dir = os.path.dirname(os.path.abspath(__file__))
+package_name = 'pynfft'
+package_dir = os.path.join(setup_dir, package_name)
+
+include_dirs = [numpy.get_include()]
+library_dirs = []
+package_data = {}
+libraries = ['nfft3_threads', 'nfft3', 'fftw3_threads', 'fftw3', 'm']
+
+ext_modules = [
+ Extension(
+ name=package_name+'.nfft',
+ sources=[os.path.join(package_dir, 'nfft.pyx')],
+ libraries=libraries,
+ library_dirs=library_dirs,
+ include_dirs=include_dirs,
+ extra_compile_args='-O3 -fomit-frame-pointer -malign-double '
+ '-fstrict-aliasing -ffast-math'.split(),
+ ),
+ Extension(
+ name=package_name+'.util',
+ sources=[os.path.join(package_dir, 'util.pyx')],
+ libraries=libraries,
+ library_dirs=library_dirs,
+ include_dirs=include_dirs,
+ extra_compile_args='-O3 -fomit-frame-pointer -malign-double '
+ '-fstrict-aliasing -ffast-math'.split(),
+ ),
+]
+
+
+class CleanCommand(Command):
+
+ description = "Force clean of build files and directories."
+ user_options = []
+
+ def initialize_options(self):
+ self.all = None
+
+ def finalize_options(self):
+ pass
+
+ def run(self):
+ for _dir in [os.path.join(setup_dir, d)
+ for d in ('build', 'dist', 'doc/build', 'pyNFFT.egg-info')]:
+ if os.path.exists(_dir):
+ shutil.rmtree(_dir)
+ for root, _, files in os.walk(package_dir):
+ for _file in files:
+ if not _file.endswith(('.py', '.pyx', '.pxd', '.pxi')):
+ os.remove(os.path.join(package_dir, _file))
+
+
+class TestCommand(Command):
+ user_options = []
+
+ def initialize_options(self):
+ pass
+
+ def finalize_options(self):
+ pass
+
+ def run(self):
+ import sys
+ import subprocess
+ errno = subprocess.call(
+ [sys.executable, '-m', 'unittest', 'discover'])
+ raise SystemExit(errno)
+
+
+version = '1.2'
+release = True
+if not release:
+ version += '-dev'
+
+long_description = '''"The NFFT is a C subroutine library for computing the
+nonequispaced discrete Fourier transform (NDFT) in one or more dimensions, of
+arbitrary input size, and of complex data."
+
+The NFFT library is licensed under GPLv2 and available at:
+ http://www-user.tu-chemnitz.de/~potts/nfft/index.php
+
+This wrapper provides a somewhat Pythonic access to some of the core NFFT
+library functionalities and is largely inspired from the pyFFTW project
+developped by Henry Gomersall (http://hgomersall.github.io/pyFFTW/).
+
+This project is still work in progress and is still considered beta quality. In
+particular, the API is not yet frozen and is likely to change as the
+development continues. Please consult the documentation and changelog for more
+information.'''
+
+classifiers = [
+ 'Programming Language :: Python',
+ 'Programming Language :: Python :: 3',
+ 'Development Status :: 5 - Production/Stable',
+ 'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
+ 'Operating System :: POSIX :: Linux',
+ 'Intended Audience :: Developers',
+ 'Intended Audience :: Science/Research',
+ 'Topic :: Scientific/Engineering',
+ 'Topic :: Scientific/Engineering :: Mathematics',
+ 'Topic :: Multimedia :: Sound/Audio :: Analysis',
+]
+
+setup_args = {
+ 'name': 'pyNFFT',
+ 'version': version,
+ 'author': 'Ghislain Vaillant',
+ 'author_email': 'ghisvail at gmail.com',
+ 'description': 'A pythonic wrapper around NFFT',
+ 'long_description': long_description,
+ 'url': 'https://github.com/ghisvail/pyNFFT.git',
+ 'classifiers': classifiers,
+ 'packages': [package_name],
+ 'ext_modules': ext_modules,
+ 'include_dirs': include_dirs,
+ 'package_data': package_data,
+ 'cmdclass': {'build_ext': build_ext,
+ 'clean': CleanCommand,
+ 'test': TestCommand},
+ 'install_requires': ['numpy', 'cython'],
+}
+
+if __name__ == '__main__':
+ setup(**setup_args)
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test_nfft.py b/tests/test_nfft.py
new file mode 100644
index 0000000..327493a
--- /dev/null
+++ b/tests/test_nfft.py
@@ -0,0 +1,209 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2013 Ghislain Vaillant
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+from __future__ import division
+import numpy
+import unittest
+from numpy import pi
+from numpy.testing import assert_allclose
+from pynfft import NFFT
+from pynfft.nfft import fftw_flags, nfft_flags, nfft_supported_flags
+from pynfft.util import vrand_unit_complex, vrand_shifted_unit_double
+
+
+class Test_NFFT_init(unittest.TestCase):
+
+ def __init__(self, *args, **kwargs):
+ super(Test_NFFT_init, self).__init__(*args, **kwargs)
+ M, N = 32, (12, 12)
+ self.x = numpy.ones(len(N) * M, dtype=numpy.float64)
+ self.f = numpy.empty(M, dtype=numpy.complex128)
+ self.f_hat = numpy.empty(N, dtype=numpy.complex128)
+ self.m = 6
+ self.flags = ('PRE_PHI_HUT', 'FG_PSI', 'PRE_FG_PSI')
+
+ def test_default_args(self):
+ Nfft = NFFT(self.f, self.f_hat, self.x)
+ default_m = 12
+ default_flags = ('PRE_PHI_HUT', 'PRE_PSI')
+ self.assertEqual(Nfft.m, default_m)
+ for each_flag in default_flags:
+ self.assertIn(each_flag, Nfft.flags)
+
+ def test_user_specified_args(self):
+ Nfft = NFFT(self.f, self.f_hat, self.x, m=self.m, flags=self.flags)
+ self.assertEqual(Nfft.d, self.f_hat.ndim)
+ self.assertEqual(Nfft.N, self.f_hat.shape)
+ self.assertEqual(Nfft.N_total, self.f_hat.size)
+ self.assertEqual(Nfft.M, self.f.size)
+ self.assertEqual(Nfft.m, self.m)
+ for each_flag in self.flags:
+ self.assertIn(each_flag, Nfft.flags)
+
+
+class Test_NFFT_runtime(unittest.TestCase):
+
+ N = (32, 32)
+ M = 1280
+
+ def fdft(self, f_hat):
+ N = self.N
+ k = numpy.mgrid[slice(N[0]), slice(N[1])]
+ k = k.reshape([2, -1]) - numpy.asarray(N).reshape([2, 1]) / 2
+ x = self.x.reshape([-1, 2])
+ F = numpy.exp(-2j * pi * numpy.dot(x, k))
+ f_dft = numpy.dot(F, f_hat.ravel())
+ return f_dft
+
+ def idft(self, f):
+ N = self.N
+ k = numpy.mgrid[slice(N[0]), slice(N[1])]
+ k = k.reshape([2, -1]) - numpy.asarray(N).reshape([2, 1]) / 2
+ x = self.x.reshape([-1, 2])
+ F = numpy.exp(-2j * pi * numpy.dot(x, k))
+ f_hat_dft = numpy.dot(numpy.conjugate(F).T, f)
+ return f_hat_dft
+
+ def generate_new_arrays(self, init_f=False, init_f_hat=False):
+ f = numpy.empty(self.M, dtype=numpy.complex128)
+ f_hat = numpy.empty(self.N, dtype=numpy.complex128)
+ if init_f:
+ vrand_unit_complex(f.ravel())
+ if init_f_hat:
+ vrand_unit_complex(f_hat.ravel())
+ return f, f_hat
+
+ def generate_nfft_plan(self):
+ Nfft = NFFT(f=self.f, f_hat=self.f_hat, x=self.x, precompute=True)
+ return Nfft
+
+ def __init__(self, *args, **kwargs):
+ super(Test_NFFT_runtime, self).__init__(*args, **kwargs)
+ self.x = numpy.empty(self.M*len(self.N), dtype=numpy.float64)
+ vrand_shifted_unit_double(self.x.ravel())
+ self.f, self.f_hat = self.generate_new_arrays()
+
+ def test_trafo(self):
+ Nfft = self.generate_nfft_plan()
+ vrand_unit_complex(self.f_hat.ravel())
+ f = Nfft.forward(use_dft=False)
+ assert_allclose(f, self.fdft(self.f_hat), rtol=1e-3)
+
+ def test_trafo_direct(self):
+ Nfft = self.generate_nfft_plan()
+ vrand_unit_complex(self.f_hat.ravel())
+ f = Nfft.forward(use_dft=True)
+ assert_allclose(f, self.fdft(self.f_hat), rtol=1e-3)
+
+ def test_adjoint(self):
+ Nfft = self.generate_nfft_plan()
+ vrand_unit_complex(self.f)
+ f_hat = Nfft.adjoint(use_dft=False)
+ assert_allclose(f_hat.ravel(), self.idft(self.f), rtol=1e-3)
+
+ def test_adjoint_direct(self):
+ Nfft = self.generate_nfft_plan()
+ vrand_unit_complex(self.f)
+ f_hat = Nfft.adjoint(use_dft=True)
+ assert_allclose(f_hat.ravel(), self.idft(self.f), rtol=1e-3)
+
+
+class Test_NFFT_errors(unittest.TestCase):
+
+ def __init__(self, *args, **kwargs):
+ super(Test_NFFT_errors, self).__init__(*args, **kwargs)
+
+ def test_for_invalid_m(self):
+ M, N = 20, 32
+ f = numpy.empty(M, dtype=numpy.complex128)
+ f_hat = numpy.empty(N, dtype=numpy.complex128)
+
+ failing_m = (-1, 1+numpy.iinfo(numpy.int32).max)
+ for some_m in failing_m:
+ self.assertRaises(ValueError,
+ lambda: NFFT(f=f, f_hat=f_hat, m=some_m))
+
+ def test_for_invalid_n(self):
+ M, N = 20, 32
+ f = numpy.empty(M, dtype=numpy.complex128)
+ f_hat = numpy.empty(N, dtype=numpy.complex128)
+
+ failing_n = (-1, 1+numpy.iinfo(numpy.int32).max,
+ (4, numpy.iinfo(numpy.int32).max / 2))
+ for some_n in failing_n:
+ self.assertRaises(ValueError,
+ lambda: NFFT(f=f, f_hat=f_hat, n=(some_n,)))
+
+ def test_for_invalid_x(self):
+ M, N = 20, 32
+ x = numpy.empty(M, dtype=numpy.float64)
+ f = numpy.empty(M, dtype=numpy.complex128)
+ f_hat = numpy.empty(N, dtype=numpy.complex128)
+ # array must be contigous
+ self.assertRaises(ValueError,
+ lambda: NFFT(f=f, f_hat=f_hat, x=x[::2]))
+ # array must be of the right size
+ self.assertRaises(ValueError,
+ lambda: NFFT(f=f, f_hat=f_hat, x=x[:-2]))
+ # array must be of the right type
+ self.assertRaises(ValueError,
+ lambda: NFFT(f=f, f_hat=f_hat,
+ x=x.astype(numpy.float32)))
+
+ def test_for_invalid_f(self):
+ M, N = 20, 32
+ x = numpy.empty(M, dtype=numpy.float64)
+ f = numpy.empty(M, dtype=numpy.complex128)
+ f_hat = numpy.empty(N, dtype=numpy.complex128)
+ # array must be contigous
+ self.assertRaises(ValueError,
+ lambda: NFFT(f=f[::2], f_hat=f_hat))
+ # array must be of the right type
+ self.assertRaises(ValueError,
+ lambda: NFFT(f=f.astype(numpy.complex64), f_hat=f_hat))
+
+ def test_for_invalid_f_hat(self):
+ M, N = 20, 32
+ x = numpy.empty(M, dtype=numpy.float64)
+ f = numpy.empty(M, dtype=numpy.complex128)
+ f_hat = numpy.empty(N, dtype=numpy.complex128)
+ # array must be contigous
+ self.assertRaises(ValueError,
+ lambda: NFFT(f=f, f_hat=f_hat[::2]))
+ # array must be of the right type
+ self.assertRaises(ValueError,
+ lambda: NFFT(f=f, f_hat=f_hat.astype(numpy.complex64)))
+
+ def test_for_invalid_flags(self):
+ M, N = 20, 32
+ x = numpy.empty(M, dtype=numpy.float64)
+ f = numpy.empty(M, dtype=numpy.complex128)
+ f_hat = numpy.empty(N, dtype=numpy.complex128)
+ # non existing flags
+ invalid_flags = ('PRE_PHI_HOT', 'PRE_FOOL_PSI', 'FG_RADIO_PSI')
+ for flag in invalid_flags:
+ self.assertRaises(ValueError,
+ lambda: NFFT(f=f, f_hat=f_hat, flags=(flag,)))
+ # managed flags
+ managed_flags = []
+ managed_flags.append([flag for flag in nfft_flags.keys()
+ if flag not in nfft_supported_flags])
+ managed_flags.append([flag for flag in fftw_flags.keys()
+ if flag not in nfft_supported_flags])
+ for flag in managed_flags:
+ self.assertRaises(ValueError,
+ lambda: NFFT(f=f, f_hat=f_hat, flags=(flag,)))
--
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