move some updated doc pages to master

docs/ackn.rst

@@ -1,36 +1,44 @@
+.. _ackn:
+
 Acknowledgments
 ===============
 
-The main code and mathematical development is by:
+FINUFFT was initiated by Jeremy Magland and Alex Barnett at the
+Center for Computational Mathematics, Flatiron Institute.
+The main developer and maintainer is:
 
-* Alex Barnett (Flatiron Institute)
-* Jeremy Magland (Flatiron Institute)
-
-Significant SIMD vectorization/acceleration of the spreader by:
+* Alex Barnett
 
-* Ludvig af Klinteberg (SFU)
+Major code contributions by:
 
-Other code contributions:
+* Jeremy Magland - multithreaded spreader, benchmark vs other codes
+* Ludvig af Klinteberg - SIMD vectorization/acceleration of spreader, julia wrapper
+* Yu-Hsuan ("Melody") Shih - 2d1many, 2d2many vectorized interface, GPU version
+* Andrea Malleo - guru interface prototype and tests
+* Libin Lu - guru Fortran, python, MATLAB/octave, julia interfaces
+
+Other significant code contributions by:
 
-* Yu-Hsuan ("Melody") Shih - 2d1many, 2d2many interface for many vectors same points
-* Leslie Greengard and June-Yub Lee - CMCL fortran drivers and test codes
-* Dan Foreman-Mackey - python wrappers
+* Joakim Andén - catching bugs, Matlab/FFTW issues, performance tests, python
+* Leslie Greengard and June-Yub Lee - CMCL Fortran test drivers
+* Dan Foreman-Mackey - early python wrappers
 * David Stein - python wrappers
-* Dylan Simon - sphinx help
-* Amit Moscovich - Mac OSX build
-
-Testing, bug reports:
+* Vineet Bansal - pypy packaging
+
+Testing, bug reports, helpful discussions:
 
-* Joakim Anden - catching memory leak, Matlab/FFTW issues, performance tests
 * Hannah Lawrence - user testing and finding bugs
-* Marina Spivak - fortran testing
+* Marina Spivak - Fortran testing
 * Hugo Strand - python bugs
-  
-Helpful discussions:
-
-* Charlie Epstein - analysis of kernel Fourier transform sums
+* Amit Moscovich - Mac OSX build
+* Dylan Simon - sphinx help
+* Zydrunas Gimbutas - explanation that NFFT uses Kaiser-Bessel backwards
+* Charlie Epstein - help with analysis of kernel Fourier transform sums
 * Christian Muller - optimization (CMA-ES) for early kernel design
 * Andras Pataki - complex number speed in C++
 * Timo Heister - pass/fail numdiff testing ideas
-* Zydrunas Gimbutas - explanation that NFFT uses Kaiser-Bessel backwards
 * Vladimir Rokhlin - piecewise polynomial approximation on complex boxes
+
+We are also indebted to the authors of other NUFFT codes
+such as NFFT3, CMCL NUFFT, MIRT, BART, etc, upon whose interfaces, code,
+and algorithms we have built.

docs/related.rst

@@ -1,35 +1,22 @@
+.. _related:
+
 Related packages
 ================
 
 Other recommended NUFFT libraries
 ---------------------------------
 
-- `NFFT3 <https://www-user.tu-chemnitz.de/~potts/nfft/>`_: well-supported and multi-featured C++ library using FFTW. Has MATLAB interface. However, significantly slower and/or more memory-intensive than FINUFFT (see reference [FIN]).
+- `NFFT3 <https://www-user.tu-chemnitz.de/~potts/nfft/>`_: well-supported and multi-featured C++ library using FFTW. Has MATLAB MEX interface. However, significantly slower and/or more memory-intensive than FINUFFT (see reference [FIN]). Has many more general abilities, eg, inverse NUFFT. We are working on this too.
+
+- `CMCL NUFFT <https://cims.nyu.edu/cmcl/nufft/nufft.html>`_: NYU single-threaded Fortran library using self-contained FFT, fast Gaussian gridding kernel. Has MATLAB MEX interface. Much (up to 50x even for one thread) slower than FINUFFT, but very easy to compile.
 
-- `CMCL NUFFT <https://cims.nyu.edu/cmcl/nufft/nufft.html>`_: NYU single-threaded Fortran library using self-contained FFT, Gaussian kernel. Has MATLAB interface. Much slower than FINUFFT.
+- `cuFINUFFT <https://github.com/flatironinstitute/cufinufft>`_: Our GPU version of FINUFFT, for single precision in 2D and 3D, type 1 and 2. Still under development by Melody Shih (NYU) and others. Often achieves speeds around 10x the CPU version.
 
-- `MIRT <https://web.eecs.umich.edu/~fessler/code/index.html>`_ Michigan Image Reconstruction Toolbox. Native MATLAB, single-threaded sparse mat-vec, prestores all kernel evaluations, thus is memory-intensive. Slower than FINUFFT for all tolerances smaller than 0.1.
+- `MIRT <https://web.eecs.umich.edu/~fessler/code/index.html>`_ Michigan Image Reconstruction Toolbox. Native MATLAB, single-threaded sparse mat-vec, prestores all kernel evaluations, thus is memory-intensive but surprisingly fast for a single-threaded implementation. However, slower than FINUFFT for all tolerances smaller than 0.1.
 
 - `PyNUFFT <https://github.com/jyhmiinlin/pynufft>`_ Python code supporting CPU and GPU operation. Have not compared against FINUFFT yet.
 
 
-Also see the summary of library performances in our paper [FIN].
+Also see the summary of library performances in our paper [FIN] in the
+:ref:`references <refs>`.
 
-
-Interfaces to FINUFFT from other languages
-------------------------------------------
-
-- `FINUFFT.jl <https://github.com/ludvigak/FINUFFT.jl>`_: a `julia <https://julialang.org/>`_ language wrapper by Ludvig af Klinteberg (SFU). This is actually a secondary wrapper around our python interface, so you should make sure that the latter is working first.
-
-- Vineet Bansal's pypi package https://pypi.org/project/finufftpy/
-
-
-Packages making use of FINUFFT
-------------------------------
-
-Here are some packages dependent on FINUFFT (please let us know others):
-
-- `ASPIRE <http://spr.math.princeton.edu>`_: software for cryo-EM, based at Amit Singer's group at Princeton. `github <https://github.com/PrincetonUniversity/ASPIRE-Python>`_
-
-- `sinctransform <https://github.com/hannahlawrence/sinctransform>`_: C++
-  and MATLAB codes to evaluate sums of the sinc and sinc^2 kernels between arbitrary nonuniform points in 1,2, or 3 dimensions, by Hannah Lawrence (2017 summer intern at Flatiron).

docs/users.rst

@@ -1,10 +1,35 @@
-Users and citations
-===================
+.. _users:
 
-Here we list papers describing work which uses FINUFFT or its new spreading
-kernel. Papers that merely cite our work are listed separately at the bottom. Please let me know if you are a user but not listed:
+Dependent packages, users, and citations
+========================================
 
-1. ASPIRE software for cryo-EM, based at Amit Singer's group at Princeton. https://github.com/PrincetonUniversity/ASPIRE-Python http://spr.math.princeton.edu/
+Here we list packages that depend on FINUFFT, and papers or groups using it.
+Papers that merely cite our work are listed separately at the bottom. Please let us know (and use github's dependent package link) if you are a user or package maintainer but not listed.
+
+Packages relying on FINUFFT
+---------------------------
+
+Here are some packages dependent on FINUFFT (please let us know of others,
+and also add them to github's Used By feature):
+
+1. `SMILI <https://github.com/astrosmili/smili>`_, very long baseline interferometry reconstruction code by `Kazu Akiyama <http://kazuakiyama.github.io/>`_ and others, uses FINUFFT (2d1, 2d2, Fortran interfaces) as a `key library <https://smili.readthedocs.io/en/latest/install.html#external-libraries>`_. Akiyama used SMILI to reconstruct the `famous black hole image <https://physicstoday.scitation.org/do/10.1063/PT.6.1.20190411a/full/>`_ in 2019 from the Event Horizon Telescope.
+
+#. `ASPIRE <http://spr.math.princeton.edu>`_: software for cryo-EM, based at Amit Singer's group at Princeton. `github <https://github.com/PrincetonUniversity/ASPIRE-Python>`_
+
+#. `sinctransform <https://github.com/hannahlawrence/sinctransform>`_: C++ and MATLAB codes to evaluate sums of the sinc and sinc^2 kernels between arbitrary nonuniform points in 1,2, or 3 dimensions, by Hannah Lawrence (2017 summer intern at Flatiron).
+
+#. `fsinc <https://github.com/gauteh/fsinc>`_:  Gaute Hope's fast sinc transform and interpolation python package.
+
+#. `FTK <https://github.com/flatironinstitute/ftk>`_: Factorization of the translation kernel for fast rigid image alignment, by Rangan, Spivak, Andén, and Barnett.
+
+#. `FINUFFT.jl <https://github.com/ludvigak/FINUFFT.jl>`_: a `julia <https://julialang.org/>`_ language wrapper by Ludvig af Klinteberg (SFU), now using pure julia rather than python.
+
+#. Vineet Bansal's pypi package https://pypi.org/project/finufftpy/. This will be updated soon.
+
+
+
+Research output using FINUFFT
+-----------------------------
 
 #. "Cryo-EM reconstruction of continuous heterogeneity by Laplacian spectral volumes", Amit Moscovich, Amit Halevi, Joakim Andén, and Amit Singer. To appear, Inv. Prob. (2020), https://arxiv.org/abs/1907.01898
 
@@ -18,20 +43,28 @@ kernel. Papers that merely cite our work are listed separately at the bottom. Pl
    series taken at unknown view angles with non-uniform distribution",
    International Conference on Image Processing (ICIP), (2019).
 
-#. Aleks Donev's group at NYU.
+#. "Factorization of the translation kernel for fast rigid image alignment,"
+   Aaditya Rangan, Marina Spivak, Joakim Andén, and Alex Barnett.
+   Inverse Problems 36 (2), 024001 (2020).
+   https://arxiv.org/abs/1905.12317
 
-Papers using our new window function but not the whole FINUFFT package:
+#. Aleks Donev's group at NYU; ongoing
+
+Papers using our new window (spreading) function but not the whole FINUFFT package:
 
 1. Davood Shamshirgar and Anna-Karin Tornberg, "Fast Ewald summation for electrostatic potentials with arbitrary periodicity", exploit our "Barnett-Magland" (BM), aka exp-sqrt, window function. https://arxiv.org/abs/1712.04732
 
-   #. Daniel Potts and Manfred Tasche, "Uniform error estimates for the NFFT", (2019) https://arxiv.org/abs/1912.09746 Claims a proof of tighter error constant for our exp-sqrt kernel, via Chebyshev expansions. See our remark on this in
-      https://arxiv.org/abs/2001.09405
+
+
 
-Citations to FINUFFT or its paper, that are not actual users:
+Citations to FINUFFT that do not appear to be actual users
+----------------------------------------------------------
 
 1. https://arxiv.org/abs/1903.08365
 
 #. https://arxiv.org/abs/1908.00041
 
 #. https://arxiv.org/abs/1908.00574
 
+#. https://arxiv.org/abs/1912.09746
+