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~~*[[Agora]] -- website for rapid collaboration related to GNU Octave. Talk to [[User:JordiGH|Jordi]]~~

import projects from Summer_of_Code_Project_Ideas that were without an associated mentor

*Evaluate harmonics and cross-correlations of unevenly sampled and nonstationary time series, as in http://www.jstatsoft.org/v11/i02 (which has C code with interface to R). (This is now partly implemented in the [http://octave.sourceforge.net/lssa/index.html lssa] package.)

== General purpose Finite Element library ==

Octave-Forge already has a set of packages for discretizing Partial Differential operators by Finite Elements and/or Finite Volumes,

namely the [[bim package]] which relies on the [http://octave.sf.net/msh msh package] (which is in turn based on [http://geuz.org/gmsh/ gmsh]) for creating and managing 2D triangular and 3D tetrahedral meshes and on the [http://octave.sf.net/fpl fpl package] for visualizing 2D results within Octave or exporting 2D or 3D results in a format compatible with [http://www.paraview.org Paraview] or [https://wci.llnl.gov/codes/visit/ VisIT]. These packages, though, offer only a limited choice of spatial discretization methods which are based on low degree polynomials and therefore have a low order of accuracy even for problems with extremely smooth solutions.

The [http://geopdes.sf.net GeoPDEs] project, on the other hand, offers a complete suite of functions for discretizing a wide range of

differential operators related to important physical problems and uses basis functions of arbitrary polynomial degree that allow the construction of methods of high accuracy. These latter, though, are based on the IsoGeometric Analysis Method which, although very powerful and often better performing, is less widely known and adopted than the Finite Elements Method. The implementation of a general purpose library of Finite Elements seems therefore a valuable addition to Octave-Forge. Two possible interesting choices for implementing this package exist, the first consists of implementing the most common Finite Element spaces in the [http://geopdes.sf.net GeoPDEs] framework, which is possible as IsoGeometric Analysis can be viewed as a superset of the Finite Element Method, the other is to construct Octave language bindings for the free software library [http://fenicsproject.org/documentation/ FEniCS] based on the existing C++ or Python interfaces. This second approach has been developed during the GSOC 2013 and the Octave-Forge package [http://octave.sf.net/fem-fenics fem-fenics] is now available. However, fem-fenics could be extended in many different ways:

* implement the bindings for the UFL language inside Octave

* add new functions already available with Fenics but not yet in Octave

* create new functions specifically suited for Octave

* improve the efficiency of the code

The main goal for the fem-fenics package is ultimately to be merged with the FEnics project itself, so that it can remain in-sync with the main library development.

== Implement solver for initial-boundary value problems for parabolic-elliptic PDEs in 1D ==

The project will deliver a solver for initial-boundary value problems for parabolic-elliptic PDEs in 1D similar to Matlab's function <tt>pdepe</tt>. A good starting point is the [http://en.wikipedia.org/wiki/Method_of_lines method of lines] for which you can find more details [http://en.wikibooks.org/wiki/Partial_Differential_Equations/Method_of_Lines here] and [http://www.scholarpedia.org/article/Method_of_lines here], whereas an example implementation can be found [http://www.scholarpedia.org/article/Method_of_Lines/Example_Implementation here]. In addition, [http://www.pdecomp.net/ this page] provides some useful material.

== Implement solver for 1D nonlinear boundary value problems ==

The project will complete the implementation of the bvp4c solver that is already available in an initial version in the odepkg package

by adding a proper error estimator and will implement a matlab-compatible version of the bvp5c solver.

Details on the methods to be implemented can be found in [http://dx.doi.org/10.1145/502800.502801 this paper] on bvp4c and [http://www.jnaiam.net/new/uploads/files/014dde86eef73328e7ab674d1a32aa9c.pdf this paper] on bvp5c. Further details are available in [http://books.google.it/books/about/Nonlinear_two_point_boundary_value_probl.html?id=s_pQAAAAMAAJ&redir_esc=y this book].

== Geometric integrators for Hamiltonian Systems ==

[http://openlibrary.org/books/OL9056139M/Geometric_Numerical_Integration Geometric (AKA Symplectic) integrators] are useful for

multi-dimensional classical mechanics problems and for molecular dynamics simulations.

The odepkg package has a number of solvers for ODE, DAE and DDE problems but none of them is currently

specifically suited for second order problems in general and Hamiltonian systems in particular.

Therefore a new package for geometric integrators would be a useful contribution.

This could be created as new package or added as a set of new functions for odepkg.

The function interface should be consistent throughout the package and should be modeled to follow

that of other functions in odepkg (or that of DASPK and LSODE) but will need specific extensions to accommodate for specific options that only make sense for this specific class of solvers.

An initial list of methods to be implemented includes (but is not limited to)

* Symplectic Euler methods, see [http://en.wikipedia.org/wiki/Semi-implicit_Euler_method here] and [http://openlibrary.org/books/OL9056139M/Geometric_Numerical_Integration here]

* Störmer-Verlet method, see [http://en.wikipedia.org/wiki/Verlet_integration here] and [http://openlibrary.org/books/OL9056139M/Geometric_Numerical_Integration here]

* Velocity Verlet method, see [http://en.wikipedia.org/wiki/Verlet_integration here] and [http://openlibrary.org/books/OL9056139M/Geometric_Numerical_Integration here]

* Symplectic partitioned Runge-Kutta methods, see [http://reference.wolfram.com/mathematica/tutorial/NDSolveSPRK.html here] or [http://dx.doi.org/10.1137/0733019 here]

* Spectral Variational Integrator methods, see [http://www3.nd.edu/~izaguirr/papers/acta_numerica.pdf here] or [http://www.math.ucsd.edu/~mleok/pdf/HaLe2012_SVI.pdf here]

For this latter there is an existing code which is already working but needs to be improved, posted on the patch tracker.

Furthermore, methods to implement solutions of problems with rigid constraints should be implemented, e.g.

* SHAKE, see [http://en.wikipedia.org/wiki/Constraint_algorithm here] or [http://dx.doi.org/10.1016/0021-9991(77)90098-5 here]

* RATTLE, see [http://dx.doi.org/10.1016/0021-9991(83)90014-1 here] or [http://dx.doi.org/10.1002/jcc.540161003 here]

== Matlab-compatible ODE solvers in core-Octave ==

* Adapt "odeset" and "odeget" from the odepkg package so that the list of supported options is more Matlab-compatible, in the sense that all option names that are supported by Matlab should be available. On the other hand, Matlab returns an error if an option which is not in the list of known options is passed to "odeset", but we would rather make this a warning in order to allow for special extensions, for example for symplectic integrators.

* Adapt the interface of "ode45" in odepkg to be completely Matlab compatible, fix its code and documentation style and move it to Octave-core.

* Build Matlab compatible versions of "ode15s" and "ode15i". jwe has prototype implementations [https://savannah.gnu.org/patch/index.php?8102|here] of these built as wrappers to "dassl" and "daspk". An initial approach could be to just improve these wrappers, but eventually it would be better to have wrappers for "IDA" from the sundials library.

* Implement Matlab compatible versions of "deval".

== High Precision Arithmetic Computation ==

The Linear Algebra Fortran libraries used by Octave make use of of single (32 bits) and double (64 bits) precision floating point numbers. Many operations are stopped when matrices condition number goes below 1e-16: such matrices are considered as ill-conditioned. There are cases where this is not enough, for instance simulations implying chemical concentrations covering the range 10^4 up to 10^34. There are a number of ways to increase the numerical resolution, like f.i. make use of 128 bits quadruple precision numbers available in GFortran. A simpler option is to build an interface over Gnu MPL arbitrary precision library, which is used internally by gcc and should be available on any platform where gcc runs. Such approach has been made available for MatLab under the name mptoolbox and is licensed under a BSD license. The author kindly provided a copy of the latest version and agreed to have it ported under Octave and re-distributed under GPL v3.0

The architecture consists of an Octave class interface implementing "mp" (multi-precision) objects. Arithmetic operations are forwarded to MPL using MEX files. This is totally transparent to the end user, except when displaying numbers. This implementation needs to be ported and tested under Octave.

=GUI/IDE=

:''See also: [[Summer of Code Project Ideas#GUI]]''

*Søren Hauberg has suggested that we need C++ code that can:

**Query defined variables, i.e. get a list of currently defined variables. Bonus points if it could tell you if anything had changed since the last time you checked the variables (could also be done with signals).

**Make the links in the "Experimental GUI info" dialog box (the one that appears when the button "More Info" is pressed) clickable. They are not clickable in the 3.8.2-2 version (at least not on Windows 7).

== Implement a Qt widget for manipulating plots ==

Octave has had for some time a native OpenGL plotter. The plotter requires some user interaction for manipulating the plots, and it's been using fltk for quite some time. We want to replace this with Qt, so it fits better with the overall GUI look-and-feel and is easier to extend in the future.

[https://github.com/goffioul/QtHandles QtHandles] is a current work in progress integrating the octave OpenGL renderer plus good support for GUI elements (uicontrol, uimenu, uitoolbar...). This project may initially consists of integrating the existing QtHandles code base into Octave. Then if time permits, further improvements can be made to QtHandles.

== Create a better (G)UI for the profiler ==

During GSoC 2011, Daniel Kraft successfully implemented a profiler for Octave. It needs a better interface and a way to generate reports. This may be done with Qt, but not necessarily, and HTML reports might also be good.

== Sisotool. Create a graphical design tool for tuning closed loop control system (control pkg) ==

When tuning a SISO feedback system it is very helpful to be able to grab a pole or a zero and move them by dragging them with the mouse. As they are moving the software must update all the plotted lines. There should be the ability to display various graphs rlocuse, bode, step, impulse etc. and have them all change dynamically as the mouse is moving. The parameters of the compensator must be displayed and updated.

== Interface to Electronic Circuit Simulator ==

[http://sourceforge.net/projects/qucs/ Qucs] is a C++ based circuit simulation package. This project aims to improve the interface to the Qucs algorithms to allow the transient, i.e. time series, simulation of circuits in Octave within a larger ODE system simulation driven by Octave. Other possible goals would be to make other analysis types available directly from Octave. There is an existing C++ interface which is based on handle class syntax available in the development version of Octave. The Qucs interface is intended to have two modes, synchronous and asynchronous. The asynchronous mode uses qucs to solve a circuit between two given time steps (internally taking as many smaller time steps as required), returning only the final result. This method is well developed. The alternative synchronous mode is intended to give full control of the time steps to Octave, and it is this mode which requires more work. A simple synchronous interface exists which can be built upon.

'''Main Goals'''

* Improve the functionality of the transient solver interface by implementing a robust synchronous simulation mode that integrates well with Octave ode solvers, particularly those from the odepkg package from OctaveForge.

* Create interface to other analysis types (AC, DC, S-Parameter and Harmonic Balance)

* Packaging the interface for Octave, to make it available through OctaveForge

=Sparse Matrices=

The paper by [http://arxiv.org/abs/cs.MS/0604006 Bateman & Adler] is good reading for understanding the sparse matrix implementation.

*Improve QR factorization functions, using idea based on CSPARSE cs_dmsol.m

=Interpreter=

The interpreter is written in C++, undocumented. There are many possible projects associated with it.

'''Required skills''': ''Very good'' C and C++ knowledge, possibly also understanding of [http://en.wikipedia.org/wiki/Gnu_bison GNU bison] and [http://en.wikipedia.org/wiki/Flex_lexical_analyser flex]. Understanding how compilers and interpreters are made plus being able to understand how to use a profiler and a debugger will probably be essential skills.

*Allow customization of the debug prompt.

* Start the development of classdef (already underway)

== Improve JIT compiling ==

Octave's interpreter is ''very'' slow on some loops. Recently, thanks to Max Brister's work, an initial implement of a just-in-time compiler (JITC) in [http://llvm.org LLVM] for GSoC 2012. This project consists in understanding Max's current implementation and extending it so that functions and exponents (e.g. 2^z) compile with the JITC. This requires knowledge of compilers, C++, LLVM, and the Octave or Matlab languages. A capable student who demonstrates the ability to acquire this knowledge quickly may also be considered. Max himself will mentor this project. [http://planet.octave.org/octconf2012/jit.pdf Here] is Max's OctConf 2012 presentation about his current implementation. See also [[JIT]].

== Improve memory management ==

From profiling the interpreter, it appears that a lot of time is spending allocating and deallocating memory. A better memory management algorithm might provide some improvement.

== Implement classdef classes ==

Matlab has two kinds of classes: old style @classes and new style classdef. Octave has only fully implemented the old style. There is partial support for new classes in [http://hg.savannah.gnu.org/hgweb/octave/shortlog/classdef our classdef branch]. There is irregular work here, and classdef is [http://www.mathworks.com/help/matlab/matlab_oop/method-attributes.html a very] [http://www.mathworks.com/help/matlab/events-sending-and-responding-to-messages.html complicated] [http://www.mathworks.com/help/matlab/enumeration-classes.html thing] to fully implement. A successful project would be to implement enough of classdef for most basic usages. Familiarity with Matlab's current classdef support would be a huge plus. Michael Goffioul and jwe can mentor this.

Although there's already a substantial classdef support in current octave code base, there are still many areas that are unimplemented or need improvements. The main ones that come to my mind are:

* support for events

* support for enums

* support for "import" (this requires good understanding of octave internals, especially he symbol table)

* improving multiple inheritance and method resolution

* honoring and computing "Sealed" attribute

* support for function handle to methods

== Improve MPI package ==

Octave Forge's [http://octave.sourceforge.net/mpi/index.html MPI package]

is a wrapper for basic MPI functions for parallel computing. It is implemented

by wrapping MPI function calls in simple DLD functions that map Octave's Datataypes to

MPI Derived Datatypes.

The proposed project deals with improving and extending the Octave MPI package, for example:

* Octave MPI applications can currently be only run in batch mode, add the ability to launch parallel jobs and collect their output in an interactive Octave session.

* Implement functions for non-blocking communication (MPI_Isend, MPI_Irecv)

* Implement one-to-many (Broadcast, Scatter), many-to-one (Reduce, Gather), and many-to-many (All Reduce, Allgather) communication routines

=Graphics=

* Add data cursor to trace data values in figure.

== Lighting ==

Implement transparency and lighting in OpenGL backend(s). A basic implementation is available in [http://octave.svn.sourceforge.net/viewvc/octave/trunk/octave-forge/extra/jhandles/ JHandles]. This needs to be ported/re-implement/re-engineered/optimized in the C++ OpenGL renderer of Octave.

== Object selection in OpenGL renderer ==

This project is about the implementation of a selection method of graphics elements within the OpenGL renderer [http://glprogramming.com/red/chapter13.html]

== Non-OpenGL renderer ==

Besides the original gnuplot backend, Octave also contains an OpenGL-based renderer for advanced and more powerful 3D plots. However, OpenGL is not perfectly suited for 2D-only plots where other methods could result in better graphics. The purpose of this project is to implement an alternate graphics renderer for 2D only plots (although 3D is definitely not the focus, extending the new graphics renderer to support basic 3D features should also be taken into account). There is no particular toolkit/library that must be used, but natural candidates are:

* [http://qt.nokia.com Qt]: the GUI is currently written in Qt and work is also in progress to provide a Qt/OpenGL based backend [https://github.com/goffioul/QtHandles]

* [http://en.wikipedia.org/wiki/Cairo_%28software%29 Cairo]: this library is widely used and known to provides high-quality graphics with support for PS/PDF/SVG output.

== TeX/LaTeX markup ==

Text objects in plots (like titles, labels, texts...) in the OpenGL renderer only support plain text mode without any formatting possibility. Support for TeX and/or LaTeX formatting needs to be added.

* The TeX formatting support actually only consists of a very limited subset of the TeX language. This can be implemented directly in C++ into Octave by extending the existing text engine, avoiding to add a dependency on a full TeX system. Essentially, support for Greek letters, super/sub-scripts, and several mathematical symbols needs to be supported. For example,

:<pre>\alpha \approx \beta_0 + \gamma^\chi</pre>

:Would be rendered as,

:α ≈ β<sub>0</sub> + γ<sup>χ</sup>

:This is analogous to how special characters may be included in a wiki using html.

:<pre>&alpha; &asymp; &beta;<sub>0</sub> + &gamma;<sup>&chi;</sup></pre>

:The text object's {{Codeline|extent}} for the rendered result needs to be calculated and the text placed the location specified by the text object's {{Codeline|position}} property. An itemized list of a text objects properties can be found [http://www.gnu.org/software/octave/doc/interpreter/Text-Properties.html here].

* On the other hand, the LaTeX formatting support is expected to provide full LaTeX capabilities. This will require to use an external LaTeX system to produce text graphics in some format (to be specified) that is then integrated into Octave plots.

:The matplotlib project [http://matplotlib.sourceforge.net/users/usetex.html has already done this in Python] and might be used as an example of how to do this in Octave. Mediawiki has also also done [http://en.wikipedia.org/wiki/Wikipedia:Texvc something similar]. There is also [http://forge.scilab.org/index.php/p/jlatexmath/ JLaTeXMath], a Java API to display LaTeX code in mathematical mode.

=History=

*Make the website prettier. Maybe a new design, maybe a more "corporate" design (if we're heading down the "paid support for Octave" path.

** FusionForge's "Submit a Snippet" and "Create A Package" would seem to be directly usable for Agora's "Post a Snippet" and "Share your Code", respectively: https://alioth.debian.org/snippet/. It is FLOSS.

** ScipyCentral, http://scipy-central.org/ has all the features we need and is also free software.

* Help prepare and deliver presentations about Octave at colleges and universities.

== Finish the Agora website ==

In 2009, the Mathworks decided to restrict the terms of use Matlab Central, a place dedicated to Matlab collaboration. The Mathworks forbade copyleft licenses and using the "free" code found in Matlab central on anything other than Mathworks products (e.g. forbidding from using it on Octave, even if the authors of the code wanted to allow this). Thus Octave users have no place to centrally, quickly, and conveniently share Octave code. See the [[FAQ#Why_can.27t_I_use_code_from_File_Exchange_in_Octave.3F_It.27s_released_under_a_BSD_license.21|FAQ]] for more details.

In response to this, a website started to form, [http://agora.octave.org/ Agora Octave].

This should be relatively easy webdev in Python using [http://en.wikipedia.org/wiki/Django_%28web_framework%29 Django].

Things to be considered when working on this:

* [http://octave-forge.blogspot.ie/2012/08/octconf2012-agora-and-pkg.html discussion of Agora during OctConf2012]

* [http://scipy-central.org/ Scipy Central] - a website with the same objective as Agora for Scipy. Their [https://github.com/scipy/SciPyCentral Code] is released under a BSD license. Might be useful to reuse some parts.

Most of the basic functionality of Agora is already in, but there are many ways in which it could be improved, such as implementing comment threads, giving it an email interface, or a ReSTful API which could be used from Octave for package management. See also [[Agora]]. Talk to [[User:JordiGH|Jordi]]

== Improve binary packaging ==

We would like to be able to easily generate binary packages for Windows and Mac OS X. Right now, it's difficult and tedious to do so. Any way to help us do this in a faster way would be appreciated. Required knowledge is understanding how building binaries in Windows and Mac OS X works. Our current approach to fixing this is to cross-compile from a GNU system using [http://mxe.cc/ MXE] or [http://lilypond.org/gub/ GUB].

'''Skills Required''': Knowledge of GNU build systems, Makefiles, configure files, chasing library dependencies, how to use a compiler. If you choose to work on GUB, Python will be required. No m-scripting or C++ necessary, beyond understanding [http://david.rothlis.net/c/compilation_model/ the C++ compilation model].

=Performance=

Retrieved from "https://wiki.octave.org/Special:MobileDiff/5630"

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