Summer of Code - Getting Started: Difference between revisions

=== 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,

=== Improve logm, sqrtm, funm ===

The goal here is to implement some missing Matlab functions related to matrix functions like the [http://en.wikipedia.org/wiki/Matrix_exponential matrix exponential]. There is [http://octave.1599824.n4.nabble.com/matrix-functions-td3137935.html a general discussion] of the problem.

=== Generalised eigenvalue problem ===

[http://www.mathworks.com/help/techdoc/ref/eig.html Certain calling forms] of the <tt>eig</tt> function are missing. The problem is to understand what those missing forms are and implement them.

=== Various sparse matrix improvements ===

The implementation of sparse matrices in Octave needs several improvements. Any of [[Projects#Sparse Matrices|these]] would be good. The paper by [http://arxiv.org/abs/cs.MS/0604006 Bateman & Adler] is good reading for understanding the sparse matrix implementation.

=== 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

=== Geometric integrators for Hamiltonian Systems ===

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

=== 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.

=== Nonlinear and constrained least squares ===

The [[Optimization package]] is missing the functions <tt>lsqcurvefit</tt>, <tt>lsqlin</tt>, <tt>lsqnonlin</tt> to conveniently solve least-squares problems that are nonlinear and/or constrained. There are free implementations of the needed algorithms in other languages, such as [http://www.netlib.org/minpack/ minpack] in Fortran and [http://users.ics.forth.gr/~lourakis/levmar/ levmar] in C. This project would link to or port these implementations and develop Matlab-compatible Octave wrappers.

=== TISEAN package ===

[http://www.mpipks-dresden.mpg.de/~tisean/Tisean_3.0.1/index.html TISEAN] is a suite of code for nonlinear time series analysis. It is old but there are many algorithms there that haven't been re-implemented as libre software. The objective is to integrate TISEAN as a

octave package as it was done for the Control package.

=== 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

=== Finish the Octave GUI ===

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The GUI is currently on its own branch in hg. It is not stable enough and its design is still in flux. It is in a very alpha stage and needs to be turned into a real usable product. At the moment, it consists of the basic building blocks (terminal window, editor, variable browser, history, file browser) that are put together into a main interface. The GUI uses the Qt library. Among the things to improve are:

=== 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.

=== 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.

=== 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:

=== 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.

=== 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.

=== 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  

=== 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.

=== 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].

=== Installation of packages ===

We would like to enhance the management of Octave-forge packages from within Octave environment. Currently there is a working (but rather monolithic) function that is used to do the job. The work would be to improve the way Octave interacts with the package server. Since the functionality is already sketched by the current function, the most important skill is software design.

=== Improvements to N-dimensional image processing ===

The image package has partial functionality for N-dimensional images. These images exist for example in medical imaging where slices from scans are assembled to form anatomical 3D images, or even exposures taken over time at different wavelengths can result in 5D images. As part of GSoC 2013, the core functions {{codeline|imwrite}} and {{codeline|imread}} were extended to better support this type of image. Likewise, many functions in the image package, mostly morphology operators, were expanded to deal with this type of image. Still, many are left, specially image transformation and analysis of ROIs.

=== Color management functions in image package ===

The goal is to implement these functions: