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*Francesco Potortì's fractal programs (Octave, GPL): http://fly.cnuce.cnr.it/software/#fractals
*Francesco Potortì's fractal programs (Octave, GPL): http://fly.cnuce.cnr.it/software/#fractals


==Ecnometrics==
==Econometrics==
*Michael Creel's Econometrics notes and octave files: http://pareto.uab.es/mcreel/Econometrics/ (try the Econometrics/MyOctaveFiles directory too)
*Michael Creel's Econometrics notes and octave files: http://pareto.uab.es/mcreel/Econometrics/ (try the Econometrics/MyOctaveFiles directory too)
* Ludwig Kanzler's Econometric software (much of it adapted to Octave):
* Ludwig Kanzler's Econometric software (much of it adapted to Octave):
**http://www2.gol.com/users/kanzler/index.htm#L.%20Kanzler:%20Software
**http://www2.gol.com/users/kanzler/index.htm#L.%20Kanzler:%20Software
**Licence: "All rights reserved", Unfree for distributing modified versions
**Licence: "All rights reserved", Unfree for distributing modified versions
*[http://www.dynare.org Dynare] is a software platform for handling a wide class of economic models, in particular dynamic stochastic general equilibrium (DSGE) and overlapping generations (OLG) models. Licensed under GNU GPL (v3 or later). Consists of a pre-processor (in C++) and of a collection of Octave/Matlab routines.


==Communications Toolbox==
==Communications Toolbox==
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*Simulate multipath fading channels: http://zeidler.ucsd.edu/~sct/code/20060112_multipath/
*Simulate multipath fading channels: http://zeidler.ucsd.edu/~sct/code/20060112_multipath/
*Signal processing package in [http://octave.sourceforge.net/signal/index.html OctaveForge]
*Signal processing package in [http://octave.sourceforge.net/signal/index.html OctaveForge]
*Wavelets: try Wavelab developed by David Donoho et al. at http://www-stat.stanford.edu/~wavelab/. For more information, see [[Wavelab on Octave]].
*Wavelets: LTFAT package in [http://octave.sourceforge.net/ltfat/ OctaveForge], see additional documentation in the [http://ltfat.sourceforge.net/doc/wavelets/index.php LTFAT web page]. Try also Wavelab developed by David Donoho et al. at http://www-stat.stanford.edu/~wavelab/. For more information, see [[Wavelab on Octave]].
* Peter Kovesi's functions for computer vision and image processing: http://www.csse.uwa.edu.au/~pk/Research/MatlabFns/
* Peter Kovesi's functions for computer vision and image processing: http://www.csse.uwa.edu.au/~pk/Research/MatlabFns/


===Data Formats===
===Data Formats===
A collection of various signal data formats can be found [http://www.dpmi.tu-graz.ac.at/~schloegl/matlab/eeg/ here]. Many formats are supported by the [http://biosig.sf.net/ BIOSIG]-toolbox for Octave and Matlab.
A collection of various signal data formats can be found [http://www.dpmi.tu-graz.ac.at/~schloegl/matlab/eeg/ here]. Many formats are supported by the [http://biosig.sf.net/ BIOSIG]-toolbox for Octave and Matlab.
===Speech and Signal Processing Links===
The following packages contain routines that can be made to work with Octave. Sometimes a little effort is required.
*OctaveForge contains a sizable collection of signal and image processing routines
*Alois Schloegl's Time series analysis toolbox is also available at OctaveForge
*Mike Brookes' Voice Box (http://www.ee.ic.ac.uk/hp/staff/dmb/voicebox/voicebox.html)
*University of Sheffield's Matlab Auditory and Speech Demos (http://www.dcs.shef.ac.uk/~martin/MAD/docs/mad.htm)
*Malcolm Slaney's Auditory Toolbox (http://rvl4.ecn.purdue.edu/~malcolm/interval/1998-010/)
*Philip Loizou's COLEA speech analysis toolbox (http://www.utdallas.edu/~loizou/speech/colea.htm)
*Levant Arslans's Speech Processing Toolbox (http://cslr.colorado.edu/software/rspl.html)
*John Hansen's Additive noise sources (http://cslr.colorado.edu/software/rspl.html)
*Dennis Brown's SPCtools (ftp://svr-ftp.eng.cam.ac.uk/pub/comp.speech/tools/spctools) has code for AR and ARMA modelling, particularly in the spcline subdirectory (Note that the version at mathworks is slightly older).
*Steve Niu's AUDI (ftp://ftp.mathworks.com/pub/contrib/v4/systemid/audidemo.tar) and Arthur Jutan's recursivels (ftp://ftp.mathworks.com/pub/contrib/v4/control/recursivels.tar) for ARMA modelling. AUDI worked well enough for me with a bit of fiddling. Haven't tried recursivels.
*Peter Assmann's Track Draw (http://www.utdallas.edu/~assmann/TRACKDRAW/trackdraw.html) has code for a klatt synthesizer
*Time-Frequency Tool box (http://www-isis.enst.fr/Applications/tftb/iutsn.univ-nantes.fr/auger/tftb.html) from CNRS & Rice has code for AM/FM modulation amongst other cool stuff
*Christophe Couvreur's octave (ftp://ftp.mathworks.com/pub/contrib/v5/signal/octave.tar) has filterbank stuff. Of course the plotting doesn't work, but with a bit of fiddling, you can get, 1/3 octave and 1 octave filter banks to work.
*Mathworks signal processing contributions directories for Matlab 4 (http://www.mathworks.com/support/ftp/signalssv4.shtml) and Matlab 5 (http://www.mathworks.com/support/ftp/signalssv5.shtml)
*University of Vienna's Linear Time-Frequency Toolbox (http://www.univie.ac.at/nuhag-php/ltfat)
The following used to be available:
*Kuo, et. al.'s Speech Signal Processing and Recognition tools (SSPR). A number of the other tools are archived at the same site (http://www.eeng.dcu.ie/~speech5/matspeech.html).
Other Software:
*ESPS has been open sourced (BSD license) and is available at http://www.speech.kth.se/software/. Finally we will have a decent pitch tracker!


==Digital communications in medicine (DICOM)==
==Digital communications in medicine (DICOM)==
At an early development stage. [http://octave.svn.sourceforge.net/viewvc/octave/trunk/octave-forge/extra/dicom/ octave-forge svn]
There is a DICOM package hosted on sourceforge: [[dicom | more information]].
*Maintainer: Andy Buckle [http://sourceforge.net/sendmessage.php?touser=1760416contact]
*Currently worked on by: Kris Thielemans


===Supporting library===
==Adding a quadl like integrator to octave==
[http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=Main_Page GCDM]. I think the libraries must be built. Getting source with subversion.


svn co https://gdcm.svn.sourceforge.net/svnroot/gdcm/branches/gdcm-2-0
quadl is an adaptive quadrature function available in MATLAB (from version 6 I think). It is very fast and accurate and surprisingly it's a small m-file. The algorithm is based on works by Prof. Walter Gander.


cmake and g++ are required. create a gdcmbin directory parallel to the gdcm-2-0 directory. Change to gdcmbin and then run cmake (Linux/cygwin).
Prof. Gander has two m files in his web page http://www.inf.ethz.ch/personal/gander/ which implement his algorithm along with a paper describing the algorithm.


> mkdir gdcmbin
I have not delved deeply into the subject, but the adaptlobe.m function looks equivalent to quadl. Compatibility with MATLAB could be achieved by writing a small quadl wrapper function which simply calles adaptlobe, or by changing adabtlobe's name to quadl.
> ls
gdcmbin gdcm-2-0
> cd gdcmbin
> cmake -DGDCM_BUILD_SHARED_LIBS=ON ../gdcm-2-0/


This creates a Makefile in your gdcmbin directory. You can easily edit cmake options with "make edit_cache", for example to build applications like gdcmdump. "make help" is also very useful.
I have contacted Prof. Gander to allow for distribution of his m-files in octave-forge.


make install
quadl, from the above source is now incorporated into octave-forge-2004-02-12.


On my system, I also had to add this to my ~/.bashrc.
==Model transformation tools==
http://mtt.sourceforge.net


export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
A set of tools for modelling dynamic physical systems using the bond-graph methodology and transforming these models into representations suitable for analysis, control and simulation. These tools use, and generate m files for, GNU Octave.


Mingw32 is similar. Get openSSL: [http://www.slproweb.com/products/Win32OpenSSL.html Win32 Openssl v1.0.0a Light]
==Optimization==
There is a variety of code in the octave-forge optimization package http://octave.sourceforge.net/optim/index.html


cmake -G "MinGW Makefile" -DGDCM_BUILD_SHARED_LIBS=ON ..\gdcm-2-0
==Parallelism ==
mingw32-make all
Operating Octave remotely and in parallel
*distributed linear algebra from octave command line via [http://icl.cs.utk.edu/netsolve/index.html GridSolve]
*OctaveForge has a parallel octave, allowing remote commands and data transfer
*OctaveServer allows net connections to Octave
*MPI toolbox for Octave http://atc.ugr.es/javier-bin/mpitb (This is included in a live CD ParallelKnoppix http://pareto.uab.es/mcreel/ParallelKnoppix/ which you can use without installation or configuration)


===Features===
==Statistics ==
All of these still need work, but they exist, and are usable to some extent.
===Statistics Functions===
*dicomdict (load different dict - file follows same format as Matlab's)
*dicominfo (load metadata into octave struct. nasty bug in SQ loading)
*dicomlookup (keyword <-> tag)
*dicomread (load pixel data, 2D or 3D int types. Does not yield colormaps, yet.)
*dicomwrite (only does some 2D int types, ATM. No metadata control, yet)


===Todo===
*[ http://www.maths.lth.se/matstat/stixbox/ Stixbox] supports Octave. It has a variety of functions not available in octave/octave-forge such as bootstrap and jackknife estimators and a variety of qq plots. GPL.


*dicomanon
*[http://www.statsci.org/matlab/statbox.html Statbox] has some regression functions which are not in Octave. Don't know license or Octave compatibility.
*dicomuid


===Questions===
*[http://pub.ist.ac.at/~schloegl/matlab/NaN/ NaN-toolbox] A statistic-toolbox for Octave and Matlab®. It handles data with and without MISSING VALUES. More background information is provided in [http://pub.ist.ac.at/~schloegl/matlab/NaN/README.TXT README]
I don't have a Matlab license available. I would like to make this package compatible with the dicom functions in Matlab's image processing toolbox, as far as possible.


*Octave (and Matlab) stores images (y,x) and DICOM is intrinsically (x,y). Does Matlab transpose images when it loads them?
===Multivariate kernel density estimation===
**matlab reads the data from the dicom file as if it's a raw block of numbers (and then converts if necessary). Therefore, current Octave/dicom behaviour is compatible with matlab.
*I would like people to try m-files that worked with Matlab to let me know of problems.
*(not necessarily) Matlab related: I need examples of odd DICOM files. I have plenty with complex metadata, but I need some with unusual images.
**More than one sample per pixel
**Colour
**Float types
*DA (date) VR: does Matlab turn them into a string?
*if the user supplies metadata (eg HighBit?, BitsStored?) that describe the type of the pixels and this is not in agreement with the type of the image matrix supplied, does Matlab
**silently convert the image pixel type to match the metadata?
**silently convert the metadata to match the pixel type?
**error and do nothing?
*What does dicominfo do when a tag is not in its dictionary: skip it or give error? I was wondering about turning the tag into a variable name, something like Tag_3243_0010. (Matlab 6.5 (2002): Private__3243_0010)
*dicominfo: Items in sequences are not necessarily the same, so cannot be stored in arrays of structs. (Matlab 6.5 (2002): makes nested structs like dcm.RTDoseROISequence?.Item_1.DoseUnits?)


== Fixed point toolbox ==
*[http://www.ics.uci.edu/~ihler/code/kde.shtml Kernel Density Estimation Toolbox] LGPL
(initial announcement can be found [http://www.octave.org/octave-lists/archive/help-octave.2004/msg01274.html here], with the corresponding thread)


When implementing algorithms in hardware, it is common to reduce the accuracy of the representation of numbers to a smaller number of bits. This allows much lower complexity in the hardware, at the cost of accuracy and potential overflow problems. Such representations are known as fixed point.
*[http://www.maths.lth.se/matstat/wafo/documentation/wafodoc/wafo/kdetools/index.html wafo/kdetools] GPL


OctaveForge now contains [http://octave.sourceforge.net/Fixedpoint/index.html a toolbox] to perform such fixed point calculations. This toolbox supplies a fixed point type that allows Octave to model the effects of such a reduction in accuracy of the representation of numbers. The major advantage of this toolbox is that with correctly written Octave scripts, the same code can be used to test both fixed and floating point representations of numbers.
*A google search for epanechnikov at the r-project.org site returns several R packages on this subject. They all should be GPL compatible. [http://www.google.com/search?hl=en&lr=&q=Epanechnikov+site%3Ar-project.org&btnG=Search]


What it does is create several new user types for fixed point scalar, complex scalars, matrices and complex matrices, and the corresponding operators on these types. As this code was first written against 2.1.50 there is no capabilities at this time for NDArray operations with this code, however I'm not sure this is a problem.
*[http://astrostatistics.psu.edu/statcodes/sc_density.html sc_density]


A typical use of the toolbox might be something like
*[http://www.cs.waikato.ac.nz/~ml/weka/ Weka] is written in Java, again, don't know how difficult... look for a file called LWL.java


n = 2;
*[http://ltilib.sourceforge.net/doc/homepage/index.shtml LTI-Lib] is an object oriented library with algorithms and data structures frequently used in image processing and computer vision. LGPL
a = rand (n, n);
b = rand (n, n);
## Create fixed-point version with 1 bit before decimal and 5 after.
af = fixed (1, 5, a);
bf = fixed (1, 5, b);
c = myfunc (a, b);
cf = myfunc (af, bf);
function y = myfunc (a, b)
    y = a * b;
endfunction


where as you can see the underlying function myfunc is unchanged, while it is called with either floating or fixed point types. The case above is for fixed-point values with 1-bit before the decimal point and 5 after, and for me gave a result of
==Symbolic==
===Symbolic Manipulation===
Octave is a matrix algebra tool, not a symbolic algebra tool, so it cannot perform symbolic operations, such as finding the derivative of sine(x) with respect to x


  octave:8> c
  y = derivative('sin(x)','x'); # Not available in Octave
c =
  0.98105  0.94436
  0.82622  0.30831
octave:9> cf
cf =
  0.93750  0.90625
  0.78125  0.25000


which clearly shows the loss of precision of a fixed-point algorithm with only 6-bits of precision in a matrix multiply. One gotcha in this toolbox is the use of the concatenation operator "[ ]" which will implicitly reconvert fixed-point values back to floating-point, with Octave 2.1.57 or earlier. This is due to an internal limitation of octave that was removed in Octave 2.1.58. So for the best experience it is suggested you use this toolbox with octave 2.1.58 or later.
The below mentioned GiNaC will add symbolic functionality to octave.


This package is only available with recent versions of OctaveForge (20040707 or later). With the package installed online help is available with the command
===Octave interfaces to GiNaC===
octave:1> fixedpoint info
There are two Octave interfaces to GiNaC[1] available


As this package is relatively new, all feedback on its use would be most welcome.
*gino -- http://www.sourceforge.net/projects/mtt (download) provides an Octave interface to GiNaC via ginsh


Matlab also recently introduced a [http://www.mathworks.com/products/fixed Fixed Point Toolbox]. The Octave toolbox has been written independently of the Matlab toolbox and doesn't follow the same syntax. This might change in the future, if the author (DavidBateman) can be bothered to put the effort into making the required changes. Mathworks [http://www.mathworks.com/access/helpdesk/help/pdf_doc/fixedpoint/FPTUG.pdf documentation] for their fixed point toolbox also includes a generic discussion of fixed point numbers that might be a useful addition to the documentation supplied with Octave itself. Another short introduction to fixed point arithmetics is [http://home.earthlink.net/~yatescr/fp.pdf this].
octave:1> df = g_diff ( "sin(x)" , "x" )
df = cos(x)
octave:2> x = pi; eval ( df );
ans = -1


==Adding a quadl like integrator to octave==
*OctaveForge provides direct access to GiNaC in the [http://octave.sourceforge.net/index/navsymbolic.html symbolic package]. Here is a http://wiki.octave.org/wiki.pl?OctaveForgeGNCIntro short tutorial] to get you started.
 
===Numerical methods===
In some instances, Octave can give reasonable results using numerical methods
 
*Octave supports numerical derivatives:
 
t = linspace(0,6,100);
y = sin(t);
dydt = diff(y) ./ diff(t)
*OctaveForge has other numerical derivative functions.


quadl is an adaptive quadrature function available in MATLAB (from version 6 I think). It is very fast and accurate and surprisingly it's a small m-file. The algorithm is based on works by Prof. Walter Gander.
===Symbolic algebra systems===
Software other than Octave may be more useful for work involving symbolic manipulations


Prof. Gander has two m files in his web page http://www.inf.ethz.ch/personal/gander/ which implement his algorithm along with a paper describing the algorithm.
Free software
*Axiom: http://www.nongnu.org/axiom/


I have not delved deeply into the subject, but the adaptlobe.m function looks equivalent to quadl. Compatibility with MATLAB could be achieved by writing a small quadl wrapper function which simply calles adaptlobe, or by changing adabtlobe's name to quadl.
*GiNaC/ginsh: http://www.ginac.de


I have contacted Prof. Gander to allow for distribution of his m-files in octave-forge.
*Maxima: http://maxima.sourceforge.net


quadl, from the above source is now incorporated into octave-forge-2004-02-12.  
*Yacas: http://yacas.sourceforge.net


==Model transformation tools==
Non-free software
http://mtt.sourceforge.net
*Maple: http://www.maplesoft.com


A set of tools for modelling dynamic physical systems using the bond-graph methodology and transforming these models into representations suitable for analysis, control and simulation. These tools use, and generate m files for, GNU Octave.
*Reduce: http://www.uni-koeln.de/REDUCE


==Optimisation==
Note that most of these systems (and Octave!) may be used from within TeXmacs http://www.texmacs.org
There is a variety of code in the octave-forge optimization package http://octave.sourceforge.net/optim/index.html


==Parallelism ==
A list of some other scientific software is available at http://sal.kachinatech.com/
Operating Octave remotely and in parallel
*distributed linear algebra from octave command line via [http://icl.cs.utk.edu/netsolve/index.html GridSolve]
*OctaveForge has a parallel octave, allowing remote commands and data transfer
*OctaveServer allows net connections to Octave
*MPI toolbox for Octave http://atc.ugr.es/javier-bin/mpitb (This is included in a live CD ParallelKnoppix http://pareto.uab.es/mcreel/ParallelKnoppix/ which you can use without installation or configuration)

Latest revision as of 21:30, 13 February 2018

Chaos and fractal contributions and toolboxes[edit]

Econometrics[edit]

  • Michael Creel's Econometrics notes and octave files: http://pareto.uab.es/mcreel/Econometrics/ (try the Econometrics/MyOctaveFiles directory too)
  • Ludwig Kanzler's Econometric software (much of it adapted to Octave):
  • Dynare is a software platform for handling a wide class of economic models, in particular dynamic stochastic general equilibrium (DSGE) and overlapping generations (OLG) models. Licensed under GNU GPL (v3 or later). Consists of a pre-processor (in C++) and of a collection of Octave/Matlab routines.

Communications Toolbox[edit]

OctaveForge now contains a fairly complete implementation of a Matlab R13 compatible communications toolbox http://octave.sourceforge.net/communications/index.html. This includes

  • Random signal creation/analysis
  • Source coding (Quantization, Compand)
  • Block coding (BCH, Reed-Solomon)
  • Modulations (QASK, PSK, etc)
  • Galois fields of even order [i.e. GF(2^m) ]

With a recent version of the OctaveForge installed (version 20030602 or later), online help is available with the command 

octave:1> comms info

There are still functions missing or with limitations, and the documentation is not complete. You are therefore welcome to send patches.

Various Communications-Related Octave Code[edit]

Data Formats[edit]

A collection of various signal data formats can be found here. Many formats are supported by the BIOSIG-toolbox for Octave and Matlab.

Speech and Signal Processing Links[edit]

The following packages contain routines that can be made to work with Octave. Sometimes a little effort is required.

The following used to be available:

Other Software:

Digital communications in medicine (DICOM)[edit]

There is a DICOM package hosted on sourceforge: more information.

Adding a quadl like integrator to octave[edit]

quadl is an adaptive quadrature function available in MATLAB (from version 6 I think). It is very fast and accurate and surprisingly it's a small m-file. The algorithm is based on works by Prof. Walter Gander.

Prof. Gander has two m files in his web page http://www.inf.ethz.ch/personal/gander/ which implement his algorithm along with a paper describing the algorithm.

I have not delved deeply into the subject, but the adaptlobe.m function looks equivalent to quadl. Compatibility with MATLAB could be achieved by writing a small quadl wrapper function which simply calles adaptlobe, or by changing adabtlobe's name to quadl.

I have contacted Prof. Gander to allow for distribution of his m-files in octave-forge.

quadl, from the above source is now incorporated into octave-forge-2004-02-12.

Model transformation tools[edit]

http://mtt.sourceforge.net

A set of tools for modelling dynamic physical systems using the bond-graph methodology and transforming these models into representations suitable for analysis, control and simulation. These tools use, and generate m files for, GNU Octave.

Optimization[edit]

There is a variety of code in the octave-forge optimization package http://octave.sourceforge.net/optim/index.html

Parallelism[edit]

Operating Octave remotely and in parallel

Statistics[edit]

Statistics Functions[edit]

  • [ http://www.maths.lth.se/matstat/stixbox/ Stixbox] supports Octave. It has a variety of functions not available in octave/octave-forge such as bootstrap and jackknife estimators and a variety of qq plots. GPL.
  • Statbox has some regression functions which are not in Octave. Don't know license or Octave compatibility.
  • NaN-toolbox A statistic-toolbox for Octave and Matlab®. It handles data with and without MISSING VALUES. More background information is provided in README

Multivariate kernel density estimation[edit]

  • A google search for epanechnikov at the r-project.org site returns several R packages on this subject. They all should be GPL compatible. [1]
  • Weka is written in Java, again, don't know how difficult... look for a file called LWL.java
  • LTI-Lib is an object oriented library with algorithms and data structures frequently used in image processing and computer vision. LGPL

Symbolic[edit]

Symbolic Manipulation[edit]

Octave is a matrix algebra tool, not a symbolic algebra tool, so it cannot perform symbolic operations, such as finding the derivative of sine(x) with respect to x 

y = derivative('sin(x)','x'); # Not available in Octave

The below mentioned GiNaC will add symbolic functionality to octave.

Octave interfaces to GiNaC[edit]

There are two Octave interfaces to GiNaC[1] available 

octave:1> df = g_diff ( "sin(x)" , "x" )
df = cos(x)
octave:2> x = pi; eval ( df );
ans = -1

Numerical methods[edit]

In some instances, Octave can give reasonable results using numerical methods

  • Octave supports numerical derivatives:
t = linspace(0,6,100);
y = sin(t);
dydt = diff(y) ./ diff(t)
  • OctaveForge has other numerical derivative functions.

Symbolic algebra systems[edit]

Software other than Octave may be more useful for work involving symbolic manipulations

Free software

Non-free software

Note that most of these systems (and Octave!) may be used from within TeXmacs http://www.texmacs.org

A list of some other scientific software is available at http://sal.kachinatech.com/

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