Re: Easy Wavelet capability added to Octave core software

[Marc Normandin]

[bumping this thread from octave-maintainers to help-octave]

PattiMichelle wrote:
> Marc Normandin wrote:
>>
>> I tinkered a bit with WavePath.m, the file that adds the WaveLab code to
>> your [Octave] path.  I made two changes: (1) eliminated the dependence
>> on the "matlabroot" variable by simply requiring that you run the script
>> from the WaveLab directory, and (2) removed some strange markup that
>> existed in the original file.  The modified WavePath.m is attached.
>>
>> Executing this file seems to successfully add all of the WaveLab stuff
>> to the Octave path on my machine.  I didn't try to compile the mex
>> files, but the documentation indicates that the functions should still
>> work, albeit more slowly.  An attempt to run one of the demos failed, it
>> seems that the demo is graphically based and incompatible with Octave
>> graphics (at least with the gnuplot backend that I'm using).  So the
>> demos may be unavailable to you, but the functions that actually perform
>> various analyses should be accessible.
>>
>> Does this help any?
>>
>>   
> Thank You, Mark!!!  I'm not really sure what you mean about "running
> waveleb.m from the wavelab850 directory" - where did you stick wavelab
> (or does that really matter)?  Is these the results you got?

I just meant that Wavelab850/ should be Octave's working directory when
you execute the WavePath.m script.  Shouldn't matter where you've put
WaveLab.

My results were quite different (see below).

> QtOctave (on Windows) which is a front end for Octave 3.0.0.  When I
> loaded wavepath.m and ran it, it didn't throw an error, but it didn't
> report a success either.  When I tried to "run a matlab script" I got
> the error at the bottom.  Next I will try Octave 3.0.1, and Octave on
> openSuSE 11.0 and see if they give the same result.    Patti

I've tested this on Octave 3.0.0 (Ubuntu 8.04) and it worked there as
well.  I'm inclined to guess that Octave versions aren't causing the
differences in observed behaviors.

> Starting Octave...

[...]

> octave:5>octave:6> cd "C:/Program Files (x86)/Octave-Qt/octave/Wavelab850"
> octave:7> WavePath
> octave:8> pkg list

I noticed that you had no output at the Octave prompt after running
WavePath...I experienced the same before I edited the file and removed
some unusual markup characters.  Are you certain that you were running
the modified one I sent and not the original?

> Package Name       | Version | Installation directory
> -------------------+---------+-----------------------
>            arpack *|   1.0.3 | ...\octave\share\octave\packages\arpack-1.0.3
>             audio *|   1.0.3 | ...\octave\share\octave\packages\audio-1.0.3
[snip]

Here's a semi-annotated walkthrough of what I saw with Octave 3.0.1 on
Debian etch.


[BEGIN SESSION]

address@hidden:~/octave/sandbox$ ls
WavePath_mdn.m
address@hidden:~/octave/sandbox$ wget
http://www-stat.stanford.edu/~wavelab/Wavelab_850/WAVELAB850.ZIP
--23:51:17--
http://www-stat.stanford.edu/~wavelab/Wavelab_850/WAVELAB850.ZIP
           => `WAVELAB850.ZIP'
Resolving www-stat.stanford.edu... 171.64.102.103
Connecting to www-stat.stanford.edu|171.64.102.103|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3,107,216 (3.0M) [application/zip]

100%[====================================>] 3,107,216    831.11K/s
ETA 00:00

23:51:22 (728.80 KB/s) - `WAVELAB850.ZIP' saved [3107216/3107216]

address@hidden:~/octave/sandbox$
address@hidden:~/octave/sandbox$ unzip -q WAVELAB850.ZIP
address@hidden:~/octave/sandbox$ cp -f WavePath_mdn.m
Wavelab850/WavePath.m #copy modified Wavelab.m
address@hidden:~/octave/sandbox$ head -n 10 Wavelab850/WavePath.m
#make sure it copied
%  WavePath -- initialize path to include WaveLab
%
% This file was modified to remove some strange markup characters and
% to remove dependency on the "matlabroot" variable.  The second
% change was implemented by simply assuming that this file is being
% run from the WaveLab directory.  If this does not suit your needs,
% you should assign the "WAVELABPATH" variable appropriately below.
%
% Marc Normandin  address@hidden
% 10 August 2008
address@hidden:~/octave/sandbox$
address@hidden:~/octave/sandbox$ octave
GNU Octave, version 3.0.1
Copyright (C) 2008 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTIBILITY or
FITNESS FOR A PARTICULAR PURPOSE.  For details, type `warranty'.

Octave was configured for "i686-pc-linux-gnu".

Additional information about Octave is available at http://www.octave.org.

Please contribute if you find this software useful.
For more information, visit http://www.octave.org/help-wanted.html

Report bugs to <address@hidden> (but first, please read
http://www.octave.org/bugs.html to learn how to write a helpful report).

For information about changes from previous versions, type `news'.

octave:1> more off
octave:2> cd Wavelab850
octave:3> WavePath
Welcome to WaveLab v 850
Setting Global Variables
WAVELABPATH = /home/normandin/octave/sandbox/Wavelab850/
Warning: This version is only supported on Matlab 6.x and 7.x
Pathnames Successfully Set
global WAVELABPATH = "/home/normandin/octave/sandbox/Wavelab850/"
global PATHNAMESEPARATOR = "/"; global MATLABVERSION = 3
global PREFERIMAGEGRAPHICS = 1
WaveLab v 802 Setup Complete

Available Demos - Figures from the following papers:
  AdaptDemo  - ``Adapting to Unknown Smoothness via Wavelet Shrinkage''
  AsympDemo  - ``Wavelet Shrinkage: Asymptopia?''
  BlockyDemo - ``Smooth Wavelet Decompositions with Blocky Coefficient
Kernels''  CorrelDemo - ``Wavelet Threshold Estimators for Data with
Correlated Noise''
  IdealDemo  - ``Ideal Spatial Adaptation via Wavelet Shrinkage''
  MESDemo    - ``Minimum Entropy Segmentation''
  MIPTDemo  - ``Nonlinear Wavelet Transforms based on Median-Interpolaton''
  RiskDemo  - ``Exact Risk Analysis of Wavelet Regression''
  SCDemo     - ``Nonlinear Wavelet Methods for Recovery of Signals,
Densities
                  and Spectra from Indirect and Noisy Data''
  CSpinDemo   - ``Translation-Invariant De-Noising''
  TourDemo   - ``Wavelet Shrinkage and W.V.D. -- A Ten-Minute Tour''
  VdLDemo    - ``WaveLab and Reproducible Research''

Available Workouts:
  BBWorkout  - Workouts for Best Basis
  MPWorkout  - Workouts for Matching Pursuit
  MultiFrac  - Workouts for Continuous Wavelet Transform
  Toons      - The Cartoon Guide to Wavelets

Available Book(s):
  WaveTour   - ``WaveLet Tour of Signal Processing''

octave:4> path

Octave's search path contains the following directories:

.
/home/normandin/octave/weights
/usr/local/share/octave/site/m/startup
/usr/local/libexec/octave/3.0.1/oct/i686-pc-linux-gnu
/usr/local/share/octave/3.0.1/m

[snip more directories in path]

/usr/local/share/octave/3.0.1/m/startup
/home/normandin/octave/sandbox/Wavelab850/
/home/normandin/octave/sandbox/Wavelab850/Biorthogonal/
/home/normandin/octave/sandbox/Wavelab850/Continuous/
/home/normandin/octave/sandbox/Wavelab850/Datasets/
/home/normandin/octave/sandbox/Wavelab850/DeNoising/
/home/normandin/octave/sandbox/Wavelab850/Documentation/
/home/normandin/octave/sandbox/Wavelab850/FastAlgorithms/
/home/normandin/octave/sandbox/Wavelab850/Fractals/
/home/normandin/octave/sandbox/Wavelab850/Interpolating/
/home/normandin/octave/sandbox/Wavelab850/MEXSource/
/home/normandin/octave/sandbox/Wavelab850/Median/
/home/normandin/octave/sandbox/Wavelab850/Median/HigherDegree/
/home/normandin/octave/sandbox/Wavelab850/Meyer/
/home/normandin/octave/sandbox/Wavelab850/Orthogonal/
/home/normandin/octave/sandbox/Wavelab850/Packets/One-D/
/home/normandin/octave/sandbox/Wavelab850/Packets/Two-D/
/home/normandin/octave/sandbox/Wavelab850/Papers/
/home/normandin/octave/sandbox/Wavelab850/Pursuit/
/home/normandin/octave/sandbox/Wavelab850/Invariant/
/home/normandin/octave/sandbox/Wavelab850/Utilities/
/home/normandin/octave/sandbox/Wavelab850/TimeFrequency/
/home/normandin/octave/sandbox/Wavelab850/Workouts/
/home/normandin/octave/sandbox/Wavelab850/Papers/Adapt/
/home/normandin/octave/sandbox/Wavelab850/Papers/Asymp/
/home/normandin/octave/sandbox/Wavelab850/Papers/Blocky/
/home/normandin/octave/sandbox/Wavelab850/Papers/Correl/
/home/normandin/octave/sandbox/Wavelab850/Papers/Ideal/
/home/normandin/octave/sandbox/Wavelab850/Papers/MinEntSeg/
/home/normandin/octave/sandbox/Wavelab850/Papers/MIPT/
/home/normandin/octave/sandbox/Wavelab850/Papers/RiskAnalysis/
/home/normandin/octave/sandbox/Wavelab850/Papers/ShortCourse/
/home/normandin/octave/sandbox/Wavelab850/Papers/SpinCycle/
/home/normandin/octave/sandbox/Wavelab850/Papers/Tour/
/home/normandin/octave/sandbox/Wavelab850/Papers/VillardDeLans/
/home/normandin/octave/sandbox/Wavelab850/Workouts/BestOrthoBasis/
/home/normandin/octave/sandbox/Wavelab850/Workouts/MatchingPursuit/
/home/normandin/octave/sandbox/Wavelab850/Workouts/Toons/
/home/normandin/octave/sandbox/Wavelab850/Workouts/MultiFractal/
/home/normandin/octave/sandbox/Wavelab850/Browsers/One-D/
/home/normandin/octave/sandbox/Wavelab850/Browsers/WaveTour/
/home/normandin/octave/sandbox/Wavelab850/Books/WaveTour/WTCh02/
/home/normandin/octave/sandbox/Wavelab850/Books/WaveTour/WTCh04/
/home/normandin/octave/sandbox/Wavelab850/Books/WaveTour/WTCh05/
/home/normandin/octave/sandbox/Wavelab850/Books/WaveTour/WTCh06/
/home/normandin/octave/sandbox/Wavelab850/Books/WaveTour/WTCh07/
/home/normandin/octave/sandbox/Wavelab850/Books/WaveTour/WTCh08/
/home/normandin/octave/sandbox/Wavelab850/Books/WaveTour/WTCh09/
/home/normandin/octave/sandbox/Wavelab850/Books/WaveTour/WTCh10/

octave:5>

[END SESSION]


At the end you can see that the WaveLab directories were successfully
added to the Octave path.  As I mentioned previously, the demos didn't
work but a few calls to basic WaveLab functions seemed to work okay.

Unless you're getting more specific errors, I'm afraid your troubles
might be beyond the scope of what I can address.  Did you have any luck
with the WaveLab authors?

--
------------------------------------------------------------------
Marc D. Normandin              http://web.ics.purdue.edu/~mdnorman
Graduate Research Assistant                     address@hidden
Indiana University School of Medicine           317-278-9841 (tel)
Department of Radiology, Division of Research   317-274-1067 (fax)
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