✎ tagwiki:help:octave [Animal Tag Tools Wiki]

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
<page-header>
=====Tag tools Octave help=====
</page-header>
You may want to double-check that you have the latest version of Octave installed. It will not necessarily work with older versions.

For Windows, Linux or BSD, refer to the GNU page: https://www.gnu.org/software/octave/download

For Mac, octave.app is a great simple option: https://octave-app.org/ or the Octave wiki has other options: https://wiki.octave.org/Octave_for_macOS
=====Tips and tricks=====
====1. Install & load packages required to run the Tag Tools functions====
Packages are the Octave equivalent of a Matlab toolbox. To be able to get started with Tag Tools in Octave you will need to have the **required** package list installed; however, many other **optional** packages are automatically installed on you system or can be installed from [[https://octave.sourceforge.io/packages.php|Octave Forge]].

<WRAP group>

<WRAP half column>
<panel title="Required packages">
|<100% 12.5% -%>|
^Package name ^ Function^
|control |Computer-Aided Control System Design, required by signal|
|io|Input/Output in external formats|
|netcdf|A MATLAB compatible NetCDF interface for Octave |
|signal|Signal processing tools, requires control |

</panel>
</WRAP>

<WRAP half column>
<panel title="Optional packages">
^Package name ^ Function^
|database |an interface to SQL databases, currently only postgresql using libpq|
|generate_html|Generate HTML pages for function help pages|
|gsl |GNU Scientific Library |
|image|Image processing   |
|load lssa |Compute spectral decompositions of irregularly-spaced time series|
|load ltfat |The Large Time/Frequency Analysis Toolbox (LTFAT) |
|load mapping |Simple mapping and GIS .shp and raster file functions |
|load miscellaneous |Miscellaneous tools|
|load optim |Non-linear optimization toolkit |
|load statistics |Additional statistics functions for Octave |
|load struct |Additional structure manipulation functions|
</panel>

</WRAP>
</WRAP>




To find out which packages you have installed, how to install and load them follow the instructions below. 
<accordion collapsed="true">
<panel title="⇓a. List all installed packages">
The latest versions of Octave automatically install base packages during the installation process. To find out which packages that you have installed on your system use the command **pkg list**. Here is an example of the packages that were automatically installed on my system when I downloaded and installed GNU Octave, version 4.2.1.
<code>
>> pkg list
Package Name         | Version | Installation directory
---------------------+---------+-----------------------
     communications  |   1.2.1 | C:\Octave\Octave-4.2.1\share\octave\packages\communications-1.2.1
            control *|   3.0.0 | C:\Octave\Octave-4.2.1\share\octave\packages\control-3.0.0
     data-smoothing  |   1.3.0 | C:\Octave\Octave-4.2.1\share\octave\packages\data-smoothing-1.3.0
           database  |   2.4.2 | C:\Octave\Octave-4.2.1\share\octave\packages\database-2.4.2
          dataframe  |   1.1.0 | C:\Octave\Octave-4.2.1\share\octave\packages\dataframe-1.1.0
              dicom  |   0.1.1 | C:\Octave\Octave-4.2.1\share\octave\packages\dicom-0.1.1
          financial  |   0.5.0 | C:\Octave\Octave-4.2.1\share\octave\packages\financial-0.5.0
               fits  |   1.0.7 | C:\Octave\Octave-4.2.1\share\octave\packages\fits-1.0.7
fuzzy-logic-toolkit  |   0.4.5 | C:\Octave\Octave-4.2.1\share\octave\packages\fuzzy-logic-toolkit-0.4.5
                 ga  |  0.10.0 | C:\Octave\Octave-4.2.1\share\octave\packages\ga-0.10.0
            general  |   2.0.0 | C:\Octave\Octave-4.2.1\share\octave\packages\general-2.0.0
      generate_html  |  0.1.13 | C:\Octave\Octave-4.2.1\share\octave\packages\generate_html-0.1.13
           geometry  |   2.1.1 | C:\Octave\Octave-4.2.1\share\octave\packages\geometry-2.1.1
                gsl  |   2.0.0 | C:\Octave\Octave-4.2.1\share\octave\packages\gsl-2.0.0
              image  |   2.6.1 | C:\Octave\Octave-4.2.1\share\octave\packages\image-2.6.1
 instrument-control  |   0.2.3 | C:\Octave\Octave-4.2.1\share\octave\packages\instrument-control-0.2.3
           interval  |   2.1.0 | C:\Octave\Octave-4.2.1\share\octave\packages\interval-2.1.0
                 io  |   2.4.5 | C:\Octave\Octave-4.2.1\share\octave\packages\io-2.4.5
     linear-algebra  |   2.2.2 | C:\Octave\Octave-4.2.1\share\octave\packages\linear-algebra-2.2.2
               lssa  |   0.1.2 | C:\Octave\Octave-4.2.1\share\octave\packages\lssa-0.1.2
              ltfat  |   2.2.0 | C:\Octave\Octave-4.2.1\share\octave\packages\ltfat-2.2.0
            mapping  |   1.2.1 | C:\Octave\Octave-4.2.1\share\octave\packages\mapping-1.2.1
      miscellaneous  |   1.2.1 | C:\Octave\Octave-4.2.1\share\octave\packages\miscellaneous-1.2.1
                nan  |   3.1.2 | C:\Octave\Octave-4.2.1\share\octave\packages\nan-3.1.2
             netcdf  |  1.0.11 | C:\Octave\Octave-4.2.1\share\octave\packages\netcdf-1.0.11
              nurbs  |  1.3.10 | C:\Octave\Octave-4.2.1\share\octave\packages\nurbs-1.3.10
                ocs  |   0.1.5 | C:\Octave\Octave-4.2.1\share\octave\packages\ocs-0.1.5
             odepkg  |   0.8.5 | C:\Octave\Octave-4.2.1\share\octave\packages\odepkg-0.8.5
              optim  |   1.5.2 | C:\Octave\Octave-4.2.1\share\octave\packages\optim-1.5.2
         quaternion  |   2.4.0 | C:\Octave\Octave-4.2.1\share\octave\packages\quaternion-2.4.0
           queueing  |   1.2.5 | C:\Octave\Octave-4.2.1\share\octave\packages\queueing-1.2.5
             signal *|   1.3.2 | C:\Octave\Octave-4.2.1\share\octave\packages\signal-1.3.2
            sockets  |   1.2.0 | C:\Octave\Octave-4.2.1\share\octave\packages\sockets-1.2.0
          sparsersb  |   1.0.2 | C:\Octave\Octave-4.2.1\share\octave\packages\sparsersb-1.0.2
            specfun  |   1.1.0 | C:\Octave\Octave-4.2.1\share\octave\packages\specfun-1.1.0
            splines  |   1.3.2 | C:\Octave\Octave-4.2.1\share\octave\packages\splines-1.3.2
         statistics  |   1.3.0 | C:\Octave\Octave-4.2.1\share\octave\packages\statistics-1.3.0
                stk  |   2.3.4 | C:\Octave\Octave-4.2.1\share\octave\packages\stk-2.3.4
            strings  |   1.2.0 | C:\Octave\Octave-4.2.1\share\octave\packages\strings-1.2.0
             struct  |  1.0.14 | C:\Octave\Octave-4.2.1\share\octave\packages\struct-1.0.14
             tisean  |   0.2.3 | C:\Octave\Octave-4.2.1\share\octave\packages\tisean-0.2.3
                tsa  |   4.4.5 | C:\Octave\Octave-4.2.1\share\octave\packages\tsa-4.4.5
              video  |   1.2.3 | C:\Octave\Octave-4.2.1\share\octave\packages\video-1.2.3
            windows  |   1.2.4 | C:\Octave\Octave-4.2.1\share\octave\packages\windows-1.2.4
             zeromq  |   1.2.1 | C:\Octave\Octave-4.2.1\share\octave\packages\zeromq-1.2.1
>>

</code>
</panel>
<panel title="⇓b. Load an installed package"> 
To load an installed package use **pkg load [package name]**. For example to load the package image:
<code>
pkg load image
</code>

</panel>
<panel title="⇓c. Install packages"> 
If the package you need has not installed automatically you can install it with the following command **pkg install -option [package name]**. For example to install:
<code>
pkg install image-1.0.0.tar.gz %Installs the package image from a file
</code>
While using **-forge** option installs a package directly from the Octave-Forge repository.  This requires an internet connection and the cURL library.
<code>
pkg install -forge signal %Installs the pkg signal from the Octave-Forge repository
</code>

</panel>
<panel title="⇓d. Load packages automatically at startup"> 

During installation Octave installs a number of base packages that add functionality to the software. Packages are the Octave equivalent of Matlab Toolboxes. In Matlab Toolboxes are automatically installed, loaded and added to the path at start-up if the Toolbox has been supplied by Matlab, user supplied Tools & Toolboxes can be add using <wrap em>Set Path</wrap>. In Octave Packages are not automatically loaded unless required by the user. To automatically install packages in Octave you will need to Open Octave and edit <wrap em> octaverc </wrap> file this is equivalent to the Matlab <wrap em>startup.m</wrap> file. 

===Editing octaverc===
At the command prompt type:
<code>
edit octaverc
</code>

octavec will open in the Editor Window or Editor Tab. You will be presented with something like this:
<code>
## System-wide startup file for Octave.
##
## This file should contain any commands that should be executed each
## time Octave starts for every user at this site.
EXEC_PATH (cstrcat (fullfile (OCTAVE_HOME, 'notepad++'), pathsep, EXEC_PATH));
EXEC_PATH (cstrcat (fullfile (OCTAVE_HOME, 'bin'), pathsep, EXEC_PATH));
EDITOR (fullfile (OCTAVE_HOME, 'notepad++', 'notepad++.exe'));
</code>
Do not delete or modify any of the above lines from octaverc, unless you are a power user. Rather, add lines below these to accomplish what you're after (i.e. loading packages automatically).

=== Loading packages ===
To add packages type <wrap em>pkg load</wrap> followed by the name of the package you want to load. For example you may want to load the control & signal packages:
<code>
## System-wide startup file for Octave.
##
## This file should contain any commands that should be executed each
## time Octave starts for every user at this site.
EXEC_PATH (cstrcat (fullfile (OCTAVE_HOME, 'notepad++'), pathsep, EXEC_PATH));
EXEC_PATH (cstrcat (fullfile (OCTAVE_HOME, 'bin'), pathsep, EXEC_PATH));
EDITOR (fullfile (OCTAVE_HOME, 'notepad++', 'notepad++.exe'));

pkg load tagtools

## Animal Tag Tools required packages
pkg load control    %Computer-Aided Control System Design, required by signal
pkg load io	    %Input/Output in external formats
pkg load netcdf     %A MATLAB compatible NetCDF interface for Octave 
pkg load signal	    %Signal processing tools

## Animal Tag Tools Optional packages
pkg load database 	 %Interface to SQL databases, currently only postgresql using libpq
pkg load generate_html   %Generate HTML pages for function help pages
pkg load gsl             % GNU Scientific Library
pkg load image 		 %Image processing  
pkg load lssa 		 %Compute spectral decompositions of irregularly-spaced time series
pkg load ltfat 		 %The Large Time/Frequency Analysis Toolbox (LTFAT) 
%pkg load mapping 	 %Simple mapping and GIS .shp and raster file functions 
%pkg load miscellaneous  % Miscellaneous tools
pkg load optim		 %Non-linear optimization toolkit 
pkg load statistics	 %Additional statistics functions for Octave 
pkg load struct		 %Additional structure manipulation functions
</code>
Save any changes that you make! 

</panel>
</accordion>

-------------
==== 2. Adding the Tag Tools to your work path ====

See this link for detailed help: https://octave.org/doc/v4.0.1/Manipulating-the-Load-Path.html