Tips and tricks: Difference between revisions

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=C++=
==Preferences==
Sometimes, Octave defaults are not the best for someone's specific use. To change the defaults, use the following on the {{Path|[[.octaverc]]}} file.
 
=== Changing default figure size ===
The default size of a figure may be appropriate for simple figures but not so much when using {{Codeline|subplot}} for example. This can be changed though.
 
{{Code|change default figure size|<pre>set (0, 'DefaultFigurePosition', [1 get(0, "screensize")(4:-1:3) get(0, "DefaultFigurePosition")(4)]);</pre>}}
 
The value of {{Codeline|DefaultFigurePosition}} must be a four element vector with the x and y coordinates for the figure, followed by its width and height. The code above sets the default image to be placed at the top of the monitor, with the width of the monitor and the same height previously set as default.
 
=== Changing default font for axes ===
 
To display tex characters such as '\alpha' or '\lambda', a TrueType font ("arial" for instance) is better for the gnuplot backend [https://savannah.gnu.org/bugs/?30681]
{{Code|change default axes font name|<pre>set (0, "DefaultAxesFontName", "Arial")</pre>}}
It can then be necessary to change the font size as well
{{Code|change default axes font size|<pre>set(0, 'DefaultAxesFontSize', 10)</pre>}}
 
 
=== Shorten help message ===
To get rid of the long help message with the link to the Octave homepage place this in your startup file usually at ~/.octaverc (if it does not exist, create it). See the [http://www.gnu.org/software/octave/doc/interpreter/Startup-Files.html documentation] for more information.
suppress_verbose_help_message(1)
 
==Tiny helper functions==
 
This is a list of tiny helper functions (the equivalent of e.g., shell aliases), the kind one would have on its {{Path|.octaverc}} file.
 
=== Reload 'octave.rc' after 'clear' ===
When using {{Codeline|clear}}, one may accidentally remove functions (alias) or other variables set on the {{Path|octave.rc}} file. This can fixed by shadowing the {{Codeline|clear}} function with the following:
 
{{Code|reload octave.rc after clear|<pre>
function clear (varargin)
  args = sprintf (', "%s"', varargin{:});
  evalin ("caller", ['builtin ("clear"' args ')']);
  source ("~/.octaverc");
endfunction</pre>}}
 
The problem with this approach is if there's path manipulation on the {{Path|octave.rc}} file, such as {{Codeline|addpath}}. A workaround is needed for each case since it is not possible to obtain a reliable list of what's in Octave load path. But basically should be to undo what the file does, before {{Codeline|source ("~/.octaverc")}}.
 
If there's a {{Codeline|pkg unload all}} on it, this would also unload all packages. The following adjustment will keep the packages loaded
 
{{Code|reload octave.rc after clear but keep packages loaded|<pre>
function clear (varargin)
  args = sprintf (', "%s"', varargin{:});
  evalin ("caller", ['builtin ("clear"' args ')']);
  pkglist = pkg ("list");
  loadedpkg = cell (0);
  for ii = 1:numel (pkglist)
    if (pkglist{ii}.loaded)
      loadedpkg{end+1} = pkglist{ii}.name;
    endif
  endfor
  source ("~/.octaverc");
  if (numel (loadedpkg) != 0)
    pkg ("load", loadedpkg{:});
  endif
endfunction</pre>}}
 
 
=== replace help with man ===
 
If you use octave too much, you'll find yourself trying to use {{Codeline|help}} instead of {{Codeline|man}} on bash. This function will fix that so you can use {{Codeline|man}} in your octave instance (you can also do the opposite, create a {{Codeline|help}} alias in bash but {{Codeline|man}} has fewer characters).
 
{{Code|alias to help|<pre>
function man (name)
  help (char (name))
endfunction</pre>}}
 
==C++==
 
=== Real matrix operations===


== Real matrix operations==
This is a table of matrix operations commonly performed in Octave and their equivalents in C++ when using the octave libraries.
This is a table of matrix operations commonly performed in Octave and their equivalents in C++ when using the octave libraries.


Line 10: Line 78:
<tr><td>element multiplication</td><td><code>A.*B</code></td><td><code>product(A,B) </code></td></tr>
<tr><td>element multiplication</td><td><code>A.*B</code></td><td><code>product(A,B) </code></td></tr>
<tr><td>element division</td><td><code>A./B</code></td><td><code>quotient(A,B) </code></td></tr>
<tr><td>element division</td><td><code>A./B</code></td><td><code>quotient(A,B) </code></td></tr>
<tr><td>transpose*</td><td><code>A'</code></td><td><code>A.transpose()</code></td></tr>
<tr><td>transpose*</td><td><code>A.'</code></td><td><code>A.transpose()</code></td></tr>
<tr><td>select element m,n of A**</td><td><code>A(m,n)</code></td><td><code>A(m-1,n-1)</code></td></tr>
<tr><td>select element m,n of A**</td><td><code>A(m,n)</code></td><td><code>A(m-1,n-1)</code></td></tr>
<tr><td>select row N of A**</td><td><code>A(N,:)</code></td><td><code>A.row(N-1)</code></td></tr>
<tr><td>select row N of A**</td><td><code>A(N,:)</code></td><td><code>A.row(N-1)</code></td></tr>
Line 30: Line 98:
<tr><td>column vector</td><td><code>A(:)</code></td><td><code>ColumnVector(A.reshape (dim_vector(A.length())))</code></td></tr>
<tr><td>column vector</td><td><code>A(:)</code></td><td><code>ColumnVector(A.reshape (dim_vector(A.length())))</code></td></tr>
<tr><td>row vector</td><td><code>A(:)'</code></td><td><code>RowVector(A.reshape (dim_vector(A.length())))</code></td></tr>
<tr><td>row vector</td><td><code>A(:)'</code></td><td><code>RowVector(A.reshape (dim_vector(A.length())))</code></td></tr>
<tr><td>check for Inf or <a href="wiki.pl?NaN">NaN</a></td><td><code>any(~isfinite(A))</code></td><td><code>A.any_element_is_inf_or_nan()</code></td></tr>
<tr><td>check for Inf or NaN</td><td><code>any(~isfinite(A))</code></td><td><code>A.any_element_is_inf_or_nan()</code></td></tr>
<tr><td>stack two matrices vertically</td><td><code>A=[B;C]</code></td><td><code>B.stack(C)</code></td></tr>
<tr><td>stack two matrices vertically</td><td><code>A=[B;C]</code></td><td><code>B.stack(C)</code></td></tr>
<tr><td>uniform random matrix</td><td><code>rand(a,b)</code></td><td><code>octave_rand::distribution("uniform"); octave_rand::matrix(a,b)</code></td></tr>
<tr><td>uniform random matrix</td><td><code>rand(a,b)</code></td><td><code>octave_rand::distribution("uniform"); octave_rand::matrix(a,b)</code></td></tr>
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<tr><td>number of rows</td><td><code>size(A,1)</code></td><td><code>A.rows()</code></td></tr>
<tr><td>number of rows</td><td><code>size(A,1)</code></td><td><code>A.rows()</code></td></tr>
<tr><td>number of columns</td><td><code>size(A,2)</code></td><td><code>A.cols()</code></td></tr>
<tr><td>number of columns</td><td><code>size(A,2)</code></td><td><code>A.cols()</code></td></tr>
<tr><td>range</td><td><code>0.1:0.2:0.9</code></td><td><code>Range (0.1, 0.9, 0.2).matrix_value ()</code></td></tr>
</table>
</table>


Notes:
Notes:
<nowiki>
*Transpose, addition, and multiplication operations also apply to RowVector, ComplexRowVector, ColumnVector, and ComplexColumnVector data types when the dimensions are in agreement.


**The difference is due to the fact that arrays are zero-based in C++, but one-based in Octave.  
* Transpose, addition, and multiplication operations also apply to RowVector, ComplexRowVector, ColumnVector, and ComplexColumnVector data types when the dimensions are in agreement.  


***The names of Octave internal functions, such as mx_el_gt, are not documented and are subject to change. Functions such as mx_el_gt may eventually be available at both the scripting level and in C++ under more common names such as gt.
* The difference is due to the fact that arrays are zero-based in C++, but one-based in Octave.
</nowiki>
 
* The names of Octave internal functions, such as mx_el_gt, are not documented and are subject to change. Functions such as mx_el_gt may eventually be available at both the scripting level and in C++ under more common names such as gt.
 
===Complex Matrix Operations===


==Complex Matrix Operations==
<table>
<table>
<tr><td><b>Operation</b></td><td><b>Octave</b></td><td><b>C++</b></td></tr>
<tr><td><b>Operation</b></td><td><b>Octave</b></td><td><b>C++</b></td></tr>
Line 62: Line 131:
</table>
</table>


==General==


=General=
===Vectorizing Tricks===
==How to declare functions inside a test block==


function experience
You can easily fill a vector with an index:
%!test
%! experience_design_mat
%! experience_obs_eqs
%! assert (experience_design_mat == pi);
%! assert (experience_obs_eqs == exp(1));
%!
%! endfunction  % this is a trick.
%! % now we can declare functions to be used by the test above.
%!
%! function a = experience_design_mat
%!    a = pi;
%! endfunction
%!
%! function b = experience_obs_eqs
%!    b = exp(1);
%! % endfunction: don't add it here. Let test() do it.


==A funny formatting trick with fprintf found by chance==
    for i=1:n, x(i) = i; end


Imagine that you want to create a text table with fprintf with 2 columns of 15 characters width and both right justified. How to do this thing?
    x = 1:n;


That's easy:
This works for expressions on the index by wrapping the index in an expression:


If the variable Text is a cell array of strings (of length <15) with two columns and a certain number of rows, simply type for the kth row of Text
    for i=1:n, x(i) = sin(2*pi*i*f/r); end
fprintf('%15.15s | %15.15s\n', Text{k,1}, Text{k,2});
The syntax '%<n>.<m>s' allocates '<n>' places to write chars and display the '<m>' first characters of the string to display.


Example:
    x = sin(2*pi*(1:n)*f/r);
octave:1> Text={'Hello','World'};
octave:2> fprintf('%15.15s | %15.15s\n', Text{1,1}, Text{1,2})
          Hello |          World


==Load Comma Separated Values (*.csv) files==
You can also work with other vectors this way:


A=textread("file.csv", "%d", "delimiter", ",");
B=textread("file.csv", "%s", "delimiter", ",");
inds = isnan(A);
B(!inds) = num2cell(A(!inds))
This gets you a 1 column cell array. You can reshape it to the original size by using the <code>reshape</function>
The next version of octave (3.6) implements the <code>CollectOutput</code> switch as seen in example 8 here:                    http://www.mathworks.com/help/techdoc/ref/textscan.html
==Using Variable Strings in Octave Commands==
For example, to plot data using a string variable as a legend:
Option 1 (simplest):
legend = "-1;My data;";
plot(x, y, legend);
Option 2 (to insert variables):
plot(x, y, sprintf("-1;%s;", dataName));
Option 3 (not as neat):
legend = 'my legend';
plot_command = ['plot(x,y,\';',legend,';\')'];
eval(plot_command);
These same tricks are useful for reading and writing data files with unique names, etc.
==Vectorizing Tricks===
You can easily fill a vector with an index:
    for i=1:n, x(i) = i; end
    x = [1:n];
This works for expressions on the index by wrapping the index in an expression:
    for i=1:n, x(i) = sin(2*pi*i*f/r); end
   
    x = sin(2*pi*[1:n]*f/r);
You can also work with other vectors this way:
     for i=1:n, x(i) = sin(2*pi*y(i)*f/r); end
     for i=1:n, x(i) = sin(2*pi*y(i)*f/r); end


Line 160: Line 168:
*tricks relying on fortran indexing
*tricks relying on fortran indexing


===Other references===
====Other references====
*MATLAB array manipulation tips and tricks by Peter Acklam: http://home.online.no/~pjacklam/matlab/doc/mtt/index.html
 
*MATLAB array manipulation tips and tricks by Peter Acklam: https://web.archive.org/web/20151030212438/http://home.online.no/~pjacklam/matlab/doc/mtt/index.html
*The MathWorks: Code Vectorization Guide: http://www.mathworks.com/support/tech-notes/1100/1109.html
*The MathWorks: Code Vectorization Guide: http://www.mathworks.com/support/tech-notes/1100/1109.html
[[Category:Tips and tricks]]
===Changing BLAS===
Many Octave functions are wrappers to optimized numerical libraries, notably BLAS and ATLAS. It is possible to achieve impressive performance gains by simply using a library tuned to your platform. One example is using OpenBLAS to replace the default BLAS implementation ([https://web.archive.org/web/20140217072457/http://www.stat.cmu.edu/~nmv/2013/07/09/for-faster-r-use-openblas-instead-better-than-atlas-trivial-to-switch-to-on-ubuntu/ further details]).
On some Linux distributions, this just takes a few commands. For instance, on Ubuntu, it usually suffices to run
sudo apt-get install libopenblas-base libatlas3gf-base
followed by
sudo update-alternatives --config libblas.so.3
and then selecting the openblas option.

Latest revision as of 21:00, 14 August 2022

Preferences[edit]

Sometimes, Octave defaults are not the best for someone's specific use. To change the defaults, use the following on the .octaverc file.

Changing default figure size[edit]

The default size of a figure may be appropriate for simple figures but not so much when using subplot for example. This can be changed though.

Code: change default figure size 
set (0, 'DefaultFigurePosition', [1 get(0, "screensize")(4:-1:3) get(0, "DefaultFigurePosition")(4)]);

The value of DefaultFigurePosition must be a four element vector with the x and y coordinates for the figure, followed by its width and height. The code above sets the default image to be placed at the top of the monitor, with the width of the monitor and the same height previously set as default.

Changing default font for axes[edit]

To display tex characters such as '\alpha' or '\lambda', a TrueType font ("arial" for instance) is better for the gnuplot backend [1]

Code: change default axes font name 
set (0, "DefaultAxesFontName", "Arial")

It can then be necessary to change the font size as well

Code: change default axes font size 
set(0, 'DefaultAxesFontSize', 10)


Shorten help message[edit]

To get rid of the long help message with the link to the Octave homepage place this in your startup file usually at ~/.octaverc (if it does not exist, create it). See the documentation for more information. 

suppress_verbose_help_message(1)

Tiny helper functions[edit]

This is a list of tiny helper functions (the equivalent of e.g., shell aliases), the kind one would have on its .octaverc file.

Reload 'octave.rc' after 'clear'[edit]

When using clear, one may accidentally remove functions (alias) or other variables set on the octave.rc file. This can fixed by shadowing the clear function with the following:

Code: reload octave.rc after clear 
function clear (varargin)
  args = sprintf (', "%s"', varargin{:});
  evalin ("caller", ['builtin ("clear"' args ')']);
  source ("~/.octaverc");
endfunction

The problem with this approach is if there's path manipulation on the octave.rc file, such as addpath. A workaround is needed for each case since it is not possible to obtain a reliable list of what's in Octave load path. But basically should be to undo what the file does, before source ("~/.octaverc").

If there's a pkg unload all on it, this would also unload all packages. The following adjustment will keep the packages loaded

Code: reload octave.rc after clear but keep packages loaded 
function clear (varargin)
  args = sprintf (', "%s"', varargin{:});
  evalin ("caller", ['builtin ("clear"' args ')']);
  pkglist = pkg ("list");
  loadedpkg = cell (0);
  for ii = 1:numel (pkglist)
    if (pkglist{ii}.loaded)
      loadedpkg{end+1} = pkglist{ii}.name;
    endif
  endfor
  source ("~/.octaverc");
  if (numel (loadedpkg) != 0)
    pkg ("load", loadedpkg{:});
  endif
endfunction


replace help with man[edit]

If you use octave too much, you'll find yourself trying to use help instead of man on bash. This function will fix that so you can use man in your octave instance (you can also do the opposite, create a help alias in bash but man has fewer characters).

Code: alias to help 
 function man (name)
   help (char (name))
 endfunction

C++[edit]

Real matrix operations[edit]

This is a table of matrix operations commonly performed in Octave and their equivalents in C++ when using the octave libraries.

OperationOctaveC++
addA+BA+B
subtractA-BA-B
matrix multiplicationA*BA*B
element multiplicationA.*Bproduct(A,B)
element divisionA./Bquotient(A,B)
transpose*A.'A.transpose()
select element m,n of A**A(m,n)A(m-1,n-1)
select row N of A**A(N,:)A.row(N-1)
select column N of A**A(:,N)A.column(N-1)
extract submatrix of AA(a:b,c:d)A.extract(a-1,c-1,b-1,d-1)
absolute value of Aabs(A)A.abs()
comparison to scalar***A>2mx_el_gt(A,2)
A<2mx_el_lt(A,2)
A==2mx_el_eq(A,2)
A~=2mx_el_ne(A,2)
A>=2mx_el_ge(A,2)
A<=2mx_el_le(A,2)
matrix of zerosA=zeros(m,n)A.fill(0.0)
matrix of onesA=ones(m,n)A.fill(1.0)
identity matrixeye(N)identity_matrix(N,N)
inverse of Ainv(A)A.inverse()
pseudoinverse of Apinv(A)A.pseudo_inverse()
diagonal elements of Adiag(A)A.diag()
column vectorA(:)ColumnVector(A.reshape (dim_vector(A.length())))
row vectorA(:)'RowVector(A.reshape (dim_vector(A.length())))
check for Inf or NaNany(~isfinite(A))A.any_element_is_inf_or_nan()
stack two matrices verticallyA=[B;C]B.stack(C)
uniform random matrixrand(a,b)octave_rand::distribution("uniform"); octave_rand::matrix(a,b)
normal random matrixrandn(a,b)octave_rand::distribution("normal"); octave_rand::matrix(a,b)
sum squares of columnssumsq(A)A.sumsq()
sum along columnssum(A,1)A.sum(0)
sum along rowssum(A,2)A.sum(1)
product along columnsprod(A,1)A.prod(0)
product along rowsprod(A,2)A.prod(1)
cumsum along columnscumsum(A,1)A.cumsum(0)
cumsum along rowscumsum(A,2)A.cumsum(1)
cumproduct along columnscumprod(A,1)A.cumprod(0)
cumproduct along rowscumprod(A,2)A.cumprod(1)
number of rowssize(A,1)A.rows()
number of columnssize(A,2)A.cols()
range0.1:0.2:0.9Range (0.1, 0.9, 0.2).matrix_value ()

Notes:

  • Transpose, addition, and multiplication operations also apply to RowVector, ComplexRowVector, ColumnVector, and ComplexColumnVector data types when the dimensions are in agreement.
  • The difference is due to the fact that arrays are zero-based in C++, but one-based in Octave.
  • The names of Octave internal functions, such as mx_el_gt, are not documented and are subject to change. Functions such as mx_el_gt may eventually be available at both the scripting level and in C++ under more common names such as gt.

Complex Matrix Operations[edit]

OperationOctaveC++
conjugate tranposeA'A.hermitian()

General[edit]

Vectorizing Tricks[edit]

You can easily fill a vector with an index: 

   for i=1:n, x(i) = i; end

   x = 1:n;

This works for expressions on the index by wrapping the index in an expression: 

   for i=1:n, x(i) = sin(2*pi*i*f/r); end

   x = sin(2*pi*(1:n)*f/r);

You can also work with other vectors this way: 

   for i=1:n, x(i) = sin(2*pi*y(i)*f/r); end

   x = sin(2*pi*y*f/r);

Conditionals in the for loop are a little bit tricky. We need to create an index vector for the true condition, and another for the false condition, then calculate the two independently. 

   for i=1:n, if y(i)<1, x(i)=y(i); else x(i) = 2*y(i); endif

   idx = y < 1;
   x(idx) = y(idx);
   x(!idx) = 2*y(!idx);

FIXME: add the following

  • examples from matrices
  • tricks with sort and cumsum (e.g., hist, lookup)
  • counter-examples such as a tridiagonal solver
  • sparse matrix tricks
  • tricks relying on fortran indexing

Other references[edit]

Changing BLAS[edit]

Many Octave functions are wrappers to optimized numerical libraries, notably BLAS and ATLAS. It is possible to achieve impressive performance gains by simply using a library tuned to your platform. One example is using OpenBLAS to replace the default BLAS implementation (further details).

On some Linux distributions, this just takes a few commands. For instance, on Ubuntu, it usually suffices to run 

sudo apt-get install libopenblas-base libatlas3gf-base

followed by 

sudo update-alternatives --config libblas.so.3

and then selecting the openblas option.

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