Cookbook
An Octave cookbook. Each entry should go in a separate section and have the following subsection: problem, solution, discussion and maybe a see also.
Programs, Libraries, and Packages
Recipes for developers of Octave programs and libraries. The type of stuff an Octave programmer should be aware when writing code for others.
Find Octave configuration
Octave can be built with many configurations so programs may end up running in a machine without features they need. Developers should never expect an Octave installation to have all features. And programs should identify if the required features are available.
This is a list of possible tests to check for features:
## support for 64 bit indexing sizemax () > intmax ("int32")
## built with support for java usejava ("jvm")
## Image IO with support for tif files any (cellfun (@(x) ismember ("tif", x), {imformats.ext})) ## Image IO with support for png files any (cellfun (@(x) ismember ("png", x), {imformats.ext}))
Find if a package is installed
Problem
You have a program that uses different functions or behaves different depending on the availability of specific packages.
Solution
Use pkg ("describe", pkgname)
like so:
if (! isempty (pkg ("describe", "foo"))) ## use functions from package foo, the prefered way elseif (! isempty (pkg ("describe", "bar"))) ## use functions from package bar, not so optimal else ## default case endif
Discussion
It's not recommended to use this if the only purpose is to then fail in the absence of the package. In such case, simply try to load the package and Octave will already give a error message that is informative enough.
There is only purpose to check this, if there is something different to
do if a package is missing. The same is true for catching an error from
pkg load
. If you only catch an error to then throw it again
then you might as well not catch it in the first place.
## This contraption doesn't add anything. If 'pkg load' fails, it ## will already give an error message to the user. try pkg load foo; catch error ("failed to load foo: %s", lasterr ()); end_try_catch
## Again, doesn't add anything. The failure of 'pkg load' is enough if (isempty (pkg ("describe", "foo"))) error ("program: package foo is not installed"); endif
Beware that an installed package is not always a guarantee that a function will be available. Some packages may disable functions at build time, or specific functions may have specific runtime requirements.
Structures
Retrieve a field value from all entries in a struct array
Problem
You have a struct array with multiple fields, and you want to access the value from a specific field from all elements. For example, you want to return the age from all patients in the following case:
samples = struct ("patient", {"Bob", "Kevin", "Bob" , "Andrew"}, "age", { 45 , 52 , 45 , 23 }, "protein", {"H2B", "CDK2" , "CDK2", "Tip60" }, "tube" , { 3 , 5 , 2 , 18 } );
Solution
Indexing the struct returns a comma separated list so use them to create a matrix.
[samples(:).age]
This however does not keep the original structure of the data, instead returning all values in a single column. To fix this, use reshape()
.
reshape ([samples(:).age], size (samples))
Discussion
Returning all values in a comma separated lists allows you to make anything out of them. If numbers are expected, create a matrix by enclosing them in square brackets. But if strings are to be expected, a cell array can also be easily generated with curly brackets
{samples(:).patient}
You are also not limited to return all elements, you may use logical indexing from other fields to get values from the others:
[samples([samples(:).age] > 34).tube] ## return tube numbers from all samples from patients older than 34 [samples(strcmp({samples(:).protein}, "CDK2")).tube] ## return all tube numbers for protein CDK2
Array manipulation
Select a slice from an nD array
Problem
For an array A
with arbitrary number of dimensions, select, for example, the first column. This would be A(:, 1)
if A
was 2D, A(:, 1, :)
if A
was 3D, and so on.
Solution
One possibility is to use subsref
with the input idx
created dynamically with repelems
to have the right number of dimensions. This can be written as a function:
function [B]= array_slice (A,k,d)
#return the kth slice (row, column...) of A, with d specifying the dimension to slice on
idx.type = "()";
idx.subs = repelems ({':'}, [1;ndims(A)]);
idx.subs(d) = k;
B = subsref (A,idx);
endfunction
#test cases
%!shared A
%! A=rand(2, 3);
%!assert (array_slice (A,1,2), A(:, 1))
%! A=rand(2, 3, 4);
%!assert (array_slice (A,2,1), A(2, :, :))
%! A=rand(2, 3, 4, 5);
%!assert (array_slice (A,1,2), A(:, 1, :, :))
%! A=rand(2, 3, 4, 5, 6);
%!assert (array_slice (A,2,3), A(:, :, 2, :, :))

To remove the singleton dimension d
from the result B
, use
B = reshape(B, [size(B)([1:d1 d+1:end])]);

Input/output
Display matched elements from different arrays
Problem
You have two, or more, arrays with paired elements and want to print out a string about them. For example:
keys = {"human", "mouse", "chicken"}; values = [ 64 72 70 ];
and you want to display:
Calculated human genome GC content is 64% Calculated mouse genome GC content is 72% Calculated chicken genome GC content is 70%
Solution
Make a two rows cell array, with each paired data in a column and supply a cslist to printf
values = num2cell (values); new = {keys{:}; values{:}}; printf ("Calculated %s genome GC content is %i%%\n", new{:})
or in a single line:
printf ("Calculated %s genome GC content is %i%%\n", {keys{:}; num2cell(values){:}}{:})
Discussion
printf
and family do not accept cell arrays as values. However, they keep repeating the template given as long as it has enough arguments to keep going. As such, the trick is on supplying a cslist of elements which can be done by using a cell array and index it with {}
.
Since values are stored in columnmajor order, paired values need to be on the same column. A new row of data can then be added later with new(end+1,:) = {"Andrew", "Bob", "Kevin"}
. Note that normal brackets are now being used for indexing.
Swap values
If you want to exchange the value between two variables without creating a dummy one, you can simply do:
Code: Swap values without dummy variable 
[b,a] = deal (a,b);

Collect all output arguments of a function
If you have a function that returns several values, e.g.
function [a b c]= myfunc ()
[a,b,c] = deal (1,2,3);
endfunction

and you want to collect them all into a single cell (similarly to Python's zip() function) you can do:
Code: Collect multiple output arguments 
outargs = nthargout (1:3, @myfunc)

Create a text table with fprintf
(a.k.a. A funny formatting trick with fprintf found by chance)
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?
That's easy:
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
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:
Code: Example create a text table with fprintf 
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
Code: Load comma separated values files 
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 reshape
function
The next version of octave (3.6) implements the CollectOutput
switch as seen in example 8 here: http://www.mathworks.com/help/techdoc/ref/textscan.html
Another option is to use the function csvread
, however this function can't handle nonnumerical data.
The probably best option is to use the function csv2cell() from the io package. This function can read mixedtype (numerical and text) .csv files, allows to specify other field separators than a comma and other text protection characters (default: " double quote) and can skip headerlines. If you have the io package installed and loaded, type "help csv2cell" at the Octave prompt for more info.
Load XML files
Reading XML in octave can be achieved using the java library Xerces (from apache).
It seems that the matlab's xmlread is just a thin wrapper around the Xerces library. One should note however, that Java functions have the working directory set to the working directory when octave starts and the working directory is not modified by a cd in octave. Matlab has the same behavior, as Java does not provide a way to change the current working directory (http://bugs.java.com/bugdatabase/view_bug.do?bug_id=4045688). To avoid any issues, it is thus better to use the absolute path to the XML file.
You need the jar files xercesImpl.jar and xmlapis.jar from e.g. https://www.apache.org/dist/xerces/j/XercesJbin.2.11.0.tar.gz (check for the latest version). Use javaaddpath to include these files:
Code: Define java path 
javaaddpath('/path/to/xerces2_11_0/xercesImpl.jar');
javaaddpath('/path/to/xerces2_11_0/xmlapis.jar');

A sample script:
Code: Load XML file 
filename = 'sample.xml';
% These 3 lines are equivalent to xDoc = xmlread(filename) in matlab
parser = javaObject('org.apache.xerces.parsers.DOMParser');
parser.parse(filename);
xDoc = parser.getDocument;
% get first data element
elem = xDoc.getElementsByTagName('data').item(0);
% get text from child
data = elem.getFirstChild.getTextContent
% get attribute named att
att = elem.getAttribute('att')

The file sample.xml:
Code: Sample XML file 
<root>
<data att="1">hello</data>
</root>

Using variable strings in commands
For example, to plot data using a string variable as a legend:
Option 1 (simplest):
Code: Using variable strings in commands. op1 
legend = "1;My data;";
plot(x, y, legend);

Option 2 (to insert variables):
Code: Using variable strings in commands. op2 
plot(x, y, sprintf("1;%s;", dataName));

Option 3 (not as neat):
Code: Using variable strings in commands. op3 
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.
Combinatorics
Combinations with string characters
Problem
You want to get all combinations of different letters but nchoosek
only accepts numeric input.
Solution
Convert your string to numbers and then back to characters.
char (nchoosek (uint8 (string), n)

Discussion
A string in Octave is just a character matrix and can easily be converted to numeric form back and forth. Each character has an associated number (the asci
function of the miscellaneous package displays a nicely formatted conversion table).
Permutations with repetition
Problem
You want to generate all possible permutations of a vector with repetition.
Solution
Use ndgrid
[x y z] = ndgrid ([1 2 3 4 5]);
[x(:) y(:) z(:)]

Discussion
It is possible to expand the code above and make it work for any length of permutations.
cart = nthargout ([1:n], @ndgrid, vector);
combs = cell2mat (cellfun (@(c) c(:), cart, "UniformOutput", false));

Mathematics
Test if a number is a integer
There are several methods to do this. The simplest method is probably fix (x) == x
Find if a number is even/odd
Problem
You have a number, or an array or matrix of them, and want to know if any of them is an odd or even number, i.e., their parity.
Solution
Check the remainder of a division by two. If the remainder is zero, the number is odd.
mod (value, 2) ## 1 if odd, zero if even
Since mod()
acceps a matrix, the following can be done:
any (mod (values, 2)) ## true if at least one number in values is even all (mod (values, 2)) ## true if all numbers in values are odd any (!logical (mod (values, 2))) ## true if at least one number in values is even all (!logical (mod (values, 2))) ## true if all numbers in values are even
Discussion
Since we are checking for the remainder of a division, the first choice would be to use rem()
. However, in the case of negative numbers mod()
will still return a positive number making it easier for comparisons. Another alternative is to use bitand (X, 1)
or bitget (X, 1)
but those are a bit slower.
Note that this solution applies to integers only. Nonintegers such as 1/2 or 4.201 are neither even nor odd. If the source of the numbers are unknown, such as user input, some sort of checking should be applied for NaN, Inf, or noninteger values.
See also
Find if a number is an integer.
Parametrized Functions
Problem
One sometimes needs to define a family of functions depending on a set of parameters, e.g., where denote a the variables on which the function operates and are the parameters used to chose one specific element of the family of functions.
For example, let's say we need to compute the time evolution of the elongation of a spring for different values of the spring constant
Solution
We could solve the problem with the following code:
Code: Solve spring equation for different values of the spring constant 
t = linspace (0, 10, 100);
function sprime = spring (s, t, k)
x = s(1);
v = s(2);
sprime(1) = v;
sprime(2) = k * x;
endfunction
k = 1;
x1 = lsode (@(x, t) spring (x, t, k), [1;0], t)(:, 1);
k = 2;
x2 = lsode (@(x, t) spring (x, t, k), [1;0], t)(:, 2);
plot (t, x1, t, x2)
legend ('x1', 'x2')

Discussion
In the above example, the function "sprime" represents a family of functions of the variables parametrized by the parameter .
@(x, t) sprime (x, t, k)

is a function of only where the parameter is 'frozen' to the value it has at the moment in the current scope.
Distance between points
Problem
Given a set of points in space we want to calculate the distance between all of them. Each point is described by its components . Asusme that the points are saved in a matrix P with N rows (one for each point) and D columns, one for each component.
Solution
One way of proceeding is to use the broadcast properties of operators in GNU Octave. The square distance between the points can be calculated with the code
Code: Calculate square distance between points 
[N, dim] = size (P);
Dsq = zeros (N);
for i = 1:dim
Dsq += (P(:,i)  P(:,i)').^2;
endfor

This matrix is symmetric with zero diagonal.
Similarly the vectors pointing from one point to the another is
Code: Calculate radius vector between points 
R = zeros (N,N,dim);
for i = 1:dim
R(:,:,i) = P(:,i)  P(:,i)';
endfor

The relation between Dsq and R is
Dsq = sumsq (R,3);

Discussion
The calculation can be implemented using functions like cellfun and avoid the loop over components of the points. However in most cases we will have more points than components and the improvement, if any, will be minimal.
Another observation is that the matrix Dsq is symmetric and we could store only the lower or upper triangular part. To use this optimization in a practical way check the help of the functions vech and unvech (this one is in the Forge package general). Two functions that haven't seen the light yet are sub2ind_tril and ind2sub_tril (currently private functions in the Forge package mechanics) that are useful to index the elements of a vector constructed with the function vech. Each page (the third index) of the multidimensional array R is an antisymmetric matrix and we could also save some memory by keeping only one of the triangular submatrices.
Check the Geometry package for many more distance functions (points, lines, polygons, etc.).