# Editing Cookbook

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===Load comma separated values (*.csv) files=== | ===Load comma separated values (*.csv) files=== | ||

− | + | {{Code|Load comma separated values files|<syntaxhighlight lang="octave" style="font-size:13px"> | |

− | A = textread("file.csv", "%d", "delimiter", ","); | + | A=textread("file.csv", "%d", "delimiter", ","); |

− | B = textread("file.csv", "%s", "delimiter", ","); | + | B=textread("file.csv", "%s", "delimiter", ","); |

inds = isnan(A); | inds = isnan(A); | ||

− | B(! inds) = num2cell (A(! inds)) | + | B(!inds) = num2cell(A(!inds)) |

− | </syntaxhighlight> | + | </syntaxhighlight>}} |

− | + | ||

− | + | This gets you a 1 column cell array. You can reshape it to the original size by using the <code>reshape</code> 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 | ||

+ | |||

+ | Another option is to use the function <code>csvread</code>, however this function can't handle non-numerical data. | ||

+ | |||

+ | The probably best option is to use the function csv2cell() from the io package. This function can read mixed-type (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=== | ===Load XML files=== | ||

− | Reading XML in octave can be achieved using the java library [ | + | Reading XML in octave can be achieved using the java library [http://xerces.apache.org/ Xerces] (from apache). |

− | It seems that the | + | 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. |

− | 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 | ||

− | 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 | + | You need the jar files xercesImpl.jar and xml-apis.jar from e.g. https://www.apache.org/dist/xerces/j/Xerces-J-bin.2.11.0.tar.gz (check for the latest version). |

− | Use | + | Use javaaddpath to include these files: |

− | <syntaxhighlight lang=" | + | {{Code|Define java path|<syntaxhighlight lang="octave" style="font-size:1.1em"> |

− | javaaddpath ( | + | javaaddpath('/path/to/xerces-2_11_0/xercesImpl.jar'); |

− | javaaddpath ( | + | javaaddpath('/path/to/xerces-2_11_0/xml-apis.jar'); |

− | </syntaxhighlight> | + | </syntaxhighlight>}} |

− | + | A sample script: | |

− | <syntaxhighlight lang=" | + | {{Code|Load XML file|<syntaxhighlight lang="octave" style="font-size:1.1em"> |

− | filename = | + | 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') | ||

+ | </syntaxhighlight>}} | ||

− | + | The file <tt>sample.xml</tt>: | |

− | |||

− | |||

− | |||

− | + | {{Code|Sample XML file|<syntaxhighlight lang="xml" style="font-size:1.1em"> | |

− | + | <root> | |

− | + | <data att="1">hello</data> | |

− | + | </root> | |

− | |||

− | {{ | ||

− | <syntaxhighlight lang="xml"> | ||

− | <root> | ||

− | |||

− | </root> | ||

</syntaxhighlight>}} | </syntaxhighlight>}} | ||

Line 339: | Line 346: | ||

For example, to plot data using a string variable as a legend: | For example, to plot data using a string variable as a legend: | ||

− | + | Option 1 (simplest): | |

− | + | {{Code|Using variable strings in commands. op1|<syntaxhighlight lang="octave" style="font-size:13px"> | |

− | |||

legend = "-1;My data;"; | legend = "-1;My data;"; | ||

− | plot (x, y, legend); | + | plot(x, y, legend); |

− | </syntaxhighlight> | + | </syntaxhighlight>}} |

− | + | ||

− | + | Option 2 (to insert variables): | |

− | + | {{Code|Using variable strings in commands. op2|<syntaxhighlight lang="octave" style="font-size:13px"> | |

− | + | plot(x, y, sprintf("-1;%s;", dataName)); | |

− | plot (x, y, sprintf("-1;%s;", dataName)); | + | </syntaxhighlight>}} |

− | </syntaxhighlight> | + | |

− | + | Option 3 (not as neat): | |

− | legend = | + | {{Code|Using variable strings in commands. op3|<syntaxhighlight lang="octave" style="font-size:13px"> |

− | plot_command = [ | + | legend = 'my legend'; |

− | eval (plot_command); | + | plot_command = ['plot(x,y,\';',legend,';\')']; |

− | </syntaxhighlight> | + | eval(plot_command); |

+ | </syntaxhighlight>}} | ||

These same tricks are useful for reading and writing data files with unique names, etc. | These same tricks are useful for reading and writing data files with unique names, etc. | ||

== Combinatorics == | == Combinatorics == | ||

− | |||

=== Combinations with string characters === | === Combinations with string characters === | ||

− | |||

==== Problem ==== | ==== Problem ==== | ||

− | + | You want to get all combinations of different letters but {{codeline|nchoosek}} only accepts numeric input. | |

− | You want to get all combinations of different letters but {{ | ||

==== Solution ==== | ==== Solution ==== | ||

− | |||

Convert your string to numbers and then back to characters. | Convert your string to numbers and then back to characters. | ||

− | <syntaxhighlight lang=" | + | {{Code||<syntaxhighlight lang="octave"> |

− | |||

− | |||

char (nchoosek (uint8 (string), n)) | char (nchoosek (uint8 (string), n)) | ||

− | </syntaxhighlight> | + | </syntaxhighlight>}} |

==== Discussion ==== | ==== 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 {{codeline|asci}} function of the {{forge|miscellaneous}} package displays a nicely formatted conversion table). | |

− | 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 {{codeline|asci}} function of the {{forge|miscellaneous}} package displays a nicely formatted conversion table). | ||

=== Permutations with repetition === | === Permutations with repetition === | ||

− | |||

==== Problem ==== | ==== Problem ==== | ||

− | |||

You want to generate all possible permutations of a vector with repetition. | You want to generate all possible permutations of a vector with repetition. | ||

==== Solution ==== | ==== Solution ==== | ||

+ | Use {{codeline|ndgrid}} | ||

− | + | {{Code||<syntaxhighlight lang="octave"> | |

− | + | [x y z] = ndgrid ([1 2 3 4 5]); | |

− | <syntaxhighlight lang=" | + | [x(:) y(:) z(:)] |

− | [x | + | </syntaxhighlight>}} |

− | [x(:) | ||

− | </syntaxhighlight> | ||

==== Discussion ==== | ==== Discussion ==== | ||

− | |||

It is possible to expand the code above and make it work for any length of permutations. | It is possible to expand the code above and make it work for any length of permutations. | ||

− | <syntaxhighlight lang=" | + | {{Code||<syntaxhighlight lang="octave"> |

cart = nthargout ([1:n], @ndgrid, vector); | cart = nthargout ([1:n], @ndgrid, vector); | ||

combs = cell2mat (cellfun (@(c) c(:), cart, "UniformOutput", false)); | combs = cell2mat (cellfun (@(c) c(:), cart, "UniformOutput", false)); | ||

− | </syntaxhighlight> | + | </syntaxhighlight>}} |

== Mathematics == | == Mathematics == | ||

− | + | === Test if a number is a integer === | |

− | === Test if a number is | + | There are several methods to do this. The simplest method is probably {{Codeline|<nowiki>fix (x) == x</nowiki>}} |

− | |||

− | The simplest method is probably {{ | ||

− | |||

− | < | ||

− | fix (x) == x | ||

− | </ | ||

=== Find if a number is even/odd === | === Find if a number is even/odd === | ||

− | |||

==== Problem ==== | ==== 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. | 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 ==== | ==== Solution ==== | ||

− | |||

Check the remainder of a division by two. If the remainder is zero, the number is even. | Check the remainder of a division by two. If the remainder is zero, the number is even. | ||

− | + | mod (value, 2) ## 1 if odd, zero if even | |

− | mod (value, 2) | ||

− | |||

− | Since {{ | + | Since {{Codeline|mod()}} acceps a matrix, the following can be done: |

− | + | any (mod (values, 2)) ## true if at least one number in values is even | |

− | any (mod (values, 2)) | + | all (mod (values, 2)) ## true if all numbers in values are odd |

− | all (mod (values, 2)) | + | |

− | + | any (!logical (mod (values, 2))) ## true if at least one number in values is even | |

− | any (!logical (mod (values, 2))) | + | all (!logical (mod (values, 2))) ## true if all numbers in values are even |

− | all (!logical (mod (values, 2))) | ||

− | |||

==== Discussion ==== | ==== Discussion ==== | ||

+ | Since we are checking for the remainder of a division, the first choice would be to use {{Codeline|rem()}}. However, in the case of negative numbers {{Codeline|mod()}} will still return a positive number making it easier for comparisons. Another alternative is to use {{Codeline|bitand (X, 1)}} or {{Codeline|bitget (X, 1)}} but those are a bit slower. | ||

− | + | Note that this solution applies to integers only. Non-integers 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 non-integer values. | |

− | |||

− | |||

− | + | ==== See also ==== | |

− | + | Find if a number is an integer. | |

− | |||

=== Parametrized Functions === | === Parametrized Functions === | ||

− | |||

==== Problem ==== | ==== Problem ==== | ||

Line 459: | Line 437: | ||

==== Solution ==== | ==== Solution ==== | ||

+ | We could solve the problem with the following code: | ||

− | + | {{Code|Solve spring equation for different values of the spring constant|<syntaxhighlight lang="octave" style="font-size:13px"> | |

− | |||

− | <syntaxhighlight lang=" | ||

t = linspace (0, 10, 100); | t = linspace (0, 10, 100); | ||

function sprime = spring (s, t, k) | function sprime = spring (s, t, k) | ||

Line 476: | Line 453: | ||

plot (t, x1, t, x2) | plot (t, x1, t, x2) | ||

legend ('x1', 'x2') | legend ('x1', 'x2') | ||

− | </syntaxhighlight> | + | </syntaxhighlight>}} |

[[File:solparfun.png|400px]] | [[File:solparfun.png|400px]] | ||

Line 485: | Line 462: | ||

The [http://www.gnu.org/software/octave/doc/interpreter/Anonymous-Functions.html#Anonymous-Functions anonymous function] | The [http://www.gnu.org/software/octave/doc/interpreter/Anonymous-Functions.html#Anonymous-Functions anonymous function] | ||

+ | {{Code||<syntaxhighlight lang="octave" style="font-size:13px"> | ||

+ | @(x, t) sprime (x, t, k) | ||

+ | </syntaxhighlight>}} | ||

− | + | is a function of only <math>x, t</math> where the parameter <math>k</math> is 'frozen' to the value it has at the moment in the current scope. | |

− | |||

− | |||

− | |||

− | is a function of only <math>x, t</math> where the parameter <math>k</math> is | ||

=== Distance between points === | === Distance between points === | ||

− | |||

==== Problem ==== | ==== 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 <math> (x_i,y_i,\ldots)</math>. Asusme that the points are saved in a matrix '''<tt>P</tt>''' with '''<tt>N</tt>''' rows (one for each point) and '''<tt>D</tt>''' columns, one for each component. | |

− | Given a set of points in space we want to calculate the distance between all of them. | ||

− | Each point is described by its components <math> (x_i,y_i,\ldots)</math>. | ||

− | |||

− | |||

==== Solution ==== | ==== 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 | |

− | One way of proceeding is to use the broadcast properties of operators in GNU Octave. | + | <!-- {{SyntaxHighlight| --> |

− | The square distance between the points can be calculated with the code | + | {{Code|Calculate square distance between points|<syntaxhighlight lang="octave" style="font-size:13px"> |

− | + | [N, dim] = size (P); | |

− | <syntaxhighlight lang=" | + | Dsq = zeros (N); |

− | [ | + | for i = 1:dim |

− | Dsq = zeros ( | ||

− | for i = 1: | ||

Dsq += (P(:,i) - P(:,i)').^2; | Dsq += (P(:,i) - P(:,i)').^2; | ||

endfor | endfor | ||

− | </syntaxhighlight> | + | </syntaxhighlight>}} |

− | |||

This matrix is symmetric with zero diagonal. | This matrix is symmetric with zero diagonal. | ||

Similarly the vectors pointing from one point to the another is | Similarly the vectors pointing from one point to the another is | ||

− | + | <!-- {{SyntaxHighlight| --> | |

− | <syntaxhighlight lang=" | + | {{Code|Calculate radius vector between points|<syntaxhighlight lang="octave" style="font-size:13px"> |

− | R = zeros ( | + | R = zeros (N,N,dim); |

− | for i = 1: | + | for i = 1:dim |

R(:,:,i) = P(:,i) - P(:,i)'; | R(:,:,i) = P(:,i) - P(:,i)'; | ||

endfor | endfor | ||

− | </syntaxhighlight> | + | </syntaxhighlight>}} |

− | The relation between < | + | The relation between <tt>Dsq</tt> and <tt>R</tt> is |

− | + | <!-- {{SyntaxHighlight| --> | |

− | <syntaxhighlight lang=" | + | {{Code||<syntaxhighlight lang="octave" style="font-size:13px"> |

− | Dsq = sumsq (R, 3); | + | Dsq = sumsq (R,3); |

− | </syntaxhighlight> | + | </syntaxhighlight>}} |

==== Discussion ==== | ==== Discussion ==== | ||

+ | The calculation can be implemented using functions like <tt>cellfun</tt> 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 <tt>vech</tt> and <tt>unvech</tt> (this one is in the Forge package ''general''). Two functions that haven't seen the light yet are <tt>sub2ind_tril</tt> and <tt>ind2sub_tril</tt> (currently private functions in the [[Mechanics_package | Forge package mechanics]]) that are useful to index the elements of a vector constructed with the function <tt>vech</tt>. Each page (the third index) of the multidimensional array <tt>R</tt> is an anti-symmetric matrix and we could also save some memory by keeping only one of the triangular submatrices. | |

− | |||

− | |||

− | Another observation is that the matrix | ||

− | To use this optimization in a practical way check the help of the functions < | ||

− | Two functions that haven't seen the light yet are < | ||

− | Each page (the third index) of the multidimensional array < | ||

Check the [[Geometry package]] for many more distance functions (points, lines, polygons, etc.). | Check the [[Geometry package]] for many more distance functions (points, lines, polygons, etc.). |