PLoS supp. material by Hermann Cuntz
The suffix „_tree“ is usually appended to indicate that a function belongs directly
to the TREES toolbox. An input tree intree is generally
the first argument which is passed on (this proved to be more comfortable in most cases).
This first argument intree can be a tree structure or an index (single value)
to the global cell array trees.
If the first input is omitted (or „“) the last entry in the trees
array is used.
In general, omitting an input argument by typing in the empty vector „“
or by simply sending out too few arguments to a function will result in replacing
the input arguments by default values.
These default values are indicated precisely in the headers
of each function (simply typing „help function_name“ will retrieve the header)
and in the code. For most functions only a subset of the full tree definition is used
(e.g. only the diameter values, only the X and Y coordinates or only the topology).
In those cases the functions will not complain if the tree is not complete
but the required fields are existent in the tree structure.
Missing fields might even be replaced: the „plot_tree“ function for example will
attribute sensible fake metrics if real ones are missing.
In most cases the last input argument to a TREES function is the options
string. This string contains concatenated flags starting with „-“.
Examples of typical options are:
‚-s‘.... show the result, this is mostly for demo purposes
‚-m‘.... demonstration movie in very few cases
‚-w‘.... waitbar to indicate the progress of long-lasting calculations
‚-e‘.... echo changes made to the tree
Note that if options is left empty (‚‘) default options will be used
rather than all flags off. To be sure that all flags are off set options
string to ‚none‘. Note also that when demo flags are on,
features of a tree as well as other TREES toolbox functions
might be required which are not required when the flags are off.
Meta-functions are generalized functions whose input of an Nx1 vector
can vary their application greatly
(see introductary explanation
of morphing a tree for one such example).
Examples are not necessarily useful but try to also exemplify typically
more unintuitive applications.
Output values and resulting plots are formatted and do not always correspond
to the correct output (e.g. rounded values) of the Matlab function.
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