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9. Hierarchical Structure

Typically, simulations are constructed of many different types of elements with different relationships to each other, mediated by the exchange of messages. In order to keep track of the structure of such a simulation, elements are organized into a tree hierarchy similar to that of the directory structure in the UNIX operating system. Obviously, as a simulation becomes more sophisticated, this tree structure can become many levels deep. Nevertheless, if you organize this structure properly, it will reflect the natural organization of the system.

9.1 The GENESIS Element Tree Hierarchy

Elements are stored in the GENESIS element tree. A particular element is uniquely identified by a path name. The root of this tree has a path of ``/''. The user can attach elements to this tree (at first as children of the root and then later as children of these children). The structure mimics that of the UNIX file system.

9.2 Traversing the Element Tree

You use the following GENESIS routines to navigate the element tree.

Routine Description
ce Changes the current working element.
el Returns list of elements matching wildcard specification.
getelementlist Alias for el routine.
getpath Returns subpart of full element pathname.
le Displays a list of elements in the element tree.
pope Restores previously stacked element as current working
element.
pushe Saves current working element on stack (for later retrieval
with pope) with option to go to new current working element.
pwe Displays full pathname of current working element.
stack Displays list of elements on working element stack.

9.3 Pathnames and Wildcards

Each element has a unique name which is fully specified by giving its pathname within the hierarchy. Pathnames are of the form: 

    name/name
or 
    /name/name
The first form specifies a path relative to the current element. The second form is an absolute path from the top or ``root'' of the hierarchy. By analogy with UNIX directory names, the name may be an actual element name, ``.'' (the current element), or ``..'' (the parent element).

Many commands can operate on more than a single element at a time. Wildcard paths can be used to specify multiple elements which satisfy the specified conditions.

A wildcard path is of the form 

    name[index][condition]
The wildcard name can be absent or can be one of 
    a#b    a?b    ##      #
If an index is specified, it can be one of 
  index:       []     [n]    [n-m]
One or more optional conditions may be specified in one of the forms 
    [field  operator value]
    [CLASS  operator classname]
    [OBJECT operator objectname]
    [TYPE   operator objectname]
    [ISA    operator objectname]

where the allowed operators are 

    = <> != > < >= <=

Note that white space is NOT allowed anywhere in the wildcard specification. The # matches strings of any length while ? matches single characters. The ## is a special name which specifies searches down the entire subtree rather than at a single level.

For example, a path that specified all elements that had name beginning with ``cell'' with x coordinates greater than 5 and less than 10 would be: 

    /cell#[x>5][x<10]

Note that the # and ## DO NOT expand indexed elements. For example, given the following list of elements: 

    /TEST[0] /TEST[1] /TEST[2] /TEST[3] /TEST[4] /THESE[0] /THESE[1]
The command 
    echo {el /#}
would produce only 
    /TEST /THESE
while 
    echo {el /#[]}
would give 
  /TEST /TEST[1] /TEST[2] /TEST[3] /TEST[4]
  /THESE /THESE[1]
Note that /TEST is the same as /TEST[0].

The use of the ``[]'' wildcard notation for indexed elements is useful for setting fields of indexed elements, for example, 

    setfield /randomspike[] rate 200
It can also be used with the addmsg command: 
    // Provide injection to soma of cell[0], cell[1], cell[2], etc.
    addmsg /waveform /cell[]/soma INJECT output

A path that would specify all elements in the hierarchy that belong to the channel class would be: 

    /##[CLASS=channel]

The OBJECT identifier (and its older name, TYPE) is used to specify elements which were created from a given object. For example, 

    setfield /##[OBJECT=xgraph] bg white
will set the background to white for all graphs which were created from the xgraph object. The X1compat libray of XODUS 1 compatible objects and commands uses the xgraph object as the basis of an extended object, x1graph. Elements which are created from the x1graph object will not be affected by the statement above. The ISA identifier is used instead of OBJECT to include elements created from objects that were derived from a specified object. For example, 
    setfield /##[ISA=xgraph] bg white
It is also possible to specify comma separated lists of wildcard path specifications, for example: 
    showfield soma/#[OBJECT=Ca_concen],basal_8/#[OBJECT=Ca_concen] Ca

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