File contents

Routine Name:	planardelay

Description:	Sets the delay fields on groups of synapses between
		specified lists of elements.  Most often used to set
		delays on groups of synapses that have been set up
		by calling the "planarconnect" command.  This function
		can assign groups of synapses to a fixed delay, can
		assign delays in proportion to the distances between
		pre- and postsynaptic elements, and can add various
		types of randomness to delay values.

Usage:		planardelay sourcepath [destination_path]  \
		-fixed delay                               \
		-radial conduction_velocity		   \
		-add					   \
		-uniform scale                             \
		-gaussian stdev maxdev                     \
		-exponential mid max                       \
		-absoluterandom

		sourcepath  A wildcarded list of elements which are the 
		        sources of the SPIKE messages connecting the
			pre- and postsynaptic elements (i.e. the presynaptic
			elements).  These must be of class "spiking" and are 
			usually spikegen or randomspike objects.

		destination_path  A wildcarded list of elements which must be
			synchans or objects derived from synchan.  If this
			(optional) argument is given, only the delays between 
			the given set of pre- and postsynaptic elements will
			be set by this command.  If this argument is not
			given, then all the synapses receiving SPIKE messages
			from the presynaptic elements will have their delays
			set by this command.  NOTE: this optional argument is 
			new and is not documented in the Book of GENESIS.

		-fixed delay  -- This option sets all the synaptic delays in
		        question to be equal to "delay".

		-radial conduction_velocity  -- This option sets the synaptic 
			delays in question to be proportional to
			the distance between the source and destination 
			elements according to the equation:

			delay = radial_distance / conduction_velocity

			Where conduction_velocity is usually measured in
			meters/sec (SI units).	"conduction_velocity"
			represents the conduction velocity of the 
			(hypothetical) axon that the spikes travel down.
			For planardelay, the distance is measured as:

			distance = 
			  sqrt((x_src - x_dest)^2 + (y_src - y_dest)^2)

			where x_src is the x component of the source element,
			x_dest is the x component of the destination element,
			and so on.  Note that the z component is not taken
			into account, which is unrealistic.  volumedelay
			uses the z component as well.

		-add  This option causes the computed delays to be added to 
		        the preexisting delays in the synapses instead of
			overwriting them.  This is useful when adding small 
			synaptic delays, among other uses.  

		The next four options are used to add random components to the
		delays established using the -fixed or -decay options.  How
		these random components are added to the delays is explained
		below.

		-uniform scale  -- This option gives a random number taken 
			from a uniform distribution in the range 
			{-scale, scale}.

		-gaussian stdev maxdev  -- This option gives a random number
			taken from a gaussian distribution centered on zero,
			with a standard deviation equal to "stdev" and with
			a maximum value of "maxdev".  The maximum value is
			used to limit the random component to a given range.

		-exponential mid max  -- This option gives a random number
			taken from an exponential distribution with a 
			minimum value of zero, a 1/e point of "mid" and a 
			maximum value of "max".  This is mainly for backwards
			compatibility with genesis 1.4.

		-absoluterandom  This option alters the way the random number
			is combined with the nominal delay to give the actual
			delay, as described below.

		Once a random component has been created for a given delay, 
		it is used to set the delay as follows.  If the 
		-absoluterandom option has not been selected the delay is set 
		to be:

		final_delay = delay + (delay * random_number)

		Whereas if the -absoluterandom option has been selected then
		we have

		final_delay = delay + random_number

		Thus the default is to have the amount of randomness as a 
		constant proportion of the delay value.

Example:	[modified from the Orient_tut simulation:]

		planardelay /retina/recplane/rec[]/input \
			    -radial {CABLE_VEL}          \
			    -gaussian 0.1 0.3

		This command will set the size of the delays of synapses 
		that are receiving their inputs from 
		/retina/recplane/rec[]/input.  It gives delays equal to the
		radial distance between elements divided by the conduction
		velocity (CABLE_VEL).  It also specifies that gaussian noise 
		be added to the delays with a mean value of 0.1 (which 
		represents 10% of the original delay, since -absoluterandom 
		has not been selected) and a maximum value of 0.3 (which is 
		30% of the original delay value).

Notes:		The "destination_path" optional argument is new and is not
		documented in the Book of GENESIS.

		This routine calculates distance using only the x and y 
		coordinates of the element positions.  It is convenient for
		objects laid out in planar arrays but ignoring the z
		direction is somewhat unrealistic.  volumedelay is identical 
		to planardelay except that it uses the positions of elements 
		in three dimensions to calculate distances and is thus more 
		realistic.

		The delays are never allowed to go negative even if a large
		negative random component is added.  Negative delays are set
		to zero.

		If the -add option is chosen, the random component modifies 
		only the delay added and not the total delay.

See also:	volumedelay, planarconnect, planarweight, syndelay; Chapter 18
                of the Book of GENESIS (2nd ed.) has a lengthy discussion on
                this and related commands.