Routine Name: abort Description: Cleanly interrupts simulation in progress. Usage: abort Example: abort Notes:See also: stop , step
Routine Name: abs
Description: Returns absolute value of number.
Usage: positive-number = abs any-number
positive-number returned as absolute value of
any_number
any-number number (float or int) for which to
compute absolute value
Example: genesis > echo { abs -22 }
22
genesis > int x
genesis > float y
genesis > y = -33.333
genesis > echo { abs {y} }
33.333000183
genesis > x = {abs {y}}
genesis > echo {x}
33
Notes:
Routine Name: acos
Description: Returns angle (in radians) corresponding to given cosine.
Usage: angle-in-radians = {acos cosine}
Example: genesis > echo { acos 1 }
0
genesis > float degrees_per_radian = 360 / (2 * 3.1415926)
genesis > echo {{ acos 0.707} * degrees_per_radian}
45.00865245
Notes:
See also:
cos
Routine Name: addaction
Description: Adds a named action to the action table used by element types.
Usage: addaction name action_func
addaction name id-number
Example: addaction NEWACTION 10
addaction K_squid_hh K_squid_hh_SET
(see Scripts/tutorials/hhchan_K.g)
Notes: Each object in a simulation is capable of performing one or
more "actions". An action can be described as an operation
that an object performs on its data. Actions are defined
within compiled functions which are attached to each object.
(You can display a list of actions which an object can perform
and the function(s) which perform using the showobject
routine.) For instance, objects of type compartment can
perform the actions:
RESTORE2 SAVE2 SET CHECK RESET PROCESS INIT
(The actions are actually performed by an underlying C
function associated with the compartment element type.)
You use the addaction routine to add the named action to the
action table. Actions are passed to the handler routines
associated with each type of GENESIS object. The handler is
expected to perform the necessary actions when a given action
type is passed to it by the simulator.
For the most part this routine will only be used when adding
new object types which require use of additional (non-default)
actions already known to GENESIS.
You use the addaction routine to define new actions to be used
by elements. There are a number of predefined actions
which are typically used by objects. PROCESS is one of them.
New actions can be added in any object. Use the 'addaction'
routine in the object definition script to inform the
simulator of the new action. The case number assigned to new
actions is relatively arbitrary as long as it does not
conflict with the case numbers of other actions defined in the
object. (you should get a compiler error if there is a
conflict).
When used as a GENESIS command, addaction is primarily used
in the construction of extended objects. It is also used as
a library intialization command during the compilation of
GENESIS libraries.
See also:
object ,
Extended Objects, Defining New
Objects and Commands (
NewObjects )
Routine Name: addalias
Description: Associates alternative name with existing GENESIS command.
Usage: addalias alias-name command-name
Example: addalias set setfield
Notes: You may put a number of addalias statements in a file and
use an include statement in the .simrc file to include the
file when GENESIS is started.
See also:
addescape
Command Name: addclass
Description: Adds a new class to list of currently recognized GENESIS
element classes.
Adds a new class tag to a given element.
Usage: addclass [element] class-name
Example: addclass /sine device
Notes: The addclass routine adds a class tag to a given element
identifying it as belonging to the given class. Omitting
the element defines a class name without assigning any
element to the class. (This is a deprecated usage which
may not be supported in future releases).
Objects can be grouped into named classes. This
grouping can be used to facilitate the specification of
operations to be performed on functionally related
elements. See scheduling (e.g., the addtask
routine, and Schedules) for an example of class use.
Classes are simply used for grouping of related
elements and do not alter the element functionality in
any way. Classes in GENESIS don't carry the full
connotations of classes within a true object-oriented
programming environment. They are simply convenient
ways of creating named groupings to which objects can be
assigned.
See also: listclasses,
deleteclass ,
showobject ,
Extended
Routine Name: addescape
Description: Adds an escape-key macro binding.
Usage: addescape esc_sequence command-string [-execute] [-id string]
esc_sequence actual keystrokes (or representation)
to associate with escape action
command-string string to insert in place when escape
sequence is issued (should be in
quotation marks if it contains blank
spaces)
-execute flag to have command-string executed
when escape sequence is called
(this puts the field EXEC in the
listescape table; if -exec is left
out, default is REPLACE, i.e., insert
command-string, unexecuted, in command
line at point escape sequence is
issued)
-id string label for this escape sequence, used
typically to identify the escape
sequence in user-understandable
language
Example: genesis > addescape [15~ "/xproto" -id "F5"
genesis > le <F5>
[line changes to:]
genesis > le /xproto
/draw
[associate command string 'echo "I am not a duck"' with key
stroke sequence escape-a:]
genesis > addescape a "echo I am not a duck" -execute
genesis > <escape-a>
I am not a duck
[from escapelist.g file, included in startup:]
addescape [A <^P> -id "up arrow"
addescape [B <^N> -id "down arrow"
addescape [C <^F> -id "right arrow"
addescape [D <^H> -id "left arrow"
addescape [1~ "execute movebol" -exec -id Find
addescape [2~ <^I> -id "Insert Here"
addescape [3~ <^D> -id Remove
addescape [11~ stop -exec -id F1
addescape [17~ "status -process" -exec -id F6
addescape [18~ status -exec -id F7
addescape [28~ "commands | more" -exec -id Help
addescape [29~ step<CR> -id Do
Notes: You use the addescape routine to create escape-key macros for
commonly used command lines. Here, the key is the key you
will depress after the escape key, and command-string is the
string which will be substituted into the SLI interpreter when
the the escape sequence occurs. (When the key is preceded by
escape -- ctrl [ -- during keyboard input, the command-string
is substituted.)
A standard set of escape-key macros is specified during
startup through the file escapelist.g.
See also:
listescape
Routine Name: addfield
Description: Add an extended (user-defined) field to an element.
Usage: addfield [element] field-name [-indirect element field]
[-description text]
field-name name of the new field to be added to element
-indirect make the field-name an alias for the a field
in another element
-description add a descriptive text string
Example: addfield /cell/soma area -d "Area of the compartment"
Notes: If you have a compartment, /soma, with a hh_channel
/soma/hh_Na, then
addfield /soma Gk -indirect hh_Na Gk
will add a field to /soma called Gk which is an alias for
/soma/hh_na Gk. Note that the path in the -indirect option
is relative to the element to which you are adding the
field. The indirect element path can also be an absolute
path.
See also:
deletefield
Routine Name: addforwmsg
Description: Forwards an incoming message to one element to another
element.
Usage: addforwmsg source-element message-number destination-element
source-element element from which the message will be
forwarded
msg-number number (index) of message in message list
(messages are numbered from 0 up)
destination-element
element to which the message will be forwarded
Notes: The destination element must accept messages of the same
name and with the same number of data slots as the message
being forwarded.
See also:
deleteforwmsg ,
showmsg ,
Extended
Routine Name: addglobal
Description: Declares a global variable of the specified type, allowing the
name of the global variable to be held in a string variable.
Usage: addglobal type name [value]
type must be one of int, float or str.
Example:
genesis > str name = "foo"
genesis > addglobal float {name} 5.55
genesis > listglobals
float foo = 5.55
str name = "foo"
(plus many others)
Notes:
Often it is useful to use a string variable name to hold the name of a
global variable. For example, one may want to pass the name of a global
variable to a function that declares a global variable, or that sets or
returns its value. However, normal GENESIS syntax for declarations and
assignments does not permit a variable name to be specified by a string
variable. The routines addglobal, getglobal, and setglobal are designed
to overcome this limitation.
Note that if addglobal is used within a function definition, the declared
variable will nevertheless be global, and not local to the function.
See also:
Variables ,
setglobal ,
getglobal ,
listglobals
Routine Name: addmsg
Description: Establishes message links between two elements.
Usage: addmsg source-element dest-delement msg-type [msg-fields]
Example: addmsg /cell/dend /cell/soma RAXIAL Ra previous_state
addmsg /cell/soma /cell/dend AXIAL previous_state
addmsg /cell/soma /graphs/Vmgraph PLOT Vm *voltage *red
Notes: addmsg sets up communication links to pass information
between elements. Messages flow along message links created
by the addmsg routine each time a simulation timestep is
executed.
For example, an asymmetric compartment connected to another
asymmetric compartment needs to send both its axial
resistance, Ra, and its membrane potential at the previous
simulation step to the second compartment. In order to update
its state, it needs to receive the second compartment's
previous membrane potential.
See also:
deletemsg ,
showmsg ,
getmsg , gen3dmsg, dd3dmsg
Routine Name: addmsgdef
Description: Adds a new message type allowing messages of that type
to be added to the element.
Usage: addmsgdef element message-name [message-arguments...]
-type message-type
element element for which to add the message
definition
message-name name of the message (the convention is
to use all upper case)
messages-arguments
zero or more names for the data slots
of the message
-type option to set the message type number
explicitly
Notes: It is normally unnecessary use the -type option as
addmsgdef assigns an unused message type number
automatically. -type should be necessary only for
specifying active messages.
See also:
deletemsgdef ,
showobject ,
Extended
Routine Name: addobject
Description: Adds a new object to GENESIS defined by the fields, message,
actions and class tags of the given element. The element
is removed and used as a prototype for initial field values
of new elements created from the new object.
Usage: addobject object-name element -author author-info
-description descriptive-text ...
object-name the new name for the object
element element from which to create the new object
-author Information about the author of the object
-description A description of the object; multiple
arguments to -description may be given
resulting in multiple lines of descriptive
text
Notes: The object name must not be the same as an existing
object. Currently, there is no corresponding
deleteobject command.
See also:
listobjects ,
showobject ,
Extended
Routine Name: addtask
Description: Adds a simulation event to the simulation schedule.
Usage: addtask function [arguments...]
function a compiled C function to be executed at each
step in the simulation phase according to its
order in the schedule table (almost always,
this fucntion will be "Simulate")
arguments arguments for the specified function
[practically speaking this means:]
addtask Simulate path -action action-name
path path specification of elements affected
(typically a wildcard path designation
with a CLASS-conditioned selection to
identify all elements of a specific type)
action-name action to perform on specified elements
(usually INIT or PROCESS; must be a valid
action, as determined by listactions)
Example:
addtask Simulate /##[CLASS=myclass] -action PROCESS
addtask myfunction myargs
from startup/schedule.g:]
deletetasks
addtask Simulate /##[CLASS=buffer] -action INIT
addtask Simulate /##[CLASS=segment] -action INIT
addtask Simulate /##[CLASS=device] -action INIT
addtask Simulate /##[CLASS=buffer] -action PROCESS
addtask Simulate /##[CLASS=projection] -action PROCESS
addtask Simulate /##[CLASS=spiking] -action PROCESS
addtask Simulate /##[CLASS=gate] -action PROCESS
addtask Simulate /##[CLASS=segment][CLASS!=membrane][CLASS!=gate]\
[CLASS!=concentration][CLASS!=concbuffer] -action PROCESS
addtask Simulate /##[CLASS=membrane] -action PROCESS
addtask Simulate /##[CLASS=hsolver] -action PROCESS
addtask Simulate /##[CLASS=concentration] -action PROCESS
addtask Simulate /##[CLASS=concbuffer] -action PROCESS
addtask Simulate /##[CLASS=device] -action PROCESS
addtask Simulate /##[CLASS=output] -action PROCESS
resched
Notes: GENESIS provides a default simulation schedule that handles
most simulation configurations (see above), but for your
simulation you may need to specify a different order in which
the simulator should process elements in the simulation. You
use addtask to enter simulation events to the simulation
schedule.
You must be careful to avoid multiple references to elements
with the same action. For instance, given a model containing
the six elements /test[1-6], the following schedule would be
an invalid specification since it would cause test[1] to be
invoked twice on each simulation step.
addtask Simulate /test[1] -action PROCESS
addtask Simulate /test[1-6] -action PROCESS
With broad path specifications, it is easy to accidentally
include multiple reference. However, you can check for these
occurrences by running the check routine. In the above case,
calling check after entering the above specifications would
generate the following message:
** Error - '/test[1]' multiply invoked
with action 'PROCESS'. Check task [2]
Task [2] refers to the second addtask command. This
command was responsible for the conflict.
Alternately, not scheduling all enabled elements (see enable)
for simulation is detected as an error by the check routine.
For instance, given the model of six elements used above, you
might define a schedule with one addtask call as follows:
addtask Simulate /test[1-5] -action PROCESS
Running check would produce the following message:
* Warning - '/test[6]' is not scheduled for simulation.
A valid schedule for this set of elements might be:
addtask Simulate /test[1] -action PROCESS
addtask Simulate /test[2-6] -action PROCESS
or
addtask Simulate /test[1-6] -action PROCESS
See also: <href id="Schedules">, <href id="resched">,
<href id="deletetasks">, <href id="showsched">, <href id="check">
Routine Name: argc
Description: Returns argument count (number of arguments passed to a
function).
Usage: int-value = {argc}
Example: if ({argc} > 3)
echo usage: foo a b c
return
end
Notes:
See also:
argc ,
argv ,
getarg ,
printargs
Routine Name: arglist
Description: Converts list of items into an argument list.
Usage: arglist string
Example:
genesis > str s ="a b c d"
genesis > echo { getarg {arglist {s}} -arg 3}
c
str s
str thingys = "foo bar baz"
foreach s ({arglist {thingys}})
echo {s}
end
Notes: In each of these examples, a single string consisting of
items separated by spaces has been converted into a list.
See also:
argc ,
argv ,
getarg ,
printargs
Routine Name: argv
Description: An array of strings containing the arguments passed to
a function.
Usage: argv position-number
Example:
function echoargs
int i
echo "Number of arguments = "{argc}
for(i=1;i<= {argc};i=i+1)
echo {argv {i}}
end
end
genesis > echoargs foo 5 1.23
Number of arguments = 3
foo
5
1.23
Notes: As with C, indices of argv should start with 1.
See also:
argc ,
arglist ,
getarg ,
printargs
Routine Name: asciidata
Description:
Converts a FMT1 formatted binary file (as produced by the
disk_out object, for example) to ASCII. Output is to stdout.
Usage:
asciidata file-name -time t -cell cell -gain g -old -xy -skip n -header
One of options -cell, -time or -header must be given.
Example: (using the horiz_disk file from Scripts/orient_tut)
genesis > asciidata horiz_disk -header
FMT1
start time = 0.000000e+00
time step = 1.000000e-05
cellnum = 25
data type = 4
data size = 4
genesis > asciidata horiz_disk -cell 24 | more
-7.006086e-02
-7.012120e-02
.
.
-7.597300e-02
-7.596859e-02
//(provides Vm at each time step; adding -xy option gives t and Vm)
genesis > asciidata horiz_disk -time 1.e-4 -xy
0 -0.0706427
1 -0.0706427
2 -0.0706427
.
.
23 -0.0706427
24 -0.0706427
//(cell number and Vm for each of the 25 cells)
See also:
disk_out
Routine Name: asin
Description: Returns angle (in radians) corresponding to given sine.
Usage: angle-in-radians = {asin sine}
Example: genesis > echo {{ asin 0.5 }*(180/3.1415926)}
30.00000135
Notes:
See also:
sin
Routine Name: atan
Description: Returns angle (in radians) corresponding to given tangent.
Usage: angle-in-radians = {atan tangent}
Example: genesis > echo { atan 0.876 }
Notes:
See also:
tan
Routine Name: call
Description: Allows an element to execute the function associated with the
named action.
Usage: call path action [args...] -parent -virtual
-parent call the action on the element using the parent object
of the current object context as the new object
context
-virtual call the action on the element using the element's
object as the object context during the action.
Example: call /form/graph RESET
call /form/graph/plot ADDPTS {x} {y}
Notes: The call routine allows the user to send an action to an
element's handler routine (outside of the simulation cycle).
An action executes in the context of a specific object which
is either the element's object or some base object for the
element. The object context determines what fields,
actions, messages and classes are known and accessibility of
fields during execution of the action function. Without any
other options to call, the object context during the call is
the element's object or the current object context if the
element is already executing an action. The -parent and
-virtual options modify this. These options are to be used
when an action is called within the function definition of
an action to be added with the addaction command. They have
no affect when used outside an action function.
See also:
addaction ,
Extended
Routine Name: callfunc
Description: Allows you to call a function whose name is stored in a
string variable.
Usage: callfunc funcname ...
Example: genesis > str foo = "echo"
genesis > callfunc {foo} a b c
a b c
Notes:
See also:
Routine Name: cd
Description: Changes current working operating system directory.
Usage: cd directory
Example: genesis > cd /usr/genesis/Scripts/neuron
Notes: This is a GENESIS implementation of the operating system
command cd, to assure that any change you make in the working
directory is known to GENESIS. (If you just issued a normal
cd command directly, via "sh cd" for instance, the
change in the current working directory would last only as
long as the subshell created to enact the command, and future
actions in GENESIS would not recognize a change. The GENESIS
implementation of cd fixes this.)
See also:
sh
Routine Name: ce
Description: Changes the current working element.
Usage: ce element-path
element-path complete or relative pathname of element to
make current working element; can also be
operating-system style hierarchy
abbreviations, such as . (current),
.. (element above current)
Example: ce /
ce /proto
ce output
ce ..
genesis > create compartment foo
genesis > ce ^
genesis > pwe
/foo
Notes: All GENESIS elements exist in a hierarchy. The root element
lives at the top of the tree (designated by /) and child
elements are created beneath the root. You use the ce routine
to move about the tree (much as you can use the "cd" command
to move about the operating system file system).
If the element-path specified in a ce call starts with a /
then the path is assumed to be an absolute path from the root
of the element hierarchy. If the first character of the path
specified is not a / then the path is assumed to be relative
to the current working element.
See also:
pwe ,
le ,
pushe ,
pope ,
stack
Routine Name: cellsheet
Description: Copies prototype cells into a 3-D sheet specified by
coordinates in a file.
Usage: cellsheet prototype dest filename [-orient][-curve]
[-randomise x y z] [-twirl theta]
prototype existing cell to copy to create cells in the
sheet (prototype is not changed by the
routine; all operations are done on the
copies)
destination element to become parent of all cells in sheet
filename file defining position and orientation of
cells (ascii file with 3 numbers for each
coordinate (cartesian only), followed by 3
coordinates for the normal vector to the
surface of the sheet at that point; this
vector does not have to be normalised; each
set of 6 numbers should be on different lines)
-orient reorients the cell to be normal to the local
region of the sheet
-curve distorts copies of prototype cell to follow
curvature of sheet of cells; the lengths (and
electrical properties) of the cell are not
changed (this option assumes that length of
each compartment is less than the radius of
curvature of the surface; also, the sampling
density over the cell sheet should be high
enough that the spacing between the points is
smaller than the length of each compartment;
does not attempt to curve compartments where
the angle of rotation would be less than 10
degrees, or more than 60)
-randomise x y z
randomises the coordinates of copied cells by
the specified factors in x, y and z before the
orienting/positioning/curving steps
(randomisation involves finding length of each
compartment in each direction, scaling it by a
random number within the range of the
specified factor, and adding it to the
original; e.g., a factor of 1 would permit a
change of up to the original length of the
compartment; the electrical properties and
channel conductances in each compartment are
scaled according to the total length change)
-twirl theta rotates the finally positioned cell about its
normal by a random angle from 0 to theta
degrees
Example:
include protodefs.g // copied from Scripts/tutorials
readcell cell.p /library/cell // use cell.p from Scripts/tutorials
plane planepoints 400e-6 400e-6 100e-6 100e-6 -normal
egg eggpoints 400e-6 400e-6 400e-6 100e-6 -normal
create neutral /planenet
create neutral /eggnet
rotcoord /library/cell {-3.1415927/2} -y // point dendrite up along z-axis
cellsheet /library/cell /planenet planepoints -orient
cellsheet /library/cell /eggnet eggpoints -orient
showfield /planenet/cell[]/dend x y z
Notes: Creates a sheet of cells by copying from a prototype, and
placing them at 3-D positions specified by an ascii file. A
number of options permit the cells to be oriented, conformed
to the curvature of the surface, randomised, and rotated, in
order to make the geometry more natural.
In the example above, the prototype cell had the apical
dendrite pointing along the x-axis, so rotcoord was used to
rotate it 90 degrees about the y-axis to point outward along
the z-axis. Then, cellsheet was used, first on a file
containing points in a plane, and then on a file containing
points distributed over the surface of an ovoid. In both
cases, the orient option was used to point the dendrite along
the outward normal to the surface.
Routine Name: check
Description: Checks various aspects of simulation to catch specification
errors.
Usage: check
Example: check
genesis > setfield /soma Rm -5000 Cm 0
genesis > check
** Error - Compartment : Invalid Rm. '/soma'
** Error - Compartment : Invalid Cm. '/soma'
Notes: The check routine sends the CHECK action to the handlers for
all enabled elements. The CHECK action should verify the
consistency and well being of the element and report any
problems with it to the user. (Each element which supports
self-checking will be invoked with the CHECK action and report
any problems.)
In the example above, the CHECK action of the compartment
checks to be sure that the Rm and Cm fields are set to
positive values, and running a check prints an error message.
See also:
addtask ,
setclock ,
enable ,
reset
Routine Name: chr
Description: Returns ASCII character specified by number code.
Usage: character = {chr ASCII-number}
Example: genesis > echo { chr 64 }
@
genesis > echo {chr 65}
A
genesis > echo {chr 97}
a
Notes:
Routine Name: clearerrors
Description: Resets error count to 0.
Usage: clearerrors
Example: clearerrors
Notes: When the number of errors reaches its maximum value (default:
10 syntax errors or 20 warnings) the current action is
interrupted, the simulator goes back to the command line, and
the errors are reset. The clearerrors routine can be used to
reset the error count before this occurs, allowing a
simulation to continue running despite errors.
See also:
maxerrors ,
maxwarnings
Routine Name: closefile
Description: Closes an ASCII file opened with the openfile routine.
Usage: closefile filename
Example: openfile myfile w
writefile myfile 10 20 30
closefile myfile
Notes: When you open a file using openfile, you work on a copy of
the file. The closefile routine writes your changes back
into the actual file and eliminates it from the list of open
files. (Closefile is automatically called for all opened
files when you exit from GENESIS).
See also:
openfile ,
listfiles ,
writefile
Converting GENESIS 1.4 Scripts to GENESIS 2.0
What Does Convert Do?
GENESIS 2.0 includes a major revision of command format and command
option naming, script language syntax changes and changes in various
GENESIS features. The convert program converts GENESIS 1.4 compatible
scripts to use GENESIS 2.0 syntax, commands and features. Some
features have changed dramatically enough that an automatic conversion
to the new features is not feasible. In these cases, convert generates
script code for compatibility libraries which support the GENESIS 1.4
features.
Some scripts can be converted and run successfully without any manual
changes to the converted scripts. In most cases, however, some changes
to the converted scripts will be necessary.
The Conversion Process
Below is the process through which a GENESIS 1.4 script is converted
to run under GENESIS 2.0.
1 - Use the convert program to convert scripts from 1.4 to
2.0 syntax.
2 - Fix any known problem areas (See, Convert Problem Areas).
3 - Try the script out and fix any remaining problems.
Using the Convert Program
The easiest way to use convert is to create a new directory for the new
scripts, cd to the new directory and convert the files from the old
directory. A simple shell procedure may be used to convert an entire
directory. For example, if your 1.4 script files are in the directory
../oldscript, then the following shell commands will convert the entire
directory placing the converted scripts in the current working
directory:
csh:
foreach script (../oldscript/*.g)
convert $script
end
sh:
for script in (../oldscript/*.g)
convert $script
end
Global Script Variables
In order for convert to handle certain script expressions involving
global script variables, it must know what globals exist for a given
set of scripts. (This is not a problem for a self contained script
where global variables are defined and used within the script.)
Often a single script file is devoted to defining and initializing
global variables and constants for a given set of scripts.
The -constants option of the convert program gives a list of script
files which define the global variables for the script set. For
example, if the file constants.g contains global variable definitions
which are used througout a set of scripts in the ../oldscripts
directory then the following csh code would convert the scripts:
foreach script (../oldscripts/*.g)
convert $script -constants ../oldscripts/constants,g
end
The -constants option will allow one or more scripts to be given.
Compatibility Libraries
Two areas of major change in GENESIS 2.0 are the Xodus GUI and support
for network modeling (e.g. GENESIS 1.4 connections). Support for use
of these facilities in GENESIS 2.0 is provided by compatibility
libraries.
While the compatibility libraries allow faster conversion of GENESIS
1.4 scripts for use under GENESIS 2.0, these libraries will not be
aggresively supported and should be viewed as a transitional step in
converting scripts to GENESIS 2.0 facilities. Those areas of your
scripts which use these libraries should eventually be recoded to use
the new GENESIS 2.0 features. Assistance for recoding of these
features may be found in the new GENESIS 2.0 Reference Manual (not
available at this time).
The X1compat Library
Compatibility for GENESIS 1.4 features of Xodus is provided as a set of
scripts using GENESIS 2.0 extended objects to implement the old Xodus
objects and script functions to implement old Xodus commands. To load
the X1compat library, include Scripts/X1compat in your SIMPATH and
include X1compat from your .simrc or your main simulation script.
Convert will not add an include statement for X1compat to your
scripts.
X1compat defines a set of old Xodus compatible objects which are named
using the prefix "x1" in place of the normal "x" prefix for Xodus
objects (e.g. xform becomes x1form, etc). Convert will automatically
transform create statements from Xodus objects in 1.4 scripts to use
the X1compat objects. Some support for field naming of old Xodus
objects is included in the new Xodus objects, which may allow direct
use of the new Xodus objects. The -noX1compat convert option causes
convert not to perform the translation to X1compat objects. This is
likely to be useful for only those scripts which use the basic Xodus
widgets (i.e. xform, xlabel, xbutton, xtoggle and xdialog). Uses of
xdraw or xgraph are likely to require use of X1compat.
Convert and the X1compat library cannot address various issues of
layout of widgets on a form. See, Convert Problem Areas, for more
information.
The Connection Compatibility Library
While GENESIS 1.4 connections are not a standard part of GENESIS 2.0, a
compatibility library may be compiled into GENESIS 2.0 which supports
the old connection feature. (See, src/Makefile or Usermake for
instructions on including the library.) The library defines the
connection related objects (e.g. axon, synapses, etc) and the
connection related commands (e.g. region_connect, expweight,
radialdelay, etc) as well as connection specific commands which support
set/get/show of connections (e.g. setconn, getconn and showconn).
Access to connection fields is not supported by the GENESIS 2.0
setfield, getfield and showfield commands.
Convert will change connection related script statements as needed to
use the Connection Compatibility Library. In particular, it will
convert uses of set, get and show on connections to use setconn, et
al. In some cases, convert will be unable to convert these statements
(See, Convert Problem Areas).
Converting User Libraries
Objects and commands defined in user libraries (for the most part) will
not need to change to run under GENESIS 2.0. To compile your libraries
and create a new GENESIS you will need to replace and update your
Usermake, Libmake(s), liblist and perhaps the library startup script.
Copy the Usermake and liblist files from the GENESIS 2.0 installation
directory to your local GENESIS directory renaming Usermake to
Makefile. Add your user libraries to the Makefile and liblist files.
In each user library you must copy the Libmake from the GENESIS 2.0
installation directory into the library directory renaming it
Makefile. Add your library specific information and files to the
Makefile.
The convert program cannot be used to convert startup scripts. The
only changes you should need to make are to modify any GENESIS 1.4
script language features which change in 2.0 and to remove any
non-startup commands from the script. (Startup commands are object,
addfunc, hashfunc, newclass and addaction.) Since a startup script is
usually straight line code and the typical commands in a 1.4 startup
script are the above named commands, there are normally no changes
required. There are, however, some GENESIS 2.0 features you may want
to take advantage of in your startup scripts. See the new GENESIS
Reference Manual section on library startup scripts for details.
Convert Problem Areas
There are a number of areas in which convert will be unable to
transform script statements or where the converted code will perform in
a less than optimal manner. Each problem area described below must be
found and fixed manually.
Script Callbacks
Commands used as callbacks to script commands or functions are not
translated by convert. As such, script callbacks like the following
would fail:
create xbutton echoButton -script "echo -n this is a test"
create xdialog vmDialog -script "set /mycompt Vm <v>"
The echoButton will result in a usage error when pressed and the
vmDialog will fail because the set command no longer exists.
Command Options in Script Variables
A command option which is passed to a command through a script variable
or as the result of a command or script function will not be
translated. For example, if leoptions is a script string variable
holding the value "-R" (a recursive listing), then the following code
will not be converted:
le {leoptions}
The code which sets leoptions must be found and changed.
Command Arguments That Look Like Options
All GENESIS 2.0 commands check for valid command options and complain
when an unkown option is given. As a result, code like
echo -notAnOption
will result in a usage error. This will also be the case if a script
variable value looks like an option, e.g.
str echoOption = "-notAnOption"
echo {echoOption} // Usage error!
The usage statement can be avoided by placing whitespace before the
value, e.g.
echo " -notAnOption"
echo " "{echoOption}
Set/Get/Show Connections in Script Variables
Commands like
set anElm:0 weight 10
will be correctly translated to use the setconn command. However, code
like
str connelm = "anElm:0"
set {connelm} weight 10
will be translated to a setfield command. Convert behaves similarly
with translating the get and show commands.
Script Variable/Command Name Conflicts
With all the command name changes in GENESIS 2.0, it is possible that a
script variable in a GENESIS 1.4 script may coinside with a new GENESIS
2.0 command name. In this case, you may receive a syntax error or
unexpected result as the script variable will take precedence over the
command name. This is may be particularly likely with the el command.
(The convert program may be updated at some future point to rename
script variables which clash with GENESIS 2.0 command names.)
Setting Integration Methods
GENESIS 2.0 removes some of the previously existing integration methods
and renumbers some of the remaining methods. Convert will handle the
renumbering as long as a number is given directly to the setmethod
command. If this is not the case, convert will issue a warning and the
command will be left unaltered. You must change the integration
numbering manually. See setmethod.txt (or type "help setmethod" in
GENESIS) for the new numbering.
Sizing of Xodus Forms
XODUS 1 made use of an unsupported feature of MIT X11 which allowed
forms to automatically adjust their height to accomodate all the
widgets which they contain, even if the form was made too short.
Although this did not work under Openwindows, it allowed users of MIT
X11 to be somewhat sloppy in the sizing of forms when writing scripts.
This feature no longer exists in XODUS, so forms which are incorrectly
sized may not show all the widgets which they contain. The most
convenient way to detemine the proper hgeom for the form is to properly
resize it with the mouse and then inspect the hgeom field for the value
to use in your script.
Apart from the preceeding issue, forms previously large enough to
encompass a given set of widgets may not be large enough under GENESIS
2.0, as the border widths of XODUS object have increased.
Positioning and Sizing of Widgets
Scripts which explicitly set the dimensions of a widget based on the
expected dimensional requirements of a 1.4 widget may cause text or
graphics within the widget to be clipped under 2.0. This is due to the
additional requirements of the Motif style borders.
Likewise, widgets which are positioned using absolute coordinates on
the form based on expected default dimensions of other widgets on the
form may overlap other widgets on the form.
The only widget layouts used under GENESIS 1.4 which are likely to work
well under 2.0 are those using relative positioning. Even if this is
the case, the form size may need to be changed (See Sizing of XODUS
Forms above).
Routine Name: copy
Description: Copies an element (and its children, if any) from one portion
of the element tree to another.
Usage: copy src-element dest-element -repeat # -autoindex
src-element element to copy (if this element has
subelements, they too are copied)
dst-element location into which to copy src-element (if
dst-element already exists, src-element is
copied beneath it with original name; if
dst-element does not exist, copy of
src-element is given that name as new name)
-repeat is followed by an integer specifying how
many duplicates of src-element to make
-autoindex automatically assigns the first free element
index to the newly created element.
Example: copy /cell1 /cell2
// create 5 cells, cell[0-4]
copy /library/protocell /cell[0] -repeat 5
Notes: This routine copies an element and its children, without
changing the original.
Simulation messages and connections between elements within
the copied subtree will be copied, but messages and
connections to elements outside of the copied subtree will not
be copied.
After it has copied the object, the copy routine issues the
COPY action for that element type, if any.
See also:
create ,
createmap ,
move
Routine Name: cos
Description: Returns cosine for given angle (specified in radians).
Usage: cosine = {cos angle-in-radians}
Example: float x
x = {cos {3.14159/4}}
Notes:
See also:
acos
Routine Name: countchar
Description: Counts occurrences of specified character in string.
Usage: number-of-occurrences = {countchar string char}
number-of-occurrences returned as integer indicating how
many occurences of char were found
in string
Example: genesis > echo {countchar "abcbdb" b}
3
Notes:
Routine Name: countelementlist
Description: Returns the number of elements in an element list.
Usage: countelementlist path [-listname listname]
path path specification, which may include
wildcards such as [] or # (note,
however, that operating-system style
use of * is not supported)
listname The listname argument tells it to look for the
field <listname> on the element in <path> and
treat that as an element list.
Example:
genesis > echo {el /#}
/proto /output /cell /control /data
genesis > echo {countelementlist /#}
5
genesis > echo {countelementlist /##}
19
Notes:
See also:
el ,
Tree
Routine Name: cpu
Description: Displays current cumulative cpu usage for user and system time.
Usage: cpu
Example: genesis > cpu
user time used = 3 sec 510000 usec
system time used = 1 sec 180000 usec
Notes: This routine calls the getrusage operating system command to
display user/system usage statistics.
See also:
showstat
Routine Name: create
Description: Creates new element of specified element type.
Usage: create element-type name -autoindex [object-specific-options]
element-type type of element; must be one of the valid
element types (objects) compiled into the
genesis executable, or an extended object
created with the GENESIS scripting language.
name element or path name where new element is to
be attached in the GENESIS element hierarchy;
if single name is given (i.e., no path
separators "/"), element is created on the
current working element [also can be indexed;
see below]
-autoindex automatically assigns the first free element
index to the newly created element.
[options] some elements can be created with additional
options which are specific to the object type
(see individual object documentation for
options)
Example: create neutral /cell
create compartment /cell/soma
create xgraph voltage_plot
Notes: The create routine is used to create new elements in the
GENESIS element tree. It generates an element of type
"element-type" and places it in the element tree with the
assigned name.
The additional options which can be specified for the create
routine depend on the element-type being created. For
example, elements which represent graphical widgets contain
data fields for screen information such as the position and
dimensions of the graphical object. This information may
also be specified as an option in the creation of an element.
create compartment soma[0]
create compartment soma[1]
create compartment soma[10]
create compartment soma -autoindex
In the example above, he name field of each element will be
"soma" but the index fields will have values 0-2 and 10.
The "-autoindex" option in the last statement creates the
element with index 2. Note that soma and soma[0] are
equivalent i.e. the absence of an index implies an index of
0 (the default). Also note that the index is an arbitrary
value and does not need to follow any order.
See also:
listobjects ,
showobject ,
le
Routine Name: createmap
Description: Copies an element multiple times to form a two-dimensional
array.
Usage: createmap source dest Nx Ny -delta dx dy -origin x y -object
source path to the element that will be copied
dest pathname of the parent of the array of copies
Nx,Ny number of elements in the x and y dimensions
of resulting array
dx,dy distance between adjacent elements in the
array in x and y dimensions, in world or
actual coordinates (default: 1,1)
x,y position of first element of array (i.e.,
corner of array, in world coordinates
(default: 0,0)
-object indicates that the source is the name of
an object, rather than the path to an element
Example: createmap /prototypes/cell /map 10 10
createmap mycell /network 3 5 -delta 0.1 0.2 -object
[from /usr/genesis/Scripts/orient_tut/retina.g:]
genesis > createmap /library/rec /retina/recplane \
{REC_NX} {REC_NY} \
-delta {REC_SEPX} {REC_SEPY} \
-origin {-REC_NX * REC_SEPX / 2} {-REC_NY * REC_SEPY / 2}
genesis > le /retina/recplane
rec[0-99]/
Notes: The createmap routine creates a two-dimensional array of the
specified source element by making copies of the source
element and assigning the copies x,y coordinates within the
specified bounds. The resulting array is placed under the
specified destination path. As with the copy command, the
entire tree of child elements and messages is copied along
with the source element. When the "-object" option is
used, the source is the name of a GENESIS object, instead of
the path to an element tree. This is most useful when a
prototype cell is created as an extended object composed from
a combination of basic objects with added fields and default
values.
The resulting array coordinates can be used by routines such
as planarconnect, planarweight, and planardelay to assign
connections, synaptic weights and propagation delays for
simulation-oriented elements. The coordinates can also be
used to display the cells in a draw widget.
See also:
copy ,
planarconnect ,
planarweight ,
planardelay ,
Extended
Routine Name: debug
Description: Sets (or displays) the debug level used by some routines.
Usage: debug [level]
level integer indicating debug level to use:
0 = disable debug (nothing printed)
1 = intermediate debug
2 = intermediate debug
3 = full Debug (print everything)
Example: genesis > debug
debug level 0
genesis > debug 2
debug level 2
Notes: Sets the debug level used by some routines to report status
information. Increasing the level typically increases the
amount of information produced. If no argument is given the
current debug level is displayed.
See also:
silent
Routine Name: delete
Description: Deletes an element and all of its children.
Usage: delete element
Example: delete /neuron
Notes: The delete routine is used to delete elements from the GENESIS
element hierarchy. Deleting an element which has children
attached to it will also delete all of the child elements.
In the course of deleting the object, the delete routine also
issues the DELETE action for the object before it is
eliminated.
When deleting interpol_structs that share tables between them
(e.g. tabchannel, tab2Dchannel, or tabcurrent), or the cells
or compartments containing them, you must call TABDELETE
first, in order to deallocate the memory for the tables.
Finally, you have to give the "reclaim" command for the memory
to actually be freed. Note that the tables are shared among
all copies of the interpol_struct that are created by copy or
readcell from a prototype. Therefore, you shouldn't call
TABDELETE unless you plan to delete all copies of the
interpol_struct.
See also:
create ,
reclaim
Routine Name: deleteaction
Description: Deletes an action from an element added by a previous
addaction command
Usage: deleteaction element action-name
element element to delete the action from
action-name name of the action to delete
Notes: An object's built in actions are permanent and may
not be deleted using deleteaction.
See also:
addaction , listactions,
Extended
Routine Name: deleteall
Description: Deletes all existing elements. [not recommended]
Usage: deleteall -force
-f flag to force deletions
Example: genesis > deleteall
*** WARNING ***
This function removes all elements from the simulation.
If you really want to do this use 'deleteall -force'.
usage: deleteall -force
genesis > deleteall -f
Simulator cleaned out.
Notes: If no flags are specified, deleteall displays a warning
message.
The deleteall routine can be used to return the simulator to
a startup state by deleting all existing elements, including
elements which may be provided by default at startup. If
this is done, running the simulation scripts again could
produce different results.
If you really need to delete all the elements in your GENESIS
session, you might as well quit exit from GENESIS completely
and start again -- deleteall just deletes all the elements
and might not reset other parameters to appropriate values.
In general, you should not use the deleteall routine.
See also:
delete
Routine Name: deleteclass
Description: Delete a class tag from an element which was previously
added using addclass.
Usage: deleteclass element class-name
element element from which to delete the class
class-name name of the class to delete
Notes: Deleteclass will not delete classes defined for the
built in objects.
See also:
addclass , listclasses,
Extended
Routine Name: deletefield
Description: Deletes an extended field which has been added to an element.
Usage: deletefield [element] field-name
Example: genesis > addfield /soma area
OK
genesis > deletefield /soma area
OK
genesis > deletefield /soma inject
deletefield: Cannot delete permanent field 'inject' on element '/soma'
Notes: Only added extended field may be deleted with deletefield.
See also:
addfield
Routine Name: deleteforwmsg
Description: Deletes a forwarded message previously forwarded using
addforwmsg.
Usage: deleteforwmsg source-element message-number destination-element
source-element element from which the message was
forwarded
msg-number number (index) of message in message list
(messages are numbered from 0 up)
destination-element
element to which the message was forwarded
Notes: The destination element must accept messages of the same
name and with the same number of data slots as the message
being forwarded.
See also:
addforwmsg ,
showmsg ,
Extended
Routine Name: deletemsg
Description: Deletes a message link between two elements.
Usage: deletemsg element msg-number -incoming -outgoing
-find srcelem type
element element receiving or sending the message
msg-number index of message in element message list
(index can be obtained with 'showmsg'
routine, or, in a script, with 'getmsg' used
with the -find option)
srcelem element sending the message
type message type (PLOT, AXIAL, VOLTAGE, etc.)
-incoming message to be deleted is incoming
-outgoing message to be deleted is outgoing
-find delete the first message (lowest index)
matching the srcelem and type
Example: deletemsg /cell/soma 2 -incoming
deletemsg /data/voltage -in 0 -find /cell/soma PLOT
Notes: The deletemsg routine is used to remove messages added using
the addmsg routine. Deleting earlier messages will change
the message numbers of the remaining messages. If
msg-number is not known for the desired message, it may be
found by using getmsg with the -find option.
When the -find option of deletemsg is used, the msg-number
argument is required, but ignored, and the message must be
an incoming one. (The -incoming and -outcoming options are
ignored, if specified.)
See also:
addmsg ,
showmsg ,
getmsg
Routine Name: deletemsgdef
Description: Deletes a message definition previously added to an element
using addmsgdef.
Usage: deletemsgdef element msg-name
element element from which to remove the message
definition
msg-name name of the message type to delete
Notes: Deletemsgdef will not delete permanent message definitions
defined by the built in objects.
See also:
addmsgdef ,
showobject ,
Extended
Routine Name: deletetasks
Description: Removes all simulation events from the simulation schedule.
Usage: deletetasks
Example: deletetasks
Notes: deletetasks removes from the simulation schedule table any
functions currently scheduled for execution during simulation.
This allows you to construct a new schedule using a sequence
of addtask calls.
See also:
Schedules ,
addtask ,
resched ,
showsched
Routine Name: disable
Description: Disables an element and its children from participating in a
simulation.
Usage: disable element
Example: disable /prototypes/mitral_cell
Notes: The specified elements are still accessible to basic
operations such as setfield and showfield, but they will not
participate in the simulation or be updated during the run of
the simulation (i.e., when you use the step routine).
You should run reset or resched after you disable an element
to be sure that the simulation properly takes into account the
disabling of the element. (The resched command may be used to
recompute the simulation schedule in order to remove the
disabled element without resetting the simulation. It is not
a good idea to call resched frequently, especially for large
simulations, as it does quite a bit of work.)
The disable command cannot be used with script_out elements.
If you need to disable a script_out element, it will be best
to use a more versatile extended object, instead. (See
Extended.txt.)
See also:
enable ,
step ,
reset
Routine Name: echo
Description: Prints out its arguments to the console.
Usage: echo [arguments] [-nonewline] [-format format-string]
arguments strings, or expressions enclosed in braces
-nonewline do not include carriage return at end of line
format-string a string of the form "%[flag][width]s", where
"width" is the minimum number of characters
to be output. If the output width is less
than this, it is padded with blanks. "flag"
is as in C; "0" means pad with zeroes, "-"
means left justify. (to construct mixed
formats, use multiple echo commands with
-nonewline to place them on a single line)
Example:
genesis > int five = 5
genesis > echo five
five
genesis > echo { five }
5
genesis > echo "Give me" -n; echo space! -f %20s
Give me space!
Notes: The echo routine is used to print output to the command
interpreter window. If echo is followed by a string (or a
quoted string) that string will be printed. If echo is
followed by a string enclosed in curly brackets, then the
value assigned the variable named by the string will be
printed.
Routine Name: egg
Description: Generates coordinates for points on the surface of an ovoid.
Usage: egg filename x y z d -normal
filename name for file into which to put generated
coordinates
x, y, z dimensions of the egg
d approximate distance between points
-normal "normal"; if selected, generates an
additional set of 3 coordinates per line,
to define the normal to the surface. This
format is used by the cellsheet routine.
Example: egg eggpoints 400e-6 400e-6 400e-6 100e-6 -normal
Notes: Generates coordinates for points on the surface of an ovoid,
(an egg) and puts them into a file, with an option for
generating the normals at each point. This is useful for
generating layers of cells on an ovoid. It tries to get
fairly even spacing. The coordinates are dumped into the
file specified by filename with one set of coordinates per
line.
See also:
plane ,
cellsheet
Routine Name: el
Description: Returns list of elements matching wildcard specification.
Usage: list-of-elements = el path [-listname listname]
list-of-elements returned as a text
path path specification, which may include
wildcards such as [] or # (note,
however, that operating-system style
use of * is not supported)
Example: genesis > echo {el /#}
/proto /output /net
genesis > echo {el /net/neuron[]}
/net/neuron /net/neuron[1] /net/neuron[2] /net/neuron[3]
genesis > str name
genesis > foreach name ({el /# })
? echo {name}
? end
/proto
/output
/net
Notes: In GENESIS 1, this was EL or element_list. getelementlist
is an alias for el in GENESIS 2.
The listname argument tells it to look for the field
<listname> on the element in <path> and treat that
as an element list.
Routine Name: enable
Description: Enables previously disabled elements to participate in a
simulation.
Usage: enable element
Example: enable /neuron
Notes: The enable routine is used to enable an element which has been
disabled using the disable routine.
You should run reset or resched after you enable a previously
disabled element to be sure that the simulation state properly
takes into account the newly enabled element.
See also:
disable ,
step ,
reset
Routine name: enddump
Description: Cleans up at the end of a dumpfile. Normally
generated by default in a dumpfile. Doesn't do much of
anything outside a dumpfile.
Usage: enddump
Example: Here is a little dumpfile using initdump that recreates a
simple 2-compartment model, and ignores the orphan element
/x/y/z.
============================================================
//genesis
initdump -version 3 -ignoreorphans 1
simobjdump neutral
simobjdump compartment activation Vm previous_state \
Im Em Rm Cm Ra inject dia len initVm
simundump neutral /x/y/z 0
simundump neutral /a 0
simundump compartment /a/compt 0 0 0.6632976405 0.6632942696 \
-0.3333315551 0 1 1 1 1 0 0 0
simundump neutral /b 0
simundump compartment /b/compt 0 0 0.3299660931 0.3299627243 \
0.3333349228 0 1 1 1 0 0 0 0
addmsg /b/compt /a/compt RAXIAL Ra Vm
addmsg /a/compt /b/compt AXIAL Vm
enddump
// End of dump
============================================================
Notes:
See also:
initdump ,
simdump ,
simobjdump ,
simundump
Routine Name: eof
Description: Tests whether at end of currently opened file.
Usage: eof-flag = {eof filename}
eof-flag returned as 1 if at end of file;
returned as 0 if not at end of file
filename name of open file to test
Example:
str line
openfile TestFile r
line = {readfile TestFile -linemode}
while (!{eof TestFile})
// process line from the file
echo {line}
line = {readfile TestFile -linemode}
end
Notes: The file must be currently open.
See also:
openfile ,
listfiles ,
readfile
Routine Name: exists
Description: Tests for existence of specified element or field.
Usage: exists-flag = {exists element [field]}
exists-flag returned as 1 if element (or element field)
exists; returned as 0 otherwise
element name or full pathname of element to test
field element field to test existence of
(does not check whether field is nonempty)
Example: if ({exists /cell/dendrite})
delete /cell/dendrite
end
genesis > create compartment soma
genesis > echo {exists soma}
1
genesis > echo {exists bogus}
0
genesis > echo {exists soma len}
1
genesis > echo {exists soma bogusfield}
0
Notes:
Routine Name: exit Description: Exits from GENESIS, terminating any simulation in progress. Usage: exit Notes: You can also use "quit", which is identical to "exit".
Routine Name: exp
Description: Returns "e" raised to specified power.
Usage: number = {exp power}
Example: genesis > echo { exp 1 }
2.718281746
Notes:
See also:
log ,
pow
Routine Name: file2tab
Description: Utility function for loading a file into an interpol struct
of an element
Usage: file2tab filename element table -table2 table -table3 table
-xy xdivs -skiplines number -calc_mode mode -autofill table
Arguments: filename: name of ascii file to load into table. Entries
must be separated by spaces, tabs or line breaks.
Line breaks in input file are ignored. In other
words, any number of numeric entries per line are
allowed, and all are used.
element: path of element containing the table
table: name of interpol_struct within the element.
Options: -table2 table
This option allows one to specify an additional table to load
the file into. Entries are loaded alternately into the first
table and table2. Note that table2 must be on the same
element as table. If there are an odd number of entries in
the file, the last one is not used.
-table3 table
This allows a third table. This option is similar to table2.
-xy xdivs
Uses xy mode for the table entries. Assumes that the points
are stored in the file as x,y pairs. Uses the xdivs argument
to set the table size, then figures out xmin, xmax
and sets the table limits and dx accordingly. Uses dx
between all points and fills up table using linear
interpolation if the x,y pairs in the file are not evenly
spaced. Assumes x is monotonically increasing, behavior
in other situations is undefined.
-skiplines number
Skips "number" lines at the start of the file. Useful
for reading in 'xplot' files into a table, since these
files usually have headers.
-calc_mode mode
'mode' is an integer representing one of the legal
interpolation modes (0 = no interpolation, 1 = linear
interpolation, 2 = fixed, see interpol doc).
-autofill table
table is the name of an interpol_struct in which we wish
to place successive integers. Useful for displaying plots
from a single series of numbers in a file:
file2tab yvalue_file /form/graph/plot ypts -autofill xpts
will load the numbers in yvalue_file into ypts, and put
successive integers into xpts.
Example: This simple example illustrates loading an xplot file into
a table using different options to file2tab. In the first
case we end up with the x and y values alternating. In
the second case we end up with the y values only. In the
third case we use the xy mode to load the values into a linear
table while preserving the x information.
Datafile name is xplot.data:
/newplot
/plotname "testplot"
0 5
4 10
8 5
10 10
script file:
//genesis
create table /tab1
file2tab xplot.data /tab1 table -skiplines 2
create table /tab2
file2tab xplot.data /tab2 table -table2 table -skiplines 2
create table /tab3
file2tab xplot.data /tab3 table -skiplines 2 -xy 50
showfield /tab1 *
showfield /tab2 *
showfield /tab3 *
-----------------------------------------------------------------------------
Notes: The control fields of the interpol are set as follows:
xdivs: for 1 table: (num_entries -1)
for 2 tables: (int)(num_entries / 2 -1)
for 3 tables: (int)(num_entries / 3 -1)
xmin : 0
xmax : 1
calc_mode: defaults to 0 (lin-interp), but may be set on the
command line.
See also:
tab2file , interpol_struct documentation
(
Tables ),
table
Routine Name: fileconnect
Description: Establishes synaptic connections and weights between groups
of elements based on a file of weights. The routine
sets up the connections by adding SPIKE messages between the
source and destination objects and then assigning a weight.
Usage: fileconnect source_elements destination_elements \
filename -wtscale w
source_elements A wildcarded list of elements which are the
sources of the SPIKE messages. These must be of
class "spiking" and are usually spikegen or
randomspike objects.
destination_elements A wildcarded list of elements which are
the destinations of the SPIKE messages. These must
be synchans or objects derived from synchan.
filename The name of an ascii file with weights
(as floats) separated by whitespace. Separation
can include spaces, line breaks etc.
The file is expected to have weights for all possible
connections, i.e., :
src_nelements * dest_nelements
entries.
The order of entries is source-first. For
example, if the source_elements list has 9 entries
and the dest_elements list has 16, then the
first 9 entries will specify weights from each of
the sources to the first destination. The next 9
entries will be to the second destination, and so on.
Weights less than or equal to zero will not
form connections at all.
Negative weights are often used to indicate
inhibitory input, so the command provides a way
around that: use a negative wtscale argument.
If a file has +ve as well as -ve weights,
it would be read twice: first with the paths of
excitatory receptor channels and a +ve wtscale,
then with the paths of the inhibitory ones and a
-ve wtscale.
-wtscale w -- This specifies a scale factor for all
weights. As noted above, it can be negative to
select for inhibitory (negative) weights.
Example:
int nx = 5
int ny = 5
int destx = 5
int desty = 5
include cellproto.g
createmap /proto/cell /lgn {nx} {ny}
createmap /proto/cell /v1 {destx} {desty}
fileconnect /lgn/##[TYPE=spikegen] /v1/cell[]/glu \
wts.file -wtscale 0.1
fileconnect /lgn/##[TYPE=spikegen] /v1/cell[]/GABA \
wts.file -wtscale -0.1
wts.file would have 5x5x5x5 entries. A centre-surround
pattern for the above example could start like this:
10 -1 0 0 0
-1 -1 0 0 0
0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
-1 10 -1 0 0
-1 -1 -1 0 0
0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
0 -1 10 -1 0
0 -1 -1 -1 0
0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
...
Notes: The routine is somewhat inefficient for large input and output
arrays with sparse connectivity, since it has to read
Nsrc x Ndest entries. This is offset by the fact that
the routine simultaneously creates synapses and sets
their weights, thereby eliminating a scan for setting
weights. The main use is for setting up large
networks based on weight files generated by other
programs.
See also:
planarconnect ,
planarweight ,
planardelay ; chapter 18 of the Book of GENESIS has a
lengthy discussion on these and related commands. A detailed
example of the use of fileconnect is given in Scripts/examples/fileconnect.
Routine Name: findchar
Description: Returns location of specified character in a given string.
Usage: position = {findchar string char}
position returned as integer indicating position of
first occurrence of char in string (positions
start with 0); returns -1 if char not found in
string
string string to search
char single character to locate in string (any
extra characters in char are ignored)
Example: genesis > echo {findchar abcbx b}
1
genesis > echo {findchar "a bcbx" b}
2
genesis > echo {findchar abcbx bx}
1
genesis > echo {findchar abcbx q}
-1
Notes:
See also:
strcat ,
strcmp ,
strncmp ,
strlen ,
substring
Routine Name: findsolvefield
Description: Returns a string giving the array location of a particular
element field value in the hines solver. Used for
input/output of values when the original element has been
taken over by the hines solver and its fields may not be
updated.
Usage: findsolvefield hsolve element field
hsolve name of the hsolve element
element name of an element which was taken over by hsolve
field the field of the element whiich is to be accessed
Example: // statements to create the hsolve element "/cell"
...
setfield /cell chanmode 4
call /cell SETUP
...
create disk_out /output
addmsg /cell /output OUTPUT \
{findsolvefield /cell /cell/soma/Na Gk}
...
reset
or:
genesis > echo {findsolvefield /cell /cell/soma/Na Gk}
givals[108]
genesis > echo {getfield /cell {findsolvefield /cell /cell/soma/Na Gk}}
2.634178326e-10
Notes: When using chanmodes 2 through 5 with the hines solver
(hsolve), you can no longer assume that all the fields of the
elements that are taken over by hsolve will be updated. The
findsolvefield function is used to access the hsolve arrays
directly to output field values instead of having to use the
old disabled elements. This allows one to establish new
messages for the output of field values after setup of the
hsolve element. The example above shows how to output the Gk
field of the Na channel from the hsolve element /cell. Note
that the fields Gk, Ik, Ek, and Im are not available for
chanmodes 2 and 3, and require the use of findsolvefield
in chanmodes 4 and 5.
See also:
hsolve
Routine Name: floatformat
Description: Sets format for display of variables of type float.
Usage: floatformat format-string
format-string "%[flag][width].[precision][type]",
indicating format to use in displaying
float-type variables. (default: "%0.10g")
The flag, width, precsion and type are
defined as in C, but only f and g type
formats are allowed.
Example:
genesis > float x = 3.12345678
genesis > echo { x }
3.12345678
genesis > floatformat %0.5g
genesis > echo { x }
3.1235
genesis > floatformat %10.5g
genesis > echo { x }
3.1235
genesis > floatformat %10.5f
genesis > echo { x }
3.12346
genesis > float y = 1e-5
genesis > floatformat %0.10g
genesis > echo {y}
1e-05
genesis > floatformat %0.10f
genesis > echo {y}
0.0000100000
genesis > floatformat %+10.2f // show sign
genesis > echo {x}
+3.12
genesis > float pi = 3.14159265
genesis > floatformat %-10.2f //left justify with width 10
genesis > echo {x} {pi}
3.12 3.14
genesis > floatformat %010.2f // "0" flag pads with zeroes
genesis > echo {x} {pi}
0000003.12 0000003.14
Notes: As in C, the width is the minimum number of characters to be
output. If the output width is less than this, it is padded
with blanks, unless the "0" flag is used. For type f, the
precision is the number of digits after the decimal point;
for type g, it is the maximum number of significant digits.
Routine Name: flushfile
Description: The contents of a file opened with ``openfile <filename> w''
and written with ``writefile <filename>'' are flushed from
the buffer onto disk. The file remains open for further
writefile operations.
Usage: flushfile file-name
Example:
genesis > openfile test w
genesis > writefile test 1.0 2.0 3.0
genesis > more test
genesis >
genesis > flushfile test
genesis > more test
1.0 2.0 3.0
genesis > writefile test 4.0 5.0 6.0
genesis > more test
1.0 2.0 3.0
genesis > closefile test
genesis > more test
1.0 2.0 3.0
4.0 5.0 6.0
Notes: This command is useful when the contents of a file need to
be checked before a simulation has terminated. (Writefile
alone does not flush the buffer, and file contents are only
available after closefile has been issued).
See also:
openfile ,
writefile ,
closefile
Routine Name: gaussian
Description: Returns a random value from a Gaussian (Normal) distribution.
Usage: value = {gaussian mean standard-deviation}
Example: genesis > echo {gaussian 0 1 }
0.5069125295
genesis > echo {gaussian 0 100 }
-63.29789352
Notes:
See also:
randseed ,
rand
Routine Name: gen2spk
Description: This program takes ascii files generated by GENESIS
containing simulation times and membrane potentials
(normally of the soma) and extracts the spike times
relative to the onset of a current-clamp square-wave
pulse. The output will be a file which will have currents
and spike times listed in the file.
Usage: gen2spk datafile current-start current-duration \
total-duration -stepsize dt -maxaccuracy
Arguments: datafile: the ascii input file. The format of the input
file is as follows: The beginning of a trial is
indicated by the following two lines:
/newplot
/plotname 0.234
i.e. the plotname is the current value for that
trial (units are arbitrary but are usually in nA).
This format is taken from Matt Wilson's xplot
program, which is useful for displaying simulation
output. The subsequent lines consist of time/Vm pairs
as follows:
0 -0.0770584
0.0002 -0.077233
etc.
which can be generated automatically by the
asc_file object of GENESIS. Multiple trials can be
put in one file, as long as they're separated by the
/newplot, /plotname ... sequence described above.
current-start: the time in the trace where current
injection begins. Most simulations allow the cell to
reach equilibrium before injecting current (e.g. for
50-100 msec or more). All spike times will be relative
to the starting time of the current injection. Units
are in seconds (SI units).
current-duration: the duration of the current injection, in
seconds.
total-duration: the total duration of the entire trace,
including the time before and after the current
injection.
Options: -stepsize dt: the output time step i.e. the time between
samples in the output file. This is usually much
larger than the simulation time step. The default
value is 0.0001 (0.1 msec).
-maxaccuracy: the output spike times are printed with ten
digits of precision rather than 4 (the default).
Obviously this is only useful if your output step
size is small enough so that the accuracy will make
a difference (i.e. less than 0.0001).
Output: A file with the same name as the input file but with
.spk.sim added. The file format is:
CURR 0.1
SPK 0.0010
SPK 0.0123
--------------------
CURR 0.2
SPK 0.0004
SPK 0.0054
SPK 0.0080
...
etc. CURR means the current value and is equal to the
value in the /plotname line in the input file. Each spike
gets a SPK line; the value to the right of the SPK is the
time in seconds when the spike occurred, relative to the
start of the current injection. Different currents are
separated by a line of dashes.
Algorithm: See the comments in the file src/param/gen2spk.c.
Notes: This routine is used mainly for generating data for the
spkcmp function for current injection simulations.
However, it is not limited to this use and will extract
spikes from any membrane potential waveform.
The /newplot and /plotname lines must be written out
explicitly to disk using writefile. Make sure they are
flushed to disk before starting the simulation so that they
don't appear in the middle of what asc_file writes. See
the parameter search demos for examples of this.
Some weird waveforms may defeat the spike-identifying
algorithm. Very small (low amplitude) spikes are a good
example of this. Be careful when using this routine in
cases like this, and check the outputs with a visual
display of the membrane potential waveform.
Example: genesis> gen2spk "Vmfile" 0.2 1.0 1.5
In this case, the current comes on at 0.2 seconds, lasts
for 1.0 seconds (i.e. until the simulation time is 1.2
seconds) and the whole trace is 1.5 seconds long.
See also: Parameter Search (
Param ),
spkcmp ,
shapematch
Routine Name: genesis
Description: Starts up the GENESIS program. (operating system command)
Usage: genesis [-usage][-nosimrc][-altsimrc filename][-notty][-nosig]
[-execdir dirname][-nice nice-level][-nox]
[-defaultcolor][-batch][script arg1 ...]
-usage print the usage message, listing options.
-nosimrc ignore the .simrc file
-altsimrc use 'filename' instead of the .simrc file
-notty do not accept terminal input
-execdir change to 'dirname' after starting genesis
-nice give genesis 'nice-level' priority
-nox start GENESIS without initializing XODUS
-defaultcolor use the display's default colormap
-batch run genesis in the background
script name of a GENESIS script to run
Example: % genesis -altsimrc ~/.backup_simrc
Starting Genesis
==========================================================================
G E N E S I S
Release Version: 2.0
Copyright 1988 - 1995, California Institute of Technology
Some components are copyright by the originating institution and are used
with the permission of the authors.
==========================================================================
Executable: /usr/genesis/genesis
----------------------- Starting XODUS 2.0 -----------------------
Startup script: ~/.backup_simrc
SIMPATH=. /usr/home/jouser/mystartup
SIMNOTES=/usr/home/jouser/.notes
GENESIS_HELP=/usr/genesis/Doc
genesis #0 >
Notes: When starting, GENESIS looks for an initialization file, .simrc,
first in the current working directory, and then in your home
directory. After installing genesis, this file is created in the
GENESIS installation directory. After making any appropriate edits,
you should copy it to your home directory and insure that the
genesis executable is in your path.
A new GENESIS command line option -defaultcolor will cause GENESIS
to use the display's default colormap, even if the default visual is
readonly. The net result is that colorscale colors will be shared
among multiple GENESIS processes, but GENESIS will fail to allocate
a colorscale if the default colortable is full. This option may be
used to avoid X protocol errors on some SGI systems where the X11
server defaults to a TrueColor (24 bit) visual.
To perform a GENESIS simulation in the background (for example if you
want to login from home over a modem, start a simulation, and logout
while the simulation continues to run), your simulation script should
use no graphics, and write all output to files.
Besides specifying the -nox option when starting genesis to avoid
starting XODUS, you also need to use the -notty and -batch options.
GENESIS will attempt to read from stdin after the .simrc and command
line script are completed. The -batch option causes genesis to exit
rather than try to read stdin. -notty will avoid doing any terminal
setup and cleanup procedures which can also cause this type of
behaviour. You must specify both on the command line (i.e. neither
option implies the other). In addition, you need to redirect output
(both stdout and stderr) to a file. For example, to run a script
``batchtest.g'' and direct startup messages and any error messages to
a log file (using the C shell) you would use:
genesis -nox -batch -notty batchtest >& batch.log &
With the Bourne shell (or bash) it would be:
genesis -nox -batch -notty batchtest > batch.log 2>&1 &
See also: src/README,
Simulations
Routine Name: getarg
Description: Returns specified item from an argument list.
Usage: getarg [arguments] -count -arg #
One of -count or -arg must be given
Example: genesis > echo {getarg 11 22 33 44 55 -arg 3}
33
genesis > echo {getarg 11 22 33 44 55 -count}
5
Notes:
See also:
argc ,
argv ,
arglist ,
printargs
Routine Name: getclock
Description: Returns value of the time interval for the specified clock.
Usage: clock-value = {getclock clock-number}
Example: genesis > echo { getclock 0 }
5.000000e-05
Notes: The getclock routine returns the current value of the step
size for the specified clock (as a floating point number).
See also:
showclocks ,
useclock ,
setclock
Routine Name: getdate
Description: Returns operating system date-time.
Usage: str-value = getdate
Example: genesis > echo { getdate }
Thu Jun 22 22:11:13 1995
Notes: This is a GENESIS implementation of the operating system
date command, to have the value returned by the routine rather
than displayed directly to the user. This allows the current
date to be used as a data value within GENESIS.
See also:
sh
Routine Name: getdefault
Description: Returns the default value of an object field.
Usage: getdefault object-name field-name
Example: genesis > echo {getdefault compartment Rm}
1
Notes:
See also:
setdefault
Routine Name: getelementlist Description: Returns list of elements matching wildcard specification. Usage: getelementlist path -listname listname Notes: This is an alias for el.
See also: el
Routine Name: getenv
Description: Returns value of operating-system environmental variable.
Usage: str-value = {getenv environment-variable}
Example: genesis > echo { getenv DISPLAY }
babel.bbb.edu:0
Notes: This is a GENESIS implementation of the operating system
printenv command, to have the value returned by the routine
rather than displayed directly to the user. (GENESIS also
includes a version of printenv to have the value displayed
directly to the user.) The getenv routine allows the value of
the particular operating system environmental variables to be
used as a data value within GENESIS.
See also:
setenv ,
printenv
Routine Name: getfield
Description: Returns value of field in data structure of specified element.
Usage: getfield [pathname] field
field-value = {getfield pathname field}
pathname path specification
defaults to current working element
field name of field in element data structure
Example: echo {getfield /cell/soma Vm}
setfield /cell/soma Rm {getfield /form/Rm_dialog value}
Notes: The getfield routine returns the value of fields in the
specified path.
See also:
setfield ,
showfield ,
getfieldnames
Routine Name: getfieldnames
Description: Returns names of all existing fields in specified element.
Usage: element-fields = {getfieldnames Element}
element-fields returned as a single line (i.e., a
string without carriage returns)
listing fields of specified element
Example: echo { getfieldnames /output }
str name
foreach name ( {getfieldnames soma })
echo {name}
end
Notes:
See also:
getfield ,
showfield ,
setfield
Routine Name: getglobal
Description: Returns the value of a global variable, allowing the name of
the global variable to be held in a string variable.
Usage: getglobal name
Example:
genesis > str variable = "EREST"
genesis > addglobal float {variable}
genesis > setglobal {variable} -0.07
genesis > echo {variable} = {getglobal {variable}}
EREST = -0.070000
Notes:
Often it is useful to use a string variable name to hold the name of a
global variable. For example, one may want to pass the name of a global
variable to a function that declares a global variable, or that sets or
returns its value. However, normal GENESIS syntax for declarations and
assignments does not permit a variable name to be specified by a string
variable. The routines addglobal, getglobal, and setglobal are designed
to overcome this limitation.
See also:
Variables ,
addglobal ,
setglobal ,
listglobals
Routine Name: getmsg
Description: Returns information about a message into or out of element.
Usage: getmsg element -incoming -outgoing -slot msg-number slot-number
-count -type msg-number -destination msg-number
-source msg-number -find srcelem type
[One of -slot, -count, -type, -destination, -source or -find
must be given]
element element for which to determine information
msg-number number (index) of message in message list
(messages are numbered from 0 up)
srcelem element sending the message
type message type (PLOT, AXIAL, VOLTAGE, etc.)
-incoming look for an incoming message
-outgoing look for an outgoing message
-slot return the slot value for the given message
and slot numbers
-count return the number of messages in or out
of this element
-type return the message type for the message
having the index msg-number
-destination return the destination element for the
message having the index msg-number
-source return the source element for the
message having the index msg-number
-find return the index (msg-number) of the first
message matching the srcelem and type
Example:
genesis > echo { getmsg /cell/dend1 -out -destination 0}
/cell/soma
genesis > echo { getmsg /cell/dend1 -out -source 0}
/cell/dend1
genesis > echo { getmsg /cell/dend1 -out -count }
5
genesis > echo { getmsg /cell/dend1 -in -destination 1 }
/cell/dend1
genesis > echo {getmsg /cell/soma -in -find /cell/dend1 RAXIAL}
2
genesis > echo {getmsg /cell/soma -in -type 2}
RAXIAL
genesis > echo {getmsg /cell/soma -in -slot 2 0}
-0.07
Notes: The -find option may only be used to find the index of
an incoming message. It returns -1 if there is no message
from the specified source element and message type.
The -count option may be useful if you want to loop over the
index in order to find multiple messages which meet some
specification.
See also:
addmsg ,
deletemsg ,
showmsg
Routine Name: getparamGA
Description: gets the value of a parameter in a paramtableGA object as a
floating-point number.
Usage: getparamGA path table param
path: The location of the paramtableGA object in the
element hierarchy.
table: The parameter table to be accessed.
param: The location of the desired parameter in the
table.
Return value: a float, representing the parameter value desired.
Example: float val
val = {getparamGA /GA 10 1}
This returns the second parameter (zero-indexed) from
the tenth parameter table in the paramtableGA object
called /GA. The value is stored in the
variable val.
Notes: The reason for having this routine and setparamGA is that
the parameter table array in paramtableGA objects is in an
object-specific binary form (optimized for the genetic
algorithm method) and thus can't be viewed or set directly
using the showfield, getfield or setfield commands (at
least not meaningfully).
This routine and setparamGA are hacks; ultimately they should
be made obsolete by overloading the SET and SHOW actions of
the paramtableGA object.
See also: Parameter Search (
Param ),
paramtableGA ,
setparamGA
Routine Name: getpath
Description: Returns subpart of full element pathname.
Usage: head-string = {getpath name -head}
tail-string = {getpath name -tail}
head-string full path leading to element, without actual
element name
tail-string only actual element name, without full path
name an element pathname
Example: genesis > echo {getpath /cell/soma/Na_channel -head}
/cell/soma/
genesis > echo {getpath /cell/soma/Na_channel -tail}
Na_channel
Notes: You use getpath to extract the parent or head of a path.
See also:
el ,
pwe ,
stack
Routine Name: getsolvechildname
Description: Returns the name of the child stored at the index value
inside the hines solver.
Usage: getsolvechildname hsolve_element index
Example:
genesis > showfield /cell/solve nchildren
[ /cell/solve ]
nchildren = 2
genesis > echo {getsolvechildname /cell/solve 1}
/cell/soma/K_mit_tchan
genesis > echo {getsolvechildname /cell/solve 2}
/cell/soma/Na_mit_tchan
Notes: Mainly used for debugging.
See also:
hsolve ,
getsolvecompname ,
findsolvefield
Routine Name: getsolvecompname
Description: Returns the name of the compartment stored at the index value
inside the hines solver.
Usage: getsolvecompname hsolve_element index
Example:
genesis > showfield /cell/solve ncompts
[ /cell/solve ]
ncompts = 1
genesis > echo {getsolvecompname /cell/solve 0}
soma[0]
Notes: Mainly used for debugging.
See also:
hsolve ,
getsolvechildname ,
findsolvefield
Routine Name: getstat
Description: Returns current simulation time, step number, or memory used
Usage: getstat -time -step -memory
Example:
genesis > echo {getstat -time}
0.1000500023
genesis > echo {getstat -step}
2001
genesis > {getstat -memory}
3704068
Notes:
See also:
showstat
Routine Name: getsyncount
Description: This function is used to count SPIKE messages coming from a
particular presynaptic element and/or synapses on a
particular postsynaptic element. If both the presynaptic
and postsynaptic elements are specified this function
returns the number of connections between the two i.e. the
number of SPIKE messages from the presynaptic element which
are sent to the given postsynaptic element. This function
is often used inside a loop to set fields in synapses
between specific elements to particular values.
Usage: getsyncount [presynaptic-element] [postsynaptic-element]
presynaptic-element The element sending SPIKE messages to
postsynaptic targets.
postsynaptic-element The synchan or derived element which
receives SPIKE messages.
Example: // Set the weights of all synapses that receive SPIKE messages
// from a given source to 10.0
int i
str dest
int nsyn = {getsyncount /input[0]/spike}
for (i = 0; i = {nsyn}; i = i + 1)
dest = {getsyndest /input[0]/spike {i}}
index = {getsyndest /input[0]/spike {i} -index}
setfield {dest} synapse[{index}].weight 10.0
end
Notes: Synchans have an "nsynapses" field which holds a count of the
number of synapses on a given element; this can be used instead
of getsyncount when getting synapse counts for postsynaptic
elements.
See also:
getsynindex ,
getsynsrc ,
getsyndest , BoG chapter 18
Routine Name: getsyndest
Description: Returns a string which is the path of the postsynaptic
element which receives the nth SPIKE message sent by the
given presynaptic element. Can also return the index of
the synapse on this element.
Usage: getsyndest presynaptic-element spikemsg-number -index
presynaptic-element The element sending SPIKE messages to
postsynaptic targets.
spikemsg-number The number of the SPIKE message whose
destination we want. This can be obtained by getmsg
or showmsg.
-index This option returns the index of the synapse which
receives the SPIKE message on the destination
element.
Example: str dest = {getsyndest input[0]/spike 0}
int index = {getsyndest input[0]/spike 0 -index}
setfield {dest} synapse[{index}].weight 10.0
Notes: getsynindex can also be used to get the index of a synapse
if you know the names of the pre- and postsynaptic elements.
See also:
getsyncount ,
getsynindex ,
getsynsrc , BoG chapter 18
Routine Name: getsynindex
Description: getsynindex is used to find the index of synapses between
particular presynaptic and postsynaptic elements.
Usage: getsynindex presynaptic-element postsynaptic-element
[-number n]
presynaptic-element The element sending SPIKE messages to
postsynaptic targets.
postsynaptic-element The synchan or derived element
receiving the SPIKE message from the presynaptic
element.
-number n If there is more than one synapse between the
given pre- and postsynaptic elements, this option
will return the index of the nth such synapse.
This option will rarely be necessary, since
usually there is at most one synapse between a
given presynaptic and postsynaptic element.
Example: int index = {getsynindex /input[0]/spike /cell/soma/Ex_channel}
if (index >= 0)
setfield /cell/soma/Ex_channel synapse[{index}].weight 10.0
end
Notes: If the desired synapse does not exist a value of -1 is
returned.
See also:
getsyncount ,
getsynsrc ,
getsyndest , BoG chapter 18
Routine Name: getsynsrc
Description: Returns a string which is the path of the presynaptic
element sending the SPIKE message to the synapse of the
postsynaptic element with the given index.
Usage: getsynsrc postsynaptic-element index
postsynaptic-element The synchan or derived element
receiving the SPIKE message from the source element.
index The index of the synapse on a synchan or derived element
whose source you want.
Example: str src = {getsynsrc /cell/soma/Ex_chan 0}
if (src == "input[0]/spike")
setfield /cell/soma/Ex_chan synapse[0].weight 10.0
else
setfield /cell/soma/Ex_chan synapse[0].weight 0.0
end
Notes:
See also:
getsyncount ,
getsynindex ,
getsyndest , BoG chapter 18
Routine Name: h
Description: Displays the contents of the command-history buffer.
Usage: h
h [start [end] ]
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