Object Type: Ca_concen
Description: Single pool model for Ca concentration.
Author: M. Wilson, Caltech (2/89)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: Ca_concen_type [in src/segment/seg_struct.h]
Size: 112 bytes
Fields: tau time constant of decay
Ca_base resting (base level) concentration
B equals 1/(ion_charge * Faraday * volume)
Ca Resulting concentraton of Ca++ ions
C Intermediate result, Ca - Ca_base
thick Holds thickness of shell (used by readcell)
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: CaConcen [in src/segment/Ca_concen.c]
Classes: concentration segment
Actions: INIT
PROCESS
RESET
CHECK
SAVE2
RESTORE2
Messages: I_Ca Ik Receives ionic current Ik from a channel
BASE Ca_base Sets Ca_base with a message
fI_Ca Ik fraction Receives fractional current Ik*fraction
INCREASE delta_Ik Add delta_Ik to incoming current
DECREASE delta_Ik Subtract delta_Ik from incoming current
------------------------------------------------------------------------------
Notes: Single shell model for Ca concentration.
Solves dC/dt = B*Ik - C/tau.
Ca = Ca_base + C.
In SI units, where concentration is moles/m^3
(milli-moles/liter) and current is in amperes, theory gives B
= 5.2e-6/(shell volume). In practice, B is a parameter to be
fitted or estimated from experiment, as buffering, non-uniform
distribution of Ca, etc., will modify this value. If thick =
0, the readcell routine calculates B by dividing the "density"
parameter in the cell parameter file by the volume of the
compartment. Otherwise, it scales as a true shell, with the
volume of a shell having thickness thick. A negative value of
the "density" parameter may be used to indicate that it should
be taken as an absolute value of B, without scaling.
Example: see Scripts/burster
See also:
readcell
OBJECT KPORES 3/14/92 (AS)
DESCRIPTION:
Simulates a population of potassium ion channel proteins (pores)
embedded in a patch of membrane over an isopotential region. Each
individual pore undergoes standard Markov kinetics through a five state
scheme:
4an-> 3an-> 2an-> an->
[n0]---------[n1]---------[n2]---------[n3]---------[n4]
<-bn <-2bn <-3bn <-4bn
where [n4] = Open State and an and bn have voltage dependencies
given by:
an = (alpha_A + alpha_B*Vk)/(alpha_C + exp((alpha_D+Vk)/alpha_F))
bn = (beta_A + beta_B*Vk)/(beta_C + exp((beta_D+Vk)/beta_F))
The total population of pores is given by Nt.
The total number of pores within each of the five stable states
at any given iteration is given by n0, n1, n2, n3, n4, respectively.
The total number of pores in the open stable state is given
by No = n4.
The open state conductance of a pore is given by Gmax.
The effective conductance for the population of pores at any
given iteration is then Gk = Gmax*No.
SPECIFICATIONS:
FUNCTION KPorePop()
DATA STRUCTURE K_pore_type
CLASS segment membrane
SIZE ?? bytes
AUTHOR A. Strassberg Caltech 3/92
ACTIONS:
CHECK null
RESET sets initial distribution of pores into the various stable
states based upon the equilibrium solutions to the Markov
matrix for given Vk.
PROCESS updates the distribution of the stable states of the
population based upon the rate constants an and bn, derived
from the current transmembrane voltage Vk.
INIT null
MESSAGES:
VOLTAGE sends transmembrane voltage Vk to the population of pores.
This Vk is used to update the state distribution after each
iteration.
FIELDS:
See DESCRIPTION
RELATED COMMANDS/TOPICS:
Napores
ERROR MESSAGES:
BUGS:
NOTES:
See Strassberg and DeFelice, 1993, Neural Computation 5:6
and the demonstration scripts in Scripts/examples/pore
Object Type: Mg_block
Description: Implementation of voltage- and [Mg]-dependent
blocking of a channel.
Author: E. De Schutter, Caltech (11/90)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: Mg_block_type [in src/segment/seg_struct.h]
Size: 120 bytes
Fields: Ik blocked value of current
Gk blocked value of current
Ek blocked value of current k
Zk charge; may also be used as
{charge / relative fraction of I},
e.g. 2/(Ica/Itot) -> msg to difpool
KMg_A A-factor K(v) in eq'n for Mg block reaction
KMg_B B-factor K(v) in eq'n for Mg block reaction
CMg [Mg] in mM
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: MgBlock [in src/segment/Mg_block.c]
Classes: segment channel
Actions: INIT [INIT does nothing]
PROCESS
RESET
CHECK
Messages: VOLTAGE Vm voltage from the compartment
CHANNEL Gk Ek unblocked Gk and Ek from compartment
CHANNEL1 Gk
CHANNEL2 Gk Ek
CHARGE Zk
------------------------------------------------------------------------------
Notes: An Mg_block element may be interposed between a synaptically
activated channel (a synchan or hebsynchan) and a compartment.
This calculates a blocked value of Gk that is reduced from
the incoming Gk by a factor of A/(A + [Mg]*exp(-Vm/B)).
The example below puts this in the form of the Zador, Koch,
and Brown equation [Proc. Natl. Acad. Sci. USA 10:6718-6722
(1990)], with A = 1/eta and B = 1/gamma.
Example:
float CMg = 2 // [Mg] in mM
float eta = 0.33 // per mM
float gamma = 60 // per Volt
create synchan {compartment}/{channel}
setfield ^ \
Ek {Ek} \
tau1 {tau1} \
tau2 {tau2} \
gmax {gmax}
create Mg_block {compartment}/{channel}/block
setfield ^ \
CMg {CMg} \
KMg_A {1.0/eta} \
KMg_B {1.0/gamma}
addmsg {compartment}/{channel} {compartment}/{channel}/block \
CHANNEL Gk Ek
addmsg {compartment}/{channel}/block {compartment} CHANNEL Gk Ek
addmsg {compartment} {compartment}/{channel}/block VOLTAGE Vm
// Even though the channel current isn't used, CHECK expects this message
addmsg {compartment} {compartment}/{channel} VOLTAGE Vm
See also:
synchan
OBJECT NAPORES 3/14/92 (AS)
DESCRIPTION:
Simulates a population of sodium ion channels proteins (pores) embedded
in a patch of membrane over an isopotential region. Each individual pore
undergoes standard Markov kinetics through an eight state scheme:
3am-> 2am-> am->
[m0h1]---------------[m1h1]---------------[m2h1]---------------[m3h1]
| <-bm | <-2bm | <-3bm |
| | | |
/\ | /\ | /\ | /\ |
ah | bh ah | bh ah | bh ah | bh
| \/ | \/ | \/ | \/
| | | |
| 3am-> | 2am-> | am-> |
[m0h0]---------------[m1h0]---------------[m2h0]---------------[m3h0]
<-bm <-2bm <-3bm
where [m3h1] = Open State and am, bm, ah and bh have voltage
dependencies given by:
am = (malpha_A + malpha_B*Vk)/(malpha_C + exp((malpha_D+Vk)/malpha_F))
bm = (mbeta_A + mbeta_B*Vk)/(mbeta_C + exp((mbeta_D+Vk)/mbeta_F))
ah = (halpha_A + halpha_B*Vk)/(halpha_C + exp((halpha_D+Vk)/halpha_F))
bh = (hbeta_A + hbeta_B*Vk)/(hbeta_C + exp((hbeta_D+Vk)/hbeta_F))
The total population of pores is given by Nt. The total number of pores
within each of the eight stable states at any given iteration is given by
m0h0, m1h0, m2h0, m3h0, m0h1, m1h1, m2h1, and m3h1, respectively. The
total number of pores in the open stable state is given by No = m3h1.
The open state conductance of a pore is given by Gmax. The effective
conductance for the population of pores at any given iteration is then
Gk = Gmax*No.
SPECIFICATIONS:
FUNCTION NaPorePop()
DATA STRUCTURE Na_pore_type
CLASS segment membrane
SIZE ?? bytes
AUTHOR A. Strassberg Caltech 3/92
ACTIONS:
CHECK null
RESET sets initial distribution of pores into the various stable
states based upon the equilibrium solutions to the Markov
matrix for given Vk.
PROCESS updates the distribution of the stable states of the
population based upon the rate constants an and bn, derived
from the current transmembrane voltage Vk.
INIT null
MESSAGES:
VOLTAGE sends transmembrane voltage Vk to the population of pores.
This Vk is used to update the state distribution after each
iteration.
FIELDS:
See DESCRIPTION
RELATED COMMANDS/TOPICS:
Kpores
ERROR MESSAGES:
BUGS:
NOTES:
See Strassberg and DeFelice, 1993, Neural Computation 5:6
and the demonstration scripts in Scripts/examples/pore
Object Type: PID
Description: PID (proportional, integral, derivative) feedback controller
Author: M. Nelson, Caltech (4/89)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: PID_type [in src/user/user_struct.h]
Size: 144 bytes
Fields: cmd inputs the command (desired) value of sns
sns inputs the sensed (measured) value
output = gain*(e + tau_d*de/dt + 1/tau_i * e_integral)
gain determines the sensitivity of the controller
tau_i integration time constant, typically = dt
tau_d derivative time constant, typically = dt/4
saturation sets permissible range of output
e internal variable (error = cmd-sns)
e_integral internal variable (integral of e dt)
e_deriv internal variable
e_previous internal variable
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: PIDcontroller [in src/user/PID.c]
Classes: device
Actions: INIT
PROCESS
RESET
Messages: CMD command
SNS sense
GAIN gain
------------------------------------------------------------------------------
Notes:
The PID is used for feedback control of dynamical systems. For example, in
a voltage clamp circuit it is used with a pulsegen, RC, and diffamp device
to provide the required injection current to maintain the membrane voltage
at the desired level. The RC-filtered command voltage is scaled by the
diffamp and then presented to the PID with a CMD message. The output is
sent to a compartment with an INJECT message, and the resulting Vm in the
compartment is fed back to the PID with a SNS message. A higher gain gives
a better clamp, but requires a smaller integration time step to avoid
numerical instability.
For more information on PID controllers see: Franklin, Powel, Emami-Naeini
(1986) "Feedback Control of Dynamic Systems", Addison-Wesley, pp. 99-106.
Example: Scripts/squid/squid_electronics.g
See also:
Object Type: RC
Description: A series resistance R, shunted by a capacitance C.
Author: M. Wilson, Caltech (6/88)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: RCunit_type [in /usr/genesis/src/segment/seg_struct.h]
Size: 96 bytes
Fields: V0 initial value of "state" (set on RESET)
R series resistance
C shunting capacitance
state output value
inject input value
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: RC_Unit [in src/segment/rcunit.c]
Classes: segment
Actions: CHECK PROCESS RESET
Messages: INJECT inject (input-value)
------------------------------------------------------------------------------
Notes:
An RC element is often used as a low-pass filter, as with a voltage clamp
circuit, in order to prevent a step change in the command voltage from
causing numerical instabilities.
Example: Scripts/squid/squid_electronics.g
See also:
Object Type: asc_file
Description:
The asc_file object is used to write data to a file in ASCII format. A new
line is written at every time step of the clock which is assigned. Unless
the notime flag is set, the first item on each line is the simulation time.
Each SAVE message which is received adds another item to the line.
Author: M. Wilson, Caltech (4/89)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: ascfile_type [in src/out/out_struct.h]
Size: 88 bytes
Fields:
filename data file name to be written
fp data file pointer
is_open flag: is file currently open?
initialize flag: has file been initialized?
leave_open flag: leave file open? 1 leaves the file open
all the time so you can write on it whenever
you want (a good idea if the file is used
frequently, but there is a limit to number of
files that can be left open at any time);
0 closes the file after every write to it
(only useful if you have more than 30 files;
this is slow)
append flag: append data after resetting?
flush flag: flush data to disk at each interval?
1 forces program to send data to the disk at
once and not store it in a buffer (slow but
secure); 0 (default) writes data in a buffer
(fast)
notime flag: if non-zero, don't output the time
float_format format specifier for output (default is %g)
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: AscFileOutput [in src/out/out_ascfile.c]
Classes: output
Actions: RESET PROCESS DELETE SAVE FLUSH OUT_OPEN OUT_WRITE
Messages: SAVE data
------------------------------------------------------------------------------
Notes:
If the filename field is not set, the output file will be given the same
name as the element which is created from the asc_file object.
When the append flag is zero, a reset will close and reopen the file,
setting the file pointer at the begining, effectively creating a new file
if the simulation is stepped again. When the append flag is set to a
non-zero value, additional steps after a reset will be appended to the
file. The OUT_WRITE action may be called to write any string to the file.
The OUT_OPEN command is used to manually initialize the file for writing,
and must be called before calling OUT_WRITE. In append mode, it must be
called after changing the filename to a new output file name, or renaming
an existing one.
The float_format field specifies the format of the data written to the
file, using the notation of the floatformat command, similar to that
used in C. The default is "%g". By setting this to a string with
a different value, for example "%0.12g", the data and the simulation time
that are written to the file can be given to to a higher precision.
There are two variations of asc_file that are not documented elsewhere:
res_asc_file has two additional fields, time_res and value_res, with
default values of 0. The data is output at intervals that are separated
by at least time_res (X-axis) OR value_res (Y-axis). With the default
values, this means that the interval will be determined by the simulation
clock that is used. To increase the interval, both time_res and value_res
should be set to appropriate larger values.
par_asc_file is a modified version of asc_file to be used with parallel
GENESIS (PGENESIS), in order to guarantee that SAVE messages coming from
various nodes provide outputs in a fixed order. For more information on
the use of par_asc_file, see the section on Parallel I/O Issues in the
PGENESIS hypertext documentation.
For binary data, use disk_out.
Example:
create asc_file /out
setfield /out flush 1 leave_open 1 append 1 float_format %0.9g
setclock 1 0.0005
useclock /out 1
// Assume the existence of /cell/soma to provide output
addmsg /cell/soma /out SAVE Vm
setfield /cell/soma inject 0
step 0.1 -t
// append the results of a new run with different injection
setfield /cell/soma inject 0.1e-9
reset
step 0.1 -t
// now do yet another injection with output to a different file
setfield /out filename out2
call /out OUT_OPEN
call /out OUT_WRITE "Run #2" // Write a header
setfield /cell/soma inject 0.2e-9
reset
step 0.1 -t
See also:
disk_out ,
disk_in ,
floatformat
Object Type: autocorr
Description: Computes the auto-correlation of a spike train
A histogram containing the count of
events for each bin is constructed.
Author: D. Jaeger, Caltech (9/92)
revised for Genesis v2.2 11/99
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: doac_type [in genesis/src/device/spike_struct.h]
Size: 100 bytes
Fields: num_bins (int) number of bins in histogram
binwidth (float) binwidth in sec
reset_mode (int) 0 or 1
threshold (float) input amplitude triggering spike event
*acarray (int) histogram array containing data
nospks (int) number of spikes from source
*sptimes (float) array of spike times from source
curridx (int) internal indexing
calcidx (int) internal indexing
maxspikes (int) internal boundary condition
wintime (float) internal boundary condition
dont (int) internal condition
allocated (int) internal condition
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Doac [in genesis/src/device/acxc.c]
Classes: datanal
Actions: PROCESS update *sptimes, *acarray, nospks
RESET if reset_mode = 0, empties *sptimes but not
*acarray
if reset_mode = 1, empties *sptimes and
recreates *acarray
Messages: SPIKE : signal amplitude from source
------------------------------------------------------------------------------
Notes:
User must setfield num_bins and binwidth (in sec) so
that a data array is created on RESET. The input is assumed to
cross the amplitude given in the threshold field only for one
timestep to generate a spike. Vm is not to be used as an input field.
Valid inputs may be derived from random, neutral or spike objects.
An internal spike time buffer is set up for a maximal
spike rate of 1000 events / second. A greater density of spikes
will lead missed events in the histogram.
The auto-corrlation histogram is updated with each timestep.
However, the first results will only be available after the
simulation time has reached the value of num_bins * binwidth.
This is due to the fact that any spike needs to be correlated
with other spikes across a time window of this duration.
The data are stored in *acarray and can be accessed with
a getfield command (see example).
Example:
create autocorr /ac
setfield ^ binwidth 0.002 num_bins 200 threshold 0.5
/* this example uses random object for input */
create random /input
setfield ^ min_amp 1 max_amp 1 rate {in1_rate} reset 1 reset_value 0
addmsg /input1 /ac SPIKE state
/* To display data on a graph, use this function after creating the graph */
function plotac(source, dest, pname, color)
str source,dest,color
int maxbin
int i,barval
maxbin = {getfield {source}, num_bins}
setfield {dest} xmax {maxbin}
call {dest} RESET
for(i=0; i < maxbin; i = i + 1)
barval = {getfield {source}, acarray[{i}]}
addpts {dest} -plotname {pname} -color {color} {i} 0
addpts {dest} -plotname {pname} -color {color} {i} {barval}
addpts {dest} -plotname {pname} -color {color} {{i}+1} 0
end
end
See also:
crosscorr ,
interspike ,
peristim ,
Scripts/examples/spike/spikes.g
Object Type: calculator
Description: Adds, subtracts, multiplies, and divides using messages.
Author: Erik De Schutter, BBF-UIA 6/98
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: calc_type [in src/device/dev_struct.h]
Size: 100 bytes
Fields: output computed value
resetclock clock # used to reset output value (default 0)
output_init value of output after reset (default 0)
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: CalculatorFunc [in src/device/calculator.c]
Classes: device
Actions: RESET PROCESS DELETE CREATE
Messages: SUM number
SUBTRACT number
MULTIPLY number
DIVIDE number
------------------------------------------------------------------------------
Notes:
The calculator is often used to sum multiple inputs. For example, the
total channel current in a cell could be calculated with:
foreach s ({el /cell/##[CLASS=channel]})
addmsg {s} /calculator_element SUM Ik
end
With the resetclock default of clock 0, the calculator is reinitialized to
output_init (default 0) at every time step, so that it may calculate a new
value of the sum from incoming messages at each time step. If resetclock is
set to a clock with a longer time step, then operations are performed on
the previous output, until it is time to reset the output to output_init.
The example below uses a resetclock with a longer time step in order to
generate a periodic ramp output.
Example:
create xform /data
create xgraph /data/calculator
create xbutton /data/RESET -script reset
create xbutton /data/RUN -script "step 100"
create xbutton /data/QUIT -script quit
xshow /data
// Create a ramp generator by summing a constant input
// The length of the ramp is given by the resetclock
setclock 0 1.0
setclock 1 25.0
create neutral /source
setfield /source x 4
create calculator /source/ramp
setfield /source/ramp resetclock 1
addmsg /source /source/ramp SUM x
addmsg /source/ramp /data/calculator PLOT output *output *red
addmsg /source /data/calculator PLOT x *input *blue
reset
See also:
Object Type: compartment
Description: Axially asymmetric compartment. Ra is located on
one side of the compartment. This is slightly more
computationally efficient than the symmetric counterpart.
Author: M. Wilson, Caltech (6/88)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: compartment_type [in src/segment/seg_struct.h]
Size: 124 bytes
Fields: Rm total membrane resistance
Cm total membrane capacitance
Em membrane resting potential
Ra axial resistance
inject injected current in membrane
dia compartment diameter
len compartment length
Vm voltage across the membrane
previous_state Vm at previous time step
Im approximation to the total membrane current
initVm initial value to set Vm on reset
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Compartment [in src/segment/compartment.c]
Classes: segment
membrane
Actions: INIT assign previous_state = Vm
PROCESS update Vm, calculate Im
RESET assign Vm = Em
CHECK make sure Rm>0, Cm>0,
Ra'>0 (if RAXIAL message is present),
Ra>0 (if AXIAL message is present)
SAVE2
RESTORE2
Messages: CHANNEL Gk Ek delivers the conductance and equilibrium
potential of channel within the compartment
RAXIAL Ra Vm delivers the Ra and Vm of a compartment
AXIAL Vm delivers the Vm of a compartment
INJECT inject sets the inject field to the message value
EREST Em sets the Em field to the message value
------------------------------------------------------------------------------
Notes: Simulates a section of passive membrane or cable. The
potential across the membrane is given by Vm. There is a
leakage path for current through the resistance Rm. This
resistance is in series with a leakage battery Em. This
compartment can be coupled to other compartments with an axial
resistance Ra. The compartment is not symmetrical, with Ra
lumped to one side of the compartment. Any number of ionic
channels can be introduced into the membrane (Gk, Ek in the
circuit diagram). The membrane also allows current
injection.
The compartment Im is the sum of axial currents and injected
current only. The (transmembrane) channel currents or the
leakage current are not included. For a multicompartment
cell, under a quasistatic approximation (C*dV/dt is small), Im
is approximately equal to the sum of the channel and leakage
currents, due to charge conservation. This approximation is
used in the efield object (see efield.txt) to allow Im to be
used to calculate external field potentials. The exception to
this is when Im is calculated with hsolve in chanmode 4. In
that case, Im is directly calculated as the sum of the channel
currents and leakage current though Rm.
When a compartment performs its RESET action (usually
invoked by the reset command), Vm is set to the value of the
initVm field. Normally, initVm follows any changes to Em,
so Vm will be initialized to Em upon reset. If, as in the
Hodgkin-Huxley model, Em is a leakage potential that is
different from the rest potential, initVm may be set to the
rest potential. It will then no longer follow Em, and Vm
will be set to the rest potential upon reset.
Calculates Vm using:
dVm/dt = {(Em - Vm)/Rm + SUM[(Ek - Vm)*Gk] +
(Vm' - Vm)/Ra' + (Vm'' - Vm)/Ra + inject}/Cm
In the diagram, the compartment shown in the middle
receives the Vm' and Ra' of the upper compartment with
an RAXIAL message, and the Vm'' of the lower compartment
with an AXIAL message. Channels deliver their Gk and Ek
with a CHANNEL message.
Vm'
o_________________________________________________
| | | | |
\
/ Ra'
\
|
|
| Vm
o_________________________________________________
| | | | |
\ | | | |
/ Ra \ \ | |
\ --/--> / | ___|___
| Gk \ Rm \ / \ _______ Cm
| | | / A \ |
| | | \ | / |
| Ek --- Em --- \ / |
| ------- ------- | Iinject|
| | | | |
| |_____________|________|________|
|
| Vm''
o_________________________________________________
| | | | |
Example:
See also:
symcompartment
Object Type: concchan
Description: Concentration-driven membrane channel. Equivalent
to 1-D diffusion of molecules across a membrane. The
concchan, like the enzyme, is a property of a pool and so
each concchan should be attached to a pool which specifies
the number of concchans.
Author: U. S. Bhalla MSSM Aug/93
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: [in src/kinetics/kin_struct.h]
Size: 124 bytes
Fields:
A, B Internal state variables, used to
communicate with pools. A represents
increase in the pool n, B is the decrease.
perm Permeability
gmax conductance (not currently used)
n number of concchans
Vm potential across channel (not currently used)
use_nernst flag (not currently used)
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: [in src/kinetics/concchan.c]
Classes: segment
Actions: SET PROCESS RESET
Messages:
SUBSTRATE n vol Number of molecules in substrate pool
PRODUCT n vol Number of molecules in product pool
NUMCHAN n Number of concchans specified by pool
Vm Vm Sets the Vm field (not currently used)
------------------------------------------------------------------------------
Notes: The concchan allows the substrate and product pools to diffuse
back and forth. The state variables A and B are used in the
return messages to the substrates and products. (However the
roles of A and B are reversed for the product pools).
If there are both substrate and product pools (as evidenced by
having both a SUBSTRATE and a PRODUCT message to the
concchan), the SUBSTRATE message calculates conc1 = n/vol, and
PRODUCT calculates conc2 = n/vol. Here, n/vol represents the
density of molecules in the pool, not the density of conchans.
Then A and B are set to
A = conc2 * perm * n
B = conc1 * perm * n
where n is the number of concchans.
Example: // numerically attach the chan to the pool
addmsg {pool} {chan} NUMCHAN n
// Attaches the pool to the chan as a substrate
addmsg {chan} {pool} REAC A B
addmsg {pool} {chan} SUBSTRATE n vol
// Attaches the pool to the chan as a product
addmsg {chan} {pool} REAC B A
addmsg {pool} {chan} PRODUCT n vol
See also:
pool
Object Type: concpool
Description: A "well-mixed" concentration pool without diffusion that can
have miscellaneous in/out flows (when coupled to other
objects). It has better controls over size/volume than
Ca_concen and does not include its own equilibration
mechanisms.
Author: E. De Schutter BBF-UIA 4/94 - 3/99
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: concpool_type [in src/concen/conc_struct.h]
Size: 132 bytes
Fields: C concentration (calculated by concpool) in mM
prev_C concentration at previous time step
Ceq equilibrium concentration in mM
val ionic valence
leak constant in/outflow in mM/sec
shape_mode Set to one of the predefined global variables
SHELL=0, SLICE=SLAB=1, TUBE=2, USERDEF=3.
SHELL: onion shell. Set len for cylindrical shell (zero
length for spherical shell), dia (outer diameter of shell)
and thick (thickness of shell); vol, is computed on RESET.
SLICE (or SLAB): salami slices of cylinder. Set dia
(diameter of cylinder) and thick (thickness of slab), len
is not used; vol is computed on RESET.
TUBE: a cylinder with diameter dia and length len. For
concpools inside a difshell: make dia negative in the
prototype; readcell will scale len so as to obtain an
appropriate change in vol relative to the difshell.
USERDEF: len, dia, thick are not used. Set vol field
to desired pool volume.
len shell length
dia shell diameter
thick shell thickness
vol shell volume
-----------------------------------------------------------------------
SIMULATION PARAMETERS
Function: ConcPool [in src/concen/concpool.c]
Classes: concentration segment
Actions: RESTORE2 SAVE2 CHECK RECALC RESET PROCESS INIT
Messages: CONCEN C (sets C with a message)
STOREINFLUX flux (flux into store in moles/sec;
increases C)
STOREOUTFLUX flux (flux out of store in moles/sec;
decreases C)
BUFFER kBf kBb Bfree Bbound (fields sent from a buffer,
e.g. a fixbuffer)
HILLPUMP vmax Kd Hill (sent from a hillpump; setting
Hill=1 is equivalent to an
MMMPUMP message from an mmpump)
------------------------------------------------------------------------------
Notes:
Unlike the difshell, the concpool provides a single shell model of a
"well-mixed" concentration pool without diffusion between shells. As it can
also couple to buffers and pumps, it provides for multiple mechanisms for
calcium removal and has better controls over size/volume than the Ca_concen.
The buffers (e.g, fixbuffer) interact with a difshell or concpool to model the
binding of calcium to buffer molecules and to calculate the concentrations of
free and bound ions using a kinetic scheme with forward and backward rate
constants for the binding and release of calcium. The BUFFER message from a
buffer passes on the rate constants and the calculated free and bound
concentrations so that the concpool may calculate the resulting ion
concentration C. Details of the fields that are passed to the concpool with
messages from buffers and the hillpump are provided in the documentation for
these objects.
For a general description of buffered calcium diffusion see: De Schutter E.,
and Smolen P., "Calcium dynamics in large neuronal models", in Methods in
neuronal modeling: From ions to networks (2nd edition), C. Koch and I. Segev
editors, pp. 211-250 (1998).
Example:
See also:
difshell ,
fixbuffer ,
hillpump
Object Type: crosscorr
Description: Computes the cross-correlation between two trains of
spike events. A histogram containing the count of
events for each bin is constructed.
Author: D. Jaeger, Caltech (9/92)
revised for Genesis v2.2 11/99
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: doxc_type [in genesis/src/device/spike_struct.h]
Size: 116 bytes
Fields: num_bins (int) number of bins in histogram
binwidth (float) binwidth in sec
reset_mode (int) 0 or 1
threshold (float) input amplitude triggering spike event
*xcarray (int) histogram array containing data
no1spks (int) number of spikes from source 1
no2spks (int) number of spikes from source 2
*sp1times (float) array of spike times from source 1
*sp2times (float) array of spike times from source 2
curr1idx (int) internal indexing
curr2idx (int) internal indexing
calc1idx (int) internal indexing
calc2idx (int) internal indexing
maxspikes (int) internal boundary condition
wintime (float) internal boundary condition
dontnow (int) internal condition
allocated (int) internal condition
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Doxc [in genesis/src/device/acxc.c]
Classes: device
Actions: PROCESS update *spktimes, *xcarray, nospks
RESET if reset_mode = 0, empties *spktimes but not
*xcarray
if reset_mode = 1, empties *spktimes and
recreates *xcarray
Messages: XSPIKE : signal amplitude from source 1
YSPIKE : signal amplitdue from source 2
------------------------------------------------------------------------------
Notes:
User must setfield num_bins (only even number of bins
are allowed) and binwidth (in sec) so that a data array
is created on RESET. The input is assumed to cross the amplitude
given in the threshold field only for one timestep to generate
a spike. Vm is not to be used as an input field. Valid inputs
may be derived from random, neutral or spike objects.
An internal spike time buffer is set up for a maximal
spike rate of 1000 events / second. A greater density of spikes
will lead to missing events in the histogram.
The cross-corrlation table is updated with each timestep.
However, the first results will only be available after the
simulation time has reached the value of num_bins * binwidth.
The data are stored in *xcarray and can be accessed with
a getfield command (see example). The 0 delay time bin is stored in
the center of the histogram, i.e. for num_bins = 100, xcarray[49]
contains the 0 delay time bin.
Example:
create autocorr /xc12
setfield ^ binwidth 0.002 num_bins 200 threshold 0.5
/* this example uses random object for input */
create random /input1
setfield ^ min_amp 1 max_amp 1 rate {in1_rate} reset 1 reset_value 0
create random /input2
setfield ^ min_amp 1 max_amp 1 rate {in1_rate} reset 1 reset_value 0
addmsg /input1 /xc12 XSPIKE state
addmsg /input2 /xc12 YSPIKE state
/* To display data on a graph, use this function after creating the graph */
function plotxc(source, dest, color)
str source, dest, color
int bins, minbin, maxbin, barval
/* display *xcarray of doxc element {source} on graph {dest}
The display could be made nicer than this. */
bins = getfield {source}, num_bins
minbin = -({bins} / 2)
maxbin = {bins} / 2
setfield {dest} xmin {minbin} xmax {maxbin}
call {dest} RESET
for(i=minbin; i < maxbin; i = i + 1)
barval = {getfield {source}, xcarray[{{i}+{maxbin}}]}
addpts {dest} -plotname xcor -color {color} {i} 0
addpts {dest} -plotname xcor -color {color} {i} {barval}
addpts {dest} -plotname xcor -color {color} {i} 0
end
end
------------------------------------------------------------------------------
Notes:
User must setfield num_bins and binwidth (in sec) so
that a data array is created on RESET. The input is assumed to
cross the amplitude given in the threshold field only for one
timestep to generate a spike. Vm is not to be used as an input field.
Valid inputs may be derived from random, neutral or spike objects.
An internal spike time buffer is set up for a maximal
spike rate of 1000 events / second. A greater density of spikes
will lead missed events in the histogram.
The cross-corrlation histogram ought to be used with clock 0.
The first results will only be available after the
simulation time has reached the value of num_bins * binwidth.
This is due to the fact that any spike needs to be correlated
with other spikes across a time window of this duration.
The data are stored in *xcarray and can be accessed with
a getfield command (see example).
See also:
autocorr ,
interspike ,
peristim ,
Scripts/examples/spike/spikes.g
Object Type: ddsyn
Description: modified synchan with table front end to transform voltage
to activation, for dendro-dendritic synapses. Calculates
channel current therefore needs membrane state.
Author: U. S. Bhalla, Caltech (5/91)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: dd_syn_type [in src/olf/olf_struct.h]
Size: 164 bytes
Fields: Gk channel conductance
Ik channel current
Ek channel reversal potential
gmax maximum conductance
tau1 open time constant of channel activation
tau2 close time constant of channel activation
transf table for transform from Vm to activation;
usual interpolation element with the normal
set of fields; set up using TABCREATE, filled
by indexing as usual, and interpolated using
TABFILL
activation channel activation; set either by a table
lookup of the transform of the incoming
VOLTAGE message or by synaptic input
transf_alloced flag for allocation of transform
X state variable for time response
Y state variable for time response
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: DDSyn [in src/olf/dd_syn.c]
Classes: segment, channel
Actions: INIT
PROCESS
RESET
CHECK
SET
DUMP
SAVE2
RESTORE2
TABCREATE
TABFILL
Messages: VOLTAGE voltage [tells channel what membrane
potential is]
ACTIVATION activation [sends activation directly to
channel; sums linearly with
other ACTIVATION input and
transformed V_PRESYN input]
V_PRESYN presynaptic-voltage [sends presynaptic voltage to
transform table; sums linearly
at output of table, so
multiple V_PRESYN inputs are
first transformed, then their
activations are summed]
RAND_ACTIVATION [rather than sending direct
probability amplitude activation signal, specifies
probability (from 0 to 1) that
activation of size amplitude
will occur at synapse (useful
for sending random synaptic
input to synapse)]
------------------------------------------------------------------------------
Notes: Dendrodendritic synapse with tabulated transform
from presyn potential to postsyn activation.
The table for the transform is created using tabcreate
and is shared with all copies of the element
The ddsyn element is the equivalent of a synchan element
with a tabulated transform from input voltage to channel
activation. This serves as a way of representing
dendro-dendritic synapses. The usual fields and messages for
the synchan element remain available. The table entries are
filled in the usual ways from the script interface, and can be
shared between ddsyn elements.
Example: Here we create a ddsyn channel to act as the synaptic input
for granule cells in an olfactory bulb model.
// for dd, ax, and centrif inputs
create ddsyn glu_gran_usb
call glu_gran_usb TABCREATE 10 -0.070 0.05
setfield glu_gran_usb \
Ek {EGlu} \
tau1 4.0e-3 \ // sec
tau2 6.0e-3 \ // sec
gmax {GGlu} \ // Siemens
// Setting up the table for transforming
// from presyn Vm to activation
transf->table[0] 0 \
transf->table[1] 0.05 \
transf->table[2] 0.1 \
transf->table[3] 0.2 \
transf->table[4] 0.5 \
transf->table[5] 0.7 \
transf->table[6] 0.8 \
transf->table[7] 0.9 \
transf->table[8] 0.95 \
transf->table[9] 0.98 \
transf->table[10] 1
call glu_gran_usb TABFILL 1000 0
See also: Scripts/examples/ddsyn
Object Type: dif2buffer
Description: Implementation of a first-order diffusible (mobile) buffer
with variable total buffer concentration. Should be coupled
to a difshell, where the change in the concentration of the
buffered ion is computed.
Author: E. De Schutter BBF-UIA 8/94 - 4/96
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: dif2buffer_type [in src/concen/conc_struct.h]
Size: 172 bytes
Fields: activation ion concentration from incoming CONCEN message
Bfree free buffer concentration (calculated) in mM
Bbound bound buffer concentration (calculated) in mM
prev_free Bfree at previous time step
prev_bound Bbound at previous time step
Btot total buffer concentration in mM (used on reset)
kBf forward rate constant in 1/(mM*sec)
kBb backward rate constant in 1/sec
Dfree diffusion constant for Bfree in m^2/sec
Dbound diffusion constant for Bbound in m^2/sec
shape_mode Set to one of the predefined global
variables SHELL=0, SLICE=SLAB=1, USERDEF=3.
SHELL: onion shell, for radial diffusion. Set len for
cylindrical shell (zero length for spherical shell), dia
(outer diameter of shell) and thick (thickness of shell);
vol, surf_up, and surf_down are computed on RESET.
SLICE (or SLAB): salami slices of cylinder, for axial
diffusion. Set dia (diameter of cylinder) and thick
(thickness of slab), len is not used; vol, surf_up, and
surf_down are computed on RESET.
USERDEF: len, dia, thick are not used. Set vol, surf_up
and surf_down.
len shell length
dia shell diameter
thick shell thickness
vol shell volume
surf_up area of upper (outer) shell surface
surf_down area of lower (inner) shell surface
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Dif2Buffer [in src/concen/dif2buffer.c]
Classes: concbuffer segment
Actions: RESTORE2 SAVE2 CHECK RECALC RESET PROCESS INIT
Messages: CONCEN C (buffered ion concentration, sent
from a difshell or concpool)
BDIFF_DOWN prev_free prev_bound thick (diffusion to inner shell,
sent from an outer shell)
BDIFF_UP prev_free prev_bound thick (diffusion to outer shell,
sent from an inner shell)
------------------------------------------------------------------------------
Notes:
The buffers (e.g, fixbuffer) interact with a difshell to model the binding of
calcium to buffer molecules and to calculate the concentrations of free and
bound buffer molecules, using a kinetic scheme with forward and backward rate
constants for the binding and release of calcium. Intracellular buffers are
often mobile, and the diffusion of buffer molecules can carry calcium with
them. This can often make a significant contribution to the transport of
calcium, in addition to the diffusion of free Ca++ ions that is modeled by the
difshell object. These diffusible buffers can be modeled with the difbuffer
and dif2buffer objects, instead of using the non-mobile fixbuffer.
Like the fixbuffer, the dif2buffer interacts with a difshell to model the
binding of calcium to buffer molecules and to calculate the concentrations of
free and bound buffer molecules using a kinetic scheme with forward and
backward rate constants for the binding and release of calcium. The rate
constants kBf and kBb are set by the user, and the concentration C is sent
with a CONCEN message from the difshell. The BUFFER message to a difshell
from a buffer passes on the rate constants and the calculated free and bound
buffer concentrations.
In addition, the dif2buffer acts like a difshell, in the sense that it allows
diffusion between adjacent buffer shells. However, it is the free and bound
buffer molecules, rather than free ions that are diffusing. Adjacent buffer
shells are coupled by BDIFF_DOWN and BDIFF_UP messages that are analogous to
the DIFF_DOWN and DIFF_UP messages that link adjacent difshells. Note that a
dif2buffer should have the same dimensions and shape_mode as the difshell to
which it is coupled.
For the difbuffer, the assumption is made that the diffusion rate for bound
and free buffer molecules is the same (as they are much larger than the Ca
atoms), so there is a single diffusion constant D, and they diffuse together,
with dBbound/dt = -dBfree/dt. The dif2buffer does not make this assumption,
and treats the diffusion of free and bound molecules separately. Thus, there
are separate diffusion constants Dfree and Dbound, and the BDIFF_DOWN and
BDIFF_UP messages pass both the previous step Bfree and Bbound values along
with the buffer shell thickness.
NOTE: When using difshell, difbuffer, or dif2buffer elements without hsolve
(or in chanmodes 0 or 1), it will be necessary to issue two reset commands
after setting up the simulation.
For a general description of buffered calcium diffusion see:
De Schutter E., and Smolen P., "Calcium dynamics in large neuronal
models", in Methods in neuronal modeling: From ions to networks
(2nd edition), C. Koch and I. Segev editors, pp. 211-250 (1998).
Example:
See also:
difshell ,
difbuffer ,
fixbuffer
Object Type: difbuffer
Description: Implementation of a first-order diffusible (mobile) buffer
with constant total buffer concentration. Should be coupled
to a difshell, where the change in the concentration of the
buffered ion is computed.
Author: E. De Schutter BBF-UIA 8/94 - 6/96
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: difbuffer_type [in src/concen/conc_struct.h]
Size: 168 bytes
Fields: activation ion concentration from incoming CONCEN message
Bfree free buffer concentration (calculated) in mM
Bbound bound buffer concentration (calculated) in mM
prev_free Bfree at previous time step
prev_bound Bbound at previous time step
Btot total buffer concentration in mM (free + bound)
kBf forward rate constant in 1/(mM*sec)
kBb backward rate constant in 1/sec
D diffusion constant of buffer molecules, m^2/sec
shape_mode Set to one of the predefined global
variables SHELL=0, SLICE=SLAB=1, USERDEF=3.
SHELL: onion shell, for radial diffusion. Set len for
cylindrical shell (zero length for spherical shell), dia
(outer diameter of shell) and thick (thickness of shell);
vol, surf_up, and surf_down are computed on RESET.
SLICE (or SLAB): salami slices of cylinder, for axial
diffusion. Set dia (diameter of cylinder) and thick
(thickness of slab), len is not used; vol, surf_up, and
surf_down are computed on RESET.
USERDEF: len, dia, thick are not used. Set vol, surf_up
and surf_down.
len shell length
dia shell diameter
thick shell thickness
vol shell volume
surf_up area of upper (outer) shell surface
surf_down area of lower (inner) shell surface
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: DifBuffer [in src/concen/difbuffer.c]
Classes: concbuffer segment
Actions: RESTORE2 SAVE2 CHECK RECALC RESET PROCESS INIT
Messages: CONCEN C (buffered ion concentration, sent
from a difshell or concpool)
BDIFF_DOWN prev_free thick (diffusion to inner shell, sent from
an outer shell)
BDIFF_UP prev_free thick (diffusion to outer shell, sent from
an inner shell)
DIFF_DOWN prev_free thick (alias for BDIFF_DOWN)
DIFF_UP prev_free thick (alias for BDIFF_UP)
------------------------------------------------------------------------------
Notes:
The buffers (e.g, fixbuffer) interact with a difshell to model the binding of
calcium to buffer molecules and to calculate the concentrations of free and
bound buffer molecules, using a kinetic scheme with forward and backward rate
constants for the binding and release of calcium. Intracellular buffers are
often mobile, and the diffusion of buffer molecules can carry calcium with
them. This can often make a significant contribution to the transport of
calcium, in addition to the diffusion of free Ca++ ions that is modeled by the
difshell object. These diffusible buffers can be modeled with the difbuffer
and dif2buffer objects, instead of using the non-mobile fixbuffer.
Like the fixbuffer, the difbuffer interacts with a difshell to model the
binding of calcium to buffer molecules and to calculate the concentrations of
free and bound buffer molecules using a kinetic scheme with forward and
backward rate constants for the binding and release of calcium. The rate
constants kBf and kBb are set by the user, and the concentration C is sent
with a CONCEN message from the difshell. The BUFFER message to a difshell
from a buffer passes on the rate constants and the calculated free and bound
buffer concentrations.
In addition, the difbuffer acts like a difshell, in the sense that it allows
diffusion between adjacent buffer shells. However, it is the free and bound
buffer molecules, rather than free ions that are diffusing. Adjacent buffer
shells are coupled by BDIFF_DOWN and BDIFF_UP messages that are analogous to
the DIFF_DOWN and DIFF_UP messages that link adjacent difshells. Note that a
difbuffer should have the same dimensions and shape_mode as the difshell to
which it is coupled.
For the difbuffer, the assumption is made that the diffusion rate for bound
and free buffer molecules is the same (as they are much larger than the Ca
atoms), so there is a single diffusion constant D, and they diffuse together,
with dBbound/dt = -dBfree/dt. The dif2buffer does not make this assumption,
and treats the diffusion of free and bound molecules separately.
NOTE: When using difshell, difbuffer, or dif2buffer elements without hsolve
(or in chanmodes 0 or 1), it will be necessary to issue two reset commands
after setting up the simulation.
For a general description of buffered calcium diffusion see:
De Schutter E., and Smolen P., "Calcium dynamics in large neuronal
models", in Methods in neuronal modeling: From ions to networks
(2nd edition), C. Koch and I. Segev editors, pp. 211-250 (1998).
Example:
See also:
difshell ,
fixbuffer ,
dif2buffer
Object Type: diffamp
Description: Difference amplifier, takes two inputs and produces an
output proportional to their difference.
Author: M. Wilson, Caltech (2/89)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: diffamp_type [in src/device/dev_struct.h]
Size: 96 bytes
Fields: gain
saturation
plus
minus
output
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: DifferenceAmp [in src/device/diffamp.c]
Classes: device
Actions: RESET sets the output to zero
PROCESS calculates and sets the output from the inputs
Messages: PLUS +input
MINUS -input
GAIN gain
------------------------------------------------------------------------------
Notes:
Adds inputs from PLUS messages and subtracts those received with MINUS
messages. The output is this total, multiplied by gain, but limited to the
range -saturation to +saturatation. If there are no MINUS messages, the
minus input is taken as zero. Normally, the gain field is set using
"setfield", but it may also be varied with a GAIN message. This object also
provides a convenient way to sum or scale quantities which are to be plotted
by sending a PLOT message to an xgraph.
Example:
See also:
Object Type: difshell
Description: Implementation of a concentration shell that can have
miscellaneous in/out flows (when coupled to other objects),
and one-dimensional diffusion between other difshells.
Author: E. De Schutter BBF-UIA 4/94 - 3/99
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: difshell_type [in src/concen/conc_struct.h]
Size: 152 bytes
Fields: C concentration (calculated by difshell) in mM
prev_C concentration at previous time step
Ceq equilibrium concentration in mM
D diffusion constant in m^2/sec
val ionic valence
leak constant in/outflow in mM/sec
shape_mode Set to one of the predefined global
variables SHELL=0, SLICE=SLAB=1, USERDEF=3.
SHELL: onion shell, for radial diffusion. Set len for
cylindrical shell (zero length for spherical shell), dia
(outer diameter of shell) and thick (thickness of shell);
vol, surf_up, and surf_down are computed on RESET.
SLICE (or SLAB): salami slices of cylinder, for axial
diffusion. Set dia (diameter of cylinder) and thick
(thickness of slab), len is not used; vol, surf_up, and
surf_down are computed on RESET.
USERDEF: len, dia, thick are not used. Set vol, surf_up
and surf_down.
len shell length
dia shell diameter
thick shell thickness
vol shell volume
surf_up area of upper (outer) shell surface
surf_down area of lower (inner) shell surface
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: DifShell [in src/concen/difshell.c]
Classes: concentration segment
Actions: RESTORE2 SAVE2 CHECK RECALC RESET PROCESS INIT
Messages: INFLUX I_Ca (current flow in A; increases C)
OUTFLUX I_Ca (current flow in A; decreases C)
FINFLUX I_Ca fraction (current flow, scaled by fraction)
FOUTFLUX I_Ca fraction (current flow, scaled by fraction)
STOREINFLUX flux (flux into store in moles/sec;
increases C)
STOREOUTFLUX flux (flux out of store in moles/sec;
decreases C)
DIFF_DOWN prev_C thick (diffusion to inner shell, sent from
an outer shell)
DIFF_UP prev_C thick (diffusion to outer shell, sent from
an inner shell)
BUFFER kBf kBb Bfree Bbound (fields sent from a buffer,
e.g. a fixbuffer)
TAUPUMP kP Ceq (sent from a taupump)
EQTAUPUMP kP (sent from a taupump; uses Ceq from
the difshell)
MMPUMP vmax Km (sent from a mmpump)
HILLPUMP vmax Kd Hill (sent from a hillpump)
------------------------------------------------------------------------------
Notes:
The concentration of intracellular calcium close to the cell membrane surface
can have a significant influence on the conductance of calcium dependent
potassium channels and on mechanisms for synaptic plasticity. Unless the
neural compartment is very small and the calcium is "well-mixed", the calcium
concentration may vary considerably within the compartment. It may then be
necessary to model diffusion within the compartment by dividing it into a
number of shells. The difshell object is used for modeling these shells and
diffusion between them. It may also be used for modeling axial diffusion
between compartments. Just as the length of a neural compartment should be
chosen to give small differences in membrane potential between adjacent
compartments, the thickness of diffusion shells should be chosen to give small
differences in concentration between adjacent shells.
A difshell is typically coupled to buffers and/or pumps, in order to provide
for multiple mechanisms for calcium removal.
The buffers (e.g, fixbuffer) interact with a difshell or concpool to model the
binding of calcium to buffer molecules and to calculate the concentrations of
free and bound ions using a kinetic scheme with forward and backward rate
constants for the binding and release of calcium. The BUFFER message from a
buffer passes on the rate constants and the calculated free and bound
concentrations so that the difshell may calculate the resulting ion
concentration C in the shell.
The ionic pumps provide various mechanisms to remove ions from the shell.
Details of the fields that are passed to the difshell with messages from
the pumps are provided in the documentation for the various pump objects.
The various FLUX messages assume SI units for the Faraday constant, currents
and dimensions. If other units are used, scale the val parameter to account
for this.
NOTE: When using difshell, difbuffer, or dif2buffer elements without hsolve
(or in chanmodes 0 or 1), it will be necessary to issue two reset commands
after setting up the simulation.
For a general description of buffered calcium diffusion see:
De Schutter E., and Smolen P., "Calcium dynamics in large neuronal
models", in Methods in neuronal modeling: From ions to networks
(2nd edition), C. Koch and I. Segev editors, pp. 211-250 (1998). The
spinedemo simulation gives a detailed example of the use of the difshell,
taupump, and fixbuffer objects for modeling calcium diffusion in dendritic
spines.
Example:
/* based on spinedemo, for spine head initial shell (headshell0) */
create difshell headshell0
setfield headshell0 C 0.000020 Ceq 0.000020 D 6.0e-10 val 2.0 leak 0.0
setfield headshell0 shape_mode {SLAB} len 0.0 dia 0.5e-6 thick 0.1e-6
/* Ca fraction of NMDA current is influx into outer shell */
addmsg Mg_block headshell0 FINFLUX Ik 0.128
/* attach fast immobile buffer */ headbuf0
create fixbuffer headbuf0
setfield headbuf0 Btot 0.2 kBf 5.0e5 kBb 500 // mM, 1/(mM*sec), 1/sec
addmsg headbuf0 headshell0 BUFFER kBf kBb Bfree Bbound
addmsg headshell0 headbuf0 CONCEN C
/* attach the pump */
create taupump headpump0
setfield headpump0 Ceq 0.000020
/* The pump rate is proportional to the surface-to-volume ratio
spine head initial shell is end of cylinder, so stv=1/thick */
setfield headpump0 T_C {thick/Pump_kP} // pump rate Pump_kP = 1.4e-5
addmsg headpump0 headshell0 TAUPUMP kP Ceq
/* set up diffusion messages, assuming the existence of headshell1 */
addmsg headshell0 headshell1 DIFF_DOWN prev_C thick
addmsg headshell1 headshell0 DIFF_UP prev_C thick
// similar statements for the other shells ...
See also:
taupump ,
fixbuffer , Scripts/examples/spinedemo
Object Type: disk_in
Description: Reads in a 2-d array of data from an ascii or binary file.
Author: U. S. Bhalla, Caltech (1/90)
Coordinate read-in added by U. S. Bhalla, Mt. Sinai, 5/95.
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: disk_in_type [in src/olf/olf_struct.h]
Size: 148 bytes + allocation for arrays and interpols
Fields: filename name of data file
leave_open flag: leave file open between steps [cycles]
nx x dimension of input val array
ny y dimension of input val array
loop flag: return to start of file on EOF
val 2D array of input values
fp pointer to file
fileformat flag: 0 (default) for ASCII, 1 for FMT1
time_offset offset from sim time for FMT1 files
is_open internal flag : is file open yet?
allocated internal flag: Is array allocated yet?
tempdata data array used for FMT1 reading
start_time field used for FMT1 handling
dt field used for FMT1 handling
datatype field used for FMT1 handling
header_size field used for FMT1 handling
lastpos field used for FMT1 handling
xpts,ypts,zpts Interpols used for storing coordinate
information when FMT1 files are read.
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: DiskIn [in src/olf/disk_in.c]
Classes: segment
Actions:
RECALC CHECK SET RESET PROCESS INIT
Messages:
none
------------------------------------------------------------------------------
Notes:
The disk_in element reads in data from a file to the val
array in the element every clock tick. This is a 2-d array
with dimensions set by the nx and ny fields.
The source file can be either in ASCII or FMT1 formats. FMT1
is the GENESIS-specific format used by disk_out. Data in
FMT1 files is time-stamped, and accessed according to the
current simulation clock.
At RESET, disk_in automatically figures out if the file
is FMT1. If not it assumes it is ASCII. The fileformat
flag is set accordingly.
FMT1 files contain information on the number of data items,
and the 3-d coordinate information for each item. On RESET,
the 'val' array is automatically allocated for the data values.
nx is set to 1, and ny is set to the number of data items.
Also on RESET, the coordinate information is loaded into the
xpts,ypts,zpts interpol-structs, which are automatically
allocated as needed. These interpols can be accessed in
the usual ways. See the interpol documentation.
ASCII files do not have coordinate information. The nx and ny
fields must be set prior to reading in an ASCII file, so
that the disk_in can figure out how many data points to
read per time-step. Changing nx and ny causes
automatic reallocation of the 'val' array, with dire
results for any messages that had been linked to earlier
incarnations of the val array. In other words, never set
the nx or ny unless you are sure that no messages
are being sent from the input array. Typically one sets
nx and ny as soon as one creates the disk_in, and
later adds messages.
The leave_open flag should normally be set to 1 to avoid
closing and reopening the file every clock tick.
The time_offset field allows one to specify the difference
between the simulation time and the FMT1 internal time stamp.
The format of the ascii file is simply a sequence of numbers,
separated by spaces, tabs or newlines, with a maximum of 16
numbers per line. They are read in sequentially to fill the
val[x][y] array, the x index being incremented more rapidly .
Every time a new clock tick is read in, the reading starts
from a new line, discarding any unread data on the previous
line.
The format of the FMT1 file is highly condensed. See the
source (in src/out/out_view.c) and the documentation for
disk_out for more details. In general, it includes information
on the size of the file, the coordinates of all elements
whose values are stored, and the time-step at which successive
data values are stored.
Example:
create disk_in /in
// read a single line with 2 variables at each time step
// from the file Vm1 (in Scripts/MultiCell)
setfield /in nx 2 ny 1 filename Vm1 dt 1 leave_open 1
create xform /form
create xgraph /form/graph
setfield /form/graph xmax 500 ymin -100 ymax 50
// The Vm value is the second one on each line
addmsg /in /form/graph PLOT val[1][0] *Vm *red
xshow /form
reset
step 500
Alternatively, the message from the disk_in element could have been an INPUT
message to a spikegen element. The spikegen element could then send a SPIKE
message to a synchan element, as in Scripts/tutorials/tutorial4.g.
If we had 100 cells, each containing a spikegen element, with names
``cell[0]/spike'' through ``cell[99]/spike'' and a data file containing
multiple groups of 10 lines with 10 Vm values each, to represent 100
simultaneous inputs, we could use statements like this:
// send a message for each spike generator
for (i=0;i<=9; i = i + 1)
for (j=0;j<=9; j = j + 1)
addmsg /in /cell[{j + 10*i}]/spike INPUT val[{i}][{j}]
end
end
Normally, you will want to use a clock with a much larger step for reading
in the data than that used for the integration of the equations for
calculating membrane potentials, etc. Otherwise, the data file would have
to be very large. The example in Scripts/examples/XODUS/fileview also
illustrates the use of arrays and the binary format.
See also: asc_file , disk_out , floatformat,
Object Type: disk_out
Description:
The disk_out object is used to write data to a file in a special binary
format. This is done at every time step of the clock which is assigned.
These files are usually used with a disk_in object and the xview widget or
the xgraph widget to "replay" the results of a simulation. An external
program (or your own compiled GENESIS function) can write files in this
format in order to provide a convenient interface to the display
capabilities of XODUS.
Author: M. Wilson, Caltech (6/88)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: file_type [in src/out/out_struct.h]
Size: 88 bytes
Fields: filename data file name to be written
fp data file pointer
is_open flag: is file currently open?
initialize flag: has file been initialized?
leave_open flag: leave file open? 1 leaves the file open
all the time so you can write on it whenever
you want (a good idea if the file is used
frequently, but there is a limit to number of
files which can be left open any any time);
0 closes the file after every write to it
(only useful if you have more than 30 files;
this is slow)
append flag: append data after resetting?
flush flag: flush data to disk at each interval?
1 forces program to send data to the disk at
once and not store it in a buffer (slow but
secure); 0 (default) writes data in a buffer
(fast)
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: FileOutput [in src/out/out_file.c]
Classes: output
Actions:
SAVE DELETE PROCESS RESET
Messages: SAVE data
------------------------------------------------------------------------------
Notes:
If the filename field is not set, the output file will be given the same
name as the element which is created from the disk_out object. Use asc_file
for writing the data in ASCII format.
Example:
(from Scripts/orient_tut/V1_output.g)
function do_disk_out(diskpath,srcpath,field)
str name
create disk_out /output/{diskpath}
setfield /output/{diskpath} leave_open 1 flush 1
addmsg {srcpath} /output/{diskpath} SAVE {field}
end
do_disk_out vert_disk /lgn/vert/soma[] Vm
do_disk_out horiz_disk /lgn/horiz/soma[] Vm
Also see the example in Scripts/examples/XODUS/fileview/generate.g.
Normally, you need not be concerned with the format of the files produced
by a disk_out element. However, you may wish to write either a GENESIS
function or an external program which produces an output file which can
be displayed with an xview widget. The code which writes a disk_out
file can be found in /usr/genesis/src/out/out_file.c, and the code which
reads the data from the file can be found in /usr/genesis/src/out/out_view.c.
The following two C programs describe this format and show how to write and
read these data files.
------------------------------------------------------------------------------
/* diskwrt.c - a demo program to write a sample file "test_disk" in the
GENESIS "disk_out" format, to be viewed with the xfileview widget. */
#include <stdio.h>
#include <math.h>
main()
{
FILE *fpr;
int width = 5;
int height = 5;
float start = 0.0;
float dt = 1.0;
float x, y, data;
int ntimes;
fpr = fopen("test_disk", "w");
headerwrt(start, dt, width, height, fpr);
data = 0.0; /* make some bogus data */
for (ntimes = 0; ntimes < 20; ntimes++)
for (y = 0.0; y < height; y++) {
for (x = 0.0; x < width; x++) {
data = x*x + y*y + height*ntimes;
fwrite (&data, sizeof (float),1, fpr);
}
}
fclose(fpr);
} /* end main */
headerwrt(start, deltat, width, height, fp)
/* Header for files compatible with GENESIS disk_out
"FMT1" - 80 byte null terminated character string as identifying label
start - starting time - float
dt - time step - float
ndata - number of data points per time step - int
datatype - int code for data type - disk_out uses only FLOAT = 4, but
display routines can use DOUBLE = 5, INT = 3, SHORT = 2.
x1,y1,z1,x2,y2,z2,....,xndata,yndata,zndata - x,y,z coordinates for icon
representing each data point - float
The header is then followed by data - ndata values for each time step,
with the data type specified by "datatype".
*/
float start, deltat;
int width, height;
FILE *fp;
{
char label[80];
float strt, dt;
int ndata, datatype;
float x, y, z;
float dx = 2.0; /* horiz spacing between icons */
float dy = 2.0; /* vert spacing between icons */
int i, j;
strt = start; /* use local variables so addresses are correct */
dt = deltat; /* otherwise fwrite gets wrong start and deltat */
strcpy(label,"FMT1");
fwrite (label, sizeof (char),80, fp);
fwrite (&strt, sizeof (float),1, fp);
fwrite (&dt, sizeof (float),1, fp);
ndata = width*height;
fwrite (&ndata, sizeof (int),1, fp);
datatype = 4; /* use float data */
fwrite (&datatype, sizeof (int),1, fp);
z = 0.0; /* 2-D display */
for (j=0, y = 0.0; j < height; j++) {
for (i=0, x = 0.0; i < width; i++) {
fwrite (&x, sizeof (float),1, fp);
fwrite (&y, sizeof (float),1, fp);
fwrite (&z, sizeof (float),1, fp);
x = x + dx;
}
y = y + dy;
}
}
------------------------------------------------------------------------------
/* diskrd.c - Reads and displays the header information of files produced by
the GENESIS disk_out widget */
#include <stdio.h>
main(argc,argv)
int argc;
char **argv;
{
char label[100];
float fval;
int i;
int ndata;
int datatype;
FILE *fp;
if(argc < 2){
printf("usage: %s filename\n",argv[0]);
exit();
}
if((fp = fopen(argv[1],"r")) == NULL){
printf("unable to find file '%s'\n",argv[1]);
exit();
}
/* read in the file header */
fread(label,sizeof(char),80,fp);
/* check the label */
if(strncmp("FMT1",label,4) != 0){
printf("file '%s' is not a valid FMT1 data file\n",argv[1]);
fclose(fp);
exit();
}
/* starting time */
fread (&fval, sizeof (float),1,fp);
printf("%-20s = %e\n","start time",fval);
/* time step */
fread (&fval, sizeof (float),1,fp);
printf("%-20s = %e\n","time step",fval);
/* number of data points */
fread (&ndata, sizeof (int),1,fp);
printf("%-20s = %d\n","ndata points",ndata);
/** data type */
fread (&datatype, sizeof (int),1,fp);
printf("%-20s = %d\n","data type",datatype);
fclose(fp);
}
----------------------------------------------------------------------------
See also:
disk_in ,
asc_file
Object Type: diskio
Description:
The diskio object can be used to open/create a binary format file on disk
(specified with -fileformat option) that can be then used to read/write
data or metadata from/to it with child objects, 'variable' or 'metadata'
respectively in this same library. Unlike disk_out/disk_in, the reading
and writing actions are combined into this one new object.
For purposes of backwards compatibility (BC), diskio responds to the
set of messages that disk_out and disk_in respond to at a minimum, and
allows the user to read/write files directly from/to the disk at every
time-step of the clock which is assigned. It also allows the "replay" of
the results of a simulation through the xview and xgraph widgets in XODUS
by message passing as well as the "xsimplot" command added in genesis 2.2.
As of GENESIS 2.2, diskio supports files in the FMT1 and Netcdf formats.
Netcdf is a portable, network transparent, public domain binary format.
Netcdf interfaces to various popular analysis/signal-processing tools
including MATLAB are available in the public domain. Specifically,
* MEXCDF
WEB: http://crusty.er.usgs.gov/mexcdf.html
FTP: crusty.er.usgs.gov (128.128.19.19) or contact
Rich Signell at rsignell@crusty.er.usgs.gov.
* MexEPS
WEB: http://www.pmel.noaa.gov/epic/mexeps.html
FTP: ftp.pmel.noaa.gov/epic/mexeps/
* fanmat
WEB: http://www.unidata.ucar.edu/packages/netcdf/contrib.html
FTP: ftp.unidata.ucar.edu/pub/netcdf/contrib/fanmat.taz
are freely available packages that allow MATLAB to read/write/visualize
netcdf data.
The implementation of the diskio library and the diskio, metadata, and
variable objects makes use of netcdf, which is Copyright
1993-1997 by University Corporation for Atmospheric Research/Unidata. the
netcdf library is provided as per the terms of the UCAR/Unidata license,
described in the copyright notice found in the src/diskio/interface/netcdf
directory tree.
Author: V.Jagadish, Caltech (9/96)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: Gen_Diskio_Type [in src/diskio/diskio_struct.h]
Size: 172 bytes + allocation for arrays and interpols
Fields: accessmode Mode with which the file is accessed
- 'r', 'w' or 'a' (Read/Write/Append)
- Read-only field specifiable on the
command line using the -accessmode option
but cannot be set/unset subsequently
using setfield
- Defaults to 'r' (Read mode) as this is the
most non-destructive
- Append 'a' mode is not supported currently
- BC NOTE: Due to the default mode being
readonly 'r', it is not sufficient to
merely replace creation-lines of disk_out
with diskio but to add the option
"-accessmode w" as well. cf. See Examples.
filename Data file name to read from or write into
- Defaults to name of object if not specified
- Can be set/unset as required : The old file
will have data and metadata written into it
till that point in time, if the accessmode
was 'w' (write).
fileformat Format of the data file
- Unlike disk_out it is a character string
field but allows numerical setting for BC.
("1" => FMT1, "2" => netcdf)
- Defaults to FMT1 if not specified
- Subsequent setting/unsetting of this
field is allowed only to preserve BC with
disk_out/disk_in. This is effectively a
NOP as far as the physical file is
concerned. Only the the value of the
field changes to reflect the setting and
is not recommended.
append Flag: 1 => data should be appended to file
after RESET. This has certain implications
from the point of view of interpreting the
'variable' object value[], input and output
fields. If the append flag is on, there
could be more than 1 value associated with
a single time instance. The output field
will always reflect the first value for the
time instant set for the input field. All
values however can be retrieved from the
value[] field and the size field of the
variable will show the total number of
values stored. The user needs to keep track
of when the reset was done and the time
step rate (dt) to interpret the values
stored in the value[] field.
is_open Read-only flag: is file currently open?
is_writable Read-only flag: is file writable?
val 2D array of input values
nx x dimension of input val array
ny y dimension of input val array
xpts,ypts,zpts Interpols used for storing coordinate
information when the binary file is read
flush Same functionality as in disk_out
leave_open Same functionality as in disk_out
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Gen_Diskio [in src/diskio/gen_diskio.c]
Classes: output
Actions: CREATE PROCESS SET ADDMSGIN DELETEMSGIN SHOW
RESET:
It is essential that the RESET action be called
on the diskio object for allocating and filling the
"xpts ypts zpts" interpol arrays before using
them to render/replay data graphically on the
xview objects.
cf. Example: Scripts/examples/diskiolib/diskio
/replayview.g
QUIT:
FLUSH:
UPDATE: when called on the diskio object, allows the user
to commit any changes done interactively
or in the process of running a simulation or script,
to the file on disk. This allows another diskio
object to simultaneously access updated data from the
same file.
DELETE: also commits changes but with the usual effect of
deleting the object and all its children. Please note
that this action does not delete the physical file on
disk.
GENERAL NOTE: The process of committing changes to disk is
time-consuming for netcdf files. This is
inherent in the implementation of the
netcdf library. So please expect high
latency after you quit or do a delete or
call one of the above 4 actions on the
diskio object, when supporting the netcdf
fileformat. In general, the netcdf library
provides its portability across
architectures at the cost of efficiency in
speed. Therefore, performance-wise one will
notice diskio is slower than
disk_out/disk_in, in this situation. The
same is however not true for FMT1 file
support.
Messages: SAVE data
IMPORTANT BACKWARDS COMPATIBILITY (BC) NOTES:
---------------------------------------------
As previously mentioned, diskio responds to the same set of
messages that disk_out and disk_in respond to as a minimum, for
purposes of BC.
Since the actual data is encapsulated within the variable object
and the design eventually envisages the exclusive use of this child
object to manipulate data, any incoming SAVE messages to the diskio
object (thro the addmsg command) will result in the automatic
creation of child variables and the forwarding of the message to
them. So the data will be stored and manipulated via these child
variables, while letting the user transparently deal only with the
diskio object as was done previously with disk_out/disk_in.
For every SAVE message there will be a specially named child
variable object - 'autoSAVE_diskio[i]', where i is the index of
the element and that corresponds to the number of the message.
The indices will be reused if any messages are deleted and added
later.
Also, for every SAVE message, the 3-D position coords of the source
element needs to be stored for possible future replay via graphical
objects like xview. This is done through the automatic creation of
specially named indexed metadata children -
'auto3-DPosSAVE_diskio[i]'.
So in applications where diskio is intended to be used as a
replacement for disk_out/disk_in, these variables & metadata will
be automatically created in the hierarchy for every SAVE message to
the object. Directly manipulating these child objects should be
avoided, since it would essentially change the contents of the
file, if committed.
Example:
* Run Scripts/examples/diskiolib/diskio/generate.g
* genesis> le /diskio
------------------------------------------------------------------------------
Notes:
As a departure from the disk_out/disk_in objects, this object internally
just serves to interface (open/create/close) with a binary file on disk.
The actual data in the file can be more flexibly managed using the child
'variable' objects in this library. For purposes of backwards
compatibility, however, the diskio object will respond to the same messages
as the disk_out and disk_in objects at a minimum to actively write/read
data to/from the file during a simulation run.
Some binary file formats notably netcdf (which this library supports) allow
descripive data (metadata) to be stored in them along with the actual data.
Child 'metadata' objects in this library allow the user to manipulate the
metadata content in these files.
Use asc_file for writing data in ASCII format.
Examples:
0. create diskio /dout -filename testfile.nc -fileformat netcdf -accessmode w
// Not specifiying a fileformat while creating a file defaults to FMT1
1. create diskio /dout_FMT1 -filename testfile.fmt1 -accessmode w
2. call /dout UPDATE
3. delete /dout
4. Also, please see Scripts/examples/diskiolib/diskio/
- generate.g
- generate_netcdf.g
- replayview.g
- replaygraph.g
- simplot.g
______________________________________________________________________________
See also:
variable ,
metadata ,
disk_out ,
disk_in ,
asc_file
Object Type: efield
Description: An extracellular field potential recording electrode that uses
current sources and their distance from the electrode site to
calculate the field.
Author: M. Wilson, Caltech (2/89)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: efield_type [in src/device/dev_struct.h]
Size: 64 bytes
Fields: scale
field
x
y
z
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: ExtracellularRecordingElectrode [in src/device/efield.c]
Classes: device
Actions: PROCESS
RESET
RECALC
Messages: CURRENT current 0.0
------------------------------------------------------------------------------
Notes: If one assumes that the medium surrounding neurons is
of homogeneous resistivity and has no capacitance,
then the field potential generated by a compartmental
model can be calculated from the following equation:
Im
1 n i
F = ------ SUM ----- (see Nunez, 1981)
4*pi*s i=1 R
i
where F is the field potential in volts, s is
conductivity in 1/(Ohms*m), Im_i is the transmembrane
current (Amperes) accoss the ith neural compartment,
and R_i is the distance from the ith neural
compartment to the recording electrode (i.e. the
efield object).
This equation is most accurate in the case of elongated
neurons oriented with the axis perpendicular to the scalp, as
is the case with cortical pyramidal cells. It is probably not
very good for a small cell. See the documentation of
compartment and symcompartment for details of the calculation
of the compartment Im.
In the case of the efield object, the term 1/(4*pi*s)
is replaced by the scale field, otherwise the same
equation is used to calculate field potentials.
The RECALC action must be called in order for efield
to calculate the distances to neural compartments.
For more information about field potentials and how
they are used in GENESIS simulations, see Chapter 9 in
The Book of GENESIS. For a derivation of the above
equation, see:
Nunez, P.L. (1981) Electric Fields of the Brain: The
Neurophysics of EEG, Oxford University Press, Oxford.
Example: create efield electrode
setfield electrode scale -1e3 x 0.00 y 0.00 x 0.00
addmsg some_compartment electrode CURRENT Im 0.0
call electrode RECALC
See also: Scripts/piriform/field.g,
compartment ,
symcompartment
Object Type: enz
Description: Enzyme activity for a pre-existing pool. An enz does two
things: it handles the reactions in the Michaelis-Menten (MM)
scheme below, and it also acts as a pool to represent the
enzyme-substrate complex. It can only be
created on a pool, it is not an independent object.
The MM scheme is modeled as:
k1 k3
Substrate + Enzyme <-----> EnzComplex ----> Enz + Prd
k2
The enz is really a utility object, as it replaces
two reacs and a pool, but does not add anything extra.
Author: U. S. Bhalla, National Centre for Biological Sciences,
Bangalore, India. (1993).
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: enz_type [in src/kinetics/kin_struct.h]
Size: bytes
Fields: CoComplex Concentration of enz-substrate complex.
CoComplex = nComplex/vol
CoComplexInit Initial concentration of enz-substrate
complex.
CoComplex gets set to this value on
RESET.
nComplex Number of molecules of complex.
nComplexInit Initial number of molecules of complex.
'nComplex'gets set to this value on
RESET.
vol Volume occupied by enzyme. Often
involves scale factor so as to have
direct conversion from 'n' to some
sensible units of Co, such as
micromolar.
sA A state variable to pass to substrate
in messages.
pA A state variable to pass to products
in messages.
eA A state variable to pass to parent
enzyme pool in messages.
B B state variable to pass to substrate
and parent enzyme pool in messages
k1,k2,k3 Michaelis-Menten parameters.
keepconc Flag determining whether to change
concs or n when volume changes
usecomplex Flag. Determines whether the enzyme
complex is used when the parent enzyme
is involved in other reactions.
Consider:
E + A <----> E.A
where E is a pool reacting with A.
Suppose E has an enzyme site. Then,
whenever some of the enzyme is complexed
with a substrate, the conc of E
decreases unless 'usecomplex' is true.
ksum Internal variable. ksum = k2 + k3.
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: EnzFunc [in src/kinetics/enz.c]
Classes: segment
Actions: PROCESS
RESET
SET
Messages: ENZYME n [n is number of molecules of enzyme
pool to which this site is attached]
SUBSTRATE n [Number of molecules of substrate]
VOL vol [volume of enzyme pool]
INTRAMOL n [Total number of molecules in an
intramolecular reaction]
------------------------------------------------------------------------------
Notes: See pool documentation for example of use.
------------------------------------------------------------------------------
Object Type: event_tofile
Description: A gizmo that collects an INPUT message. When value
in message exceeds threshold, current simulation
time is written to asci file.
Designed to allow ascii output from a range of
objects, like channelC3, synchan, timetable.
Author: D. Jaeger, Caltech (3/95)
---------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: event_tofile_type [in genesis/src/device/spike_struct.h]
Size: 64 bytes
Fields: fname File name of asci output
fp file pointer
open flag
threshold threshold above which time is written to file
-----------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Event_tofileFunc [in genesis/src/device/event_tofile.c]
Classes: device
Actions: PROCESS
SET
OPEN
CLOSE
FLUSH
Messages: INPUT compared against threshold
-----------------------------------------------------------------------
Notes: An ascii file containing simulation times at which an event
occurred is generated. The event arrives via an INPUT
message, and is generated when the input value exceeds
threshold. Only positive thresholds are implemented.
Before activation the file needs to be opened with a reset or call
OPEN statement. The generic openfile, writefile, and closfile
commands can NOT be used with the same file.
Example:
create synchan syn
create event_tofile etf
set etf fname test.asc
sendmsg syn etf INPUT activation
reset
... // run simulation
call etf CLOSE
See also:
openfile ,
writefile ,
closefile
(for general asci file control),
timetable ,
spikegen ,
randomspike (for good source elements
to feed into event_tofile), Scripts/examples/spike/spikes.g.
Object Type: facsynchan
Description: Synaptically activated channel with synaptic facilitation
and/or synaptic depression.
Author: Mike Vanier
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: fac_synchan_type [in src/newconn/newconn_struct.h]
Size: 252 bytes
Fields: activation driving force ("transmitter") for channel
conductance
Ik channel current
Gk time varying channel conductance
Ek reversal potential of channel
tau1 first time constant of channel activation
tau2 second time constant of channel activation
gmax peak channel conductance (but see Notes below)
nsynapses number of incoming spike messages
(readonly)
event_buffer_size size of event buffer (readonly)
pending_events number of pending spike events in event
buffer (readonly)
nodes_per_synapse number of event nodes to allocate per
synapse (default 1)
synapse synapse buffer
fac_depr_on flag: no fac/depr if 0
max_fac upper limit on facilitation
fac_per_spike synaptic facilitation per spike
fac_tau time constant of synaptic facilitation
depr_per_spike synaptic depression per spike
depr_tau time constant of synaptic depression
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: FacSynchan [in src/newconn/facsynchan.c]
Classes: segment channel synchannel
Actions: CREATE Set default values and initialize object.
PROCESS Update Gk, calculate Ik, update facilitation/
depression state of synaptic weights.
RESET Assign activation = 0, Gk = 0; calculate
time-step-dependent coefficients; remove
all pending SPIKE events; reset facilitation/
depression state of synaptic weights.
RECALC Recalculate time-step-dependent coefficients.
CHECK Make sure tau1>0, tau2>0, gmax>0; make sure a
VOLTAGE message is present (in order to
calculate Ik); make sure facilitation/
depression parameters are reasonable.
SAVE2 Called by the save command.
RESTORE2 Called by the restore command
EVENT Put a spike event into the event buffer.
ADDMSGIN Add a new message.
DELETEMSGIN Delete a message.
MSGINDELETED Do cleanup after message is deleted.
RESETBUFFER Reset size of event buffer to
(nodes_per_synapse * nsynapses) nodes.
DELETE Delete the element.
COPY Copies the element.
Messages: VOLTAGE Vm
SPIKE
------------------------------------------------------------------------------
Notes: The `facsynchan' object is a version of the synchan object
that can exhibit synaptic facilitation, synaptic depression,
or some combination of the two.
1) General information about synchans.
The `facsynchan' object, like all synchan objects, simulates a
time dependent synaptically activated ionic channel. A
variable channel conductance `Gk' is activated by the
application of transmitter. This conductance then changes with
damped second-order characteristics with a time course given
by two time constants `tau1' and `tau2'. This gives rise to
an alpha function/dual exponential conductance waveform for an
impulse spike input. The channel also calculates channel
current (`Ik') and therefore needs the membrane state (`Vm').
Each SPIKE message to a synchan establishes a synaptic
connection and increments `nsynapses'. The synapses are
numbered starting with 0, and each contains a field for a
synaptic weight and a propagation delay. For example, the
weight of the first synaptic connection is held in the field
`synapse[0].weight' while the delay is `synapse[0].delay'.
`Gk' reaches a value (`gmax' * `weight') for a single event
delivered with a SPIKE message. Note that even though
synapses are not elements, they do have fields that can be
accessed individually. They can be thought of as
"sub-elements" or substructures of the element. Note also
that `gmax' is not the absolute maximum conductance of the
synapse; it is just the maximum conductance given a single
synaptic connection with a weight of 1.0 only. Multiple
synapses onto a particular synchan, weights higher than 1.0,
and/or synaptic facilitation can all give rise to total
conductances that are greater than `gmax'.
Any number of spike events can be pending per synapse. The
`facsynchan' object stores all spike events in a buffer until
they are scheduled to occur. If enough events come in to
overload the buffer, the buffer will dynamically expand to
enable storage of all events. The size of the buffer in
events is stored in the `event_buffer_size' field which is
readonly. The number of actual spikes in the buffer which
have not yet hit the channel are stored in the
`pending_events' field (also readonly). The
`nodes_per_synapse' field controls how many large the event
buffer is initially. The default is to have one node per
synapse, but if you expect a lot of events or very few events
you can change this number to be greater or less than the
default (1), respectively. This will speed up the simulation
slightly in the first case and save memory in the second. If
you leave this field alone the object will still work fine.
The "resetsynchanbuffers" command will cause all the buffers
in all synchan and derived objects to be reset to a size of
`nodes_per_synapse' * `nsynapses' (which will also cause all
pending events to be flushed).
The "copy" command will fail for any synchan type which is
receiving SPIKE messages. The correct way to set up
simulations is to set up prototype cells which do not receive
any SPIKE messages on their synchans, copy these cells, and
then add the appropriate SPIKE messages (by hand or by using
planarconnect or volumeconnect). We may eventually build a
more intelligent copy command which will permit copying of
synchans with SPIKE messages, but for now, don't do it.
2) Specific information about implementing synaptic
facilitation and depression.
Each synapse, in addition to its `weight' and `delay' fields,
has two other fields called `fac' and `depr' which represent
the current level of synaptic facilitation and depression,
respectively. Each time a spike hits, the facilitation and
depression values are incremented by a fixed amount
(`fac_per_spike' and `depr_per_spike', respectively) which can
be zero but not negative. The facilitation and depression
values decay away with a time constant equal to `fac_tau' and
`depr_tau', respectively. The effective synaptic weight when
a spike hits is calculated from these equations:
wt_multiplier = max((1 + fac) / (1 + depr), max_fac)
wt_effective = wt * wt_multiplier
Thus, a `fac' value of 1.0 and a `depr' value of 0.0 will give
rise to a wt_multiplier value of 2.0 (assuming that `max_fac'
> 2.0), so the effective weight at that point in time will be
twice the listed synaptic weight. The `max_fac' field allows
you to limit the amount that a particular synaptic weight can
grow; however, there is no limit to how low a weight can
shrink due to depression. If `max_fac' is negative, there is
no maximum facilitation level. This is the default (`max_fac'
= -1, to be precise).
You can switch facilitation/depression off by setting
`fac_dep_on' to 0. The default is 1 (facilitation on).
Example: Scripts/examples/facsynchan/facdemo.g
Bugs: The SAVE2/RESTORE2 actions have not been tested and may
contain bugs. Please report any bugs you find.
Caveats: The facsynchan object is not supported by the cell reader
(readcell), so if it is to be used in a model described
by a cell parameter (.p) file, you will need to use it in
a prototype compartment that is included with the readcell
"*compt" option.
See also:
synchan ,
resetsynchanbuffers ,
Connections ,
NewSynapticObjects ,
readcell
Object Type: fixbuffer
Description: Implementation of a first-order fixed (non-mobile) buffer.
Should be coupled to a difshell or concpool, where the change
in the concentration of the buffered ion is computed.
Author: E. De Schutter BBF-UIA 8/94 - 9/95
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: fixbuffer_type [in src/concen/conc_struct.h]
Size: 124 bytes
Fields: activation ion concentration from incoming CONCEN message
Bfree free buffer concentration (calculated) in mM
Bbound bound buffer concentration (calculated) in mM
prev_free Bfree at previous time step
prev_bound Bbound at previous time step
Btot total buffer concentration in mM (free + bound)
kBf forward rate constant in 1/(mM*sec)
kBb backward rate constant in 1/sec
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: FixBuffer [in src/concen/fixbuffer.c]
Classes: concbuffer segment
Actions: RESTORE2 SAVE2 CHECK RESET PROCESS INIT
Messages: CONCEN C (buffered ion concentration, sent from a
difshell or concpool)
------------------------------------------------------------------------------
Notes:
The fixbuffer interacts with a difshell or concpool to model the binding of
calcium to buffer molecules and to calculate the concentrations of free and
bound buffer molecules using a kinetic scheme with forward and backward rate
constants for the binding and release of calcium:
dBfree/dt = kBb*Bbound - kBf*Bfree*C
Bbound = Btot - Bfree, where Btot == constant
The rate constants kBf and kBb are set by the user, and the concentration C is
sent with a CONCEN message from the difshell or concpool. The BUFFER message
to a difshell or concpool from a buffer passes on the rate constants and the
calculated free and bound buffer concentrations.
For a general description of buffered calcium diffusion see: De Schutter E.,
and Smolen P., "Calcium dynamics in large neuronal models", in Methods in
neuronal modeling: From ions to networks (2nd edition), C. Koch and I. Segev
editors, pp. 211-250 (1998). The spinedemo simulation gives a detailed
example of the use of the difshell, taupump, and fixbuffer objects for
modeling calcium diffusion in dendritic spines.
Example: create fixbuffer headbuf0
setfield headbuf0 Btot 0.2 \ // Total buffer conc in mM
kBf 5.0e5 \// Forward binding rate 1/(mM*sec)
kBb 500 // Backward rate, 1/sec
addmsg headbuf0 headshell0 BUFFER kBf kBb Bfree Bbound
addmsg headshell0 headbuf0 CONCEN C
See also:
difshell ,
taupump , Scripts/examples/spinedemo
Object Type: freq_monitor
Description: Calculates running event (spike) frequency over a given time
window using exponential weighting.
Author: M. Wilson, Caltech (2/89), modified by D. Jaeger
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: freq_mon_type [in src/device/dev_struct.h]
Size: 84 bytes
Fields: tmin minimum time interval which must be held by
the buffer
size buffer size, in number of events
current current buffer location
start starting buffer location - 1
end last occupied buffer location
event_size size of each event data structure
event circular event buffer
exponent power by which to weight
frequency curent calculated value of the frequency
(set to zero on reset)
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: FrequencyMonitor [in src/device/new_frequency.c]
Classes: device
Actions: PROCESS RESET CREATE
Messages: NONZERO_TRIG input trigger on nonzero input
ZERO_TRIG input trigger only when input is zero
POSITIVE_TRIG input trigger on positive input
NEGATIVE_TRIG input trigger on negtive input
WINDOW tmin sets the window size tmin
CONTINUOUS input triggers every time
------------------------------------------------------------------------------
Notes: This is a frequency measuring device which computes the
running event frequency over a time interval using exponential
weighting. The field "tmin" should be set in order to specify
the interval or "window" for averaging. Larger values give a
smoother result. If "exponent" is unequal to the default
value of zero, inputs are weighted by exp(exponent*time). The
frequency field may be examined or sent to a graph.
The first four messages are used to give it an input, and the
counting of input events is triggered by one of the four
conditions. The most common way to use the frequency monitor
is to set the "tmin" field to an appropriate timing window,
send it a POSITIVE_TRIG message with the state of a spiking
element, and send a "PLOT frequency" message from the monitor
to a graph.
Example: See the demonstration script Scripts/examples/spike/freqmon.g.
See also:
Object Type: funcgen
Description:
This is a function generator which produces periodic output with a waveform
set by the mode field.
Author: M. Wilson, Caltech (4/89)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: funcgen_type [in src/device/dev_struct.h]
Size: 96 bytes
Fields: mode flag: 0=sine; 1=square; 2=triangle; 3=constant
amplitude peak-to-peak amplitude
dc_offset constant to be added to output
phase phase in degrees
frequency frequency
output output waveform
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: FunctionGenerator [in src/device/funcgen.c]
Classes: device
Actions: CHECK PROCESS RESET
Messages: AMPLITUDE amplitude
DC_OFFSET dc_offset
PHASE phase
FREQUENCY frequency
------------------------------------------------------------------------------
Notes:
In a simulation, you would set up messages between the funcgen element
(in our example it is called "funky") and other elements which are to
receive its output. For example:
addmsg funky funcplot PLOT output *function *red // funcplot is an xgraph
addmsg funky Exc_channel ACTIVATION output // Exc_channel is a synchan
Example: Scripts/examples/sigmoid
See also:
Object Type: fura2
Description: Computes fura2 fluorescence in a single difshell.
Author: E. De Schutter BBF-UIA 1/95
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: fura2_type [in src/concen/conc_struct.h]
Size: 104 bytes
Fields: F340 F340 fluorescence
F380 F380 fluorescence
ratio F340/F380
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: FuraRatio [in src/concen/fura2.c]
Classes: concentration segment
Actions: RESET PROCESS
Messages: CONCEN Bfree Bbound vol (from all fura2 difbuffers)
------------------------------------------------------------------------------
Notes: Computes the fluorescence signal of the fura-2 calcium
indicator dye by adding together information from a series of
difbuffers (representing the fura2 in shells).
In order to use the fura2 object, create difbuffers to model
the diffusion of the fura-2 dye and Ca buffering for each
difshell that is associated with a compartment. The Btot, D,
kBf, and kBb fields for the difbuffers should be set to values
that are typical of the ionic environment of the dye. The
difbuffers are linked to their difshells with the usual
messages.
Then send "CONCEN Bfree Bbound vol" messages to a single fura2
element from each difbuffer that corresponds to the
compartment for which you wish to calculate the fura-2
fluorescence signal.
For a general description of buffered calcium diffusion see:
De Schutter E., and Smolen P., "Calcium dynamics in large
neuronal models", in Methods in neuronal modeling: From ions
to networks (2nd edition), C. Koch and I. Segev editors, pp.
211-250 (1998). Details of the GENESIS implementation of the
fura2 object are given in Sec. 6.6.4. Also see Blumenfeld et.
al., Biophys. J. 63: 1146-1164 (1992) for additional
discussion of fura-2 parameters.
Example:
See also:
difshell ,
difbuffer
Object Type: ghk
Description: Calculates the Goldman-Hodgkin-Katz (constant field) equation
for a single ionic species. Provides current as well as
reversal potential and slope conductance.
Author: Subba Shankar 8/25/91, modified by EDS 9/93-10/96
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: ghk_type [in src/segment/seg_struct.h]
Size: 136 bytes
Fields: Ik channel current (calculated)
Gk channel conductance (calculated)
Ek channel reversal potential (calculated)
T temperature (degrees Celcius)
p permeability
Vm membrane potential
Cin concentration inside the compartment in mM
Cout concentration outside the cell in mM
valency charge on ion
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Ghk [in src/segment/ghk.c]
Classes: device channel
Actions: CHECK PROCESS RESET
Messages: Cin concentration
Cout concentration
VOLTAGE Vm
PERMEABILITY p
------------------------------------------------------------------------------
Notes:
The general equation used is:
Cin * exp(K * Vm) - Cout
Ik = -p * F * K * Vm ------------------------
exp(K * Vm) - 1
valency * F
where K = -------------
R * (T + 273)
F = Faraday's constant (9.6487e4 coul/mol)
R = universal gas constant (8.314 volts*coul/(deg K * mol))
Unlike the tabchannel or tab2Dchannel, it is not assumed that the current
obeys Ohm's law and is proportional to the membrane potential Vm. However, a
compartment (or symcompartment) will expect a channel element to provide Gk
and the reversal potential Ek in a "CHANNEL Gk Ek" message, and use these to
calculate the incoming ionic current from Ik = Gk*(Ek - Vm). In order for
a ghk element to be used like a channel, suitable values of Gk and Ek must
be provided. This may be done by making the assumption that over a single time
step, Gk and Ek vary slowly compared to Vm. Then the approximation can be
made that dIk/dVm = - Gk, and that Ek = (Ik + Gk*Vm)/Gk. Thus, Ek is
calculated by the ghk element, rather than being set by the user or by
an incoming message. Note that the sign of the current expresses the GENESIS
convention that current flow into a compartment is positive.
One way to use this object would be to let a voltage or ligand gated channel
element determine the permeability of the channel as a function of time,
voltage, concentration of ligand, etc., and then send that permeability to a
ghk element (as a message) to determine the net current through the channel.
The resulting Gk and Ek could be sent to the compartment that contains the
channel. If you are keeping track of the concentration of your ion with a
concentration type element, you could send it the Ik field of the ghk element.
You could then get Cin or Cout messages from the concentration element into
the ghk element.
In the example below, the conductance Gk is sent to the ghk element in
a PERMEABILITY message. Although the permeability p and conductance Gk
have differnet units, the scaling has been taken into account in the ghk
object, as long as SI (MKS) units are used.
A full explanation of the constant field equation can be found in:
1) From Neuron to Brain, Kuffler, et al., Sinauer Assoc.
2nd edition, (1984) p. 123, 130.
2) Electric Current Flow in Excitable Cells, Jack, et al.,
Oxford Press, (1983) p. 237.
3) Ionic Channels of Ecitable Membranes, Hille, Sinauer Assoc.
2nd edition, (1992) pp 345-347.
Example: create ghk soma/Ca_ghk
setfield soma/Ca_ghk Cin {CCaI} Cout {CCaO} valency 2.0 T {Temp}
addmsg soma soma/Ca_ghk VOLTAGE Vm
addmsg soma/Ca_ghk soma CHANNEL Gk Ek
addmsg soma soma/CaT VOLTAGE Vm
setfield soma/CaT Gbar {GCaTs*surf}
addmsg soma/CaT soma/Ca_ghk PERMEABILITY Gk
addmsg soma soma/CaP VOLTAGE Vm
setfield soma/CaP Gbar {GCaPs*surf}
addmsg soma/CaP soma/Ca_ghk PERMEABILITY Gk
See also:
tabcurrent ,
setupghk ,
setupNaCa
Object Type: hebbsynchan
Description: Synaptically activated channel with a simple mechanism for
hebbian weight changes as a function of pre- and postsynaptic
activities.
Author: Mike Vanier 9/95; revised 4/96
--------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: HebbSynchan_type [in src/newconn/newconn_struct.h]
Size: 296 bytes
Fields: activation driving force (transmitter) for channel
conductance
Ik channel current
Gk time varying channel conductance
Ek reversal potential of channel
tau1 first time constant of channel activation
tau2 second time constant of channel activation
gmax peak channel conductance
frequency random activation frequency (default = 0)
nsynapses number of incoming spike messages (read only)
event_buffer_size size of event buffer (read only)
pending_events number of pending spike events in event
buffer (read only)
nodes_per_synapse number of event nodes to allocate per
synapse (default = 1)
synapse synapse buffer
pre_tau1 rise time constant for presynaptic averaging
pre_tau2 decay time constant for presynaptic averaging
pre_thresh_lo lower presynaptic threshold
pre_thresh_hi upper presynaptic threshold
avg_Vm averaged membrane potential (read only)
post_tau time constant for postsynaptic averaging
post_thresh_lo lower postsynaptic threshold
post_thresh_hi upper postsynaptic threshold
post_scale scaling factor for postsynaptic activities
weight_change_rate rate of weight change (roughly in units/sec)
min_weight minimum weight
max_weight maximum weight
change_weights flag: nonzero means weights can be changed
--------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: HebbSynchan [in src/newconn/hebbsynchan.c]
Classes: segment channel synchannel
Actions: CREATE set synapse_size hidden field
INIT assign activation = 0
PROCESS update Gk, calculate Ik; calculate hebbian
presynaptic and postsynaptic activities
RESET assign activation = 0, Gk = 0; calculate
time-step-dependent coefficients
RECALC recalculate time-step-dependent coefficients
CHECK make sure tau1 > 0, tau2 > 0; make sure a
VOLTAGE message is present (in order to
calculate Ik); check hebbian fields, etc.
SAVE2 called by the save command
RESTORE2 called by the restore command
EVENT put a spike event into the event buffer
ADDMSGIN
DELETEMSGIN
MSGINDELETED
RESETBUFFER reset size of event buffer to
(nodes_per_synapse * nsynapses) nodes
DELETE delete the element
COPY copies the element
Messages: VOLTAGE Vm
ACTIVATION activation
RAND_ACTIVATION probability amplitude
MOD modulation
WEIGHT_CHANGE_MOD modulation
SPIKE
------------------------------------------------------------------------------
Notes: This object simulates a time-dependent synaptically
activated ionic channel. A variable channel conductance Gk
is activated by the application of transmitter. This
conductance then changes with damped second-order
characteristics with a time course given by two time
constants tau1 and tau2. This gives rise to an
alpha-function/dual-exponential conductance waveform for an
impulse spike input. The channel also calculates channel
current Ik and therefore needs the membrane state (Vm).
Each SPIKE message to a synchan or hebbsynchan establishes a
synaptic connection and increments nsynapses. The synapses
are numbered starting with 0, and each contains a field for a
synaptic weight and a propagation delay. For example, the
weight of the first synaptic connection is held in the field
"synapse[0].weight". Gk reaches a value gmax*weight for a
single event delivered with a SPIKE message. Note that even
though synapses are not elements, they do have fields that can
be accessed individually. They can be thought of as
"sub-elements" or substructures of the element. The fields
the user should be concerned about in the synapse are "weight"
and "delay".
The above description is also true for the synchan object.
Hebbsynchans also have a "pre_activity" field, described
below. Note that this field was named "pre_avg" in GENESIS
version 2.0.1. The hebbsynchan object also updates the
synaptic weights of the synapses based on the presynaptic
"activities" (which are calculated separately for each
synapse) and the postsynaptic activity (which is the same for
all synapses which are part of a given hebbsynchan). The
activities are artificial values which do not have a direct
relationship to any real biological entities; very loosely we
can think of the presynaptic activity as being the amount of
calcium current through an NMDA receptor while the
postsynaptic activity is derived from an average of the
postsynaptic membrane potential (which will affect NMDA
receptors in reality). The pre- and postsynaptic activities
are used to update the weights in a roughly Hebbian manner
described below, which is similar but by no means identical to
the way NMDA-dependent LTP works. For serious GENESIS
hackers, we have isolated the actual weight change algorithm
in a single function in "hebbsynchan.c" which can be altered
if you need a different algorithm. If you want to calculate
pre- or postsynaptic activities differently you have to do a
lot more work.
The presynaptic activity is calculated by having each spike
generate a generalized alpha-function waveform with a
maximum size of 1 in the "pre_activity" field of the
synapse. This is meant to be analogous to an NMDA channel
conductance so the rise and fall times should be slow; for
instance we might use pre_tau1 of 10 msec and pre_tau2 of
100 msec. Note that this activity value doesn't mean that
there is a slow conductance being simulated here; it's just
used to determine a measure of presynaptic spiking
activity. When weight updates occur, the presynaptic
activity relative to two thresholds (pre_thresh_lo and
pre_thresh_hi) are used to calculate the weight change (see
below).
Also at each time step, the membrane potential of the
compartment the hebbsynchan is connected to is used to
update the "avg_Vm" field. This is done by running the Vm
of the compartment through a leaky integrator with a time
constant of post_tau. When weight updates occur, the
postsynaptic activity relative to two thresholds
(post_thresh_lo and post_thresh_hi) are used to calculate
the weight change (see below). Also, since presynaptic
activity values are dimensionless but avg_Vm has the
dimensions of volts, postsynaptic activities are internally
calculated by dividing the difference between avg_Vm and
the nearest threshold by "post_scale", which is also in
units of volts. You can think of post_scale as the amount
that avg_Vm has to be above threshold to give a
postsynaptic activity of 1.0.
The 2-d space defined by the pre- and postsynaptic
activities are separated into 9 regions based on two
presynaptic and two postsynaptic thresholds (called
"pre_thresh_lo", "pre_thresh_hi", "post_thresh_lo", and
"post_thresh_hi"). The values of the thresholds are fixed
and are specified by the user. The weight changes in each
of the nine regions are as follows:
---------> Presynaptic activity ----->
low medium high
Post- | |
synaptic | |
activity: | |
no | no change | decrease
low change | |
| | |
| | |
| -------------------------------------------------- <--- post_thresh_lo
| | |
| | |
\|/ no change | no change | no change
medium | |
| | |
| | |
| | |
| -------------------------------------------------- <--- post_thresh_hi
| | |
| | |
\|/ decrease | no change | increase
high | |
| |
| |
| |
^^^ ^^^
pre_thresh_lo pre_thresh_hi
The diagram shows what happens for various combinations of
pre- and postsynaptic activities. Note that if
pre_thresh_lo = pre_thresh_hi and post_thresh_lo =
post_thresh_hi then there are only four regions and the
weights will always be changing unless both presynaptic and
postsynaptic activities are below the thresholds. The
weight change algorithm used converts pre_activity into a
value which is the difference between the pre_activity of
the synapse and the nearest threshold value i.e.
real_pre_activity = pre_activity - pre_thresh_hi
(if pre_activity > pre_thresh_hi), OR
= pre_activity - pre_thresh_lo
(if pre_activity < pre_thresh_lo;
note that this gives a negative number), OR
= 0 otherwise
Similarly, the weight change algorithm calculates a "real"
postsynaptic activity as follows:
real_post_activity = (avg_Vm - post_thresh_hi) / post_scale
(if avg_Vm > post_thresh_hi), OR
= (avg_Vm - post_thresh_lo) / post_scale
(if post_activity < post_thresh_lo;
note that this gives a negative number), OR
= 0 otherwise
Note that the post_thresh values are both in units of
volts, like avg_Vm.
Once we have the "real" pre- and postsynaptic activities we
can update the weights. Essentially the algorithm now is
just the Hebb algorithm:
weight_change = real_pre_activity * real_post_activity *
weight_change_rate * dt;
where dt is the time step size in seconds. The
weight_change_rate is a field in the object and has units
of (1/time). Thus the overall weight change is
dimensionless, as is the weight itself. If
(real_pre_activity * real_post_activity *
weight_change_rate) equalled 1.0, then the weight would
increase roughly at the rate of 1 unit per second. One
neat feature of this scheme is that if weight_change_rate
is negative you get an anti-Hebbian synapse.
Unfortunately, there's more to it than this. There are
also two fields called "min_weight" and "max_weight" which
keep the weights of synapses connected to the hebbsynchan
within specified limits. We could in theory just truncate
the weights if the weight change algorithm tried to push it
beyond the limits, but in order to make it more smooth the
weight change calculated above is modified depending on how
close you are to min_weight or max_weight. The effect of
this is that the weight change rate is reduced when you
approach either limit.
There is also a field called "change_weights". If this is
set to zero, no weight changes will occur. Otherwise,
weight updates will occur according to the above algorithm.
In addition, hebbsynchans can receive a WEIGHT_CHANGE_MOD
message (or multiple messages of this type) which will
modify the effective value of weight_change_rate based on
the message value. In this case the effective
weight_change_rate is the product of the value in the field
of the object and the value in the message. The field
value is not changed. Thus you can have, say, a
sinusoidally varying weight change rate by setting
weight_change_rate to 1.0 and adding a WEIGHT_CHANGE_MOD
message from a sine wave generator (funcgen object) where
the sine wave varies from 0 to 2.0, say.
The "copy" command will fail for any synchan or hebbsynchan
which is receiving SPIKE messages. The correct way to set
up simulations is to set up prototype cells which do not
receive any SPIKE messages on their synchans, copy these
cells, and then add the appropriate SPIKE messages (by hand
or by using planarconnect or volumeconnect). We are
working on a more "intelligent" copy command which will
permit copying of synchans with SPIKE messages, but for
now, don't do it.
Default values of hebbian parameters (SI units are assumed
here):
pre_tau1 0.010 // seconds
pre_tau2 0.100 // seconds
pre_thresh_lo 3.0
pre_thresh_hi 3.0
post_thresh_lo -0.065 // Volts
post_thresh_hi -0.065 // Volts
post_scale 0.002 // Volts
weight_change_rate 1.0
min_weight 0.0
max_weight 100.0
change_weights 1
The RESET action does not restore the weights to the original
(unlearned) values. If you wish to re-run a simulation
starting from the initial state, write a script function that
sets the weights to the original values and then performs a
reset.
Example: Scripts/examples/hebb/hebb.g
See also:
synchan ,
resetsynchanbuffers ,
Connections ,
NewSynapticObjects
Object Type: hh_channel
Description: Implements the channel model described in A.L.Hodgkin and
A.F.Huxley, J.Physiol(Lond) 117, pp 500-544 (1952)
In the Hodgkin-Huxley model, the general form for the
channel conductance is represented as being proportional to
an activation state variable raised to an integer power
times an inactivation state variable raised to another
integer power. The hh_channel object calculates the channel
conductance from the equation
Gk = Gbar*X^Xpower * Y^Ypower
In the usual Hodgkin-Huxley notation for the Na channel, X
corresponds to the activation variable, m, with Xpower = 3,
and Y corresponds to the inactivation variable, h, with
Ypower = 1.
Channel elements which are created from the hh_channel
object calculate both X and Y by solving differential
equations of the form
dX/dt = alpha*(1-X) - beta*X
The voltage-dependent rate variables, alpha and beta, can
each assume one of the three functional forms:
1 (EXPONENTIAL): alpha(v) = A exp((v-V0)/B)
2 (SIGMOID): alpha(v) = A / (exp((v-V0)/B) + 1)
3 (LINOID): alpha(v) = A (v-V0) / (exp((v-V0)/B) - 1)
The form to be used and the constants A, B and V0 are
specified for each rate variable by setting fields in the
hh_channel element.
Author: M. Nelson, Caltech (8/88)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: hh_channel_type [in src/hh/hh_struct.h]
Size: 184 bytes
Fields: activation channel activation
Gk channel conductance
Ik channel current
Ek channel reversal potential
Gbar channel maximum conductance
X value of X gate (m)
Y value of Y gate (h)
Xpower power to raise X gate to
Ypower power to raise Y gate to
X_alpha_FORM Equation form for X gate alpha rate constant
1 = EXPONENTIAL, 2 = SIGMOID, 3 = LINOID
X_alpha_A A constant for X gate alpha rate constant
X_alpha_B B constant for X gate alpha rate constant
X_alpha_V0 V0 constant for X gate alpha rate constant
X_beta_FORM Equation form for X gate beta rate constant
1 = EXPONENTIAL, 2 = SIGMOID, 3 = LINOID
X_beta_A A constant for X gate beta rate constant
X_beta_B B constant for X gate beta rate constant
X_beta_V0 V0 constant for X gate beta rate constant
Y_alpha_FORM Equation form for Y gate alpha rate constant
1 = EXPONENTIAL, 2 = SIGMOID, 3 = LINOID
Y_alpha_A A constant for Y gate alpha rate constant
Y_alpha_B B constant for Y gate alpha rate constant
Y_alpha_V0 V0 constant for Y gate alpha rate constant
Y_beta_FORM Equation form for Y gate beta rate constant
1 = EXPONENTIAL, 2 = SIGMOID, 3 = LINOID
Y_beta_A A constant for Y gate beta rate constant
Y_beta_B B constant for Y gate beta rate constant
Y_beta_V0 V0 constant for Y gate beta rate constant
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: hh_channel [in src/hh/channel.c]
Classes: segment channel
Actions: INIT
PROCESS
RESET
CHECK
CALC_ALPHA
CALC_BETA
CALC_MINF
Messages: VOLTAGE Vm
------------------------------------------------------------------------------
Notes: The tabchannel object provides a faster and more general way
to implement this type of channel.
The CALC_ALPHA, CALC_BETA, and CALC_MINF actions are used with
calls of the form
y = {call <element> CALC_ALPHA <gate> <x-value>}
in order to access values of alpha, beta or m_inf (the steady
state activation, alpha/(alpha + beta)) for the specified gate
(X or Y) and a particular value of the independent variable.
This feature is most often used for making plots of these
quantities. Note that the activation time constant can be
calculated from tau = 1/(alpha + beta).
Example: Scripts/neurokit/prototypes/hhchan.g
See also:
tabchannel ,
vdep_channel
Object Type: hillpump
Description: A simple model for the store membrane pump (SERCA), similar
to the mmpump, but with a Hill exponent.
Author: E. De Schutter BBF-UIA 11/97
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: hillpump_type [in src/concen/conc_struct.h]
Size: 92 bytes
Fields: vmax maximum pump velocity, scaled by mebrane
surface area. i.e., max ion flux in moles/sec.
Kd disassociation constant
Hill Hill exponent
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: HillPump [in src/concen/hillpump.c]]
Classes:: gate segment
Actions: CHECK RESET PROCESS INIT
Messages: MMKD Kd (changes Kd value)
------------------------------------------------------------------------------
Notes:
The hillpump is similar to the mmpump, and is coupled to a difshell to reduce
the concentration in the shell, and to a concpool to increase the
concentration. The message "HILLPUMP vmax Kd Hill" to a difshell causes the
concentration to change as dC/dt = -vmax*(C^Hill/(C^Hill+Kd)/vol. When sent
to a concpool, it changes the concentration with the opposite sign. Note that
the maximum pump velocity vmax should have previously been multiplied by the
membrane surface area, so that it is in moles/sec.
This does not have the electrogenic effect (Ik) calculation of the mmpump. It
gets Kd from a MMKD message (or a setfield), and simply stores Kd, vmax, Hill,
letting the difshell or concpool do the calculations.
Example:
See also:
mmpump ,
difshell ,
concpool
Object Type: hsolve
Description: An object used for implementing the Hines method for the
implicit solution of dendritic trees, as well as a set of
routines that maximize speed. This allows faster, more
stable numerical integration methods to be used with GENESIS,
particularly when there are many compartments in a cell.
Author: U. S. Bhalla and E. De Schutter Caltech 91-93,
E. De Schutter BBF-UIA 94-99.
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: hsolve_type [in src/hines/hines_struct.h]
Size: 552 bytes
Fields: path wildcard list of compartments to be
integrated; specifies all compartments
belonging to cell which hsolve element will
deal with. The default is
./##[][TYPE=compartment]
chanmode flag that controls channel computations and
chip-array use.
0 = default. It is the most general, uses least memory
and is slowest (no chip-array). It takes over the
actions of compartments only, computing all other
object types as before. As a consequence, all
computed fields of the original elements are updated,
and all user-setable fields may be set, just as before
the element was taken over by the hsolve element.
This means that you can add and delete outgoing
messages to compartments or other elements whenever
you like and easily change parameters during the
course of the simulation, making this the easiest mode
to use. It is also the most compatible mode of
operation, and is guaranteed to work with any future
new object type. One significant limitation is that
you cannot add or delete AXIAL, RAXIAL or CHANNEL
messages, once the hsolve element has been created.
In order to calculate the compartment Im field,
the compute_Im flag must be set.
1 = like chanmode 0, but optimizes calculations for
tabchannel equations. This will be faster than
chanmode 0 for models containing tabchannels and
tab2Dchannels.
2 = assumes integer exponents (maximum = 6) for
tabchannel and tab2Dchannel gate variables. Chanmodes
2-5 are the fastest because of the large 'chip-array'.
Under these moses, you can no longer assume that all
the fields of the elements that are taken over by
hsolve will be updated. Incoming and outgoing
messages to and from the disabled elements will work
properly, provided that they were added prior to
setting up the hsolve element. However, the Vm fields
of all compartments are automatically updated under
chanmode 2, whether or not there were pre-existing
messages to output Vm. Note also that several fields
(Gk, Ik, Ek, and Im) are not available for output in
chanmodes 2 and 3, so you have to use chanmode 4 or 5
with findsolvefield if you want to output these fields.
3 = as chanmode 2, but Vm fields of compartments are
not automatically updated. This mode is faster than
chanmode 2, at the expense of somewhat greater memory
usage. All disabled elements (including compartments)
that had outgoing messages to non-hsolved objects
during the SETUP call are updated at a rate determined
by outclock. Thus SAVE and PLOT messages will work
properly, except with the fields Gk, Ik, Ek, and Im.
4 = as chanmode 3, but more variables (e.g. Gk, Ik,
Ek, Im and leak) are stored by hsolve so that they can
be accessed by SAVE or PLOT messages (see
findsolvefield documentation for more details). The
added field, leak, is available for each compartment
to give the current flowing through the membrane
resistance Rm. Im is calculated directly as the sum
of the channel currents and the leakage current.
5 = as chanmode 4, but normalizes the currents and
conductances stored in the hsolve givals array (for
display purposes only).
computeIm flag to determine whether the compartment Im field
is calculated in chanmodes 0 and 1. If set, Im is
approximated by the sum of axial currents and injected
current, as done for non-hsolved compartments and
symcompartments.
0 = the default, does not calculate Im.
1 = calculates Im, with a decrease in speed.
comptmode flag that selects option for compartment computations
0 = uses least memory, and is slightly slower. However
the amount of time spent in this part is usually less
than 10% of the total, so this should not matter.
1 = the default, uses a lot of memory and is twice as
fast for the actual Hines matrix calculation. This
may be only a 5% difference. comptmode 1 is
required for chanmodes 2-5.
calcmode flag affecting operations for chanmodes 2-5.
0 = no interpolation will be performed in lookup
tables. This mode is for backward compatibility with
older versions of hsolve (prior to GENESIS 2.1) which
did not use interpolation.
1 = default mode with linear interpolation of values
in lookup tables.
storemode flag, only valid for chanmodes 4 and 5, to allow the
output of total currents and conductances. For each
type of voltage gated channel in the model, the total
currents or conductances are the sum of the
corresponding Ik or Gk fields for all compartments
where the channel is present. This assumes that these
channels have the same name in each compartment.
These are stored in an array called itotal. When the
hsolve element is set up, a message will be output
giving a list of channel names and corresponding
itotal indices, if the 'silent' command has previously
been given with a negative argument.
0 = no sums are stored.
1 = total currents are stored.
2 = total conductances are stored.
no_elminfo = 0/1; flag that controls whether the HPUT and HSET
actions will work. Is relevant only for chanmodes
2-5. Default is zero (HPUT and HSET work).
Saves memory if non-zero value is used (HPUT, HSET
do not work; HRESTORE and HSAVE do).
outclock number [0-99] of the clock used for all element
updates if chanmode = 3, 4, or 5, will affect SAVE and
PLOT messages. The element update routines are not
very efficient, so setting them to a slower clock will
speed up things. Note however that any object that is
not computed by the hines solver and that depends on a
message from a hsolve-computed object will be affected.
The other fields displayed with the showobject command are NOT
to be set by the user.
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: HinesSolver [in src/hines/hsolve.c]
Classes: hsolver
Actions: RESET does the standard reset functions, but also for
chanmodes 2-5, it will update all parameters in
the chip-array (equivalent to a HRESTORE call) and
recompute rate factor tables if clocks were changed.
DELETE standard actions
PROCESS standard actions
SETUP setup all internal tables. Must be called before the
hsolve element is used. User accessible fields
(path, chanmode, etc.) should have been set. Model
changes after the SETUP call may have no effect on
the computations.
DUPLICATE does an efficient duplication of an hsolve element.
Use this in a network simulation for identical
copies of a neuron. Only the tables containing
changing parameters (Vm, etc.) will be duplicated.
Syntax: call hsolve1 DUPLICATE hsolve2 duplic_path
HPUT updates chip-array. Fields from a single element are
put into the chip-array (chanmodes 2 or 3). Do this
call after a setfield command on the element.
Syntax: call hsolve HPUT element_path
HGET updates hsolve-computed element. Computed values are
put from the chip-array into a single element
(chanmodes 2-5). Do this call before a getfield on
the element. Syntax: call hsolve HGET element_path
HRESTORE the complete chip-array is updated. Fields from all
hsolve-computed elements are put into chip-array
(chanmodes 2-5). Do this call after a restore
command or after multiple setfield commands.
Syntax: call hsolve HRESTORE
HSAVE all hsolve-computed elements are updated. Computed
values are put from the chip array into all elements
(chanmodes 2-5). Do this call before a save
command or before multiple getfield commands.
Syntax: call hsolve HSAVE
Messages: None.
Example:
// Do all the preparatory grunge work
.
.
// create the cell as an hsolve element
readcell test.p /test -hsolve
// set the chanmode, comptmode and calcmode (if other than defaults)
setfield /test chanmode 2
// set up the arrays and tables for the solver
call /test/solve SETUP
// use the Crank-Nicholson method for the hsolve element
setmethod 11
// It is essential to call reset (or reschedule) after setting
// up an hsolver, so that the process list gets updated.
reset
------------------------------------------------------------------------------
Notes:
The hsolve element completely takes over the calculations for compartment and
symcompartment elements and certain other elements specified as part of the
cell. Each hsolve element should only solve one cell. The timestep for the
integration is determined by the clock assigned to the hsolve element, and the
clocks for these elements which are taken over are ignored.
When using the Hines solver with a neuron, it is best to think of the entire
neuron as a single object since the individual compartments within the cell
are no longer responsible for their own computations. This loss of object
orientedness is mitigated to some degree by the ability of the solver to
transparently interact with elements utilizing other integration schemes.
There are 2 basic modes for hsolve operation: without chip-array (chanmode 0
or 1), or with chip-array (chanmodes 2-5). Without chip-array is the most
compatible mode, but is the slowest. With the chip-array, hsolve is much
faster because the original elements are no longer used, instead all
simulation parameters are stored in a huge array (this improves memory access
times). Unfortunately you can no longer expect that it will update the fields
in computed objects (like Vm in a compartment or Ca in Ca_concen) so that
graphic or file output might not work. Vice versa, if you change a field
(like inject in compartment) it might not affect the simulation. However,
there are methods available to get values in and out of the chip-array, which
involve special settings and/or the use of the HPUT, HGET, HSAVE and HRESTORE
actions listed above. This is ilustrated in another example below. The
documentation for findsolvefield describes another method, introduced in
GENESIS 2.1, that also allows access to these values.
The example above illustrates the process of setting up the hsolve element.
First, one should create the cell as an hsolve element at the root of the cell
element tree. This may be done in one step by using the "-hsolve" option with
readcell. Note that, starting with GENESIS version 2.2, it is necessary to
provide the full path to the cell when using readcell to directly create an
hsolve. (e.g. you can't use "readcell test.p test -hsolve", even if "/" is
the current working element.)
If readcell is not used, then the hsolved cell should be created with
statements like
create hsolve /test
create compartment /test/soma
create tabchannel /test/soma/Na_channel
...
It is required that only compartments (or symcompartments) be children of the
cell, and that channel, concentration, etc. elements should be children or
grandchildren of the compartment to which they are attached.
Next, set any fields of the hsolve which are needed to specify non-default
values of chanmode, comptmode, calcmode, storemode, etc. Then, one needs to
call the SETUP action in order to tell the hsolve element to create all the
solution arrays and tables. Finally, chose either method 10 (backwards Euler)
or 11 (Crank-Nicholson) as the method to be used. All elements that lie
outside this tree will continue to be treated by the previous explicit method
(typically exponential Euler). The Scripts/examples/hines directory contains
an example that which demonstrates both chanmodes 0 and 2.
Although it is not presently necessary to create the hsolve element as the
root of the element tree, future versions of hsolve may require this. The
older method of creating the hsolve is to create the cell as a neutral
element, create the hsolve element as a child element, and then set the hsolve
path field to indicate which elements will be taken over. Typically, a
wildcard path is used to refer to all compartment elements in the simulation.
This includes all hsolvable sublelements of these compartments. For example,
// readcell will place the compartments below the neutral '/test'
readcell test.p /test
// create the hines solver element below the cell '/test'
create hsolve /test/solve
// Specify the path for the solver
setfield /test/solve path /test/##[][TYPE=compartment]
RESTRICTIONS
It is important to be aware of some of the restrictions imposed by the use
of hsolve:
Only the objects compartment, symcompartment, tabchannel, tab2Dchannel,
tabcurrent, spikegen, Ca_concen, concpool, nernst, Mg_block, ghk, taupump,
mmpump, hillpump, difshell, fixbuffer, difbuffer, dif2buffer, fura2, synchan,
and the oldconn library channels channelC2 and channelC3 are handled by
hsolve. If your simulation uses these listed objects, the use of hsolve will
increase speed significantly. Note that as of GENESIS version 2.2,
symcompartment objects are handled by hsolve.
An important restriction introduced in GENESIS version 2.1 is that, for
chanmodes 2-5, the element tree of your cell (or other element tree to be
taken over by hsolve) must not contain any non-hsolvable elements other than
neutral elements. For existing simulations which violate this restriction, it
will be easiest to switch to chanmode 0 or 1.
It is not guaranteed that messages from unlisted objects to listed objects
will work, though solve should alert you about any such incompatibilities.
Most incoming messages will work if you use chanmodes 2-5, however you will
receive a warning if the source of the message is not hsolved. This is to let
you know that the source element is being solved by a less accurate explicit
method. Messages from listed to unlisted objects will only work for certain
chanmode settings.
hsolve does not keep track of changes made to the model after the hsolve SETUP
command (particularly the following commands: create, copy, delete, addmsg,
deletemsg). In chanmode 0 or 1 this only affects the listed objects and
messages between them; in chanmodes 2-5 this affects the listed objects and
ALL messages going in or out from them. The hsolver should be used in these
modes only for finished models (you can use it for parameter searches); do not
use it if you are still constructing and testing a model.
hsolve may miscalculate if you change clocks used by tabchannels,
tab2Dchannels, synchans, or channelC2/C3 objects without doing a reset (only
in chanmodes 2-5).
The Hines solver utilizes a considerable amount of memory. Memory use
increases as the result of comptmode + chanmode - no_elminfo flags. In
particular, going from chanmode 0 or 1 to chanmode 2, 3, or 4 causes a big
jump in memory usage. Approximately 100 bytes are required per compartment if
the speed-optimized version of the hsolve element is used. Most of this
storage is for tables describing the sequence of calculations. These tables
can, however, be shared between cells which are identical in topology and
differ only in parameter values.
FURTHER EXAMPLES
* Copying cells with the hsolve element
When a cell using the hsolve element is copied, the pointers in the
duplicated hsolve element are unchanged. In other words, they refer back to
the original cell. One could simply change the path to refer to the current
cell and call SETUP again, but that would unnecessarily duplicate a lot of
tables. The efficient option would be to use the original tables where they
are identical, and construct new ones where they refer to the current cell.
This is done using the DUPLICATE sction, which takes the name of the new
hsolve element and a wildcard path duplic_path as arguments. duplic_path
points to all compartments that should be taken over by the new solver.
For example,
// Copy the original cell to /test2
copy /test /test2
// create the hines solver element below the cell '/test'
create hsolve /test/solve
// Specify the path for the solver and the chanmode
setfield /test/solve path /test/##[][TYPE=compartment] chanmode 4
call /test/solve SETUP
// Duplicate the hsolver
call /test/solve DUPLICATE /test2/solve /test2/##[][TYPE=compartment]
reset
There are several commands, including createmap and cellsheet, that copy
cells. The DUPLICATE command should be issued for the hsolvers on each copy.
When using chanmodes 3 or higher, findsolvefield must be used with messages in
order to access fields of duplicated hsolves, as shown in the documentation
for findsolvefield.
* Deleting hsolve elements
When an hsolve element is set up it removes the relevant channels and
compartments from the list of elements to be processed, by setting a bit
(0x100) on the flag field of those elements. These elements are re-enabled
and the bit set back to 0 when the hsolve element is deleted.
WARNING: in the present implementation, the hsolve element does not check
whether it has had duplicates made using the DUPLICATE command. This makes it
possible to delete the tables for all of the copies by deleting any one of
them, resulting in segmentation violations and similar amusements. In other
words, do not delete hsolves on duplicated cells.
* Accessing data fields in chanmodes 2-5.
A script similar to this example might be used for running a long simulation
as a background job, using no graphics. The HPUT and HSAVE actions are used
in chanmode 2 or 3 to allow the simulation results and the final state of
the simulation to be saved to disk. A disk_out element is used to output the
Vm of a soma compartment in a compressed binary format. However, it is
equally possible to output Vm from every compartment, or from an array of
cells. Later, a script using a disk_in element can display the results using
messages from the disk_in to an xgraph or xview. The save command is used
here to save field values of all elements except nernst elements and the
hsolve element. This will allow the simulation to be resumed from its final
state by using the restore command.
For more details, see Scripts/examples/XODUS/fileview and the documentation
for disk_out, disk_in, save, and restore.
/* load scripts and global variables */
include defaults
include other_stuff
pushe /library
make_my_stuff
pope
/* make the model */
readcell my_cell {my_cellpath} -hsolve
/* set the clocks */
setclock 0 1e-5 /* integration */
setclock 1 1e-4 /* output */
/* create the output or graphics elements */
/* note that if you want to output Vm only, but from multiple
** compartments, you should use chanmode == 2; if you want to
** output other fields or Vm from only one compartment,
** use chanmode == 3 */
create disk_out /output/disk
useclock /output/disk 1
addmsg {my_cellpath}/soma /output/disk Vm
addmsg ...
/* create any other elements */
....
/* setup the hines solver */
setfield {my_cellpath} \
comptmode 1 \
chanmode 3 \
outclock 1
call {my_cellpath} SETUP
setmethod 11 // Crank-Nicholson integration method
/* initialize output */
setfield /output/plot_out filename {filename} initialize 1
setfield /output/plot_out filename {filename} append 1 leave_open 1
reset
step 0.10 -t
/* do a current injection */
setfield {my_cellpath}/soma inject 1.0e-9 /* in Amps */
/* update chip array */
call {my_cellpath} HPUT {my_cellpath}/soma
step 2.00 -t
/* save the integration values to disk */
call {my_cellpath} HSAVE
save {my_cellpath}/##[][TYPE!=nernst][TYPE!=hsolve] {savename}
quit
---------------------------------------------------------------------------
DETAILED DESCRIPTION
The Hines library provides elements and functions for the efficient implicit
solution of the systems of differential equations arising in single-neuron
models. The sparse matrix arising from the the branched structure of neurons
is ordered by the method described by Michael Hines, which permits it to be
solved in order N operations using Gaussian elimination without pivoting.
The nonlinear equations resulting from the Hodgkin-Huxley description of ion
channels are treated as conditionally linear, and also solved in an
efficient, second-order manner. Compatibility with other integration
schemes is maintained so that mixed integration schemes are feasible.
The element sets up a data structure whereby the only change needed for
other identical cells is to reassign pointers to the compartment and channel
elements. This avoids having to reallocate and rederive the solving
scheme. Solutions are done using gaussian forward and backward elimination
without pivoting. The numbering and evaluation sequence ensures that no new
off-diagonal terms are formed which might mess up the sparse matrix
representation. The sparse matrix is represented by a single 'values' array
indexed using the ri and cip arrays. The actual solution system is stored
as a linear sequence of operations on the 'values' array, in an attempt to
speed things up a bit.
The implicit method leads to numerically stable solutions for all time
steps. Numerical accuracy, however, imposes limits on the integration time
step which must be empirically evaluated for each simulation. Typical
values are 100 microsecond time steps for purely passive membranes and 20
microsecond time steps for membranes with active channels. This confers a
considerable speed up in detailed neuronal simulations where the presence of
electrotonically small compartments (such as dendritic spines) leads to
systems of equations which are numerically very stiff. In order to obtain
similar accuracy using explicit integration methods, time steps in the
nanosecond range may be required.
In addition to the substantial speed advantage gained from the use of an
implicit solution, the coding of the Hines solver element has been done with
a view to computational efficiency. This results in a speed up of around 50%
compared to the same model with the same time step, using the conventional
explicit Euler integration scheme.
Code changes needed for the Hines library
This section is probably of interest only to individuals who have developed
their own code libraries and who are deeply entangled in GENESIS coding
issues. For most users the changes are transparent, once the .simrc and
schedule.g file have been updated to reflect the addition of a new library.
The incorporation of a completely new integration scheme to the simulator can
be expected to have numerous repercussions. Fortunately, the changes needed for
the Hines library turned out to be relatively painless. No changes were needed
for the code of any of the existing elements. There is a slight rearrangement
of the order of fields in the various channel objects, and a new globally
#define'd type called CHAN_TYPE has been created so that all these channel
objects have the following common fields at identical memory offsets: Ik, Gk
and Ek (See src/sim/struct_defs.h). All channels whose structures obey this
convention can be used in cells utilizing the hsolve element. A very small
number of channel objects (such as channelC) do not share these fields and
therefore cannot be part of cell models which use the hines solver.
A new flag (0x100) has been employed for the Hines solver, which causes the
removal of compartment and tabchannel elements from the action list (the list
of elements whose action functions are to be called according to the clocks).
This flag is similar to the disable option except that it leaves the children
of these elements intact.
In the interests of speed (which is, after all, what the Hines method is all
about) I have 'unrolled' the sparse matrix solution into a single giant
function array. This is done at setup time, so the actual solution does not
involve any conditionals and minimises array lookups. This is moderately
expensive in terms of memory. The size of the function array allocated is
S = FA * sizeof (int) ; FA = 10 + 1.5 * M^2 / N
where S is the size of the array, FA is the number of functions allocated, M
is the number of non-zero coefficients in the solution matrix and N is the
number of compartments. M depends strongly on the branching pattern of the
cell. FA is an approximation to, and is greater than F, which is the actual
number of locations needed in the function table. For example, in a mitral
cell model, which has limited branching:
N = 286 ; M = 856 ; FA = 3853 ; S = 15412 ; F = 3710
In a granule cell model with numerous dendritic spines:
N = 944 ; M = 2830 ; FA = 12736 ; S = 50944 ; F = 12264
A reasonable approximation is that each compartment requires about 54 bytes in
the function table, which is not too bad.
References: Hines, M. (1984) Efficient computation of branched nerve
equations. Int. J. Bio-Med. Comp. 15: 69-76
Mascagni, M.V. (1989) Methods in Neuronal Modeling Ed: Koch
and Segev. Chapter 13. 439-484
See also:
setmethod ,
findsolvefield
Object Type: interspike
Description: Generates an interspike interval histogram.
Author: E. De Schutter Caltech 8/91
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: interspike_type [in src/device/dev_struct.h]
Size: 116 bytes
Fields: output gives the most recent interspike interval
threshold voltage threshold for determining when a spike
occurs
binwidth time interval between bins
num_bins number of table entries (bins)
trigger_mode 0 (free run) or 1 (triggered)
reset_mode if 1 then bins will be emptied upon RESET
table table with the number of spikes for that bin
prev_time time of last event (not set by user)
triggered set to 1 on RESET if trigger_mode = 0 (free run),
else is 0 until a TRIGGER message is received
(not set by user)
spiking flag indicating spike in progress
(not set by user)
allocated flag indicating table has been allocated
(not set by user)
------------------------------------------------------------------------------
Function: InterSpikeInterval [in src/device/interspike.c]
Classes: device
Actions: CHECK PROCESS RESET
Messages: SPIKE time (Time of occurrence of a spike.)
TRIGGER state (If state is > 0, the previous spike time is
set to the current time, and binning starts
at first bin.)
INPUT voltage (The Vm value sent to be compared with
threshold.)
------------------------------------------------------------------------------
Notes: interspike produces an interspike interval histogram (ISI).
Incoming data is used to fill an internal array (called table)
that contains num_bins entries from which the histogram values
can be read. These objects can collect data on-line during a
simulation, but do not produce much useful information during
the simulation (the output field of interspike can be used to
look at the most recent interspike interval). At the end of
the run, the histogram results can be retrieved with commands
such as "getfield /interspike table[{i}]", with i taking on
values from 0 through nbins-1. The example script reads the
table entries and and plots a histogram after the run phase of
the simulation.
The last bin also contains the number of intervals with
values larger than that of the last bin.
There are two modes that may be used, as determined by the
"trigger_mode" field. If the field is 0, the system is
free-running and begins accumulating data right away.
Otherwise, the system waits until it receives a trigger to
start binning incoming events. The trigger should be a single
time step event like the state field of a 'spikegen' or
'randomspike' object, sent with a TRIGGER message.
Events can be defined in one of two ways. They can be
determined from the time that the value of an INPUT message
first exceeds threshold. The voltage must then fall below
threshold before another spike event can be recorded.)
Alternatively, a SPIKE message can be sent giving the time
that a spike occurs. Note that this is NOT like the SPIKE
message of a synchan, which does not require an argument.
Example: See Scripts/examples/spike.
See also:
peristim
Object Type: leakage
Description: Provides a constant conductance in series with a battery.
This is often used to implement a passive "leakage" channel
having a fixed conductance.
Author: M. Wilson, Caltech (6/88)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: leakage_type [in src/segment/seg_struct.h]
Size: 96 bytes
Fields: Gk the Gk to be sent in a CHANNEL message
Ek the leakage battery
activation the leakage conductance used to calculate Ik
Ik channel current
inject not used
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Leakage [in src/segment/leakage.c]
Classes: segment
channel
Actions: PROCESS Calculates Ik
RESET Sets Ik = 0
CHECK Checks to see if an incoming VOLTAGE
message has been established.
Messages: VOLTAGE Vm
------------------------------------------------------------------------------
Notes: This object is intended to be used as a flexible leakage
term in conjunction with the membrane model. As with any
other type of channel, it normally is used to send its
conductance (Gk) and reversal potential (the battery in series
with Gk) to the parent compartment using a CHANNEL message.
In this case, Gk has a constant value, to be set by the user.
Although this feature is not often used, a leakage element
also calculates the current, Ik = (Ek - Vm)*activation. Here,
Vm is the compartment membrane potential received with a
VOLTAGE message, and "activation" is a conductance. This
would normally be set by the user to the same value as Gk, but
this is not done automatically. As Gk does not depend on Vm,
a VOLTAGE message is not strictly required if Ik not is
needed. However, the check command will issue a warning if
one has not been established.
Example:
create leakage K_leak
setfield K_leak Ek {EK} Gk {Gleak}
addmsg K_leak .. CHANNEL Gk Ek
addmsg .. K_leak VOLTAGE Vm
See also:
Object Type: metadata
Description:
File formats such as netcdf allow the inclusion of descriptive content in
addition to actual data. This is extremely useful from the perspective of
having important documentation, such as time of creation, author, purpose
or critical information about individual variables or the file as a whole,
alongside the actual data in the same file.
The genesis metadata object allows the user to manipulate this descriptive
data that is in an existing file or write new metadata content into it. As
already mentioned, descriptive data can describe individual variables in
the file (local metadata) or the file as a whole (global metadata). This
distinction is replicated well, through the hierarchical element structure
in genesis. So a metadata object will be identified as a local attribute if
the immediate parent is a 'variable' object and global if the 'diskio' object
is the immediate parent.
FMT1 files do not support the notion of metadata and hence arbitrary
creation of metadata objects in this case will not be allowed. For the sake
of consistency, however, when SAVE messages are sent to the diskio object,
automatically created metadata elements (auto3-DPosSAVE_diskio[]) store
relevant information for inspection. The fields are made readonly in the
case of FMT1.
Author: V.Jagadish (9/96)
------------------------------------------------------------------------------
ELEMENT PARAMETERS:
DataStructure: Gen_Metadata_Type [in src/diskio/diskio_struct.h]
Size: 92 bytes
Fields: datatype The type of the value(s) held in the metadata
- The list of valid types are given in the
notes section of this document.
- Defaults to 'char8' (8-bit char)
- readonly for FMT1 files.
size The maximum number of descriptive values the
object can hold.
- Like variables, metadata objects can hold
an array of descriptive values the size of
which is limited by the value of this field.
- If the datatype is 'char8' (default) the
user could provide a string as an argument
to the value field without
specifying a size or index, and the size
(which is the number of chars in the string
including the '/0' character) is
internally calculated and set in this field.
- The default value is 1.
- readonly for FMT1 files.
value The value(s) held by the metadata.
- Since metadata can hold an array of
values or a single one, an index (with
the genesis style indexing syntax) needs
to be specified while setting or showing
this field. The index defaults to 0 if
not specified, the exception to it being
the case that the datatype is 'char8'.
- Not specifying the index for a 'char8' type
metadata will translate to mean the entire
string and individual indices will mean the
character in that position.
- As in the case of the variable object,
multiple argument values can be specified
for this field (see examples) and the values
will be accessed starting with index 0.
- The default value is 0 for numerical
datatypes and ''(blank) for character types
- readonly for FMT1 files.
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Gen_Metadata [in src/diskio/gen_metadata.c]
Classes: output
Actions: CREATE PROCESS RESET SET SHOW ADDMSGIN
FLUSH:
UPDATE: the object commits the underlying metadata values
to the file on disk.
DELETE: commits any changes to disk if necessary and then
deletes the object but does not remove the
underlying attribute on file.
------------------------------------------------------------------------------
Notes:
The default metadata is an 8-bit single blank character (char8)
The datatype field stores the type of the variable as a string. The types
are chosen to be as generic as possible. They are not based on the usual
'C' data types but rather on the user's perspective.
Table 1.2 shows the valid datatype names and what they mean to the user.
Please note that not all these types are supported by all file formats.
An error to that effect will be printed if a metadata obeject of an
unsupported type is attempted to be created.
As opposed to variables, the size and datatype fields of metadata objects
can be reset within netcdf.
A smaller size setting than the original truncates values and a larger size
does not disturb the old values but adds the appropriate number of default
values (0 or '').
Changing the datatype for a metadata object defaults all the values
(as specified by the size field) to the new type. The old values will be lost.
Table 1.2 - Valid datatypes
Name Description
____ | ___________
|
|
uint8 | 8-bit unsigned int
|
int8 | 8-bit signed int
|
uint16 | 16-bit unsigned int
|
int16 | 16-bit signed int
|
uint32 | 32-bit unsigned int
|
int32 | 32-bit signed int
|
uint64 | 64-bit unsigned int
|
int64 | 64-bit signed int
|
float32 | 32-bit float
|
float64 | 64-bit float
|
uchar8 | 8-bit unsigned char
|
char8 | 8-bit signed char
|
char16 | 16-bit (unicode) char
|
string | string type (i.e not an array of chars)
|
________________+______________________________________________________
Examples:
create diskio /dout -filename "testfile.nc" -accessmode w
create metadata /dout/author -value "Venkat Jagadish"
showfield /dout/author value // This will print out the entire string
showfield /dout/author value[2] // This will print the 3rd char - 'n'
create variable /dout/Vmtrace -datatype float32
create metadata /dout/Vmtrace/starttimes -datatype float32 -size 3 \
-value "5 45 65"
create metadata /dout/Vmtrace/stoptimes -datatype float32 -size 3 \
-value "20 60 80"
setfield /dout/Vmtrace/starttimes value[1] 55
setfield /dout/Vmtrace/stoptimes value[1] 70
setfield /dout/Vmtrace/starttimes datatype float64
showfield /dout/Vmtrace/starttimes value[1] // Setting datatype resets
// values to default - 0
// (in this case)
_______________________________________________________________________
See also:
diskio ,
variable
Object Type: mmpump
Description: Implementation of a simple pump with Michaelis Menten kinetics,
to be coupled to a difshell.
Author: E. De Schutter BBF-UIA 9/94 - 3/99
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: mmpump_type [in src/concen/conc_struct.h]
Size: 108 bytes
Fields: Ik computed electrogenic effect (if val!=0)
vmax maximum pump velocity, scaled by mebrane
surface area. i.e., max ion flux in moles/sec.
val charge of ion
Kd half-maximal activating concentration in mM
mmconst mmconst=vmax*val*FARADAY (calculated on reset)
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: MMPump [in src/concen/mmpump.c]
Classes: gate segment
Actions: CHECK RESET PROCESS INIT
Messages: CONCEN C (use for electrogenic effect only)
MMKD Kd (changes Kd value)
------------------------------------------------------------------------------
Notes:
The mmpump and other ionic pumps provide various mechanisms to remove ions
from a concentration shell (difshell). The mmpump is a simple model
for the plasma membrane pump (PMCA) with Michaelis Menten kinetics.
For a general description of buffered calcium diffusion and ionic pumps, see:
De Schutter E., and Smolen P., "Calcium dynamics in large neuronal models", in
Methods in neuronal modeling: From ions to networks (2nd edition), C. Koch and
I. Segev editors, pp. 211-250 (1998). Sec. 6.3.2 and Eq. 6.10 describe the
Michaelis Menten pump, which may be used to model a Ca-ATPase pump. This is
also discussed in A. Zador, C. koch, and T. H. Brown, Proc. Natl. Acad. Sci.
(USA) 87: 6718-6722 (1990).
Note that this object does not compute anything by itself, unless the
electrogenic action is simulated by specifying a non-zero value of val. When
coupled to a difshell with a MMPUMP message that sends the vmax and Kd field
values, the difshell computes its change in ion concentration from dC/dt =
-vmax*(C/(Kd + C))/vol. This corresponds to De Schutter and Smolen Eq. 6.10,
if the maximum pump velocity vmax has previously been multiplied by the
membrane surface area, so that it is in moles/sec.
The current outflow across the membrane due to the electrogenic effect of the
pump can also be simulated by using a CONCEN message into the pump, and using
a non-zero value for the valence (e.g. val = 2, for Ca++ ions). In this case,
the mmpump calculates Ik = mmconst * C/(Kd + C), where the constant mmconst is
set to vmax * val * FARADAY on reset. Note that, in contrast to the GENESIS
channel objects, the Ik calculated by the mmpump has a positive sign for an
outward current, rather than obeying the usual GENESIS convention of "inward
positive".
Example: addmsg mmpump0 shell0 MMPUMP vmax Kd
See also:
difshell ,
taupump , Scripts/examples/spinedemo
Object Type: nernst
Description: Calculates the Nernst potential for the given
ionic concentrations and temperature.
Author: M. Wilson, Caltech (3/89)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: nernst_type [in src/device/dev_struct.h]
Size: 96 bytes
Fields: E equilibrium (Nernst) potential
T temperature in degrees Celsius
valency ionic valency z
scale voltage scale factor
Cin internal ionic concentration
Cout external ionic concentration
constant scale*(R/zF)*(T + 273.15)
This is set by the element,
and should not be set by the user.
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Nernst [in src/device/nernst.c]
Classes: device
channel
Actions: PROCESS sets the fields from incoming messages
and calculates constant and E.
RESET similar to a single PROCESS step.
CHECK checks for valid messages and parameters.
Messages: CIN Cin sets the Cin field.
COUT Cout sets the Cout field.
TEMP T sets the T field, and calculates constant.
------------------------------------------------------------------------------
Notes: A nernst element calculates E = constant * ln(Cout/Cin)
= scale*(R/zF)*(T + 273.15)*ln(Cout/Cin), where R is the
universal gas constant (1.9872 cal/mol deg) and F is Faraday's
constant (23061 cal/volt mol). Note that the temperature in
degrees Celsius is internally converted to degrees Kelvin. A
scale factor of 1 gives E in volts, and a scale factor of
1e3 gives E in millivolts.
A nernst element is usually used with a channel and a
Ca_concen element to calculate the channel equilibrium
potential (Ek) from the internal ionic concentration in a
shell near the compartment surface. The equilibrium potential
is sent from the nernst element to the channel with an EK
message, and the nernst element receives the concentration
from the Ca_concen element with a Cin message. The Ca_concen
element calculates this concentration from ionic currents
delivered with an I_k message.
It is also possible to perform a "one-time" calculation of E
with fixed values of the ionic concentrations by setting these
fields instead of setting up messages, and performing a reset.
If this is done, the nernst element should be disabled to
avoid wasting time performing the PROCESS action.
Example:
// assume that a tabchannel `Ca' has been set up
create Ca_concen conc
setfield conc \
B {5.2e-6/(area*shell_thick)} \
Ca_base 4.0e-5 \
tau 1e-4 \
thick {shell_thick}
create nernst nernst
setfield nernst \
Cout 4.0 \ // external Ca concentration of 4 mM.
T 21 \ // near room temperature
valency 2 \ // Ca++
scale 1 // E in volts
addmsg Ca conc I_Ca Ik
addmsg conc nernst CIN Ca
addmsg nernst Ca EK E
function reset_nernst // Insure that resets are done in proper order
call Ca RESET
call conc RESET // Ca_concen must be reset before nernst
reset // reset everything
end
See also:
Ca_concen
Object Type: neutral
Description: empty object used for grouping
Author: Caltech
ELEMENT PARAMETERS
DataStructure: element_type [in src/sim/sim_struct.h]
Size: 68 bytes
Fields: [none]
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: NULL [i.e., none]
Classes: element
Actions: [none]
Messages: [none]
------------------------------------------------------------------------------
Notes: A set of default element types is distributed with GENESIS.
One of the simplest is the "neutral" object which can be
used to create an empty element used for grouping, much like
a directory in the UNIX file system. It is often used to
represent a cell, containing subelements for compartments,
channels, etc. Although it has no other fields, it has the
usual setable [x,y,z] coordinate fields possesed by other
objects. This allows it to be given a position in a network.
The addfield, addaction, and addmsgdef commands can be used
to give a neutral element new fields, actions, and messages,
allowing it to be used as customizable element, or the basis
of an extended object
Example:
See also:
Object Type: paramtableBF
Description: This object implements a brute-force search as part of a
parameter search process, and also stores the parameter
tables and various bookkeeping information relating to the
parameter search process. It is mainly for use in
systematically mapping out the parameter space of a model.
Author: Mike Vanier, Caltech
-------------------------------------------------------------------------
ELEMENT PARAMETERS
Data structure: paramtableBF_type [in src/param/param_struct.h]
Size: 168 bytes (more when tables are loaded)
Fields:
iteration_number iteration number
num_params total number of parameters
num_params_to_search number of parameters to search over
search array of flags:
0 = don't search this parameter,
1 = do search this parameter
type type of parameter:
0 = additive,
1 = multiplicative
range of parameter values
min of parameter values
max of parameter values
label label of parameter,
for documentation purposes only
current array of parameter values
to be simulated next
current_match match value of current parameter set
being simulated
best array of parameter values
giving best match so far
best_match best match value
new_best_match flag: 1 if last match was the best so far
done flag: 1 when the simulation is finished
filename where parameter information is
stored/saved as a binary file
alloced flag: 1 means tables are allocated
orig array of original parameter values
search_divisions number of points on the range
to test
search_rangemod fraction of the full range to
search over
search_count where we are in the search for
each param
-------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: ParamtableBF [in src/param/paramtableBF.c]
Classes: param
Actions: Note: required arguments to actions are in <angle brackets>;
optional arguments are in [square brackets].
CREATE Creates the object (not invoked directly).
TABCREATE <num_params>
Initializes the object for a given number of
parameters.
DELETE Deletes all allocated memory.
TABDELETE Same as DELETE.
INITSEARCH Initializes the search process.
Usage: ParamtableBF_INITSEARCH \
<param-number1> <npts1> <scale1> ... \
<param-numbern> <nptsn> <scalen>
This function expects its arguments to be in the
form of (<param_number> <npts> <scale>) triplets,
where <param_number> is the index of the parameter
to be varied, <npts> is the number of
equally-spaced points along the parameter axis to
test, and <scale> is the proportion of the total
range to use; 1.0 means use the entire range. Note
that the range is relative to a center point which
is where the parameter search starts from.
EVALUATE <match>
Copies the match value into the current_match field.
If this match is the best match so far, this action
copies the current parameter set into the best
parameter set and the current_match field into the
best_match field.
UPDATE_PARAMS
Chooses the next set of parameters to simulate.
This object systematically works its way through
parameter space, simulating all points on a
multidimensional grid whose features are specified
in the INITSEARCH action.
SAVE [filename]
Saves the object as a binary file. If no
argument given, use the "filename" field
of the element.
SAVEBEST <filename>
Saves the best parameter set to an ascii file.
RESTORE [filename]
Restores the object from a binary file. If no
argument given, use the "filename" field of the
element.
RESTOREBEST Restores the best parameter table from a text file.
DISPLAY Displays the best parameter set obtained so
far on stdout.
CHECK Runs a series of self-check diagnostics on this
object.
Messages: none
-------------------------------------------------------------------------
Notes: This object stores parameter tables and calculates new tables
to be simulated in a parameter search process using a
brute-force algorithm. The algorithm divides the parameter
space into a multidimensional grid where all points are
equidistant to their neighbors in each dimension. Then it
systematically walks through the space, calculating and
outputting a match value for each point.
This algorithm is effectively useless for searching parameter
space per se because of the combinatorial explosion that occurs
when you have more than a few parameters (e.g. 3 or 4).
However, it can be used effectively to map out parameter space
very coarsely for a small number of parameters. For instance,
you could keep all but two parameters fixed and map out the
two-dimensional parameter space that consists of varying values
for each of the two parameters. This may give some insight
into various aspects of a model. Alternatively, you could map
out all the parameters at a very coarse scale, which can be
used (for instance) to give a reasonable starting point for
other algorithms. In practice, this is still not feasible for
more than 5 or 6 parameters.
Example: See Scripts/param/BF for demo scripts.
See also: Parameter Search (
Param ),
Paramtable ,
setsearch ,
initparamBF ,
paramtableCG ,
paramtableGA ,
paramtableSA ,
paramtableSS
Object Type: paramtableCG
Description: This object implements a conjugate gradient descent
algorithm as part of a parameter search process, and also
stores the parameter tables and various bookkeeping
information relating to the parameter search process.
Author: Mike Vanier, Caltech
-------------------------------------------------------------------------
ELEMENT PARAMETERS
Data structure: paramtableCG_type [in src/param/param_struct.h]
Size: 308 bytes (more when tables are loaded)
Fields: iteration_number iteration number
num_params total number of parameters
num_params_to_search number of parameters to search over
search array of flags:
0 = don't search this parameter,
1 = do search this parameter
type type of parameter:
0 = additive,
1 = multiplicative
center of parameter values in range
range of parameter values
min of parameter values
max of parameter values
label label of parameter,
for documentation purposes only
current array of parameter values
to be simulated next
current_match match value of current parameter set
being simulated
best array of parameter values
giving best match so far
best_match best match value
new_best_match flag: 1 if last match was the best so far
done flag: 1 when the simulation is finished
filename where parameter information is
stored/saved as a binary file
alloced flag: 1 means tables are allocated
linemin_number which line minimization we're doing;
for bookkeeping only
state state of parameter search:
0 = random searches at startup
1 = gradient calculation
2 = line minimization
deriv_method 0 = do a proper derivative;
1 = quick-and-dirty estimate
(not yet implemented)
deriv_index index of parameter we're taking
the derivative of
deriv_h_init initial values of h (the spatial step
size) to use in derivative
calculations
deriv_h_decrease how fast to decrease h
deriv_h_min lowest permissible value of h
deriv array of 1st partial derivatives:
d(match)/d(param)
dir direction vector
tolerance tolerance of parameter search as a whole
linemin_tolerance tolerance of line minimization
routines
-------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: ParamtableCG [in src/param/paramtableCG.c]
Classes: param
Actions: Note: required arguments to actions are in <angle brackets>;
optional arguments are in [square brackets].
CREATE Creates the object (not invoked directly).
TABCREATE <num_params>
Initializes the object for a given number of
parameters.
DELETE Deletes all allocated memory.
TABDELETE Same as DELETE.
INITSEARCH Initializes the search process.
RANDOMIZE Picks a random parameter set from the parameter
space as a potential starting point for the search.
EVALUATE <match>
Copies the match value into the current_match field.
If this match is the best match so far, this action
copies the current parameter set into the best
parameter set and the current_match field into the
best_match field.
UPDATE_PARAMS
Chooses the next set of parameters to
simulate based on past results.
UPDATE_PARAMS2
Increments iteration_number. Only used in
random searches at the beginning of a CG
parameter search.
LOADBEST Copies best parameter values to current values;
can be used to start the search at the best values
found so far.
RESTART Re-initializes parameter search at the
best point found so far.
SAVE [filename]
Saves the object as a binary file. If no
argument given, use the "filename" field
of the element.
SAVEBEST <filename>
Saves the best parameter set to an ascii file.
RESTORE [filename]
Restores the object from a binary file. If no
argument given, use the "filename" field of the
element.
RESTOREBEST Restores the best parameter table from a text file.
DISPLAY Displays the best parameter set obtained so
far on stdout.
CHECK Runs a series of self-check diagnostics on this
object.
Messages: none
-------------------------------------------------------------------------
Notes: This object stores parameter tables and calculates new tables
to be simulated in a parameter search process using a
conjugate gradient-descent algorithm. Here is a brief
description of the algorithm:
The conjugate-gradient (CG) method is a type of gradient
descent algorithm. In this method the gradient of the match
function at a given point in parameter space and the direction
of steepest descent with respect to this function are computed.
A line minimization in the direction of steepest descent is
done to find the point on the line with the best match value.
A new gradient is calculated at this point and the procedure is
iterated until the method converges to a local minimum of the
matching function. Successive line minimizations are done in
directions which are "conjugate" to one another so that
successive minimizations are as nearly independent of each
other as possible. In theory this will guarantee that the
parameter search will find a local minimum of the objective
function.
The termination criteria used by the algorithm is that either
(a) the gradient must be very close to zero, or (b) successive
line minimizations must produce nearly identical results. Note
that this can happen fairly early in the search, resulting in
rapid convergence to a local minimum which is nowhere near the
global minimum. Welcome to gradient-descent algorithms :-) One
way around this is to simply rerun the search from random
starting points again and again until you find better matches.
A better alternative is to use the simulated annealing (SA)
method instead of this one, which also incorporates a
(modified) gradient descent algorithm so that you get the best
of both worlds (i.e. ability to escape from local minima
characteristic of SA methods, and convergence to local minima
characteristic of gradient descent algorithms).
The fields deriv_h_init, deriv_h_decrease, deriv_h_min do not
have to be set explicitly; they are set to "reasonable" values
by default. deriv_h_init is actually an array of values, one
per parameter. The (hidden) field h represents the spatial
step size used in the derivative calculation. You can find
more information about this in the source code; don't mess with
it unless you know what you're doing or your results will
probably be worse.
The code for this routine was adapted from the conjugate
gradient code in Numerical Recipes in C, 2nd Ed., by Press
et. al. (chapter 10). The actual code is substantially
different but the algorithm is essentially the same.
Example: See Scripts/param/CG for demo scripts.
See also: Parameter Search (
Param ),
Paramtable ,
setsearch ,
initparamCG ,
paramtableGA ,
paramtableSA ,
paramtableSS
Object Type: paramtableGA
Description: This object implements a simple genetic algorithm as part
of a parameter search process, and also stores the
parameter tables and various bookkeeping information
relating to the parameter search process.
Author: Mike Vanier, Caltech
-------------------------------------------------------------------------
ELEMENT PARAMETERS
Data structure: paramtableGA_type [in src/param/param_struct.h]
Size: 272 bytes (more when tables are loaded)
Fields: generation generation number
num_tables number of parameter tables
num_params number of parameters per table
num_params_to_search number of parameters to search over
search array of flags:
0 = don't search this parameter,
1 = do search this parameter
type type of parameter:
0 = additive,
1 = multiplicative
center of parameter values in range
range of parameter values
label label of parameter,
for documentation purposes only
best array of parameter values
giving best match (fitness) so far
best_match best match (fitness) value
filename where parameter information is
stored/saved as a binary file
alloced flag: 1 means tables are allocated
param_size size of parameters in bytes:
1, 2, 4 are the only choices
param two-dimensional parameter array
fitness array of fitness values for
parameter sets
min_fitness minimum fitness value
max_fitness maximum fitness value
avg_fitness average fitness value
stdev_fitness standard deviation of fitness values
min_fitness_index index of minimum fitness in fitness
array
max_fitness_index index of maximum fitness in fitness
array
normfitness array of normalized fitness values
cumulfitness array of cumulative normalized
fitness values
preserve number of best matches to
retain unchanged
crossover_type type of crossover algorithm:
0 = choose exactly <crossover_number>
crossover points for all
parameter sets that are being
crossed over
1 = choose an average of
<crossover_number> crossover points
for all parameter sets that are
being crossed over
crossover_probability probability of crossover
crossover_number number of crossovers per parameter
string
crossover_break_param flag: if 0, crossovers can't
occur inside parameter values.
mutation_probability probability of mutation per bit
use_gray_code flag: if nonzero, use Gray code
for encoding numbers (see below).
do_restart flag for whether to restart ever
restart_after restart after this many
unproductive generations
restart_count count of unproductive generations
old_fitness old fitness value, that we have
to do better than
restart_thresh need to get this much above
old_fitness to not restart
-------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: ParamtableGA [in src/param/paramtableGA.c]
Classes: param
Actions: Note: required arguments to actions are in <angle brackets>;
optional arguments are in [square brackets].
CREATE Creates the object (not invoked directly).
TABCREATE <num_tables> <num_params>
Initializes the object for a given number of
parameter tables and a given number of
parameters.
DELETE Deletes all allocated memory.
TABDELETE Same as DELETE.
INITSEARCH [random]
Initializes the search process. If "random" is
given as the argument then the first parameter
set is the original parameter set and all other
sets are chosen randomly within the given
ranges; if "random" is not given as the
argument then *all* parameter sets are chosen
randomly.
RANDOMIZE Randomizes parameters in tables. Not
normally called directly.
UPDATE_PARAMS Chooses the next set of parameters to
simulate based on past results.
Calls the REPRODUCE, CROSSOVER, and MUTATE
actions.
REPRODUCE Performs fitness-proportional reproduction.
Not normally invoked directly.
CROSSOVER Performs crossing-over between parameter sets.
Not normally invoked directly.
MUTATE Mutates each bit of the parameter sets with
a fixed (low) probability. Not normally
invoked directly.
FITSTATS Calculates statistics on the fitnesses of
the parameter sets currently stored in the
tables.
RECENTER Moves the center points of the parameter
ranges to correspond to the best parameter
set obtained so far.
RESTART Re-seeds the all the parameter tables with
random values in the allowed range, except
for the protected tables (see below).
SAVE [filename]
Saves the object as a binary file. If no
argument given, use the "filename" field
of the element.
SAVEBEST <filename>
Saves the best parameter set to an ascii file.
RESTORE [filename]
Restores the object from a binary file. If no
argument given, use the "filename" field of the
element.
RESTOREBEST Restores a parameter set from a text file,
normally the best set so far obtained. You
can use INITSEARCH without the "random"
option to keep this set and randomize the rest
of the table.
CHECK Runs a series of self-check diagnostics on this
object.
Messages: none
-------------------------------------------------------------------------
Notes: This object stores parameter tables and calculates new tables
to be simulated in a parameter search process using a
simple genetic algorithm. Here is a short description of the
algorithm:
The genetic algorithm (GA) method treats each parameter set as
an individual in a large breeding population. A new generation
of the population is derived from the preceding generation by
reproduction, crossing-over and mutation. This is accomplished
by discretizing the parameter values into bit strings and
crossing-over and mutating the different bit strings. A
population of parameter sets is selected randomly from the
parameter space and the fitness of each one is evaluated.
Fitness values, unlike the match values calculated by functions
like `spkcmp', are increasing for better and better models; a
perfect parameter set would have infinite fitness. Typically,
you take the inverse (or some power of the inverse) of the
value returned by `spkcmp' or `shape_match' to get the fitness
value.
Once fitnesses are calculated, the next generation is
determined by reproducing the current generation, with each
parameter set being chosen for reproduction in proportion to
its fitness (fitness-proportional reproduction). Then a fixed
percentage of the resulting parameter sets are crossed over by
choosing pairs of parameter sets at random, choosing one or
more breakpoints within the bit string and exchanging the bit
strings above the breakpoint (single-point recombination).
Finally, each parameter set is subjected to mutation with a low
probability per bit. In this way, highly fit parameter sets
are selected for and less fit sets are eliminated from the
population over a series of generations. Furthermore, the
processes of crossing-over and recombination can generate new
parameter combinations whose fitness is greater than that of
its predecessors.
Parameters can be stored as bit strings in one of two ways. In
the first way, the parameter range can be divided up into even
increments and the position of the parameter within that range
can be encoded by converting its relative position from a
floating-point number into an integer, where 0 represents one
end of the parameter range and the maximum possible integer
(which depends on the param_size field) represents the other
end. Successive binary numbers represent successively higher
parameter values. This is specified by setting the
"use_gray_code" field to 0. If "use_gray_code" is 1, then the
binary encoding is a Gray code encoding in which successive
values are guaranteed to differ by one bit exactly. This turns
out to be mildly advantageous for genetic algorithms, so
"use_gray_code" is set to 1 by default. If you don't
understand any of this, don't worry; just use the defaults and
you'll be fine.
By default, a crossover in a bit string can occur anywhere,
even inside the bit string that represents a single parameter.
Note that a crossover occurring inside a parameter is
effectively mutating that parameter too. If you don't want
this, set the field "crossover_break_param" to 0. This is the
default as well. In practice, this makes very little
difference.
There are two different kinds of crossover algorithms that can
be used, which are determined by the field "crossover_type".
In one case (crossover_type = 0), the field "crossover_number"
represents the exact number of crossovers for each pair of
parameter sets that is crossed over. Thus, if crossover_number
is 1, you have single-point crossovers; if crossover_number is
2, you have two-point crossovers, etc. In the other case
(crossover_type = 1) the crossover_number field represents the
*average* number of crossovers per pair of parameter sets. In
this case, there is a low probability for a crossover for each
possible crossover location between a pair of parameter sets.
This leads to a roughly Poisson distribution of crossovers for
the parameter sets chosen. The advantage of this is that you
can get single, double, triple etc. crossovers within the same
population, which can be useful in selecting for highly fit
parameter sets. The disadvantage is that some parameter sets
which are meant to be crossed over will not be. I suspect that
having crossover_type set to 1 is advantageous, although I have
no hard data to back me up. It is the default.
Note that the "mutation_probability" field is calculated per
bit, not per parameter. For each bit of each parameter table,
a separate random number is generated to determine whether to
mutate that bit.
A non-standard (but not original) feature of the genetic
algorithm implemented here is the ability to preserve the best
tables unchanged from generation to generation. This is very
useful (in fact, I consider it essential) because GA parameter
searches in genesis often use fairly small populations. This
means that genetic drift can easily cause the best parameter
sets to be crossed-over and/or mutated out of existence. To
prevent this, the field "preserve" sets the number of best
parameter tables to retain unchanged (unmutated,
uncrossed-over) between generations. For instance, if preserve
is 5, the 5 best parameter tables will be copied unchanged from
one generation to the next. These tables can also participate
in crossing-over and mutations, but you are guaranteed that one
unaltered copy of each of the tables will be present in the
next generation. The default value of preserve is 1 (preserve
only the best table); I recommend you leave it at that.
Another non-standard feature of the genetic algorithm
implemented here is that if no real progress has been achieved
after a large number of generations, then the parameter tables
can be reseeded (i.e. replaced with random values from the
allowable parameter ranges for all parameters). This is called
"restarting", which is a bit of a misnomer since the best
parameter tables are not altered. This is controlled by the
"do_restart" field, which is 1 if restarts are enabled and 0 if
not (1 is the default). If restarts are enabled, then the
object keeps track of the best fitness value and the generation
that it was first achieved at. If, after a certain number of
generations (set by the field "restart_after" which defaults to
25), the best fitness has not improved substantially (set by
the field "restart_thresh" which defaults to 1.0), then all the
parameter tables will be replaced by random values except for
the best table(s) (set by the preserve field as described
above) which are preserved unaltered. This can be useful if
you get into a suboptimal region of parameter space which is
difficult to get out of by crossing over and mutating, for
whatever reason.
If you are running genesis on a 64-bit machine (e.g. DEC
alpha), then you may have to change the definitions of
Param_short, Param_medium, and/or Param_long in
src/param/param_struct.h. All of these should be unsigned
integer types. Param_short should be one byte long,
Param_medium should be two bytes long, and Param_long should be
four bytes long.
Note that this object only instantiates one kind of genetic
algorithm. There are as many variations of the genetic
algorithm concept as there are people working on them. Feel
free to come up with your own variants and tell us all about
them :-)
Finally, if all the above has left you hopelessly confused,
don't worry; just use the default values for all the fields and
use the GA demo as a template, and you should do fine. The
options are mainly for experts and/or hackers to play with.
Example: See Scripts/param/GA for demo scripts.
See also: Parameter Search (
Param ),
Paramtable ,
setsearch ,
initparamGA ,
getparamGA ,
setparamGA ,
paramtableBF ,
paramtableCG ,
paramtableSA ,
paramtableSS
Object Type: paramtableSA
Description: This object implements a continuous version of simulated
annealing as part of a parameter search process, and also
stores the parameter tables and various bookkeeping
information relating to the parameter search process.
Author: Mike Vanier, Caltech
-------------------------------------------------------------------------
ELEMENT PARAMETERS
Data structure: paramtableSA_type [in src/param/param_struct.h]
Size: 276 bytes (more when tables are loaded)
Fields: iteration_number iteration number
num_params total number of parameters
num_params_to_search number of parameters to search over
search array of flags:
0 = don't search this parameter,
1 = do search this parameter
type type of parameter:
0 = additive,
1 = multiplicative
center of parameter values in range
range of parameter values
min of parameter values
max of parameter values
label label of parameter,
for documentation purposes only
current array of parameter values
to be simulated next
current_match match value of current parameter set
being simulated
best array of parameter values
giving best match so far
best_match best match value
new_best_match flag: 1 if last match was the best so far
done flag: 1 when the simulation is finished
filename where parameter information is
stored/saved as a binary file
alloced flag: 1 means tables are allocated
iterations_per_temp number of iterations per temperature level
temperature of annealing process
inittemp initial temperature of annealing process
annealing_method 0 = manual,
1 = linear decay,
2 = exponential decay
max_iterations maximum number of iterations;
for linear decay only
annealing_rate how fast the temperature drops;
for proportional decay only
testtemp test for whether simulation is finished
when temperature is below this value
tolerance if matches are within this distance
of each other we're done
stop_after if best match hasn't changed after
this many iterations then stop
restart_every call RESTART action every x iterations
state of search process (0-5)
simplex_init_noise proportion of initial noise in
simplex; a number in (0,1); default = 0
simplex points on the simplex:
(num_params + 1) x (num_params)
simplex_match match values for each point in the simplex
scale "typical" length scale of starting points
scalemod modifiers of length scales in
(num_params) dimensions; default: all = 1
-------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: ParamtableSA [in src/param/paramtableSA.c]
Classes: param
Actions: Note: required arguments to actions are in <angle brackets>;
optional arguments are in [square brackets].
CREATE Creates the object (not invoked directly).
TABCREATE <num_params>
Initializes the object for a given number of
parameters.
DELETE Deletes all allocated memory.
TABDELETE Same as DELETE.
INITSEARCH [random]
Initializes the search process; sets up initial
simplex values (see below); if "random" is given as
the argument then the simplex is populated by
random points in the parameter space; otherwise one
point on the simplex represents the original model.
EVALUATE <match>
Copies the match value into the current_match field.
If this match is the best match so far, this action
copies the current parameter set into the best
parameter set and the current_match field into the
best_match field.
UPDATE_PARAMS
Chooses the next set of parameters to
simulate based on past results.
RECENTER Moves the center points of the parameter
ranges to correspond to the best parameter
set obtained so far.
RESTART Replaces the worst point on simplex with the
point corresponding to the best match.
RESTART2 Like INITSEARCH, but preserves the best
match obtained so far.
SAVE [filename]
Saves the object as a binary file. If no
argument given, use the "filename" field
of the element.
SAVEBEST <filename>
Save the best parameter set to an ascii file.
RESTORE [filename]
Restores the object from a binary file. If no
argument given, use the "filename" field of the
element.
DISPLAY Displays the best parameter set obtained so
far on stdout.
DISPLAY2 Same as DISPLAY, but also prints the current
parameters.
CHECK Runs a series of self-check diagnostics on this
object.
Messages: none
-------------------------------------------------------------------------
Notes: This object stores parameter tables and calculates new tables
to be simulated in a parameter search process using a
continuous-space simulated annealing algorithm. The algorithm
is taken from Press et. al., Numerical Recipes in C,
2nd. edition, chapter 10, pp. 451-455. This algorithm is much
too complex to describe in detail here, but here is the
two-second summary:
The algorithm constructs a geometrical object called a simplex.
If there are N parameters, the simplex has N+1 points
(vertices) and conceptually occupies a volume in parameter
space. For instance, a triangle is a 3-simplex in 2 dimensions
and a tetrahedron is a 4-simplex in three dimensions.
Confused? There's more :-) Each vertex of the simplex
corresponds to a particular parameter set in parameter space.
Each vertex's corresponding parameter set is simulated and its
match value is calculated. Depending on the state of the
algorithm, several different things can happen, but typically
the worst point is discarded and a new point is selected. By
itself, this describes a gradient-descent algorithm; the
simulated annealing process comes in by adding noise to the
match values based on a temperature parameter (the higher the
temperature, the more noise). At high temperatures, the
simplex performs essentially a random walk in parameter space,
but as the temperature lowers, the simplex spends more and more
time exploring areas of the space which correspond to good
match values. As the temperature drops to zero, the simplex
will perform a gradient descent in the parameter space and find
a local minimum (which is hopefully close to the global minimum
as well).
Example: See Scripts/param/SA for demo scripts.
See also: Parameter Search (
Param ),
Paramtable ,
setsearch ,
initparamSA ,
paramtableBF ,
paramtableCG ,
paramtableGA ,
paramtableSS
Object Type: paramtableSS
Description: This object implements a stochastic-search (SS)
algorithm as part of a parameter search process, and also
stores the parameter tables and various bookkeeping
information relating to the parameter search process.
Author: Mike Vanier, Caltech
-------------------------------------------------------------------------
ELEMENT PARAMETERS
Data structure: paramtableSS_type [in src/param/param_struct.h]
Size: 184 bytes (more when tables are loaded)
Fields: iteration_number iteration number
num_params total number of parameters
search array of flags:
0 = don't search this parameter,
1 = do search this parameter
type type of parameter:
0 = additive,
1 = multiplicative
range of parameter values
min of parameter values
max of parameter values
label label of parameter,
for documentation purposes only
current array of parameter values
to be simulated next
best array of parameter values
giving best match so far
best_match best match value
filename where parameter information is
stored/saved as a binary file
alloced flag: 1 means tables are allocated
round_number number of expansion-contraction cycles
we have completed
variance current variance of gaussian
distribution
minvariance minimum variance of algorithm
maxvariance maximum variance of algorithm
addvarscale scaling factor for variances of
additive parameters
multvarscale scaling factor for variances of
multiplicative parameters
contract rate of variance contraction
-------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: ParamtableSS [in src/param/paramtableSS.c]
Classes: param
Actions: Note: required arguments to actions are in <angle brackets>;
optional arguments are in [square brackets].
CREATE Creates the object (not invoked directly).
TABCREATE <num_params>
Initializes the object for a given number of
parameters.
DELETE Deletes all allocated memory.
TABDELETE Same as DELETE.
INITSEARCH Initializes the search process. Note that
TABCREATE must be called before calling this
action. Also, the maxvariance field must
be set before calling this action. This action
will start the search off at the parameters set
by the initparamSS function.
RANDOMIZE Randomizes parameters in tables; uses a uniform
distribution from (best - range, best + range).
Can be used after INITSEARCH to pick a random
point in the parameter space to start with.
UPDATE_PARAMS
Chooses the next set of parameters to
simulate based on past results.
ACCEPT <match>
Copies the match value to the best_match field
and the current parameters to the best fields.
RECENTER Recalculates the min and max values based on
the best and range values. You might try doing
this after a best match is found to allow you
to search through a larger search space than
the initial limits would allow.
SAVE [filename]
Saves the object as a binary file. If no
argument given, use the "filename" field
of the element.
SAVEBEST <filename>
Saves the best parameter set to an ascii file.
RESTORE [filename]
Restores the object from a binary file. If no
argument given, use the "filename" field of the
element.
DISPLAY Displays the best parameter set obtained so
far on stdout.
CHECK Runs a series of self-check diagnostics on this
object.
Messages: none
-------------------------------------------------------------------------
Notes: This object stores parameter tables and calculates new tables
to be simulated in a parameter search process using a
stochastic-search algorithm. Here is a brief description of
this algorithm:
A random starting point in parameter space is chosen. New
points are selected from a multidimensional Gaussian
distribution centered on the starting point with a given
(initially large) variance. These new points are evaluated,
and if one is found that is a better match than the previous
best match, the Gaussian distribution is moved so that it is
centered on the new (best) point. In addition, the variance of
the distribution decreases each iteration until it reaches some
minimum value, at which time it is increased to the original
value. This constitutes one "round", and successive
expansion-contraction rounds are performed for as long as the
modeler wants. In principle, choosing points from a
distribution with a large variance will allow the modeler to
search over large regions of parameter space, while choosing
points from a distribution with a much smaller variance will
allow the modeler to find locally optimal points in small
regions of parameter space.
In general, this algorithm performs more poorly than the
simulated annealing and the genetic algorithm methods. It was
included mostly for comparison purposes, since some
investigators have used this method for parameterizing neural
models. Nevertheless, we recommend that you skip this method
entirely and instead use the GA or SA methods.
You can modify the variance separately for additive and
multiplicative parameters using the addvarscale and
multvarscale fields. This can be useful since the scales of
additive and multiplicative parameters can be very different
(e.g. of order 1.0 for Gbar scaling (multiplicative) and of
order 0.001 (1 mV) for minf offsets (additive)). Ideally you'd
like to be able to modify the variance on a per-parameter basis
(like the scalemod fields in paramtableSA) but we haven't
gotten around to that yet.
Example: See Scripts/param/SS for demo scripts.
See also: Parameter Search (
Param ),
Paramtable ,
setsearch ,
initparamSS ,
paramtableBF ,
paramtableCG ,
paramtableGA ,
paramtableSA
Object Type: peristim
Description: Generates a peristimulus spike histogram.
Author: E. De Schutter Caltech 8/91; embellished by D. Jaeger 8/92
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: new_peristim_type [in src/device/dev_struct.h]
Size: 112 bytes
Fields: output gives the most recent peristimulus value
threshold voltage threshold for determining when a spike
occurs
binwidth time interval between bins
num_bins number of table entries (bins)
trigger_mode 0 (free run) or 1 (triggered)
reset_mode if 1 then bins will be emptied upon RESET
table contains num_bins entries of histogram values
bin_index index into the table, giving current bin
(not set by user)
bin_steps time steps since the start of the current bin
(not set by user)
spiking flag indicating spike in progress
(not set by user)
allocated flag indicating table has been allocated
(not set by user)
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: NewPeriStimulusDistribution [in src/device/new_peristim.c]
Classes: device
Actions: CHECK PROCESS RESET
Messages: INVM voltage (Records a spike event when voltage first
exceeds threshold. The voltage must then
fall below threshold before another spike
event can be recorded.)
TRIGGER state (Starts recording spikes starting with the
first bin, when state is non-zero.)
READTIME time (Adds a spike event to the table in the
bin appropriate for the value of time.
This could be used with a timetable,
table, or asc_file element to retrieve
spike times from a table or a file.)
INSPIKE state (Records a spike event whenever state
exceeds threshold. This message would be
sent by an element, such as a spikegen,
that represents a spike by a state that
lasts for a single time step.)
------------------------------------------------------------------------------
Notes: In the example below, there are 1000 bins to process 1 second
of spike events, using a 1 msec bin width. The typical use
would be to run the simulation, and send a trigger event to
the peristim element at 1 second intervals. This would
normally coincide with the application of some stimulus to the
cell.
Each time the triggering device generates a triggering event
and stimulates the cell, the resulting action potentials will
be counted and placed in bins according to the time that they
occurred since the trigger event. At the end of the run, the
histogram results can be retrieved with commands such as
"getfield /peristim table[{i}]", with i taking on values from
0 through nbins-1.
If trigger_mode is set to zero (free run mode), then spike
data is gathered continously, looping through all the bins and
then starting again in the first bin. Otherwise, data after
the last bin is ignored until a TRIGGER message is received.
When a non-zero TRIGGER message is received, subseqent spike
events are binned starting with the the first bin, table[0].
This is true regardless of the value of trigger_mode.
Normally the source of the TRIGGER message is an element, such
as a spikegen, that sends the value of a state field that
lasts for a single time step.
Example:
float binwidth = 0.001; int nbins = 1000
create peristim /peristim
setfield /peristim threshold 0 num_bins {nbins} binwidth {binwidth}
setfield /peristim trigger_mode 1
// Assume that /trigger_device generates spike events in its state field
addmsg /trigger_device /peristim TRIGGER state
// Assume a cell, generating action potentials in the soma compartment
addmsg /cell/soma /peristim INVM Vm
See also:
interspike
Object Type: playback
Description: update a pre-filled buffer
Author: M. Wilson, Caltech (6/88)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: playback_type [in src/buffer/buf_struct.h]
Size: 100 bytes
Fields:
tmin
size
current
start
end
event_size
event
state
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: PlaybackBuffer [in src/buffer/playback.c]
Classes: buffer
Actions: PROCESS
RESET
COPY BufferCopy
CREATE BufferCreate
Messages: none
------------------------------------------------------------------------------
Notes: The putevent command may be used to fill the buffer
Example:
create playback /test
putevent /test 10 10.0 20 0.0 30 30.0 40 0.0 50 50.0 60 0.0
create xform /testform
create xgraph /testform/graph
addmsg /test /testform/graph PLOT state *playback *blue
xshow /testform
reset
step 100
See also:
putevent
Object Type: pool
Description: Pool of molecules involved in chemical reactions and
transport between cellular compartments. Keeps track of the
number of molecules resulting from forward and backward
reactions. Uses mean-rate theory which assumes large numbers
of molecules, not probabilities of transitions of individual
molecules.
Does Michaelis-Menten enzyme kinetics when hooked to the 'enz'
object, and standard kinetic reactions with the 'reac' object.
The MM scheme is modeled as:
k1 k3
Substrate + Enzyme <-----> EnzComplex ----> Enz + Prd
k2
The generic reaction scheme is:
kf
Substrate1 + S2 + .. <----> Prd1 + Prd2 + ...
kb
Note that vol, n and Co are interdependent. vol is never
changed except by the user or by messages. n changes if Co is
changed. Co changes if either vol or n is changed. Volume is
typically scaled by the Avogadro number, so that Co is in
convenient units such as micromolar.
During integration, all calculations are done in terms of
n, and, where needed, vol. Co is calculated as n / vol on
each timestep.
Author: U. S. Bhalla, National Centre for Biological Sciences,
Bangalore, India. (1993).
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: pool_type [in src/kinetics/kin_struct.h]
Size: bytes
Fields: Co Concentration of molecule. Calculated
from 'n' as n/vol.
CoInit Initial concentration of molecule.
Co gets set to this value on RESET.
CoTotal Total concentration of molecule. Used
when applying conservation rules.
CoRemaining CoTotal - Co.
n Number of molecules. This is the
value used for all calcultions.
nInit Initial number of molecules.
'n 'gets set to this value on RESET.
nTotal Total number of molecules. Used
when applying conservation rules.
nRemaining nTotal - n
nMin Minimum allowed number of molecules.
Normally zero.
vol Volume occupied by pool. Often involves
extra units so as to have direct
conversion from 'n' to some sensible
units of Co, such as micromolar.
slave_enable Flag used to control buffering and
other overrides. Values:
1 - Obey slave message, representing n
2 - Obey slave message, representing Co
4 - Buffering on: n is set to nInit,
Co to CoInit, every timestep.
See below for details.
keepconc Flag determining whether to change
concs or n when volume changes
consv_flag Internal flag keeping track of presence
of CONSERVE and SUMTOTAL msgs
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: PoolFunc [in src/kinetics/pool.c]
Classes: segment, concentration
Actions: CREATE
PROCESS
RESET
SET
Messages: REAC A B [A is increment to n,
B is decrement to n,
where n is number of molecules in pool.
This message is used for hooking up
all reactions and enzymes.]
MM_PRD A [increment n by A. This message is
used for the product of enzymes.
We assume it is irreversible, so there
is no B term]
SLAVE number [Sets n or Co to this command number
depending on the slave_enable status,
described below. This message is
used to make concentrations in the pool
follow an external signal.]
REMAINING n [decrement to nRemaining]
CONSERVE n nInit [This message is used for setting up
conservation relationships.
n from all derived molecules is summed
to do the conservation. nInit is used
during RESET to calculate the total
number of molecules. See notes.]
VOL vol [volume of pool]
SUMTOTAL n nInit [This message is used to make a pool
whose n is the sum of that of several
other pools. nInit is used at
RESET to get the initial levels]
------------------------------------------------------------------------------
Notes:
The pool has numerous extras used in practical simulations.
Most of these are readily accessed from within kinetikit, which is
the recommended way of developing kinetic simulations. For
completeness, here is a list of features of the pool:
1. Buffering. When slave_enable is set to 4, then all the pool
does is assign n to nInit and Co to CoInit every timestep.
2. Following an external signal. This works when the SLAVE
message is passing in the external number. if slave_enable is
1 then the external number represents n. If it is 2 the
external number represents Co.
3. Conservation relationships. In some cases it helps stability
and accuracy to apply explicit conservation relationships,
rather than rely on the implicit ones that arise from the
numerical integrations. Warning: in some cases explicit
conservation relationships actually worsen stability ! So
try it for each case before relying on it. Conservation
relationships are set up in two phases:
- identify the pool whose value you want to be calculated
from conservation.
- Send CONSERVE messages from all pools to which this molecule
gets converted. Be sure you have found ALL the pools: this is
a very common source of error. For example, you may need to
send a CONSERVE message from enzyme intermediates, which
are represented by 'enz' objects.
4. Summation. In some cases the final amount of an active
species recieves contributions from several independent pathways.
An example is an enzyme whose active site always has the same
activity regardless of the means of activation. The total amount
of the active enzyme could then be represented as the sum of
the active forms from several independent activation pathways.
The SUMTOTAL message is used for such cases.
5. Calculating the amount of the molecule that has reacted, and is
no longer in this pool.
The nRemaining field plus the REMAINING message are used for this.
Again, the REMAINING message must come in from all other molecules
into which this pool may convert. This is mainly useful for checking
accuracy and stability.
The combination of pools, reacs, and tables is capable in principle of
implementing very complicated ODEs, not restricted to
chemical reactions. The pools represent the variables, reacs represent
processes increasing and decreasing variables, and the tables can
twiddle the rate constants of the reacs according to arbitrary
complicated functions. It should be stressed that this is an
extremely inefficient but reasonably general way of doing this.
Example:
Message setup between pools, reacs and enzymes:
For the reaction
kf
2X + Y <======> Z
kb
we would have 3 pools, and 1 reac. The messaging would be as follows:
addmsg X reac SUBSTRATE n
addmsg X reac SUBSTRATE n
addmsg reac X REAC A B
addmsg reac X REAC A B
addmsg Y reac SUBSTRATE n
addmsg reac Y REAC A B
addmsg Z reac SUBSTRATE n
addmsg reac Z REAC B A
Some points about this messaging scheme:
1. We need N sets of SUBSTRATE and REAC messages between a pool and
a reac, where the order of the reaction for that pool is N.
2. The Z pool, which is the product, has the A and B state variables
reversed in the message. This is because any decrease in X or Y is an
_increase_ in Z.
Setting up the enzymatic reaction:
Sub + X --> Prd
We normally put the enzyme site enz as a child of the pool which
represents the enzyme.
create enz X/enz
A given pool can have any number of enzyme
'sites'. This is required when an enzyme has different levels
of activity for different substrates, as each of the enzyme 'sites'
can then be given different rates. The messaging would look like this:
addmsg X X/enz ENZYME n
addmsg X/enz X REAC eA B
addmsg sub X/enz SUBSTRATE n
addmsg X/enz sub REAC sA B
addmsg X/enz prd MM_PRD pA
Some points about this messaging scheme:
1. In the irreversible Michaelis-Menten model we are using, the
enzyme cannot reduce the level of the product. So there is only one
term required in the outgoing message, and no incoming message from
the product to the enzyem
2. If this scheme doesn't suit you, you can always build better
enzyme models using combinations of reacs and intermediate pools.
Object Type: pulsegen
Description: General purpose pulse generator
Author: M. Nelson, Caltech (4/89)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: pulsegen_type [in src/user/user_struct.h]
Size: 120 bytes
Fields: level1 level of pulse1
width1 width of pulse1
delay1 delay of pulse1
(wrt ext. input - trig or gate mode)
(wrt pulse2 - free run mode)
level2 level of pulse2
width2 width of pulse2
delay2 delay of pulse2 (wrt pulse1)
baselevel baseline level
trig_mode flag: 0=free run, 1=ext. trig, 2=ext. gate
output output
trig_time internal state variable
previous_input internal state variable
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: PulseGen [in src/user/pulsegen.c]
Classes: device
Actions: PROCESS RESET
Messages: INPUT "gate/trig" (0 = low, non-0 = high)
LEVEL pulse# level
WIDTH pulse# width
DELAY pulse# delay
------------------------------------------------------------------------------
Notes:
This device can generate a variety of pulse patterns: single pulses, double
pulses (each with its own level and width), and pulse trains (of single
pulses or pairs). It can be triggered, gated, or allowed to free run.
In combination with a spikegen object, it can be used to generate bursts of
spikes for use as synaptic input. (See Scripts/neuron/inputs.g.)
The following diagram illustrates the relationships between the fields:
+-----------------+ level1
trigger | |
| | | +-------------+ level2
| | | | |
V | | | |
+--- baselevel --+ +--------+ +----
<---- delay1 ----><---- width1 ----> <-- width2 -->
<--------- delay2 -------->
If delay2 <= width1, then level2 starts imediately after the end of the
pulse at level1. This means that if delay2, width2 and level2 are not set
and remain at their default values of 0, there will be only one type of
pulse. It will repeat after a time delay1 after the end of the pulse
(free run mode) or a time delay1 after it is triggered (trigger or gate
mode).
Example: Scripts/examples/pulsegen/PulseGenDemo.g
See also:
Object Type: randomspike
Description: place a random event into the buffer
Author: M. Wilson, Caltech 6/88, Dave Bilitch 1/94
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: Randomspike_type [src/newconn/newconn_struct.h]
Size: 100 bytes
Fields: min_amp minimum amplitude of event
max_amp maximum amplitude of event
rate rate of generation of events
reset flag for whether to reset after each event
reset_value what to reset state to
state current state of object
abs_refract minimum time between events
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: RandomEvent [in src/newconn/randomspike.c]
Classes: buffer
Actions: INIT
RESET
PROCESS
Messages: RATE rate
MINMAX min max
------------------------------------------------------------------------------
Notes: Generates a time series of events at a rate given by the rate
parameter. The probability of an event for a single time step
is given by rate*dt where dt is the clock rate of the
element. However, no event will be generated at a time less
than abs_refract. When an event has been generated, the
amplitude of the event is a random variable uniformly
distributed between min_amp and max_amp. The state field
has the value of the event amplitude if an event has been
generated. If an event is not generated then the value of
the state field depends on the reset field. If reset is
non-zero then the state is takes on the value given in
reset_value. Otherwise the state will behave like a latch
containing the amplitude of the previous event.
Example: Scripts/tutorials/tutorial4.g
See also:
Object Type: reac
Description: Chemical reaction object. Works with pools to provide kf and
kb. Reacs calculate the changes in concs for each pool hooked
into them. The pool is responsible for adding up all the
up and down changes resulting from various reactions it is
involved in. Each reac can handle any number of substrates
and products, though reactions of order greater than 2 are
rare. Any number of reacs can be hooked up to a given pool.
The generic reaction scheme is:
kf
Substrate1 + S2 + .. <----> Prd1 + Prd2 + ...
kb
Author: U. S. Bhalla, National Centre for Biological Sciences,
Bangalore, India. (1996).
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: reac_type [in src/kinetics/kin_struct.h]
Size: bytes
Fields: kf Forward rate constant. Units depend
on the order of the reaction, ie,
the number of molecules on the
left hand side. First
order is sec^-1, second order is
sec^-1.num^-1, etc.
kb Backward rate constant. Units depend
on the number of molecules on the
right hand side, in a similar way.
A, B Internal state variables, used to
communicate with pools. A represents
increase in the pool n, B is the
decrease.
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: ReacFunc [in src/kinetics/reac.c]
Classes: segment
Actions: PROCESS
RESET
SET
Messages: SUBSTRATE n [Number of molecules in substrate pool]
PRODUCT n [Number of molecules in product pool]
KF kf [Forward rate constant]
KB kb [Backward rate constant]
------------------------------------------------------------------------------
Notes: See pool documentation for complete example.
------------------------------------------------------------------------------
Object Type: receptor
Description: takes the weighted sum of up to 10 odors to determine membrane
voltage and spike rates.
Author: U. S. Bhalla, Caltech (1/90)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: olf_receptor_type [in src/olf/olf_struct.h]
Size: 144 bytes
Fields: response table of weights to apply to incoming odor
messages
Vmin minimum bound of membrane potential
Vmax maximum bound of membrane potential
gain scaling factor on input odors
Vm calculated current membrane potential
min_rate minimum bound of spike firing rate
max_rate maximum bound of spike firing rate
state spike flag; will be 1 if receptor has fired,
0 otherwise
activation not used
transfer_form not used
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: OlfReceptor [in src/olf/receptor.c]
Classes: segment
Actions: INIT
PROCESS
RESET
RECALC
CHECK
SAVE2
RESTORE2
Messages: ODOR strength strength of odor
GAIN sensitivity sets gain field in element; globally
scales sensitivity of receptor to odors
------------------------------------------------------------------------------
Notes:
The receptor is used as an olfactory receptor, taking a
weighted sum of up to 10 ODOR messages, to represent
components of olfactory stimulus. The weights are defined in
an array on the element, this enables one to construct any
combination of odor sensitivities on the neuron. The output
is both in the form of a membrane potential and a spike.
The receptor element takes the weighted sum of up to 10 odors
to determine membrane voltage and spike rates. The odor inputs
arrive as messages. These can be scaled by the gain field
which can also be set by messages. Each odor is weighted by
the appropriate entry in the response table.
response - table of 10 weights for incoming odor messages
(messages are multiplied by weights before being scaled by
gain and summed to get Vm).
Vm is meant to be the equivalent of membrane potential,
calculated by:
sum [from i=0 to i=nodors-1] of odor_i x response[i] x gain
(always bounded by Vmin and Vmax). There is no time course
involved in Vm, it is simply recalculated every time step.
state is calculated in a probabilistic manner every time step
as follows:
state is set to 1 if:
min_rate + Vm * (max_rate - min_rate) >
a random number (calculated every time step)
between 0 and 1
State is meant to be used as the origin of a message to an
axon, for connecting to other neurons.
This element had been largely superseded by the receptor2
element, which is is a much more realistic version of an
olfactory receptor protein-membrane channel complex.
Example:
See also:
receptor2
Object Type: receptor2
Description: Olfactory Receptor. Takes weighted sum of any number of
messages to get the activation for a channel. The messages
represent components of an olfactory stimulus.
Author: U. S. Bhalla, Caltech (1/90)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: olf_receptor2_type [in src/olf/olf_struct.h]
Size: 172 bytes
Fields: response table of weights to be set for each odor
nodors number of odors
tau1 open time constant of channel
tau2 close time constant of channel
gmax peak conductance
Ik channel current
modulation scale all odors; gain control on responses
Gk resulting channel conductance
Ek equilibrium potential
activation channel activation calculated from incoming
messages
allocated internal flag
X state variable for time response
Y state variable for time response
xconst1 internal variable, not normally set by user
xconst2 internal variable, not normally set by user
yconst1 internal variable, not normally set by user
yconst2 internal variable, not normally set by user
norm internal variable, not normally set by user
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: OlfReceptor2 [in src/olf/receptor2.c]
Classes: segment
channel
Actions: INIT
PROCESS
RESET
RECALC
SET
CHECK
SAVE2
RESTORE2
Messages: VOLTAGE Vm usual message from parent compartment
to channel to tell what the membrane
potential is
ODOR activation odor_no describes odor; activation = strength
of particular odor; odor_no = integer
specifying response table index having
weight for that odor
MODULATION modulation sets modulation field; provides means
for scaling the overall sensitivity of
receptor up or down
------------------------------------------------------------------------------
Notes: Does a weighted sum of odors to get activation
of a channel with usual conductance properties.
The receptor2 element is a much more realistic version of an
olfactory receptor protein-membrane channel complex than the
receptor element. The receptor2 is a channel similar to the
synchan element, except that this channel responds to odors
via ODOR messages, and does not have synapses with weights and
delays.
Any number of odor messages may be sent to the receptor2.
They are scaled by the weights in the response table, and then
their summed effects act as the activation of the channel. The
channel has the usual time courses and conductance fields, and
can be incorporated into membrane compartments just like
ordinary synaptic channels.
Example: Scripts/neurokit/prototypes/newbulbchan.g
Here is a section of script that puts random numbers from 0
to 1 in each of the entries of the response array. You will
need to set the other fields (especially modulation) to
sensible values, of course.
create receptor2 /foo
setfield /foo nodors 10
int i
for (i = 0; i < 10; i = i + 1)
setfield /foo response[{i}] {rand 0 1}
end
See also:
receptor
Object Type: script_out
Description: executes a script command at each step of a simulation
Author: M. Wilson, Caltech (2/89)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: script_output_type [in src/out/out_struct.h]
Size: 80 bytes
Fields: command Command string (function name + optional args)
argc Number of arguments, including function name
argv array of arguments (argv[0] = function name)
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: ScriptOutput [in src/out/out_script.c]
Classes: output
Actions: PROCESS
SET
RESET
RECALC
Messages: none
------------------------------------------------------------------------------
Notes:
The command field of a script_out element is used to hold the name of a script
language function which will be executed at every step of the clock used by
the script_out. This will normally by clock 0, the default simulation clock.
As the definition of this script function will be interpreted by the SLI,
execution will be much slower than with the compiled PROCESS action of other
predefined GENESIS objects. For that reason it is best to assign a slower
clock to the script_out element.
If the command field is set to a string consisting of the function name
plus one or more optional arguments, then argv[{n}] will contain the
nth argument. Extended objects provide a much more flexible alternative
to the script_out object.
Example:
// spikebeep.g - illustrate the use of the script_out element to beep
// whenever a spike is produced (assuming your terminal window
// beeps when a ctrl-G is echoed).
// Include this file at the end of Scripts/tutorials/tutorial4.g
// The script_out element checks for a spike at every simulation step
create script_out /catchspike
setfield /catchspike command "checkspike"
useclock /catchspike 0
function checkspike
if ({getfield /cell/soma/spike state} != 0)
echo {chr 7} -nonewline
end
end
reset
See also:
Extended , Scripts/orient_tut/ret_input.g
Object Type: sigmoid
Description:
Computes the sigmoidal transformation of the input and places the result in
'state'. The equation being applied is
state = amplitude*(tanh(gain*(input - thresh)) + 1)/2.0
This gives a ``squashing'' function which is commonly used in connectionist
models as an approximation to the relation between the amount of synaptic
input to a cell and its firing rate.
Author: M. Wilson, Caltech (6/88)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
Data Structure: sigmoid_type [in src/buffer/buf_struct.h]
Size: 116 bytes
Fields: thresh
amplitude
input
state
gain
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: SigmoidEvent [in src/buffer/sigmoid.c]
Classes: buffer
segment
Actions: PROCESS RESET COPY CREATE
Messages: INPUT input
THRESH threshold
GAIN gain
AMP amplitude
------------------------------------------------------------------------------
Notes:
Example: Scripts/examples/sigmoid.
See also:
Object Type: spikegen
Description: Performs threshold spike discrimination.
Generates an impulse each time an input crosses the
spike threshold at a maximal rate set by abs_refract.
Author: M. Wilson, Caltech 6/88, ave Bilitch 1/94
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: Spikegen_type [in src/newconn/newconn_struct.h]
Size: 88 bytes
Fields:
state current spiking state
thresh threshold level for spike generation
abs_refract minimum interval between spikes
output_amp spike event amplitude
lastevent time of last generated spike
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: SpikeEvent [in src/newconn/spikegen.c]
Class: spiking
Actions: RESET clear the history buffer, removing
any existing events
PROCESS determine whether a spike is
generated, set the state to 0 for no
spike or to output_amp for a spike
CHECK make sure there is a source of input
to drive spike generation
RESTORE2 called by the restore command
SAVE2 called by the save command
Messages: INPUT input
THRESH threshold
------------------------------------------------------------------------------
Notes: Simulates a thresholded spike generation mechanism. When the
input exceeds the specified threshold and there has not been a
spike for at least the interval specified by 'abs_refract' a
single spike event is generated with amplitude given by
'output_amp'. The spikegen typically receives action
potentials from a compartment via the INPUT message and
sends spike events to a synchan or synchan2 element with
a SPIKE message.
Example: Scripts/tutorials/tutorial4.g
Object Type: spikehistory
Description:
The spikehistory object is used to record into an ASCII file the spikes
produced by a neuron or by a network of neurons. When the network is large or
when it is simulated during several seconds, it becomes impractical to record
the complete membrane potential traces of the constituent neurons through
messagess to an asc_file or to a graph element. In addition, one is usually
only interested in the spike responses, which could be compared with
"extracellularly" recorded spike potentials.
The occurrence of a spike must be sent from a spikegen element to the
spikehistory element through a SPIKESAVE message, which is established with
the usual addmsg command (no parameters needed). A SPIKESAVE message is an
active message. This means that a nonzero state field of a spikegen element
actively triggers the execution of the EVENT action of the spikehistory
element. (Note that the spikehistory object does not have the usual PROCESS
action, normally executed on each time step.) This EVENT action consists of
adding a line to the ASCII file. The first item on each line is the
identification of the spikegen element that sent the spike. Depending on the
initialization value of the ident_toggle field of the spikehistory element,
this item is either the index assigned to the spikegen element (or to its
parents) in a map created with createmap (ident_toggle 0) or the full path
name of the spikegen element (ident_toggle 1). Each EVENT action triggered by
a SPIKESAVE message adds another line.
Author: R. Maex, UI Antwerp (1/96) (reinoud@bbf.uia.ac.be)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: spikehistory_type [in src/out/out_struct.h]
Size: 88 bytes
Fields:
filename data file name to be written
fp data file pointer
is_open flag: is file currently open?
initialize flag: has file been initialized?
leave_open flag: leave file open? 1 leaves the file open
all the time so you can write on it whenever
you want (a good idea if the file is used
frequently, but there is a limit to number of
files which can be left open any any time);
0 closes the file after every write to it
(only useful if you have more than 30 files;
this is slow)
append flag: append data after resetting?
flush flag: flush data to disk at each interval?
1 forces program to send data to the disk at
once and not store it in a buffer (slow but
secure); 0 (default) writes data in a buffer
(fast)
ident_toggle flag: if zero, output as an identifier
the map index of the sending spikegen element;
if non-zero, output the full path name
of the sending spikegen element
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: SpikeHistory [in src/out/spike_history.c]
Classes: output
Actions: RESET EVENT SAVE
Messages: SPIKESAVE
------------------------------------------------------------------------------
Notes:
When indices are used as sender specification, it is required that the
sequence in which the SPIKESAVE messages are established to the spikehistory
element be the same as the order of the sender elements in the map of sender
elements. Indeed, the SpikeHistory EVENT action loops through the MsgIn list
to find the sender element. It assumes that this loop index is the same as the
index of the sender in the afferent map. This requires of course also that
every map has its private spikehistory element!
If the filename field is not set, the output file will be given the
same name as the element which is created from the asc_file object.
For binary data, use disk_out.
Example with index specification:
str cellpath = "/Granule"
// read cell data from .p file
readcell Gran1M0.p {cellpath}
// add a spikegen object
create spikegen {cellpath}/soma/spike
setfield {cellpath}/soma/spike thresh -0.02 \
abs_refract 0.005 \
output_amp 1
addmsg {cellpath}/soma {cellpath}/soma/spike INPUT Vm
// create a map
create neutral /granule_cell_layer
createmap {cellpath} /granule_cell_layer \
20 1 -delta 1.0 0.0 -origin 0.0 0.0
// create a spikehistory element
create spikehistory granule_cells.history
setfield granule_cells.history ident_toggle 0 \ // index specification
filename "granule_cells.spikes" \
initialize 1 leave_open 1 flush 1
// add messages from the spikegen elements to the spikehistory element
addmsg /granule_cell_layer/Granule[]/soma/spike \
granule_cells.history SPIKESAVE
See also:
asc_file ,
spikegen
Object Type: stdp_rules
Description: Performs a weight modification of synchan connections,
according to spike timing dependent (STDP) rules and
settable parameters. Works with hsolved cells.
Author: Dave Beeman, University of Colorado, June 2014
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: stdp_rules_type [in src/newconn/stdp_rules_struct.h]
Size: 208 bytes
Fields:
synpath relative path to synchan to be modified
spikepath relative path to the cell spikegen
tau_pre decay constant for pre before post spike
tau_post decay constant for post before pre spike
min_dt minimum time diff to account for latency
max_weight maximum synaptic weight allowed
min_weight minimum synaptic weight allowed
dAplus increment for postive weight changes
dAminus increment for negative weight changes
change_weights flag: 0 = plasticity off, otherwise on
debug_level flag: 0 = no messages, 1 = some messages, 2 = more
celllist GENESIS ElementList of cells to modify
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: StdpRules [in src/newconn/stdp_rules.c]
Class: output
Actions: CHECK RESET PROCESS INIT CREATE
Messages: None
------------------------------------------------------------------------------
Notes: A clocked object to modify synaptic weights for all synapses of
a specified (wildcarded) cell and synchan, e.g. '/layer4/pyr[]'
and 'apical3/AMPA'. The spike timing dependent plasticity
(STDP) rules algorithm is from Song, Miller, and Abbott (2000).
Example: Scripts/stdp_rules/README.txt
See also:
synchan ,
spikegen
Object Type: symcompartment
Description: Axially symmetric compartment. Ra is divided into
two equal components across the compartment.
Author: M. Wilson, Caltech (6/88)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: symcompartment_type [in src/segment/seg_struct.h]
Size: 132 bytes
Fields: Rm total membrane resistance
Cm total membrane capacitance
Em membrane resting potential
Ra axial resistance
inject injected current in membrane
dia compartment diameter
len compartment length
Vm voltage across the membrane
previous_state Vm at previous time step
Im approximation to the total membrane current
initVm initial value to set Vm on reset
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: SymCompartment [in src/segment/symcompartment.c]
Classes: segment
membrane
Actions: INIT assign previous_state = Vm
PROCESS update Vm, calculate Im
RESET assign Vm = Em, set internal constants
depending on the types of incoming messages.
CHECK make sure Rm>0, Cm>0, Ra>0
SAVE2
RESTORE2
Messages: CHANNEL Gk Ek delivers the conductance and equilibrium
potential of channel within the compartment
INJECT inject sets the inject field to the message value
EREST Em sets the Em field to the message value
CONNECTHEAD Ra Vm used to connect to the child compartment
CONNECTTAIL Ra Vm used to connect to the parent compartment
CONNECTCROSS Ra Vm used to cross-connect the first
compartments after a binary or multiple
branch.
RAXIAL Ra Vm alias for CONNECTTAIL
AXIAL Ra Vm alias for CONNECTHEAD; note that for the
asymmetric compartment, AXIAL only receives Vm.
RAXIAL2 Ra Vm alias for CONNECTHEAD
RAXIALC Ra Vm alias for CONNECTCROSS
------------------------------------------------------------------------------
Notes: Like the compartment object, the symcompartment simulates
a section of passive membrane or cable. The potential across
the membrane is given by Vm. There is a leakage path for
current through the resistance Rm. This resistance is in
series with a leakage battery Em, and there is a membrane
capacitance in parallel with Rm and Em. This compartment can
be coupled to other compartments with an axial resistance Ra,
which is divided into two pieces of resistance Ra/2 on either
side of the point having the potential Vm. In most respects,
the symcompartment is similar to the asymetric compartment
object, and its use is more fully described in the
documentation for compartment. However, the division of Ra
requires different messages to be used when linking
symcompartments.
For linear chains of symmetric compartments, all of the
connection messages are equivalent, and all compartments may
be linked by exchanging RAXIAL messages. However, for
branched structures, the the incoming current must be
calculated differently, depending on whether it is from a
parent, child, or connected sibling in the tree of
compartments, using the messages described above. Because of
this added complexity, it is best to use the readcell routine
with a cell parameter file when constructing cells with
symcompartments. This will link the compartments with the
proper messages.
Prior to GENESIS version 2.2, the CONNECTSPHERE message was
use to connect a cylinder to a sphere, assuming that all the
dendrites are distributed perfectly over the soma/sphere.
This is now performed automatically by readcell, and this
message is no longer needed. Using CONNECTHEAD or CONNECTTAIL
instead connects all denrites to one point on the soma/sphere.
A note on spherical compartments by Erik De Schutter: If you
use readcell, spherical compartments will have zero length (a
GENESIS convention) and the Ra field will NOT be zero. This
means that the (small) resistive component of the spherical
compartment will be used in computing the axial current
between the spherical soma and dendrite. This is very
different from the asymmetric case (where the connections are
usually arranged to go through the larger Ra of the adjacent
dendritic cylinder instead of the small soma Ra). This may
look strange for the case of a single dendrite. It makes more
sense in the case of an apical and basal dendrite: if synaptic
current flows from one to the other, one imagines that the
soma has some effect. Note also that whether you use a
CONNECTCROSS message between cylindrical compartments onto the
same sphere really should depend on their topological
relation. For example, basal dendrites should probably be
cross-connected to each other but not to an apical one.
readcell will issue all the possible CONNECTCROSS messages
automatically, so you may want to delete some which are not
consistent with your intended topology.
The compartment Im is the sum of axial currents and injected
current only. The (transmembrane) channel currents or the
leakage current are not included. For a multicompartment
cell, under a quasistatic approximation (C*dV/dt is small), Im
is approximately equal to the sum of the channel and leakage
currents, due to charge conservation. This approximation is
used in the efield object (see efield.txt) to allow Im to be
used to calculate external field potentials. The exception to
this is when Im is calculated with hsolve in chanmode 4. In
that case, Im is directly calculated as the sum of the channel
currents and leakage current though Rm.
As of GENESIS version 2.2, symcompartments may be used
with the hsolve method, allowing the use of fast implicit
numerical integration methods.
Example: Use the showmsg command to examine the messages to and from
/CA3/soma, /CA3/apical_10, /CA3/basal_8, etc. in the traub91
simulation.
See also:
compartment ,
readcell
Object Type: synchan
Description: Synaptically activated channel.
Author: Mike Vanier 11/94
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: Synchan_type [in src/newconn/newconn_struct.h]
Size: 200 bytes
Fields: activation driving force (transmitter) for channel
conductance
Ik channel current
Gk time varying channel conductance
Ek reversal potential of channel
tau1 first time constant of channel activation
tau2 second time constant of channel activation
gmax peak channel conductance
frequency random activation frequency (default = 0)
nsynapses number of incoming spike messages (readonly)
time_last_event arrival time (including delay) of last spike (readonly)
Aplus unused field available to store positive weight changes
Aminus unused field available to store negative weight changes
event_buffer_size size of event buffer (readonly)
pending_events number of pending spike events in event
buffer (readonly)
nodes_per_synapse number of event nodes to allocate per
synapse (default 1)
synapse synapse buffer
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Synchan [in src/newconn/synchan.c]
Classes: segment channel synchannel
Actions: CREATE set synapse_size hidden field
INIT assign activation = 0
PROCESS update Gk, calculate Ik
RESET assign activation = 0, Gk = 0; calculate
time-step-dependent coefficients
RECALC recalculate time-step-dependent coefficients
CHECK make sure tau1>0, tau2>0; make sure a VOLTAGE
message is present (in order to calculate Ik)
SAVE2 called by the save command
RESTORE2 called by the restore command
EVENT put a spike event into the event buffer
ADDMSGIN
DELETEMSGIN
MSGINDELETED
RESETBUFFER reset size of event buffer to
(nodes_per_synapse * nsynapses) nodes
DELETE delete the element
COPY copies the element
Messages: VOLTAGE Vm
ACTIVATION activation
RAND_ACTIVATION probability amplitude
MOD modulation
SPIKE
------------------------------------------------------------------------------
Notes: Simulates a time dependent synaptically activated ionic
channel. A variable channel conductance Gk is activated by
the application of transmitter. This conductance then changes
with damped second-order characteristics with a time course
given by two time constants tau1 and tau2. This gives rise to
an alpha function/dual exponential conductance waveform for an
impulse spike input. The channel also calculates channel
current Ik and therefore needs the membrane state (Vm).
Each SPIKE message to a synchan establishes a synaptic
connection and increments nsynapses. The synapses are
numbered starting with 0, and each contains a field for a
synaptic weight and a propagation delay. Thus, a synchan has
some of the characteristics of the axons that make synaptic
connections to activate the conductance. For example, the
weight of the first synaptic connection is held in the field
"synapse[0].weight" while the delay is "synapse[0].delay". Gk
reaches a value gmax*weight for a single event delivered with
a SPIKE message. Note that even though synapses are not
elements, they do have fields that can be accessed
individually. They can be thought of as "sub-elements" or
substructures of the element.
Any number of spike events can be pending per synapse.
synchan stores all spike events in a buffer until they are
scheduled to occur. If enough events come in to overload
the buffer, the buffer will dynamically expand to enable
storage of all events. The size of the buffer in events is
stored in the "event_buffer_size" field which is readonly.
The number of actual spikes in the buffer which have not
yet hit the channel are stored in the "pending_events"
field (also readonly). The "nodes_per_synapse" field
controls how many large the event buffer is initially. The
default is to have one node per synapse, but if you expect
a lot of events or very few events you can change this
number to be greater or less than the default (1),
respectively. This will speed up the simulation slightly
in the first case and save memory in the second. If you
leave this field alone the object will still work fine.
The "resetsynchanbuffers" command will cause all the
buffers in all synchan and derived objects to be reset to
a size of nodes_per_synapse*nsynapses (which will also
cause all pending events to be flushed).
Unlike most messages, a SPIKE message may only be sent from
certain objects, e.g. the spikegen and randomspike objects.
The example in Scripts/tutorials/tutorial4.g illustrates the
use of synaptic connections with a very simple model of a
neuron that translates action potentials generated in the soma
into spike events using a spikegen, and then creates a
feedback synaptic connection to a synchan in its dendrite.
The synchan also receives random background activation with
spikes provided by a randomspike element. Chapters in "The
Book of GENESIS" describe this tutorial in detail, the
construction of networks with synchans, and the use of GENESIS
utility functions to create synaptic connections and provide
information about connections in a network. The documentation
for Connections also provides information about ways to make
synaptic conections.
The ACTIVATION message can be used to directly activate the
synchan conductance without creating a synapse. ACTIVATION
messages do not create synapses with weight and delay fields.
One use would be to deliver spikes to a synchan from objects
that cannot deliver SPIKE messages, without using an
intermediate spikegen object to create SPIKE messages. In
this case the activation that is sent with the SPIKE message
should last for a single time step dt, and have an amplitude
of 1/dt to normalize the activation to a unit area when
integrated over this single time step. Then, it will have the
same effect as a SPIKE message, and the result will be
independent of dt. The other case would be one in which an
activation is given that persists over multiple time steps, as
in an in vitro experiment that provides synaptic activation
that does not arise from axonal spikes. In that case, no
normalization by 1/dt is needed. The activation will be
integrated over the duration of the stimulus, and will not
depend on dt.
The MOD message is used to to implement neuromodulation.
The MOD message simply scales the channel activation for
that time step by the factor which is sent with the MOD
message. Note that this globally affects all the synapses
in the synchan. If you want synchans where some synapses
are modifiable but not others, you should divide it into two
synchans and only have a MOD message on the modifiable one.
The MOD message could also be used to implement learned
time-dependent modification of activation, by using a
script_out or extended object to implement an algorithm for
synaptic plasticity and to send the MOD message. The
hebbsynchan and facsynchan objects provide other mechanisms
for implementing synaptic plasticity.
The "copy" command will fail for any synchan, facsynchan, or
hebbsynchan which is receiving SPIKE messages. The correct
way to set up simulations is to set up prototype cells which
do not receive any SPIKE messages on their synchans, copy
these cells, and then add the appropriate SPIKE messages (by
hand or by using planarconnect or volumeconnect). We are
working on a more "intelligent" copy command which will permit
copying of synchans with SPIKE messages, but for now, don't do
it.
This object used to be called synchan2 in genesis 2.0.1.
Since it does everything that the old synchan does without
the limitations of that object we have retired the old
synchan and renamed synchan2 to be synchan. "synchan2" is
now just an alias for synchan -- they are identical.
Additions for GENESIS 2.4:
The individual synapse substructures of the synchan now have
four additional fields that can be used to implement synaptic
plasticity in hsolved synchans.
'last_spike_time' records the arrival time (including delay) of the
last presynaptic spike. It can be used along with the
'lastevent' field of the cell spikegen to determine the times
of presynaptic and postsynaptic spikes. It is set to -1 on
RESET.
The settable fields 'Aplus' and 'Aminus' are set to 0.0 on
RESET. Otherwise, they are not used by the synchan. They are
available to store positive and negative weight when synaptic
plasticity rules are applied with an external function or
object, such as the stdp_rules object. Likewise, 'lastupdate'
is not directly used by the synchan, except to set it to -1 on
RESET. It is used by plasticity objects such as stdp_rules to
keep track of when the synapse weight, Aplus, and Aminus
fields were last updated.
Example: (Using Scripts/tutorials/tutorial4.g)
genesis > showfield /cell/dend/Ex_channel synapse[1].weight
[ /cell/dend/Ex_channel ]
synapse[1].weight = 10
genesis > echo {getfield /cell/dend/Ex_channel synapse[1].delay}
0.004999999888
genesis > showfield /cell/soma/Ex_channel synapse[0].last_spike_time
[ /cell/soma/Ex_channel ]
synapse[0].last_spike_time = 99.92880249
See also:
resetsynchanbuffers ,
Connections ,
NewSynapticObjects ,
hebbsynchan ,
facsynchan ,
getsyncount ,
getsynindex ,
getsynsrc ,
getsyndest ,
New Synaptic Plasticity Objects,
stdp_rules
Object Type: synchan2
Description: Synaptically activated channel.
Author: Mike Vanier 11/94
Notes: This object is just an alias for synchan, for
backwards-compatibility. The synchan2 object from genesis
2.0.1 has been renamed synchan, since it has all the
functionality of the old synchan object without its
limitations.
See also:
synchan
Object Type: tab2Dchannel
Description: Hodgkin-Huxley type channel with two-dimensional tables
for alpha (A) and alpha + beta (B), allowing the rate variables to
have dependencies on two variables, x and y (e.g., membrane voltage
and an ion concentration).
Author: E. De Schutter, BBF-UIA Aug 94Caltech (1/91)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: tab2channel_type [in src/olf/olf_struct.h]
Size: 184 bytes
Fields: Gk channel conductance
Ik channel current
Ek channel reversal potential
Gbar channel maximum conductance
X value of X gate; optional gate, X=m
Y value of Y gate; optional gate, X=h
Z value of Z gate; optional gate, Z is
concentration dependent if Z_conc is set (default)
Z_conc indicates Z gate is concentration dependent (default 1)
X_A table for alpha function for X
X_B table for alpha + beta function for X
X_alloced flag for allocation of X_A and X_B
Y_A table for alpha function for Y
Y_B table for alpha + beta function for Y
Y_alloced flag for allocation of Y_A and Y_B
Z_A table for alpha function for Z
Z_B table for alpha + beta function for Z
Z_alloced flag for allocation of Z_A and Z_B
Xpower power to raise X gate to
Ypower power to raise Y gate to
Zpower power to raise Z gate to
instant {INSTANTX}, {INSTANTY}, or {INSTANTZ} to
determine the gate to instantly set to A/B
Xindex specifies role of x and y for X gate
Yindex specifies role of x and y for Y gate
Zindex specifies role of x and y for Z gate
surface compartment surface area used with DOMAINCONC
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Tab2DChannel [in src/olf/tab2channel.c]
Classes: segment channel
Actions: TABREAD TABSAVE RESTORE2 SAVE2 SHOW SET TABCREATE
CHECK PROCESS RESET INIT
Messages: VOLTAGE voltage [membrane voltage of compartment]
EK Ek [reversal potential]
CONCEN concen [ion concentration sent to channel]
CONCEN1 concen [ion concentration sent to channel]
CONCEN2 concen [ion concentration sent to channel]
DOMAINCONC Ik scale [ion current from another channel, to
be multiplied by scale, and divided by
the surface field]
ADD_GBAR offset [increment to be added to Gbar]
------------------------------------------------------------------------------
Notes: The tab2Dchannel object is very similar to the tabchannel, and
calculates the channel conductance and current from the
equations
Gk = Gbar*X^Xpower * Y^Ypower * Z^Zpower
Ik = Gk * (Ek - V)
where the gates obey the Hodgkin-Huxley equations
dX/dt = A_X - B_X*X
dY/dt = A_Y - B_Y*Y
dZ/dt = A_Z - B_Z*Z
Note that, as with the tabchannel, A corresponds to the
Hodgkin-Huxley alpha rate variable, and that B = alpha + beta
= 1/tau.
However, the TABCREATE action for the tab2Dchannel takes
additional arguments ydivs, ymin, and ymax, in in order to
allocate the two-dimensional tables for X_A, X_B, Y_A, etc.
The tables now have two indices, where the first one runs from
0 to xdivs and the second one from 0 to ydivs. Typical
commands for allocating tables and setting values would be
call {chanpath} TABCREATE X {xdivs} {xmin} {xmax} \
{ydivs} {ymin} {ymax}
setfield {chanpath} X_B->table[{i}][{j}] {alpha + beta}
As there are currently no utilities like setupalpha or
setuptau for filling tab2Dchannel tables, the setfield command
above would be used in a doubly-nested for loop that
calculates the A and B values for the two indices.
When using two-dimensional tables, it may be necessary to
experiment with the table size in order to obtain the desired
accuracy without using large tables, which would result in
both excessive memory use and setup time. When using a
one-dimensional table, it is customary to use a large table,
either by setting xdivs to a large value, or by using TABFILL
to expand the table with interpolated values. Then the
calc_mode field for each table would be set to zero
(NO_INTERP), in order to save computation time. For objects
that use 2-D tables, it is best to use a smaller values of
xdivs and ydivs and to perform linear interpolation is
performed at run time. This is the default. In the unlikely
event that you want to disable interpolation, set the table
calc_mode to NO_INTERP (zero). For example:
setfield {chanpath} X_A->calc_mode {NO_INTERP}
As with the tabchannel, a message carrying the membrane
voltage or a concentration is sent to the channel so that the
channel can retrieve the appropriate A and B table values to
calculate the gate activations (X, Y and Z) and the resulting
channel conductance. However, the tab2Dchannel can have two
messages, in order to specify both the x and y variables.
There are two new messages for sending concentrations (or
anything else), CONCEN1 (the same as CONCEN) and CONCEN2.
Another message DOMAINCONC provides a highly simplified model
to obtain the ionic concentration directly, using the current
sent from another channel, times a scale factor, and dividing
by the surface area of the parent compartment.
There are also three fields Xindex, Yindex, and Zindex. These
fields are used for each gate to define which message refers
to the x variable and which refers to the y variable. The
index fields may each be assigned to one of the pre-defined
global variables VOLT_INDEX, C1_INDEX, C2_INDEX, DOMAIN_INDEX,
VOLT_C1_INDEX, VOLT_C2_INDEX, VOLT_DOMAIN_INDEX, C1_C2_INDEX,
and DOMAIN_C2_INDEX.
The first four of these are used when a gate depends on only
one variable. In this case, xdivs should be set to zero for
that gate, and the y variable (corresponding to the second
index) used to fill the A and B tables. Then, the prefix
(VOLT, C1, C2 or DOMAIN) specifies whether the VOLTAGE,
CONCEN1, CONCEN2, or DOMAINCONC message is used to provide the
y variable. The remaining five of these index variables are
of the form x_y_INDEX, and similarly specify which of two
messages are used to specify the x and y variables. Thus if
Xindex is set to VOLT_C1_INDEX, a VOLTAGE message would
specify the x variable of the X_A and X_B tables, and a
CONCEN1 message would specify the y variable. If you wanted
to have a second gate Y which depended on another ionic
concentration, you would also send a CONCEN2 message, and set
Yindex to C2_INDEX.
The instant field may be set to {INSTANTX}, {INSTANTY}, or
{INSTANTZ} to specify that the X, Y, or Z gate value will be
instantly set to A/B, rather than using the A and B table
values in the differential equations above. This allows the
channel conductance to have a multiplicative factor of A/B.
This is often used to model a conductance having a
multiplicative Ca-dependent factor, or to implement
Morris-Lecar models with zero time constant for activation.
The TABSAVE and TABREAD functions may be called to save the
channel tables to a file to be read in when making a
subsequent simulation run. These are described in the
documentation for the tabchannel.
See the documentation for tabchannel for explanations of the
other actions that are often called in a simulation script.
Example: see Scripts/neurokit/prototypes/MoczydKC.g
See also: Interpol documentation (
Tables ),
tabchannel
Object Type: tabchannel
Description: Hodgkin-Huxley type voltage activated channel with tabulated
equations.
Author: E. De Schutter, Caltech (1/91)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: tab_channel_type [in src/olf/olf_struct.h]
Size: 168 bytes
Fields:
activation channel activation
Gk channel conductance
Ik channel current
Ek channel reversal potential
Gbar channel maximum conductance
X value of X gate; optional gate, X=m
Y value of Y gate; optional gate, X=h
Z value of Z gate; optional gate, Z is concen-
tration dependent if Z_conc is set (default),
voltage dependent otherwise.
Z_conc indicates Z gate is concentration dependent
(default 1), or voltage dependent (if 0)
X_A table for alpha function for X
X_B table for beta function for X
X_alloced flag for allocation of X_A and X_B
Y_A table for alpha function for Y
Y_B table for beta function for Y
Y_alloced flag for allocation of Y_A and Y_B
Z_A table for alpha function for Z
Z_B table for beta function for Z
Z_alloced flag for allocation of Z_A and Z_B
Xpower power to raise X gate to
Ypower power to raise Y gate to
Zpower power to raise Z gate to
instant {INSTANTX}, {INSTANTY}, or {INSTANTZ} to
determine the gate to instantly set to A/B
surface compartment surface area used with DOMAINCONC
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: TabChannel [in src/olf/tabchannel.c]
Classes: segment channel
Actions: CALC_BETA CALC_ALPHA CALC_MINF DUMP RESTORE2 SAVE2
SHOW SET TABDELETE TABFILL TABCREATE TABREAD TABSAVE
CHECK PROCESS RESET INIT
Messages: VOLTAGE voltage [membrane voltage of compartment]
EK Ek [reversal potential]
CONCEN concen [ion concentration sent to channel]
DOMAINCONC Ik scale [ion current from another channel, to
be multiplied by scale, and divided by
surface field]
ADD_GBAR offset [increment to be added to Gbar]
------------------------------------------------------------------------------
Notes: Tabulated hh-like channel. The standard voltage dependent
activation (X) and inactivation (Y) factors are present. For
concentration dependent processes a third factor (Z) has been
added. Z can do a lot of things; the most important is that
it can get a different message (CONCEN) than X and Y (VOLTAGE).
Standard use for Z is concentration dependent inactivation,
using a Zpower > 0. An alternative is to use it for
codependent activation; using Zpower<0, Z will equal concen
value times v-dependent table-value. The Z_conc flag can be
unset (set to zero) to allow a voltage-dependent Z gate.
The DOMAINCONC message provides a highly simplified model
to obtain the ionic concentration directly, using the current
sent from another channel, times a scale factor, and dividing
by the surface area of the parent compartment.
The table for the object is created using a call to the
TABCREATE action of the object. For computational efficiency
the forward rate factor alpha (A) and 1/tau (B) are tabulated
in A-table and B-table.
The tabchannel element is very similar to the hh_channel
element, except that it uses tables for the voltage and other
dependencies. It speeds up computation by using table lookups
rather than calculations depending on exponentials. It also
provides more flexibility, being able to specify voltage
dependencies not falling in the traditional Hodgkin-Huxley
forms.
The gate obeys the following equations:
dX/dt = A_X - B_X*X
dY/dt = A_Y - B_Y*Y
dZ/dt = A_Z - B_Z*Z
Gk = Gbar X^Xpower} Y^Ypower} Z^Zpower}
Ik = Gk * (Ek - V)
NOTE: These equations are slightly different from the usual
Hodgkin-Huxley equations where:
dX/dt = alpha*(1 - X) - beta*X
The tables in this element are therefore actually A = alpha,
and B = 1/tau = alpha + beta. This change reduces the number
of calculations to be made on the table output during the
integration.
The alpha and beta functions of the X, Y and Z gates are
implemented as tables and therefore have to be explicitly
allocated using the TABCREATE function. Copies of tabchannel
use the original arrays unless new arrays are explicitly
allocated. The X and Y gates use the same VOLTAGE message.
The Z gate uses the CONCEN message, which can be any field. It
allows for dependencies on other parameters.
The instant field may be set to {INSTANTX}, {INSTANTY}, or
{INSTANTZ} to specify that the X, Y, or Z gate value will
be instantly set to A/B, rather than using the A and B
table values in the differential equations above. This
allows the channel conductance to have a multiplicative
factor of A/B. This is often used with the Z gate to model
a Ca-dependent conductance, or to implement Morris-Lecar
models having zero time constant for activation. For an
example, see the implementation of the Ca-dependent K
Channel in Scripts/neurokit/prototypes/traub91chan.g.
The TABCREATE function
TABCREATE here is different from the table and tabgate
elements. We only need to specify which gate to set up, and
both tables for the gate will be filled.
call <element> TABCREATE <X/Y/Z> <xdivs> <xmin> <xmax>
This call creates two tables for X, Y, or Z with indices from
0 to xdivs, i.e. xdvivs + 1 entries which span the range xmin
to xmax. Values outside this range are linearly extrapolated
using the nearest 2 table entries.
Entries in these tables are made with statements like
setfield Na_chan X_A->table[0] 0.05
There are several alternatives to using a long sequence of
setfield commands to fill the tables. The file2tab command
can be used to fill the tables from a file of values. If the
rate (alpha and beta) or state (tau and minf) variables can be
expressed as a mathematical function, a for loop may be used
to fill the tables. For functions of the form (A + B * x) /
(C + exp((x + D) / F)), the setupalpha or setuptau commands
may be used. This is also discussed in Chapter 19 of The
Book of GENESIS (2nd ed.)
The TABDELETE function
When deleting tabchannels, 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 tabchannels
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 tabchannel.
The TABFILL function
TABFILL expands the table by using interpolation on the
existing table entries. Again, the syntax is different from
that for table and tabgate elements, and one just has to call
TABFILL once to fill both the arrays corresponding to that
gate:
call <element> TABFILL <X/Y/Z> <xdivs> <fill_mode>
xdivs specifies the number of divisions that the expanded
tables should have.
fill_mode is one of
0 = B-spline fill (default)
1 = cubic spline fill (not yet implemented)
2 = Linear fill
Tables have a calc_mode field that is by default set to
LIN_INTERP (a pre-defined global variable equal to one), so
that linear interpolation is performed at run time, allowing
the use of a smaller table. If sufficient memory is
available, it will be faster to perform the interpolation when
the table is created, by expanding it with TABFILL. Then, run
time interpolation should be disabled by setting the calc_mode
of the tables to NO_INTERP (zero). For example:
setfield {chanpath} X_A->calc_mode {NO_INTERP}
setfield {chanpath} X_B->calc_mode {NO_INTERP}
The TABSAVE and TABREAD functions
As filling the tables can be time-consuming (particularly if
it is done using a for loop in a script), the TABSAVE and
TABREAD functions can be useful for saving channel tables and
re-loading them when the simulation is run again.
TABSAVE may be called after the channel has been created and
set up, in order wto save the tables to a file. For example:
call Purk_Kdr TABSAVE Purk_Kdr.tab
TABREAD is called after the channel has been created and the
tables have been allocated. For example:
if (!{exists Purk_Kdr})
create tabchannel Purk_Kdr
setfield Purk_Kdr Ek {EK} Gbar {GK} Ik 0 Gk 0 \
Xpower 2 Ypower 1 Zpower 0
call Purk_Kdr TABCREATE X {xdivs} {xmin} {xmax}
call Purk_Kdr TABCREATE Y {xdivs} {xmin} {xmax}
end
call Purk_Kdr TABREAD Purk_Kdr.tab
Scaling tables
When the fields X_A->sx, X_A->sy, X_A->ox, X_A->oy, and the
corresponding fields on X_B, Y_A, Y_B, Z_A, Z_B are set, the
tabgate element automatically scales on the entries in the
interpol_struct array so as to avoid scaling computations
during simulations. Care must be taken since the B table
contains 1/tau rather than the beta values. It is recommended,
therefore, that both alpha and beta be adjusted simultaneously
and identically. Alternatively, the scaletabchan function may
be used to scale the two tables in such a way as to scale
alpha, beta, tau, or the steady state activation (minf).
The CALC_ALPHA, CALC_BETA, and CALC_MINF functions
The CALC_ALPHA, CALC_BETA, and CALC_MINF actions are used with
calls of the form
y = {call <element> CALC_ALPHA <X/Y/Z> <x-value>}
in order to access values of alpha, beta or m_inf (the steady
state activation, alpha/(alpha + beta)) for the specified gate
(X, Y, or Z) and a particular value of the independent
variable. This feature is most often used for making plots of
these quantities. Note that the activation time constant can
be calculated from tau = 1/(alpha + beta).
Example: see Scripts/neurokit/prototypes/traub91chan.g
See also: Interpol documentation (
Tables ),
scaletabchan ,
setupalpha ,
setuptau ,
tweakalpha ,
tweaktau ,
hh_channel ,
tab2Dchannel
Object Type: tabcurrent
Description: A non-ohmic ionic current that provides instantaneous values
for Ik and the slope conductance Gk from 2-D tables.
Author: E. De Schutter, BBF-UIA 2/95-6/98
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: tab_current_type [in src/olf/olf_struct.h]
Size: 120 bytes
Fields: Ik channel current (calculated)
Gk channel conductance (calculated)
Ek channel reversal potential (calculated)
Gbar scaling factor for Gk and Ik
Gindex specifies role of x and y for G_tab and I_tab
alloced flag (= 2 when both tables have been allocated
surface compartment surface area used with DOMAINCONC
G_tab 2-D table for Gk
I_tab 2-D table for Ik
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: TabCurrent [in src/olf/tabcurrent.c]
Classes: channel segment
Actions: TABREAD TABSAVE TABCREATE SHOW CHECK PROCESS RESET
Messages: VOLTAGE voltage [membrane voltage of compartment]
CONCEN concen [alias for CONCEN1]
CONCEN1 concen [ion concentration sent to channel]
CONCEN2 concen [ion concentration sent to channel]
DOMAINCONC Ik scale [ion current from another channel, to
be multiplied by scale, and divided by
the surface field]
ADD_GBAR Gbar [increment to be added to Gbar]
------------------------------------------------------------------------------
Notes:
The tabcurrent object provides a fairly general way to compute non-ohmic
currents that depend on voltage or (more typically) both voltage and
concentration. The resulting current Ik and conductance Gk are obtained (with
interpolation, by default) from the two-dimensional tables I_tab and G_tab,
which are then scaled by the Gbar value. The cell reader (readcell) sets the
Gbar value by multiplying the conductance density specified in a cell
parameter file by the compartment area, as is does for other channels.
Unlike the tabchannel or tab2Dchannel, it is not assumed that the current
obeys Ohm's law and is proportional to the membrane potential Vm. However, a
compartment (or symcompartment) will expect a channel element to provide Gk
and the reversal potential Ek in a "CHANNEL Gk Ek" message, and use these to
calculate the incoming ionic current from Ik = Gk*(Ek - Vm). In order for a
tabcurrent element to be used like a channel, the G_tab table must contain
values that will produce the proper result for Ik when this calculation is
performed. This may be done by making the assumption that over a single time
step, Gk and Ek vary slowly compared to Vm. Then the approximation can be
made that dIk/dVm = - Gk, and that Ek = (Ik + Gk*Vm)/Gk. Thus, Ek is
calculated by the tabcurrent object, rather than being set by the user or by
an incoming message. Note that the sign of the current expresses the GENESIS
convention that current flow into a compartment is positive.
Thus, the I_tab table should be filled with values of Ik/Gbar and the G_tab
table should be filled with -dI_tab/dVm. GENESIS has two commands, setupNaCa
and setupghk, that will create and fill these tables for the special cases of
the Na-Ca exchanger pump and the Goldman-Hodgkin-Katz constant field equation.
For other cases, you will have to create and fill the tables yourself.
A table is allocated by calling the the TABCREATE function, for example:
call mytabcurrent TABCREATE I_tab {xdivs} {xmin} {xmax} {ydivs} {ymin} {ymax}
As the I_tab and G_tab tables are related, and must have the same dimensions,
calling TABCREATE for one of them automatically allocates memory for the
other. Thus, it is not necessary to call TABCREATE again for G_tab. As with
the table2D and tab2Dchannel objects, xdivs and ydivs refer to the number of
divisions in the tables, with the first index running from 0 to xdivs and the
second one from 0 to ydivs.
The tables are filled by commands of the form:
setfield mytabcurrent I_tab->table[{i}][{j}] {Ivalue}
setfield mytabcurrent G_tab->table[{i}][{j}] {Gvalue}
The source code for setupNaCa and setupghk (in src/concen/tabcurrent.c)
provides examples of filling the tables using C, rather than the scripting
language. This would be a good starting point for adding your own GENESIS
commands for setting up specialized non-ohmic currents.
By default, objects that use tables have the calc_mode for the tables set to
LIN_INTERP (a pre-defined global variable equal to one), so that linear
interpolation is performed at run time, allowing the use of a smaller table.
In the unlikely event that you want to disable interpolation, set the
calc_mode to NO_INTERP (zero). For example:
setfield mytabcurrent G_tab->calc_mode {NO_INTERP}
setfield mytabcurrent I_tab->calc_mode {NO_INTERP}
The TABSAVE and TABREAD functions may be called to save the channel tables to
a file to be read in when making a subsequent simulation run. These are
described in the documentation for the tabchannel.
The units to be used when setting the Gbar field depend on the units used for
the G_tab table, and should be chosen to that it results in the proper units
of conductance for Gk, e.g. Siemens. For example, the setupNaCa command
creates I_tab with units of (mM)^4 and G_tab with units of (mM)^4/Volts Then,
Gbar should be in units of Amperes/(mM)^4.
The Gindex field is similar to the Xindex, Yindex, and Zindex fields of the
tab2Dchannel, and is used to specify which message refers to the x variable
and which refers to the y variable when performing the table lookups. The
Gindex field may be assigned to one of the pre-defined global variables
VOLT_INDEX, C1_INDEX, C2_INDEX, DOMAIN_INDEX, VOLT_C1_INDEX, VOLT_C2_INDEX,
VOLT_DOMAIN_INDEX, C1_C2_INDEX, and DOMAIN_C2_INDEX.
The first four of these are used when a gate depends on only one variable. In
this case, xdivs should be set to zero for that gate, and the y variable
(corresponding to the second index) used to fill the I_tab and G_tab tables.
Then, the prefix (VOLT, C1, C2 or DOMAIN) specifies whether the VOLTAGE,
CONCEN1, CONCEN2, or DOMAINCONC message is used to provide the y variable.
The remaining five of these index variables are of the form x_y_INDEX, and
similarly specify which of two messages are used to specify the x and y
variables. Thus if Gindex is set to VOLT_C1_INDEX, a VOLTAGE message would
specify the x variable of the I_tab and G_tab tables, and a CONCEN1 message
would specify the y variable.
In principle, any of these values for Gindex are allowed by the tabcurrent
object. But, a VOLTAGE message is required in order to calculate Ek.
Although tabcurrent does not check to be sure that the VOLTAGE message is used
as an index into the tables, the tables would have to depend on voltage, in
order to have G_tab = -dI_tab/dV. So, in practice, Gindex is restricted to be
VOLT_INDEX, VOLT_C1_INDEX, VOLT_C2_INDEX, or VOLT_DOMAIN_INDEX. The most
common use of tabcurrent is when Ik depends on both membrane potential Vm and
an ionic concentration. Then, both VOLTAGE and CONCEN1 (or CONCEN) messages
are used, and Gindex is set to VOLT_C1_INDEX.
Example:
See also:
tab2Dchannel ,
setupNaCa ,
setupghk ,
Tables
Object Type: tabgate
Description: A gate with tabulated dependencies on any field for
opening and closing.
Author: U. S. Bhalla, Caltech (2/90)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: tab_gate_type [in src/olf/olf_struct.h]
Size: 96 bytes
Fields: activation input field, usually accessed by messages
m state of gate
alpha rate variable table filled by TABCREATE
alpha_alloced internal flag for table allocation
beta rate variable table filled by TABCREATE
beta_alloced internal flag for table allocation
instantaneous flag for looking at instantaneous response
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: TabGate [in src/olf/tabgate.c]
Classes: segment
gate
Actions: PROCESS
CHECK
RESET
SET
SAVE2
RESTORE2
TABCREATE
TABFILL
CALC_MINF
CALC_ALPHA
CALC_BETA
Messages: VOLTAGE compartment-voltage
SUM_ALPHA value-to-sum-onto-alpha-func
PRD_ALPHA value-to-multiply-alpha-func-by
SUM_BETA value-to-sum-onto-beta-func
PRD_BETA value-to-multiply-beta-func-by
EREST resting-potential-for-resets
Notes: A gate with tabulated dependencies on any variable for opening
and closing. Voltage and ion concentration are the most common
variables for dependencies. The tabgate object is very
similar to the vdep_gate object, except that it uses tables
for the voltage and other dependencies. It also has message
slots for additional dependencies. It is normally used to
send MULTGATE messages to a vdep_channel. However, this
combination has been largely supplanted by the tabchannel
object.
A gate state is calculated from the following differential
equation:
dm/dt = alpha(1 - m) - beta * m
The alpha and beta functions are implemented as tables and
therefore have to be explicitly allocated using the TABCREATE
function. Copies of tabgate use the original arrays unless new
arrays are explicitly allocated.
The TABCREATE function
TABCREATE here is different from the table element since we
need to specify which table to create:
call <element> TABCREATE <alpha/beta> <xdivs> <xmin> <xmax>
This call creates an array on alpha or on beta with xdivs
entries, which spans the range xmin to xmax. Values outside
this range are linearly extrapolated using the nearest 2 table
entries.
The TABFILL function
TABFILL expands the table by using interpolation on the
existing table entries. The syntax is different from the
table element, as one has to specify the array (alpha or beta)
being filled:
call <element> TABFILL <alpha/beta> <xdivs> <fill_mode>
xdivs + 1 specifies the number of entries that the expanded
tables should have.
fill_mode is one of
0 = B-spline fill (default)
1 = cubic spline fill (not yet implemented)
2 = Linear fill
Scaling tables
When the fields alpha->sx, alpha->sy, alpha->ox, alpha->oy,
and the corresponding fields on beta are set, the table
element automatically scales on the entries in the
interpol_struct array so as to avoid scaling computations
during simulations.
The CALC_ALPHA, CALC_BETA, and CALC_MINF functions
The CALC_ALPHA, CALC_BETA, and CALC_MINF actions are used with
calls of the form
y = {call <element> CALC_ALPHA <x-value>}
In order to access values of alpha, beta or m_inf (the steady
state activation, alpha/(alpha + beta)) for a particular value
of the dependent variable. This feature is most often used
for making plots of these quantities. Note that the
activation time constant can be calculated from tau = 1/(alpha
+ beta).
Example: see Scripts/neurokit/prototypes/traub91chan.g
See also: Interpol documentation (
Tables ),
tabchannel ,
vdep_channel
Object Type: table
Description: A table with a couple of message slots for adding
dependencies on other fields.
The table can be used in several modes, depending on the
step_mode field. These include:
Table lookup - incoming messages are used as an
index to the contents of the table. The output
is calculated using interpolation if the appropriate
mode is selected in the interpol_struct.
Function generation - The table steps through
its entries and emits the values. The
stepsize determines the rate at which the table is
scanned. Again, interpolation may be used.
Output buffering - Input message values arriving at the
table are stored on each timestep, and the table index
is incremented, till the table is full
Delay line - Input message values arriving at the table
are stored on each timestep, using the table as a
ring buffer. The output is the input from an earlier
time.
Spike output buffering - Input message values arriving at
the table are checked for threshold crossing. If
they pass, then the current simulation time is
stored in a table entry, and the table index
incremented.
Monitoring a large number of incoming messages -
Input message values are placed into successive
or defined table entries on every clock tick. This
is made much more useful because of a hack which
allows the table values to be sent backwards along
the messages using the TAB2FIELDS action.
The usual options for interpol_struct manipulations are
available for the table. These include special set options
for setting an entire interpol_struct at a time, file-
interface commands like tab2file and file2tab, and the
loadtab command for filling the table from the command line.
Author: U. S. Bhalla, Caltech (2/90)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: table_type [in src/olf/olf_struct.h]
Size: 80 bytes (minimum)
Fields: input input field to table, usually set by
messages. If step_mode=1, input field keeps
track of the current position in the table
output output value
table interpol struct for table; assigned by
TABCREATE
alloced internal flag for table allocation
step_mode This flag selects between several modes of
operation of the table.
0 = TAB_IO - Default mode. Table does lookup.
1 = TAB_LOOP - Table acts as a function
generator, looping back to the beginning
when all the entries have been scanned.
The input field is incremented by
step_size on each timestep, and
is used to perform the lookup.
2 = TAB_ONCE - Table acts as a function
generator, terminating when
all the entries have been scanned.
At this stage the output is fixed
at the last entry in the table.
3 = TAB_BUF - Table acts as a buffer.
Incoming msg values are stored in
successive table entries on each
timestep. The output field keeps
track of the table index.
4 = TAB_SPIKE - Table acts as a buffer
for spike times. Incoming msg values
are checked for crossing a
threshold, which is stored in the
'stepsize' field. If they pass,
then the simulation time is stored
in the table entry. The output
field keeps track of the table index.
5 = TAB_FIELDS - Table acts as a buffer for
many incoming messages. If the
messages are INPUT messages, each
message value is placed in a successive
table entry. If the messages are INPUT2,
then the second slot of the message
holds the table index.
The TAB2FIELDS action will go
back along these messages and place
the table values into the source fields.
This option does not work in parallel
or with extended fields.
6 = TAB_DELAY - Table acts as a delay line. Input to
the table arrives from the INPUT message as
usual, and output from the table is available
at the 'output' field as usual. The delay is
implemented as a simple ring buffer, in which
the 'input' field indexes the table to specify
which entry should receive input and supply
output. The 'input' field is incremented by
one each timestep. (This is unlike the
TAB_BUF mode, where the current sample number
is stored in the 'output' field.) The
duration of the delay is therefore equal to
xdivs * dt, where xdivs is the size of the
interpol struct and dt is the timestep of the
clock used by the table. Note that the
'stepsize' field is not used, and that the
contents of the table are NOT erased on RESET.
This restriction is necessary in case a
predefined input is required in the delay
line. If the user wishes to wipe out the table
then the command "setfield /table table ===0"
will set all entries to zero. (See the
documentation for Tables for an explanation of
this enhanced setfield syntax.)
stepsize increment to input for stepping through table
with each clock tick in step_modes 1 and 2.
In the case of step_mode 4, stepsize acts
as the spike threshold.
In step_modes 1 and 2, stepsize can also be
set to zero to use the current simulation time
to look up a value. The table uses the sum of
the current simulation time and the value of the
'input' field. This is designed for generating
a predefined stimulus waveform controlled by
the simulation time, even if the timesteps are
changing. Thus, if the input field has value -3,
and the simulation time is 10, the stimulus waveform
will be looked up for a time of 7. In this manner,
by using negative values in the input field, one
can delay the start of a stimulus waveform.
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: TableFunc [in src/olf/table.c]
Classes: segment
Actions: PROCESS
RESET
SET
TABCREATE Must be called to allocate the interpol_struct
of the table.
syntax:
call table TABCREATE xdivs xmin xmax
This produces a table with indices from 0 to
xdivs, i.e. xdvivs + 1 entries
which span the range xmin to xmax.
TABFILL Expands the table by using interpolation
on the existing table entries.
syntax:
call table TABFILL xdivs fill_mode
xdivs + 1 specifies the number of entries that
the expanded table should have.
fill_mode is one of
0 = B-spline fill (default)
1 = C_Spline fill (not yet implemented)
2 = Linear fill
TAB2FIELDS Sends values from the table back to the
originating element fields, only works with
the TAB_FIELDS stepmode.
syntax:
call table TAB2FIELDS
TABOP Carries out an operation on the entries in
the table, putting the result in the
'output' field.
syntax:
call table TABOP op [min max]
where op is the operation to perform and
min and max are the x range on the table
on which to operate
The available operations are:
a = average
m = min
M = Max
r = range (i.e., max - min)
s = slope
i = intercept
f = freq
S = Sqrt(sum of squares)
DUMP Saves the table fields and interpol entries
in a script-readable file. This is an
internal action only.
Messages: INPUT input-value-for-lookup
SUM value-to-sum-onto-output
PRD value-to-multiply-output-by
INPUT2 input-value-for-table index-for-value-to-go-to
------------------------------------------------------------------------------
Notes: A table with a couple of message slots for adding dependencies
on other fields. The table for the object is created using
tabcreate.
Does a table lookup with interpolation. Also permits one to
modify the table with sum and product messages, so as to
extend the dimensionality of the table.
The table element is a way of defining arbitrary input-output
functions. It is based on the interpol_struct described
above, and provides the simplest form of access to it. Other
values (possibly generated by other tables) may be summed or
multiplied into the output value by means of messages, to
permit pseudo-multidimensional functions to be generated by
the table. Tables can also be used as function generators.
The array with the table values has to be explicitly allocated
using the TABCREATE function. Copies of a table use the
original array unless a new array is explicitly allocated.
Basically:
output = lookup[input] * (prd values) + (sum values)
TABCREATE
The syntax for tables is simple, since there is only one
interpol_struct to worry about:
call <element> TABCREATE <xdivs> <xmin> <xmax>
This call creates the interpol_struct data structure, which is
rather badly named ``table''.
Scaling tables
When the fields table->sx, table->sy, table->ox, table->oy
are set, the table element automatically scales on the
entries in the interpol_struct array so as to avoid scaling
computations during simulations.
Example : Using the TAB_FIELDS options
============================CUT HERE======================================
//genesis
// This example illustrates the use of the TAB_FIELDS options in
// the table element.
// First, we create a bunch of neutrals. The createmap command
// lays them out in a 10x10 square array with unit spacing.
createmap neutral /foo 10 10 -object
// Then we create a table
create table /bar
call /bar TABCREATE 100 0 100
// We now assign the TAB_FIELDS step_mode. In this mode, incoming
// messages are sent to successive table entries, and updated
// on every clock tick.
setfield /bar step_mode 5 // TAB_FIELDS
addmsg /foo/proto[] /bar INPUT x
reset
step // To do the clock tick and assign the table values.
int i
/* Here we show the x fields */
echo
echo Showing x fields before:
for (i = 0; i < 100; i = i + 1)
echo {getfield /foo/proto[{i}] x} " " -n
end
// Here we show that the table entries are now equal to the
// x fields
echo
echo Showing table array
for (i = 0; i < 100; i = i + 1)
echo {getfield /bar table->table[{i}]} " " -n
end
// here we add 0.5 to each of the values in the table array.
for (i = 0; i < 100; i = i + 1)
setfield /bar table->table[{i}] \
{{getfield /bar table->table[{i}]} + 0.5}
end
// here we call the action in the table which goes back through
// the messages and puts the new values in the source fields,
// in this case the x coords of the array of neutrals.
call /bar TAB2FIELDS
// Here we look to see what happened.
echo
echo Showing x fields after:
for (i = 0; i < 100; i = i + 1)
echo {getfield /foo/proto[{i}] x} " " -n
end
echo
============================CUT HERE======================================
Bugs: All of the interpolation options depend on an internal field
of the interpol_struct, called invdx, which is set up during
table allocation using TABCREATE. Unfortunately this field is
not updated upon subsequent manipulations of the table or
interpol structure. Invdx has the value 1/dx where dx = (xmax
- xmin)/xdivs. To work around the bug please explicitly set it
when you need to use the interpolation options.
See also: Interpol documentation (
Tables ).
Object Type: table2D
Description: A two-dimensional table with interpolation.
Author: U. S. Bhalla MSSM May/93
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: [in src/olf/olf_struct.h]
Size: 124 bytes (minimum)
Fields: input x value input to table
input2 yvalue input to table
output Output of table lookup
negoutput Negative of table output
table 2d interpol struct for table
alloced Internal flag for table allocation
step_mode Not implemented
stepsize Not implemented
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: [in src/olf/table2d.c]
Classes: segment
Actions: SET TABCREATE PROCESS RESET
Messages: INPUT x-value-for-lookup y-value-for-lookup
SUM value-to-sum-onto-output
PRD value-to-multiply-output-by
X x-value-for-lookup
Y y-value-for-lookup
------------------------------------------------------------------------------
Notes: TABCREATE must be called to allocate the interpol_struct
of the table. The syntax is:
call table-element TABCREATE xdivs xmin xmax [ydivs ymin ymax]
As with other interpol_structs, xdivs and ydivs refer to the
number of divisions in the table, with the first index running
from 0 to xdivs and the second one from 0 to ydivs. If the
ydivs, ymin, and ymax parameters are not given, these will be
set to the values used for the x variable.
By default, objects that use 2-D tables (tab2Dchannel,
table2D, and tabcurrent) have the calc_mode for the tables set
to LIN_INTERP (a pre-defined global variable equal to one), so
that linear interpolation is performed at run time, allowing
the use of a smaller table. In order to disable
interpolation, set the calc_mode to NO_INTERP (zero). For
example:
setfield my2Dtable table->calc_mode {NO_INTERP}
Example: genesis > create table2D /foo
genesis > call /foo TABCREATE 5 0 1 5 0 1
genesis > setfield /foo table->table[0][0] 5
genesis > setfield /foo table->table[1][1] 10
genesis > setfield /foo table->table[3][3] 105
genesis > echo {getfield /foo table->table[3][3]}
105
See also:
table , Interpol documentation (
Tables ).
Object Type: taupump
Description: Implementation of a simple pump with a variable time constant
of removal. Should be coupled to a difshell, where the change
in concentration is computed.
Author: E. De Schutter, Caltech (11/90)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: taupump_type [in /usr/genesis/src/concen/conc_struct.h]
Size: 108 bytes
Fields: kP pump rate = inverse of tau in s
Ceq equilibrium concentration in mM
T_A factor for Tau
T_B exp factor for Tau
T_V half-voltage for Tau
T_C constant offset for Tau
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: TauPump [in src/concen/taupump.c]
Classes: gate segment
Actions: INIT
PROCESS
RESET
CHECK
Messages: VOLTAGE Vm
------------------------------------------------------------------------------
Notes:
The taupump and other ionic pumps provide various mechanisms to remove ions
from a concentration shell (difshell).
If a VOLTAGE message is received, carrying a membrane potential Vm (or any
other parameter used to vary the pump rate), the time constant is given
by tau = T_A*exp((Vm - T_V)/T_B) + T_C, and the pump rate is kP = 1.0/tau.
If there is no VOLTAGE message, tau is fixed to T_C, or to T_A if T_C = 0.
The pump rate kP and equilibrium concentration Ceq are sent with a
TAUPUMP message to a difshell, which uses them to produce a change in
its ion concentration dC/dt = -kPump*(C-Ceq).
For a general description of buffered calcium diffusion see:
De Schutter E., and Smolen P., "Calcium dynamics in large neuronal
models", in Methods in neuronal modeling: From ions to networks
(2nd edition), C. Koch and I. Segev editors, pp. 211-250 (1998). The
spinedemo simulation gives a detailed example of the use of the difshell,
taupump, and fixbuffer objects for modeling calcium diffusion in dendritic
spines.
Example: addmsg headpump0 headshell0 TAUPUMP kP Ceq
See also:
difshell ,
fixbuffer , Scripts/examples/spinedemo
Object Type: timetable
Description: A table of time values at which an activation variable
is set to different value for one timestep.
Designed to allow timestep independent synaptic activation
with controlled sequences of input.
Author: D. Jaeger, Caltech (3/95)
revised and extended for GENESIS 2.2 4/00
------------------------------------------------------------------------
ELEMENT PARAMTERS
DataStructure: timetable_type [in genesis/src/device/spike_struct.h]
Size: 176 bytes
Fields: method 1 = exponential inter-time interval
2 = gamma iti
3 = regular iti
4 = read times from ascii file
meth_desc1 method parameter
meth_desc2 method parameter
meth_dexc3 method parameter
seed random number generator seed
act_val value of activation when set to on
maxtime max. time up to which table is filled
maxpos table size
tabpos current table index
fname name of file if times are read from file
------- fields below should not be touched by user ----
*timetable floating point array
allocated allocation flag
------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: TimetableFunc [in genesis/src/device/timetable.c]
Classes: device
Actions: SET
RESET
PROCESS
TABCREATE
TABFILL
TUPDATE
Messages: [none]
-------------------------------------------------------------------------
Notes: The timetable consists of a floating point array of values
at which an activation variable is set to on.
The table can be filled with various distributions of inter-
time intervals. This procedure is controlled by the
TABCREATE, TABFILL, and TUPDATE actions. The fields
method, meth_desc1, meth_desc2, and meth_desc3 control
the process. Here is how it works:
TABCREATE: a table of size maxpos is allocated and filled with zeros.
TABFILL: a table is created and filled according to the following
rules:
method=1: exponential iti distribution.
-> meth_desc1 = mean iti.
method=2: gamma iti distribution with added refractory period
-> meth_desc1 = mean iti.
-> meth_desc2 = absolute refractory period.
-> meth_desc3 = order of gamma distribution
(integer between 1 and 6)
method=3: regular iti distribution
-> meth_desc1 = iti
method=4: read times from ascii file
-> filename = filename
maxtime: table is filled up to maximal value of maxtime
and appropriate table is allocated and maxpos is
set automatically.
seed: if seed != 0 then random number generator is
seeded before filling table with methods 1 or 2.
TUPDATE: the table is changed in the following way.
example: call timetable TUPDATE mode mintime maxtime new_iti [new_iti2]
i.e. the TUPDATE is done with a call statement and
4 variables need to be supplied.
mode=1: The time values are randomly jitterd for
+- 0.5 new_iti
mode=2: A new distribution following the current
method field is inserted between mintime and
maxtime. The old values in this time range
are thrown out, but surrounding values stay
intact. The new_iti field determines the new
mean iti. If a new_iti2 is given, the new iti is
changed linearly from new_iti to new_iti2 during
the period between mintime and maxtime.
mode=3: A specified number of spikes can be inserted
into a given time window. Usage:
call <tt> TUPDATE 3 starttime endtime n jitval
The first spike is inserted at starttime. If more
than one spike is to be inserted, subsequent spikes
are inserted at regular intervals until the nth
spike is inserted at endtime. If jitval <> 0 then
each inserted spike is randomly jittered by a value
of max. +-jitval.
Example:
create timetable tt
setfield tt maxtime 1 act_val 1.0 method 1 meth_desc1 0.02
/* create table with exponential distribution of mean 0.02 */
call tt TABFILL
/* connect table to synaptic events */
create synchan c3
addmsg tt c3 ACTIVATION activation
/* put burst with faster itis (iti 0.001) at time 0.1 to 0.2 */
call tt TUPDATE 2 0.1 0.2 0.001
/* put burst of diminishing itis (iti 0.001 to 0.01) at time 0.5 to 0.7 */
call tt TUPDATE 2 0.5 0.7 0.001 0.01
See also:
event_tofile , Scripts/examples/spike/spikes.g
Object Type: variable
Description:
The variable object allows the user to manipulate the actual
simulation data that is in an existing file or write new data into
it. It responds to incoming SAVE messages to write data to the file
and users can use its 'output' field to send messages to other
elements to display traces and so on. The functionality to replay
data in a variable on through an xview element is currently not in
place.
Values may need to be stored in a single variable at every time
step. File formats(including netcdf) allow variables to be arrays
so multiple values can be stored. The access of individual values in
a variable is done by indexing it. This index is associated with the
value of the simulation time.
As an example, if the Vm of the soma is saved every time step for 100 steps,
* values will be stored sequentially along the array. Assuming the
clockrate of the variable object (rate of acquisition) is 1.0
second, Vm at the 0th, 45th and 99th second can be got from
value[0], value[45] and value[99] respectively.
* Now if the rate at which the data was saved i.e the clockrate of
the variable object was set at 1e-03 (1 msec), the above values
would reflect the Vm values at times 0, 45 and 99 milliseconds
respectively.
* A better way for the user to establish/understand this relationship
can be achieved through the 'input' and 'output' fields of the
variable. The input field values represent the actual time values
and the output field reflects the value corresponding to the input,
i.e the value corresponding to a specific time instant.
* In the previous example for the acquisition rate being 1 msec, one
could set the input field to 45e-03 and expect to show a valid
output value. However if the input were set to just 45 (45 secs),
the output value will be undefined (usually a very large +ve number
or an extremely small +ve number not equal to 0. This indeterminate
value depends on the file format used as well as the operating
system in which it is executing)
* The append field in the diskio element also has an effect on how these
values should be interpreted. See Doc/diskio.txt for an explanation.
* Another important issue to note is that interpolated values will
not be returned for inputs that do not match the time instants
precisely. For instance, if the input field were set to 45.5 e-03,
the value returned in the output field will be the one that
corresponds to the prior time instant, in this case 45msec and not
a value interpolated between values at 45 msec and 46 msec.
* Also, for a correct acquisition of data at proper time instants,
the clockrate of the variable object should match that of the
parent diskio. If this is not the case, a reset would print a
warning to this effect but continue to function without crashing
the sytem. However, the values returned by the output values will
not directly correspond to the actual simulation time instant at
which the value was saved.
The file itself has to be initially opened or created by the parent
diskio object. In other words, a variable can be created only as the
child of a diskio object. The results of a simulation stored in the
file can be replayed through an xgraph widget by sending the
appropriate message and data(output field) to it from the variable
object. At present, the mechanics to replay data written by the
variable object through an xview/xvar widget are not in place but will
be made available in the near future.
NOTE: Variable objects can be created only for fileformats that
support creation of arbitrary variables, such as
Netcdf. Variables and metadata CANNOT BE CREATED ARBITRARILY
for FMT1 files, for example.
For purposes of consistency, however, when SAVE messages are
directly sent to the diskio object, the autoSAVE_diskio and
auto3-DPosSAVE_diskio child elements are automatically created
in both cases. These should NOT BE MANIPULATED but can be used
to inspect values in the file.
Since FMT1 files do not support the notion of arbitrary
variables the 'input' and 'output' fields are hidden and the
other fields are made readonly.
Author: V.Jagadish (9/96)
------------------------------------------------------------------------------
ELEMENT PARAMETERS:
DataStructure: Gen_Variable_Type [in src/diskio/diskio_struct.h]
Size: 120 bytes
Fields: datatype The type of the value(s) held in the variable
- The list of valid types are specified in the notes
section. - Defaults to 'float64' (64-bit float) if
not specified in the create command line - readonly
for FMT1 files
size The maximum number of data values the object
can hold.
- Can be specified on the create command
line with the -size option.
- The special size value 'unlimited' allows
any number of values to be written into
the variable.
- Defaults to 'unlimited' if not specified.
- If the datatype is char8 (8-bit char) the
user could provide a string as the argument
to the 'value' field without specifying a
size or index, and the size (which is the
number of chars in the string including the
trailing '\0') is internally
calculated and set in this field.
- readonly for FMT1 files
value The value(s) held by the variable.
- Since variables
can hold an array of values or a single one,
an index (with the genesis-style indexing
mechanism) needs to be specified while
setting or showing this field. The index
defaults to 0 if not specified, the
exception to it being the case that the
datatype is 'char8'.
- If the type is 'char8', not
specifying an index would translate
to mean the entire string and
individual indices would return the
character at that location.(See
examples)
- Multiple argument values can be
specified for this field (see
examples) and the values will be
accessed starting with index 0.
- The default value is undefined for all
data types
- readonly for FMT1 files
input This field stores the actual simulation time
for analog traces. In combination
with the output field it thus provides a way
for the user to see what trace (output) value
is associated with a particular simulation
time value(input). - See examples.
- Datatype of this field is hard-coded as
float64 (64-bit float)
- Default value is 0
- hidden for FMT1 files
output This read-only field serves as the data for
outgoing messages from the variable object to
other elements such as xgraph. The value
of this field always reflects the one
associated with the particular simulation
time value stored in the input field. It
acquires also the value specified through the
incoming SAVE message to the variable object.
- Datatype of this field is hard-coded as
float64 (64-bit float)
- Default value would be the value of the
variable corresponding to the default
input field value of 0 seconds.
(starting simulation time)
- hidden for FMT1 files
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: Gen_Variable [in src/diskio/gen_variable.c]
Classes: output
Actions: CREATE PROCESS RESET SET SHOW ADDMSGIN
FLUSH:
UPDATE: allows the object to commit to the file on disk
by writing out its contents
DELETE: allows committing to the file on disk,
if necessary and then deletes the
object and any children but does not
delete the underlying variable or any
of its attributes on file.
Messages: SAVE data
- An incoming message of this type to the variable
object indicates that the value of the field
(specified in the 'data' argument) of the source
element needs to be saved in it.
- These values will be stored in the value field
and the output field of the variable every time
step and if the variable is an array
the location for this value is determined according
to the current time as explained earlier.
------------------------------------------------------------------------------
Notes:
The default variable is an unlimited size array of 64-bit floating point
values and associated with the actual simulation time.
So, if the -size option is not specified while creating a variable
the size would be internally set to 'unlimited' but an attempt to show
the size field would show a number. This number is the maximum number of
elements written so far, maybe in another variable associated with
the simulation time. If no values had been written or if this were the first
variable created, then the size would indicate 0. Any number of values
could be subsequently set on this variable.
In order to create a scalar variable (that holds a single value) not
associated with time, use the -valuetype option with 'scalar'
as the argument. There is, however, no field named valuetype.
The datatype field stores the type of the variable as a string. The
types are chosen to be as generic as possible. They are not based on
the usual 'C' data types but rather on the user's perspective.
Table 1.1 shows the valid datatype names and what they mean to
the user.
Please note that not all these types are supported by all file formats.
An error to that effect will be printed if a variable of an unsupported
type is attempted to be created. Netcdf, in particular does not allow
resetting of datatypes or sizes for variables at all and an error will
be issued if setfield attempts to change the values of these fields.
Table 1.1 - Valid datatypes
Name Description
____ | ___________
|
|
uint8 | 8-bit unsigned int
|
int8 | 8-bit signed int
|
uint16 | 16-bit unsigned int
|
int16 | 16-bit signed int
|
uint32 | 32-bit unsigned int
|
int32 | 32-bit signed int
|
uint64 | 64-bit unsigned int
|
int64 | 64-bit signed int
|
float32 | 32-bit float
|
float64 | 64-bit float
|
uchar8 | 8-bit unsigned char
|
char8 | 8-bit signed char
|
char16 | 16-bit (unicode) char
|
string | string type (i.e not an array of chars)
|
________________+______________________________________________________
Examples:
create diskio /dout -filename "testfile.nc" -accessmode w
create variable /dout/stringvar -datatype char8 -value "This is a string variable";
showfield /dout/stringvar value // Would display the whole string
showfield /dout/stringvar value[1] // Would display the character h
create variable /dout/fixedsizevar -size 3 -datatype float64 -value \
"1.0 2.0 3.0"
create variable /dout/scalarvar -valuetype scalar -datatype int32 \
-value 10
create variable /dout/variablesizevar -datatype float32 -value \
"100.0 200.0 300.0"
showfield /dout/variablesizevar value[0] value[2]
showfield /dout/variablesizevar value[3] // This would show a very large +ve or
// -ve number => undefined
setfield /dout/variablesizevar value[0] 150.0 value[2] 250.0
showfield /dout/variablesizevar value[0] value[2]
create xform /f
create xgraph /f/g
addmsg /path/to/some-element /dout/variablesizevar SAVE <some-element-field>
addmsg /dout/variablesizevar /f/g PLOT output *<plotname> *<color>
step 100
setfield /dout/variablesizevar input 30
showfield /dout/variablesizevar output
delete /dout
For a clear example dealing with the SAVE message and replays,
please see :
Scripts/examples/diskiolib/variable/generate.g
Scripts/examples/diskiolib/variable/replaygraph.g
------------------------------------------------------------------------------
See also:
diskio ,
metadata
Object Type: vdep_channel
Description: A Hodgkin-Huxley type voltage-dependent channel, which
receives activation gate values from other elements.
Author: M. Wilson, Caltech (2/89)
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: vdep_channel_type [in src/hh/hh_struct.h]
Size: 96 bytes
Fields: Gk channel conductance
Ik channel current
Ek channel reversal potential
gbar channel maximum conductance
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: VDepChannel [in src/hh/vchannel.c]
Classes: segment channel
Actions: RESET
PROCESS
CHECK [CHECK does nothing]
SAVE2 invoked with the save command
RESTORE2 invoked with the restore command
Messages: VOLTAGE voltage
MULTGATE gate_state power
ADDGATE gate_state power
GMAX gmax
EK Ek
------------------------------------------------------------------------------
Notes: A vdep_channel calculates Gk by multiplying gbar by any number of
factors of the form (gate_state)^(power). These are typically
received with the MULTGATE message from a tabgate element. For
example, Gk = gbar*h*m^3 could be implemented with:
addmsg Na_squid/m Na_squid MULTGATE m 3
addmsg Na_squid/h Na_squid MULTGATE m 1
Here, m and h are vdep_gate or tabgate elements, and Na_squid is a
vdep_channel. Note that the field for the gate variable is called
'm', regardless of the name of the gate element.
For most uses, the vdep_channel has been superseded by the
tabchannel. It is sometimes used with a table and tabgate element
to implement conductances which depend on both concentration and
voltage (e.g. the potassium C-current).
Example: see Scripts/neurokit/prototypes/traub91chan.g
See also:
hh_channel ,
tabchannel ,
tabgate
Object Type: xbutton
Description: Executes script actions from button presses
Author: Maneesh Sahani / Upi Bhalla Caltech Feb/93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xbutton_type [in src/Xodus/widg/xbutton_struct.h]
Size: 132 bytes
Fields: fg Foreground color of text in button
bg Background color.
onfg Foreground color of text in button,
for on (pressed) state.
onbg Foreground color for on (pressed) state.
offfg Background color of text in button,
for off (unpressed) state.
offbg Background color for off (unpressed) state.
xgeom Position of left edge of button.
ygeom Position of upper edge of button.
wgeom Width of button.
hgeom Height of button.
onlabel optional text string to display in on state
Defaults to widget name in the GENESIS hierarchy.
offlabel optional text string to display in off state
Defaults to widget name in the GENESIS hierarchy.
onfont optional font for text in on state.
offfont optional font for text in on state.
script string representing actions to be performed
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XButton [in src/Xodus/widg/xbutton.c]
Classes: widget output
Actions:
B1DOWN: Button 1 pressed (left button)
B2DOWN: Button 2 pressed (middle button on 3 button mouse)
B3DOWN: Button 3 pressed (right button on 3 button mouse)
ANYBDOWN: Any button pressed.
XUPDATE: update internal fields when
displayed widget is changed.
Messages: none.
----------------------------------------------------------------------------
Notes: Can only be displayed in a form widget
The xbutton does not perbutton any computational operations.
It issues script calls depending on button presses.
Example:
create xform /form [0,0,500,100]
create xbutton /form/button1 [0,0,100%,100%] \
-onlabel "This button widget is on" \
-offlabel "This button widget is off" \
-onfg red \
-offfg blue \
-onfont 12x24 \
-script "echo.d1 left button; echo.d3 right button; echo any button"
xshow /form
See also: Widget documentation. Mouse events documentation
(
Clicks ), Scripts/examples/XODUS/widgets.g.
Object Type: xcell
Description: The cell pix is similar to the view pix, but is specialized to
display the geometry and state of compartments in
multicompartmental cell models. Each compartment is
represented by a line segment of variable thickness and color.
The position and length of each line segment comes from the
3-D coordinates of the element that the line represents. Each
compartment is drawn from the coordinates of the previous
compartment (electrically speaking) to the current one. The
color of the compartment may be used to represent the value of
a field of the compartment or of one of its subelements.
As with the view pix, it is displayed within a draw widget,
and refreshes itself every time its assigned clock ticks.
Therefore, care should be taken to ensure that the cell is
only being refreshed as often as you really want it to be.
For refreshes that are not associated with a running
simulation, the xupdate command can be used on the parent draw
widget.
Author: Upi Bhalla Mount Sinai June/93
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xcell_type [in src/Xodus/draw/xcell_struct.h]
Size: ? Depends on the number of compartments in the cell
being displayed.
Fields:
fg foreground color of cell, applies to labels for
compartments, which are as yet unimplemented.
script Script operation(s) to perform on a mouse click.
tx Translation distance in the x dimension. The
cell is displaced in the draw by this amount.
ty Translation in y.
tz Translation in z.
value contains path to the compartment which is clicked on.
pixflags set of flags specifying visibility, refreshes,
mouse sensitivity, and many other options. Use
the 'pixflags' utility command to find out more.
dia table of compartment diameters. For example,
"showfield cell dia->table[10]".
color table showing the current value of the field which
is used to set the color of a compartment.
colmin value of the displayed field corresponding to the
minimum of the color scale.
colmax value of the displayed field corresponding to the
maximum of the color scale.
diamin Compartments of this diameter or less are drawn at
minimum thickness (as a line).
diamax Compartments of this diameter or less are drawn at
maximum thickness, specified by diarange.
diarange specifies the maximum thickness of the line that
represents a compartment. There are two modes: if it
is a negative number, then the absolute value is
taken as the thickness of the line in pixels. If it
is positive, then the value is taken as the diameter
of the compartment in real space. The pixel
specification is easier to use, but does not scale
when the user zooms in or out in the draw widget. The
real space option requires one to have good values
for diameters, and take care that the units are
correct, or the lines may be so thick that they fill
the screen. Note that these values are the thickness
of the thickest compartment (usually the soma). The
remaining compartments will be scaled linearly
towards zero. The dependence on diamin and diamax is
described above. The default value of diarange is
-20, meaning that the thickest compartment will be
drawn with a line 20 pixels wide.
autocol When set to 1 (or TRUE), colmin and colmax are set to
the minimum and maximum values of the displayed field
in the cell, each time the pix is updated. The
default is 0 (FALSE), meaning that colmin and colmax
should be set by the user.
autodia When set to the default value of 1 (or TRUE), the
diamin and diamax values are automatically set to the
minimum and maxiumum compartment diameters of the cell
being represented. In order to set diamin and diamax
to other values, set autodia to 0 (or FALSE) before
setting diamin and diamax.
soma contains the index of the compartment to be displayed
as a spherical soma. When the xcell is created with
the default value of -1, the soma field is
automatically reset to the index of the compartment
having the largest diameter. When it has a value of
-2, all compartments are displayed as cylinders.
names array of compartment names, eg. "showfield cell
names[10]".
path sets the path (as a wildcard list) of all the
compartments (or symcompartments) to be displayed.
For example, /cell/##[TYPE=compartment] is a valid
path for a cell whose parent element is called /cell.
field the field to be displayed by color.
fieldpath may be used to optionally specify the path to a
child element of the compartments, so that "field"
will refer to a field of this element, rather than a
field of the compartment. For instance, one might
wish to display the current in an ion channel present
in some compartments.
labelmode when set, will allow compartments to be labeled by
number or name (not yet implemented).
cellmode specifies how to draw the cell. The allowed values
are endcoords (the default) or midcoords. (One will
usually not want to change this.)
npts When path is set, npts gives the number of compartments
which are represented. This value is useful when
looping over the names, color, or dia tables.
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XCell [in src/Xodus/draw/xcell.c]
Classes: output gadget
Actions: DELETE COPY SET CREATE RESET PROCESS
XUPDATE: update internal fields when
displayed widget is changed.
B1DOWN: Invoked when mouse Button 1 is pressed.
B2DOWN: Invoked when mouse Button 2 is pressed.
B3DOWN: Invoked when mouse Button 3 is pressed.
ANYBDOWN: Invoked when any mouse button is pressed.
B1DOUBLE: Invoked on a double click on mouse button 1.
B2DOUBLE: Invoked on a double click on mouse button 2.
B3DOUBLE: Invoked on a double click on mouse button 3.
XOCOMMAND: an action that can invoke the functions
in the 'script' field
XODROP: Called when a another pix is dropped onto this one.
XODRAG: Called when the mouse is clicked on this pix, and
the mouse moves while the mouse button is held down.
XOWASDROPPED: Called after this pix has been dropped onto
another one.
Messages: COLDIAPOS color dia x y z
COLDIA color dia
POSITION x y z
DIAMETER dia
COLOR color
------------------------------------------------------------------------------
Notes: The xmin, xmax, ymin, and ymax fields of the parent draw
widget should be set to values which are appropriate for the
dimensions of the cell. As with other pixes displayed in a
draw widget, the arrow keys may be used to translate the image
in the draw, and "<" and ">" to zoom out (smaller) and in
(larger). Likewise, the coordinate transformations described
in the xdraw documentation are available. You may find these
keyboard commands useful for fine tuning the xmin, xmax, ymin,
and ymax fields. Then, after inspecting them with showfield,
you may enter the final values in your script.
The messages which are accepted by the cell pix are usually
issued automatically, and not explicitly added by SLI addmsg
commands. As may be verified with the showmsg command, each
compartment which is represented in the xcell sends a COLOR
message to the xcell, giving the value of the field which is
to be mapped to a color.
Example:
// traub91proto.g and CA3.p should be copied from Scripts/traub91
include traub91proto.g
// Create a library of prototype elements to be used by the cell reader
create neutral /library
pushe /library
create symcompartment symcompartment
make_Na
make_Ca
make_K_DR
make_K_AHP
make_K_C
make_K_A
make_Ca_conc
pope
// Build the cell from a parameter file using the cell reader
readcell CA3.p /cell
// create and display the xcell
create xform /cellform [620,50,400,400]
create xdraw /cellform/draw [0,0,100%,100%]
setfield /cellform/draw xmin -0.003 xmax 0.001 ymin -5e-5 ymax 5e-5 \
zmin -1e-3 zmax 1e-3
xshow /cellform
echo creating xcell
create xcell /cellform/draw/cell
// Note that this particular cell uses symcompartments, not compartments
setfield /cellform/draw/cell colmin -0.1 colmax 0.1 \
path /cell/##[TYPE=symcompartment] field Vm \
script "echo widget clicked on = <w> value = <v>"
xcolorscale hot
reset
See also:
xpix ,
xview ,
xdraw ,
Clicks
Object Type: xcoredraw
Description: Foundation object class for displaying pixes. All other
draw classes (at present: dumbdraw, draw, and graph) are
subclassed from coredraw. Therefore these subclasses perform
a superset of the operations described here.
Coredraw and its subclasses can be thought of as providing
a window into a space where pixes reside, or a screen onto
which pixes are projected. One can select the size,
orientation and other parameters of this window/screen
according to the set of functions described below.
The functions provided by coredraw, which are inherited or
overridden by its subclasses, include:
Displaying and managing pixes.
Handling forward transforms for drawing pixes
Handling backward transforms for identifying
location of mouse events
Keyboard control over transformation parameters
such as zoom and pan.
Providing a mechanism for deciding which child
pix should recieve mouse events
Coredraw and subclassses do not display anything on their own.
The pixes provide the actual images and drawing routines
displayed in a coredraw widget/subclasses. It is important
to note that since the pix display, transformation and event
handling functions are present in the coredraw class, any pix
can be displayed in any draw subclass.
The coredraw widget can only display pixes using planar
orthographic projections in the xy plane. In other
words, x is to the right, y is up and the z coordinate
of pixes is ignored.
In a future revision the z coordinate will be used to determine
the order of redrawing pixes to enable pixes to obscure
each other according to depth.
Unless flexibility in transformation options would be
a handicap (e.g., in displaying a simulation layout where
alternative projections would just confuse matters) the
coredraw widget is not especially useful for displays.
The draw widget is recommended for all cases where
flexibility is desired, since the overhead in performing
the general transformations is minimal.
Author: Upi Bhalla Caltech April 93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xcoredraw_type [in src/Xodus/draw/xcoredraw_struct.h
Size: ?
Fields: fg Foreground color of coredraw (not used)
bg Background color.
xgeom Position of left edge of coredraw.
ygeom Position of upper edge of coredraw.
wgeom Width of coredraw
hgeom Height of coredraw
xmin left edge of window for displaying pixes.
ymin bottom edge of window for displaying pixes.
xmax right edge of window for displaying pixes.
ymax top edge of window for displaying pixes.
script Script operation(s) to perform on a mouse
click. The script calls to the coredraw widget
are only made if none of the child pixes has
expressed an interest in the event.
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XCoreDraw [in src/Xodus/widg/xcoredraw.c]
Classes: widget output
Actions: XUPDATE: update internal fields when
displayed widget is changed.
XOCOMMAND: an action that can invoke the functions
in the 'script' field
XODROP: Called when a pix is dropped into the widget.
Messages: none.
----------------------------------------------------------------------------
Notes: Can only be displayed in a form widget
The xcoredraw does not perform any computational operations
driven by the simulation clock.
Example:
create xform /form [0,0,500,500]
create xcoredraw /form/coredraw [0,0,100%,100%] \
-bg red -script "echo Hello, I am a coredraw widget"
setfield /form/coredraw xmin -2 xmax 2 ymin -2 ymax 2
// display the pixes here
create xsphere /form/coredraw/sphere -fg green -r 1\
-script "echo Hello, I am a sphere pix"
xshow /form
See also:
XODUS documentation, pix documentation, documentation
for coredraw subclasses.
Object Type: xdialog
Description: Maintains dialog state and executes script actions
from mouse button presses.
Author: Maneesh Sahani / Upi Bhalla Caltech May/93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xdialog_type [in src/Xodus/widg/xdialog_struct.h]
Size: 116 bytes
Fields: fg Foreground color of text in dialog
bg Background color.
xgeom Position of left edge of dialog.
ygeom Position of upper edge of dialog.
wgeom Width of dialog.
hgeom Height of dialog.
label optional text string to display in button.
Defaults to widget name in the GENESIS hierarchy.
font optional font for text in on state.
value Maintains character string displayed in widget.
fvalue Maintains float containing converted value of
widget.
script string representing operations to be performed
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XDialog [in src/Xodus/widg/xdialog.c]
Classes: widget output
Actions:
B1DOWN: Button 1 pressed to turn on dialog (left mouse button)
B2DOWN: Button 2 pressed to turn on dialog
(middle button on 3 button mouse)
B3DOWN: Button 3 pressed to turn on dialog
(right button on 3 button mouse)
ANYBDOWN: Any button pressed.
KEYPRESS: Any key pressed.
XPDATE: update internal fields when widget is changed.
Messages: INPUT.
----------------------------------------------------------------------------
Notes: Can only be displayed in a form widget
The xdialog does not perform any computational operations.
It issues script calls depending on button presses and
'returns'. It can also display the value of incoming messages.
Example
create xform /form [0,0,500,100]
create xdialog /form/dialog1 [0,0,100%,100%] \
-label "dialog" \
-fg green \
-bg black \
-font r24 \
-script "echo The value on <widget> is: <value>"
xshow /form
See also: Widget documentation. Mouse events documentation
(
Clicks )
Object Type: xdraw
Description: Main object class for displaying pixes. Subclassed
from coredraw. This widget provides general projection
transforms for pixes.
Like other coredraw subclasses, draw can be thought of as
providing a window into a space where pixes reside, or a
screen onto which pixes are projected. One can select the size,
orientation and other parameters of this window/screen
according to the set of functions described below.
The functions provided by draw, which are inherited or
overridden from the coredraw class, include:
Displaying and managing pixes.
Handling forward transforms for drawing pixes
Handling backward transforms for identifying
location of mouse events
Keyboard control over transformation parameters
such as zoom and pan.
Providing a mechanism for deciding which child
pix should recieve mouse events
Draw does not display anything on its own. The pixes
provide the actual images and drawing routines displayed
in a draw widget.
Keyboard commands may be used to translate or zoom the display
of pixes within a draw widget. Use the arrow keys to
translate the image in the draw, and "<" and ">" to zoom out
(make smaller) and in (make larger).
The draw widget can display pixes using both orthographic
and perspective projections. One can select between these
using keyboard commands as follows:
plane perspective key
-------------------------------------------
xy off z
xy on Z
yz off x
yz on X
xz off y
xz on Y
general orthographic off o
general perspective on p
In a future revision the z coordinate will be used to determine
the order of redrawing pixes to enable pixes to obscure
each other according to depth.
Author: Upi Bhalla Caltech April 93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xdraw_type [in src/Xodus/draw/xdraw_struct.h
Size: 172 bytes
Fields: fg Foreground color of draw (not used)
bg Background color.
xgeom Position of left edge of draw.
ygeom Position of upper edge of draw.
wgeom Width of draw
hgeom Height of draw
xmin x lower limit for displaying pixes.
ymin y lower limit for displaying pixes.
zmin z lower limit for displaying pixes.
xmax x upper limit for displaying pixes.
ymax y upper limit for displaying pixes.
zmax z upper limit for displaying pixes.
cx x coord of point in space which is to be located
at center of projection
cy y coord of point at center of projection
cz z coord of point at center of projection
wx window 'width'. Provided for backwards compatibility.
wy window 'height'. Provided for backwards compatibility.
vx x coord of viewpoint for 'o' and 'p' projections.
vy y coord of viewpoint for 'o' and 'p' projections.
vz z coord of viewpoint for 'o' and 'p' projections.
script Script operation(s) to perform on a mouse
click. The script calls to the draw widget
are only made if none of the child pixes has
expressed an interest in the event.
transform The projection transformation to
perform while displaying the pixes. One of
(z, Z, x, X, y, Y, o, p), described in the table
above.
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XDraw [in src/Xodus/draw/xdraw.c]
Classes: widget output
Actions: XUPDATE: update internal fields when
displayed widget is changed.
XOCOMMAND: an action that can invoke the functions
in the 'script' field
XODROP: Called when a pix is dropped into a draw widget.
Messages: CENTER cx cy cz
ZOOM wx wy
VIEWPOINT vx vy vz
where the values of these messages set the
specified projection controlling fields.
----------------------------------------------------------------------------
Notes: Can only be displayed in a form widget
If the xdraw is receiving messages it will recalculate
the projections each clock tick.
Example
create xform /form [0,0,500,500]
create xdraw /form/draw [0,0,100%,100%] \
-bg red -script "echo Hello, I am a draw widget"
setfield /form/draw xmin -2 xmax 2 ymin -2 ymax 2
// display the pixes here
create xsphere /form/coredraw/sphere -fg green \
-script "echo Hello, I am a sphere pix"
xshow /form
See also: Widget documentation, pix documentation, documentation
for coredraw and other subclasses.
Object Type: xdumbdraw
Description: Demonstration object class for displaying pixes. Subclassed
from coredraw. While this widget is functional, it is not
particularly useful for anything other than demo purposes for
code developers.
The coredraw widget should be used if the projections need
to be restricted to the xy plane, and the draw widget in
other cases.
Like other coredraw subclasses, dumbdraw can be thought of as
providing a window into a space where pixes reside, or a
screen onto which pixes are projected. One can select the size,
orientation and other parameters of this window/screen
according to the set of functions described below.
The functions provided by coredraw, which are inherited or
overridden by its subclasses, include:
Displaying and managing pixes.
Handling forward transforms for drawing pixes
Handling backward transforms for identifying
location of mouse events
Keyboard control over transformation parameters
such as zoom and pan.
Providing a mechanism for deciding which child
pix should recieve mouse events
Dumbdraw does not display anything on its own. The pixes
provide the actual images and drawing routines displayed
in a dumbdraw widget.
The dumbdraw widget can only display pixes using planar
orthographic projections. One can select between the
xy, yz and xz planes using the keyboard commands
z, x, and y respectively.
In a future revision the z coordinate will be used to determine
the order of redrawing pixes to enable pixes to obscure
each other according to depth.
Author: Upi Bhalla Caltech April 93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xdumbdraw_type [in src/Xodus/draw/xdumbdraw_struct.h
Size: ?
Fields: fg Foreground color of dumbdraw (not used)
bg Background color.
xgeom Position of left edge of dumbdraw.
ygeom Position of upper edge of dumbdraw.
wgeom Width of dumbdraw
hgeom Height of dumbdraw
xmin x lower limit for displaying pixes.
ymin y lower limit for displaying pixes.
zmin z lower limit for displaying pixes.
xmax x upper limit for displaying pixes.
ymax y upper limit for displaying pixes.
zmax z upper limit for displaying pixes.
script Script operation(s) to perform on a mouse
click. The script calls to the dumbdraw widget
are only made if none of the child pixes has
expressed an interest in the event.
transform The projection transformation to
perform while displaying the pixes.
z = xy plane
y = xz plane
x = yz plane.
(think of it as looking down from the selected
axis (eg, z) onto a plane (eg, xy).
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XDumDraw [in src/Xodus/widg/xdumbdraw.c]
Classes: widget output
Actions: XUPDATE: update internal fields when
displayed widget is changed.
XOCOMMAND: an action that can invoke the functions
in the 'script' field
XODROP: Called when a pix is dropped into a draw widget.
Messages: none.
----------------------------------------------------------------------------
Notes: Can only be displayed in a form widget
The xdumbdraw does not perform any computational operations
driven by the simulation clock.
Example:
create xform /form [0,0,500,500]
create xdumbdraw /form/dumbdraw [0,0,100%,100%] \
-bg red -script "echo Hello, I am a dumbdraw widget"
setfield /form/dumbdraw xmin -2 xmax 2 ymin -2 ymax 2
// display the pixes here
create xsphere /form/dumbdraw/sphere -fg green -r 1 \
-script "echo Hello, I am a sphere pix"
xshow /form
See also: XODUS documentation, pix documentation, documentation
for coredraw and other subclasses.
Object Type: xfastplot
Description: Optimised but limited graphing widget. Designed mainly for
high-speed display similar to an oscilloscope. Also designed
to use minimal memory so that large numbers of xfastplots
can be in use simultaneously. Limitations are that the number
of points on the plot must be known in advance, axes are
rudimentary, and only single plots are possible.
Plots in 6 modes, related to what an oscilloscope might do.
roll, oscilloscope, ring, xyring, waveplot, xywaveplot.
roll: New data points appear on the right and the old data
points shift leftwards.
oscilloscope: Trace fills in data points from left to right,
clearing after screen is full. Various trigger options.
ring: Similar to oscilloscope except that screen does not
clear. Instead the oldest points are overwritten. No triggering.
xyring: Same as ring except both x and y coordinates are
specified by separate messages for each point. Oldest points
are overwritten.
waveplot: All the Y points on the plot are simultaneously
specified. X points increase linearly across the plot.
Previous plot is lost.
xywaveplot: X and Y coordinates for all points are
simultaneously specified by separate messages for each point.
Each mode can be displayed using points or lines. Overlay
can be enabled for any mode, in which case old points are not
erased.
The color of each new set of data points can be
specified by the COLOR message.
Data points can abe added a variable number of points at a
time (Roll, oscilloscope, ring and xyring modes). Here the
NPLOT message is used. The first argument is the first entry
in an array of data points (e.g. an interpol_struct). The
second argument is the number of points to be plotted, and the
third is the starting index in the array. Scalar fields (e.g.
Vm) can be plotted as single-entry arrays with a starting
index of 0. The XPLOT message can be used along with NPLOT to
specify xyring mode. In this case, the argument to the XPLOT
message is the first entry in the corresponding X array of
data points.
Data points can also be plotted a full screen at a time
(waveplot or xywaveplot modes). The WAVEPLOT message
is used, and the argument of the message is the first
entry in the array of Y data points. If the XPLOT message
is also present, this becomes an xywaveplot. Again, the
argument of the XPLOT message is the first entry in the
array of X data points.
The fastplot widget has a number of special key and mouse
mappings:
event operation
-------------------------------------------------------
arrow keys Move the little tick marks on the x and
y axes up and down. The xval and yval
fields are updated to match the position
of the tick marks. This event triggers script
function calls if the function has the
.k suffix.
Mouse button Standard click operations. Passes x and y
coordinate values to the script using
the <x> and <y> special arguments.
Author: Upi Bhalla NCBS Bangalore May 1998
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xfastplot_type [in src/Xodus/widg/xfastplot_struct.h]
Size: 384 bytes (element) + 236 bytes (graphics) + 4 * npts (data)
Fields: fg Foreground color of graph (used for axes and labels)
bg Background color.
xgeom Position of left edge of graph.
ygeom Position of upper edge of graph.
wgeom Width of graph
hgeom Height of graph
npts int, number of points in plot.
overlay_flag If 1, overlay output traces rather than clearing
line_flag If 1, draw lines rather than dots
roll_flag If 1, use roll mode rather than ring mode
oscope_flag If 1, use oscilloscope mode rather than ring
trig_sign 0: Auto triggering
1: Trigger on +ve going events
-1: Trigger on -ve going events
ac_trig_flag 0: DC trig
1: AC trig
trig_thresh (double): Threshold for triggering.
update_dt average dt to maintain between X updates
request_dt Not yet used
xval Position of x tick mark
yval Position of y tick mark
xaxis_flag Draw x axis and tick if 1
yaxis_flag Draw y axis and tick if 1
color Color (0 - 64) to use for next point(s)
title Title text, top middle of graph
xtextmax X axis top text, lower right of graph
xtextmid X axis middle text, lower middle of graph
xtextmin X axis origin text, lower left of graph
ytextmax Y axis top text, top left of graph
ytextmid Y axis middle text, middle left of graph
ytextmin Y axis origin text, lower left of graph
script Script function to execute on clicks and
key events.
shortptr_flag If 1, treat the message as a pointer to
a short. Needed to work around a GENESIS
messaging limitation.
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: FastPlot [in src/Xodus/widg/xfastplot.c]
Classes: widget output
Actions: XUPDATE: update internal fields when
displayed widget is changed.
XOCOMMAND: an action that can invoke the functions
in the 'script' field
PROCESS: Update the plot display with new values
RESET: Clear out the plot display, zero out the values
CREATE: Make the plot
SET: used to handle special cases of set where memory
allocation is involved. The remainder
use the generic GENESIS set methods.
DELETE: Destroys the element and widget and storage
Messages:
NPLOT data_array n index
The first argument is the first entry in the data
array. The second argument is the number of entries
to use for data, and the third argument is the index
of the starting data entry.
WAVEPLOT data_array n
The first argument is the first entry in the data
array. The second argument is the number of points to
use.
XPLOT data
This message is only used in combination with NPLOT or
WAVEPLOT. The data argument is the first entry in the
x data array.
COLOR data
An integer from 1 to 64.
UPDATE_DT
Not yet implemented.
----------------------------------------------------------------------------
Notes: Can only be displayed in a form widget
Example: This example sets up 20 xfastplots getting various kinds of inputs.
The inputs are shown in the conventional xgraph on the left of the screen.
Most of this example is actually devoted to setting up interesting inputs.
The type of the xfastplot is indicated in the title of each plot.
The display mode is indicated at the bottom.
================================= cut here =================================
//genesis
int i, j
xcolorscale rainbow
create xform /form [0,0,1000,600]
create xgraph /form/graph [0,0,30%,100%] \
-xmax 400 -ymax 4 -yoffset 1 -ymin -1
for (i = 0; i < 5; i = i + 1)
for (j = 0; j < 4; j = j + 1)
create xfastplot /form/plot{i}{j} \
[{i * 12 + 30}%,{j * 15}%,12%,15%]
end
end
xshow /form
create xform /form2 [500,500,200,220]
create xbutton /form2/quit -script quit
create xtoggle /form2/overlay \
-onlabel "Overlay ON" -offlabel "Overlay OFF" \
-script "do_set overlay_flag <v>"
create xtoggle /form2/line \
-onlabel "Line mode" -offlabel "Dot mode" \
-script "do_set line_flag <v>"
create xtoggle /form2/xaxis \
-onlabel "X axis on" -offlabel "X axis off" \
-script "do_set xaxis_flag <v>"
create xtoggle /form2/yaxis \
-onlabel "Y axis on" -offlabel "Y axis off" \
-script "do_set yaxis_flag <v>"
create xbutton /form2/run -script "step 400"
create xbutton /form2/reset -script reset
xshow /form2
create table /tab[0]
call /tab[0] TABCREATE 100 0 100
for (i = 0; i < 101; i = i + 1)
setfield /tab[0] table->table[{i}] {sin {i / 10.0}}
end
setfield /tab[0] step_mode 1
create table /tab[1]
call /tab[1] TABCREATE 1 0 100
setfield /tab[1] table->table[0] 0
setfield /tab[1] table->table[1] 1
setfield /tab[1] step_mode 1
create table /tab[2]
call /tab[2] TABCREATE 100 0 100
for (i = 0; i < 101; i = i + 1)
setfield /tab[2] table->table[{i}] {sin {0.5 + i / 17.0}}
end
setfield /tab[2] step_mode 1
create table /tab[3]
call /tab[3] TABCREATE 100 0 100
for (i = 0; i < 101; i = i + 1)
setfield /tab[3] table->table[{i}] {rand 0 1}
end
setfield /tab[3] step_mode 1
create table /tab[4]
call /tab[4] TABCREATE 100 0 100
for (i = 1; i < 51; i = i + 1)
addmsg /tab[4] /tab[4] INPUT2 table->table[{i}] {i - 1}
addmsg /tab[4] /tab[4] INPUT2 table->table[{100 - i}] {101 - i}
end
addmsg /tab[0] /tab[4] INPUT2 output 50
setfield /tab[4] step_mode 5
create table /tab[5]
call /tab[5] TABCREATE 100 0 100
for (i = 1; i < 51; i = i + 1)
addmsg /tab[5] /tab[5] INPUT2 table->table[{i}] {i - 1}
addmsg /tab[5] /tab[5] INPUT2 table->table[{100 - i}] {101 - i}
end
addmsg /tab[2] /tab[5] INPUT2 output 50
setfield /tab[5] step_mode 5
create table /tab[6]
call /tab[6] TABCREATE 63 0 63
for (i = 0; i < 64; i = i + 1)
setfield /tab[6] table->table[{i}] {i}
end
setfield /tab[6] step_mode 1
addmsg /tab[6] /form/plot# COLOR output
addmsg /tab[0] /form/graph PLOT output *tab0 *red
addmsg /tab[1] /form/graph PLOT output *tab1 *green
addmsg /tab[2] /form/graph PLOT output *tab2 *blue
addmsg /tab[3] /form/graph PLOT output *tab3 *black
for (i = 0; i < 4; i = i + 1)
addmsg /tab[{i}] /form/plot0{i} NPLOT output 1 0
setfield /form/plot0{i} title NPLOT npts 256
addmsg /tab[{i %2 + 4}] /form/plot1{i} NPLOT table->table[0] index 0
setfield /form/plot1{i} title NPLOT npts 256
addmsg /tab[{i % 2 + 4}] /form/plot2{i} WAVEPLOT table->table[0] 100
setfield /form/plot2{i} title WAVEPLOT npts 100
addmsg /tab[{i}] /form/plot3{i} NPLOT output 1 0
addmsg /tab[{(i + 1)%4}] /form/plot3{i} XPLOT output
setfield /form/plot3{i} title XYRING npts 256 xmin -1 xmax 1
addmsg /tab[{i % 2 + 4}] /form/plot4{i} WAVEPLOT table->table[0] 100
addmsg /tab[{(i + 1)%2 + 4}] /form/plot4{i} XPLOT table->table[0]
setfield /form/plot4{i} title XYWAVEPLOT npts 100 xmin -1 xmax 1
end
setfield /form/plot00 xtextmid ring
setfield /form/plot01 xtextmid ring
setfield /form/plot02 roll_flag 1 xtextmid roll
setfield /form/plot03 oscope_flag 1 xtextmid oscope
setfield /form/plot10 xtextmid ring
setfield /form/plot11 xtextmid ring
setfield /form/plot12 roll_flag 1 xtextmid roll
setfield /form/plot13 oscope_flag 1 xtextmid oscope
setfield /form/plot# script "echo Hi from <w>; show_val.k <w>" ymin -1
function do_set(field, value)
str field
int value
setfield /form/plot# {field} {value}
end
function show_val(widget)
echo xval={getfield {widget} xval}, yval={getfield {widget} yval}
end
reset
================================= cut here =================================
See also:
xgraph ,
XODUS documentation
Object Type: xform
Description: Containing window for other graphical interface objects.
Author: Maneesh Sahani Caltech July/92
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xform_type [in src/Xodus/widg/xform_struct.h
Size: 124 bytes
Fields: fg Foreground color (not used)
bg Background color (not used)
xgeom Position of left edge of form with respect to screen.
This value is an integer. If it is suffixed with a
'%' symbol (eg set form xgeom 20%) then percent of
screen size is used.
ygeom Position of upper edge of form with respect to screen.
wgeom Width of form
hgeom Height of form
The geometry fields can optionally be set on the
create line using the square brackets notation:
[xgeom,ygeom,wgeom,hgeom]
title Optional text string to be placed on top of widget.
Currently only available at create time.
nested Read-only flag that indicates if the form was created
as an embedded form or not.
(1 => embedded, 0 => top-level)
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XForm [in src/Xodus/widg/xform.c]
Classes: widget
Actions: XUPDATE: update internal fields when
displayed widget is changed.
Messages: none.
----------------------------------------------------------------------------
Notes: Invisible until 'xshow' command is issued unless it is
created as an embedded form with the '-nested' option.
One could also create an embedded form and
make it invisible by default using the '-noautomap' option
in conjunction with the '-nested' option. For obvious
reasons, the '-noautomap' option is superfluous when used
with top-level forms.
The xform does not perform any computational operations.
Important: xforms are top-level unless created with the
-nested option.
Example
create xform /foo [0,0,500,50%] -title "I am a top-level form"
xshow /foo
create xform /foo/embedded_foo [0,0,100%,40%] -nested -title \
"I am an embedded form"
create xform /foo/popup_foo [20,20:embedded_foo,,] -nested \
-noautomap -title "xshow/xhide to map/unmap me"
See also: Scripts/examples/XODUS/widgets.g,
XODUS documentation.
Object Type: xgif
Description: Displays gif images as a pix within a draw.
Author: Upi Bhalla / Jason Leigh Aug/93
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xgif_type [in src/Xodus/draw/xgif_struct.h]
Size: 124 bytes
Fields:
fg Foreground color (not currently used).
script Script operation(s) to perform on a mouse
click. The script calls of the pix are only made
if the draw determines that the pix is the nearest
to the event and if the event occurred within the
bounding region of the pix.
value Set with setfield, and accessible in script functions
with the <v> or <value> argument.
tx Transposition distance in the x dimension. The
pix is transposed (ie, displaced, offset) by this
amount.
ty Transposition in y.
tz Transposition in z.
pixflags Set of flags specifying visibility,
refreshes, mouse sensitivity and many other options.
Use the 'pixflags' utility function to find out more.
filename Name of the file containing the image.
format Image format. The default, gif, is the only format
currently supported.
srcx left margin of image in gif file (not currently used).
srcy top margin of image in gif file (not currently used).
dstx left margin of image in draw (not currently used).
dsty top margin of image in draw (not currently used).
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XGif [in src/Xodus/draw/xgif.c]
Classes: output, gadget
Actions: DELETE COPY SET CREATE RESET PROCESS
XUPDATE: update internal fields when
displayed widget is changed.
B1DOWN: Invoked when mouse Button 1 is pressed.
B2DOWN: Invoked when mouse Button 2 is pressed.
B3DOWN: Invoked when mouse Button 3 is pressed.
ANYBDOWN: Invoked when any mouse button is pressed.
B1DOUBLE: Invoked on a double click on mouse button 1.
B2DOUBLE: Invoked on a double click on mouse button 2.
B3DOUBLE: Invoked on a double click on mouse button 3.
XOCOMMAND: an action that can invoke the functions
in the 'script' field
XODROP: Called when a another pix is dropped onto this one.
XODRAG: Called when the mouse is clicked on this pix, and
the mouse moves while the mouse button is held down.
XOWASDROPPED: Called after this pix has been dropped onto
another one.
Messages: none
------------------------------------------------------------------------------
Notes: Unlike ximage, which displays a gif image in a form, xgif
displays the image as a pix inside a draw widget.
Example: Scripts/examples/XODUS/draws.g
See also:
ximage ,
xpix
Object Type: xgraph
Description: Main object class for displaying graphs. Subclassed
from coredraw. This widget provides many special functions
for helping to display graphs.
Like other coredraw subclasses, graph can be thought of as
providing a window into a space where pixes reside, or a
screen onto which pixes are projected. Usually the only
pixes displayed in a graph widget are xplots and xaxis
pixes. Furthermore, xplots are usually not created explicitly
and are instead automatically generated when the graph is
created or receives messages. The axis pixes for the x and
y axes are created automatically when the xgraph is created.
The functions provided by xgraph, which are inherited or
overridden from the coredraw class, include:
Displaying and managing pixes.
Handling forward transforms for drawing pixes
Handling backward transforms for identifying
location of mouse events
Keyboard control over transformation parameters
such as zoom and pan.
Providing a mechanism for deciding which child
pix should recieve mouse events
The graph widget can only display pixes in the xy plane.
The graph widget has a number of special key and mouse
mappings:
event operation
-------------------------------------------------------
'a' 'all' : Change the axes to display all
the plots in their entirety.
arrow keys change the x and y axis offsets.
shift-arrow Change the scale on the x and y axes.
keys
ctrl-arrow Change the lower boundaries of the graph
keys
shift-ctrl-arrow Change the upper boundaries of the graph
keys
Mouse events Selects plots, and passes appropriate
on labels actions to the scripts associated with the
for plots plots.
Click and drag Changes the selected axis range
on upper/lower
values of axes
Click and drag Changes the selected axis offset.
on middle
values of axes
ctrl-p Prints the graph to a postscript
printer/file
Author: Upi Bhalla Mt. Sinai May 93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xgraph_type [in src/Xodus/graph/xgraph_struct.h]
Size: 184 bytes
Fields: fg Foreground color of graph (not used)
bg Background color.
xgeom Position of left edge of graph.
ygeom Position of upper edge of graph.
wgeom Width of graph
hgeom Height of graph
xmin x lower limit for axis for plots. Note that the is
NOT the lower limit of the region in which pixes
can be drawn. That is given by cdxmin.
ymin y lower limit for axis
xmax x upper limit for axis
ymax y upper limit for axis
cdxmin x lower limit for draw region of graph
cdymin y lower limit for draw region of graph
cdxmax x upper limit for draw region of graph
cdymax y upper limit for draw region of graph
xoffset X-offset to apply to successive plots in the graph.
yoffset Y-offset to apply to successive plots in the graph.
overlay Flag for whether or not to save old plots. If
set to 0, old plots are discarde. If set to 1,
old plots are retained and moved into the
subelement 'xoverlay' which is a child of the
graph.
script Script operation(s) to perform on a mouse
click. The script calls to the graph widget
are only made if none of the child pixes has
expressed an interest in the event.
title Title text, top middle of graph
xlabel Label text, centered under x-axis
XUnits Units text, at end of x-axis
ylabel Label text, vertically to left of y-axis
YUnits Units text, at end of y-axis
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XGraph [in src/Xodus/widg/xgraph.c]
Classes: widget output
Actions: XUPDATE: update internal fields when
displayed widget is changed.
XOCOMMAND: an action that can invoke the functions
in the 'script' field
XODROP: Called when a pix is dropped into a draw widget.
ADDMSGIN: Monitors commands for adding messages. If a
PLOT, PLOTSCALE or WAVEPLOT message is received,
the appropriate xplot pixes are created.
Messages: PLOT data name color
In this mode successive data points are added to
the end of the plot as the simulation progresses.
PLOTSCALE data name color scale yoffset
Similar to PLOT, except that the scale and yoffset
of this plot are also included in the message.
X x-coordinate-of-PLOT-msg name-of-corresponding-PLOT-msg
This is used for creating xy (phase) plots. To use
this, first the PLOT msg must be sent, then the
corresponding X msg can be set up. See the
example below.
WAVEPLOT data name color
This is used to create a plot whose y coordinates
vary as the simulation progresses. For example,
if we have 10 waveplot messages with the same name,
they will specify 10 successive y coordinates on
a line. With every timestep the y coordinates get
updated so the effect is like the profile of a
travelling wave.
----------------------------------------------------------------------------
Notes: Can only be displayed in a form widget
The xgraph does not actually handle messages itself.
Instead it forwards them to the appropriate xplot
pix.
Example.
================================= cut here =================================
//genesis
// This example tests the various graph modes. First click 'runit',
// then click reset and then runit again.
// Click on any of the plots to toggle their visibility
create xform /form [1,1,500,800] -title "OUTPUT" -fg black
ce /form
create xbutton runit
setfield runit script \
"step 1000; setfield /form/instr1 fg black; setfield /form/instr2 fg blue"
create xbutton reset -wgeom 50% -script reset
create xbutton quit -ygeom 0:runit -xgeom 50% -wgeom 50% -script quit
create xgraph /form/graph -hgeom 30%
ce /form/graph
setfield script "echo in graph" xmin 0 xmax 100 ymin -1 ymax 5
setfield yoffset 2
setfield xmax 1000 ymax 15
setfield overlay 1
create xgraph /form/phasegraph -hgeom 30%
ce /form/phasegraph
setfield script "echo in graph" xmin 0 xmax 100 ymin -1 ymax 5
setfield yoffset 2
setfield xmin -1 xmax 1 ymin -1 ymax 3
setfield overlay 1
create xgraph /form/wavegraph -hgeom 20%
ce /form/wavegraph
setfield script "echo in graph" xmin 0 xmax 100 ymin -1 ymax 5
setfield xmin -0.5 xmax 1.5 ymin -1 ymax 1
create xlabel /form/instr1 \
-label "First click 'runit' to activate the demo." -fg blue
create xlabel /form/instr2 \
-label "After the run ends, click 'reset' and 'runit' again."
create xlabel /form/instr3 \
-label "Click on any of the plot names to toggle their visibility"
int i
create xplot /form/graph/foo
ce /form/graph/foo
for(i = 0; i < 200 ; i = i + 1)
setfield xpts->table[{i}] {i}
setfield ypts->table[{i}] {sin {i/10.0} }
end
setfield npts 200 fg blue wx 1 wy 1
//set xmin 0 xmax 100 ymin -1 ymax 1 wx 1 wy 1
ce ..
create table /tab
call /tab TABCREATE 400 0 400
setfield /tab step_mode 1 stepsize 1
for(i = 0; i < 400 ; i = i + 1)
setfield /tab table->table[{i}] {cos {5+ i/30.0} }
end
create table /tab2
call /tab2 TABCREATE 400 0 400
setfield /tab2 step_mode 1 stepsize 1
for(i = 0; i < 400 ; i = i + 1)
setfield /tab2 table->table[{i}] {sin {4 +i/16.0} }
end
addmsg /tab /form/graph PLOT output *output *yellow
addmsg /tab2 /form/graph PLOT output *output *green
addmsg /tab2 /form/graph PLOTSCALE output *plotscale *red -0.5 0.5
addmsg /tab /form/phasegraph PLOT output *output *yellow
addmsg /tab2 /form/phasegraph X output *output
addmsg /tab /form/wavegraph WAVEPLOT output *wave *blue
addmsg /tab2 /form/wavegraph WAVEPLOT output *wave *blue
setfield /form/#[TYPE=xgraph]/#[TYPE=xplot] script "toggle_visibility <w>"
function toggle_visibility(widget)
str widget
if ({getfield {widget} pixflags} & 1)
setfield {widget} pixflags ~v
else
setfield {widget} pixflags v
end
end
xshow /form
================================= cut here =================================
See also:
xplot , xaxis,
XODUS
documentation, pix documentation,documentation for coredraw and other
subclasses.
Object Type: ximage
Description: Displays a gif image in a form.
Author: Jason Leigh U Illinois @ Chicago / Upi Bhalla Caltech Feb/93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: ximage_type [in src/Xodus/widg/ximage_struct.h]
Size: depends on the image
Fields: fg Not used
bg Not used
xgeom Position of left edge of image.
ygeom Position of upper edge of image.
wgeom Width of image.
hgeom Height of image.
srcx left margin of image in gif file
srcy top margin of image in gif file
dstx left margin of image in widget
dsty top margin of image in widget
script Script function to execute on button event.
filename name of gif file to load.
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XImage [in src/Xodus/widg/ximage.c]
Classes: widget
Actions:
B1DOWN: Button 1 pressed (left)
B2DOWN: Button 2 pressed (middle)
B3DOWN: Button 3 pressed (right)
ANYBDOWN: Any button pressed.
XUPDATE: update internal fields when
displayed widget is changed.
Messages: none.
----------------------------------------------------------------------------
Notes: An ximage can only be displayed in a form widget.
The ximage does not perform any computational operations,
but can issue script calls when the mouse is clicked in it.
srcx and srcy control the coordinates of the upper left corner
of the image to be displayed expressed relative to the origin
of the image itself. dstx and dsty control the positioning of
the image relative to the parent form. In the example below,
the changes to srcx and srcy would would strip out 40 pixels
from the left-side of the image and 50 pixels from the bottom
of the image. The changes to dstx and dsty would shift the
image 40 pixels to the left and 20 pixels down from the parent
form.
Example:
create xform /form [0,0,400,250]
create ximage /form/image [0,0,100%,100%] \
-filename xodus.gif // in Scripts/examples/XODUS
xshow /form
// try these interactively, one at a time
setfield /form/image srcx 40 srcy -50
setfield /form/image dstx 40 dsty 20
See also:
xgif ,
XODUS documentation,
Mouse events documentation (
Clicks )
Object Type: xlabel
Description: Static display for a text string.
Author: Maneesh Sahani Caltech July/92
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xlabel_type [in src/Xodus/widg/xlabel_struct.h]
Size: 104 bytes
Fields: fg Foreground color of text in label
bg Background color.
xgeom Position of left edge of label with respect to parent
form. This value is an integer. If it is suffixed with
a '%' symbol (eg set label xgeom 20%) then percent of
form size is used. Relative positions with respect
to other widgets can be specified by following the
distance with a :widgetname
(eg set label xgeom 20:otherwidget)
ygeom Position of upper edge of label with respect to form.
wgeom Width of label
hgeom Height of label
The geometry fields can optionally be set on the
create line using the square brackets notation:
[xgeom,ygeom,wgeom,hgeom]
label optional text string to display. Defaults to
widget name in the GENESIS hierarchy.
font optional font for text.
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XLabel [in src/Xodus/widg/xlabel.c]
Classes: widget
Actions: XUPDATE: update internal fields when
displayed widget is changed.
Messages: none.
----------------------------------------------------------------------------
Notes: Can only be displayed in a form widget
The xlabel does not perform any computational operations.
Example
create xform /form [0,0,500,500]
create xlabel /form/label1 [0,0,30%,50%] \
-label "I am a label" \
-fg red
create xlabel /form/label2 [0:/form/label1,0,50%,20%] \
-label "I am another label" \
-font r24 \
-bg red
xshow /form
See also:
XODUS documentation.
Object Type: xpix
Description: Foundation object class for pixes. All other
pix classes are subclassed from pix. Therefore
these subclasses perform a superset of the operations
described here.
Pix and its subclasses can be thought of as being
graphical objects in a 3-d space, which can be viewed
using the coredraw widget and its subclasses. In the same
way that other widgets can only be created in a form,
pixes can only be created in a coredraw or a subclass
thereof. However, a pix need not be the direct child element
of a draw widget as long as the draw widget is somewhere
there among its ancestors.
The functions provided by pix, which are inherited or
overridden by its subclasses, include:
Specifying a set of coordinates.
Calling the transformation routines (which
are specified by the draws).
Drawing an image based on the transformed coordinates.
Providing information to the draw for determining
which pix should respond to a mouse click
Executing script functions in response to mouse or
keyboard events.
Coredraw and subclassses do not display anything on their own.
The pixes provide the actual images and drawing routines
displayed in a coredraw widget/subclasses. It is important
to note that since the pix display, transformation and event
handling functions are present in the coredraw class, any pix
can be displayed in any draw subclass.
The exact transformation used to display the pix is defined
by the draw widget it lives in. Note that the coordinates of
the pix are not changed by any of the transformations.
In a future revision the z coordinate will be used to determine
the order of redrawing pixes to enable pixes to obscure
each other according to depth.
All pixes have a special field 'pixflags' which contains
a large number of options for drawing, projecting and so
on. The 'pixflags' utility function allows one to see the
options for this field. While pixflags can be set directly
to the appropriate hexadecimal number, there is a special
parser which will interpret options as set out by the
pixflags utility funciton.
Author: Upi Bhalla Caltech April 93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xpix_type [in src/Xodus/draw/xpix_struct.h
Size: ?
Fields: fg Foreground color of pix.
script Script operation(s) to perform on a mouse
click. The script calls of the pix are only made
if the draw determines that the pix is the nearest
to the event and if the event occurred within the
bounding region of the pix.
tx Transposition distance in the x dimension. The
pix is transposed (ie, displaced, offset) by this
amount.
ty Transposition in y.
tz Transposition in z.
pixflags Set of flags specifying visibility,
refreshes, mouse sensitivity and many other options.
Use the 'pixflags' utility function to find out more.
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XPix [in src/Xodus/widg/xpix.c]
Classes: gadget
Actions: XUPDATE: update internal fields when
displayed widget is changed.
B1DOWN: Invoked when mouse Button 1 is pressed.
B2DOWN: Invoked when mouse Button 2 is pressed.
B3DOWN: Invoked when mouse Button 3 is pressed.
ANYBDOWN: Invoked when any mouse button is pressed.
B1DOUBLE: Invoked on a double click on mouse button 1.
B2DOUBLE: Invoked on a double click on mouse button 2.
B3DOUBLE: Invoked on a double click on mouse button 3.
XOCOMMAND: an action that can invoke the functions
in the 'script' field
XODROP: Called when a another pix is dropped onto this one.
XODRAG: Called when the mouse is clicked on this pix, and
the mouse moves while the mouse button is held down.
XOWASDROPPED: Called after this pix has been dropped onto
another one.
Example: If pix A is moved onto pix B, the following sequence of
events is issued:
B1DOWN on A
XODRAG on A
XODROP on B
XOWASDROPPED on A.
Messages: none.
----------------------------------------------------------------------------
Notes: Can only be displayed in a coredraw widget subclass.
The xpix does not perform any computational operations
driven by the simulation clock.
Example: Scripts/examples/XODUS/clicks.g
See also:
xcoredraw ,
Clicks
Object Type: xplot
Description: Main object class for displaying graphs. Subclassed
from pix. The xplot pix stores and plots sequences of points.
Like xpix, xplot can be thought of as being
graphical objects in a 3-d space, which can be viewed
using the coredraw widget and its subclasses. In the same
way that other widgets can only be created in a form,
xplots can only be created in a coredraw or a subclass
thereof. xplots are usually created in xgraph widgets,
which are a subclass of coredraw specialized for plotting
graphs.
Xplot at this time displays line plots only. There is no
facility at present for adding markers or error bars
to the points plotted.
SPECIAL XPLOT CREATION FACILITY
For reasons of convenience and backwards compatibility,
there is a special facility for the automatic creation of
xplots when the appropriate messages are sent to the parent
xgraph. In particular, the messages
PLOT, PLOTSCALE, and WAVEPLOT
sent to the parent xgraph, will cause a new xplot to be
created if necessary, and then copies of these messages
will be sent to the new xplot. This does not affect the
normal commands for creation and message-passing to xplots.
In other words, the commands
create xgraph /form/graph
addmsg /foo /form/graph PLOT *plot *red
will produce the same plot as
create xgraph /form/graph
create xplot /form/graph/plot
addmsg /foo /form/graph/plot PLOT *plot *red
DATA STORAGE IN XPLOT
The points displayed by xplots are stored in two
interpol_structs called xpts and ypts respectively.
As is obvious from their names, point #i displayed in
the xplot is stored in location
(xpts->table[i],ypts->table[i])
There are several options for passing information into
the xpts/ypts arrray.
1. The points can be filled in explicitly through the usual
script commands for handling tables, e.g.:
setfield /form/graph/plot \
xpts->table[0] 10
ypts->table[0] 20
....
or
loadtab /form/graph/plot xpts 1 10 0 10 \
1 2 3 4 5 6 7 8 9 10
loadtab /form/graph/plot ypts 1 10 0 10 \
1 2 1 4 1 6 1 8 1 10
or
setfield /form/graph/plot ypts /foo/table
2. The points can be loaded in from a file using the
file2tab function, e.g.:
file2tab ypointsfile /form/graph/plot \
ypts -autofill xpts
(see the file2tab documentation for more information and
other options.)
3. The points can be filled in during the course of a
simulation using messages, which are described in more
detail below. This option is the most commonly used one,
for watching the progress of a simulation.
Note that once the data is in the xpts and ypts tables,
it is accessible just like any other data in GENESIS
tables.
MEMORY HANDLING OPTIONS
An obvious problem resulting from monitoring a
very long simulation is that all those data points will
fill up all the available memory. There are a number
of ways around this.
1. Don't store all the data. One very rarely needs to
monitor the output of the simulation at the same fine
time-step that the numerical calculations use. Typically
the plots can be run at 10 to 100 times longer time-steps.
This makes the simulation run faster, too.
2. Compress the data. There is an option (on by default)
which compresses the incoming data on the fly using a very
simplistic, lossy compression scheme. All this does is
to discard points which are closer than a defined number
in the y-coordinate. The 'ysquish' field stores this
number, which is initialized to 1/100 of the range
of the y axis of the graph. If it ever looks like the
plotted data is seriously distorted, this is a likely
culprit and 'ysquish' should be squished. A value of zero
will result, obviously, in no compression.
3. Set a maximum limit for the number of points allowed
(the 'limit' mode). This is unlikely to be useful to anybody.
4. Use the 'oscilloscope' mode, where the plot starts
over from zero after filling up.
5. Use the 'roll' mode to scroll the points like a
stripchart, except that unlike a paper stripchart the
scrolled points are lost.
To recapitulate, the available memory handling modes
are :
s[quish] : default, attempts lossy compression
depending on the ysquish parameter.
Expands memory use as required.
l[imit] : Prevent plotting points past predefined
allocation.
r[oll] : Roll the data like a stripchart.
o[scilloscope]: Start over at zero once the
allocated memory is used up.
MANIPULATING XPLOTS.
Xplots can be created copied, moved and deleted in just the
same way as other pixes, which is almost the same as
ordinary elements with the following restrictions:
1. A an instance of the coredraw subclass must be an ancestor
of the xplot. In other words, there must be an element which
is a subclass of xcoredraw somewhere in the heirarchy above
(closer to the root) the point where the xplot is created.
2. An xplot can only be moved within the subtree arising
from this ancestral coredraw element.
Author: Upi Bhalla Mt. Sinai May 93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xplot_type [in src/Xodus/draw/xplot_struct.h]
Size: Variable depending on number of points stored. Makes
extensive use of realloc, so it may fragment memory.
Fields: fg Foreground color of plot.
script Script operation(s) to perform on a mouse
click. The script calls of the pix are only made
if the draw determines that the pix is the nearest
to the event and if the event occurred within the
bounding region of the pix.
tx Transposition distance in the x dimension. The
pix is transposed (ie, displaced, offset) by this amount.
ty Transposition in y.
tz Transposition in z.
pixflags Set of flags specifying visibility,
refreshes, mouse sensitivity and many other options.
Use the 'pixflags' utility function to find out more.
The most commonly used pixflag option with xplot is 'f',
which prevents flushing the entire display every time a point
is added. This greatly speeds up the display if there are many
xplots or other widgets being updated each timestep.
xpts interpol-struct containing x-coords for plot
ypts interpol-struct containing y-coords for plot
npts Number of points currently being displayed in plot
linewidth Width (in pixels) of plotted line
linestyle One of: LineSolid (default), LineOnOffDash,
LineDoubleDash
xmin,ymin,xmax,ymax: Determine range of plotted values.
The offsets and scaling factors are handled
by adjusting these. Normally managed by the
parent xgraph, but must be assigned explicitly
when in another coredraw subclass.
wx, wy: Window size for plot. Normally both are 1.0.
memory_mode: One of:
s[quish]: default. Attempts lossy compression.
l[imit]: limit number of plotted points
r[oll] : Roll the data like a stripchart.
o[scilloscope]: Start over at zero once the
allocated memory is used up.
auto_mode: For future extensions.
ysquish: cutoff for 'squish' mode data compression.
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XPlot [in src/Xodus/draw/xplot.c]
Classes: gadget output
Actions: XUPDATE: update internal fields when
displayed widget is changed.
XOCOMMAND: an action that can invoke the functions
in the 'script' field
XODROP: Called when a pix is dropped into a draw widget.
XODRAG: Called when a pix is dropped into a draw widget.
XOWASDROPPED: Called when a pix is dropped into a draw widget.
B1DOWN: Invoked when mouse Button 1 is pressed.
B2DOWN: Invoked when mouse Button 2 is pressed.
B3DOWN: Invoked when mouse Button 3 is pressed.
ANYBDOWN: Invoked when any mouse button is pressed.
B1DOUBLE: Invoked on a double click on mouse button 1.
B2DOUBLE: Invoked on a double click on mouse button 2.
B3DOUBLE: Invoked on a double click on mouse button 3.
PROCESS: Handle plot input.
RESET: Checks various message options.
SET: Handles special set options including table sets.
ADDPTS: Plots (x,y) values as points; equivalent to old
xaddpts: call {plot-name} ADDPTS {x} {y}
Messages: PLOT data name color
In this mode successive data points are added to
the end of the plot as the simulation progresses.
PLOTSCALE data name color scale yoffset
Similar to PLOT, except that the scale and yoffset
of this plot are also included in the message.
X x-coordinate-of-PLOT-msg name-of-corresponding-PLOT-msg
This is used for creating xy (phase) plots. To use
this, first the PLOT msg must be sent, then the
corresponding X msg can be set up. See the
example below.
WAVEPLOT data name color
This is used to create a plot whose y coordinates
vary as the simulation progresses. For example,
if we have 10 waveplot messages with the same name,
they will specify 10 successive y coordinates on
a line. With every timestep the y coordinates get
updated so the effect is like the profile of a
travelling wave.
----------------------------------------------------------------------------
Notes: Can only be displayed in a xcoredraw widget subclass
Example 1.
================================= cut here =================================
//genesis
// This example tests the various graph modes. First click 'runit',
// then click reset and then runit again.
// Click on any of the plots to toggle their visibility
create xform /form [1,1,500,800] -title "OUTPUT" -fg black
ce /form
create xbutton runit
setfield runit script \
"step 1000; setfield /form/instr1 fg black; setfield /form/instr2 fg blue"
create xbutton reset -wgeom 50% -script reset
create xbutton quit -ygeom 0:runit -xgeom 50% -wgeom 50% -script quit
create xgraph /form/graph -hgeom 30%
ce /form/graph
setfield script "echo in graph" xmin 0 xmax 100 ymin -1 ymax 5
setfield yoffset 2
setfield xmax 1000 ymax 15
setfield overlay 1
create xgraph /form/phasegraph -hgeom 30%
ce /form/phasegraph
setfield script "echo in graph" xmin 0 xmax 100 ymin -1 ymax 5
setfield yoffset 2
setfield xmin -1 xmax 1 ymin -1 ymax 3
setfield overlay 1
create xgraph /form/wavegraph -hgeom 20%
ce /form/wavegraph
setfield script "echo in graph" xmin 0 xmax 100 ymin -1 ymax 5
setfield xmin -0.5 xmax 1.5 ymin -1 ymax 1
create xlabel /form/instr1 \
-label "First click 'runit' to activate the demo." -fg blue
create xlabel /form/instr2 \
-label "After the run ends, click 'reset' and 'runit' again."
create xlabel /form/instr3 \
-label "Click on any of the plot names to toggle their visibility"
int i
create xplot /form/graph/foo
ce /form/graph/foo
for(i = 0; i < 200 ; i = i + 1)
setfield xpts->table[{i}] {i}
setfield ypts->table[{i}] {sin {i/10.0} }
end
setfield npts 200 fg blue wx 1 wy 1
//set xmin 0 xmax 100 ymin -1 ymax 1 wx 1 wy 1
ce ..
create table /tab
call /tab TABCREATE 400 0 400
setfield /tab step_mode 1 stepsize 1
for(i = 0; i < 400 ; i = i + 1)
setfield /tab table->table[{i}] {cos {5+ i/30.0} }
end
create table /tab2
call /tab2 TABCREATE 400 0 400
setfield /tab2 step_mode 1 stepsize 1
for(i = 0; i < 400 ; i = i + 1)
setfield /tab2 table->table[{i}] {sin {4 +i/16.0} }
end
addmsg /tab /form/graph PLOT output *output *yellow
addmsg /tab2 /form/graph PLOT output *output *green
addmsg /tab2 /form/graph PLOTSCALE output *plotscale *red -0.5 0.5
addmsg /tab /form/phasegraph PLOT output *output *yellow
addmsg /tab2 /form/phasegraph X output *output
addmsg /tab /form/wavegraph WAVEPLOT output *wave *blue
addmsg /tab2 /form/wavegraph WAVEPLOT output *wave *blue
setfield /form/#[TYPE=xgraph]/#[TYPE=xplot] script "toggle_visibility <w>"
function toggle_visibility(widget)
str widget
if ({getfield {widget} pixflags} & 1)
setfield {widget} pixflags ~v
else
setfield {widget} pixflags v
end
end
xshow /form
================================= cut here =================================
See also:
xgraph , xaxis,
XODUS documentation, pix documentation, documentation for
coredraw and other subclasses.
Object Type: xshape
Description: The shape pix draws assorted shapes, and was developed in
order to allow users to design their own graphical objects
such as clickable labels, arrows, and other icons under the
draw widget. It provides access to the primitive graphical
operations of drawing geometrical shapes and text, as well as
to the `higher functions' such as icons, mouse clicks and
hilighting. It is also automatically created as a subordinate
pix for the xvar, xview, and xtree widgets. For example, two
filled rectangle xshapes, shape[0] and shape[1], are created
as child elements of a view widget when the view is created.
The shape pix contains fields for the coordinates of the
shape, and assorted fields for controlling draw modes using
the coordinates, a set of fields related to the text string
that the pix can display, and a field for setting a return
value when the shape is clicked on.
Author: Upi Bhalla Caltech Apr/93
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xshape_type [in src/Xodus/draw/xshape_struct.h]
Size: 156 bytes
Fields: fg Color of the shape
script Script operation(s) to perform on a mouse
click. The script calls of the shape are only made
if the draw determines that the shape is the nearest
to the event and if the event occurred within the
bounding region of the shape.
value Set with setfield, or with a PATH message, and
accessible in script functions with the <v> or
<value> argument.
tx Transposition distance in the x dimension. The
shape is displaced in the draw by this amount.
ty Transposition in y.
tz Transposition in z.
pixflags Set of flags specifying visibility,
refreshes, mouse sensitivity and many other options.
Use the 'pixflags' utility function to find out more.
xpts Interpol struct (table) of x coordinates.
ypts Interpol struct (table) of y coordinates.
zpts Interpol struct (table) of z coordinates.
npts Contains the number of points which were set.
drawmode One of: DrawLines (default), DrawPoints, DrawSegs
(takes coordinate pairs and draws lines between
them; The last coordinate is ignored if there is
an odd number of coordinates.), DrawArrows (same
as DrawSegs, only arrows are drawn instead of
segments), FillPoly (draws a filled polygon
bounded by the coordinates specified. It will
close the polygon if the last point is different
from the first.), or FillRects (takes coordinate
pairs and draws filled rectangles from one to the
next. If there are an odd number of coordinates
specified, then the last coordinate is ignored.).
linewidth Line width in pixels.
linestyle One of: LineSolid (solid line of fg color, the
default), LineOnOffDash (dashed line of fg color),
or LineDoubleDash (dashed line of fg color, with
white between the dashes).
capstyle End of line style; One of: CapButt (rectangular
end, the default), CapRound (round end),
CapProjecting (adds an extra pixel to the end), or
CapNotLast (skips the last pixel of the line).
joinstyle Style of line joints; One of: JoinMiter (sharp
corners, the default), JoinRound (rounded
corners), or JoinBevel (beveled corners).
text Text string to display (if any).
textcolor Color of the text string.
textmode Mode for drawing text; One of: draw (print the
text on the draw background, the default), fill
(add a white background to the text), or nodraw
(do not display the text).
textfont Font used for the text string.
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XShape [in src/Xodus/draw/xshape.c]
Classes: output, gadget
Actions: XUPDATE: update internal fields when
displayed widget is changed.
B1DOWN: Invoked when mouse Button 1 is pressed.
B2DOWN: Invoked when mouse Button 2 is pressed.
B3DOWN: Invoked when mouse Button 3 is pressed.
ANYBDOWN: Invoked when any mouse button is pressed.
B1DOUBLE: Invoked on a double click on mouse button 1.
B2DOUBLE: Invoked on a double click on mouse button 2.
B3DOUBLE: Invoked on a double click on mouse button 3.
XOCOMMAND: an action that can invoke the functions
in the 'script' field.
XODROP: Called when a another pix is dropped onto this one.
XODRAG: Called when the mouse is clicked on this pix, and
the mouse moves while the mouse button is held down.
XOWASDROPPED: Called after this pix has been dropped onto
another one.
XSHAPE_ADDPT x y z: adds a point to the arrays, and
increments npts.
XSHAPE_MOVEPT x y z: finds the nearest point to [x,y,z] and
moves it there.
Messages: PATH dummy
When a PATH message is present, then the value field
is set to the full path of the source of the message
on PROCESS.
------------------------------------------------------------------------------
Notes: After changing some of the fields related to the display
modes, it will be necessary to perform an xupdate of the
parent draw widget for the changes to take effect.
The coordinates of the shape can be set in the xpts, ypts, and
zpts tables, using the usual commands for interpol_structs,
e.g. "setfield shape xpts->table[0] 0.5". However, there is a
shorthand notation for setting several coordinate sets at
once, for example:
setfield shape2 coords [1,0,0][0,1,0][0,0,1]
The example below shows how this notation may be used at the
time the shape is created. The use of this notation has the
additional advantage of automatically setting npts to the
number of coordinate sets which were specified. Otherwise,
npts must be explicitly set before the shape will be
displayed.
Example: create xform /form
create xdraw /form/draw [0,0,100%,100%] \
-xmin -1 -xmax 2 -ymin -2 -ymax 2
create xshape /form/draw/shape -fg green -drawmode FillPoly \
-coords [0,0,0][0.5,1,0][1,0,0][0,0,0] \
-text "I am a green triangle" \
-script "echo You clicked on <w>"
xshow form
See also:
xview ,
xvar ,
xpix ,
Clicks ,
Tables , and the scripts
Scripts/examples/XODUS/draws.g, Scripts/CPG/viewform.g
Object Type: xsphere
Description: Example pix which draws a filled circle.
Author: Upi Bhalla Caltech Apr/93
------------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xsphere_type [in src/Xodus/draw/xsphere_struct.h]
Size: 104 bytes
Fields:
fg Color of sphere.
script Script operation(s) to perform on a mouse
click.
tx Transposition distance in the x dimension. The
pix is transposed (ie, displaced, offset) by this
amount.
ty Transposition in y.
tz Transposition in z.
value
pixflags Set of flags specifying visibility,
refreshes, mouse sensitivity and many other options.
r Radius of the sphere.
------------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XSphere [in src/Xodus/draw/xsphere.c]
Classes: output, gadget
Actions:
XOWASDROPPED XODRAG XOCOMMAND XODROP XUPDATE B3ENTER B2ENTER B1ENTER
B3DOUBLE B2DOUBLE B1DOUBLE ANYBDOWN B3DOWN B2DOWN B1DOWN DELETE COPY
SET CREATE RESET PROCESS
Messages: none
------------------------------------------------------------------------------
Notes:
Example: Scripts/examples/XODUS/draws.g
See also:
xpix ,
Clicks
Object Type: xtext
Description: Display and optional editor for text.
Author: Maneesh Sahani Caltech/ Jason Leigh U Illinois@Chicago July 93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xtext_type [in src/Xodus/widg/xtext_struct.h]
Size: ?
Fields: fg Foreground color of text in text
bg Background color.
xgeom Position of left edge of xtext.
ygeom Position of upper edge of xtext.
wgeom Width of text
hgeom Height of text
font optional font for text.
initialtext optional text string to display.
editable Flag determining if text can be altered.
filename Optional name of an ascii file for widget
to display.
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XText [in src/Xodus/widg/xtext.c]
Classes: widget
Actions: XUPDATE: update internal fields when
displayed widget is changed.
Messages: none.
----------------------------------------------------------------------------
Notes: Can only be displayed in a form widget
The xtext does not perform any computational operations.
Example
create xform /form [0,0,500,500]
create xtext /form/text1 [0,0,100%,100%] \
-initialtext "I am a text widget" \
-fg red \
-font r24 \
-bg green
xshow /form
See also: Scripts/examples/XODUS/widgets.g,
XODUS documentation.
Object Type: xtoggle
Description: Maintains toggle state and executes script actions
from mouse button presses.
Author: Maneesh Sahani / Upi Bhalla Caltech Feb/93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xtoggle_type [in src/Xodus/widg/xtoggle_struct.h]
Size: 136 bytes
Fields: fg Foreground color of text in toggle
bg Background color.
onfg Foreground color of text in toggle,
for on (pressed) state.
onbg Foreground color for on (pressed) state.
offfg Background color of text in toggle,
for off (unpressed) state.
offbg Background color for off (unpressed) state.
xgeom Position of left edge of toggle.
ygeom Position of upper edge of toggle.
wgeom Width of toggle.
hgeom Height of toggle.
onlabel optional text string to display in on state.
Defaults to widget name in the GENESIS hierarchy.
offlabel optional text string to display in off state.
Defaults to widget name in the GENESIS hierarchy.
onfont optional font for text in on state.
offfont optional font for text in on state.
state Maintains state of widget. 1 if on, 0 if off.
Defaults to 0.
script string representing operations to be performed
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XToggle [in src/Xodus/widg/xtoggle.c]
Classes: widget
Actions:
B1DOWN: Button 1 pressed to turn on toggle (left mouse button)
B2DOWN: Button 2 pressed to turn on toggle
(middle button on 3 button mouse)
B3DOWN: Button 3 pressed to turn on toggle
(right button on 3 button mouse)
ANYBDOWN: Any button pressed.
B1UP: Button 1 pressed to turn off toggle (left button)
B2UP: Button 2 pressed to turn off toggle
(middle button on 3 button mouse)
B3UP: Button 3 pressed to turn off toggle
(right button on 3 button mouse)
ANYBUP: Any button pressed to turn off toggle.
XPDATE: update internal fields when widget is changed.
Messages: none.
----------------------------------------------------------------------------
Notes: Can only be displayed in a form widget
The xtoggle does not perform any computational operations.
It issues script calls depending on button presses and
internal state.
Example:
create xform /form [0,0,500,100]
create xtoggle /form/toggle1 [0,0,100%,100%] \
-onlabel "This toggle widget is on" \
-offlabel "This toggle widget is off" \
-onfg green \
-offfg black \
-onfont r24 \
- script "echo.d1 LMB <value> ; echo.u3 released RMB <v> ; echo any MB <v>"
xshow /form
See also:
XODUS documentation. Mouse events documentation
(
Clicks )
Object Type: xtree
Description: Object for displaying and manipulating the relationships
between elements and objects in a simulation. This is an extremely
complex widget designed for building click-and-drag interfaces
within Xodus. The default mode provides a heirarchical
tree display of a simulation. The additional options include
alternative display modes, issuing script calls based on the
source and destinations of mouse-drag operations, and options
for changing the appearance of individual items in the tree.
Xtree is subclassed from pix and can only be displayed in coredraw
or its subclasses.
xtree is not designed to be updated every time step. It is quite
expensive to recalculate. The contents of xtree are updated by
calling the RESET action.
Like xvar and xview, xtree maintains a set of child xshapes named
shape[0], shape[1], ... The items displayed by the xtree use
the coordinate and drawing information in these shapes for display.
When drawing an item, the tree finds a string associated with
the item (usually its object name, see below). It then scans the
list of child shapes to find a match between the 'value' field of
the xshape and this string. The selected shape is used as the icon
for representing the item in the tree. If no match is found, shape[0]
is used. The child xshape shape[0] is created automatically when
the xtree is created.
The 'items' that the xtree can represent include elements and
objects. In addition to representing these items, xtree can also
display heirarchical (parent-child-sibling) relationships between
them in the form of a tree structure as one of the display options.
Furthermore, xtree can display messages between elements in the
form of arrows.
Display options
Several display options are available:
tree: a heirarchical display, eg, of a directory structure or
a GENESIS heirarchy. Any orientation can be selected.
treenotrunc: ?
custom: The coordinates of the items are user-specified and just
stored in an array.
grid: The items are placed on a rectangular grid or as a single
row or column, as specified by the orientation option.
geometry: The items are located according to their x,y,z coords.
obj_grid: The objects are located on a rectangular grid. This
may be modified depending on the orientation option.
obj_custom: The objects are located according to user-specified
positions.
orientation: Determines two kinds of things: first, the orientation
of the heirarchy in the tree mode. Second, the orientation
and layout of the grid.
In the tree mode the orientation can be one of
u: up - the leaves are up , the root is down
d: down - the leaves are down, the root is up.
l: left - the leaves are on the left, the root on the right.
r: right - the leaves are on the right, the root on the left.
In the grid or obj-grid modes, the orientation can be
u: Grid with horizontal long axis
U: Grid with horizontal long axis and staggered entries.
d: Single column
l: Grid with vertical long axis
r: Single row
R: Single row with staggered entries
m<n>: multiple rows with n entries each.
M<n>: multiple rows with n entries each, staggered in the y
direction to minimize text overlap.
Displaying messages
The tree is frequently used to display messages between elements.
Messages can be displayed in any treemode, except, of course,
between objects. Messages are displayed as arrows which start and
end a few pixels from the item on the screen. If the pair of items
being displayed is very close, the messages are not displayed.
The details of the message display are determined by the MSGARROW
array, which is manipulated using the ADDMSGARROW action.
Executing functions in response to graphical events.
Trees are especially useful for performing drag-and-drop operations,
though the usual set of actions on the tree is also allowed. The
ADDMSGARROW action, in addition to loading in the specification
for msg display, is also used to set up the script functions to
be performed under various sets of drag-drop operations between
specified object classes.
The ADDMSGARROW action.
As already described, ADDMSGARROW is used both to specify how to
display msgs between elements of particular object-classes, and
also to execute functions in response to particular graphical
operations like drag-and-drop.
The syntax of ADDMSGARROW is:
call tree ADDMSGARROW msgsrc msgdest msgtype msgdesttype fg index
fliparrow script script_add script_drop
msgsrc and msgdest are wildcard paths to two sets of elements.
msgtype is a string defining the type of msg.
msgdesttype is the type of the element at the destination of the msg
fg is the color of the arrow used to draw the msg
index is for identifying this ADDMSGARROW entry among the array
of other entries. If it is >= 0, the msgarrow
information is placed at the specified index, overwriting
whatever else may have been stored there. If it is
less than 0, the the information is first checked to ensure
that it does not duplicate an existing entry. If not, then
the information is placed in the first free entry.
fliparrow is a flag (0 or 1) to tell the display routines to draw
the arrow backwards. Normally (fliparrow = 0) the arrowhead
points to the destination of the msg.
script, script_add and script_drop are strings with the standard
Xodus syntax for specifying functions and arguments.
The msgsrc and msgdest wildcards are used in two ways. If one is
drawing messages, they are used to specify the elements that the
tree is supposed to check for the sources and the dests of the message,
respectively. If one is executing functions, then the lists are
scanned to check if the source and dest elms of a drag-drop operation
lie on the lists. If so, then the function named in "script" is
executed every time; the function named in "script_add" is executed if
there is NO message of the specified msgtype between the src and dest,
and the function named in "script_drop" is executed if there is
already a message between src and dest. The intention is that
operations involving creation of messages be specified with the
"script_add", deletion by "script_drop", and other operations by the
function defined in "script".
SIMULATION PARAMETERS
Function: XTree [in src/Xodus/widg/xtree.c]
Classes: gadget output
Actions: PROCESS: redraws tree - does NOT check for changes to contents.
RESET: rebuilds tree from scratch, thereby updating any
changes.
CREATE: Creates the tree and the default child xshape
COPY : currently incomplete
SET: Special handling for the fields
pixflags
sizescale
DELETE: Frees up allocated entries.
DUMP: Saves all the internal information for the tree,
specially the ADMMSGARROW info and the coords of
the display items in certain modes.
UNDUMP: Loads in the information stored using DUMP
ADDMSGARROW: Sets modes for displaying msgs and handling
drag-drop operations. See above.
SHOWMSGARROW: Lists existing msgarrows
MOVECUSTOM: args: elmpath x y z recurse_flag
Handles xyz moves of tree items in custom mode
TRUNCATE: args: elmname [mode]
Applies to treemode 'tree'. Sets truncation of the tree
at the element 'elmname'. If mode is 0, truncation is
turned on. If 1, it is turned off. If -1 (default),
it is toggled.
XUPDATE: update internal fields when
displayed widget is changed.
Xodus actions: handled normally, with the following
exceptions
1. In treemode 'tree', action B1DOUBLE toggles
the truncation of the the tree at the clicked item.
2. Drags and drops are checked against entries
in the msgarrow table to decide if the scriptfuncs
specified by ADDMSGARROW should be called. These
are only called for operations within the same tree.
3. B1DOWN, B2DOWN and B3DOWN are checked against
the hlmode. If it is "one", then one element is
highlit. If it is "multi" then the element is added
to the list of entries to be highlit. If it is "none"
or the default, then no permanent highlight flags are
set.
Messages: none.
----------------------------------------------------------------------------
Notes: Can only be displayed in a coredraw widget subclass.
Not meant to be clocked.
Examples: Scripts/examples/XODUS/xtree_example
See also:
xshape ,
xview
Object Type: xvar
Description: Object for displaying numerical values graphically. Xvar is
subclassed from pix and can only be displayed in coredraw
subclasses.
The following parameters of the graphical display can be
used to display values in xvar:
1. Color
2-4. x,y and z offsets
5. Coordinates (morphing)
6. Line thickness. *
7. Text color *
8. Text
9. Minigraph. *
10. Surface *
11. Contour *
* Not yet available.
While these parameters can in principle be used to
simultaneously display 9 independent parameters, in practice
it gets rather confusing if more than 2 or 3 are used at a
time.
Values are specified either through messages or by directly
setting the 'values' array in the xvar. At this time 5 such
messages are permitted (VAL1, VAL2, VAL3, VAL4, VAL5).
The color_val, xoffset_val, morph_val etc.
fields are used to bind the message number to the specified
display variable. Thus setting color_val to 1 means that
message VAL1 will be used to control the color of the xvar pix.
By default all _vals are set to 0, which disables them.
The xvar pix displays values (except text and minigraph) by linear
interpolation. Every xvar has at least two child elements of class
xshape, named shape[0], shape[1], etc. These shapes determine the
extreme points for the linear interpolation. Therefore if shape[0]
has foreground color 0, and shape[1] has color 10, the range of
colors displayed would be interpolated between 0 and 10. Likewise,
if shape[0] displays a tall thin rectangle, and shape[1] a short
wide rectangle, the shapes displayed would be 'morphed' between
these two extremes. Of course, to get these effects one would have
to set the color_val and morph_val to the appropriate values.
In addition to the shapes themselves, three arrays are used to specify
how the xvar does interpolation. As already mentioned, the 'values'
array specifies the actual values to be displayed. 'value_min'
contains the values that correspond to the lower end of the
interpolated range. Thus if value[0] was equal to value_min[0],
the parameter displayed would correspond to shape[0]. Likewise,
value_max contains the upper end of the interpolated range.
One can have multiple xshapes. In this case the interpolation
first decides which pair of shapes to use. In this version, each pair
of shapes handles an equal range between value_min and value_max.
Having selected the appropriate pair of shapes,
the algorithm then proceeds as outlined above.
The 'text' option simply prints out the floating point value of the
appropriate message. The 'minigraph' option (which will be
implemented one of these days) displays a little graph of the
value, without any optional extras like axes.
By default, the xvar object is created along with two child shapes,
shape[0] and shape[1]. The default shapes are squares, shape[0] being
a small one with color 0 and shape[1] a big (1x1) square in color 63.
The child shapes can have parameters set in the usual ways, but are
not displayed independently of the xvar pix. For the technically
minded, this is because their pixflags have been set to visible_not.
Note on 'morphing': Morphing in the xvar pix is simply linear
interpolation between corresponding points. When one shape has a
different number of points from the other, then the algorithm
assumes that the missing points are [0,0,0] and does interpolation
accordingly. This may lead to peculiar effects, so usually one
uses the same number of points in all xshapes.
Author: Upi Bhalla Caltech Dec 93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xvar_type [in src/Xodus/draw/xvar_struct.h
Size: ? Depends on number of associated shapes.
Fields: fg Foreground color of var.
script Script operation(s) to perform on a mouse
click. The script calls of the var are only made
if the draw determines that the var is the nearest
to the event and if the event occurred within the
bounding region of the var.
tx Transposition distance in the x dimension. The
var is transposed (ie, displaced, offset) by this
amount.
ty Transposition in y.
tz Transposition in z.
pixflags Set of flags specifying visibility,
refreshes, mouse sensitivity and many other options.
Use the 'pixflags' utility function to find out more.
varmode Specifies the mode of operation of the xvar. Can be
one of:
shape - Does interpolation between shapes
graph - draws a minigraph (Not yet implemented)
surface - Draws a plane in 3-d, specified by 3
points in space (not yet implemented)
contour - Draws contour lines for a plane in 3-d. NYI.
colorview - Backwards compatibility hack. Uses 'shape'
mode to display boxes of different color.
boxview - Backwards compatibility hack. Uses 'shape'
mode to display boxes of different sizes.
colorboxview - Backwards compatibility hack. Default
varmode. Uses 'shape' mode to display VAL1
using both the morph and color modes for
a box.
fillboxview - Backwards compatibility hack. Uses 'shape'
mode to display filled boxes of different sizes.
value_min 1-d array with lower limits for shape parameters.
value_max 1-d array with upper limits for shape parameters.
values 1-d array with display values.
color_val Specifies message to use for color
display values. 0=disabled is default.
If you wish to cause var to change colors,
use color_val.
morph_val Specifies message to use for morphing.
If you wish to have the var change
shape, use morph_val.
xoffset_val Specifies message to use for xoffset.
If you wish to cause a var to
bounce around on the screen,
use the offset_vals.
yoffset_val Specifies message to use for yoffset.
zoffset_val Specifies message to use for zoffset.
text_val Specifies message whose value should
be printed out.
textcolor_val Specifies message which determines
the color of the text.
linethickness_val Specifies message determining the
line thickness used in the var.
sizescale Rescales all the shapes. The default
shapes have a size of 1.
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XVar [in src/Xodus/draw/xvar.c]
Classes: gadget output
Actions: PROCESS: Redo interpolation and display.
RESET: Required when changing child xshapes.
CREATE: Automatically creates 2 child xshapes.
XUPDATE: update internal fields when
displayed widget is changed.
B1DOWN: Invoked when mouse Button 1 is pressed.
B2DOWN: Invoked when mouse Button 2 is pressed.
B3DOWN: Invoked when mouse Button 3 is pressed.
ANYBDOWN: Invoked when any mouse button is pressed.
B1DOUBLE: Invoked on a double click on mouse button 1.
B2DOUBLE: Invoked on a double click on mouse button 2.
B3DOUBLE: Invoked on a double click on mouse button 3.
XOCOMMAND: an action that can invoke the functions
in the 'script' field
XODROP: Called when a another pix is dropped onto this one.
XODRAG: Called when the mouse is clicked on this pix, and
the mouse moves while the mouse button is held down.
XOWASDROPPED: Called after this pix has been dropped onto
another one.
Messages: COORDS x y z
VAL1 data
VAL2 data
VAL3 data
VAL4 data
VAL5 data
All messages can contain values for any display parameter.
----------------------------------------------------------------------------
Notes: Can only be displayed in a coredraw widget subclass.
The xvar performs the interpolation between shapes and
redraws them on every clock tick.
Example:
See also:
xview ,
xshape
Object Type: xview
Description: Object for displaying large numbers of numerical values
graphically. Xview can be thought of as an array of xvars, though it
uses much less memory than multiple xvars would. It also provides
many more features for accessing the fields and messages of groups
of elements. Xview is subclassed from pix and can only be displayed
in coredraw or its subclasses.
Xview displays multiple 'points' in space, each behaving rather like
an xvar. Each 'point' in xview usually represents a single entity
in the simulation, such as a compartment.
Each 'point' in xview can be clicked to select, and the 'value'
field of the xview will be set according to the 'valuemode'. By
default the 'valuemode' is set to "path", so a click action will
place the path of the element represented by the clicked point in
xview into the 'value' field. Alternative valuemodes are "index",
which returns the index of clicked point in the internal xview list;
and "lookup", which looks up the value displayed for the clicked
point.
Values in xview are specified in three ways.
- First, one can set the 'values' array directly (e.g., using the set
command). Note that 'values' is 2-dimensional in xview.
- Second, one can send up to 5 messages (VAL1, VAL2, VAL3, VAL4,
VAL5), for each point. The points themselves must be previously
specified using the COORDS message. It is assumed that the order of
sending the COORDS messages is identical to the order of sending the
values. This is guaranteed if a wildcard list is used to set up the
messages. This method is recommended for all dynamic displays, as
it is far and away the most efficient. The use of messages also
enables displays on parallel machines.
- Third, one can specify 'path' for looking up the coords. 'path' is
usually a wildcard list of elements. 'relpath' is used for finding
the actual elements containing the fields, relative to the coords.
This is NOT a wildcard list. If no relpath is used, it can be set to
"" or ".". Only two values can be displayed in this mode, using
'field' and 'field2'.
In addition, one can set 'field' to one of "msgout" or "msgin". If
these options are selected, one can view values that are contained
in messages. The 'msgpath' is a wildcard list of elements connected
to the 'path' by the message type specified in 'msgtype'. The
direction of the messages is specified, as mentioned above, by
'field'. The view looks for the first message that satisfies all the
above criteria for each coordinate, and displays the appropriate
value. If it fails to find a suitable message the value becomes 0.
This option enables one to display connectivity patterns in a
network. Using 'path' and its related options for displaying values
is the most flexible option, and the slowest. Connections can only be
displayed using this option. It is recommended for static displays
such as during setup.
The display options outlined below are essentially identical to
the 'xvar' widget.
The following parameters of the graphical display can be
used to display values in xview:
1. Color
2-4. x,y and z offsets
5. Coordinates (morphing)
6. Line thickness. *
7. Text color *
8. Text
9. Minigraph. *
10. Surface *
11. Contour *
* Not yet available.
Any or all of the display parameters can in principle be used to
simultaneously display values pertaining to each point.
In practice it gets rather confusing if more than 2 or 3 are
used at a time.
The color_val, xoffset_val, morph_val etc.
fields are used to bind the message number to the specified
display variable. Thus setting color_val to 1 means that
message VAL1 will be used to control the color of the xview pix.
By default all _vals are set to 0, which disables them.
The xview pix displays values (except text and minigraph) by linear
interpolation. Every xview has at least two child elements of class
xshape, named shape[0], shape[1], etc. These shapes determine the
extreme points for the linear interpolation. Therefore if shape[0]
has foreground color 0, and shape[1] has color 10, the range of
colors displayed would be interpolated between 0 and 10. Likewise,
if shape[0] displays a tall thin rectangle, and shape[1] a short
wide rectangle, the shapes displayed would be 'morphed' between
these two extremes. Of course, to get these effects one would have
to set the color_val and morph_val to the appropriate values.
In addition to the shapes themselves, three arrays are used to specify
how the xview does interpolation. As already mentioned, the 'values'
array specifies the actual values to be displayed. 'value_min'
contains the values that correspond to the lower end of the
interpolated range. Thus if value[0][0] was equal to value_min[0],
the parameter displayed would correspond to shape[0]. Likewise,
value_max contains the upper end of the interpolated range.
One can have multiple xshapes. In this case the interpolation first
decides which pair of shapes to use. In this version, each pair of
shapes handles an equal range between value_min and value_max.
Having selected the appropriate pair of shapes, the algorithm then
proceeds as outlined above.
The 'text' option simply prints out the floating point value of the
appropriate message. The 'minigraph' option (which will be
implemented one of these days) displays a little graph of the
value, without any optional extras like axes.
By default, the xview object is created along with two child shapes,
shape[0] and shape[1]. The default shapes are squares, shape[0] being
a small one with color 0 and shape[1] a big (1x1) square in color 63.
The child shapes can have parameters set in the usual ways, but are
not displayed independently of the xview pix. For the technically
minded, this is because their pixflags have been set to visible_not.
Note on 'morphing': Morphing in the xview pix is simply linear
interpolation between corresponding points. When one shape has a
different number of points from the other, then the algorithm
assumes that the missing points are [0,0,0] and does interpolation
accordingly. This may lead to peculiar effects, so usually one
uses the same number of points in all xshapes.
Note on 'value_min' and 'value_max' arrays: The same min and max
apply to all points in an xview. At this time autoscaling has
not been implemented, but this should be easy.
Author: Upi Bhalla Caltech Dec 93
-----------------------------------------------------------------------------
ELEMENT PARAMETERS
DataStructure: xview_type [in src/Xodus/draw/xview_struct.h]
Size: ? Depends on number of associated shapes and number of
points being displayed.
Fields:
The following fields are the same as for xvar:
fg Foreground color of view.
script Script operation(s) to perform on a mouse
click. The script calls of the view are only made
if the draw determines that the view is the nearest
to the event and if the event occurred within the
bounding region of the view.
tx Transposition distance in the x dimension. The
view is transposed (ie, displaced, offset) by this
amount.
ty Transposition in y.
tz Transposition in z.
pixflags Set of flags specifying visibility,
refreshes, mouse sensitivity and many other options.
Use the 'pixflags' utility function to find out more.
viewmode Specifies the mode of operation of the
xview. Can be one of:
shape - Does interpolation between shapes
graph - draws a minigraph (Not yet implemented)
surface - Draws a plane in 3-d, specified by 3
points in space (not yet implemented)
contour - Draws contour lines for a plane in 3-d. NYI.
colorview - Backwards compatibility hack. Uses 'shape'
mode to display boxes of different color.
boxview - Backwards compatibility hack. Uses 'shape'
mode to display boxes of different sizes.
colorboxview - Backwards compatibility hack. Default
viewmode. Uses 'shape' mode to display VAL1
using both the morph and color modes for
a box.
fillboxview - Backwards compatibility hack. Uses
'shape' mode to display filled boxes of
different sizes.
value_min 1-d array with lower limits for shape
parameters.
value_max 1-d array with upper limits for shape
parameters.
values 2-d array with display values.
color_val Specifies message to use for color
display values. 0=disabled is default.
If you wish to cause view to change
colors, use color_val.
morph_val Specifies message to use for morphing.
If you wish to have the view change
shape, use morph_val.
xoffset_val Specifies message to use for xoffset.
If you wish to cause a view to
bounce around on the screen,
use the offset_vals.
yoffset_val Specifies message to use for yoffset.
zoffset_val Specifies message to use for zoffset.
text_val Specifies message whose value should
be printed out.
textcolor_val Specifies message which determines
the color of the text.
linethickness_val Specifies message determining the
line thickness used in the view.
sizescale Rescales all the shapes. The default
shapes have a size of 1.
The following fields are new for xview:
xpts 1-d array with x-coordinates of points.
This is automatically set if the 'path' field
is set, or if COORD messages are present.
ypts 1-d array with y-coordinates of points.
This is automatically set if the 'path' field
is set, or if COORD messages are present.
zpts 1-d array with z-coordinates of points.
This is automatically set if the 'path' field
is set, or if COORD messages are present.
ncoords Number of points.
This is automatically set if the 'path' field
is set, or if COORD messages are present.
autoscale Flag for determining if the xview should
calculate value_min and max by itself. Options:
0 = off. 1 = max ever reached. 2 = max current.
(Not Yet Implemented)
undraw_by_blanking
Flag for deciding if the xview should clear
the whole display every step for redrawing.
This may be faster in some cases, but may also
leads to flicker.
(Not Yet Implemented)
path Wildcard path for elements specifying
coordinates. (xpts, ypts and zpts)
relpath Relative path for child elements off 'path',
determining where the fields are located.
field Name of field to display. Can have the
special values "msgin" or "msgout".
field2 An extra field to display. Cannot have
"msgin" or "msgout"
msgpath Wildcard path for elements connected via
msgs to 'path'. Only used for "msgin" or
"msgout" modes of 'field'.
msgtype Specifies type of msgs to display.
msgslotno Specifies slot number of msgs to display.
value Set by a click action, according to valuemode.
valuemode Specifies how xview fills the 'value' field
when a click event occurs on the view.
Can be one of "path"; "index"; "lookup"
Default = "path".
path: Finds the path of the element represented
at the click site
index: Returns the internal xview
index of the click site
lookup: Returns the value displayed at
the click site from values[0].
----------------------------------------------------------------------------
SIMULATION PARAMETERS
Function: XVar [in src/Xodus/draw/xview.c]
Classes: gadget output
Actions: PROCESS: Redo interpolation and display.
RESET: Required when changing child xshapes,
looks up coordinates.
CREATE: Automatically creates 2 child xshapes.
XUPDATE: update internal fields when
displayed widget is changed.
B1DOWN: Invoked when mouse Button 1 is pressed.
B2DOWN: Invoked when mouse Button 2 is pressed.
B3DOWN: Invoked when mouse Button 3 is pressed.
ANYBDOWN: Invoked when any mouse button is pressed.
B1DOUBLE: Invoked on a double click on mouse button 1.
B2DOUBLE: Invoked on a double click on mouse button 2.
B3DOUBLE: Invoked on a double click on mouse button 3.
XOCOMMAND: an action that can invoke the functions
in the 'script' field
XODROP: Called when a another pix is dropped onto this one.
XODRAG: Called when the mouse is clicked on this pix, and
the mouse moves while the mouse button is held down.
XOWASDROPPED: Called after this pix has been dropped onto
another one.
Messages: VAL1 data
VAL2 data
VAL3 data
VAL4 data
VAL5 data
All messages can contain values for any display parameter.
----------------------------------------------------------------------------
Notes: Can only be displayed in a coredraw widget subclass.
The xview performs the interpolation between shapes and
redraws them on every clock tick.
Examples:
//=================================CUT HERE=================================
//genesis
//
// This example demonstrates how xview can use the fields
// 'path', 'field' and 'field2' to display a combination of message
// values and field values. Note how the
// color of the boxes (displaying msgin) in the view display is
// related to the size of the boxes (displaying the 'output' field
// of the tables) preceding them.
//
int side = 10
xcolorscale rainbow2
create xform /form [0,0,500,550]
xshow /form
create xdraw /form/draw [0,0,100%,500]
setfield /form/draw xmin -1 xmax 11 ymin -1 ymax 11
create xview /form/draw/view
create xbutton /form/run -wgeom 50% -script "step 100"
create xbutton /form/quit -ygeom 0:draw -xgeom 50% -wgeom 50% \
-script quit
/* Set up the connectivity that the view will look at */
create table /tab
call /tab TABCREATE 1 0 1
setfield /tab \
stepsize 1 \
step_mode 0 \
table->table[0] 0 \
table->table[1] 1
addobject tabobj /tab
createmap tabobj /manytabs {side} {side}
gen_3d_msg /manytabs/tab[] /manytabs/tab[] 0.5 1 INPUT output -o -1 0 0
gen_3d_msg /manytabs/tab[] /manytabs/tab[] 0.5 1 INPUT output -o 9 -1 0
call /manytabs/tab[99] TABCREATE 100 0 1
setfield /manytabs/tab[99] \
stepsize 0.01 \
step_mode 1
/* Set up some values for the tabs to display */
int i
for(i = 0 ; i < 100 ; i = i + 1)
setfield /manytabs/tab[99] table->table[{i}] {{rand 0 100 }/100.0}
end
/* Set up the view widget */
setfield /form/draw/view \
path /manytabs/tab[] \
field msgin \
field2 output \
morph_val 2 \
relpath "" \
msgpath "" \
msgtype INPUT \
msgslotno 0
reset
//=================================CUT HERE=================================
See also:
xvar ,
xshape