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26. GENESIS Object Reference

26.1 Ca_concen

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

26.2 Kpores

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

26.3 Mg_block

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

26.4 Napores

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

26.5 PID

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:       

26.6 RC


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:

26.6.1 SynE_object

Object Type:    SynE_object
 
Description:    Implements electrical synaptic transmission in the leech
 
Author:         J. Lu and A. Hill, Calabrese Lab, 5/99
 
------------------------------------------------------------------------------
 
ELEMENT PARAMETERS
 
DataStructure:  SynE_type  [in src/newconn/SynGS_struct.h]
 
Size:           148 bytes
 
Fields:         TauPre       Tau for RC filter of presynaptic Vm
                TauPost      Tau for RC filter of presynaptic Vm
                Vpre         RC filtered presynaptic Vm
                Vpost        RC filtered postsynaptic Vm
                Gbar         maximal conductance
                rectify      0 = no rectify, 1 = pass pos., -1 pass neg.

------------------------------------------------------------------------------

SIMULATION PARAMETERS
 
Function:       SynE  [in src/newconn/SynE.c]
 
Classes:        device synchannel
 
Actions:        RESTORE2  SAVE2  CHECK  RESET  PROCESS  INIT
 
Messages:       VOLTAGE         presynaptic membrane potential
                POSTVOLTAGE     postsynaptic membrane potential
 
--------------------------------------------------------------------------

Notes:          Simulates electrical synaptic transmission designed
                specifically for leech HN cells, based on the synchan object.
		Needs presynaptic and postsynaptic membrane potential as
		input.  The output is the synaptic current that is added to
		the postsynaptic compartment via an inject message.  In
		addition, the pre- and postsynaptic membrane potentials can be
		lowpass filtered with an RC circuit.  The time contants can be
		set for both potentials. The synapse is unidirectional, that
		is, the current is injected into only the postsynaptic cell.
		To make a bidirectional synapse, another element must be
		created.  The synapse can be configured to be non-rectifying
		(passes both positive and negative current) or retifying
		(passes only either positive or negative current).  This is
		done by setting the rectify field to 0 for non-retifying, 1
		for passes positve current, or -1 for passes negative current.  

Example:        See http://calabreselx.biology.emory.edu/software.html.

See also: synchan, SynG_object, SynS_object.

26.6.2 SynG_object

Object Type:    SynG_object
 
Description:    Implements graded synaptic inhibition in the leech
 
Author:         J. Lu and A. Hill, Calabrese Lab, 3/97
 
------------------------------------------------------------------------------
 
ELEMENT PARAMETERS
 
DataStructure:  SynG_type  [in src/newconn/SynGS_struct.h]
 
Size:           196 bytes
 
Fields:         Ik                 channel current
                Gk                 time varying channel conductance
                Ek                 reversal potential of channel
                A                  shunts effective Ca current
                B                  buffering parameter
                P                  Ca factor governing transmitter release
                C                  limit parameter(limits release to Gbar)
                R                  release = p^3/(p^3+C)
                Gbar               maximal conductance
                A1                 A1 in Ainf=A1+A2/(1+exp(A3+(Vm+A4)))
                A2                 A2
                A3                 A3
                A4                 A4
                A5                 A5 is the time constant
                POWER              POWER

------------------------------------------------------------------------------

SIMULATION PARAMETERS
 
Function:       SynG  [in src/newconn/SynG.c]

Classes:        device synchannel
 
Actions:        RESTORE2  SAVE2  CHECK  RESET  PROCESS  INIT
 
Messages:       VOLTAGE         presynaptic membrane potential
                CAF             presynaptic fast Ca current, ICaF
                CAS             presynaptic slow Cacurrent, ICaS
                POSTVOLTAGE     postsynaptic membrane potential
 
------------------------------------------------------------------------------
 
Notes:          Simulates graded synaptic transmission designed specifically
                for leech HN cells, based on the synchan object.  Needs
		presynaptic calcium currents (ICaF and ICaS) and presynaptic
		membrane potential as input.  The output is the synaptic
		conductance.  In addition, this object can calculate the
		synpatic current if it is given the postsynaptic membrane
		potential.  This is useful only for the purpose of plotting
		the synaptic current.  The simuation will work without
		calculating synaptic current because the postsynaptic
		compartment calculates the current based on the postsynaptic
		Vm and the synaptic reversal potential.

Example:        See http://calabreselx.biology.emory.edu/software.html.

See also: See also: synchan, SynE_object, SynS_object.

26.6.3 SynS_object

Object Type:    SynS_object
 
Description:    Implements voltage-dependent modulation of spike-mediated
                synaptic transmission.
 
Author:         Calabrese Lab, 3/97
 
------------------------------------------------------------------------------
 
ELEMENT PARAMETERS
 
DataStructure:  SynS_type  [in src/newconn/SynGS_struct.h]
 
Size:           148 bytes
 
Fields:         m_SynS       modulation factor = A+B/(1+exp(C*(Vm+D)))
                A            A
                B            B
                C            C
                D            D
                E            E = time constant  

------------------------------------------------------------------------------

SIMULATION PARAMETERS
 
Function:       SynS  [in src/newconn/SynS.c]
 
Classes:        device synchannel
 
Actions:        RESTORE2  SAVE2  CHECK  RESET  PROCESS  INIT
 
Messages:       VOLTAGE         membrane potential Vm

 
------------------------------------------------------------------------------

Notes:          Calculates the voltage dependent modulation of spike mediated
                transmission in the leech HN cells.  Therefore, it needs the
		presynaptic membrane potential.  Modulation is a sigmoidal
		function of the membrane potential given by
		m_SynS = A+B/(1+exp(C*(Vm+D))), with a time constant E.

Example:        See http://calabreselx.biology.emory.edu/software.html.

See also: synchan, SynG_object, SynE_object.

26.7 asc_file

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

26.8 autocorr

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

26.9 calculator

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:       

26.10 compartment

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

26.11 concchan

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

26.12 concpool

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

26.13 crosscorr

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

26.14 ddsyn

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

26.15 dif2buffer

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

26.16 difbuffer

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

26.17 diffamp

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:       

26.18 difshell

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

26.19 disk_in

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,

26.20 disk_out

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

26.21 diskio

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

26.22 efield

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

26.23 enz

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.

------------------------------------------------------------------------------

26.24 event_tofile

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.

26.25 facsynchan

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

26.26 fixbuffer

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

26.27 freq_monitor

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:       

26.28 funcgen

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:       

26.29 fura2

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

26.30 ghk

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

26.31 hebbsynchan

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

26.32 hh_channel

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

26.33 hillpump

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

26.34 hsolve

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

26.35 interspike

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

26.36 leakage

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:       

26.37 metadata

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

26.38 mmpump

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

26.39 nernst

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

26.40 neutral

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:       

26.41 paramtableBF

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

26.42 paramtableCG

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

26.43 paramtableGA

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

26.44 paramtableSA

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

26.45 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

26.46 peristim

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

26.47 playback

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

26.48 pool

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.

26.49 pulsegen

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:       

26.50 randomspike

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:       

26.51 reac

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.

------------------------------------------------------------------------------

26.52 receptor

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

26.53 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

26.54 script_out

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

26.55 sigmoid

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:       

26.56 spikegen

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

26.57 spikehistory

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

26.57.1 stdp_rules

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

26.58 symcompartment

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

26.59 synchan

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

26.60 synchan2

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

26.61 tab2Dchannel

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

26.62 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

26.63 tabcurrent

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

26.64 tabgate

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

26.65 table

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 ).

26.66 table2D

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 ).

26.67 taupump

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

26.68 timetable

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

26.69 variable

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

26.70 vdep_channel

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

26.71 xbutton

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.

26.72 xcell

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

26.73 xcoredraw

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.

26.74 xdialog

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 )

26.75 xdraw

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.

26.76 xdumbdraw

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.

26.77 xfastplot

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

26.78 xform

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.

26.79 xgif

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

26.80 xgraph

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.

26.81 ximage

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 )

26.82 xlabel

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.

26.83 xpix

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

26.84 xplot

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.

26.85 xshape

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

26.86 xsphere

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

26.87 xtext

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.

26.88 xtoggle

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 )

26.89 xtree

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

26.90 xvar

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

26.91 xview

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


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