// Created 10/09/03 08:18:39 by /usr/site/scripts/loadfiles
//================================================================
// INSERTED cells.hoc
// $Id: cells.hoc,v 1.15 2003/10/09 12:18:33 billl Exp $
// load_file("modeldb/cells.hoc")
load_file("stdgui.hoc")
//================================================================
// INSERTED /usr/site/nrniv/local/hoc/setup.hoc
// $Id: setup.hoc,v 1.17 2003/07/23 17:44:26 billl Exp $
// variables normally controlled by SIMCTRL
// load_file("setup.hoc")
show_panel=0
proc setup () {}
strdef simname, filename, output_file, datestr, uname, comment, section, osname
objref tmpfile,nil,graphItem
tmpfile = new File()
simname = "sim" // helpful if running multiple simulations simultaneously
runnum = 2 // updated at end of run
datestr = "99aug01" // updated at end of day
output_file = "data/99aug01.01" // assumes a subdir called data
comment = "current comment for saving sim"
uname = "i686" // keep track of type of machine for byte compatibility
osname = "Linux" // will want to grab this from env
printStep = 0.25 // time interval for saving to vector
graph_flag=1
xwindows = 1 // can still save but not look without xwindows
// load_file("nrnoc.hoc")
// END /usr/site/nrniv/local/hoc/setup.hoc
//================================================================
//================================================================
// INSERTED /usr/site/nrniv/simctrl/hoc/nrnoc.hoc
// $Id: nrnoc.hoc,v 1.58 2003/10/01 13:01:01 billl Exp $
proc nrnoc () {}
// Users should not edit nrnoc.hoc or default.hoc. Any local
// changes to these files should be made in local.hoc.
// key '*&*' is picked up by to indicate command for emacs
proc elisp () { printf("*&* %s\n",$s1) }
// if (not exists(simname)) { strdef simname, output_file, datestr, comment }
// Simctrl.hoc will automatically load stdgraph.hoc which automatically
// loads stdrun.hoc
strdef temp_string_, user_string_ // needed for simctrl
/* Global variable default values. NOTE that stdrun.hoc, stdgraph.hoc
and simctrl.hoc all contain variable definitions and thus default.hoc
should be loaded after these files */
//================================================================
// INSERTED /usr/site/nrniv/simctrl/hoc/default.hoc
// $Id: default.hoc,v 1.5 2003/07/08 16:16:52 billl Exp $
/* This file contains various global defaults for hoc
** Users should not edit nrnoc.hoc or default.hoc. Any local
changes to these files should be made in local.hoc.
----------------------------------------------------------------*/
/*------------------------------------------------------------
Object defaults
------------------------------------------------------------*/
/*** Define a "nil" object ***/
objectvar nil
/*------------------------------------------------------------
String defaults
------------------------------------------------------------*/
/*** "Section" is used if errors are found in the initializiations ***/
strdef section
/*** Misc defines used by graphic routines ***/
temp_string_ = "t"
tempvar = 0
/*------------------------------------------------------------
Simulation defaults
------------------------------------------------------------*/
/* To be consistent w/the nmodl values */
FARADAY = 96520. /* Hoc default = 96484.56 */
PI = 3.14159 /* Hoc default = 3.1415927 */
/* 0=off, 1=on */
print_flag = 0 /* Write to output file */
graph_flag = 1 /* Plot output */
iv_flag = 1 /* Using Interviews plotting */
batch_flag = 0 /* Using batch_run() */
compress_flag = 0 /* Compress output file when saved */
stoprun = 0 /* 0=running, 1=stopped */
iv_loaded = 0 /* Load initial iv stuff on once */
init_seed = 830529
run_seed = 680612
t = 0 /* msec */
dt = .01 /* msec */
tstop = 100 /* msec */
printStep = 0.1 /* msec */
plotStep = 0.1 /* msec */
flushStep = 0.1 /* msec */
eventStep = 50 /* Number of nstep's before a doEvent */
secondorder = 0
celsius = 6.3 /* degC */
v_init = -70 /* (mV) */
global_ra = 200 /* (ohm-cm) specific axial resisitivity */
/*** Ion parameters ***/
ca_init = 50e-6 /* mM */
na_init = 10 /* mM */
k_init = 54.4 /* mM */
// END /usr/site/nrniv/simctrl/hoc/default.hoc
//================================================================
/* Allows arrays of strings */
objref hoc_obj_[2]
//================================================================
// INSERTED /usr/site/nrniv/simctrl/hoc/simctrl.hoc
// $Id: simctrl.hoc,v 1.14 2000/11/27 21:59:33 billl Exp $
// Graphic routines for neuremacs simulation control
proc sim_panel () {
xpanel(simname)
xvarlabel(output_file)
xbutton("Init", "stdinit()")
xbutton("Init & Run", "run()")
xbutton("Stop", "stoprun=1")
xbutton("Continue till Tstop", "continueRun(tstop)")
xvalue("Continue till", "runStopAt", 1, "{continueRun(runStopAt) stoprun=1}", 1, 1)
xvalue("Continue for", "runStopIn", 1, "{continueRun(t + runStopIn) stoprun=1}", 1,1)
xbutton("Single Step", "steprun()")
xvalue("Tstop", "tstop", 1, "tstop_changed()", 0, 1)
graphmenu()
sim_menu_bar()
misc_menu_bar()
xpanel()
}
proc misc_menu_bar() {
xmenu("Miscellaneous")
xbutton("Label Graphs", "labelgrs()")
xbutton("Label With String", "labelwith()")
xbutton("Label Panel", "labelpanel()")
xbutton("Parameterized Function", "load_template(\"FunctionFitter\") makefitter()")
xmenu()
}
proc sim_menu_bar() {
xmenu("Simulation Control")
xbutton("File Vers", "elisp(\"sim-current-files\")")
xbutton("File Status...", "elisp(\"sim-rcs-status\")")
xbutton("Sim Status", "elisp(\"sim-portrait\")")
xbutton("Load Current Files", "elisp(\"sim-load-sim\")")
xbutton("Load Templates", "elisp(\"sim-load-templates\")")
xbutton("Load File...", "elisp(\"sim-load-file\")")
xbutton("Save Sim...", "elisp(\"sim-save-sim\")")
xbutton("Set File Vers...", "elisp(\"sim-set-file-ver\")")
xbutton("Read Current Vers From Index", "elisp(\"sim-read-index-file\")")
xbutton("Read Last Saved Vers", "elisp(\"sim-read-recent-versions\")")
xbutton("Output to sim buffer", "elisp(\"sim-direct-output\")")
xmenu()
}
proc labelpanel() {
xpanel(simname,1)
xvarlabel(output_file)
xpanel()
}
proc labels () {
labelwith($s1)
labelgrs()
}
proc labelgrs () { local i, j, cnt
for j=0,n_graph_lists-1 {
cnt = graphList[j].count() - 1
for i=0,cnt labelgr(graphList[j].object(i))
}
}
proc labelwith () { local i, j, cnt
temp_string_ = user_string_ // save the old one
if (numarg() == 1) { /* interactive mode */
user_string_ = $s1
} else {
string_dialog("write what?", user_string_)
}
for j=0,n_graph_lists-1 {
cnt = graphList[j].count() - 1
for i=0,cnt {
graphList[j].object(i).color(0)
graphList[j].object(i).label(0.5,0.9,temp_string_)
graphList[j].object(i).color(1)
graphList[j].object(i).label(0.5,0.9,user_string_)
}
}
}
proc labelgr () { local i
$o1.color(0) // white overwrite
for (i=0;i<10;i=i+1) { // erase every possible runnum for this date
sprint(temp_string_,"%s %d%d",datestr,i,i)
$o1.label(0.1,0.7,temp_string_) }
$o1.color(1) // back to basic black
sprint(temp_string_,"%s %02d",datestr,runnum)
$o1.label(0.1,0.7,temp_string_)
}
// END /usr/site/nrniv/simctrl/hoc/simctrl.hoc
//================================================================
proc run () {
stdinit()
if (batch_flag == 1) {
cvode.solve(tstop)
} else {
continueRun(tstop)
}
finish()
}
proc continueRun () { local eventCount
eventCount=0
eventslow=1
stoprun = 0
if (cvode_active()) cvode.event($1)
while (t < tstop && stoprun == 0) {
advance()
outputData()
if (graph_flag) { fastflushPlot() doEvents() }
}
}
proc advance () { fadvance() }
proc stdinit() {
realtime=0 startsw()
t = 0
stoprun = 0
if (batch_flag == 1) {
}
init()
if (graph_flag == 1) {
if (iv_flag == 1) {
initPlot()
} else {
initGraph()
}
}
if (print_flag == 1) { initPrint() }
}
proc init () {
initMech()
initMisc1()
// Initialize state vars then calculate currents
// If user hand-set v in initMisc1() then v_init should be > 1000,
// else all compartments will be set to v_init
if (v_init < 1000) {
finitialize(v_init)
} else {
finitialize()
}
fcurrent()
// Set ca pump and leak channel for steady state
setMemb()
// Recalculate currents with new pump and leak kinetics
fcurrent()
fcurrent()
initMisc2()
if (cvode_active()) cvode.re_init()
}
// Initialization of mechanism variables
// NOTE: if any changes are made to the NEURON block of any local mod
// file, the user must add the necessary inits to initMisc1()
proc initMech () {
forall {
if ((!ismembrane("pas")) && (!ismembrane("Passive"))) {
// Allow for either pas or Passive mod file usage
// errorMsg("passive not inserted")
}
if (ismembrane("na_ion")) {
nai = na_init
nai0_na_ion = na_init
}
if (ismembrane("k_ion")) {
ki = k_init
ki0_k_ion = k_init
}
if (ismembrane("ca_ion")) {
cai = ca_init
cai0_ca_ion = ca_init
}
}
}
//* setMemb complex -- multiple names for passive mech
//** declarations
iterator scase() { local i
for i = 1, numarg() { temp_string_ = $si iterator_statement }}
objref paslist,pasvars[3],XO
double pasvals[2],x[1]
paslist = new List()
for ii=0,2 pasvars[ii]= new String()
for scase("pas","Pass","Passive") paslist.append(new String(temp_string_))
//** getval(),setval() -- return/set the hoc value of a string
func retval () { return getval($s1) }
func getval () {
sprint(temp_string2_,"x=%s",$s1)
execute(temp_string2_)
return x
}
proc setval () {
sprint(temp_string2_,"%s=%g",$s1,$2)
execute(temp_string2_)
}
//** findpas()
// assumes that we are starting in a live section since looks for pass mech there
qx_=0
proc findpas () {
for ii=0,paslist.count-1 {
XO=paslist.object(ii)
if (ismembrane(XO.s)) {
// print XO.s,"found"
pasvars[2].s=XO.s
sprint(pasvars[0].s,"g_%s(qx_)",XO.s)
for scase("e","erev","XXXX") { // look for the proper prefix
sprint(temp_string_,"%s_%s",temp_string_,XO.s)
if (name_declared(temp_string_)==1) break
}
if (name_declared(temp_string_)==0) { // not found
printf("SetMemb() in nrnoc.hoc: Can't find proper 'erev' prefix for %s\n",XO.s)
} else {
sprint(pasvars[1].s,"%s(qx_)",temp_string_)
}
}
}
}
proc setMemb () {
findpas() // assume that passive name is the same in all sections
forall for (qx_) { // will eventually want 'for (x)' to handle all the segments
if (ismembrane(pasvars[2].s)) {
for ii=0,1 pasvals[ii]=getval(pasvars[ii].s)
setmemb2()
for ii=0,1 setval(pasvars[ii].s,pasvals[ii])
}
}
}
func setother () {return 0} // callback stub
proc setmemb2 () { local iSum, ii, epas, gpas
gpas=pasvals[0] epas=pasvals[1]
// Setup steady state voltage using leak channel
iSum = 0.0
if (ismembrane("na_ion")) { iSum += ina(qx_) }
if (ismembrane("k_ion")) { iSum += ik(qx_) }
if (ismembrane("ca_ion")) { iSum += ica(qx_) }
iSum += setother()
// print iSum
if (iSum == 0) { // Passive cmp so set e_pas = v
epas = v
} else {
if (gpas > 0) { // Assume g set by user, calc e
epas = v + iSum/gpas
} else { // Assume e set by user, calc g
if (epas != v) {
gpas = iSum/(epas - v)
} else { gpas=0 }
}
if (gpas < 0) errorMsg("bad g", gpas)
if (epas < -100 || epas > 0) {
printf(".")
// printf("%s erev: %g %g %g\n",secname(),e_pas,ina,ik)
}
}
pasvals[0]=gpas pasvals[1]=epas
}
proc finish() {
/* Called following completion of continueRun() */
finishMisc()
if (graph_flag == 1) {
if (iv_flag == 1) {
flushPlot()
doEvents()
} else {
graphmode(-1)
plt(-1)
}
}
if (print_flag == 1) {
wopen("")
}
}
/*------------------------------------------------------------
User definable GRAPHICS and PRINTING routines
------------------------------------------------------------*/
proc outputData() {
// Default procedure - if outputData() doesn't exist in the run file
if (graph_flag == 1) {
if (iv_flag == 1) {
Plot()
rt = stopsw()
if (rt > realtime) {
realtime = rt
fastflushPlot()
doNotify()
if (realtime == 2 && eventcount > 50) {
eventslow = int(eventcount/50) + 1
}
eventcount = 0
}else{
eventcount = eventcount + 1
if ((eventcount%eventslow) == 0) {
doEvents()
}
}
} else {
graph(t)
}
}
if (print_flag == 1) {
if (t%printStep <= printStep) { printOut() }
}
}
proc printOut() {
/* Default procedure - if printOut() doesn't exist in the run file */
}
proc initGraph() {
/* Default procedure - if initGraph() doesn't exist in the run file */
graph()
}
proc initPrint() {
/* Default procedure - if initPrint() doesn't exist in the run file */
wopen(output_file)
}
/*------------------------------------------------------------
User definable BATCH RUN routines
------------------------------------------------------------*/
proc nextrun() {
// Called from finishmisc() following completion of batch in an autorun
wopen("")
runnum = runnum + 1
sprint(output_file,"data/b%s.%02d", datestr, runnum)
}
// commands for emacs
proc update_runnum() {
runnum = $1
sprint(output_file,"data/%s.%02d", datestr, runnum)
print "^&^ (progn (sim-index-revert)(setq sim-runnum ",runnum,"))" }
proc nrn_write_index() { printf("&INDEX& %s\n",$s1) }
proc nrn_update () { elisp("nrn-update") }
proc nrn_message () { printf("!&! %s\n",$s1) }
/*------------------------------------------------------------
User definable INITIALIZATION and FINISH routines
------------------------------------------------------------*/
// Default procedure - if initMisc1() doesn't exist in the run file
// Initializations performed prior to finitialize()
// This should contain point process inits and inits for any changes
// made to the NEURON block of any local mod file
proc initMisc1() { }
// Default procedure - if initMisc2() doesn't exist in the run file
// Initializations performed after finitialize()
proc initMisc2() { }
// Default procedure - if finishMisc() doesn't exist in the run file
proc finishMisc() { }
/*------------------------------------------------------------
Miscellaneous routines
------------------------------------------------------------*/
proc errorMsg() {
/* Print warning, assumes arg1 is string and arg2 if present is a
variable value */
sectionname(section)
if (numarg() == 0) {
printf("ERROR in errorMsg(): Needs at least 1 argument.\n")
} else if (numarg() == 1) {
printf("ERROR: %s in section %s.\n", $s1, section)
} else {
printf("ERROR: %s in section %s (var=%g).\n", $s1, section, $2)
}
}
proc clear() {
/* Clear non-interviews plot window */
plt(-3)
}
func mod() { local x, y
/* Mod function for non-integers */
x=$1
y=$2
return (x/y - int(x/y))
}
proc whatSection() { print secname() }
proc print_pp_location() { local x //arg1 must be a point process
x = $o1.get_loc()
sectionname(temp_string_)
printf("%s located at %s(%g)\n", $o1, temp_string_, x)
pop_section()
}
//* set method with method()
proc method () {
if (strcmp($s1,"global")==0) {
cvode_active(1)
} else if (strcmp($s1,"local")==0) {
cvode_local(1)
} else if (strcmp($s1,"implicit")==0) {
secondorder=0
cvode_active(0)
} else if (strcmp($s1,"CN")==0) {
secondorder=2
cvode_active(1) // this turns off local
cvode_active(0)
} else {
printf("Integration method %s not recognized\n",$s1)
}
}
//* Load local modifications to nrnoc.hoc and default.hoc
//================================================================
// INSERTED /usr/site/nrniv/simctrl/hoc/local.hoc
// $Header: /usr/site/nrniv/simctrl/hoc/RCS/local.hoc,v 1.15 2003/02/13 15:32:06 billl Exp $
//
// This file contains local modifications to nrnoc.hoc and default.hoc
//
// Users should not edit nrnoc.hoc or default.hoc. Any local
// changes to these files should be made in this file.
// ------------------------------------------------------------
//* MODIFICATIONS TO NRNOC.HOC
// The procedures declared here will overwrite any duplicate
// procedures in nrnoc.hoc.
// ------------------------------------------------------------
//*MODIFICATIONS TO DEFAULT.HOC
//
// Vars added here may not be handled properly within nrnoc.hoc
//------------------------------------------------------------
//** String defaults
//** Simulation defaults
long_dt = .001 // msec
objref sfunc,tmpfile
sfunc = hoc_sf_ // needed to use is_name()
tmpfile = new File() // check for existence before opening a user's local.hoc file
proc write_comment () {
tmpfile.aopen("index")
tmpfile.printf("%s\n",$s1)
tmpfile.close()
}
func asin () { return atan($1/sqrt(1-$1*$1)) }
func acos () { return atan(sqrt(1-$1*$1)/$1) }
objref mt[2]
mt = new MechanismType(0)
proc uninsert_all () { local ii
forall for ii=0,mt.count()-1 {
mt.select(ii)
mt.selected(temp_string_)
if (strcmp(temp_string_,"morphology")==0) continue
if (strcmp(temp_string_,"capacitance")==0) continue
if (strcmp(temp_string_,"extracellular")==0) continue
if (sfunc.substr(temp_string_,"_ion")!=-1) continue
mt.remove()
// print ii,temp_string_
}
}
condor_run = 0 // define for compatability
// END /usr/site/nrniv/simctrl/hoc/local.hoc
//================================================================
if (xwindows && graph_flag) { nrnmainmenu() } // pwman_place(50,50)
print "Init complete.\n"
// END /usr/site/nrniv/simctrl/hoc/nrnoc.hoc
//================================================================
//================================================================
// INSERTED /usr/site/nrniv/local/hoc/grvec.hoc
// $Id: grvec.hoc,v 1.337 2003/09/27 14:35:27 billl Exp $
// 0 -> double, ie $1
// 1 -> object, ie $o1
// 2 -> string, ie $s1
// 3 -> address,ie $&1
// main panel is 'vecpanel()'
proc grvec () {}
//================================================================
// INSERTED /usr/site/nrniv/local/hoc/declist.hoc
// $Id: declist.hoc,v 1.51 2003/10/08 17:51:45 billl Exp $
strdef mchnms
objref tmplist,tmplist2,tmpobj,stack,SO,aa
tmplist = new List()
stack = new List()
proc declist() {}
//* Declarations
begintemplate String2
public s,t,append,prepend,exec
strdef s,t
proc init() {
if (numarg() == 1) { s=$s1 }
if (numarg() == 2) { s=$s1 t=$s2 }
}
proc append () { local i
if (argtype(1)==2) sprint(t,"%s%s",s,$s1)
for i=2,numarg() sprint(t,"%s%s",t,$si)
}
proc prepend () { local i
if (argtype(1)==2) sprint(t,"%s%s",$s1,s)
for i=2,numarg() sprint(t,"%s%s",$si,t)
}
proc exec () {
if (numarg()==1) sprint(t,"%s%s",$s1,s)
execute(t)
}
endtemplate String2
//* SNO: generic template to store strings numbers and objects
begintemplate SNO
public s,t,u,n,o,set
public ov,ol,set,get,pr,init
strdef s,t,u,tstr
objref o[3],this
double n[3]
proc init() {
if (numarg() >= 2) {s=$s1 n[0]=$2}
if (numarg() >= 4) {t=$s3 n[1]=$4}
if (numarg() == 6) {u=$s5 n[2]=$6}
}
proc ov () { local a,sz
if (numarg()>=1) a=$1 else a=0
if (numarg()==1) sz=$2 else sz=100
o[a]=new Vector(sz)
}
proc ol () {
if (numarg()==1) a=$1 else a=0
o[a]=new List()
}
proc set () { local ii
if (numarg()==1) ii=$1 else ii=0
if (ii==0) tstr=s else if (ii==1) tstr=t else if (ii==2) tstr=u else {
printf("ERROR: only 3 items in SNO: %s\n",this) return }
sprint(tstr,"%s = %s.n[%d]",tstr,this,ii)
execute(tstr)
}
proc get () { local ii
if (numarg()==1) ii=$1 else ii=0
if (ii==0) {
sprint(tstr,"%s.n[%d] = %s",this,ii,this.s)
} else if (ii==1) {
sprint(tstr,"%s.n[%d] = %s",this,ii,this.t)
} else if (ii==2) {
sprint(tstr,"%s.n[%d] = %s",this,ii,this.u)
} else { printf("ERROR: only 3 items in SNO: %s\n",this) return }
execute(tstr)
}
proc pr () { local ii
if (numarg()==1) ii=$1 else ii=0
if (ii==0) {
sprint(tstr,"print %s.s,\" \",%s,\" \",%s.n[%d]",this,s,this,ii)
} else if (ii==1) {
sprint(tstr,"print %s.t,\" \",%s,\" \",%s.n[%d]",this,t,this,ii)
} else if (ii==2) {
sprint(tstr,"print %s.u,\" \",%s,\" \",%s.n[%d]",this,u,this,ii)
} else { printf("ERROR: only 3 items in SNO: %s\n",this) return }
execute(tstr)
}
endtemplate SNO
//* list iterator ltr
// usage 'for ltr(tmplist) { print XO }' :: 1 arg, assumes XO as dummy
// usage 'for ltr(YO, tmplist) { print YO }' 2 arg, specify dummy
// usage 'for ltr(XO, tmplist, &x) { print XO,x }' :: 3 args, define counter (else i1 default)
// :: note that x, i1 must be defined
iterator ltr () { local i
if (numarg()==3) {$&3=0} else {i1 = 0}
if (numarg()==1) {
for i = 0, $o1.count() - 1 {
XO = $o1.object(i)
iterator_statement
i1+=1
}
tmpobj=$o1
} else {
for i = 0, $o2.count() - 1 {
$o1 = $o2.object(i)
iterator_statement
if (numarg()==3) { $&3+=1 } else { i1+=1 }
}
tmpobj=$o2
$o1 = nil
}
}
// lswap(list,#1,#2) swap items on a list
proc lswap () { local a,b
if ($2<$3) {a=$2 b=$3} else {a=$3 b=$2}
$o1.insrt(a,$o1.object(b))
$o1.remove(b+1)
$o1.insrt(b+1,$o1.object(a+1))
$o1.remove(a+1)
}
// proc shl() show a list
proc shl () {
if (numarg()==1) tmpobj=$o1 else tmpobj=tmplist
if (tmpobj.count==0) return
if (isstring(tmpobj.object(0),tstr)) {
for ltr(XO,tmpobj) print XO.s
} else for ltr(XO,tmpobj) print XO
}
// lfu() = ltr follow-up, pick out a single item from the last ltr request
// lfu(list,num[,obj])
proc lfu () {
if (numarg()==1) {
if (argtype(1)==0) XO=tmpobj.object($1)
if (argtype(1)==1) tmpobj=$o1
}
if (numarg()==2) {
if (argtype(1)==1 && argtype(2)==0) {tmpobj=$o1 XO=$o1.object($2)}
if (argtype(1)==0 && argtype(2)==1) {$o2=tmpobj.object($1)}
}
if (numarg()==3) {
if (argtype(1)==1 && argtype(2)==0 && argtype(3)==1) { tmpobj=$o1 $o3=$o1.object($2) }
}
if (numarg()==4) {
$o2=tmpobj.object($1) $o4=tmpobj.object($3)
}
}
//* list iterator ltr2
// usage 'for ltr2(XO, YO, list1, list2) { print XO,YO }'
iterator ltr2() { local i
if (numarg()==5) $&5=0 else i1=0
if ($o3.count != $o4.count) { print "ltr2 ERROR: lists have different lengths" return }
for i = 0, $o3.count() - 1 {
$o1 = $o3.object(i)
$o2 = $o4.object(i)
iterator_statement
if (numarg()==5) { $&5+=1 } else { i1+=1 }
}
$o1=nil $o2=nil
}
//* list pairwise iterator ltrp
// usage 'for ltrp(XO, YO, list) { print XO,YO }' takes them pairwise
iterator ltrp() { local i
if (numarg()==4) {$&4=0} else {i1 = 0}
for (i=0;i<$o3.count()-1;i+=2) {
$o1 = $o3.object(i) $o2 = $o3.object(i+1)
iterator_statement
if (numarg()==4) { $&4+=1 } else { i1+=1 }
}
$o1=nil $o2=nil
}
//* list iterator sltr
// usage 'for sltr(XO, string) { print XO }'
iterator sltr() { local i
tmplist = new List($s2)
if (numarg()==3) {$&3=0} else {i1=0}
for i = 0, tmplist.count() - 1 {
$o1 = tmplist.object(i)
iterator_statement
if (numarg()==3) { $&3+=1 } else { i1+=1 }
}
$o1 = nil
}
//* listedit() allows you to remove things by clicking
proc listedit () {
if (numarg()==0) { print "listedit(list,str) gives browser(list,str) for removing items" return}
if (numarg()==1) {
if (! isstring($o1.object(0),temp_string_)) {print "Give name for string of object?" return }
sprint(temp_string_,"proc ledt1 () {sprint(temp_string_,%s,hoc_ac_,%s.object(hoc_ac_).%s)}","\"%d:%s\"",$o1,"s")
} else {
sprint(temp_string_,"proc ledt1 () {sprint(temp_string_,%s,hoc_ac_,%s.object(hoc_ac_).%s)}","\"%d:%s\"",$o1,$s2)
}
execute1(temp_string_)
$o1.browser("Double click on item to remove",temp_string_,"ledt1()")
sprint(temp_string_,"%s.remove(hoc_ac_)",$o1)
$o1.accept_action(temp_string_)
}
//* listXO() connects stuff to XO from a list
proc listXO () {
if (numarg()==1) {
$o1.browser("Double click")
sprint(temp_string_,"print hoc_ac_,\":XO -> \",%s.object(hoc_ac_) XO = %s.object(hoc_ac_)",$o1,$o1)
$o1.accept_action(temp_string_)
} else if (numarg()==2) {
$o1.browser($s2)
sprint(temp_string_,"XO = %s.object(hoc_ac_) print %s.object(hoc_ac_).%s",$o1,$o1,$s2)
$o1.accept_action(temp_string_)
} else if (numarg()==3) {
$o1.browser($s2)
sprint(temp_string_,"XO = %s.object(hoc_ac_) print %s.object(hoc_ac_).%s,%s.object(hoc_ac_).%s",$o1,$o1,$s2,$o1,$s3)
$o1.accept_action(temp_string_)
}
}
//* lcatstr(list,s1,s2,...) make new List("s1") new List("s2") ... in one list
proc lcatstr() { local i
if (numarg()<3) { print "lcatstr(l1,s1,s2,...) puts new Lists into l1" return }
$o1 = new List($s2)
for i=3,numarg() {
tmplist2 = new List($si)
for ltr(XO,tmplist2) { $o1.append(XO) }
}
}
//* sublist() places a sublist in LIST0 from LIST1 index BEGIN to END inclusive
proc sublist () { local ii
$o1.remove_all
for ii=$3,$4 {
$o1.append($o2.object(ii))
}
}
//* catlist() concats LIST2...LISTN on end of LIST1
proc catlist () { local i
for i = 2, numarg() {
for ltr(YO,$oi) {
$o1.append(YO)
}
}
}
//* mechlist() creates a LIST of all this CELL type's TEMPLATE type
// list, cell, template
// make a list of mechanisms belonging to a certain template
proc mechlist () { local num,ii
// mchnms = "" // not a good storage since runs out of room
if (numarg()==0) { print "mechlist(list, cell, template)" return}
$o1 = new List($s2)
num = $o1.count
for ii=0,num-1 {
sprint(temp_string_,"%s.append(%s.%s)",$o1,$o1.object(ii),$s3)
execute(temp_string_)
sprint(mchnms,"%s/%d/%s.%s",mchnms,ii,$o1.object(ii),$s3)
}
for (ii=num-1;ii>=0;ii=ii-1) { $o1.remove(ii) }
}
//* lp() loop through a list running command in object's context
// assumes list in tmplist
// with 1 args run $o1.object().obj_elem
// with 2 args run comm($o1.object().obj_elem)
proc lp () {
for ii=0,tmplist.count-1 {
printf("%s ",tmplist.object(ii))
if (numarg()==2) {
sprint(temp_string_,"%s(%s.%s)",$s2,tmplist.object(ii),$s1)
} else {
sprint(temp_string_,"%s.%s",tmplist.object(ii),$s1)
}
execute(temp_string_)
}
}
//* prlp() loop through a list printing object name and result of command
proc prlp () {
for ii=0,tmplist.count-1 {
printf("%s ",tmplist.object(ii))
if (numarg()==1) {
sprint(temp_string_,"print %s.%s",tmplist.object(ii),$s1)
execute(temp_string_)
} else { print "" }
}
}
//** repl_str(str,stra,strb,scratch): replace stra with strb in string
// will only replace first string match
proc repl_str() {
if (sfunc.substr($s1,$s2) == -1) { print $s2," not in ",$s1 return }
sfunc.tail($s1,$s2,$s4)
sprint($s4,"%s%s",$s3,$s4)
sfunc.head($s1,$s2,$s1)
sprint($s1,"%s%s",$s1,$s4)
}
proc aaaa () { local flag
if (numarg()==2) { tmpfile.ropen($s1) aa=$o2 flag=0
} else if (numarg()==1) { tmpfile.ropen($s1) flag=1
} else { tmpfile.ropen("aa") flag=1 }
if (flag==1) if (isobj(aa,"List")) { aa.remove_all() } else { aa=new List() }
while (tmpfile.gets(temp_string_)>0) {
chop(temp_string_)
tmpobj=new String(temp_string_)
aa.append(tmpobj)
}
tmpobj=nil
}
//* var2obj() and canobj() -- find true object names
// var2obj("tstr"[,"objvar"]) replaces variable name with actual name of the object
// default into XO; optional second arg allows to place somewhere else
// eg tstr="TC[0].ampa" var2obj(tstr) -> AMPA[0]
proc var2obj () { local flag
if (numarg()==1) flag=1 else flag=0
if (flag) sprint($s1,"XO=%s",$s1) else sprint($s1,"%s=%s",$s2,$s1)
execute($s1) // change variable name to object name
if (flag) sprint($s1,"%s",XO) else sprint($s1,"%s",$s2)
}
//** objnum(OBJ) -- find object number
func objnum () {
sprint(temp_string_,"%s",$o1)
if (sscanf(temp_string_,"%*[^[][%d]",&x) != 1) x=-1
return x
}
//** canobj(obj[,"OBJVAR"]) -- default will assign to XO
// canonical object -- return canonical identity for an object
// eg canobj(tc,"YO") -- figure out what tc is and assign it to YO
proc canobj () { local flag
if (numarg()==1) flag=1 else flag=0
if (flag) sprint(tstr,"XO=%s",$o1) else sprint(tstr,"%s=%s",$s2,$o1)
execute(tstr) // change variable name to object name
sprint(tstr,"%s",$o1)
}
//* push() and pop() for objects -- returns
proc push () { local i
for i=1,numarg() stack.append($oi)
}
proc pop () { local i
if ((numarg()>0 && stack.count<numarg()) || stack.count==0) {
print "ERR: stack underflow" return
}
if (numarg()>=1) {
for i=1,numarg() {
$oi=stack.object(stack.count-1)
stack.remove(stack.count-1)
}
} else {
SO=stack.object(stack.count-1)
stack.remove(stack.count-1)
}
}
proc time () { local tti
prtime()
if (numarg()==1) execute1($s1) else execute1("run()")
tti=prtime()
if (tti<60) print tti,"s" else print tti/60,"m"
}
// END /usr/site/nrniv/local/hoc/declist.hoc
//================================================================
//================================================================
// INSERTED /usr/site/nrniv/local/hoc/decvec.hoc
// $Id: decvec.hoc,v 1.118 2003/10/08 17:46:54 billl Exp $
proc decvec() {}
//* Declarations
objref ind, tvec, vec, vec0, vec1, tmpvec, vrtmp, veclist, veccollect
objref tmpobj, XO, YO, rdm, dir
dir = new List()
print "Loading decvec"
{ MSONUM=100 MSOSIZ=100 msomax=0 msoptr=0 objref mso[MSONUM] }
double x[4],y[4]
xx=0 // declare a scalar
ind = new Vector(100)
tvec = new Vector(100)
vec = new Vector(100)
vec0 = new Vector()
vec1 = new Vector()
vrtmp = new Vector()
veclist = new List()
veccollect = new List()
rdm = new Random()
if (!(xwindows && name_declared("xwindows"))) {
xwindows=0
objref graphItem
strdef temp_string_, temp_string2_
}
strdef xtmp,space
if (wopen("xtmp")) xtmp = "xtmp" else xtmp="/tmp/xtmp" // scratch file to save system output to
//* stuff that doesn't belong here
//** dired(list,file) - put together list of files matching 'file', calls 'ls -1 file'
// dired(list,file,1) file name to read for list of files
proc dired () {
if (numarg()==0) { print "dired(list,filename) adds the filename to list (use wildcards)"
return }
if (numarg()==3) {
tmpfile.ropen($s2)
} else {
sprint(temp_string_,"ls -1R %s > %s",$s2,xtmp) // list in order of creation time
system(temp_string_)
tmpfile.ropen(xtmp)
}
while (tmpfile.scanstr(temp_string_) != -1) {
tmpobj=new String()
tmpobj.s=temp_string_
$o1.append(tmpobj)
tmpfile.gets(temp_string_) // get rid of the rest of the line
}
}
//** lbrw(list,action) is used to put up a browser
// note action given without '()'
proc lbrw () {
$o1.browser($s2,"s")
sprint($s2,"%s()",$s2)
$o1.accept_action($s2)
}
//** l2v(S1,S2) makes a list(S1) and puts all the XO.S2 into vec
// eg l2v("IClamp","amp")
proc l2v () {
tmpobj=new List($s1)
if (numarg()==3) YO=$o3 else YO=vec
YO.resize(tmpobj.count) YO.resize(0)
for ltr(tmpobj) {
sprint(tstr,"YO.append(%s.%s)",XO,$s2)
execute(tstr)
}
}
//* vector iterator vtr
// usage 'for vtr(&x, vec) { print x }'
iterator vtr() { local i
if (numarg()==3) {$&3=0} else {i1 = 0}
if (numarg()==1) {
for i = 0,$o1.size()-1 {
x = $o1.x[i]
iterator_statement
i1+=1
}
} else {
for i = 0,$o2.size()-1 {
$&1 = $o2.x[i]
iterator_statement
if (numarg()==3) { $&3+=1 } else { i1+=1 }
}
}
}
//* vector iterator vtr2, treat two vectors as pairs
// usage 'for vtr2(&x, &y, vec1, vec2) { print x,y }'
iterator vtr2() { local i,pairwise,noi1
noi1=pairwise=0
if (numarg()==3) { pairwise=1 i1=0 }
if (numarg()==4) if (argtype(4)==3) { pairwise=1 $&4=0 noi1=1}
if (pairwise) if ($o3.size%2!=0) { print "vtr2 ERROR: vec not even sized." return }
if (! pairwise) {
if ($o3.size != $o4.size) { print "vtr2 ERROR: sizes differ." return }
if (numarg()==5) {$&5=0 noi1=1} else {i1 = 0}
}
for i = 0,$o3.size()-1 {
$&1 = $o3.x[i]
if (pairwise) $&2=$o3.x[i+=1] else $&2=$o4.x[i]
iterator_statement
if (noi1) { if (pairwise) $&4+=1 else $&5+=1 } else i1+=1
}
}
//* iterator lvtr, step through a list and a vector together
// usage 'for lvtr(XO, &x, list, vec) { print XO,x }'
iterator lvtr() { local i
if ($o3.count < $o4.size) { printf("lvtr ERROR: vecsize > listsize: list %d,vec %d.\n",$o3.count,$o4.size) return }
if ($o3.count != $o4.size) { printf("lvtr WARNING: sizes differ: list %d,vec %d.\n",$o3.count,$o4.size) }
if (numarg()==5) {$&5=0} else {i1 = 0}
for i = 0, $o4.size()-1 {
$o1 = $o3.object(i)
$&2 = $o4.x[i]
iterator_statement
if (numarg()==5) { $&5+=1 } else { i1+=1 }
}
}
//* other iterators: case, scase, ocase
iterator case() { local i
i1 = 0
for i = 2, numarg() {
$&1 = $i
iterator_statement
i1+=1
}
}
iterator scase() { local i
i1 = 0
for i = 1, numarg() {
temp_string_ = $si
iterator_statement
i1+=1
}
}
// eg for scase2("a","b","c","d","e","f") print tmpobj.s,tmpobj.t
iterator scase2() { local i
i1 = 0
if (numarg()%2==1) {print "ERROR: scase2 needs even number of args" return }
for i = 1, numarg() {
tmpobj=new String2()
tmpobj.s=$si i+=1 tmpobj.t=$si
iterator_statement
i1+=1
}
}
iterator ocase() { local i
i1 = 0
for i = 1, numarg() {
XO = $oi
iterator_statement
}
i1+=1
}
//* strm(STR,REGEXP) == regexp string match
func strm () { return sfunc.head($s1,$s2,"")!=-1 }
//* nind(targ,data,ind) fill the target vector with data NOT index by ind (opposite of v.index)
proc nind () {
if (! eqobj($o1,$o2)) $o1.copy($o2)
$o1.indset($o3,-1e20)
$o1.where($o1,">",-1e20)
}
//* vlk(vec)
// vlk(vec,max)
// vlk(vec,min,max)
// prints out a segment of a vector
vlk_width=20
space=" "
proc vlk () { local i,j,min,max,dual,wdh,nonl
j=dual=0 nl=1 wdh=vlk_width
if (numarg()==1) { min=0 max=$o1.size-1 }
if (numarg()==2) {
if (argtype(2)==0) {
if ($2==0) {
nl=min=0 max=$o1.size-1 // vlk(vec,0) flag to suppress new lines
} else if ($2>0) { min=0 max=$2-1 } else { min=$o1.size+$2 max=$o1.size-1 }
} else { dual=1 min=0 max=$o1.size-1 }
}
if (numarg()==3) {
if (argtype(2)==0) if ($3>-1) { min=$2 max=$3 }
if (argtype(2)==1) { dual=1
if ($3>=0) { min=0 max=$3 } else { min=$o1.size+$3 max=$o1.size-1 }
}
}
if (numarg()==4) { min=$3 max=$4 dual=1 }
if (min<0) min=0
if (max>$o1.size-1) { max=$o1.size-1 printf("vlk: max beyond $o1 size\n") }
if (dual) if (max>$o2.size-1) { max=$o2.size-1 printf("vlk: max beyond $o2 size\n") }
for i=min,max {
if (dual) printf("%g:%g%s",$o1.x[i],$o2.x[i],"\n") else printf("%g%s",$o1.x[i],space)
if ((j=j+1)%vlk_width==0 && nl && strcmp(space," ")==0) { print "" }
}
if (nl) print ""
}
//* vprf() prints 1,2 or 3 vectors in parallel to output file
proc vprf () { local x2
if (! tmpfile.isopen()) {
print "Writing to temp file 'temp'"
tmpfile.wopen("temp")
}
if (numarg()==1) {
for vtr(&x,$o1) { tmpfile.printf("%g\n",x) }
} else if (numarg()==2) {
for vtr2(&x,&y,$o1,$o2) { tmpfile.printf("%g %g\n",x,y) }
} else if (numarg()==3) {
for vtr2(&x,&y,$o1,$o2,&ii) { x2=$o3.x[ii] tmpfile.printf("%g %g %g\n",x,y,x2) }
}
tmpfile.close
}
//* vpr() prints 1,2 or 3 vectors in parallel to STDOUT
proc vpr () { local x2
if (numarg()==1) {
for vtr(&x,$o1) { printf("%g ",x) }
} else if (numarg()==2) {
for vtr2(&x,&y,$o1,$o2) { printf("%g:%g ",x,y) }
} else if (numarg()==3) {
for vtr2(&x,&y,$o1,$o2,&ii) { x2=$o3.x[ii] printf("%g:%g:%g ",x,y,x2) }
}
print ""
}
//* readvec(vec) read from line
proc readvec () {
$o1.resize(0)
while (read(xx)) $o1.append(xx)
vlk($o1)
}
//* popvec(), savenums, readnums, vecsprint, savevec, savestr
proc pushvec () { local i // same as .append, retained for compatability
for i=2, numarg() $o1.append($i)
}
proc insvec () { local i // insert a value into the vector
for i=2, numarg() $o1.append($i)
}
proc revec () { local i // clear vector then append
if (! isobj($o1,"Vector")) $o1 = new Vector()
$o1.resize(0)
if (numarg()>1) if (argtype(2)==1) {
for i=2, numarg() $oi.resize(0)
} else {
for i=2, numarg() $o1.append($i)
}
}
// vrsz() -- vector resize -- to size of first arg
proc vrsz () { local i,sz
if (argtype(1)==1) sz=$o1.size else sz=$1
for i=2, numarg() $oi.resize(sz)
}
proc zvec () { local i // make vectors zero size
for i=1, numarg() $oi.resize(0)
}
// savenums(x[,y,...]) save numbers to tmpfile via a vector
proc savenums () { local vv,i
vv=allocvecs(1)
for i=1, numarg() mso[vv].append($i)
mso[vv].vwrite(tmpfile)
dealloc(vv)
}
// readnums(&x[,&y...]) recover nums from tmpfile via a vector
proc readnums () { local vv,i
vv=allocvecs(1)
mso[vv].vread(tmpfile)
if (numarg()!=mso[vv].size) printf("readnums WARNING: args=%d;vec.size=%d\n",numarg(),mso[vv].size)
for i=1,numarg() if (i<=mso[vv].size) $&i = mso[vv].x[i-1]
dealloc(vv)
}
//** wrvstr(str) save string to a file by converting to ascii
proc wrvstr () { local vv,i
vv=allocvecs(1)
str2v($s1,mso[vv])
mso[vv].vwrite(tmpfile)
dealloc(vv)
}
// rdvstr(str) read string from a file via vread and conversion
proc rdvstr () { local vv,i
vv=allocvecs(1)
mso[vv].vread(tmpfile)
if (numarg()==1) v2str(mso[vv],$s1) else v2str(mso[vv],tstr)
// print tstr
dealloc(vv)
}
// str2v() overwrites temp_string2_
proc str2v () {
$o2.resize(0)
temp_string2_=$s1
while (sfunc.len(temp_string2_)>0) {
sscanf(temp_string2_,"%c%*s",&x)
sfunc.right(temp_string2_,1)
$o2.append(x)
}
}
proc v2str () {
$s2=""
for vtr(&x,$o1) sprint($s2,"%s%c",$s2,x)
}
//* remove last entry
func popvec () { local sz, ret
sz = $o1.size-1
ret = $o1.x[sz]
$o1.resize[sz]
return ret
}
//* chkvec (look at last entry)
func chkvec () { if ($o1.size>0) return $o1.x[$o1.size-1] else return -1e10 }
// vecsprint(strdef,vec)
proc vecsprint () { local ii
if ($o2.size>100) { return }
for ii=0,$o2.size-1 { sprint($s1,"%s %g ",$s1,$o2.x[ii]) }
}
// savevec([list,]vec1[,vec2,...]) add vector onto veclist or other list if given as 1st arg
// don't throw out vectors
proc savevec () { local i,flag,beg
if (isobj($o1,"List")) beg=2 else beg=1
for i=beg, numarg() {
if (veccollect.count>0) { // grab a vector from garbage collection
tmpvec=veccollect.object(veccollect.count-1)
veccollect.remove(veccollect.count-1)
} else tmpvec = new Vector($oi.size)
tmpvec.copy($oi)
if (beg==2) $o1.append(tmpvec) else veclist.append(tmpvec)
tmpvec = nil
}
}
proc prveclist () {
if (tmpfile.ropen($s1)) {
printf("%s exists; save anyway? (y/n) ",$s1)
getstr(temp_string_) chop(temp_string_)
if (strcmp(temp_string_,"y")!=0) return
}
tmpfile.wopen($s1)
if (numarg()==2) {
for ltr(XO,$o2) XO.vwrite(tmpfile)
} else {
for ltr(XO,veclist) XO.vwrite(tmpfile)
}
tmpfile.close()
}
proc rdveclist () { local flag,a
flag=0
a=allocvecs(1)
if (numarg()==1) { flag=1 clrveclist() } else $o2.remove_all
tmpfile.ropen($s1)
while (mso[a].vread(tmpfile)) {
if (flag) savevec(mso[a]) else savevec($o2,mso[a])
}
tmpfile.close()
tmpobj=veclist
dealloc(a)
}
proc rdxy () { local a
a = allocvecs(1)
revec(ind,vec)
tmpfile.ropen("aa")
mso[a].scanf(tmpfile)
if (mso[a].size%2!=0) {print "rdxy ERR1 ",mso[a].size return}
for vtr2(&x,&y,mso[a]) {ind.append(x) vec.append(y)}
print ind.size," points read from aa into ind and vec"
dealloc(a)
}
// closest(vec,num) -- return ind for vec member closest to num
func closest () { local a,ret
a=allocvecs(1)
mso[a].copy($o1) mso[a].sub($2) mso[a].abs
ret=mso[a].min_ind
dealloc(a)
return ret
}
proc clrveclist () {
for ltr(XO,veclist) { XO.resize(0) veccollect.append(XO) }
veclist.remove_all()
}
// savestr(str1...) add string obj onto tmplist
proc savestr () { local i
if (argtype(1)==1) for i=2, numarg() $o1.append(new String($si)) else {
for i=1, numarg() tmplist.append(new String($si))
}
}
// redund with v.count in vecst.mod
func vcount () { local val,sum
val=$2 sum=0
for vtr(&x,$o1) if (x==val) sum+=1
return sum
}
// tvecl() -- transpose veclist
proc tvecl () { local cnt,sz,err,ii,p
err = 0
cnt = veclist.count
sz = veclist.object(0).size
for ltr(XO,veclist) if (XO.size!=sz) err=i1
if (err) { print "Wrong size vector is #",i1 return }
p = allocvecs(1,cnt) mso[p].resize(cnt)
for ii=0,sz-1 {
for jj=0,cnt-1 {
XO=veclist.object(jj)
mso[p].x[jj] = XO.x[ii]
}
savevec(mso[p])
}
for (jj=cnt-1;jj>=0;jj-=1) { veccollect.append(veclist.object(jj)) veclist.remove(jj) }
}
//* vinsect(v1,v2,v3) -- v1 gets intersection (common members) of v2,v3
// replaced by v.insct() in vecst.mod
proc vinsect () {
$o1.resize(0)
for vtr(&x,$o2) for vtr(&y,$o3) if (x==y) $o1.append(x)
}
//* vecsplit(vec,vec1,vec2[,vec3,...])
// splits vec into other vecs given
proc vecsplit () { local num,ii,i
num = numarg()-1 // how many
for i=2,numarg() $oi.resize(0)
for (ii=0;ii<$o1.size;ii+=num) {
for i=2,numarg() if (ii+i-2<$o1.size) $oi.append($o1.x[ii+i-2])
}
}
//* vecsort(vec,vec1,vec2[,vec3,...])
// sorts n vecs including first vec by first one
proc vecsort () { local i,inv,scr,narg
narg=numarg()
if (narg<2 || narg>10) {print "Wrong #args in decvec.hoc:vecsort" return}
scr=inv=allocvecs(2) scr+=1
$o1.sortindex(mso[inv])
mso[scr].resize(mso[inv].size)
sprint(temp_string_,"%s.fewind(%s,%s,%s",mso[scr],mso[inv],$o1,$o2)
for i=3,narg sprint(temp_string_,"%s,%s",temp_string_,$oi)
sprint(temp_string_,"%s)",temp_string_)
execute(temp_string_)
dealloc(inv)
}
//* vdelind() -- delete a single index
proc vdelind () { local i,iin
iin = $2
if (iin<0) iin=$o1.size+iin
if (iin>$o1.size-1 || iin<0) {
printf("vdelind Error: index %d doesn't exist.\n",iin) return }
if (iin<$o1.size-1) $o1.copy($o1,iin,iin+1,$o1.size-1)
$o1.resize($o1.size-1)
}
//* mkveclist(num[,sz]) recreate veclist to have NUM vecs each of size SZ (or MSOSIZ)
proc mkveclist () { local ii,num,sz,diff
num=$1
diff = num-veclist.count
if (numarg()==2) { sz=$2 } else { sz = MSOSIZ }
if (diff>0) {
for ii=0,diff-1 {
tmpvec = new Vector(sz)
veclist.append(tmpvec)
}
} else if (diff<0) {
for (ii=veclist.count-1;ii>=num;ii=ii-1) { veclist.remove(ii) }
}
for ltr(XO,veclist) { XO.resize(sz) }
}
//* allocvecs
// create temp set of vectors on mso
// returns starting point on mso
// eg p = allocvecs(3)
// access these vectors by mso[p+0] ... [p+2]
func allocvecs () { local ii, llen, sz, newv
if (numarg()==0) { print "p=allocvecs(#), access with mso[p], mso[p+1]..." return 0}
newv = $1
if (numarg()==2) { sz=$2 } else { sz=MSOSIZ }
llen = msoptr
for ii=msomax,msoptr+newv-1 { // may need new vectors
if (ii>=MSONUM) { print "alloc ERROR: MSONUM exceeded." return 0 }
mso[ii] = new Vector(sz)
}
for ii=0,newv-1 {
mso[msoptr].resize(0)
msoptr = msoptr+1
}
if (msomax<msoptr) msomax = msoptr
return llen
}
//** dealloc(start)
// remove temp set of vectors from mso
proc dealloc () { local ii,min
if (numarg()==0) { min = 0 } else { min = $1 }
msomax = msoptr
msoptr = min
}
//* vecconcat(vec1,vec2,...)
// destructive: concatenates all vecs onto vec1
proc vecconcat () { local i
if (numarg()<2) { print "vecconcat(v1,v2,...) puts all into v1" return }
for i=2,numarg() {
$o1.copy($oi,$o1.size)
}
}
//** vecelim(v1,v2) eliminates items in v1 given by index vec v2
proc vecelim () {
for vtr(&x,$o2) { $o1.x[x]= -1e20 }
$o1.where($o1,"!=",-1e20)
}
//** vwh() returns a v.where(==)
func vwh() { return $o1.indwhere("==",$2) }
//** redundout(vec) eliminates sequential redundent entries
// destructive
proc redundout () { local x,ii,p1
p1=allocvecs(1)
$o1.sort
x = $o1.x[0]
for ii=1,$o1.size-1 {
if ($o1.x[ii]==x) { $o1.x[ii]=-1e20 } else { x=$o1.x[ii] }
}
mso[p1].where($o1,">",-1e20)
$o1.copy(mso[p1])
dealloc(p1)
}
// vecconv() convert $o1 by replacing instances in $o2 by corresponding instances in $o3
proc vecconv () { local a,b
a=b=allocvecs(2) b+=1
vrsz($o1,mso[b])
for vtr2(&x,&y,$o2,$o3) { // x -> y
mso[a].indvwhere($o1,"==",x)
mso[b].indset(mso[a],y)
}
$o1.copy(mso[b])
}
//** veceq() like vec.eq but don't have to be same size and shows discrepency
func veceq () { local sz1,sz2,eq,beg,ii,jj,kk
sz1=$o1.size sz2=$o2.size
if (numarg()==3) beg=$3 else beg=0
if (sz1!=sz2) printf("%s %d; %s %d\n",$o1,sz1,$o2,sz2)
ii=0 jj=beg
while (ii<sz1 && jj<sz2) {
if ($o1.x[ii]!=$o2.x[jj]) {
eq=0
printf("Differ at %d %d\n",ii,jj)
for kk=-10,10 if ((ii+kk)>=0 && (ii+kk)<sz1 && (jj+kk)>=0 && (jj+kk)<sz2) {
printf("(%d)%g:(%d)%g ",(ii+kk),$o1.x[ii+kk],(jj+kk),$o2.x[jj+kk]) }
print ""
break
} else eq=1
ii+=1 jj=ii+beg
}
return eq
}
//* isstring() determine if object $o1 is of type string, if so return the string in [$s2]
func isstring () {
sprint(tstr,"%s",$o1)
if (sfunc.substr(tstr,"String")==0) {
if (numarg()==2) sprint($s2,"%s",$o1.s)
return 1
} else {
if (numarg()==2) sprint($s2,"%s",$o1)
return 0
}
}
//** isassigned() checks whether an object is Null
func isassigned () {
sprint(temp_string_,"%s",$o1)
if (sfunc.substr(temp_string_,"NULLobject")==0) {
return 0
} else {
return 1
}
}
//** isit() like isassigned() but takes a string instead
func isit () {
sprint(temp_string_,"XO=%s",$s1)
execute(temp_string_) // XO points to the thing
sprint(temp_string_,"%s",XO) // what is XO
if (sfunc.substr(temp_string_,"NULLobject")==0) {
return 0
} else {
return 1
}
}
//** isob(s1,s2) like isobj but takes string statt obj
func isob () {
sprint(temp_string_,"XO=%s",$s1)
execute(temp_string_) // XO points to the thing
sprint(temp_string_,"%s",XO)
if (sfunc.substr(temp_string_,$s2)==0) {
return 1
} else {
return 0
}
}
//** eqobj(o1,o2) checks whether 2 objects are the same
func eqobj () { return object_id($o1) == object_id($o2) }
//** isobj(o1,s2) checks whether object $o1 is of type $s2
func isobj () {
sprint(temp_string_,"%s",$o1)
if (sfunc.substr(temp_string_,$s2)==0) {
return 1
} else {
return 0
}
}
// destructive of $s1
func str2num () { local ii
sscanf($s1,"%d",&x)
return x
}
// like perl chop -- removes the last character
proc chop () { sfunc.left($s1,sfunc.len($s1)-1) }
proc concat () { local i
for i=2,numarg() sprint($s1,"%s%s",$s1,$si)
}
proc concat () { local i
for i=2,numarg() sprint($s1,"%s%s",$s1,$si)
}
// eg split("534, 43 , 2, 1.4, 34",vec)
proc split () {
revec($o2) temp_string2_=$s1
while (sfunc.len(temp_string2_)>0) {
sscanf(temp_string2_,"%lf",&x) $o2.append(x)
if (numarg()==3) sfunc.tail(temp_string2_,$s3,temp_string2_) else {
sfunc.tail(temp_string2_,",",temp_string2_) }
}
}
// intervals(TRAIN,OUTPUT)
proc intervals () { local a
if ($o1.size<=1) { printf("%s size <2 in intervals()\n",$o1) return }
$o2.deriv($o1,1,1)
}
proc downcase () { local len,ii,let,diff,min,max
diff=32 min=65 max=90
if (numarg()==2) { diff=-diff min=97 max=122 } // if flag -> upcase
len = sfunc.len($s1)
for ii=1,len {
sscanf($s1,"%c%*s",&x)
sfunc.right($s1,1)
if (x>=min&&x<=max) {
sprint($s1,"%s%c",$s1,x+diff)
} else sprint($s1,"%s%c",$s1,x) // just rotate the letter
}
}
// newlst() puts a newline in the middle of a string
proc newlst () { local l
if (numarg()>1) l=$2 else l=int(sfunc.len($s1)/2)
temp_string_=$s1
temp_string2_=$s1
sfunc.left(temp_string_,l)
sfunc.right(temp_string2_,l)
sprint($s1,"%s\n%s",temp_string_,temp_string2_)
}
//* hist(g,vec,max,width)
proc hist () { local a,b,c,max,wid,ii,jj
max=$3 wid=$4
a=b=c=allocvecs(3) b+=1 c+=2
$o1.erase()
mso[c].hist($o2,0,int((max+wid)/wid),wid)
mso[a].resize(2*mso[c].size())
mso[a].indgen(.5)
mso[a].apply("int")
mso[b].index(mso[c], mso[a])
mso[a].mul(wid)
mso[b].rotate(1)
mso[b].x[0] = 0
mso[b].append(mso[b].x[mso[b].size-1],0)
mso[a].append(max,max)
mso[b].plot($o1, mso[a])
jj=-1
for (ii=0;ii<max;ii+=wid) {
$o1.beginline() $o1.line(ii,0) $o1.line(ii,mso[c].x[jj+=1])
if (mso[c].x[jj]!=0) $o1.mark(ii+wid/2,mso[c].x[jj],"O",6,2,2)
}
$o1.flush()
$o1.size(0,max,0,mso[b].max)
dealloc(a)
}
// END /usr/site/nrniv/local/hoc/decvec.hoc
//================================================================
strdef grep // LINUX grep requires -a to handle a binary file
strdef ddir,msg,symb
if (sfunc.substr(osname,"inux")==1) grep="grep -a" else grep="grep"
ddir = "data"
symb = "O"
gvmarkflag=gveraseflag=0
//* abbreviated proc alls
proc pwpl () { pwman_place(500,500) }
proc vp () { vecpanel() }
proc ap () {if (numarg()==1) attrpanl($1) else attrpanl(0) }
proc wp () {if (numarg()==1) wvpanl($1) else wvpanl(0) }
proc gp () {if (numarg()==1) rpanel($1) else pbrgr("Graph","gv") }
proc tog (){if (numarg()==0) print gvmarkflag=1-gvmarkflag else print $&1=1-$&1}
//* templates
//** attrpanl(attribute panel) template stores the information about
// the attributes of a particular set of graphs including line colors,
// world coordinates, ...
// glist is a list of all graphs created from this panel
// llist is a list of available names and associated vectors or locations
begintemplate panattr
public color,line,super,curcol,graph,filename,comment
public glist,llist,tvec,size,shift,vsz,vjmp,tloc,vloc,remote
public printStep,entries,segments,bytes
public clear
double color[1],line[1],super[1],curcol[1],printStep[1],remote[1]
double size[4],entries[1],segments[1],bytes[1],shift[1]
double vsz[2],tloc[1],vloc[1],vjmp[1]
objref glist,llist,tvec
strdef filename,comment
proc init() {
if (numarg()==1) filename = $s1
color=1 line=1 curcol=1 tloc=-1 super=0 bytes=0 vjmp=50 entries=1 segments=1
vsz[0] = 300 vsz[1] = 200
glist = new List()
llist = new List()
tvec = new Vector(0)
}
proc remgrs () {
glist.remove_all
glist = nil
glist = new List()
}
proc clear() {
bytes=0 entries=1 segments=1
comment = ""
llist.remove_all()
}
endtemplate panattr
//** vfile_line (vector file line) template gives information about a line
// in a file that gives a vector: name, size and location
begintemplate vfile_line
public name, size, loc, num
strdef name
double size[1],loc[1],num[1],tvec[1]
proc init () {
name=$s1 size=$2 num=$4
double loc[num],tvec[num]
loc[0] = $3
}
endtemplate vfile_line
//** vitem (vector item) is an internal vector used to store output from
// new vitem(var_name,vec_size,friendly_name)
// new vitem(var_name,vec_size,1) -- force tvec creation even if not cvode_local
// a simulation holds the name and the vector itself
begintemplate vitem
external cvode_local
public tvec,vec,var
objref tvec,vec // vector
strdef var // variable name
proc init () { local tvflag
var=$s1 tvflag=0
if (cvode_local()==1) tvflag=1 else {
// print "WARNING CVODE LOCAL IS NOT SET"
}
vec=new Vector($2)
// NB label is labile
vec.label("") // use label for friendly name
if (numarg()==3) {
if (argtype(3)==2) vec.label($s3)
if (argtype(3)==0) if ($3==1) tvflag=1
}
if (tvflag=1) tvec=new Vector($2)
}
endtemplate vitem
//* object declarations
objref vite, scob, printlist, panobj, panobjl, szstr[4], g[10]
panobj = new panattr(simname)
panobjl = new List()
proc pno () { panobj=panobjl.object($1) }
printlist = new List()
panobjl.append(panobj) // global graphing attributes
panobj.llist = printlist
tmpfile = new File()
strdef filename, recstr, grvecstr, readtag
readtag = "^//[:pbCM ]" // regexp used to identify header in mixed binary files
for ii=0,3 { szstr[ii] = new String() }
{ szstr[0].s="Set xmin" szstr[1].s="Set xmax" szstr[2].s="Set ymin" szstr[3].s="Set ymax" }
multi_files = 1 // set 0 to show individual segments of multi-seg files
dec_runnum = 1 // whether to decrement runnum when saving a new file
byte_store = 4 // store as ascii (0), byte (1), int (2), float (3), double (4)
tvec_bytesize = 4 // always store tvecs with more precision
show_panel = 1 // whether or not to put a full panel up when a file is read
outvecint = 0 // dump vectors every outvecint time if not 0
outvect = 0 // time for next vec dump
labelm = 1 // set to 0 to turn off labeling
strdef rvvec_name
rvvec_name = "vec"
//* store cvode state in a double in form active.local
func cvode_status () { return cvode_active() + cvode_local()/10 }
ulvflag=1
proc ulv () {
if (ulvflag || numarg()==1) { // else leave these other flags alone
using_cvode_ = cvode_active()
use_lvardt_ = cvode_active() && cvode_local()
}
}
cvode_state = cvode_status()
//** return true and update cvode_state if cvode state has changed
func cvode_change () {
if (cvode_state!=cvode_status()) {
cvode_state=cvode_status() return 1
} else { return 0 }
}
//** verbose form of cvode_change
func cvode_what () { local act,loc,newstat,newact,newloc
act=int(cvode_state) loc=(cvode_state-act)*10
newstat = cvode_status()
if (cvode_state!=newstat) {
newact=int(newstat) newloc=(newstat-newact)*10
printf("Updating active/local from %d/%d to %d/%d\n",act,loc,newact,newloc)
cvode_state=cvode_status() return 1
} else {
printf("cvode_state: active %d, local %d\n",act,loc)
return 0
}
}
if (xwindows) scob = new SymChooser()
//* vecpanel() main panel
proc vecpanel() {
fchooser_flag = 0 // used to initialize the file chooser
sprint(temp_string_,"%s Vectors",simname)
xpanel(temp_string_)
xbutton("Graph from file","fchooser(-1)")
xbutton("Graph vector","pbrgr(\"Graph\",\"gv\")")
xbutton("Archive to file:","pbrgr(\"Archive\",\"pv\")")
xbutton("Archive all to output_file","pvall()")
xstatebutton("Superimpose",&panobjl.object(0).super)
xbutton("Attributes","attrpanl(0)")
redo_printlist()
redo_attrlist()
xpanel()
}
//* pbrgr(browser name,action) is used to put up a browser
// note action given without '()'
proc pbrgr () {
if (printlist.count == 1) {
gv(0)
} else if (printlist.count <= 8) {
mkpanel("Vector",$s1,$s2)
} else {
sprint(temp_string_,"%s:%s",simname,$s1)
printlist.browser(temp_string_,"var")
sprint(temp_string2_,"%s()",$s2)
printlist.accept_action(temp_string2_)
}
}
//* record(list,what,vecptr) from items in $o1 object(ii).$s2 in vectors
// $o1 is the list arg $s2 is the thing to be recorded [eg soma.v(0.5)]
// optional $3 is the name of an object belonging to list items that will
// serve as a pointer to the recording vector
proc record () { local ii, dur, na3
for ltr(XO,$o1) {
sprint(recstr,"%s.%s",XO,$s2)
new_printlist_item(recstr)
if (numarg()==3) {
sprint(temp_string_,"%s.%s=printlist.object(printlist.count-1).vec",XO,$s3)
execute(temp_string_) // only way to get call by ref for object
}
}
}
//* record_spks(list[,what]) takes a list of netcons and puts in printlist objects for them
// assumes that the PP will be called pp
proc record_spks () { local ii,flag
ulv(1)
for ltr(XO,$o1) {
flag=1
if (cvode.netconlist(XO, "", "").count>0) {
YO=cvode.netconlist(XO, "", "").object(0)
sprint(recstr,"%s%s",YO.precell,"_spks")
} else if (cvode.netconlist(XO.pp, "", "").count>0) {
YO=cvode.netconlist(XO.pp, "", "").object(0)
sprint(recstr,"%s%s",YO.pre,"_spks")
} else { printf("%s not connected.\n",XO) flag=0 }
if (flag) {
vite = new vitem(recstr,100)
if (use_lvardt_) { YO.record(vite.tvec) vite.vec.resize(0) } else YO.record(vite.vec)
printlist.append(vite)
}
}
YO=nil
}
//* redo_printlist() menu allows removal or addition of inidividual items
proc redo_printlist() {
xmenu("Print list")
xbutton("Add var to printlist","redolist(0)")
xbutton("Clear printlist","printlist.remove_all()")
xbutton("Remove item from printlist","redolist(1)")
xbutton("Vector.op","redolist(2)")
xbutton("Proc(vector)","redolist(6)")
xbutton("Link XO->vec,YO->tvec","redolist(7)")
xbutton("Graph vector","redolist(4)")
xbutton("Save printlist","redolist(5)")
xbutton("Add all obj's of this type to printlist","redolist(3)")
xmenu()
}
//* redolist() set of functions for altering the printlist called by redo_printlist()
proc redolist () { local ii,flag
flag = $1 rdstr = 1
if (numarg()==2) { recstr=$s2 rdstr=0 }
if (flag==0) {
if (scob.run()) {
scob.text(temp_string_)
new_printlist_item(temp_string_)
}
} else if (flag==1) { // remove item
printlist.browser("Double click on item to remove","var")
printlist.accept_action("printlist.remove(hoc_ac_)")
} else if (flag==2) { // .op
if (rdstr) string_dialog("Enter operation to be run on vec",recstr)
temp_string_ = "\"%s.%s = %g\\n\""
sprint(temp_string_,"printf(%s,printlist.object(hoc_ac_).var,\"%s\",x=printlist.object(hoc_ac_).vec.%s)",temp_string_,recstr,recstr)
printlist.browser(recstr,"var")
printlist.accept_action(temp_string_)
} else if (flag==3) { // put another set of things on list
if (rdstr) string_dialog("String to be used as suffix for all items on list",recstr)
scob.run()
scob.text(temp_string_)
tmplist = new List(temp_string_)
record(tmplist,recstr)
} else if (flag==4) { // show it
pbrgr("Graph","gv")
} else if (flag==5) {
fchooser_flag = 0
tmpfile.chooser("a","Add printlist to file")
if (tmpfile.chooser()==1) {
tmpfile.printf("\nproc make_printlist() { \n")
tmpfile.printf(" printlist.remove_all()\n")
for ii=0,printlist.count-1 {
tmpfile.printf(" new_printlist_item(\"%s\")\n",printlist.object(ii).var)
}
tmpfile.printf("}\nmake_printlist()\n")
tmpfile.close()
}
} else if (flag==6) { // proc(vec)
if (rdstr) string_dialog("Enter procedure name \"proc\",called as proc(vec,var,num)",recstr)
printlist.browser(recstr,"var")
sprint(temp_string_,"%s(printlist.object(hoc_ac_).vec,printlist.object(hoc_ac_).var,hoc_ac_)",recstr)
printlist.accept_action(temp_string_)
} else if (flag==7) { // XO is pointer to vec
printlist.browser("XO","var")
sprint(temp_string_,"{tmpobj=printlist.object(hoc_ac_) print hoc_ac_,tmpobj.var XO=tmpobj.vec YO=tmpobj.tvec}")
printlist.accept_action(temp_string_)
}
}
//** lkprl([num]) link X0 to vector in printlist, optional arg can be pos or neg
proc lkprl () { local num,cnt
cnt = printlist.count
if (numarg()==1) {if ($1>=0) num=$1 else num=cnt+$1} else num=cnt-1
if (num>cnt-1 || num<0) {
printf("%d!: Only %d items (0-%d) in list.\n",num,cnt,cnt-1) return
}
print num,":XO -> ",printlist.object(num).var
XO = printlist.object(num).vec
YO = printlist.object(num).tvec
}
//** cpplitem([num]) copy X0 to new item in printlist, optional arg can be pos or neg
proc cpplitem () { local num,cnt
cnt = printlist.count
if (numarg()>0) {if ($1>=0) num=$1 else num=cnt+$1} else num=cnt-1
if (num>cnt-1 || num<0) {
printf("%d!: Only %d items (0-%d) in list.\n",num,cnt,cnt-1) return
}
if (numarg()>1) grvecstr=$s2 else sprint(grvecstr,"Copy_of_%s",printlist.object(num).var)
new_printlist_item(grvecstr,printlist.object(num).vec)
print printlist.count-1,":XO -> ",grvecstr
XO = printlist.object(printlist.count-1).vec
}
//** cpplitem([num]) copy X0 to new item in printlist, optional arg can be pos or neg
proc chgplname () { local num,cnt
cnt = printlist.count
if (numarg()>0) {if ($1>=0) num=$1 else num=cnt+$1} else num=cnt-1
if (num>cnt-1 || num<0) {
printf("%d!: Only %d items (0-%d) in list.\n",num,cnt,cnt-1) return
}
printlist.object(num).var=$s2
}
//* new_printlist_item(name) adds this item to the printlist
// new_printlist_item(name,vec) adds this vec to the printlist
// new_printlist_item(name,num,vec) adds this vec to the printlist under name_num0,name_num1,...
proc new_printlist_item () { local dur,pln
ulv(1)
panobj = panobjl.object(0)
if (outvecint == 0) dur = tstop else dur = outvecint
grvecstr = $s1
remove_spaces(grvecstr,temp_string2_) // splits on '/'
// eg new_printlist_item(name,ii,vec)
if (numarg()>=3) { // allows formation of tags on the fly
sprint(temp_string_,"%s%s",grvecstr,":%d")
sprint(temp_string_,temp_string_,$2)
vite = new vitem(temp_string_,$o3.size,temp_string2_)
vite.vec.copy($o3)
if (numarg()==4) vite.tvec.copy($o4)
printlist.append(vite)
return
}
if (numarg()==2) { // second arg is a vector to store
if (argtype(2)==1) {
vite = new vitem(grvecstr,$o2.size,temp_string2_)
vite.vec.copy($o2)
printlist.append(vite)
return
} else if (argtype(2)==2) sprint(grvecstr,"%s%s",grvecstr,$s2)
}
if (use_lvardt_) {
if (isobj(panobj.tvec,"Vector")) if (panobj.tvec.size!=0) { panobj.tvec.resize(0) panobj.tvec.play_remove() }
vite = new vitem(grvecstr,dur/printStep+10,temp_string2_)
panobj.printStep=-2
} else if (using_cvode_) {
vite = new vitem(grvecstr,dur/printStep+10,temp_string2_)
panobj.printStep=-1
if (panobj.tvec.buffer_size==0) {
panobj.tvec.resize(dur/printStep+10) panobj.tvec.resize(0)
}
panobj.tvec.record(&t)
} else {
if (panobj.tvec.size!=0) { panobj.tvec.resize(0) panobj.tvec.play_remove()}
panobj.printStep=printStep
vite = new vitem(grvecstr,dur/printStep+10,temp_string2_)
}
printlist.append(vite)
pln = printlist.count-1 // current printlist number
if (numarg()==2) $o2=vite.vec // allow user to assign a pointer
vite = nil
if (use_lvardt_) {
printlist.object(pln).vec.resize(dur/printStep+10)
printlist.object(pln).tvec.resize(dur/printStep+10)
find_secname(grvecstr,temp_string_)
sprint(temp_string_,\
"%s {cvode.record(&%s,printlist.object(%d).vec,printlist.object(%d).tvec)}",\
temp_string_,grvecstr,pln,pln)
} else if (using_cvode_) { // don't give an explicit printStep
printlist.object(pln).vec.resize(dur/printStep+10)
sprint(temp_string_,\
"{printlist.object(%d).vec.record(&%s)}",pln,grvecstr)
} else {
sprint(temp_string_,\
"printlist.object(%d).vec.record(&%s,%g)",pln,grvecstr,printStep)
}
execute(temp_string_)
}
// new_pri(NAME,TVEC,VEC) quick and dirty new_printlist_item
proc new_pri () {
vite = new vitem($s1,$o2.size)
if (numarg()==3) { vite.tvec.copy($o2) vite.vec.copy($o3) } else vite.vec.copy($o2)
printlist.append(vite)
vite=nil
}
//* prlexp(sz) expands all the vectors in printlist to size sz
proc prlexp () {
sz = $1
tvec.resize(sz)
for ltr(XO,printlist) { XO.vec.resize(sz) }
}
//* redo_attrlist() menu allows removal or addition of inidividual items
proc redo_attrlist() {
xmenu("Attribute panels")
xbutton("Read file","attrlist(0)")
xbutton("Remove","attrlist(1)")
xbutton("Show","attrlist(2)")
xbutton("Clear list","attrlist(3)")
xbutton("New","attrlist(4)")
xmenu()
}
//* attrlist() set of functions for altering panobjl (list of graph attributes)
proc attrlist() { local ii
if ($1==0) {
fchooser(-1)
} else if ($1==1) { // remove item
panobjl.browser("Double click on item to remove","filename")
panobjl.accept_action("panobjl.remove(hoc_ac_)")
} else if ($1==2) {
panobjl.browser("Double click on item",temp_string_,"numovecs()")
panobjl.accept_action("attrpanl(hoc_ac_)")
} else if ($1==3) { // clear but leave #0
for (ii=panobjl.count-1;ii>0;ii=ii-1) { panobjl.remove(ii) }
} else if ($1==4) { // create a new one without reading a file in
panobj = new panattr()
panobj.filename = "EMPTY"
panobjl.append(panobj)
panobj.remote = panobjl.count()-1
attrpanl(panobjl.count()-1)
} else if ($1==5) { // create one with given num and name
for ii=panobjl.count,$2 { // create more if needed
panobj = new panattr()
panobjl.append(panobj)
panobj.remote = ii
}
panobj = panobjl.object($2)
panobj.filename = $s3
panobj.comment = $s4
panobj.printStep = $5
}
}
// show the number of vectors as well as the name of the file
proc numovecs() { local num
if (hoc_ac_==0) num=printlist.count() else num=panobjl.object(hoc_ac_).llist.count()
sprint(temp_string_,"#%d %s: %d",hoc_ac_,panobjl.object(hoc_ac_).filename,num)
}
//* fchooser(attrnum) finds file and then create panel from it using rpanel
proc fchooser () { local attr0
attr0=$1
if (fchooser_flag == 0) { // create panel first time only
sprint(temp_string_,"v0*")
tmpfile.chooser("","Read from a file",temp_string_)
}
fchooser_flag = 1
if (tmpfile.chooser() == 1) {
// find out whether this is a vector file or not
tmpfile.getname(filename)
sfunc.tail(filename,"/data.*/",grvecstr) // just take the file name without the leading stuff
attrnum = read_vfile(attr0)
if (attrnum == 0) {print "ERROR in fchooser" return }// error
// a new one so should show something
if (attr0==-1) if (show_panel) rpanel(attrnum) else attrpanl(attrnum)
}
}
//* routines for reading in a vector file
//** read_vfile(attrnum) creates a panattr object from information in a file
// (uses grep to avoid loading big file)
// assumes file in tmpfile
func read_vfile () { local flag, ii, sz, loc, mult, sze, cloc, segs
if (numarg()==0) { print "read_vfile(attrnum,filename)" return 0 }
if (numarg()==2) filename = $s2
read_findattr($1) // set panobj and attrnum
// grab hold of the different lines using grep
file_with_dot(filename,temp_string_,temp_string2_) // put .filename into temp_string_
if (!tmpfile.ropen(temp_string_)) {
if (! tmpfile.ropen(filename)) { print "E1: Can't open ",filename // avoid grep error
return 0 }
sprint(temp_string2_,"%s '%s' %s > %s",grep,readtag,filename,temp_string_)
system(temp_string2_)
tmpfile.close()
if (! tmpfile.ropen(temp_string_)) { print "E2: Can't open ",temp_string_," (",filename,")"
return 0 }
flag = 0
} else flag = 1 // signifies that .file exists to use as key
while ((numr = tmpfile.scanstr(temp_string_)) != -1) { // throw out the leading '//'
// read the line
cloc = tmpfile.tell - numr // location of the beginning of this line
if (sfunc.head(temp_string_,"//[^b]",temp_string2_)==0) {
read_vinfo() // a line giving info about the file (eg comment)
} else { // NB: code in v60:516 to pickup byte_store value
if (panobj.bytes==0 && \
sfunc.head(temp_string_,"//b[1-9]",temp_string2_)==0) { panobj.bytes = 1 }
if (flag && panobj.entries>1) { // a .file with MULTI segs
tmpfile.seek(-numr,1) // backup to beginning of line
read_vdotfile()
} else if (panobj.segments > 1) { // mult segs: different times for same var
tmpfile.seek(-numr,1) // backup to beginning of line
panobj.segments = read_vsegs()
} else { // read each line in for itself
tmpfile.scanstr(temp_string_) // name of a var
sze = tmpfile.scanvar() // size of the vector or time it was dumped
loc = tmpfile.scanvar() // location of the vector
if (panobj.bytes) { tmpfile.seek(cloc) // go back and measure the line length
loc = loc + tmpfile.gets(temp_string2_) }
// create the item
if (! strcmp(temp_string_,"tvec")==0) {
tmpobj = new vfile_line(temp_string_,sze,loc,1)
panobjl.object(attrnum).llist.append(tmpobj)
tmpobj = nil
} else {
panobj.tvec.resize(0)
panobj.printStep=-1
panobj.tloc = loc // where to find tvec later
}
}
}
}
if (panobj.entries==1) panobj.entries = panobj.llist.count
if (! flag && panobj.segments>1) write_vsegs() // create key .file
if (! tmpfile.ropen(panobj.filename)) { print "E3: Can't open ",panobj.filename
return 0 }
if (panobj.printStep==-1) { rtvec(attrnum) // code for cvode_active()
} else if (panobj.printStep==0) panobj.printStep = printStep
return attrnum
}
//** read_findattr()
// see if want to use old attributes or start new ones
proc read_findattr () {
if ($1 > -1 && $1 < panobjl.count()) {
attrnum = $1
panobj = panobjl.object(attrnum)
panobj.clear()
panobj.filename = filename
} else { // create a new panel attribute object to hold color and line type
panobj = new panattr(filename)
panobjl.append(panobj)
panobj.remote = panobjl.index(panobj)
attrnum = panobjl.index(panobj)
}
}
//** read_vinfo()
// fill in panobj entries based on an information line in a vector file
proc read_vinfo () {
if (strcmp(temp_string_,"//printStep")==0) {
panobj.printStep = tmpfile.scanvar() // printstep==-1 means cvode
} else if (strcmp(temp_string_,"//:")==0) { // a comment
tmpfile.gets(temp_string_)
sfunc.head(temp_string_,"\n",panobj.comment) // chop final newline
} else if (strcmp(temp_string_,"//CPU")==0) { // the machine type for byte storage
tmpfile.scanstr(temp_string_)
if (strcmp(temp_string_,uname)!=0) {
printf("%s written from %s\n",filename,temp_string_)
}
} else if (strcmp(temp_string_,"//MULTI")==0) { // multiple lines for each entry
panobj.entries = tmpfile.scanvar()
if (multi_files) { panobj.segments = tmpfile.scanvar() }
} else {
printf("Line:\t%s\n\tnot recognized in %s\n",temp_string_,panobj.filename)
tmpfile.seek(-1,1)
tmpfile.gets(temp_string_) // clear this line out
}
}
//** read_vdotfile() read .file in abbreviated format (see write_vsegs)
proc read_vdotfile() { local loc,entries,segments,ii
entries=panobj.entries segments=panobj.segments
panobj.bytes = 1
for i=1,entries { // read this abbreviated file version (much faster)
tmpfile.scanstr(temp_string_)
loc = tmpfile.scanvar()
tmpobj = new vfile_line(temp_string_,-1,loc,segments) // don't set size
panobj.llist.append(tmpobj)
for ii=1,segments-1 { tmpobj.loc[ii] = tmpfile.scanvar() }
}
}
//** read_vsegs() read a file that is segmented with diff vectors at diff times
// (see outvecs)
func read_vsegs () { local segments,entries,i,ii,jj,sze,loc,ret,cloc,clocend,llen
entries=panobj.entries segments=panobj.segments ret=1
for i=1,entries { // usually will be the number of cells recorded
cloc = tmpfile.tell() // starting location in the file
tmpfile.scanstr(temp_string_)
tmpfile.scanstr(temp_string_) // name of a var
sze = tmpfile.scanvar() // size of the vector or time it was dumped
loc = tmpfile.scanvar() + (tmpfile.tell() - cloc) // add line length
cloc = tmpfile.tell() // a location where a vec begins
tmpobj = new vfile_line(temp_string_,sze,loc,segments)
panobj.llist.append(tmpobj)
for ii=1,segments-1 { // go through all the different time segs
for jj=1,entries-1 { // go through all the cells
if ((ret = tmpfile.gets(temp_string_))==-1) { break } // EOF error
}
clocend = tmpfile.tell() // loc of end of this seg
tmpfile.scanstr(temp_string_) tmpfile.scanstr(temp_string_) // name of a var
if (strcmp(temp_string_,tmpobj.name)!=0) { // name should match
printf("ERROR: %d not %d segs found (%s)\n",ii,segments,tmpobj.name)
segments = ii
break
}
tmpfile.scanvar() // a time
tmpobj.loc[ii] = tmpfile.scanvar()+(tmpfile.tell()-clocend) // where the vector starts
clocend = tmpfile.tell()
}
tmpfile.seek(cloc) // go back for next entry
}
tmpfile.seek(clocend) // go to end of all this stuff
return segments
}
//** write_vsegs()
// write out names of all entries along with locations where the vecs start
proc write_vsegs () { local ii
file_with_dot(filename,temp_string_,temp_string2_) // put .filename into temp_string_
sprint(temp_string2_,"grep '^//[^bM]' %s > %s",xtmp,temp_string_)
system(temp_string2_) // copy the non-location lines into the new file
tmpfile.aopen(temp_string_)
tmpfile.printf("//MULTI %d %d\n",panobj.entries,panobj.segments) // redo in case differs
for ltr(XO,panobj.llist) {
tmpfile.printf("%s ",XO.name)
for ii=0,panobj.segments-1 { tmpfile.printf("%d ",XO.loc[ii]) }
tmpfile.printf("\n")
}
tmpfile.close()
}
//** make_vdot_files() go through a list of filenames to convert into .file format
proc make_vdot_files () { local ii,sav,cnt
cnt = panobjl.count()
for ltr(XO,$o1) {
filename = XO.s
print "Processing ",filename
read_vfile(cnt) // don't overwrite one that's being used
}
}
//* print out the CPU name
proc vfcpu () {
sprint(temp_string_,"%s '^//CPU' %s",grep,$s1)
system(temp_string_)
}
//* rpanel() creates a panel from information in llist
proc rpanel () { local ii
print $1
attrnum = $1
panobj = panobjl.object(attrnum)
if (panobj.llist.count > 8) { rlist($1) return }
sprint(temp_string_,"#%d:%s ",attrnum,simname)
xpanel(temp_string_)
xlabel(panobj.filename)
for ii=0,panobj.llist.count-1 {
sprint(temp_string2_,"rv(%d,%d)",attrnum,ii)
xbutton(panobj.llist.object(ii).name,temp_string2_)
}
sprint(temp_string_,"attrpanl(%d)",attrnum)
xbutton("Attributes",temp_string_)
sprint(temp_string_,"lpvec(filename,vrtmp,%g)",panobj.printStep)
xbutton("Print last vec",temp_string_)
xbutton("Erase","ge()")
xpanel()
}
//* rlist(): like rpanel() but puts up a browser list instead of a panel
proc rlist () {
panobjl.object($1).llist.browser(panobjl.object($1).filename,"name")
sprint(temp_string_,"rv(%d,hoc_ac_)",$1)
panobjl.object($1).llist.accept_action(temp_string_)
}
//* rvlist(): like rpanel() but puts up a browser list instead of a panel
proc rvlist () { local flag,attrnum,rdstr
rdstr = 1
flag = $1 attrnum = $2
if (numarg()==3) { recstr=$s3 rdstr=0 }
if (flag==0) {
panobjl.object(attrnum).llist.browser(panobjl.object(attrnum).filename,"name")
sprint(temp_string_,"rvec(%d,hoc_ac_)",attrnum)
panobjl.object(attrnum).llist.accept_action(temp_string_)
} else if (flag==1) { // proc(vec)
if (rdstr) string_dialog("Procedure name: proc, called as proc(vec)",recstr)
panobjl.object(attrnum).llist.browser(recstr,"name")
sprint(temp_string_,"{rvec(%d,hoc_ac_) %s(%s)}",attrnum,recstr,rvvec_name)
panobjl.object(attrnum).llist.accept_action(temp_string_)
print attrnum,":",recstr,":",temp_string_,":",rvvec_name
} else if (flag==2) { // vec.command
if (rdstr) string_dialog("comm: print vec.comm",recstr)
panobjl.object(attrnum).llist.browser(recstr,"name")
sprint(temp_string_,"{rvec(%d,hoc_ac_) print %s.%s}",attrnum,rvvec_name,recstr)
panobjl.object(attrnum).llist.accept_action(temp_string_)
}
}
proc disptray() { print "Must load boxes.hoc to get trays" }
//* attrpanl() gives attributes for a set of graphs
proc attrpanl () { local ii,jj
attrnum = $1 // use global for xbuttn
sfunc.tail(panobjl.object(attrnum).filename,"data.*/",grvecstr)
sprint(temp_string_,"#%d:%s:%s (ATTRPANL)",attrnum,simname,grvecstr)
xpanel(temp_string_)
xvarlabel(panobjl.object(attrnum).filename)
xvarlabel(msg) msg = panobjl.object(attrnum).comment
sprint(temp_string_,"panobjl.object(%d).color",attrnum)
xvalue("Color(-1=multi)",temp_string_,1)
sprint(temp_string_,"panobjl.object(%d).line",attrnum)
xvalue("Line",temp_string_,1)
xstatebutton("Superimpose",&panobjl.object(attrnum).super,"gnum=-1")
xvalue("Superimpose - Graph[#]","gnum",1)
xbuttn("Graph limits","wvpanl(")
xmenu("Manipulate graphs")
xbutton("Mark","gvmarkflag=-(gvmarkflag-1) sprint(msg,\"Mark: %d\",gvmarkflag)")
xbutton("Erase/redraw","gveraseflag=-(gveraseflag-1) sprint(msg,\"Erase: %d\",gveraseflag)")
xbuttn("Label graphs","lblall(")
xbuttn("Erase graphs","geall(")
xbuttn("Remove graphs","remgrs(")
sprint(temp_string2_,"disptray(%d)",attrnum)
xbutton("Make tray",temp_string2_)
sprint(temp_string2_,"setrange(%d,3)",attrnum)
xbutton("Erase axes",temp_string2_)
sprint(temp_string2_,"for ltr(XO,panobjl.object(%d).glist) XO.exec_menu(\"View = plot\")",attrnum)
xbutton("View = plot",temp_string2_)
sprint(temp_string2_,"for ltr(XO,panobjl.object(%d).glist) XO.exec_menu(\"Crosshair\")",attrnum)
xbutton("Crosshair",temp_string2_)
sprint(temp_string2_,"for ltr(XO,panobjl.object(%d).glist) XO.exec_menu(\"NewView\")",attrnum)
xbutton("New view",temp_string2_)
sprint(temp_string2_,"for ltr(XO,panobjl.object(%d).glist) XO.exec_menu(\"Delete\")",attrnum)
xbutton("Delete Text",temp_string2_)
sprint(temp_string2_,"for ltr(XO,panobjl.object(%d).glist) XO.exec_menu(\"Move Text\")",attrnum)
xbutton("Move Text",temp_string2_)
sprint(temp_string2_,"for ltr(XO,panobjl.object(%d).glist) XO.exec_menu(\"Change Text\")",attrnum)
xbutton("Change Text",temp_string2_)
xmenu()
sprint(temp_string_,"panobjl.object(%d).remote",attrnum)
sprint(temp_string2_,"grall(%d)",attrnum)
xvalue("Graph all",temp_string_,0,temp_string2_)
if (attrnum != 0) {
xmenu("Manipulate vectors")
xbutton("Vector name","string_dialog(\"Change Vector name\",rvvec_name)")
xbuttn("Write to vector","rvlist(0,")
xbuttn("Proc(vector)","rvlist(1,")
xbuttn("vector.command","rvlist(2,")
xmenu()
xbuttn("Show full panel","rpanel(")
xbuttn("Change file","fchooser(")
} else {
xbutton("Show full panel","pbrgr(\"Graph\",\"gv\")")
}
xpanel()
}
// allows inclusion of attrnum for each item
proc xbuttn () { sprint(temp_string2_,"%s%d)",$s2,attrnum) xbutton($s1,temp_string2_) }
//* set something for attrpanl() to value
func attrset () { local attrnum, ii
if (numarg()==0) { printf("attrset(attrnum,\"thing\",val)\n")
} else if (numarg()==2) {
sprint(temp_string_,"tempvar = panobjl.object(%d).%s",$1,$s2)
execute(temp_string_)
return tempvar
} else {
sprint(temp_string_,"panobjl.object(%d).%s=%g",$1,$s2,$3)
execute(temp_string_)
return $3
}
}
proc wvpanl () { local attrnum, ii
attrnum = $1
sfunc.tail(panobjl.object(attrnum).filename,"data.*/",grvecstr)
sprint(temp_string_,"#%d:%s:%s (WVPANL)",attrnum,simname,grvecstr)
xpanel(temp_string_)
sprint(temp_string_,"%d Vectors",panobjl.object(attrnum).llist.count)
xlabel(temp_string_)
for ii=0,3 {
sprint(temp_string_,"panobjl.object(%d).size[%d]",attrnum,ii)
sprint(temp_string2_,"chrange(%d,%d)",attrnum,ii)
xvalue(szstr[ii].s,temp_string_,0,temp_string2_)
}
sprint(temp_string_,"panobjl.object(%d).shift",attrnum)
sprint(temp_string2_,"chrange(%d,-2)",attrnum)
xvalue("Shift L/R",temp_string_,0,temp_string2_)
sprint(temp_string2_,"chrange(%d,%d)",attrnum,-1)
xmenu("Other")
xbutton("Clear/Set to G0",temp_string2_)
sprint(temp_string2_,"viewplot(%d)",attrnum)
xbutton("View=plot",temp_string2_)
sprint(temp_string2_,"setrange(%d,0,tstop,-90,50)",attrnum)
xbutton("0,tstop,-90,50",temp_string2_)
xbutton("Clean graph list","collapsegrs()")
sprint(temp_string2_,"attrpanl(%d)",attrnum)
xbutton("Attributes",temp_string2_)
xmenu()
xpanel()
for ii=0,3 if (panobj.size[ii]==0) panobj.size[ii]=panobj.glist.object(0).size(ii+1)
}
//* remgrs() gets rid of all of the graphs (called from attrpanl)
proc remgrs () { local ii,cnt
if (isobj(graphItem,"Graph")) { graphItem.unmap graphItem = nil }
panobj = panobjl.object($1)
for ltr (XO,panobj.glist) XO.unmap()
panobj.glist.remove_all
}
//* collapsegrs () take off of glist graphs that have been closed on screen
proc collapsegrs () { local ii
if (numarg()==0) { panobj = panobjl.object(0)
} else { panobj = panobjl.object($1) }
for (ii=panobj.glist.count-1;ii>=0;ii-=1) {
if (panobj.glist.object(ii).view_count() == 0) {
panobj.glist.remove(ii)
}
}
}
//* viewplot() set the world for each graph correctly
proc viewplot () { local cnt,ii,flag,sz1,sz2,sz3,sz4
if (numarg()==2) flag=$2 else flag=-1
if (flag==0) { sz1=sz3=1e10 sz2=sz4=-1e10 }
panobj = panobjl.object($1)
for ltr(XO,panobj.glist) {
XO.size(&x[0])
if (flag==0) {
if (x[0]<sz1) sz1=x[0]
if (x[1]>sz2) sz2=x[1]
if (x[2]<sz3) sz3=x[2]
if (x[3]>sz4) sz4=x[3]
} else if (flag==9) {
XO.size(0,tstop,x[2],x[3])
} else { XO.size(x[0],x[1],x[2],x[3]) }
}
if (flag==9) { panobj.size[0]=0 panobj.size[1]=tstop }
if (flag==0) for ltr(XO,panobj.glist) XO.size(sz1,sz2,sz3,sz4)
}
//* nvwall() changes the size of the graphs
proc nvwall () { local cnt,ii,sz1,sz2,sz3,sz4,wd,ht
panobj = panobjl.object($1)
if (numarg()==3) { wd=$2 ht=$3 } else { wd=panobj.vsz[0] ht=panobj.vsz[1] }
cnt = panobj.glist.count()
for (ii=cnt-1;ii>=0;ii=ii-1) {
if (panobj.glist.object(ii).view_count()==0) {panobj.glist.remove(ii)
} else {
sz1 = panobj.glist.object(ii).size(1)
sz2 = panobj.glist.object(ii).size(2)
sz3 = panobj.glist.object(ii).size(3)
sz4 = panobj.glist.object(ii).size(4)
panobj.glist.object(ii).unmap()
panobj.vloc = panobj.vloc+panobj.vjmp
if (panobj.vloc > 700) { panobj.vloc = 0 }
panobj.glist.object(ii).view(sz1,sz3,sz2-sz1,sz4-sz3,0,panobj.vloc,wd,ht)
}
}
}
//* geall() erases all of the graphs
proc geall () { local cnt,ii
panobj = panobjl.object($1)
cnt = panobj.glist.count()
for ii=0,cnt-1 {
panobj.glist.object(ii).erase_all()
}
}
//* lblall(attrnum,label,#,xloc,yloc) put label on all of the graphs
// arg3 tells which single graph to put it on
proc lblall () { local cnt,ii,min,max,attrnum,lx,ly
if (numarg()==0) { printf("lblall(attrnum[,loc])\n") return }
attrnum = $1 panobj = panobjl.object(attrnum)
cnt = panobj.glist.count()
if (numarg()>2) { min=max=$3 } else { min=0 max=cnt-1 }
if (numarg()==5) { lx=$4 ly=$5 } else { lx=0.1 ly=0.8 }
if (numarg()>1) { if (sfunc.len($s2)>0) { temp_string_ = $s2
}} else if (attrnum==0) { temp_string_ = comment
} else sprint(temp_string_,"%s",panobjl.object(0).comment)
for ii=min,max {
panobj.glist.object(ii).color(panobj.color)
panobj.glist.object(ii).label(lx,ly,temp_string_)
// if (attrnum!=0&&ii<panobj.llist.count()) panobj.glist.object(ii).label(panobj.llist.object(ii).name)
}
}
//* relbl() put appropriate label on all of the graphs
proc relbl () { local cnt,ii,min,max,attrnum,lx,ly
if (numarg()==0) { printf("relbl(attrnum[,str])\n") return }
attrnum = $1 panobj = panobjl.object(attrnum)
cnt = panobj.glist.count()
if (numarg()==4) { lx=$3 ly=$4 } else { lx=0.1 ly=0.8 }
if (numarg()>1) panobj.glist.object(0).label($s2)
for ltr2(XO,YO,panobj.glist,panobj.llist) {
XO.color(0)
if (attrnum==0) XO.label(0.,.9,YO.var) else XO.label(0.,.9,YO.name)
XO.color(panobj.color)
XO.label(lx,ly,YO.vec.label)
}
}
//* grall() graphs all of the lines from the file
// use vector $o2 as indices for vectors (see tposvec)
proc grall () { local attrnum,cnt,ii,min,max,gr,skip,iskp,vind
if (numarg()==0) {printf("grall(attrnum[,min,max,remote,gr_offset,skipgr,iskp]): graph vectors.\n")
return }
attrnum=$1 vind=0
panobj = panobjl.object(attrnum)
if (attrnum == 0) cnt = printlist.count() else cnt = panobj.llist.count()
// will reset max if is vector with numarg()==2
if (numarg()>2) { min=$2 max=$3 } else { min=0 max=cnt-1 }
// with 2 args, vector $o2 gives indices for vectors (see tposvec)
if (numarg()>=2) if (argtype(2)==1) { vind=1 min=0 max=$o2.size-1 }
if (numarg()>3) { panobj.super=1 panobj.remote=$4 }
if (numarg()>4) gr=$5 else gr=0
if (numarg()>5) skip=$6 else skip=1
if (numarg()>6) iskp=$7 else iskp=1
if (iskp==0) iskp=1 if (skip==0) skip=1
if (panobj.super==1 && panobj.remote==attrnum && panobj.glist.count==0) {
remgrs(attrnum)
print "Creating plot"
skip=0
newPlot(0,tstop,-100,100) panobj.glist.append(graphItem)}
if (panobj.super==0 && panobj.glist.count==0) panobj.size[1]=0
for (ii=min;ii<=max;ii+=iskp) {
if (panobj.super == 1) {
if (gr >= panobjl.object(panobj.remote).glist.count()) break
graphItem = panobjl.object(panobj.remote).glist.object(gr)
gr=gr+skip
}
if (vind) rv($1,$o2.x[ii]) else rv($1,ii)
}
}
// tposvec(rows,cols): generate the indices for a transposed matrix of rows x cols
proc tposvec () { local rows,cols,i,j
rows=$2 cols=$3
$o1.resize($2*$3)
for (i=0;i<rows;i+=1) for (j=0;j<cols;j+=1) $o1.x[j*rows+i]=i*cols+j
}
// fliptb(rows,cols): generate the indices for a transposed matrix of rows x cols
proc fliptb () { local rows,cols,i,j,p
rows=$2 cols=$3
if ($o1.size != $2*$3) {print "Wrong size vector in fliptb()" return}
p = allocvecs(1) mso[p].resize(rows)
for (j=0;j<cols;j+=1) {
mso[p].copy($o1,j*rows,(j+1)*rows-1)
mso[p].reverse
$o1.copy(mso[p],j*rows)
}
}
//* setrange() sets the range
// setrange(attrnum,x0,x1,y0,y1)
proc setrange () { local i,ii
if (numarg()==0){print "setrange(attrnum,x0,x1,y0,y1)\n setrange(attrnum,3) erases axes" return}
panobj = panobjl.object($1)
if (numarg()==1) { for ltr(XO,panobj.glist) XO.size(0,tstop,-100,50)
} else if (numarg()==2) { for ltr(XO,panobj.glist) XO.xaxis(3)
} else if (numarg()==3) { for ltr(XO,panobj.glist) XO.size(0,tstop,$2,$3)
} else {
panobj.size[0]=$2
for ltr(XO,panobj.glist) XO.size($2,$3,$4,$5)
for i=2,5 panobj.size[i-2]=$i
}
for ii=0,3 if (panobj.size[ii]==0) panobj.size[ii]=panobj.glist.object(0).size(ii+1)
}
//* grransel() -- graph range select
proc setgrransel () { local attrnum
attrnum=$1
panobj = panobjl.object(attrnum)
for ltr(XO,panobj.glist) {
XO.menu_remove("REVIEW")
sprint(tstr,"proc p%d%d(){grransel($1,$2,$3,$4,%d,%d,%s)}",attrnum,i1,attrnum,i1,XO)
execute1(tstr)
sprint(tstr,"p%d%d",attrnum,i1)
XO.menu_tool("REVIEW", tstr)
XO.exec_menu("REVIEW")
}
}
//** grransel(): CTL-hit == Crosshair
// SHT-hit == resize
// hit-drag-release == show in square
// SHT-hit-drag-release == show new thing there
// Type: press (2), drag (1), release (3)
// Keystate: META-SHT-CTL eg 101=5 is META-CTL
grrcnt=-1
proc grransel () { local type, x0, y0, keystate, ii, attrnum, gr
type=$1 x0=$2 y0=$3 keystate=$4 attrnum=$5 gr=$6
graphItem=$o7 // = panobj.glist.object(gr)
panobj=panobjl.object(attrnum)
if (keystate==1 && type==2) { graphItem.exec_menu("Crosshair") // CTL-MOUSE-1
} else if (keystate==3 && type==3) {
print grrcnt
if (grrcnt>-1) { printf("Graphing %s\n",printlist.object(grrcnt).var)
graphItem.erase_all()
rv(attrnum,grrcnt)
graphItem.exec_menu("View = plot")
}
graphItem.size(panobj.size[0],panobj.size[1],panobj.size[2],panobj.size[3])
} else if (keystate==2 && type==2) { grrcnt=-1
} else if (keystate==2 && type==1) {
x+=1 // slow it down five-fold
if (x>5) { grrcnt=(grrcnt+1)%printlist.count
printf("%d: %s\n",grrcnt,printlist.object(grrcnt).var)
x=0
}
} else if (keystate==0 && type==2) { x=x0 y=y0 } else if (keystate==0 && type==3) {
graphItem.size(x,x0,y,y0) // resize to chosen square
}
}
//* chrange() changes range for a set of graphs (called from attrpanl)
luprd=0
proc chrange () { local cnt, flag, ii, sz1, sz2, sz3, sz4
if (numarg()==2) { flag = $2 } else { flag = -1 }
panobj = panobjl.object($1)
cnt = panobj.glist.count()
for (ii=cnt-1;ii>=0;ii=ii-1) if (panobj.glist.object(ii).view_count() == 0) panobj.glist.remove(ii)
cnt = panobj.glist.count() // check again after removing any with no views
if (cnt==0) { for ii=0,3 panobj.size[ii]=0 return }
// flag -1 means set everything from the first graph
if (flag==-1) for ii=0,3 panobj.size[ii] = panobj.glist.object(0).size(ii+1)
if (flag==-2) for ii=0+luprd,1+luprd panobj.size[ii] += panobj.shift // shift right or left
if (flag==5) { panobj.size[0]=0 panobj.size[1]=tstop } // just set x
// for each of the graphs
for ltr(XO,panobj.glist) {
sz1=XO.size(1) sz2=XO.size(2) sz3=XO.size(3) sz4=XO.size(4)
if (flag==0) XO.size(panobj.size[0],sz2,sz3,sz4)
if (flag==1) XO.size(sz1,panobj.size[1],sz3,sz4)
if (flag==2) XO.size(sz1,sz2,panobj.size[2],sz4)
if (flag==3) XO.size(sz1,sz2,sz3,panobj.size[3])
if (flag==-1 || flag==4) XO.size(panobj.size[0],panobj.size[1],panobj.size[2],panobj.size[3])
if ((flag==-2 && !luprd) || flag==5) XO.size(panobj.size[0],panobj.size[1],sz3,sz4)
if (flag==-2 && luprd) XO.size(sz1,sz2,panobj.size[2],panobj.size[3])
}
for ii=0,3 if (panobj.size[ii]==0) panobj.size[ii]=panobj.glist.object(0).size(ii+1)
}
//* rtvec() reads tvec if it exists, returns -1 if it doesn't
// rtvec(attrnum)
func rtvec () { local attrnum,inx,inx2
attrnum = $1
panobj = panobjl.object(attrnum)
if (panobj.tloc > 0) {
tmpfile.seek(panobj.tloc)
panobj.tvec.vread(tmpfile)
return 1
} else {
return 0
}
}
//* rv() reads line of vector file into IV graph via vector
// rv(attrnum,llist_ind1[,llist_ind2])
func round () { if ($1>0) return int($1+0.5) else return int($1-0.5) } // round off to nearest integer
// rvaltdisp(tvec,vec,name)
func rvaltdisp () { return 0 } // if returns 1 means there is an alternate display for rv
proc rv2 () { } // stub for manipulating the vectors before graphing
proc rv () { local attrnum,inx,inx2
// open the file and go to correct position
if (numarg() == 0) { print "rv(attrnum,ind1,ind2) reads into vrtmp bzw vec" return }
attrnum = $1
inx = $2
if (panobj.printStep>0 && numarg() > 2) { inx2 = $3 } else { inx2 = -1 }
if (attrnum==0) { gv(inx) return }
rv_readvec(attrnum,inx,vrtmp) // will set panobj
rv2(vrtmp)
// create a new plot if necessary and set color
nvplt(vrtmp)
if (vrtmp.size==0) { // assume this is a spike train in tvec
ind.resize(panobj.tvec.size) ind.fill(0)
ind.mark(graphItem,panobj.tvec,"O",panobj.line+4,panobj.curcol)
// grrtsize()
} else if (inx2>-1) {
rv_readvec(attrnum,inx2,vec)
graphItem.size(0,vrtmp.max,0,vec.max)
if (numarg() > 3) {
vec.mark(graphItem,vrtmp,$s4,6,panobj.curcol)
} else {
vec.mark(graphItem,vrtmp,"O",6,panobj.curcol)
}
} else if (panobj.printStep<0) {
if (gvmarkflag) {
if (! rvaltdisp(panobj.tvec,vrtmp,panobj.llist.object(inx).name)) {
vrtmp.mark(graphItem,panobj.tvec,"O",4,panobj.curcol,panobj.line)
graphItem.exec_menu("View = plot")
}
} else if (numarg() >= 3) {
vrtmp.apply("round") // round off this index vector
vrtmp.mark(graphItem,panobj.tvec,"O",$3,panobj.curcol,panobj.line)
} else {
vrtmp.line(graphItem,panobj.tvec,panobj.curcol,panobj.line) }
} else {
vrtmp.line(graphItem,panobj.printStep,panobj.curcol,panobj.line) }
// graph it and label the graph
if (sfunc.substr(panobj.filename,"batch")!=-1 || \
sfunc.substr(panobj.filename,"data")==-1) {
grvecstr = panobj.filename
} else { sfunc.tail(panobj.filename,"data",grvecstr) }
sprint(grvecstr,"%s:%s",grvecstr,panobj.llist.object(inx).name)
if (panobj.super == 0 && labelm) { graphItem.label(0,0.9,grvecstr)
} else if (labelm) graphItem.label(0.5,0.9,grvecstr)
}
// rv_readvec(attrnum,index,vec)
// read vector #index from file associated with attrnum into vector vec
proc rv_readvec () { local size,attrnum,inx,ii
attrnum = $1
inx = $2
panobj = panobjl.object(attrnum)
tmpfile.getname(temp_string_)
if (strcmp(temp_string_,panobj.filename)!=0 || tmpfile.isopen()==0) {
if (! tmpfile.ropen(panobj.filename)) {
print "ERROR rv() can't read ",panobj.filename return }}
tmpfile.seek(panobj.llist.object(inx).loc)
if (panobj.bytes) {
if (panobj.printStep==-2) { panobj.tvec.vread(tmpfile) }
if (numarg()==4) { $o3.vread(tmpfile) $o4.vread(tmpfile) } else {
$o3.vread(tmpfile) }
if (panobj.segments>1) {
tmpvec = new Vector($o3.size)
for ii=1,panobj.segments-1 {
tmpfile.seek(panobj.llist.object(inx).loc[ii])
tmpvec.vread(tmpfile)
$o3.copy(tmpvec,$o3.size)
}
tmpvec = nil
}
} else {
tmpfile.scanstr(temp_string_) // get rid of '//'
size = tmpfile.scanvar()
tmpfile.scanvar() // get rid of the seek number
$o3.scanf(tmpfile,size)
}
}
//* read vector iterator rvtr
// usage 'for rvtr(vec,#) XO.vec.printf' where # is attrpanl#
// not debugged for presence of tvec in cvode
iterator rvtr() { local i
if (numarg()==3) {$&3=0} else {i1 = 0}
attrnum=$2
panobj=panobjl.object(attrnum)
for i = 0, panobj.entries - 1 {
rv_readvec(attrnum,i,$o1)
iterator_statement
if (numarg()==3) { $&3+=1 } else { i1+=1 }
}
}
//* rvec(attrnum,num[,vec]) writes to vec, or contents of rvvec_name or
// to vector of same name if rvvec_name is empty
proc rvec () { local flag,ln,on
flag=0 ln=$1
if (sfunc.len(rvvec_name)==0) flag=1
if (numarg()<2) on=hoc_ac_ else on=$2
if (numarg()>2) sprint(rvvec_name,"%s",$o3)
if (sfunc.len(rvvec_name)==0) rvvec_name=panobjl.object(ln).llist.object(on).name
printf("Copying %s to %s\n",panobjl.object(ln).llist.object(on).name,rvvec_name)
sprint(temp_string_,"rv_readvec(%d,%d,%s)",ln,on,rvvec_name)
if (flag) rvvec_name="" // clear it again
if (! execute1(temp_string_)) print "ERROR: Declare target as a vector"
if (numarg()==4) $o4.copy(panobj.tvec)
}
//* rvl() reads line of vector file into IV graph via vector
// rvl(attrnum,name,pos[,pos2,pos3,...])
proc rvl () { local i
// open the file and go to correct position
panobj=panobjl.object($1)
tmpfile.getname(temp_string_)
if (strcmp(temp_string_,panobj.filename)!=0 || tmpfile.isopen()==0) {
tmpfile.ropen(panobj.filename) } // only open if necessary
if (tmpfile.isopen==0) { printf("ERROR: %s not found.\n",panobj.filename)
return }
if (numarg() == 3) {
tmpfile.seek($3)
tmpfile.gets(temp_string_) // throw away line
vrtmp.vread(tmpfile)
} else {
tmpvec = new Vector()
for i=3,numarg() {
tmpfile.seek($i)
tmpvec.vread(tmpfile)
vrtmp.copy(tmpvec,vrtmp.size)
}
}
tmpvec = nil
nvplt(vrtmp)
vrtmp.line(graphItem,panobj.printStep,panobj.curcol,panobj.line)
// graph it and label the graph
if (sfunc.substr(panobj.filename,"batch")!=-1) { grvecstr = panobj.filename
} else { sfunc.tail(panobj.filename,"data",grvecstr) }
sprint(grvecstr,"%s:%s",grvecstr,$s2)
if (panobj.super==0 && labelm) { graphItem.label(0,0.9,grvecstr)
} else if (labelm) graphItem.label(grvecstr)
}
//* read_file(file,cols[,length]): read multicolumn file
// see /u/billl/nrniv/jun/tidata/proc.hoc for improved version
func read_file() { local ii,cols,pt,length
if (numarg()==0) { print "\tread_file(\"file\",cols)"
print "\t(must set tstop and printStep.)"
return 0
}
panobjl.object(0).printStep = use_lvardt_ = using_cvode_ = 0
print "WARNING: Turning off cvode."
if (numarg()==3) { length = $3 } else { length=tstop/printStep }
cols = $2
if (! tmpfile.ropen($s1)) { printf("\tERROR: can't open file \"%s\"\n",$s1) return 0}
printlist.remove_all()
tmpfile.scanstr(temp_string_) pt = 0
// skip over a comment line; note that this will skip extra line if comment line is
// just one word long
while (sfunc.head(temp_string_,"[^-+0-9.e]",temp_string2_) != -1) {
tmpfile.gets(temp_string_) // first word in line was not a number so next line
pt = tmpfile.tell() // location at next line
tmpfile.scanstr(temp_string_) // get first word here
print temp_string2_
}
for ii=1,cols { // pick up all of the columns
tmpfile.seek(pt)
vrtmp.scanf(tmpfile,length,ii,cols)
new_printlist_item("col",ii,vrtmp)
}
return 1
}
//* read_rfile(file): read multirow file
// use col2row to transpose columnar file first
proc read_rfile() { local num
if (numarg()==0) { print "\tread_rfile(\"file\")" return }
if (! tmpfile.ropen($s1)) { printf("\tERROR: can't open file \"%s\"\n",$s1) return}
printlist.remove_all()
while (tmpfile.scanstr(temp_string_) != -1) { // read lines
num = tmpfile.scanvar() // pick up number of items in col
vrtmp.scanf(tmpfile,num)
new_printlist_item(temp_string_,vrtmp)
}
}
// restore_plist() restores the plist from a file in an attrnum
proc restore_plist () { local cnt,ii,attrnum,savlvar
printlist.remove_all
attrnum = $1
panobj=panobjl.object(attrnum)
panobjl.object(0).printStep=panobj.printStep
if (panobj.printStep == -2) use_lvardt_=1 else use_lvardt=0
cnt = panobj.llist.count()
for ii=0,cnt-1 {
vite = new vitem(panobj.llist.object(ii).name,0)
rv_readvec(attrnum,ii,vite.vec)
if (use_lvardt_) vite.tvec.copy(panobj.tvec)
printlist.append(vite)
vite=nil
}
if (use_lvardt_) tstop=panobj.tvec.max
}
//* sgv() print out spikes from IF recordings like spkt()
proc sgv () { local cl
if (numarg()==1) cl=$1 else cl=1
sgv1()
nvplt(ind)
panobj.curcol=cl
// g.erase_all()
vec.mark(graphItem,ind,"O",panobj.line+4,panobj.curcol,4)
graphItem.size(0,ind.max+1,0,tstop)
}
proc sgv1 () {
revec(ind) revec(vec)
for ltr(XO,printlist) if (XO.vec.size==0) {
szt=XO.tvec.size
if (szt>0) {
szi=ind.size
vec.append(XO.tvec)
ind.resize(szi+szt)
ind.fill(i1,szi,szi+szt-1)
}
}
}
//* gv(vnum) graphs vector
proc gv () { local inx
ulv()
inx=-1
if (numarg()==0) { inx = hoc_ac_ } else {
if (argtype(1)==0) inx = $1
if (argtype(1)==2) {
for ltr(XO,printlist) if (strm(XO.var,$s1)) inx=i1
if (inx==-1) {print $s1," not found" return }}
}
panobj = panobjl.object(0)
if (use_lvardt_) { panobj.tvec = printlist.object(inx).tvec }
XO = printlist.object(inx).vec
if (XO.size==0) { // assume that this is spk trace
if (panobj.tvec.size==0) { printf("\tNO SPIKES IN %s\n",printlist.object(inx).var)
} else {
nvplt(panobj.tvec)
ind.resize(panobj.tvec.size) ind.fill(1)
ind.mark(graphItem,panobj.tvec,"O",panobj.line+3,panobj.curcol)
// grrtsize()
}
return
} else nvplt(XO)
if (gvmarkflag) {
XO.mark(graphItem,panobj.tvec,"O",panobj.line+3,panobj.curcol)
graphItem.exec_menu("View = plot")
} else if (using_cvode_) {
XO.line(graphItem,panobj.tvec,panobj.curcol,panobj.line)
} else {
XO.line(graphItem,printStep,panobj.curcol,panobj.line)
}
if (labelm) graphItem.label(0.,0.9,printlist.object(inx).var)
}
proc gvmt () { gvmarkflag=-(gvmarkflag-1) printf("gv Mark: %d\n",gvmarkflag) }
//* dispspks() display spike times
proc dispspks () { local attrnum,n
attrnum = $1 n=0
panobj=panobjl.object(attrnum)
if (panobj.super == 1) {
graphItem = panobj.glist.object(panobj.glist.count-1)
} else {
newPlot(0,1,0,1)
panobj.glist.append(graphItem)
}
if (attrnum==0) {for ltr(XO,printlist) dispspks2(XO.var,XO.tvec,i1)
} else for ltr(XO,panobj.llist) {
rv_readvec(attrnum,i1,ind) // ind is scratch here since info in tvec
dispspks2(XO.name,panobj.tvec,i1)
}
grrtsize()
}
// $s1 name, $o2 tvec, $3 n
proc dispspks2 () { local n,col
n=$3
col = panobj.curcol
if (sfunc.substr($s1,"_spks")) {
if ($o2.size>0) {
ind.resize($o2.size) ind.fill(n)
if (sfunc.substr($s1,"NetStim")!=-1) col+=1
ind.mark(graphItem,$o2,"O",panobj.line+4,col)
}
}
}
//** grrtsize() use view=plot and then pad a little
proc grrtsize () { local h,w,frac
if (numarg()>=1) tmpobj=$o1 else tmpobj=graphItem
if (numarg()>=2) frac = $2 else frac=.05
tmpobj.exec_menu("View = plot")
tmpobj.size(&x)
w=frac*(x[1]-x[0]) h=frac*(x[3]-x[2])
x[0]-=2*w x[1]+=w x[2]-=4*h x[3]+=h // need extra padding on bottom
tmpobj.size(x[0],x[1],x[2],x[3])
}
//* gvv() like gv() but give it vector statt vnum
proc gvv () { local inx
nvplt($o1)
if (numarg()==1) {
$o1.line(graphItem,printStep,panobj.curcol,panobj.line)
} else {
$o1.line(graphItem,$o2,panobj.curcol,panobj.line)
graphItem.size($o2.min,$o2.max,$o1.min,$o1.max)
}
}
//* ge() erases IV graph
proc ge () { if (numarg()==0) graphItem.erase_all() else g[$1].erase_all }
//* pvall() dumps all vectors to output_file
// Save logic:
// 1) Interactive mode: you're watching simulations while printing out
// data. You see something you like and save it - the runnum in the
// index file then corrsponds to the number on the data file, it is
// subsequently augmented
// 2) Batch mode: you're running very long sims and saving directly to
// vector files. You put together a simulation you want and save it
// immediately rather than waiting for the sim to return (in 1 or 2
// days). To correspond, the data file (v*) must then be numbered
// 'runnum-dec_runnum'
proc pvall () {
sprint(output_file,"%s/v%s.%02d",ddir,datestr,runnum-dec_runnum)
while (tmpfile.ropen(output_file)) { runnum = runnum+1
sprint(output_file,"%s/v%s.%02d",ddir,datestr,runnum-dec_runnum)
}
if (numarg()>0) { comment = $s1 // a comment
} else {
sprint(temp_string_,"%s.%02d",datestr,runnum-dec_runnum)
if (sfunc.substr(comment,temp_string_) == -1) { comment = "" } // clear comment
}
printf("Saving to %s\n",output_file)
pvplist(output_file,comment)
sprint(output_file,"%s/v%s.%02d",ddir,datestr,runnum)
}
// pvplist(file,comment) print out the printlist with comment at head
proc pvother () {} // user can dump other vectors at top with prvec()
proc pvplist () { local inx
ulv()
file_with_dot($s1,temp_string_,temp_string2_) // put .filename into temp_string_
if (tmpfile.ropen(temp_string_)) { printf("WARNING: removing %s\n",temp_string_)
sprint(temp_string_,"rm %s",temp_string_) system(temp_string_) }
if (tmpfile.wopen($s1)==0) { print "Can't open ",$s1 return}
tmpfile.printf("//: %s\n",$s2) // comment
pvplist1()
if (byte_store) {tmpfile.printf("//CPU %s\n",uname)}
pvout()
tmpfile.close()
}
proc pvplist1 () {
if (use_lvardt_) {
tmpfile.printf("//printStep -2\n")
} else if (using_cvode_) {
tmpfile.printf("//printStep -1\n")
} else {
tmpfile.printf("//printStep %g\n",printStep)
}
}
// pvnext() append another printlist set to same file
proc pvnext() { local ii
if ($1==0) {
pvall(comment)
sprint(output_file,"%s/v%s.%02d",ddir,datestr,runnum-1) // decrement back to name
return
}
tmpfile.aopen(output_file)
pvout()
printf("Append to %s\n",output_file)
tmpfile.close()
}
// prout() called by pvplist() and pvnext(), actually puts out the vecs
proc pvout () {
ulv()
if (!use_lvardt_ && using_cvode_) { prvec("tvec",panobjl.object(0).tvec,tvec_bytesize) } // save precise times
pvother()
for ltr(XO,printlist) { // no whitespace allowed
if (sfunc.len(XO.vec.label)>0) sprint(temp_string_,"%s__(%s)",XO.vec.label,XO.var) else {
temp_string_=XO.var }
if (byte_store) {
tmpfile.printf("//b%d %s %d %d\n",byte_store,temp_string_,XO.vec.size,tmpfile.tell())
if (use_lvardt_==1) if (eqobj(XO.tvec,nil)) {
print "ERROR: can't save under cvode_local, must recreate printlist\n"
return
} else { XO.tvec.vwrite(tmpfile,tvec_bytesize) }
XO.vec.vwrite(tmpfile,byte_store)
tmpfile.printf("\n")
} else {
tmpfile.printf("// %s %d %d\n",temp_string_,XO.vec.size,tmpfile.tell())
XO.vec.printf(tmpfile)
}
}
}
// prvec(name,vec,byte_flag[,file]) byte_flag=0 means printf
proc prvec () { local bflag
if (numarg()==0) { print "prvec(name,vec,byte_flag[,file])" return}
if (numarg()>3) { tmpfile.aopen($s4) }
bflag = $3
tmpfile.printf("//b%d %s %d %d\n",bflag,$s1,$o2.size,tmpfile.tell())
if (bflag==0) {
$o2.printf(tmpfile)
} else { $o2.vwrite(tmpfile,bflag) tmpfile.printf("\n") }
if (numarg()>3) { tmpfile.close() }
}
//* pv() dumps a single vector into output_file
proc pv () { local inx
sprint(output_file,"%s/v%s.%02d",ddir,datestr,runnum-dec_runnum)
if (numarg()==0) { inx = hoc_ac_ } else { inx = $1 }
printf("Printing %s to %s\n",printlist.object(inx).var,output_file)
temp_string_ = printlist.object(inx).var
// string_dialog("Name for saved vector",temp_string_)
if (tmpfile.ropen(output_file)) { // file exists already
tmpfile.close()
tmpfile.aopen(output_file)
printf("Appending to ",output_file)
} else {
tmpfile.wopen(output_file)
tmpfile.printf("//: %s\n",comment)
pvplist1()
}
if (byte_store) {
tmpfile.printf("//b%d %s %d %d\n",byte_store,temp_string_,\
printlist.object(inx).vec.size,tmpfile.tell())
if (use_lvardt_==1) if (eqobj(printlist.object(inx).tvec,nil)) {
print "ERROR: can't save under cvode_local, must recreate printlist\n"
return
} else { printlist.object(inx).tvec.vwrite(tmpfile,tvec_bytesize) }
printlist.object(inx).vec.vwrite(tmpfile,byte_store)
tmpfile.printf("\n")
} else {
tmpfile.printf("// %s %d %d\n",temp_string_,\
printlist.object(inx).vec.size,tmpfile.tell())
printlist.object(inx).vec.printf(tmpfile)
}
tmpfile.close()
}
//* lpv() calls lpvec from printlist
proc lpv () { local inx
if (numarg()==0) { inx = hoc_ac_ } else { inx = $1 }
sprint(temp_string_,"%s.%02d:%s",datestr,runnum-dec_runnum,printlist.object(inx).var)
lpvec(temp_string_,printlist.object(inx).vec,printStep)
}
//* lpvec(title,vector,printstep) dumps a single vector onto the printer using jgraph
proc lpvec () { local inx,ii
tmpfile.wopen("lptmp")
tmpfile.printf("newgraph\nnewcurve pts\n")
for ii = 0,$o2.size-1 {
tmpfile.printf("%g ",ii*$3)
$o2.printf(tmpfile,"%g",ii,ii)
}
tmpfile.printf("marktype none\nlinetype solid\ntitle : %s\n",$s1)
tmpfile.close()
system("jgraph -P lptmp > lptmp2")
system("lpt lptmp2")
}
//* phase planes
//** gppl(n1,n2) graph phase planes from printlist
proc gppl () {
newPlot(0,1,0,1)
panobjl.object(0).glist.append(graphItem)
printlist.object($2).vec.line(graphItem,printlist.object($1).vec)
}
//* routines for printing out in sections
//** outvec_init([output_file,comment])
proc outvec_init() { local segs
if (numarg()>0) { output_file = $s1 } else {
sprint(output_file,"%s/v%s.%02d",ddir,datestr,runnum-dec_runnum)
while (tmpfile.ropen(output_file)) { runnum = runnum+1 // don't allow an overwrite
sprint(output_file,"%s/v%s.%02d",ddir,datestr,runnum-dec_runnum) }
}
if (numarg()>1) { comment = $s2 }
print "\nOutput to ",output_file
if (print_flag) { print "WARNING: print_flag=1 --> 0\n"
print_flag = 0 }
if (outvecint==0 || outvecint>tstop) {
printf("WARNING: outvecint being set to tstop\n")
outvecint = tstop }
outvect = outvecint
segs = int(tstop/outvecint)
if (tstop/outvecint > segs) { segs=segs+1 }
tmpfile.wopen(output_file)
if (strcmp(comment,"")!=0) { tmpfile.printf("//: %s\n",comment) }
tmpfile.printf("//printStep %g\n",printStep)
tmpfile.printf("//MULTI %d %d\n",printlist.count,segs)
tmpfile.close()
}
//** outvecs() : print out the vectors and reset them for recording
proc outvecs () { local ii
if (t<outvect || outvecint == 0) { return }
tmpfile.aopen(output_file)
for ii=0,printlist.count-1 {
tmpfile.printf("//b%d %s %d %d\n",byte_store,printlist.object(ii).var,t-outvecint,tmpfile.tell())
printlist.object(ii).vec.vwrite(tmpfile,byte_store)
tmpfile.printf("\n")
printlist.object(ii).vec.play_remove()
sprint(temp_string_,"printlist.object(%d).vec.record(&%s,%g)",\
ii,printlist.object(ii).var,printStep)
execute(temp_string_)
}
tmpfile.close
outvect = outvect+outvecint
}
//** outvec_finish () : put out the last section if needed, update the output_file name
proc outvec_finish() {
if (t > outvect-outvecint+2*dt) {
tmpfile.aopen(output_file)
for ii=0,printlist.count-1 {
tmpfile.printf("//b%d %s %d %d\n",byte_store,printlist.object(ii).var,t-outvecint,tmpfile.tell())
printlist.object(ii).vec.vwrite(tmpfile,byte_store)
tmpfile.printf("\n")
}
tmpfile.close()
}
}
//* utility programs (not all used)
gnum=-1
proc nvplt () { local xs,ys,flag
if (panobj.super == 0) flag=1 else {
if (gnum>-1) {
sprint(tstr,"x=Graph[%d].view_count",gnum)
if (execute1(tstr,0)) if (x>0) { // use Graph[gnum] if exists and has views
graphItem=Graph[gnum] flag=0
} // else use graphItem if has views
} else if (isobj(graphItem,"Graph")) if (graphItem.view_count() > 0) {
flag=0
} else { flag=1 } // else need new graph
}
if (flag) {
if (panobj.printStep==0) { panobj.printStep=printStep }
if (panobj.size[1] != 0) { // xmax is set
newpl(panobj.size[0],panobj.size[1],panobj.size[2],panobj.size[3])
} else if (panobj.printStep<0) {
newpl(0,panobj.tvec.max,$o1.min,$o1.max)
} else {
newpl(0,$o1.size()*panobj.printStep,$o1.min,$o1.max)
}
panobj.glist.append(graphItem)
} else if (gveraseflag) graphItem.erase_all
if (panobj.color == -1) {
panobj.curcol += 1
if (panobj.curcol == 0 || panobj.curcol>7) panobj.curcol = 1
} else panobj.curcol = panobj.color
graphItem.color(panobj.curcol)
g=graphItem
}
double wvloc[4]
{wvloc[0]=50 wvloc[1]=50 wvloc[2]=800 wvloc[3]=150}
proc newpl () { local w,h
if (numarg()==5) newPlot($1,$2,$3,$4) // 5th arg is flag
if (numarg()==8) {wvloc[0]=$5 wvloc[1]=$6 wvloc[2]=$7 wvloc[3]=$8}
graphItem = new Graph(0)
graphItem.xaxis() // view axis for x and y
graphItem.view($1,$3,$2-$1,$4-$3,wvloc[0],wvloc[1],wvloc[2],wvloc[3])
}
proc gs () { g=Graph[$1] graphItem=g }
proc gg () { local ii,na,a1,a2,a3,newgr,clr
na=a1=a2=a3=-1 newgr=1
clr=panobj.color lne=panobj.line
na=numarg() if (na>=1) a1=argtype(1) if (na>=2) a2=argtype(2) if (na>=3) a3=argtype(3)
if (a1==0) ii=$1 else ii=0
if (a1==0 && isassigned(g[ii])) if (g[ii].view_count>0) newgr=0
if (newgr) g[ii]=new Graph()
graphItem=g[ii]
graphList[0].append(g[ii]) panobj.glist.append(g[ii])
if (gvmarkflag) tstr="mark" else tstr="line"
if (na==1 && a1==1) sprint(tstr,"%s.%s(%s,%s",$o1,tstr,g[ii],"1") // gg(vec)
if (na==2) {
if (a1==0 && a2==1) sprint(tstr,"%s.%s(%s,1",$o2,tstr,g[ii]) // gg(g[i],vec)
if (a1==1 && a2==0) sprint(tstr,"%s.%s(%s,%g",$o1,tstr,g[ii],$2) // gg(vec,step)
if (a1==1 && a2==1) sprint(tstr,"%s.%s(%s,%s",$o1,tstr,g[ii],$o2) // gg(vec,ind)
}
if (na>=3) {
if (a2==1 && a3==1) sprint(tstr,"%s.%s(%s,%s",$o2,tstr,g[ii],$o3) // gg(g[i],vec,ind)
if (a2==1 && a3==0) sprint(tstr,"%s.%s(%s,%g",$o2,tstr,g[ii],$3) // gg(g[i],vec,step)
}
if (na>=4) { clr=$4 } if (na>=5) { lne=$5 } if (na>=6) { symb=$s6 }
if (sfunc.len(tstr)>4) {
if (gvmarkflag) { sprint(tstr,"%s,\"%s\",%d,%d,1)",tstr,symb,lne+5,clr)
} else { sprint(tstr,"%s,%d,%d)",tstr,clr,lne) }
execute1(tstr)
}
}
//** remove_spaces(string,scratch) removes spaces and splits on '/'
// ie remove_spaces(temp_string_,temp_string2_)
proc remove_spaces () {
$s2="" // clear it out
while (sfunc.substr($s1," ") != -1) { // still have spaces
sfunc.tail($s1," ",$s2)
sfunc.head($s1," ",$s1)
sprint($s1,"%s%s",$s1,$s2)
}
if (sfunc.substr($s1,"/") != -1) { // split it up
sfunc.tail($s1,"/",$s2)
sfunc.head($s1,"/",$s1)
}
}
//** dirname(full,path) filname(full,file) splits up path/file
// eg filname("/home/billl/nrniv/thal/params.hoc",temp_string_)
// temp_string_ => params.hoc
proc dirname () { sfunc.head($s1,"[^/]+$",$s2) }
proc filname () { local ii,cnt
cnt = 0
$s2=$s1 while (sfunc.tail($s2,"/",$s2) != -1) cnt += 1
$s2=$s1 for ii=1,cnt sfunc.tail($s2,"/",$s2)
}
//** file_with_dot(filename,result,scratch): put .filename into result
proc file_with_dot() {
if (sfunc.substr($s1,"/") == -1) {
sprint($s2,".%s",$s1)
} else {
sfunc.tail($s1,".*/",$s3)
sfunc.head($s1,"/[^/]+$",$s2)
sprint($s2,"%s/.%s",$s2,$s3)
}
}
//** find_secname(variable,result): put secname into result
proc find_secname() {
sfunc.head($s1,"\.[_a-z]+$",$s2) // strip off stuff after terminal .
if ( strm($s1,"\.[_a-z]+[(][0-9.]+[)]$")) { // form eg v(0.5)
sfunc.head($s1,"\.[_a-z]+[(][0-9.]+[)]$",$s2)
} else if (isit($s2)) { // the the stem an obj
XO.get_loc() // isit sets XO
sectionname($s2)
pop_section()
} else {
printf("grvec.hoc:f_s ERR0: Can't find sec: %s\n",$s1) err()
}
if (sfunc.len($s2)==0) { printf("grvec.hoc:f_s ERR: %s\n",$s1) err() }
}
//** mkmenu(title,action,proc) makes a menu from printlist
proc mkmenu () { local ii
xmenu($s1)
for ii=0,printlist.count-1 {
sprint(temp_string_,"%s %s",$s2,printlist.object(ii).var)
sprint(temp_string2_,"%s(%d)",$s3,ii)
xbutton(temp_string_,temp_string2_)
}
sprint(temp_string_,"mkpanel(\"%s\",\"%s\",\"%s\")",$s1,$s2,$s3)
xbutton("Leave up",temp_string_)
xmenu()
}
//** mkpanel(title,action,proc) makes a panel from printlist
proc mkpanel () { local ii
sprint(temp_string_,"%s:%s",simname,$s1)
xpanel(temp_string_)
for ii=0,printlist.count-1 {
sprint(temp_string_,"%s %s",$s2,printlist.object(ii).var)
sprint(temp_string2_,"%s(%d)",$s3,ii)
xbutton(temp_string_,temp_string2_)
}
xpanel()
}
//** drline(x0,y0,x1,y1,OPT graph)
proc drline () {
if (numarg()==0) { print "drline(x0,y0,x1,y1,OPT graph)"
return }
if (numarg()>4) { graphItem = $o5 }
graphItem.beginline(panobj.color,panobj.line)
graphItem.line($1,$2)
graphItem.line($3,$4)
graphItem.flush()
}
//** seevec(varname,min,max) -- uses a stringmatch to find a particular vector
proc shprl () {
if (numarg()==1) {
print panobjl.object($1).filename
for ltr(XO,panobjl.object($1).llist) print i1," ",XO.name
} else for ltr(XO,printlist) print i1," ",XO.var,XO.vec,XO.tvec
}
proc remprl () { local flag
flag=0
if (numarg()==2) flag=1 else print "LISTING ONLY; rerun with 2 args to remove"
for (ii=printlist.count-1;ii>=0;ii-=1) {
XO=printlist.object(ii)
if (strm(XO.var,$s1)) if (flag) printlist.remove(ii) else print XO.var
}
}
//** seevec(regexp,flag)
// flag: 1 savevec, 2 save sections
proc seevec2 () {} // stub
proc seevec () { local min,max,flag,a,b,n
flag=0
if (numarg()==2) flag=$2
if (numarg()==3) { min=$2 max=$3 flag=2 b=a=allocvecs(2) b+=1}
if (flag==1 || flag==2) clrveclist()
for ltr(XO,printlist) {
if (strm(XO.var,$s1)) {
printf("%d %s: %s/%s\n",i1,XO.var,printlist.object(i1).vec,printlist.object(i1).tvec)
if (flag==3) seevec2(XO)
if (flag==1) savevec(XO.vec,XO.tvec)
if (flag==2) {
mso[b].indvwhere(XO.tvec,"()",min,max)
mso[a].index(XO.vec,mso[b])
mso[b].where(XO.tvec,"()",min,max)
savevec(mso[a],mso[b])
}
n+=1
}
}
if (flag==2) dealloc(a)
}
//** file_len(fname): retrieve file length; uses global x
func file_len () {
sprint(temp_string_,"wc %s",$s1)
sassign(temp_string_,temp_string_)
sscanf(temp_string_,"%d",&x)
return x
}
//** count_substr(str,sub): count occurences of substring in str
func count_substr () { local cnt
cnt = 0
while (sfunc.tail($s1,$s2,$s1) != -1) { cnt += 1}
return cnt
}
// for ltr(XO,panobj.glist) { print XO,XO.view_count }
//** xgetargs(panel_name,command,arg1[,arg2,...],defaults)
// eg xgetargs("Random session","newrand","# of patts","patt size ","overlap ","5,33,7")
objref argvl,argv
argvl = new List()
strdef mesg
proc xgetargs () { local i,args
args=numarg()-3 i=numarg()
argv = new Vector(args)
argvl.append(argv)
argv.resize(0)
sprint(temp_string_,"argv.append(%s)",$si)
execute(temp_string_)
if (argv.size!=args) argv.resize(args)
xpanel($s1)
mesg="" xvarlabel(mesg)
for i=3,numarg()-1 {
sprint(temp_string_,"%s.x[%d]",argv,i-3)
xvalue($si,temp_string_)
}
sprint(temp_string_,"xgetexec(\"%s\",%d,%s)",$s2,args,argv)
xbutton($s1,temp_string_)
xpanel()
}
proc xgetexec () { local i,args
args = $2
if ($o3.size!=args) { mesg="Error-close & relaunch panel" return }
sprint(temp_string_,"%s(",$s1)
for i=0,args-2 sprint(temp_string_,"%s%g,",temp_string_,$o3.x[i])
sprint(temp_string_,"%s%g)",temp_string_,$o3.x[i])
// print temp_string_
execute(temp_string_)
}
//** procbutt() put up a single proc in a button
proc procbutt () {
xpanel($s1)
xbutton($s1,$s1)
xpanel(500,500)
}
proc prlclr () {
for ltr(XO,printlist) {
cvode.record_remove(XO.vec)
}
printlist.remove_all
}
// op([obj,list],num) -- create object pointer
proc op () {
if (numarg()==1) { XO=tmpobj.object($1) } else\
if (numarg()==2) { tmpobj=$o1 XO=tmpobj.object($2) } else\
if (numarg()==3) { tmpobj=$o2 $o1=tmpobj.object($3) }
}
// END /usr/site/nrniv/local/hoc/grvec.hoc
//================================================================
//================================================================
// INSERTED /usr/site/nrniv/local/hoc/shape.hoc
// $Id: shape.hoc,v 1.83 2003/09/29 12:35:35 billl Exp $
// load_file("shape.hoc")
objref pls,sh,sl,rvpl,rvp,sec,dl[1]
rvpl = new List() // list of RangeVarPlot's
d=0
proc newshp () {
objref sh
forall ifsec "soma" distance()
sh = new Shape()
sh.color_all(1)
sh.menu_tool("test", "p")
sh.exec_menu("test")
}
//* template TRE
begintemplate TRE
public sec,xv,dv,min,max,iv,n,ypv,xpv,zpv,sf,par,chl,codes,name,i
objref sec,xv,dv,ypv,xpv,zpv,chl,codes
double min[1],max[1],n[1],sf[1],par[1],i[1]
strdef name
proc init () {
sec=new SectionRef()
name=secname()
par=-1
xv=new Vector(0) dv=xv.c ypv=xv.c xpv=xv.c zpv=xv.c chl=xv.c codes=xv.c
sf=0
if (issection(".*soma.*")) sf=1
if (issection(".*axon.*")) sf=-1
for (x) { xv.append(x)
dv.append(distance(x))
if (n3d()>0) {
xpv.append(x3d(int(x*(n3d()-1))))
ypv.append(y3d(int(x*(n3d()-1))))
zpv.append(z3d(int(x*(n3d()-1))))
}
}
min=distance(0) max=distance(1)
n=xv.size-1
}
iterator iv () { local ii
sec.sec {
for ii=0,n {
if (numarg()>=2) { $&1=xv.x[ii] $&2=dv.x[ii] }
if (numarg()>=3) $&3=ypv.x[ii]
if (numarg()>=4) $&4=xpv.x[ii]
if (numarg()==5) $&5=zpv.x[ii]
iterator_statement
}
}
}
endtemplate TRE
// trifsec(TRE_list,string)
proc trifsec () {
for ltr(XO,$o1) XO.sec.sec if (strm(secname(),$s2)) YO=XO
if (isassigned(YO)) XO=YO else print $s2," not found"
}
// trifloc(TRE_list,code) -- looks for that code
func trifloc () { local flag,ret,loc
flag=1 loc=$2
for ltr(XO,$o1) if (flag) for vtr2(&x,&y,XO.codes) if (x==loc) { flag=0 ret=y YO=XO}
XO=YO
return ret
}
// trl(XO,TRE_list,regexp)
iterator trl () { local ii,flag
flag=0
for ii=0,$o2.count-1 {
$o1=$o2.object(ii)
if (strm($o1.name,$s3)) $o1.sec.sec {
flag+=1
iterator_statement
}
}
if (!flag) print $s3," not found (trl)"
if (flag>1) printf("%s matched %d secs (trl)\n",$s3,flag)
}
//** trm(XO,TRE_list,str) same as trl() except string-match is exact
iterator trm () { local ii,flag
flag=0
for ii=0,$o2.count-1 {
$o1=$o2.object(ii)
if (strcmp($o1.name,$s3)==0) $o1.sec.sec {
flag+=1
iterator_statement
}
}
if (!flag) print $s3," not found (trm)"
if (flag>1) printf("%s matched %d secs (trm)\n",$s3,flag)
}
//* trunc() build a database of distances throughout tree
// trunc(seclist,list)
proc trunc () { local flag,ii
$o2.remove_all
if (isassigned($o1)) {
tmpobj=$o1
forsec tmpobj ifsec "soma" distance()
forsec tmpobj $o2.append(new TRE())
} else {
forall ifsec "soma" distance()
forall $o2.append(new TRE())
}
// second pass sets up children and parents
for ltr(XO,$o2) {
XO.i=i1
if (XO.sec.has_parent) {
XO.sec.parent tstr=secname()
flag=1
for ltr(YO,$o2,&y) if (flag) {
if (strcmp(tstr,YO.name)==0) {
XO.par=y flag=0 } // break
}
}
for ii=0,XO.sec.nchild-1 {
XO.sec.child(ii) tstr=secname()
flag=1
for ltr(YO,$o2,&y) if (flag) {
if (strcmp(tstr,YO.name)==0) {
XO.chl.append(y) flag=0 } // break
}
}
}
}
//* trak(mainLIST,LOC,outputLIST) -- track() rewritten to use TRE statt seclist
// give location as a regular expression for strm()
// puts the indices for the track into vec
proc trak () {
$o3.remove_all
for trl(XO,$o1,$s2) {
$o3.append(XO)
while (XO.par>-1) { // till reach soma
XO=$o1.object(XO.par)
$o3.append(XO)
}
}
}
//* bktrak(mainLIST,LOC,dist) -- back track for dist distance
// func returns index with associated TRE in XO
// eg bktrak(dl[ee],"\\[21",100) returns 3 then XO.xv.x[3] is closest
func bktrak () { local dist,loc,flag,ret
dist=$3 flag=1
for trl(XO,$o1,$s2) {
loc = XO.dv.max-dist // location being sought
if (loc<0) { print "bktrak ERR1: too far" flag=0 ret=-1}
while (flag) { // till reach soma
if (loc>=XO.dv.min && loc<=XO.dv.max) {
flag=0 ret=closest(XO.dv,loc) YO=XO
}
if (XO.par==-1) {flag=0 ret=-1}
XO=$o1.object(XO.par)
}
}
XO=YO
return ret
}
//* track from recording site down to soma
// start at location with sec=new SectionRef()
proc track () {
$o1.remove($o1)
sec = new SectionRef()
sec.sec $o1.append()
while (sec.has_parent) {
sec.parent sec = new SectionRef()
if (sec.has_parent) sec.sec $o1.append()
}
}
//* prune(SECLIST,NUM,NEWSECLIST) grab NUM separated sections from SECLIST and add to NEWSECLIST
proc prune () { local sum,ii,jj,n,skp,keep
n=$2 sum=0
forsec $o1 sum+=1
skp=int(sum/(n+1))
printf("Keeping every %d of %d secs in %s\n",skp,sum,$o1)
ii=0 jj=0 keep=skp
forsec $o1 {
if (ii==keep && jj<n) {
$o3.append()
print "Keeping ",secname()
keep+=skp
jj+=1 // counter for those kept
}
ii+=1 // counter through SECLIST
}
}
// for dsr(DISTLIST)
// eg for dsr(list) gmax_kdr(dix)=dis/max * val
// dis will be distance and dix will be location on the sec
// distance, location, sec count, seg count
double dis[1], dix[1], secn[1], segn[1]
iterator dsr () {
max=-1
for secn=0,$o1.count-1 if ($o1.object(secn).dv.max>max) max=$o1.object(secn).dv.max
for secn=0,$o1.count-1 for segn=0,$o1.object(secn).dv.size-1 {
dis=$o1.object(secn).dv.x[segn]
dix=$o1.object(secn).xv.x[segn]
$o1.object(secn).sec.sec { iterator_statement }
}
}
// find the point in the sectionlist that's furthest -- must set distance()
func maxdist () { local max
max=-1e10
forsec $o1 if (distance(1)>max) max=distance(1) // find the end of the list
return max
}
// dcls(SECLIST,TARG)
// eg for dcls(seclist,0.72) printf("%s(%.2f) @ %.2f\n",secname(),i1,distance(i1))
iterator dcls () { local targ,min,max,n,dist,sc
tmpobj=$o1
if (numarg()==3) { max=$3 } else {
max=-1e10
forsec tmpobj if (distance(1)>max) max=distance(1) // find the end of the list
}
targ=$2*max min=1e10 x=0 n=0 // targ is target distance
forsec tmpobj { n+=1 // loop to find closest point
for (x) { // sc=n is sect count, i1=x is seg loc
dist=distance(x)
if (abs(dist-targ)<min) { min=abs(dist-targ) i1=x sc=n }
}}
n=0
forsec tmpobj { n+=1 // count to find the same sec
if (n==sc) {
printf("%s(%.2f) @ %.2f ~ %.2f\n",secname(),i1,distance(i1),targ)
iterator_statement // do something here
}
}
}
//** markloc()
proc markloc () { local colr
if (isobj($o1,"List")) {
if (numarg()==4) colr=$4 else colr=2
$o1.object($2).sec.sec tmpobj=new PointProcessMark($o1.object($2).xv.x[$3])
} else {
if (numarg()==3) colr=$3 else colr=2
$o1.sec.sec tmpobj=new PointProcessMark($o1.xv.x[$2])
}
sh.point_mark(tmpobj,colr)
tmplist.append(tmpobj)
tmpobj=nil
}
//* p()
proc p () { local d, a, l
if ($1 == 2) {
sh.color_all(1)
sh.point_mark_remove()
d = sh.nearest($2,$3)
a = sh.push_selected()
if (a >= 0) {
sh.select()
l=a*(n3d()-1)
sh.erase
XO = new PointProcessMark(0)
sh.point_mark(XO,2)
YO = new PointProcessMark(1)
sh.point_mark(YO,3)
printf("%s(%g): %d,%g,%g,%g,%d\n", secname(), a, l, x3d(l), y3d(l), z3d(l),distance(a))
// printf("%s(%g): %g,%g,%g - %g,%g,%g\n", secname(), a, x3d(0), y3d(0), z3d(0), x3d(n3d()-1), y3d(n3d()-1), z3d(n3d()-1)) // x,y,z coordinates
printf("%s L=%g diam=%g-%g\n",secname(),L,diam(0),diam(1)) // L and diam
// printf("%s: %g -> %g\n", secname(), z3d(0), z3d(n3d()-1)) // z coordinates
// printf("%s d(0)=%g d(1)=%g nseg=%d\n",secname(),distance(0),distance(1),nseg)// distance
pop_section()
}
}
}
//* proc psec -- modified psection()
proc psec () { local d,l
if (numarg()==1) { sprint(tstr,"%s sec = new SectionRef()",$s1)
execute(tstr) } else sec = new SectionRef()
// if (sec.has_parent()) sec.parent sprint(tstr,"%s",secname())
sec.sec printf("%s->%s: %g x %g\n",tstr,secname(),L,diam)
// sec.sec printf("%s->%s: %.2f\n",tstr,secname(),diam)
// sec.sec printf("%g %g %g\n",x3d(0),y3d(0),z3d(0))
// sec.sec printf("%s: %g,%g,%g -> %g,%g,%g\n", secname(), x3d(0), y3d(0), z3d(0), x3d(n3d()-1), y3d(n3d()-1), z3d(n3d()-1))
vec.resize(0)
for ii=0,sec.nchild-1 sec.child[ii] { vec.append(diam(0)) print secname() }
vec.sort
sec.sec printf("%s has %d branches (%.1f): ",secname(),sec.nchild,vec.sum)
vlk(vec)
sec=nil
}
//* move cells around, crm(), translate(), zrotate()
// $o1 is sectionlist for this neuron, $2 is theta in degrees
proc crm () { local theta,ii
if (numarg()==0) {print "crm(SECLIST,ROT_DEG)" return }
tmpobj=$o1
theta = $2
ind.resize(0) vec.resize(0)
forsec tmpobj for ii=0,n3d()-1 { ind.append(x3d(ii)) vec.append(y3d(ii)) }
forsec tmpobj translate(-ind.mean,-vec.mean)
forsec tmpobj zrotate(theta)
}
//** rotate and translate
// zrotate(seclist,theta) OR forsec seclist zrotate(theta)
proc zrotate () { local theta,ii
if (numarg()==2) { // include the list as 1st arg
theta= -$2/360*2*PI // don't know why it is negative here
forsec $o1 for ii=0,n3d()-1 pt3dchange(ii,x3d(ii)*cos(theta) - y3d(ii)*sin(theta),\
y3d(ii)*cos(theta) + x3d(ii)*sin(theta),\
z3d(ii), diam3d(ii))
} else {
theta= -$1/360*2*PI // don't know why it is negative here
for ii=0,n3d()-1 pt3dchange(ii,x3d(ii)*cos(theta) - y3d(ii)*sin(theta),\
y3d(ii)*cos(theta) + x3d(ii)*sin(theta),\
z3d(ii), diam3d(ii))
}
}
//** translate in x,y plane
// translate(seclist,x,y) OR forsec seclist translate(x,y)
proc translate () { local x,y,ii
if (numarg()==2) {
x=$1 y=$2
for ii=0,n3d()-1 pt3dchange(ii,x3d(ii)+x,y3d(ii)+y,z3d(ii), diam3d(ii))
} else {
x=$2 y=$3
forsec $o1 for ii=0,n3d()-1 pt3dchange(ii,x3d(ii)+x,y3d(ii)+y,z3d(ii), diam3d(ii))
}
}
//* graphics -- space plot to graph v from one location to another
//* newspaceplot("SECNAME1","SECNAME2"[,TRE_LIST]) -- 3rd arg optional for back compatability
proc newspaceplot () {
if (numarg()==3) tmpobj=$o3 else tmpobj=dl[ee] // assume location of TRE_LIST
rvp = new RangeVarPlot("v")
rvpl.append(rvp)
for trm(XO,tmpobj,$s1) XO.sec.sec rvp.begin(1)
for trm(XO,tmpobj,$s2) XO.sec.sec rvp.end(1)
rvp.origin(0)
}
//** grspaceplot(g,rvp)
proc grspaceplot () {
$o1.addobject($o2, 2, 1, 0.8, 0.9)
$o1.size(-600,600,-80,40)
$o1.view(-600, -80, 1200, 120, 150, 40, 450, 300)
}
//** drawspace("SECNAME1","SECNAME2",TRE_LIST) will trak from both directions to draw rvp locs on shape
proc drawspace () { local colr
if (numarg()==4) colr=$4 else colr=2
for trm(XO,$o3,$s1) while (XO.par>-1) {
XO.sec.sec sh.color(colr)
XO=$o3.object(XO.par)
}
for trm(XO,$o3,$s2) while (XO.par>-1) {
XO.sec.sec sh.color(colr)
XO=$o3.object(XO.par)
}
sh.flush()
}
//* grdm(cel# or obj,graph,label) graph diameters
proc grdm () { local a,b,cel
cel=$1
g=$o2
a=b=allocvecs(2) b+=1
g.erase
for ltr(XO,dl[cel],&y) if (XO.chl.size==0) {
mso[a].resize(0) mso[b].resize(0)
YO=dl[cel].object(XO.par) // parent
YO.sec.sec {
for vtr(&x,YO.xv) mso[a].append(diam(x))
mso[b].append(YO.dv)
}
XO.sec.sec {
for vtr(&x,XO.xv) mso[a].append(diam(x))
mso[b].append(XO.dv)
}
if (XO.ypv.min<-10) mso[b].mul(-1) // show basal dends
mso[a].line(g,mso[b],y%9+1,2)
}
if (numarg()==3) g.label(0.8,0.8,$s3)
g.size(0,800,0.1,1)
dealloc(a)
}
// END /usr/site/nrniv/local/hoc/shape.hoc
//================================================================
tstop=300
objref ce[4]
//* template SWC
begintemplate SWC
public soma,dend,ndend,name,file,sl
create soma, dend[1]
objref sl
double ndend[1], soma_L[1], soma_diam[1]
strdef name,file
external filname,sfunc
proc init () {
file=$s1
filname($s1,name)
sfunc.head(name,"\\.",name) // strip off the .hoc
xopen(file)
sl=new SectionList()
soma sl.wholetree()
}
endtemplate SWC
for scase("rlgncb54_99jan20.hoc","rlgntc5-10-95.hoc","rlgnI8-4-95.hoc","rlgnti4-13-96.hoc") ce[i1] = new SWC(temp_string_)
proc movece () {
crm(ce[2].sl,270)
translate(ce[2].sl,0,500) // top cell in A , TI
crm(ce[3].sl,90)
translate(ce[3].sl,0,100) // bottom cell in A, TI
crm(ce[0].sl,-90)
translate(ce[0].sl,-50,-180) // top cell in B, TC
translate(ce[1].sl,-30,-400) // bottom cell in B, TC
}
movece()
sh = new Shape()
objref stim[4]
for ii=0,3 ce[ii].soma stim[ii]=new IClamp(0.5)
for ii=0,1 { // TCs
stim[ii].amp=-.05
stim[ii].dur=tstop
forsec ce[ii].sl {
Ra=100 Cm=0.85
insert pas e_pas=-62.7 g_pas=1/30.3e3
v=-62.7
}
}
for ii=2,3 { // TCs
stim[ii].amp=-.0125
stim[ii].dur=tstop
forsec ce[ii].sl {
Ra=70 Cm=1
insert pas e_pas=-54.5 g_pas=1/95.2e3
v=-54.5
}
}
newPlotV()
g=graphItem
g.erase_all
g.size(0,tstop,-90,-50)
for ii=0,3 {
sprint(tstr,"ce[%d].soma.v(0.5)",ii) g.addvar(tstr,ii+1,2)
forsec ce[ii].sl sh.color(ii+1) // match colors on shape
}
tstop=400
cvode_local(1)
v_init=1e4 // prevent v from being reset
run()
// END cells.hoc
//================================================================