Hippocampus temporo-septal engram shift model (Lytton 1999)

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Accession:7400
Temporo-septal engram shift model of hippocampal memory. The model posits that memories gradually move along the hippocampus from a temporal encoding site to ever more septal sites from which they are recalled. We propose that the sense of time is encoded by the location of the engram along the temporo-septal axis.
Reference:
1 . Lytton WW, Lipton P (1999) Can the hippocampus tell time? The temporo-septal engram shift model. Neuroreport 10:2301-6 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Hippocampus;
Cell Type(s):
Channel(s): I Na,t; I K;
Gap Junctions:
Receptor(s): GabaA; AMPA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Pattern Recognition; Temporal Pattern Generation; Spatio-temporal Activity Patterns; Simplified Models;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu];
Search NeuronDB for information about:  GabaA; AMPA; I Na,t; I K;
/
lytton99
README
AMPA.mod
GABAA.mod
kdr.mod
matrix.mod *
naf.mod *
passiv.mod *
pulse.mod *
sinstim.mod *
vecst.mod
vecst.mod.orig
bg.inc *
bg_cvode.inc
boxes.hoc *
declist.hoc *
decvec.hoc *
default.hoc *
directory
fig1.gif
grvec.hoc
init.hoc
ivl.vecs
labels.hoc
loadr.hoc *
local.hoc
mosinit.hoc
net.hoc
netcon.inc
nrnoc.hoc
ovl.vecs
params.hoc *
params.hoc.SAV *
proc.hoc
run.hoc
simctrl.hoc *
spkts.hoc
syncode.hoc
tmpl.hoc
                            
// $Id: grvec.hoc,v 1.220 2002/04/22 15:08:40 billl Exp $

// main panel is 'vecpanel()'
proc grvec () {}
load_file("declist.hoc","declist")  // declare lists
load_file("decvec.hoc","decvec")  // declare vectors
strdef grep // LINUX grep requires -a to handle a binary file 
if (sfunc.substr(osname,"inux")==1) grep="grep -a" else grep="grep"

//* 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,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],vloc[1],vjmp[1]
  objref glist,llist,tvec
  strdef filename,comment
  proc init() {
    if (numarg()==1) filename = $s1
    color=1 line=1 curcol=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)
// 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 () {
    var=$s1
    if (cvode_local()==1) tvec=new Vector($2)
    vec=new Vector($2)
    // NB label is labile
    if (numarg()==3) vec.label($s3) else vec.label("") // use label for friendly name
  }
endtemplate vitem

//* object declarations
objref vite, scob, printlist, panobj, panobjl, szstr[4], tvec
panobj = new panattr(simname)
tvec = panobj.tvec // use as a pointer to the tvec being recorded
panobjl = new List()
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 }
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,$s1)
    printlist.browser(temp_string_,"var")
    sprint($s2,"%s()",$s2)
    printlist.accept_action($s2)
  }
}

//* 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
  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)
//    sprint(temp_string_,"print printlist.object(hoc_ac_).var,\"%s = \",printlist.object(hoc_ac_).vec.%s",recstr,recstr)
    temp_string_ = "\"%s.%s = %g\\n\""
    sprint(temp_string_,"printf(%s,printlist.object(hoc_ac_).var,\"%s\",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_)
  } 
}

//** linkxo2vec([num]) link X0 to vector in printlist, optional arg can be pos or neg
proc linkxo2vec () { 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
}

//** 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
  panobj = panobjl.object(0)  tvec=panobj.tvec
  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($o3)
    printlist.append(vite)
    return
  }
  if (numarg()==2) { // second arg is a vector to store
    vite = new vitem(grvecstr,$o2.size,temp_string2_)
    vite.vec.copy($o2)
    printlist.append(vite)
    return
  }
  if (use_lvardt_) { 
    if (isobj(panobj.tvec,"Vector")) if (panobj.tvec.size!=0) { tvec.resize(0) 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.size==0) { 
      tvec.resize(dur/printStep+10) panobj.tvec.record(&t) }
  } else { 
    if (panobj.tvec.size!=0) { tvec.resize(0) 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)
    sprint(temp_string_,\
           "{cvode.record(&%s,printlist.object(%d).vec,printlist.object(%d).tvec)}",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_)
}

//* 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
      return 0 }
    sprint(temp_string2_,"%s '%s' %s > %s",grep,readtag,filename,xtmp)
    system(temp_string2_)
    tmpfile.close()
    if (! tmpfile.ropen(xtmp)) { print "E2: Can't open ",xtmp," (",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) { // a .file with locs has been written previously
        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 {
          tvec = panobj.tvec
          tvec.resize(0)
          panobj.printStep = -loc // where to find tvec later
        }
      }
    }
  }
  if (panobj.printStep==0) panobj.printStep = printStep
  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 }
  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
  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_,"%s (#%d)",simname,attrnum)
  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_,"%s:%s (#%d)",simname,grvecstr,attrnum)
  xpanel(temp_string_)
  xvarlabel(panobjl.object(attrnum).filename)
  xvarlabel(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)
  xbuttn("Graph limits","wvpanl(")
  xmenu("Manipulate graphs")
  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_,"%s:%s (#%d)",simname,grvecstr,attrnum)
  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)
  xbutton("Clear/Set to G0",temp_string2_)
  xbutton("Clean graph list","collapsegrs()")
  sprint(temp_string2_,"viewplot(%d)",attrnum)
  xbutton("View=plot",temp_string2_)
  xpanel()
}

//* 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=1 else flag=0
  if (flag) { sz1=sz3=1e10 sz2=sz4=-1e10 }
  panobj = panobjl.object($1)
  for ltr(XO,panobj.glist) {
    XO.size(&x[0])
    if (flag) { 
      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 { XO.size(x[0],x[1],x[2],x[3]) }
  }
  if (flag) 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
  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 $o2 gives indices for vectors (see tposvec)
  if (numarg()==2) { vind=1 min=0 max=$o2.size-1 } else vind=0 
  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 () {
  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 {
  panobj.size[0]=$2
  for ltr(XO,panobj.glist) XO.size($2,$3,$4,$5)
  }
}



//* chrange() changes range for a set of graphs (called from attrpanl)
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=0,1 panobj.size[ii] += panobj.shift // shift right or left
  // 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) XO.size(panobj.size[0],panobj.size[1],panobj.size[2],panobj.size[3])
    if (flag==-2) XO.size(panobj.size[0],panobj.size[1],sz3,sz4)
  }
  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.printStep < 0) {
    tmpfile.seek(-panobj.printStep)
    panobj.tvec.vread(tmpfile)
    tvec = panobj.tvec
    return 1
  } else {
    return 0
  }
}

//* rv() reads line of vector file into IV graph via vector
// rv(attrnum,llist_ind1[,llist_ind2])
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 (numarg() > 2) { inx2 = $3 } else { inx2 = -1 }
  if (attrnum==0) { gv(inx) return }
  rv_readvec(attrnum,inx,vrtmp)  // will set panobj
  // create a new plot if necessary and set color
  nvplt(vrtmp)
  if (vrtmp.size==0) { // assume this is a spike train in tvec
    ind.resize(panobj.tvec.size) ind.fill(0)
    ind.mark(graphItem,panobj.tvec,"O",panobj.line+4,panobj.curcol)        
    grrtsize()
  } else if (inx2>-1) {
    rv_readvec(attrnum,inx2,vec)
    graphItem.size(0,vrtmp.max,0,vec.max)
    if (numarg() > 3) {
      vec.mark(graphItem,vrtmp,$s4,6,panobj.curcol)
    } else {
      vec.mark(graphItem,vrtmp,"O",6,panobj.curcol)
    }
  } else if (panobj.printStep<0) {
    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) }
    $o3.vread(tmpfile)
    if (panobj.segments>1) {
      tmpvec = new Vector($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"
}

//* 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
}

//* gv(vnum) graphs vector
proc gv () {  local inx
  if (numarg()==0) { inx = hoc_ac_ } else { inx = $1 }
  panobj = panobjl.object(0)
  if (use_lvardt_) { tvec = panobj.tvec = printlist.object(inx).tvec }
  XO = printlist.object(inx).vec
  if (XO.size==0) { // assume that this is spk trace
    if (tvec.size==0) { printf("\tNO SPIKES IN %s\n",printlist.object(inx).var)
    } else {
      newPlot(0,1,0,1)
      ind.resize(tvec.size) ind.fill(1)
      ind.mark(graphItem,tvec,"O",panobj.line+4,panobj.curcol)
      grrtsize()
    }
    return
  } else nvplt(XO)
  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)
}

//* 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 () { graphItem.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,"data/v%s.%02d",datestr,runnum-dec_runnum)
  while (tmpfile.ropen(output_file)) { runnum = runnum+1
    sprint(output_file,"data/v%s.%02d",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,"data/v%s.%02d",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
  if (tmpfile.wopen($s1)==0) { print "Can't open ",$s1  return}
  tmpfile.printf("//: %s\n",$s2) // comment
  if (use_lvardt_) {
    tmpfile.printf("//printStep -2\n")
  } else if (using_cvode_) {
    tmpfile.printf("//printStep -1\n")
  } else {
    tmpfile.printf("//printStep %g\n",printStep)
  }
  if (byte_store) {tmpfile.printf("//CPU %s\n",uname)}
  pvother()
  pvout()
  tmpfile.close()
}

// pvnext() append another printlist set to same file
proc pvnext() { local ii
  if ($1==0) { 
    pvall(comment)
    sprint(output_file,"data/v%s.%02d",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 () {
  if (!use_lvardt_ && using_cvode_) { prvec("tvec",panobjl.object(0).tvec,tvec_bytesize) } // save precise times
  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 (! eqobj(XO.tvec,nil)) 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,"data/v%s.%02d",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)
  } else {
    tmpfile.wopen(output_file)
    tmpfile.printf("//printStep %g\n",printStep)
    tmpfile.printf("//: %s\n",comment)
  }
  if (byte_store) {
    tmpfile.printf("//b%d %s %d %d\n",byte_store,temp_string_,\
                   printlist.object(inx).vec.size,tmpfile.tell())
    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,"data/v%s.%02d",datestr,runnum-dec_runnum)
    while (tmpfile.ropen(output_file)) { runnum = runnum+1 // don't allow an overwrite
      sprint(output_file,"data/v%s.%02d",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)
proc nvplt () { local xs,ys,flag
  flag=0
  if (panobj.super == 0) flag=1
  if (isobj(graphItem,"Graph")) if (graphItem.view_count() == 0) flag=1 
  if (flag) {
    if (panobj.printStep==0) { panobj.printStep=printStep }
    if (panobj.size[1] != 0) { // xmax is set
      newPlot(panobj.size[0],panobj.size[1],panobj.size[2],panobj.size[3])
    } else if (panobj.printStep<0) {
      newPlot(0,panobj.tvec.max,$o1.min,$o1.max)
    } else {
      newPlot(0,$o1.size()*panobj.printStep,$o1.min,$o1.max)
    }
    panobj.glist.append(graphItem)
  }
  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)
}

//** 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)
  }
}

//** 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 seevec () { local min,max,flag
  if (numarg()==3) { min=$2 max=$3 flag=1} else flag=0
  if (numarg()==2) flag=-1
  for ltr(XO,printlist) {
    if (strcmp(XO.var,$s1)==0) {
      printf("printlist.object(%d).vec\n",i1)
      if (flag==0) XO.vec.printf
      if (flag==-1) $o2 = XO.vec
      if (flag==1) {
        vec.resize(max-min+1)
        vec.copy(XO.vec,min,max)
        vec.printf
      } 
      flag = -2
      break
    }
  }
  if (flag!=-2) printf("%s not found.\n",$s1)
}

//** 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)
}

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