Ih tunes oscillations in an In Silico CA3 model (Neymotin et al. 2013)

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Accession:151282
" ... We investigated oscillatory control using a multiscale computer model of hippocampal CA3, where each cell class (pyramidal, basket, and oriens-lacunosum moleculare cells), contained type-appropriate isoforms of Ih. Our model demonstrated that modulation of pyramidal and basket Ih allows tuning theta and gamma oscillation frequency and amplitude. Pyramidal Ih also controlled cross-frequency coupling (CFC) and allowed shifting gamma generation towards particular phases of the theta cycle, effected via Ih’s ability to set pyramidal excitability. ..."
Reference:
1 . Neymotin SA, Hilscher MM, Moulin TC, Skolnick Y, Lazarewicz MT, Lytton WW (2013) Ih Tunes Theta/Gamma Oscillations and Cross-Frequency Coupling In an In Silico CA3 Model PLoS ONE 8(10):e76285 [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): Hippocampus CA3 pyramidal cell; Hippocampus CA3 basket cell; Hippocampus CA3 stratum oriens lacunosum-moleculare interneuron;
Channel(s): I Na,t; I A; I K; I K,leak; I h; I K,Ca; I Sodium; I Potassium;
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA; Glutamate;
Gene(s): HCN1; HCN2;
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON; Python;
Model Concept(s): Oscillations; Brain Rhythms; Conductance distributions; Multiscale;
Implementer(s): Lazarewicz, Maciej [mlazarew at gmu.edu]; Neymotin, Sam [samn at neurosim.downstate.edu];
Search NeuronDB for information about:  Hippocampus CA3 pyramidal cell; Hippocampus CA3 basket cell; GabaA; AMPA; NMDA; Glutamate; I Na,t; I A; I K; I K,leak; I h; I K,Ca; I Sodium; I Potassium; Gaba; Glutamate;
/
ca3ihdemo
readme.txt
CA3ih.mod
CA3ika.mod
CA3ikdr.mod
CA3ina.mod
caolmw.mod *
HCN1.mod
icaolmw.mod *
iholmw.mod
ihstatic.mod
kcaolmw.mod *
kdrbwb.mod *
misc.mod *
MyExp2SynBB.mod *
MyExp2SynNMDABB.mod *
nafbwb.mod *
stats.mod *
vecst.mod *
aux_fun.inc *
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
geom.py
grvec.hoc *
init.hoc
labels.hoc *
local.hoc *
misc.h *
network.py
nqs.hoc *
nrnoc.hoc *
params.py
pyinit.py *
pywrap.hoc
run.py
sim.py
simctrl.hoc *
stats.hoc *
syncode.hoc *
xgetargs.hoc *
                            
//* $Id: grvec.hoc,v 1.672 2011/10/25 16:16:14 billl Exp $

//* Objects argtype: 0:double; 1:obj; 2:str; 3:double pointer
objref g[100],printlist,grv_,panobj,panobjl
strdef symb
symb = "O"
load_file("nqs.hoc")  // declare vectors
gnum=-1
declare("show_panel",1)
obfunc file_with_dot(){} // stubs to declare later, otherwise external barfs
obfunc filname(){} 
obfunc dirname(){}
func file_len(){}
proc tog (){if (numarg()==1) print $&1=1-$&1 else print gvmarkflag=1-gvmarkflag}
proc pvout2 () { }  // stub for manipulating printlist
proc rv2 () { }  // stub for manipulating the vectors before graphing
proc rv3 () { }  // stub for manipulating the label
func setfilt2 () { return 0 }  // stub for setting filter
func dir2mf2() {return 1} // stub for checking whether to include a trace

//* template 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, segs, num, ix, f, ty
  strdef name,f
  double loc[1]
  proc init () { 
    segs=1 ty=4
    if (argtype(5)==0) segs=$5 else if (argtype(5)==2) f=$s5
    name=$s1 size=$2 num=$4
    double loc[segs]
    loc[0] = $3
    ix=-1 // can be used as index if needed
  }
endtemplate vfile_line

//* template 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
tvflag_on=1
begintemplate vitem
  external cvode,tvflag_on,isassigned
  public tvec,vec,name,tvflag,pstep,o,code,resize
  objref tvec,vec,o,this // o not set here but used for Acells
  strdef tstr,name // variable name
  proc init () {
    name=$s1  tvflag=0 pstep=0 code=0
    if (cvode.active()) { if (cvode.use_local_dt()) tvflag=1 else tvflag=-1 }
    if (tvflag_on) tvflag=1
    if (argtype(2)==0) vec=new Vector($2) else if (argtype(2)==1) vec=$o2
    if (argtype(3)==0) { // very sloppy -- what if pstep=1??
      if ($3==1) tvflag=1 else {tvflag=0 pstep=$3} 
    } else if (argtype(3)==1) {
      tvec=$o3
      tvflag=1 // don't create another one
    }
    if (argtype(4)==0) if ($4==1) tvflag=1 else {tvflag=0 pstep=$4}
    if (tvflag==1 && !isassigned(tvec)) tvec=new Vector($2) 
    if (tvflag==-1) {
      sprint(tstr,"if (!isassigned(tvec)) tvec=new Vector(%d)",$2) execute(tstr) 
      sprint(tstr,"%s.tvec=tvec",this) execute(tstr)
    }
  }
  proc resize () {
    vec.resize($1) 
    if (isassigned(tvec)) tvec.resize($1)
    if (numarg()==2) { vec.resize($2)   // typically sizeup and then resize to 0
      if (isassigned(tvec)) tvec.resize($2) }
  }
endtemplate vitem

//* main template: GRV
// the attributes of a particular set of graphs including line colors,
// world coordinates, etc
// glist is a list of all graphs created from this panel
// llist is a list of available names and associated vectors or locations
begintemplate GRV
  public color,line,super,curcol,comment,vecpanel,mesg,tmplist,gxpan
  public glist,oglist,llist,tvec,size,shift,vsz,vjmp,tloc,vloc,remote
  public entries,segments,clear,keepgr
  public read_vfile,rvaltdisp,read_file,grvec,remgrs,clear,record,read_pclamp
  public cpplitem,chgplname,npl,new_pri,prlexp,numovecs,fchooser
  public read_vdotfile,rpanel,panobjl,ddir,filter
  public rlist,rvlist,attrpanl,wvpanl,remgrs,collapsegrs,viewplot,nvwall
  public geall,lblall,relbl,grall,grsel,tposvec,fliptb,setrange,setgrransel,grransel
  public chrange,rv,rv_readvec,rvec,rvl,read_rfile,gv
  public grrtsize,ge,pvall,pvother,pvplist,pvclose,vf2fwf
  public pvnext,pvout,prvec,pv,lpvec,nvplt,apbrowse,apkill
  public newpl,find_secname,mkmenu,dir2pr,dir2mf,read_mf
  public mkpanel,pbrgr,remprl,filename,onum,po,stub,go
  public rvtr,vrdr,prdr,tmpobj,printlist,output_file,attr0,attrnum,s,vite
  public glist,llist,tvec,ind,vec,vrtmp,tmpvec,tf1,tmpobj,apvb,printStep
  public gvmarkflag,gveraseflag,fchooser_flag,byte_store,bst,szstr,regexp,tmpfile
  public magga,mvga,ll,labelm,tstr

  double size[4],vsz[2],wvloc[4],x[4]
  objref glist, oglist, llist, tvec, ind, vec, vrtmp, tmpvec, tf1, tmpobj, apvb, ovb, printlist
  objref vite,scob,printlist,szstr[4],g,this,tmplist,panobj,panobjl,Xo,Yo,tmpfile, gcomms
  strdef comment,recstr,grvecstr,readtag,rvvec_name,grep,tstr,tstr2,ddir,filter
  strdef temp_string_,temp_string2_,output_file,s,filename,mesg,regexp
  external sfunc,osname,vfile_line,vitem,uname,nil,simname,gnum,XO,YO,graphList,isassigned
  external isobj,isit,mso,msoptr,allocvecs,dealloc,tstop,method,cvode,show_panel,rv2,rv3,setfilt2
  external cvode_active,cvode_local,datestr,runnum,i1,graphItem,GRV,strm,objnum,DBL,dir2mf2
  external file_with_dot,count_substr,file_len,filname,dirname,dir,grv_,repl_mstr,pvout2,symb

// list iterator ltr
// usage 'for ltr(YO, tmplist) { print YO }'
iterator ltr () { local i
  ii1=0
  for i = 0,$o2.count-1 {
    $o1 = $o2.object(i)
    iterator_statement
    ii1+=1
  }
  $o1=nil
}

proc init () { local flag,nopan
  flag=1e9
  if (numarg()==1) if (argtype(1)==0) flag=$1 
  if (numarg()==2) if (argtype(2)==0) flag=$2 else printf("2nd arg for GRV should be flag\n")
  nopan=0 color=1 line=1 curcol=1 keepgr=tloc=-1 nvec=bvec=super=0 vjmp=50 entries=1 segments=1
  fchooser_flag=0
  vsz[0] = 300  vsz[1] = 200
  glist = new List()
  tmpfile = new File()
  oglist = glist // save old glist for after superimpose
  llist=new List() gcomms=new List() printlist=llist
  tvec=new Vector(0) ind=tvec.c vec=tvec.c vrtmp=tvec.c tmpvec=tvec.c
  rvvec_name = "vec"
  ddir = "data/"
  printStep=gvmarkflag=gveraseflag=mff=0
  remote=0
  entries=segments=shift=0
  tloc=vloc=vjmp=x=y=luprd=0
  wvloc[0]=50 wvloc[1]=50 wvloc[2]=800 wvloc[3]=150
  onum=objnum(this)

  for ii=0,3 { szstr[ii] = new String() }
  if (sfunc.substr(osname,"inux")==1) grep="grep -a" else grep="grep"
  readtag = "^//[:pbCM ]"  // regexp used to identify header in mixed binary files
  { 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 = 0  // 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
  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
  attr0=0 // default is a panel for reading files
  if (flag==0) { // make a sim-recording panel
    if (numarg()>1) printf("GRV WARNING: creating simpan, ignoring filename\n")
    attr0=1 attrnum=0
    if (! isobj(panobjl,"List")) panobjl = new List() 
    attrnum=panobjl.append(this)-1
    if (attrnum!=0) printf("GRV WARNING: attr0 with attrnum=%d!\n",attrnum)
    if (show_panel) vecpanel()
    sprint(tstr,"printlist=%s.printlist",this)
    execute(tstr)
    sprint(s,"GRV[%d]:%s (sim vecs)",objnum(this),simname)
    return
  }
  panobjl=grv_.panobjl
  attrnum=panobjl.append(this)-1
  if (flag==-2) nopan=1 
  if (flag==-1) { fchooser() // ask user for filename
  } else if (numarg()>=1) {
    if (argtype(1)==2) read_vfile($s1)
  }
  if (!nopan) attrpanl()
}

//** newfile() calls fchooser
proc newfile () { localobj o
  o = apvb
  fchooser() 
  attrpanl()
}

//** bst() selects byte_store
func bst () { 
  if (numarg()>=1) byte_store=$1 
  if (numarg()>=2) tvec_bytesize=$2
  return byte_store 
}

//* attrpanl() gives attributes for a set of graphs
proc attrpanl () { local ii,jj
  sfunc.tail(filename,"data.*/",grvecstr)
  apvb=new VBox() 
  apvb.intercept(1) 
  xpanel(temp_string_)
  xvarlabel(filename)
  if (sfunc.len(mesg)>40) sfunc.left(mesg,40)
  xvarlabel(mesg)
  xvalue("Color(-1=multi)","color",1,"if (color==0) curcol=0",0,1)
  xvalue("Line","line",1,"",0,1)
  xpanel()
  xpanel("",1)
  xbutton("Superimpose: ","tog(&super) if (super==0) gnum=-1 sprint(mesg,\"super=%d\",super)")
  xbutton("Where?","sprimp()")
  xbutton("Restore","glist=oglist sprint(mesg,\"Restore graph list\")")
  xpanel()
  xpanel("",1)
  xbutton("Limits","wvpanl()")
  xbutton("Erase","geall()")
  xbutton("Mark","togmark()")
  if (attr0) xbutton("Panel","pbrgr(\"Graph\",\"gv\")") else {
    xbutton("New file","newfile()") }
  xpanel()
  xpanel("",1)
  xmenu("Graphs")
  xbutton("Erase/redraw","gveraseflag=-(gveraseflag-1) if (gveraseflag==1) super=1 else super=0 sprint(mesg,\"Erase=%d\",gveraseflag)")
  xbutton("Erase graphs","geall()")
  xbutton("Remove graphs","remgrs()")
  xbutton("Clean graph list","collapsegrs()")
  xbutton("Erase axes","setrange(3)")
  xbutton("Draw axes","setrange(0)")
  xbutton("Label graphs","lblall()")
  sprint(tstr,"execute(\"disptray(%d)\")",onum)
  xbutton("Make tray",tstr)
  xbutton("View = plot","for ltr(Xo,glist) Xo.exec_menu(\"View = plot\")")
  xbutton("Crosshair","for ltr(Xo,glist) Xo.exec_menu(\"Crosshair\")")
  xbutton("New view","for ltr(Xo,glist) Xo.exec_menu(\"NewView\")")
  xbutton("Zoom","for ltr(Xo,glist) Xo.exec_menu(\"Zoom in/out\")")
  xbutton("Delete Text","for ltr(Xo,glist) Xo.exec_menu(\"Delete\")")
  xbutton("Move Text","for ltr(Xo,glist) Xo.exec_menu(\"Move Text\")")
  xbutton("Change Text","for ltr(Xo,glist) Xo.exec_menu(\"Change Text\")")
  xmenu()
  // sprint(temp_string_,"remote",attrnum)
  // sprint(temp_string2_,"grall(%d)",attrnum)
  // xvalue("Graph all",temp_string_,0,temp_string2_)
  if (attr0) redo_printlist() else xbutton("Show full panel","rpanel()")
  xpanel()
  apvb.intercept(0) 
  if (attr0) {   sprint(s,"GRV[%d] %s SIM CONTROL",objnum(this),simname)
  } else       { 
    if (sfunc.len(filename)>0) filname(filename,grvecstr)
    sprint(s,"GRV[%d] %s:%s",objnum(this),simname,grvecstr) 
  }
  apvb.map(s)
}

//** sprimp() superimpose on another sim
proc sprimp () {
  super=1
  sprint(tstr,"SUPERIMPOSE %s ON?",s)
  ovb=new VBox() 
  ovb.intercept(1) 
  xpanel(tstr)
  xvalue("Superimpose on Graph[#]","gnum",1)
  for ltr(Xo,panobjl) {
    sprint(temp_string2_,"glist=%s.glist sprint(mesg,\"Using graph list from %s\") ovb.unmap() ovb=nil",Xo,Xo)
    xbutton(Xo.s,temp_string2_)
  }
  xpanel()
  ovb.intercept(0) 
  ovb.map(tstr)
  ovb.dismiss_action("ovb.unmap ovb=nil")
}

//** fchooser() finds file and then create panel from it using rpanel
proc fchooser () { 
  if (fchooser_flag == 0) {  // create panel first time only
    if (setfilt2(filter)) { // do nothing
    } else if (strm(filter,"\\*")) { // do nothing
    } else sprint(filter,"*%s*",datestr)
    tmpfile.chooser("","Read from a file",filter,"Open","Cancel",ddir)
  }
  fchooser_flag = 1
  if (tmpfile.chooser()) {
    // find out whether this is a vector file or not
    tmpfile.getname(filename)
    if (strm(filename,"\.mf")) read_mf() else read_vfile() 
  }
}

//** newpan() create a new panel and call fchooser from there
proc newpan () { tmpobj=new GRV(-1) }

//** read_vfile() 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()>=2) if (strcmp(filename,$s1)==0) return 2 // check if file is already active 
  if (attr0) {
    if (!boolean_dialog("Look at file data instead of sim?","YES","NO")) {
      printf("Read file cancelled\n")
      return 0
    }
  } else { attr0=0 }
  if (numarg()>=1) filename=$s1 else tmpfile.getname(filename)
  if (strm(filename,"\.mf$")) return read_mf(filename)
  sprint(s,"GRV[%d] %s: %s",objnum(this),simname,filename)
  clear()
  // grab hold of the different lines using grep
  file_with_dot(filename,temp_string_) // put .filename into temp_string_
  if (!tmpfile.ropen(temp_string_)) {
    print "E1: Can't open ",temp_string_ // avoid grep error
    return 0
  } else flag = 1 // signifies that .file exists to use as key
  while ((numr = tmpfile.gets(tstr)) != -1) {  // throw out the leading '//'
    // read the line
    if (sfunc.head(tstr,"//[^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 (flag && entries > 1) { // a .file with MULTI segs
        tmpfile.seek(-numr,1) // backup to beginning of line
        read_vdotfile()
      } else if (segments > 1) { // mult segs: different times for same var
        tmpfile.seek(-numr,1) // backup to beginning of line
        segments = read_vsegs() //**** NEEDS to be recovered from grvec.hoc442
      } else {  // read each line in for itself
        if (  sscanf(tstr,"//b%1ld %g %s %ld %ld",&bvec,&nvec,tstr2,&sze,&loc)!=5) {
          if (sscanf(tstr,"//b%1ld %s %ld %ld",&bvec,tstr2,&sze,&loc)!=4) {
            printf("**** GRV read_vfile() parse ERR on %s in %s",tstr,filename)
          } else if (printStep==-2) nvec=-2 else nvec=-1 // guess
        }
        if (nvec==2) {
          printf("read_vfile forward compat. **** WARNING ****\n\t****consider edit of %s dot file to change 2 to -2\n",filename)
          nvec=-2
        }
        if (strcmp(tstr2,"CVODE1.0 tvec")==0) {
          tvec.resize(0)
          printStep=-1
          tloc = loc // where to find tvec later
        } else {
          tmpobj = new vfile_line(tstr2,sze,loc,nvec) // name size loc num
          tmpobj.ty=bvec
          llist.append(tmpobj)
          tmpobj = nil
        }
      }
    }
  }
  if (llist.count==0) {
    printf("grvec.hoc::read_vfile ERR no vecs read from %s\n",filename)}
  if (entries==1) entries = llist.count
  if (! flag && segments>1) write_vsegs()  // create key .file
  if (! tmpfile.ropen(filename)) { print "E3: Can't open ",filename
    return 0
  }
  if (printStep==-1) rtvec() // code for cvode_active()
  mff=0
  return 1
}

//** rtvec() reads tvec if it exists, returns -1 if it doesn't
func rtvec () {
  if (tloc > -1) {
    tmpfile.seek(tloc)
    tvec.vread(tmpfile)
    return 1
  } else {
    return 0
  }
}

proc write_vsegs () { print "NEEDS to be ported from grvec.hoc442" }

//** read_vinfo()
proc read_vinfo () {
  if (strm(tstr,"//printStep")) {
    sfunc.tail(tstr," ",tstr) // just take end of string following space
    sscanf(tstr,"%g",&printStep) // printstep==-1 means cvode
  } else if (strm(tstr,"^//:")) { // a comment
    sfunc.tail(tstr,"//: *",tstr)
    sfunc.head(tstr,"\n",comment) // chop final newline
    mesg=comment
  } else if (strm(tstr,"^//CPU")) { // the machine type for byte storage
    sfunc.tail(tstr," ",tstr)
    if (! strm(tstr,uname)) {
      printf("%s written from %s\n",filename,tstr)
    }
  } else if (strm(tstr,"^//MULTI")) { // multiple lines for each entry
    sfunc.tail(tstr," ",tstr)
    if (sscanf(tstr,"%d %d",&entries,&segments)==2) {
      if (! multi_files) printf("**************** GRV read_vinfo ERRa\n") 
    } else segments=1
  } else {
    printf("Line:\t%s\n\tnot recognized in %s\n",tstr,filename)
  }
}

//** read_vdotfile() read .file in abbreviated format (see write_vsegs)
proc read_vdotfile() { local loc,entries,segments,ii
  entries=entries segments=segments
  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
    llist.append(tmpobj)
    for ii=1,segments-1 { tmpobj.loc[ii] = tmpfile.scanvar() }
  }
}

//** rpanel() creates a panel from information in llist
proc rpanel () { local ii
  if (llist.count > 8) { rlist() return }
  sprint(temp_string_,"%s ",simname)
  xpanel(temp_string_)
  xlabel(filename)
  for ii=0,llist.count-1 {
    sprint(temp_string2_,"rv(%d)",ii)
    xbutton(llist.object(ii).name,temp_string2_)
  }
  xbutton("Attributes","attrpanl()")
  sprint(temp_string_,"lpvec(filename,vrtmp,%g)",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 () {
  sprint(tstr,"%d items on list: Enter regexp for subset or \"All\"",llist.count)
  if (llist.count>50 || numarg()>=1) {
    if (numarg()>=1) regexp=$s1 else if (!string_dialog(tstr,regexp)) return
    if (! strm(regexp,"[Aa][Ll][Ll]")) {
      if (! isobj(tmplist,"List")) tmplist = new List()
      tmplist.remove_all
      for ltr(Xo,llist) {
        Xo.ix=ii1
        if (strm(Xo.name,regexp)) tmplist.append(Xo)
      }
      tmplist.browser(filename,"name")
      tmplist.accept_action("rv(tmplist.object(hoc_ac_).ix)")
      printf("%d selected\n",tmplist.count)
      return
    }
  }
  llist.browser(filename,"name")
  llist.accept_action("rv(hoc_ac_)")
}

//** rvlist(): like rpanel() but puts up a browser list instead of a panel
proc rvlist () { local flag,rdstr
  rdstr = 1
  flag = $1
  if (numarg()==2) { recstr=$s2  rdstr=0 }
  if (flag==0) {
    llist.browser(filename,"name")
    llist.accept_action("rvec(hoc_ac_)")
  } else if (flag==1) { // proc(vec)
    if (rdstr) string_dialog("Procedure name: proc, called as proc(vec)",recstr)
    llist.browser(recstr,"name")
    sprint(temp_string_,"rv_readvec(hoc_ac_,%s) execute1(\"%s(%s)\")",rvvec_name,recstr,rvvec_name)
    llist.accept_action(temp_string_)
    print ":",recstr,":",temp_string_,":",rvvec_name
  } else if (flag==2) { // vec.command
    if (rdstr) string_dialog("comm: print vec.comm",recstr)
    llist.browser(recstr,"name")
    sprint(temp_string_,"{rvec(hoc_ac_) print %s.%s}",rvvec_name,recstr)
    llist.accept_action(temp_string_)
  }
}

//* rv() reads line of vector file into IV graph via vector
// rv(llist_ind1[,llist_ind2])
// rvaltdisp(tvec,vec,name)
func rvaltdisp () { return 0 } // if returns 1 means there is an alternate display for rv
obfunc rv () { local inx,inx2 localobj o
  // open the file and go to correct position
  if (numarg() == 0) { print "rv(ind1,ind2) reads into vrtmp bzw vec" return this}
  inx = $1
  if (attr0) {return gv(inx)}
  o=llist.object(inx)
  if (numarg()>1) inx2 = $2 else inx2 = -1 // to graph one vec against another 
  rv_readvec(inx,vrtmp)
  rv2(vrtmp,tvec)
  // create a new plot if necessary and set color
  if (vrtmp.size==0) { // assume this is a spike train in tvec
    nvplt(ind,vrtmp)
    ind.resize(tvec.size) ind.fill(0)
    ind.mark(graphItem,tvec,symb,line,curcol)
  } else if (inx2>-1) { // only make sense if they share the same tvec
    rv_readvec(inx2,vec)
    nvplt(vec,vrtmp)
    if (numarg() >= 3) {
      vec.mark(graphItem,vrtmp,$s3,line,curcol)
    } else {
      vec.mark(graphItem,vrtmp,symb,line,curcol)
    }
  } else if (o.num==-2) {
    nvplt(vrtmp,tvec)
    if (gvmarkflag) {
      if (! rvaltdisp(tvec,vrtmp,llist.object(inx).name)) {
        vrtmp.mark(graphItem,tvec,symb,line,curcol,4) }
    } else vrtmp.line(graphItem,tvec,curcol,line)
  } else if (o.num==-1) {
    printf("rv() PROBLEM: CVODE global read not implemented\n")
  } else {
    if (o.num==0) {
      printf("rv WARNING: taking printstep %g for %s\n",printStep,o.name)
      o.num=printStep
    }
    nvplt(vrtmp,o.num)
    if (gvmarkflag) {
           vrtmp.mark(graphItem,o.num,symb,line,curcol,4)
    } else vrtmp.line(graphItem,o.num,curcol,line)
  }
  // too much fussing with labels
  if (sfunc.substr(filename,"batch")!=-1 || \
      sfunc.substr(filename,"data")==-1) {
    grvecstr = filename
    } else sfunc.tail(filename,"data",grvecstr)
  if (sfunc.len(llist.object(inx).name)>40) {
    grvecstr=llist.object(inx).name } else {
    sprint(grvecstr,"%s:%s",grvecstr,llist.object(inx).name) }
  rv3(grvecstr)
  if (super == 0 && labelm) { graphItem.label(0,0.9,grvecstr)
  } else if (labelm) graphItem.label(0.0,0.95,grvecstr)
  return graphItem
}

//* gv(vnum) graphs vector
obfunc gv () {  local a,inx,lin localobj o,v1,vtmp
  inx=-1
  lin=line
  a=allocvecs(vtmp)
  if (numarg()==0) { inx = hoc_ac_ } else { 
    if (argtype(1)==0) inx = $1
    if (argtype(1)==2) {
      for ltr(Xo,printlist) if (strm(Xo.name,$s1)) inx=ii1
      if (inx==-1) {print $s1," not found" return this}}
  }
  if (numarg()>=2) { color=curcol=$2 }
  if (numarg()>=3) { lin=$3 }
  o = printlist.object(inx)
  vtmp.copy(o.vec)
  rv2(o.vec) // alters vtmp
  if (o.vec.size==0) { // assume that this is spk trace
    if (o.tvec.size==0) { printf("\tNO SPIKES IN %s\n",printlist.object(inx).name)
    } else {
      nvplt(o.tvec)
      ind.resize(o.tvec.size) ind.fill(1)
      ind.mark(graphItem,o.tvec,symb,lin,curcol)
    }
  } else { 
    if (o.tvflag!=0) { // o.tvec should point to tvec if tvflag==-1
      nvplt(o.vec,o.tvec)
      if (gvmarkflag) { o.vec.mark(graphItem,o.tvec,symb,lin,curcol)
      } else {          o.vec.line(graphItem,o.tvec,curcol,lin) }
    } else {
      if (o.pstep==0) {
        printf("gv WARNING: vitem.pstep not set with tvflag==0 (%s)\n",o)
        o.pstep=printStep
      }
      nvplt(o.vec,o.pstep)
      if (gvmarkflag) { o.vec.mark(graphItem,o.pstep,symb,lin,curcol)
      } else {          o.vec.line(graphItem,o.pstep,curcol,lin) }
    }
    if (labelm) {
      grvecstr=printlist.object(inx).name
      rv3(grvecstr) graphItem.label(0.,0.9,grvecstr) 
    }
  }
  o.vec.copy(vtmp) // in case has been changed by rv2()
  dealloc(a)
  return graphItem
}


// go(n) will goto location in the data file
obfunc go () { localobj o
  if (argtype(1)==0) { inx=$1 o=llist.object(inx) } else o=$o1
  tmpfile.seek(o.loc)
  return o
}

// rv_readvec(index,vec)
// read vector #index from file into vector vec
func rv_readvec () { local inx,ii,n,bvec localobj o
  if (argtype(1)==0) { inx=$1 o=llist.object(inx) } else o=$o1
  n=o.num
  if (mff) {tstr=filename filename=o.f}
  tmpfile.getname(temp_string_) // may not be necessary?
  if (strcmp(temp_string_,filename)!=0 || tmpfile.isopen()==0) { // don't reopen file if there
    if (! tmpfile.ropen(filename)) {
      print "ERROR rv() can't read ",filename 
      return 0
    }
  }
  tmpfile.seek(o.loc)
  bvec=o.ty
  if (numarg()>=3) { 
    if (n!=-2) {
      printf("ERROR rv() called with 2 vecs but only find 1 in %s %s %d\n",filename,o.name,inx)
      return 0
    }
    if (bvec>5) {
      $o2.fread(tmpfile,o.size,bvec-5) $o3.fread(tmpfile,o.size,bvec-5) 
    } else {
      $o2.vread(tmpfile) $o3.vread(tmpfile) 
    }
  } else if (n==-2) {
    if (n==-2) {
      if (bvec>5) {
        tvec.fread(tmpfile,o.size,bvec-5) // no error check
      } else if (!tvec.vread(tmpfile)) {
        printf("rv_readvec tvec READ failure in %s %s %d\n",filename,o.name,inx) return 0 }
      if (bvec>5) {
        $o2.fread(tmpfile,o.size,bvec-5) // no error check
      } else  if (! $o2.vread(tmpfile)) {
        printf("rv_readvec vec READ failure in %s %s %d\n",filename,o.name,inx) return 0 }
    }
    if (n==-2 && (tvec.size != $o2.size)) {
      printf("rv_readvec size mismatch in %s %s %d\n",filename,o.name,inx)
      return 0
    }
  } else $o2.vread(tmpfile) // fixed dt
  if (segments>1) { // needs rewrite
    tmpvec = new Vector($o2.size)
    for ii=1,segments-1 {
      tmpfile.seek(llist.object(inx).loc[ii])
      tmpvec.vread(tmpfile)
      $o2.copy(tmpvec,$o2.size)
    }
    tmpvec = nil
  }
  if (mff) filename=tstr // restore
  return n
}

//** vf2fwf() take a file in vformat and prints out as multiple fwrites
proc vf2fwf () { local ii localobj f
  f=new File()
  f.wopen($s1)
  for ii=0,entries-1 {
    rv_readvec(ii,vrtmp)
    vrtmp.fwrite(f)
    printf("%d ",vrtmp.size)
  }
  f.close
  printf("\n dt=%g\n",printStep)
}

//** rvec(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,on
  flag=0
  if (sfunc.len(rvvec_name)==0) flag=1
  if (numarg()<1) on=hoc_ac_ else on=$1
  if (numarg()>1) sprint(rvvec_name,"%s",$o2)
  if (sfunc.len(rvvec_name)==0) rvvec_name=llist.object(on).name 
  printf("Copying %s to %s\n",llist.object(on).name,rvvec_name) 
  sprint(temp_string_,"%s.rv_readvec(%d,%s)",this,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(tvec)
}

//** rvl() reads line of vector file into IV graph via vector
// rvl(name,pos[,pos2,pos3,etc])
proc rvl () { local i
  // open the file and go to correct position
  tmpfile.getname(temp_string_)
  if (strcmp(temp_string_,filename)!=0 || tmpfile.isopen()==0) {
    tmpfile.ropen(filename) }  // only open if necessary
  if (tmpfile.isopen==0) { printf("ERROR: %s not found.\n",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,printStep,curcol,line)
  // graph it and label the graph
  if (sfunc.substr(filename,"batch")!=-1) { grvecstr = filename
  } else { sfunc.tail(filename,"data",grvecstr) }
  sprint(grvecstr,"%s:%s",grvecstr,$s2)
  if (super==0 && labelm) { graphItem.label(0,0.9,grvecstr)
  } else if (labelm) graphItem.label(grvecstr)
}

//* utility programs (not all used or even all usable)
//** nvplt() put up new voltage plot
obfunc nvplt () { local xs,ys,flag,prstep
  prstep=10
  if (super == 0) flag=1 else {
    if (gnum>-1) {
      sprint(tstr,"{Graph[%d]}",gnum)
      if (execute1(tstr,0)) { // Graph[gnum] exists
        if (Graph[gnum].view_count>0) { 
          graphItem=Graph[gnum] flag=0
        }               
      } 
    } else if (isobj(graphItem,"Graph")) if (graphItem.view_count() > 0) { 
      flag=0
    } else { flag=1 }                   // else need new graph
  }
  if (flag) {
    if (numarg()==2) if (argtype(2)==0) prstep=$2 else prstep=-1
    if (size[1] != 0) { // xmax is set
      newpl(size[0],size[1],size[2],size[3])
    } else if (prstep<0) {
      newpl(0,$o2.max,$o1.min,$o1.max)
    } else {
      newpl(0,$o1.size()*prstep,$o1.min,$o1.max)
    }
  } else if (gveraseflag) graphItem.erase_all
  if (color == -1) {
    curcol += 1
    if (curcol == 0 || curcol>7) curcol = 1 
  } else curcol = color
  graphItem.color(curcol)
  g=graphItem
  return g
}

//** 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])
}

//** newpl()
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) 
  g=graphItem
  graphItem.xaxis()	// view axis for x and y
  graphItem.view($1,$3,$2-$1,$4-$3,wvloc[0],wvloc[1],wvloc[2],wvloc[3])
  glist.append(graphItem)
}

//** find_secname(variable,result): put secname into result
proc find_secname () { localobj o
  if ((sfunc.head($s1,"\.[_A-Za-z0-9]+$",$s2))==0) { // strip off stuff after terminal .
    printf("grvec.hoc:find_secname ERR: no section found: %s\n",$s1) err() }
  if (    strm($s1,"\.[_A-Za-z0-9]+[(][0-9.]+[)]$")) {  // form eg v(0.5)
    sfunc.head($s1,"\.[_A-Za-z0-9]+[(][0-9.]+[)]$",$s2)
  } else {
    o=isit($s2)
    if (o.x) {  // the stem is an obj
    o.o.get_loc() 
    sectionname($s2)
    pop_section()
    } else {
      printf("grvec.hoc:f_s ERR0: Can't find sec: %s\n",$s1) err() 
    }
  }
}

//** vecpanel() main panel
proc vecpanel () {
  if (! attr0) {printf("vecpanel (main panel) can only be run from attr0\n") return }
  fchooser_flag = 0  // used to initialize the file chooser
  sprint(temp_string_,"%s Vectors",simname)
  xpanel(temp_string_)
  xbutton("Graph from file","newpan()")
  xbutton("Sim vectors","pbrgr(\"Graph\",\"gv\")")
  xbutton("Sim attributes","attrpanl(0)")
  xbutton("Save Sim","pvall()")
  xbutton("Panels","apbrowse()")
  redo_printlist()
  xpanel()
}

//** 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")
}

//** remgrs() -- clears glist
proc remgrs () { local ii
  for ltr(Xo,glist) Xo.unmap
  if (keepgr!=-1) {
    for (ii=glist.count-1;ii>0;ii-=1) glist.remove(ii) // leave #1
  } else glist.remove_all
}

//** clear() -- clears llist
proc clear () {
  entries=1 segments=1
  comment = ""
  llist.remove_all()
}

//** ll() same as external llist
proc ll () { 
  if (numarg()==1) {
    if (attr0==1) { for ltr(XO,printlist) if (strm(XO.name,$s1)) print ii1,XO.name,XO.vec.size
    } else          for ltr(XO,llist) if (strm(XO.name,$s1)) print ii1,XO.name,XO.size
  } else {
    if (attr0==1) { for ltr(XO,printlist) print ii1,XO.name,XO.vec.size
    } else          for ltr(XO,llist) print ii1,XO.name,XO.size
  }
}

//* read_pclamp(file,vscale,tscale): read physiol data file, similar to read_file()
proc read_pclamp () { local ii,cols,pt,length,pstep,tscale,vscale
  if (! tmpfile.ropen($s1)) { printf("\tERROR: can't open file \"%s\"\n",$s1) }
  if (numarg()>=2) vscale=$2 else vscale=1
  if (numarg()>=3) tscale=$3 else tscale=1e3
  printlist.remove_all()
  method("implicit") printStep=0.1
  tmpfile.gets(temp_string_)  
  length=1
  while (! strm(temp_string_,"^\"Time")) {
    length += 1
    tmpfile.gets(temp_string_)  // first word in line was not a number so next line
  }
  temp_string2_ = temp_string_ // column def line
  cols = count_substr(temp_string_,"[(]") // destructive function
  pt = tmpfile.tell()
  length = file_len($s1) - length
  vrtmp.scanf(tmpfile,length,1,cols) // tvec
  pstep=vrtmp.x[1]-vrtmp.x[0]
  pstep*=tscale // typically gives it in s statt ms
  print "Reading ", cols, " columns; ", length, " lines; tstep=",pstep
  for ii=2,cols { // pick up all of the columns
    tmpfile.seek(pt)
    vrtmp.scanf(tmpfile,length,ii,cols)
    vrtmp.mul(vscale) // correct for a common scaling
    npl("col",ii,vrtmp,pstep)
  }
  if (1) {
    sprint(temp_string2_,"%s:%s",$s1,temp_string2_)
    file_with_dot($s1,filename,"v") // put vfilename into name
    print "Saving to ",filename
    pvplist(filename,temp_string2_)
  }
}

//* read_file(file,cols[,length]): read multicolumn file
//  see also read_pclamp() above
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
  }
  printStep=10
  if (cvode_status()!=0) print "WARNING: Turn 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)
    npl("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)
    npl(temp_string_,vrtmp)
  }
}

//* redo_printlist() menu allows removal or addition of inidividual items
proc redo_printlist () {
  xmenu("Printlist")
  xbutton("Save Sim","pvall()")
  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("Archive to file:","pbrgr(\"Archive\",\"pv\")")
  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
  if (! isobj(printlist,"List")) printlist = new List()
  flag = $1  rdstr = 1
  if (numarg()==2) { recstr=$s2  rdstr=0 }
  if (flag==0) {
    if (! isobj(scob,"SymChooser")) scob = new SymChooser()
    if (scob.run()) {
      scob.text(temp_string_)
      npl(temp_string_)
    }
  } else if (flag==1) { // remove item
    printlist.browser("Double click on item to remove","name")
    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_).name,\"%s\",x=printlist.object(hoc_ac_).vec.%s)",temp_string_,recstr,recstr)
    printlist.browser(recstr,"name")
    printlist.accept_action(temp_string_)
  } else if (flag==3) { // put another set of things on list
    if (! isobj(scob,"SymChooser")) scob = new SymChooser()
    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("  npl(\"%s\")\n",printlist.object(ii).name)
      }
      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,"name")
    sprint(temp_string_,"%s(printlist.object(hoc_ac_).vec,printlist.object(hoc_ac_).name,hoc_ac_)",recstr)
    printlist.accept_action(temp_string_)
  } else if (flag==7) { // XO is pointer to vec
    printlist.browser("XO","name")
    sprint(temp_string_,"{tmpobj=printlist.object(hoc_ac_) print hoc_ac_,tmpobj.name XO=tmpobj.vec YO=tmpobj.tvec}")
    printlist.accept_action(temp_string_)
  } 
}

//** 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).name)
    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()
}

//** 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,$s1)
    printlist.browser(temp_string_,"name")
    sprint(temp_string2_,"%s()",$s2)
    printlist.accept_action(temp_string2_)
  }
}

//** 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).name)
    sprint(temp_string2_,"%s(%d)",$s3,ii)
    xbutton(temp_string_,temp_string2_)
  }
  xpanel()
}

//** remprl() -- remove printlist item by name
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.name,$s1)) if (flag) printlist.remove(ii) else print Xo.name
  }
}

// for ltr(XO,glist) { print XO,XO.view_count }

//** wvpanl() 
proc wvpanl () { local  ii
  sfunc.tail(filename,"data.*/",grvecstr)
  sprint(temp_string_,"%s:%s (WVPANL)",simname,grvecstr)
  xpanel(temp_string_)
  sprint(temp_string_,"%d Vectors",llist.count)
  xlabel(temp_string_)
  for ii=0,3 {
     sprint(temp_string_,"size[%d]",ii)
     sprint(temp_string2_,"chrange(%d)",ii)
     xvalue(szstr[ii].s,temp_string_,0,temp_string2_,0,1)
  }
  xvalue("Shift L/R","shift",0,"chrange(-2)",0,1)
  xmenu("Other")
  xbutton("Clear/Set to G0","chrange(-1)")
  xbutton("View=plot","viewplot()")
  xbutton("0,tstop,-90,50","setrange(0,tstop,-90,50)")
  // xbutton("Clean graph list","collapsegrs()")
  xbutton("Attributes","attrpanl()")
  xmenu()
  xpanel()
  if (glist.count>0) for ii=0,3 if (size[ii]==0) size[ii]=glist.object(0).size(ii+1)
}

//** chrange() changes range for a set of graphs (called from attrpanl)
proc chrange () { local cnt, flag, ii, sz1, sz2, sz3, sz4
  if (numarg()==1) { flag = $1 } else { flag = -1 }
  cnt = glist.count()
  for (ii=cnt-1;ii>=0;ii=ii-1) if (glist.object(ii).view_count() == 0) glist.remove(ii)
  cnt = glist.count() // check again after removing any with no views
  if (cnt==0) { for ii=0,3 size[ii]=0 return }
  // flag -1 means set everything from the first graph
  if (flag==-1) for ii=0,3 size[ii] = glist.object(0).size(ii+1)
  if (flag==-2) for ii=0+luprd,1+luprd size[ii] += shift // shift right or left
  if (flag==5) { size[0]=0 size[1]=tstop } // just set x
  // for each of the graphs
  for ltr(Xo,glist) {
    sz1=Xo.size(1) sz2=Xo.size(2) sz3=Xo.size(3) sz4=Xo.size(4)
    if (flag==0) Xo.size(size[0],sz2,sz3,sz4)
    if (flag==1) Xo.size(sz1,size[1],sz3,sz4)
    if (flag==2) Xo.size(sz1,sz2,size[2],sz4)
    if (flag==3) Xo.size(sz1,sz2,sz3,size[3])
    if (flag==-1 || flag==4) Xo.size(size[0],size[1],size[2],size[3])
    if ((flag==-2 && !luprd) || flag==5) Xo.size(size[0],size[1],sz3,sz4)
    if (flag==-2 && luprd) Xo.size(sz1,sz2,size[2],size[3])
  }
  for ii=0,3 if (size[ii]==0) size[ii]=glist.object(0).size(ii+1)
}

//** grall() graphs all of the lines from the file
// use vector $o2 as indices for vectors (see tposvec)
proc grall () { local cnt,ii,min,max,gr,skip,iskp,vind,sind,a
  if (numarg()==0) {printf("grall(min,max,gr_offset,skipgr,iskp]): graph vectors.\n") return }
  sind=vind=0
  cnt = llist.count()
  min=0 max=cnt-1
  // will reset max if is vector with numarg()==2
  // with 2 args, vector $o2 gives indices for vectors (see tposvec)
  if (numarg()>=1) {
    if (argtype(1)==0) { min=$1
    } else { // a vector of indices or a string for prdr/vrdr
      a=allocvecs(1)
      if (argtype(1)==1) { vind=1 mso[a].copy($o1) } else sind=1
    }
  }
  if (numarg()>1) { max=$2 if (max<0) max+=llist.count }
  if (numarg()>2) gr=$3 else gr=0
  if (numarg()>3) skip=$4 else skip=1
  if (numarg()>4) iskp=$5 else iskp=1
  if (iskp==0) iskp=1
  if (super==1 && glist.count==0) { 
    remgrs()
    print "Creating plot"
    skip=0
    newPlot(0,tstop,-100,100) glist.append(graphItem)}
  if (super==0 && glist.count==0) size[1]=0
  if (sind) { 
    // for vrdr(aa,$s2,1,1) aa.x(0).append(ii1)
    vind=1
  }
  if (vind) { min=0 max=mso[a].size-1 }
  for (ii=min;ii<=max;ii+=iskp) {
    if (super == 1) { 
      if (gr >= glist.count()) break
      graphItem = glist.object(gr) 
      gr=gr+skip
    }
    if (vind) rv(mso[a].x[ii]) else rv(ii)
  }
  if (vind) dealloc(a)
}

// go through tmplist selected in rlist and graph onto glist
proc grsel () { localobj o
  for ii=0,tmplist.count-1 {
    rv_readvec((o=tmplist.o(ii)),vrtmp)
    if (ii<glist.count) graphItem=glist.o(ii) else {
      printf("GRV grsel() glist exhausted\n")
      return }
    if (o.num==-2) { // guess should do mark
      vrtmp.mark(graphItem,tvec,symb,line+2,curcol,4)
    } else vrtmp.line(graphItem,o.num,curcol,line)
  }
}    

// 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(x0,x1,y0,y1)
proc setrange () { local i,ii
  if (numarg()==0){print "setrange(x0,x1,y0,y1)\n setrange(3) erases axes"}
  if (numarg()==0) { for ltr(Xo,glist) Xo.size(0,tstop,-100,50)
  } else if (numarg()==1) { for ltr(Xo,glist) Xo.xaxis($1)
  } else if (numarg()==2) { for ltr(Xo,glist) Xo.size(0,tstop,$1,$2)
  } else {
    size[0]=$1
    for ltr(Xo,glist) Xo.size($1,$2,$3,$4)
    for i=1,4 size[i-1]=$i
  }
  for ii=0,3 if (size[ii]==0) size[ii]=glist.object(0).size(ii+1)
}

//* gxpan()
proc gxpan () { local x localobj xo,yo,g1
  gcomms.remove_all
  gcomms.append(new String2("Move","mvga"))
  gcomms.append(new String2("Mag","magga"))
  for ltr(xo,gcomms) for ltr(yo,glist) {
    yo.menu_remove(xo.s)
    yo.menu_tool(xo.s,xo.t)
  }
  gcomms.append(new String2("Crosshair",""))
  xpanel("Manipulate graphs",1)
  x=-1
  for ltr(xo,gcomms) {sprint(tstr,"mvgaset(%d)",x+=1) xradiobutton(xo.s,tstr)}
  xpanel()
}  

proc mvgaset () { localobj yo
  print $1,gcomms.o($1).s
  for ltr(yo,glist) yo.exec_menu(gcomms.o($1).s) 
}

proc mvga () { local type,x,y,keystate,sz1,sz2,sz3,sz4 localobj xo,yo
  type=$1 x=$2 y=$3 keystate=$4 // 2 for press, 1 for dragging, and 3 for release
  xo=glist.o(0)
  sz1=xo.size(1) sz2=xo.size(2) sz3=xo.size(3) sz4=xo.size(4)
  if (type == 2) {
    begx=x begy=y
  } else if (type==3) {
    x-=begx y-=begy
    size[0]=sz1-x size[1]=sz2-x size[2]=sz3-y size[3]=sz4-y
    for ltr(xo,glist) xo.size(sz1-x,sz2-x,sz3-y,sz4-y)
  }
}

proc magga () { local tmp,type,x,y,begx,begy,keystate,sz1,sz2,sz3,sz4 localobj xo,yo
  type=$1 x=$2 y=$3 keystate=$4 // 2 for press, 1 for dragging, and 3 for release
  xo=glist.o(0)
  sz1=xo.size(1) sz2=xo.size(2) sz3=xo.size(3) sz4=xo.size(4)
  if (type == 2) {
    begx=x begy=y
  } else if (type==3) {
    if (x<begx) { tmp=x x=begx begx=tmp }
    if (y<begy) { tmp=y y=begy begy=tmp }
    size[0]=begx size[1]=x size[2]=begy size[3]=y
    for ltr(xo,glist) xo.size(size[0],size[1],size[2],size[3])
  }
}

//* grransel() -- graph range select
proc setgrransel () {
  for ltr(Xo,glist) { 
    Xo.menu_remove("REVIEW")
    sprint(tstr,"proc p%d(){grransel($1,$2,$3,$4,%d,%s)}",ii1,ii1,Xo)
    execute1(tstr)
    sprint(tstr,"p%d",ii1)
    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
// not debugged
proc grransel () { local type, x0, y0, keystate, ii, gr
  type=$1 x0=$2 y0=$3 keystate=$4 gr=$5
  graphItem=$o7 // = glist.object(gr)
  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).name)
      graphItem.erase_all()
      rv(grrcnt) 
      graphItem.exec_menu("View = plot")
    }
    graphItem.size(size[0],size[1],size[2],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).name)
      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
  } 
}

//** remgrs() gets rid of all of the graphs (called from attrpanl)
proc remgrs () { local ii,cnt
  if (isobj(graphItem,"Graph")) { graphItem.unmap graphItem = nil }
  for ltr (Xo,glist) Xo.unmap()
  glist.remove_all
}

//** collapsegrs () take off of glist graphs that have been closed on screen
proc collapsegrs () { local ii
  for (ii=glist.count-1;ii>=0;ii-=1) {
    if (glist.object(ii).view_count() == 0) { 
      glist.remove(ii)
    }
  }
}

//** viewplot() set the world for each graph correctly
proc viewplot () { local cnt,ii,flag,sz1,sz2,sz3,sz4
  if (numarg()==1) flag=$1 else flag=-1
  if (flag==0) { sz1=sz3=1e10 sz2=sz4=-1e10 }
  for ltr(Xo,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) { size[0]=0 size[1]=tstop }
  if (flag==0) for ltr(Xo,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
  if (numarg()==2) { wd=$1 ht=$2 } else { wd=vsz[0] ht=vsz[1] }
  cnt = glist.count()
  for (ii=cnt-1;ii>=0;ii=ii-1) { 
    if (glist.object(ii).view_count()==0) {glist.remove(ii)
    } else {
      sz1 = glist.object(ii).size(1)
      sz2 = glist.object(ii).size(2)
      sz3 = glist.object(ii).size(3)
      sz4 = glist.object(ii).size(4)
      glist.object(ii).unmap()
      vloc = vloc+vjmp
      if (vloc > 700) { vloc = 0 }
      glist.object(ii).view(sz1,sz3,sz2-sz1,sz4-sz3,0,vloc,wd,ht)
    }
  }
}

//** geall() erases all of the graphs
proc geall () { local cnt,ii
  cnt = glist.count()
  for ii=0,cnt-1 { 
    glist.object(ii).erase_all()
  }
}

//** lblall(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,lx,ly
  if (numarg()==0) { printf("lblall([,loc])\n")  return }
  cnt = glist.count()
  if (numarg()>1) { min=max=$2 } else { min=0 max=cnt-1 }
  if (numarg()==5) { lx=$3 ly=$4 } else { lx=0.1 ly=0.8 }
  if (numarg()>1) { if (sfunc.len($s1)>0) { temp_string_ = $s1
  }}
  for ii=min,max { 
    glist.object(ii).color(color)
    glist.object(ii).label(lx,ly,temp_string_)
  }
}

//** relbl() put appropriate label on all of the graphs
proc relbl () { local cnt,ii,min,max,lx,ly
  if (numarg()==0) { printf("relbl([str])\n")  return }
  cnt = glist.count()
  if (numarg()==4) { lx=$3 ly=$4 } else { lx=0.1 ly=0.8 }
  if (numarg()>1) glist.object(0).label($s2)
  for ii=0,glist.count-1 {
    Xo=glist.object(0) Yo=llist.object(0)
    Xo.color(0)
    Xo.label(0.,.9,Yo.name) 
    Xo.color(color)
    Xo.label(lx,ly,Yo.vec.label)
  }
}

//** toggle functions
proc tog (){if (numarg()==0) print super=1-super else print $&1=1-$&1}
proc togmark () {
  if (gvmarkflag==0) { gvmarkflag=1 if (line<4) line+=1
  } else {             gvmarkflag=0 if (line>6) line-=1
  }
  sprint(tstr,"gvmarkflag=%d",gvmarkflag) // set external gvmarkflag as well
  execute(tstr)
  sprint(mesg,"mark=%d",gvmarkflag)
}

//* panobjl stuff
proc apbrowse () {
  panobjl.browser("attrpanls","s")
  panobjl.accept_action("panobjl.object(hoc_ac_).attrpanl()")
}

//** po(NUM) set global panobj to that number
proc po () { 
  sprint(tstr,"panobj=GRV[%d]",$1)
  execute(tstr)
}

proc apkill () {
  panobjl.browser("attrpanls","s")
  panobjl.accept_action("panobjl.remove(hoc_ac_)")
}

//* printlist stuff

//** 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 $3 is the name of an object belonging to list items that will
// serve as a pointer to the recording vector
proc record () { local ii, dur, na3
  if (isobj($o1,"List")) for ltr(Xo,$o1) {
    sprint(recstr,"%s.%s",Xo,$s2)
    npl(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
    }
  } else forsec $o1 { // assume sectionlist
    sprint(recstr,"%s.%s",secname(),$s2)
    npl(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
    }
  } 
}

//** npl(name) adds this item to the printlist
//  npl(name,vec) adds this vec to the printlist
//  npl(name,vec,step) adds this vec to the printlist with printStep step
//  npl(name,vec,tvec) adds this vec to the printlist
//  npl(var,name) use name instead of variable name
//  npl(var,ptr) provide an objref to point to the vec
//  npl(name,num,vec)??adds this vec to the printlist under name_num0,name_num1,etc
proc npl () { local dur,nflag,tvflag,prstep  // METHOD DEPENDENT
  if (! isobj(printlist,"List")) printlist = new List()
  tvflag=nflag=0  prstep=0.05
  if (argtype(3)==0) {
    vite = new vitem($s1,$o2.size)
    vite.vec.copy($o2)
    vite.pstep=$3
    printlist.append(vite)
    return
  } else if (cvode_status()==0.0) {
    sprint(tstr,"%s.printStep=printStep",this)
    execute(tstr)
    prstep=printStep
  } else if (cvode_status()==1.1) {
    tvflag=1
  } else if (cvode_status()==1.0) { // ??
    printf("WARNING: Method 'global' is not currently supported for recording via grvec\n")
  }
  if (outvecint == 0) dur = tstop else dur = outvecint
  grvecstr = $s1
  repl_mstr(grvecstr," ","",temp_string2_) // no longer splits on '/'
  // eg npl(name,ii,vec)
  if (numarg()>=4) if ($4<=0) tvflag=1 else { tvflag=0 prstep=$4 }
  if (numarg()>=3) { // allows formation of tags on the fly
    if (argtype(3)==0) { 
      if ($3<=0) tvflag=1 else { tvflag=0 prstep=$3 }
    } else if (argtype(2)==0) {
      sprint(temp_string_,"%s%s",grvecstr,":%d")
      sprint(temp_string_,temp_string_,$2)
      vite = new vitem(temp_string_,$o3.size)
      vite.vec.copy($o3)
      if (numarg()==4) if (argtype(4)==1) {
        vite.tvec.copy($o4) vite.tvflag=1 vite.pstep=0
      } else if (argtype(4)==0) { vite.pstep=$4
      } else printf("Arg 4 unrecognized in npl?\n")
      printlist.append(vite)
      return
    } else if (argtype(2)==1) { 
      vite = new vitem(grvecstr,$o2.size,1)
      vite.vec.copy($o2) vite.tvec.copy($o3)
      printlist.append(vite)
      return
    }
  } 
  if (numarg()>=2) { // second arg is a vector to store
    if (argtype(2)==1) {
      vite = new vitem(grvecstr,$o2.size)
      vite.tvflag=tvflag vite.pstep=prstep
      vite.vec.copy($o2)
      printlist.append(vite)
      return
    } else if (argtype(2)==2) {  // give explicit name for the thing to store
      nflag=1
    }
  }
  if (cvode_status()==1.0) { 
    if (tvec.buffer_size==0){tvec.resize(dur/prstep+10) tvec.resize(0)}
    tvec.record(&t) 
  } else if (isobj(tvec,"Vector")) if (tvec.size!=0) { 
    tvec.resize(0) tvec.play_remove()          
  }
  if (nflag) { 
    if (tvflag) { vite = new vitem($s2,dur/prstep+10,1) } else {
                  vite = new vitem($s2,dur/prstep+10,prstep)   }
  } else {
    if (tvflag) { vite = new vitem(grvecstr,dur/prstep+10,1) } else {
                  vite = new vitem(grvecstr,dur/prstep+10,prstep) }
  }
  if (numarg()==2) if (argtype(2)==1) $o2=vite.vec // allow user to assign a pointer
  printlist.append(vite)
  if (tvflag) {
    vite.vec.resize(dur/prstep+10) vite.tvec.resize(dur/prstep+10)
    find_secname(grvecstr,temp_string_) // with lvardt, need to assign in proper context
    sprint(temp_string_,"%s {cvode.record(&%s,%s.vite.vec,%s.vite.tvec)}",temp_string_,grvecstr,this,this)
  } else if (cvode_status()==1.0) { // don't give an explicit prstep
    vite.vec.resize(dur/prstep+10)
    sprint(temp_string_,"%s.vite.vec.record(&%s)",this,grvecstr)
  } else {
    sprint(temp_string_,"%s.vite.vec.record(&%s,%g)",this,grvecstr,prstep)
  }
  if (! execute1(temp_string_)) print "Unable to excute ",temp_string_
  vite=nil
}

//** store cvode state in a double in form active.local
func cvode_status () { return cvode.active() + cvode.use_local_dt()/10 }

proc ulv () {  }

//** 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 () { 
  if (numarg()>=1) { 
    comment = $s1 // a comment
  } else if (sfunc.len(comment)==0) {
    sprint(tstr,"%s.comment=comment",this) execute(tstr)
    sprint(tstr,"Use: %s ?",comment)
    if (!boolean_dialog(tstr)) return
  }
  if (numarg()>=2) output_file=$s2 else {
    sprint(output_file,"%sv%s.%02d",ddir,datestr,runnum-dec_runnum)
    while (tmpfile.ropen(output_file)) { runnum = runnum+1
      printf("%s found, trying %sv%s.%02d\n",output_file,ddir,datestr,runnum-dec_runnum)
      sprint(output_file,"%sv%s.%02d",ddir,datestr,runnum-dec_runnum) 
    }
  }
  printf("Saving to %s\n",output_file)
  pvplist(output_file,comment)
  sprint(output_file,"%sv%s.%02d",ddir,datestr,runnum)
  comment=""
}

//** pvplist(file,comment,tback) print out the printlist with comment at head
proc pvother () {}  // user can dump other vectors at top with prvec()
proc pvplist () { local inx,tmin,tmax,tback localobj oq,xo
  output_file=$s1
  if (! pvplist0()) return // open file(s)
  pvplist1($s2) // print string header
  if (numarg()==3) if ($3>1) {
    tback=$3 tmax=printlist.o(0).tvec.max
    if (tmax>tback) {
      tmin=tmax-tback
      oq=new NQS() 
      for ltr(xo,printlist) {
        oq.setcols(xo.tvec,xo.vec)
        oq.select(0,">",tmin)
        oq.cpout()
        oq.resize(0)
      }
    }
  }
  pvout() 
  if (numarg()<3) { // leave for appending if $3==1
                     tmpfile.close() tf1.close()
  } else if ($3>1) { tmpfile.close() tf1.close() }
}

//** pvclose() -- close files used for writing
proc pvclose () {
  tmpfile.close()
  tf1.close()
}

//** pvplist0() -- open output_file and ancillary dot file if needed
func pvplist0 () { localobj st
  st=new String2()
  file_with_dot(output_file,st.s) // put .filename into st.s
  if (numarg()==0) {
    if (tmpfile.ropen(st.s)) { printf("WARNING: removing %s\n",st.s)
      sprint(st.t,"rm %s",st.s) system(st.t) }
    if (tmpfile.wopen(st.s)==0) { print "Can't open ",st.s  return 0}
    if (! isojt(tf1,tmpfile)) tf1=new File()
    tf1.wopen(output_file)
  } else {
    if (tmpfile.aopen(st.s)==0) { print "Can't open ",st.s," to append" return 0}
    if (! isojt(tf1,tmpfile)) tf1=new File()
    tf1.aopen(output_file)
  }
  return 1
}

//** prplist1()
proc pvplist1 () {
  tmpfile.printf("//: %s\n",$s1) // comment
  if (cvode_status()==1.1) {
    tmpfile.printf("//printStep -2\n")
  } else if (cvode_status()==1.0) {
    tmpfile.printf("//printStep -1\n")
  } else {
    sprint(tstr,"%s.printStep=printStep",this)
    execute(tstr)
    tmpfile.printf("//printStep %g\n",printStep)
  }
  if (byte_store) tmpfile.printf("//CPU %s\n",uname)
}

//** pvnext() append another printlist set to same file
proc pvnext () { local ii
  if ($1==0) { 
    pvplist(output_file,comment,1)
    return
  }
  pvplist0(0) // open for appending
  pvout()
  printf("Append to %s\n",output_file)
  tmpfile.close()
  tf1.close
}

//** pvout() called by pvplist() and pvnext(), actually puts out the vecs
proc pvout () {  // METHOD DEPENDENT
  pvout2()
  if (cvode_status()==1.0 && tvec.max>0) { 
    tmpfile.printf("//b%d 1 %s %d %d\n",tvec_bytesize,"CVODE1.0 tvec",tvec.size,tf1.tell)
    tvec.vwrite(tf1,tvec_bytesize) 
  }
  for ltr(Xo,printlist) { // no whitespace allowed
    if (Xo.code==2) continue
    if (sfunc.len(Xo.vec.label)>0) sprint(temp_string_,"%s__(%s)",Xo.vec.label,Xo.name) else {
      temp_string_=Xo.name } 
    pvpone(Xo)
  }
}

//** dir2pr(item#[,OUTFILE,OUTCOMMENT]) read the files in dir and add one item to printlist
// see also collect.hoc for batch use
proc dir2pr () { local ix,ps
  printlist.remove_all 
  ix=$1
  for ltr(Xo,dir) {
    read_vfile(Xo.s)
    rv_readvec(ix,vrtmp)
    ps=llist.o(ix).num // pstep: need if want to save a fixed step entry
    grv_.npl(comment,vrtmp,tvec)
  }
  if (numarg()==3) { grv_.pvplist($s2,$s3) read_vfile($s2) }
}

//** dir2mf(FILENAME,COMMENT) read the files in dir and create a master file
proc dir2mf () { local ix,ps,n localobj f
  f=new File()
  f.wopen($s1)
  f.printf("//: %s\n",$s2)
  for ltr(Xo,dir) {
    read_vfile(Xo.s)
    n=-1
    for ltr(Yo,llist) if (dir2mf2(n+=1)) {
      // repl_mstr(comment," ",";",temp_string2_) // no spaces allowed
      // sprint(temp_string_,"%s_%s",Yo.name,comment)
      f.printf("//b%d %g %s %d %d %s\n",bvec,Yo.num,Yo.name,Yo.size,Yo.loc,filename)
    }
  }
  f.close()
}

//** read_mf() reads a master file
// assumes file in tmpfile
func read_mf () { local ii,sz,loc,mult,sze,cloc,segs localobj o
  if (attr0) {
    if (!boolean_dialog("Look at file data instead of sim?","YES","NO")) {
      printf("Read file cancelled\n")
      return 0
    }
  } else { attr0=0 }
  if (numarg()==1) filename=$s1 else tmpfile.getname(filename)
  sprint(s,"GRV[%d] %s: %s",objnum(this),simname,filename)
  clear()
  if (!tmpfile.ropen(filename)) { print "E1: Can't open ",filename return 0 }
  while ((numr = tmpfile.gets(tstr)) != -1 && (sfunc.head(tstr,"//[^b]",temp_string2_)==0)) {
    read_vinfo()  // a line giving info about the file (eg comment)
  }
  tmpfile.seek(-numr,1) // back up
  ii=0
  while ((numr = tmpfile.gets(tstr)) != -1) {
    if (((ii+=1)%10000)==0) printf("%d ",ii)
    if (sscanf(tstr,"//b%1ld %g %s %ld %ld %s",&bvec,&nvec,tstr2,&sze,&loc,tstr)!=6) {
      printf("**** GRV read_mf() parse ERR on %s in %s",tstr,filename)
      return 0
    }
    llist.append(new vfile_line(tstr2,sze,loc,nvec,tstr))  // name size loc num
  }
  if (llist.count==0) {
    printf("grvec.hoc::read_mf ERR nothing read from %s\n",filename)
    return 0
  }
  entries=llist.count
  mff=1
  return 1
}

//** prvec(name,vec,byte_flag[,file])
proc prvec () { local bflag
  if (numarg()>3) { tmpfile.aopen($s4) }
  bflag = $3
  tmpfile.printf("//b%d 1 %s %d %d\n",bflag,$s1,$o2.size,tf1.tell())
  $o2.vwrite(tf1,bflag) 
  if (numarg()>3) { tmpfile.close() }
}

//** pv() dumps a single vector into output_file
proc pv () { local inx  
  sprint(output_file,"%sv%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).name,output_file)
  // string_dialog("Name for saved vector",printlist.object(inx).name)
  if (tmpfile.ropen(output_file)) { // file exists already
    file_with_dot(output_file,temp_string_) // put .filename into temp_string_
    tmpfile.aopen(temp_string_) tf1.aopen(output_file)
    printf("Appending to %s\n",output_file)
  } else { 
    pvplist0()
    pvplist1(comment)
  }
  pvpone()
  tmpfile.close()
  tf1.close
}

//** pvpone() -- write out a vector or vector pair to the file
proc pvpone () {  // METHOD DEPENDENT
  if (byte_store) {
    if ($o1.tvflag==1 && isassigned($o1.tvec)) {
      tmpfile.printf("//b%d -2 %s %d %d\n",byte_store,temp_string_,$o1.vec.size,tf1.tell)
      $o1.tvec.vwrite(tf1,tvec_bytesize) 
    } else if ($o1.pstep>0) {
      tmpfile.printf("//b%d %g %s %d %d\n",byte_store,$o1.pstep,temp_string_,$o1.vec.size,tf1.tell)
    } else {
      tmpfile.printf("//b%d -1 %s %d %d\n",byte_store,temp_string_,$o1.vec.size,tf1.tell)
    }
    $o1.vec.vwrite(tf1,byte_store)
  }
}

//** 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).name)
  npl(grvecstr,printlist.object(num).vec)
  print printlist.count-1,":XO -> ",grvecstr
  XO = printlist.object(printlist.count-1).vec
}

//** chgplname([num],STR) change name of item in printlist
proc chgplname () { local num,cnt
  cnt = printlist.count
  if (numarg()>0) {if ($1>=0) num=$1 else num=cnt+$1} else num=cnt-1
  if (num>cnt-1 || num<0) {
    printf("%d!: Only %d items (0-%d) in list.\n",num,cnt,cnt-1) return 
  }
  printlist.object(num).name=$s2
}

// 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) }
}

//* iterators for printlist and files
//** rvtr() read vector iterator
// usage 'for rvtr(vec) XO.vec.printf' where # is attrpanl#
iterator rvtr () { local i,flag,s4flag
  if (numarg()>=2) {$&2=0} else {i1 = 0}
  if (numarg()==3) s4flag=1 else s4flag=0
  flag=1
  for i = 0, entries-1 {
    tstr = llist.object(i).name
    if (s4flag) {if (strm(tstr,$s3)) flag=1 else flag=0}
    if (flag) {
      rv_readvec(i,$o1) 
      if (numarg()>=2) { $&2=i } else { i1=i }
      iterator_statement // rvtr(vec) -- name in .tstr, tvec in .tvec
    }
  }
}

//** vrdr(vlist[,REGEXP or INDV,flag,&y]) -- used for llist
// similar to rvtr() but does interpolation
// use regexp eg for prdr("PYR2.8") { etc }
// optional flag to NOT interpolate
// indv gives set of llist nums to search through (can use with "" as regexp)
// sets 4 vectors in vlist: voltage,times,interp v, interp t
iterator vrdr () { local flag,a,ii localobj rxp,v1,tv1,v2,tv2,ipt
  if (numarg()==0) printf("\t**** HELP::  vrdr(vlist[,REGEXP or INDV,flag,&y]) ****\n")
  curcol=0
  rxp=new String()
  a=allocvecs(ipt)
  if (!isojt($o1,llist)) $o1=new List()
  if ($o1.count==4) { // use the list we're given
    for ii=0,3 if (!isojt($o1.o(ii),vrtmp)) {
      printf("vrdr: Nonvector in vlist:%s\n",$o1.o(ii))
      return
    }
  } else {
    $o1.remove_all 
    for ii=0,3 $o1.append(new Vector())
  }
  v1=$o1.o(0) tv1=$o1.o(1) v2=$o1.o(2) tv2=$o1.o(3) 
  ipt.indgen(0,llist.count-1,1)
  if (numarg()>=2) if (argtype(2)==1) { ipt.copy($o2) 
            } else if (argtype(2)==2) { rxp.s=$s2
            } else { printf("vrdr() ERR arg 2 should be vector or string\n") }
  if (numarg()>=3) flag=$3 else flag=0
  if (numarg()>=4) {$&4=0} else {ii1 = 0}
  if (!flag) {
    if (tvec.max != tstop) printf("WARNING: tvec set?: %g %g\n",tstop,tvec.max)
    tv2.copy(tvec)  // tvec must be preassigned for interpolation
  }
  tmpfile.ropen(filename)
  for (ii1=0;ii1<llist.count;ii1+=1) {
    if (ipt.contains(ii1) && strm(llist.object(ii1).name,rxp.s)) {
      XO=llist.object(ii1)
      if (mff) if (strcmp(filename,XO.f)!=0) { filename=XO.f tmpfile.ropen(filename) }
      tmpfile.seek(XO.loc)
      if (XO.num==-2) tv1.vread(tmpfile) else {
        if (XO.num<=0) {printf("vrdr INTERR; ?printStep for interpolation\n") err()}
        tv1.indgen(0,tstop+0.01,XO.num) }
      v1.vread(tmpfile)
      v2.resize(0)
      if (XO.num==-2 && !flag) v2.interpolate(tv2,tv1,v1)
      i1=ii1
      iterator_statement
      if (numarg()>=4) { $&4+=1 }
    }
  }
  tmpfile.close
  dealloc(a)
}

//** prdr() -- used for printlist
// use regexp eg for prdr("PYR2.8") { etc }
// optional flag to NOT interpolate
// ind=tvec, vec1=original trace, vec interpolated on tvec
// note that i1 here gives list number, not sequential
// eg for panobj.prdr("V$",1) gv(i1)
iterator prdr () { local flag
  if (numarg()>1) flag=$2 else flag=0
  if (numarg()==3) {$&3=0} else {i1 = 0}
  v1=tv1=v2=tv2=allocvecs(4) tv1+=1 v2+=2 tv2+=3
  if (!flag) {
    if (tvec.max != tstop) printf("WARNING: tvec set?: %g %g\n",tstop,tvec.max)
    mso[tv2].copy(tvec)  // tvec must be preassigned for interpolation
  }
  curcol=0
  if (attr0) for (ii1=0;ii1<printlist.count;ii1+=1) {
    XO=printlist.object(ii1)
    if (strm(XO.name,$s1)) {
      sprint(tstr,"tstr=\"%s\"",XO.name) execute(tstr) // set global tstr
      mso[v1].copy(XO.vec) 
      if (isit(XO.tvec)) mso[tv1].copy(XO.tvec) 
      if (!flag && isit(XO.tvec)) mso[v2].interpolate(mso[tv2],XO.tvec,XO.vec)
      i1=ii1
      iterator_statement
      if (numarg()==3) { $&3+=1 }
    }    
  } else for (ii1=0;ii1<llist.count;ii1+=1) {
    if (strm(llist.object(ii1).name,$s1)) {
      XO=llist.object(ii1)
      i1=ii1
      iterator_statement
      if (numarg()>=3) { $&3+=1 }
    }
  }
  dealloc(v1)
}

//* outvec() routines for printing out in sections - NOT DEBUGGED

//** outvec_init([output_file,comment])
proc outvec_init() { local segs
  if (numarg()>0) { output_file = $s1 } else {
    sprint(output_file,"%sv%s.%02d",ddir,datestr,runnum-dec_runnum)
    while (tmpfile.ropen(output_file)) { runnum = runnum+1 // don't allow an overwrite
      sprint(output_file,"%sv%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 1 %s %d %d\n",byte_store,printlist.object(ii).name,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).name,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 1 %s %d %d\n",byte_store,printlist.object(ii).name,t-outvecint,tmpfile.tell())
      printlist.object(ii).vec.vwrite(tmpfile,byte_store)
      tmpfile.printf("\n")
    }
    tmpfile.close()
  }
}

//* endtemplate; assignments:
endtemplate GRV

printStep=0.1
grv_ = new GRV(0)
{panobj=grv_ printlist=grv_.printlist panobjl=grv_.panobjl}

//* external routines
//** 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,vec,tvec) adds this vec to the printlist
//  new_printlist_item(var,name) use name instead of variable name
//  new_printlist_item(var,ptr) provide an objref to point to the vec
//  new_printlist_item(name,num,vec)??adds this vec to the printlist under name_num0,name_num1,etc
proc new_printlist_item () { local dur,nflag,tvflag
  if (! isassigned(grv_)) { grv_ = new GRV(0) printlist=grv_.printlist }
  if (numarg()==1) { grv_.npl($s1)
  } else if (numarg()==2) {
    if (argtype(2)==1) {
      grv_.npl($s1,$o2)
    } else if (argtype(2)==2) {
      grv_.npl($s1,$s2)
    } else grv_.npl($s1,$2)
  } else if (numarg()==3) {
    if (argtype(2)==1) {
      grv_.npl($s1,$o2,$o3)
    } else if (argtype(2)==0) {
      grv_.npl($s1,$2,$o3)
    }
  }
}

//** llist() print out contents of a list
proc llist () { local done localobj o,st,xo
  st=new String()  o=panobj
  if (numarg()==2) st.s=$s2
  if (numarg()>=1) { 
    if (argtype(1)==1) {
      if (isobj($o1,"List")) { 
        if ($o1.count==0) {print "empty list" return}
        if (isobj($o1.object(0),"String2")) {
          for ltr(xo,$o1) if (strm(xo.s,st.s)) print xo.s,xo.t
        } else if (isobj($o1.object(0),"String")) { 
          for ltr(xo,$o1) if (strm(xo.s,st.s))  print xo.s
        } else if (isobj($o1.object(0),"Vector")) {
          done=0
          if (name_declared("oform")) if (oform(vec)!=NOP) {
            for ltr(xo,$o1) print xo,oform(xo) 
            done=1 
          }
          if (!done) for ltr(xo,$o1) print xo,xo.size
        } else if (isobj($o1.object(0),"Union")) {
          for ltr(xo,$o1) if (strm(xo.s,st.s)) print xo,xo.s,xo.t,xo.u,xo.v
        } else for ltr(xo,$o1) print xo
        return
      } else o=$o1
    } else if (argtype(1)==2) st.s=$s1
  }
  if (o.attr0) { for ltr(xo,printlist) if (strm(xo.name,st.s)) print i1,xo.name,xo.vec.size
  } else         for ltr(xo,o.llist) if (strm(xo.name,st.s)) print i1,xo.name,xo.size      
}

//** cpprl(PRINTLIST,TMPLIST) copies printlist vitem's to tmplist
proc cpprl () { localobj xo,yo
  $o2.remove_all
  for ltr(xo,$o1) {
    $o2.append((yo=new vitem(xo.name,xo.vec.size)))
    yo.tvflag=xo.tvflag yo.pstep=xo.pstep yo.o=xo.o yo.vec.copy(xo.vec)
    if (yo.tvflag) {yo.tvec=new Vector() yo.tvec.copy(xo.tvec)}
  }
}

//** abbreviated proc calls
proc gvpwpl () { pwman_place(500,500) }
proc vp () { grv_.vecpanel }
obfunc gvnew () { 
  if (numarg()==1) {
    if (argtype(1)==0) {
      panobj=new GRV($1)
    } else if (argtype(1)==2) {
      panobj=new GRV($s1)
    } else if (argtype(1)==1) {
      $o1=new GRV(-2)
      panobj=$o1
    }
  } else if (numarg()==2) {
    if ($2>0) {
      panobj=panobjl.object($2)
      panobj.read_vfile($s1)
    } else panobj=new GRV($s1,$2) // file,flag
  } else panobj=new GRV(1) // default
  return panobj
}

proc ap () { local ii,attr0,nopan localobj o
  nopan=ii=0
  if (numarg()==0) { o=panobj 
  } else if (numarg()>=1) {
    if (argtype(1)==0) { ii=$1 
      o=grv_.panobjl.object(ii)
      if (ii<0 || ii>=grv_.panobjl.count) { 
        printf("**** ap(%d) ERR panobj #%d not found -- run gvnew() \n",ii,ii) return }
    } else o=$o1
  }
  if (numarg()>=2) if (argtype(2)==0) if ($2==-2) nopan=1
  attr0=o.attr0
  o.attrpanl()
  if (!nopan) if (attr0) o.pbrgr("Graph","gv") else o.rpanel()
  panobj=o
}
proc disptray () { print "Must load boxes.hoc to get trays" }

//** gg() graph vectors and functions directly
//** gs(#) select graph (by setting g and graphItem to this Graph#
proc gs () { 
  if (argtype(1)==1) {      g=$o1 graphItem=g 
  } else if (numarg()==2) { g[$1]=Graph[$2] 
  } else {                  g=Graph[$1] graphItem=g }
}
// gg(g[i],vec) gg(vec,step) gg(vec,ind) gg(g,"FUNC","min,max") [color,line,symbol]
gvmarkflag=0
obfunc gg () { local gp,na,newgr,clr,a,stp,i,tmp localobj ty,ts,abs,ord,o,go
  if (argtype(1)==2) if (strc($s1,"help")) {
    printf("eg gg(g[i],vec) gg(vec,step) gg(vec,ind) gg(g,'FUNC','min,max') [color,line,symbol]\n")
    return nil
  }
  a=allocvecs(ty,abs,ord)
  ts=new String2()
  na=numarg() newgr=1
  ty.resize(10) ty.fill(-1)
  for i=1,na ty.x[i]=argtype(i)
  i=1
  clr=panobj.color lne=panobj.line
  if (ty.x[i]==0) { 
    gp=$i                                         i+=1
  } else gp=0
  if (gp<100) {
    if (isassigned(g[gp])) if (g[gp].view_count>0) newgr=0
    if (newgr) g[gp]=new Graph()
    go=graphItem=g[gp]
    graphList[0].append(g[gp])  panobj.glist.append(g[gp])
  } else {
    graphItem=go=new Graph()
    graphList[0].append(go)  panobj.glist.append(go)
  }
  if (gvmarkflag) ts.t="mark" else ts.t="line"

  if (na==1 && ty.x[0]==0) { return  // gg(#) just put up the graph
  } else if (na==i && ty.x[i]==1) { 
    sprint(ts.t,"%s.%s(%s,1",$oi,ts.t,go)   // gg(vec)
  } else if (ty.x[i]==2) { // gg("FUNC","min,max,step")
    min=0 max=10 stp=0
    ts.s=$si                                      i+=1
    if (ty.x[i]==2) {
      split($si,abs,"[,:/]") min=abs.x[0] max=abs.x[1] 
      if (abs.size==3) stp=abs.x[2]               i+=1
    }
    if (stp==0) stp=(max-min)/200
    abs.indgen(min,max,stp) ord.copy(abs) 
    if (!name_declared(ts.s)) { // look for an x that will become $1
      if (!strm(ts.s,"[$]1")) { printf("gg ERR Can't find '$1' in %s\n",ts.s) return nil }
      sprint(ts.s,"func _gg_f(){return %s}",ts.s) execute1(ts.s)
      print ts.s
      ts.s="_gg_f"
    }
    ord.apply(ts.s)
    sprint(ts.t,"%s.%s(%s,%s",ord,ts.t,go,abs)
  } else if (ty.x[i]==1 && ty.x[i+1]==0) {     // gg(vec,step)
    o=$oi                                         i+=1
    if (isobj(o,"List")) {
      tmp=$i   i+=1
      if (int($i)!=$i) { // a timestep
        sprint(ts.t,"%s.%s(%s,%g",o.o(tmp),ts.t,go,$i)      i+=1  
      } else {
        sprint(ts.t,"%s.%s(%s,%s",o.o(tmp),ts.t,go,o.o($i)) i+=1  
      }
    } else { // vector
      sprint(ts.t,"%s.%s(%s,%g",o,ts.t,go,$i)     i+=1  
    }                                          
  } else if (ty.x[i]==1 && ty.x[i+1]==1) {     // gg(vec,ind)
    o=$oi                                         i+=1
    sprint(ts.t,"%s.%s(%s,%s",o,ts.t,go,$oi)   i+=1
  }
  if (ty.x[i]==0) { clr=$i                        i+=1 }
  if (ty.x[i]==0) { lne=$i                        i+=1 }
  if (ty.x[i]==2) { symb=$si                      i+=1 }
  if (sfunc.len(ts.t)>4) {
    if (gvmarkflag) { sprint(ts.s,"%s,\"%s\",%d,%d,4)",ts.t,symb,lne,clr)
    } else { sprint(ts.s,"%s,%d,%d)",ts.t,clr,lne) }
    execute(ts.s)
  }
  dealloc(a)
  return graphItem
}

//*** ge() erases IV graph
proc ge () { if (numarg()==0) graphItem.erase_all() else g[$1].erase_all }

//** gv() calls internal gv
proc gv () {  local inx,na // EXTERNAL VERSION -- same name in template
  na=numarg()
  if        (argtype(1)==0) { inx = $1
  } else if (argtype(1)==2) {
      for ltr(XO,printlist) if (strm(XO.name,$s1)) inx=i1
      if (inx==-1) {print $s1," not found" return }
  }
  if (na==1) grv_.gv(inx) else if (na==2) grv_.gv(inx,$2) else if (na==3) grv_.gv(inx,$2,$3)
}

//** restore_printlist() restores the plist from a file in an attrnum
objref vite
proc restore_printlist () { local cnt,ii,attrnum,savlvar localobj aa,st
  printf("NOT WORKING\n")
  st=new String()
  attrnum=$1
  printlist.remove_all
  panobj=grv_.panobjl.object(attrnum)
  for panobj.vrdr(aa,"",1) {
    vite= new vitem(st.s,aa.o(0).size)
    vite.vec.copy(aa.o(0))
    printlist.append(vite)
  }
}

//** dirname(full,path) filname(full,file) splits up path/file
// eg filname("/home/billl/nrniv/thal/params.hoc",temp_string_)
//    temp_string_ => params.hoc
obfunc dirname () { localobj st
  st=new String2()
  if (argtype(1)==1) st.s=$o1.s else st.s=$s1
  st.t=st.s
  sfunc.head(st.s,"[^/]+$",st.s)
  sfunc.tail(st.t,st.s,st.t)
  if (numarg()==2) $s2=st.s
  return st
}

//** filname()
obfunc filname () { localobj st
  st=new String2()
  if (argtype(1)==1) st.s=$o1.s else st.s=$s1
  sfunc.head(st.s,"[^/]+$",st.t)
  sfunc.tail(st.s,st.t,st.s)
  if (numarg()==2) $s2=st.s
  return st
}

//** filsuf()
obfunc filsuf () { localobj st
  st=new String2()
  if (argtype(1)==1) st.s=$o1.s else st.s=$s1
  sfunc.tail(st.s,"\\.",st.s)
  if (numarg()==2) $s2=st.s
  return st
}

//** filstem()
// allows composition: filstem(filname(aa)).s
obfunc filstem () { localobj st
  st=new String2()
  if (argtype(1)==1) st.s=$o1.s else st.s=$s1
  sfunc.head(st.s,"\\.",st.s)
  if (numarg()==2) $s2=st.s
  return st
}

//** file_with_dot(filename,[result,prefix]): put .filename into result
obfunc file_with_dot () { localobj st
  st=dirname($s1)
  if (numarg()==3) { sprint(st.s,"%s%s%s",st.s,$s3,st.t)
  } else             sprint(st.s,"%s.%s", st.s,    st.t)
  if (numarg()>=2) $s2=st.s
  return st
}

//* using grvec to save vectors 
proc grvclr () { printlist.remove_all() }
//* grvsv,grvwr,etc
//* grvsv(name,vec[,dt or tvec]) save a named vector
proc grvsv () { local ddt,tvf localobj st,dv,tv
  st=new String()
  tvf=0 ddt=1
  if (argtype(1)==2) st.s=$s1
  if (argtype(2)==1) dv=$o2
  if (argtype(3)==-1){tvf=0 ddt=0.025
  } else if (argtype(3)==1) {tv=$o3 tvf=1
  } else if (argtype(3)==0) ddt=$3
  if (ddt==1) ddt=1.00001 // since dt of 1 is used as a flag (bad hack)
  if (tvf) printlist.append(new vitem(st.s,dv,tv)) else printlist.append(new vitem(st.s,dv,ddt))
}
// grvwr(filename[,comment]) // comment appends date,user,hg tip
proc grvwr () { localobj st
  st=new String2()
  if (argtype(2)==2) st.t=$s2
  system("date",st.s)       
  chop(st.s) sprint(st.t,"%s:%s",st.t,st.s)
  system("echo $USER",st.s) 
  chop(st.s) sprint(st.t,"%s:%s",st.t,st.s)
  system("hg tip --template '{rev}:{node}:{date|isodate}'",st.s) // mysteriously adds a newline??
  if (sfunc.len(st.s)>2) {chop(st.s) sprint(st.t,"%s:%s",st.t,st.s)}
  GRV[0].pvplist($s1,st.t)
}
//** datasource=grvrd("filename"[,showflag]); with showflag puts up attribute panel; returns a datasource
obfunc grvrd () { local showflag
  showflag= 0 // default don't show
  if (argtype(2)==0) showflag=1
  if (showflag) panobj=new GRV($s1) else panobj=new GRV($s1,-2)
  return panobj
}

//** grvlist([GRV]) // list names and sizes
proc grvlist () { local x localobj xo,po
  po=panobj
  if (po.llist.count()==0) return
  if (argtype(1)==1) if (isobj($o1,"GRV")) po=$o1
  printf("# name size\n")
  if (eqobj(po.llist,printlist)) { for ltr(xo,po.llist,&x) print x,xo.name,xo.vec.size
  } else                           for ltr(xo,po.llist,&x) print x,xo.name,xo.size
}

//** vec=grvrv(datasource,num OR name, datavec, timevec) // read data vec(s) from a datasource
//   all arguments are optional but order of args not
//    datasource defaults to current datasource given by 'panobj' object pointer
//    num or dataname defaults to 0 (first vector in datasource)
//    if vec1 is missing routine creates a vector, fills with datavec and returns
//    vec2 if missing is ignored -- in order to pick up vec2 must also give a vector for vec1
//    examples: grvrv(3) grvrv(vec,tvec) grvrv("dataname",vec,tvec)
obfunc grvrv () { local i,num,x localobj po,st,v1,v2,xo
  i=1 st=new String2() po=panobj
  if (argtype(i)==1) if (isobj($oi,"GRV")) {po=$oi i+=1}
  if (argtype(i)==0) {num=$i i+=1} else num=0
  if (argtype(i)==2) { 
    st.s=$si i+=1 // name will overwrite num if redundantly given as num,name 
    for ltr(xo,po.llist,&x) if (strm(xo.name,st.s)) {num=x break}
    if (x==po.llist.count) printf("grvrv(): %s NOT FOUND in datasource %s; returning first item\n",st.s,po)
  }
  if (num>=po.llist.count || num<0) { 
    printf("grvrv(): %d not in datasource %s (max %d); returning first item\n",num,po,po.llist.count-1) 
    num=0 
  }
  if (argtype(i)==-1) { v1=new Vector(1e3)
  } else { // pick up 1 or 2 vectors or vector names
    if (argtype(i)==1) { v1=$oi i+=1 // vector
      if (isobj(v1,"NULLobject")) { v1=new Vector(1e3)
      } else if (!isobj(v1,"Vector")) {printf("grvrv ERRA: arg %d should be a vector\n",i) err()}
    } 
    if (argtype(i)==1) {v2=$oi i+=1 // vector
      if (isobj(v2,"NULLobject")) { v2=new Vector(1e3)
      } else if (!isobj(v2,"Vector")) {printf("grvrv ERRA: arg %d should be a vector\n",i) err()}
    }   
  }
  if (i!=numarg()+1) printf("grvrv ERRB: some args not parsed (%d %d)\n",i,numarg())
  tstr=po.llist.o(num).name // name of that data item
  if (v2==nil) po.rv_readvec(num,v1) else po.rv_readvec(num,v2,v1)
  return v1
}

//** vec=grvnq(datasource,num OR name, nq) // read data vec(s) from a datasource
//    all arguments are optional but order of args not
//    datasource defaults to current datasource given by 'panobj' object pointer
//    num or dataname defaults to 0 (first vector in datasource)
obfunc grvnq () { local i,num,x,a localobj po,st,oq,xo,v1,v2
  i=1 st=new String2() po=panobj
  if (argtype(i)==1) if (isobj($oi,"GRV")) {po=$oi i+=1}
  if (argtype(i)==0) {num=$i i+=1} else num=0
  a=allocvecs(v1,v2)
  if (argtype(i)==2) { 
    st.s=$si i+=1 // name will overwrite num if redundantly given as num,name 
    for ltr(xo,po.llist,&x) if (strm(xo.name,st.s)) {num=x break}
    if (x==po.llist.count) printf("grvnq(): %s NOT FOUND in datasource %s; returning first item\n",st.s,po)
  }
  if (num>=po.llist.count || num<0) { 
    printf("grvnq(): %d not in datasource %s (max %d); returning first item\n",num,po,po.llist.count-1) 
    num=0 
  }
  if (argtype(i)!=1) { oq=new NQS("t","ind")
  } else oq=$oi
  if (i!=numarg()+1) printf("grvnq ERRB: some args not parsed (%d %d)\n",i,numarg())
  tstr=po.llist.o(num).name // name of that data item
  if (po!=panobjl.o(0)) po.rv_readvec(num,v2,v1) else { v1.copy(printlist.o(num).vec) v2.copy(printlist.o(num).tvec) }
  oq.v[0].append(v2) oq.v[1].append(v1)
  return oq
}

//* misc routines
//** fexists()
func fexists () { localobj o
  o=new File()
  return o.ropen($s1)
}

//** ftype()
func ftype () { local ty localobj st
  ty=0
  st=new String2()
  sprint(st.t,"stat -c %%F %s 2>&1",$s1)
  system(st.t,st.s)
  chop(st.s)
  if (strm(st.s,"\n")) {               return 10 //  more than 1 file -- ie * used
  } else if (strm(st.s,"No such"))   { return -1
  } else if (strm(st.s,"directory")) { return 0
  } else if (strm(st.s,"symbolic")) {  return 8
  } else if (strm(st.s,"regular"))  {  return 2
  } else { // not identified
    printf("File %s is a %s\n",$s1,st.s)
    return -2
  }
}

//** file_len() uses wc
func file_len () { local x localobj st
  st=new String()
  sprint(st.s,"wc -l \"%s\"",$s1)
  system(st.s,st.s)
  sscanf(st.s,"%d",&x)
  return x
}

func cvode_status () { return cvode.active() + cvode.use_local_dt()/10 }

proc pvall () { local n localobj o
  o=panobjl.o(0)
  if (! o.attr0) { printf("pvall() ERR %s not attr0==0\n",o)
  } else { 
    n=numarg()
    if (n==1) o.pvall($s1) else if (n==2) o.pvall($s1,$s2) else o.pvall()
  }
}

//** procbutt() put up a single proc in a button
proc procbutt () {
  xpanel($s1)
  xbutton($s1,$s1)
  xpanel(500,500)
}

// mdl2view(g,X,Y) converts world coordinates to view coordinates
// eg {XO=mdl2view(g,12,533.7) g.label(XO.x,XO.x[1],"AA",2,2,0.5,0.5,1)}
// translate from world coordinates into view coordinates
// view coordinates are different from Graph model coordinates
//  3 coordinate systems: view, world, panel  -- ie the 0,1 used by g.label
obfunc mdl2view () { local a,ii,x0,y0 localobj o,v1,g
  g=$o1 x0=$2 y0=$3
  if (argtype(4)==1) v1=$o4 else {
    v1=new Vector(4)
    for ii=0,3 v1.x[ii]=g.size(ii+1) 
  }
  o=new Union()
  o.x=   (x0-v1.x[0])/(v1.x[1]-v1.x[0])
  o.x[1]=(y0-v1.x[2])/(v1.x[3]-v1.x[2])  
  o.x[2]=o.x[0]*0.8+0.1 
  o.x[3]=o.x[1]*0.8+0.1 // scale and move over to where graph usually is
  return o
}

//* cart2north() -- identify 0-360 degree N up for cartesian vector
// cart2north(x0,y0,x1,y1[,vec]) -- with vec also return amplitude in vec.x[1]
// cart2north(delx,dely[,vec]) 
func cart2north () { local theta,delx,dely,i
  if (numarg()<4) {delx=$1 dely=$2 i=3} else {delx=$3-$1 dely=$4-$2 i=5}
  theta=atan2(dely,delx)
  theta*=(180/PI)
  if (theta<0) theta+=360
  if (theta>=0 && theta<90) { theta= abs(theta-90)
  } else if (theta>=90 && theta<=360) theta = abs(450 - theta)
  if (numarg()==i) revec($oi,theta,sqrt(dely*dely+delx*delx))
  return theta
}

//** rmallgrs() gets rid of all extant graphs
proc rmallgrs () { local ii,cnt localobj xo,glist
  glist=new List("Graph")
  for ltr (xo,glist) xo.unmap()
}

proc stopper () {
  xpanel("STOP")
  xbutton("STOP","stoprun=1")
  xbutton("FINI","finish()")
  xbutton("CONT","time(\"cvode.solve(tstop)\")")
  xbutton("RUN","time()")
  xpanel()
}


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