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grvec.hoc
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grvec.hoc
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//* $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_)
}