show.hoc

{load_file("viewspikes.hoc")}
{load_file("viewspikes1.hoc")}

begintemplate ShowConnect
public smode_, mgrsmap, syns, grasterm_
external ring, len, Lsec, nmitral, ngranule, mitral_x, granule_x, sparse_connection_matrix_
external reload_onecell, reload_wholenet, pc, weight_movie
external allsyn, somesyn, cells, flush_list, cvode, addplot, tstop
external pattern_tvec_, pattern_idvec_, mgconnect
external clear, create_stim, mknet, gidvec, classname
external moi, goi
public msel, gsel, create_subnet // for record.hoc
public g, draw, fi_cond_vec
objref g, syns, msel, gsel, mgrsel, msynsel, gsynsel, synsel1, deck
objref b, v_rvp_, keepsyn, keepnc, hinton_shape, tplots
objref exc_hinton_shape, inh_hinton_shape
objref syn_movie_fih, syn_movie_list, syn_movie_nclist, this
objref grasterm_, grasterg_, scm, mgrsmap
objref fih_spikes, fih_bar, fih_cond
strdef sel_str_
create keepsyn_sec
proc init() {local i
	spike_viewer_ = 0
	show_soma_spikes_ = 1
	show_fi_cond_ = 0
	rasterm_ = 0
	rasterg_ = 0
	tplots = new List()
	hinton_movie = 0
	exc_hinton_movie = 0
	inh_hinton_movie = 0
	keepsyn_sec { delete_section() }
	smode_ = -1
	wholenet_ = 1
	sel_str_ = "no selection"
	sel_gid_ = -1
	cells = $o1
	//ls = cells.object(0).secden[1].L
	ls = Lsec
	//nmitral = $2
	//ngranule = $3
	scm = sparse_connection_matrix_
	nsyn = 0
	for i=0, scm.nrow-1 {
		nsyn += scm.sprowlen(i)
	}
	syns = $o4
	msel = new Vector(nmitral)
	gsel = new Vector(ngranule)
	msynsel = new Vector(nmitral) // all synapses assocated with mitral
	gsynsel = new Vector(ngranule)
	mgrsel = new Vector(nsyn)
	synsel1 = new Matrix(nmitral, ngranule, 2)
	build()
	draw()
}

proc build() {local mx1, mx2, gx1, gx2
	b = new HBox()
	b.intercept(1)
	b.full_request(1)
	b.adjuster(520)
	g = new Graph(0)
	g.view(0,0,1,1,0,0,520,120)
	//cells.object(0).soma mx1 = x3d(0)
	//cells.object(nmitral-1).soma mx2 = x3d(0)
	//cells.object(nmitral).soma gx1 = x3d(0)
	//cells.object(nmitral+ngranule-1).soma gx2 = x3d(0)
	mx1 = mitral_x.x[0]
	mx2 = mitral_x.x[nmitral-1]
	gx1 = granule_x.x[0]
	gx2 = granule_x.x[ngranule-1]
	if ( gx1 < mx1) mx1 = gx1
	if ( gx2 > mx2) mx2 = gx2
	g.size(mx1, mx2, -1, nmitral)
//	g.size(-ls + mx1, ls + mx2, -1, nmitral)
	
	g.xaxis(3)

	deck = new Deck()
	deck.intercept(1)
	xpanel("")
	g.menu_tool("Select cells", "select", "smode(1)")
	g.menu_tool("Select all synapses of cells", "select", "smode(2)")
	g.menu_tool("Select a few synapses", "select", "smode(3)")
	xmenu("Select")
	xbutton("Mitrals", "mansel(0)")
	xbutton("Granules", "mansel(1)")
	xmenu()
	xcheckbox("Exc+Inh Hinton synapse movie", &hinton_movie)
	xcheckbox("Exc Hinton synapse movie", &exc_hinton_movie)
	xcheckbox("Inh Hinton synapse movie", &inh_hinton_movie)
	xcheckbox("Mitral soma raster", &rasterm_, "mraster()")
	xcheckbox("Granule soma raster", &rasterg_, "graster()")
	xcheckbox("Show soma spikes", &show_soma_spikes_, "show_fi_cond_ = (show_fi_cond_ && show_soma_spikes_)")
	xcheckbox(" and fih conductance", &show_fi_cond_, "show_fi_cond_ = (show_fi_cond_ && show_soma_spikes_)")
	xmenu("Spike Viewers")
	xbutton("All Mitrals", "view_spikes(0)")
	xbutton("Mitral at all granule positions", "view_spikes(1)")
	xmenu()
//	xcheckbox("Spike Viewer", &spike_viewer_, "view_spikes()")
//	xvarlabel(sel_str_)
	xbutton("Simulate", "sim()")
	xpanel()
	xpanel("")
	xbutton("Selection Tool", "whole_net()")
	xmenu("Spike Viewers")
	xbutton("All Mitrals", "view_spikes(0)")
	xbutton("Mitral at all granule positions", "view_spikes(1)")
	xmenu()
	xbutton("Time plots to file", "p2f(\"temp.tplot\")")
//	xcheckbox("Spike Viewer", &spike_viewer_, "view_spikes()")
	xpanel()
	deck.intercept(0)
	deck.flip_to(0)
	deck.map()
	b.intercept(0)
	b.map("Select Subset", 400, 30, 700, 300)
	g.exec_menu("Select cells")
}
proc mraster() {local i  localobj tv, yv, mi, mt
//	objref grasterm_
	if (rasterm_) {
		grasterm_ = new Graph()
		grasterm_.size(0, tstop, 0, nmitral)
		grasterm_.xaxis(3)
		grasterm_.xaxis(0, tstop,    0, 5,        0,0,1)
		grasterm_.yaxis(0, nmitral, 0, 5, 0,0,1)
		mi = new Vector()
		mi.indvwhere(pattern_idvec_, "[)", 0, nmitral)
		mt = new Vector()
		mt.index(pattern_tvec_.c, mi)
		mi.index(pattern_idvec_, mi)
		for i=0, mi.size-1 {
			grasterm_.mark(mt.x[i], mi.x[i], "|", 10, (i%8)+1, 1)
		}
	execute("barinit()")
	fih_bar = new FInitializeHandler(0, "cvode.event(0, \"bar()\")")
	}
}
proc graster() {local i, x  localobj tv, yv, gi, gt
	objref grasterg_
	if (rasterg_) {
		grasterg_ = new Graph()
		grasterg_.size(0, tstop, nmitral-1, nmitral+ngranule-1)
		grasterg_.xaxis(3)
		grasterg_.xaxis(0, tstop,    -.5, 5,        0,0,1)
		grasterg_.yaxis(nmitral-1, nmitral+ngranule-1, 0, 5,0,0,1)
		gi = new Vector()
		gi.indvwhere(pattern_idvec_, "[)", nmitral, nmitral+ngranule)
		gt = new Vector()
		gt.index(pattern_tvec_.c, gi)
		gi.index(pattern_idvec_, gi)
		gi.sub(nmitral)
		for i=0, gi.size-1 {
			grasterg_.mark(gt.x[i], gi.x[i], "|", 10, 1, 1)
		}
	}
}

proc p2f() {local i, j, sz  localobj sf, f, g1, glist, xvec, yvec, lines
	sf = new StringFunctions()
	glist = new List("Graph")
	lines = new List()
	xvec = new Vector()  yvec = new Vector()
	// Yuguo wants text output in matrix form for time plots
	//  (only save lines that have the same size)
	for i=0, glist.count-1 {
		g1 = glist.o(i)
		if (g1 != grasterg_ && g1 != grasterm_ && g1 != g) {
  for (j=-1; (j = g1.getline(j, xvec, yvec)) != -1; ) {
			if (sf.len(yvec.label()) > 1 && yvec.size > 1000) {
				if (lines.count == 0) {
					lines.append(xvec.c)
					lines.o(0).label("t")
					sz = xvec.size
				}
				if (sz == yvec.size) {
					lines.append(yvec.cl)
				}
			}
  }
		}
	}
	if (lines.count == 0) {
		return
	}
	f = new File()
	f.wopen($s1)
	f.printf("%d %d\n", lines.count, lines.o(0).size)
	for i=0, lines.count-1 {
		f.printf("\"%s\"\n",lines.o(i).label())
	}
	for i = 0, sz-1 {
		f.printf("%g", lines.o(0).x[i])
		for j=1, lines.count-1 {
			f.printf(" %g", lines.o(j).x[i])
		}
		f.printf("\n")
	}
	f.close()
}

proc draw() {local i, j, k, x, x0, x1, mx, mn, gi, b, def_color, i1   localobj mgr, sr
	def_color = 1
	if (wholenet_ == 0) { def_color = 9 }
	g.erase_all()
	for i1=0, moi.size-1 { i=moi.x[i1]
		x = mitral_x.x[i]
		g.beginline(9, 1)
	    if (ring) {
		x0 = -ls + x
		x1 = ls + x
		if (x0 < 0) {
			g.line(len + x0, i) g.line(len, i)
			x0 = 0
			g.flush() g.beginline(9, 1)
		}
		if (x1 > len) {
			g.line(0, i) g.line(x1-len, i)
			x1 = len
			g.flush() g.beginline(9, 1)
		}
		g.line(x0, i)
		g.line(x1, i)
	    }else{
		g.line(-ls + x, i)
		g.line(ls + x, i)	
	    }
//		g.flush()
		if (msel.x[i] == 1) {
			g.mark(x, i, "T", 10, 2, 1)
		}else{
			g.mark(x, i, "t", 10, def_color, 2)
		}
	}
	for i1=0, goi.size-1  {i = goi.x[i1]
		x = granule_x.x[i]
		if (gsel.x[i] == 1) {
			g.mark(x, -1, "O", 8, 3, 1)
		}else{
			g.mark(x, -1, "o", 8, def_color, 1)
		}
		g.beginline(9, 1)
		g.line(x, nmitral-.5)
		g.line(x, -1)
//		g.flush()
	}
//	for k=0, syns.count-1 {
//		mgr = syns.object(k)
//		mi = mgr.mitral_gid
//		gi = mgr.granule_gid - nmitral
	for i1 = 0, moi.size-1  {mi=moi.x[i1] for k=0, scm.sprowlen(mi)-1 {
		scm.spgetrowval(mi, k, &gi)
		x = granule_x.x[gi]
		j = mi
		b = 0
		if (msynsel.x[mi] || gsynsel.x[gi]) {
			b = 1
			g.mark(x, j, "O", 6, 4, 1)
		}else{
			if (msel.x[mi]) {
				b = 1
				if (gsel.x[gi]) {
					g.mark(x, j, "O", 5, 2, 1)
					g.mark(x, j, "o", 6, 3, 2)
				}else{
					g.mark(x, j, "O", 6, 2, 1)
				}
			}else if (gsel.x[gi]) {
				b = 1
				g.mark(x, j, "O", 6, 3, 1)
			}
		}
		if (b == 0) {
			if (wholenet_ == 1) {
				g.mark(x, j, "o", 4, 1, 1)
			}else if (hinton_movie) {
				g.mark(x, j, "O", 3, 1, 1)
			}
		}
		if (synsel1.getval(mi, gi)) {
			g.mark(x, j, "O", 6, 6, 1)
		}
	}}
	if (show_fi_cond_ && wholenet_ == 0) {
		fi_cond_init()
	}
	g.flush()
}
proc smode() {
	if (smode_ != $1) {
//		whole_net()
	}
	smode_ = $1
	sel_gid_ = -1
}
proc view_spikes() {localobj sv
	spike_viewer_ = 0
	if ($1 == 0) {
		sv = new SpikeViewer(pattern_tvec_, pattern_idvec_)
	}else{
		sv = new SpikeViewer1(pattern_tvec_, pattern_idvec_)
	}
}

proc select() {local m, g, min, x, i, j  localobj mgr, s
	if (wholenet_ != 1) { return }
	if ($1 == 2) { //press
		//print $1, $2, $3, $4
		if ($3 < -.5) {
			 m = -1
		} else {
			m = int($3+.5)
		}
		if (m >= nmitral) { m = -1}
		if (0 && m >= 0) { // closest to moi
			if (moi.indwhere("==", m) == -1) {
				//s = new String()
				//sprint(s.s, "Mitral %g not displayed", m)
				//continue_dialog(s.s)
				m = -1
			}
		}
		min = 1e9
		g = -1
		// assume granules evenly distributed from 0 to len
		g = int(ngranule*$2/len)
		if (g < 0) g = 0
		if (g >= ngranule) g = ngranule-1
		if (g >= 0) { // closest to g
			if (0 && goi.indwhere("==", g) == -1) {
				//s = new String()
				//sprint(s.s, "Mitral %g not displayed", g)
				//continue_dialog(s.s)
				g = -1
			}
		}
		//print smode_, m, g
	    if (smode_ == 1) { // selecting a cell
		if (m >= 0) {
			msel.x[m] = (msel.x[m] == 0)
			sel_gid_ = m
			sprint(sel_str_, "mitral gid %d", sel_gid_)
		}else if (g >= 0) {
			gsel.x[g] = (gsel.x[g] == 0)
			sel_gid_ = g + nmitral
			sprint(sel_str_, "granule gid %d", sel_gid_)
		}else{
			sel_gid_ = -1
			sel_str_ = "no selection" 
		}
	    }else if (smode_ == 2) { // selecting all syn for a cell
		if (m >= 0) {
			msynsel.x[m] = (msynsel.x[m] == 0)
			sel_gid_ = m
			sprint(sel_str_, "mitral gid %d", sel_gid_)
		}else if (g >= 0) {
			gsynsel.x[g] = (gsynsel.x[g] == 0)
			sel_gid_ = g + nmitral
			sprint(sel_str_, "granule gid %d", sel_gid_)
		}else{
			sel_gid_ = -1
			sel_str_ = "no selection" 
		}
	    }else{ // select individual synapses
		if (m > -1 && g > -1) {
//printf("%d %d %d\n", m, g, scm.getval(m, g))
			if (scm.getval(m, g)) {
				synsel1.x[m][g] = synsel1.x[m][g]==0
			}
		}
	    }
		sel2coi(0)
		sel2coi(1)
		draw()
	}
}

obfunc sellist() {localobj a
	if (smode_ == 1) {
		if ($1 == 0) { a = msel } else { a = gsel }
	}else if (smode_ == 2) {
		if ($1 == 0) { a = msynsel } else { a = gsynsel }
	}
	return a
}
proc str2sel() {local i  localobj s, a, sf
	sf = new StringFunctions()
	a = sellist($1)
	a.fill(0)
	while(sf.len($s2) > 0 && sscanf($s2,"%d", &i)) {
		if (i < 0) { continue }
		if ($1 == 0) {
			if (i >= nmitral) { continue }
		}else{
			if (i >= ngranule) { continue }
		}
		a.x[i] = 1
		sf.tail($s2, " ", $s2)
	}
}
obfunc sel2str() {local i localobj s, a
	s = new String()
	a = sellist($1)
	if(object_id(a) == 0){
		s.s = "Not Allowed"
	}else{
		for i=0, a.size-1 if (a.x[i]) {
			sprint(s.s, "%s %d", s.s, i)
		}
	}
	return s
}

proc sel2coi() {
	if ($1 == 0) {
		moi.indvwhere(msel.c.add(msynsel), ">", 0)
	} else {
		goi.indvwhere(gsel.c.add(gsynsel), ">", 0)
	}
}

proc mansel() {localobj label, s
	label = new String()
	if ($1 == 0) {
		label.s = "Space separated list of mitral id's"
	}else{
		label.s = "Space separated list of granule id's"
	}
	s = sel2str($1)
	if (string_dialog(label.s, s.s)) {
		str2sel($1, s.s)
		sel2coi($1)
		draw()
	}
}

proc sim() {local i, j, jx, x, mk
	if (wholenet_ != 1) { return }
//	if (smode_ != 1) { return }
	deck.flip_to(1)
	wholenet_ = 0
//	prune()
	create_subnet()
	draw()
	for i=0, synsel1.nrow-1 {
		for jx = 0, synsel1.sprowlen(i)-1 {
			x = synsel1.spgetrowval(i, jx, &j)
			syn_graph(mgfind(i, j))
		}
	}
	for i=0, msel.size-1 if (msel.x[i]) {
		v_movie(i)
		t_movie(i)
	}
	for i=0, gsel.size-1 if (gsel.x[i]) {
		t_movie(i + nmitral)
	}
	mk = 0
	for i=0, msynsel.size-1 if (msynsel.x[i]) {
		mk = 1
		if (object_id(syn_movie_list) == 0) {
			syn_movie_list = new List()
			syn_movie_nclist = new List()
		}
		syn_movie(i)
	}
	if (hinton_movie) {
		mkhinton(1)
		mk = 1
	}
	if (exc_hinton_movie) {
		mkhinton(2)
		mk = 1
	}
	if (inh_hinton_movie) {
		mkhinton(3)
		mk = 1
	}
	if (mk) {
syn_movie_fih = new FInitializeHandler("cvode.event(0, \"show_weight()\")", this)
	}
	show_weight()
	if (show_soma_spikes_) {
		fih_spikes = new FInitializeHandler(0, "cvode.event(0, \"spikesinit()\")")
	}
	if (show_fi_cond_) {
		fih_cond = new FInitializeHandler("cvode.event(20, \"fi_cond_update()\")", this)
	}
	execute("stdinit()")
}

objref fi_cond_vec[1]
proc fi_cond_init() {local i
	objref fi_cond_vec[nmitral]
	for i=0, nmitral-1 {
		fi_cond_vec[i] = new Vector(ngranule)
	}
	fi_cond_update1()
	for i=0, nmitral-1 {
		fi_cond_vec[i].plot(g, granule_x, 1, 1)
	}
	g.flush()
}
proc fi_cond_update() {
	fi_cond_update1()
	g.flush()
	cvode.event(t+20, "fi_cond_update()")
}

proc fi_cond_update1() {local i, m, g, scl  localobj mgrs, cvec, fi
	scl = 200
	for i=0, syns.count-1 {
		mgrs = syns.o(i)
		m = mgrs.mitral_gid
		g = mgrs.granule_gid - nmitral
		cvec = fi_cond_vec[m]
		fi = mgrs.fi
		if (object_id(fi)) {
			cvec.x[g] = fi.g*scl + m
		}
	}
}

proc whole_net() {local i
	pc.gid_clear()
	objref mgrsmap
	objref fih_spikes
	objref fih_cond
	for i=0, tplots.count-1 {
		tplots.o(i).unmap()
	}
	tplots.remove_all()
	objref keepsyn, keepnc, syn_movie_nclist, syn_movie_fih, syn_movie_list
	objref hinton_shape, exc_hinton_shape, inh_hinton_shape
	create keepsyn_sec
	keepsyn_sec { delete_section() }
	sel_gid_ = -1
	sel_str_ = "no selection"
//	reload_wholenet()
	clear()
	wholenet_ = 1
	deck.flip_to(0)
	draw()
}

proc v_movie() {localobj g, s
	s = new String()
	g = new Graph(0)	
	g.view(-Lsec, -80, 2*Lsec, 120, 400, 500+$1*300/nmitral, 700, 200)
	v_rvp_ = new RangeVarPlot("v")
	pc.gid2cell($1).secden[1] v_rvp_.begin(1)	
	pc.gid2cell($1).secden[0] v_rvp_.end(1)
	v_rvp_.origin(12.5)
	g.addobject(v_rvp_, 2, 1, 0.8, 0.9)
	sprint(s.s, "mitral gid %d", $1)
	g.label(.3,.9,s.s,2)
	flush_list.append(g)
	tplots.append(g)
}

proc t_movie() {localobj g, s
	s = new String()
	sprint(s.s, "gid %d: %s.soma.v(.5)", $1, pc.gid2cell($1))
	g = new Graph()
	addplot(g, 0)
	g.size(0, tstop, -80, 40)
	tplots.append(g)
	g.label(.3, 1, "", 2)
	pc.gid2cell($1).soma g.addvar(s.s, "v(0.5)", 1, 1) 
}

proc syn_graph() {localobj g, s, mgr
	mgr = $o1
	if (object_id(mgr) == 0) {
		execerror("syn_graph arg is nil")
	}
	s = new String()
	sprint(s.s, "syn (%d, %d)", mgr.mitral_gid, mgr.granule_gid)
	g = new Graph()
	addplot(g, 0)
	g.size(0, tstop, 0, 1)
	tplots.append(g)
	g.label(.3, .9, s.s, 2)
	sprint(s.s, "%s.weight[2]", mgr.gd2fi)
	g.addvar("fi", s.s, 3, 1)
	sprint(s.s, "%s.weight[2]", mgr.md2ampanmda)
	g.addvar("an", s.s, 2, 1)
}

proc syn_movie() {local i localobj g, s, nc, nclist1, nclist2, syn
	s = new String()
	g = new Graph(0)
	g.view(0, 0, len, 1, 400, 250+$1*400/nmitral, 700, 200)
	
	sprint(s.s, "mitral gid %d", $1)
	g.label(.3,.9,s.s,2)
	syn_movie_list.append(g)
	nclist1 = new List()
	nclist2 = new List()
	for i = 0, syns.count-1 {
		syn = syns.o(i)
		if (syn.mitral_gid == $1) {
			nclist1.append(syn.gd2fi)
			nclist2.append(syn.md2ampanmda)
		}
	}
	syn_movie_nclist.append(nclist1)
	syn_movie_nclist.append(nclist2)
}

proc show_weight() {local i, j, k, x, w  localobj g, nc, syn, nclist
	if (object_id(syn_movie_list)) for i=0, syn_movie_list.count-1 {
		g = syn_movie_list.o(i)
		g.erase()
		for j=0,1 {
			nclist = syn_movie_nclist.o(2*i + j)
			for k = 0, nclist.count - 1 {
				nc = nclist.o(k)
				syn = nc.syn
				x = syn.x
				w = nc.weight[2]
				if (j == 1) {
					g.mark(x, w, "S", 8, 2, 1)
				}else{
					g.mark(x, w, "s", 10, 3, 1)
				}
			}
		}
	}			
	if (object_id(hinton_shape)) {
		hinton_shape.flush()
	}
	if (object_id(exc_hinton_shape)) {
		exc_hinton_shape.flush()
	}
	if (object_id(inh_hinton_shape)) {
		inh_hinton_shape.flush()
	}
	cvode.event(t + 100, "show_weight()")
}

proc prune() {local i, mi, gi  localobj pc, keepa, keepf, mgr, nil, cell
	pc = new ParallelContext()
	pc.gid_clear()
	// 0 - destroy, 1 - keep where it is, 2 - move to safe place
	keepa = new Vector(syns.count)
	keepf = new Vector(syns.count)
	if (hinton_movie) { keepa.fill(2)  keepf.fill(2) }
	if (exc_hinton_movie) { keepa.fill(2) }
	if (inh_hinton_movie) { keepf.fill(2) }
	for i=0, syns.count-1 {
		mgr = syns.o(i)
		mi = mgr.mitral_gid
		gi = mgr.granule_gid - nmitral
		if (msynsel.x[mi]) {keepa.x[i] = 2  keepf.x[i] = 2 }
		if (gsynsel.x[gi]) {keepa.x[i] = 2  keepf.x[i] = 2 }
		if (synsel1.x[i]) {keepa.x[i] = 2  keepf.x[i] = 2 }
	}
	for i=0, syns.count-1 {
		mgr = syns.o(i)
		mi = mgr.mitral_gid
		gi = mgr.granule_gid - nmitral
		if (msel.x[mi]) {keepf.x[i] = 1}
		if (gsel.x[gi]) {keepa.x[i] = 1}
	}
	// move/destroy syns
	for i=0, syns.count-1 {
		mgr = syns.o(i)
		mgr.gd = nil
		mgr.md = nil
		if (keepf.x[i] == 2) {
			if (!section_exists("keepsyn_sec", this)) {
				create keepsyn_sec
			}
			keepsyn_sec mgr.fi.loc(.5)
			mgr.mitral = nil
		}
		if (keepa.x[i] == 2) {
			if (!section_exists("keepsyn_sec", this)) {
				create keepsyn_sec
			}
			keepsyn_sec mgr.ampanmda.loc(.5)
			mgr.granule = nil
			mgr.spine = nil
		}
		if (keepf.x[i] == 0) {
			mgr.gd2fi = nil
			mgr.fi = nil
			mgr.mitral = nil
			mgr.granule = nil
		}
		if (keepa.x[i] == 0) {
			mgr.md2ampanmda = nil
			mgr.ampanmda = nil
			mgr.mitral = nil
			mgr.granule = nil
			mgr.spine = nil
		}
	}
	// destroy cells
	for (i = cells.count-1; i >= 0; i -= 1) {
		cell = cells.o(i)
		if (i < nmitral) if(msel.x[i]) {
			pc.set_gid2node(i, pc.id)
			cell.soma pc.cell(i, new NetCon(&v(.5), nil))
			continue
		}
		if (i > nmitral) if (gsel.x[i - nmitral]) {
			pc.set_gid2node(i, pc.id)
			cell.soma pc.cell(i, new NetCon(&v(.5), nil))
			continue
		}
		cells.remove(i)
		cell = nil
	}
	// recreate connection using the original NetCon
	for i=0, syns.count-1 {
		mgr = syns.o(i)
		if (mgr.fi != nil) {
			pc.gid_connect(mgr.gd_gid, mgr.fi, mgr.gd2fi)
		}
		if (mgr.ampanmda != nil) {
			pc.gid_connect(mgr.md_gid, mgr.ampanmda, mgr.md2ampanmda)
		}
	}
}

proc create_subnet() {local i, m, j, x, g  localobj mgr, nil
	// first the cells, then synapses not on cells
	objref mgrsmap
	gidvec.resize(0)
	for i=0, msel.size-1 if (msel.x[i]) { gidvec.append(i) }
	for i=0, gsel.size-1 if (gsel.x[i]) { gidvec.append(i + nmitral) }
	mknet()
	create_stim()
	// if hinton we need all remaining syn, otherwise the msynsel...
	if (hinton_movie || exc_hinton_movie || inh_hinton_movie) {
		mk_mgrsmap()
		if (!section_exists("keepsyn_sec", this)) {
			create keepsyn_sec
		}
		keepsyn_sec for m=0, nmitral-1 for j=0, scm.sprowlen(m)-1 {
			scm.spgetrowval(m, j, &g)
			mgrs_extra(m, g)
		}
		objref mgrsmap
	}
	if (msynsel.indwhere("==", 1) >= 0) {
		mk_mgrsmap()
		if (!section_exists("keepsyn_sec", this)) {
			create keepsyn_sec
		}
		keepsyn_sec for m=0, nmitral-1 if (msynsel.x[m]) for j=0, scm.sprowlen(m)-1 {
			scm.spgetrowval(m, j, &g)
			mgrs_extra(m, g)
		}
		objref mgrsmap
	}
	if (gsynsel.indwhere("==", 1) >= 0) {
		mk_mgrsmap()
		if (!section_exists("keepsyn_sec", this)) {
			create keepsyn_sec
		}
		keepsyn_sec for g=0, ngranule-1 if (gsynsel.x[g]) for m=0, nmitral-1 {
			mgrs_extra(m, g)
		}
		objref mgrsmap
	}
	j=0
	for i=0, synsel1.nrow-1 if (synsel1.sprowlen(i) > 0) { j=1 break}
	if (j) {
		mk_mgrsmap()
		if (!section_exists("keepsyn_sec", this)) {
			create keepsyn_sec
		}
		keepsyn_sec for m=0, synsel1.nrow-1 for j=0, synsel1.sprowlen(m)-1 {
			if (synsel1.spgetrowval(m, j, &g)) {
				mgrs_extra(m, g)
			}
		}
	}
	objref mgrsmap
	mk_mgrsmap()
}

// create any synapses onto the cas for m,g that do not already exist
proc mgrs_extra() {localobj mgrs
	mgrs = mgfind($1, $2)
	if (object_id(mgrs)) {
		mgrs.complete()
		mgrs.fi.x = granule_x.x[$2]
		mgrs.ampanmda.x = granule_x.x[$2]
	}else{
		mgconnect($1, $2, 1)
	}
}

proc mk_mgrsmap() {local i  localobj po, keys, s
	if (object_id(mgrsmap) != 0) { return }
	po = new PythonObject()
	mgrsmap = po.dict()
	keys = new Vector(syns.count)
	for i=0, syns.count-1 {
		s = syns.o(i)
		keys.x[i] = s.mitral_gid + (s.granule_gid-nmitral)*nmitral
	}
	mgrsmap = mgrsmap.fromkeys(keys)
	for i=0, syns.count-1 {
		mgrsmap.__setitem__(keys.x[i], syns.o(i))
	}
//nrnpython("a = None")
//po.a = mgrsmap
//nrnpython("print a")
//print "hello"
}

obfunc mgfind() {
	return mgrsmap.get($1+nmitral*$2)
}

objref cmap

proc mkhinton() {local i, mx1, mx2, xmin, xmax, dx, ymin, ymax, yscl \
  localobj syn, sl, g
	xmin = 0  xmax = len
	dx = len/ngranule
//print "dx=", dx
	ymin = 0  ymax = nmitral
	yscl = (xmax - xmin)/(ymax - ymin) * 250/700 *.9
//	if (dx > yscl/2) { dx = yscl/2 * .9 }
//	hinton_build()
//proc hinton_build() {local mx1, mx2, sl
	sl = new SectionList()
	g = new PlotShape(sl,0)
	if ($1 == 1) hinton_shape = g else if ($1 == 2) exc_hinton_shape = g else inh_hinton_shape = g
	g.view(xmin, ymin, xmax-xmin, (ymax-ymin)*yscl, 400, 250, 700, 250)
	g.colormap(11)
	i = -1
g.colormap(i+=1, 111,  0,    111)
g.colormap(i+=1, 143,  0,    127)
g.colormap(i+=1, 175,  0,    95)
g.colormap(i+=1, 207,  0,    63)
g.colormap(i+=1, 223,  47,   47)
g.colormap(i+=1, 255,  79,   15)
g.colormap(i+=1, 255,  111,  0)
g.colormap(i+=1, 255,  143,  0)
g.colormap(i+=1, 255,  175,  0)
//g.colormap(i+=1, 255,  207,  0)
g.colormap(i+=1, 255,  239,  0)
//g.colormap(i+=1, 255,  255,  0)
g.colormap(i+=1, 255,  255,  200)

	g.scale(0,1)
	g.exec_menu("Shape Plot")
	hinton_draw(dx, $1, g)
}
proc hinton_draw() {local i, x, m, b, dx  localobj ncl, nc, syn, sr, s
	dx = $1
	s = new String()
	ncl = new List("NetCon")
	for i=0, ncl.count-1 {
		nc = ncl.object(i)
		syn = nc.syn
		classname(syn, s.s)
		if (strcmp(s.s, "FastInhib") == 0) {
			b = 1
		}else if (strcmp(s.s, "AmpaNmda") == 0) {
			b = 0
		}else{
			continue
		}
		x = syn.x
		m = syn.mgid		
		nc.weight[2] = 0
		if ($2 == 1) {
			$o3.hinton(&nc.weight[2], x, 3*m*dx+(dx)*b, dx)
		}else{
			if ($2 == 2 && b == 0) {
				$o3.hinton(&nc.weight[2], x, m*dx, dx)
			}
			if ($2 == 3 && b == 1) {
				$o3.hinton(&nc.weight[2], x, m*dx, dx)
			}
		}
	}
}

endtemplate ShowConnect

objref sc_
proc showconnect() {
	sc_ = new ShowConnect(cells, nmitral, ngranule, mgrs_list)
}
showconnect()

load_file("michele_movie.hoc")