function three_neuron_circuit_sim
% 3-neuron conductance network UI (compact, robust playback)
% - Three plots (A,B,C), fixed y [-80, 40] mV, linked x
% - DC sliders, momentary pulses (buttons + A/B/C keys)
% - Drug toggles (TTX / Picrotoxin / CNQX) with LED lamps + Reset
% - Play/Stop + Playback speed (0.1x..20x), visible spike peaks, final-frame flush

%% ----------------- Model params -----------------
P.T       = 2.0;         % s total
P.dt      = 1e-4;        % s step (0.1 ms)
P.t       = 0:P.dt:P.T;  P.nT = numel(P.t);

% Intrinsic (per neuron)
leakConductance = 1e-14 ;
% P.Cm      = 150e-12;            % F
P.Cm      = 100e-12;            % F
P.gL      = [12;12;12]*leakConductance;    % S [A;B;C]
P.EL      = -65e-3;             % V
P.Vreset  = -70e-3;             % V
P.Vthr0   = -48e-3;             % V
P.dVthr   = 12e-3;              % V
P.tau_thr = 0.12;               % s
P.t_ref   = 0.002;              % s

% Synapses (bi-exponential)
P.E_AMPA  = 0e-3;
P.E_GABA  = -70e-3;
P.tau_e   = 0.005;  P.rise_e = 0.001;  P.alpha_e = 1/(P.rise_e*P.tau_e);
P.tau_i   = 0.010;  P.rise_i = 0.002;  P.alpha_i = 1/(P.rise_i*P.tau_i);

% Synaptic weights (S)
excitSynConductance = 1e-11 ;
inhibSynConductance = 5e-9 ;
P.w_A_to_B_exc = excitSynConductance;  % A->B (AMPA)
P.w_C_to_A_exc = excitSynConductance;  % C->A (AMPA)
P.w_C_to_B_exc = excitSynConductance;  % C->B (AMPA)
P.w_B_to_A_inh = inhibSynConductance;  % B->A (GABA)

% Animation
P.play_speed  = 1.0;      % playback speed factor (0.1x ... 20x)
P.showSpikeMv = 30e-3;    % V (plot-only spike marker height)

%% ---- Figure with scrollable shell + fixed minimum content ----
%% ---- Figure + responsive main grid (no fixed content canvas) ----
f = uifigure('Name','3-Neuron Circuit','Color','w','Position',[100 100 900 600]);

% Main grid: plots left, controls right. This grid resizes with the window.
g = uigridlayout(f,[3 2], ...
    'RowHeight',{'1x','1x','1x'}, ...
    'ColumnWidth',{'3x','2x'}, ...
    'Padding',6,'RowSpacing',6,'ColumnSpacing',8);



%% ----------------- Axes (A/B/C) -----------------
axA = uiaxes(g); axA.Layout.Row=1; axA.Layout.Column=1; setupAxis(axA,'Neuron A',P);
axB = uiaxes(g); axB.Layout.Row=2; axB.Layout.Column=1; setupAxis(axB,'Neuron B',P);
axC = uiaxes(g); axC.Layout.Row=3; axC.Layout.Column=1; setupAxis(axC,'Neuron C',P);
linkaxes([axA,axB,axC],'x');

% Pre-create lines
lnA = plot(axA,nan,nan,'LineWidth',1.2);
lnB = plot(axB,nan,nan,'LineWidth',1.2);
lnC = plot(axC,nan,nan,'LineWidth',1.2);

%% ----------------- Right side: 3 rows x 2 cols -----------------
% --- Right side: scrollable column with a fixed-minimum canvas ---
rightScroll = uipanel(g, ...
    'Scrollable','on', ...
    'AutoResizeChildren','off');          % critical: don't auto-shrink children
rightScroll.Layout.Row    = [1 3];
rightScroll.Layout.Column = 2;

% A canvas that can be taller than the viewport -> triggers scrollbars
minRightHeight = 720;                     % tweak this to taste
rightCanvas = uipanel(rightScroll, ...
    'Units','pixels', ...
    'Position',[0 0 1 minRightHeight], ...
    'AutoResizeChildren','on');

% Keep the canvas at least minRightHeight tall; match width to viewport
rightScroll.SizeChangedFcn = @(~,~) ...
    set(rightCanvas,'Position',[0, 0, rightScroll.InnerPosition(3), ...
                               max(minRightHeight, rightScroll.InnerPosition(4))]);

% Your existing right-hand grid now lives INSIDE the canvas, not directly in g
rightStack = uigridlayout(rightCanvas,[3 2], ...
    'RowHeight',{200, 260, 140}, ...      % pixel heights ensure a real min size
    'ColumnWidth',{'1x','1x'}, ...
    'Padding',6,'RowSpacing',6,'ColumnSpacing',6);




% (1) DC Currents (Row 1, span both columns)
RH_DC_01 = 20 ;
RH_DC_02 = 40 ;

pDC = uipanel(rightStack,'Title','DC Current (pA)'); pDC.Layout.Row=1; pDC.Layout.Column=[1 2];
gc = uigridlayout(pDC,[6 2],'Padding',5,'RowSpacing',5,'ColumnWidth',{'1x',52},'RowHeight',{RH_DC_01,RH_DC_02,RH_DC_01,RH_DC_02,RH_DC_01,RH_DC_02});
uilabel(gc,'Text','A','FontWeight','bold');    rdA = uilabel(gc,'Text','0','HorizontalAlignment','right');
sA = uislider(gc,'Limits',[-300 300],'Value',0,'MajorTicks',-300:150:300); sA.Layout.Column=[1 2];
uilabel(gc,'Text','B','FontWeight','bold');    rdB = uilabel(gc,'Text','0','HorizontalAlignment','right');
sB = uislider(gc,'Limits',[-300 300],'Value',0,'MajorTicks',-300:150:300); sB.Layout.Column=[1 2];
uilabel(gc,'Text','C','FontWeight','bold');    rdC = uilabel(gc,'Text','0','HorizontalAlignment','right');
sC = uislider(gc,'Limits',[-300 300],'Value',0,'MajorTicks',-300:150:300); sC.Layout.Column=[1 2];
sA.ValueChangedFcn = @(src,~) set(rdA,'Text',sprintf('%+4.0f',src.Value));
sB.ValueChangedFcn = @(src,~) set(rdB,'Text',sprintf('%+4.0f',src.Value));
sC.ValueChangedFcn = @(src,~) set(rdC,'Text',sprintf('%+4.0f',src.Value));

% (2) Pulses (Row 2, Column 1)
pPulse = uipanel(rightStack,'Title','Pulses'); pPulse.Layout.Row=2; pPulse.Layout.Column=1;
RH_Pulses_01 = 20 ;
RH_Pulses_02 = 20 ;

gp = uigridlayout(pPulse,[6 3],'Padding',6,'RowSpacing',6,'ColumnWidth',{72,66,'1x'},'RowHeight',{RH_Pulses_01,RH_Pulses_02,RH_Pulses_01,RH_Pulses_02,RH_Pulses_01,RH_Pulses_02});
uilabel(gp,'Text','Pulse A','FontWeight','bold');
btnPulseA = uibutton(gp,'state','Text','OFF','Value',false,'ValueChangedFcn',@(bt,~) set(bt,'Text',tern(bt.Value,'ON','OFF')));
ampA = uieditfield(gp,'numeric','Limits',[-500 500],'Value',150,'ValueDisplayFormat','%+g'); ampA.Layout.Column=3; ampA.Layout.Row=1;
uilabel(gp,'Text','Pulse B','FontWeight','bold');
btnPulseB = uibutton(gp,'state','Text','OFF','Value',false,'ValueChangedFcn',@(bt,~) set(bt,'Text',tern(bt.Value,'ON','OFF')));
ampB = uieditfield(gp,'numeric','Limits',[-500 500],'Value',150,'ValueDisplayFormat','%+g'); ampB.Layout.Column=3; ampB.Layout.Row=2;
uilabel(gp,'Text','Pulse C','FontWeight','bold');
btnPulseC = uibutton(gp,'state','Text','OFF','Value',false,'ValueChangedFcn',@(bt,~) set(bt,'Text',tern(bt.Value,'ON','OFF')));
ampC = uieditfield(gp,'numeric','Limits',[-500 500],'Value',150,'ValueDisplayFormat','%+g'); ampC.Layout.Column=3; ampC.Layout.Row=3;
% uilabel(pPulse,'Text','Hold keys A/B/C to inject while held.','FontAngle','italic','Position',[6 2 220 16]);

% (2b) Pharmacology (Row 2, Column 2) with LEDs + Reset
pDrug = uipanel(rightStack,'Title','Pharmacology'); pDrug.Layout.Row=2; pDrug.Layout.Column=2;
gd = uigridlayout(pDrug,[4 3],'Padding',6,'RowSpacing',6,'ColumnWidth',{18,'1x',100},'RowHeight',{24,24,24,24});
LED_ON=[0 0.75 0]; LED_OFF=[0.6 0.6 0.6];
lampTTX = uilamp(gd);  lampTTX.Color=LED_OFF;    btnTTX  = uibutton(gd,'state','Text','TTX: OFF','Value',false);
btnTTX.ValueChangedFcn  = @(bt,~) drugToggle(bt,lampTTX,'TTX',LED_ON,LED_OFF);
lampPIC = uilamp(gd);  lampPIC.Color=LED_OFF;    btnPicro= uibutton(gd,'state','Text','Picrotoxin: OFF','Value',false);
btnPicro.ValueChangedFcn= @(bt,~) drugToggle(bt,lampPIC,'Picrotoxin',LED_ON,LED_OFF);
lampCNQX= uilamp(gd);  lampCNQX.Color=LED_OFF;   btnCNQX = uibutton(gd,'state','Text','CNQX: OFF','Value',false);
btnCNQX.ValueChangedFcn = @(bt,~) drugToggle(bt,lampCNQX,'CNQX',LED_ON,LED_OFF);
btnResetDrugs = uibutton(gd,'Text','Reset','ButtonPushedFcn',@(~,~) resetAllDrugs());
lampTTX.Layout.Row=1; lampTTX.Layout.Column=1; btnTTX.Layout.Row=1; btnTTX.Layout.Column=[2 3];
lampPIC.Layout.Row=2; lampPIC.Layout.Column=1; btnPicro.Layout.Row=2; btnPicro.Layout.Column=[2 3];
lampCNQX.Layout.Row=3; lampCNQX.Layout.Column=1; btnCNQX.Layout.Row=3; btnCNQX.Layout.Column=[2 3];
btnResetDrugs.Layout.Row=4; btnResetDrugs.Layout.Column=[2 3];

% (3) Run controls (Row 3, span both columns)
pRun = uipanel(rightStack,'Title','Run'); pRun.Layout.Row=3; pRun.Layout.Column=[1 2];
RW_Play_01 = 30 ;
RW_Play_02 = 40 ;
gr = uigridlayout(pRun,[2 3],'Padding',6,'RowSpacing',6,'ColumnWidth',{86,86,'1x'},'RowHeight',{RW_Play_01,RW_Play_02});
btnPlay = uibutton(gr,'push','Text','Play','ButtonPushedFcn',@(~,~) runOnce());
btnStop = uibutton(gr,'push','Text','Stop','ButtonPushedFcn',@(~,~) setappdata(f,'stopFlag',true),'Enable','off');
lbl     = uilabel(gr,'Text','Ready','HorizontalAlignment','right'); lbl.Layout.Column=3;

% Playback speed (0.1x .. 20x), visibly different at low vs high
lblSpeed = uilabel(gr,'Text','Speed (×): 1.00','HorizontalAlignment','left');
sSpeed = uislider(gr, ...
    'Limits',[0.1 20], ...
    'Value',P.play_speed, ...
    'MajorTicks',[0.1 2 5 10 20], ...
    'MinorTicks',[], ...
    'ValueChangingFcn',@(s,evt) set(lblSpeed,'Text',sprintf('Speed (×): %.2f',evt.Value)) );
sSpeed.Layout.Column=[2 3];

%% ----------------- Keyboard hold-to-inject -----------------
set(f,'WindowKeyPressFcn',  @(~,evt) keyHold(evt,true));
set(f,'WindowKeyReleaseFcn',@(~,evt) keyHold(evt,false));
setappdata(f,'keysHeld',struct('a',false,'b',false,'c',false));

%% ----------------- Store shared handles -----------------
setappdata(f,'P',P);
setappdata(f,'axes',{axA,axB,axC});
setappdata(f,'lines',{lnA,lnB,lnC});
setappdata(f,'sDC',{sA,sB,sC});
setappdata(f,'pulseBtns',{btnPulseA,btnPulseB,btnPulseC});
setappdata(f,'pulseAmps',{ampA,ampB,ampC});
setappdata(f,'drugBtns',struct('TTX',btnTTX,'Picro',btnPicro,'CNQX',btnCNQX));
setappdata(f,'drugLamps',struct('TTX',lampTTX,'Picro',lampPIC,'CNQX',lampCNQX));
setappdata(f,'drugColors',struct('ON',LED_ON,'OFF',LED_OFF));
setappdata(f,'speedSlider',sSpeed);
setappdata(f,'statusLabel',lbl);

%% ----------------- Callbacks -----------------
    function runOnce()
        P = getappdata(f,'P'); t = P.t;
        sDC = getappdata(f,'sDC');
        IA = sDC{1}.Value*1e-12; IB = sDC{2}.Value*1e-12; IC = sDC{3}.Value*1e-12;
        Ibase = [IA; IB; IC];

        btnPlay.Enable='off'; btnStop.Enable='on';
        sDC{1}.Enable='off'; sDC{2}.Enable='off'; sDC{3}.Enable='off';
        setappdata(f,'stopFlag',false);

        lbl = getappdata(f,'statusLabel');
        lbl.Text = sprintf('Running: I_A=%+g pA, I_B=%+g pA, I_C=%+g pA', sDC{1}.Value, sDC{2}.Value, sDC{3}.Value);

        [VA_plot,VB_plot,VC_plot] = simulateAndAnimate(Ibase);

        % Final frame flush
        L = getappdata(f,'lines'); tms = t*1e3;
        set(L{1},'XData',tms,'YData',VA_plot*1e3);
        set(L{2},'XData',tms,'YData',VB_plot*1e3);
        set(L{3},'XData',tms,'YData',VC_plot*1e3);
        drawnow;

        if getappdata(f,'stopFlag'), lbl.Text='Stopped'; else, lbl.Text='Done'; end
        btnPlay.Enable='on'; btnStop.Enable='off';
        sDC{1}.Enable='on'; sDC{2}.Enable='on'; sDC{3}.Enable='on';
    end

    function [VA_plot,VB_plot,VC_plot] = simulateAndAnimate(Ibase)
        P   = getappdata(f,'P');   t = P.t;
        L   = getappdata(f,'lines'); lnA=L{1}; lnB=L{2}; lnC=L{3};
        pulseBtns = getappdata(f,'pulseBtns'); pulseAmps = getappdata(f,'pulseAmps');
        drugBtns  = getappdata(f,'drugBtns');
        axs = getappdata(f,'axes'); axA=axs{1};

        % Playback speed factor (0.1x .. 20x)
        speed = max(0.1, getappdata(f,'speedSlider').Value);
        frameSkip = max(1, round(speed * 6));             % ~6 at 1x, ~120 at 20x
pausePerFrame = 0;                                 % default: no pause= 1:P
if speed < 1
    % gentle pause only when slowing down
    pausePerFrame = min(0.02, 0.008 / speed);      % 8 ms @1x -> 80 ms @0.1x (capped at 20 ms)
end

% NEW: UI event poll cadence (process button changes even if not drawing)
uiPollEvery = 10;   % steps between event polls (~1 ms if dt=0.1 ms)


        % State
        V   = repmat(P.EL,3,1);  Vthr = repmat(P.Vthr0,3,1);  tref = zeros(3,1);
        rE = zeros(3,1); sE = zeros(3,1); rI = zeros(3,1); sI = zeros(3,1);
        VA = zeros(1,P.nT); VB = zeros(1,P.nT); VC = zeros(1,P.nT);
        VA_plot = VA; VB_plot = VB; VC_plot = VC;

        % Clear traces; with linked x, set once on A
        set(lnA,'XData',[],'YData',[]); set(lnB,'XData',[],'YData',[]); set(lnC,'XData',[],'YData',[]);
        xlim(axA,[0 t(end)*1e3]);

        for k = 1:P.nT
            % Process queued UI events regularly for snappy buttons
            if mod(k, uiPollEvery) == 0
                drawnow limitrate;   % processes callbacks without heavy repaints
            end
            
            % Quick stop check (stop button sets stopFlag)
            if getappdata(f,'stopFlag')
                % draw whatever we have to the plots, then exit cleanly
                tms = t(1:max(k-1,1))*1e3;
                set(lnA,'XData',tms,'YData',VA_plot(1:max(k-1,1))*1e3);
                set(lnB,'XData',tms,'YData',VB_plot(1:max(k-1,1))*1e3);
                set(lnC,'XData',tms,'YData',VC_plot(1:max(k-1,1))*1e3);
                drawnow;
                return;
            end

            % Drugs
            TTX_on   = drugBtns.TTX.Value;
            PICRO_on = drugBtns.Picro.Value;
            CNQX_on  = drugBtns.CNQX.Value;

            % Currents (base + pulses + key holds)
            I = Ibase;
            if pulseBtns{1}.Value, I(1)=I(1)+pulseAmps{1}.Value*1e-12; end
            if pulseBtns{2}.Value, I(2)=I(2)+pulseAmps{2}.Value*1e-12; end
            if pulseBtns{3}.Value, I(3)=I(3)+pulseAmps{3}.Value*1e-12; end
            KH = getappdata(f,'keysHeld');
            if KH.a, I(1)=I(1)+pulseAmps{1}.Value*1e-12; end
            if KH.b, I(2)=I(2)+pulseAmps{2}.Value*1e-12; end
            if KH.c, I(3)=I(3)+pulseAmps{3}.Value*1e-12; end

            % Record current Vm (and default plot values)
            VA(k)=V(1); VB(k)=V(2); VC(k)=V(3);
            VA_plot(k)=V(1); VB_plot(k)=V(2); VC_plot(k)=V(3);

            % Refractory countdown
            tref = max(0, tref - P.dt);

            % Receptor block (instant)
            if CNQX_on, rE(:)=0; sE(:)=0; end
            if PICRO_on, rI(:)=0; sI(:)=0; end

            % Syn conductances for this step
            gE = sE; if CNQX_on, gE(:)=0; end
            gI = sI; if PICRO_on, gI(:)=0; end

            % Membrane ODE
            dV = ( -P.gL.*(V-P.EL) - gE.*(V-P.E_AMPA) - gI.*(V-P.E_GABA) + I ) ./ P.Cm;

            % Refractory clamp
            mask_ref = (tref > 0); dV(mask_ref)=0; V(mask_ref)=P.Vreset;

            % Integrate membrane
            V = V + P.dt*dV;

            % Threshold relaxation
            Vthr = Vthr + P.dt*((P.Vthr0 - Vthr)/P.tau_thr);

            % Spike detection (TTX blocks spiking)
            if TTX_on, spk = [false;false;false];
            else,      spk = (V >= Vthr) & (tref == 0);
            end

            % Spike events (with receptor gating)
            if spk(1)
                VA_plot(k)=P.showSpikeMv; V(1)=P.Vreset; Vthr(1)=Vthr(1)+P.dVthr; tref(1)=P.t_ref;
                if ~CNQX_on, rE(2)=rE(2)+P.w_A_to_B_exc*P.alpha_e; sE(2)=sE(2)+P.w_A_to_B_exc; end
            end
            if spk(2)
                VB_plot(k)=P.showSpikeMv; V(2)=P.Vreset; Vthr(2)=Vthr(2)+P.dVthr; tref(2)=P.t_ref;
                if ~PICRO_on, rI(1)=rI(1)+P.w_B_to_A_inh*P.alpha_i; sI(1)=sI(1)+P.w_B_to_A_inh; end
            end
            if spk(3)
                VC_plot(k)=P.showSpikeMv; V(3)=P.Vreset; Vthr(3)=Vthr(3)+P.dVthr; tref(3)=P.t_ref;
                if ~CNQX_on
                    rE(1)=rE(1)+P.w_C_to_A_exc*P.alpha_e; sE(1)=sE(1)+P.w_C_to_A_exc;
                    rE(2)=rE(2)+P.w_C_to_B_exc*P.alpha_e; sE(2)=sE(2)+P.w_C_to_B_exc;
                end
            end

            % Synapse kinetics
            rE = rE + P.dt*(-rE/P.rise_e);  sE = sE + P.dt*(-sE/P.tau_e + rE);
            rI = rI + P.dt*(-rI/P.rise_i);  sI = sI + P.dt*(-sI/P.tau_i + rI);

            % --------- Animate with speed control (frameSkip + pause) ---------
          % --------- Animate with speed control (frameSkip + optional pause) ---------
            if mod(k, frameSkip) == 0 || k == P.nT
                tms = t(1:k)*1e3;
                set(lnA,'XData',tms,'YData',VA_plot(1:k)*1e3);
                set(lnB,'XData',tms,'YData',VB_plot(1:k)*1e3);
                set(lnC,'XData',tms,'YData',VC_plot(1:k)*1e3);
            
                if getappdata(f,'stopFlag')
                    drawnow;              % final flush with callbacks
                    return;
                else
                    drawnow limitrate;    % service callbacks & throttle repaint rate
                    if pausePerFrame > 0
                        pause(pausePerFrame);   % only at slow speeds
                    end
                end
            end


        end

        % Ensure last frame draws fully
        tms = t*1e3;
        set(lnA,'XData',tms,'YData',VA_plot*1e3);
        set(lnB,'XData',tms,'YData',VB_plot*1e3);
        set(lnC,'XData',tms,'YData',VC_plot*1e3);
        drawnow;
    end

    function keyHold(evt,isDown)
        KH = getappdata(f,'keysHeld');
        if isfield(evt,'Key')
            switch lower(evt.Key)
                case 'a', KH.a = isDown;
                case 'b', KH.b = isDown;
                case 'c', KH.c = isDown;
            end
            setappdata(f,'keysHeld',KH);
        end
    end
end

%% ----------------- Helpers -----------------
function setupAxis(ax,label,P)
title(ax,label);
xlim(ax,[0 P.t(end)*1e3]); ylim(ax,[-80 40]);
yline(ax,P.Vthr0*1e3,'k--','Baseline thr');
xlabel(ax,'Time (ms)'); ylabel(ax,'V_m (mV)');
ax.Box='on'; ax.FontSize=10;
end

function drugToggle(bt,lamp,labelTxt,ON,OFF)
if bt.Value
    set(bt,'Text',[labelTxt ': ON']); set(lamp,'Color',ON);
else
    set(bt,'Text',[labelTxt ': OFF']); set(lamp,'Color',OFF);
end
end

function resetAllDrugs()
db = getappdata(gcf,'drugBtns'); dl = getappdata(gcf,'drugLamps'); C = getappdata(gcf,'drugColors');
set(db.TTX,'Value',false);   set(db.TTX,'Text','TTX: OFF');           set(dl.TTX,'Color',C.OFF);
set(db.Picro,'Value',false); set(db.Picro,'Text','Picrotoxin: OFF');  set(dl.Picro,'Color',C.OFF);
set(db.CNQX,'Value',false);  set(db.CNQX,'Text','CNQX: OFF');         set(dl.CNQX,'Color',C.OFF);
end

function out = tern(cond,a,b)
if cond, out=a; else, out=b; end
end

function localResizeContent(shell, content, baseW, baseH)
ip = shell.InnerPosition;      % [x y w h] of the scrollable viewport
content.Position(3) = max(baseW, ip(3));   % grow with window, but never below baseW
content.Position(4) = max(baseH, ip(4));   % grow with window, but never below baseH
end