function varargout=axontp(varargin)
%
% AXONTP 
%
%    VARARGOUT = AXONTP
%         Testpulse program for Axon amplifier using one shot
%         acquisition.
%         Assumes the following: 
%           - Frequency = 10KHz 
%           - Command sensitivity = 100 mV/V
%           - Output gain = 1 V/nA
%
%         This program delivers a testpulse (currently 2mV in amplitude
%         and 20msec wide) on both output channels, and monitors the output
%         current.  Also plots the access resistance over time.
%

	global handles datafighandles

	% If we were called with no arguments means we were called straight
	% from matlab; so we will set up the figure.

	if nargin==0

		% Set up the main figure

		mainfig = figure;
		uicontrol('style','checkbox','units','inches','position',[4.2 6.5 1.2 .3],'string','testpulse (on)','tag','power','backgroundcolor',[.1 .4 .9],'callback','axontp(''conflute'')');
		axes('units','inches','position',[1.25 4 3 2],'tag','axes1'); ...
			xlabel('time, ms'); 
		axes('units','inches','position',[5.25 4 3 2],'tag','axes2'); ...
			xlabel('time, ms'); 
		axes('units','inches','position',[1.25 1 3 2],'tag','axes3'); ...
			xlabel('time, s');
		axes('units','inches','position',[5.25 1 3 2],'tag','axes4'); ...
			xlabel('time, s');
		set(mainfig,'Units','inches','color',[.8 .3 0],'pointer','custom', ...
			'position',[.1 3.5 9.25 7],'handlevisibility','on',...
			'name','Axon Testpulse');
		handles=guihandles(mainfig);

		%----------------------------------------

		% Set up the accessory figure with the data values

		datafig = figure;


		yvalue = 6.4;

		for ichannel = 1:2

			% Amplifier 1 Label
			uicontrol('style','text','units','inches','position',[.2 yvalue 2.1 .2], ...
				'FontName', 'helvetica', 'FontSize',12, 'FontWeight', 'bold',...
				'HorizontalAlignment', 'left', 'string',sprintf('Amplifier %d', ichannel), ...
				'backgroundcolor',[.9 .9 0]);

			%% Rtotal
			yvalue = yvalue - 0.3;
			uicontrol('style','text','units','inches','position',[.2 yvalue .5 .2], ...
				'FontName', 'helvetica', 'FontSize',12, ...
				'HorizontalAlignment', 'left', 'string','Rtot.', ...
				'backgroundcolor',[.9 .9 0]);
            uicontrol('style','text','units','inches','position',[.75 yvalue 1 .2], ...
				'FontName', 'helvetica', 'FontSize',12, ...
				'HorizontalAlignment', 'left', 'string','no value', ...
				'tag',sprintf('rtot%d',ichannel),'backgroundcolor',[.9 .9 0]);
			uicontrol('style','text','units','inches','position',[1.8 yvalue .5 .2], ...
				'FontName', 'helvetica', 'FontSize',10, ...
				'tag',sprintf('rtot%d_units',ichannel), 'HorizontalAlignment', 'left',...
				'string','Mohms', 'backgroundcolor',[.9 .9 0]);
    
			%% Rseries
			yvalue = yvalue - .3;
			uicontrol('style','text','units','inches','position',[.2 yvalue .5 .2], ...
				'FontName', 'helvetica', 'FontSize',12, ...
				'HorizontalAlignment', 'left', 'string','Rser.', ...
				'backgroundcolor',[.9 .9 0]);
			uicontrol('style','text','units','inches','position',[.75 yvalue 1 .2], ...
				'FontName', 'helvetica', 'FontSize',12, ...
				'HorizontalAlignment', 'left', 'string','no value', ...
				'tag',sprintf('rser%d',ichannel),'backgroundcolor',[.9 .9 0]);
			uicontrol('style','text','units','inches','position',[1.8 yvalue .5 .2], ...
				'FontName', 'helvetica', 'FontSize',10, ...
				'HorizontalAlignment', 'left', 'string','Mohms', ...
				'backgroundcolor',[.9 .9 0]);

			%% Rpipette
			yvalue = yvalue - .3;
			uicontrol('style','text','units','inches','position',[.2 yvalue .5 .2], ...
				'FontName', 'helvetica', 'FontSize',12, ...
				'HorizontalAlignment', 'left', 'string','Rpip.', ...
				'backgroundcolor',[.9 .9 0]);
			uicontrol('style','text','units','inches','position',[.75 yvalue 1 .2], ...
				'FontName', 'helvetica', 'FontSize',12, ...
				'HorizontalAlignment', 'left', 'string','not set', ...
				'tag',sprintf('rpip%d',ichannel),'backgroundcolor',[.9 .9 0]);
			uicontrol('style','text','units','inches','position',[1.8 yvalue .5 .2], ...
				'FontName', 'helvetica', 'FontSize',10, ...
				'HorizontalAlignment', 'left', 'string','Mohms', ...
				'backgroundcolor',[.9 .9 0]);
			uicontrol('style','checkbox','units','inches','position',[.75 (yvalue-.35) ...
				1.6 .3], 'FontName', 'helvetica', 'FontSize',10, ...
				'tag',sprintf('rpip%dc',ichannel),'HorizontalAlignment', 'left', ...
				'string','Set Rpipette', 'backgroundcolor',[.9 .9 0], ...
				'callback', sprintf('axontp(''setrpipette'')', ichannel));
    
			%% Ra
			yvalue = yvalue - .75;
			uicontrol('style','text','units','inches','position',[.2 yvalue .5 .2], ...
				'FontName', 'helvetica', 'FontSize',12, ...
				'HorizontalAlignment', 'left', 'string','Ra', ...
				'backgroundcolor',[.9 .9 0]);
			uicontrol('style','text','units','inches','position',[.75 yvalue 1 .2], ...
				'FontName', 'helvetica', 'FontSize',12, ...
				'HorizontalAlignment', 'left', 'string','no value', ...
				'tag',sprintf('ra%d',ichannel),'backgroundcolor',[.9 .9 0]);
			uicontrol('style','text','units','inches','position',[1.8 yvalue .5 .2], ...
				'FontName', 'helvetica', 'FontSize',10, ...
				'HorizontalAlignment', 'left', 'string','Mohms', ...
				'backgroundcolor',[.9 .9 0]);

			%% Rm
			yvalue = yvalue - .3;
			uicontrol('style','text','units','inches','position',[.2 yvalue .5 .2], ...
				'FontName', 'helvetica', 'FontSize',12, ...
				'HorizontalAlignment', 'left', 'string','Rm', ...
				'backgroundcolor',[.9 .9 0]);
			uicontrol('style','text','units','inches','position',[.75 yvalue 1 .2], ...
				'FontName', 'helvetica', 'FontSize',12, ...
				'HorizontalAlignment', 'left', 'string','no value', ...
				'tag',sprintf('rm%d',ichannel),'backgroundcolor',[.9 .9 0]);
			uicontrol('style','text','units','inches','position',[1.8 yvalue .5 .2], ...
				'FontName', 'helvetica', 'FontSize',10, ...
				'HorizontalAlignment', 'left', 'string','Mohms', ...
				'backgroundcolor',[.9 .9 0]);
    
			%% Cm
			yvalue = yvalue -.3;
			uicontrol('style','text','units','inches','position',[.2 yvalue .5 .2], ...
				'FontName', 'helvetica', 'FontSize',12, ...
				'HorizontalAlignment', 'left', 'string','Cm', ...
				'backgroundcolor',[.9 .9 0]);
			uicontrol('style','text','units','inches','position',[.75 yvalue 1 .2], ...
				'FontName', 'helvetica', 'FontSize',12, ...
				'HorizontalAlignment', 'left', 'string','no value', ...
				'tag',sprintf('cm%d',ichannel), 'backgroundcolor',[.9 .9 0]);
			uicontrol('style','text','units','inches','position',[1.8 yvalue .5 .2], ...
				'FontName', 'helvetica', 'FontSize',10, ...
				'HorizontalAlignment', 'left', 'string','pFarads', ...
				'backgroundcolor',[.9 .9 0]);

			yvalue = yvalue - 1.3;

		end
    
		set(datafig,'Units','inches','color',[.8 .3 0],'pointer','custom', ...
			'position',[10 3.5 2.5 7],'handlevisibility','on','name','Axon Datascreen');

		datafighandles = guihandles(datafig);

		% -- Both the figures have now been set up ------------------------------

		if nargout > 0
			varargout{1} = fig;
		end

	% The elseif below goes with the "if nargin == 0" above
	%

	elseif ischar(varargin{1}) % INVOKE NAMED SUBFUNCTION OR CALLBACK

		try
			if (nargout)
				[varargout{1:nargout}] = feval(varargin{:});
			else
				feval(varargin{:}); % FEVAL switchyard
			end

		catch
			disp(lasterr);

		end

	end


%-------------------------------------------------------------------
% This is the main function, the one that gets called when the
% testpulse button is pressed.
%-------------------------------------------------------------------

function varargout=conflute(varargin)

	% We need the Rtotal to be global because it is  used to transfer
	% data to setrpipette.
	global handles datafighandles Rtotal

	%init parameters
	Fs = 10000;         % Frequency (in Hz)
	stimlength = 1000;  % in samples
	pulsewidth = 200;   % in samples
	scaling = 100;      % mV/V, the command sensitivity of the amplifier
	gain = 1;           % V/nA, the output gain of the amplifier
	amplitude = 2;      % mV, amplitude of test pulse
	nrepeat = 1;        % number of times we want the testpulse repeated

	% We will only do things here if the "testpulse" button is on.  If
	% not, we will just lie here and shrivel.
    
	power = get(handles.power,'value');

	if power == 1

		% We will have two x axes: one called time, in msecs, to
		% plot the output current, and one called rrtime, in secs,
		% to plot the access resistance over time.
    
		chan0 = zeros(1,600);
		chan1 = zeros(1,600);
		rr = zeros(999,2);
		time = [1:600] * 1000 / Fs;          %units in msec
		rrtime=[1:999] * stimlength / Fs;    %units in sec
 
		% create handles to plots in respective axes				      
		axes(handles.axes1); 
		pl1 = plot(time,chan0); xlabel('Time (ms)'); ylabel('current (pA)');
		axes(handles.axes2); 
		pl2 = plot(time,chan1); xlabel('Time (ms)'); ylabel('current (pA)');
		axes(handles.axes3);
		pl3 = plot(rrtime,rr(:,1)); xlabel('Time (s)'); set(gca,'ylim',[0 ...
			200],'xlim',[0 100]); ylabel('R_{access} (M\Omega)');
		axes(handles.axes4);
		pl4 = plot(rrtime,rr(:,2)); xlabel('Time (s)'); set(gca,'ylim',[0 ...
			200],'xlim',[0 100]); ylabel('R_{access} (M\Omega)');
		set(gcf, 'doublebuffer', 'on');
      
		% While the "testpulse" button is pressed, this while loop will
		% execute, sending out a testpulse and plotting the output appropriately
		
		while get(handles.power,'value')==1;

			% Call testpulse now
			[Rtotal Rseries Rmem Cmem Ileak current] = testpulse(Fs, scaling, gain, amplitude, pulsewidth, nrepeat);
			
			% Rseries is returned in ohms, and we want to plot it in megaohms,
			% so we convert it here.
			for ichannel = 1:2
				rr(:,ichannel) = [rr(2:999,ichannel); Rseries(ichannel)*10^-6];
			end
			
			% First we update the four graphs
			
			set(pl1, 'ydata', current(:,1));  
			set(pl2, 'ydata', current(:,2));  
			set(pl3, 'ydata', rr(:,1));
			set(pl4, 'ydata', rr(:,2));
			drawnow;
			
			% Now we update the text fields with the different resistance
			% and capacitance values
			%
			% We check to see that the datascreen window exists, because
			% we allow the user to turn it off.
			
			if (findobj('name', 'Axon Datascreen'))
			
				% We will display the total resistance in Mohms or Gohms depending
				% on the approximate range
				if (Rtotal(1) > 10^9)
					set(datafighandles.rtot1,'string',sprintf('%3.1f', (Rtotal(1)*10^-9)));
					set(datafighandles.rtot1_units,'string','Gohms');
				else
					set(datafighandles.rtot1,'string',sprintf('%3.1f', (Rtotal(1)*10^-6)));
					set(datafighandles.rtot1_units,'string','Mohms');
				end

				if (Rtotal(2) > 10^9)
					set(datafighandles.rtot2,'string',sprintf('%3.1f', (Rtotal(2)*10^-9)));
					set(datafighandles.rtot2_units,'string','Gohms');
				else
					set(datafighandles.rtot2,'string',sprintf('%3.1f', (Rtotal(2)*10^-6)));
					set(datafighandles.rtot2_units,'string','Mohms');
				end

				set(datafighandles.rser1,'string',sprintf('%2.1f', (Rseries(1)*10^-6)));
				set(datafighandles.rser2,'string',sprintf('%2.1f', (Rseries(2)*10^-6)));

				if (strcmp(get(datafighandles.rpip1,'string'), 'not set'))
					set(datafighandles.ra1,'string',sprintf('%2.1f', (Rseries(1)*10^-6)));
				else
					rpipette = str2num(get(datafighandles.rpip1,'string')) * 10^6;
					set(datafighandles.ra1,'string',sprintf('%2.1f', ((Rseries(1)-rpipette)*10^-6)));
				end
				if (strcmp(get(datafighandles.rpip2,'string'), 'not set'))
					set(datafighandles.ra2,'string',sprintf('%2.1f', (Rseries(2)*10^-6)));
				else
					rpipette = str2num(get(datafighandles.rpip2,'string')) * 10^6;
					set(datafighandles.ra2,'string',sprintf('%2.1f', ((Rseries(2)-rpipette)*10^-6)));
				end
				
				set(datafighandles.rm1,'string',sprintf('%2.1f', (Rmem(1)*10^-6)));
				set(datafighandles.rm2,'string',sprintf('%2.1f', (Rmem(2)*10^-6)));
				
				set(datafighandles.cm1,'string',sprintf('%2.1f', (Cmem(1)*10^12)));
				set(datafighandles.cm2,'string',sprintf('%2.1f', (Cmem(2)*10^12)));
				
				drawnow;

			end
    
			% Now we're done updating everything.  Yahoo!

			pause(0.1)

		end

	end

%-------------------------------------------------------------------

% When user clicks on Set R_pipette, this transfers the resistance
% during the voltage step (should be just rt since there are no
% capacitors involved), to the R_pipette value.
%
% This should be done ONLY when the pipette is in the bath not near
% a cell. Setting R_pipette ensures accurate calculation of the
% access resistance Ra during the patch.

function setrpipette

	% We need the Rtotal to be global because that's how we
	% get data from the acquisition routine.  The return value
	% is not transferred in a variable; the acquisition function
	% simply reads the string that we set here.
	
	global datafighandles Rtotal
	
	if (strcmp (get(gcbo, 'tag'), 'rpip1c'))
		if get(gcbo, 'value') == 1
			set(datafighandles.rpip1,'string',sprintf('%2.1f', (Rtotal(1)*10^-6)));
		else
			set(datafighandles.rpip1,'string', 'not set');
		end
	else
		if get(gcbo, 'value') == 1
			set(datafighandles.rpip2,'string',sprintf('%2.1f', (Rtotal(2)*10^-6)));
		else
			set(datafighandles.rpip2,'string', 'not set');
		end
	end


%-------------------------------------------------------------------