SCN9A/clamp.m

function varargout = clamp(varargin)
% CLAMP MATLAB code for clamp.fig
%      CLAMP, by itself, creates a new CLAMP or raises the existing
%      singleton*.
%
%      H = CLAMP returns the handle to a new CLAMP or the handle to
%      the existing singleton*.
%
%      CLAMP('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in CLAMP.M with the given input arguments.
%
%      CLAMP('Property','Value',...) creates a new CLAMP or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before clamp_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to clamp_OpeningFcn via varargin.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES

% Edit the above text to modify the response to help clamp

% Last Modified by GUIDE v2.5 01-Aug-2018 17:00:38

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
    'gui_Singleton',  gui_Singleton, ...
    'gui_OpeningFcn', @clamp_OpeningFcn, ...
    'gui_OutputFcn',  @clamp_OutputFcn, ...
    'gui_LayoutFcn',  [] , ...
    'gui_Callback',   []);
if nargin && ischar(varargin{1})
    gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT


% --- Executes just before clamp is made visible.
function clamp_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   command line arguments to clamp (see VARARGIN)

% Update the current L&F
%originalLnF = javax.swing.UIManager.getLookAndFeel;  %class
%newLnF = 'javax.swing.plaf.metal.MetalLookAndFeel';  %string
%javax.swing.UIManager.setLookAndFeel(newLnF);

% Restore the original L&F
%javax.swing.UIManager.setLookAndFeel(originalLnF);

%Create a data acquisition session
handles.devices = daq.getDevices;
handles.daqSession = daq.createSession('ni');

%  Add channels specified by subsystem type and device
chAI0=addAnalogInputChannel(handles.daqSession,'Dev1', 0, 'Voltage');
chAI0.TerminalConfig = 'SingleEndedNonReferenced';
chAI1=addAnalogInputChannel(handles.daqSession,'Dev1', 1, 'Voltage');
chAI1.TerminalConfig = 'SingleEndedNonReferenced';
chAO0=addAnalogOutputChannel(handles.daqSession,'Dev1', 0, 'Voltage');

%  Configure Data Acquisition Properties
handles.daqSession.Rate = 100000;
handles.secToAccuire=1;%Sample period in seconds
handles.vHold=-100;
handles.scaleFactorI=0.1; %0.1 V per uA
handles.scaleFactorV=10; %V output scaled 10x on OC-725C
handles.mVconversion=1000; %To mV
handles.mSconversion=1000; %To mS
handles.msToSamples=handles.daqSession.Rate/handles.mSconversion;
handles.saveData=0;
handles.leakSubtraction=0;
handles.PathName='C:\Users\Hugo\Documents\MATLAB';
handles.FileName='clamp.mat';
handles.btnStop=0;

% Axis lim
handles.xMin = 300;
handles.xMax = 350;
handles.yMinI = -5;
handles.yMaxI = 0;
handles.yMinV = -120;
handles.yMaxV = 80;

% Info
handles.newCell=0;
handles.human=0;
handles.neandertal=0;
handles.iData=[];
handles.vData=[];
handles.time=[];

plot(handles.axes1,[],[]);
xlabel(handles.axes1,'Time (ms)');
ylabel(handles.axes1,'Current (uA)');
axis(handles.axes1,[handles.xMin handles.xMax handles.yMinI handles.yMaxI]);

plot(handles.axes2,[],[]);
xlabel(handles.axes2,'Time (ms)');
ylabel(handles.axes2,'Voltage (mV)');
axis(handles.axes2,[handles.xMin handles.xMax handles.yMinV handles.yMaxV]);

% Choose default command line output for clamp
handles.output = hObject;

% Update handles structure
guidata(hObject, handles);



% UIWAIT makes clamp wait for user response (see UIRESUME)
% uiwait(handles.figure1);


% --- Outputs from this function are returned to the command line.
function varargout = clamp_OutputFcn(hObject, eventdata, handles)
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure
varargout{1} = handles.output;

% --- Executes on button press in actFastInact.
function actFastInact_Callback(hObject, eventdata, handles)
% hObject    handle to actFastInact (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
handles.btnStop=0;
guidata(hObject, handles);

hold(handles.axes1,'off');
hold(handles.axes2,'off');

holdingVoltage=handles.vHold;
testPulsStart=holdingVoltage;
testPulsEnd=20;
testPulsInactivation=0;
sleepTime=10;
%Stockholmsprotokollet. 9-11 grader. Oklart vilken paus mellan?

preStimulusTime=60;        %ms   
stimulus1Time=300;          %ms
stimulus2Time=40;          %mS
postStimulusTime=120;        %mS

samplesToAcquire=(preStimulusTime+stimulus1Time+stimulus2Time+postStimulusTime)*handles.msToSamples;

nrOfSweeps=(testPulsStart-(testPulsEnd))/-10+1;
iData=zeros(samplesToAcquire,nrOfSweeps);
vData=zeros(samplesToAcquire,nrOfSweeps);
time=zeros(samplesToAcquire,nrOfSweeps);

testPuls=testPulsStart;

i=1;
while testPuls<=testPulsEnd% used to be 10 steps
    
    if i>1
    pause(sleepTime);
    end
        
    drawnow() %Give the abort callback a chance to interrupt
    handles = guidata(hObject); %Update the GUI data
    if handles.btnStop==1 % stop condition
        disp('Aborted.')
		break;
    end
    

    preStimulusVoltage=holdingVoltage;        %mV    
    preStimulus=preStimulusVoltage*ones(preStimulusTime*handles.msToSamples,1);
    
    stimulus1Voltage=holdingVoltage+(i-1)*10;  %mV
    stimulus1=stimulus1Voltage*ones(stimulus1Time*handles.msToSamples,1);
    
    stimulus2Voltage=testPulsInactivation;             %mV
    stimulus2=stimulus2Voltage*ones(stimulus2Time*handles.msToSamples,1);
    
    postStimulusVoltage=holdingVoltage;       %mV
    postStimulus=postStimulusVoltage*ones(postStimulusTime*handles.msToSamples,1);
    
    line0=vertcat(preStimulus,stimulus1,stimulus2,postStimulus); 
    
    queueOutputData(handles.daqSession,line0*(handles.scaleFactorV/handles.mVconversion));
    [inputData,time(:,i),triggerTime] = handles.daqSession.startForeground();
    
    iData(:,i)=(1/handles.scaleFactorI)*inputData(:,1); %data in uA
    vData(:,i)=(handles.mVconversion/handles.scaleFactorV)*inputData(:,2); %data in mV
    
    %Leak subtraction
    if 1>0 %(handles.leakSubtraction==0)
        iDataPlot=iData(:,i);
    else
        iDataPlot=iData(:,i)-mean(iData(38000:40000,i));
    end
    
    iDataPlot=movmean(iDataPlot,20);
    
    plot(handles.axes1,handles.mSconversion*time(:,1),iDataPlot);
    xlabel(handles.axes1,'Time (ms)');
    ylabel(handles.axes1,'Current (uA)');
    axis(handles.axes1,[handles.xMin handles.xMax handles.yMinI handles.yMaxI]);
    hold(handles.axes1,'on');
        
    plot(handles.axes2,handles.mSconversion*time(:,1),vData(:,i));
    xlabel(handles.axes2,'Time (ms)');
    ylabel(handles.axes2,'Voltage (mV)');
    axis(handles.axes2,[handles.xMin handles.xMax handles.yMinV handles.yMaxV]);
    hold(handles.axes2,'on');
    
    disp(['Clamped ', num2str(stimulus1Voltage),' mV']);
    
    testPuls=testPuls+10;
    i=i+1;
end

handles.type='fast';
handles.iData=iData;
handles.vData=vData;
handles.time=time;
guidata(hObject, handles);

% --- Executes on button press in slowkinetics.
function slowkinetics_Callback(hObject, eventdata, handles)
% hObject    handle to slowkinetics (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% hObject    handle to actFastInact (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

hold(handles.axes1,'off');
hold(handles.axes2,'off');

preStimulusTime=100;        %ms   
stimulus1Time=10000;        %mS
stimulus2Time=100;          %mS
stimulus3Time=200;          %mS
postStimulusTime=100;       %mS

holdingVoltage=-120;
testPulsStart=-120;
testPulsEnd=-20;
sleepTime=10; %Seconds

samplesToAcquire=(preStimulusTime+stimulus1Time+stimulus2Time+stimulus3Time+postStimulusTime)*handles.msToSamples;

nrOfSweeps=(testPulsStart-(testPulsEnd))/-10+1;
iData=zeros(samplesToAcquire,nrOfSweeps);
vData=zeros(samplesToAcquire,nrOfSweeps);
time=zeros(samplesToAcquire,nrOfSweeps);

testPuls=testPulsStart;
i=1;
while testPuls<=testPulsEnd% used to be 10 steps
   
    if i>1
    pause(sleepTime);
    end
    
    preStimulusVoltage=holdingVoltage;        %mV    %Used to be minus 120
    preStimulus=preStimulusVoltage*ones(preStimulusTime*handles.msToSamples,1);
        
    stimulus1Voltage=testPuls;   %mV %Used to be minus 140  * 10
    stimulus1=stimulus1Voltage*ones(stimulus1Time*handles.msToSamples,1);
    
    stimulus2Voltage=holdingVoltage;   %mV %Used to be minus 120
    stimulus2=stimulus2Voltage*ones(stimulus2Time*handles.msToSamples,1);
    
    stimulus3Voltage=0;   %mV
    stimulus3=stimulus3Voltage*ones(stimulus3Time*handles.msToSamples,1);
    
    postStimulusVoltage=holdingVoltage;       %mV
    postStimulus=postStimulusVoltage*ones(postStimulusTime*handles.msToSamples,1);
    
    line0=vertcat(preStimulus,stimulus1,stimulus2,stimulus3,postStimulus); 
    
    queueOutputData(handles.daqSession,line0*(handles.scaleFactorV/handles.mVconversion));
    [inputData,time(:,i),triggerTime] = handles.daqSession.startForeground();
    
    iData(:,i)=(1/handles.scaleFactorI)*inputData(:,1); %data in uA
    vData(:,i)=(handles.mVconversion/handles.scaleFactorV)*inputData(:,2); %data in mV
    
    %Leak subtraction
    if 1<0%(handles.leakSubtraction==0)
       iDataPlot=iData(:,i);
    else
       iDataPlot=iData(:,i)-max(iData((preStimulusTime+stimulus1Time+stimulus2Time+0.5*stimulus3Time:preStimulusTime+stimulus1Time+stimulus2Time+stimulus3Time)*handles.msToSamples,i));
    end
    
    iDataPlot=movmean(iDataPlot,20);
    
    plot(handles.axes1,handles.mSconversion*time(:,1),iDataPlot);
    xlabel(handles.axes1,'Time (ms)');
    ylabel(handles.axes1,'Current (uA)');
    axis(handles.axes1,[handles.xMin handles.xMax handles.yMinI handles.yMaxI]);
    hold(handles.axes1,'on');
        
    plot(handles.axes2,handles.mSconversion*time(:,1),vData(:,i));
    xlabel(handles.axes2,'Time (ms)');
    ylabel(handles.axes2,'Voltage (mV)');
    axis(handles.axes2,[handles.xMin handles.xMax handles.yMinV handles.yMaxV]);
    hold(handles.axes2,'on');
    
    disp(['Clamped ', num2str(stimulus1Voltage),' mV']);
    
    testPuls=testPuls+10;
    i=i+1;
end

handles.type='slow';
handles.iData=iData;
handles.vData=vData;
handles.time=time;
guidata(hObject, handles);

% --- Executes on button press in resurgent.
function resurgent_Callback(hObject, eventdata, handles)
% hObject    handle to resurgent (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
hold(handles.axes1,'off');
hold(handles.axes2,'off');

preStimulusTime=100;        %ms   
stimulus1Time=20;           %ms
stimulus2Time=500;          %mS
postStimulusTime=100;       %mS

samplesToAcquire=(preStimulusTime+stimulus1Time+stimulus2Time+postStimulusTime)*handles.msToSamples;

iData=zeros(samplesToAcquire,11);
vData=zeros(samplesToAcquire,11);
time=zeros(samplesToAcquire,11);

for i=1:1%11
    
    preStimulusVoltage=-100;        %mV    
    preStimulus=preStimulusVoltage*ones(preStimulusTime*handles.msToSamples,1);
    
    stimulus1Voltage=30;             %mV
    stimulus1=stimulus1Voltage*ones(stimulus1Time*handles.msToSamples,1);
    
    stimulus2Voltage=-80+(i-1)*10;           %mV
    stimulus2=stimulus2Voltage*ones(stimulus2Time*handles.msToSamples,1);
      
    postStimulusVoltage=-100;       %mV
    postStimulus=postStimulusVoltage*ones(postStimulusTime*handles.msToSamples,1);
    
    line0=vertcat(preStimulus,stimulus1,stimulus2,postStimulus); 
    
    queueOutputData(handles.daqSession,line0*(handles.scaleFactorV/handles.mVconversion));
    [inputData,time(:,i),triggerTime] = handles.daqSession.startForeground();
    
    iData(:,i)=(1/handles.scaleFactorI)*inputData(:,1); %data in uA
    vData(:,i)=(handles.mVconversion/handles.scaleFactorV)*inputData(:,2); %data in mV
    
    %Leak subtraction
    if(handles.leakSubtraction==0)
       iDataPlot=iData(:,i);
    else
       iDataPlot=iData(:,i)-mean(iData(500*handles.msToSamples:600*handles.msToSamples,i));
    end
    
    iDataPlot=movmean(iDataPlot,200);
    
    plot(handles.axes1,handles.mSconversion*time(:,1),iDataPlot);
    xlabel(handles.axes1,'Time (ms)');
    ylabel(handles.axes1,'Current (uA)');
    axis(handles.axes1,[handles.xMin handles.xMax handles.yMinI handles.yMaxI]);
    hold(handles.axes1,'on');
        
    plot(handles.axes2,handles.mSconversion*time(:,1),vData(:,i));
    xlabel(handles.axes2,'Time (ms)');
    ylabel(handles.axes2,'Voltage (mV)');
    axis(handles.axes2,[handles.xMin handles.xMax handles.yMinV handles.yMaxV]);
    hold(handles.axes2,'on');
    
    disp(['Clamped ', num2str(stimulus2Voltage),' mV']);
    pause(2.5);
end

handles.type='resurgent';
handles.iData=iData;
handles.vData=vData;
handles.time=time;
guidata(hObject, handles);

% --- Executes on button press in pushbutton2.
function pushbutton2_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% Run Session & Acquire Data
%line0=vertcat(ones(handles.daqSession.Rate*1,1), ones(handles.daqSession.Rate*0,1));

handles.vHold = str2double(get(handles.edit1,'String'));
line0=handles.vHold*ones(handles.daqSession.Rate,1);

%vHold = str2double(get(handles.edit1,'String'));
%line0=vHold*ones(handles.daqSession.Rate,1);

queueOutputData(handles.daqSession,line0*(handles.scaleFactorV/handles.mVconversion));
[data,time,triggerTime] = handles.daqSession.startForeground();
guidata(hObject, handles);


% --- Executes on button press in save.
function save_Callback(hObject, eventdata, handles)
% hObject    handle to save (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
%'iData','vData','time',

iData=handles.iData;
vData=handles.vData;
time=handles.time;
newCell=handles.newCell;
human=handles.human;
neandertal=handles.neandertal;
%type=handles.type;
temp=str2double(get(handles.temp,'String'));
conc=str2double(get(handles.conc,'String'));
days=str2double(get(handles.days,'String'));
fileNr=length(dir('*.mat'))+1;

if newCell==1
    str='_newcell';
else
    str='';
end

if human==1
    save(strcat(date,'_',num2str(fileNr),'_human',str),'human','neandertal','iData','vData','time','days','conc','temp');
    disp('Data saved.')
elseif neandertal==1
    save(strcat(date,'_',num2str(fileNr),'_neandertal_M932L',str),'human','neandertal','iData','vData','time','days','conc','temp');
    disp('Data saved.')
else
    disp('No species set. Data could not be saved.')
end


% --- Executes on button press in newcell.
function newcell_Callback(hObject, eventdata, handles)
% hObject    handle to newcell (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
if (get(hObject,'Value') == get(hObject,'Max'))
    handles.newCell=1;
else
    handles.newCell=0;
end
% Update handles structure
guidata(hObject, handles);

% --- Executes on button press in pushbutton3.
function pushbutton3_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

[handles.FileName,handles.PathName] = uiputfile('*.mat','Save data to');
% Update handles structure
guidata(hObject, handles);


function edit1_Callback(hObject, eventdata, handles)
% hObject    handle to edit1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit1 as text
%        str2double(get(hObject,'String')) returns contents of edit1 as a double


% --- Executes during object creation, after setting all properties.
function edit1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function xminset_Callback(hObject, eventdata, handles)
% hObject    handle to xminset (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of xminset as text
%        str2double(get(hObject,'String')) returns contents of xminset as a double


% --- Executes during object creation, after setting all properties.
function xminset_CreateFcn(hObject, eventdata, handles)
% hObject    handle to xminset (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end


% --- Executes on button press in setaxes.
function setaxes_Callback(hObject, eventdata, handles)
% hObject    handle to setaxes (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
axis(handles.axes1,[str2double(get(handles.xminset,'String')) str2double(get(handles.xmaxset,'String')) str2double(get(handles.yminset,'String')) str2double(get(handles.ymaxset,'String'))]);
handles.xMin = str2double(get(handles.xminset,'String'));
handles.xMax = str2double(get(handles.xmaxset,'String'));
handles.yMinI = str2double(get(handles.yminset,'String'));
handles.yMaxI = str2double(get(handles.ymaxset,'String'));
handles.yMinV = -120;
handles.yMaxV = 80;
guidata(hObject, handles);




function xmaxset_Callback(hObject, eventdata, handles)
% hObject    handle to xmaxset (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of xmaxset as text
%        str2double(get(hObject,'String')) returns contents of xmaxset as a double


% --- Executes during object creation, after setting all properties.
function xmaxset_CreateFcn(hObject, eventdata, handles)
% hObject    handle to xmaxset (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function yminset_Callback(hObject, eventdata, handles)
% hObject    handle to yminset (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of yminset as text
%        str2double(get(hObject,'String')) returns contents of yminset as a double


% --- Executes during object creation, after setting all properties.
function yminset_CreateFcn(hObject, eventdata, handles)
% hObject    handle to yminset (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function ymaxset_Callback(hObject, eventdata, handles)
% hObject    handle to ymaxset (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of ymaxset as text
%        str2double(get(hObject,'String')) returns contents of ymaxset as a double


% --- Executes during object creation, after setting all properties.
function ymaxset_CreateFcn(hObject, eventdata, handles)
% hObject    handle to ymaxset (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function checkbox5_Callback(hObject, eventdata, handles)
% hObject    handle to save (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of save

if (get(hObject,'Value') == get(hObject,'Max'))
    handles.leakSubtraction=1;
else
    handles.leakSubtraction=0;
end
% Update handles structure
guidata(hObject, handles);


% --- Executes on button press in pushbutton9.
function pushbutton9_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton9 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
handles.sweep=9999;
%Update handles structure
guidata(hObject, handles);


% --- Executes on button press in human.
function human_Callback(hObject, eventdata, handles)
% hObject    handle to human (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
if (get(hObject,'Value') == get(hObject,'Max'))
    handles.human=1;
else
    handles.human=0;
end
% Update handles structure
guidata(hObject, handles);



% --- Executes on button press in neandertal.
function neandertal_Callback(hObject, eventdata, handles)
% hObject    handle to neandertal (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
if (get(hObject,'Value') == get(hObject,'Max'))
    handles.neandertal=1;
else
    handles.neandertal=0;
end
% Update handles structure
guidata(hObject, handles);



function days_Callback(hObject, eventdata, handles)
% hObject    handle to days (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of days as text
%        str2double(get(hObject,'String')) returns contents of days as a double


% --- Executes during object creation, after setting all properties.
function days_CreateFcn(hObject, eventdata, handles)
% hObject    handle to days (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function conc_Callback(hObject, eventdata, handles)
% hObject    handle to conc (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of conc as text
%        str2double(get(hObject,'String')) returns contents of conc as a double


% --- Executes during object creation, after setting all properties.
function conc_CreateFcn(hObject, eventdata, handles)
% hObject    handle to conc (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function temp_Callback(hObject, eventdata, handles)
% hObject    handle to temp (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of temp as text
%        str2double(get(hObject,'String')) returns contents of temp as a double


% --- Executes during object creation, after setting all properties.
function temp_CreateFcn(hObject, eventdata, handles)
% hObject    handle to temp (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end


% --- Executes on button press in checkbox9.
function checkbox9_Callback(hObject, eventdata, handles)
% hObject    handle to checkbox9 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of checkbox9


% --- Executes on button press in pushbutton14.
function pushbutton14_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton14 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

preStimulusTime=100;        %ms   
stimulus1Time=100;          %ms
postStimulusTime=100;        %mS

samplesToAcquire=(preStimulusTime+stimulus1Time+postStimulusTime)*handles.msToSamples;

nrOfSweeps=1;
iData=zeros(samplesToAcquire,nrOfSweeps);
vData=zeros(samplesToAcquire,nrOfSweeps);
time=zeros(samplesToAcquire,nrOfSweeps);

for i=1:nrOfSweeps
    preStimulusVoltage=handles.vHold;        %mV    
    preStimulus=preStimulusVoltage*ones(preStimulusTime*handles.msToSamples,1);
    
    stimulus1Voltage=handles.vHold+10;  %mV
    stimulus1=stimulus1Voltage*ones(stimulus1Time*handles.msToSamples,1);
 
    postStimulusVoltage=handles.vHold;       %mV
    postStimulus=postStimulusVoltage*ones(postStimulusTime*handles.msToSamples,1);
    
    line0=vertcat(preStimulus,stimulus1,postStimulus); 
    
    queueOutputData(handles.daqSession,line0*(handles.scaleFactorV/handles.mVconversion));
    [inputData,time(:,i),triggerTime] = handles.daqSession.startForeground();
    
    iData(:,i)=(1/handles.scaleFactorI)*inputData(:,1); %data in uA
    vData(:,i)=(handles.mVconversion/handles.scaleFactorV)*inputData(:,2); %data in mV
end

disp(['Membrane resistance is ', num2str(0.01/(mean(iData(150*handles.msToSamples:200*handles.msToSamples,1))-mean(iData(1*handles.msToSamples:50*handles.msToSamples,1)))),' MOhm at ', num2str(handles.vHold), 'mV' ]);


% --- Executes on button press in pushbutton15.
function pushbutton15_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton15 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
handles.btnStop=1;
guidata(hObject, handles);