measure.m

function varargout = measure(varargin)
% MEASURE MATLAB code for measure.fig
%      MEASURE, by itself, creates a new MEASURE or raises the existing
%      singleton*.
%
%      H = MEASURE returns the handle to a new MEASURE or the handle to
%      the existing singleton*.
%
%      MEASURE('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in MEASURE.M with the given input arguments.
%
%      MEASURE('Property','Value',...) creates a new MEASURE or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before measure_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to measure_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 measure

% Last Modified by GUIDE v2.5 08-Aug-2017 14:49:54

% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @measure_OpeningFcn, ...
                   'gui_OutputFcn',  @measure_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 measure is made visible.
function measure_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 measure (see VARARGIN)

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

% Update handles structure
guidata(hObject, handles);

% Storing the handle to the sweepset object
handles.paired_sweepset=varargin{1};

% Drawing all elements, but not making them visible
figure(handles.paired_sweepset.handles.figure)
handles.display_handles.peak_up=text(1,1,'empty','visible','off');
handles.display_handles.peak_down=text(1,1,'empty','visible','off');

% Deal with input arguments
for i=1:length(varargin)
    if ischar(varargin{i}) && strcmp(varargin{i},'start interval')
        % A start interval is suplied
        set(handles.measurement_start,'String',num2str(round(varargin{i+1}(1))));
        set(handles.measurement_end,'String',num2str(round(varargin{i+1}(2))));
    end
    if ischar(varargin{i}) && strcmp(varargin{i},'mode')
        % Measure either average or current trace
        if strcmp(varargin{i+1}, 'average')
            set(handles.select_current,'value',0)
            set(handles.select_average,'value',1)
        elseif strcmp(varargin{i+1}, 'current')
            set(handles.select_current,'value',1)
            set(handles.select_average,'value',0)
        else
            error([varargin{i+1}, ' is not a valid measurement mode.']);
        end 
        % Display the peak
        set(handles.display_handles.peak_up,'visible','on')
        set(handles.display_handles.peak_down,'visible','on')
        set(handles.display,'value',1)
    end
end

% Add listener
handles.listener=addlistener(handles.paired_sweepset,'state_change',@(scr, ev) update_everything(scr, ev, handles));

% Update handles structure
guidata(hObject, handles);

% Filling variables in the GUI (Voltage clamp by defaults, this switches to
% curent clamp)
set(handles.filename,'String',handles.paired_sweepset.filename)
if strcmp(handles.paired_sweepset.clamp_type,'Voltage (mV)')
    set(handles.text3,'String','Maximum (mV)')
    set(handles.text4,'String','Minimum (mV)')
end

% Find peaks
find_peak(handles);

% Setting a callback for then this GUI is closed and other callbacks
set(hObject,'CloseRequestFcn',{@close_req, handles})

% Putting the measure GUI at a location next to the active sweepset on the
% screen.
% Location of the sweepset figure:
hObject.Units='pixels';
Current_position=hObject.Position;
Sweepset_position=handles.paired_sweepset.handles.figure.Position;
hObject.Position=[Sweepset_position(1)+Sweepset_position(3),Sweepset_position(2)+Sweepset_position(4)-Current_position(4),Current_position(3), Current_position(4)];


% --- Outputs from this function are returned to the command line.
function varargout = measure_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;

function measurement_start_Callback(hObject, eventdata, handles)
% hObject    handle to measurement_start (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 measurement_start as text
%        str2double(get(hObject,'String')) returns contents of measurement_start as a double

find_peak(handles);

% --- Executes during object creation, after setting all properties.
function measurement_start_CreateFcn(hObject, eventdata, handles)
% hObject    handle to measurement_start (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 measurement_end_Callback(hObject, eventdata, handles)
% hObject    handle to measurement_end (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 measurement_end as text
%        str2double(get(hObject,'String')) returns contents of measurement_end as a double

find_peak(handles);

% --- Executes during object creation, after setting all properties.
function measurement_end_CreateFcn(hObject, eventdata, handles)
% hObject    handle to measurement_end (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 display.
function display_Callback(hObject, eventdata, handles)
% hObject    handle to display (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')==1;
    set(handles.display_handles.peak_up,'visible','on')
    set(handles.display_handles.peak_down,'visible','on')
else
    set(handles.display_handles.peak_up,'visible','off')
    set(handles.display_handles.peak_down,'visible','off')
end

% --- Executes on button press in select_current.
function select_current_Callback(hObject, eventdata, handles)
% hObject    handle to select_current (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 select_current

if get(handles.select_average,'value')==1
    set(handles.select_average,'value',0)
    find_peak(handles);
else
    set(hObject,'value',1)
end

% --- Executes on button press in select_average.
function select_average_Callback(hObject, eventdata, handles)
% hObject    handle to select_average (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 select_average

if get(handles.select_current,'value')==1 
    set(handles.select_current,'value',0)
    find_peak(handles);
else
    set(hObject,'value',1)
end


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

paired_sweepset=handles.paired_sweepset;
start_time=str2num(get(handles.measurement_start,'String'));
end_time=str2num(get(handles.measurement_end,'String'));

[~, start_index]=min(abs(paired_sweepset.X_data-start_time));
[~, end_index]=min(abs(paired_sweepset.X_data-end_time));

results=zeros(paired_sweepset.number_of_sweeps,1);
for i=1:paired_sweepset.number_of_sweeps
    results(i)=sum(paired_sweepset.data(start_index:end_index,paired_sweepset.current_channel,i));
end
results=results(paired_sweepset.sweep_selection);

figure()
plot(results)
xlabel('sweep #')
ylabel('Y values')
assignin('base','AUC_data',results)
disp('Data stored in workspace as AUC_data.')

% Calculate AUC of the average sweep
data=sum(paired_sweepset.average_trace(start_index:end_index));
disp(['AUC of average trace: ' num2str(data)]);


%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Callbacks %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% just to make sure that not only this GUI, but also it's associated
% doodles are closed.

function close_req(src,ev,handles)
delete(handles.display_handles.peak_up)
delete(handles.display_handles.peak_down)

 
delete(src)
delete(handles.listener)
 
function update_everything(scr,ev,handles)

find_peak(handles);

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Other %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function find_peak(handles)
paired_sweepset=handles.paired_sweepset;

if get(handles.select_average,'value')==1

    average_trace_handle=paired_sweepset.handles.average_trace;
    trace_to_analyse=get(average_trace_handle,'YData');

else
    trace_to_analyse=paired_sweepset.data(:,paired_sweepset.current_channel,paired_sweepset.current_sweep);
end    
    
SF=paired_sweepset.sampling_frequency;
timeline=squeeze(paired_sweepset.X_data);
start_time=str2num(get(handles.measurement_start,'String'));
end_time=str2num(get(handles.measurement_end,'String'));


[~, measurement_start]=min(abs(timeline-start_time));
[~, measurement_end]=min(abs(timeline-end_time));
%measurement_start=round(str2num(get(handles.measurement_start,'String'))*SF);
%measurement_end=round(str2num(get(handles.measurement_end,'String'))*SF);


[peak.up, peak.location_up]=max(trace_to_analyse(measurement_start:measurement_end));
[peak.down, peak.location_down]=min(trace_to_analyse(measurement_start:measurement_end));

peak.location_up=timeline(peak.location_up+measurement_start);
peak.location_down=timeline(peak.location_down+measurement_start);

display_text_up= ['\leftarrow     ',num2str(peak.up)];
display_text_down= ['\leftarrow     ',num2str(peak.down)];

set(handles.display_handles.peak_up,'Position',[peak.location_up,peak.up,0],'String',display_text_up);
set(handles.display_handles.peak_down,'Position',[peak.location_down,peak.down,0],'String',display_text_down);

% updating displayed vallues
set(handles.maximum,'String',num2str(peak.up))
set(handles.minimum,'String',num2str(peak.down))