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

% Last Modified by GUIDE v2.5 08-Oct-2003 14:19:46

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @PBC_OpeningFcn, ...
                   'gui_OutputFcn',  @PBC_OutputFcn, ...
                   'gui_LayoutFcn',  [] , ...
                   'gui_Callback',   []);
if nargin & isstr(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 PBC is made visible.
function PBC_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 PBC (see VARARGIN)

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

% Update handles structure
guidata(hObject, handles);

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


% --- Outputs from this function are returned to the command line.
function varargout = PBC_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 pushbutton1.
function pushbutton1_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)


% --- Executes on button press in togglebutton1.
function togglebutton1_Callback(hObject, eventdata, handles)
% hObject    handle to togglebutton1 (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 togglebutton1


% --- Executes on button press in checkbox1.
function checkbox1_Callback(hObject, eventdata, handles)
% hObject    handle to checkbox1 (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 checkbox1


% --- Executes during object creation, after setting all properties.
function number_CreateFcn(hObject, eventdata, handles)
% hObject    handle to number (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
    set(hObject,'BackgroundColor','white');
else
    set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end



function number_Callback(hObject, eventdata, handles)
% hObject    handle to number (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 number as text
%        str2double(get(hObject,'String')) returns contents of number as a double
  I=str2double(get(hObject, 'String'));
  handles.num_data = I;
  guidata(hObject, handles);
  
% --- Executes during object creation, after setting all properties.
function File_name_CreateFcn(hObject, eventdata, handles)
% hObject    handle to File_name (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
    set(hObject,'BackgroundColor','white');
else
    set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end



function File_name_Callback(hObject, eventdata, handles)
% hObject    handle to File_name (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 File_name as text
%        str2double(get(hObject,'String')) returns contents of File_name as a double
  fname=get(hObject, 'String');
  handles.fname = fname;
  guidata(hObject, handles);

% --- Executes during object creation, after setting all properties.
function PB_name_CreateFcn(hObject, eventdata, handles)
% hObject    handle to PB_name (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
    set(hObject,'BackgroundColor','white');
else
    set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end



function PB_name_Callback(hObject, eventdata, handles)
% hObject    handle to PB_name (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 PB_name as text
%        str2double(get(hObject,'String')) returns contents of PB_name as a double
  dname=get(hObject, 'String');
  handles.dname = dname;
  guidata(hObject, handles);


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

dname=handles.dname;
I=handles.num_data;

DNAMEIN=sprintf('%s.xls', dname);
data_all = xlsread(DNAMEIN);
   Plane_initial = data_all(1:I);                      % Plane array goes from 1 to I
   num_Int = data_all(I+1:2*I);                % absolute value intensities for the numerator
   denom_Int = data_all(2*I+1:3*I);            % absolute value intensities for the denominator
      num_Int_norm = num_Int ./ num_Int(1);        % calculates normalized intensity values for numerator, normalized to t=0  
      denom_Int_norm = denom_Int ./ denom_Int(1);  % calculates normalized intensity values for denominator, normalized to t=0

Plane = (Plane_initial - 1).';                       % makes plane array start from zero instead of 1 for data fitting purposes      
      
Ratio = (num_Int_norm ./ denom_Int_norm).';        % calculates the ratio of the normalized instensities 

outliers = ~excludedata(Plane, Ratio, 'range', [0 0.1]);  % sets fit exclusion range in Y values

[fresult,gof] = fit(Plane, Ratio, 'exp2', 'exclude', outliers);        % double exponential fit, Plane numbers as X and normalized Ratio as Y 
% display (fresult);                  % displays fitted parameters and coefficients
% display (gof);                      % displays goodness of fit parameters

Fit_ratio = fresult(Plane);      % producing fitted curve using the plane numbers

CF = 1 ./ Fit_ratio;           % correction factor is 1 over the ratio decay function

    a=num2str(fresult.a); b=num2str(fresult.b); c=num2str(fresult.c); d=num2str(fresult.d); rsq=num2str(gof.rsquare);  
    coef=sprintf('a = %s ; b = %s', a, b);
    coef2=sprintf('c = %s ; d = %s', c, d);
    coef3=sprintf('r^2 = %s', rsq);
    
     plot(Plane, Ratio,'rd', Plane, fresult(0:I-1),'b-');   % Plots results
     title('Double exponential fit to Photobleach data');
     xlabel('Plane Number'); 
     ylabel('Normalized Ratio Decay'); 
     legend('Data', 'Fit');
     axis([0, I, 0, 1.2]);
     text (2, 0.4, 'y = a exp(b*x) + c exp(d*x)');
     text (2, 0.33, coef);
     text (2, 0.26, coef2);
     text (2, 0.19, coef3);
     
set(gcf,'PaperUnits','inches'); 
width = 7.5;         % Initialize a variable for width.
height = 9.6;          % Initialize a varible for height.

myfiguresize = [0.5, 0.7, width, height];
set(gcf, 'PaperPosition', myfiguresize);  
% PRINT;   % prints graph

handles.CF=CF;
guidata(hObject, handles);


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

CF=handles.CF;
fname=handles.fname;
I=handles.num_data

%% Image processing starting at this point, using the CF as the correction
if I < 100;
   if I < 10;
       for mult_rep=1:I;
           counter=mult_rep;
           FNAMEIN=sprintf('%s%i.tif', fname, counter);
           ratio=imread(FNAMEIN,'tif');
           R=double(ratio);
           CR=R .* CF(counter);   %Array element by element multiplication
           CR_out=uint16(CR);
           FNAMEOUT=sprintf('out_%i.tif',counter);
           imwrite(CR_out, FNAMEOUT, 'tif','compression','none');   % write output file
       end;
   else;
       for mult_rep=1:I;
           counter=mult_rep;
           if counter < 10;
              FNAMEIN=sprintf('%s0%i.tif', fname, counter);
           else;
              FNAMEIN=sprintf('%s%i.tif', fname, counter);
           end;
           ratio=imread(FNAMEIN,'tif');
           R=double(ratio);
           CR=R .* CF(counter);   %Array element by element multiplication
           CR_out=uint16(CR);
           if counter < 10;
              FNAMEOUT=sprintf('out_0%i.tif',counter);
           else;
              FNAMEOUT=sprintf('out_%i.tif',counter);
           end;
           imwrite(CR_out, FNAMEOUT, 'tif','compression','none');   % write output file
       end;
   end;
elseif I >= 100;
      for mult_rep=1:I;
           counter=mult_rep;
           if counter < 10;  
              FNAMEIN=sprintf('%s00%i.tif', fname, counter);
              ratio=imread(FNAMEIN,'tif');
              R=double(ratio);
              CR=R .* CF(counter);   %Array element by element multiplication
              CR_out=uint16(CR);
              FNAMEOUT=sprintf('out_00%i.tif',counter);
              imwrite(CR_out, FNAMEOUT, 'tif','compression','none');   % write output file
          elseif counter < 100;
              FNAMEIN=sprintf('%s0%i.tif', fname, counter);
              ratio=imread(FNAMEIN,'tif');
              R=double(ratio);
              CR=R .* CF(counter);   %Array element by element multiplication
              CR_out=uint16(CR);
              FNAMEOUT=sprintf('out_0%i.tif',counter);
              imwrite(CR_out, FNAMEOUT, 'tif','compression','none');   % write output file
          elseif counter >= 100;
              FNAMEIN=sprintf('%s%i.tif', fname, counter);
              ratio=imread(FNAMEIN,'tif');
              R=double(ratio);
              CR=R .* CF(counter);   %Array element by element multiplication
              CR_out=uint16(CR);
              FNAMEOUT=sprintf('out_%i.tif',counter);
              imwrite(CR_out, FNAMEOUT, 'tif','compression','none');   % write output file
          end;
      end;   
end;


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