CalculateCellsGUI.m

function varargout = CalculateCellsGUI(varargin)
% CALCULATECELLSGUI MATLAB code for CalculateCellsGUI.fig
%      CALCULATECELLSGUI, by itself, creates a new CALCULATECELLSGUI or raises the existing
%      singleton*.
%
%      H = CALCULATECELLSGUI returns the han15.dle to a new CALCULATECELLSGUI or the handle to
%      the existing singleton*.
%
%      CALCULATECELLSGUI('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in CALCULATECELLSGUI.M with the given input arguments.
%
%      CALCULATECELLSGUI('Property','Value',...) creates a new CALCULATECELLSGUI or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before CalculateCellsGUI_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to CalculateCellsGUI_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 CalculateCellsGUI

% Last Modified by GUIDE v2.5 07-Jun-2021 13:04:47

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @CalculateCellsGUI_OpeningFcn, ...
                   'gui_OutputFcn',  @CalculateCellsGUI_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 CalculateCellsGUI is made visible.
function CalculateCellsGUI_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 CalculateCellsGUI (see VARARGIN)
handles.threshold = 0.1;
handles.image1 = '4512-4 KO';
handles.image2 = '4522-5 WT';

handles.newMap = containers.Map;

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

% Update handles structure
guidata(hObject, handles);

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


% --- Outputs from this function are returned to the command line.
function varargout = CalculateCellsGUI_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 during object creation, after setting all properties.
function nicknametext_CreateFcn(hObject, eventdata, handles)
% hObject    handle to nicknametext (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 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)
handles.threshold = get(handles.slider1, 'Value');
[startingIMG, overlapIMG, intensityLevel] = CalculateCellsForGUI(handles.valueSet, handles.threshold);

 axes(handles.axes1);
 imshow(startingIMG);
 axes(handles.axes2);
 imshow(overlapIMG);
 handles.intensityLevel = intensityLevel*100;
 
set(handles.edit2, 'String', sprintf('Intensity level of green on red areas: %0.3f%% \n', handles.intensityLevel));

% --- Executes on selection change in popupmenu1.
function popupmenu1_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% Determine the selected data set.
str = get(hObject, 'string');
val = get(hObject,'Value');
keyset = {str(val)};
handles.valueSet = values(handles.newMap, str(val));

% Set current data to the selected data set.

% switch str{val}
% case '4512-4 KO' 
%    handles.current_data = handles.image1;
% case '4522-5 WT' 
%    handles.current_data = handles.image2;
% end
% Save the handles structure.
guidata(hObject,handles)

% Hints: contents = cellstr(get(hObject,'String')) returns popupmenu1 contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu1


% --- Executes during object creation, after setting all properties.
function popupmenu1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: popupmenu 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 slider movement.
function slider1_Callback(hObject, eventdata, handles)
% hObject    handle to slider1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

handles.threshold = get(hObject, 'Value');
set(handles.edit3, 'String', sprintf('%0.3f', get(hObject, 'Value')));


% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider


% --- Executes during object creation, after setting all properties.
function slider1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called
set(hObject, 'Max', 0.3, 'Min', 0, 'Value', 0.1);
set(hObject, 'SliderStep', [0.001, 0.01]);
handles.threshold = get(hObject, 'Value');

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end



function edit2_Callback(hObject, eventdata, handles)
% hObject    handle to edit2 (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 edit2 as text
%        str2double(get(hObject,'String')) returns contents of edit2 as a double


% --- Executes during object creation, after setting all properties.
function edit2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit2 (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 edit3_Callback(hObject, eventdata, handles)
% hObject    handle to edit3 (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 edit3 as text
%        str2double(get(hObject,'String')) returns contents of edit3 as a double


% --- Executes during object creation, after setting all properties.
function edit3_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit3 (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 finddatabutton.
function finddatabutton_Callback(hObject, eventdata, handles)
% hObject    handle to finddatabutton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
[filename, filepath] = uigetfile({'*.*';'*.tif'}, 'Search images');
fullnametotal = [filepath filename];
set(handles.totalimagename, 'String', filename);


% --- 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)
[filename, filepath] = uigetfile({'*.*';'*.tif'}, 'Search images');
fullnamecolor1 = [filepath filename];
set(handles.color1name, 'String', filename);

% --- Executes on button press in pushbutton5.
function pushbutton5_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton5 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
[filename, filepath] = uigetfile({'*.*';'*.tif'}, 'Search images');
fullnamecolor2 = [filepath filename];
set(handles.color2name, 'String', filename);


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

handles.popupmenu1.String{end+1} = get(handles.nicknametext, 'string');


total = get(handles.totalimagename, 'String');
color1 = get(handles.color1name, 'String');
color2 = get(handles.color2name, 'String');

handles.newMap(get(handles.nicknametext, 'string')) = {total, color1, color2};




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


% --- Executes during object creation, after setting all properties.
function fullimagetextbox_CreateFcn(hObject, eventdata, handles)
% hObject    handle to fullimagetextbox (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 color1textbox_Callback(hObject, eventdata, handles)
% hObject    handle to color1textbox (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 color1textbox as text
%        str2double(get(hObject,'String')) returns contents of color1textbox as a double


% --- Executes during object creation, after setting all properties.
function color1textbox_CreateFcn(hObject, eventdata, handles)
% hObject    handle to color1textbox (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 color2textbox_Callback(hObject, eventdata, handles)
% hObject    handle to color2textbox (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 color2textbox as text
%        str2double(get(hObject,'String')) returns contents of color2textbox as a double


% --- Executes during object creation, after setting all properties.
function color2textbox_CreateFcn(hObject, eventdata, handles)
% hObject    handle to color2textbox (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 edit7_Callback(hObject, eventdata, handles)
% hObject    handle to edit7 (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 edit7 as text
%        str2double(get(hObject,'String')) returns contents of edit7 as a double


% --- Executes during object creation, after setting all properties.
function edit7_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit7 (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 nicknametext_Callback(hObject, eventdata, handles)
% hObject    handle to nicknametext (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 nicknametext as text
%        str2double(get(hObject,'String')) returns contents of nicknametext as a double