Cycle_Picker.m

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

% Last Modified by GUIDE v2.5 02-Oct-2017 12:34:01

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @Cycle_Picker_OpeningFcn, ...
                   'gui_OutputFcn',  @Cycle_Picker_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 Cycle_Picker is made visible.
function Cycle_Picker_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 Cycle_Picker (see VARARGIN)

% clear all;
clc;
% close all;

parameters % load parameters

%-------------start pre-prosessing-----------
handles.dir_name = data_dir;
handles.cell_data = load(cell_foci_file_path);
handles.px_to_mu = px_to_mu;
handles.IW_thr = IW_thr; % threshold of intensity weighting
handles.n_oc = 1; %number of overlapping cell cycle. Leave as 1
handles.xlim_max = 1;	% ignore
handles.ylim_max = ylim_maximum;	%handles.ylim_max = 30;
handles.time_int = 1;	% Leave as 1
%%%

if exist([handles.dir_name 'picked/']) == 0
    mkdir([handles.dir_name 'picked/']);
end

if exist([handles.dir_name 'picked_png/']) == 0
    mkdir([handles.dir_name 'picked_png/']);
end


L = length(fieldnames(handles.cell_data));
fnames = fieldnames(handles.cell_data);

fnames_array = cell2mat(fnames);

fnames_array_num = zeros(L,4);

fnames_array_num(:,1) = str2num(fnames_array(:,2:3));
fnames_array_num(:,2) = str2num(fnames_array(:,5:8));
fnames_array_num(:,3) = str2num(fnames_array(:,10:13));
fnames_array_num(:,4) = str2num(fnames_array(:,15:16));

fnames_sort = sortrows(fnames_array_num,4);
fnames_sort = sortrows(fnames_sort,3);
fnames_sort = sortrows(fnames_sort,2);
fnames_sort = sortrows(fnames_sort,1);

fovs = unique(fnames_sort(:,1));

handles.channels = [0 0];
for i = fovs'
    fov_index = find(fnames_sort(:,1) == i);
    fnames_fov = fnames_sort(fov_index,:);

    channels_tmp(:,2) = unique(fnames_fov(:,2));
    channels_tmp(:,1) = i + zeros(length(channels_tmp(:,2)),1);

    handles.channels = [handles.channels; channels_tmp];
    clear channels_tmp;
end
handles.channels(1,:) = [];

handles.fnames_sort = fnames_sort;
handles.channle_idx = channel_start;

[handles.length_list, handles.foci_list, handles.birth_list, handles.division_list, handles.cell_list, handles.cell_names, handles.save_name, handles.save_name_png, handles.display_name] ...
    = plot_channel(handles.dir_name, handles.cell_data, handles.px_to_mu, handles.IW_thr, handles.fnames_sort, handles.channels, handles.channle_idx, handles.xlim_max, handles.ylim_max, handles.time_int);

set(handles.display, 'String' , handles.display_name );

handles.clicks = 0;

handles.n_oc_curr = handles.n_oc; %the number of overlapping cycle for current cell
handles.initiation_time = [];
handles.initiation_time_n = [];
handles.termination_time = [];
handles.division_time = [];

handles.birth_time_m = [];
handles.initiation_mass = [];
handles.initiation_mass_n = [];
handles.termination_mass = [];

handles.cell_name_m_tmp = [];
handles.cell_name_n_tmp = [];
handles.cell_name_tmp = [];

handles.p1 = [];
handles.p2 = [];
handles.p3 = [];
handles.p4 = [];
handles.l1 = [];
handles.l2 = [];
handles.l3 = [];

set(handles.text3, 'String' , num2str(handles.n_oc_curr, '%1d'));

%-------------end pre-prosessing-----------

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

% Update handles structure
guidata(hObject, handles);

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


% --- Outputs from this function are returned to the command line.
function varargout = Cycle_Picker_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 axes2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to axes2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called
hold on;
% Hint: place code in OpeningFcn to populate axes2

% --- Executes on mouse press over axes background.
function axes2_ButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to axes2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

parameters

a = get(hObject, 'Currentpoint');

handles.clicks = handles.clicks + 1;
guidata(hObject, handles);

color_idx =  mod(handles.clicks,3);

% scale for changing y value to x as the axis are different units
x_y_scale = (xlim_maximum - xlim_minimum) / (ylim_maximum + 1);

% calculate distance between clicked point and all foci. X and Y
for i = 1:size(handles.foci_list, 1)
    d_1(i) = ((a(1, 1)-handles.foci_list(i, 1))^2 + ((a(1, 2)-handles.foci_list(i,2))*x_y_scale)^2)^0.5;
end

% % calculate distance but only use y
% for i = 1:size(handles.foci_list, 1)
%     d_1(i) = (((a(1, 1)-handles.foci_list(i, 1))*10)^2 + ((a(1, 2)-handles.foci_list(i,2)))^2)^0.5;
% end

[R_1, j_1] = min(d_1); % miniminum distance 

if color_idx == 1

    handles.p1 = plot( handles.foci_list(j_1, 1), handles.foci_list(j_1, 2), 'p', 'LineWidth',1 , 'MarkerEdgeColor','r','MarkerFaceColor','none','MarkerSize',15);
    handles.initiation_time = handles.foci_list(j_1, 1);
    handles.initiation_pos = handles.foci_list(j_1, 2);
    handles.initiation_mass = handles.length_list(2, find(handles.length_list(1,:) == handles.initiation_time)) / (2^(handles.n_oc_curr-1)); %note that number of origins at initiation is updated to the current OC number;

    %saving the cell name in the mother generation
    for i = 1:size(handles.division_list, 1)
        if  handles.initiation_time >= handles.birth_list(i, 1) && handles.initiation_time < handles.division_list(i, 1) %if the initiation is right at division, then regard it as happening at the birth of new cell
            cell_idx_m = i;
        end
    end
    handles.cell_name_m_tmp = handles.cell_names{cell_idx_m,1};

    handles.initiation_time_n = handles.initiation_time;
    handles.initiation_mass_n = handles.initiation_mass;

    %saving as the current initiation time & initiaion mass in the current generation
    for i = 1:size(handles.division_list, 1)
        if  handles.initiation_time_n >= handles.birth_list(i, 1) && handles.initiation_time_n < handles.division_list(i, 1) %if the initiation is right at division, then regard it as happening at the birth of new cell
            cell_idx_n = i;
        end
    end
    handles.cell_name_n_tmp = handles.cell_names{cell_idx_n,1};

    %save the second initiation event in the current generation if double-initiation happens
    if isfield(handles.cell_list.(handles.cell_name_n_tmp),'initiation_time_n') == 0
        handles.cell_list.(handles.cell_name_n_tmp).initiation_time_n = handles.initiation_time_n;
        handles.cell_list.(handles.cell_name_n_tmp).initiation_mass_n = handles.initiation_mass_n;
        handles.cell_list.(handles.cell_name_n_tmp).n_oc_n = handles.n_oc_curr;
    else
        handles.cell_list.(handles.cell_name_n_tmp).initiation_time_n2 = handles.initiation_time_n;
        handles.cell_list.(handles.cell_name_n_tmp).initiation_mass_n2 = handles.initiation_mass_n;
        handles.cell_list.(handles.cell_name_n_tmp).n_oc_n2 = handles.n_oc_curr;
    end
    

    j_3 = sum(handles.birth_list <= handles.initiation_time); % index of birth time before initiation click
    handles.p3 = plot( handles.birth_list(j_3, 1), handles.initiation_pos, 's', 'LineWidth',1 , 'MarkerEdgeColor','r','MarkerFaceColor','None','MarkerSize',10);
    handles.birth_time_m = handles.birth_list(j_3, 1);
    handles.l2 = plot( [handles.birth_time_m handles.initiation_time], [handles.initiation_pos handles.initiation_pos], '-', 'LineWidth',1 , 'MarkerEdgeColor','b','MarkerFaceColor','none','MarkerSize',10, 'Color', [0.75 0.75 0.75]);

elseif color_idx == 2

    handles.p2 = plot( handles.foci_list(j_1, 1), handles.foci_list(j_1, 2), 'o', 'LineWidth',1 , 'MarkerEdgeColor','b','MarkerFaceColor','none','MarkerSize',10);
    handles.termination_time = handles.foci_list(j_1, 1);
    handles.termination_pos = handles.foci_list(j_1, 2);
    handles.termination_mass = handles.length_list(2, find(handles.length_list(1,:) == handles.termination_time));

    handles.l1 = plot( [handles.initiation_time handles.termination_time], [handles.initiation_pos handles.termination_pos], '-', 'LineWidth',1 , 'MarkerEdgeColor','b','MarkerFaceColor','none','MarkerSize',10, 'Color', [0.75 0.75 0.75]);

% birth before initiation is handled automatically now. 
% elseif color_idx == 3
%     beep= 0;

%     for i = 1:size(handles.birth_list, 1)
%         d_3(i) = abs(a(1, 1)-handles.birth_list(i, 1));
%     end
%     [R_3, j_3] = min(d_3);
%     handles.p3 = plot( handles.birth_list(j_3, 1), handles.initiation_pos, 's', 'LineWidth',1 , 'MarkerEdgeColor','r','MarkerFaceColor','None','MarkerSize',10);
%     handles.birth_time_m = handles.birth_list(j_3, 1);
%     handles.l2 = plot( [handles.birth_time_m handles.initiation_time], [handles.initiation_pos handles.initiation_pos], '-', 'LineWidth',1 , 'MarkerEdgeColor','b','MarkerFaceColor','none','MarkerSize',10, 'Color', [0.75 0.75 0.75]);

elseif color_idx == 0

    for i = 1:size(handles.division_list, 1)
        d_4(i) = abs(a(1, 1)-handles.division_list(i, 1));
    end
    [R_4, j_4] = min(d_4);
    handles.p4 = plot( handles.division_list(j_4, 1), handles.termination_pos, 's', 'LineWidth',1 , 'MarkerEdgeColor','b','MarkerFaceColor','None','MarkerSize',10);
    handles.division_time = handles.division_list(j_4, 1);
    handles.l3 = plot( [handles.termination_time handles.division_time], [handles.termination_pos handles.termination_pos], '-', 'LineWidth',1 , 'MarkerEdgeColor','b','MarkerFaceColor','none','MarkerSize',10, 'Color', [0.75 0.75 0.75]);

    cell_idx = find(handles.division_list == handles.division_time);

    handles.cell_name_tmp = handles.cell_names{cell_idx,1};

    handles.cell_list.(handles.cell_name_tmp).birth_time_m = handles.birth_time_m;
    handles.cell_list.(handles.cell_name_tmp).cell_name_m = handles.cell_name_m_tmp; %saving the cell name in the mother generation

    %saving as the mother initiation time & initiaion mass in the current generation
    handles.cell_list.(handles.cell_name_tmp).initiation_time = handles.initiation_time;
    handles.cell_list.(handles.cell_name_tmp).initiation_mass = handles.initiation_mass;
    handles.cell_list.(handles.cell_name_tmp).n_oc = handles.n_oc_curr;

    handles.cell_list.(handles.cell_name_tmp).termination_time = handles.termination_time;
    handles.cell_list.(handles.cell_name_tmp).termination_mass = handles.termination_mass;

    handles.n_oc_curr = handles.n_oc; %restore the current number of overlapping cycles to default
    set(handles.text3, 'String' , num2str(handles.n_oc_curr, '%1d'));

    guidata(hObject, handles);
end

guidata(hObject, handles);


% --- Executes on button press in pushbutton1. Save 
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)

cell_list = handles.cell_list;

save(handles.save_name,'cell_list');
saveas(handles.axes2,handles.save_name_png,'png');

guidata(hObject, handles);


% --- Executes on button press in pushbutton2. Back
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)

handles.channle_idx = handles.channle_idx-1;
cla;

handles.n_oc_curr = handles.n_oc; %restore the current number of overlapping cycles to default
set(handles.text3, 'String' , num2str(handles.n_oc_curr, '%1d'));

[handles.length_list, handles.foci_list, handles.birth_list, handles.division_list, handles.cell_list, handles.cell_names, handles.save_name, handles.save_name_png, handles.display_name] ...
    = plot_channel(handles.dir_name, handles.cell_data, handles.px_to_mu, handles.IW_thr, handles.fnames_sort, handles.channels, handles.channle_idx, handles.xlim_max, handles.ylim_max, handles.time_int);
set(handles.display, 'String' , handles.display_name );

handles.clicks = 0;
handles.initiation_time = [];
handles.termination_time = [];
handles.division_time = [];

handles.birth_time_m = [];
handles.initiation_mass = [];
handles.termination_mass = [];

guidata(hObject, handles);


% --- Executes on button press in pushbutton3. Forward
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.channle_idx = handles.channle_idx+1;

cla;

handles.n_oc_curr = handles.n_oc; %restore the current number of overlapping cycles to default
set(handles.text3, 'String' , num2str(handles.n_oc_curr, '%1d'));

[handles.length_list, handles.foci_list, handles.birth_list, handles.division_list, handles.cell_list, handles.cell_names, handles.save_name, handles.save_name_png, handles.display_name] ...
    = plot_channel(handles.dir_name, handles.cell_data, handles.px_to_mu, handles.IW_thr, handles.fnames_sort, handles.channels, handles.channle_idx, handles.xlim_max, handles.ylim_max, handles.time_int);
set(handles.display, 'String' , handles.display_name );

handles.clicks = 0;
handles.initiation_time = [];
handles.termination_time = [];
handles.division_time = [];

handles.birth_time_m = [];
handles.initiation_mass = [];
handles.termination_mass = [];

guidata(hObject, handles);


% --- Executes on button press in pushbutton4. Change oc
function pushbutton4_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton4 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

handles.n_oc_curr = handles.n_oc_curr+1;
set(handles.text3, 'String' , num2str(handles.n_oc_curr, '%1d'));

guidata(hObject, handles);


% --- Executes on button press in pushbutton5. Change oc
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)

handles.n_oc_curr = handles.n_oc_curr-1;
set(handles.text3, 'String' , num2str(handles.n_oc_curr, '%1d'));

guidata(hObject, handles);


% --- Executes on button press in pushbutton6. Undo
function pushbutton6_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton6 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

color_idx =  mod(handles.clicks,3);

%can only undo one generation
if color_idx == 1

    if isempty(handles.p1)==0
        handles.p1.Visible = 'off';
    end

    %remove the second initiation event in the current generation if double-initiation happens
    if isfield(handles.cell_list.(handles.cell_name_n_tmp),'initiation_time_n2') == 1
        handles.cell_list.(handles.cell_name_n_tmp) = rmfield(handles.cell_list.(handles.cell_name_n_tmp),'initiation_time_n2');
        handles.cell_list.(handles.cell_name_n_tmp) = rmfield(handles.cell_list.(handles.cell_name_n_tmp),'initiation_mass_n2');
        handles.cell_list.(handles.cell_name_n_tmp) = rmfield(handles.cell_list.(handles.cell_name_n_tmp),'n_oc_n2');
    else
        handles.cell_list.(handles.cell_name_n_tmp) = rmfield(handles.cell_list.(handles.cell_name_n_tmp),'initiation_time_n');
        handles.cell_list.(handles.cell_name_n_tmp) = rmfield(handles.cell_list.(handles.cell_name_n_tmp),'initiation_mass_n');
        handles.cell_list.(handles.cell_name_n_tmp) = rmfield(handles.cell_list.(handles.cell_name_n_tmp),'n_oc_n');
    end
    
    % undo line from initiation to birth
    if isempty(handles.p3)==0
        handles.p3.Visible = 'off';
    end
    if isempty(handles.l2)==0
        handles.l2.Visible = 'off';
    end

    
elseif color_idx == 2

    if isempty(handles.p2)==0
        handles.p2.Visible = 'off';
    end
    if isempty(handles.l1)==0
        handles.l1.Visible = 'off';
    end

% birth time is handled automatically now
% elseif color_idx == 3
% 
%     if isempty(handles.p3)==0
%         handles.p3.Visible = 'off';
%     end
%     if isempty(handles.l2)==0
%         handles.l2.Visible = 'off';
%     end

elseif color_idx == 0

    if isempty(handles.p4)==0
        handles.p4.Visible = 'off';
    end
    if isempty(handles.l3)==0
        handles.l3.Visible = 'off';
    end

    handles.cell_list.(handles.cell_name_tmp) = rmfield(handles.cell_list.(handles.cell_name_tmp),'birth_time_m');
    handles.cell_list.(handles.cell_name_tmp) = rmfield(handles.cell_list.(handles.cell_name_tmp),'cell_name_m');
    handles.cell_list.(handles.cell_name_tmp) = rmfield(handles.cell_list.(handles.cell_name_tmp),'initiation_time');
    handles.cell_list.(handles.cell_name_tmp) = rmfield(handles.cell_list.(handles.cell_name_tmp),'initiation_mass');
    handles.cell_list.(handles.cell_name_tmp) = rmfield(handles.cell_list.(handles.cell_name_tmp),'n_oc');
    handles.cell_list.(handles.cell_name_tmp) = rmfield(handles.cell_list.(handles.cell_name_tmp),'termination_time');
    handles.cell_list.(handles.cell_name_tmp) = rmfield(handles.cell_list.(handles.cell_name_tmp),'termination_mass');

end

if handles.clicks >0
    handles.clicks = handles.clicks - 1;
else
    handles.clicks = 0;
end

guidata(hObject, handles);

% --- Executes during object deletion, before destroying properties.
function axes2_DeleteFcn(hObject, eventdata, handles)
% hObject    handle to axes2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)