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function varargout = CellTrackerSettingsGeneral(varargin)
% CELLTRACKERSETTINGSGENERAL M-file for CellTrackerSettingsGeneral.fig
% CELLTRACKERSETTINGSGENERAL, by itself, creates a new CELLTRACKERSETTINGSGENERAL or raises the existing
% singleton*.
%
% H = CELLTRACKERSETTINGSGENERAL returns the handle to a new CELLTRACKERSETTINGSGENERAL or the handle to
% the existing singleton*.
%
% CELLTRACKERSETTINGSGENERAL('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in CELLTRACKERSETTINGSGENERAL.M with the given input arguments.
%
% CELLTRACKERSETTINGSGENERAL('Property','Value',...) creates a new CELLTRACKERSETTINGSGENERAL or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before CellTrackerSettingsGeneral_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to CellTrackerSettingsGeneral_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 CellTrackerSettingsGeneral
% Last Modified by GUIDE v2.5 26-Jun-2015 16:36:13
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @CellTrackerSettingsGeneral_OpeningFcn, ...
'gui_OutputFcn', @CellTrackerSettingsGeneral_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 CellTrackerSettingsGeneral is made visible.
function CellTrackerSettingsGeneral_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 CellTrackerSettingsGeneral (see VARARGIN)
global f_handles
% Choose default command line output for CellTrackerSettingsGeneral
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes CellTrackerSettingsGeneral wait for user response (see UIRESUME)
% uiwait(handles.figure1);
%% set parameters to show
try
% Close the other windows
%if ishandle(f_handles.h_GUIsetG); close(f_handles.h_GUIsetG); end;
if ishandle(f_handles.h_GUIsetT); close(f_handles.h_GUIsetT); end;
if ishandle(f_handles.h_GUIsetS); close(f_handles.h_GUIsetS); end;
if ishandle(f_handles.h_GUIsetM); close(f_handles.h_GUIsetM); end;
if ishandle(f_handles.h_GUIstatistics); close(f_handles.h_GUIstatistics); end;
inpImage = imread(f_handles.PathImgOriginal, 1);
[rowI, colI, chI] = size(inpImage);
numImages = length(imfinfo(f_handles.PathImgOriginal));
% background correction
if f_handles.backCorrMethod == 1
set(handles.radiobutton1, 'Value', 1);
elseif f_handles.backCorrMethod == 2
set(handles.radiobutton2, 'Value', 1);
end;
% Check parameters
if f_handles.backCorrSize<1 || f_handles.backCorrSize>=min([rowI, colI])
f_handles.backCorrSize = 1;
end
if f_handles.maxAlignDistance<0 || f_handles.maxAlignDistance>=min([rowI, colI])
f_handles.maxAlignDistance = ceil(min([rowI, colI])/10);
end
% Set parameters
set(handles.edit1, 'String', num2str(f_handles.backCorrSize));
% auto aligner
set(handles.edit3, 'String', num2str(f_handles.maxAlignDistance));
catch ME1
Message = {'Wrong parameter set.', ...
' '};
msgbox(Message,'Message')
end
% --- Outputs from this function are returned to the command line.
function varargout = CellTrackerSettingsGeneral_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 deletion, before destroying properties.
function figure1_DeleteFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --- Executes when user attempts to close figure1.
function figure1_CloseRequestFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: delete(hObject) closes the figure
delete(hObject);
% --- Executes on button press in pb_saveSettings.
function pb_saveSettings_Callback(hObject, eventdata, handles)
% hObject handle to pb_saveSettings (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%% OK button to save settings
global f_handles;
try
%Reset input
f_handles.PathImgCurrent = f_handles.PathImgOriginal;
f_handles.startIm = 1;
f_handles.lastImage = length(imfinfo(f_handles.PathImgOriginal));
% Errors check
inpImage = imread(f_handles.PathImgCurrent, 1);
[rowI, colI, chI] = size(inpImage);
numImages = length(imfinfo(f_handles.PathImgCurrent));
testBackCorrSize = str2num(get(handles.edit1, 'String'));
testMaxAlignDistance = str2num(get(handles.edit3, 'String'));
flag_ComputationOn = 1;
if testBackCorrSize<1 || testBackCorrSize>=min([rowI, colI])
flag_ComputationOn = 0;
end
if testMaxAlignDistance<0 || testMaxAlignDistance>=min([rowI, colI])
flag_ComputationOn = 0;
end
if flag_ComputationOn == 1
if get(handles.radiobutton1, 'Value')== 1
f_handles.backCorrMethod = 1;
elseif get(handles.radiobutton2, 'Value') == 1
f_handles.backCorrMethod = 2;
end;
f_handles.backCorrSize = str2num(get(handles.edit1, 'String'));
% auto aligner
f_handles.maxAlignDistance = str2num(get(handles.edit3, 'String'));
% Reset GUI
set(f_handles.h_FCpb02, 'BackgroundColor', 'yellow');
set(f_handles.h_FCpb03, 'BackgroundColor', 'yellow');
set(f_handles.h_FCpb04, 'BackgroundColor', 'yellow');
set(f_handles.h_FCpb05, 'BackgroundColor', 'yellow');
set(f_handles.h_FCpb06, 'BackgroundColor', 'yellow');
set(f_handles.h_FCpb07, 'BackgroundColor', 'red');
% Update visualization
% Save output
path = [pwd filesep 'tmpct' filesep];
fileNameMat = 'TracksCoordinates.mat';
fileNameExcel = 'TracksCoordinates.xls';
pathFileNameMat = [path fileNameMat];
pathFileNameExcel = [path fileNameExcel];
if ~isempty(f_handles.pos)
pos = f_handles.pos;
if isequal(exist(pathFileNameMat, 'file'),2); delete(pathFileNameMat); save(pathFileNameMat, 'pos'); else save(pathFileNameMat, 'pos'); end;
if isequal(exist(pathFileNameExcel, 'file'),2); delete(pathFileNameExcel); xlswrite(pathFileNameExcel, pos); else xlswrite(pathFileNameExcel, pos); end;
f_handles.pos = [];
else
if isequal(exist(pathFileNameMat, 'file'),2); delete(pathFileNameMat); end;
if isequal(exist(pathFileNameExcel, 'file'),2); delete(pathFileNameExcel); end;
end
f_handles.PathImgCurrent = f_handles.PathImgOriginal;
guidata(hObject, handles);
updateSliceWindows(f_handles.startIm, f_handles.PathImgCurrent, handles);
if ishandle(f_handles.h_GUIsetG); close(f_handles.h_GUIsetG); end;
else
Message = {'Wrong parameter set.', ...
' '};
msgbox(Message,'Message')
end
catch ME1
Message = {'Wrong parameter set.', ...
' '};
msgbox(Message,'Message')
end
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 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
function edit4_Callback(hObject, eventdata, handles)
% hObject handle to edit4 (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 edit4 as text
% str2double(get(hObject,'String')) returns contents of edit4 as a double
% --- Executes during object creation, after setting all properties.
function edit4_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit4 (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 edit5_Callback(hObject, eventdata, handles)
% hObject handle to edit5 (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 edit5 as text
% str2double(get(hObject,'String')) returns contents of edit5 as a double
% --- Executes during object creation, after setting all properties.
function edit5_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit5 (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 edit6_Callback(hObject, eventdata, handles)
% hObject handle to edit6 (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 edit6 as text
% str2double(get(hObject,'String')) returns contents of edit6 as a double
% --- Executes during object creation, after setting all properties.
function edit6_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit6 (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