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gui_select.m
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gui_select.m
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function varargout = gui_select(varargin)
% GUI_SELECT MATLAB code for gui_select.fig
% GUI_SELECT, by itself, creates a new GUI_SELECT or raises the existing
% singleton*.
%
% H = GUI_SELECT returns the handle to a new GUI_SELECT or the handle to
% the existing singleton*.
%
% GUI_SELECT('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in GUI_SELECT.M with the given input arguments.
%
% GUI_SELECT('Property','Value',...) creates a new GUI_SELECT or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before gui_select_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to gui_select_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 gui_select
% Last Modified by GUIDE v2.5 22-Mar-2023 22:10:02
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @gui_select_OpeningFcn, ...
'gui_OutputFcn', @gui_select_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 gui_select is made visible.
function gui_select_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 gui_select (see VARARGIN)
% Choose default command line output for gui_select
handles.out = hObject;
if nargin>3
setappdata(handles.figure1,'arg',varargin);
% if isempty(varargin{2})
% handles.bt_sim.Enable='off';
% end
h=varargin{1}; %pks
pks=getappdata(h.figure1,'pks');
msi=getappdata(h.figure1,'msi');
dt=pks.data;
ordering=pks.ordering;
sz=size(dt,2);
handles.uitable1.ColumnName=[pks.header,'select'];
else
dt={'met1';'met2';'met3'};
pks.data=dt;
pks.ordering=[1,2,3];
sz=1;
handles.uitable1.ColumnName={'name','select'};
end
set(handles.uitable1, 'ColumnFormat', [repmat({'char'},1,sz),'logical']);
selected=1;
col2=false(size(dt,1),1);
col2(selected)=1;
col2=num2cell(col2);
dt=[dt(ordering,:),col2];
set(handles.uitable1, 'Data', dt);
set_uitable_color(handles,dt,size(dt,2));
handles.uitable1.ColumnEditable(length(pks.header)+1)=true;
handles.text_total.String=num2str(size(dt,1));
% Update handles structure
handles.pks=pks;
handles.msi=msi;
R=msi.R;
S=msi.S;
str=[];ct=0;
for i=1:length(R)
str=[str;['R(',num2str(i),')']];
ct=ct+1;
subID{ct}=R(i).subID;
end
for i=1:length(S)
str=[str;['S(',num2str(i),')']];
ct=ct+1;
subID{ct}=S(i).subID;
end
handles.subID=subID;
handles.pop1.String=str;
handles.h=h;
guidata(hObject, handles);
eventdata.Indices=[1,2];
uitable1_CellSelectionCallback(hObject, eventdata, handles)
% UIWAIT makes gui_select wait for user response (see UIRESUME)
uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = gui_select_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.pks;
delete(hObject);
function select(handles)
pks=handles.pks;
dt=handles.uitable1.Data;
%pkid=pks.pkid;
pkid=handles.pkid;
ordering=pks.ordering;
corref_new=pks.corref(ordering,ordering); %reordered corref
if handles.checkbox1.Value==0
[A,B]=sort(corref_new(pkid,:),'descend'); %correlation
else
[A,B]=sort(corref_new(pkid,:),'ascend'); %anti-correlation
end
c1=str2num(handles.edit1.String); %top n
c1=min(c1,length(B));
handles.edit1.String=num2str(c1);
c2=str2num(handles.edit2.String); %score cutoff
if handles.radiobutton4.Value
selected=B(1:c1);
elseif handles.radiobutton5.Value
if handles.checkbox1.Value==0
selected=B(A>c2);
else
selected=B(A<-c2);
end
end
col_end=false(size(dt,1),1); %update last column checks
if ~isempty(selected)
corref_new(pkid,selected)
col_end(selected)=1;
end
col_end=num2cell(col_end);
dt(:,end)=col_end;
set(handles.uitable1, 'Data', dt);
handles.text_num.String=num2str(length(selected));
dt=handles.uitable1.Data;
set_uitable_color(handles,dt,size(dt,2));
handles.text_stat.String=[num2str(length(selected)),' qualifying peaks detected!'];
% --- Executes on button press in bt_OK.
function bt_OK_Callback(hObject, eventdata, handles)
% hObject handle to bt_OK (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
ckecked=handles.uitable1.Data(:,end);
idx=[];
for i=1:size(ckecked,1)
if ckecked{i,end}
idx=[idx,i];
end
end
pks=handles.pks;
pks.data=pks.data(pks.ordering(idx),:);
T=cell2table(pks.data(:,1:3));
T.Properties.VariableNames = {'Name','Formula','m_z'};
pks.sdata=table2struct(T);
pks.corref=pks.corref(pks.ordering(idx),pks.ordering(idx));
pks.ordering=1:size(pks.data,1); %update ordering
handles.pks=pks;
guidata(hObject, handles);
figure1_CloseRequestFcn(handles.figure1, eventdata, handles);
% --- Executes on button press in bt_cancel.
function bt_cancel_Callback(hObject, eventdata, handles)
% hObject handle to bt_cancel (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
figure1_CloseRequestFcn(handles.figure1, eventdata, handles);
% --- 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
uiresume(hObject);
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 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
% --- Executes on button press in radiobutton1.
function bt_all_Callback(hObject, eventdata, handles)
% hObject handle to radiobutton1 (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 radiobutton1
dt=handles.uitable1.Data;
col2=true(size(dt,1),1);
col2=num2cell(col2);
dt(:,end)=col2;
set(handles.uitable1, 'Data', dt);
set_uitable_color(handles,dt,size(dt,2));
handles.text_num.String=num2str(size(dt,1));
% --- Executes on button press in radiobutton2.
function bt_none_Callback(hObject, eventdata, handles)
% hObject handle to radiobutton2 (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 radiobutton2
dt=handles.uitable1.Data;
col2=false(size(dt,1),1);
col2=num2cell(col2);
dt(:,end)=col2;
set(handles.uitable1, 'Data', dt);
set_uitable_color(handles,dt,size(dt,2));
handles.text_num.String='0';
% --- Executes on button press in bt_reverse.
function bt_reverse_Callback(hObject, eventdata, handles)
% hObject handle to bt_reverse (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
dt=handles.uitable1.Data;
selected=dt(:,end);
for i=1:length(selected)
selected{i}=~selected{i};
end
dt(:,end)=selected;
set(handles.uitable1, 'Data', dt);
set_uitable_color(handles,dt,size(dt,2));
handles.text_num.String=num2str(sum(cell2mat(selected)));
% --- Executes on button press in radiobutton4.
function radiobutton4_Callback(hObject, eventdata, handles)
% hObject handle to radiobutton4 (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 radiobutton4
% --- Executes on button press in radiobutton5.
function radiobutton5_Callback(hObject, eventdata, handles)
% hObject handle to radiobutton5 (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 radiobutton5
% --- Executes when entered data in editable cell(s) in uitable1.
function uitable1_CellEditCallback(hObject, eventdata, handles)
% hObject handle to uitable1 (see GCBO)
% eventdata structure with the following fields (see MATLAB.UI.CONTROL.TABLE)
% Indices: row and column indices of the cell(s) edited
% PreviousData: previous data for the cell(s) edited
% EditData: string(s) entered by the user
% NewData: EditData or its converted form set on the Data property. Empty if Data was not changed
% Error: error string when failed to convert EditData to appropriate value for Data
% handles structure with handles and user data (see GUIDATA)
dt=handles.uitable1.Data;
ct=sum(cell2mat(dt(:,end)));
handles.text_num.String=num2str(ct);
set_uitable_color(handles,dt,size(dt,2));
% --- Executes on button press in bt_top.
function bt_top_Callback(hObject, eventdata, handles)
% hObject handle to bt_top (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
dt=handles.uitable1.Data;
col2=false(size(dt,1),1);
N=str2num(handles.edit_N.String);
for i=1:N
col2(i)=true;
end
col2=num2cell(col2);
dt(:,end)=col2;
set(handles.uitable1, 'Data', dt);
set_uitable_color(handles,dt,size(dt,2));
handles.text_num.String=N;
% --- Executes on button press in bt_bottom.
function bt_bottom_Callback(hObject, eventdata, handles)
% hObject handle to bt_bottom (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
dt=handles.uitable1.Data;
col2=false(size(dt,1),1);
N=str2num(handles.edit_N.String);
for i=1:N
col2(end-i+1:end)=true;
end
col2=num2cell(col2);
dt(:,end)=col2;
set(handles.uitable1, 'Data', dt);
set_uitable_color(handles,dt,size(dt,2));
handles.text_num.String=N;
function edit_N_Callback(hObject, eventdata, handles)
% hObject handle to edit_N (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 edit_N as text
% str2double(get(hObject,'String')) returns contents of edit_N as a double
% --- Executes during object creation, after setting all properties.
function edit_N_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_N (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 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 when selected cell(s) is changed in uitable1.
function uitable1_CellSelectionCallback(hObject, eventdata, handles)
% hObject handle to uitable1 (see GCBO)
% eventdata structure with the following fields (see MATLAB.UI.CONTROL.TABLE)
% Indices: row and column indices of the cell(s) currently selecteds
% handles structure with handles and user data (see GUIDATA)
if ~isempty(eventdata.Indices)
id=eventdata.Indices(1);
handles.uitable1.UserData=id;
handles.text_id.String=num2str(id);
msi=handles.msi;
if isempty(msi.imax)
pk=Mzpk(handles.pks.sdata(id));
pk.ppm=str2num(handles.h.edit_ppm.String);%ppm pass over
pk.offset=str2num(handles.h.edit_offset.String);%offset pass over
pk.z=handles.h.popup_z.Value-3; %z pass over
pk.addType=handles.h.popup_addtype.Value;%addType pass over
pk.isoType=handles.h.popup_isotype.Value; %isoType pass over
msi=msi_get_idata(msi,pk); % get idata from pk
else
msi.idata=msi.imax(:,id); %directly get idata from msi.imax
end
msi=msi_update_imgdata(msi); % update to get 2d imgdata
msi=msi_get_imgC(msi,handles.h);
imshow(msi.imgC,'Parent',handles.axes1);
handles.pkid=id;
handles.msi=msi;
guidata(hObject, handles);
end
function filterline_Callback(hObject, eventdata, handles)
% hObject handle to filterline (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 filterline as text
% str2double(get(hObject,'String')) returns contents of filterline as a double
% --- Executes during object creation, after setting all properties.
function filterline_CreateFcn(hObject, eventdata, handles)
% hObject handle to filterline (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 bt_filter.
function bt_filter_Callback(hObject, eventdata, handles)
% hObject handle to bt_filter (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
msi=handles.msi;
R=msi.R;
S=msi.S;
id=[];
dt=handles.uitable1.Data;
if size(dt,1)~=length(R(1).c)
warndlg('Please click cancel and run targeted analysis to update the intensity matrix first!','warning')
return
end
filterline=handles.filterline.String;
try
handles.text_stat.String='applying filters...' ;
id=eval(['find(', filterline,');']);
catch
handles.text_stat.String='Filterline error!';
return
end
if isempty(id) % no peaks found
handles.text_stat.String='no peaks found!';
else
ct=length(id);
col2=false(size(dt,1),1);
col2(id)=true;
col2=num2cell(col2);
dt(:,end)=col2;
set(handles.uitable1, 'Data', dt);
set_uitable_color(handles,dt,size(dt,2));
handles.text_num.String=num2str(ct);
handles.text_stat.String=[num2str(ct),' qualifying peaks detected!'];
id_next=id(1);
handles.text_id.String=id_next;
ev.Indices=[id_next,1];
uitable1_CellSelectionCallback(hObject, ev, handles)
end
% --- Executes on selection change in pop1.
function pop1_Callback(hObject, eventdata, handles)
% hObject handle to pop1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = cellstr(get(hObject,'String')) returns pop1 contents as cell array
% contents{get(hObject,'Value')} returns selected item from pop1
subID=handles.subID{handles.pop1.Value};
msi=handles.msi;
meta=msi.metadata;
imgdata=zeros(max(meta(:,2))+10,max(meta(:,1))+10);
for i=1:length(subID)
idx=subID(i);
imgdata(meta(idx,2),meta(idx,1))=1;
end
imshow(msi.imgC,'Parent',handles.axes1);
hold(handles.axes1,'on')
f=imshow(imgdata,'parent',handles.axes1);
f.AlphaData = 0.4;
% --- Executes during object creation, after setting all properties.
function pop1_CreateFcn(hObject, eventdata, handles)
% hObject handle to pop1 (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 key press with focus on uitable1 and none of its controls.
function uitable1_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to uitable1 (see GCBO)
% eventdata structure with the following fields (see MATLAB.UI.CONTROL.TABLE)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
id=handles.uitable1.UserData;
dt=handles.uitable1.Data;
if strcmp(eventdata.Key,'g')
dt{id,end}=true;
handles.uitable1.Data{id,end}=true;
ct=sum(cell2mat(dt(:,end)));
handles.text_num.String=num2str(ct);
set_uitable_color(handles,dt,size(dt,2));
elseif strcmp(eventdata.Key,'b')
dt{id,end}=false;
handles.uitable1.Data{id,end}=false;
ct=sum(cell2mat(dt(:,end)));
handles.text_num.String=num2str(ct);
set_uitable_color(handles,dt,size(dt,2));
end
% --- Executes on button press in bt_select.
function bt_select_Callback(hObject, eventdata, handles)
% hObject handle to bt_select (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
select(handles);
% --- Executes on button press in pushbutton14.
function pushbutton14_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton14 (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 bt_left.
function bt_right_Callback(hObject, eventdata, handles)
% hObject handle to bt_left (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
idx=find(cell2mat(handles.uitable1.Data(:,end)));
id=str2num(handles.text_id.String);
tp=find((idx-id)>0);
if ~isempty(tp)
id_next=idx(tp(1));
handles.text_id.String=id_next;
ev.Indices=[id_next,1];
uitable1_CellSelectionCallback(hObject, ev, handles)
end
% --- Executes on button press in bt_right.
function bt_left_Callback(hObject, eventdata, handles)
% hObject handle to bt_right (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
idx=find(cell2mat(handles.uitable1.Data(:,end)));
id=str2num(handles.text_id.String);
tp=find((idx-id)<0);
if ~isempty(tp)
id_next=idx(tp(end));
handles.text_id.String=id_next;
ev.Indices=[id_next,1];
uitable1_CellSelectionCallback(hObject, ev, handles)
end