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PAS_analyzer.m
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PAS_analyzer.m
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function varargout = PAS_analyzer(varargin)
% PAS_ANALYZER MATLAB code for PAS_analyzer.fig
% PAS_ANALYZER, by itself, creates a new PAS_ANALYZER or raises the existing
% singleton*.
%
% H = PAS_ANALYZER returns the handle to a new PAS_ANALYZER or the handle to
% the existing singleton*.
%
% PAS_ANALYZER('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in PAS_ANALYZER.M with the given input arguments.
%
% PAS_ANALYZER('Property','Value',...) creates a new PAS_ANALYZER or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before PAS_analyzer_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to PAS_analyzer_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 PAS_analyzer
% Last Modified by GUIDE v2.5 13-Feb-2021 12:15:39
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @PAS_analyzer_OpeningFcn, ...
'gui_OutputFcn', @PAS_analyzer_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
% End initialization code - DO NOT EDIT
% --- Executes just before PAS_analyzer is made visible.
function PAS_analyzer_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 PAS_analyzer (see VARARGIN)
% Choose default command line output for PAS_analyzer
handles.output = hObject;
handles.data_array = {};
handles.data_select = [];
handles.pathname = '';
handles.filename = '';
handles.MEPs = [];
handles.params = struct(...
'emg_vec' , [1],...
'time_before' , 100,...
'time_after' , 500,...
'amp_gain' , 1,...
'rectify' , false,...
'dc' , true,...
'bar_plot_select', 'int_ave',...
'time_window' , [10 20]);
% Update handles structure
guidata(hObject, handles);
end
% UIWAIT makes PAS_analyzer wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = PAS_analyzer_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;
end
%-------------------------------------------------------------------------------------------------------
%% BUTTONS
%IMPORT
function import_button_Callback(hObject, eventdata, handles)
[handles.data_array, num_data_files, handles.pathname] = TDT_import();
if ~isempty(handles.pathname)
handles.data_table.Data = handles.data_array(:,2:end);
else
disp('Import cancelled');
end
%update handles in guidata
guidata(hObject, handles);
end
% --- Executes on button press in import_lc_button.
function import_lc_button_Callback(hObject, eventdata, handles)
% hObject handle to import_lc_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
[handles.data_array, num_data_files, handles.pathname] = LC_import('time_before',handles.params.time_before/1000,'time_after',handles.params.time_after/1000);
if ~isempty(handles.pathname)
handles.data_table.Data = handles.data_array(:,2:end);
else
disp('Import cancelled');
end
%update handles in guidata
guidata(hObject, handles);
end
%LOAD
function load_button_Callback(hObject, eventdata, handles)
% load matlab file from folder:
disp('Select .mat to analyze');
[filename, pathname] = uigetfile(fullfile(handles.pathname,'*.mat'),'Select .mat file to analyze');
if pathname
%user did not press cancel
handles.filename = filename;
handles.pathname = pathname;
data_tmp = load(fullfile(handles.pathname,handles.filename));
if ~isfield(data_tmp,'matdata')
warning('Incompatible data file. Data load failed');
return;
end
%load data_array
handles.data_array = data_tmp.matdata;
handles.data_table.Data = handles.data_array(:,2:end);
handles.data_table.ColumnName = handles.data_table.ColumnName(1);
%load MEPs if any
if isfield(data_tmp,'MEPs')
handles.MEPs = data_tmp.MEPs;
assignin('base','MEPs',handles.MEPs);
%update data table with MEP values
handles = update_meps(handles);
end
clear data_tmp;
%update handles in guidata
guidata(hObject, handles);
end
end
%SAVE
function save_button_Callback(hObject, eventdata, handles)
% hObject handle to save_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
[filename, pathname] = uiputfile(fullfile(handles.pathname,handles.filename),'Save data array');
if pathname
% user did not press cancel, update file info in handles
handles.filename = filename;
handles.pathname = pathname;
matdata = handles.data_array;
MEPs = handles.MEPs;
rat_name = get(handles.rat_name, 'String');
session_date = handles.session_date;
STDP_condition = handles.STDP_condition;
window = handles.params.time_window;
save(fullfile(handles.pathname,handles.filename),'matdata','MEPs','rat_name','session_date','STDP_condition','window');
fprintf('File %s\n saved successfully. Open quickload.mat to see measurement time window.\n',fullfile(handles.pathname,handles.filename));
clear data_array;
% update handles in guidata
guidata(hObject, handles);
end
end
%CLEAR
function clear_button_Callback(hObject, eventdata, handles)
clear_data = questdlg('Are you sure you want to clear all data?', ...
'Confirm clear', ...
'Yes', 'Cancel', 'Yes');
if strcmp(clear_data,'Yes')
handles.data_array = {};
handles.data_select = [];
handles.pathname = '';
handles.filename = '';
handles.MEPs = [];
set ([handles.amp_gain, handles.session_date, handles.STDP_condition], 'String','');
handles.data_table.Data = [];
handles.data_table.ColumnName = handles.data_table.ColumnName(1);
else
disp('Clear data cancelled');
end
% update handles in guidata
guidata(hObject, handles);
end
%LOAD WS
function load_ws_button_Callback(hObject, eventdata, handles)
% hObject handle to load_ws_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
for i = 1:length(handles.data_select)
assignin('base',handles.data_array{handles.data_select(i),2},handles.data_array{handles.data_select(i),1});
end
assignin('base','rat_name',get(handles.rat_name, 'String'));
assignin('base','session_date',get(handles.session_date, 'String'));
assignin('base','exp_condition',get(handles.STDP_condition, 'String'));
end
%CONV2ELF
function conv2ELF_button_Callback(hObject, eventdata, handles)
% hObject handle to conv2ELF_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if ~isfield(handles.data_array{1,1},'format')
handles.data_array = convertTDT2ELformat(handles.data_array);
disp('Data converted to ELF format');
elseif ~strcmpi(handles.data_array{1,1}.format,'ELF')
handles.data_array = convertTDT2ELformat(handles.data_array);
disp('Data converted to ELF format');
else
disp('Data already in ELF format');
end
% update handles in guidata
guidata(hObject, handles);
end
%VALIDATE
function validate_snips_button_Callback(hObject, eventdata, handles)
% hObject handle to validate_snips_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if length(handles.data_select)>1
msgbox('Please select only one data block at a time','Wô les moteurs!','warn')
else
if isfield(handles.data_array{1,1},'format')
if strcmpi(handles.data_array{1,1}.format,'ELF')
data = validate_EMG_snips_ELF(handles.data_array{handles.data_select,1},handles.params);
handles.data_array{handles.data_select,1} = data;
set(handles.data_table,'Data',handles.data_array(:,2));
clear data;
end
else
warning('Please convert to ELF format first');
end
end
% update handles in guidata
guidata(hObject, handles);
end
%GET MEP
function get_mep_button_Callback(hObject, eventdata, handles)
% hObject handle to get_mep_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles.data_array{1,1},'format')
if strcmpi(handles.data_array{1,1}.format,'ELF')
MEPs = calc_mean_MEPs(handles.data_array,...
'window',handles.params.time_window,...
'emg_vec',handles.params.emg_vec,...
'amp_gain',handles.params.amp_gain);
assignin('base','MEPs',MEPs);
end
handles.MEPs = MEPs;
%update data table with MEP values
handles = update_meps(handles);
else
warning('Please convert to ELF format first');
return;
end
% update handles in guidata
guidata(hObject, handles);
end
function handles = update_meps(handles)
%update data table with MEP values
handles.data_table.Data = handles.data_table.Data(:,1);
handles.data_table.ColumnName = handles.data_table.ColumnName(1);
if ~isempty(handles.MEPs)
num_ch = length(handles.MEPs.chan_list);
for c = 1:num_ch
%column label:
handles.data_table.ColumnName{c+1} = sprintf('MEP p2p ch%d (mVpp)',handles.MEPs.chan_list(c));
handles.data_table.ColumnName{c+1+num_ch} = sprintf('MEP int ch%d (mV*ms)',handles.MEPs.chan_list(c));
%display mean meps for each block
for b=1:size(handles.data_array,1)
handles.data_table.Data{b,c+1} = handles.MEPs.p2p.mean(b,c);
handles.data_table.Data{b,c+1+num_ch} = handles.MEPs.integral.mean(b,c);
end
end
end
end
%PLOT EMG
function plot_emg_button_Callback(hObject, eventdata, handles)
if isempty(handles.data_select)
warning('Please select a data set first');
return;
end
if isfield(handles.data_array{1,1},'format')
if strcmpi(handles.data_array{1,1}.format,'ELF')
meanEMGs = mean_EMG_traces(handles.data_array(handles.data_select,:),...
handles.params.emg_vec,'rectify',handles.params.rectify,...
'time_range',[-handles.params.time_before handles.params.time_after]/1000,...
'amp_gain', handles.params.amp_gain);
assignin('base','meanEMGs',meanEMGs);
end
else
disp('Please convert to ELF format first');
end
end
%BAR PLOT
function bar_plot_button_Callback(hObject, eventdata, handles)
% hObject handle to bar_plot_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isempty(handles.data_select)
warning('Please select rows in data tables');
return;
end
if isempty(handles.MEPs)
warning('Please calculate MEPs first');
return;
end
PAS_plot_bar(handles.MEPs,handles.data_select,handles.params.emg_vec,handles.params.bar_plot_select)
end
%-------------------------------------------------------------------------------------------------------
%% TABLE
function data_table_CellSelectionCallback(hObject, eventdata, handles)
% hObject handle to data_table (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)
handles.data_select = unique(eventdata.Indices(:,1));
guidata(hObject, handles);
end
%% PARAMS
%EMG VEC
function emg_vec_edit_Callback(hObject, eventdata, handles)
% hObject handle to emg_vec_edit (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 emg_vec_edit as text
% str2double(get(hObject,'String')) returns contents of emg_vec_edit as a double
val = hObject.String;
if strcmpi(val,':')
%if ':', use all available emgs, set handles.emg_vec to empty array
handles.params.emg_vec = [];
else
%otherwise, set handles.emg_vec to value in emg_vec_edit textbox
try val = eval(val);
catch
warning('Invalid EMG chan vector format. Use standard matlab vector format.');
handles.params.emg_vec_edit.String = ':';
end
handles.params.emg_vec = val;
end
% update handles in guidata
guidata(hObject, handles);
end
function emg_vec_edit_CreateFcn(hObject, eventdata, handles)
% hObject handle to emg_vec_edit (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
end
%TIME BEFORE / TIME AFTER
function time_before_edit_Callback(hObject, eventdata, handles)
% hObject handle to time_before_edit (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 time_before_edit as text
% str2double(get(hObject,'String')) returns contents of time_before_edit as a double
handles.params.time_before = str2double(hObject.String);
% update handles in guidata
guidata(hObject, handles);
end
function time_before_edit_CreateFcn(hObject, eventdata, handles)
% hObject handle to time_before_edit (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
end
function time_after_edit_Callback(hObject, eventdata, handles)
% hObject handle to time_after_edit (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 time_after_edit as text
% str2double(get(hObject,'String')) returns contents of time_after_edit as a double
handles.params.time_after = str2double(hObject.String);
% update handles in guidata
guidata(hObject, handles);
end
function time_after_edit_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
end
% GAIN
% --- Executes during object creation, after setting all properties.
function amp_gain_edit_CreateFcn(hObject, eventdata, handles)
% hObject handle to amp_gain_edit (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
end
function amp_gain_edit_Callback(hObject, eventdata, handles)
handles.params.amp_gain = str2double(hObject.String);
guidata(hObject, handles);
end
%RECTIFY
function rectify_cbx_Callback(hObject, eventdata, handles)
% hObject handle to rectify_cbx (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 rectify_cbx
handles.params.rectify = get(hObject,'Value');
% update handles in guidata
guidata(hObject, handles);
end
function time_window_edit_Callback(hObject, eventdata, handles)
val = hObject.String;
try val = eval(val);
if numel(val)~=2
warning('Invalid time window vector format. Enter a 2-element vecgtor in strandard matlab format.');
handles.time_window_edit.String = [ '[' num2str(handles.params.time_window) ']'];
else
handles.params.time_window = val;
end
catch
warning('Invalid time window vector format. Use standard matlab vector format.');
handles.time_window_edit.String = [ '[' num2str(handles.params.time_window) ']'];
end
% update handles in guidata
guidata(hObject, handles);
end
function time_window_edit_CreateFcn(hObject, eventdata, handles)
% hObject handle to time_window_edit (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
end
function int_radio_Callback(hObject, eventdata, handles)
handles.params.bar_plot_select = 'integral';
% update handles in guidata
guidata(hObject, handles);
end
function p2p_radio_Callback(hObject, eventdata, handles)
handles.params.bar_plot_select = 'p2p';
% update handles in guidata
guidata(hObject, handles);
end
% --- Executes on button press in int_ave_radio.
function int_ave_radio_Callback(hObject, eventdata, handles)
handles.params.bar_plot_select = 'int_ave';
% update handles in guidata
guidata(hObject, handles);
end
% --- Executes during object creation, after setting all properties.
function amp_gain_CreateFcn(hObject, eventdata, handles)
% hObject handle to amp_gain (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
end
function session_date_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)
handles.session_date = get(hObject, 'String');
% Hints: get(hObject,'String') returns contents of edit7 as text
% str2double(get(hObject,'String')) returns contents of edit7 as a double
guidata(hObject, handles);
end
% --- Executes during object creation, after setting all properties.
function session_date_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
end
function exp_notes_Callback(hObject, eventdata, handles)
% hObject handle to edit8 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles.STDP_condition = get(hObject, 'String');
% Hints: get(hObject,'String') returns contents of edit8 as text
% str2double(get(hObject,'String')) returns contents of edit8 as a double
guidata(hObject, handles);
end
% --- Executes during object creation, after setting all properties.
function exp_notes_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit8 (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
end
function rat_name_Callback(hObject, eventdata, handles)
% hObject handle to rat_name (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles.rat_name = get(hObject, 'String');
% Hints: get(hObject,'String') returns contents of rat_name as text
% str2double(get(hObject,'String')) returns contents of rat_name as a double
guidata(hObject, handles);
end
% --- Executes during object creation, after setting all properties.
function rat_name_CreateFcn(hObject, eventdata, handles)
% hObject handle to rat_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 && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
end
% --- Executes on button press in dc.
function dc_Callback(hObject, eventdata, handles)
% hObject handle to dc (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles.dc = get(hObject, 'Value');
guidata(hObject, handles);
% Hint: get(hObject,'Value') returns toggle state of dc
end