Unverified Commit 61db9ee2 authored by jayd1860's avatar jayd1860 Committed by GitHub
Browse files

Merge pull request #16 from sstucker/master 

Stim to aux interface, pan tool for PlotProbe, update prompt
parents b55438c5 d8415165

AppSettings.cfg

+2 −2
Original line number Diff line number Diff line
@@ -15,7 +15,7 @@ SNIRF 
On



% Last Checked For Update

17-Jul-2020 16:07:16

17-Jul-1998 16:07:16



% Check For Updates

on
@@ -24,7 +24,7 @@ on 
file



% Auto Save Acquisition Files

Yes

No





% END

DataTree/AcquiredData/Snirf/StimClass.m

+2 −2
Original line number Diff line number Diff line
@@ -47,8 +47,8 @@ classdef StimClass < FileLoadSaveClass 
                t        = varargin{2};

                CondName = varargin{3};

                obj.name = CondName;

                k = s>0;

                obj.data = [t(k), 5*ones(length(t(k)),1), ones(length(t(k)),1)];

                k = s>0 | s==-1 | s==-2;  % Include stim marks with these values

                obj.data = [t(k), 5*ones(length(t(k)),1), s(k)];

            elseif nargin==0

                obj.name = '';

                obj.data = [];

PlotProbeGUI/PlotProbeGUI.fig

+6.04 KiB (45 KiB)

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StimEditGUI/StimEditGUI.fig

+12.2 KiB (44.5 KiB)

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StimEditGUI/StimEditGUI.m

+186 −34
Original line number Diff line number Diff line
@@ -26,7 +26,6 @@ global stimEdit 
if ~isempty(stimEdit.updateParentGui)

    stimEdit.updateParentGui('StimEditGUI', 'close');

end

Save()
@@ -81,7 +80,6 @@ stimEdit.updateParentGui = []; 
cfg = ConfigFileClass();

stimEdit.config.autoSaveAcqFiles = cfg.GetValue('Auto Save Acquisition Files');





if ~isempty(maingui)

    stimEdit.groupDirs = maingui.groupDirs;

    stimEdit.format = maingui.format;
@@ -147,8 +145,6 @@ EnableGuiObjects('on', handles); 
stimEdit.status=0;









% --------------------------------------------------------------------

function pushbuttonExit_Callback(hObject, eventdata, handles)

if ishandles(handles.figure)
@@ -156,7 +152,6 @@ if ishandles(handles.figure) 
end







% --------------------------------------------------------------------

function popupmenuConditions_Callback(hObject, eventdata, handles)

conditions = get(hObject, 'string');
@@ -165,7 +160,6 @@ condition = conditions{idx}; 
SetUitableStimInfo(condition, handles);







%---------------------------------------------------------------------------

function editSelectTpts_Callback(hObject, eventdata, handles)

global stimEdit
@@ -188,7 +182,6 @@ figure(handles.figure); 
stimEdit.status=0;







%---------------------------------------------------------------------------

function uitableStimInfo_CellEditCallback(hObject, eventdata, handles)

global stimEdit
@@ -209,7 +202,6 @@ end 
figure(handles.figure);







%---------------------------------------------------------------------------

function pushbuttonRenameCondition_Callback(hObject, eventdata, handles)

global stimEdit
@@ -304,7 +296,6 @@ s2 = sum(abs(s(tPts_idxs_select,:)),2); 
stims_select = find(s2>=1);







% ------------------------------------------------

function h = HighlightStims(t, t_select, s, handles)

h = [];
@@ -324,7 +315,6 @@ hold off 
drawnow







% ------------------------------------------------

function EditSelectRange(t1, t2, handles)

global stimEdit
@@ -456,13 +446,10 @@ end 
if menu_choice==nActions || menu_choice==0

    return;

end





%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% New stim

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

if isempty(iS_lst)

    

    % If stim added to new condition update group conditions

    if menu_choice==nCond+1

        CondNameNew = inputdlg('','New Condition name');
@@ -479,7 +466,6 @@ if isempty(iS_lst) 
    else

        CondName = CondNamesGroup{menu_choice};

    end

    

    %%%% Add new stim to currElem's condition

    stimEdit.dataTree.currElem.AddStims(tc(tPts_idxs_select), CondName);

    stimEdit.status = 1;
@@ -525,7 +511,6 @@ iG = stimEdit.dataTree.GetCurrElemIndexID(); 
stimEdit.dataTree.groups(iG).SetConditions();







% ------------------------------------------------

function SetStimDuration(icond, duration)

global stimEdit
@@ -541,9 +526,8 @@ end 
stimEdit.dataTree.currElem.SetStimDuration(icond, duration);







% ------------------------------------------------

function duration = GetStimDuration(icond)

function duration = GetStimDuration(icond) %#ok<*DEFNU>

global stimEdit

if isempty(stimEdit)

    return;
@@ -557,14 +541,12 @@ end 
duration = stimEdit.dataTree.currElem.GetStimDuration(icond);







% -------------------------------------------------------------------

function [tpts, duration, vals] = GetStimData(icond)

global stimEdit

[tpts, duration, vals] = stimEdit.dataTree.currElem.GetStimData(icond);







% -------------------------------------------------------------------

function SetStimData(icond, data)

global stimEdit
@@ -573,27 +555,31 @@ stimEdit.dataTree.currElem.SetStimDuration(icond, data(:,2)); 
stimEdit.dataTree.currElem.SetStimValues(icond, data(:,3));







% -------------------------------------------------------------------

function Save()

global stimEdit



% If nothing changes, nothing to save, so exit

if ~stimEdit.dataTree.currElem.AcquiredDataModified()

    errordlg('There are no changes to save!','Unmodified file')

    return

end



% Check auto-save config parameter

if ~strcmpi(stimEdit.config.autoSaveAcqFiles, 'yes')

if ~strcmpi(stimEdit.config.autoSaveAcqFiles, 'Yes')

    % Ask user if they want to save, before changing contents of acquisition file

    if stimEdit.dataTree.currElem.IsRun()

        msg = sprintf('Do you want to save stimulus edits directly in the acquisition file %s?', stimEdit.dataTree.currElem.name);

        msg = sprintf('Are you sure you want to save stimulus edits directly in the acquisition file %s?', stimEdit.dataTree.currElem.name);

    else

        msg = sprintf('Do you want to save stimulus edits directly in acquisition files in %s?', stimEdit.dataTree.currElem.name);

        msg = sprintf('Are you sure you want to save stimulus edits directly in acquisition files in %s?', stimEdit.dataTree.currElem.name);

    end

    q = MenuBox(msg, {'YES','NO'});

    q = MenuBox(msg, {'Yes','No','Don''t ask again'});

    if q==2

        return;

    elseif q==3

        cfg = ConfigFileClass();

        cfg.SetValue('Auto Save Acquisition Files', 'Yes');

        cfg.Save()

    end

else

    % Otherwise auto-save
@@ -601,8 +587,15 @@ else 
end



% Update acquisition file with new contents

h = waitbar_improved(0, 'Saving new stim marks to %s...', stimEdit.dataTree.currElem.name);

stimEdit.dataTree.currElem.SaveAcquiredData()

waitbar_improved(1, h, 'Saving new stim marks to %s...', stimEdit.dataTree.currElem.name);

close(h)





% --------------------------------------------------------------------

function pushbuttonWriteToFile_Callback(hObject, eventdata, handles)

Save()





% -------------------------------------------------------------------
@@ -610,7 +603,6 @@ function StimEditGUI_DeleteFcn(hObject, eventdata, handles) 
Save()







% --------------------------------------------------------------------

function menuItemChangeGroup_Callback(hObject, eventdata, handles)

pathname = uigetdir(pwd, 'Select a NIRS data group folder');
@@ -621,7 +613,6 @@ cd(pathname); 
StimEditGUI();







% --------------------------------------------------------------------

function menuItemSaveGroup_Callback(hObject, eventdata, handles)

global stimEdit
@@ -631,7 +622,6 @@ end 
stimEdit.dataTree.currElem.Save();







% --------------------------------------------------------------------

function Update(handles)

global stimEdit
@@ -677,7 +667,6 @@ if eval( sprintf('ishandles(obj.handles.%s)', handle) ) 
end







% -----------------------------------------------------------

function [icond, conditions] = GetConditionIdxFromPopupmenu(conditions, handles)

conditions_menu = get(handles.popupmenuConditions, 'string');
@@ -693,7 +682,6 @@ if isempty(icond) 
end







% -----------------------------------------------------------

function SetTextFilename(name, handles)

if isempty(handles)
@@ -710,11 +698,9 @@ set(handles.textFilename, 'units','normalized'); 
set(handles.textFilename, 'string',name);







% -----------------------------------------------------------

function Display(handles)

global stimEdit



if isempty(stimEdit.dataTree)

    return;

end
@@ -727,7 +713,6 @@ end 


axes(handles.axes1)

cla(handles.axes1);

set(handles.axes1, 'ytick','');

hold(handles.axes1, 'on');



% As of now this operation is undefined for non-Run nodes (i.e., Subj and Group)
@@ -748,6 +733,30 @@ t = stimEdit.dataTree.currElem.GetTimeCombined(); 
s              = stimEdit.dataTree.currElem.GetStims(t);

stimVals       = stimEdit.dataTree.currElem.GetStimValSettings();



% Aux preview

if get(handles.checkboxPreview, 'Value')  % If preview is enabled, plot

    iaux = handles.listboxAuxSelect.Value;

    currAux = stimEdit.dataTree.currElem.acquired.aux(iaux);

    [onsets, auxFiltered, timeFiltered] = StimEditGUI_StimFromAux(currAux,...

                                                            handles.editThresh.Value,...          % Stim threshold

                                                            handles.editLPF.Value,...             % LPF window width

                                                            handles.radiobuttonRisingEdge.Value); % rising vs falling

    % Plot selected aux signal after applying filter

    auxPlot = plot(timeFiltered + currAux.timeOffset, auxFiltered, 'k-');  % TODO is this what timeOffset is for?

    auxPlot.Color(4) = 0.5;  % Stim opacity

    % Plot stim preview

    yy = get(handles.axes1, 'ylim');

    for iOnset = 1:length(onsets)

        plot([1 1]*onsets(iOnset), yy, 'k:', 'LineWidth', 2.5, 'parent', handles.axes1);

    end

    if length(onsets) > 9999

        nmarks = '>9999';

    else

        nmarks = num2str(length(onsets));

    end

    set(handles.pushbuttonGenerate, 'String', ['Generate ', nmarks, ' stim marks']);

end



[lstR,lstC] = find(abs(s) ~= stimVals.none);

[lstR,k] = sort(lstR);

lstC = lstC(k);
@@ -764,6 +773,8 @@ for ii=1:nStim 
        linestyle = '--';

    elseif(s(lstR(ii),lstC(ii))==stimVals.excl_auto)

        linestyle = '-.';

    else

        linestyle = '-';

    end

    Lines(ii).handle = plot([1 1]*t(lstR(ii)), yy, linestyle, 'parent',handles.axes1);
@@ -786,6 +797,7 @@ for ii=1:nStim 
end



% Update legend

set(0,'DefaultLegendAutoUpdate','off')  % Required to keep aux signals from appearing

[idxLg,k] = sort(idxLg);

if ~isempty(hLg)

    hLg = legend(hLg(k), CondNamesGroup(idxLg));
@@ -808,8 +820,6 @@ end 
Lines = repmat( struct('handle',[], 'color',[], 'widthReg',2, 'widthHighl',4), n,1);









% -----------------------------------------------------------

function SetUitableStimInfo(condition, handles)

global stimEdit
@@ -838,3 +848,145 @@ data(:,3) = vals(idx); 
set(handles.uitableStimInfo, 'data',data);





% --------------------------------------------------------------------

function [onsets, aux_filt, time_filt] = StimEditGUI_StimFromAux(currElemAux, thresh, lpf_len, rising_edge)

T = currElemAux.time(2) - currElemAux.time(1);  % Aux sample period

moving_avg_filter = ones(lpf_len,1) / lpf_len;

auxMax = max(currElemAux.dataTimeSeries);

auxMin = min(currElemAux.dataTimeSeries);

% Apply filter

if lpf_len > 0

   aux_filt = filter(moving_avg_filter, 1, currElemAux.dataTimeSeries);

   time_filt = currElemAux.time - T*(lpf_len/2);  % Remove group delay induced by LPF

   aux_filt(aux_filt > auxMax) = auxMax;

   aux_filt(aux_filt < auxMin) = auxMin;

else

   aux_filt = currElemAux.dataTimeSeries;

   time_filt = currElemAux.time;

end

onsets = [];

last = currElemAux.dataTimeSeries(1);

% Naive search for threshold crossings

for i = (lpf_len + 1):length(time_filt)  % Exclude LPF artifact

    next = aux_filt(i);

    if rising_edge

        if ((last <= thresh) && (next > thresh))

           onsets = [onsets, time_filt(i) + currElemAux.timeOffset];  %#ok<*AGROW>

        end

    else

        if ((last >= thresh) && (next < thresh))

            onsets = [onsets, time_filt(i) + currElemAux.timeOffset];

        end

    end

    last = aux_filt(i);

end



% --------------------------------------------------------------------

function editThresh_Callback(hObject, eventdata, handles)

val = str2double(hObject.String);

if isnan(val)

   set(hObject ,'String', hObject.Value);

else

    hObject.Value = val;

end

Display(handles);





% --------------------------------------------------------------------

function pushbuttonGenerate_Callback(hObject, eventdata, handles)

global stimEdit; 

iaux = handles.listboxAuxSelect.Value;

currAux = stimEdit.dataTree.currElem.acquired.aux(iaux);

[onsets, ~, ~] = StimEditGUI_StimFromAux(currAux,...

                                         handles.editThresh.Value,...          % Stim threshold

                                         handles.editLPF.Value,...             % LPF window width

                                         handles.radiobuttonRisingEdge.Value); % rising vs falling

% Add stim to dataTree element

cond = char(handles.listboxAuxSelect.String(handles.listboxAuxSelect.Value));

for i = 1:length(onsets)

    stimEdit.dataTree.currElem.AddStims(onsets(i), cond);

end

iG = stimEdit.dataTree.GetCurrElemIndexID();

stimEdit.dataTree.groups(iG).SetConditions();

if ~isempty(stimEdit.updateParentGui)

    stimEdit.updateParentGui('StimEditGUI', 'close');

end

Display(handles);

    



% --------------------------------------------------------------------

function listboxAuxSelect_Callback(hObject, eventdata, handles)

Display(handles);





% --------------------------------------------------------------------

function listboxAuxSelect_CreateFcn(hObject, eventdata, handles)

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end

try

    % Try to populate listbox with aux channels

    global stimEdit

    aux = stimEdit.dataTree.currElem.acquired.aux;

    names = cell(1, length(aux));

    for i = 1:length(aux)

        names{i} = aux(i).name;

    end

    set(hObject, 'string', names);

    set(stimEdit.handles.editCondition, 'String', names{1});

catch

    return

end





% --------------------------------------------------------------------

function editThresh_CreateFcn(hObject, eventdata, handles)

set(hObject ,'String', '0.0');





% --------------------------------------------------------------------

function checkboxPreview_Callback(hObject, eventdata, handles)

Display(handles);





% --------------------------------------------------------------------

function radiobuttonFallingEdge_Callback(hObject, eventdata, handles)

Display(handles);





% --------------------------------------------------------------------

function radiobuttonRisingEdge_Callback(hObject, eventdata, handles)

Display(handles);





% --------------------------------------------------------------------

function editLPF_Callback(hObject, eventdata, handles)

val = abs(floor(str2num(hObject.String))); %#ok<ST2NM>

if isnan(val)

   set(hObject ,'String', hObject.Value);

else

    hObject.Value = val;

    set(hObject ,'String', val);

end

Display(handles);





% --------------------------------------------------------------------

function editLPF_CreateFcn(hObject, eventdata, handles)

hObject.Value = floor(str2double(hObject.String));





% --------------------------------------------------------------------

function editDuration_Callback(hObject, eventdata, handles)

val = str2double(hObject.String);

if isnan(val)

   set(hObject ,'String', hObject.Value);

else

    hObject.Value = val;

end





% --------------------------------------------------------------------

function editDuration_CreateFcn(hObject, eventdata, handles)

val = str2double(hObject.String);

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