Commit d1b58597 authored by Jay Dubb's avatar Jay Dubb
Browse files

Merge branch 'locDataTree' of https://github.com/chrsthur/Homer3

parents 1e245ec3 4a06914b

DataTree/DataTreeClass.m

+17 −1
Original line number Diff line number Diff line
@@ -26,6 +26,11 @@ classdef DataTreeClass < handle 
            obj.dirnameGroups       = {};

            obj.logger              = InitLogger(logger, 'DataTree');

            

            if isa(groupDirs, 'DataTreeClass')

                   obj.Copy(groupDirs);

                   return;

            end

            

            cfg = ConfigFileClass();

            obj.dataStorageScheme = cfg.GetValue('Data Storage Scheme');
@@ -89,6 +94,17 @@ classdef DataTreeClass < handle 
            end

        end

        

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

        function Copy(obj, obj2)

            idx = obj2.currElem.GetIndexID();

            iG = idx(1);

            iS = idx(2);

            iR = idx(3);

            obj.groups = GroupClass();

            obj.groups.Copy(obj2.groups(iG))

            obj.groups.CondNames = obj2.groups(iG).CondNames;

            obj.currElem = obj.groups(iG).subjs(iS).runs(iR);

        end

        

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

        function status = FoundDataFilesInOtherFormat(obj, dataInit, kk)

DataTree/ProcStream/ProcInputClass.m

+3 −2
Original line number Diff line number Diff line
@@ -63,6 +63,8 @@ classdef ProcInputClass < handle 
                eval( sprintf('obj.misc.%s = CopyHandles(obj2.misc.%s, obj.misc.%s);', fields{ii}, fields{ii}) );

            end

            if isempty(obj.acquired)

                obj.acquired = SnirfClass();

                obj.acquired.Copy(obj2.acquired);

                return;

            end

            obj.acquired.Copy(obj2.acquired);
@@ -447,4 +449,3 @@ classdef ProcInputClass < handle 
    end   

    

end
 
 No newline at end of file

DataTree/RunClass.m

+2 −2
Original line number Diff line number Diff line
@@ -183,6 +183,7 @@ classdef RunClass < TreeNodeClass 
                    end

                end

                obj.acquired.Copy(R.acquired);

                obj.CondNames = R.CondNames;

            end

        end
@@ -752,4 +753,3 @@ classdef RunClass < TreeNodeClass 
    end  % Private methods



end
 
 No newline at end of file

StimEditGUI/StimEditGUI.m

+81 −73
Original line number Diff line number Diff line
@@ -76,6 +76,7 @@ stimEdit.groupDirs = {}; 
stimEdit.format = '';

stimEdit.pos = [];

stimEdit.updateParentGui = [];

stimEdit.locDataTree = DataTreeClass(maingui.dataTree);



cfg = ConfigFileClass();

stimEdit.config.autoSaveAcqFiles = cfg.GetValue('Auto Save Acquisition Files');
@@ -172,9 +173,9 @@ if stimEdit.status==0 
    return;

end

Display(handles);

if ~isempty(stimEdit.updateParentGui)

    stimEdit.updateParentGui('StimEditGUI');

end

% if ~isempty(stimEdit.updateParentGui)

%     stimEdit.updateParentGui('StimEditGUI');

% end

figure(handles.figure);



% Reset status only should be set/reset in top-level gui functions (ie
@@ -187,7 +188,7 @@ function uitableStimInfo_CellEditCallback(hObject, eventdata, handles) 
global stimEdit



data = get(hObject,'data') ;

conditions =  stimEdit.dataTree.currElem.GetConditions();

conditions =  stimEdit.locDataTree.currElem.GetConditions();

icond = GetConditionIdxFromPopupmenu(conditions, handles);

SetStimData(icond, data);

r=eventdata.Indices(1);
@@ -196,9 +197,9 @@ if c==2 
    return;

end

Display(handles);

if ~isempty(stimEdit.updateParentGui)

    stimEdit.updateParentGui('StimEditGUI');

end

% if ~isempty(stimEdit.updateParentGui)

%     stimEdit.updateParentGui('StimEditGUI');

% end

figure(handles.figure);
@@ -233,17 +234,17 @@ oldname = conditions{idx}; 
% in keeping the condition colors straight. Therefore we comment out the 

% following line in favor of the one after it. 



iG = stimEdit.dataTree.GetCurrElemIndexID();

stimEdit.dataTree.groups(iG).RenameCondition(oldname, newname{1});

iG = stimEdit.locDataTree.GetCurrElemIndexID();

stimEdit.locDataTree.groups(iG).RenameCondition(oldname, newname{1});

if stimEdit.status ~= 0

    return;

end

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

set(handles.popupmenuConditions, 'string', stimEdit.dataTree.groups(iG).GetConditions());

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

set(handles.popupmenuConditions, 'string', stimEdit.locDataTree.groups(iG).GetConditions());

Display(handles);

if ~isempty(stimEdit.updateParentGui)

    stimEdit.updateParentGui('StimEditGUI');

end

% if ~isempty(stimEdit.updateParentGui)

%     stimEdit.updateParentGui('StimEditGUI');

% end

figure(handles.figure);
@@ -263,9 +264,9 @@ if stimEdit.status==0 
    return;

end

Display(handles);

if ~isempty(stimEdit.updateParentGui)

    stimEdit.updateParentGui('StimEditGUI');

end

% if ~isempty(stimEdit.updateParentGui)

%     stimEdit.updateParentGui('StimEditGUI');

% end

figure(handles.figure);



% Reset status
@@ -281,17 +282,17 @@ global stimEdit 
if isempty(stimEdit.dataTree)

    return;

end

if isempty(stimEdit.dataTree.currElem)

if isempty(stimEdit.locDataTree.currElem)

    return;

end

if ~isa(stimEdit.dataTree.currElem, 'RunClass')

if ~isa(stimEdit.locDataTree.currElem, 'RunClass')

    return;

end



% Now that we made sure legit dataTree exists, we can match up

% the selected stims to the stims in currElem

t = stimEdit.dataTree.currElem.GetTimeCombined();

s = stimEdit.dataTree.currElem.GetStims(t);

t = stimEdit.locDataTree.currElem.GetTimeCombined();

s = stimEdit.locDataTree.currElem.GetStims(t);

s2 = sum(abs(s(tPts_idxs_select,:)),2);

stims_select = find(s2>=1);
@@ -318,7 +319,7 @@ drawnow 
% ------------------------------------------------

function EditSelectRange(t1, t2, handles)

global stimEdit

t = stimEdit.dataTree.currElem.GetTime();

t = stimEdit.locDataTree.currElem.GetTime();

if ~all(t1==t2)

    tPts_idxs_select = find(t>=t1 & t<=t2);

else
@@ -342,7 +343,7 @@ end 
% ------------------------------------------------

function EditSelectTpts(tPts_select)

global stimEdit

t = stimEdit.dataTree.currElem.GetTime();

t = stimEdit.locDataTree.currElem.GetTime();

if isempty(t)

    MessageBox('Current processing element has no time course data for stim editing. In MainGUI, change current processing element to Run to edit stim marks.');

    return;
@@ -378,9 +379,9 @@ if ~exist('iS_lst','var') || isempty(iS_lst) 
    iS_lst = [];

end



iG = stimEdit.dataTree.GetCurrElemIndexID();

CondNamesGroup = stimEdit.dataTree.groups(iG).GetConditions();

tc             = stimEdit.dataTree.currElem.GetTime();

iG = stimEdit.locDataTree.GetCurrElemIndexID();

CondNamesGroup = stimEdit.locDataTree.groups(iG).GetConditions();

tc             = stimEdit.locDataTree.currElem.GetTime();



% Create menu actions list

actionLst = CondNamesGroup;
@@ -424,9 +425,9 @@ if ~exist('mode','var') || isempty(mode) 
    mode = 'interactive';

end



iG = stimEdit.dataTree.GetCurrElemIndexID();

CondNamesGroup = stimEdit.dataTree.groups(iG).GetConditions();

tc             = stimEdit.dataTree.currElem.GetTime();

iG = stimEdit.locDataTree.GetCurrElemIndexID();

CondNamesGroup = stimEdit.locDataTree.groups(iG).GetConditions();

tc             = stimEdit.locDataTree.currElem.GetTime();

nCond          = length(CondNamesGroup);



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -467,7 +468,7 @@ if isempty(iS_lst) 
        CondName = CondNamesGroup{menu_choice};

    end

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

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

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

    stimEdit.status = 1;

    

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -480,12 +481,12 @@ else 


        % Delete stim entry from userdata first

        % because it depends on stim.currElem.s

        stimEdit.dataTree.currElem.DeleteStims(tc(tPts_idxs_select));

        stimEdit.locDataTree.currElem.DeleteStims(tc(tPts_idxs_select));



    %%%% Toggle active/inactive stim

    elseif menu_choice==nActions-2 & nActions==nCond+4



        stimEdit.dataTree.currElem.ToggleStims(tc(tPts_idxs_select));

        stimEdit.locDataTree.currElem.ToggleStims(tc(tPts_idxs_select));

    

    %%%% Edit stim

    elseif menu_choice<=nCond+1
@@ -500,15 +501,15 @@ else 
        else

            CondName = CondNamesGroup{menu_choice};

        end

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

        stimEdit.locDataTree.currElem.MoveStims(tc(tPts_idxs_select), CondName);

        

    end

    stimEdit.status = 1;

    

end



iG = stimEdit.dataTree.GetCurrElemIndexID();

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

iG = stimEdit.locDataTree.GetCurrElemIndexID();

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





% ------------------------------------------------
@@ -520,10 +521,10 @@ end 
if isempty(stimEdit.dataTree)

    return;

end

if isempty(stimEdit.dataTree.currElem)

if isempty(stimEdit.locDataTree.currElem)

    return;

end

stimEdit.dataTree.currElem.SetStimDuration(icond, duration);

stimEdit.locDataTree.currElem.SetStimDuration(icond, duration);





% ------------------------------------------------
@@ -535,24 +536,24 @@ end 
if isempty(stimEdit.dataTree)

    return;

end

if isempty(stimEdit.dataTree.currElem)

if isempty(stimEdit.locDataTree.currElem)

    return;

end

duration = stimEdit.dataTree.currElem.GetStimDuration(icond);

duration = stimEdit.locDataTree.currElem.GetStimDuration(icond);





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

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

global stimEdit

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

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





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

function SetStimData(icond, data)

global stimEdit

stimEdit.dataTree.currElem.SetStimTpts(icond, data(:,1));

stimEdit.dataTree.currElem.SetStimDuration(icond, data(:,2));

stimEdit.dataTree.currElem.SetStimValues(icond, data(:,3));

stimEdit.locDataTree.currElem.SetStimTpts(icond, data(:,1));

stimEdit.locDataTree.currElem.SetStimDuration(icond, data(:,2));

stimEdit.locDataTree.currElem.SetStimValues(icond, data(:,3));





% -------------------------------------------------------------------
@@ -560,17 +561,17 @@ function Save() 
global stimEdit



% If nothing changes, nothing to save, so exit

if ~stimEdit.dataTree.currElem.AcquiredDataModified()

if ~stimEdit.locDataTree.currElem.AcquiredDataModified()

    return

end



% Check auto-save config parameter

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

    if stimEdit.locDataTree.currElem.IsRun()

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

    else

        msg = sprintf('Are you sure 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.locDataTree.currElem.name);

    end

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

    if q==2
@@ -580,15 +581,22 @@ if ~strcmpi(stimEdit.config.autoSaveAcqFiles, 'Yes') 
        cfg.SetValue('Auto Save Acquisition Files', 'Yes');

        cfg.Save()

    end

    stimEdit.dataTree.Copy(stimEdit.locDataTree);

else

    % Otherwise auto-save 

    fprintf('StimEditGUI: auto-saving ...\n')

    stimEdit.dataTree.Copy(stimEdit.locDataTree);

end



% Update acquisition file with new contents

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

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

stimEdit.dataTree.currElem.SaveAcquiredData()

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

idx = stimEdit.dataTree.currElem.GetIndexID();

stimEdit.dataTree.groups(idx(1)).Save()    %Need to save derived data on disk for consistency (groupResults.mat)

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

if ~isempty(stimEdit.updateParentGui)

    stimEdit.updateParentGui('StimEditGUI');

end

close(h)
@@ -618,7 +626,7 @@ global stimEdit 
if ~ishandles(hObject)

    return;

end

stimEdit.dataTree.currElem.Save();

stimEdit.locDataTree.currElem.Save();





% --------------------------------------------------------------------
@@ -631,8 +639,8 @@ end 
if ~ishandles(handles.figure)

    return;

end

conditions =  stimEdit.dataTree.currElem.GetConditions();

filename = stimEdit.dataTree.currElem.GetName();

conditions =  stimEdit.locDataTree.currElem.GetConditions();

filename = stimEdit.locDataTree.currElem.GetName();

[~, fname, ext] = fileparts(filename);

SetTextFilename([fname, ext, ' :'], handles);
@@ -717,26 +725,26 @@ hold(handles.axes1, 'on'); 


% As of now this operation is undefined for non-Run nodes (i.e., Subj and Group)

% So we clear the axes and exit

if stimEdit.dataTree.currElem.iRun==0

if stimEdit.locDataTree.currElem.iRun==0

    return;

end



% Load current element data from file

if stimEdit.dataTree.currElem.IsEmpty()

    stimEdit.dataTree.currElem.Load();

if stimEdit.locDataTree.currElem.IsEmpty()

    stimEdit.locDataTree.currElem.Load();

end



iG = stimEdit.dataTree.GetCurrElemIndexID();

CondNamesGroup = stimEdit.dataTree.groups(iG).GetConditions();

CondColTbl     = stimEdit.dataTree.groups(iG).CondColTbl();

t              = stimEdit.dataTree.currElem.GetTimeCombined();

s              = stimEdit.dataTree.currElem.GetStims(t);

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

iG = stimEdit.locDataTree.GetCurrElemIndexID();

CondNamesGroup = stimEdit.locDataTree.groups(iG).GetConditions();

CondColTbl     = stimEdit.locDataTree.groups(iG).CondColTbl();

t              = stimEdit.locDataTree.currElem.GetTimeCombined();

s              = stimEdit.locDataTree.currElem.GetStims(t);

stimVals       = stimEdit.locDataTree.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);

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

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

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

                                                            handles.editLPF.Value,...             % LPF window width
@@ -805,7 +813,7 @@ end 
set(handles.axes1,'xlim', [t(1), t(end)]);



% Update conditions popupmenu

set(handles.popupmenuConditions, 'string', sort(stimEdit.dataTree.currElem.GetConditions()));

set(handles.popupmenuConditions, 'string', sort(stimEdit.locDataTree.currElem.GetConditions()));

conditions = get(handles.popupmenuConditions, 'string');

idx = get(handles.popupmenuConditions, 'value');

condition = conditions{idx};
@@ -827,7 +835,7 @@ global stimEdit 
if ~exist('condition','var')

    return;

end

conditions =  stimEdit.dataTree.currElem.GetConditions();

conditions =  stimEdit.locDataTree.currElem.GetConditions();

if isempty(conditions)

    return;

end
@@ -835,7 +843,7 @@ icond = find(strcmp(conditions, condition)); 
if isempty(icond)

    return;

end

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

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

if isempty(tpts)

    set(handles.uitableStimInfo, 'data',[]);

    return;
@@ -896,7 +904,7 @@ Display(handles); 
function pushbuttonGenerate_Callback(hObject, eventdata, handles)

global stimEdit; 

iaux = handles.listboxAuxSelect.Value;

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

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

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

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

                                         handles.editLPF.Value,...             % LPF window width
@@ -904,13 +912,13 @@ currAux = stimEdit.dataTree.currElem.acquired.aux(iaux); 
% 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');

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

end

iG = stimEdit.locDataTree.GetCurrElemIndexID();

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

% if ~isempty(stimEdit.updateParentGui)

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

% end

Display(handles);
@@ -927,7 +935,7 @@ end 
try

    % Try to populate listbox with aux channels

    global stimEdit

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

    aux = stimEdit.locDataTree.currElem.acquired.aux;

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

    for i = 1:length(aux)

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

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