ERPLAB v11.04

Includes new MVPC Decoding tab in Estudio, currently in BETA.
ucdavis · Aug 6, 2024 · c5450a8 · c5450a8
1 parent 120867c
commit c5450a8
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Showing 128 changed files with 16,551 additions and 2,257 deletions.
diff --git a/GUIs/binselectorGUI.mlapp b/GUIs/binselectorGUI.mlapp
diff --git a/GUIs/decodingGUI.mlapp b/GUIs/decodingGUI.mlapp
diff --git a/GUIs/mvpa_save_multi_file.fig b/GUIs/mvpa_save_multi_file.fig
diff --git a/GUIs/mvpa_save_multi_file.m b/GUIs/mvpa_save_multi_file.m
@@ -55,8 +55,8 @@ function mvpa_save_multi_file_OpeningFcn(hObject, eventdata, handles, varargin)
 catch
     suffix  = '';
     ERPLAB = [];
-    ERPLAB.erpname = 'No erpset was selected';
-    ERPLAB.filename ='No erpset was selected';
+    ERPLAB.bestname = 'No mvpcset was selected';
+    ERPLAB.filename ='No mvpcset was selected';
     ERPLAB.event = [];
     ERPLAB.chanlocs = [];
     ERPLAB.nbchan = 0;
@@ -74,14 +74,14 @@ function mvpa_save_multi_file_OpeningFcn(hObject, eventdata, handles, varargin)
 %erplab_studio_default_values;
 erplab_default_values; 
 version = erplabver;
-set(handles.gui_chassis,'Name', ['ERPLAB ' version '   -   Save multiple MVPAsets GUI'])
+set(handles.gui_chassis,'Name', ['ERPLAB ' version '   -   Save multiple MVPCsets GUI'])
 
 
 % set(handles.checkbox1_suffix,'Value',1);
 set(handles.edit_suffix_name,'String',suffix);
 set(handles.checkbox2_save_label,'Value',0);
 
-ColumnName_table = {'MVPA name','File name'};
+ColumnName_table = {'MVPC name','File name'};
 
 set(handles.uitable1_erpset_table,'ColumnName',cellstr(ColumnName_table));
 set(handles.uitable1_erpset_table,'RowName',cellstr(num2str(Selected_ERP_label')));
@@ -141,12 +141,7 @@ function checkbox1_suffix_Callback(hObject, eventdata, handles)
 Selected_ERP_label = handles.Selected_ERP_label;
 suffix_edit = handles.edit_suffix_name.String;
 
-if isempty(suffix_edit)
-    msgboxText =  'You must enter a suffix at least!';
-    title = 'EStudio: f_ERP_save_multi_file() error';
-    errorfound(msgboxText, title);
-    return
-end
+
 
 
 DataString_before = handles.uitable1_erpset_table.Data;
@@ -217,9 +212,9 @@ function checkbox2_save_label_Callback(hObject, eventdata, handles)
         fileName= char(ALLERP(Selected_ERP_label(Numofselectederp)).filename);
         [pathstr, file_name, ext] = fileparts(fileName);
         if isempty(file_name)
-            file_name = [num2str(Selected_ERP_label(Numofselectederp)),'_ERP.mvpa'];
+            file_name = [num2str(Selected_ERP_label(Numofselectederp)),'_ERP.mvpc'];
         else
-            file_name = [file_name,'.mvpa'];
+            file_name = [file_name,'.mvpc'];
         end
         DataString{Numofselectederp,2} = file_name;
 
@@ -255,13 +250,13 @@ function checkbox3_filename_erpname_Callback(hObject, eventdata, handles)
     DataString{Numofselectederp,1} = DataString_before{Numofselectederp,1};
     fileName = char(DataString_before{Numofselectederp,1});
     if isempty(fileName)
-        fileName = strcat(num2str(Numofselectederp),'mvpa');
+        fileName = strcat(num2str(Numofselectederp),'mvpc');
     end
     [pathstr, file_name, ext] = fileparts(fileName);
     if isempty(file_name)
-     file_name = [num2str(Selected_ERP_label(Numofselectederp)),'_ERP.mvpa'];
+     file_name = [num2str(Selected_ERP_label(Numofselectederp)),'_ERP.mvpc'];
     else
-     file_name = [file_name,'.mvpa'];  
+     file_name = [file_name,'.mvpc'];  
     end
     DataString{Numofselectederp,2} = file_name;
 end
@@ -279,16 +274,16 @@ function uitable1_erpset_table_CellEditCallback(hObject, eventdata, handles)
 DataString = handles.uitable1_erpset_table.Data;
 Selected_ERP_label = handles.Selected_ERP_label;
 if size(DataString,1) < numel(Selected_ERP_label)
-    msgboxText =  'Erpname and filename for one of erpsets are empty at least! Please give name to erpname and filename';
-    title = 'EStudio: f_ERP_save_multi_file empty erpname';
+    msgboxText =  'MVPC name and filename for one of erpsets are empty at least! Please give name to mvpcname and filename';
+    title = 'EStudio: mvpa_save_multi_file empty erpname';
     errorfound(msgboxText, title);
     return
 end
 
 for Numofselected = 1:numel(Selected_ERP_label)
     if  isempty(DataString{Numofselected,1})
-        msgboxText =  'Erpname for one of erpsets is empty at least! Please give name to that erpset';
-        title = 'EStudio: f_ERP_save_multi_file empty erpname';
+        msgboxText =  'MVPCname for one of mvpcsets is empty at least! Please give name to that mvpcset';
+        title = 'EStudio: mvpa_save_multi_file empty mvpcname';
         errorfound(msgboxText, title);
         return
     end
@@ -326,16 +321,16 @@ function pushbutton4_okay_Callback(hObject, eventdata, handles)
 Selected_ERP_label = handles.Selected_ERP_label;
 
 if size(Data_String,1)< numel(Selected_ERP_label)%
-    msgboxText =  'MVPAname for one of MVPAsets is empty at least! Please give a name';
+    msgboxText =  'MVPCname for one of MVPCsets is empty at least! Please give a name';
     title = 'ERPLAB: mvpa_save_multi_file empty MVPAname';
     errorfound(msgboxText, title);
     return
 end
 
 
 if size(Data_String,1)> numel(Selected_ERP_label)%
-    msgboxText =  'More MVPAname is given. Please delete it!!!';
-    title = 'ERPLAB: mvpa_save_multi_file empty MVPAname';
+    msgboxText =  'More MVPCname is given. Please delete it!!!';
+    title = 'ERPLAB: mvpa_save_multi_file empty MVPCname';
     errorfound(msgboxText, title);
     return
 end
@@ -344,8 +339,8 @@ function pushbutton4_okay_Callback(hObject, eventdata, handles)
 
 for Numofselected = 1:numel(Selected_ERP_label)
     if  isempty(Data_String{Numofselected,1})
-        msgboxText =  'MVPAname for one of MVPAsets is empty at least! Please give a name';
-        title = 'ERPLAB: mvpa_save_multi_file empty MVPAname';
+        msgboxText =  'MVPCname for one of MVPCsets is empty at least! Please give a name';
+        title = 'ERPLAB: mvpa_save_multi_file empty MVPCname';
         errorfound(msgboxText, title);
         return
     end
@@ -363,9 +358,9 @@ function pushbutton4_okay_Callback(hObject, eventdata, handles)
 
     [pathstr, file_name, ext] = fileparts(fileName);
     if isempty(file_name)
-     file_name = [num2str(Selected_ERP_label(Numofselectederp)),'_mvpa.mvpa'];
+     file_name = [num2str(Selected_ERP_label(Numofselectederp)),'_mvpc.mvpc'];
     else
-     file_name = [file_name,'.mvpa'];  
+     file_name = [file_name,'.mvpc'];  
     end
 
     ALLERP(Selected_ERP_label(Numofselectederp)).filename = file_name;

diff --git a/GUIs/mvpc2textGUI.mlapp b/GUIs/mvpc2textGUI.mlapp
diff --git a/GUIs/plotConfusionGUI.mlapp b/GUIs/plotConfusionGUI.mlapp
diff --git a/README.md b/README.md
@@ -4,10 +4,10 @@ Click the Wiki icon at the top of the page for documentation, tutorials, and FAQ
 </p>
 To ask questions, subscribe to the ERPLAB email list (https://erpinfo.org/erplab-email-list). Bug reports can be submitted via GitHub or by sending an email to erplab-bugreports@ucdavis.edu.
 
-## ERPLAB v11.03
+## ERPLAB v11.04
 
 <p align="center" >
-  <a href="https://github.com/ucdavis/erplab/releases/download/11.0/erplab11.03.zip"><img src="https://github.com/ucdavis/erplab/blob/master/images/erplab-and-studio-logo.png">
+  <a href="https://github.com/ucdavis/erplab/releases/download/11.0/erplab11.04.zip"><img src="https://github.com/ucdavis/erplab/blob/master/images/erplab-and-studio-logo.png">
 <br/>
 
   <img src="https://cloud.githubusercontent.com/assets/5808953/8663301/1ff9a26a-297e-11e5-9e15-a7085569058f.png" width=300px >
@@ -25,7 +25,7 @@ We encourage most users to use this latest major version.
 
 ## Release Notes
 
-### ERPLAB v11.03 Release Notes
+### ERPLAB v11.04 Release Notes
 
 ERPLAB can now be accessed from two different user interfaces: 
 - [ERPLAB Classic](https://github.com/ucdavis/erplab/wiki/Manual) (our original software, which operates as an EEGLAB plugin)

diff --git a/erplab_default_values.m b/erplab_default_values.m
@@ -1,5 +1,5 @@
-erplabver = '11.03';                  % current erplab version
-erplabrel = '18-July-2024';             % DOB
+erplabver = '11.04';                  % current erplab version
+erplabrel = '06-August-2024';             % DOB
 erplabdeveloper = 'Simmons,Zhang,Garrett'; 
 %ColorB = [170 180 195]/255;          % old background color (until version 3)
 %ColorB = [0.9216 0.8353 0.6078];     % background color for version 4

diff --git a/functions/averager.m b/functions/averager.m
@@ -462,7 +462,7 @@
 L      = size(datax,2);
 fnyq   = fs/2;
 f      = fnyq*linspace(0,1,NFFT/2);
-y      = pagetranspose(datax);
+y      = datax';
 tapwin = zeros(L,1);
 if ~isempty(apodization)
     aponame  = strtrim(apodization{1}); % taper function name
@@ -485,7 +485,7 @@
     y  = y.*repmat(tapwin, 1, size(y,2)); % data tapered
 end
 
-Y = pagetranspose(fft(y,NFFT))/L;
+Y = fft(y,NFFT)'/L;
 fftepo = abs(Y(:,1:NFFT/2)).^2; % power
 if rem(NFFT, 2)                 % odd NFFT excludes Nyquist point
     fftepo(:, 2:end) = fftepo(:, 2:end).*2;

diff --git a/functions/crossnobis.m b/functions/crossnobis.m
@@ -1,23 +1,23 @@
 
-function [MVPC, ALLMVPC] = crossnobis(ALLBEST, nIter, nCrossBlocks, DataTimes,relevantChans,classcoding,equalT,ParWorkers,method)
+function [MVPC, ALLMVPC] = crossnobis(ALLBEST, nIter, nCrossBlocks, DataTimes,relevantChans,classcoding,equalT,ParWorkers,method,Tooltype)
 
-%% Subject List: 
+%% Subject List:
 nSubs = length(ALLBEST); % # files = # subjects
-
+global observe_DECODE;
 %% Step 9: Loop through participants
 for s = 1:nSubs %crossnobis is performed within each subject independently
 
-    %% Parameters to set per subject 
-    BEST = ALLBEST(s);   
-    mvpc = buildMVPCstruct(BEST,relevantChans, nIter, nCrossBlocks, DataTimes,equalT,classcoding,method); 
+    %% Parameters to set per subject
+    BEST = ALLBEST(s);
+    mvpc = buildMVPCstruct(BEST,relevantChans, nIter, nCrossBlocks, DataTimes,equalT,classcoding,method);
 
     % for brevity in analysis
     nBins =         mvpc.nClasses;
     nIter =         mvpc.nIter;
     nPerms =        nchoosek(nBins,2); %total # pairwise comparisions
     dataTime = BEST.times; %times of imported data
     %nBlocks =       mvpc.nCrossfolds;
-   % nElectrodes =   length(mvpc.electrodes); 
+    % nElectrodes =   length(mvpc.electrodes);
     nSamps =        length(mvpc.times);
     try
         sn =            BEST.mvpcname; %if data went through decoding GUI
@@ -26,19 +26,19 @@
     end
 
     %progress output to command window
-    fprintf('*** Currently Decoding (Crossnobis) Subject:\t%s ***\n ',sn); %is Decoding the word to use for crossnobis? 
+    fprintf('*** Currently Decoding (Crossnobis) Subject:\t%s ***\n ',sn); %is Decoding the word to use for crossnobis?
 
-     % grab EEG data from bin-list organized data 
+    % grab EEG data from bin-list organized data
     eegs = BEST.binwise_data;
     nPerBin = BEST.n_trials_per_bin;
     % we create index of timpoint of interests from original data
     tois = ismember(dataTime,dataTime);
-
 
-%     % Preallocate Matrices
-     final_xDist = nan(nSamps,nIter,nPerms);
-%     %BetaWeights_Raw = nan(nIter,nSamps,nBlocks,nElectrodes);
-%     %BetaWeights_Corr = BetaWeights_Raw;
+
+    %     % Preallocate Matrices
+    final_xDist = nan(nSamps,nIter,nPerms);
+    %     %BetaWeights_Raw = nan(nIter,nSamps,nBlocks,nElectrodes);
+    %     %BetaWeights_Corr = BetaWeights_Raw;
 
 
     if nBins ~= max(size(eegs))
@@ -66,18 +66,18 @@
     % (NChan x nTP x nTrials(ideally randomized) x Nlabels)
 
     for b = 1:numel(nPerBin)
-        ntrial = size(eegs(b).data,3); 
-        shuff_list = randperm(ntrial); 
+        ntrial = size(eegs(b).data,3);
+        shuff_list = randperm(ntrial);
 
         %so we always allow the specified number of trials per bin
         %(nPerBin) by choosing from a (potentially) larger set of trials
         %within the bin
 
-        idx_list = shuff_list(1:nPerBin(b)); 
+        idx_list = shuff_list(1:nPerBin(b));
 
         indexed_data = eegs(b).data(:,:,idx_list);
-        eegs(b).data = indexed_data; 
-
+        eegs(b).data = indexed_data;
+        
     end
 
 
@@ -86,14 +86,19 @@
     xdata = xdata(:,tois,:); %resampled data
 
 
-      %% Step 8: Loop through each iteration with random shuffling
+    %% Step 8: Loop through each iteration with random shuffling
     tic % start timing iteration loop
 
     %% Perform Cross-Nobis analysis at each requested time-point
     for iter = 1:nIter
         fprintf('Subject: %s, Iteration: %i / %i \n', sn, iter, nIter);
+        if ~strcmpi(Tooltype,'erplab')
+            messg = ['Subject:',32, sn,', Iteration:',32,num2str(iter),'/', num2str(nIter)]; %%GH
+            estudioworkingmemory('f_Decode_proces_messg',messg);
+            observe_DECODE.Process_messg =1;
+        end
         parfor (nTp = 1:nSamps,ParWorkers)
-
+            
             % structs to hold shuffled data
             a_full_bin_label= struct();
             b_full_bin_label= struct();
@@ -162,29 +167,29 @@
             final_xDist(nTp,iter,:) = xDist;
         end
     end
-
+    
     toc % stop timing the iteration loop
 
-    mvpc.details = []; 
-    mvpc.raw_predictions = final_xDist; 
+    mvpc.details = [];
+    mvpc.raw_predictions = final_xDist;
 
-    avg_distance_iter = squeeze(mean(final_xDist,2))'; 
-    avg_distance_scores =  squeeze(mean(avg_distance_iter,1)); 
+    avg_distance_iter = squeeze(mean(final_xDist,2))';
+    avg_distance_scores =  squeeze(mean(avg_distance_iter,1));
 
     mvpc.average_score = avg_distance_scores;
-    mvpc = avgconfusionCM(mvpc, final_xDist);  
-    mvpc.stderror = std(avg_distance_iter)/sqrt(size(final_xDist,1)); 
+    mvpc = avgconfusionCM(mvpc, final_xDist);
+    mvpc.stderror = std(avg_distance_iter)/sqrt(size(final_xDist,1));
 
 
-     %probably a better way
+    %probably a better way
     if nSubs == 1
-
+        
         MVPC = mvpc;
         ALLMVPC = mvpc;
     else
-
-        MVPC = mvpc; 
-        ALLMVPC(s) = mvpc; 
+        
+        MVPC = mvpc;
+        ALLMVPC(s) = mvpc;
     end
 
 

diff --git a/functions/erpAutoYLim.m b/functions/erpAutoYLim.m
@@ -90,32 +90,13 @@
             else
                 aux_xxlim(2) = xxlim(2);
             end
-
-        elseif strcmpi(datatype, 'TFFT')
-
-            aux_xxlim(1) = 1;
-            if xxlim(2)>round(ERP.xmax*1000)
-                aux_xxlim(2) = round(ERP.xmax*1000);
-            else
-                aux_xxlim(2) = xxlim(2);
-            end
-
-        elseif strcmpi(datatype, 'EFFT')
-
-            aux_xxlim(1) = 0;
-            if xxlim(2)>round(ERP.xmax*1000)
-                aux_xxlim(2) = round(ERP.xmax*1000);
-            else
-                aux_xxlim(2) = xxlim(2);
-            end
-
         else  % fft
             if xxlim(1)<5
                 aux_xxlim(1) = 5; % to avoid including the spectrum under 5 Hz in calculating Y auto (too big!)
             else
                 aux_xxlim(1) = xxlim(1);
             end
-            if xxlim(2)>round(fs/2)
+            if xxlim(2)>round(fs/2);
                 aux_xxlim(2) = round(fs/2);
             else
                 aux_xxlim(2) = xxlim(2);
@@ -139,7 +120,7 @@
             yymax   = max(datresh);
             yymin   = min(datresh);
         end
-
+            
         if abs(yymax)<1 && abs(yymin)<1
             yylim(1:2) = [yymin*1.2 yymax*1.1]; % JLC. Mar 11, 2015
         else