pull v3.1.1 (#6)

* suppPrep4stats re-write

* Fixed error when plotting more than 6 conditions

* new epp_makegrands function

* Improvments to speed when combining data

* support for plotting over time windows

+ Removed plotting t-values
+ Added control of color-map

* Fix bug when measuring from average of channels

* Fix to bad chars in condition names

* minor fix

* minor fix

* improvment to loading data

* major fix to flipped time axes

* update README

* new author

README.Rmd

@@ -66,6 +66,7 @@ If a wavelet analysis has been preformed, the Data field is replaced with:
 These functions can be used to compute new conditions or manipulate existing data:
 
 - Merge 2 or more conditions with `epp_combineconds`.
+- Make grand-average ERP/ERSP/ITC with `epp_makegrands` (useful for plotting large data sets).
 - Compute differences between 2 conditions with `epp_diffwave`.
 - Compute LRP with `epp_LRP`
 - Compute global field potentials with `epp_GFP`.
@@ -411,6 +412,7 @@ The function `epp_getTF` measure the *mean* ersp / itc from selected channels, w
 
 - **Mattan S. Ben-Shachar** [aut, cre].
 - **Rachel Rac** [ctb].
+- **Micael Shmueli** [ctb].
 
 ## Acknowledgments
 

README.md

@@ -53,6 +53,7 @@ If a wavelet analysis has been preformed, the Data field is replaced with:
 These functions can be used to compute new conditions or manipulate existing data:
 
 -   Merge 2 or more conditions with `epp_combineconds`.
+-   Make grand-average ERP/ERSP/ITC with `epp_makegrands` (useful for plotting large data sets).
 -   Compute differences between 2 conditions with `epp_diffwave`.
 -   Compute LRP with `epp_LRP`
 -   Compute global field potentials with `epp_GFP`.
@@ -182,6 +183,7 @@ Authors
 
 -   **Mattan S. Ben-Shachar** \[aut, cre\].
 -   **Rachel Rac** \[ctb\].
+-   **Micael Shmueli** \[ctb\].
 
 Acknowledgments
 ---------------

_depricated_/suppPrep4export.m

@@ -8,6 +8,7 @@
 %{
 Change log:
 -----------
+14-04-2018  Support new jackknife function
 19-01-2017  Support for saving data
 19-12-2016  Support for Jackknife adjustment
 25-11-2016  New function (written in MATLAB R2015a)
@@ -22,7 +23,7 @@
 for c = 1:length(study) % for each condition
     % Correct for jackknifing:
     if pResults.jackknife
-        study(c).measure = suppJackknife('out',study(c).measure);
+        study(c).measure = suppJackknife('out',study(c).measure,1);
     end
 
     % Make variable name:

_depricated_/suppPrep4stats.m

@@ -8,6 +8,7 @@
 %{
 Change log:
 -----------
+14-04-2018  Support new jackknife function
 07-04-2018  Added samplingRate calculation
 06-03-2018  Removed samplingRate & baseLine fields from study struct.
 29-01-2017  Support for sampling interpolation
@@ -32,7 +33,7 @@
 
     %% Jackknife
     if jackknife
-        studyIn(c).Data = suppJackknife('in',studyIn(c).Data);
+        studyIn(c).Data = suppJackknife('in',studyIn(c).Data,3);
     end
 
     %% Interpolate

data_reduction/epp_GFP.m

@@ -24,7 +24,7 @@
 %                       (SES) is calculated, as per  Milivojevic, Johnson,
 %                       Hamm, & Corballis (2003).
 %
-% See also epp_combineconds, epp_LRP, epp_diffwave
+% See also epp_combineconds, epp_LRP, epp_diffwave, epp_makegrands
 %
 %
 % Author: Mattan S. Ben Shachar, BGU, Israel

data_reduction/epp_LRP.m

@@ -26,7 +26,7 @@
 % NOTE that output has only the number of selected electrodes (ordered as
 % they were input).
 %
-% See also epp_combineconds, epp_GFP, epp_diffwave
+% See also epp_combineconds, epp_GFP, epp_diffwave, epp_makegrands
 % 
 % 
 % Author: Mattan S. Ben Shachar, BGU, Israel

data_reduction/epp_combineconds.m

@@ -19,7 +19,7 @@
 %           'name'      - name of new combined condition. Defults is to
 %                         concatenate the condition names.
 %
-% See also epp_LRP, epp_GFP, epp_diffwave
+% See also epp_LRP, epp_GFP, epp_diffwave, epp_makegrands
 %
 % Author: Mattan S. Ben Shachar, BGU, Israel
 
@@ -56,9 +56,16 @@
 
 IDs = {};
 for c = 1:length(study)
-    IDs = {IDs{:}, study(c).IDs.ID{:}};
+    if ~any(isstr(study(c).IDs.ID))
+        study(c).IDs.ID = cellfun(@(X) num2str(X),study(c).IDs.ID,'UniformOutput',false);
+    end
+    IDs = [IDs, study(c).IDs.ID];
+end
+try
+    IDs = unique(IDs);
+catch
+    IDs = arrayfun(@(X) {X},unique(cell2mat(IDs)));
 end
-IDs = unique(IDs);
 
 %% Combine
 for id = 1:length(IDs)
@@ -130,6 +137,6 @@
 if has_erp,  out.Data = data; end
 if has_ersp, out.ersp = ersp; end
 if has_itc,  out.itc  = itc; end
-out.IDs         = table(IDs',nTrials','VariableNames',{'ID' 'nTrials'});
+out.IDs         = table(IDs,nTrials','VariableNames',{'ID' 'nTrials'});
 
 end

data_reduction/epp_diffwave.m

@@ -18,7 +18,7 @@
 %           'name'      - name of new combined condition. Defults is to
 %                         concatenate the condition names.
 %
-% See also epp_combineconds, epp_LRP, epp_GFP
+% See also epp_combineconds, epp_LRP, epp_GFP, epp_makegrands
 %
 %
 % Author: Mattan S. Ben Shachar, BGU, Israel

data_reduction/epp_makegrands.m

@@ -0,0 +1,38 @@
+% PURPOSE:  Collapes all data across subjects. This is useful for plotting
+%           data of large data sets.
+%
+%
+% FORMAT
+% ------
+% study = epp_makegrands(study)
+%
+%
+% See also epp_combineconds, epp_GFP, epp_diffwave, epp_LRP
+%
+%
+% Author: Mattan S. Ben Shachar & Rachel Rac, BGU, Israel
+
+%{
+Change log:
+-----------
+23-04-2018  Minor fix
+16-04-2018  New function (written in MATLAB R2017a)
+%}
+function study = epp_makegrands(study)
+for c = 1:length(study)
+    %% IDs
+    study(c).IDs = table(000,size(study(c).IDs,1),'VariableNames',{'ID' 'nTrials'});
+
+    %% Data
+    if isfield(study,'Data')
+        study(c).Data = mean(study(c).Data,3);
+    end
+
+    if isfield(study,'ersp')
+        study(c).ersp = mean(study(c).ersp,4);
+    end
+
+    if isfield(study,'itc')
+        study(c).itc = mean(study(c).itc,4);
+    end
+end

import_export/epp_loadeeglab.m

@@ -43,6 +43,9 @@
 %{
 Change log:
 -----------
+25-04-2018  Fix when combining
+16-04-2018  Improvments to speed when combining data
+15-04-2018  Reduced printing from eeglab pop_*
 13-04-2018  A million little bug fixes
 11-04-2018  Added errors when subject ID
 20-03-2018  Fix naming of subject files.
@@ -133,13 +136,14 @@
 
 if p.Results.wavelet || p.Results.erp    
     for f = 1:nFiles
+        fprintf('Processing file %d of %d\n',f,nFiles)
         % Load and validate sub\group\condition
         % =====================================
         try
-            temp_EEG = pop_loadset('filename',EEG_list{f});
+            evalc('temp_EEG = pop_loadset(''filename'',EEG_list{f});');
         catch
             eeglab; close
-            temp_EEG = pop_loadset('filename',EEG_list{f});
+            evalc('temp_EEG = pop_loadset(''filename'',EEG_list{f});');
         end
 
         if isempty(temp_EEG.condition) && isempty(temp_EEG.group)
@@ -194,37 +198,100 @@
 
 %% Combine all files
 
+study = struct;
+
 if p.Results.combine
     % list files in savePath
     all_files   = dir([savePath '\\*.eppf']);
     nFiles      = length(all_files);
 
     study.Condition = '';
+    % Load and append data
+    % --------------------
+    fprintf('\n\n')
     for f = 1:nFiles
         % Load
+        fprintf('Loading file %d of %d\n',f,nFiles)
         load(fullfile(savePath, all_files(f).name), '-mat')
 
         % Orgenize
         for c = 1:length(output)
             c_ind = find(strcmpi(output(c).Condition,{study.Condition}));
-            if isempty(c_ind)
-                if strcmpi(study(end).Condition,'')
+            if isempty(c_ind) % if there is no such condition
+                if isempty(study(end).Condition) % if this is the first condition
                     study = output(c);
                 else
                     study(end+1) = output(c);
                 end
-            else
-                try study(c_ind).ersp(:,:,:,end+1)  = output(c).ersp;   end
-                try study(c_ind).itc(:,:,:,end+1)   = output(c).itc;    end
-                try study(c_ind).Data(:,:,end+1)    = output(c).Data;   end
+
+                % build data
+                if isfield(study,'Data')
+                    study(end).Data     = cell([1 nFiles]);
+                    study(end).Data{1}  = output(c).Data;  
+
+                end
+
+                % build ersp
+                if isfield(study,'ersp')
+                    study(end).ersp     = cell([1 nFiles]);
+                    study(end).ersp{1}  = output(c).ersp;  
+                end
+
+                % build itc
+                if isfield(study,'itc')
+                    study(end).itc      = cell([1 nFiles]);
+                    study(end).itc{1}   = output(c).itc;  
+                end
+
+
+            else % condition exists
                 study(c_ind).IDs = [study(c_ind).IDs;output(c).IDs];
+
+                % append data
+                if isfield(study,'Data')
+                    next_ind = find(cellfun(@isempty, study(c_ind).Data),1);
+                    study(c_ind).Data{next_ind} = output(c).Data;  
+                end
+
+                % append ersp
+                if isfield(study,'ersp')
+                    next_ind = find(cellfun(@isempty, study(c_ind).ersp),1);
+                    study(c_ind).ersp{next_ind} = output(c).ersp;  
+                end
+
+                % append itc
+                if isfield(study,'itc')
+                    next_ind = find(cellfun(@isempty, study(c_ind).itc),1);
+                    study(c_ind).itc{next_ind} = output(c).itc;  
+                end                
             end
         end
         clear output c_ind
     end
-else
-    % return an empty struct
-    study = struct;
+
+    % Collaps Data/ersp/itc
+    % ---------------------
+    fprintf('\nCleaning up (this can take a while)..')
+    for c = 1:length(study)
+        % Collaps data
+        if isfield(study,'Data')
+            next_ind = cellfun(@(X) ~isempty(X), study(c).Data);
+            study(c).Data = cat(3,study(c).Data{next_ind});
+        end
+
+        % Collaps ersp
+        if isfield(study,'ersp')
+            next_ind = cellfun(@(X) ~isempty(X), study(c).ersp);
+            study(c).ersp = cat(4,study(c).ersp{next_ind});
+        end
+
+        % Collaps itc
+        if isfield(study,'itc')
+            next_ind = cellfun(@(X) ~isempty(X), study(c).itc);
+            study(c).itc = cat(4,study(c).itc{next_ind});
+        end
+    end
+    fprintf('. Done!\n',f,nFiles)
 end
 
 

measuring/epp_getTF.m

@@ -23,6 +23,8 @@
 % The available parameters are as follows:
 %           'average'       - average across electrodes before measuring?
 %                             (false my default). 
+%           'jackknife'     - measure using the jackknife technique?
+%                             (default: false)
 %           'save'          - 'long' / 'wide'; will save the results in the
 %                             current directory in the specified format.
 %
@@ -34,6 +36,8 @@
 %{
 Change log:
 -----------
+18-04-2018  Fix bug when sending to suppPrep4statsTF
+14-04-2018  Support for jackknife
 07-04-2018  Rewrite of function.
 28-02-2018  ITC (abs) is now computed in function, to allow for the
             combination of conditions.
@@ -56,7 +60,7 @@
     addRequired(p,'freqs',@(x) isnumeric(x) && size(x,2)==2);
 
     addParameter(p,'average',false,@islogical);
-    addParameter(p,'jackknife',false,@islogical); % not supported
+    addParameter(p,'jackknife',false,@islogical);
     addParameter(p,'plot',false,@islogical);
     addParameter(p,'save','no', @ischar);
 parse(p, measure ,study, conditions, electrodes, timeWindow, freqs, varargin{:}); % validate
@@ -66,7 +70,7 @@
 
 [study, timeWindow_ind, freqs_name] = suppPrep4statsTF(study, conditions, electrodes,...
     timeWindow, freqs,...
-    p.Results.average, p.Results.average);
+    p.Results.average, p.Results.jackknife);
 
 %% Get Measure