Updated PREP to version 0.55.4

Author: VisLab

EEGLABPlugin/PrepPipeline0.55.3.zip EEGLABPlugin/PrepPipeline0.55.4.zipEEGLABPlugin/PrepPipeline0.55.3.zip renamed to EEGLABPlugin/PrepPipeline0.55.4.zip

@@ -15,7 +15,7 @@
 params.lineFrequencies = [60, 120, 180, 212, 240];
 params.referenceChannels = 1:64;
 params.evaluationChannels = 1:64;
-params.rereferencedChannels = 1:83;
+params.rereferencedChannels = 1:70;
 params.detrendChannels = 1:70;
 params.lineNoiseChannels = 1:70;
 
@@ -32,7 +32,7 @@
 %% Get the filelist
 fileList = getFileList('FILES', indir);
 %% Run the pipeline
-for k = 1%:length(fileList)
+for k = 1:length(fileList)
     [~, thisName, ~] = fileparts(fileList{k});
     EEG = pop_loadset(fileList{k});
     params.name = thisName;

PrepPipeline/examples/runVEPPrepPipeline.m

@@ -24,7 +24,11 @@
 %% Run the pipeline
 
 for k = 1:length(inNames)
-    sessionReportName = [inNames{k}(1:(end-4)) '.pdf'];
+    [~, theName, theExt] = fileparts(inNames{k});
+    if ~strcmpi(theExt, '.set') && ~strcmpi(theExt, '.mat')
+        continue;
+    end
+    sessionReportName = [theName '.pdf'];
     fname = [dataDir filesep inNames{k}];
     load(fname, '-mat');
     sessionFileName = [summaryFolder filesep sessionReportName];

PrepPipeline/examples/runVEPPrepReport.m

@@ -46,7 +46,7 @@
 if isempty(tmp)
     myPath = fileparts(which('prepPipeline'));
     addpath(genpath(myPath));
-end;
+end
 
 %% Pop up window
 if nargin < 2

PrepPipeline/pop_prepPipeline.m

@@ -41,7 +41,7 @@
     computationTimes= struct( 'detrend', 0, 'lineNoise', 0, 'reference', 0);
     errorMessages = struct('status', 'good', 'boundary', 0, ...
                    'detrend', 0, 'lineNoise', 0, 'reference', 0, ...
-                   'postprocess', 0);
+                   'postProcess', 0);
     [backupOptionsFile, currentOptionsFile, warningsState] = setupForEEGLAB();
     finishup = onCleanup(@() cleanup(backupOptionsFile, currentOptionsFile, ...
         warningsState));

PrepPipeline/prepPipeline.m

@@ -9,29 +9,48 @@
         warningsState));
 
 %% Check the parameters
-    if nargin < 1 || ~isstruct(EEG)
-        error('postProcess:NotEnoughArguments', 'first argument must be a structure');
-    elseif nargin < 2 || ~exist('postIn', 'var') || isempty(postIn)
-        postIn = struct();
-    end
-    if ~isstruct(postIn)
-        error('postProcess:NoData', 'second argument must be a structure')
-    end
-    postOut = struct('keepFiltered', [], 'removeInterpolatedChannels', [], ...
-                      'cleanupReference', []);
-    defaults = getPrepDefaults(EEG, 'postprocess');
+postOut = struct();
 
-    [postOut, errors] = checkPrepDefaults(postIn, postOut, defaults);
-    if ~isempty(errors)
-        error('postProcess:BadParameters', ['|' sprintf('%s|', errors{:})]);
-    end
-    defaults = getPrepDefaults(EEG, 'general');
-    [postOut, errors] = checkPrepDefaults(postOut, postOut, defaults);
-    if ~isempty(errors)
-        error('postProcess:BadGeneralParameters', ['|' sprintf('%s|', errors{:})]);
+%% Initial setup
+    try
+        %% Check the input
+        if nargin < 1 || ~isstruct(EEG)
+            error('postProcess:NotEnoughArguments', 'first argument must be a structure');
+        elseif nargin < 2 || ~exist('postIn', 'var') || isempty(postIn)
+            postIn = struct();
+        end
+        if ~isstruct(postIn)
+            error('postProcess:NoData', 'second argument must be a structure')
+        end
+        if ~isfield(EEG, 'etc') || ~isfield(EEG.etc, 'noiseDetection') || ...
+                hasPrepErrors(EEG.etc.noiseDetection)
+            error('postProcess:NoPrep', 'Prep has not executed or has errors');
+        end
+
+        %% Set up the output structure
+        postOut = struct('keepFiltered', [], 'removeInterpolatedChannels', [], ...
+            'cleanupReference', []);
+        defaults = getPrepDefaults(EEG, 'postprocess');
+
+        [postOut, errors] = checkPrepDefaults(postIn, postOut, defaults);
+        if ~isempty(errors)
+            error('postProcess:BadParameters', ['|' sprintf('%s|', errors{:})]);
+        end
+        defaults = getPrepDefaults(EEG, 'general');
+        [postOut, errors] = checkPrepDefaults(postOut, postOut, defaults);
+        if ~isempty(errors)
+            error('postProcess:BadGeneralParameters', ['|' sprintf('%s|', errors{:})]);
+        end
+        EEG.etc.noiseDetection.postProcess = postOut;
+
+    catch mex
+        errorMessages.setup = ...
+            ['postProcessing failed due to previous issues: ' ...
+            getReport(mex, 'basic', 'hyperlinks', 'off')];
+        EEG.etc.noiseDetection.errors.postProcess = errorMessages;
+        return;
     end
-    EEG.etc.noiseDetection.postProcess = postOut;
-    
+     
 %% Perform filtering if requested
      try
         if postOut.keepFiltered
@@ -100,6 +119,9 @@
         end
         return;
      end
+     
+     %% If we got this far everything was good
+     EEG.etc.noiseDetection.errors.postProcess = 0;
 end
 
 %% Cleanup callback

PrepPipeline/prepPostProcess.m

@@ -6,6 +6,18 @@
 end
 
 function changeLog = getChangeLog()
+   changeLog(5) = ...
+     struct('version', '0', 'status', 'Unreleased', 'date', '', 'changes', '');
+
+    changeLog(5).version = '0.55.4';
+    changeLog(5).status = 'Released';
+    changeLog(5).date = '7/26/2020';
+    changeLog(5).changes = { ...
+       'Correctly restored EEGLAB options after execution'; ...
+       'Added functions to output errors from etc.noiseDetection'; ...
+       'Corrected findpeaks naming conflict in Chronux'; ...
+       'Post process does not execute if Prep had errors'};
+ 
    changeLog(4) = ...
      struct('version', '0', 'status', 'Unreleased', 'date', '', 'changes', '');
 

PrepPipeline/utilities/getPrepVersion.m

@@ -0,0 +1,25 @@
+function hasErrors = hasPrepErrors(noiseDetection)
+% Return false if Prep has executed successfully
+%
+% Parameters:
+%     noiseDetection   Structure containing prep execution information
+%     hasErrors        (output) true if Prep did not execute or has errors
+
+%% Check for defaults
+   hasErrors = false;
+%% Make sure that noiseDetection has an errors field
+    if isempty(noiseDetection) || ~isstruct(noiseDetection) ||...
+        ~isfield(noiseDetection, 'errors') || ...
+        ~isstruct(noiseDetection.errors)
+        hasErrors = true;
+        return;
+    end
+    errors = noiseDetection.errors;
+    errors = rmfield(errors, 'status');
+    errorFields = fieldnames(errors);
+    for k = 1:length(errorFields)
+        if errors.(errorFields{k}) ~= 0
+            hasErrors = true;
+            break;
+        end
+    end

PrepPipeline/utilities/hasPrepErrors.m

@@ -33,6 +33,12 @@ authorized to reproduce and distribute reprints for Government purposes
 notwithstanding any copyright notation herein.
 
 ### Releases 
+Version 0.55.4 Released 7/26/2020  
+* Correctly restored EEGLAB options after execution
+* Added functions to output errors from etc.noiseDetection
+* Corrected findpeaks naming conflict in Chronux
+* Post process does not execute if Prep had errors  
+
 Version 0.55.3 Released 10/19/2017
 * Fixed issue with interpolated channels when interpolation order is pre-process
 * Fixed issue with correct removal of interpolated channels during post-processing