Merge pull request #29 from VisLab/check-issues

Resolved parfor issue and updateNoisyChannels issue

PrepPipeline/eegplugin_prepPipeline.m

@@ -1,47 +1,47 @@
-% eegplugin_prepPipeline() - a wrapper to the prepPipeline, which does early stage
-% 
-% Usage:
-%   >> eegplugin_prepPipeline(fig, try_strings, catch_strings);
-%
-%   see also: prepPipeline
-
-% Author: Kay Robbins, with contributions from Nima Bigdely-Shamlo, Tim Mullen, Christian Kothe, and Cassidy Matousek.
-
-% This program is free software; you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published by
-% the Free Software Foundation; either version 2 of the License, or
-% (at your option) any later version.
-%
-% This program is distributed in the hope that it will be useful,
-% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program; if not, write to the Free Software
-% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-
-%function eegplugin_clean_rawdata(fig,try_strings,catch_strings)
-
-% create menu
-% toolsmenu = findobj(fig, 'tag', 'tools');
-% uimenu( toolsmenu, 'label', 'Clean continuous data using ASR', 'separator','on',...
-%    'callback', 'EEG = pop_clean_rawdata(EEG); [ALLEEG EEG CURRENTSET] = eeg_store(ALLEEG, EEG); eeglab redraw');
-
-% eegplugin_prepPipeline() - the PREP pipeline plugin
-function vers = eegplugin_prepPipeline(fig, trystrs, catchstrs) 
-
-%% Add path to prepPipeline subdirectories if not in the list
-tmp = which('getPrepDefaults');
-if isempty(tmp)
-    myPath = fileparts(which('prepPipeline'));
-    addpath(genpath(myPath));
-end;
-vers = getPrepVersion(); 
-
-% create menu
-comprep = [trystrs.no_check '[EEG LASTCOM] = pop_prepPipeline(EEG);' catchstrs.new_and_hist];
-menu = findobj(fig, 'tag', 'tools');
-uimenu( menu, 'Label', 'Run PREP pipeline', 'callback', comprep, ...
-    'separator', 'on');
-
+% eegplugin_prepPipeline() - a wrapper to the prepPipeline, which does early stage
+% 
+% Usage:
+%   >> eegplugin_prepPipeline(fig, try_strings, catch_strings);
+%
+%   see also: prepPipeline
+
+% Author: Kay Robbins, with contributions from Nima Bigdely-Shamlo, Tim Mullen, Christian Kothe, and Cassidy Matousek.
+
+% This program is free software; you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation; either version 2 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program; if not, write to the Free Software
+% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+%function eegplugin_clean_rawdata(fig,try_strings,catch_strings)
+
+% create menu
+% toolsmenu = findobj(fig, 'tag', 'tools');
+% uimenu( toolsmenu, 'label', 'Clean continuous data using ASR', 'separator','on',...
+%    'callback', 'EEG = pop_clean_rawdata(EEG); [ALLEEG EEG CURRENTSET] = eeg_store(ALLEEG, EEG); eeglab redraw');
+
+% eegplugin_prepPipeline() - the PREP pipeline plugin
+function vers = eegplugin_prepPipeline(fig, trystrs, catchstrs) 
+
+%% Add path to prepPipeline subdirectories if not in the list
+tmp = which('getPrepDefaults');
+if isempty(tmp)
+    myPath = fileparts(which('prepPipeline'));
+    addpath(genpath(myPath));
+end
+vers = getPrepVersion(); 
+
+% create menu
+comprep = [trystrs.no_check '[EEG LASTCOM] = pop_prepPipeline(EEG);' catchstrs.new_and_hist];
+menu = findobj(fig, 'tag', 'tools');
+uimenu( menu, 'Label', 'Run PREP pipeline', 'callback', comprep, ...
+    'separator', 'on');
+

PrepPipeline/examples/runVEPPrepPipeline.m

@@ -1,51 +1,50 @@
-%% Example: Running the pipeline on a directory of EEG files
-
-%% Set up the input and the output directories
-basename = 'vep';
-indir = 'F:\DataPool\CTADATA\VEP\BiosemiOriginalSetCorrected';
-outdir = 'D:\TempCTA';
-
-%% Make the output directory if needed
-if ~exist(outdir, 'dir')
-    mkdir(outdir)
-end
-
-%% Set up the params structure
-params = struct();
-params.lineFrequencies = [60, 120, 180, 212, 240];
-params.referenceChannels = 1:64;
-params.evaluationChannels = 1:64;
-params.rereferencedChannels = 1:70;
-params.detrendChannels = 1:70;
-params.lineNoiseChannels = 1:70;
-
-params.detrendType = 'high pass';
-params.detrendCutoff = 1;
-params.referenceType = 'robust';
-params.meanEstimateType = 'median';
-params.interpolationOrder = 'post-reference';
-params.removeInterpolatedChannels = true;
-params.keepFiltered = false;
-basenameOut = [basename 'robust_1Hz_post_median_unfiltered'];
-
-
-%% Get the filelist
-fileList = getFileList('FILES', indir);
-%% Run the pipeline
-for k = 1:length(fileList)
-    [~, thisName, ~] = fileparts(fileList{k});
-    EEG = pop_loadset(fileList{k});
-    params.name = thisName;
-    [EEG, params, computationTimes] = prepPipeline(EEG, params);
-    fprintf('Computation times (seconds):\n   %s\n', ...
-        getStructureString(computationTimes));
-    fprintf('Post-process\n')
-    EEG = prepPostProcess(EEG, params);
-    fname = [outdir filesep thisName '.set'];
-    save(fname, 'EEG', '-mat', '-v7.3'); 
-    if strcmpi(params.errorMsgs, 'verbose')
-        outputPrepParams(params, 'Prep parameters (non-defaults)');
-        outputPrepErrors(EEG.etc.noiseDetection, 'Prep error status');
-    end
-
-end
+%% Example: Running the pipeline on a directory of EEG files
+
+%% Set up the input and the output directories
+basename = 'vep';
+indir = 'F:\DataPool\CTADATA\VEP\BiosemiOriginalSetCorrected';
+outdir = 'F:\TempData';
+
+%% Make the output directory if needed
+if ~exist(outdir, 'dir')
+    mkdir(outdir)
+end
+
+%% Set up the params structure
+params = struct();
+params.lineFrequencies = [60, 120, 180, 212, 240];
+params.referenceChannels = 1:64;
+params.evaluationChannels = 1:64;
+params.rereferencedChannels = 1:70;
+params.detrendChannels = 1:70;
+params.lineNoiseChannels = 1:70;
+
+params.detrendType = 'high pass';
+params.detrendCutoff = 1;
+params.referenceType = 'robust';
+params.meanEstimateType = 'median';
+params.interpolationOrder = 'post-reference';
+params.removeInterpolatedChannels = true;
+params.keepFiltered = false;
+basenameOut = [basename 'robust_1Hz_post_median_unfiltered'];
+
+%% Get the filelist
+fileList = getFileList('FILES', indir);
+%% Run the pipeline
+for k = 1:length(fileList)
+    [~, thisName, ~] = fileparts(fileList{k});
+    EEG = pop_loadset(fileList{k});
+    params.name = thisName;
+    [EEG, params, computationTimes] = prepPipeline(EEG, params);
+    fprintf('Computation times (seconds):\n   %s\n', ...
+        getStructureString(computationTimes));
+    fprintf('Post-process\n')
+    EEG = prepPostProcess(EEG, params);
+    fname = [outdir filesep thisName '.set'];
+    save(fname, 'EEG', '-mat', '-v7.3'); 
+    if strcmpi(params.errorMsgs, 'verbose')
+        outputPrepParams(params, 'Prep parameters (non-defaults)');
+        outputPrepErrors(EEG.etc.noiseDetection, 'Prep error status');
+    end
+
+end

PrepPipeline/examples/runVEPPrepReport.m

@@ -1,37 +1,36 @@
-%% Read in the file and set the necessary parameters
-
-% dataDir = 'O:\ARL_Data\VEP\VEP_Robust_1Hz';
-% summaryFolder  = 'O:\ARL_Data\VEP\VEP_Robust_1Hz_New_Report_B';
-
-dataDir = 'D:\TempCTA';
-summaryFolder = 'D:\TempCTA';
-publishOn = true;
-%% Get the directory list
-inList = dir(dataDir);
-inNames = {inList(:).name};
-inTypes = [inList(:).isdir];
-inNames = inNames(~inTypes);
-
-%%
-basename = 'vep';
-summaryReportName = [basename '_summary.html'];
-sessionFolder = '.';
-summaryFileName = [summaryFolder filesep summaryReportName];
-if exist(summaryFileName, 'file') 
-   delete(summaryFileName);
-end
-
-%% Run the pipeline
-
-for k = 1:length(inNames)
-    [~, 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];
-    consoleFID = 1;
-    publishPrepReport(EEG, summaryFileName, sessionFileName, consoleFID, publishOn);
+%% This script takes a directory of files that have been processed by PREP
+% and produces reports.
+
+%% Read in the file and set the necessary parameters
+dataDir = 'F:\TempData';
+summaryFolder = 'F:\TempDataReports';
+publishOn = true;
+
+%% Get the directory list
+inList = dir(dataDir);
+inNames = {inList(:).name};
+inTypes = [inList(:).isdir];
+inNames = inNames(~inTypes);
+
+%% Setup up the names
+basename = 'vep';
+summaryReportName = [basename '_summary.html'];
+sessionFolder = '.';
+summaryFileName = [summaryFolder filesep summaryReportName];
+if exist(summaryFileName, 'file') 
+   delete(summaryFileName);
+end
+
+%% Publish the reports
+for k = 1:length(inNames)
+    [~, 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];
+    consoleFID = 1;
+    publishPrepReport(EEG, summaryFileName, sessionFileName, consoleFID, publishOn);
 end