Neuroscan plugin

bcilab_config.m

@@ -8,9 +8,16 @@
 % argument to the "bcilab" function (e.g. cd /your/path/to/bcilab; bcilab
 % /your/path/to/your/bcilab_config.m)
 
+% This file is loaded by bcilab.m -- note that you can have a version of the file in your ~/.bcilab/
+% directory, which will take precedence over a file of same name placed in the bcilab folder (see
+% bcilab.m), and that you can specify a custom config file to load.
+%
+% The options in this configuration file can also be edited via the GUI (under Settings); the GUI
+% always edits the file that was used when the toolbox was loaded.
+
 % this is your data path, i.e., where your studies and data sets are stored
-data = {'/data/projects'};
-data = [];
+% (if empty, will default to your bcilab:/userdata folder)
+data = []; % e.g., {'/data/myprojects','bcilab:/userdata','home:/mydata'};
 
 % this is a path where results can be stored (you must have write permission)
 % (if empty, it is set to equal the data path)
@@ -28,7 +35,8 @@
 else
     cache = [];
 end
-% comment out this line to enable caching of intermediate results
+% comment out this line to enable caching of intermediate results in one of the above default linux
+% temp folders
 cache = [];
 
 % This is the memory capacity that is being reserved for in-memory caching of intermediate results.
@@ -56,9 +64,14 @@
 data_reuses = 3;
 
 % this is a directory for temporary results (e.g. IC decompositions); if this is empty, it will be
-% set to a directory next to your BCILAB path
+% set to a directory that is your BCILAB installation path with -temp appended.
 temp = [];
 
+% if you have private plugins that you manage separately from the bcilab directory tree, you can set
+% the path to these here (using the same sub-directory structure as ~/.bcilab/, see that folder for
+% reference)
+private = [];
+
 % whether to show the main BCILAB menu by default (if this is set to 'separate', the menu is 
 % always detached from the EEGLAB main menu; otherwise it is under Tools>BCILAB)
 menu = 'separate';
@@ -75,5 +88,3 @@
 acquire_options = {'Hostnames',{'localhost'},'ShutdownTimeout',300};
 
 
-
-

code/dataset_editing/set_concat.m

@@ -48,7 +48,7 @@
         end
         % count events, epochs and samples in each set
         event_count = cellfun(@(x)length(x.event),varargin);
-        sample_count = cellfun(@(x)x.pnts,varargin).*epoch_count;
+        sample_count = cellfun(@(x)x.pnts,varargin);
         % concatenate .event and .epoch fields
         event = cellfun(@(x)x.event,varargin,'UniformOutput',false); result.event = [event{:}];
         % shift event latencies based on cumulative sample counts

code/environment/env_startup.m

@@ -24,6 +24,9 @@ function env_startup(varargin)
 %                       (default: path/to/bcilab-temp, or path/to/cache/bcilab_temp if a cache
 %                       directory was specified)
 %
+%               'private': optional private plugin directory, separate from bcilab/*; can have
+%                          the same directory structure as ~/.bcilab/ (default: [])
+%
 %               --- caching settings ---
 %
 %               'cache': Path where intermediate data sets are cached. Should be located on a fast 
@@ -209,7 +212,7 @@ function env_startup(varargin)
     disp('Note: Your version of MATLAB is not supported by BCILAB any more. You may try BCILAB version 0.9, which supports old MATLAB''s back to version 2006a.'); end    
 
 % get options
-opts = hlp_varargin2struct(varargin,'data',[],'store',[],'cache',[],'temp',[],'mem_capacity',2,'data_reuses',3, ...
+opts = hlp_varargin2struct(varargin,'data',[],'store',[],'cache',[],'temp',[],'private',[],'mem_capacity',2,'data_reuses',3, ...
     'parallel',{'use','local'}, 'menu',true, 'configscript','', 'worker',false, 'autocompile',true, 'acquire_options',{}, ...
     'show_experimental',false,'show_guru',false);
 
@@ -218,6 +221,8 @@ function env_startup(varargin)
 env_load_dependencies(dependency_dir,opts.autocompile);
 if exist(env_translatepath('home:/.bcilab/code/dependencies'),'dir')
     env_load_dependencies(env_translatepath('home:/.bcilab/code/dependencies'),opts.autocompile); end
+if ~isempty(opts.private) && exist(env_translatepath([opts.private '/code/dependencies']),'dir')
+    env_load_dependencies(env_translatepath([opts.private '/code/dependencies']),opts.autocompile); end
 
 if ischar(opts.worker)
     try
@@ -248,7 +253,7 @@ function env_startup(varargin)
     opts.data = {opts.data}; end
 for d = 1:length(opts.data)
     opts.data{d} = path_normalize(opts.data{d}); end
-if isempty(opts.data) || ~any(cellfun(@exist,opts.data))
+if isempty(opts.data)
     opts.data = {[base_dir 'userdata']}; end
 
 % process store directory
@@ -297,7 +302,7 @@ function env_startup(varargin)
 
 % set global variables
 global tracking
-tracking.paths = struct('bcilab_path',{base_dir(1:end-1)}, 'function_path',{function_dir}, 'data_paths',{opts.data}, 'store_path',{opts.store}, 'dependency_path',{dependency_dir},'resource_path',{resource_dir},'temp_path',{opts.temp});
+tracking.paths = struct('bcilab_path',{base_dir(1:end-1)}, 'function_path',{function_dir}, 'data_paths',{opts.data}, 'store_path',{opts.store}, 'dependency_path',{dependency_dir},'resource_path',{resource_dir},'temp_path',{opts.temp}, 'private_path',{opts.private});
 for d=1:length(opts.cache)
     location = rmfield(opts.cache{d},'tag');
     % convert GiB to bytes
@@ -406,6 +411,8 @@ function env_startup(varargin)
     disp('cache is disabled');
 end
 disp(['temp is in ' opts.temp]);
+if ~isempty(opts.private)
+    disp(['private plugins are in ' opts.private]); end
 fprintf('\n');
 
 
@@ -463,6 +470,22 @@ function env_startup(varargin)
         end
     catch,end
 
+    % add private plugin directories to the path
+    if ~isempty(opts.private)
+        try
+            private_codedirs = {['code' filesep 'filters'],['code' filesep 'dataset_editing'], ...
+                ['code' filesep 'machine_learning'], ['code' filesep 'paradigms'], ['code' filesep 'scripts']};
+            % and add the code directories to the path
+            for d = private_codedirs
+                tmpdir  = env_translatepath([opts.private filesep d{1}]);
+                if exist(tmpdir,'dir')
+                    addpath(genpath(tmpdir)); end
+            end
+        catch e
+            disp(['Could not add private code directories to path: ' e.message]);
+        end
+    end
+
     % create a menu
     if ~(isequal(opts.menu,false) || isequal(opts.menu,0))
         try

code/environment/env_translatepath.m

@@ -10,6 +10,11 @@
 % 30])", and this in turn allows to share the same data set caches (which are indexed by expression)
 % across machines and operating systems, minimizing redundant computations.
 %
+% Some of the path references, such as data:/, temp:/, store:/, private:/ can be set in the startup
+% arguments of bcilab.m or bcilab_config.m (see documentation in those files). It is permitted to
+% use other relative paths, such as home:/ when specifying those arguments (but circular references
+% must be avoided).
+%
 % In:
 %   IndependentPath : platform-independent path; may contain forward and/or backward slashes
 %                     (forward slashes generally preferred), and may refer to locations such as
@@ -42,7 +47,6 @@
 %   % resolve a reference to the resources directory
 %   env_translatepath('resources:/workspaces/testing.mat')
 %
-%
 % See also:
 %   env_startup, io_loadset
 %
@@ -51,47 +55,56 @@
 
 global tracking;
 
-% turn the path into a system-dependent one
-filename = strrep(strrep(filename,'\',filesep),'/',filesep);
+% function to sanitize file names (replace file separators by system-dependent version)
+sanitize = @(filename) strrep(strrep(strrep(filename,'\',filesep),'/',filesep),[filesep filesep],filesep);
 
-% resolve location references
-if strncmp('store:',filename,6)
-    filename = [tracking.paths.store_path filename(1+length('store:'):end)]; 
-elseif strncmp('resources:',filename,10)
-    filename = [tracking.paths.resource_path filename(1+length('resources:'):end)]; 
-elseif strncmp('temp:',filename,5)
-    filename = [tracking.paths.temp_path filename(1+length('temp:'):end)]; 
-elseif strncmp('functions:',filename,10)
-    filename = [tracking.paths.function_path filename(1+length('functions:'):end)]; 
-elseif strncmp('bcilab:',filename,7)
-    filename = [tracking.paths.bcilab_path filename(1+length('bcilab:'):end)]; 
-elseif strncmp('dependencies:',filename,13)
-    filename = [tracking.paths.dependency_path filename(1+length('dependencies:'):end)];
-elseif strncmp('home:',filename,5)
-    filename = [hlp_homedir filename(1+length('home:'):end)];
-elseif strncmp('data:',filename,5)
-    rest = filename(1+length('data:'):end);
-    bestpath = 1; bestlen = -1;
-    if length(tracking.paths.data_paths) > 1
-        fpieces = hlp_split(rest,filesep);
-        % find the data path that contains the longest prefix of the filename
-        for pidx=1:length(tracking.paths.data_paths)
-            p = tracking.paths.data_paths{pidx};
-            % for each prefix of the filename (starting with the longest one)
-            for k=length(fpieces):-1:0
-                % check if the data path plus the first k pieces of the filename exists
-                if exist([p sprintf([filesep '%s'],fpieces{1:k})],'file')
-                    % found a match - check if it is a new length record among all our data paths...
-                    if k>bestlen
-                        bestlen = k;
-                        bestpath = pidx;
+% loop until all path references have been resolved
+while true
+    % resolve location references
+    if strncmp('store:',filename,6)
+        filename = [tracking.paths.store_path filename(1+length('store:'):end)]; 
+    elseif strncmp('resources:',filename,10)
+        filename = [tracking.paths.resource_path filename(1+length('resources:'):end)]; 
+    elseif strncmp('temp:',filename,5)
+        filename = [tracking.paths.temp_path filename(1+length('temp:'):end)]; 
+    elseif strncmp('functions:',filename,10)
+        filename = [tracking.paths.function_path filename(1+length('functions:'):end)]; 
+    elseif strncmp('bcilab:',filename,7)
+        filename = [tracking.paths.bcilab_path filename(1+length('bcilab:'):end)]; 
+    elseif strncmp('dependencies:',filename,13)
+        filename = [tracking.paths.dependency_path filename(1+length('dependencies:'):end)];
+    elseif strncmp('private:',filename,8)
+        filename = [tracking.paths.private_path filename(1+length('private:'):end)];
+    elseif strncmp('home:',filename,5)
+        filename = [hlp_homedir filename(1+length('home:'):end)];
+    elseif strncmp('data:',filename,5)
+        rest = filename(1+length('data:'):end);
+        bestpath = 1; bestlen = -1;
+        if length(tracking.paths.data_paths) > 1
+            % find the data path that contains the longest prefix of the filename
+            fpieces = hlp_split(sanitize(rest),filesep);
+            for pidx=1:length(tracking.paths.data_paths)
+                p = env_translatepath(tracking.paths.data_paths{pidx});
+                % for each prefix of the filename (starting with the longest one)
+                for k=length(fpieces):-1:0
+                    % check if the data path plus the first k pieces of the filename exists
+                    if exist([p filesep fpieces{1:k}],'file')
+                        % found a match - check if it is a new length record among all our data paths...
+                        if k>bestlen
+                            bestlen = k;
+                            bestpath = pidx;
+                        end
+                        break;
                     end
-                    break;
                 end
             end
         end
+        % resolve the reference using that data path which matches most of the filename,
+        % where, if multiple data paths are equally well suited, the first one of them is taken
+        filename = [tracking.paths.data_paths{bestpath} rest];
+    else
+        break;
     end
-    % resolve the reference using that data path which matches most of the filename,
-    % where, if multiple data paths are equally well suited, the first one of them is taken
-    filename = [tracking.paths.data_paths{bestpath} rest];
 end
+
+filename = sanitize(filename);

code/filters/flt_pipeline.m

@@ -391,6 +391,10 @@
              dir(env_translatepath('functions:/dataset_editing/set_*.m'));
              dir(env_translatepath('functions:/filters/in_development/flt_*.m'));
              dir(env_translatepath('functions:/dataset_editing/in_development/set_*.m'));
+             dir(env_translatepath('private:/code/filters/flt_*.m'));
+             dir(env_translatepath('private:/code/dataset_editing/set_*.m'));
+             dir(env_translatepath('private:/code/filters/in_development/flt_*.m'));
+             dir(env_translatepath('private:/code/dataset_editing/in_development/set_*.m'));
              dir(env_translatepath('home:/.bcilab/code/filters/flt_*.m'));
              dir(env_translatepath('home:/.bcilab/code/dataset_editing/set_*.m'))];
 

code/gui/gui_batchanalysis.m

@@ -81,6 +81,7 @@ function gui_batchanalysis_OpeningFcn(hObject, eventdata, handles, varargin)
 % hObject    handle to figure
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
+global tracking;
 
 % turn all large edit panes to multi-line editors
 for obj = {handles.edit1,handles.edit20,handles.edit19}
@@ -93,7 +94,10 @@ function gui_batchanalysis_OpeningFcn(hObject, eventdata, handles, varargin)
 
 % get all paradigm names
 para_files = [];
-for p = {'functions:/paradigms', 'home:/.bcilab/code/paradigms'}
+para_paths = {'functions:/paradigms', 'functions:/paradigms/in_development', 'home:/.bcilab/code/paradigms'};
+if ~isempty(tracking.paths.private_path)
+    para_paths = [para_paths {'private:/code/paradigms','private:/code/paradigms/in_development'}]; end
+for p = para_paths
     para_files = [para_files dir([env_translatepath(p{1}) filesep 'Paradigm*.m'])]; end
 para_acronyms = cellfun(@(s)s(9:end-2),{para_files.name},'UniformOutput',false);
 

code/gui/utils/gui_listapproaches.m

@@ -27,6 +27,11 @@
     {'Built-in Paradigms', {'functions:/paradigms'}}, ...
     {'User Paradigms', {'home:/.bcilab/code/paradigms'}}, ...
     {'Experimental Paradigms',quickif(tracking.gui.show_experimental,{'functions:/paradigms/in_development'},{})}};
+if ~isempty(tracking.paths.private_path)
+    paradigm_locations = [paradigm_locations { ...
+        {'Private Paradigms', {'private:/code/paradigms'}}, ...
+        {'Private Experimental Paradigms',quickif(tracking.gui.show_experimental,{'private:/code/paradigms/in_development'},{})}}];
+end
 
 for loc=1:length(paradigm_locations)
     if ~isempty(paradigm_locations{loc}{2})
@@ -68,7 +73,7 @@
 for v=find(strcmp({vars.class},'cell'))
     var = evalin('base',vars(v).name);
     if length(var)>1 && ischar(var{1}) && ((strncmp(var{1},'Paradigm',8) && length(var{1})>8 && any(strcmp(var{1}(9:end),paradigm_names))) || any(strcmp(var{1},paradigm_names)))
-        approaches{end+1} = struct('paradigm',quickif(strncmp(var{1},'Paradigm',8),var{1},['Paradigm',var{1}]),'name',vars(v).name,'parameters',{var(2:end)}); end
+        approaches{end+1} = struct('paradigm',quickif(strncmp(var{1},'Paradigm',8),var{1},['Paradigm',var{1}]),'name',vars(v).name,'parameters',{var(2:end)},'description',''); end
 end
 
 list = [list {'From Workspace', approaches}];
@@ -77,6 +82,8 @@
 % --- aggregate all approaches in the approaches directory (and the user's home directory, too) ---
 approaches = {};
 approach_dirs = {env_translatepath('home:/.bcilab/approaches'),env_translatepath('resources:/approaches')};
+if ~isempty(tracking.paths.private_path)
+    approach_dirs = [approach_dirs {env_translatepath('private:/approaches')}]; end
 for d = approach_dirs
     approach_dir = d{1};
     files = dir([approach_dir filesep '*.apr']);

code/machine_learning/ml_train.m

@@ -180,10 +180,14 @@
 
 function learners = list_learners(update_list)
 % list all the learning functions in code/machine_learning/
+global tracking;
 persistent memo;
 if isempty(memo) || exist('update_list','var') && update_list
     memo = {};
-    for p = {'functions:/machine_learning/ml_train*.m','home:/.bcilab/code/machine_learning/ml_train*.m'}
+    ml_paths = {'functions:/machine_learning/ml_train*.m','home:/.bcilab/code/machine_learning/ml_train*.m'};
+    if ~isempty(tracking.paths.private_path)
+        ml_paths = [ml_paths {'private:/code/machine_learning/ml_train*.m'}]; end
+    for p = ml_paths
         modules = dir(env_translatepath(p{1}));
         names = setdiff({modules.name},{'ml_train.m','ml_trainvote.m'});
         tags = cellfun(@(n) n(9:end-2),names,'UniformOutput',false);

code/online_plugins/Neuroscan/BCILAB.readme

@@ -0,0 +1,18 @@
+README for Neuroscan Scan Plugin for BCILAB
+Author: Visual Attention and Cognition Lab, Dan Roberts, and Nick Pe�aranda, George Mason University, Spring 2014
+         Released under the GPLv3, see COPYING.txt
+         Based on the BrainVision BCILAB plug-in by Hal Greenwald
+
+
+Plugin to stream EEG data and event markers from Neuroscan Scan software to BCILAB. Has been tested with Scan 4.3 and a NuAmps 40-channel amplifier
+
+Associated Files:
+
+BCILAB/code/online_plugins/Neuroscan:
+ns_close.m
+ns_open.m
+ns_parseheader.m
+ns_parseinfo.m
+ns_read.m
+ns_sendpacket.m
+run_readneuroscan.m