* Fixed the lack of a min-phase highpass FIR filter.

* Added the ability to read "private" plugins from ~/.bcilab/code

Author: chkothe

RELEASE NOTES.TXT

@@ -80,8 +80,6 @@ The latest versions of the toolbox can be found at github.com/sccn/BCILAB, and r
 
 === Known Issues in Beta Version ===
 - utl_kernelize has a bug that renders it non-working (affects ml_trainsvm and ml_trainrvm)
-- flt_fir has no minimum-phase implementation for high-pass filters yet, which means that it will incur possibly 
-  intolerable delay (workaround: use flt_iir, or, if working with epochs, flt_spectrum)
 - flt_standardize with the sphere setting turned on is not robust to signals that are (almost) rank-deficient
 - flt_iir flips the signal sign under some settings (though consistently) and causes rather high CPU load during 
   online processing
@@ -236,6 +234,8 @@ Minor New Features
 - flt_standardize: can now also do multivariate sphering (whitening)
 - tutorial_erp1.m: added a few new approaches to demo new features
 - added UnLocBox toolbox to dependencies (primarily for some of its prox operators)
+- added the ability to read private plugins from ~/.bcilab/code
+- added robust re-referencing
 
 Major Changes:
 - arg_tovals: now by default sets the arg_direct flag to false rather than true, meaning that some 

code/environment/bcilab_crashreport.mat

@@ -113,8 +113,10 @@ function env_load_dependencies(dependency_dir,autocompile)
     end
 
     % rebuild path
-    rmpath(added_paths{:});
-    addpath(added_paths{:});
+    if ~isempty(added_paths)
+        rmpath(added_paths{:});
+        addpath(added_paths{:});
+    end
 end
 
 

code/environment/env_load_dependencies.m

@@ -216,6 +216,8 @@ function env_startup(varargin)
 % load all dependencies, recursively...
 disp('Loading BCILAB dependencies...');
 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 ischar(opts.worker)
     try
@@ -421,21 +423,45 @@ function env_startup(varargin)
     end
     tracking.logfile = env_translatepath('home:/.bcilab/logs/bcilab_console.log');
     try 
-        if ~exist([hlp_homedir filesep '.bcilab' filesep 'logs'],'dir')
-            mkdir([hlp_homedir filesep '.bcilab' filesep 'logs']); end
+        diary(tracking.logfile); 
         if exist(tracking.logfile,'file')
             warning off MATLAB:DELETE:Permission
             delete(tracking.logfile); 
             warning on MATLAB:DELETE:Permission
         end
     catch,end
-    try diary(tracking.logfile); catch,end
-
-    if ~exist([hlp_homedir filesep '.bcilab' filesep 'models'],'dir')
-        mkdir([hlp_homedir filesep '.bcilab' filesep 'models']); end
-    if ~exist([hlp_homedir filesep '.bcilab' filesep 'approaches'],'dir')
-        mkdir([hlp_homedir filesep '.bcilab' filesep 'approaches']); end
 
+    try 
+        % create directories in the user's .bcilab folder...
+        home_basedir = [hlp_homedir filesep '.bcilab' filesep];
+        home_codedirs = {['code' filesep 'filters'],['code' filesep 'dataset_editing'], ...
+            ['code' filesep 'machine_learning'], ['code' filesep 'paradigms']};
+        home_miscdirs = {'models','approaches','code',['code' filesep 'dependencies'],'logs'};
+        for d = [home_codedirs home_miscdirs]
+            try
+                subdir = [home_basedir d{1}];
+                if ~exist(subdir,'dir')
+                    mkdir(subdir); end
+            catch e
+                disp(['Could not create directory: ' subdir ': ' e.message]);
+            end
+        end
+        % and add the code directories to the path
+        for d = home_codedirs
+            addpath(genpath([home_basedir d{1}])); end
+        % add the env_add.m file to the dependencies folder
+        add_file = [home_basedir 'code' filesep 'dependencies' filesep 'env_add.m'];
+        if ~exist(add_file,'file')
+            try                
+                f = fopen(add_file,'w');
+                fwrite(f,' ');
+                fclose(f);
+            catch e
+                disp(['Could not create file ' add_file ': ' e.message]);
+            end
+        end
+    catch,end
+
     % create a menu
     if ~(isequal(opts.menu,false) || isequal(opts.menu,0))
         try

code/environment/env_startup.m

@@ -59,7 +59,7 @@
 % a function that creates a list of cleaning parameters, for some defaults
 make_clean_params = @(flatlines,drifts,regression,windows,channels,dropouts,peaks,spikes,shaping) { ...
     arg_subtoggle({'flatlines','FlatlineRemoval'},flatlines,@flt_clean_flatlines,'Removal of flat-line channels.'), ...
-    arg({'drifts','DriftCutoff'},drifts,[],'Drift-correction high-pass filter. This is the frequency specification of a (zero-phase) filter: [transition-start, transition-end], in Hz'), ...
+    arg({'drifts','DriftCutoff'},drifts,[],'Drift-correction high-pass filter. This is the frequency specification of the filter: [transition-start, transition-end], in Hz'), ...
     arg_subtoggle({'regression','ArtifactRegression'},regression,@flt_eog,'Removal of artifacts based on reference channels.'), ...
     arg_subtoggle({'channels','BadChannelRemoval'},channels,@flt_clean_channels,'Rejection of channels with uncorrelated signals.'), ...
     arg_subtoggle({'dropouts','ChannelDropoutRepair'},dropouts,@flt_repair_channels,'Repair of channels that temporarily glitch out.'), ...

code/filters/flt_clean_settings.m

@@ -209,7 +209,7 @@
         n = length(state.b);
 
         % use cepstral windowing to calculate a minimum-phase filter (note: the min-phase change applies
-        if strcmp(ftype,'minimum-phase') && ~any(strcmp(fmode,{'highpass','hp'}))
+        if strcmp(ftype,'minimum-phase')
             wnd = [1 2*ones(1,(n+mod(n,2))/2-1) ones(1,1-mod(n,2)) zeros(1,(n+mod(n,2))/2-1)];
             state.b = real(ifft(exp(fft(wnd.*real(ifft(log(abs(fft(state.b))+stopripple)))))));
         end

code/filters/flt_fir.m

@@ -390,7 +390,9 @@
     found = [dir(env_translatepath('functions:/filters/flt_*.m')); 
              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('functions:/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'))];
 
     % get file names, function names, function handles, function tags (names without prefix)
     files = setdiff({found.name},{'flt_pipeline.m','set_new.m','set_chanid.m','set_infer_chanlocs.m'});

code/filters/flt_pipeline.m

@@ -72,7 +72,7 @@
     arg({'ref_chn','ReferenceChannels','chn'}, [], [], 'Cell array of reference channels. The signal data is be referenced to these, defaults to average reference if empty.','type','cellstr','shape','row'),...
     arg({'exclude_chn','ExcludeChannels','exclude'}, [], [], 'Cell array of channels to exclude.','type','cellstr','shape','row'),...
     arg({'keepref','KeepReference'}, false, [], 'Keep the reference channel.'), ...
-    arg({'ref_type','ReferenceType'}, 'mean', {'mean','median','huber'}, 'Type of reference. The traditional average reference operation uses the mean. If this is set to median, the median of the reference channels will be removed, and if set to huber the robust mean under the Huber loss will be removed (slower than median but closer to the mean).'), ...
+    arg({'ref_type','ReferenceType'}, 'mean', {'mean','median','huber'}, 'Type of reference. The traditional average reference operation uses the mean. If this is set to median, the median of the reference channels will be removed, and if set to huber the robust mean under the Huber loss will be removed (slower than median but statistically a more efficient estimator).'), ...
     arg({'huber_cut','HuberCutoff'}, [], [], 'Cutoff for huber function. If left empty this is set to one (robust) standard deviation of the signal.','guru',true), ...
     arg({'huber_iters','HuberIterations'}, 100, [], 'Iterations for huber fitting. A larger number yields tolerance to larger outliers.','guru',true));
 

code/filters/flt_reref.m

@@ -92,8 +92,9 @@ function gui_batchanalysis_OpeningFcn(hObject, eventdata, handles, varargin)
 end
 
 % get all paradigm names
-paradir = env_translatepath('functions:/paradigms');
-para_files = dir([paradir filesep 'Paradigm*.m']);
+para_files = [];
+for p = {'functions:/paradigms', 'home:/.bcilab/code/paradigms'}
+    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);
 
 % populate the list of approaches with available in the workspace

code/gui/gui_batchanalysis.m

@@ -24,12 +24,16 @@
 % --- aggregate all paradigms ---
 approaches = {};
 
-paradir = env_translatepath('functions:/paradigms');
-para_files = dir([paradir filesep 'Paradigm*.m']);
-para_names = {para_files.name};
+para_paths = {};
+for p = {'functions:/paradigms', 'home:/.bcilab/code/paradigms'}
+    rootpath = env_translatepath(p{1});
+    files = dir([rootpath filesep 'Paradigm*.m']);
+    para_paths = [para_paths cellfun(@(n)[rootpath filesep n],{files.name},'UniformOutput',false)];
+end
 
-for p=1:length(para_names)
-    filename = para_names{p};
+for p=1:length(para_paths)
+    [paradir,filename,ext] = fileparts(para_paths{p});
+    filename = [filename ext];
     tag = filename(1:end-2);
     try
         % try lookup from a tiny cache of approach descriptions