Added landing point for the notion of a staging script

.gitignore

@@ -10,7 +10,7 @@ code/eeg_init
 code/misc
 
 # Specifically hide the staging script
-derivatives/lossless/code/scripts/staging
+# derivatives/lossless/code/scripts/staging/*
 
 # BIDS ignores:
 sourcedata/*

derivatives/lossless/code/scripts/staging/staging_script.m

+%load corresponding coordinate file
+EEG = warp_locs( EEG, 'derivatives/lossless/code/misc/standard_1005.elc', ...
+      'mesh','derivatives/lossless/code/misc/standard_vol_SCCN.mat', ...
+      'transform',[0.6,-22,-3,-0.05,-0.003,-1.57,10.2,11,11.6], ...
+      'manual','off');
+
+EEG = pop_eegfiltnew(EEG,[],1,[],true,[],0);
+
+if ~isfield(EEG,'marks');
+    EEG.marks = marks_init(size(EEG.data));
+end
+
+% Apply trimmed average re-reference
+chan_inds = marks_label2index(EEG.marks.chan_info,{'manual'},'indexes','invert','on');
+trm_m = ve_trimmean(EEG.data(chan_inds,:),30,1);
+trm_m_mat = repmat(trm_m,size(EEG.data,1),1);
+EEG.data = EEG.data - trm_m_mat;
+clear trm_m_mat;
+
+% epoch the continuous data
+EEG = marks_continuous2epochs(EEG,'recurrence',[1],'limits',[0 1]);
+
+% flag fixed criteria time points
+chan_inds = marks_label2index(EEG.marks.chan_info,{'manual'},'indexes','invert','on');
+epoch_inds = marks_label2index(EEG.marks.time_info,{'manual'},'indexes','invert','on');
+[EEG,data_s_sd_t]=chan_variance(EEG,'data_field','data', ...
+         'chan_inds',chan_inds, ...
+         'epoch_inds',epoch_inds, ...
+         'plot_figs','off');
+
+[~,flag_s_sd_t_inds]=marks_array2flags(data_s_sd_t, ...
+             'flag_dim','col', ...
+             'init_method','fixed', ...
+             'init_vals',[0 50], ...
+             'init_crit',[], ...
+             'flag_method','fixed', ...
+             'flag_val',.3, ...
+             'plot_figs','off');
+chsd_epoch_flags = zeros(size(EEG.data(1,:,:)));
+chsd_epoch_flags(1,:,epoch_inds(flag_s_sd_t_inds))=1;
+chsd_epoch_flags=padflags(EEG,chsd_epoch_flags,1,'value',.5);
+EEG.marks = marks_add_label(EEG.marks,'time_info', ...
+            {'ch_s_sd',[1,0,0],chsd_epoch_flags});
+EEG = pop_marks_merge_labels(EEG,'time_info',{'ch_s_sd'},'target_label','manual');
+
+% concatenate the epoched data
+EEG = marks_epochs2continuous(EEG);
+EEG = eeg_checkset(EEG,'eventconsistency');
+