Diagnostic output added as well as overlay bug fix.

eeglab_asr_amica @ 0917d2a7

-Subproject commit eb58a1e067347780e855649ba59351ffcf47015d
+Subproject commit 0917d2a77293fd978331afb26ff407edf7692b4a

derivatives/lossless/code/misc/standard_1020_Fpz_FT7_FT8_Cz_PO7_PO8_Oz.elc

+# ASA electrode file
+ReferenceLabel	avg
+UnitPosition	mm
+NumberPositions= 7
+Positions
+0.1123 88.2470 -1.7130
+-80.7750 14.1203 -11.1350
+81.8151 15.4167 -11.3300
+0.4009 -9.1670 100.2440
+-54.8404 -97.5279 2.7920
+55.6666 -97.6251 2.7300
+0.1076 -114.8920 14.6570
+Labels
+Fpz
+FT7
+FT8
+Cz
+PO7
+PO8
+Oz

derivatives/lossless/code/scripts/qc.htb

@@ -14,26 +14,35 @@ set(bfh,'Position',[1986 1 348 973]);
 %PLOT CHAN DATA SCROLL PLOT USING VISED PLUGIN...
 EEG_scalp = pop_vised(EEG,'data_type','EEG', ...
     'pop_gui','off', ...
+    'event_type',[], ...
     'spacing',80, ...
     'command','', ...
     'tag','ve_eeg', ...
-    'keyselectcommand',{'t,ve_eegplot(''topoplot'',gcbf)';'r,ve_eegplot(''drawp'',0)';'o,qc_ovl_tog';'u,qc_ovl_upd'});
+    'keyselectcommand',{'t,ve_eegplot(''topoplot'',gcbf)';'r,ve_eegplot(''drawp'',0)';'o,qc_ovl_tog';'u,qc_ovl_upd'}, ...
+    'dispchans',32);
+
 sfh = gcf;
 set(sfh,'Position',[66 1 1484 1003]);
 
 %PLOT FULL DURATION NON-MANUAL ICAACT SURFACE PLOT
-notman_pnts = marks_label2index(EEG.marks.time_info,{'manual'},'indexes','invert','on');
-normact=zeros(size(EEG.icaact(:,notman_pnts)));
+%notman_pnts = marks_label2index(EEG.marks.time_info,{'manual'},'indexes','invert','on');
+%normact=zeros(size(EEG.icaact(:,notman_pnts)));
+fullnormact=zeros(size(EEG.icaact));
 
-sortnormact=zeros(size(EEG.icaact(:,notman_pnts)));
+%sortnormact=zeros(size(EEG.icaact(:,notman_pnts)));
 for i=1:min(size(EEG.icaweights));
-    normact(i,:)=(EEG.icaact(i,notman_pnts)-min(EEG.icaact(i,notman_pnts)))/(max(EEG.icaact(i,notman_pnts))-min(EEG.icaact(i,notman_pnts)));
-    sortnormact(i,:)=sort(normact(i,:));
+    %normact(i,:)=(EEG.icaact(i,notman_pnts)-min(EEG.icaact(i,notman_pnts)))/(max(EEG.icaact(i,notman_pnts))-min(EEG.icaact(i,notman_pnts)));
+    fullnormact(i,:) = (EEG.icaact(i,:)-min(EEG.icaact(i,:)))/(max(EEG.icaact(i,:))-min(EEG.icaact(i,:)));
+    %sortnormact(i,:)=sort(normact(i,:));
 end
 
-nash=figure;
-surf(normact,'linestyle','none');axis('tight');view(0,270);
-set(nash,'Position',[1550 1 371 973]);
+%nash=figure;
+%surf(normact,'linestyle','none');axis('tight');view(0,270);
+%set(nash,'Position',[1550 1 371 973]);
+
+fullnash=figure;
+surf(fullnormact,'linestyle','none');axis('tight');view(0,270);
+set(fullnash,'Position',[1550 1 371 973]);
 
 %snash=figure;
 %surf(sortnormact,'linestyle','none');axis('tight');view(0,270);
@@ -62,7 +71,8 @@ close(tfh(find(strncmp('View components properties - pop_viewprops() (dataset:',
 
 %CLOSE/CLEAR ICLABEL BAR GRAPH
 try close(bfh),clear bfh, catch clear bfh, end
-try close(nash),clear nash, catch clear nash, end
+try close(fullnash),clear fullnash, catch clear fullnash, end
+%try close(nash),clear nash, catch clear nash, end
 %try close(snash),clear snash, catch clear snash, end
 
 %CLOSE/CLEAR EEG SCROLL PLOT HANDLES

derivatives/lossless/code/tools/diagnostics/main_diagnostics.m

@@ -8,7 +8,7 @@ function main_diagnostics(filePath)
     fOut = fopen(fName,'w');
     
     % Update this eventually...
-    header = 'fname,nbchan,pnts,srate,manual,ch_s_sd-m,ch_s_sd_b-m,ch_s_sd_b-m-ch_sd_b,ch_s_sd_b-m-ic_sd1_b,ch_sd-m,ch_sd_b-m,ch_sd_b-m-ic_sd1_b,low_r-m,ic_sd1-m,ic_sd1_b-m,ic_sd2,ch_s_sd,ch_sd,low_r,bridge,LtModelMean,LtModelStd,Lt_quant_0.05,Lt_quant_0.15,Lt_quant_0.25,Lt_quant_0.5,Lt_quant_0.75,Lt_quant_0.85,Lt_quant_0.95,manual_comp_1,ic_rt_1,linkpvaluesMean,linkpvaluesStd,lpv_quant_0.05,lpv_quant_0.15,lpv_quant_0.25,lpv_quant_0.5,lpv_quant_0.75,lpv_quant_0.85,lpv_quant_0.95,tvar_mean, tvar_std, tvar_quant_0.05,tvar_quant_0.15,tvar_quant_0.25,tvar_quant_0.5,tvar_quant_0.75,tvar_quant_0.85,tvar_quant_0.95, pvar_mean, pvar_std,pvar_quant_0.05,pvar_quant_0.15,pvar_quant_0.25,pvar_quant_0.5,pvar_quant_0.75,pvar_quant_0.85,pvar_quant_0.95';
+    header = 'fname,nbchan,pnts,srate,manual,ch_s_sd_m,ch_s_sd_b_m,ch_sd_m,ch_sd_b_m,low_r_m,ic_sd1_m,ic_sd1_b_m,ic_sd2_m,mark_gap,ch_s_sd_b-ch_sd_b,ch_s_sd_b-ic_sd1_b,ch_sd_b-ic_sd1_b,low_r_m-ic_sd1_b,manual_only,non_manual,remaining,ch_s_sd,ch_sd,low_r,bridge,LtModelMean,LtModelStd,Lt_quant_0.05,Lt_quant_0.15,Lt_quant_0.25,Lt_quant_0.5,Lt_quant_0.75,Lt_quant_0.85,Lt_quant_0.95,manual_comp_1,ic_rt_1,linkpvaluesMean,linkpvaluesStd,lpv_quant_0.05,lpv_quant_0.15,lpv_quant_0.25,lpv_quant_0.5,lpv_quant_0.75,lpv_quant_0.85,lpv_quant_0.95,tvar_mean, tvar_std, tvar_quant_0.05,tvar_quant_0.15,tvar_quant_0.25,tvar_quant_0.5,tvar_quant_0.75,tvar_quant_0.85,tvar_quant_0.95, pvar_mean, pvar_std,pvar_quant_0.05,pvar_quant_0.15,pvar_quant_0.25,pvar_quant_0.5,pvar_quant_0.75,pvar_quant_0.85,pvar_quant_0.95';
     fprintf(fOut,'%s\n',header);
     
     % Read line by line of the specified diag list
@@ -16,6 +16,7 @@ function main_diagnostics(filePath)
     tline = fgetl(fIn);
     while ischar(tline)
         single_diagnostic(fOut,tline);
+        single_spect_diag(tline);
         tline = fgetl(fIn);
     end
     

derivatives/lossless/code/tools/diagnostics/single_diagnostic.m

@@ -18,31 +18,42 @@ function single_diagnostic(fOutID, singleSetFile)
     outString = [outString, num2str(EEG.pnts), ','];
     outString = [outString, num2str(EEG.srate), ','];
     
-    % All time_info flag enables in seconds:
+    % All time_info flags in seconds:
     % Manual
-    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags==1)) / EEG.srate), ','];
-    % ch_s_sd m
+    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags== 1)) / EEG.srate), ','];
+    % ch_s_sd_m
     outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(3).flags == 1)) / EEG.srate), ','];
-    % ch_s_sd b m
+    % ch_s_sd_b_m (padding of ch_s_sd_m)
     outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(3).flags == 0.5)) / EEG.srate), ','];
-    % ch_s_sd b m ch_sd b
-    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(3).flags == 0.5 & EEG.marks.time_info(4).flags == 0.5)) / EEG.srate), ','];
-    % ch_s_sd b m ic_sd1 b
-    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(3).flags == 0.5 & EEG.marks.time_info(8).flags == 0.5)) / EEG.srate), ','];
-    % ch_sd m
+    % ch_sd_m
     outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(4).flags == 1)) / EEG.srate), ','];
-    % ch_sd b m
+    % ch_sd_b_m (padding of ch_sd_m)
     outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(4).flags == 0.5)) / EEG.srate), ','];
-    % ch_sd b m ic_sd1 b
-    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(4).flags == 0.5 & EEG.marks.time_info(8).flags == 0.5)) / EEG.srate), ','];
-    % low_r m
+    % low_r_m
     outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(5).flags == 1)) / EEG.srate), ','];
-    % ic_sd1 m
+    % ic_sd1_m
     outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(8).flags == 1)) / EEG.srate), ','];
-    % ic_sd1 b m
+    % ic_sd1_b_m
     outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(8).flags == 0.5)) / EEG.srate), ','];
-    % ic_sd2
-    outString = [outString, num2str(length(find(EEG.marks.time_info(12).flags==1)) / EEG.srate), ','];
+    % ic_sd2_m
+    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(12).flags == 1)) / EEG.srate), ','];
+    % mark_gap
+    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(6).flags == 1)) / EEG.srate), ','];
+    % overlap between ch_s_sd_b_m  and ch_sd_b_m
+    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(3).flags == 0.5 & EEG.marks.time_info(4).flags == 0.5)) / EEG.srate), ','];
+    % overlap between ch_s_sd_b_m  and ic_sd1_b_m
+    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(3).flags == 0.5 & EEG.marks.time_info(8).flags == 0.5)) / EEG.srate), ','];
+    % overlap between ch_sd_b_m and ic_sd1_b_m
+    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(4).flags == 0.5 & EEG.marks.time_info(8).flags == 0.5)) / EEG.srate), ','];
+    % overlap between low_r_m and ic_sd1_b_m
+    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(5).flags == 1 & EEG.marks.time_info(8).flags == 0.5)) / EEG.srate), ','];
+    % manual only
+    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(3).flags == 0 & EEG.marks.time_info(4).flags == 0 & ...
+            EEG.marks.time_info(5).flags == 0 & EEG.marks.time_info(6).flags == 0 & EEG.marks.time_info(8).flags == 0 & EEG.marks.time_info(12).flags == 0)) / EEG.srate), ','];
+    % non-manual but flagged for other reason
+    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 0 & (EEG.marks.time_info(3).flags > 0 | EEG.marks.time_info(4).flags > 0 | EEG.marks.time_info(5).flags > 0 | EEG.marks.time_info(6).flags > 0 | EEG.marks.time_info(8).flags > 0 | EEG.marks.time_info(12).flags > 0))) / EEG.srate), ','];
+    % all non-manual
+    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 0)) / EEG.srate), ','];
 
     % Single chan_info flag enables in seconds:
     for i=2:5 % [2,5] are ch_s_sd, ch_sd, low_r, and bridge respectively.

derivatives/lossless/code/tools/diagnostics/single_spect_diag.m

+% This function loads a single file and gathers all of the needed
+% information. fOutID should be the output file handle from
+% main_diagnostics. singleSetFile should reflect its name.
+function single_spect_diag(singleSetFile)
+    % Storing what's going to be written to the csv in a variable to act as
+
+    % Load:
+    EEG = pop_loadset('filepath','','filename',singleSetFile);
+    EEG = eeg_checkset( EEG );
+    
+    % Removed flagged channels and time segments
+    sprintf('%s','Purging flagged channels...\n');
+    EEG = pop_marks_select_data(EEG,'channel marks',[],'labels',{'manual'},'remove','on');
+    EEG = pop_marks_select_data(EEG,'time marks',[],'labels',{'manual'},'remove','on');
+%    EEG = pop_marks_select_data(EEG,'component marks',[],'labels',{'manual'},'remove','on');
+    EEG = eeg_checkset(EEG);
+    
+    EEG= warp_locs(EEG,'derivatives/lossless/code/misc/standard_1020_Fpz_FT7_FT8_Cz_PO7_PO8_Oz.elc','transform',[0,0,0,0,0,-1.57,1,1,1],'manual','off');
+    EEG = interp_mont(EEG,'derivatives/lossless/code/misc/standard_1020_Fpz_FT7_FT8_Cz_PO7_PO8_Oz.elc','manual','off');
+    EEG = eeg_checkset(EEG);
+    
+    EEG.icaact=[];
+    EEG.icawinv=[];
+    EEG.icasphere=[];
+    EEG.icaweights=[];
+    EEG.icachansind=[];
+    
+    % Window the continuous data
+    logging_log('INFO', 'Windowing the continous data...');
+    EEG = marks_continuous2epochs(EEG,'recurrence',0.5,'limits',[0,1],'keepboundary','off');
+    EEG = eeg_checkset(EEG);
+    
+    if EEG.srate==500;
+        EEG.data=EEG.data(:,1:2:end,:);
+        %EEG.srate=250;
+    end
+    %EEG = eeg_checkset(EEG);    
+
+    h=hanning(250);
+    hr=repmat(h,1,EEG.trials);
+
+    for i=1:size(EEG.data,1);
+        d=squeeze(EEG.data(i,:,:));    
+        dh=d.*hr;
+        f=fft(dh);
+        out.tfm(:,i)=mean(abs(f(1:125,:)),2);
+    end
+
+    
+    
+    % Load:
+    EEG = pop_loadset('filepath','','filename',singleSetFile);
+    EEG = eeg_checkset( EEG );
+    
+    % Removed flagged channels and time segments
+    sprintf('%s','Purging flagged channels...\n');
+    EEG = pop_marks_select_data(EEG,'channel marks',[],'labels',{'manual'},'remove','on');
+    EEG = pop_marks_select_data(EEG,'time marks',[],'labels',{'manual'},'remove','on');
+    EEG = pop_marks_select_data(EEG,'component marks',[],'labels',{'manual'},'remove','on');
+    EEG = eeg_checkset(EEG);
+    
+    EEG= warp_locs(EEG,'derivatives/lossless/code/misc/standard_1020_Fpz_FT7_FT8_Cz_PO7_PO8_Oz.elc','transform',[0,0,0,0,0,-1.57,1,1,1],'manual','off');
+    EEG = interp_mont(EEG,'derivatives/lossless/code/misc/standard_1020_Fpz_FT7_FT8_Cz_PO7_PO8_Oz.elc','manual','off');
+    EEG = eeg_checkset(EEG);
+    
+    EEG.icaact=[];
+    EEG.icawinv=[];
+    EEG.icasphere=[];
+    EEG.icaweights=[];
+    EEG.icachansind=[];
+    
+    % Window the continuous data
+    logging_log('INFO', 'Windowing the continous data...');
+    EEG = marks_continuous2epochs(EEG,'recurrence',0.5,'limits',[0,1],'keepboundary','off');
+    EEG = eeg_checkset(EEG);
+    
+    if EEG.srate==500;
+        EEG.data=EEG.data(:,1:2:end,:);
+        %EEG.srate=250;
+    end
+    %EEG = eeg_checkset(EEG);
+    
+    h=hanning(250);
+    hr=repmat(h,1,EEG.trials);
+
+    for i=1:size(EEG.data,1);
+        d=squeeze(EEG.data(i,:,:));    
+        dh=d.*hr;
+        f=fft(dh);
+        out.pfm(:,i)=mean(abs(f(1:125,:)),2);
+    end
+
+    
+    [path, name, ~]= fileparts(singleSetFile);
+    outfname = [path,'/',name, '_spect_diag.mat'];
+    disp(['Saving ' outfname '...']);
+    save(outfname,'out');
+end
+