Update new diagnostics to include more info

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,quant_0.05,quant_0.15,quant_0.25,quant_0.5,quant_0.75,quant_0.85,quant_0.95,pre_qc_comp';
+    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';
     fprintf(fOut,'%s\n',header);
     
     % Read line by line of the specified diag list

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

@@ -6,6 +6,9 @@ function single_diagnostic(fOutID, singleSetFile)
     % a buffer. Line starts with filename.
     outString = [singleSetFile, ','];
 
+    % Quantile breakdown used as a constant:
+    quantBreakdown = [0.05,0.15,0.25,0.5,0.75,0.85,0.95];
+    
     % Load:
     EEG = pop_loadset('filepath','','filename',singleSetFile);
     EEG = eeg_checkset( EEG );
@@ -49,12 +52,29 @@ function single_diagnostic(fOutID, singleSetFile)
     % Amica diagnostic info:
     outString = [outString, num2str(mean(EEG.amica(2).models.Lt)), ','];
     outString = [outString, num2str(std(EEG.amica(2).models.Lt)), ','];
-    quants = quantile(EEG.amica(2).models.Lt,[0.05,0.15,0.25,0.5,0.75,0.85,0.95]);
+    quants = quantile(EEG.amica(2).models.Lt,quantBreakdown);
     for i=1:length(quants)
         outString = [outString, num2str(quants(i)), ','];
     end
-    % Pre QC comp count:
-    outString = [outString, num2str(length(EEG.icachansind)), ','];
+    % Manual QC comp count:
+    outString = [outString, num2str(length(find(EEG.marks.comp_info(1).flags == 1))), ','];
+    % Components marked as ic_rt
+    outString = [outString, num2str(length(find(EEG.marks.comp_info(2).flags == 1))), ','];
+    
+    % ISCtest:
+    a = [];
+    for i=2:length(EEG.amica);
+        a(:,:,i-1)=EEG.amica(i).models(1).A;
+    end
+    [~,~,linkpvalues,~] = isctest(a,0.05,0.05,'mixing');
+    outString = [outString, num2str(mean(linkpvalues)), ','];
+    outString = [outString, num2str(std(linkpvalues)), ','];
+    quants = quantile(linkpvalues,quantBreakdown);
+    for i=1:length(quants)
+        outString = [outString, num2str(quants(i)), ','];
+    end
+    
+    % disp('hold');
     
     % Final write - includes newline
     fprintf(fOutID,'%s\n',outString);