New diagnostics scripts which build csvs added.

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

+% Root diagnostics file.
+% Argument should be a plaintext file listing the qcr's to be loaded
+% newFolder=$(date +%Y_%m_%d_%H_%M_%S)
+function main_diagnostics(filePath)
+    % Generate unique csv file
+    [~,fMod] = system('(date +%Y_%m_%d_%H_%M_%S)');
+    fName = ['diag_',strtrim(fMod),'.csv'];
+    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';
+    fprintf(fOut,'%s\n',header);
+    
+    % Read line by line of the specified diag list
+    fIn = fopen(filePath,'r');
+    tline = fgetl(fIn);
+    while ischar(tline)
+        single_diagnostic(fOut,tline);
+        tline = fgetl(fIn);
+    end
+    
+    % Proper form!
+    fclose(fIn);
+    fclose(fOut);
+end
\ No newline at end of file

derivatives/lossless/code/tools/diagnostics/single_diagnostic.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_diagnostic(fOutID, singleSetFile)
+    % Storing what's going to be written to the csv in a variable to act as
+    % a buffer. Line starts with filename.
+    outString = [singleSetFile, ','];
+
+    % Load:
+    EEG = pop_loadset('filepath','','filename',singleSetFile);
+    EEG = eeg_checkset( EEG );
+    
+    % Basic row info:
+    outString = [outString, num2str(EEG.nbchan), ','];
+    outString = [outString, num2str(EEG.pnts), ','];
+    outString = [outString, num2str(EEG.srate), ','];
+    
+    % All time_info flag enables 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.marks.time_info(3).flags == 1)) / EEG.srate), ','];
+    % ch_s_sd b 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
+    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
+    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
+    outString = [outString, num2str(length(find(EEG.marks.time_info(1).flags == 1 & EEG.marks.time_info(5).flags == 1)) / EEG.srate), ','];
+    % 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
+    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), ','];
+    
+    % Single chan_info flag enables in seconds:
+    for i=2:5 % [2,5] are ch_s_sd, ch_sd, low_r, and bridge respectively.
+        outString = [outString, num2str(length(find(EEG.marks.chan_info(i).flags==1))), ','];
+    end
+    
+    % 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]);
+    for i=1:length(quants)
+        outString = [outString, num2str(quants(i)), ','];
+    end
+    % Pre QC comp count:
+    outString = [outString, num2str(length(EEG.icachansind)), ','];
+    
+    % Final write - includes newline
+    fprintf(fOutID,'%s\n',outString);
+end
\ No newline at end of file