Merge remote-tracking branch 'cpp-lln-lab/master' into cer-readme_suggest

Author: CerenB

.travis.yml

@@ -44,7 +44,7 @@ before_script:
 jobs:
   include:
     - name: "BIDS validator: create and check dataset"
-      script: octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/rawdata/ --ignoreNiftiHeaders
+      script: octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/raw/ --ignoreNiftiHeaders
     - name: "miss_hit: checking code quality"
       script: mh_metric . --ci
     - name: "miss_hit: checking code style"

README.md

@@ -125,6 +125,10 @@ future BEP format in a dedicated eyetracker folder
 `<matches>[_recording-<label>]_stim.tsv.gz`
 `<matches>[_recording-<label>]_stim.json`
 
+### change log
+
+ <!-- 93b4c584bf22883a3c4f8b9031b70e381deef272 -->
+
 ###  3.3. <a name='Contributors'></a>Contributors ✨
 
 Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):

src/checkCFG.m

@@ -12,7 +12,9 @@
 
     %% list the defaults to set
 
-    fieldsToSet.verbose = false;
+    fieldsToSet.verbose = 0;
+
+    fieldsToSet.useGUI = false;
 
     fieldsToSet.fileName.task = '';
     fieldsToSet.fileName.zeroPadding = 3;

src/convertSourceToRaw.m

@@ -10,7 +10,7 @@ function convertSourceToRaw(cfg)
     % Only covers func folder at the moment
 
     sourceDir = fullfile(cfg.dir.output, 'source');
-    rawDir = fullfile(cfg.dir.output, 'rawdata');
+    rawDir = fullfile(cfg.dir.output, 'raw');
 
     % add dummy README and CHANGE file
     copyfile(fullfile( ...

src/createFilename.m

@@ -105,7 +105,7 @@
         'echo', ...
         'phaseEncodingDirection', ...
         'reconstruction', ...
-        'recording', ...
+        'recording' ...
         };
 
     targetFields = { ...
@@ -114,7 +114,7 @@
         'echo', ...
         'dir', ...
         'rec', ...
-        'recording', ...
+        'recording' ...
         };
 
     for iField = 1:numel(fields2Check)
@@ -146,10 +146,10 @@
     pattern = cfg.fileName.pattern;
 
     runSuffix = cfg.fileName.suffix.run;
-    acqSuffix = cfg.fileName.suffix.acquisition ;
-    ceSuffix = cfg.fileName.suffix.contrastEnhancement ;
-    dirSuffix = cfg.fileName.suffix.phaseEncodingDirection ;
-    recSuffix = cfg.fileName.suffix.reconstruction ;
+    acqSuffix = cfg.fileName.suffix.acquisition;
+    ceSuffix = cfg.fileName.suffix.contrastEnhancement;
+    dirSuffix = cfg.fileName.suffix.phaseEncodingDirection;
+    recSuffix = cfg.fileName.suffix.reconstruction;
     echoSuffix = cfg.fileName.suffix.echo;
     recordingSuffix = cfg.fileName.suffix.recording;
 
@@ -201,7 +201,7 @@
 
 function talkToMe(cfg)
 
-    if cfg.verbose
+    if cfg.verbose > 0
 
         fprintf(1, '\nData will be saved in this directory:\n\t%s\n', ...
             fullfile(cfg.dir.outputSubject, cfg.fileName.modality));

src/miss_hit.cfg

@@ -1,3 +1,10 @@
+# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
 regex_function_name: "[a-z]+(([A-Z]){1}[A-Za-z]+)*"
-suppress_rule: "copyright_notice"
+suppress_rule: "copyright_notice"
+
+# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
+metric "cnest": limit 4
+metric "file_length": limit 500
+metric "cyc": limit 15
+metric "parameters": limit 6

src/saveEventsFile.m

@@ -219,14 +219,14 @@ function printHeaderExtraColumns(logFile)
             warning('saveEventsFile:missingData', ...
                 'Missing some %s data for this event.', namesExtraColumns{iExtraColumn});
 
-            if cfg.verbose
+            if cfg.verbose > 1
                 disp(logFile(iEvent));
             end
 
         elseif ~ischar(data) && all(isnan(data))
             warning('Missing %s data for this event.', namesExtraColumns{iExtraColumn});
 
-            if cfg.verbose
+            if cfg.verbose > 1
                 disp(logFile(iEvent));
             end
         end
@@ -297,11 +297,11 @@ function printHeaderExtraColumns(logFile)
 
         else
 
-            printData(logFile(1).fileID, onset);
-            printData(logFile(1).fileID, duration);
-            printData(logFile(1).fileID, trial_type);
+            printData(logFile(1).fileID, onset, cfg);
+            printData(logFile(1).fileID, duration, cfg);
+            printData(logFile(1).fileID, trial_type, cfg);
 
-            printExtraColumns(logFile, iEvent);
+            printExtraColumns(logFile, iEvent, cfg);
 
             fprintf(logFile(1).fileID, '\n');
             fprintf(1, '\n');
@@ -311,7 +311,7 @@ function printHeaderExtraColumns(logFile)
 
 end
 
-function printExtraColumns(logFile, iEvent)
+function printExtraColumns(logFile, iEvent, cfg)
     % loops through the extra columns and print them
 
     namesExtraColumns = returnNamesExtraColumns(logFile);
@@ -320,26 +320,32 @@ function printExtraColumns(logFile, iEvent)
 
         data = logFile(iEvent).(namesExtraColumns{iExtraColumn});
 
-        printData(logFile(1).fileID, data);
+        printData(logFile(1).fileID, data, cfg);
 
     end
 
 end
 
-function printData(output, data)
+function printData(output, data, cfg)
     % write char
     % for numeric data we replace any nan by n/a
     if ischar(data)
         fprintf(output, '%s\t', data);
-        fprintf(1, '%s\t', data);
+        if cfg.verbose > 0
+            fprintf(1, '%s\t', data);
+        end
     else
         for i = 1:numel(data)
             if isnan(data(i))
                 fprintf(output, '%s\t', 'n/a');
-                fprintf(1, '%s\t', 'n/a');
+                if cfg.verbose > 0
+                    fprintf(1, '%s\t', 'n/a');
+                end
             else
                 fprintf(output, '%f\t', data(i));
-                fprintf(1, '%f\t', data(i));
+                if cfg.verbose > 0
+                    fprintf(1, '%f\t', data(i));
+                end
             end
         end
     end
@@ -384,7 +390,7 @@ function errorSaveEventsFile(identifier)
 
 function talkToMe(cfg, logFile)
 
-    if cfg.verbose
+    if cfg.verbose > 0
 
         fprintf(1, '\nData were saved in this file:\n\n%s\n\n', ...
             fullfile( ...

src/checkCppBidsDependencies.m src/subfun/checkCppBidsDependencies.msrc/checkCppBidsDependencies.m renamed to src/subfun/checkCppBidsDependencies.m

@@ -12,7 +12,7 @@ function checkCppBidsDependencies(cfg)
 
     elseif isempty(GITHUB_WORKSPACE)  % local
 
-        pth = fullfile(fileparts(mfilename('fullpath')), '..');
+        pth = fullfile(fileparts(mfilename('fullpath')), '..', '..');
         checkSubmodule(fullfile(pth, 'lib', 'JSONio'));
         checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'));
 

src/printCreditsCppBids.m src/subfun/printCreditsCppBids.msrc/printCreditsCppBids.m renamed to src/subfun/printCreditsCppBids.m

@@ -1,20 +1,25 @@
 function printCreditsCppBids(cfg)
 
-    verbose = true;
+    try
+        version = fileread(fullfile(fileparts(mfilename('fullpath')), ...
+            '..', '..', 'version.txt'));
+    catch
+        version = 'v1.0.0';
+    end
+
+    verbose = 2;
     if ~isempty(cfg) && isfield(cfg, 'verbose') && ~isempty(cfg.verbose)
         verbose = cfg.verbose;
     end
 
-    if verbose
-
-        version = '0.0.1';
+    if verbose > 1
 
         contributors = { ...
             'Rémi Gau', ...
             'Marco Barilari', ...
             'Ceren Battal'};
 
-        % DOI_URL = 'https://doi.org/10.5281/zenodo.3554331.';
+        DOI_URL = 'https://doi.org/10.5281/zenodo.4007674';
 
         repoURL = 'https://github.com/cpp-lln-lab/CPP_BIDS';
 
@@ -39,7 +44,7 @@ function printCreditsCppBids(cfg)
         end
         fprintf('\b\n\n');
 
-        % fprintf('Please cite using the following DOI: \n %s\n\n', DOI_URL)
+        fprintf('Please cite using the following DOI: \n %s\n\n', DOI_URL);
 
         fprintf('For bug report, suggestions or contributions see: \n %s\n\n', repoURL);
 

src/userInputs.m

@@ -15,16 +15,26 @@
         cfg = struct('debug', []);
     end
 
+    cfg = checkCFG(cfg);
+
     [cfg, responses] = setDefaultResponses(cfg);
 
     if ~cfg.debug.do
 
         questions = createQuestionList(cfg);
 
-        try
-            responses = askUserGui(questions, responses);
-        catch
+        if cfg.useGUI
+
+            try
+                responses = askUserGui(questions, responses);
+            catch
+                responses = askUserCli(questions, responses);
+            end
+
+        else
+
             responses = askUserCli(questions, responses);
+
         end
 
     end