final touches

Author: Remi-Gau

.travis.yml

@@ -19,11 +19,8 @@ before_install:
 
 
 install:
-  # Install JSONio
-  #- travis_retry git clone git://github.com/gllmflndn/JSONio.git --depth 1
+  # make octave file for JSONio
   - cd lib/JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ../..
-  #- octave $OCTFLAGS --eval "addpath (fullfile (pwd, 'JSONio')); savepath ();"
-  # Install BIDS-MATLAB
   - octave $OCTFLAGS --eval "addpath (pwd); savepath ();"
   # Install BIDS-Validator
   - sudo npm install -g bids-validator
@@ -41,5 +38,5 @@ jobs:
       name: "miss_hit linter" # names the second job
     - stage: "BIDS validator"
       name: "create and check dataset" # names the second job
-    - script: octave $OCTFLAGS --eval "makeRawDataset_test" && bids-validator `pwd`/../output/rawdata/ --ignoreNiftiHeaders
+      script: octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/../output/rawdata/ --ignoreNiftiHeaders
 

README.md

@@ -127,16 +127,17 @@ logFile.extraColumns = {'Speed', 'is_Fixation'};
 
 [cfg, expParameters] = createFilename(cfg, expParameters);
 
-% dummy call to initialize the logFile variable
-logFile = saveEventsFile('open', expParameters, logFile);
+% initialize the logFile variable
+[logFile] = saveEventsFile('init', expParameters, logFile);
 
 % set the real length we really want
 logFile.extraColumns.Speed.length = 12;
 
-% actual inititalization
+% open the file
 logFile = saveEventsFile('open', expParameters, logFile);
 ```
 
+
 ## Functions descriptions
 
 ### userInputs

saveEventsFile.m

@@ -171,6 +171,8 @@
 end
 
 function logFile = initializeFile(expParameters, logFile)
+    
+    createDataDictionary(expParameters, logFile);
 
     logFile = initializeExtraColumns(logFile);
 
@@ -214,36 +216,6 @@ function printHeaderExtraColumns(logFile)
 
 end
 
-function data = checkInput(data, expectedLength)
-    % check the data to write
-    % default will be 'n/a' for chars and NaN for numeric data
-    % for numeric data that don't have the expected length, it will be padded with NaNs
-
-    if nargin < 2
-        expectedLength = [];
-    end
-
-    if ischar(data) && isempty(data) || strcmp(data, ' ')
-        data = 'n/a';
-    elseif isempty(data)
-        % important to not set this to n/a as we still need to check if this
-        % numeric valur has the right length and needs to be nan padded
-        data = nan;
-    end
-
-    if islogical(data) && data
-        data = 'true';
-    elseif islogical(data) && ~data
-        data = 'false';
-    end
-
-    if ~isempty(expectedLength) && isnumeric(data) && max(size(data)) < expectedLength
-        padding = expectedLength - max(size(data));
-        data(end + 1:end + padding) = nan(1, padding);
-    end
-
-end
-
 function logFile = checkExtracolumns(logFile, iEvent)
     % loops through the extra columns
     % if the field we are looking for does not exist or is empty in the
@@ -277,6 +249,40 @@ function printHeaderExtraColumns(logFile)
 
 end
 
+function data = checkInput(data, expectedLength)
+    % check the data to write
+    % default will be 'n/a' for chars and NaN for numeric data
+    % for numeric data that don't have the expected length, it will be padded with NaNs
+
+    if nargin < 2
+        expectedLength = [];
+    end
+    
+    if islogical(data) && data
+        data = 'true';
+    elseif islogical(data) && ~data
+        data = 'false';
+    end
+    
+
+    if ischar(data) && isempty(data) || strcmp(data, ' ')
+        data = 'n/a';
+    elseif isempty(data)
+        % important to not set this to n/a as we still need to check if this
+        % numeric valur has the right length and needs to be nan padded
+        data = nan;
+    end
+
+    if ~isempty(expectedLength) && isnumeric(data) && max(size(data)) < expectedLength
+        padding = expectedLength - max(size(data));
+        data(end + 1:end + padding) = nan(1, padding);
+    elseif ~isempty(expectedLength) && isnumeric(data) && max(size(data)) > expectedLength
+        data = data(1:expectedLength);
+        warning('A field for this event is longer than expected. Truncating the extra values.')
+    end
+
+end
+
 function printExtraColumns(logFile, iEvent)
     % loops through the extra columns and print them
 

tests/test_makeRawDataset.m

@@ -27,8 +27,6 @@ function test_makeRawDataset()
 
     cfg.testingDevice = 'mri';
 
-    cfg.testingDevice = 'pc';
-
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
     logFile.extraColumns.is_Fixation.length = 1;
@@ -40,7 +38,6 @@ function test_makeRawDataset()
     % create the events file and header
     logFile = saveEventsFile('open', expParameters, logFile);
 
-    createDataDictionary(expParameters, logFile);
     createBoldJson(expParameters);
     createDatasetDescription(expParameters);