update converting scripts

Author: Remi-Gau

.travis.yml

@@ -36,7 +36,7 @@ jobs:
       script: octave $OCTFLAGS --eval "results = runTests; assert(all(~[results.Failed]))"
     - stage: "BIDS validator"
       name: "Create and check dataset"
-      script: octave $OCTFLAGS --eval "testmanual_makeRawDataset" && bids-validator `pwd`/../output/rawdata/ --ignoreNiftiHeaders
+      script: cd manualTests && octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/../output/rawdata/ --ignoreNiftiHeaders
     - stage: "Linter"
       name: "miss_hit"
       script: cd .. && mh_style `pwd`

convertSourceToRaw.m

@@ -1,11 +1,15 @@
 function convertSourceToRaw(cfg)
 
-    sourceDir = fullfile(cfg.outputDir, 'source');
-    rawDir = fullfile(cfg.outputDir, 'rawdata');
+    sourceDir = fullfile(cfg.dir.output, 'source');
+    rawDir = fullfile(cfg.dir.output, 'rawdata');
 
     % add dummy readme and change file
-    copyfile(fullfile('..', 'dummyData', 'README'), sourceDir);
-    copyfile(fullfile('..', 'dummyData', 'CHANGES'), sourceDir);
+    copyfile(fullfile( ...
+        fileparts(mfilename('fullpath')), 'dummyData', 'README'), ...
+        sourceDir);
+    copyfile(fullfile( ...
+        fileparts(mfilename('fullpath')), 'dummyData', 'CHANGES'), ...
+        sourceDir);
 
     copyfile(sourceDir, rawDir);
 

tests/manualTests/test_makeRawDataset.m

@@ -14,16 +14,16 @@ function test_makeRawDataset()
 
     %%% set up
 
-    cfg.subjectNb = 1;
-    cfg.runNb = 1;
-    cfg.task = 'testtask';
-    cfg.outputDir = outputDir;
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+    cfg.task.name = 'testtask';
+    cfg.dir.output = outputDir;
 
     cfg.bids.datasetDescription.Name = 'dummy';
     cfg.bids.datasetDescription.BIDSVersion = '1.0.0';
     cfg.bids.datasetDescription.Authors = {'Jane Doe', 'John Doe'};
 
-    cfg.bids.MRI.RepetitionTime = 1.56;
+    cfg.bids.mri.RepetitionTime = 1.56;
 
     cfg.testingDevice = 'mri';
 
@@ -74,10 +74,10 @@ function test_makeRawDataset()
     saveEventsFile('close', cfg, logFile);
 
     % add dummy functional data
-    funcDir = fullfile(cfg.outputDir, 'source', 'sub-001', 'ses-001', 'func');
+    funcDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001', 'func');
     boldFilename = 'sub-001_ses-001_task-testtask_run-001_bold.nii.gz';
     copyfile( ...
-        fullfile('..', 'dummyData', 'dummyData.nii.gz'), ...
+        fullfile('..', '..', 'dummyData', 'dummyData.nii.gz'), ...
         fullfile(funcDir, boldFilename));
 
     %%