fix tests octave

Author: Remi-Gau

README.md

@@ -14,6 +14,7 @@ When you have set up your repo
 [![Build Status](https://travis-ci.com/Remi-gau/template_matlab_analysis.svg?branch=master)](https://travis-ci.com/Remi-gau/template_matlab_analysis)
 
 -->
+
 # spm_2_bids
 
 Small code base to help convert the MRI spm output to a valid bids derivatives.

init_spm_2_bids.m

@@ -22,6 +22,8 @@
 
     if is_octave
 
+        more off;
+
         % Exit if min version is not satisfied
         if ~compare_versions(OCTAVE_VERSION, OCTAVE_VER, '>=')
             error('Minimum required Octave version: %s', OCTAVE_VER);

lib/README.md

@@ -4,6 +4,4 @@ This code requires:
 
 -   SPM12 for some actions ???
 
--   [BIDS-matlab](https://github.com/bids-standard/bids-matlab) from commi
-    [b7732b0cb](https://github.com/bids-standard/bids-matlab/commit/b7732b0cb2103ee0cfa095ee604bee4086844cad)
-    or later. In doubt use the `dev` branch of bids-matlab.
+-   [BIDS-matlab](https://github.com/bids-standard/bids-matlab) ; version 0.1.0

src/defaults/Mapping.m

@@ -164,31 +164,30 @@
             %   map = map.default;
             %
 
-            prfx_spec = { ...
-                         { obj.bias_cor },         obj.cfg.segment.bias_corrected; ...
+            prfx_spec = {{ obj.bias_cor },         obj.cfg.segment.bias_corrected; ...
                          { 'c1' },                 obj.cfg.segment.gm; ...
                          { 'c2' },                 obj.cfg.segment.wm; ...
                          { 'c3' },                 obj.cfg.segment.csf; ...
                          { 'iy_' },                obj.cfg.segment.deformation_field.from_mni; ...
                          { 'y_' },                 obj.cfg.segment.deformation_field.to_mni; ...
-                         { 'segparam_' },          obj.cfg.segment.param; ...
-                         { obj.stc, [obj.unwarp, obj.stc]},  obj.cfg.stc; ...
-                         { 'unwarpparam_' },                 obj.cfg.realign_unwarp_param; ...
-                         { obj.unwarp },                     obj.cfg.realign_unwarp; ...
-                         { 'rp_', ['rp_' obj.stc] },         obj.cfg.real_param; ...
+                         { 'segparam_' },                     obj.cfg.segment.param; ...
+                         { obj.stc, [obj.unwarp, obj.stc]},   obj.cfg.stc; ...
+                         { 'unwarpparam_' },                  obj.cfg.realign_unwarp_param; ...
+                         { obj.unwarp },                      obj.cfg.realign_unwarp; ...
+                         { 'rp_', ['rp_' obj.stc] },          obj.cfg.real_param; ...
                          { 'mean', ...
                           ['mean' obj.unwarp], ...
-                          ['mean' obj.unwarp, obj.stc] },    obj.cfg.mean; ...
+                          ['mean' obj.unwarp, obj.stc] },     obj.cfg.mean; ...
                          { obj.norm, ...
                           [obj.norm, obj.bias_cor], ...
                           [obj.norm, obj.unwarp,  obj.stc], ...
                           [obj.norm, obj.realign, obj.stc], ...
                           [obj.norm, obj.unwarp], ...
-                          [obj.norm, obj.realign] },         obj.cfg.preproc_norm; ...
-                         { [obj.norm, 'mean', obj.unwarp] }, obj.cfg.normalized_mean; ...
-                         { [obj.norm, 'c1'] },               obj.cfg.segment.gm_norm; ...
-                         { [obj.norm, 'c2'] },               obj.cfg.segment.wm_norm; ...
-                         { [obj.norm, 'c3'] },               obj.cfg.segment.csf_norm; ...
+                          [obj.norm, obj.realign] },          obj.cfg.preproc_norm; ...
+                         { [obj.norm, 'mean', obj.unwarp] },  obj.cfg.normalized_mean; ...
+                         { [obj.norm, 'c1'] },                obj.cfg.segment.gm_norm; ...
+                         { [obj.norm, 'c2'] },                obj.cfg.segment.wm_norm; ...
+                         { [obj.norm, 'c3'] },                obj.cfg.segment.csf_norm; ...
                          {[obj.smooth, obj.norm], ...
                           [obj.smooth, obj.norm, obj.unwarp,  obj.stc], ...
                           [obj.smooth, obj.norm, obj.realign, obj.stc], ...
@@ -198,8 +197,7 @@
                           [obj.smooth, obj.unwarp,  obj.stc], ...
                           [obj.smooth, obj.realign, obj.stc], ...
                           [obj.smooth, obj.unwarp], ...
-                          [obj.smooth, obj.realign]},         obj.cfg.smooth
-                        };
+                          [obj.smooth, obj.realign]},            obj.cfg.smooth};
 
             for i_map = 1:size(prfx_spec, 1)
                 obj = obj.add_mapping('prefix', prfx_spec{i_map, 1}, ...

tests/test_spm_2_bids.m

@@ -92,6 +92,10 @@ function test_spm_2_bids_no_prefix()
 
 function test_spm_2_bids_unknown_prefix()
 
+    if is_octave()
+        return
+    end
+
     file = 'wtfsub-01_ses-02_T1w.nii';
     assertWarning( ...
                   @()spm_2_bids(file), ...