fix realign unwarp and stc

Remi-Gau · Remi-Gau · commit be3fdc24e500 · 2022-05-19T09:13:34.000+02:00
diff --git a/run_tests.m b/run_tests.m
@@ -1,7 +1,13 @@
 % (C) Copyright 2019 spm_2_bids developers
 
-folderToCover = fullfile(pwd, 'src');
-testFolder = fullfile(pwd, 'tests');
+thisDir = fullfile(fileparts(mfilename('fullpath')));
+
+if isdir(fullfile(thisDir, 'lib', 'bids-matlab'))
+    addpath(fullfile(thisDir, 'lib', 'bids-matlab'));
+end
+
+folderToCover = fullfile(thisDir, 'src');
+testFolder = fullfile(thisDir, 'tests');
 
 success = moxunit_runtests(testFolder, ...
                            '-verbose', '-recursive', '-with_coverage', ...
diff --git a/src/defaults/Mapping.m b/src/defaults/Mapping.m
@@ -180,7 +180,7 @@
                          { obj.unwarp, [obj.unwarp, obj.stc] }, obj.cfg.realign_unwarp; ...
                          { 'rp_', ['rp_' obj.stc] },          obj.cfg.real_param; ...
                          { 'mean', ...
-                          ['mean' obj.unwarp], ...      
+                          ['mean' obj.unwarp], ...
                           ['mean' obj.unwarp, obj.stc] },     obj.cfg.mean; ...
                          { obj.norm, ...
                           [obj.norm, obj.bias_cor], ...
diff --git a/src/defaults/check_cfg.m b/src/defaults/check_cfg.m
@@ -68,6 +68,7 @@
 
     fields_to_set.space = SPM_SPACE;
 
+    % just to keep track of all the BIDS entities in the cfg
     bidsFile = bids.File('sub-01_T1.nii', 'use_schema', false);
     bidsFile = bidsFile.reorder_entities;
     fields_to_set.all_entity_order = bidsFile.entity_order;
diff --git a/src/defaults/get_spm_prefix_list.m b/src/defaults/get_spm_prefix_list.m
@@ -1,6 +1,9 @@
 function prefix_list = get_spm_prefix_list()
     %
     % load SPM default prefix values
+    % or use a hard coded one it this fails:
+    % can be useful for testing when spm
+    % is not there.
     %
     %
     % (C) Copyright 2021 spm_2_bids developers

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,9 @@`
`1`	`1`	`function prefix_list = get_spm_prefix_list()`
`2`	`2`	`%`
`3`	`3`	`% load SPM default prefix values`
	`4`	`+ % or use a hard coded one it this fails:`
	`5`	`+ % can be useful for testing when spm`
	`6`	`+ % is not there.`
`4`	`7`	`%`
`5`	`8`	`%`
`6`	`9`	`% (C) Copyright 2021 spm_2_bids developers`