rely on prefixes stored in map rather than rely on hardcoded values

Author: Remi-Gau

src/utils/identify_rawsources.m

@@ -27,8 +27,6 @@
     %                 'wmeanu'
     %                };
 
-    % TODO adapt in case prefixes have been changed from SPM defaults
-
     rawsource = '';
 
     if nargin < 1 || isempty(derivatives)

src/utils/identify_sources.m

@@ -97,7 +97,7 @@
     % anything prefix based
     if prefix_based
 
-        [status, bf] = update_prefix(bf);
+        [status, bf] = update_prefix(bf, map);
 
         if status == 0
             return
@@ -119,7 +119,7 @@
 
 function sources = add_deformation_field(bf, sources, map, verbose)
 
-    if ~startsWith(bf.prefix, 'w')
+    if ~startsWith(bf.prefix, map.norm)
         return
     end
 
@@ -143,7 +143,7 @@
 
 end
 
-function [status, bf] = update_prefix(bf)
+function [status, bf] = update_prefix(bf, map)
 
     status = 2;
 
@@ -155,7 +155,7 @@
     end
 
     % remove the prefix of the last step
-    if startsWith(bf.prefix, 's')
+    if startsWith(bf.prefix, map.smooth)
 
         % in case the prefix includes a number to denotate the FXHM used
         % for smoothing
@@ -166,13 +166,13 @@
             bf = shorten_prefix(bf, 1);
         end
 
-    elseif startsWith(bf.prefix, 'u')
+    elseif startsWith(bf.prefix, map.unwarp)
         bf = shorten_prefix(bf, 1);
 
-    elseif startsWith(bf.prefix, 'w')
+    elseif startsWith(bf.prefix, map.norm)
         bf = shorten_prefix(bf, 1);
 
-    elseif startsWith(bf.prefix, 'rp_a')
+    elseif startsWith(bf.prefix, ['rp_' map.stc])
         bf = shorten_prefix(bf, 3);
 
     elseif startsWith(bf.prefix, 'mean')

tests/test_spm_2_bids_metadata.m

@@ -31,9 +31,9 @@ function test_spm_2_bids_metadata_func()
 
     assertEqual(fieldnames(json), {'filename'; 'content'});
     assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_task-foo_bold.nii.gz');
-    assertEqual(json.content.Sources{1}, ...
+    assertEqual(json.content.Sources{2}, ...
                 'sub-01/sub-01_task-foo_space-individual_desc-realignUnwarp_bold.nii');
-    assertEqual(json.content.Sources{2}, 'TODO: add deformation field');
+    assertEqual(json.content.Sources{1}, 'TODO: add deformation field');
 
     bids.util.jsonencode(json.filename, json.content);
 
@@ -47,7 +47,7 @@ function test_spm_2_bids_non_raw_suffix()
 
     assertEqual(fieldnames(json), {'filename'; 'content'});
     assertEqual(json.content.RawSources{1}, 'TODO');
-    assertEqual(json.content.Sources{1}, 'TODO');
+    assertEqual(json.content.Sources{end}, 'TODO');
 
     bids.util.jsonencode(json.filename, json.content);
 
@@ -61,7 +61,7 @@ function test_spm_2_bids_metadata_surface()
 
     assertEqual(fieldnames(json), {'filename'; 'content'});
     assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_T1w.nii.gz');
-    assertEqual(json.content.Sources{1}, ...
+    assertEqual(json.content.Sources{end}, ...
                 'sub-01/sub-01_space-IXI549Space_desc-preproc_T1w.nii');
 
     bids.util.jsonencode(json.filename, json.content);
@@ -90,7 +90,7 @@ function test_spm_2_bids_metadata_smoothed_data()
 
     assertEqual(fieldnames(json), {'filename'; 'content'});
     assertEqual(json.content.RawSources{1}, 'sub-01/sub-01_task-auditory_bold.nii.gz');
-    assertEqual(json.content.Sources{1}, ...
+    assertEqual(json.content.Sources{end}, ...
                 'sub-01/sub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii');
 
     bids.util.jsonencode(json.filename, json.content);