refactor

Author: Remi-Gau

src/utils/add_deformation_field.m

@@ -0,0 +1,46 @@
+function sources = add_deformation_field(sources, bf, map, verbose, deformation_field_needed)
+    % (C) Copyright 2021 spm_2_bids developers
+    
+    deformation_field = 'TODO: add deformation field';
+
+    % TODO? grab all the anat suffixes from BIDS schema?
+    covered_suffixes = {'T1w', ...
+                        'T2w', ...
+                        'PDw', ...
+                        'T2starw', ...
+                        'inplaneT1', ...
+                        'inplaneT2', ...
+                        'PD', ...
+                        'PDT2', ...
+                        'T2star', ...
+                        'FLASH', ...
+                        'T1map', ...
+                        'T2map', ...
+                        'T2starmap', ...
+                        'R1map', ...
+                        'R2map', ...
+                        'R2starmap', ...
+                        'PDmap', ...
+                        'UNIT1'};
+
+    if deformation_field_needed
+
+        % for anatomical data we assume that
+        % the deformation field comes from the anatomical file itself
+        if (~isempty(bf.modality) && ismember(bf.modality, {'anat'})) || ...
+           (~isempty(bf.suffix) && ismember(bf.suffix, covered_suffixes))
+
+            bf.prefix = 'y_';
+            bf = bf.update;
+            new_filename = spm_2_bids(bf.filename, map, verbose);
+            deformation_field = fullfile(bf.bids_path, new_filename);
+
+            % otherwise we can't guess it just from the file name
+        else
+
+        end
+
+        sources{2, 1} = deformation_field;
+
+    end
+end

src/utils/identify_sources.m

@@ -136,48 +136,3 @@
 
 end
 
-function sources = add_deformation_field(sources, bf, map, verbose, deformation_field_needed)
-
-    deformation_field = 'TODO: add deformation field';
-
-    % TODO? grab all the anat suffixes from BIDS schema?
-    covered_suffixes = {'T1w', ...
-                        'T2w', ...
-                        'PDw', ...
-                        'T2starw', ...
-                        'inplaneT1', ...
-                        'inplaneT2', ...
-                        'PD', ...
-                        'PDT2', ...
-                        'T2star', ...
-                        'FLASH', ...
-                        'T1map', ...
-                        'T2map', ...
-                        'T2starmap', ...
-                        'R1map', ...
-                        'R2map', ...
-                        'R2starmap', ...
-                        'PDmap', ...
-                        'UNIT1'};
-
-    if deformation_field_needed
-
-        % for anatomical data we assume that
-        % the deformation field comes from the anatomical file itself
-        if (~isempty(bf.modality) && ismember(bf.modality, {'anat'})) || ...
-           (~isempty(bf.suffix) && ismember(bf.suffix, covered_suffixes))
-
-            bf.prefix = 'y_';
-            bf = bf.update;
-            new_filename = spm_2_bids(bf.filename, map, verbose);
-            deformation_field = fullfile(bf.bids_path, new_filename);
-
-            % otherwise we can't guess it just from the file name
-        else
-
-        end
-
-        sources{2, 1} = deformation_field;
-
-    end
-end