extract sub function in identify sources

Author: Remi-Gau

.gitignore

@@ -3,6 +3,7 @@
 .vscode
 
 *.json
+mapping.md
 
 env/
 

miss_hit.cfg

@@ -17,5 +17,5 @@ copyright_entity: "spm_2_bids developers"
 # metric for code quality
 metric "cnest": limit 5
 metric "file_length": limit 500
-metric "cyc": limit 16
+metric "cyc": limit 15
 metric "parameters": limit 6

src/utils/identify_sources.m

@@ -32,28 +32,7 @@
 
     prefix_based = true;
 
-    add_deformation_field = false;
-    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'};
+    deformation_field_needed = false;
 
     args = inputParser;
 
@@ -118,12 +97,12 @@
 
                 bf.prefix = bf.prefix(2:end);
 
-                add_deformation_field = true;
+                deformation_field_needed = true;
 
             elseif bids.internal.starts_with(bf.prefix, 'w')
 
                 bf.prefix = bf.prefix(2:end);
-                add_deformation_field = true;
+                deformation_field_needed = true;
 
             elseif bids.internal.starts_with(bf.prefix, 'rp_a')
 
@@ -153,7 +132,35 @@
 
     sources{1, 1} = fullfile(bf.bids_path, new_filename);
 
-    if add_deformation_field
+    sources = add_deformation_field(sources, bf, map, verbose, deformation_field_needed);
+
+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
@@ -173,5 +180,4 @@
         sources{2, 1} = deformation_field;
 
     end
-
 end