make the copy atlas functional optionally verbose

Author: Remi-Gau

docs/source/atlas.rst

@@ -6,3 +6,4 @@ Atlas
 .. autofunction:: extractRoiFromAtlas
 .. autofunction:: extractRoiByLabel
 .. autofunction:: labelClusters
+.. autofunction:: copyAtlasToSpmDir

src/atlas/copyAtlasToSpmDir.m

@@ -1,54 +1,68 @@
-function copyAtlasToSpmDir(atlas)
+function copyAtlasToSpmDir(varargin)
   %
-  % copies a given atlas to the SPM atlas dir
+  % Copies a given atlas to the SPM atlas directory.
   %
   % USAGE::
   %
-  %   copyAtlasToSpmDir(atlas)
+  %   copyAtlasToSpmDir(atlas, 'verbose', false)
   %
   % :param atlas: Any of ``{'AAL'}``. Defaults to ``'AAL'``
   % :type  atlas: char
   %
-  % (C) Copyright 2022 CPP_SPM developers
-  
-  if nargin < 1
-    atlas = 'AAL';
-  end
-  
+  % :param verbose: Defaults to ``false``
+  % :type  verbose: boolean
+  %
+  %
+  % (C) Copyright 2022 CPP ROI developers
+
+  args = inputParser;
+
+  addOptional(args, 'atlas', 'AAL', @ischar);
+  addParameter(args, 'verbose', false, @islogical);
+
+  parse(args, varargin{:});
+
+  atlas = args.Results.atlas;
+  verbose = args.Results.verbose;
+
   spmAtlasDir = fullfile(spm('dir'), 'atlas');
   cppRoiAtlasDir = returnAtlasDir();
-  
+
   switch lower(atlas)
-    
+
     case 'aal'
       sourceAtlasImage = fullfile(cppRoiAtlasDir, 'AAL3', 'AAL3v1_1mm.nii.gz');
       sourceAtlasXml = fullfile(cppRoiAtlasDir, 'AAL3', 'AAL3v1_1mm.xml');
   end
-  
+
   targetAtlasImage = fullfile(spmAtlasDir, spm_file(sourceAtlasImage, 'filename'));
   targetAtlasXml = fullfile(spmAtlasDir, spm_file(sourceAtlasXml, 'filename'));
-  
+
   atlasPresent = isdir(spmAtlasDir) && ...
-                 exist(targetAtlasImage(1:end-3), 'file') && ...
+                 exist(targetAtlasImage(1:end - 3), 'file') && ...
                  exist(targetAtlasXml, 'file');
-  
+
   if ~atlasPresent
-    fprintf('\nCopying atlas "%s" to spm atlas directory:\n\t%s\n', ...
-            atlas, ...
-            spmAtlasDir)
+    if verbose
+      fprintf('\nCopying atlas "%s" to spm atlas directory:\n\t%s\n', ...
+              atlas, ...
+              spmAtlasDir);
+    end
     spm_mkdir(spmAtlasDir);
-    
+
     copyfile(sourceAtlasImage, spmAtlasDir);
-    gunzip(fullfile(spmAtlasDir, '*.nii.gz'))
-    delete(fullfile(spmAtlasDir, '*.nii.gz'))
-    
+    gunzip(fullfile(spmAtlasDir, '*.nii.gz'));
+    delete(fullfile(spmAtlasDir, '*.nii.gz'));
+
     copyfile(sourceAtlasXml, spmAtlasDir);
-    
+
   else
-    fprintf('\nAtlas "%s" already in spm atlas directory:\n\t%s\n', ...
-      atlas, ...
-      spmAtlasDir)
-    
+    if verbose
+      fprintf('\nAtlas "%s" already in spm atlas directory:\n\t%s\n', ...
+              atlas, ...
+              spmAtlasDir);
+    end
+
   end
-  
-end
+
+end