mh fix

Author: Remi-Gau

src/defaults/Mapping.m

@@ -7,15 +7,15 @@
     %
     %   - mapping : (n X 1) structure with the following fiels
     %
-    %         - prefix 
-    %         - suffix 
-    %         - entities 
-    %         - ext 
+    %         - prefix
+    %         - suffix
+    %         - entities
+    %         - ext
     %         - name_spec: structure that must resemble the output of bids.internal.parse_filename
-    % 
+    %
     %   - cfg : describes the common properties to be used for several names in the output.
     %           See ``check_cfg``
-    % 
+    %
     %   - list of SPM prefixes from ``get_spm_prefix_list()``
     %
     %    - stc = ''
@@ -27,8 +27,8 @@
     %    - smooth = ''
     %
     % (C) Copyright 2021 spm_2_bids developers
-    
-    %TODO add a print_mapping method to allow easy visualization 
+
+    % TODO add a print_mapping method to allow easy visualization
     % of the input --> output relationship
 
     properties
@@ -61,7 +61,7 @@
             %
             %  map = Mapping(cfg)
             %
-            % 
+            %
 
             if nargin == 1
                 obj.cfg = cfg;
@@ -91,15 +91,15 @@
             %  map = add_mapping('prefix', prefix, 'suffix', 'entities', 'ext', 'name_spec')
             %
 
-            %TODO add possibility to pass "filter" arugment that is a structure
+            % TODO add possibility to pass "filter" arugment that is a structure
             % with shape (allows to chain the output from bids parsing)
             %
             % filter.prefix
             % filter.suffix
             % filter.entities
             % filter.ext
-            % 
-            
+            %
+
             p = inputParser;
 
             addParameter(p, 'prefix', obj.default_value);
@@ -163,7 +163,7 @@
             %
             %   map = map.default;
             %
-            
+
             prfx_spec = { ...
                          { obj.bias_cor },         obj.cfg.segment.bias_corrected; ...
                          { 'c1' },                 obj.cfg.segment.gm; ...
@@ -217,18 +217,18 @@
             addParameter(p, 'prefix', @ischar);
 
             parse(p, varargin{:});
-            
+
             available_mapped_prefixes = {obj.mapping.prefix}';
-            
+
             idx = strcmp(p.Results.prefix, available_mapped_prefixes);
 
         end
-        
+
         function obj = rm_mapping(obj, idx)
 
-              obj.mapping(idx) = [];
+            obj.mapping(idx) = [];
 
-        end        
+        end
 
     end
 end

src/defaults/check_cfg.m

@@ -122,8 +122,8 @@
                                                        'mode', 'image'), ...
                                                 'suffix', 'xfm');
 
-    segment.param = struct('label', 'TBD', 'suffix', 'segparam');                                            
-                                            
+    segment.param = struct('label', 'TBD', 'suffix', 'segparam');
+
     fields_to_set.segment = segment;
 
     % Preprocessed data

src/spm_2_bids.m

@@ -10,7 +10,7 @@
     % :param file: SPM preprocessed filename (can be fullpath);
     %              for example ``wmsub-01_ses-01_T1w.nii``
     % :type file: string
-    % :param map: optional spm_2_bids map to overwrite the default 
+    % :param map: optional spm_2_bids map to overwrite the default
     %             map (see Mapping)
     % :param map: Mapping object
     %
@@ -33,9 +33,9 @@
 
     mapping = map.mapping;
     cfg = map.cfg;
-    
+
     use_suffix_as_label = false;
-    
+
     % deal with suffixes modified by SPM
     % turns them into prefixes that can be handled by the default mapping
     if strfind(file, '_uw.mat') %#ok<*STRIFCND>
@@ -64,13 +64,13 @@
 
     % TODO se if some of the bids-query machinery cannot be kept for identifying
     % the right mapping
-    
+
     % look for the right prefix in the mapping
     prefix_match = map.find_mapping('prefix', p.prefix);
 
     % TODO implement methods in Mapping to filter by suffix / extention /
     % entities
-    
+
     % if any suffix / extention mentioned in the mapping we check for that as well
     % if none is mentioned anywhere in the mapping then anything goes
     suffix_match = true(size(mapping));
@@ -118,7 +118,7 @@
     end
 
     if isempty(spec)
-        %TODO this warning should probably go in the find_mapping methods
+        % TODO this warning should probably go in the find_mapping methods
         msg = sprintf('Unknown prefix: %s', p.prefix);
         warning('spm_2_bids:unknownPrefix', msg); %#ok<SPWRN>
         return
@@ -127,7 +127,7 @@
     spec = add_fwhm_to_smooth_label(spec, cfg);
 
     spec = adapt_from_label_to_input(spec, p);
-    
+
     if use_suffix_as_label
         spec.entities.label = p.suffix;
     end

tests/test_spm_2_bids.m

@@ -11,14 +11,14 @@
 function test_spm_2_bids_suffix()
 
     input_output = {
-    'sub-01_T1w_seg8.mat', 'sub-01_label-T1w_segparam.mat';
-    'sub-01_task-auditory_bold_uw.mat', 'sub-01_task-auditory_label-bold_unwarpparam.mat'};
+                    'sub-01_T1w_seg8.mat', 'sub-01_label-T1w_segparam.mat'
+                    'sub-01_task-auditory_bold_uw.mat', 'sub-01_task-auditory_label-bold_unwarpparam.mat'};
 
     for i = 1:numel(size(input_output, 1))
 
-        print_here('%s\n', input_output{i,1});
+        print_here('%s\n', input_output{i, 1});
 
-        filename = spm_2_bids(input_output{i,1});
+        filename = spm_2_bids(input_output{i, 1});
 
         expected = input_output{i, 2};
         assertEqual(filename, expected);