refactor and update copyright format

Author: Remi-Gau

src/Mapping.m

@@ -26,6 +26,7 @@
     %           - ``norm = ''``
     %           - ``smooth = ''``
     %
+
     % (C) Copyright 2021 spm_2_bids developers
 
     properties

src/defaults/check_cfg.m

@@ -48,6 +48,7 @@
     %
     %
     %
+
     % (C) Copyright 2021 spm_2_bids developers
 
     if nargin < 1

src/defaults/get_spm_prefix_list.m

@@ -6,6 +6,7 @@
     % is not there.
     %
     %
+
     % (C) Copyright 2021 spm_2_bids developers
 
     try

src/spm_2_bids.m

@@ -24,6 +24,7 @@
     % adapting the ``cfg``.
     %
     %
+
     % (C) Copyright 2021 spm_2_bids developers
 
     if nargin < 2 || isempty(map)

src/utils/add_deformation_field.m

@@ -0,0 +1,25 @@
+function sources = add_deformation_field(bf, sources, map, verbose)
+    % (C) Copyright 2021 spm_2_bids developers
+    if ~startsWith(bf.prefix, map.norm)
+        return
+    end
+
+    % 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) && ~isempty(map.cfg.schema.find_suffix_group('anat', bf.suffix)))
+
+        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
+        deformation_field = 'TODO: add deformation field';
+
+    end
+
+    sources{end + 1, 1} = deformation_field;
+
+end

src/utils/check_dependencies.m

@@ -8,6 +8,7 @@ function check_dependencies()
     %   check_dependencies()
     %
     %
+
     % (C) Copyright 2019 spm_2_bids developers
 
     fprintf('Checking dependencies\n');

src/utils/check_field_content.m

@@ -1,5 +1,6 @@
 function status = check_field_content(struct_one, struct_two)
     %
+
     % (C) Copyright 2021 spm_2_bids developers
 
     status = true;

src/utils/get_version.m

@@ -9,6 +9,7 @@
     %
     % :returns: :version_number: (string) Use semantic versioning format (like v0.1.0)
     %
+
     % (C) Copyright 2020 spm_2_bids developers
 
     try

src/utils/identify_rawsources.m

@@ -16,6 +16,7 @@
     % :type verbose: boolean
     %
     %
+
     % (C) Copyright 2021 spm_2_bids developers
 
     % TODO mean may involve several files from the source (across runs

src/utils/identify_sources.m

@@ -16,6 +16,7 @@
     % :param verbose: Defaults to ``true``
     % :type verbose: boolean
     %
+
     % (C) Copyright 2021 spm_2_bids developers
 
     % "r" could mean realigned or resliced...
@@ -117,89 +118,6 @@
 
 end
 
-function sources = add_deformation_field(bf, sources, map, verbose)
-
-    if ~startsWith(bf.prefix, map.norm)
-        return
-    end
-
-    % 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) && ~isempty(map.cfg.schema.find_suffix_group('anat', bf.suffix)))
-
-        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
-        deformation_field = 'TODO: add deformation field';
-
-    end
-
-    sources{end + 1, 1} = deformation_field;
-
-end
-
-function [status, bf] = update_prefix(bf, map)
-
-    status = 2;
-
-    if length(bf.prefix) < 2
-        % TODO: files that have been realigned but not resliced have no
-        % "prefix" so we may miss some transformation
-        status = 0;
-        return
-    end
-
-    % remove the prefix of the last step
-    if startsWith(bf.prefix, map.smooth)
-
-        % in case the prefix includes a number to denotate the FXHM used
-        % for smoothing
-        starts_with_fwhm = regexp(bf.prefix, '^s[0-9]*', 'match');
-        if ~isempty(starts_with_fwhm)
-            bf = shorten_prefix(bf, length(starts_with_fwhm{1}));
-        else
-            bf = shorten_prefix(bf, 1);
-        end
-
-    elseif startsWith(bf.prefix, map.unwarp)
-        bf = shorten_prefix(bf, 1);
-
-    elseif startsWith(bf.prefix, map.norm)
-        bf = shorten_prefix(bf, 1);
-
-    elseif startsWith(bf.prefix, ['rp_' map.stc])
-        bf = shorten_prefix(bf, 3);
-
-    elseif startsWith(bf.prefix, 'mean')
-        % TODO mean may involve several files from the source (across runs
-        % and sessions
-        %     prefixes = {
-        %                 'mean'
-        %                 'meanu'
-        %                 'meanua'
-        %                };
-        status = 1;
-        return
-
-    elseif ismember(bf.prefix(1:2), {'c1', 'c2', 'c3', 'c4', 'c5'})
-        % bias corrected image
-        status = 1;
-        return
-
-    else
-        % no idea
-        status = 1;
-        return
-
-    end
-
-end
-
 function bf = shorten_prefix(bf, len)
     bf.prefix = bf.prefix((len + 1):end);
 end