From bb4f7e447daf3076271e3059b54b92fe024cf57b Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 8 Apr 2024 17:41:25 +0200
Subject: [PATCH] fix

---
 src/Mapping.m                    | 103 +++++++++++++------------------
 src/utils/prepare_for_printing.m |   8 ++-
 2 files changed, 48 insertions(+), 63 deletions(-)

diff --git a/src/Mapping.m b/src/Mapping.m
index 062b744..90e3e3e 100644
--- a/src/Mapping.m
+++ b/src/Mapping.m
@@ -170,39 +170,36 @@ function print_mapping(obj, filename)
 
             obj = flatten_mapping(obj);
 
-            % print to screen be default;
-            output_is_json = false;
+            if nargin > 1 && strcmp(bids.internal.file_utils(filename, 'ext'), 'json')
+                output_is_json = true;
+                content = {};
+                for i = 1:size(obj.mapping, 1)
+                    input = obj.mapping(i);
+                    input = rmfield(input, 'name_spec');
+                    content{i, 1} = struct('input', input, ...
+                                           'output', obj.mapping(i).name_spec);
+                end
+                bids.util.jsonencode(filename, content);
+                return
+            end
+
+            % print to screen by default
+            fid = 1;
 
             % what to separate input and output with
             left = ' ';
             separator = ' --> ';
             right = ' ';
 
-            if nargin < 2
-
-                fid = 1;
-
-            elseif ~strcmp(bids.internal.file_utils(filename, 'ext'), 'json')
-
+            if nargin > 1
                 fid = fopen(filename, 'Wt');
                 if fid == -1
                     error('Unable to write file %s.', filename);
                 end
-
+                % markdown table separators
                 left = '| ';
                 separator = ' | ';
                 right = ' |';
-
-            elseif strcmp(bids.internal.file_utils(filename, 'ext'), 'json')
-
-                output_is_json = true;
-
-                content = {};
-
-            else
-
-                fid = 1;
-
             end
 
             header = ['<!--\n', ...
@@ -212,60 +209,44 @@ function print_mapping(obj, filename)
                       '# Mapping\n\n', ...
                       left, 'input', separator, 'output', right,  '\n', ...
                       left, '-',     separator, '-',      right,  '\n'];
-            if ~output_is_json
-                fprintf(fid, '\n');
-                if fid ~= 1
-                    fprintf(fid, header);
-                end
+
+            fprintf(fid, '\n');
+            if fid ~= 1
+                fprintf(fid, header);
             end
 
             for i = 1:size(obj.mapping, 1)
 
-                if ~output_is_json
-                    %%
-                    input = obj.mapping(i);
-                    input = prepare_for_printing(input);
+                %%
+                input = obj.mapping(i);
+                input = prepare_for_printing(input);
 
-                    input_filename = input.filename;
+                input_filename = input.filename;
 
-                    %%
-                    output = obj.mapping(i).name_spec;
-                    output = prepare_for_printing(output);
+                %%
+                output = obj.mapping(i).name_spec;
+                output = prepare_for_printing(output);
 
-                    output_filename = output.filename;
+                output_filename = output.filename;
 
-                    output_filename = ['*' output_filename];
-                    output_filename = strrep(output_filename, 'add-star', '*');
-
-                    if fid ~= 1
-                        input_filename = strrep(input_filename, '*', '\*');
-                        input_filename = strrep(input_filename, '_', '\_');
-                        output_filename = strrep(output_filename, '*', '\*');
-                        output_filename = strrep(output_filename, '_', '\_');
-                    end
-
-                    fprintf(fid, '%s%s%s%s%s\n', ...
-                            left, input_filename, separator, output_filename, right);
-
-                else
-
-                    input = obj.mapping(i);
-                    input = rmfield(input, 'name_spec');
-                    content{i, 1} = struct('input', input, ...
-                                           'output', obj.mapping(i).name_spec);
+                output_filename = ['*' output_filename];
+                output_filename = strrep(output_filename, 'add-star', '*');
 
+                if fid ~= 1
+                    input_filename = strrep(input_filename, '*', '\*');
+                    input_filename = strrep(input_filename, '_', '\_');
+                    output_filename = strrep(output_filename, '*', '\*');
+                    output_filename = strrep(output_filename, '_', '\_');
                 end
 
-            end
+                fprintf(fid, '%s%s%s%s%s\n', ...
+                        left, input_filename, separator, output_filename, right);
 
-            if ~output_is_json
-                fprintf(fid, '\n');
-                if fid ~= 1
-                    fclose(fid);
-                end
-            else
-                bids.util.jsonencode(filename, content);
+            end
 
+            fprintf(fid, '\n');
+            if fid ~= 1
+                fclose(fid);
             end
 
         end
diff --git a/src/utils/prepare_for_printing.m b/src/utils/prepare_for_printing.m
index a4d1bc9..b049d7f 100644
--- a/src/utils/prepare_for_printing.m
+++ b/src/utils/prepare_for_printing.m
@@ -2,8 +2,12 @@
     %
     % (C) Copyright 2022 spm_2_bids developers
 
-    if isfield(spec, 'entities') && strcmp(spec.entities, '*')
-        spec.entities = struct('add', 'joker');
+    if isfield(spec, 'entities')
+        if strcmp(spec.entities, '*')
+            spec.entities = struct('add', 'joker');
+        elseif strcmp(spec.entities, '')
+            spec.entities = struct();
+        end
     end
     bf = bids.File(spec, 'tolerant', true);