move space to each action cli

cpp-lln-lab · Aug 10, 2023 · 5a55992 · 5a55992
1 parent 9bad6bc
commit 5a55992
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Showing 11 changed files with 141 additions and 92 deletions.
diff --git a/bidspm.m b/bidspm.m
@@ -10,7 +10,6 @@
     parse(args, varargin{:});
   catch ME
     disp('arguments passed were :');
-    varargin{i};
     for i = 1:numel(varargin)
       fprintf(1, '- ');
       fprintf(varargin{i});

diff --git a/demos/MoAE/test_moae.m b/demos/MoAE/test_moae.m
@@ -54,6 +54,11 @@
   output_dir = fullfile(tempname, 'outputs', 'derivatives');
   spm_mkdir(output_dir);
 
+  disp(bids_dir);
+  disp(output_dir);
+  disp(ignore{iOption});
+  disp(space(iOption));
+  disp(optionsFile);
   bidspm(bids_dir, output_dir, 'subject', ...
          'participant_label', {'01'}, ...
          'action', 'preprocess', ...

diff --git a/src/cli/baseInputParser.m b/src/cli/baseInputParser.m
@@ -23,7 +23,6 @@
   addParameter(args, 'action', defaultAction, isChar);
 
   addParameter(args, 'participant_label', {}, isCellStr);
-  addParameter(args, 'space', {}, isCellStr);
   addParameter(args, 'bids_filter_file', struct([]), isFileOrStruct);
 
   addParameter(args, 'verbosity', 2, isPositiveScalar);

diff --git a/src/cli/inputParserForCopy.m b/src/cli/inputParserForCopy.m
@@ -7,12 +7,14 @@
   % (C) Copyright 2023 bidspm developers
   isLogical = @(x) islogical(x) && numel(x) == 1;
   isCharOrCellstr = @(x) ischar(x) || iscellstr(x);  %#ok<*ISCLSTR>
+  isCellStr = @(x) iscellstr(x);
 
   args = baseInputParser();
 
   % allow unmatched in case this is called from cliSmooth
   args.KeepUnmatched = true;
 
+  addParameter(args, 'space', {}, isCellStr);
   addParameter(args, 'task', {}, isCharOrCellstr);
   addParameter(args, 'force', false, isLogical);
   addParameter(args, 'anat_only', false, isLogical);

diff --git a/src/cli/inputParserForCreateModel.m b/src/cli/inputParserForCreateModel.m
@@ -9,6 +9,7 @@
 
   isEmptyOrCellstr = @(x) isempty(x) || iscellstr(x);  %#ok<*ISCLSTR>
 
+  addParameter(args, 'space', {}, isCellStr);
   addParameter(args, 'task', {}, isEmptyOrCellstr);
 
   % :param ignore: Optional. Cell string that can contain:

diff --git a/src/cli/inputParserForCreateRoi.m b/src/cli/inputParserForCreateRoi.m
@@ -16,6 +16,7 @@
   isCellStr = @(x) iscellstr(x);
   isLogical = @(x) islogical(x) && numel(x) == 1;
 
+  addParameter(args, 'space', {}, isCellStr);
   addParameter(args, 'roi_dir', '', isDir);
   addParameter(args, 'preproc_dir', '', isDir);
   addParameter(args, 'hemisphere', {'L', 'R'}, isCellStr);

diff --git a/src/cli/inputParserForPreprocess.m b/src/cli/inputParserForPreprocess.m
@@ -11,7 +11,9 @@
   isLogical = @(x) islogical(x) && numel(x) == 1;
   isEmptyOrCellstr = @(x) isempty(x) || iscellstr(x);  %#ok<*ISCLSTR>
   isEmptyOrisChar = @(x) isempty(x) || ischar(x);  %#ok<*ISCLSTR>
+  isCellStr = @(x) iscellstr(x);
 
+  addParameter(args, 'space', {}, isCellStr);
   addParameter(args, 'task', '', isEmptyOrisChar);
   addParameter(args, 'fwhm', 6, isPositiveScalar);
   addParameter(args, 'dry_run', false, isLogical);

diff --git a/src/cli/inputParserForSmooth.m b/src/cli/inputParserForSmooth.m
@@ -9,7 +9,9 @@
 
   isPositiveScalar = @(x) isnumeric(x) && numel(x) == 1 && x >= 0;
   isLogical = @(x) islogical(x) && numel(x) == 1;
+  isCellStr = @(x) iscellstr(x);
 
+  addParameter(args, 'space', {}, isCellStr);
   addParameter(args, 'fwhm', 6, isPositiveScalar);
   addParameter(args, 'dry_run', false, isLogical);
 end
diff --git a/src/cli/inputParserForStats.m b/src/cli/inputParserForStats.m
@@ -16,6 +16,7 @@
   isCellStr = @(x) iscellstr(x);
   isEmptyOrCellstr = @(x) isempty(x) || iscellstr(x);  %#ok<*ISCLSTR>
 
+  addParameter(args, 'space', {}, isCellStr);
   addParameter(args, 'task', {}, isCellStr);
   addParameter(args, 'preproc_dir', pwd, isFolder);
   addParameter(args, 'model_file', struct([]), isFileOrStructOrIsDir);