Merge pull request #202 from adelavega/fix/missing_ignore

FIX: Don't pass ignore and force index to init_fitlins_wf

Author: effigies

fitlins/cli/run.py

@@ -94,9 +94,9 @@ def get_parser():
                         default='MNI152NLin2009cAsym',
                         help='registered space of input datasets. '
                              'Empty value for no explicit space.')
-    g_bids.add_argument('--force-index', action='store', default=None,
+    g_bids.add_argument('--force-index', action='store', default=None, nargs='+',
                         help='regex pattern or string to include files')
-    g_bids.add_argument('--ignore', action='store', default=None,
+    g_bids.add_argument('--ignore', action='store', default=None, nargs='+',
                         help='regex pattern or string to ignore files')
     g_bids.add_argument('--desc-label', action='store', default='preproc',
                         help="use BOLD files with the provided description label")
@@ -207,7 +207,6 @@ def run_fitlins(argv=None):
         database_path = opts.database_path
         reset_database = False
 
-
     layout = BIDSLayout(opts.bids_dir,
                         derivatives=derivatives,
                         ignore=ignore,
@@ -232,7 +231,6 @@ def run_fitlins(argv=None):
         analysis_level=opts.analysis_level, model=model,
         space=opts.space, desc=opts.desc_label,
         participants=subject_list, base_dir=work_dir,
-        force_index=opts.force_index, ignore=opts.ignore,
         smoothing=opts.smoothing, drop_missing=opts.drop_missing,
         )
 

fitlins/workflows/base.py

@@ -4,7 +4,6 @@
 
 def init_fitlins_wf(database_path, out_dir, analysis_level, space,
                     desc=None, model=None, participants=None,
-                    ignore=None, force_index=None,
                     smoothing=None, drop_missing=False,
                     base_dir=None, name='fitlins_wf'):
     from nipype.pipeline import engine as pe
@@ -39,10 +38,6 @@ def init_fitlins_wf(database_path, out_dir, analysis_level, space,
                                  'space': space}),
         name='loader')
 
-    if ignore is not None:
-        loader.inputs.ignore = ignore
-    if force_index is not None:
-        loader.inputs.force_index = force_index
     if participants is not None:
         loader.inputs.selectors['subject'] = participants
     if database_path is not None: