Merge pull request #496 from dbic/bf-noderivativesetc

ENH+BF: find_files to take list of topdirs, look for _bold only under  sub-* directories

Author: yarikoptic

heudiconv/bids.py

@@ -114,7 +114,8 @@ def populate_aggregated_jsons(path):
     # way too many -- let's just collect all which are the same!
     # FIELDS_TO_TRACK = {'RepetitionTime', 'FlipAngle', 'EchoTime',
     #                    'Manufacturer', 'SliceTiming', ''}
-    for fpath in find_files('.*_task-.*\_bold\.json', topdir=path,
+    for fpath in find_files('.*_task-.*\_bold\.json',
+                            topdir=glob(op.join(path, 'sub-*')),
                             exclude_vcs=True,
                             exclude="/\.(datalad|heudiconv)/"):
         #

heudiconv/parser.py

@@ -24,6 +24,7 @@
 
 _VCS_REGEX = '%s\.(?:git|gitattributes|svn|bzr|hg)(?:%s|$)' % (op.sep, op.sep)
 
+
 @docstring_parameter(_VCS_REGEX)
 def find_files(regex, topdir=op.curdir, exclude=None,
                exclude_vcs=True, dirs=False):
@@ -36,12 +37,16 @@ def find_files(regex, topdir=op.curdir, exclude=None,
     exclude_vcs:
       If True, excludes commonly known VCS subdirectories.  If string, used
       as regex to exclude those files (regex: `{}`)
-    topdir: basestring, optional
+    topdir: basestring or list, optional
       Directory where to search
     dirs: bool, optional
       Either to match directories as well as files
     """
-
+    if isinstance(topdir, (list, tuple)):
+        for topdir_ in topdir:
+            yield from find_files(
+                regex, topdir=topdir_, exclude=exclude, exclude_vcs=exclude_vcs, dirs=dirs)
+        return
     for dirpath, dirnames, filenames in os.walk(topdir):
         names = (dirnames + filenames) if dirs else filenames
         paths = (op.join(dirpath, name) for name in names)