Merge pull request #359 from mgxd/fix/group

ENH: grouping

Author: yarikoptic

heudiconv/cli/run.py

@@ -124,7 +124,6 @@ def main(argv=None):
 
     if args.debug:
         setup_exceptionhook()
-
     process_args(args)
 
 
@@ -154,8 +153,7 @@ def get_parser():
                         'If not provided, DICOMS would first be "sorted" and '
                         'subject IDs deduced by the heuristic')
     parser.add_argument('-c', '--converter',
-                        default='dcm2niix',
-                        choices=('dcm2niix', 'none'),
+                        choices=('dcm2niix', 'none'), default='dcm2niix',
                         help='tool to use for DICOM conversion. Setting to '
                         '"none" disables the actual conversion step -- useful'
                         'for testing heuristics.')
@@ -219,7 +217,7 @@ def get_parser():
                         help='custom actions to be performed on provided '
                         'files instead of regular operation.')
     parser.add_argument('-g', '--grouping', default='studyUID',
-                        choices=('studyUID', 'accession_number'),
+                        choices=('studyUID', 'accession_number', 'all', 'custom'),
                         help='How to group dicoms (default: by studyUID)')
     parser.add_argument('--minmeta', action='store_true',
                         help='Exclude dcmstack meta information in sidecar '
@@ -343,7 +341,8 @@ def process_args(args):
                         seqinfo=seqinfo,
                         min_meta=args.minmeta,
                         overwrite=args.overwrite,
-                        dcmconfig=args.dcmconfig,)
+                        dcmconfig=args.dcmconfig,
+                        grouping=args.grouping,)
 
         lgr.info("PROCESSING DONE: {0}".format(
             str(dict(subject=sid, outdir=study_outdir, session=session))))

heudiconv/convert.py

@@ -80,8 +80,8 @@ def conversion_info(subject, outdir, info, filegroup, ses):
 
 
 def prep_conversion(sid, dicoms, outdir, heuristic, converter, anon_sid,
-                   anon_outdir, with_prov, ses, bids_options, seqinfo, min_meta,
-                   overwrite, dcmconfig):
+                    anon_outdir, with_prov, ses, bids_options, seqinfo, 
+                    min_meta, overwrite, dcmconfig, grouping):
     if dicoms:
         lgr.info("Processing %d dicoms", len(dicoms))
     elif seqinfo:
@@ -157,16 +157,17 @@ def prep_conversion(sid, dicoms, outdir, heuristic, converter, anon_sid,
         # So either it would need to be brought back or reconsidered altogether
         # (since no sample data to test on etc)
     else:
-        # TODO -- might have been done outside already!
-        # MG -- will have to try with both dicom template, files
         assure_no_file_exists(target_heuristic_filename)
         safe_copyfile(heuristic.filename, target_heuristic_filename)
         if dicoms:
             seqinfo = group_dicoms_into_seqinfos(
                 dicoms,
+                grouping,
                 file_filter=getattr(heuristic, 'filter_files', None),
                 dcmfilter=getattr(heuristic, 'filter_dicom', None),
-                grouping=None)
+                flatten=True,
+                custom_grouping=getattr(heuristic, 'grouping', None))
+
         seqinfo_list = list(seqinfo.keys())
         filegroup = {si.series_id: x for si, x in seqinfo.items()}
         dicominfo_file = op.join(idir, 'dicominfo%s.tsv' % ses_suffix)