fix: temp directory problems with tarfiles

Author: mgxd

heudiconv/convert.py

@@ -256,6 +256,14 @@ def convert(items, converter, scaninfo_suffix, custom_callable, with_prov,
         if op.exists(outname):
             set_readonly(outname)
 
+    if items:
+        common = op.commonprefix(item_dicoms)
+        tmp = '/'.join(common.split(op.sep)[:3])
+        if (op.dirname(tmp) == '/tmp'
+            and op.basename(tmp).startswith('heudiconvDCM')):
+            # clean up directory holding dicoms
+            shutil.rmtree(tmp)
+
     if custom_callable is not None:
         custom_callable(*item)
 

heudiconv/parser.py

@@ -7,9 +7,10 @@
 from collections import defaultdict, OrderedDict
 
 import tarfile
+from tempfile import mkdtemp
 
 from .dicoms import group_dicoms_into_seqinfos
-from .utils import (TempDirs, docstring_parameter, StudySessionInfo, load_json,
+from .utils import (docstring_parameter, StudySessionInfo, load_json,
                     save_json, create_file_if_missing, json_dumps_pretty)
 
 lgr = logging.getLogger(__name__)
@@ -62,9 +63,8 @@ def get_extracted_dicoms(fl):
     # strategy: extract everything in a temp dir and assemble a list
     # of all files in all tarballs
 
-    tempdirs = TempDirs()
-
-    tmpdir = tempdirs(prefix='heudiconvDCM')
+    # cannot use TempDirs since will trigger cleanup with __del__
+    tmpdir = mkdtemp(prefix='heudiconvDCM')
 
     sessions = defaultdict(list)
     session = 0
@@ -99,8 +99,6 @@ def get_extracted_dicoms(fl):
         # None
         sessions[None] += sessions.pop(0)
 
-    tempdirs.cleanup() # will this affect anything?
-
     return sessions.items()