fix: remove temp dicoms if not actually converting as well

Author: mgxd

heudiconv/convert.py

@@ -3,8 +3,9 @@
 import logging
 import shutil
 
-from .utils import (read_config, load_json, save_json, write_config,
-                    TempDirs, safe_copyfile, treat_infofile, set_readonly)
+from .utils import (read_config, load_json, save_json, write_config, TempDirs,
+                    safe_copyfile, treat_infofile, set_readonly,
+                    clear_temp_dicoms)
 from .bids import (convert_sid_bids, populate_bids_templates, save_scans_key,
                    tuneup_bids_json_files, add_participant_record)
 from .dicoms import (group_dicoms_into_seqinfos, embed_metadata_from_dicoms,
@@ -143,6 +144,10 @@ def prep_conversion(sid, dicoms, outdir, heuristic, converter, anon_sid,
                 outdir=tdir,
                 min_meta=min_meta,
                 overwrite=overwrite,)
+
+    for item_dicoms in filegroup.values():
+        clear_temp_dicoms(item_dicoms)
+
     if bids:
         if seqinfo:
             keys = list(seqinfo)
@@ -256,14 +261,6 @@ 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/utils.py

@@ -1,17 +1,18 @@
 """Utility objects and functions"""
 
 import os
-import os.path as op
-from tempfile import mkdtemp
-from glob import glob
+import tempfile
 import json
 import re
 import sys
 import shutil
-from collections import namedtuple
 import copy
 import logging
 import stat
+import os.path as op
+from pathlib import Path
+from collections import namedtuple
+from glob import glob
 
 SeqInfo = namedtuple(
     'SeqInfo',
@@ -64,7 +65,7 @@ def __init__(self):
         self.lgr = logging.getLogger('tempdirs')
 
     def __call__(self, prefix=None):
-        tmpdir = mkdtemp(prefix=prefix)
+        tmpdir = tempfile.mkdtemp(prefix=prefix)
         self.dirs.append(tmpdir)
         return tmpdir
 
@@ -319,3 +320,16 @@ def is_readonly(path):
     perms = stat.S_IMODE(os.lstat(os.path.realpath(path)).st_mode)
     # should be true if anyone is allowed to write
     return not bool(perms & ALL_CAN_WRITE)
+
+
+def clear_temp_dicoms(item_dicoms):
+    """Ensures DICOM temporary directories are safely cleared"""
+    try:
+        tmp = Path(op.commonprefix(item_dicoms).parents[1])
+    except IndexError:
+        return
+    if (op.dirname(tmp) == tempfile.gettempdir()
+        and op.basename(tmp).startswith('heudiconvDCM')
+        and op.exists(tmp)):
+        # clean up directory holding dicoms
+        shutil.rmtree(tmp)