Deal with double-detection of to-be-gzipped files (fixes gh-1269)

Author: mih

nipype/interfaces/dcm2nii.py

@@ -108,11 +108,17 @@ def _parse_stdout(self, stdout):
                     out_file = line[len("Saving "):]
                 elif line.startswith("GZip..."):
                     # for gzipped outpus files are not absolute
+                    fname = line[len("GZip..."):]
+                    if len(files) and os.path.basename(files[-1]) == fname[:-3]:
+                        # we are seeing a previously reported conversion
+                        # as being saved in gzipped form -- remove the
+                        # obsolete, uncompressed file
+                        files.pop()
                     if isdefined(self.inputs.output_dir):
                         output_dir = self.inputs.output_dir
                     else:
                         output_dir = self._gen_filename('output_dir')
-                    out_file = os.path.abspath(os.path.join(output_dir, line[len("GZip..."):]))
+                    out_file = os.path.abspath(os.path.join(output_dir, fname))
                 elif line.startswith("Number of diffusion directions "):
                     if last_added_file:
                         base, filename, ext = split_filename(last_added_file)