enh: improve robustness of dcm2niix parsing

Author: mgxd

nipype/interfaces/dcm2nii.py

@@ -7,6 +7,8 @@
 import os
 import re
 from copy import deepcopy
+import itertools as it
+from glob import iglob
 
 from ..utils.filemanip import split_filename
 from .base import (CommandLine, CommandLineInputSpec, InputMultiPath, traits,
@@ -410,52 +412,36 @@ def _run_interface(self, runtime):
         # may use return code 1 despite conversion
         runtime = super(Dcm2niix, self)._run_interface(
             runtime, correct_return_codes=(0, 1, ))
-        if self.inputs.bids_format:
-            (self.output_files, self.bvecs, self.bvals,
-             self.bids) = self._parse_stdout(runtime.stdout)
-        else:
-            (self.output_files, self.bvecs, self.bvals) = self._parse_stdout(
-                runtime.stdout)
+        (self.output_files, self.bvecs,
+         self.bvals, self.bids) = self._parse_stdout(runtime.stdout)
         return runtime
 
     def _parse_stdout(self, stdout):
-        files = []
-        bvecs = []
-        bvals = []
-        bids = []
-        skip = False
-        find_b = False
+        outfiles, bvals, bvecs, bids = [], [], [], []
         for line in stdout.split("\n"):
-            if not skip:
-                out_file = None
-                if line.startswith("Convert "):  # output
-                    fname = str(re.search('\S+/\S+', line).group(0))
-                    out_file = os.path.abspath(fname)
-                    # extract bvals
-                    if find_b:
-                        bvecs.append(out_file + ".bvec")
-                        bvals.append(out_file + ".bval")
-                        find_b = False
-                # next scan will have bvals/bvecs
-                elif 'DTI gradients' in line or 'DTI gradient directions' in line or 'DTI vectors' in line:
-                    find_b = True
-                if out_file:
-                    ext = '.nii' if self.inputs.compress == 'n' else '.nii.gz'
-                    files.append(out_file + ext)
-                    if self.inputs.bids_format:
-                        bids.append(out_file + ".json")
-            skip = False
-        # just return what was done
-        if not bids:
-            return files, bvecs, bvals
-        else:
-            return files, bvecs, bvals, bids
+            if line.startswith("Convert "):  # output
+                fname = str(re.search('\S+/\S+', line).group(0))
+                outtypes = (".nii", ".nii.gz", ".bval", ".bvec", ".json")
+                # search for relevant files, and sort accordingly
+                for fl in search_files(fname, outtypes):
+                    if fl.endswith(".nii") or fl.endswith(".gz"):
+                        outfiles.append(fl)
+                    elif fl.endswith(".bval"):
+                        bvals.append(fl)
+                    elif fl.endswith(".bvec"):
+                        bvecs.append(fl)
+                    elif fl.endswith(".json"):
+                        bids.append(fl)
+        return outfiles, bvecs, bvals, bids
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs['converted_files'] = self.output_files
         outputs['bvecs'] = self.bvecs
         outputs['bvals'] = self.bvals
-        if self.inputs.bids_format:
-            outputs['bids'] = self.bids
+        outputs['bids'] = self.bids
         return outputs
+
+# https://stackoverflow.com/a/4829130
+def search_files(prefix, outtypes):
+    return it.chain.from_iterable(iglob(prefix + outtype) for outtype in outtypes)