Merge pull request #312 from matthew-brett/fix-par-parsing

MRG: fix and test for bug in PAR header reading

Fix for reading empty parrec fields, floating point window values.

Add test.

Closes #311

Author: matthew-brett

COPYING

@@ -204,3 +204,8 @@ The files::
 
 are from https://github.com/yarikoptic/nitest-balls1, also released under the
 the PDDL version 1.0 available at http://opendatacommons.org/licenses/pddl/1.0/
+
+    nibabel/nibabel/tests/data/umass_anonymized.PAR
+
+is courtesy of the University of Massachusetts Medical School, also released
+under the PDDL.

nibabel/parrec.py

@@ -185,8 +185,9 @@
     ('rescale intercept', float),
     ('rescale slope', float),
     ('scale slope', float),
-    ('window center', int,),
-    ('window width', int,),
+    # Window center, width recorded as integer but can be float
+    ('window center', float,),
+    ('window width', float,),
     ('image angulation', float, (3,)),
     ('image offcentre', float, (3,)),
     ('slice thickness', float),
@@ -244,6 +245,9 @@ class PARRECError(Exception):
     pass
 
 
+# Value after colon may be absent
+GEN_RE = re.compile(r".\s+(.*?)\s*:\s*(.*)")
+
 def _split_header(fobj):
     """ Split header into `version`, `gen_dict`, `image_lines` """
     version = None
@@ -276,7 +280,6 @@ def _split_header(fobj):
     return version, gen_dict, image_lines
 
 
-GEN_RE = re.compile(r".\s+(.*?)\s*:\s+(.*)")
 
 
 def _process_gen_dict(gen_dict):

nibabel/tests/data/README.rst

@@ -6,3 +6,6 @@ Nibabel data files
 
 ``phantom_truncated.PAR`` is a slightly edited copy of
 ``phantom_EPI_asc_CLEAR_2_1.PAR``.
+
+``umass_anonymized.PAR`` courtesy of Github user ``cccbauer``, data from the
+University of Massachusetts medical school.