add test + misc

Author: agramfort

nibabel/freesurfer/io.py

@@ -1,5 +1,6 @@
 from __future__ import division, print_function, absolute_import
 
+import warnings
 import numpy as np
 import getpass
 import time
@@ -107,20 +108,31 @@ def read_geometry(filepath, read_metadata=False, read_stamp=False):
 
             extra = fobj.read() if read_metadata else b''
             if extra:
+                volume_info = OrderedDict()
+
                 if extra[:4] != b'\x00\x00\x00\x14':
                     warnings.warn("Unknown extension code.")
-                volume_info = OrderedDict()
-                try:
-                    for line in extra[4:].split(b'\n'):
-                        key, val = map(bytes.strip, line.split(b'=', 1))
-                        key = key.decode('utf-8')
-                        if key in ('voxelsize', 'xras', 'yras', 'zras'):
-                            val = np.fromstring(val, sep=' ')
-                        elif key == 'volume':
-                            val = np.fromstring(val, sep=' ', dtype=np.uint)
-                        volume_info[key] = val
-                except ValueError:
-                    raise ValueError("Error parsing volume info")
+                else:
+                    try:
+                        for line in extra[4:].split(b'\n'):
+                            if len(line) == 0:
+                                continue
+                            key, val = map(bytes.strip, line.split(b'=', 1))
+                            print(key, val)
+                            key = key.decode('utf-8')
+                            if key in ('voxelsize', 'xras', 'yras', 'zras', 'cras'):
+                                val = np.fromstring(val, sep=' ')
+                                val = val.astype(np.float)
+                            elif key == 'volume':
+                                val = np.fromstring(val, sep=' ', dtype=np.uint)
+                                val = val.astype(np.int)
+                            volume_info[key] = val
+                    except ValueError:
+                        raise ValueError("Error parsing volume info")
+
+                if len(volume_info) == 0:
+                    warnings.warn("Volume geometry info is either "
+                                  "not contained or not valid.")
 
         else:
             raise ValueError("File does not appear to be a Freesurfer surface")
@@ -160,10 +172,10 @@ def write_geometry(filepath, coords, faces, create_stamp=None,
                                                 time.ctime())
 
     postlude = b''
-    if volume_info is not None:
+    if volume_info is not None and len(volume_info) > 0:
         postlude = [b'\x00\x00\x00\x14']
         for key, val in volume_info.items():
-            if key in ('voxelsize', 'xras', 'yras', 'zras'):
+            if key in ('voxelsize', 'xras', 'yras', 'zras', 'cras'):
                 val = '{:.3f} {:.3f} {:.3f}'.format(*val)
             elif key == 'volume':
                 val = '{:d} {:d} {:d}'.format(*val)

nibabel/freesurfer/tests/test_io.py

@@ -4,6 +4,7 @@
 import getpass
 import time
 import hashlib
+import warnings
 
 
 from ...tmpdirs import InTemporaryDirectory
@@ -17,7 +18,7 @@
 
 from ...tests.nibabel_data import get_nibabel_data
 from ...fileslice import strided_scalar
-
+from ...testing import clear_and_catch_warnings
 
 DATA_SDIR = 'fsaverage'
 
@@ -55,21 +56,31 @@ def test_geometry():
     assert_equal(coords.shape[0], faces.max() + 1)
 
     # Test quad with sphere
-    surf_path = pjoin(data_path, "surf", "%s.%s" % ("lh", "sphere"))
-    coords, faces = read_geometry(surf_path)
-    assert_equal(0, faces.min())
-    assert_equal(coords.shape[0], faces.max() + 1)
+    with clear_and_catch_warnings() as w:
+        warnings.filterwarnings('always', category=DeprecationWarning)
+        surf_path = pjoin(data_path, "surf", "%s.%s" % ("lh", "sphere"))
+        coords, faces, volume_info, create_stamp = \
+            read_geometry(surf_path, read_metadata=True, read_stamp=True)
+        assert_equal(0, faces.min())
+        assert_equal(coords.shape[0], faces.max() + 1)
+        assert_equal(0, len(volume_info))
+        assert_equal(u'created by greve on Thu Jun  8 19:17:51 2006',
+                     create_stamp)
+        assert_equal(len(w), 2)
 
     # Test equivalence of freesurfer- and nibabel-generated triangular files
     # with respect to read_geometry()
     with InTemporaryDirectory():
         surf_path = 'test'
         create_stamp = "created by %s on %s" % (getpass.getuser(),
                                                 time.ctime())
-        write_geometry(surf_path, coords, faces, create_stamp)
+        volume_info['cras'] = np.array([1., 2., 3.])
+        write_geometry(surf_path, coords, faces, create_stamp, volume_info)
 
-        coords2, faces2 = read_geometry(surf_path)
+        coords2, faces2, volume_info2 = \
+            read_geometry(surf_path, read_metadata=True)
 
+        assert_equal(volume_info2['cras'], volume_info['cras'])
         with open(surf_path, 'rb') as fobj:
             np.fromfile(fobj, ">u1", 3)
             read_create_stamp = fobj.readline().decode().rstrip('\n')