RF: Header=>SpatialHeader

Author: Ben Cipollini

nibabel/minc1.py

@@ -14,7 +14,7 @@
 
 from .externals.netcdf import netcdf_file
 
-from .spatialimages import Header, SpatialImage
+from .spatialimages import SpatialHeader, SpatialImage
 from .fileslice import canonical_slicers
 
 from .deprecated import FutureWarningMixin
@@ -264,7 +264,7 @@ def __getitem__(self, sliceobj):
         return self.minc_file.get_scaled_data(sliceobj)
 
 
-class MincHeader(Header):
+class MincHeader(SpatialHeader):
     """ Class to contain header for MINC formats
     """
     # We don't use the data layout - this just in case we do later

nibabel/parrec.py

@@ -97,7 +97,7 @@
 from locale import getpreferredencoding
 
 from .keywordonly import kw_only_meth
-from .spatialimages import SpatialImage, Header
+from .spatialimages import SpatialHeader, SpatialImage
 from .eulerangles import euler2mat
 from .volumeutils import Recoder, array_from_file
 from .affines import from_matvec, dot_reduce, apply_affine
@@ -615,7 +615,7 @@ def __getitem__(self, slicer):
         return raw_data * slopes[slicer] + inters[slicer]
 
 
-class PARRECHeader(Header):
+class PARRECHeader(SpatialHeader):
     """PAR/REC header"""
     def __init__(self, info, image_defs, permit_truncated=False):
         """
@@ -645,10 +645,9 @@ def __init__(self, info, image_defs, permit_truncated=False):
                               % bitpix)
         # REC data always little endian
         dt = np.dtype('uint' + str(bitpix)).newbyteorder('<')
-        Header.__init__(self,
-                        data_dtype=dt,
-                        shape=self._calc_data_shape(),
-                        zooms=self._calc_zooms())
+        super(PARRECHeader, self).__init__(data_dtype=dt,
+                                           shape=self._calc_data_shape(),
+                                           zooms=self._calc_zooms())
 
     @classmethod
     def from_header(klass, header=None):

nibabel/spatialimages.py

@@ -154,7 +154,7 @@ class HeaderTypeError(Exception):
     pass
 
 
-class Header(FileBasedHeader):
+class SpatialHeader(FileBasedHeader):
     ''' Template class to implement header protocol '''
     default_x_flip = True
     data_layout = 'F'
@@ -308,20 +308,21 @@ def supported_np_types(obj):
     return set(supported)
 
 
+class Header(SpatialHeader):
+    '''Alias for SpatialHeader; kept for backwards compatibility.'''
+    def __init__(self, *args, **kwargs):
+        warnings.warn('Header is deprecated, use SpatialHeader',
+                      DeprecationWarning, stacklevel=2)
+        super(Header, self).__init__(*args, **kwargs)
+
+
 class ImageDataError(Exception):
     pass
 
 
 class SpatialImage(FileBasedImage):
-    ''' Template class for images '''
-    header_class = Header
-    _meta_sniff_len = 0
-    files_types = (('image', None),)
-    valid_exts = ()
-    _compressed_suffixes = ()
-
-    makeable = True  # Used in test code
-    rw = True  # Used in test code
+    ''' Template class for volumetric (3D/4D) images '''
+    header_class = SpatialHeader
 
     def __init__(self, dataobj, affine, header=None,
                  extra=None, file_map=None):

nibabel/tests/test_spatialimages.py

@@ -9,21 +9,22 @@
 """ Testing spatialimages
 
 """
-from ..externals.six import BytesIO
+
+import warnings
+
 import numpy as np
 
-from ..spatialimages import (Header, SpatialImage, HeaderDataError,
-                             ImageDataError)
+from ..externals.six import BytesIO
+from ..spatialimages import (SpatialHeader, SpatialImage, HeaderDataError,
+                             Header, ImageDataError)
 
 from unittest import TestCase
-
 from nose.tools import (assert_true, assert_false, assert_equal,
                         assert_not_equal, assert_raises)
-
 from numpy.testing import assert_array_equal, assert_array_almost_equal
 
 from .test_helpers import bytesio_round_trip
-from ..testing import suppress_warnings
+from ..testing import clear_and_catch_warnings, suppress_warnings
 from ..tmpdirs import InTemporaryDirectory
 from .. import load as top_load
 
@@ -110,7 +111,7 @@ def test_shape_zooms():
     assert_equal(hdr.get_data_shape(), (1,2,3))
     assert_equal(hdr.get_zooms(), (1.0,1.0,1.0))
     hdr.set_zooms((4, 3, 2))
-    assert_equal(hdr.get_zooms(), (4.0,3.0,2.0))    
+    assert_equal(hdr.get_zooms(), (4.0,3.0,2.0))
     hdr.set_data_shape((1, 2))
     assert_equal(hdr.get_data_shape(), (1,2))
     assert_equal(hdr.get_zooms(), (4.0,3.0))
@@ -159,9 +160,9 @@ def test_affine():
 
 
 def test_read_data():
-    class CHeader(Header):
-        data_layout='C'
-    for klass, order in ((Header, 'F'), (CHeader, 'C')):
+    class CHeader(SpatialHeader):
+        data_layout = 'C'
+    for klass, order in ((SpatialHeader, 'F'), (CHeader, 'C')):
         hdr = klass(np.int32, shape=(1,2,3), zooms=(3.0, 2.0, 1.0))
         fobj = BytesIO()
         data = np.arange(6).reshape((1,2,3))
@@ -187,6 +188,7 @@ class CHeader(Header):
 class DataLike(object):
     # Minimal class implementing 'data' API
     shape = (3,)
+
     def __array__(self):
         return np.arange(3)
 
@@ -384,3 +386,15 @@ def test_load_mmap(self):
                 # Check invalid values raise error
                 assert_raises(ValueError, func, param1, mmap='rw')
                 assert_raises(ValueError, func, param1, mmap='r+')
+
+
+def test_header_deprecated():
+    with clear_and_catch_warnings() as w:
+        warnings.simplefilter('always', DeprecationWarning)
+
+        class MyHeader(Header):
+            pass
+        assert_equal(len(w), 0)
+
+        MyHeader()
+        assert_equal(len(w), 1)