Use Opener (which contains .mgz) instead of BinOpener (which is no longer needed).

Author: Ben Cipollini

bin/nib-nifti-dx

@@ -25,8 +25,8 @@ def main():
     (opts, files) = parser.parse_args()
 
     for fname in files:
-        with nib.volumeutils.BinOpener(fname) as fobj:
-            hdr =  fobj.read(nib.nifti1.header_dtype.itemsize)
+        with nib.openers.Opener(fname) as fobj:
+            hdr = fobj.read(nib.nifti1.header_dtype.itemsize)
         result = nib.Nifti1Header.diagnose_binaryblock(hdr)
         if len(result):
             print('Picky header check output for "%s"\n' % fname)

nibabel/arrayproxy.py

@@ -27,9 +27,10 @@
 """
 import warnings
 
-from .volumeutils import BinOpener, array_from_file, apply_read_scaling
+from .volumeutils import array_from_file, apply_read_scaling
 from .fileslice import fileslice
 from .keywordonly import kw_only_meth
+from .openers import Opener
 
 
 class ArrayProxy(object):
@@ -130,7 +131,7 @@ def get_unscaled(self):
 
         This is an optional part of the proxy API
         '''
-        with BinOpener(self.file_like) as fileobj:
+        with Opener(self.file_like) as fileobj:
             raw_data = array_from_file(self._shape,
                                        self._dtype,
                                        fileobj,
@@ -145,7 +146,7 @@ def __array__(self):
         return apply_read_scaling(raw_data, self._slope, self._inter)
 
     def __getitem__(self, slicer):
-        with BinOpener(self.file_like) as fileobj:
+        with Opener(self.file_like) as fileobj:
             raw_data = fileslice(fileobj,
                                  slicer,
                                  self._shape,

nibabel/fileholders.py

@@ -10,7 +10,7 @@
 
 from copy import copy
 
-from .volumeutils import BinOpener
+from .openers import Opener
 
 
 class FileHolderError(Exception):
@@ -63,10 +63,10 @@ def get_prepare_fileobj(self, *args, **kwargs):
            ``self.pos``
         '''
         if self.fileobj is not None:
-            obj = BinOpener(self.fileobj)  # for context manager
+            obj = Opener(self.fileobj)  # for context manager
             obj.seek(self.pos)
         elif self.filename is not None:
-            obj = BinOpener(self.filename, *args, **kwargs)
+            obj = Opener(self.filename, *args, **kwargs)
             if self.pos != 0:
                 obj.seek(self.pos)
         else:

nibabel/loadsave.py

@@ -12,7 +12,7 @@
 import numpy as np
 
 from .filename_parser import types_filenames, splitext_addext
-from .volumeutils import BinOpener, Opener
+from .openers import Opener
 from .analyze import AnalyzeImage
 from .spm2analyze import Spm2AnalyzeImage
 from .nifti1 import Nifti1Image, Nifti1Pair, header_dtype as ni1_hdr_dtype
@@ -72,14 +72,14 @@ def guessed_image_type(filename):
             signature = fobj.read(4)
             klass = Minc2Image if signature == b'\211HDF' else Minc1Image
     elif lext == '.nii':
-        with BinOpener(filename) as fobj:
+        with Opener(filename) as fobj:
             binaryblock = fobj.read(348)
         ft = which_analyze_type(binaryblock)
         klass = Nifti2Image if ft == 'nifti2' else Nifti1Image
     else:  # might be nifti 1 or 2 pair or analyze of some sort
         files_types = (('image', '.img'), ('header', '.hdr'))
         filenames = types_filenames(filename, files_types)
-        with BinOpener(filenames['header']) as fobj:
+        with Opener(filenames['header']) as fobj:
             binaryblock = fobj.read(348)
         ft = which_analyze_type(binaryblock)
         if ft == 'nifti2':
@@ -208,7 +208,7 @@ def read_img_data(img, prefer='scaled'):
             hdr.set_data_offset(dao.offset)
         if default_scaling and (dao.slope, dao.inter) != (1, 0):
             hdr.set_slope_inter(dao.slope, dao.inter)
-    with BinOpener(img_file_like) as fileobj:
+    with Opener(img_file_like) as fileobj:
         if prefer == 'scaled':
             return hdr.data_from_fileobj(fileobj)
         return hdr.raw_data_from_fileobj(fileobj)

nibabel/nicom/dicomwrappers.py

@@ -18,7 +18,7 @@
 
 from . import csareader as csar
 from .dwiparams import B2q, nearest_pos_semi_def, q2bg
-from ..volumeutils import BinOpener
+from ..openers import Opener
 from ..onetime import setattr_on_read as one_time
 
 
@@ -51,7 +51,7 @@ def wrapper_from_file(file_like, *args, **kwargs):
     """
     import dicom
 
-    with BinOpener(file_like) as fobj:
+    with Opener(file_like) as fobj:
         dcm_data = dicom.read_file(fobj, *args, **kwargs)
     return wrapper_from_data(dcm_data)
 

nibabel/parrec.py

@@ -99,10 +99,11 @@
 from .keywordonly import kw_only_meth
 from .spatialimages import SpatialImage, Header
 from .eulerangles import euler2mat
-from .volumeutils import Recoder, array_from_file, BinOpener
+from .volumeutils import Recoder, array_from_file
 from .affines import from_matvec, dot_reduce, apply_affine
 from .nifti1 import unit_codes
 from .fileslice import fileslice, strided_scalar
+from .openers import Opener
 
 # PSL to RAS affine
 PSL_TO_RAS = np.array([[0, 0, -1, 0],  # L -> R
@@ -581,13 +582,13 @@ def is_proxy(self):
         return True
 
     def get_unscaled(self):
-        with BinOpener(self.file_like) as fileobj:
+        with Opener(self.file_like) as fileobj:
             return _data_from_rec(fileobj, self._rec_shape, self._dtype,
                                   self._slice_indices, self._shape,
                                   mmap=self._mmap)
 
     def __array__(self):
-        with BinOpener(self.file_like) as fileobj:
+        with Opener(self.file_like) as fileobj:
             return _data_from_rec(fileobj,
                                   self._rec_shape,
                                   self._dtype,
@@ -603,7 +604,7 @@ def __getitem__(self, slicer):
             return np.asanyarray(self)[slicer]
         # Slices all sequential from zero, can use fileslice
         # This gives more efficient volume by volume loading, for example
-        with BinOpener(self.file_like) as fileobj:
+        with Opener(self.file_like) as fileobj:
             raw_data = fileslice(fileobj, slicer, self._shape, self._dtype, 0,
                                  'F')
         # Broadcast scaling to shape of original data

nibabel/tests/test_openers.py

@@ -57,7 +57,6 @@ def test_Opener():
         # mode is gently ignored
         fobj = Opener(obj, mode='r')
 
-
 def test_Opener_various():
     # Check we can do all sorts of files here
     message = b"Oh what a giveaway"
@@ -85,6 +84,13 @@ def test_Opener_various():
                     # Just check there is a fileno
                     assert_not_equal(fobj.fileno(), 0)
 
+def test_OpenerAgain():
+    # Test that ImageOpener does add '.mgz' as gzipped file type
+    with InTemporaryDirectory():
+        with ImageOpener('test.gz', 'w') as fobj:
+            assert_true(hasattr(fobj.fobj, 'compress'))
+        with ImageOpener('test.mgz', 'w') as fobj:
+            assert_true(hasattr(fobj.fobj, 'compress'))
 
 def test_file_like_wrapper():
     # Test wrapper using BytesIO (full API)

nibabel/tests/test_utils.py

@@ -23,12 +23,11 @@
 import numpy as np
 
 from ..tmpdirs import InTemporaryDirectory
-
+from ..openers import ImageOpener
 from ..volumeutils import (array_from_file,
                            _is_compressed_fobj,
                            array_to_file,
-                           allopen, # for backwards compatibility
-                           BinOpener,
+                           allopen,  # for backwards compatibility
                            fname_ext_ul_case,
                            calculate_scale,
                            can_cast,
@@ -928,7 +927,7 @@ def test_seek_tell():
             st = functools.partial(seek_tell, write0=write0)
             bio.seek(0)
             # First write the file
-            with BinOpener(in_file, 'wb') as fobj:
+            with ImageOpener(in_file, 'wb') as fobj:
                 assert_equal(fobj.tell(), 0)
                 # already at position - OK
                 st(fobj, 0)
@@ -949,7 +948,7 @@ def test_seek_tell():
                 fobj.write(b'\x02' * tail)
             bio.seek(0)
             # Now read back the file testing seek_tell in reading mode
-            with BinOpener(in_file, 'rb') as fobj:
+            with ImageOpener(in_file, 'rb') as fobj:
                 assert_equal(fobj.tell(), 0)
                 st(fobj, 0)
                 assert_equal(fobj.tell(), 0)
@@ -961,22 +960,22 @@ def test_seek_tell():
                 st(fobj, 0)
             bio.seek(0)
             # Check we have the expected written output
-            with BinOpener(in_file, 'rb') as fobj:
+            with ImageOpener(in_file, 'rb') as fobj:
                 assert_equal(fobj.read(),
                              b'\x01' * start + b'\x00' * diff + b'\x02' * tail)
         for in_file in ('test2.gz', 'test2.bz2'):
             # Check failure of write seek backwards
-            with BinOpener(in_file, 'wb') as fobj:
+            with ImageOpener(in_file, 'wb') as fobj:
                 fobj.write(b'g' * 10)
                 assert_equal(fobj.tell(), 10)
                 seek_tell(fobj, 10)
                 assert_equal(fobj.tell(), 10)
                 assert_raises(IOError, seek_tell, fobj, 5)
             # Make sure read seeks don't affect file
-            with BinOpener(in_file, 'rb') as fobj:
+            with ImageOpener(in_file, 'rb') as fobj:
                 seek_tell(fobj, 10)
                 seek_tell(fobj, 0)
-            with BinOpener(in_file, 'rb') as fobj:
+            with ImageOpener(in_file, 'rb') as fobj:
                 assert_equal(fobj.read(), b'g' * 10)
 
 
@@ -1004,15 +1003,6 @@ def seek(self, *args):
     assert_equal(bio.getvalue(), ZEROB * 20)
 
 
-def test_BinOpener():
-    # Test that BinOpener does add '.mgz' as gzipped file type
-    with InTemporaryDirectory():
-        with BinOpener('test.gz', 'w') as fobj:
-            assert_true(hasattr(fobj.fobj, 'compress'))
-        with BinOpener('test.mgz', 'w') as fobj:
-            assert_true(hasattr(fobj.fobj, 'compress'))
-
-
 def test_fname_ext_ul_case():
     # Get filename ignoring the case of the filename extension
     with InTemporaryDirectory():

nibabel/trackvis.py

@@ -10,7 +10,7 @@
 
 from .py3k import asstr
 from .volumeutils import (native_code, swapped_code, endian_codes, rec2dict)
-from .volumeutils import BinOpener
+from .openers import Opener
 from .orientations import aff2axcodes
 from .affines import apply_affine
 
@@ -143,7 +143,7 @@ def read(fileobj, as_generator=False, points_space=None):
     coordinate along the first image axis, multiplied by the voxel size for
     that axis.
     '''
-    fileobj = BinOpener(fileobj)
+    fileobj = Opener(fileobj)
     hdr_str = fileobj.read(header_2_dtype.itemsize)
     # try defaulting to version 2 format
     hdr = np.ndarray(shape=(),
@@ -334,7 +334,7 @@ def write(fileobj, streamlines,  hdr_mapping=None, endianness=None,
     except StopIteration:  # empty sequence or iterable
         # write header without streams
         hdr = _hdr_from_mapping(None, hdr_mapping, endianness)
-        with BinOpener(fileobj, 'wb') as fileobj:
+        with Opener(fileobj, 'wb') as fileobj:
             fileobj.write(hdr.tostring())
         return
     if endianness is None:
@@ -375,7 +375,7 @@ def write(fileobj, streamlines,  hdr_mapping=None, endianness=None,
         mm2vx = npl.inv(affine)
         mm2tv = np.dot(vx2tv, mm2vx).astype('f4')
     # write header
-    fileobj = BinOpener(fileobj, mode='wb')
+    fileobj = Opener(fileobj, mode='wb')
     fileobj.write(hdr.tostring())
     # track preliminaries
     f4dt = np.dtype(endianness + 'f4')

nibabel/volumeutils.py

@@ -1584,16 +1584,16 @@ def fname_ext_ul_case(fname):
 def allopen(fileish, *args, **kwargs):
     """ Compatibility wrapper for old ``allopen`` function
 
-    Wraps creation of ``BinOpener`` instance, while picking up module global
+    Wraps creation of ``Opener`` instance, while picking up module global
     ``default_compresslevel``.
 
-    Please see docstring for ``BinOpener`` and ``Opener`` for details.
+    Please see docstring for ``Opener`` for details.
     """
-    warnings.warn("Please use BinOpener class instead of this function",
+    warnings.warn("Please use Opener class instead of this function",
                   DeprecationWarning,
                   stacklevel=2)
 
-    class MyOpener(BinOpener):
+    class MyOpener(Opener):
         default_compresslevel = default_compresslevel
 
     return MyOpener(fileish, *args, **kwargs)