Merge pull request #708 from nipy/rel/2.3.2

REL: 2.3.2

.travis.yml

@@ -96,7 +96,7 @@ before_install:
     - virtualenv --python=python venv
     - source venv/bin/activate
     - python --version # just to check
-    - pip install -U pip wheel  # needed at one point
+    - pip install -U pip setuptools>=27.0 wheel
     - retry pip install nose flake8 mock  # always
     - pip install $EXTRA_PIP_FLAGS $DEPENDS $OPTIONAL_DEPENDS
     - if [ "${COVERAGE}" == "1" ]; then

Changelog

@@ -24,6 +24,45 @@ Gerhard (SG), Eric Larson (EL), Yaroslav Halchenko (YOH) and Chris Cheng (CC).
 
 References like "pr/298" refer to github pull request numbers.
 
+2.3.2 (Wedmesday 2 January 2019)
+================================
+
+Enhancements
+------------
+* Enable toggling crosshair with ``Ctrl-x`` in ``OrthoSlicer3D`` viewer (pr/701)
+  (Miguel Estevan Moreno, reviewed by CM)
+
+Bug fixes
+---------
+* Read .PAR files corresponding to ADC maps (pr/685) (Gregory R. Lee, reviewed
+  by CM)
+* Increase maximum number of items read from Siemens CSA format (Igor Solovey,
+  reviewed by CM, MB)
+* Check boolean dtypes with ``numpy.issubdtype(..., np.bool_)`` (pr/707)
+  (Jon Haitz Legarreta Gorroño, reviewed by CM)
+
+Maintenance
+-----------
+* Fix small typos in parrec2nii help text (pr/682) (Thomas Roos, reviewed by
+  MB)
+* Remove deprecated calls to ``numpy.asscalar`` (pr/686) (CM, reviewed by
+  Gregory R. Lee)
+* Update QA directives to accommodate Flake8 3.6 (pr/695) (CM)
+* Update DOI links to use ``https://doi.org`` (pr/703) (Katrin Leinweber,
+  reviewed by CM)
+* Remove deprecated calls to ``numpy.fromstring`` (pr/700) (Ariel Rokem,
+  reviewed by CM, MB)
+* Drop ``distutils`` support, require ``bz2file`` for Python 2.7 (pr/700)
+  (CM, reviewed by MB)
+* Replace mutable ``bytes`` hack, disabled in numpy pre-release, with
+  ``bytearray``/``readinto`` strategy (pr/700) (Ariel Rokem, CM, reviewed by
+  CM, MB)
+
+API changes and deprecations
+----------------------------
+* Add ``Opener.readinto`` method to read file contents into pre-allocated buffers
+  (pr/700) (Ariel Rokem, reviewed by CM, MB)
+
 2.3.1 (Tuesday 16 October 2018)
 ===============================
 

appveyor.yml

@@ -22,6 +22,7 @@ install:
   - SET PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
 
   # Install the dependencies of the project.
+  - python -m pip install --upgrade pip setuptools wheel
   - pip install numpy scipy matplotlib nose h5py mock pydicom
   - pip install .
   - SET NIBABEL_DATA_DIR=%CD%\nibabel-data

doc/source/conf.py

@@ -87,7 +87,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = u'2006-2018, %(MAINTAINER)s <%(AUTHOR_EMAIL)s>' % rel
+copyright = u'2006-2019, %(MAINTAINER)s <%(AUTHOR_EMAIL)s>' % rel
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/source/devel/make_release.rst

@@ -301,7 +301,7 @@ Release checklist
   text for adding a DOI badge in various formats. Copy the DOI Markdown text.
   The markdown will look something like this::
 
-    [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.60847.svg)](http://dx.doi.org/10.5281/zenodo.60847)
+    [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.60847.svg)](https://doi.org/10.5281/zenodo.60847)
 
   Go back to the Github release page for this release, click "Edit release".
   and copy the DOI into the release notes.  Click "Update release".

doc/source/index.rst

@@ -87,6 +87,11 @@ contributed code and discussion (in rough order of appearance):
 * Mathias Goncalves
 * Jakub Kaczmarzyk
 * Dimitri Papadopoulos Orfanos
+* Miguel Estevan Moreno
+* Thomas Roos
+* Igor Solovey
+* Jon Haitz Legarreta Gorroño
+* Katrin Leinweber
 
 License reprise
 ===============

nibabel/affines.py

@@ -6,7 +6,7 @@
 import numpy as np
 
 from six.moves import reduce
-from .testing import setup_test  # flake8: noqa F401
+from .testing import setup_test  # noqa
 
 
 class AffineError(ValueError):

nibabel/analyze.py

@@ -1057,10 +1057,8 @@ def to_file_map(self, file_map=None):
         # Store consumable values for later restore
         offset = hdr.get_data_offset()
         # Scalars of slope, offset to get immutable values
-        slope = (np.asscalar(hdr['scl_slope']) if hdr.has_data_slope
-                 else np.nan)
-        inter = (np.asscalar(hdr['scl_inter']) if hdr.has_data_intercept
-                 else np.nan)
+        slope = hdr['scl_slope'].item() if hdr.has_data_slope else np.nan
+        inter = hdr['scl_inter'].item() if hdr.has_data_intercept else np.nan
         # Check whether to calculate slope / inter
         scale_me = np.all(np.isnan((slope, inter)))
         if scale_me:

nibabel/casting.py

@@ -8,7 +8,7 @@
 from platform import processor, machine
 
 import numpy as np
-from .testing import setup_test  # flake8: noqa F401
+from .testing import setup_test  # noqa
 
 
 class CastingError(Exception):
@@ -268,7 +268,7 @@ def type_info(np_type):
         # 80) but in calculations nexp in fact appears to be 11 as for float64
         ret.update(dict(width=width))
         return ret
-    if vals == (105, 11, 16): # correctly detected double double
+    if vals == (105, 11, 16):  # correctly detected double double
         ret.update(dict(nmant=nmant, nexp=nexp, width=width))
         return ret
     # Oh dear, we don't recognize the type information.  Try some known types

nibabel/cifti2/tests/test_cifti2.py

@@ -58,7 +58,7 @@ def test_cifti2_metadata():
     assert_equal(md.data, dict(metadata_test))
 
     assert_equal(list(iter(md)), list(iter(collections.OrderedDict(metadata_test))))
-    
+
     md.update({'a': 'aval', 'b': 'bval'})
     assert_equal(md.data, dict(metadata_test))
 
@@ -310,7 +310,7 @@ def test_matrix():
 
     assert_raises(ci.Cifti2HeaderError, m.insert, 0, mim_none)
     assert_equal(m.mapped_indices, [])
-   
+
     h = ci.Cifti2Header(matrix=m)
     assert_equal(m.mapped_indices, [])
     m.insert(0, mim_0)

nibabel/cmdline/parrec2nii.py

@@ -89,7 +89,7 @@ def get_opt_parser():
     p.add_option(
         Option("--minmax", action="store", nargs=2, dest="minmax",
                help=one_line(
-                   """Mininum and maximum settings to be stored in the NIfTI
+                   """Minimum and maximum settings to be stored in the NIfTI
                    header. If any of them is set to 'parse', the scaled data is
                    scanned for the actual minimum and maximum.  To bypass this
                    potentially slow and memory intensive step (the data has to
@@ -103,7 +103,7 @@ def get_opt_parser():
                default=False,
                help=one_line(
                    """If set, all information from the PAR header is stored in
-                   an extension ofthe NIfTI file header.  Default: off""")))
+                   an extension of the NIfTI file header.  Default: off""")))
     p.add_option(
         Option("--scaling", action="store", dest="scaling", default='dv',
                help=one_line(

nibabel/ecat.py

@@ -657,8 +657,8 @@ def data_from_fileobj(self, frame=0, orientation=None):
         subhdr = self.subheaders[frame]
         raw_data = self.raw_data_from_fileobj(frame, orientation)
         # Scale factors have to be set to scalars to force scalar upcasting
-        data = raw_data * np.asscalar(header['ecat_calibration_factor'])
-        data = data * np.asscalar(subhdr['scale_factor'])
+        data = raw_data * header['ecat_calibration_factor'].item()
+        data = data * subhdr['scale_factor'].item()
         return data
 
 

nibabel/externals/netcdf.py

@@ -37,7 +37,7 @@
 
 import numpy as np  # noqa
 from ..py3k import asbytes, asstr
-from numpy import fromstring, ndarray, dtype, empty, array, asarray
+from numpy import frombuffer, ndarray, dtype, empty, array, asarray
 from numpy import little_endian as LITTLE_ENDIAN
 from functools import reduce
 
@@ -519,7 +519,7 @@ def _read(self):
         if not magic == b'CDF':
             raise TypeError("Error: %s is not a valid NetCDF 3 file" %
                             self.filename)
-        self.__dict__['version_byte'] = fromstring(self.fp.read(1), '>b')[0]
+        self.__dict__['version_byte'] = frombuffer(self.fp.read(1), '>b')[0]
 
         # Read file headers and set data.
         self._read_numrecs()
@@ -608,7 +608,7 @@ def _read_var_array(self):
                 # Calculate size to avoid problems with vsize (above)
                 a_size = reduce(mul, shape, 1) * size
                 if self.file_bytes >= 0 and begin_ + a_size > self.file_bytes:
-                    data = fromstring(b'\x00'*a_size, dtype=dtype_)
+                    data = frombuffer(b'\x00'*a_size, dtype=dtype_)
                 elif self.use_mmap:
                     mm = mmap(self.fp.fileno(), begin_+a_size, access=ACCESS_READ)
                     data = ndarray.__new__(ndarray, shape, dtype=dtype_,
@@ -622,7 +622,7 @@ def _read_var_array(self):
                     buf = self.fp.read(a_size)
                     if len(buf) < a_size:
                         buf = b'\x00'*a_size
-                    data = fromstring(buf, dtype=dtype_)
+                    data = frombuffer(buf, dtype=dtype_)
                     data.shape = shape
                     self.fp.seek(pos)
 
@@ -644,7 +644,7 @@ def _read_var_array(self):
             else:
                 pos = self.fp.tell()
                 self.fp.seek(begin)
-                rec_array = fromstring(self.fp.read(self._recs*self._recsize), dtype=dtypes)
+                rec_array = frombuffer(self.fp.read(self._recs*self._recsize), dtype=dtypes)
                 rec_array.shape = (self._recs,)
                 self.fp.seek(pos)
 
@@ -687,7 +687,7 @@ def _read_values(self):
         self.fp.read(-count % 4)  # read padding
 
         if typecode is not 'c':
-            values = fromstring(values, dtype='>%s' % typecode)
+            values = frombuffer(values, dtype='>%s' % typecode)
             if values.shape == (1,):
                 values = values[0]
         else:
@@ -705,14 +705,14 @@ def _pack_int(self, value):
     _pack_int32 = _pack_int
 
     def _unpack_int(self):
-        return int(fromstring(self.fp.read(4), '>i')[0])
+        return int(frombuffer(self.fp.read(4), '>i')[0])
     _unpack_int32 = _unpack_int
 
     def _pack_int64(self, value):
         self.fp.write(array(value, '>q').tostring())
 
     def _unpack_int64(self):
-        return fromstring(self.fp.read(8), '>q')[0]
+        return frombuffer(self.fp.read(8), '>q')[0]
 
     def _pack_string(self, s):
         count = len(s)

nibabel/gifti/parse_gifti_fast.py

@@ -47,7 +47,7 @@ def read_data_block(encoding, endian, ordering, datatype, shape, data):
         dec = base64.b64decode(data.encode('ascii'))
         dt = data_type_codes.type[datatype]
         sh = tuple(shape)
-        newarr = np.fromstring(dec, dtype=dt)
+        newarr = np.frombuffer(dec, dtype=dt)
         if len(newarr.shape) != len(sh):
             newarr = newarr.reshape(sh, order=ord)
 
@@ -59,7 +59,7 @@ def read_data_block(encoding, endian, ordering, datatype, shape, data):
         zdec = zlib.decompress(dec)
         dt = data_type_codes.type[datatype]
         sh = tuple(shape)
-        newarr = np.fromstring(zdec, dtype=dt)
+        newarr = np.frombuffer(zdec, dtype=dt)
         if len(newarr.shape) != len(sh):
             newarr = newarr.reshape(sh, order=ord)
 

nibabel/info.py

@@ -19,8 +19,8 @@
 _version_major = 2
 _version_minor = 3
 _version_micro = 2
-_version_extra = 'dev'
-# _version_extra = ''
+# _version_extra = 'dev'
+_version_extra = ''
 
 # Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z"
 __version__ = "%s.%s.%s%s" % (_version_major,
@@ -209,4 +209,5 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__):
 ISRELEASE = _version_extra == ''
 VERSION = __version__
 PROVIDES = ["nibabel", 'nisext']
-REQUIRES = ["numpy (>=%s)" % NUMPY_MIN_VERSION]
+REQUIRES = ["numpy>=%s" % NUMPY_MIN_VERSION,
+            'bz2file; python_version < "3.0"']

nibabel/nicom/csareader.py

@@ -18,7 +18,7 @@
     'IS': int,    # integer string
 }
 
-MAX_CSA_ITEMS = 199
+MAX_CSA_ITEMS = 1000
 
 
 class CSAError(Exception):

nibabel/nicom/dwiparams.py

@@ -21,7 +21,7 @@
 '''
 import numpy as np
 import numpy.linalg as npl
-from ..testing import setup_test as setup_module # flake8: noqa F401
+from ..testing import setup_test as setup_module  # noqa
 
 
 def B2q(B, tol=None):

nibabel/nicom/tests/test_csareader.py

@@ -21,7 +21,7 @@
 CSA2_B1000 = open(pjoin(IO_DATA_PATH, 'csa2_b1000.bin'), 'rb').read()
 CSA2_0len = gzip.open(pjoin(IO_DATA_PATH, 'csa2_zero_len.bin.gz'), 'rb').read()
 CSA_STR_valid = open(pjoin(IO_DATA_PATH, 'csa_str_valid.bin'), 'rb').read()
-CSA_STR_200n_items = open(pjoin(IO_DATA_PATH, 'csa_str_200n_items.bin'), 'rb').read()
+CSA_STR_1001n_items = open(pjoin(IO_DATA_PATH, 'csa_str_1001n_items.bin'), 'rb').read()
 
 
 @dicom_test
@@ -70,15 +70,15 @@ def test_csa_len0():
 
 def test_csa_nitem():
     # testing csa.read's ability to raise an error when n_items >= 200
-    assert_raises(csa.CSAReadError, csa.read, CSA_STR_200n_items)
-    # OK when < 200
+    assert_raises(csa.CSAReadError, csa.read, CSA_STR_1001n_items)
+    # OK when < 1000
     csa_info = csa.read(CSA_STR_valid)
     assert_equal(len(csa_info['tags']), 1)
     # OK after changing module global
     n_items_thresh = csa.MAX_CSA_ITEMS
     try:
-        csa.MAX_CSA_ITEMS = 1000
-        csa_info = csa.read(CSA_STR_200n_items)
+        csa.MAX_CSA_ITEMS = 2000
+        csa_info = csa.read(CSA_STR_1001n_items)
         assert_equal(len(csa_info['tags']), 1)
     finally:
         csa.MAX_CSA_ITEMS = n_items_thresh

nibabel/nifti1.py

@@ -27,7 +27,7 @@
 from .spm99analyze import SpmAnalyzeHeader
 from .casting import have_binary128
 from .pydicom_compat import have_dicom, pydicom as pdcm
-from .testing import setup_test  # flake8: noqa F401
+from .testing import setup_test  # noqa
 
 # nifti1 flat header definition for Analyze-like first 348 bytes
 # first number in comments indicates offset in file header in bytes
@@ -579,7 +579,7 @@ def from_fileobj(klass, fileobj, size, byteswap):
             # otherwise there should be a full extension header
             if not len(ext_def) == 8:
                 raise HeaderDataError('failed to read extension header')
-            ext_def = np.fromstring(ext_def, dtype=np.int32)
+            ext_def = np.frombuffer(ext_def, dtype=np.int32)
             if byteswap:
                 ext_def = ext_def.byteswap()
             # be extra verbose
@@ -1330,7 +1330,7 @@ def get_intent(self, code_repr='label'):
             raise TypeError('repr can be "label" or "code"')
         n_params = len(recoder.parameters[code]) if known_intent else 0
         params = (float(hdr['intent_p%d' % (i + 1)]) for i in range(n_params))
-        name = asstr(np.asscalar(hdr['intent_name']))
+        name = asstr(hdr['intent_name'].item())
         return label, tuple(params), name
 
     def set_intent(self, code, params=(), name='', allow_unknown=False):
@@ -1679,7 +1679,7 @@ def _chk_qfac(hdr, fix=False):
     @staticmethod
     def _chk_magic(hdr, fix=False):
         rep = Report(HeaderDataError)
-        magic = np.asscalar(hdr['magic'])
+        magic = hdr['magic'].item()
         if magic in (hdr.pair_magic, hdr.single_magic):
             return hdr, rep
         rep.problem_msg = ('magic string "%s" is not valid' %
@@ -1693,8 +1693,8 @@ def _chk_magic(hdr, fix=False):
     def _chk_offset(hdr, fix=False):
         rep = Report(HeaderDataError)
         # for ease of later string formatting, use scalar of byte string
-        magic = np.asscalar(hdr['magic'])
-        offset = np.asscalar(hdr['vox_offset'])
+        magic = hdr['magic'].item()
+        offset = hdr['vox_offset'].item()
         if offset == 0:
             return hdr, rep
         if magic == hdr.single_magic and offset < hdr.single_vox_offset:
@@ -1788,7 +1788,6 @@ def __init__(self, dataobj, affine, header=None,
     has been created - see those methods, and the :ref:`manual
     <default-sform-qform-codes>` for more details.  '''
 
-
     def update_header(self):
         ''' Harmonize header with image data and affine