Merge pull request #667 from nipy/rel/2.3.1

REL: 2.3.1

Author: effigies

.mailmap

@@ -29,6 +29,7 @@ Basile Pinsard <[email protected]> bpinsard <[email protected]>
 Nguyen, Ly <[email protected]> lxn2 <[email protected]>
 Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
 Chris Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
+Chris Markiewicz <[email protected]> Chris Markiewicz <[email protected]>
 Chris Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
 Chris Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
 Chris Markiewicz <[email protected]> Chris Johnson <[email protected]>

.travis.yml

@@ -4,11 +4,10 @@
 # for it to be on multiple physical lines, so long as you remember: - There
 # can't be any leading "-"s - All newlines will be removed, so use ";"s
 
+dist: xenial
+sudo: true
 language: python
 
-# Run jobs on container-based infrastructure, can be overridden per job
-sudo: false
-
 cache:
   directories:
     - $HOME/.cache/pip
@@ -22,11 +21,14 @@ env:
         - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
         - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
 python:
-    - 3.4
     - 3.5
     - 3.6
+    - 3.7
 matrix:
   include:
+    - python: 3.4
+      dist: trusty
+      sudo: false
     - python: 2.7
       env:
         - COVERAGE=1

COPYING

@@ -121,36 +121,40 @@ Sphinx 0.6 doesn't work properly.
   OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
   DAMAGE.
 
-Ordereddict
+OrderedSet
 -----------
 
-In ``nibabel/externals/ordereddict.py``
+In ``nibabel/externals/oset.py``
 
-Copied from: https://pypi.python.org/packages/source/o/ordereddict/ordereddict-1.1.tar.gz#md5=a0ed854ee442051b249bfad0f638bbec
+Copied from: https://files.pythonhosted.org/packages/d6/b1/a49498c699a3fda5d635cc1fa222ffc686ea3b5d04b84a3166c4cab0c57b/oset-0.1.3.tar.gz
 
 ::
 
-  Copyright (c) 2009 Raymond Hettinger
-
-  Permission is hereby granted, free of charge, to any person
-  obtaining a copy of this software and associated documentation files
-  (the "Software"), to deal in the Software without restriction,
-  including without limitation the rights to use, copy, modify, merge,
-  publish, distribute, sublicense, and/or sell copies of the Software,
-  and to permit persons to whom the Software is furnished to do so,
-  subject to the following conditions:
-
-      The above copyright notice and this permission notice shall be
-      included in all copies or substantial portions of the Software.
-
-      THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-      EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-      OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-      NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-      HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-      WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-      FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-      OTHER DEALINGS IN THE SOFTWARE.
+    Copyright (c) 2009, Raymond Hettinger, and others All rights reserved.
+
+    Package structured based on the one developed to odict Copyright (c) 2010, BlueDynamics Alliance, Austria
+
+    - Redistributions of source code must retain the above copyright notice, this
+      list of conditions and the following disclaimer.
+
+    - Redistributions in binary form must reproduce the above copyright notice, this
+      list of conditions and the following disclaimer in the documentation and/or
+      other materials provided with the distribution.
+
+    - Neither the name of the BlueDynamics Alliance nor the names of its
+      contributors may be used to endorse or promote products derived from this
+      software without specific prior written permission.
+
+    THIS SOFTWARE IS PROVIDED BY BlueDynamics Alliance AS IS AND ANY EXPRESS OR
+    IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+    MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
+    SHALL BlueDynamics Alliance BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+    PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+    BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+    IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
+    OF SUCH DAMAGE.
 
 mni_icbm152_t1_tal_nlin_asym_09a
 --------------------------------

Changelog

@@ -20,10 +20,46 @@ Nibabel releases
 
 Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH)
 Ben Cipollini (BC), Marc-Alexandre Côté (MC), Chris Markiewicz (CM), Stephan
-Gerhard (SG) and Eric Larson (EL).
+Gerhard (SG), Eric Larson (EL), Yaroslav Halchenko (YOH) and Chris Cheng (CC).
 
 References like "pr/298" refer to github pull request numbers.
 
+Upcoming release
+================
+
+New features
+------------
+* ``nib-diff`` command line tool for comparing image files (pr/617, pr/672,
+  pr/678) (CC, reviewed by YOH, Pradeep Raamana and CM)
+
+Enhancements
+------------
+* Speed up reading of numeric arrays in CIFTI2 (pr/655) (Michiel Cottaar,
+  reviewed by CM)
+* Add ``ndim`` property to ``ArrayProxy`` and ``DataobjImage`` (pr/674) (CM,
+  reviewed by MB)
+
+Bug fixes
+---------
+* Deterministic deduction of slice ordering in degenerate cases (pr/647)
+  (YOH, reviewed by CM)
+* Allow 0ms TR in MGH files (pr/653) (EL, reviewed by CM)
+* Allow for PPC64 little-endian long doubles (pr/658) (MB, reviewed by CM)
+* Correct construction of FreeSurfer annotation labels (pr/666) (CM, reviewed
+  by EL, Paul D. McCarthy)
+* Fix logic for persisting filehandles with indexed-gzip (pr/679) (Paul D.
+  McCarthy, reviewed by CM)
+
+Maintenance
+-----------
+* Fix semantic error in coordinate systems documentation (pr/646) (Ariel
+  Rokem, reviewed by CM, MB)
+* Test on Python 3.7, minor associated fixes (pr/651) (CM, reviewed by Gregory
+  R. Lee, MB)
+
+API changes and deprecations
+----------------------------
+
 2.3 (Tuesday 12 June 2018)
 ==========================
 

appveyor.yml

@@ -12,6 +12,8 @@ environment:
     - PYTHON: C:\Python35-x64
     - PYTHON: C:\Python36
     - PYTHON: C:\Python36-x64
+    - PYTHON: C:\Python37
+    - PYTHON: C:\Python37-x64
 
 install:
   # Prepend newly installed Python to the PATH of this build (this cannot be
@@ -20,8 +22,7 @@ install:
   - SET PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
 
   # Install the dependencies of the project.
-  - pip install numpy scipy matplotlib nose h5py mock
-  - pip install pydicom
+  - pip install numpy scipy matplotlib nose h5py mock pydicom
   - pip install .
   - SET NIBABEL_DATA_DIR=%CD%\nibabel-data
 

bin/nib-diff

@@ -0,0 +1,17 @@
+#!python
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+"""
+Quick diff summary for a set of neuroimaging files
+"""
+
+from nibabel.cmdline.diff import main
+
+if __name__ == '__main__':
+    main()

doc/source/coordinate_systems.rst

@@ -255,7 +255,7 @@ axes *starts* on the right, anterior, superior of the subject, rather than
 *ending* on the right, anterior, superior.  In other words, they would use
 "RAS" to refer to a coordinate system we would call "LPI".  To be safe, we'll
 call our interpretation of the RAS convention "RAS+", meaning that Right,
-Anterior, Posterior are all positive values on these axes.
+Anterior, Superior are all positive values on these axes.
 
 Some people also use "right" to mean the right hand side when an observer
 looks at the front of the scanner, from the foot the scanner bed.

nibabel/arrayproxy.py

@@ -42,11 +42,14 @@
 used for the lifetime of the ``ArrayProxy``. It should be set to one of
 ``True``, ``False``, or ``'auto'``.
 
-If ``True``, a single file handle is created and used. If ``False``, a new
-file handle is created every time the image is accessed. For gzip files, if
-``'auto'``, and the optional ``indexed_gzip`` dependency is present, a single
-file handle is created and persisted. If ``indexed_gzip`` is not available,
-behaviour is the same as if ``keep_file_open is False``.
+Management of file handles will be performed either by ``ArrayProxy`` objects,
+or by the ``indexed_gzip`` package if it is used.
+
+If this flag is set to ``True``, a single file handle is created and used. If
+``False``, a new file handle is created every time the image is accessed. For
+gzip files, if ``'auto'``, and the optional ``indexed_gzip`` dependency is
+present, a single file handle is created and persisted. If ``indexed_gzip`` is
+not available, behaviour is the same as if ``keep_file_open is False``.
 
 If this is set to any other value, attempts to create an ``ArrayProxy`` without
 specifying the ``keep_file_open`` flag will result in a ``ValueError`` being
@@ -160,8 +163,10 @@ def __init__(self, file_like, spec, mmap=True, keep_file_open=None):
         # Permit any specifier that can be interpreted as a numpy dtype
         self._dtype = np.dtype(self._dtype)
         self._mmap = mmap
-        self._keep_file_open = self._should_keep_file_open(file_like,
-                                                           keep_file_open)
+        # Flags to keep track of whether a single ImageOpener is created, and
+        # whether a single underlying file handle is created.
+        self._keep_file_open, self._persist_opener = \
+            self._should_keep_file_open(file_like, keep_file_open)
         self._lock = RLock()
 
     def __del__(self):
@@ -184,16 +189,64 @@ def __setstate__(self, state):
         self._lock = RLock()
 
     def _should_keep_file_open(self, file_like, keep_file_open):
-        """Called by ``__init__``, and used to determine the final value of
-        ``keep_file_open``.
+        """Called by ``__init__``.
+
+        This method determines how to manage ``ImageOpener`` instances,
+        and the underlying file handles - the behaviour depends on:
+
+         - whether ``file_like`` is an an open file handle, or a path to a
+           ``'.gz'`` file, or a path to a non-gzip file.
+         - whether ``indexed_gzip`` is present (see
+           :attr:`.openers.HAVE_INDEXED_GZIP`).
+
+        An ``ArrayProxy`` object uses two internal flags to manage
+        ``ImageOpener`` instances and underlying file handles.
+
+          - The ``_persist_opener`` flag controls whether a single
+            ``ImageOpener`` should be created and used for the lifetime of
+            this ``ArrayProxy``, or whether separate ``ImageOpener`` instances
+            should be created on each file access.
+
+          - The ``_keep_file_open`` flag controls qwhether the underlying file
+            handle should be kept open for the lifetime of this
+            ``ArrayProxy``, or whether the file handle should be (re-)opened
+            and closed on each file access.
+
+        The internal ``_keep_file_open`` flag is only relevant if
+        ``file_like`` is a ``'.gz'`` file, and the ``indexed_gzip`` library is
+        present.
+
+        This method returns the values to be used for the internal
+        ``_persist_opener`` and ``_keep_file_open`` flags; these values are
+        derived according to the following rules:
 
-        The return value is derived from these rules:
+        1. If ``file_like`` is a file(-like) object, both flags are set to
+        ``False``.
 
-          - If ``file_like`` is a file(-like) object, ``False`` is returned.
-            Otherwise, ``file_like`` is assumed to be a file name.
-          - If ``keep_file_open`` is ``auto``, and ``indexed_gzip`` is
-            not available, ``False`` is returned.
-          - Otherwise, the value of ``keep_file_open`` is returned unchanged.
+        2. If ``keep_file_open`` (as passed to :meth:``__init__``) is
+           ``True``, both internal flags are set to ``True``.
+
+        3. If ``keep_file_open`` is ``False``, but ``file_like`` is not a path
+           to a ``.gz`` file or ``indexed_gzip`` is not present, both flags
+           are set to ``False``.
+
+        4. If ``keep_file_open`` is ``False``, ``file_like`` is a path to a
+           ``.gz`` file, and ``indexed_gzip`` is present, ``_persist_opener``
+           is set to ``True``, and ``_keep_file_open`` is set to ``False``.
+           In this case, file handle management is delegated to the
+           ``indexed_gzip`` library.
+
+        5. If ``keep_file_open`` is ``'auto'``, ``file_like`` is a path to a
+           ``.gz`` file, and ``indexed_gzip`` is present, both internal flags
+           are set to ``True``.
+
+        6. If ``keep_file_open`` is ``'auto'``, and ``file_like`` is not a
+           path to a ``.gz`` file, or ``indexed_gzip`` is not present, both
+           internal flags are set to ``False``.
+
+        Note that a value of ``'auto'`` for ``keep_file_open`` will become
+        deprecated behaviour in version 2.4.0, and support for ``'auto'`` will
+        be removed in version 3.0.0.
 
         Parameters
         ----------
@@ -206,8 +259,10 @@ def _should_keep_file_open(self, file_like, keep_file_open):
         Returns
         -------
 
-        The value of ``keep_file_open`` that will be used by this
-        ``ArrayProxy``, and passed through to ``ImageOpener`` instances.
+        A tuple containing:
+          - ``keep_file_open`` flag to control persistence of file handles
+          - ``persist_opener`` flag to control persistence of ``ImageOpener``
+            objects.
         """
         if keep_file_open is None:
             keep_file_open = KEEP_FILE_OPEN_DEFAULT
@@ -216,12 +271,15 @@ def _should_keep_file_open(self, file_like, keep_file_open):
                              '\'auto\', True, False}')
         # file_like is a handle - keep_file_open is irrelevant
         if hasattr(file_like, 'read') and hasattr(file_like, 'seek'):
-            return False
-        # don't have indexed_gzip - auto -> False
-        if keep_file_open == 'auto' and not (openers.HAVE_INDEXED_GZIP and
-                                             file_like.endswith('.gz')):
-            return False
-        return keep_file_open
+            return False, False
+        # if the file is a gzip file, and we have_indexed_gzip,
+        have_igzip = openers.HAVE_INDEXED_GZIP and file_like.endswith('.gz')
+        if keep_file_open == 'auto':
+            return have_igzip, have_igzip
+        elif keep_file_open:
+            return True, True
+        else:
+            return False, have_igzip
 
     @property
     @deprecate_with_version('ArrayProxy.header deprecated', '2.2', '3.0')
@@ -232,6 +290,10 @@ def header(self):
     def shape(self):
         return self._shape
 
+    @property
+    def ndim(self):
+        return len(self.shape)
+
     @property
     def dtype(self):
         return self._dtype
@@ -265,13 +327,14 @@ def _get_fileobj(self):
             A newly created ``ImageOpener`` instance, or an existing one,
             which provides access to the file.
         """
-        if self._keep_file_open:
+        if self._persist_opener:
             if not hasattr(self, '_opener'):
                 self._opener = openers.ImageOpener(
                     self.file_like, keep_open=self._keep_file_open)
             yield self._opener
         else:
-            with openers.ImageOpener(self.file_like) as opener:
+            with openers.ImageOpener(
+                    self.file_like, keep_open=False) as opener:
                 yield opener
 
     def get_unscaled(self):

nibabel/casting.py

@@ -268,6 +268,9 @@ 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
+        ret.update(dict(nmant=nmant, nexp=nexp, width=width))
+        return ret
     # Oh dear, we don't recognize the type information.  Try some known types
     # and then give up. At this stage we're expecting exotic longdouble or
     # their complex equivalent.