REVERT: Restore dfd113c for testing

Author: effigies

.travis.yml

@@ -4,10 +4,11 @@
 # 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:
     - $HOME/.cache/pip
@@ -21,14 +22,11 @@ env:
         - EXTRA_PIP_FLAGS="--find-links=$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

@@ -121,40 +121,36 @@ Sphinx 0.6 doesn't work properly.
   OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
   DAMAGE.
 
-OrderedSet
+Ordereddict
 -----------
 
-In ``nibabel/externals/oset.py``
+In ``nibabel/externals/ordereddict.py``
 
-Copied from: https://files.pythonhosted.org/packages/d6/b1/a49498c699a3fda5d635cc1fa222ffc686ea3b5d04b84a3166c4cab0c57b/oset-0.1.3.tar.gz
+Copied from: https://pypi.python.org/packages/source/o/ordereddict/ordereddict-1.1.tar.gz#md5=a0ed854ee442051b249bfad0f638bbec
 
 ::
 
-    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.
+  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.
 
 mni_icbm152_t1_tal_nlin_asym_09a
 --------------------------------

Changelog

@@ -24,68 +24,25 @@ Gerhard (SG) and Eric Larson (EL).
 
 References like "pr/298" refer to github pull request numbers.
 
-2.3 (Tuesday 12 June 2018)
-==========================
+Upcoming Release
+================
 
 New features
 ------------
-* TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed by CM)
 * Image slicing for SpatialImages (pr/550) (CM)
 
 Enhancements
 ------------
 * Simplfiy MGHImage and add footer fields (pr/569) (CM, reviewed by MB)
-* Force sform/qform codes to be ints, rather than numpy types (pr/575) (Paul
-  McCarthy, reviewed by MB, CM)
-* Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul McCarthy,
-  reviewed by CM, MB)
-* Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves,
-  reviewed by CM, Satra Ghosh, MB, Tim Coalson)
-* Raise informative error on empty files (pr/611) (Pradeep Raamana, reviewed
-  by CM, MB)
-* Accept degenerate filenames such as ``.nii`` (pr/621) (Dimitri
-  Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko)
-* Take advantage of ``IndexedGzipFile`` ``drop_handles`` flag to release
-  filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB)
 
 Bug fixes
 ---------
-* Preserve first point of `LazyTractogram` (pr/588) (MC, reviewed by Nil
-  Goyette, CM, MB)
-* Stop adding extraneous metadata padding (pr/593) (Jon Stutters, reviewed by
-  CM, MB)
-* Accept lower-case orientation codes in TRK files (pr/600) (Kesshi Jordan,
-  MB, reviewed by MB, MC, CM)
-* Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB)
-* Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro,
-  reviewed by MC, MB, Eleftherios Garyfallidis, CM)
-* Resolve ``UnboundLocalError`` in Python 3 (pr/607) (Jakub Kaczmarzyk,
-  reviewed by MB, CM)
-* Do not crash on non-``ImportError`` failures in optional imports (pr/618)
-  (Yaroslav Halchenko, reviewed by CM)
-* Return original array from ``get_fdata`` for array image, if no cast
-  required (pr/638, MB, reviewed by CM)
 
 Maintenance
 -----------
-* Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB)
-* Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by CM)
-* Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM)
-* Increase test coverage, remove unreachable code (pr/602) (CM, reviewed by 
-  Yaroslav Halchenko, MB)
-* Move ``nib-ls`` and other programs to a new cmdline module (pr/601, pr/615)
-  (Chris Cheng, reviewed by MB, Yaroslav Halchenko)
-* Remove deprecated numpy indexing (EL, reviewed by CM)
-* Update documentation to encourage ``get_fdata`` over ``get_data`` (pr/637,
-  MB, reviewed by CM)
 
 API changes and deprecations
 ----------------------------
-* Support for ``keep_file_open = 'auto'`` as a parameter to ``Opener()`` will
-  be deprecated in 2.4, for removal in 3.0. Accordingly, support for
-  ``openers.KEEP_FILE_OPEN_DEFAULT = 'auto'`` will be dropped on the same
-  schedule.
-* Drop-in support for ``indexed_gzip < 0.7`` has been removed.
 
 
 2.2.1 (Wednesday 22 November 2017)

appveyor.yml

@@ -12,8 +12,6 @@ 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
@@ -22,7 +20,8 @@ install:
   - SET PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
 
   # Install the dependencies of the project.
-  - pip install numpy scipy matplotlib nose h5py mock pydicom
+  - pip install numpy scipy matplotlib nose h5py mock
+  - pip install pydicom
   - pip install .
   - SET NIBABEL_DATA_DIR=%CD%\nibabel-data
 

bin/nib-diff

@@ -87,7 +87,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = u'2006-2018, %(MAINTAINER)s <%(AUTHOR_EMAIL)s>' % rel
+copyright = u'2006-2017, %(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/conf.py

@@ -34,7 +34,7 @@ We can load up the EPI image to get the image data array:
 
     >>> import nibabel as nib
     >>> epi_img = nib.load('downloads/someones_epi.nii.gz')
-    >>> epi_img_data = epi_img.get_fdata()
+    >>> epi_img_data = epi_img.get_data()
     >>> epi_img_data.shape
     (53, 61, 33)
 
@@ -64,7 +64,7 @@ and look at slices in the three axes:
     :context:
 
     >>> anat_img = nib.load('downloads/someones_anatomy.nii.gz')
-    >>> anat_img_data = anat_img.get_fdata()
+    >>> anat_img_data = anat_img.get_data()
     >>> anat_img_data.shape
     (57, 67, 56)
     >>> show_slices([anat_img_data[28, :, :],
@@ -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, Superior are all positive values on these axes.
+Anterior, Posterior 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.

doc/source/coordinate_systems.rst

@@ -77,10 +77,10 @@ flag when anyone asks for the data, on the basis that the user may then
 do something to the data and you can't know if they have::
 
    img = nibabel.load('some_image.nii')
-   data = img.get_fdata()
+   data = img.get_data()
    data[:] = 0
    img2 = nibabel.load('some_image.nii')
-   assert not np.all(img2.get_fdata() == img.get_fdata())
+   assert not np.all(img2.get_data() == img.get_data())
 
 The image consists of the data, the affine and a header.  In order to
 keep track of the header and affine, we could cache them when loading
@@ -96,7 +96,7 @@ When we need to know whether the image object and image file correspond, we
 could check the current header and current affine (the header may be separate
 from the affine for an SPM Analyze image) against their cached copies, if they
 are the same and the 'dirty' flag has not been set by a previous call to
-``get_fdata()``, we know that the image file does correspond to the image
+``get_data()``, we know that the image file does correspond to the image
 object.
 
 This may be OK for small bits of memory like the affine and the header,

doc/source/devel/modified_images.rst

@@ -66,7 +66,7 @@ This information is available without the need to load anything of the main
 image data into the memory. Of course there is also access to the image data as
 a NumPy_ array
 
->>> data = img.get_fdata()
+>>> data = img.get_data()
 >>> data.shape
 (128, 96, 24, 2)
 >>> type(data)