Merge remote-tracking branch 'upstream/master' into rel/2.3.1

Author: effigies

.travis.yml

@@ -4,29 +4,31 @@
 # 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:
     - $HOME/.cache/pip
 env:
     global:
-        - DEPENDS="six numpy scipy matplotlib h5py pillow pydicom"
+        - DEPENDS="six numpy scipy matplotlib h5py pillow pydicom hypothesis"
         - OPTIONAL_DEPENDS=""
         - INSTALL_TYPE="setup"
         - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
         - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
         - EXTRA_PIP_FLAGS="--find-links=$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
@@ -95,7 +97,7 @@ before_install:
     - source venv/bin/activate
     - python --version # just to check
     - pip install -U pip wheel  # needed at one point
-    - retry pip install nose flake8 mock  # always
+    - retry pip install nose flake8 mock hypothesis  # always
     - pip install $EXTRA_PIP_FLAGS $DEPENDS $OPTIONAL_DEPENDS
     - if [ "${COVERAGE}" == "1" ]; then
       pip install coverage;

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
 --------------------------------

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 hypothesis 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()

dev-requirements.txt

@@ -2,3 +2,4 @@
 -r requirements.txt
 nose
 mock
+hypothesis

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/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.

nibabel/cifti2/parse_cifti2.py

@@ -517,28 +517,28 @@ def flush_chardata(self):
             # conversion to numpy array
             c = BytesIO(data.strip().encode('utf-8'))
             vertices = self.struct_state[-1]
-            vertices.extend(np.genfromtxt(c, dtype=np.int))
+            vertices.extend(np.loadtxt(c, dtype=np.int))
             c.close()
 
         elif self.write_to == 'VoxelIndices':
             # conversion to numpy array
             c = BytesIO(data.strip().encode('utf-8'))
             parent = self.struct_state[-1]
-            parent.voxel_indices_ijk.extend(np.genfromtxt(c, dtype=np.int).reshape(-1, 3))
+            parent.voxel_indices_ijk.extend(np.loadtxt(c, dtype=np.int).reshape(-1, 3))
             c.close()
 
         elif self.write_to == 'VertexIndices':
             # conversion to numpy array
             c = BytesIO(data.strip().encode('utf-8'))
             index = self.struct_state[-1]
-            index.extend(np.genfromtxt(c, dtype=np.int))
+            index.extend(np.loadtxt(c, dtype=np.int))
             c.close()
 
         elif self.write_to == 'TransformMatrix':
             # conversion to numpy array
             c = BytesIO(data.strip().encode('utf-8'))
             transform = self.struct_state[-1]
-            transform.matrix = np.genfromtxt(c, dtype=np.float)
+            transform.matrix = np.loadtxt(c, dtype=np.float)
             c.close()
 
         elif self.write_to == 'Label':