Merge branch 'master' of github.com:nipy/nibabel

Author: raamana

.gitmodules

@@ -13,3 +13,6 @@
 [submodule "nibabel-data/parrec_oblique"]
 	path = nibabel-data/parrec_oblique
 	url = https://github.com/grlee77/parrec_oblique.git
+[submodule "nibabel-data/nitest-cifti2"]
+	path = nibabel-data/nitest-cifti2
+	url = https://github.com/demianw/nibabel-nitest-cifti2.git

.mailmap

@@ -17,7 +17,7 @@ Cindee Madison <cindee@berkeley.edu> CindeeM <cindee@berkeley.edu>
 Cindee Madison <cindee@berkeley.edu> cindeem <cindee@berkeley.edu>
 Ian Nimmo-Smith <iannimmosmith@gmail.com> Ian Nimmo-Smith <ian.nimmo-smith@mrc-cbu.cam.ac.uk>
 Jean-Baptiste Poline <jbpoline@gmail.com> jbpoline <jbpoline@gmail.com>
-Félix C. Morency <felix.morency@gmail.com> Felix C. Morency <felix.c.morency@usherbrooke.ca> Félix C. Morency <felix.c.morency@usherbrooke.ca>
+Félix C. Morency <felix.morency@gmail.com> Felix C. Morency <felix.c.morency@usherbrooke.ca>
 Félix C. Morency <felix.morency@gmail.com> Félix C. Morency <felix.c.morency@usherbrooke.ca>
 Krish Subramaniam <krish.subramaniam@gmail.com> Krish Subramaniam <krish@monster.nmr.mgh.harvard.edu>
 Eric Larson <larson.eric.d@gmail.com> Eric89GXL <larson.eric.d@gmail.com>
@@ -28,10 +28,16 @@ Basile Pinsard <basile.pinsard@gmail.com> bpinsard <basile.pinsard@gmail.com>
 Basile Pinsard <basile.pinsard@gmail.com> bpinsard <bpinsard@imed.jussieu.fr>
 Nguyen, Ly <nguyen60@seattleu.edu> lxn2 <lxn2@uw.edu>
 Ben Cipollini <ben.cipollini@gmail.com> Ben Cipollini <bcipolli@ucsd.edu>
+Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <markiewicz@stanford.edu>
 Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@bu.edu>
 Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@gmail.com>
 Chris Markiewicz <effigies@gmail.com> Chris Johnson <effigies@bu.edu>
 Jaakko Leppäkangas <jaeilepp@student.jyu.fi> jaeilepp <jaeilepp@student.jyu.fi>
 Ariel Rokem <arokem@gmail.com> arokem <arokem@gmail.com>
 Oliver P. Hinds <ohinds@gmail.com> ohinds <ohinds@gmail.com>
 Marc-Alexandre Côté <marc.cote.19@gmail.com> Marc-Alexandre Cote <marc.cote.19@gmail.com>
+Satrajit Ghosh <satra@mit.edu> Satrajit Ghosh <satrajit.ghosh@gmail.com>
+Jasper J.F. van den Bosch <japsai@gmail.com> Jasper <japsai@gmail.com>
+Gregory R. Lee <grlee77@gmail.com> Gregory R. Lee <gregory.lee@cchmc.org>
+Demian Wassermann <demian@bwh.harvard.edu> Demian Wassermann <demian.wassermann@inria.fr>
+Paul McCarthy <pauldmccarthy@gmail.com> Paul McCarthy <pauld.mccarthy@gmail.com>

.travis.yml

@@ -15,6 +15,7 @@ cache:
 env:
     global:
         - DEPENDS="six numpy scipy matplotlib h5py pillow"
+        - OPTIONAL_DEPENDS=""
         - PYDICOM=1
         - INSTALL_TYPE="setup"
         - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
@@ -33,19 +34,19 @@ matrix:
     # Absolute minimum dependencies
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.6.0" PYDICOM=0
+        - DEPENDS="numpy==1.7.1" PYDICOM=0
     # Absolute minimum dependencies plus oldest MPL
     # Check these against:
     # nibabel/info.py
     # doc/source/installation.rst
     # requirements.txt
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.6.0 matplotlib==1.3.1" PYDICOM=0
+        - DEPENDS="numpy==1.7.1 matplotlib==1.3.1" PYDICOM=0
     # Minimum pydicom dependency
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.6.0 pydicom==0.9.7 pillow==2.6"
+        - DEPENDS="numpy==1.7.1 pydicom==0.9.7 pillow==2.6"
     # test against numpy 1.7
     - python: 2.7
       env:
@@ -84,6 +85,13 @@ matrix:
     - python: 3.5
       env:
         - DOC_DOC_TEST=1
+    # Run tests with indexed_gzip present
+    - python: 2.7
+      env:
+        - OPTIONAL_DEPENDS="indexed_gzip"
+    - python: 3.5
+      env:
+        - OPTIONAL_DEPENDS="indexed_gzip"
 before_install:
     - source tools/travis_tools.sh
     - python -m pip install --upgrade pip
@@ -93,7 +101,7 @@ before_install:
     - python --version # just to check
     - pip install -U pip wheel  # needed at one point
     - retry pip install nose flake8 mock  # always
-    - pip install $EXTRA_PIP_FLAGS $DEPENDS
+    - pip install $EXTRA_PIP_FLAGS $DEPENDS $OPTIONAL_DEPENDS
     # pydicom <= 0.9.8 doesn't install on python 3
     - if [ "${TRAVIS_PYTHON_VERSION:0:1}" == "2" ]; then
         if [ "$PYDICOM" == "1" ]; then

Changelog

@@ -24,6 +24,84 @@ Gerhard (SG) and Eric Larson (EL).
 
 References like "pr/298" refer to github pull request numbers.
 
+2.2.1 (Wednesday 22 November 2017)
+==================================
+
+Bug fixes
+---------
+
+* Set L/R labels in orthoview correctly (pr/564) (CM)
+* Defer use of ufunc / memmap test - allows "freezing" (pr/572) (MB, reviewed
+  by Satra Ghosh)
+* Fix doctest failures with pre-release numpy (pr/582) (MB, reviewed by CM)
+
+Maintenance
+-----------
+
+* Update documentation around NIfTI qform/sform codes (pr/576) (Paul McCarthy,
+  reviewed by MB, CM) + (pr/580) (Bennet Fauber, reviewed by Paul McCarthy)
+* Skip precision test on macOS, newer numpy (pr/583) (MB, reviewed by CM)
+* Simplify AppVeyor script, removing conda (pr/584) (MB, reviewed by CM)
+
+2.2 (Friday 13 October 2017)
+============================
+
+New features
+------------
+
+* CIFTI support (pr/249) (Satra Ghosh, Michiel Cottaar, BC, CM, Demian
+  Wassermann, MB)
+* Support for MRtrix TCK streamlines file format (pr/486) (MC, reviewed by
+  MB, Arnaud Bore, J-Donald Tournier, Jean-Christophe Houde)
+* Added ``get_fdata()`` as default method to retrieve scaled floating point
+  data from ``DataobjImage``s (pr/551) (MB, reviewed by CM, Satra Ghosh)
+
+Enhancements
+------------
+
+* Support for alternative header field name variants in .PAR files
+  (pr/507) (Gregory R. Lee)
+* Various enhancements to streamlines API by MC: support for reading TRK
+  version 1 (pr/512); concatenation of tractograms using `+`/`+=` operators
+  (pr/495); function to concatenate multiple ArraySequence objects (pr/494)
+* Support for numpy 1.12 (pr/500, pr/502) (MC, MB)
+* Allow dtype specifiers as fileslice input (pr/485) (MB)
+* Support "headerless" ArrayProxy specification, enabling memory-efficient
+  ArrayProxy reshaping (pr/521) (CM)
+* Allow unknown NIfTI intent codes, add FSL codes (pr/528) (Paul McCarthy)
+* Improve error handling for ``img.__getitem__`` (pr/533) (Ariel Rokem)
+* Delegate reorientation to SpatialImage classes (pr/544) (Mark Hymers, CM,
+  reviewed by MB)
+* Enable using ``indexed_gzip`` to reduce memory usage when reading from
+  gzipped NIfTI and MGH files (pr/552) (Paul McCarthy, reviewed by MB, CM)
+
+Bug fixes
+---------
+
+* Miscellaneous MINC reader fixes (pr/493) (Robert D. Vincent, reviewed by CM,
+  MB)
+* Fix corner case in ``wrapstruct.get`` (pr/516) (Paul McCarthy, reviewed by
+  CM, MB)
+
+Maintenance
+-----------
+
+* Fix documentation errors (pr/517, pr/536) (Fernando Perez, Venky Reddy)
+* Documentation update (pr/514) (Ivan Gonzalez)
+* Update testing to use pre-release builds of dependencies (pr/509) (MB)
+* Better warnings when nibabel not on path (pr/503) (MB)
+
+API changes and deprecations
+----------------------------
+
+* ``header`` argument to ``ArrayProxy.__init__`` is renamed to ``spec``
+* Deprecation of ``header`` property of ``ArrayProxy`` object, for removal in
+  3.0
+* ``wrapstruct.get`` now returns entries evaluating ``False``, instead of ``None``
+* ``DataobjImage.get_data`` to be deprecated April 2018, scheduled for removal
+  April 2020
+
+
 2.1 (Monday 22 August 2016)
 ===========================
 

Makefile

@@ -288,4 +288,4 @@ rm-orig:
 	# Remove .orig temporary diff files generated by git
 	find . -name "*.orig" -print | grep -v "fsaverage" | xargs rm
 
-.PHONY: orig-src pylint
+.PHONY: orig-src pylint all build

appveyor.yml

@@ -1,60 +1,34 @@
 # vim ft=yaml
 # CI on Windows via appveyor
-# This file was based on Olivier Grisel's python-appveyor-demo
 
 environment:
 
   matrix:
-    - PYTHON: "C:\\Python27-conda32"
-      PYTHON_VERSION: "2.7"
-      PYTHON_ARCH: "32"
-
-    - PYTHON: "C:\\Python34-conda32"
-      PYTHON_VERSION: "3.4"
-      PYTHON_ARCH: "32"
-
-    - PYTHON: "C:\\Python34-conda64"
-      PYTHON_VERSION: "3.4"
-      PYTHON_ARCH: "64"
-
-    - PYTHON: "C:\\Python35-conda64"
-      PYTHON_VERSION: "3.5"
-      PYTHON_ARCH: "64"
-
-    - PYTHON: "C:\\Python35-conda32"
-      PYTHON_VERSION: "3.5"
-      PYTHON_ARCH: "32"
+    - PYTHON: C:\Python27
+    - PYTHON: C:\Python27-x64
+    - PYTHON: C:\Python34
+    - PYTHON: C:\Python34-x64
+    - PYTHON: C:\Python35
+    - PYTHON: C:\Python35-x64
+    - PYTHON: C:\Python36
+    - PYTHON: C:\Python36-x64
 
 install:
-  # Install miniconda Python
-  - "powershell ./tools/install_python.ps1"
-
   # Prepend newly installed Python to the PATH of this build (this cannot be
   # done from inside the powershell script as it would require to restart
   # the parent CMD process).
-  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
-
-  # Set up a conda environment:
-  - conda config --set always_yes yes
-  - conda update -q conda
-  - conda info -a
-  - conda create -q -n test-environment python=%PYTHON_VERSION%
-  - activate test-environment
-
-  # Check that we have the expected version and architecture for Python
-  - "python --version"
-  - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
+  - SET PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
 
   # Install the dependencies of the project.
-  - "conda install --yes --quiet numpy scipy matplotlib nose h5py mock"
-  - "pip install pydicom"
-  - "python setup.py install"
-  - "SET NIBABEL_DATA_DIR=%CD%\\nibabel-data"
+  - pip install numpy scipy matplotlib nose h5py mock
+  - pip install pydicom
+  - pip install .
+  - SET NIBABEL_DATA_DIR=%CD%\nibabel-data
 
 build: false  # Not a C# project, build stuff at the test step instead.
 
 test_script:
   # Change into an innocuous directory and find tests from installation
-  - "mkdir for_testing"
-  - "cd for_testing"
-  - "nosetests --with-doctest nibabel"
+  - mkdir for_testing
+  - cd for_testing
+  - nosetests --with-doctest nibabel

doc-requirements.txt

@@ -1,6 +1,7 @@
 # Requirements for building docs
 -r requirements.txt
-sphinx
+# Sphinx >= 1.6 breaks the math_dollar extension
+sphinx<=1.5.6
 numpydoc
 texext
 matplotlib>=1.3

doc/Makefile

@@ -1,6 +1,10 @@
 # Makefile for Sphinx documentation
 #
 
+# The Python executable to be used
+#
+PYTHON ?= python
+
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
@@ -98,4 +102,3 @@ gitwash-update:
 	python ../tools/gitwash_dumper.py source nibabel --github-user=nipy \
 		--project-url=http://nipy.org/nibabel \
 		--project-ml-url=https://mail.python.org/mailman/listinfo/neuroimaging
-

doc/source/conf.py

@@ -42,7 +42,7 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.append(os.path.abspath('../sphinxext'))
+# sys.path.append(os.path.abspath('../sphinxext'))
 
 # -- General configuration ----------------------------------------------------
 

doc/source/coordinate_systems.rst

@@ -216,7 +216,7 @@ From scanner to subject
 If the subject is lying in the usual position for a brain scan, face up
 and head first in the scanner, then scanner-left/right is also the left-right
 axis of the subject's head, scanner-floor/ceiling is the anterior-posterior
-axis of the head and scanner-bore is the inferior-posterior axis of the head.
+axis of the head and scanner-bore is the inferior-superior axis of the head.
 
 Sometimes the subject is not lying in the standard position.  For example, the
 subject may be lying with their face pointing to the right (in terms of the
@@ -239,7 +239,7 @@ scanner-floor/ceiling, but reversed so that positive values are towards the
 floor.  This axis goes from left to right in the subject, with positive values
 to the right.  The second (Y) axis would be scanner-left/right
 (anterior-posterior in the subject), and the Z axis would be scanner-bore
-(inferior-posterior).
+(inferior-superior).
 
 Naming reference spaces
 =======================
@@ -386,8 +386,8 @@ A rotation of $\gamma$ radians around the first array axis:
     \end{bmatrix} =
     \begin{bmatrix}
     1 & 0 & 0 \\
-    0 & \cos(\gamma) & 0 & -\sin(\gamma) \\
-    0 & \sin(\gamma) & 0 & \cos(\gamma) \\
+    0 & \cos(\gamma) & -\sin(\gamma) \\
+    0 & \sin(\gamma) & \cos(\gamma) \\
     \end{bmatrix}
     \begin{bmatrix}
     i\\