Merge branch 'master' into orthoview_vlim

Author: effigies

.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 +28,15 @@ 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>

.travis.yml

@@ -12,21 +12,19 @@ sudo: false
 cache:
   directories:
     - $HOME/.cache/pip
-addons:
-  apt:
-    packages:
-      - libhdf5-serial-dev
-      # For numpy --pre wheels
-      - libatlas-base-dev
 env:
     global:
-        - DEPENDS="numpy scipy matplotlib h5py pillow"
+        - DEPENDS="six numpy scipy matplotlib h5py pillow"
         - PYDICOM=1
         - INSTALL_TYPE="setup"
+        - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
+        - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
+        - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
+        - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
 python:
-    - 3.3
     - 3.4
     - 3.5
+    - 3.6
 matrix:
   include:
     - python: 2.7
@@ -35,19 +33,19 @@ matrix:
     # Absolute minimum dependencies
     - python: 2.7
       env:
-        - DEPENDS=numpy==1.5.1 PYDICOM=0
+        - DEPENDS="numpy==1.7.1" PYDICOM=0
     # Absolute minimum dependencies plus oldest MPL
     # Check these against:
+    # nibabel/info.py
     # doc/source/installation.rst
     # requirements.txt
-    # .travis.yml
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.5.1 matplotlib==1.3.1" PYDICOM=0
+        - DEPENDS="numpy==1.7.1 matplotlib==1.3.1" PYDICOM=0
     # Minimum pydicom dependency
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.5.1 pydicom==0.9.7 pillow==2.6"
+        - DEPENDS="numpy==1.7.1 pydicom==0.9.7 pillow==2.6"
     # test against numpy 1.7
     - python: 2.7
       env:
@@ -56,10 +54,14 @@ matrix:
     - python: 2.7
       env:
         - PYDICOM="v1.0"
-    # test against pre-release builds
+    # test 2.7 against pre-release builds of everything
     - python: 2.7
       env:
-        - EXTRA_PIP_FLAGS="--pre"
+        - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
+    # test 3.5 against pre-release builds of everything
+    - python: 3.5
+      env:
+        - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
     # Documentation doctests
     - python: 2.7
       env:
@@ -84,12 +86,14 @@ matrix:
         - DOC_DOC_TEST=1
 before_install:
     - source tools/travis_tools.sh
+    - python -m pip install --upgrade pip
+    - pip install --upgrade virtualenv
     - virtualenv --python=python venv
     - source venv/bin/activate
     - python --version # just to check
-    - pip install -U pip wheel  # upgrade to latest pip find 3.5 wheels; wheel to avoid errors
+    - pip install -U pip wheel  # needed at one point
     - retry pip install nose flake8 mock  # always
-    - wheelhouse_pip_install $EXTRA_PIP_FLAGS $DEPENDS
+    - pip install $EXTRA_PIP_FLAGS $DEPENDS
     # pydicom <= 0.9.8 doesn't install on python 3
     - if [ "${TRAVIS_PYTHON_VERSION:0:1}" == "2" ]; then
         if [ "$PYDICOM" == "1" ]; then
@@ -111,13 +115,13 @@ install:
       elif [ "$INSTALL_TYPE" == "sdist" ]; then
           python setup_egg.py egg_info  # check egg_info while we're here
           python setup_egg.py sdist
-          wheelhouse_pip_install $EXTRA_PIP_FLAGS dist/*.tar.gz
+          pip install $EXTRA_PIP_FLAGS dist/*.tar.gz
       elif [ "$INSTALL_TYPE" == "wheel" ]; then
           pip install wheel
           python setup_egg.py bdist_wheel
-          wheelhouse_pip_install $EXTRA_PIP_FLAGS dist/*.whl
+          pip install $EXTRA_PIP_FLAGS dist/*.whl
       elif [ "$INSTALL_TYPE" == "requirements" ]; then
-          wheelhouse_pip_install $EXTRA_PIP_FLAGS -r requirements.txt
+          pip install $EXTRA_PIP_FLAGS -r requirements.txt
           python setup.py install
       fi
     # Point to nibabel data directory

Changelog

@@ -24,6 +24,58 @@ Gerhard (SG) and Eric Larson (EL).
 
 References like "pr/298" refer to github pull request numbers.
 
+Upcoming Release
+================
+
+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)
+
+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)
+
+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
+-----------
+
+* 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``
+
+
 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

bin/nib-ls

@@ -19,11 +19,9 @@ import numpy as np
 import nibabel as nib
 
 from math import ceil
-from collections import defaultdict
 from optparse import OptionParser, Option
 from io import StringIO
 from nibabel.py3k import asunicode
-from nibabel.externals.six.moves import xrange
 
 __author__ = 'Yaroslav Halchenko'
 __copyright__ = 'Copyright (c) 2011-2016 Yaroslav Halchenko ' \

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

@@ -22,8 +22,6 @@
 import sys
 import os
 
-import nibabel
-
 # Check for external Sphinx extensions we depend on
 try:
     import numpydoc
@@ -34,6 +32,13 @@
 except ImportError:
     raise RuntimeError('Need to install "texext" package for doc build')
 
+# Need nibabel installed as well
+try:
+    import nibabel
+except ImportError:
+    raise RuntimeError('Need nibabel on Python PATH; consider "make htmldoc" '
+                       'from nibabel root directory')
+
 # 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.
@@ -82,7 +87,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = u'2006-2016, %(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/coordinate_systems.rst

@@ -97,11 +97,11 @@ middle voxel in the EPI data array like this:
     :nofigs:
 
     >>> n_i, n_j, n_k = epi_img_data.shape
-    >>> center_i = (n_i - 1) / 2.
-    >>> center_j = (n_j - 1) / 2.
-    >>> center_k = (n_k - 1) / 2.
+    >>> center_i = (n_i - 1) // 2  # // for integer division
+    >>> center_j = (n_j - 1) // 2
+    >>> center_k = (n_k - 1) // 2
     >>> center_i, center_j, center_k
-    (26.0, 30.0, 16.0)
+    (26, 30, 16)
     >>> center_vox_value = epi_img_data[center_i, center_j, center_k]
     >>> center_vox_value
     81.549287796020508
@@ -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\\
@@ -515,16 +515,16 @@ We could record the parameters necessary for $f$ as the 3 by 3 matrix, $M$
 and the 3 by 1 vector $(a, b, c)$.
 
 In fact, the 4 by 4 image *affine array* does include exactly this
-information. If $m_{ij}$ is the value in row $i$ column $j$ of matrix $M$,
+information. If $m_{i,j}$ is the value in row $i$ column $j$ of matrix $M$,
 then the image affine matrix $A$ is:
 
 .. math::
 
     A =
     \begin{bmatrix}
-    m_{11} & m_{12} & m_{13} & a \\
-    m_{21} & m_{22} & m_{23} & b \\
-    m_{31} & m_{32} & m_{33} & c \\
+    m_{1,1} & m_{1,2} & m_{1,3} & a \\
+    m_{2,1} & m_{2,2} & m_{2,3} & b \\
+    m_{3,1} & m_{3,2} & m_{3,3} & c \\
     0 & 0 & 0 & 1 \\
     \end{bmatrix}
 
@@ -546,9 +546,9 @@ vectors:
     1\\
     \end{bmatrix} =
     \begin{bmatrix}
-    m_{11} & m_{12} & m_{13} & a \\
-    m_{21} & m_{22} & m_{23} & b \\
-    m_{31} & m_{32} & m_{33} & c \\
+    m_{1,1} & m_{1,2} & m_{1,3} & a \\
+    m_{2,1} & m_{2,2} & m_{2,3} & b \\
+    m_{3,1} & m_{3,2} & m_{3,3} & c \\
     0 & 0 & 0 & 1 \\
     \end{bmatrix}
     \begin{bmatrix}
@@ -614,6 +614,19 @@ matrix.  Put another way:
     1\\
     \end{bmatrix}
 
+    A^{-1}\begin{bmatrix}
+    x\\
+    y\\
+    z\\
+    1\\
+    \end{bmatrix} = A^{-1} A
+    \begin{bmatrix}
+    i\\
+    j\\
+    k\\
+    1\\
+    \end{bmatrix}
+
     \begin{bmatrix}
     i\\
     j\\

doc/source/dicom/dicom_orientation.rst

@@ -58,12 +58,12 @@ Section 10.7.1.3:  Pixel Spacing
 DICOM voxel to patient coordinate system mapping
 ================================================
 
-See: 
+See:
 
-* http://www.dclunie.com/medical-image-faq/html/part2.html
-* http://fixunix.com/dicom/50449-image-position-patient-image-orientation-patient.html
+* http://www.dclunie.com/medical-image-faq/html/part2.html;
+* `this dicom mailing list post <https://groups.google.com/forum/#!topic/comp.protocols.dicom/-Nms_GgmdRc>`_;
 
-See `wikipedia direction cosine`_ for a definition of direction cosines. 
+See `wikipedia direction cosine`_ for a definition of direction cosines.
 
 From section C.7.6.2.1.1 of the `DICOM object definitions`_ (2009):
 

doc/source/index.rst

@@ -70,6 +70,14 @@ contributed code and discussion (in rough order of appearance):
 * `Ariel Rokem`_
 * Eleftherios Garyfallidis
 * Jaakko Leppäkangas
+* Syam Gadde
+* Robert D. Vincent
+* Ivan Gonzalez
+* Demian Wassermann
+* Paul McCarthy
+* Fernando Pérez García
+* Venky Reddy
+* Mark Hymers
 
 License reprise
 ===============