fix: conflict with cifti additions

Author: satra

.coveragerc

@@ -3,7 +3,7 @@ branch = True
 source = nibabel, nisext
 include = */nibabel/*, */nisext/*
 omit =
-    nibabel/externals/*
-    nibabel/benchmarks/*
-    nisext/ast.py
-    nisext/codegen.py
+    */externals/*
+    */benchmarks/*
+    */ast.py
+    */codegen.py

.gitignore

@@ -77,3 +77,4 @@ Thumbs.db
 ###################################
 doc/source/reference
 venv/
+.buildbot.patch

.gitmodules

@@ -0,0 +1,12 @@
+[submodule "nibabel-data/nitest-balls1"]
+	path = nibabel-data/nitest-balls1
+	url = https://github.com/yarikoptic/nitest-balls1
+[submodule "nibabel-data/nitest-minc2"]
+	path = nibabel-data/nitest-minc2
+	url = git://github.com/matthew-brett/nitest-minc2.git
+[submodule "nipy-ecattest"]
+	path = nibabel-data/nipy-ecattest
+	url = https://github.com/freec84/nipy-ecattest
+[submodule "nibabel-data/nitest-freesurfer"]
+	path = nibabel-data/nitest-freesurfer
+	url = https://bitbucket.org/nipy/nitest-freesurfer.git

.mailmap

@@ -20,3 +20,10 @@ Jean-Baptiste Poline <[email protected]> jbpoline <[email protected]>
 Félix C. Morency <[email protected]> Felix C. Morency <[email protected]> Félix C. Morency <[email protected]>
 Félix C. Morency <[email protected]> Félix C. Morency <[email protected]>
 Krish Subramaniam <[email protected]> Krish Subramaniam <[email protected]>
+Eric Larson <[email protected]> Eric89GXL <[email protected]>
+Alexandre Gramfort <[email protected]> Alexandre Gramfort <[email protected]>
+Gael Varoquaux <[email protected]> GaelVaroquaux <[email protected]>
+Kevin S. Hahn <[email protected]> Kevin S. Hahn <[email protected]>
+Basile Pinsard <[email protected]> bpinsard <[email protected]>
+Basile Pinsard <[email protected]> bpinsard <[email protected]>
+Nguyen, Ly <[email protected]> lxn2 <[email protected]>

.travis.yml

@@ -4,6 +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
 language: python
+env:
+    global:
+        - DEPENDS="numpy scipy matplotlib h5py"
+        - PYDICOM=1
 python:
     - 2.6
     - 3.2
@@ -13,26 +17,59 @@ matrix:
   include:
     - python: 2.7
       env:
-        - COVERAGE=--with-coverage
+        - COVERAGE=1
+    # Absolute minimum dependencies
+    - python: 2.7
+      env:
+        - DEPENDS=numpy==1.5.1 PYDICOM=0
+    # Minimum pydicom dependency
+    - python: 2.7
+      env:
+        - DEPENDS="numpy==1.5.1 pydicom==0.9.7"
+    # Documentation doctests
+    - python: 2.7
+      env:
+        - DOC_DOC_TEST=1
 before_install:
+    - virtualenv --python=python venv
+    - source venv/bin/activate
+    - python --version # just to check
+    - pip install nose # always
+    - pip install --no-index -f http://travis-wheels.scikit-image.org $DEPENDS
     # pydicom <= 0.9.8 doesn't install on python 3
-    - if [[ "${TRAVIS_PYTHON_VERSION:0:1}" < "3" ]]; then
-      pip install pydicom;
+    - if [ "${TRAVIS_PYTHON_VERSION:0:1}" == "2" ]; then
+        if [ "$PYDICOM" == "1" ]; then
+            pip install pydicom;
+        fi
       fi
-    - if [ "${COVERAGE}" == "--with-coverage" ]; then
+    - if [ "${COVERAGE}" == "1" ]; then
       pip install coverage;
       pip install coveralls;
       fi
+    - if [[ $DEPENDS == *h5py* ]]; then
+      sudo apt-get install libhdf5-serial-dev;
+      fi
 # command to install dependencies
-# e.g. pip install -r requirements.txt # --use-mirrors
 install:
     - python setup.py install
+    # Point to nibabel data directory
+    - export NIBABEL_DATA_DIR="$PWD/nibabel-data"
 # command to run tests, e.g. python setup.py test
 script:
     # Change into an innocuous directory and find tests from installation
     - mkdir for_testing
     - cd for_testing
-    - if [ "${COVERAGE}" == "--with-coverage" ]; then cp ../.coveragerc .; fi
-    - nosetests --with-doctest $COVERAGE `python -c "import os; import nibabel; print(os.path.dirname(nibabel.__file__))"`
+    - if [ "${COVERAGE}" == "1" ]; then
+      cp ../.coveragerc .;
+      COVER_ARGS="--with-coverage --cover-package nibabel";
+      fi
+    - if [ "$DOC_DOC_TEST" == "1" ]; then
+      pip install sphinx;
+      cd ../doc;
+      make html;
+      make doctest;
+      else
+      nosetests --with-doctest $COVER_ARGS nibabel;
+      fi
 after_success:
-    - if [ "${COVERAGE}" == "--with-coverage" ]; then coveralls; fi
+    - if [ "${COVERAGE}" == "1" ]; then coveralls; fi

COPYING

@@ -2,7 +2,6 @@
 .. ex: set sts=4 ts=4 sw=4 et tw=79:
 .. vim:syntax=rest
 
-
 .. _license:
 
 **********************
@@ -19,12 +18,12 @@ documentation is covered by the MIT license.
 
   The MIT License
 
-  Copyright (c) 2009-2011 Matthew Brett <[email protected]>
-  Copyright (c) 2010-2011 Stephan Gerhard <[email protected]>
-  Copyright (c) 2006-2010 Michael Hanke <[email protected]>
+  Copyright (c) 2009-2014 Matthew Brett <[email protected]>
+  Copyright (c) 2010-2013 Stephan Gerhard <[email protected]>
+  Copyright (c) 2006-2014 Michael Hanke <[email protected]>
   Copyright (c) 2011 Christian Haselgrove <[email protected]>
   Copyright (c) 2010-2011 Jarrod Millman <[email protected]>
-  Copyright (c) 2011-2012 Yaroslav Halchenko <[email protected]>
+  Copyright (c) 2011-2014 Yaroslav Halchenko <[email protected]>
 
   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
@@ -45,8 +44,8 @@ documentation is covered by the MIT license.
   THE SOFTWARE.
 
 
-3rd Party Code
-==============
+3rd party code and data
+=======================
 
 Some code distributed within the nibabel sources was developed by other
 projects. This code is distributed under its respective licenses that are
@@ -151,7 +150,6 @@ subject to the following conditions:
     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
 --------------------------------
 
@@ -171,3 +169,38 @@ following license (where 'softwware' refers to the image):
     implied warranty.  The authors are not responsible for any data loss,
     equipment damage, property loss, or injury to subjects or patients
     resulting from the use or misuse of this software package.
+
+Philips PAR/REC data
+--------------------
+
+The files::
+
+    nibabel/tests/data/phantom_EPI_asc_CLEAR_2_1.PAR
+    nibabel/tests/data/phantom_EPI_asc_CLEAR_2_1.REC
+    nibabel/tests/data/Phantom_EPI_3mm_cor_20APtrans_15RLrot_SENSE_15_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_cor_SENSE_8_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_sag_15AP_SENSE_13_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_sag_15FH_SENSE_12_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_sag_15RL_SENSE_11_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_sag_SENSE_7_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_tra_-30AP_10RL_20FH_SENSE_14_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_tra_15FH_SENSE_9_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_tra_15RL_SENSE_10_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_tra_SENSE_6_1.PAR
+
+are from http://psydata.ovgu.de/philips_achieva_testfiles, and released under
+the PDDL version 1.0 available at http://opendatacommons.org/licenses/pddl/1.0/
+
+The files::
+
+    nibabel/nibabel/tests/data/DTI.PAR
+    nibabel/nibabel/tests/data/NA.PAR
+    nibabel/nibabel/tests/data/T1.PAR
+    nibabel/nibabel/tests/data/T2-interleaved.PAR
+    nibabel/nibabel/tests/data/T2.PAR
+    nibabel/nibabel/tests/data/T2_-interleaved.PAR
+    nibabel/nibabel/tests/data/T2_.PAR
+    nibabel/nibabel/tests/data/fieldmap.PAR
+
+are from https://github.com/yarikoptic/nitest-balls1, also released under the
+the PDDL version 1.0 available at http://opendatacommons.org/licenses/pddl/1.0/

Changelog

@@ -9,10 +9,6 @@ NiBabel Development Changelog
 NiBabel is the successor to the much-loved PyNifti package. Here we list the
 releases for both packages.
 
-'Close gh-' statements refer to GitHub issues that are available at::
-
-  http://github.com/nipy/nibabel/issues
-
 The full VCS changelog is available here:
 
   http://github.com/nipy/nibabel/commits/master
@@ -23,20 +19,76 @@ Releases
 NiBabel
 +++++++
 
-Most work on NiBabel so far has been by Matthew Brett (MB) and Michael Hanke
-(MH) and Stephan Gerhard (SG). Recently there have been large contributions from
-Krish Subramaniam, Alexandre Gramfort, Cindee Madison, Félix C. Morency,
-Christian Haselgrove.
-
-* Upcoming (TBA)
-
-  * Nifti2 read / write support
-  * Read support for Minc2
-  * bug fix in freesurfer.read_annot with orig_ids=False when annot contains
-    vertices with no label.
+Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH)
+and Stephan Gerhard (SG).
+
+* 2.0.0 (Tuesday 9 December 2014)
+
+  This release had large contributions from Eric Larson, Brendan Moloney,
+  Nolan Nichols, Basile Pinsard, Chris Johnson and Nikolaas N. Oosterhof.
+
+  * New feature, bugfix release with minor API breakage;
+  * Minor API breakage: default write of NIfTI / Analyze image data offset
+    value. The data offset is the number of bytes from the beginning of file
+    to skip before reading the image data.  Nibabel behavior changed from
+    keeping the value as read from file, to setting the offset to zero on
+    read, and setting the offset when writing the header. The value of the
+    offset will now be the minimum value necessary to make room for the header
+    and any extensions when writing the file. You can override the default
+    offset by setting value explicitly to some value other than zero. To read
+    the original data offset as read from the header, use the ``offset``
+    property of the image ``dataobj`` attribute;
+  * Minor API breakage: data scaling in NIfTI / Analyze now set to NaN when
+    reading images.  Data scaling refers to the data intercept and slope
+    values in the NIfTI / Analyze header.  To read the original data scaling
+    you need to look at the ``slope`` and ``inter`` properties of the image
+    ``dataobj`` attribute.  You can set scaling explicitly by setting the
+    slope and intercept values in the header to values other than NaN;
+  * New API for managing image caching; images have an ``in_memory`` property
+    that is true if the image data has been loaded into cache, or is already
+    an array in memory; ``get_data`` has new keyword argument ``caching`` to
+    specify whether the cache should be filled by ``get_data``;
+  * Images now have properties ``dataobj``, ``affine``, ``header``. We will
+    slowly phase out the ``get_affine`` and ``get_header`` image methods;
+  * The image ``dataobj`` can be sliced using an efficient algorithm to avoid
+    reading unnecessary data from disk.  This makes it possible to do very
+    efficient reads of single volumes from a time series;
+  * NIfTI2 read / write support;
+  * Read support for MINC2;
+  * Much extended read support for PAR / REC, largely due to work from Eric
+    Larson and Gregory R. Lee on new code, advice and code review. Thanks also
+    to Jeff Stevenson and Bennett Landman for helpful discussion;
+  * ``parrec2nii`` script outputs images in LAS voxel orientation, which
+    appears to be necessary for compatibility with FSL ``dtifit`` /
+    ``fslview`` diffusion analysis pipeline;
+  * Preliminary support for Philips multiframe DICOM images (thanks to Nolan
+    Nichols, Ly Nguyen and Brendan Moloney);
+  * New function to save Freesurfer annotation files (by Github user ohinds);
+  * Method to return MGH format ``vox2ras_tkr`` affine (Eric Larson);
+  * A new API for reading unscaled data from NIfTI and other images, using
+    ``img.dataobj.get_unscaled()``. Deprecate previous way of doing this,
+    which was to read data with the ``read_img_data`` function;
+  * Fix for bug when replacing NaN values with zero when writing floating
+    point data as integers.  If the input floating point data range did not
+    include zero, then NaN would not get written to a value corresponding to
+    zero in the output;
+  * Improvements and bug fixes to image orientation calculation and DICOM
+    wrappers by Brendan Moloney;
+  * Bug fixes writing GIfTI files. We were using a base64 encoding that didn't
+    match the spec, and the wrong field name for the endian code. Thanks to
+    Basile Pinsard and Russ Poldrack for diagnosis and fixes;
+  * Bug fix in ``freesurfer.read_annot`` with ``orig_ids=False`` when annot
+    contains vertices with no label (Alexandre Gramfort);
+  * More tutorials in the documentation, including introductory tutorial on
+    DICOM, and on coordinate systems;
+  * Lots of code refactoring, including moving to common code-base for Python
+    2 and Python 3;
+  * New mechanism to add images for tests via git submodules.
 
 * 1.3.0 (Tuesday 11 September 2012)
 
+  Special thanks to Chris Johnson, Brendan Moloney and JB Poline.
+
   * New feature and bugfix release
   * Add ability to write Freesurfer triangle files (Chris Johnson)
   * Relax threshold for detecting rank deficient affines in orientation
@@ -55,7 +107,8 @@ Christian Haselgrove.
 
 * 1.2.1 (Wednesday 13 June 2012)
 
-  Particular thanks to Yaroslav Halchecko for fixes and cleanups in this release
+  Particular thanks to Yaroslav Halchecko for fixes and cleanups in this
+  release.
 
   * Bugfix release
   * Make compatible with pydicom 0.9.7
@@ -67,6 +120,9 @@ Christian Haselgrove.
 
 * 1.2.0 (Sunday 6 May 2012)
 
+  This release had large contributions from Krish Subramaniam, Alexandre
+  Gramfort, Cindee Madison, Félix C. Morency and Christian Haselgrove.
+
   * New feature and bugfix release
   * Freesurfer format support by Krish Subramaniam and Alexandre Gramfort.
   * ECAT read write support by Cindee Madison and Félix C. Morency.
@@ -83,6 +139,8 @@ Christian Haselgrove.
 
 * 1.1.0 (Thursday 28 April 2011)
 
+  Special thanks to Chris Burns, Jarrod Millman and Yaroslav Halchenko.
+
   * New feature release
   * Python 3.2 support
   * Substantially enhanced gifti reading support (SG)

Makefile

@@ -281,5 +281,8 @@ tox-stale:
 	# installed)
 	tox -e python25,python26,python27,python32,np-1.2.1
 
+refresh-readme:
+	$(PYTHON) tools/refresh_readme.py
+
 .PHONY: orig-src pylint