Merge branch 'master' into loadsave-pathlib_compat

Author: CRiddler

.azure-pipelines/windows.yml

@@ -10,6 +10,7 @@ jobs:
     vmImage: ${{ parameters.vmImage }}
   variables:
     EXTRA_WHEELS: "https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
+    DEPENDS: numpy scipy matplotlib h5py pydicom
   strategy:
     matrix:
       ${{ insert }}: ${{ parameters.matrix }}
@@ -20,11 +21,14 @@ jobs:
         versionSpec: '$(PYTHON_VERSION)'
         addToPath: true
         architecture: '$(PYTHON_ARCH)'
+    - script: |
+        echo %PYTHONHASHSEED%
+      displayName: 'Display hash seed'
     - script: |
         python -m pip install --upgrade pip setuptools>=30.3.0 wheel
       displayName: 'Update build tools'
     - script: |
-        python -m pip install --find-links %EXTRA_WHEELS% numpy scipy matplotlib h5py pydicom
+        python -m pip install --find-links %EXTRA_WHEELS% %DEPENDS%
         python -m pip install nose mock coverage codecov
       displayName: 'Install dependencies'
     - script: |

.gitmodules

@@ -16,3 +16,6 @@
 [submodule "nibabel-data/nitest-cifti2"]
 	path = nibabel-data/nitest-cifti2
 	url = https://github.com/demianw/nibabel-nitest-cifti2.git
+[submodule "nibabel-data/nitest-dicom"]
+	path = nibabel-data/nitest-dicom
+	url = https://github.com/effigies/nitest-dicom

.pep8speaks.yml

@@ -0,0 +1,12 @@
+scanner:
+    diff_only: True  # Only show errors caused by the patch
+    linter: flake8
+
+message:  # Customize the comment made by the bot
+    opened:  # Messages when a new PR is submitted
+        header: "Hello @{name}, thank you for submitting the Pull Request!"
+        footer: "To test for issues locally, `pip install flake8` and then run `flake8 nibabel`."
+    updated:  # Messages when new commits are added to the PR
+        header: "Hello @{name}, Thank you for updating!"
+        footer: "To test for issues locally, `pip install flake8` and then run `flake8 nibabel`."
+    no_errors: "Cheers! There are no style issues detected in this Pull Request. :beers: "

.travis.yml

@@ -8,38 +8,39 @@ dist: xenial
 sudo: true
 language: python
 
-cache:
-  directories:
-    - $HOME/.cache/pip
+cache: pip
 env:
     global:
-        - DEPENDS="six numpy scipy matplotlib h5py pillow pydicom"
-        - OPTIONAL_DEPENDS=""
+        - SETUP_REQUIRES="pip setuptools>=30.3.0 wheel"
+        - DEPENDS="numpy scipy matplotlib h5py pillow pydicom indexed_gzip"
         - INSTALL_TYPE="setup"
         - CHECK_TYPE="test"
         - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
         - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
         - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
         - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
+
 python:
     - 3.6
     - 3.7
+
 matrix:
   include:
-    # Absolute minimum dependencies
+    # Basic dependencies only
     - python: 3.5
       env:
-        - DEPENDS="-r min-requirements.txt setuptools==30.3.0"
+        - DEPENDS="-r requirements.txt"
+    # Clean install
+    - python: 3.5
+      env:
+        - DEPENDS=""
+        - CHECK_TYPE=skiptests
     # Absolute minimum dependencies
     - python: 3.5
       env:
+        - SETUP_REQUIRES="setuptools==30.3.0"
         - DEPENDS="-r min-requirements.txt"
-        - CHECK_TYPE="import"
     # Absolute minimum dependencies plus oldest MPL
-    # Check these against:
-    # nibabel/info.py
-    # doc/source/installation.rst
-    # requirements.txt
     - python: 3.5
       env:
         - DEPENDS="-r min-requirements.txt matplotlib==1.3.1"
@@ -51,8 +52,8 @@ matrix:
     - python: 3.5
       env:
         - DEPENDS="numpy git+https://github.com/pydicom/pydicom.git@master"
-    # test 3.5 against pre-release builds of everything
-    - python: 3.5
+    # test 3.7 against pre-release builds of everything
+    - python: 3.7
       env:
         - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
     - python: 3.5
@@ -61,9 +62,6 @@ matrix:
     - python: 3.5
       env:
         - INSTALL_TYPE=wheel
-    - python: 3.5
-      env:
-        - INSTALL_TYPE=requirements
     - python: 3.5
       env:
         - INSTALL_TYPE=archive
@@ -73,62 +71,55 @@ matrix:
     # Documentation doctests
     - python: 3.5
       env:
-        - CHECK_TYPE="doc_doctests"
-    # Run tests with indexed_gzip present
-    - python: 3.5
-      env:
-        - OPTIONAL_DEPENDS="indexed_gzip"
+        - CHECK_TYPE="doc"
+
+# Set up virtual environment, build package, build from depends
 before_install:
-    - travis_retry python -m pip install --upgrade pip
-    - travis_retry pip install --upgrade virtualenv
+    - travis_retry python -m pip install --upgrade pip virtualenv
     - virtualenv --python=python venv
     - source venv/bin/activate
     - python --version # just to check
-    - travis_retry pip install -U pip setuptools>=27.0 wheel
-    - travis_retry pip install coverage
-    - if [ "${CHECK_TYPE}" == "test" ]; then
-      travis_retry pip install nose mock;
-      fi
-    - if [ "${CHECK_TYPE}" == "style" ]; then
-      travis_retry pip install flake8;
+    - travis_retry pip install -U $SETUP_REQUIRES
+    - |
+      if [ "$INSTALL_TYPE" == "sdist" ]; then
+        python setup.py egg_info  # check egg_info while we're here
+        python setup.py sdist
+        export ARCHIVE=$( ls dist/*.tar.gz )
+      elif [ "$INSTALL_TYPE" == "wheel" ]; then
+        python setup.py bdist_wheel
+        export ARCHIVE=$( ls dist/*.whl )
+      elif [ "$INSTALL_TYPE" == "archive" ]; then
+        export ARCHIVE="package.tar.gz"
+        git archive -o $ARCHIVE HEAD
       fi
-    - travis_retry pip install $EXTRA_PIP_FLAGS $DEPENDS $OPTIONAL_DEPENDS
+    - if [ -n "$DEPENDS" ]; then pip install $EXTRA_PIP_FLAGS $DEPENDS; fi
+
 # command to install dependencies
 install:
     - |
       if [ "$INSTALL_TYPE" == "setup" ]; then
           python setup.py install
-      elif [ "$INSTALL_TYPE" == "sdist" ]; then
-          python setup_egg.py egg_info  # check egg_info while we're here
-          python setup_egg.py sdist
-          pip install $EXTRA_PIP_FLAGS dist/*.tar.gz
-      elif [ "$INSTALL_TYPE" == "wheel" ]; then
-          python setup_egg.py bdist_wheel
-          pip install $EXTRA_PIP_FLAGS dist/*.whl
-      elif [ "$INSTALL_TYPE" == "requirements" ]; then
-          pip install $EXTRA_PIP_FLAGS -r requirements.txt
-          python setup.py install
-      elif [ "$INSTALL_TYPE" == "archive" ]; then
-          git archive -o package.tar.gz HEAD
-          pip install $EXTRA_PIP_FLAGS package.tar.gz
+      else
+          pip install $EXTRA_PIP_FLAGS $ARCHIVE
       fi
+    # Basic import check
+    - python -c 'import nibabel; print(nibabel.__version__)'
+    - if [ "$CHECK_TYPE" == "skiptests" ]; then exit 0; fi
+
+before_script:
     # Point to nibabel data directory
     - export NIBABEL_DATA_DIR="$PWD/nibabel-data"
+    # Because nibabel is already installed, will just look up the extra
+    - pip install $EXTRA_PIP_FLAGS "nibabel[$CHECK_TYPE]"
+
 # command to run tests, e.g. python setup.py test
 script:
     - |
       if [ "${CHECK_TYPE}" == "style" ]; then
           # Run styles only on core nibabel code.
           flake8 nibabel
-      elif [ "${CHECK_TYPE}" == "import" ]; then
-          # Import nibabel without attempting to test
-          # Allows us to check missing dependencies masked by testing libraries
-          printf 'import nibabel\nprint(nibabel.__version__)\n' > import_only.py
-          cat import_only.py
-          coverage run import_only.py
-      elif [ "${CHECK_TYPE}" == "doc_doctests" ]; then
+      elif [ "${CHECK_TYPE}" == "doc" ]; then
           cd doc
-          pip install -r ../doc-requirements.txt
           make html;
           make doctest;
       elif [ "${CHECK_TYPE}" == "test" ]; then
@@ -140,12 +131,10 @@ script:
       else
           false
       fi
-after_success:
-    - |
-      if [ "${CHECK_TYPE}" == "test" ]; then
-        travis_retry pip install codecov
-        codecov
-      fi
+
+after_script:
+    - travis_retry pip install codecov
+    - codecov
 
 notifications:
     webhooks: http://nipy.bic.berkeley.edu:54856/travis

.zenodo.json

@@ -87,6 +87,11 @@
     {
       "name": "Moloney, Brendan"
     },
+    {
+      "affiliation": "MIT",
+      "name": "Goncalves, Mathias",
+      "orcid": "0000-0002-7252-7771"
+    },
     {
       "name": "Burns, Christopher"
     },
@@ -130,11 +135,6 @@
     {
       "name": "Baker, Eric M."
     },
-    {
-      "affiliation": "MIT",
-      "name": "Goncalves, Mathias",
-      "orcid": "0000-0002-7252-7771"
-    },
     {
       "name": "Hayashi, Soichi"
     },
@@ -244,6 +244,11 @@
       "name": "P\u00e9rez-Garc\u00eda, Fernando",
       "orcid": "0000-0001-9090-3024"
     },
+    {
+      "affiliation": "Center for Magnetic Resonance Research, University of Minnesota",
+      "name": "Braun, Henry",
+      "orcid": "0000-0001-7003-9822"
+    },
     {
       "name": "Solovey, Igor"
     },

Changelog

@@ -25,6 +25,33 @@ Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.
 
 References like "pr/298" refer to github pull request numbers.
 
+2.5.1 (Monday 23 September 2019)
+================================
+
+Enhancements
+------------
+* Ignore endianness in ``nib-diff`` if values match (pr/799) (YOH, reviewed
+  by CM)
+
+Bug fixes
+---------
+* Correctly handle Philips DICOMs w/ derived volume (pr/795) (Mathias
+  Goncalves, reviewed by CM)
+* Raise CSA tag limit to 1000, parametrize for future relaxing (pr/798,
+  backported to 2.5.x in pr/800) (Henry Braun, reviewed by CM, MB)
+* Coerce data types to match NIfTI intent codes when writing GIFTI data
+  arrays (pr/806) (CM, reported by Tom Holroyd)
+
+Maintenance
+-----------
+* Require h5py 2.10 for Windows + Python < 3.6 to resolve unexpected dtypes
+  in Minc2 data (pr/804) (CM, reviewed by YOH)
+
+API changes and deprecations
+----------------------------
+* Deprecate ``nicom.dicomwrappers.Wrapper.get_affine()`` in favor of ``affine``
+  property; final removal in nibabel 4.0 (pr/796) (YOH, reviewed by CM)
+
 2.5.0 (Sunday 4 August 2019)
 ============================
 

azure-pipelines.yml

@@ -11,6 +11,11 @@ jobs:
       py35-x64:
         PYTHON_VERSION: '3.5'
         PYTHON_ARCH: 'x64'
+      py35-h5py-check:
+        PYTHON_VERSION: '3.5'
+        PYTHON_ARCH: 'x64'
+        PYTHONHASHSEED: 283137131
+        DEPENDS: "h5py==2.9.0"
       py36-x86:
         PYTHON_VERSION: '3.6'
         PYTHON_ARCH: 'x86'

doc/source/coordinate_systems.rst

@@ -215,7 +215,7 @@ 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 subject's head, scanner-floor/ceiling is the posterior-anterior
 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
@@ -231,14 +231,14 @@ position of the subject.  The most common subject-centered scanner coordinate
 system in neuroimaging is called "scanner RAS" (right, anterior, superior).
 Here the scanner axes are reordered and flipped so that the first axis is the
 scanner axis that is closest to the left to right axis of the subject, the
-second is the closest scanner axis to the anterior-posterior axis of the
+second is the closest scanner axis to the posterior-anterior axis of the
 subject, and the third is the closest scanner axis to the inferior-superior
 axis of the subject.  For example, if the subject was lying face to the right
 in the scanner, then the first (X) axis of the reference system would be
 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
+(posterior-anterior in the subject), and the Z axis would be scanner-bore
 (inferior-superior).
 
 Naming reference spaces

doc/source/index.rst

@@ -98,6 +98,7 @@ contributed code and discussion (in rough order of appearance):
 * Matt Cieslak
 * Egor Pafilov
 * Jath Palasubramaniam
+* Henry Braun
 
 License reprise
 ===============

nibabel-data/nitest-dicom

@@ -23,7 +23,7 @@
    img2 = nib.load('other_file.nii.gz')
    img3 = nib.load('spm_file.img')
 
-   data = img1.get_data()
+   data = img1.get_fdata()
    affine = img1.affine
 
    print(img1)

nibabel/__init__.py

@@ -0,0 +1,12 @@
+import sys
+import os
+from .optpkg import optional_package
+
+# PY35: A bug affected Windows installations of h5py in Python3 versions <3.6
+# due to random dictionary ordering, causing float64 data arrays to sometimes be
+# loaded as longdouble (also 64 bit on Windows). This caused stochastic failures
+# to correctly handle data caches, and possibly other subtle bugs we never
+# caught. This was fixed in h5py 2.10.
+# Please see https://github.com/nipy/nibabel/issues/665 for details.
+min_h5py = '2.10' if os.name == 'nt' and (3,) <= sys.version_info < (3, 6) else None
+h5py, have_h5py, setup_module = optional_package('h5py', min_version=min_h5py)