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Commit 6374ede

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Merge branch 'loadsave-pathlib_compat' of https://github.com/CRiddler/nibabel into loadsave-pathlib_compat
2 parents 6056014 + cf63106 commit 6374ede

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‎.azure-pipelines/windows.yml‎

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

‎.gitmodules‎

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[submodule "nibabel-data/nitest-cifti2"]
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path = nibabel-data/nitest-cifti2
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url = https://github.com/demianw/nibabel-nitest-cifti2.git
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[submodule "nibabel-data/nitest-dicom"]
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path = nibabel-data/nitest-dicom
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url = https://github.com/effigies/nitest-dicom

‎.pep8speaks.yml‎

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‎.travis.yml‎

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

‎.zenodo.json‎

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

‎Changelog‎

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

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py35-x64:
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PYTHON_VERSION: '3.5'
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PYTHON_ARCH: 'x64'
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py35-h5py-check:
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PYTHON_VERSION: '3.5'
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PYTHON_ARCH: 'x64'
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PYTHONHASHSEED: 283137131
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DEPENDS: "h5py==2.9.0"
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py36-x86:
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PYTHON_VERSION: '3.6'
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PYTHON_ARCH: 'x86'

‎doc/source/coordinate_systems.rst‎

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If the subject is lying in the usual position for a brain scan, face up
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and head first in the scanner, then scanner-left/right is also the left-right
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axis of the subject's head, scanner-floor/ceiling is the posterior-anterior
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axis of the subject's head, scanner-floor/ceiling is the anterior-posterior
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axis of the head and scanner-bore is the inferior-superior axis of the head.
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Sometimes the subject is not lying in the standard position. For example, the
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system in neuroimaging is called "scanner RAS" (right, anterior, superior).
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Here the scanner axes are reordered and flipped so that the first axis is the
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scanner axis that is closest to the left to right axis of the subject, the
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second is the closest scanner axis to the posterior-anterior axis of the
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second is the closest scanner axis to the anterior-posterior axis of the
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subject, and the third is the closest scanner axis to the inferior-superior
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axis of the subject. For example, if the subject was lying face to the right
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in the scanner, then the first (X) axis of the reference system would be
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scanner-floor/ceiling, but reversed so that positive values are towards the
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floor. This axis goes from left to right in the subject, with positive values
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to the right. The second (Y) axis would be scanner-left/right
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(posterior-anterior in the subject), and the Z axis would be scanner-bore
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(anterior-posterior in the subject), and the Z axis would be scanner-bore
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(inferior-superior).
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Naming reference spaces

‎doc/source/index.rst‎

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* Matt Cieslak
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* Egor Pafilov
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* Jath Palasubramaniam
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* Henry Braun
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License reprise
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===============

‎nibabel-data/nitest-dicom‎

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