Merge branch 'master' of git://github.com/nipy/nipype into enh/selectdirs

Author: mgxd

.travis.yml

@@ -11,6 +11,7 @@ env:
 - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler"
 - INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler"
 - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit"
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre"
 before_install:
 - function apt_inst {
   if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi &&
@@ -36,12 +37,17 @@ before_install:
   conda install python=${TRAVIS_PYTHON_VERSION} &&
   conda config --add channels conda-forge &&
   conda install -y nipype icu &&
-  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*; }
+  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*;
+  pushd $HOME;
+  git clone https://github.com/INCF/pybids.git;
+  cd pybids;
+  pip install -e .;
+  popd; }
 #  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi
 - travis_retry apt_inst
 - travis_retry conda_inst
 install:
-- travis_retry pip install -e .[$NIPYPE_EXTRAS]
+- travis_retry pip install $PIP_FLAGS -e .[$NIPYPE_EXTRAS]
 script:
 - py.test -v --doctest-modules nipype
 deploy:

.zenodo.json

@@ -523,6 +523,16 @@
       "affiliation": "University of Amsterdam",
       "name": "Lukas Snoek",
       "orcid": "0000-0001-8972-204X"
+    },
+    {
+      "affiliation": "Vrije Universiteit, Amsterdam",
+      "name": "Gilles de Hollander",
+      "orcid": "0000-0003-1988-5091"
+    },
+    {
+      "affiliation": "University of Texas at Austin",
+      "name": "De La Vega, Alejandro",
+      "orcid": "0000-0001-9062-3778"
     }
   ],
   "keywords": [

Dockerfile

@@ -87,6 +87,9 @@ COPY requirements.txt requirements.txt
 RUN pip install -r requirements.txt && \
     rm -rf ~/.cache/pip
 
+RUN git clone https://github.com/INCF/pybids.git && \
+    cd pybids && python setup.py develop
+
 # Installing nipype
 COPY . /src/nipype
 RUN cd /src/nipype && \

doc/devel/gitwash/known_projects.inc

@@ -6,7 +6,7 @@
 .. _`PROJECTNAME mailing list`: http://projects.scipy.org/mailman/listinfo/nipy-devel
 
 .. numpy
-.. _numpy: hhttp://numpy.scipy.org
+.. _numpy: http://numpy.scipy.org
 .. _`numpy github`: http://github.com/numpy/numpy
 .. _`numpy mailing list`: http://mail.scipy.org/mailman/listinfo/numpy-discussion
 

doc/users/install.rst

@@ -47,7 +47,7 @@ use the following command::
 While `all` installs everything, one can also install select components as
 listed below::
 
-    'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus'],
+    'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],
     'tests': ['pytest-cov', 'codecov'],
     'nipy': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'],
     'profiler': ['psutil'],

docker/base.Dockerfile

@@ -109,7 +109,7 @@ ENV PATH=/usr/lib/fsl/5.0:/usr/lib/afni/bin:$ANTSPATH:$PATH
 
 # Installing and setting up c3d
 RUN mkdir -p /opt/c3d && \
-    curl -sSL "http://downloads.sourceforge.net/project/c3d/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz" \
+    curl -sSL "https://files.osf.io/v1/resources/nefdp/providers/osfstorage/59ca96a9b83f69025d6b8985?action=download&version=1&direct" \
     | tar -xzC /opt/c3d --strip-components 1
 
 ENV C3DPATH=/opt/c3d/
@@ -149,4 +149,3 @@ ENV MATLABCMD="/opt/mcr/v85/toolbox/matlab" \
     FORCE_SPMMCR=1
 
 WORKDIR /work
-

examples/dmri_dtk_dti.py

@@ -37,7 +37,6 @@
 
 package_check('numpy', '1.3', 'tutorial1')
 package_check('scipy', '0.7', 'tutorial1')
-package_check('networkx', '1.0', 'tutorial1')
 package_check('IPython', '0.10', 'tutorial1')
 
 

examples/dmri_dtk_odf.py

@@ -37,7 +37,6 @@
 
 package_check('numpy', '1.3', 'tutorial1')
 package_check('scipy', '0.7', 'tutorial1')
-package_check('networkx', '1.0', 'tutorial1')
 package_check('IPython', '0.10', 'tutorial1')
 
 

examples/dmri_fsl_dti.py

@@ -37,7 +37,6 @@
 
 package_check('numpy', '1.3', 'tutorial1')
 package_check('scipy', '0.7', 'tutorial1')
-package_check('networkx', '1.0', 'tutorial1')
 package_check('IPython', '0.10', 'tutorial1')
 
 

examples/fmri_ants_openfmri.py

@@ -26,7 +26,7 @@
 import nipype.pipeline.engine as pe
 import nipype.algorithms.modelgen as model
 import nipype.algorithms.rapidart as ra
-from nipype.algorithms.misc import TSNR
+from nipype.algorithms.misc import TSNR, CalculateMedian
 from nipype.interfaces.c3 import C3dAffineTool
 from nipype.interfaces import fsl, Function, ants, freesurfer as fs
 import nipype.interfaces.io as nio
@@ -55,33 +55,6 @@
     'from scipy.special import legendre'
 ]
 
-def median(in_files):
-    """Computes an average of the median of each realigned timeseries
-
-    Parameters
-    ----------
-
-    in_files: one or more realigned Nifti 4D time series
-
-    Returns
-    -------
-
-    out_file: a 3D Nifti file
-    """
-    average = None
-    for idx, filename in enumerate(filename_to_list(in_files)):
-        img = nb.load(filename, mmap=NUMPY_MMAP)
-        data = np.median(img.get_data(), axis=3)
-        if average is None:
-            average = data
-        else:
-            average = average + data
-    median_img = nb.Nifti1Image(average / float(idx + 1), img.affine,
-                                img.header)
-    filename = os.path.join(os.getcwd(), 'median.nii.gz')
-    median_img.to_filename(filename)
-    return filename
-
 
 def create_reg_workflow(name='registration'):
     """Create a FEAT preprocessing workflow together with freesurfer
@@ -818,11 +791,7 @@ def check_behav_list(behav, run_id, conds):
     wf.connect(preproc, "outputspec.realigned_files", tsnr, "in_file")
 
     # Compute the median image across runs
-    calc_median = Node(Function(input_names=['in_files'],
-                                output_names=['median_file'],
-                                function=median,
-                                imports=imports),
-                       name='median')
+    calc_median = Node(CalculateMedian(), name='median')
     wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
 
     """