Re-pulled in changes from github

Author: pintohutch

.noserc

@@ -0,0 +1,11 @@
+[nosetests]
+verbosity=3
+
+with-coverage=1
+cover-branches=1
+cover-xml=1
+cover-xml-file=./coverage.xml
+cover-min-percentage=50
+
+
+with-xunit=1

.travis.yml

@@ -23,6 +23,8 @@ before_install:
 - if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq fsl-atlases;
   fi
 - if $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; fi
+- if $INSTALL_DEB_DEPENDECIES; then source /etc/afni/afni.sh; fi
+- export FSLOUTPUTTYPE=NIFTI_GZ
 install:
 - conda update --yes conda
 - conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION

CHANGES

@@ -1,6 +1,10 @@
 Next release
 ============
 
+* ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
+* ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
+* TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)
+* ENH: Add new flags to the BRAINSABC for new features (https://github.com/nipy/nipype/pull/1322)
 * ENH: Provides a Nipype wrapper for ANTs DenoiseImage (https://github.com/nipy/nipype/pull/1291)
 * FIX: Minor bugfix logging hash differences (https://github.com/nipy/nipype/pull/1298)
 * FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)

circle.yml

@@ -1,83 +1,71 @@
 dependencies:
   cache_directories:
+    - "~/.apt-cache"
     - "~/examples/data"
     - "~/examples/fsdata"
-    - "~/examples/feeds"
     - "~/mcr"
     - "~/spm12"
-    - "~/fsl"
     - "~/examples/fsl_course_data"
+  pre:
+    # Let CircleCI cache the apt archive
+    - sudo rm -rf /var/cache/apt/archives && sudo ln -s ~/.apt-cache /var/cache/apt/archives && mkdir -p ~/.apt-cache/partial
+    - wget -O- http://neuro.debian.net/lists/precise.us-ca.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
+    - sudo apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9
+    - sudo apt-get update
   override:
+    # Install apt packages
+    - sudo apt-get install -y fsl-core fsl-atlases fsl-mni152-templates fsl-feeds afni
+    - echo "source /etc/fsl/fsl.sh" >> $HOME/.profile
+    - echo "source /etc/afni/afni.sh" >> $HOME/.profile
+    - mkdir -p ~/examples/ && ln -sf /usr/share/fsl-feeds/ ~/examples/feeds
+    # Set up python environment
     - pip install --upgrade pip
     - pip install -e .
-    - pip install matplotlib sphinx ipython boto
+    - pip install matplotlib sphinx ipython boto coverage
     - gem install fakes3
-    - if [[ ! -d ~/fsl ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.9-centos6_64.tar.gz"; tar zxvf fsl-5.0.9-centos6_64.tar.gz; mv fsl ~/fsl; fi
-    - if [[ ! -d ~/examples/data ]]; then wget "http://tcpdiag.dl.sourceforge.net/project/nipy/nipype/nipype-0.2/nipype-tutorial.tar.bz2"; tar jxvf nipype-tutorial.tar.bz2; mkdir ~/examples; mv nipype-tutorial/* ~/examples/; fi
-    # we download this manually because CircleCI does not cache apt
-    - if [[ ! -d ~/examples/feeds ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.9-feeds.tar.gz"; tar zxvf fsl-5.0.9-feeds.tar.gz; mv feeds ~/examples/; fi
-    - if [[ ! -d ~/examples/fsl_course_data ]]; then wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" ; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz"; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz"; mkdir ~/examples/fsl_course_data; tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data; tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data; tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data; fi
+    - if [[ ! -d ~/examples/data ]]; then wget "http://tcpdiag.dl.sourceforge.net/project/nipy/nipype/nipype-0.2/nipype-tutorial.tar.bz2" && tar jxvf nipype-tutorial.tar.bz2 && mv nipype-tutorial/* ~/examples/; fi
+    - if [[ ! -d ~/examples/fsl_course_data ]]; then wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" && wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz" && wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz" && mkdir ~/examples/fsl_course_data && tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data && tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data && tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data; fi
     - bash ~/nipype/tools/install_spm_mcr.sh
-    - mkdir -p ~/.nipype && echo "[logging]" > ~/.nipype/nipype.cfg && echo "workflow_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "interface_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "filemanip_level = DEBUG" >> ~/.nipype/nipype.cfg
+    - mkdir -p ~/.nipype && echo '[logging]' > ~/.nipype/nipype.cfg && echo 'workflow_level = DEBUG' >> ~/.nipype/nipype.cfg && echo 'interface_level = DEBUG' >> ~/.nipype/nipype.cfg && echo 'filemanip_level = DEBUG' >> ~/.nipype/nipype.cfg
+machine:
+  environment:
+    FSLOUTPUTTYPE: NIFTI_GZ
 test:
   override:
-    - nosetests --with-doctest --logging-level=DEBUG --verbosity=3:
+    - mkdir -p ${CIRCLE_TEST_REPORTS}/nose
+    - source $HOME/.profile; nosetests --with-doctest --xunit-file="${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml" -c ./.noserc --logging-level=DEBUG --verbosity=3:
         environment:
           SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
           FORCE_SPMMCR: 1
           FSL_COURSE_DATA: "$HOME/examples/fsl_course_data"
-          FSLDIR: "$HOME/fsl/"
-          PATH: "$HOME/fsl/bin:$PATH"
-          LD_LIBRARY_PATH: "$HOME/fsl/lib"
-          FSLOUTPUTTYPE: "NIFTI_GZ"
         timeout: 2600
     - set -o pipefail && cd doc && make html 2>&1 | tee ~/log.txt
     - cat ~/log.txt && if grep -q "ERROR" ~/log.txt; then false; else true; fi
-    - python ~/nipype/tools/run_examples.py test_spm Linear workflow3d workflow4d:
+    - source $HOME/.profile; python ~/nipype/tools/run_examples.py test_spm Linear workflow3d workflow4d:
         pwd: ../examples
         environment:
           SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
           FORCE_SPMMCR: 1
-          FSLDIR: "$HOME/fsl/"
-          PATH: "$HOME/fsl/bin:$PATH"
-          LD_LIBRARY_PATH: "$HOME/fsl/lib"
-          FSLOUTPUTTYPE: "NIFTI_GZ"
         timeout: 1600
-    - python ~/nipype/tools/run_examples.py fmri_fsl_feeds Linear l1pipeline:
+    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_fsl_feeds Linear l1pipeline:
         pwd: ../examples
-        environment:
-          FSLDIR: "$HOME/fsl/"
-          PATH: "$HOME/fsl/bin:$PATH"
-          LD_LIBRARY_PATH: "$HOME/fsl/lib"
-          FSLOUTPUTTYPE: "NIFTI_GZ"
-    - python ~/nipype/tools/run_examples.py fmri_spm_dartel Linear level1 l2pipeline:
+    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_spm_dartel Linear level1 l2pipeline:
         pwd: ../examples
         environment:
           SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
           FORCE_SPMMCR: 1
-          FSLDIR: "$HOME/fsl/"
-          PATH: "$HOME/fsl/bin:$PATH"
-          LD_LIBRARY_PATH: "$HOME/fsl/lib"
-          FSLOUTPUTTYPE: "NIFTI_GZ"
         timeout: 1600
-    - python ~/nipype/tools/run_examples.py fmri_fsl_reuse Linear level1_workflow:
+    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_fsl_reuse Linear level1_workflow:
         pwd: ../examples
-        environment:
-          FSLDIR: "$HOME/fsl/"
-          PATH: "$HOME/fsl/bin:$PATH"
-          LD_LIBRARY_PATH: "$HOME/fsl/lib"
-          FSLOUTPUTTYPE: "NIFTI_GZ"
-    - python ~/nipype/tools/run_examples.py fmri_spm_nested Linear level1 l2pipeline:
+    - source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_spm_nested Linear level1 l2pipeline:
         pwd: ../examples
         environment:
           SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
           FORCE_SPMMCR: 1
-          FSLDIR: "$HOME/fsl/"
-          PATH: "$HOME/fsl/bin:$PATH"
-          LD_LIBRARY_PATH: "$HOME/fsl/lib"
-          FSLOUTPUTTYPE: "NIFTI_GZ"
 
 general:
   artifacts:
     - "doc/_build/html"
     - "~/log.txt"
+    - "nosetests.xml"
+    - "coverage.xml"

nipype/algorithms/misc.py

@@ -263,6 +263,14 @@ class TSNRInputSpec(BaseInterfaceInputSpec):
     in_file = InputMultiPath(File(exists=True), mandatory=True,
                              desc='realigned 4D file or a list of 3D files')
     regress_poly = traits.Range(low=1, desc='Remove polynomials')
+    tsnr_file = File('tsnr.nii.gz', usedefault=True, hash_files=False,
+                     desc='output tSNR file')
+    mean_file = File('mean.nii.gz', usedefault=True, hash_files=False,
+                     desc='output mean file')
+    stddev_file = File('stdev.nii.gz', usedefault=True, hash_files=False,
+                       desc='output tSNR file')
+    detrended_file = File('detrend.nii.gz', usedefault=True, hash_files=False,
+                          desc='input file after detrending')
 
 
 class TSNROutputSpec(TraitedSpec):
@@ -288,24 +296,18 @@ class TSNR(BaseInterface):
     input_spec = TSNRInputSpec
     output_spec = TSNROutputSpec
 
-    def _gen_output_file_name(self, suffix=None):
-        _, base, ext = split_filename(self.inputs.in_file[0])
-        if suffix in ['mean', 'stddev']:
-            return os.path.abspath(base + "_tsnr_" + suffix + ext)
-        elif suffix in ['detrended']:
-            return os.path.abspath(base + "_" + suffix + ext)
-        else:
-            return os.path.abspath(base + "_tsnr" + ext)
-
     def _run_interface(self, runtime):
         img = nb.load(self.inputs.in_file[0])
         header = img.header.copy()
         vollist = [nb.load(filename) for filename in self.inputs.in_file]
         data = np.concatenate([vol.get_data().reshape(
-            vol.shape[:3] + (-1,)) for vol in vollist], axis=3)
+            vol.get_shape()[:3] + (-1,)) for vol in vollist], axis=3)
+        data = data.nan_to_num()
+
         if data.dtype.kind == 'i':
             header.set_data_dtype(np.float32)
             data = data.astype(np.float32)
+
         if isdefined(self.inputs.regress_poly):
             timepoints = img.shape[-1]
             X = np.ones((timepoints, 1))
@@ -318,26 +320,28 @@ def _run_interface(self, runtime):
                                              betas[1:, :, :, :], 0, 3)),
                                   0, 4)
             data = data - datahat
-            img = nb.Nifti1Image(data, img.affine, header)
-            nb.save(img, self._gen_output_file_name('detrended'))
+            img = nb.Nifti1Image(data, img.get_affine(), header)
+            nb.save(img, op.abspath(self.inputs.detrended_file))
+
         meanimg = np.mean(data, axis=3)
         stddevimg = np.std(data, axis=3)
-        tsnr = meanimg / stddevimg
-        img = nb.Nifti1Image(tsnr, img.affine, header)
-        nb.save(img, self._gen_output_file_name())
-        img = nb.Nifti1Image(meanimg, img.affine, header)
-        nb.save(img, self._gen_output_file_name('mean'))
-        img = nb.Nifti1Image(stddevimg, img.affine, header)
-        nb.save(img, self._gen_output_file_name('stddev'))
+        tsnr = np.zeros_like(meanimg)
+        tsnr[stddevimg > 1.e-3] = meanimg[stddevimg > 1.e-3] / stddevimg[stddevimg > 1.e-3]
+        img = nb.Nifti1Image(tsnr, img.get_affine(), header)
+        nb.save(img, op.abspath(self.inputs.tsnr_file))
+        img = nb.Nifti1Image(meanimg, img.get_affine(), header)
+        nb.save(img, op.abspath(self.inputs.mean_file))
+        img = nb.Nifti1Image(stddevimg, img.get_affine(), header)
+        nb.save(img, op.abspath(self.inputs.stddev_file))
         return runtime
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        outputs['tsnr_file'] = self._gen_output_file_name()
-        outputs['mean_file'] = self._gen_output_file_name('mean')
-        outputs['stddev_file'] = self._gen_output_file_name('stddev')
+        for k in ['tsnr_file', 'mean_file', 'stddev_file']:
+            outputs[k] = op.abspath(getattr(self.inputs, k))
+
         if isdefined(self.inputs.regress_poly):
-            outputs['detrended_file'] = self._gen_output_file_name('detrended')
+            outputs['detrended_file'] = op.abspath(self.inputs.detrended_file)
         return outputs
 
 

nipype/algorithms/tests/test_auto_TSNR.py

@@ -4,12 +4,24 @@
 
 
 def test_TSNR_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
+    input_map = dict(detrended_file=dict(hash_files=False,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
     in_file=dict(mandatory=True,
     ),
+    mean_file=dict(hash_files=False,
+    usedefault=True,
+    ),
     regress_poly=dict(),
+    stddev_file=dict(hash_files=False,
+    usedefault=True,
+    ),
+    tsnr_file=dict(hash_files=False,
+    usedefault=True,
+    ),
     )
     inputs = TSNR.input_spec()
 

nipype/interfaces/afni/base.py

@@ -6,13 +6,14 @@
 
 
 import os
-import warnings
 
+from ... import logging
 from ...utils.filemanip import split_filename
 from ..base import (
     CommandLine, traits, CommandLineInputSpec, isdefined, File, TraitedSpec)
 
-warn = warnings.warn
+# Use nipype's logging system
+iflogger = logging.getLogger('interface')
 
 
 class Info(object):
@@ -37,10 +38,33 @@ def version():
            Version number as string or None if AFNI not found
 
         """
-        clout = CommandLine(command='afni_vcheck',
-                            terminal_output='allatonce').run()
-        out = clout.runtime.stdout
-        return out.split('\n')[1]
+        try:
+            clout = CommandLine(command='afni_vcheck',
+                                terminal_output='allatonce').run()
+
+            # Try to parse the version number
+            currv = clout.runtime.stdout.split('\n')[1].split('=', 1)[1].strip()
+        except IOError:
+            # If afni_vcheck is not present, return None
+            iflogger.warn('afni_vcheck executable not found.')
+            return None
+        except RuntimeError as e:
+            # If AFNI is outdated, afni_vcheck throws error.
+            # Show new version, but parse current anyways.
+            currv = str(e).split('\n')[4].split('=', 1)[1].strip()
+            nextv = str(e).split('\n')[6].split('=', 1)[1].strip()
+            iflogger.warn(
+                'AFNI is outdated, detected version %s and %s is available.' % (currv, nextv))
+
+        if currv.startswith('AFNI_'):
+            currv = currv[5:]
+
+        v = currv.split('.')
+        try:
+            v = [int(n) for n in v]
+        except ValueError:
+            return currv
+        return tuple(v)
 
     @classmethod
     def outputtype_to_ext(cls, outputtype):
@@ -160,3 +184,10 @@ def _list_outputs(self):
                     if ext == "":
                         outputs[name] = outputs[name] + "+orig.BRIK"
         return outputs
+
+
+def no_afni():
+    """ Checks if AFNI is available """
+    if Info.version() is None:
+        return True
+    return False

nipype/interfaces/afni/preprocess.py

@@ -8,10 +8,10 @@
     >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
     >>> os.chdir(datadir)
 """
-import warnings
 
 import os
 import re
+from warnings import warn
 
 from .base import AFNICommand, AFNICommandInputSpec, AFNICommandOutputSpec
 from ..base import CommandLineInputSpec, CommandLine, OutputMultiPath
@@ -20,8 +20,6 @@
 from ...utils.filemanip import (load_json, save_json, split_filename)
 from ...utils.filemanip import fname_presuffix
 
-warn = warnings.warn
-
 
 class To3DInputSpec(AFNICommandInputSpec):
     out_file = File(name_template="%s", desc='output image file name',
@@ -1235,6 +1233,17 @@ class SkullStrip(AFNICommand):
     input_spec = SkullStripInputSpec
     output_spec = AFNICommandOutputSpec
 
+    def __init__(self, **inputs):
+        from .base import Info, no_afni
+        super(SkullStrip, self).__init__(**inputs)
+
+        if not no_afni():
+            v = Info.version()
+
+            # As of AFNI 16.0.00, redirect_x is not needed
+            if isinstance(v[0], int) and v[0] > 15:
+                self._redirect_x = False
+
 
 class TCatInputSpec(AFNICommandInputSpec):
     in_files = InputMultiPath(

nipype/interfaces/dipy/preprocess.py

@@ -23,9 +23,6 @@
     package_check('dipy', version='0.6.0')
 except Exception as e:
     have_dipy = False
-else:
-    from dipy.align.aniso2iso import resample
-    from dipy.core.gradients import GradientTable
 
 
 class ResampleInputSpec(TraitedSpec):
@@ -172,6 +169,7 @@ def resample_proxy(in_file, order=3, new_zooms=None, out_file=None):
     """
     Performs regridding of an image to set isotropic voxel sizes using dipy.
     """
+    from dipy.align.aniso2iso import resample
 
     if out_file is None:
         fname, fext = op.splitext(op.basename(in_file))

nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py

@@ -16,6 +16,7 @@ def test_Surface2VolTransform_inputs():
     usedefault=True,
     ),
     mkmask=dict(argstr='--mkmask',
+    xor=['source_file'],
     ),
     projfrac=dict(argstr='--projfrac %s',
     ),
@@ -26,6 +27,7 @@ def test_Surface2VolTransform_inputs():
     source_file=dict(argstr='--surfval %s',
     copyfile=False,
     mandatory=True,
+    xor=['mkmask'],
     ),
     subject_id=dict(argstr='--identity %s',
     xor=['reg_file'],