Do not open nifti files with mmap if numpy < 1.12.0

.travis.yml

@@ -10,11 +10,7 @@ env:
 - INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler"
 - INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit"
 before_install:
-- function bef_inst {
-  wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
-  -O /home/travis/.cache/miniconda.sh &&
-  bash /home/travis/.cache/miniconda.sh -b -p /home/travis/miniconda &&
-  export PATH=/home/travis/miniconda/bin:$PATH &&
+- function apt_inst {
   if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi &&
   if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi &&
   bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh) &&
@@ -26,18 +22,20 @@ before_install:
     source /etc/fsl/fsl.sh;
     source /etc/afni/afni.sh;
     export FSLOUTPUTTYPE=NIFTI_GZ; fi }
-- travis_retry bef_inst
-install:
-#  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi &&
-- function inst {
+- function conda_inst {
+  export CONDA_HOME=/home/travis/anaconda &&
+  bash /home/travis/.cache/anaconda.sh -b -p ${CONDA_HOME} &&
+  export PATH=${CONDA_HOME}/bin:$PATH &&
   conda config --add channels conda-forge &&
-  conda update --yes conda &&
   conda update --all -y python=$TRAVIS_PYTHON_VERSION &&
   conda install -y nipype icu==56.1 &&
-  rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* &&
-  pip install -r requirements.txt &&
-  pip install -e .[$NIPYPE_EXTRAS]; }
-- travis_retry inst
+  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*; }
+#  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi
+- travis_retry apt_inst
+- travis_retry if [ ! -f /home/travis/.cache/anaconda.sh]; then wget https://repo.continuum.io/archive/Anaconda${TRAVIS_PYTHON_VERSION:0:1}-4.3.0-Linux-x86_64.sh -O /home/travis/.cache/anaconda.sh; fi
+- travis_retry conda_inst
+install:
+- travis_retry pip install -e .[$NIPYPE_EXTRAS]
 script:
 - py.test --doctest-modules nipype
 deploy:

nipype/algorithms/confounds.py

@@ -16,6 +16,7 @@
 
 import os
 import os.path as op
+from distutils.version import LooseVersion
 
 import nibabel as nb
 import numpy as np
@@ -29,6 +30,8 @@
                                InputMultiPath)
 IFLOG = logging.getLogger('interface')
 
+NUMPY_MMAP = LooseVersion(np.__version__) >= LooseVersion('1.12.0')
+
 class ComputeDVARSInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='functional data, after HMC')
     in_mask = File(exists=True, mandatory=True, desc='a brain mask')
@@ -127,9 +130,9 @@ def _run_interface(self, runtime):
         dvars = compute_dvars(self.inputs.in_file, self.inputs.in_mask,
                               remove_zerovariance=self.inputs.remove_zerovariance)
 
-        self._results['avg_std'] = float(dvars[0].mean())
-        self._results['avg_nstd'] = float(dvars[1].mean())
-        self._results['avg_vxstd'] = float(dvars[2].mean())
+        (self._results['avg_std'],
+         self._results['avg_nstd'],
+         self._results['avg_vxstd']) = np.mean(dvars, axis=1).astype(float)
 
         tr = None
         if isdefined(self.inputs.series_tr):
@@ -329,8 +332,8 @@ class CompCor(BaseInterface):
                    }]
 
     def _run_interface(self, runtime):
-        imgseries = nb.load(self.inputs.realigned_file).get_data()
-        mask = nb.load(self.inputs.mask_file).get_data()
+        imgseries = nb.load(self.inputs.realigned_file, mmap=NUMPY_MMAP).get_data()
+        mask = nb.load(self.inputs.mask_file, mmap=NUMPY_MMAP).get_data()
 
         if imgseries.shape[:3] != mask.shape:
             raise ValueError('Inputs for CompCor, func {} and mask {}, do not have matching '
@@ -435,15 +438,15 @@ class TCompCor(CompCor):
     output_spec = TCompCorOutputSpec
 
     def _run_interface(self, runtime):
-        imgseries = nb.load(self.inputs.realigned_file).get_data()
+        imgseries = nb.load(self.inputs.realigned_file, mmap=NUMPY_MMAP).get_data()
 
         if imgseries.ndim != 4:
             raise ValueError('tCompCor expected a 4-D nifti file. Input {} has {} dimensions '
                              '(shape {})'
                              .format(self.inputs.realigned_file, imgseries.ndim, imgseries.shape))
 
         if isdefined(self.inputs.mask_file):
-            in_mask_data = nb.load(self.inputs.mask_file).get_data()
+            in_mask_data = nb.load(self.inputs.mask_file, mmap=NUMPY_MMAP).get_data()
             imgseries = imgseries[in_mask_data != 0, :]
 
         # From the paper:
@@ -521,9 +524,9 @@ class TSNR(BaseInterface):
     output_spec = TSNROutputSpec
 
     def _run_interface(self, runtime):
-        img = nb.load(self.inputs.in_file[0])
+        img = nb.load(self.inputs.in_file[0], mmap=NUMPY_MMAP)
         header = img.header.copy()
-        vollist = [nb.load(filename) for filename in self.inputs.in_file]
+        vollist = [nb.load(filename, mmap=NUMPY_MMAP) for filename in self.inputs.in_file]
         data = np.concatenate([vol.get_data().reshape(
             vol.get_shape()[:3] + (-1,)) for vol in vollist], axis=3)
         data = np.nan_to_num(data)
@@ -626,8 +629,8 @@ def compute_dvars(in_file, in_mask, remove_zerovariance=False):
     from nitime.algorithms import AR_est_YW
     import warnings
 
-    func = nb.load(in_file).get_data().astype(np.float32)
-    mask = nb.load(in_mask).get_data().astype(np.uint8)
+    func = nb.load(in_file, mmap=NUMPY_MMAP).get_data().astype(np.float32)
+    mask = nb.load(in_mask, mmap=NUMPY_MMAP).get_data().astype(np.uint8)
 
     if len(func.shape) != 4:
         raise RuntimeError(

requirements.txt

@@ -3,7 +3,7 @@ scipy>=0.11
 networkx>=1.7
 traits>=4.3
 python-dateutil>=1.5
-nibabel>=2.0.1
+nibabel
 future>=0.15.2
 simplejson>=3.8.0
 prov>=1.4.0