fix import NUMPY_MMAP location in examples

Author: oesteban

examples/dmri_camino_dti.py

@@ -26,7 +26,6 @@
 import nipype.interfaces.fsl as fsl
 import nipype.interfaces.camino2trackvis as cam2trk
 import nipype.algorithms.misc as misc
-from nipype.utils import NUMPY_MMAP
 
 """
 We use the following functions to scrape the voxel and data dimensions of the input images. This allows the
@@ -37,6 +36,7 @@
 
 def get_vox_dims(volume):
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
     if isinstance(volume, list):
         volume = volume[0]
     nii = nb.load(volume, mmap=NUMPY_MMAP)
@@ -47,6 +47,7 @@ def get_vox_dims(volume):
 
 def get_data_dims(volume):
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
     if isinstance(volume, list):
         volume = volume[0]
     nii = nb.load(volume, mmap=NUMPY_MMAP)
@@ -57,6 +58,7 @@ def get_data_dims(volume):
 
 def get_affine(volume):
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
     nii = nb.load(volume, mmap=NUMPY_MMAP)
     return nii.affine
 

examples/dmri_connectivity.py

@@ -60,7 +60,6 @@
 import nipype.interfaces.freesurfer as fs    # freesurfer
 import nipype.interfaces.cmtk as cmtk
 import nipype.algorithms.misc as misc
-from nipype.utils import NUMPY_MMAP
 
 """
 We define the following functions to scrape the voxel and data dimensions of the input images. This allows the
@@ -75,6 +74,7 @@
 
 def get_vox_dims(volume):
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
     if isinstance(volume, list):
         volume = volume[0]
     nii = nb.load(volume, mmap=NUMPY_MMAP)
@@ -85,6 +85,7 @@ def get_vox_dims(volume):
 
 def get_data_dims(volume):
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
     if isinstance(volume, list):
         volume = volume[0]
     nii = nb.load(volume, mmap=NUMPY_MMAP)
@@ -95,6 +96,7 @@ def get_data_dims(volume):
 
 def get_affine(volume):
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
     nii = nb.load(volume, mmap=NUMPY_MMAP)
     return nii.affine
 

examples/fmri_spm_auditory.py

@@ -28,7 +28,6 @@
 import nipype.pipeline.engine as pe          # pypeline engine
 import nipype.algorithms.modelgen as model   # model specification
 import os                                    # system functions
-from nipype.utils import NUMPY_MMAP
 
 
 """
@@ -122,6 +121,7 @@
 
 def get_vox_dims(volume):
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
     if isinstance(volume, list):
         volume = volume[0]
     nii = nb.load(volume, mmap=NUMPY_MMAP)

examples/fmri_spm_face.py

@@ -27,7 +27,6 @@
 import nipype.interfaces.utility as util     # utility
 import nipype.pipeline.engine as pe          # pypeline engine
 import nipype.algorithms.modelgen as model   # model specification
-from nipype.utils import NUMPY_MMAP
 
 """
 
@@ -115,6 +114,7 @@
 
 def get_vox_dims(volume):
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
     if isinstance(volume, list):
         volume = volume[0]
     nii = nb.load(volume, mmap=NUMPY_MMAP)

examples/rsfmri_vol_surface_preprocessing.py

@@ -75,7 +75,6 @@
 import numpy as np
 import scipy as sp
 import nibabel as nb
-from nipype.utils import NUMPY_MMAP
 
 
 imports = ['import os',
@@ -119,6 +118,7 @@ def median(in_files):
     """
     import numpy as np
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
     average = None
     for idx, filename in enumerate(filename_to_list(in_files)):
         img = nb.load(filename, mmap=NUMPY_MMAP)
@@ -147,6 +147,7 @@ def bandpass_filter(files, lowpass_freq, highpass_freq, fs):
     from nipype.utils.filemanip import split_filename, list_to_filename
     import numpy as np
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
     out_files = []
     for filename in filename_to_list(files):
         path, name, ext = split_filename(filename)
@@ -262,6 +263,7 @@ def extract_noise_components(realigned_file, mask_file, num_components=5,
     from scipy.linalg.decomp_svd import svd
     import numpy as np
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
     import os
     imgseries = nb.load(realigned_file, mmap=NUMPY_MMAP)
     components = None
@@ -331,6 +333,7 @@ def extract_subrois(timeseries_file, label_file, indices):
     """
     from nipype.utils.filemanip import split_filename
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
     import os
     img = nb.load(timeseries_file, mmap=NUMPY_MMAP)
     data = img.get_data()
@@ -354,6 +357,7 @@ def combine_hemi(left, right):
     """
     import os
     import numpy as np
+    from nipype.utils import NUMPY_MMAP
     lh_data = nb.load(left, mmap=NUMPY_MMAP).get_data()
     rh_data = nb.load(right, mmap=NUMPY_MMAP).get_data()