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BF: Local imports in helper functions (maybe not?)
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  • nipype/workflows/dmri/fsl

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nipype/workflows/dmri/fsl/epi.py

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,6 @@
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import warnings
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8-
from nipype.utils import NUMPY_MMAP
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from ....pipeline import engine as pe
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from ....interfaces import utility as niu
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from ....interfaces import fsl as fsl
@@ -722,6 +721,7 @@ def _prepare_phasediff(in_file):
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import nibabel as nb
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import os
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import numpy as np
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from nipype.utils import NUMPY_MMAP
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img = nb.load(in_file, mmap=NUMPY_MMAP)
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max_diff = np.max(img.get_data().reshape(-1))
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min_diff = np.min(img.get_data().reshape(-1))
@@ -741,6 +741,7 @@ def _dilate_mask(in_file, iterations=4):
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import nibabel as nb
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import scipy.ndimage as ndimage
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import os
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from nipype.utils import NUMPY_MMAP
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img = nb.load(in_file, mmap=NUMPY_MMAP)
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img._data = ndimage.binary_dilation(img.get_data(), iterations=iterations)
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@@ -756,6 +757,7 @@ def _fill_phase(in_file):
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import nibabel as nb
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import os
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import numpy as np
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from nipype.utils import NUMPY_MMAP
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img = nb.load(in_file, mmap=NUMPY_MMAP)
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dumb_img = nb.Nifti1Image(np.zeros(img.shape), img.affine, img.header)
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out_nii = nb.funcs.concat_images((img, dumb_img))
@@ -772,6 +774,7 @@ def _vsm_remove_mean(in_file, mask_file, in_unwarped):
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import os
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import numpy as np
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import numpy.ma as ma
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from nipype.utils import NUMPY_MMAP
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img = nb.load(in_file, mmap=NUMPY_MMAP)
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msk = nb.load(mask_file, mmap=NUMPY_MMAP).get_data()
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img_data = img.get_data()
@@ -794,6 +797,7 @@ def _ms2sec(val):
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def _split_dwi(in_file):
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import nibabel as nb
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import os
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from nipype.utils import NUMPY_MMAP
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out_files = []
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frames = nb.funcs.four_to_three(nb.load(in_file, mmap=NUMPY_MMAP))
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name, fext = os.path.splitext(os.path.basename(in_file))

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