profile_near_roi.py

"""
To use:

load_ext line_profiler
import profile_near_roi as p
lprun -f p.ut.near_roi p.func()

"""

import dipy.data as dpd
import nibabel.trackvis as trk
import dipy.tracking.utils as ut
import numpy as np

fornix_file = dpd.get_data('fornix')
fornix_content = trk.read(fornix_file)
streamlines = [t[0] for t in fornix_content[0]]

mask = np.zeros((150, 150, 100), dtype=bool)

mask[90:100, 100:110, 90] = 1

def func():
    ans = ut.near_roi(streamlines, mask, affine=None, tol=0)