def test_sd_from_ball():
dom = domain_from_array(np.ones((10, 10)))
radii = np.array([2, 2, 2])
positions = np.array([[3, 3], [3, 7], [7, 7]])
subdomain = subdomain_from_balls(dom, positions, radii)
assert subdomain.k == 3
assert (subdomain.size == np.array([9, 9, 9])).all()
# paths
data_dir = os.path.expanduser(os.path.join('~', '.nipy', 'tests', 'data'))
input_image = os.path.join(data_dir,'spmT_0029.nii.gz')
mask_image = os.path.join(data_dir,'mask.nii.gz')
#get_data_light.get_it()
# write dir
swd = tempfile.mkdtemp()
# -----------------------------------------------------
# example 1: create the ROI froma a given position
# -----------------------------------------------------
position = np.array([[0, 0, 0]])
domain = grid_domain_from_image(mask_image)
roi = mroi.subdomain_from_balls(domain, position, np.array([5.0]))
roi_domain = domain.mask(roi.label>-1)
roi_domain.to_image(os.path.join(swd, "myroi.nii"))
print 'Wrote an ROI mask image in %s' %os.path.join(swd, "myroi.nii")
# fixme: pot roi feature ...
# ----------------------------------------------------
# ---- example 2: create ROIs from a blob image ------
# ----------------------------------------------------
# --- 2.a create the blob image
# parameters
threshold = 3.0 # blob-forming threshold
smin = 5 # size threshold on bblobs
contrast_image = Nifti1Image(zmap, mask.get_affine())
# if you want to save the contrast as an image
# contrast_path = op.join(swd, 'zmap.nii')
# save(contrast_image, contrast_path)
########################################
# Create ROIs
########################################
positions = np.array([[60, -30, 5], [50, 27, 5]])
# in mm (here in the MNI space)
radii = np.array([8, 6])
domain = grid_domain_from_image(mask)
my_roi = mroi.subdomain_from_balls(domain, positions, radii)
# to save an image of the ROIs
my_roi.to_image(op.join(swd, "roi.nii"))
# exact the time courses with ROIs
my_roi.make_feature("signal", fmri_data.get_data()[mask.get_data() > 0])
# ROI average time courses
avg_signal = my_roi.representative_feature("signal")
my_roi.set_roi_feature("signal", avg_signal)
# roi-level contrast average
my_roi.make_feature("contrast", contrast_image.get_data()[mask.get_data() > 0])
my_roi.set_roi_feature("contrast", my_roi.representative_feature("contrast"))
