def make_subdomain():
"""Create a multiple ROI instance
"""
labels = np.zeros(shape)
labels[4:,5:,6:] = 1
labels[:2,:2,:2] = 2
labels[:2, 5:, 6:] = 3
labels[:2, :2, 6:] = 4
labels[4:, :2, 6:] = 5
labels[4:, :2, :2] = 6
labels[4:, 5:, :2] = 7
labels[:2, 5:, :2] = 8
mroi = subdomain_from_array(labels-1, affine=None)
return mroi
def make_hroi():
"""Create a mulmtiple ROI instance
"""
labels = np.zeros(shape)
labels[4:,5:,6:] = 1
labels[:2,:2,:2] = 2
labels[:2, 5:, 6:] = 3
labels[:2, :2, 6:] = 4
labels[4:, :2, 6:] = 5
labels[4:, :2, :2] = 6
labels[4:, 5:, :2] = 7
labels[:2, 5:, :2] = 8
parents = np.zeros(9)
sd = subdomain_from_array(labels, affine=None, nn=0)
hroi = make_hroi_from_subdomain(sd, parents)
return hroi
# compute the nested roi object
nroi = hroi.HROI_as_discrete_domain_blobs(domain, values,
threshold=threshold, smin=smin)
# saving the blob image,i. e. a label image
wlabel = -2*np.ones(shape)
wlabel[data!=0] = nroi.label
blobPath = os.path.join(swd, "blob.nii")
wim = Nifti1Image(wlabel, affine)
wim.get_header()['descrip'] = 'blob image extracted from %s'%input_image
save(wim, blobPath)
# --- 2.b take blob labelled "1" as an ROI
roi = mroi.subdomain_from_array((wlabel==1)-1, affine=affine)
roi_path_2 = os.path.join(swd, "roi_blob_1.nii")
roi.to_image(roi_path_2)
# --- 2.c take the blob closest to 'position as an ROI'
roi_path_3 = os.path.join(swd, "blob_closest_to_%d_%d_%d.nii")%\
(position[0][0], position[0][1], position[0][2])
roi = mroi.subdomain_from_position_and_image(wim, position[0])
roi.to_image(roi_path_3)
# --- 2.d make a set of ROIs from all the blobs
roi = mroi.subdomain_from_image(blobPath)
roi_path_4 = os.path.join(swd, "roi_all_blobs.nii")
roi.to_image(roi_path_4)
roi.make_feature('activ', load(input_image).get_data().ravel())
