for dim in xrange(3):
offsets[dim,
coords_reg[i:j,0],
coords_reg[i:j,1],
coords_reg[i:j,2]] = y[:,dim]
del x
_ = gc.collect()
irtk.imwrite( args.output + "/offsets_heart.nii.gz",
offsets_heart )
hough_header = img.get_header()
hough_header['dim'][:3] += 2*args.padding
votes_heart = hough_votes(np.ascontiguousarray(np.round(offsets_heart).astype('int32')),
proba[1], padding=args.padding )
irtk.imwrite(args.output + "/votes_heart.nii.gz",
irtk.Image(votes_heart,hough_header))
# mask using narrow_band
if args.padding:
# update the narrow band without forgetting to
# translate the brain_center
narrow_band = get_narrow_band( votes_heart.shape,
args.brain_center+args.padding,
r_min=40,
r_max=120 )
votes_heart[narrow_band==0] = 0
_ = gc.collect()
if not args.score:
irtk.imwrite( args.output + "/offsets_left_lung.nii.gz",
offsets_left_lung )
irtk.imwrite( args.output + "/offsets_right_lung.nii.gz",
offsets_right_lung )
irtk.imwrite( args.output + "/offsets_heart.nii.gz",
offsets_heart )
irtk.imwrite( args.output + "/offsets_liver.nii.gz",
offsets_liver )
hough_header = img.get_header()
hough_header['dim'][:3] += 2*args.padding
votes_left_lung = hough_votes(np.ascontiguousarray(np.round(offsets_left_lung).astype('int32')),
proba[1], padding=args.padding )
votes_right_lung = hough_votes(np.ascontiguousarray(np.round(offsets_right_lung).astype('int32')),
proba[2], padding=args.padding )
if not args.score:
irtk.imwrite(args.output + "/votes_left_lung.nii.gz",
irtk.Image(votes_left_lung,hough_header))
irtk.imwrite(args.output + "/votes_right_lung.nii.gz",
irtk.Image(votes_right_lung,hough_header))
votes_heart = hough_votes(np.ascontiguousarray(np.round(offsets_heart).astype('int32')),
proba[3], padding=args.padding )
if not args.score:
irtk.imwrite(args.output + "/votes_heart.nii.gz",
irtk.Image(votes_heart,hough_header))
votes_liver = hough_votes(np.ascontiguousarray(np.round(offsets_liver).astype('int32')),