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@timemory.util.auto_timer()
def generate(phantom="shepp3d", nsize=512, nangles=360):
with timemory.util.auto_timer("[tomopy.misc.phantom.{}]".format(phantom)):
obj = getattr(tomopy.misc.phantom, phantom)(size=nsize)
with timemory.util.auto_timer("[tomopy.angles]"):
ang = tomopy.angles(nangles)
with timemory.util.auto_timer("[tomopy.project]"):
prj = tomopy.project(obj, ang)
return [prj, ang, obj]
def generate(phantom="shepp3d", nsize=512, nangles=360):
with timemory.util.auto_timer("[tomopy.misc.phantom.{}]".format(phantom)):
obj = getattr(tomopy.misc.phantom, phantom)(size=nsize)
with timemory.util.auto_timer("[tomopy.angles]"):
ang = tomopy.angles(nangles)
with timemory.util.auto_timer("[tomopy.project]"):
prj = tomopy.project(obj, ang)
return [prj, ang, obj]
# use the accelerated version
if algorithm in ["mlem", "sirt"]:
_kwargs["accelerated"] = True
# don't assign "num_iter" if gridrec or fbp
if algorithm not in ["fbp", "gridrec"]:
_kwargs["num_iter"] = nitr
sname = os.path.join(args.output_dir, 'proj_{}'.format(args.algorithm))
print(proj.shape)
tmp = np.zeros((proj.shape[0], proj.shape[2]))
tmp[:,:] = proj[:,0,:]
output_image(tmp, sname + "." + args.format)
# Reconstruct object.
with timemory.util.auto_timer(
"[tomopy.recon(algorithm='{}')]".format(algorithm)):
print("Starting reconstruction with kwargs={}...".format(_kwargs))
rec = tomopy.recon(data, theta, **_kwargs)
print("Completed reconstruction...")
# Mask each reconstructed slice with a circle.
rec = tomopy.circ_mask(rec, axis=0, ratio=0.95)
obj = np.zeros(rec.shape, dtype=rec.dtype)
label = "{} @ {}".format(algorithm.upper(), h5fname)
quantify_difference(label, obj, rec)
return rec
@timemory.util.auto_timer()
def convert_image(fname, current_format, new_format):
"""Create a copy of an image in a new_format.
Parameters
----------
fname : string
The current image filename sans extension.
current_format : string
The current image file extension.
new_fromat : string
The new image file extension.
"""
_fext = new_format
_success = True