def main():
normalized = i3.normalize(ct_series,
dfs,
obs,
workdir=os.path.join(workdir, 'normalization'))
tilt_corrected = i3.correct_tilt(normalized,
workdir=os.path.join(
workdir, 'tilt-correction'))
if_corrected = i3.correct_intensity_fluctuation(
tilt_corrected,
workdir=os.path.join(workdir, 'intensity-fluctuation-correction'))
angles, sinograms = i3.build_sinograms(if_corrected,
workdir=os.path.join(
workdir, 'sinogram'))
# take the middle part to calculate the center of rotation
sino = [s.data for s in sinograms[900:1100]]
sino = np.array(sino)
proj = np.swapaxes(sino, 0, 1)
rot_center = tomopy.find_center(proj,
theta,
emission=False,
init=1024,
tol=0.5)
rot_center = rot_center[0]
# reconstruct
recon = i3.reconstruct(angles,
sinograms,
workdir=outdir,
center=rot_center)
return
def test():
normalized = i3.normalize(ct_series, dfs, obs, workdir=workdir)
tilt_corrected = i3.correct_tilt(normalized, workdir=workdir)
if_corrected = i3.correct_intensity_fluctuation(tilt_corrected,
workdir=workdir)
angles, sinograms = i3.build_sinograms(if_corrected, workdir=workdir)
recon = i3.reconstruct(angles, sinograms, workdir=outdir)
return
def main():
normalized = i3.normalize(ct_series, dfs, obs, workdir=os.path.join(workdir, 'normalization'))
tilt_corrected = i3.correct_tilt(normalized, workdir=os.path.join(workdir, 'tilt-correction'))
if_corrected = i3.correct_intensity_fluctuation(tilt_corrected, workdir=os.path.join(workdir, 'intensity-fluctuation-correction'))
angles, sinograms = i3.build_sinograms(if_corrected, workdir=os.path.join(workdir, 'sinogram'))
# take the middle part to calculate the center of rotation
sino = [s.data for s in sinograms[900:1100]]
sino= np.array(sino)
proj = np.swapaxes(sino, 0, 1)
rot_center = tomopy.find_center(proj, theta, emission=False, init=1024, tol=0.5)
rot_center = rot_center[0]
# reconstruct
recon = i3.reconstruct(angles, sinograms, workdir=outdir, center=rot_center)
return
def reconstruct(
self,
ct_series, workdir=None, outdir=None,
rot_center=None, explore_rot_center=True):
workdir = workdir or self.workdir;
outdir = outdir or self.outdir
theta = self.theta
# preprocess
angles, sinograms = i3.build_sinograms(
ct_series, workdir=os.path.join(workdir, 'sinogram'),
parallel = self.parallel_preprocessing,
parallel_nodes = self.parallel_nodes)
# take the middle part to calculate the center of rotation
NSINO = len(sinograms)
sino = [s.data for s in sinograms[NSINO//3: NSINO*2//3]]
# sino = [s.data for s in sinograms]
sino= np.array(sino)
proj = np.swapaxes(sino, 0, 1)
import tomopy
X = proj.shape[-1]
DEVIATION = 40 # max deviation of rot center from center of image
if explore_rot_center:
print("* Exploring rotation center using tomopy...")
tomopy.write_center(
proj.copy(), theta,
cen_range=[X//2-DEVIATION, X//2+DEVIATION, 1.],
dpath=os.path.join(workdir, 'tomopy-findcenter'),
emission=False)
if rot_center is None:
print("* Computing rotation center using 180deg pairs...")
from .tilt import find_rot_center
rot_center = find_rot_center.find(
ct_series, workdir=os.path.join(workdir, 'find-rot-center'))
print('* Rotation center: %s' % rot_center)
open(os.path.join(workdir, 'rot_center'), 'wt').write(str(rot_center))
# reconstruct
if self.vertical_range:
sinograms = sinograms[self.vertical_range]
recon = i3.reconstruct(
angles, sinograms,
workdir=outdir, center=rot_center,
nodes=self.parallel_nodes)
return
def reconstruct(
self,
ct_series, workdir=None, outdir=None,
rot_center=None, explore_rot_center=True,
outfilename_template=None,
remove_rings_at_sinograms=False,
mirror=True,
**kwds):
workdir = workdir or self.workdir;
outdir = outdir or self.outdir
theta = self.theta
# preprocess
angles, sinograms = i3.build_sinograms(
ct_series, workdir=os.path.join(workdir, 'sinogram'),
parallel = self.parallel_preprocessing,
parallel_nodes = self.parallel_nodes)
# take the middle part to calculate the center of rotation
NSINO = len(sinograms)
sino = [s.data for s in sinograms[NSINO//3: NSINO*2//3]]
# sino = [s.data for s in sinograms]
sino= np.array(sino)
proj = np.swapaxes(sino, 0, 1)
import tomopy
X = proj.shape[-1]
DEVIATION = 40 # max deviation of rot center from center of image
if explore_rot_center:
print("* Exploring rotation center using tomopy...")
dpath=os.path.join(workdir, 'tomopy-findcenter')
if not os.path.exists(dpath): # skip if already done
tomopy.write_center(
proj.copy(), theta,
cen_range=[X//2-DEVIATION, X//2+DEVIATION, 1.],
dpath=dpath,
emission=False)
if rot_center is None:
print("* Computing rotation center using 180deg pairs...")
from .tilt import find_rot_center
rot_center = find_rot_center.find(
ct_series, workdir=os.path.join(workdir, 'find-rot-center'))
print('* Rotation center: %s' % rot_center)
self.rot_center = rot_center
open(os.path.join(workdir, 'rot_center'), 'wt').write(str(rot_center))
# reconstruct
if self.vertical_range:
sinograms = sinograms[self.vertical_range]
self.r.sinograms = sinograms
# sometimes the rotation angles and the stacking sequence coulb be not in the right convention
if mirror:
angles = -np.array(angles)
# reconstruct using original sinograms
recon = i3.reconstruct(
angles, sinograms,
workdir=outdir, filename_template=outfilename_template,
center=rot_center,
nodes=self.parallel_nodes,
**kwds)
self.r.reconstructed = recon
# reconstruct using rar filtered sinograms
if remove_rings_at_sinograms:
if remove_rings_at_sinograms is True:
remove_rings_at_sinograms = {}
self.r.rar_sino = sinograms = i3.ring_artifact_removal_Ketcham(
sinograms, workdir=os.path.join(workdir, 'rar_sinograms'),
parallel = self.parallel_preprocessing,
**remove_rings_at_sinograms)
recon = i3.reconstruct(
angles, sinograms,
workdir=os.path.join(outdir, 'rar_sinograms'),
filename_template=outfilename_template,
center=rot_center,
nodes=self.parallel_nodes,
**kwds)
self.r.reconstructed_using_rar_sinograms = recon
return recon