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 preprocess(self, workdir=None, outdir=None):
workdir = workdir or self.workdir
outdir = outdir or self.outdir
# get image objs
dfs = self.dfs; obs = self.obs
ct_series = self.ct_series
theta = self.theta
# preprocess
gamma_filtered = i3.gamma_filter(
ct_series, workdir=os.path.join(workdir, 'gamma-filter'),
parallel = self.parallel_preprocessing)
normalized = i3.normalize(gamma_filtered, dfs, obs, workdir=os.path.join(workdir, 'normalization'))
if self.clean_on_the_fly:
gamma_filtered.removeAll()
if_corrected = i3.correct_intensity_fluctuation(normalized, workdir=os.path.join(workdir, 'intensity-fluctuation-correction'))
if self.clean_on_the_fly:
normalized.removeAll()
return if_corrected
