tomo: tomo.py comparison

comparison tomo.py @ 39:8a3036b0a34c draft

"planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8"

author	rv43
date	Tue, 19 Apr 2022 18:43:00 +0000
parents	c09b8ee8f68f
children	fa94fe25ca46

comparison

equal deleted inserted replaced

-:c09b8ee8f68f
+:8a3036b0a34c
 recon_clean = np.expand_dims(recon_sinogram, axis=0)
 del recon_sinogram
 t1 = time()
 logging.info(f'running tomopy.misc.corr.remove_ring on {num_core} cores ...')
 recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=17, ncore=num_core)
-logging.info('... tomopy.misc.corr.remove_ring took {time()-t1:.2f} seconds!')
+logging.info(f'... tomopy.misc.corr.remove_ring took {time()-t1:.2f} seconds!')
 logging.debug(f'filtering and removing ring artifact took {time()-t0:.2f} seconds!')
 return recon_clean
 def _plotEdgesOnePlane(self, recon_plane, title, path=None, weight=0.001):
 # RV parameters for the denoise, gaussian, and ring removal will be different for different feature sizes
 logging.info('running tomopy.find_center_vo on 24 cores ...')
 tomo_center = tomopy.find_center_vo(sinogram, ncore=24)
 else:
 logging.info(f'running tomopy.find_center_vo on {num_core} cores ...')
 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core)
-logging.info('... tomopy.find_center_vo took {time()-t0:.2f} seconds!')
+logging.info(f'... tomopy.find_center_vo took {time()-t0:.2f} seconds!')
 center_offset_vo = tomo_center-center
 if self.test_mode:
 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
 del sinogram_T
 return float(center_offset_vo)
 elif self.galaxy_flag:
 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
 t0 = time()
-logging.info('running self._reconstructOnePlane on {num_core} cores ...')
+logging.info(f'running self._reconstructOnePlane on {num_core} cores ...')
 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
 eff_pixel_size, cross_sectional_dim, False, num_core)
-logging.info('... self._reconstructOnePlane took {time()-t0:.2f} seconds!')
+logging.info(f'... self._reconstructOnePlane took {time()-t0:.2f} seconds!')
 title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'
 self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs')
 del recon_plane
 if not galaxy_param['center_type_selector']:
 del sinogram_T
 for center_offset in center_offsets:
 if center_offset == center_offset_vo:
 continue
 logging.info(f'center_offset = {center_offset:.2f}')
 t0 = time()
-logging.info('running self._reconstructOnePlane on {num_core} cores ...')
+logging.info(f'running self._reconstructOnePlane on {num_core} cores ...')
 recon_plane = self._reconstructOnePlane(sinogram_T, center_offset+center,
 thetas_deg, eff_pixel_size, cross_sectional_dim, False, num_core)
-logging.info('... self._reconstructOnePlane took {time()-t0:.2f} seconds!')
+logging.info(f'... self._reconstructOnePlane took {time()-t0:.2f} seconds!')
 title = f'edges row{row} center_offset{center_offset:.2f}'
 if self.galaxy_flag:
 self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs')
 else:
 self._plotEdgesOnePlane(recon_plane, title)
 raise ValueError('center_offsets dimension mismatch in reconstructOneTomoStack')
 centers = center_offsets
 centers += tomo_stack.shape[2]/2
 # RV hangs here with more than 24 cores and sge_64G_4
 if True:
+t0 = time()
+logging.info(f'running tomopy.prep.stripe.remove_stripe_fw on {num_core} cores ...')
 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(
 tomo_stack[row_bounds[0]:row_bounds[1]], sigma=sigma, ncore=num_core)
+logging.info(f'... tomopy.prep.stripe.remove_stripe_fw took {time()-t0:.2f} seconds!')
 else:
 tomo_stack = tomo_stack[row_bounds[0]:row_bounds[1]]
 logging.info('performing initial reconstruction')
+t0 = time()
+logging.info(f'running tomopy.recon on {num_core} cores ...')
 tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers, sinogram_order=True,
 algorithm=algorithm, ncore=num_core)
+logging.info(f'... tomopy.recon took {time()-t0:.2f} seconds!')
 if run_secondary_sirt and secondary_iter > 0:
 logging.info(f'running {secondary_iter} secondary iterations')
 #options = {'method':'SIRT_CUDA', 'proj_type':'cuda', 'num_iter':secondary_iter}
 #RV: doesn't work for me: "Error: CUDA error 803: system has unsupported display driver /
 #                          cuda driver combination."
 #options = {'method':'SIRT', 'proj_type':'linear', 'MinConstraint': 0, 'num_iter':secondary_iter}
 #SIRT did not finish while running overnight
 #options = {'method':'SART', 'proj_type':'linear', 'num_iter':secondary_iter}
 options = {'method':'SART', 'proj_type':'linear', 'MinConstraint': 0,
 'num_iter':secondary_iter}
+t0 = time()
+logging.info(f'running tomopy.recon on {num_core} cores ...')
 tomo_recon_stack  = tomopy.recon(tomo_stack, thetas, centers,
 init_recon=tomo_recon_stack, options=options, sinogram_order=True,
 algorithm=tomopy.astra, ncore=num_core)
+logging.info(f'... tomopy.recon took {time()-t0:.2f} seconds!')
 if True:
+t0 = time()
+logging.info(f'running tomopy.misc.corr.remove_ring on {num_core} cores ...')
 tomopy.misc.corr.remove_ring(tomo_recon_stack, rwidth=rwidth, out=tomo_recon_stack,
 ncore=num_core)
+logging.info(f'... tomopy.misc.corr.remove_ring took {time()-t0:.2f} seconds!')
 return tomo_recon_stack
 def findImageFiles(self):
 """Find all available image files.
 """
 """Reconstruct tomography stacks.
 """
 if num_core is None:
 num_core = self.num_core
 logging.info(f'num_core available = {num_core}')
-if num_core > 24:
+#if num_core > 24:
-num_core = 24
+#    num_core = 24
 logging.info(f'num_core used = {num_core}')
 if self.galaxy_flag:
 assert(galaxy_param)
 if not os.path.exists('center_slice_pngs'):
 os.mkdir('center_slice_pngs')
 continue
 assert(0 <= lower_row < upper_row < self.tomo_stacks[i].shape[0])
 center_offsets = [lower_center_offset-lower_row*center_slope,
 upper_center_offset+(self.tomo_stacks[i].shape[0]-1-upper_row)*center_slope]
 t0 = time()
+logging.info(f'running self._reconstructOneTomoStack on {num_core} cores ...')
 self.tomo_recon_stacks[i]= self._reconstructOneTomoStack(self.tomo_stacks[i],
 thetas, center_offsets=center_offsets, sigma=0.1, num_core=num_core,
 algorithm='gridrec', run_secondary_sirt=True, secondary_iter=25)
-logging.info(f'Reconstruction of stack {index} took {time()-t0:.2f} seconds!')
+logging.info(f'... self._reconstructOneTomoStack took {time()-t0:.2f} seconds!')
+#logging.info(f'Reconstruction of stack {index} took {time()-t0:.2f} seconds!')
 if self.galaxy_flag:
 x_slice = int(self.tomo_stacks[i].shape[0]/2)
 title = f'{basetitle} {index} xslice{x_slice}'
 msnc.quickImshow(self.tomo_recon_stacks[i][x_slice,:,:], title=title,
 path='center_slice_pngs', save_fig=True, save_only=True)

Mercurial > repos > rv43 > tomo

comparison tomo.py @ 39:8a3036b0a34c draft