Mercurial > repos > rv43 > tomo

comparison tomo.py @ 30:c4a90d5b1ed2 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit c853b415951c80548544c495f99a1ebc5bac7287"
author rv43
date Mon, 18 Apr 2022 21:40:06 +0000
parents 59c5c0b53579
children 063e1e847d95
comparison
equal deleted inserted replaced
29:59c5c0b53579 30:c4a90d5b1ed2
1321 if True: 1321 if True:
1322 tomo_stack = tomopy.prep.stripe.remove_stripe_fw( 1322 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(
1323 tomo_stack[row_bounds[0]:row_bounds[1]], sigma=sigma, ncore=num_core) 1323 tomo_stack[row_bounds[0]:row_bounds[1]], sigma=sigma, ncore=num_core)
1324 else: 1324 else:
1325 tomo_stack = tomo_stack[row_bounds[0]:row_bounds[1]] 1325 tomo_stack = tomo_stack[row_bounds[0]:row_bounds[1]]
1326 print('OK AA')
1326 tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers, sinogram_order=True, 1327 tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers, sinogram_order=True,
1327 algorithm=algorithm, ncore=num_core) 1328 algorithm=algorithm, ncore=num_core)
1329 print('OK BB')
1328 if run_secondary_sirt and secondary_iter > 0: 1330 if run_secondary_sirt and secondary_iter > 0:
1329 #options = {'method':'SIRT_CUDA', 'proj_type':'cuda', 'num_iter':secondary_iter} 1331 #options = {'method':'SIRT_CUDA', 'proj_type':'cuda', 'num_iter':secondary_iter}
1330 #RV: doesn't work for me: "Error: CUDA error 803: system has unsupported display driver / 1332 #RV: doesn't work for me: "Error: CUDA error 803: system has unsupported display driver /
1331 # cuda driver combination." 1333 # cuda driver combination."
1332 #options = {'method':'SIRT', 'proj_type':'linear', 'MinConstraint': 0, 'num_iter':secondary_iter} 1334 #options = {'method':'SIRT', 'proj_type':'linear', 'MinConstraint': 0, 'num_iter':secondary_iter}
1335 options = {'method':'SART', 'proj_type':'linear', 'MinConstraint': 0, 1337 options = {'method':'SART', 'proj_type':'linear', 'MinConstraint': 0,
1336 'num_iter':secondary_iter} 1338 'num_iter':secondary_iter}
1337 tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers, 1339 tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers,
1338 init_recon=tomo_recon_stack, options=options, sinogram_order=True, 1340 init_recon=tomo_recon_stack, options=options, sinogram_order=True,
1339 algorithm=tomopy.astra, ncore=num_core) 1341 algorithm=tomopy.astra, ncore=num_core)
1342 print('OK CC')
1340 if True: 1343 if True:
1341 tomopy.misc.corr.remove_ring(tomo_recon_stack, rwidth=rwidth, out=tomo_recon_stack, 1344 tomopy.misc.corr.remove_ring(tomo_recon_stack, rwidth=rwidth, out=tomo_recon_stack,
1342 ncore=num_core) 1345 ncore=num_core)
1343 return tomo_recon_stack 1346 return tomo_recon_stack
1344 1347