Mercurial > repos > rv43 > tomo

comparison tomo.py @ 37:51dc93d0806a draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 87acf8a257d5d51cf249de085e555bb11d1dbd88"
author rv43
date Tue, 19 Apr 2022 18:13:10 +0000
parents 7ffde31e1e07
children c09b8ee8f68f
comparison
equal deleted inserted replaced
36:7ffde31e1e07 37:51dc93d0806a
1145 t0 = time() 1145 t0 = time()
1146 # recon_sinogram = filters.gaussian(recon_sinogram, 3.0) 1146 # recon_sinogram = filters.gaussian(recon_sinogram, 3.0)
1147 recon_sinogram = spi.gaussian_filter(recon_sinogram, 0.5) 1147 recon_sinogram = spi.gaussian_filter(recon_sinogram, 0.5)
1148 recon_clean = np.expand_dims(recon_sinogram, axis=0) 1148 recon_clean = np.expand_dims(recon_sinogram, axis=0)
1149 del recon_sinogram 1149 del recon_sinogram
1150 logging.info('tomopy.misc.corr.remove_ring start') 1150 logging.info(f'tomopy.misc.corr.remove_ring start on {num_core} cores')
1151 recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=17, ncore=num_core) 1151 recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=17, ncore=num_core)
1152 logging.info('tomopy.misc.corr.remove_ring end') 1152 logging.info('tomopy.misc.corr.remove_ring end')
1153 logging.debug(f'filtering and removing ring artifact took {time()-t0:.2f} seconds!') 1153 logging.debug(f'filtering and removing ring artifact took {time()-t0:.2f} seconds!')
1154 return recon_clean 1154 return recon_clean
1155 1155
1183 # need index order column,theta for iradon, so take transpose 1183 # need index order column,theta for iradon, so take transpose
1184 sinogram_T = sinogram.T 1184 sinogram_T = sinogram.T
1185 center = sinogram.shape[1]/2 1185 center = sinogram.shape[1]/2
1186 1186
1187 # try automatic center finding routines for initial value 1187 # try automatic center finding routines for initial value
1188 logging.info('tomopy.find_center_vo start') 1188 if num_core > 24:
1189 #tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core) 1189 logging.info('tomopy.find_center_vo start on 24 cores')
1190 tomo_center = tomopy.find_center_vo(sinogram, ncore=1) 1190 tomo_center = tomopy.find_center_vo(sinogram, ncore=24)
1191 else:
1192 logging.info(f'tomopy.find_center_vo start on {num_core} cores')
1193 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core)
1191 logging.info('tomopy.find_center_vo end') 1194 logging.info('tomopy.find_center_vo end')
1192 center_offset_vo = tomo_center-center 1195 center_offset_vo = tomo_center-center
1193 if self.test_mode: 1196 if self.test_mode:
1194 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}') 1197 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
1195 del sinogram_T 1198 del sinogram_T