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comparison tomo.py @ 35:20829cd7aaef draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2ddb1147cf5ad2fedfa2d9323c07ff16f8d9c869"
author rv43
date Tue, 19 Apr 2022 17:58:05 +0000
parents 63de912323e5
children 7ffde31e1e07
comparison
equal deleted inserted replaced
34:63de912323e5 35:20829cd7aaef
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 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')
1151 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!')
1152 return recon_clean 1154 return recon_clean
1153 1155
1154 def _plotEdgesOnePlane(self, recon_plane, title, path=None, weight=0.001): 1156 def _plotEdgesOnePlane(self, recon_plane, title, path=None, weight=0.001):
1155 # RV parameters for the denoise, gaussian, and ring removal will be different for different feature sizes 1157 # RV parameters for the denoise, gaussian, and ring removal will be different for different feature sizes
1181 # need index order column,theta for iradon, so take transpose 1183 # need index order column,theta for iradon, so take transpose
1182 sinogram_T = sinogram.T 1184 sinogram_T = sinogram.T
1183 center = sinogram.shape[1]/2 1185 center = sinogram.shape[1]/2
1184 1186
1185 # 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')
1186 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core) 1189 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core)
1190 logging.info('tomopy.find_center_vo end')
1187 center_offset_vo = tomo_center-center 1191 center_offset_vo = tomo_center-center
1188 if self.test_mode: 1192 if self.test_mode:
1189 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}') 1193 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
1190 del sinogram_T 1194 del sinogram_T
1191 return float(center_offset_vo) 1195 return float(center_offset_vo)
1537 def findCenters(self, galaxy_param=None, num_core=None): 1541 def findCenters(self, galaxy_param=None, num_core=None):
1538 """Find rotation axis centers for the tomography stacks. 1542 """Find rotation axis centers for the tomography stacks.
1539 """ 1543 """
1540 if num_core is None: 1544 if num_core is None:
1541 num_core = self.num_core 1545 num_core = self.num_core
1542 logging.info(f'num_core = {num_core}') 1546 # logging.info(f'num_core available = {num_core}')
1547 # if num_core > 24:
1548 # num_core = 24
1549 logging.info(f'num_core used = {num_core}')
1543 logging.debug('Find centers for tomography stacks') 1550 logging.debug('Find centers for tomography stacks')
1544 stacks = self.config['stack_info']['stacks'] 1551 stacks = self.config['stack_info']['stacks']
1545 available_stacks = [stack['index'] for stack in stacks if stack.get('preprocessed', False)] 1552 available_stacks = [stack['index'] for stack in stacks if stack.get('preprocessed', False)]
1546 logging.debug('Available stacks: {available_stacks}') 1553 logging.debug('Available stacks: {available_stacks}')
1547 if self.galaxy_flag: 1554 if self.galaxy_flag: