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comparison tomo.py @ 28:c7211931fc99 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 99f399daf512578b317aca74314e0246faa65cec"
author rv43
date Mon, 18 Apr 2022 21:26:01 +0000
parents 9d631a5e118f
children 59c5c0b53579
comparison
equal deleted inserted replaced
27:9d631a5e118f 28:c7211931fc99
1181 # need index order column,theta for iradon, so take transpose 1181 # need index order column,theta for iradon, so take transpose
1182 sinogram_T = sinogram.T 1182 sinogram_T = sinogram.T
1183 center = sinogram.shape[1]/2 1183 center = sinogram.shape[1]/2
1184 1184
1185 # try automatic center finding routines for initial value 1185 # try automatic center finding routines for initial value
1186 num_core=1 1186 #num_core=1
1187 #tomo_center = tomopy.find_center_vo(sinogram, ncore=1)
1188 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core) 1187 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core)
1189 center_offset_vo = tomo_center-center 1188 center_offset_vo = tomo_center-center
1190 if self.test_mode: 1189 if self.test_mode:
1191 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}') 1190 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
1192 del sinogram_T 1191 del sinogram_T
1971 if self.tomo_stacks[i].size: 1970 if self.tomo_stacks[i].size:
1972 self.tomo_stacks[i] = np.array([]) 1971 self.tomo_stacks[i] = np.array([])
1973 assert(stack.get('preprocessed', False) == True) 1972 assert(stack.get('preprocessed', False) == True)
1974 assert(stack.get('reconstructed', False) == True) 1973 assert(stack.get('reconstructed', False) == True)
1975 continue 1974 continue
1976 print(f'OK4 {i} b') 1975 print(f'OK4 {i} b size = {self.tomo_stacks[i].size}')
1977 stack['reconstructed'] = False 1976 stack['reconstructed'] = False
1978 if not self.tomo_stacks[i].size: 1977 if not self.tomo_stacks[i].size:
1979 self.tomo_stacks[i], available = self._loadTomo('red stack', index, 1978 self.tomo_stacks[i], available = self._loadTomo('red stack', index,
1980 required=True) 1979 required=True)
1981 if not self.tomo_stacks[i].size: 1980 if not self.tomo_stacks[i].size:
1982 logging.error(f'Unable to load tomography stack {index} for reconstruction') 1981 logging.error(f'Unable to load tomography stack {index} for reconstruction')
1983 stack[i]['preprocessed'] = False 1982 stack[i]['preprocessed'] = False
1984 load_error = True 1983 load_error = True
1985 continue 1984 continue
1985 print(f'lower_row = {lower_row} upper_row = {upper_row} self.tomo_stacks[i].shape[0] = {self.tomo_stacks[i].shape[0]}')
1986 assert(0 <= lower_row < upper_row < self.tomo_stacks[i].shape[0]) 1986 assert(0 <= lower_row < upper_row < self.tomo_stacks[i].shape[0])
1987 print(f'OK4 {i} c')
1987 center_offsets = [lower_center_offset-lower_row*center_slope, 1988 center_offsets = [lower_center_offset-lower_row*center_slope,
1988 upper_center_offset+(self.tomo_stacks[i].shape[0]-1-upper_row)*center_slope] 1989 upper_center_offset+(self.tomo_stacks[i].shape[0]-1-upper_row)*center_slope]
1989 t0 = time() 1990 t0 = time()
1990 self.tomo_recon_stacks[i]= self._reconstructOneTomoStack(self.tomo_stacks[i], 1991 self.tomo_recon_stacks[i]= self._reconstructOneTomoStack(self.tomo_stacks[i],
1991 thetas, center_offsets=center_offsets, sigma=0.1, num_core=num_core, 1992 thetas, center_offsets=center_offsets, sigma=0.1, num_core=num_core,
1992 algorithm='gridrec', run_secondary_sirt=True, secondary_iter=25) 1993 algorithm='gridrec', run_secondary_sirt=True, secondary_iter=25)
1993 logging.info(f'Reconstruction of stack {index} took {time()-t0:.2f} seconds!') 1994 logging.info(f'Reconstruction of stack {index} took {time()-t0:.2f} seconds!')
1994 print(f'OK4 {i} c') 1995 print(f'OK4 {i} d')
1995 if self.galaxy_flag: 1996 if self.galaxy_flag:
1996 x_slice = int(self.tomo_stacks[i].shape[0]/2) 1997 x_slice = int(self.tomo_stacks[i].shape[0]/2)
1997 title = f'{basetitle} {index} xslice{x_slice}' 1998 title = f'{basetitle} {index} xslice{x_slice}'
1998 msnc.quickImshow(self.tomo_recon_stacks[i][x_slice,:,:], title=title, 1999 msnc.quickImshow(self.tomo_recon_stacks[i][x_slice,:,:], title=title,
1999 path='center_slice_pngs', save_fig=True, save_only=True) 2000 path='center_slice_pngs', save_fig=True, save_only=True)
2023 stack['reconstructed'] = True 2024 stack['reconstructed'] = True
2024 combine_stacks = self.config.get('combine_stacks') 2025 combine_stacks = self.config.get('combine_stacks')
2025 if combine_stacks and index in combine_stacks.get('stacks', []): 2026 if combine_stacks and index in combine_stacks.get('stacks', []):
2026 combine_stacks['stacks'].remove(index) 2027 combine_stacks['stacks'].remove(index)
2027 self.cf.saveFile(self.config_out) 2028 self.cf.saveFile(self.config_out)
2028 print(f'OK4 {i} d') 2029 print(f'OK4 {i} e')
2029 2030
2030 # Save reconstructed tomography stack to file 2031 # Save reconstructed tomography stack to file
2031 print('OK5') 2032 print('OK5')
2032 if self.galaxy_flag: 2033 if self.galaxy_flag:
2033 t0 = time() 2034 t0 = time()