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comparison tomo.py @ 29:59c5c0b53579 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit dbc4ff10f088b0217bab0ce5d6d5a7763619c779"
author rv43
date Mon, 18 Apr 2022 21:38:30 +0000
parents c7211931fc99
children c4a90d5b1ed2
comparison
equal deleted inserted replaced
28:c7211931fc99 29:59c5c0b53579
1982 stack[i]['preprocessed'] = False 1982 stack[i]['preprocessed'] = False
1983 load_error = True 1983 load_error = True
1984 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]}') 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')
1988 center_offsets = [lower_center_offset-lower_row*center_slope, 1987 center_offsets = [lower_center_offset-lower_row*center_slope,
1989 upper_center_offset+(self.tomo_stacks[i].shape[0]-1-upper_row)*center_slope] 1988 upper_center_offset+(self.tomo_stacks[i].shape[0]-1-upper_row)*center_slope]
1990 t0 = time() 1989 t0 = time()
1990 num_core = 1
1991 print(f'OK4 {i} c')
1991 self.tomo_recon_stacks[i]= self._reconstructOneTomoStack(self.tomo_stacks[i], 1992 self.tomo_recon_stacks[i]= self._reconstructOneTomoStack(self.tomo_stacks[i],
1992 thetas, center_offsets=center_offsets, sigma=0.1, num_core=num_core, 1993 thetas, center_offsets=center_offsets, sigma=0.1, num_core=num_core,
1993 algorithm='gridrec', run_secondary_sirt=True, secondary_iter=25) 1994 algorithm='gridrec', run_secondary_sirt=True, secondary_iter=25)
1995 print(f'OK4 {i} d')
1996 exit('Done')
1994 logging.info(f'Reconstruction of stack {index} took {time()-t0:.2f} seconds!') 1997 logging.info(f'Reconstruction of stack {index} took {time()-t0:.2f} seconds!')
1995 print(f'OK4 {i} d')
1996 if self.galaxy_flag: 1998 if self.galaxy_flag:
1997 x_slice = int(self.tomo_stacks[i].shape[0]/2) 1999 x_slice = int(self.tomo_stacks[i].shape[0]/2)
1998 title = f'{basetitle} {index} xslice{x_slice}' 2000 title = f'{basetitle} {index} xslice{x_slice}'
1999 msnc.quickImshow(self.tomo_recon_stacks[i][x_slice,:,:], title=title, 2001 msnc.quickImshow(self.tomo_recon_stacks[i][x_slice,:,:], title=title,
2000 path='center_slice_pngs', save_fig=True, save_only=True) 2002 path='center_slice_pngs', save_fig=True, save_only=True)