Mercurial > repos > rv43 > tomo

comparison tomo.py @ 2:b8977c98800b draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0c40fb274acc13ebf7054379bb49ed13acec918e"
author rv43
date Thu, 31 Mar 2022 20:48:17 +0000
parents e4778148df6b
children f9c52762c32c
comparison
equal deleted inserted replaced
1:e4778148df6b 2:b8977c98800b
479 if not self.cf.load_flag: 479 if not self.cf.load_flag:
480 self.is_valid = False 480 self.is_valid = False
481 return 481 return
482 482
483 if self.galaxy_flag: 483 if self.galaxy_flag:
484 self.num_core = 1 #RV can I set this? mp.cpu_count()
485 assert(self.output_folder == '.') 484 assert(self.output_folder == '.')
486 assert(self.test_mode is False) 485 assert(self.test_mode is False)
487 self.save_plots = True 486 self.save_plots = True
488 self.save_plots_only = True 487 self.save_plots_only = True
489 else: 488 else:
526 num_tomo_stacks = self.config['stack_info']['num'] 525 num_tomo_stacks = self.config['stack_info']['num']
527 if num_tomo_stacks: 526 if num_tomo_stacks:
528 self.tomo_stacks = [np.array([]) for _ in range(num_tomo_stacks)] 527 self.tomo_stacks = [np.array([]) for _ in range(num_tomo_stacks)]
529 self.tomo_recon_stacks = [np.array([]) for _ in range(num_tomo_stacks)] 528 self.tomo_recon_stacks = [np.array([]) for _ in range(num_tomo_stacks)]
530 529
531 logging.info(f'num_core = {self.num_core}') 530 logging.debug(f'num_core = {self.num_core}')
532 logging.debug(f'config_file = {config_file}') 531 logging.debug(f'config_file = {config_file}')
533 logging.debug(f'config_dict = {config_dict}') 532 logging.debug(f'config_dict = {config_dict}')
534 logging.debug(f'config_out = {self.config_out}') 533 logging.debug(f'config_out = {self.config_out}')
535 logging.debug(f'output_folder = {self.output_folder}') 534 logging.debug(f'output_folder = {self.output_folder}')
536 logging.debug(f'log_stream = {log_stream}') 535 logging.debug(f'log_stream = {log_stream}')
1436 self._genTomo(tomo_stack_files, available_stacks) 1435 self._genTomo(tomo_stack_files, available_stacks)
1437 1436
1438 # Save tomography stack to file 1437 # Save tomography stack to file
1439 if self.galaxy_flag: 1438 if self.galaxy_flag:
1440 t0 = time() 1439 t0 = time()
1441 logging.info(f'Saving preprocessed tomography stack to file ...') 1440 logging.info(f'Saving preprocessed tomography stack to {output_name} ...')
1442 save_stacks = {f'set_{stack["index"]}':tomo_stack 1441 save_stacks = {f'set_{stack["index"]}':tomo_stack
1443 for stack,tomo_stack in zip(stacks,self.tomo_stacks)} 1442 for stack,tomo_stack in zip(stacks,self.tomo_stacks)}
1444 np.savez(output_name, **save_stacks) 1443 np.savez(output_name, **save_stacks)
1445 logging.info(f'... done in {time()-t0:.2f} seconds!') 1444 logging.info(f'... done in {time()-t0:.2f} seconds!')
1446 1445