Mercurial > repos > rv43 > chess_tomo

comparison workflow/run_tomo.py @ 29:551d1ea2416d draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Tue, 21 Mar 2023 18:46:02 +0000
parents 562fc79de827
children 3342c0518d4c
comparison
equal deleted inserted replaced
28:562fc79de827 29:551d1ea2416d
299 if not isinstance(nxroot, NXroot): 299 if not isinstance(nxroot, NXroot):
300 raise ValueError(f'Invalid parameter nxroot ({nxroot})') 300 raise ValueError(f'Invalid parameter nxroot ({nxroot})')
301 nxentry = nxroot[nxroot.attrs['default']] 301 nxentry = nxroot[nxroot.attrs['default']]
302 if not isinstance(nxentry, NXentry): 302 if not isinstance(nxentry, NXentry):
303 raise ValueError(f'Invalid nxentry ({nxentry})') 303 raise ValueError(f'Invalid nxentry ({nxentry})')
304 if self.galaxy_flag: 304 if center_rows is not None:
305 if center_rows is not None: 305 if self.galaxy_flag
306 center_rows = tuple(center_rows) 306 is not is_int_pair(center_rows, ge=-1):
307 if not is_int_pair(center_rows):
308 raise ValueError(f'Invalid parameter center_rows ({center_rows})') 307 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
309 elif center_rows is not None: 308 if (center_rows[0] != -1 and center_rows[1] != -1 and
310 logger.warning(f'Ignoring parameter center_rows ({center_rows})') 309 center_rows[0] > center_rows[1]):
311 center_rows = None 310 center_rows = (center_rows[1], center_rows[0])
311 else:
312 center_rows = tuple(center_rows)
313 else:
314 logger.warning(f'Ignoring parameter center_rows ({center_rows})')
315 center_rows = None
312 if self.galaxy_flag: 316 if self.galaxy_flag:
313 if center_stack_index is not None and not is_int(center_stack_index, ge=0): 317 if center_stack_index is not None and not is_int(center_stack_index, ge=0):
314 raise ValueError(f'Invalid parameter center_stack_index ({center_stack_index})') 318 raise ValueError(f'Invalid parameter center_stack_index ({center_stack_index})')
315 elif center_stack_index is not None: 319 elif center_stack_index is not None:
316 logger.warning(f'Ignoring parameter center_stack_index ({center_stack_index})') 320 logger.warning(f'Ignoring parameter center_stack_index ({center_stack_index})')
375 lower_row = self.test_config['lower_row'] 379 lower_row = self.test_config['lower_row']
376 elif self.galaxy_flag: 380 elif self.galaxy_flag:
377 if center_rows is None or center_rows[0] == -1: 381 if center_rows is None or center_rows[0] == -1:
378 lower_row = 0 382 lower_row = 0
379 else: 383 else:
380 lower_row = min(center_rows) 384 lower_row = center_rows[0]
381 if not 0 <= lower_row < tomo_fields_shape[2]-1: 385 if not 0 <= lower_row < tomo_fields_shape[2]-1:
382 raise ValueError(f'Invalid parameter center_rows ({center_rows})') 386 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
383 else: 387 else:
384 lower_row = select_one_image_bound( 388 lower_row = select_one_image_bound(
385 nxentry.reduced_data.data.tomo_fields[center_stack_index,0,:,:], 0, bound=0, 389 nxentry.reduced_data.data.tomo_fields[center_stack_index,0,:,:], 0, bound=0,
386 title=f'theta={round(thetas[0], 2)+0}', 390 title=f'theta={round(thetas[0], 2)+0}',
387 bound_name='row index to find lower center', default=default, raise_error=True) 391 bound_name='row index to find lower center', default=default, raise_error=True)
388 logger.debug('Finding center...') 392 logger.debug('Finding center...')
389 t0 = time() 393 t0 = time()
390 lower_center_offset = self._find_center_one_plane( 394 lower_center_offset = self._find_center_one_plane(
391 #np.asarray(nxentry.reduced_data.data.tomo_fields[center_stack_index,:,lower_row,:]),
392 nxentry.reduced_data.data.tomo_fields[center_stack_index,:,lower_row,:], 395 nxentry.reduced_data.data.tomo_fields[center_stack_index,:,lower_row,:],
393 lower_row, thetas, eff_pixel_size, cross_sectional_dim, path=path, 396 lower_row, thetas, eff_pixel_size, cross_sectional_dim, path=path,
394 num_core=self.num_core) 397 num_core=self.num_core)
395 logger.debug(f'... done in {time()-t0:.2f} seconds') 398 logger.debug(f'... done in {time()-t0:.2f} seconds')
396 logger.debug(f'lower_row = {lower_row:.2f}') 399 logger.debug(f'lower_row = {lower_row:.2f}')
401 upper_row = self.test_config['upper_row'] 404 upper_row = self.test_config['upper_row']
402 elif self.galaxy_flag: 405 elif self.galaxy_flag:
403 if center_rows is None or center_rows[1] == -1: 406 if center_rows is None or center_rows[1] == -1:
404 upper_row = tomo_fields_shape[2]-1 407 upper_row = tomo_fields_shape[2]-1
405 else: 408 else:
406 upper_row = max(center_rows) 409 upper_row = center_rows[1]
407 if not lower_row < upper_row < tomo_fields_shape[2]: 410 if not lower_row < upper_row < tomo_fields_shape[2]:
408 raise ValueError(f'Invalid parameter center_rows ({center_rows})') 411 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
409 else: 412 else:
410 upper_row = select_one_image_bound( 413 upper_row = select_one_image_bound(
411 nxentry.reduced_data.data.tomo_fields[center_stack_index,0,:,:], 0, 414 nxentry.reduced_data.data.tomo_fields[center_stack_index,0,:,:], 0,
511 tomo_recon_stacks[i] = tomo_recon_stack 514 tomo_recon_stacks[i] = tomo_recon_stack
512 515
513 # Resize the reconstructed tomography data 516 # Resize the reconstructed tomography data
514 # reconstructed data order in each stack: row/z,x,y 517 # reconstructed data order in each stack: row/z,x,y
515 if self.test_mode: 518 if self.test_mode:
516 x_bounds = self.test_config.get('x_bounds') 519 x_bounds = tuple(self.test_config.get('x_bounds'))
517 y_bounds = self.test_config.get('y_bounds') 520 y_bounds = tuple(self.test_config.get('y_bounds'))
518 z_bounds = None 521 z_bounds = None
519 elif self.galaxy_flag: 522 elif self.galaxy_flag:
520 if x_bounds is not None and not is_int_pair(x_bounds, ge=-1, 523 x_max = tomo_recon_stacks[0].shape[1]
521 lt=tomo_recon_stacks[0].shape[1]): 524 if x_bounds is None:
525 x_bounds = (0, x_max)
526 elif is_int_pair(x_bounds, ge=-1, le=x_max):
527 x_bounds = tuple(x_bounds)
528 if x_bounds[0] == -1:
529 x_bounds = (0, x_bounds[1])
530 if x_bounds[1] == -1:
531 x_bounds = (x_bounds[0], x_max)
532 if not is_index_range(x_bounds, ge=0, le=x_max):
522 raise ValueError(f'Invalid parameter x_bounds ({x_bounds})') 533 raise ValueError(f'Invalid parameter x_bounds ({x_bounds})')
523 if y_bounds is not None and not is_int_pair(y_bounds, ge=-1, 534 y_max = tomo_recon_stacks[0].shape[1]
524 lt=tomo_recon_stacks[0].shape[1]): 535 if y_bounds is None:
536 y_bounds = (0, y_max)
537 elif is_int_pair(y_bounds, ge=-1, le=y_max):
538 y_bounds = tuple(y_bounds)
539 if y_bounds[0] == -1:
540 y_bounds = (0, y_bounds[1])
541 if y_bounds[1] == -1:
542 y_bounds = (y_bounds[0], y_max)
543 if not is_index_range(y_bounds, ge=0, le=y_max):
525 raise ValueError(f'Invalid parameter y_bounds ({y_bounds})') 544 raise ValueError(f'Invalid parameter y_bounds ({y_bounds})')
526 z_bounds = None 545 z_bounds = None
527 else: 546 else:
528 x_bounds, y_bounds, z_bounds = self._resize_reconstructed_data(tomo_recon_stacks) 547 x_bounds, y_bounds, z_bounds = self._resize_reconstructed_data(tomo_recon_stacks)
529 if x_bounds is None: 548 if x_bounds is None:
987 x_sum_max = x_sum.max() 1006 x_sum_max = x_sum.max()
988 if self.galaxy_flag: 1007 if self.galaxy_flag:
989 if img_x_bounds is None: 1008 if img_x_bounds is None:
990 img_x_bounds = (0, first_image.shape[0]) 1009 img_x_bounds = (0, first_image.shape[0])
991 elif is_int_pair(img_x_bounds, ge=-1, le=first_image.shape[0]): 1010 elif is_int_pair(img_x_bounds, ge=-1, le=first_image.shape[0]):
1011 img_x_bounds = tuple(img_x_bounds)
992 if img_x_bounds[0] == -1: 1012 if img_x_bounds[0] == -1:
993 img_x_bounds[0] = 0 1013 img_x_bounds = (0, img_x_bounds[1])
994 if img_x_bounds[1] == -1: 1014 if img_x_bounds[1] == -1:
995 img_x_bounds[1] = first_image.shape[0] 1015 img_x_bounds = (img_x_bounds[0], first_image.shape[0])
996 if not is_index_range(img_x_bounds, ge=0, le=first_image.shape[0]): 1016 if not is_index_range(img_x_bounds, ge=0, le=first_image.shape[0]):
997 raise ValueError(f'Invalid parameter img_x_bounds ({img_x_bounds})') 1017 raise ValueError(f'Invalid parameter img_x_bounds ({img_x_bounds})')
998 else: 1018 else:
999 quick_imshow(first_image, title=title) 1019 quick_imshow(first_image, title=title)
1000 print('Select vertical data reduction range from first tomography image') 1020 print('Select vertical data reduction range from first tomography image')