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comparison tomo.py @ 20:c033f8843dc0 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9ffb1cf41954e073c15a9b2a9ef7f3fd9b643cd0"
author rv43
date Mon, 18 Apr 2022 18:10:07 +0000
parents 4eba03628711
children 3caba2116858
comparison
equal deleted inserted replaced
19:4eba03628711 20:c033f8843dc0
1554 set_center = galaxy_param['set_center'] 1554 set_center = galaxy_param['set_center']
1555 else: 1555 else:
1556 logging.error('Illegal center_type_selector entry in galaxy_param '+ 1556 logging.error('Illegal center_type_selector entry in galaxy_param '+
1557 f'({center_type_selector})') 1557 f'({center_type_selector})')
1558 galaxy_param['center_type_selector'] = None 1558 galaxy_param['center_type_selector'] = None
1559 logging.info(f'row_bounds = {row_bounds}')
1560 logging.info(f'center_rows = {center_rows}')
1561 logging.info(f'center_type_selector = {center_type_selector}')
1559 else: 1562 else:
1560 if galaxy_param: 1563 if galaxy_param:
1561 logging.warning('Ignoring galaxy_param in findCenters (only for Galaxy)') 1564 logging.warning('Ignoring galaxy_param in findCenters (only for Galaxy)')
1562 galaxy_param = None 1565 galaxy_param = None
1563 1566
1714 # Lower row center 1717 # Lower row center
1715 use_row = 'no' 1718 use_row = 'no'
1716 use_center = 'no' 1719 use_center = 'no'
1717 row = center_rows[0] 1720 row = center_rows[0]
1718 if self.test_mode or self.galaxy_flag: 1721 if self.test_mode or self.galaxy_flag:
1722 logging.info(f'row = {row} n1 = {n1} n2 = {n2}')
1719 assert(msnc.is_int(row, n1, n2-2)) 1723 assert(msnc.is_int(row, n1, n2-2))
1720 if msnc.is_int(row, n1, n2-2): 1724 if msnc.is_int(row, n1, n2-2):
1721 if self.test_mode or self.galaxy_flag: 1725 if self.test_mode or self.galaxy_flag:
1722 use_row = 'yes' 1726 use_row = 'yes'
1723 else: 1727 else:
1729 if use_row != 'no': 1733 if use_row != 'no':
1730 center_offset = find_center.get('lower_center_offset') 1734 center_offset = find_center.get('lower_center_offset')
1731 if msnc.is_num(center_offset): 1735 if msnc.is_num(center_offset):
1732 use_center = pyip.inputYesNo('Current lower center offset = '+ 1736 use_center = pyip.inputYesNo('Current lower center offset = '+
1733 f'{center_offset}, use this value ([y]/n)? ', blank=True) 1737 f'{center_offset}, use this value ([y]/n)? ', blank=True)
1738 logging.info(f'use_center = {use_center}')
1739 logging.info(f'use_row = {use_row}')
1734 if use_center == 'no': 1740 if use_center == 'no':
1735 if use_row == 'no': 1741 if use_row == 'no':
1736 if not self.test_mode: 1742 if not self.test_mode:
1737 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', 1743 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}',
1738 aspect='auto') 1744 aspect='auto')
1745 # center_stack order: row,theta,column 1751 # center_stack order: row,theta,column
1746 center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg, 1752 center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg,
1747 eff_pixel_size, cross_sectional_dim, num_core=num_core, 1753 eff_pixel_size, cross_sectional_dim, num_core=num_core,
1748 galaxy_param=galaxy_param) 1754 galaxy_param=galaxy_param)
1749 logging.info(f'lower_center_offset = {center_offset:.2f} {type(center_offset)}') 1755 logging.info(f'lower_center_offset = {center_offset:.2f} {type(center_offset)}')
1750 print(center_offset)
1751 1756
1752 # Update config and save to file 1757 # Update config and save to file
1753 find_center['row_bounds'] = [n1, n2] 1758 find_center['row_bounds'] = [n1, n2]
1754 find_center['lower_row'] = row 1759 find_center['lower_row'] = row
1755 find_center['lower_center_offset'] = center_offset 1760 find_center['lower_center_offset'] = center_offset
1759 # Upper row center 1764 # Upper row center
1760 use_row = 'no' 1765 use_row = 'no'
1761 use_center = 'no' 1766 use_center = 'no'
1762 row = center_rows[1] 1767 row = center_rows[1]
1763 if self.test_mode or self.galaxy_flag: 1768 if self.test_mode or self.galaxy_flag:
1769 logging.info(f'row = {row} lower_row = {lower_row} n2 = {n2}')
1764 assert(msnc.is_int(row, lower_row+1, n2-1)) 1770 assert(msnc.is_int(row, lower_row+1, n2-1))
1765 if msnc.is_int(row, lower_row+1, n2-1): 1771 if msnc.is_int(row, lower_row+1, n2-1):
1766 if self.test_mode or self.galaxy_flag: 1772 if self.test_mode or self.galaxy_flag:
1767 use_row = 'yes' 1773 use_row = 'yes'
1768 else: 1774 else: