Mercurial > repos > rv43 > tomo

comparison tomo.py @ 44:0ac719053d6f draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit ffffe9eee44b5fb4f5fcdf34b06de5a9bd1eff74"
author rv43
date Thu, 21 Apr 2022 16:49:37 +0000
parents 0b9ce9489ecc
children f7c75e9643f2
comparison
equal deleted inserted replaced
43:0b9ce9489ecc 44:0ac719053d6f
1269 1269
1270 # try automatic center finding routines for initial value 1270 # try automatic center finding routines for initial value
1271 t0 = time() 1271 t0 = time()
1272 if num_core > num_core_tomopy_limit: 1272 if num_core > num_core_tomopy_limit:
1273 logging.debug(f'running find_center_vo on {num_core_tomopy_limit} cores ...') 1273 logging.debug(f'running find_center_vo on {num_core_tomopy_limit} cores ...')
1274 print(f'running find_center_vo on {num_core_tomopy_limit} cores ...')
1274 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core_tomopy_limit) 1275 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core_tomopy_limit)
1275 else: 1276 else:
1276 logging.debug(f'running find_center_vo on {num_core} cores ...') 1277 logging.debug(f'running find_center_vo on {num_core} cores ...')
1278 print(f'running find_center_vo on {num_core} cores ...')
1277 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core) 1279 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core)
1278 logging.debug(f'... find_center_vo took {time()-t0:.2f} seconds!') 1280 logging.debug(f'... find_center_vo took {time()-t0:.2f} seconds!')
1281 print(f'... find_center_vo took {time()-t0:.2f} seconds!')
1279 center_offset_vo = tomo_center-center 1282 center_offset_vo = tomo_center-center
1280 if self.test_mode: 1283 if self.test_mode:
1281 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}') 1284 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
1282 del sinogram_T 1285 del sinogram_T
1283 return float(center_offset_vo) 1286 return float(center_offset_vo)
1284 elif self.galaxy_flag: 1287 elif self.galaxy_flag:
1285 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}') 1288 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
1286 t0 = time() 1289 t0 = time()
1287 logging.debug(f'running _reconstructOnePlane on {num_core} cores ...') 1290 logging.debug(f'running _reconstructOnePlane on {num_core} cores ...')
1291 print('OK AA')
1288 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg, 1292 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
1289 eff_pixel_size, cross_sectional_dim, False, num_core) 1293 eff_pixel_size, cross_sectional_dim, False, num_core)
1294 print('OK BB')
1290 logging.debug(f'... _reconstructOnePlane took {time()-t0:.2f} seconds!') 1295 logging.debug(f'... _reconstructOnePlane took {time()-t0:.2f} seconds!')
1291 title = f'edges row{row} center offset{center_offset_vo:.2f} Vo' 1296 title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'
1292 self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs') 1297 self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs')
1298 print('OK CC')
1293 del recon_plane 1299 del recon_plane
1294 if not galaxy_param['center_type_selector']: 1300 if not galaxy_param['center_type_selector']:
1295 del sinogram_T 1301 del sinogram_T
1296 return float(center_offset_vo) 1302 return float(center_offset_vo)
1297 else: 1303 else:
1327 del sinogram_T 1333 del sinogram_T
1328 del recon_plane 1334 del recon_plane
1329 return float(center_offset) 1335 return float(center_offset)
1330 1336
1331 # perform center finding search 1337 # perform center finding search
1338 print('OK DD')
1332 while True: 1339 while True:
1333 if self.galaxy_flag and galaxy_param and galaxy_param['center_type_selector']: 1340 if self.galaxy_flag and galaxy_param and galaxy_param['center_type_selector']:
1334 set_center = center_offset_vo 1341 set_center = center_offset_vo
1335 if galaxy_param['center_type_selector'] == 'user': 1342 if galaxy_param['center_type_selector'] == 'user':
1336 set_center = galaxy_param['set_center'] 1343 set_center = galaxy_param['set_center']
1372 else: 1379 else:
1373 self._plotEdgesOnePlane(recon_plane, title) 1380 self._plotEdgesOnePlane(recon_plane, title)
1374 if self.galaxy_flag or pyip.inputInt('\nContinue (0) or end the search (1): ', 1381 if self.galaxy_flag or pyip.inputInt('\nContinue (0) or end the search (1): ',
1375 min=0, max=1): 1382 min=0, max=1):
1376 break 1383 break
1384 print('OK EE')
1377 1385
1378 del sinogram_T 1386 del sinogram_T
1379 del recon_plane 1387 del recon_plane
1380 if self.galaxy_flag: 1388 if self.galaxy_flag:
1381 center_offset = center_offset_vo 1389 center_offset = center_offset_vo