Mercurial > repos > rv43 > tomo
changeset 35:20829cd7aaef draft
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2ddb1147cf5ad2fedfa2d9323c07ff16f8d9c869"
author | rv43 |
---|---|
date | Tue, 19 Apr 2022 17:58:05 +0000 |
parents | 63de912323e5 |
children | 7ffde31e1e07 |
files | tomo.py |
diffstat | 1 files changed, 8 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- a/tomo.py Tue Apr 19 16:40:34 2022 +0000 +++ b/tomo.py Tue Apr 19 17:58:05 2022 +0000 @@ -1147,7 +1147,9 @@ recon_sinogram = spi.gaussian_filter(recon_sinogram, 0.5) recon_clean = np.expand_dims(recon_sinogram, axis=0) del recon_sinogram + logging.info('tomopy.misc.corr.remove_ring start') recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=17, ncore=num_core) + logging.info('tomopy.misc.corr.remove_ring end') logging.debug(f'filtering and removing ring artifact took {time()-t0:.2f} seconds!') return recon_clean @@ -1183,7 +1185,9 @@ center = sinogram.shape[1]/2 # try automatic center finding routines for initial value + logging.info('tomopy.find_center_vo start') tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core) + logging.info('tomopy.find_center_vo end') center_offset_vo = tomo_center-center if self.test_mode: logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}') @@ -1539,7 +1543,10 @@ """ if num_core is None: num_core = self.num_core - logging.info(f'num_core = {num_core}') +# logging.info(f'num_core available = {num_core}') +# if num_core > 24: +# num_core = 24 + logging.info(f'num_core used = {num_core}') logging.debug('Find centers for tomography stacks') stacks = self.config['stack_info']['stacks'] available_stacks = [stack['index'] for stack in stacks if stack.get('preprocessed', False)]