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)]