Mercurial > repos > rv43 > tomo

changeset 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
files tomo.py
diffstat 1 files changed, 8 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/tomo.py	Thu Apr 21 16:12:21 2022 +0000
+++ b/tomo.py	Thu Apr 21 16:49:37 2022 +0000
@@ -1271,11 +1271,14 @@
         t0 = time()
         if num_core > num_core_tomopy_limit:
             logging.debug(f'running find_center_vo on {num_core_tomopy_limit} cores ...')
+            print(f'running find_center_vo on {num_core_tomopy_limit} cores ...')
             tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core_tomopy_limit)
         else:
             logging.debug(f'running find_center_vo on {num_core} cores ...')
+            print(f'running find_center_vo on {num_core} cores ...')
             tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core)
         logging.debug(f'... find_center_vo took {time()-t0:.2f} seconds!')
+        print(f'... find_center_vo took {time()-t0:.2f} seconds!')
         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}')
@@ -1285,11 +1288,14 @@
             logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
             t0 = time()
             logging.debug(f'running _reconstructOnePlane on {num_core} cores ...')
+            print('OK AA')
             recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
                     eff_pixel_size, cross_sectional_dim, False, num_core)
+            print('OK BB')
             logging.debug(f'... _reconstructOnePlane took {time()-t0:.2f} seconds!')
             title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'
             self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs')
+            print('OK CC')
             del recon_plane
             if not galaxy_param['center_type_selector']:
                 del sinogram_T
@@ -1329,6 +1335,7 @@
                 return float(center_offset)
 
         # perform center finding search
+        print('OK DD')
         while True:
             if self.galaxy_flag and galaxy_param and galaxy_param['center_type_selector']:
                 set_center = center_offset_vo
@@ -1374,6 +1381,7 @@
             if self.galaxy_flag or pyip.inputInt('\nContinue (0) or end the search (1): ',
                     min=0, max=1):
                 break
+        print('OK EE')
 
         del sinogram_T
         del recon_plane