Mercurial > repos > rv43 > tomo
changeset 40:fa94fe25ca46 draft
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100"
| author | rv43 |
|---|---|
| date | Tue, 19 Apr 2022 19:11:59 +0000 |
| parents | 8a3036b0a34c |
| children | ef5c2f7b49ec |
| files | tomo.py |
| diffstat | 1 files changed, 15 insertions(+), 19 deletions(-) [+] |
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--- a/tomo.py Tue Apr 19 18:43:00 2022 +0000 +++ b/tomo.py Tue Apr 19 19:11:59 2022 +0000 @@ -915,8 +915,8 @@ if not msnc.is_int(num_theta_skip, 0): msnc.illegal_value('num_theta_skip', num_theta_skip, 'config file') num_theta_skip = 0 - logging.info(f'zoom_perc = {zoom_perc}') - logging.info(f'num_theta_skip = {num_theta_skip}') + logging.debug(f'zoom_perc = {zoom_perc}') + logging.debug(f'num_theta_skip = {num_theta_skip}') # Update config and save to file if preprocess is None: @@ -1333,12 +1333,16 @@ raise ValueError('center_offsets dimension mismatch in reconstructOneTomoStack') centers = center_offsets centers += tomo_stack.shape[2]/2 - # RV hangs here with more than 24 cores and sge_64G_4 if True: t0 = time() - logging.info(f'running tomopy.prep.stripe.remove_stripe_fw on {num_core} cores ...') - tomo_stack = tomopy.prep.stripe.remove_stripe_fw( - tomo_stack[row_bounds[0]:row_bounds[1]], sigma=sigma, ncore=num_core) + if num_core > 24: + logging.info(f'running tomopy.prep.stripe.remove_stripe_fw on 24 cores ...') + tomo_stack = tomopy.prep.stripe.remove_stripe_fw( + tomo_stack[row_bounds[0]:row_bounds[1]], sigma=sigma, ncore=24) + else: + logging.info(f'running tomopy.prep.stripe.remove_stripe_fw on {num_core} cores ...') + tomo_stack = tomopy.prep.stripe.remove_stripe_fw( + tomo_stack[row_bounds[0]:row_bounds[1]], sigma=sigma, ncore=num_core) logging.info(f'... tomopy.prep.stripe.remove_stripe_fw took {time()-t0:.2f} seconds!') else: tomo_stack = tomo_stack[row_bounds[0]:row_bounds[1]] @@ -1567,10 +1571,7 @@ """ if num_core is None: num_core = self.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.info(f'num_core = {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)] @@ -1592,9 +1593,9 @@ logging.error('Illegal center_type_selector entry in galaxy_param '+ f'({center_type_selector})') galaxy_param['center_type_selector'] = None - logging.info(f'row_bounds = {row_bounds}') - logging.info(f'center_rows = {center_rows}') - logging.info(f'center_type_selector = {center_type_selector}') + logging.debug(f'row_bounds = {row_bounds}') + logging.debug(f'center_rows = {center_rows}') + logging.debug(f'center_type_selector = {center_type_selector}') else: if galaxy_param: logging.warning('Ignoring galaxy_param in findCenters (only for Galaxy)') @@ -1722,7 +1723,7 @@ n1 = int((1.+(tomo_ref_heights[0]+center_stack.shape[0]*eff_pixel_size- tomo_ref_heights[1])/eff_pixel_size)/2) n2 = center_stack.shape[0]-n1 - logging.info(f'n1 = {n1}, n2 = {n2} (n2-n1) = {(n2-n1)*eff_pixel_size:.3f} mm') + logging.debug(f'n1 = {n1}, n2 = {n2} (n2-n1) = {(n2-n1)*eff_pixel_size:.3f} mm') if not center_stack.size: RuntimeError('Center stack not loaded') if not self.test_mode and not self.galaxy_flag: @@ -1770,8 +1771,6 @@ if msnc.is_num(center_offset): use_center = pyip.inputYesNo('Current lower center offset = '+ f'{center_offset}, use this value ([y]/n)? ', blank=True) - #logging.info(f'use_center = {use_center}') - #logging.info(f'use_row = {use_row}') if use_center == 'no': if use_row == 'no': if not self.test_mode: @@ -1801,7 +1800,6 @@ use_center = 'no' row = center_rows[1] if self.test_mode or self.galaxy_flag: - logging.info(f'row = {row} lower_row = {lower_row} n2 = {n2}') assert(msnc.is_int(row, lower_row+1, n2-1)) if msnc.is_int(row, lower_row+1, n2-1): if self.test_mode or self.galaxy_flag: @@ -1817,8 +1815,6 @@ if msnc.is_num(center_offset): use_center = pyip.inputYesNo('Current upper center offset = '+ f'{center_offset}, use this value ([y]/n)? ', blank=True) - #logging.info(f'use_center = {use_center}') - #logging.info(f'use_row = {use_row}') if use_center == 'no': if use_row == 'no': if not self.test_mode: