Mercurial > repos > rv43 > chess_tomo
changeset 5:543dba81eb15 draft
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
| author | rv43 |
|---|---|
| date | Mon, 20 Mar 2023 18:54:48 +0000 |
| parents | 9aa288729b9a |
| children | 05335876d167 |
| files | tomo_reduce.py tomo_reduce.xml workflow/run_tomo.py |
| diffstat | 3 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/tomo_reduce.py Mon Mar 20 18:44:23 2023 +0000 +++ b/tomo_reduce.py Mon Mar 20 18:54:48 2023 +0000 @@ -73,13 +73,14 @@ logging.debug(f'log = {args.log}') logging.debug(f'is log stdout? {args.log is sys.stdout}') logging.debug(f'log_level = {args.log_level}') - return # Instantiate Tomo object tomo = Tomo(galaxy_flag=args.galaxy_flag) # Read input file data = tomo.read(args.input_file) + print('data:\n{data.tree}') + return # Generate reduced tomography images data = tomo.gen_reduced_data(data, img_x_bounds=args.img_x_bounds)
--- a/tomo_reduce.xml Mon Mar 20 18:44:23 2023 +0000 +++ b/tomo_reduce.xml Mon Mar 20 18:54:48 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="tomo_reduce" name="Tomo Reduce" version="0.1.1" python_template_version="3.9"> +<tool id="tomo_reduce" name="Tomo Reduce" version="0.1.2" python_template_version="3.9"> <description>Reduce tomography images</description> <macros> <import>tomo_macros.xml</import>
--- a/workflow/run_tomo.py Mon Mar 20 18:44:23 2023 +0000 +++ b/workflow/run_tomo.py Mon Mar 20 18:54:48 2023 +0000 @@ -873,7 +873,10 @@ # Select image bounds title = f'tomography image at theta={round(theta, 2)+0}' - if (img_x_bounds is not None and not is_index_range(img_x_bounds, ge=0, + if img_x_bounds is not None: + if is_int_pair(img_x_bounds)i and img_x_bounds[0] == -1 and img_x_bounds[1] == -1 + img_x_bounds = None + elif not is_index_range(img_x_bounds, ge=0, le=first_image.shape[0])): raise ValueError(f'Invalid parameter img_x_bounds ({img_x_bounds})') if nxentry.instrument.source.attrs['station'] in ('id1a3', 'id3a'):