Mercurial > repos > rv43 > tomo
changeset 2:b8977c98800b draft
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0c40fb274acc13ebf7054379bb49ed13acec918e"
| author | rv43 |
|---|---|
| date | Thu, 31 Mar 2022 20:48:17 +0000 |
| parents | e4778148df6b |
| children | f9c52762c32c |
| files | tomo.py tomo_setup.py tomo_setup.xml |
| diffstat | 3 files changed, 16 insertions(+), 17 deletions(-) [+] |
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--- a/tomo.py Thu Mar 31 18:24:16 2022 +0000 +++ b/tomo.py Thu Mar 31 20:48:17 2022 +0000 @@ -481,7 +481,6 @@ return if self.galaxy_flag: - self.num_core = 1 #RV can I set this? mp.cpu_count() assert(self.output_folder == '.') assert(self.test_mode is False) self.save_plots = True @@ -528,7 +527,7 @@ self.tomo_stacks = [np.array([]) for _ in range(num_tomo_stacks)] self.tomo_recon_stacks = [np.array([]) for _ in range(num_tomo_stacks)] - logging.info(f'num_core = {self.num_core}') + logging.debug(f'num_core = {self.num_core}') logging.debug(f'config_file = {config_file}') logging.debug(f'config_dict = {config_dict}') logging.debug(f'config_out = {self.config_out}') @@ -1438,7 +1437,7 @@ # Save tomography stack to file if self.galaxy_flag: t0 = time() - logging.info(f'Saving preprocessed tomography stack to file ...') + logging.info(f'Saving preprocessed tomography stack to {output_name} ...') save_stacks = {f'set_{stack["index"]}':tomo_stack for stack,tomo_stack in zip(stacks,self.tomo_stacks)} np.savez(output_name, **save_stacks)
--- a/tomo_setup.py Thu Mar 31 18:24:16 2022 +0000 +++ b/tomo_setup.py Thu Mar 31 20:48:17 2022 +0000 @@ -52,17 +52,17 @@ logging.basicConfig(format=logging_format, level=level, force=True, handlers=[logging.StreamHandler()]) - logging.info(f'config = {args.config}') - logging.info(f'theta_range = {args.theta_range.split()}') - logging.info(f'dark = {args.dark}') - logging.info(f'bright = {args.bright}') - logging.info(f'tomo = {args.tomo}') - logging.info(f'detectorbounds = {args.detectorbounds}') - logging.info(f'output_config = {args.output_config}') - logging.info(f'output_data = {args.output_data}') - logging.info(f'log = {args.log}') - logging.info(f'is log stdout? {args.log is sys.stdout}') - logging.info(f'tomoranges = {args.tomo_ranges}') + logging.debug(f'config = {args.config}') + logging.debug(f'theta_range = {args.theta_range.split()}') + logging.debug(f'dark = {args.dark}') + logging.debug(f'bright = {args.bright}') + logging.debug(f'tomo = {args.tomo}') + logging.debug(f'detectorbounds = {args.detectorbounds}') + logging.debug(f'output_config = {args.output_config}') + logging.debug(f'output_data = {args.output_data}') + logging.debug(f'log = {args.log}') + logging.debug(f'is log stdout? {args.log is sys.stdout}') + logging.debug(f'tomoranges = {args.tomo_ranges}') # Read input files and collect data files info datasets = []
--- a/tomo_setup.xml Thu Mar 31 18:24:16 2022 +0000 +++ b/tomo_setup.xml Thu Mar 31 20:48:17 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="tomo_setup" name="Tomo Setup" version="0.1.0" python_template_version="3.9"> +<tool id="tomo_setup" name="Tomo Setup" version="0.1.1" python_template_version="3.9"> <description>Preprocess tomography images</description> <requirements> <requirement type="package" version="1.11.0">tomopy</requirement> @@ -14,7 +14,7 @@ --bright 'bright_field.png' --tomo 'tomo.png' --detectorbounds 'detectorbounds.png' - --output_data '$output_data' + --output_data 'output.npz' --output_config 'output_config.yaml' -l '$log' #for $s in $tomo_sets# ${s.offset} ${s.num} #end for @@ -47,7 +47,7 @@ <data name="bright_field" format="png" label="Bright field" from_work_dir="bright_field.png"/> <data name="tomo" format="png" label="First tomography image" from_work_dir="tomo.png"/> <data name="detectorbounds" format="png" label="Detector bounds" from_work_dir="detectorbounds.png"/> - <data name="output_data" format="npz" label="Preprocessed tomography data"/> + <data name="output_data" format="npz" label="Preprocessed tomography data" from_work_dir="output_data.npz"/> <data name="output_config" format="yaml" label="Output config" from_work_dir="output_config.yaml"/> <data name="log" format="txt" label="Log"/> </outputs>