Mercurial > repos > rv43 > chess_tomo
changeset 21:7a7233e212be draft
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
| author | rv43 |
|---|---|
| date | Tue, 21 Mar 2023 15:45:42 +0000 |
| parents | b2d1826279f8 |
| children | b156e4cee6d7 |
| files | tomo_find_center.xml tomo_reconstruct.py tomo_reconstruct.xml tomo_reduce.xml workflow/.run_tomo.py.swp |
| diffstat | 5 files changed, 5 insertions(+), 166 deletions(-) [+] |
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--- a/tomo_find_center.xml Tue Mar 21 15:38:25 2023 +0000 +++ b/tomo_find_center.xml Tue Mar 21 15:45:42 2023 +0000 @@ -3,10 +3,10 @@ <macros> <import>tomo_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"/> <command detect_errors="exit_code"> <![CDATA[ - mkdir find_center_pngs; + mkdir tomo_find_centers_plots; $__tool_directory__/tomo_find_center.py --input_file "$input_file" --output_file "output.yaml" @@ -24,8 +24,8 @@ </inputs> <outputs> <expand macro="common_outputs"/> - <collection name="find_center_pngs" type="list" label="Recontructed slice images"> - <discover_datasets pattern="__name_and_ext__" directory="find_center_pngs"/> + <collection name="tomo_find_centers_plots" type="list" label="Find center images"> + <discover_datasets pattern="__name_and_ext__" directory="tomo_find_centers_plots"/> </collection> <data name="output_file" format="yaml" label="Center axis info" from_work_dir="output.yaml"/> </outputs>
--- a/tomo_reconstruct.py Tue Mar 21 15:38:25 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,113 +0,0 @@ -#!/usr/bin/env python3 - -import logging - -import argparse -import pathlib -import sys -#import tracemalloc - -from workflow.run_tomo import Tomo - -#from memory_profiler import profile -#@profile -def __main__(): - # Parse command line arguments - parser = argparse.ArgumentParser( - description='Perform a tomography reconstruction') - parser.add_argument('-i', '--input_file', - required=True, - type=pathlib.Path, - help='''Full or relative path to the input file (in Nexus format).''') - parser.add_argument('-c', '--center_file', - required=True, - type=pathlib.Path, - help='''Full or relative path to the center info file (in yaml format).''') - parser.add_argument('-o', '--output_file', - required=False, - type=pathlib.Path, - help='''Full or relative path to the output file (in Nexus format).''') - parser.add_argument('--galaxy_flag', - action='store_true', - help='''Use this flag to run the scripts as a galaxy tool.''') - parser.add_argument('-l', '--log', -# type=argparse.FileType('w'), - default=sys.stdout, - help='Logging stream or filename') - parser.add_argument('--log_level', - choices=logging._nameToLevel.keys(), - default='INFO', - help='''Specify a preferred logging level.''') - parser.add_argument('--x_bounds', - required=False, - nargs=2, - type=int, - help='''Boundaries of reconstructed images in x-direction.''') - parser.add_argument('--y_bounds', - required=False, - nargs=2, - type=int, - help='''Boundaries of reconstructed images in y-direction.''') - args = parser.parse_args() - - # Set log configuration - # When logging to file, the stdout log level defaults to WARNING - logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s' - level = logging.getLevelName(args.log_level) - if args.log is sys.stdout: - logging.basicConfig(format=logging_format, level=level, force=True, - handlers=[logging.StreamHandler()]) - else: - if isinstance(args.log, str): - logging.basicConfig(filename=f'{args.log}', filemode='w', - format=logging_format, level=level, force=True) - elif isinstance(args.log, io.TextIOWrapper): - logging.basicConfig(filemode='w', format=logging_format, level=level, - stream=args.log, force=True) - else: - raise(ValueError(f'Invalid argument --log: {args.log}')) - stream_handler = logging.StreamHandler() - logging.getLogger().addHandler(stream_handler) - stream_handler.setLevel(logging.WARNING) - stream_handler.setFormatter(logging.Formatter(logging_format)) - - # Starting memory monitoring -# tracemalloc.start() - - # Log command line arguments - logging.info(f'input_file = {args.input_file}') - logging.info(f'center_file = {args.center_file}') - logging.info(f'output_file = {args.output_file}') - logging.info(f'galaxy_flag = {args.galaxy_flag}') - 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}') - logging.info(f'x_bounds = {args.x_bounds}') - logging.info(f'y_bounds = {args.y_bounds}') - - # Instantiate Tomo object - tomo = Tomo(galaxy_flag=args.galaxy_flag) - - # Read input file - data = tomo.read(args.input_file) - - # Read center data - center_data = tomo.read(args.center_file) - - # Find the calibrated center axis info - data = tomo.reconstruct_data(data, center_data, x_bounds=args.x_bounds, y_bounds=args.y_bounds) - - # Write output file - data = tomo.write(data, args.output_file) - - # Displaying memory usage -# logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}') - - # stopping memory monitoring -# tracemalloc.stop() - - logging.info('Completed tomography reconstruction') - - -if __name__ == "__main__": - __main__()
--- a/tomo_reconstruct.xml Tue Mar 21 15:38:25 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ -<tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.3.0" python_template_version="3.9"> - <description>Perform a tomography reconstruction</description> - <macros> - <import>tomo_macros.xml</import> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"> - <![CDATA[ - mkdir center_slice_pngs; - $__tool_directory__/tomo_reconstruct.py - --input_file '$input_file' - --center_file '$center_file' - --output_file 'output.nex' - --galaxy_flag - #if str($center_offsets.type_selector) == "offsets_manual" - --center_offsets $center_offsets.low $center_offsets.upp - #end if - -l '$log' - ]]> - </command> - <inputs> - <expand macro="common_inputs"/> - <param name="input_file" type='data' format='nex' optional='false' label="Reduced tomography data"/> - <param name="center_file" type='data' format='yaml' optional='false' label="Center axis input file"/> - <conditional name="center_offsets"> - <param name="type_selector" type="select" label="Read reconstruction center axis offsets from file or enter enter manually"> - <option value="offsets_from_file" selected="true">Read center axis offsets from file</option> - <option value="offsets_manual">Manually enter center axis offsets</option> - </param> - <when value="offsets_from_file"/> - <when value="offsets_manual"> - <param name="low" type="float" value = "0" optional="false" label="Lower center offset"/> - <param name="upp" type="float" value = "0" optional="false" label="Upper center offset"/> - </when> - </conditional> - </inputs> - <outputs> - <expand macro="common_outputs"/> - <collection name="center_slice_pngs" type="list" label="Recontructed slices midway in each dimension"> - <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/> - </collection> - <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/> - </outputs> - <help><![CDATA[ - Reconstruct tomography images. - ]]></help> - <expand macro="citations"/> -</tool>
--- a/tomo_reduce.xml Tue Mar 21 15:38:25 2023 +0000 +++ b/tomo_reduce.xml Tue Mar 21 15:45:42 2023 +0000 @@ -3,7 +3,7 @@ <macros> <import>tomo_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"/> <command detect_errors="exit_code"> <![CDATA[ mkdir tomo_reduce_plots;