# HG changeset patch
# User rv43
# Date 1679336173 0
# Node ID 3fd7398a3a7fdbba53fc4e97d10d40aabfc5ad89
# Parent 07647d52d7d3cdcf2e1c54798ea7be704f5a8735
planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0814301cace61040b468d4185a9056a1aed4050d-dirty
diff -r 07647d52d7d3 -r 3fd7398a3a7f tomo_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo_macros.xml Mon Mar 20 18:16:13 2023 +0000
@@ -0,0 +1,30 @@
+
+
+
+ lmfit
+ matplotlib
+ nexusformat
+ tomopy
+
+
+
+
+
+@misc{github_files,
+ author = {Verberg, Rolf},
+ year = {2022},
+ title = {Tomo Reconstruction},
+}
+
+
+
+
+
+
+
+
diff -r 07647d52d7d3 -r 3fd7398a3a7f tomo_reduce.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo_reduce.py Mon Mar 20 18:16:13 2023 +0000
@@ -0,0 +1,96 @@
+#!/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='Reduce tomography data')
+ parser.add_argument('-i', '--input_file',
+ required=True,
+ type=pathlib.Path,
+ help='''Full or relative path to the input file (in yaml or nxs format).''')
+ parser.add_argument('-o', '--output_file',
+ required=True,
+ 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('--img_x_bounds',
+ required=False,
+ nargs=2,
+ type=int,
+ help='Vertical data reduction image range')
+ 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.''')
+ 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))
+
+ # Start memory monitoring
+# tracemalloc.start()
+
+ # Log command line arguments
+ logging.info(f'input_file = {args.input_file}')
+ logging.info(f'output_file = {args.output_file}')
+ logging.info(f'galaxy_flag = {args.galaxy_flag}')
+ logging.info(f'img_x_bounds = {args.img_x_bounds}')
+ 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}')
+
+ # Instantiate Tomo object
+ tomo = Tomo(galaxy_flag=args.galaxy_flag)
+
+ # Read input file
+ data = tomo.read(args.input_file)
+
+ # Generate reduced tomography images
+ data = tomo.gen_reduced_data(data, img_x_bounds=args.img_x_bounds)
+
+ # Write output file
+ data = tomo.write(data, args.output_file)
+
+ # Displaying memory usage
+# logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
+
+ # Stop memory monitoring
+# tracemalloc.stop()
+
+if __name__ == "__main__":
+ __main__()
diff -r 07647d52d7d3 -r 3fd7398a3a7f tomo_reduce.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo_reduce.xml Mon Mar 20 18:16:13 2023 +0000
@@ -0,0 +1,34 @@
+
+ Reduce tomography images
+
+ tomo_macros.xml
+
+
+
+
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