--- /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 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.0.3">lmfit</requirement>
+            <requirement type="package" version="3.5.2">matplotlib</requirement>
+            <requirement type="package" version="1.0.0">nexusformat</requirement>
+            <requirement type="package" version="1.12.2">tomopy</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+@misc{github_files,
+  author = {Verberg, Rolf},
+  year = {2022},
+  title = {Tomo Reconstruction},
+}</citation>
+        </citations>
+    </xml>
+    <!--
+    <xml name="common_inputs">
+        <param name="config" type='data' format='yaml' optional='false' label="Input config"/>
+        <param name="config" type='data' format='tomo.config.yaml' optional='true' label="Input config"/>
+    </xml>
+    -->
+    <xml name="common_outputs">
+        <data name="log" format="txt" label="Log"/>
+    </xml>
+</macros>
+ 

--- /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__()

--- /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 @@
+<tool id="tomo_reduce" name="Tomo Reduce" version="0.1.0" python_template_version="3.9">
+    <description>Reduce tomography images</description>
+    <macros>
+        <import>tomo_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+        <![CDATA[
+            mkdir tomo_reduce_plots;
+            $__tool_directory__/tomo_reduce.py
+            --input_file '$input_file'
+            --output_file 'output.nxs'
+            --galaxy_flag
+            --img_x_bounds $x_bounds.x_bound_low $x_bounds.x_bound_upp
+            -l '$log'
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_file" type="data" optional="false" label="Input file"/>
+    </inputs>
+    <outputs>
+        <expand macro="common_outputs"/>
+        <collection name="tomo_reduce_plots" type="list" label="Tomo data reduction images">
+            <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/>
+        </collection>
+        <data name="output_file" format="nxs" label="Reduced tomography data" from_work_dir="output.nxs"/>
+    </outputs>
+    <help>
+        <![CDATA[
+            Reduce tomography images.
+        ]]>
+    </help>
+    <expand macro="citations"/>
+</tool>