--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo_reconstruct.py	Tue Mar 21 15:38:25 2023 +0000
@@ -0,0 +1,113 @@
+#!/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__()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo_reconstruct.xml	Tue Mar 21 15:38:25 2023 +0000
@@ -0,0 +1,48 @@
+<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>