--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_smb_tiff.py	Fri Mar 10 20:57:05 2023 +0000
@@ -0,0 +1,132 @@
+#!/usr/bin/env python3
+
+import logging
+
+import argparse
+import matplotlib.pyplot as plt
+import os
+#from re import compile as re_compile
+import sys
+
+def __main__():
+
+    # Parse command line arguments
+    parser = argparse.ArgumentParser(
+            description='Plot an image for the SMB schema')
+    parser.add_argument('--cycle',
+            required=True,
+            help='''Run cycle.''')
+    parser.add_argument('--station',
+            required=True,
+            choices=['id1a3', 'id3a'],
+            help='''Beamline station.''')
+    parser.add_argument('--btr',
+            required=True,
+            help='''BTR.''')
+    parser.add_argument('--sample',
+            required=True,
+            help='''Sample name.''')
+    parser.add_argument('--scan_number',
+            default=-1,
+            type=int,
+            help='SPEC scan number')
+    parser.add_argument('--image_index',
+            default=0,
+            type=int,
+            help='Image index relative the first')
+    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))
+
+    # Log command line arguments
+    logging.info(f'cycle = {args.cycle}')
+    logging.info(f'station = {args.station}')
+    logging.info(f'btr = {args.btr}')
+    logging.info(f'sample = {args.sample}')
+    logging.info(f'scan_number = {args.scan_number}')
+    logging.info(f'image_index = {args.image_index}')
+    logging.debug(f'log = {args.log}')
+    logging.debug(f'is log stdout? {args.log is sys.stdout}')
+
+    # Check input parameters
+    if args.image_index < 0:
+        raise ValueError(f'Invalid "image_index" parameter ({args.image_index})')
+
+    # Check work directory
+    workdir = f'/nfs/chess/{args.station}/{args.cycle}/{args.btr}/{args.sample}'
+    logging.info(f'workdir = {workdir}')
+    if not os.path.isdir(workdir):
+        raise ValueError('Invalid work directory: {workdir}')
+
+    # Get all available scan_numbers
+    scan_numbers = [int(v) for v in os.listdir(workdir) if v.isdigit() and
+            os.path.isdir(f'{workdir}/{v}')]
+
+    if args.scan_number == -1:
+        # Pick lowest scan_number with image files
+        image_file = None
+        for scan_number in sorted(scan_numbers):
+            if 'nf' in os.listdir(f'{workdir}/{scan_number}'):
+#                indexRegex = re_compile(r'\d+')
+                path = f'{workdir}/{scan_number}/nf'
+#                image_files = [f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f)) and
+#                        f.endswith(".tif") and indexRegex.search(f)]
+                image_files = [f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f))
+                        and f.endswith(".tif")]
+                if len(image_files):
+                    image_file = f'{path}/{image_files[0]}'
+                    break
+    else:
+        # Pick requested image file
+        scan_number = args.scan_number
+        if not os.path.isdir(f'{workdir}/{scan_number}'):
+            raise ValueError('Invalid scan_number (non-existing directory {workdir}/{scan_number})')
+        path = f'{workdir}/{scan_number}/nf'
+        if 'nf' not in os.listdir(f'{workdir}/{scan_number}'):
+            raise ValueError('Unable to find directory {path}')
+        image_files = [f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f))
+                        and f.endswith(".tif")]
+        if args.image_index >= len(image_files):
+            raise ValueError('Unable to open the {args.image_index}th image file in {path}')
+        image_file = f'{path}/{image_files[args.image_index]}'
+
+    # Plot image to file
+    if image_file is None:
+        raise ValueError('Unable to find a valid image')
+    data = plt.imread(image_file)
+    title = 'image_files[0]'
+    plt.figure(title)
+    plt.imshow(data)
+    plt.savefig('image.jpg')
+    plt.close(fig=title)
+
+if __name__ == "__main__":
+    __main__()
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_smb_tiff.xml	Fri Mar 10 20:57:05 2023 +0000
@@ -0,0 +1,38 @@
+<tool id="plot_smb_tiff" name="Plot SMB Image" version="0.1.0" python_template_version="3.9">
+    <description>Plot an image for the SMB file schema</description>
+    <command detect_errors="exit_code"><![CDATA[
+        $__tool_directory__/plot_smb_tiff.py
+        --cycle '$cycle'
+        --station '$station'
+        --btr '$btr'
+        --sample '$sample'
+        --scan_number $scan_number
+        --image_index $image_index
+        -l '$log'
+    ]]></command>
+    <inputs>
+        <param name="cycle" type="text" optional="false" label="Run cycle"/>
+        <param name="station" type="select" label="Beamline station">
+            <option value="id1a3">id1a3</option>
+            <option value="id3a">id3a</option>
+        </param>
+        <param name="btr" type="text" optional="false" label="BTR"/>
+        <param name="sample" type="text" optional="false" label="Sample name"/>
+        <param name="scan_number" type='integer' value="-1" label="SPEC scan number"/>
+        <param name="image_index" type='integer' value="0" min="0" label="Image index relative the first"/>
+    </inputs>
+    <outputs>
+        <data name="log" format="txt" label="Log"/>
+    </outputs>
+    <help><![CDATA[
+        Plot an image for the SMB file schema
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{github_files,
+  author = {Verberg, Rolf},
+  year = {2022},
+}
+        </citation>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_plot_smb_tiff	Fri Mar 10 20:57:05 2023 +0000
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+# As Galaxy tool:
+python plot_smb_tiff.py --cycle '2021-3' --station 'id3a' --btr 'z-3234-A' --sample 'tenstom_1304r-1' --scan_number 370 --image_index 5
+display image.jpg