diff read_image.py @ 49:26f99fdd8d61 draft

"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
author rv43
date Thu, 28 Jul 2022 16:05:24 +0000
parents
children 97c4e2cbbad9
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/read_image.py	Thu Jul 28 16:05:24 2022 +0000
@@ -0,0 +1,41 @@
+#!/usr/bin/env python3
+
+import logging
+
+import sys
+import argparse
+import numpy as np
+
+def __main__():
+
+    # Parse command line arguments
+    parser = argparse.ArgumentParser(
+            description='Read a reconstructed image')
+    parser.add_argument('-i', '--input_image',
+            help='Reconstructed image file')
+    parser.add_argument('-l', '--log', 
+            type=argparse.FileType('w'),
+            default=sys.stdout,
+            help='Log file')
+    args = parser.parse_args()
+
+    # Set basic log configuration
+    logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
+    log_level = 'INFO'
+    level = getattr(logging, log_level.upper(), None)
+    if not isinstance(level, int):
+        raise ValueError(f'Invalid log_level: {log_level}')
+    logging.basicConfig(format=logging_format, level=level, force=True,
+            handlers=[logging.StreamHandler()])
+
+    logging.info(f'input_image = {args.input_image}')
+    logging.debug(f'log = {args.log}')
+    logging.debug(f'is log stdout? {args.log is sys.stdout}')
+
+    # Load image
+    f = np.load(args.input_image)
+    logging.info(f'f shape = {f.shape}')
+
+if __name__ == "__main__":
+    __main__()
+