add timestamps to logging and default to info (#96)

* add timestamps to logging and default to info

* formatting

* format

* fix imports

* format

* bump version to 0.2.14

Author: philippotto

setup.py

@@ -3,7 +3,7 @@
 setup(
     name="wkcuber",
     packages=find_packages(exclude=("tests",)),
-    version="0.2.13",
+    version="0.2.14",
     install_requires=["scipy", "numpy", "pillow", "pyyaml", "wkw", "cluster_tools>=1.19"],
     description="A cubing tool for webKnossos",
     author="Norman Rzepka",

wkcuber/__main__.py

@@ -6,7 +6,12 @@
 from .downsampling import downsample_mags, downsample_mags_anisotropic, DEFAULT_EDGE_LEN
 from .compress import compress_mag_inplace
 from .metadata import write_webknossos_metadata
-from .utils import add_verbose_flag, add_distribution_flags, add_anisotropic_flag
+from .utils import (
+    add_verbose_flag,
+    add_distribution_flags,
+    add_anisotropic_flag,
+    setup_logging,
+)
 from .mag import Mag
 
 
@@ -44,9 +49,7 @@ def create_parser():
 
 if __name__ == "__main__":
     args = create_parser().parse_args()
-
-    if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+    setup_logging(args)
 
     scale = tuple(float(x) for x in args.scale.split(","))
     bounding_box = cubing(

wkcuber/compress.py

@@ -15,6 +15,7 @@
     add_distribution_flags,
     get_executor_for_args,
     wait_and_ensure_success,
+    setup_logging,
 )
 from .metadata import detect_resolutions
 from typing import List
@@ -148,6 +149,5 @@ def compress_mags(
 
 if __name__ == "__main__":
     args = create_parser().parse_args()
-    if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+    setup_logging(args)
     compress_mags(args.source_path, args.layer_name, args.target_path, args.mag, args)

wkcuber/convert_knossos.py

@@ -15,6 +15,7 @@
     add_distribution_flags,
     get_executor_for_args,
     wait_and_ensure_success,
+    setup_logging,
 )
 from .knossos import KnossosDataset, CUBE_EDGE_LEN
 
@@ -98,9 +99,7 @@ def convert_knossos(
 
 if __name__ == "__main__":
     args = create_parser().parse_args()
-
-    if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+    setup_logging(args)
 
     convert_knossos(
         args.source_path,

wkcuber/cubing.py

@@ -15,6 +15,7 @@
     add_distribution_flags,
     get_executor_for_args,
     wait_and_ensure_success,
+    setup_logging,
 )
 from .image_readers import image_reader
 
@@ -216,9 +217,7 @@ def cubing(source_path, target_path, layer_name, dtype, batch_size, args=None) -
 
 if __name__ == "__main__":
     args = create_parser().parse_args()
-
-    if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+    setup_logging(args)
 
     cubing(
         args.source_path,

wkcuber/downsampling.py

@@ -23,6 +23,7 @@
     get_executor_for_args,
     wait_and_ensure_success,
     add_anisotropic_flag,
+    setup_logging,
 )
 
 DEFAULT_EDGE_LEN = 256
@@ -530,9 +531,7 @@ def detect_larger_and_smaller_dimension(scale):
 
 if __name__ == "__main__":
     args = create_parser().parse_args()
-
-    if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+    setup_logging(args)
 
     from_mag = Mag(args.from_mag)
     max_mag = Mag(args.max)

wkcuber/metadata.py

@@ -10,6 +10,7 @@
 from typing import Optional
 from .mag import Mag
 from typing import List
+from .utils import add_verbose_flag, setup_logging
 
 
 def get_datasource_path(dataset_path):
@@ -41,6 +42,8 @@ def create_parser():
     )
     group.add_argument("--max_id", help="set max id of segmentation.", default=0)
 
+    add_verbose_flag(parser)
+
     return parser
 
 
@@ -288,8 +291,9 @@ def detect_layers(dataset_path, max_id, compute_max_id, exact_bounding_box=None)
 
 
 if __name__ == "__main__":
-    logging.basicConfig(level=logging.DEBUG)
     args = create_parser().parse_args()
+    setup_logging(args)
+
     if not args.refresh:
         assert (
             args.name is not None

wkcuber/tile_cubing.py

@@ -17,6 +17,7 @@
     add_distribution_flags,
     get_executor_for_args,
     wait_and_ensure_success,
+    setup_logging,
 )
 from .cubing import create_parser, read_image_file
 from .image_readers import image_reader
@@ -170,9 +171,7 @@ def tile_cubing(
 
 if __name__ == "__main__":
     args = create_parser().parse_args()
-
-    if args.verbose:
-        logging.basicConfig(level=logging.DEBUG)
+    setup_logging(args)
 
     tile_cubing(
         args.source_path,

wkcuber/utils.py

@@ -76,6 +76,14 @@ def add_anisotropic_flag(parser):
     parser.set_defaults(anisotropic=False)
 
 
+def setup_logging(args):
+
+    logging.basicConfig(
+        level=(logging.DEBUG if args.verbose else logging.INFO),
+        format="%(asctime)s %(levelname)s %(message)s",
+    )
+
+
 def find_files(source_path, extensions):
     # Find all files with a matching file extension
     return (