Replace logging.info with a logger for each file (#1335)

markbader · fm3 · web-flow · commit 9554718bf6d4 · 2025-07-10T12:00:54.000+02:00
* replace logging.info with a logger for each file.

* Update changelog.

* Update webknossos/Changelog.md

Co-authored-by: Florian M &lt;fm3@users.noreply.github.com&gt;

---------

Co-authored-by: Florian M &lt;fm3@users.noreply.github.com&gt;
diff --git a/webknossos/Changelog.md b/webknossos/Changelog.md
@@ -17,6 +17,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Added
 
 ### Changed
+- Every file that sends logging messages has its own logger now. This can be used to selectively disable loggers. [#1335](https://github.com/scalableminds/webknossos-libs/pull/1335)
 
 ### Fixed
 
diff --git a/webknossos/webknossos/annotation/annotation.py b/webknossos/webknossos/annotation/annotation.py
@@ -774,7 +774,7 @@ def merge_fallback_layer(
         fallback_layer_name = volume_layer.fallback_layer_name
 
         if fallback_layer_name is None:
-            logging.info("No fallback layer found, save annotation as dataset.")
+            logger.info("No fallback layer found, save annotation as dataset.")
             self.export_volume_layer_to_dataset(output_dataset)
 
         else:
@@ -833,9 +833,9 @@ def merge_fallback_layer(
 
                     output_mag.merge_with_view(input_annotation_mag, executor)
 
-                logging.info("Delete temporary annotation layer")
+                logger.info("Delete temporary annotation layer")
                 output_dataset.delete_layer(tmp_annotation_layer_name)
-                logging.info("Done.")
+                logger.info("Done.")
 
     def upload(self) -> str:
         """Uploads the annotation to WEBKNOSSOS.
diff --git a/webknossos/webknossos/cli/check_equality.py b/webknossos/webknossos/cli/check_equality.py
@@ -116,7 +116,7 @@ def compare_layers(
     """Compares one layer with another layer"""
 
     layer_name = source_layer.name
-    logging.info("Checking layer_name: %s", layer_name)
+    logger.info("Checking layer_name: %s", layer_name)
 
     assert source_layer.bounding_box == target_layer.bounding_box, (
         f"The bounding boxes of '{layer_name}' layer of source and target \
@@ -135,7 +135,7 @@ def compare_layers(
         source_mag = source_layer.mags[mag]
         target_mag = target_layer.mags[mag]
 
-        logging.info("Start verification of %s in mag %s", layer_name, mag)
+        logger.info("Start verification of %s in mag %s", layer_name, mag)
         with get_executor_for_args(args=executor_args) as executor:
             assert source_mag.content_is_equal(target_mag, executor=executor), (
                 f"The contents of {source_mag} and {target_mag} differ."
diff --git a/webknossos/webknossos/cli/convert_raw.py b/webknossos/webknossos/cli/convert_raw.py
@@ -50,7 +50,7 @@ def _raw_chunk_converter(
     order: Literal["C", "F"],
     flip_axes: int | tuple[int, ...] | None,
 ) -> None:
-    logging.info("Conversion of %s", bounding_box.topleft)
+    logger.info("Conversion of %s", bounding_box.topleft)
     source_data: np.ndarray = np.memmap(
         source_raw_path,
         dtype=np.dtype(input_dtype),
diff --git a/webknossos/webknossos/cli/convert_zarr.py b/webknossos/webknossos/cli/convert_zarr.py
@@ -54,7 +54,7 @@ def _zarr_chunk_converter(
     target_mag_view: MagView,
     flip_axes: int | tuple[int, ...] | None,
 ) -> int:
-    logging.info("Conversion of %s", bounding_box.topleft)
+    logger.info("Conversion of %s", bounding_box.topleft)
 
     slices = bounding_box.to_slices()
     zarr_file = _try_open_zarr(source_zarr_path)
diff --git a/webknossos/webknossos/cli/export_as_tiff.py b/webknossos/webknossos/cli/export_as_tiff.py
@@ -26,6 +26,8 @@
     parse_vec2int,
 )
 
+logger = logging.getLogger(__name__)
+
 
 def _make_tiff_name(name: str, slice_index: int) -> str:
     if name is None or name == "":
@@ -96,7 +98,7 @@ def export_tiff_slice(
 
             image = _slice_to_image(tiff_data[:, :, :, slice_index], downsample)
             image.save(tiff_file_path)
-            logging.debug("Saved slice %s", slice_name_number)
+            logger.debug("Saved slice %s", slice_name_number)
 
         else:
             for y_tile_index in range(ceil(tiff_bbox.size.y / tiling_size[1])):
@@ -120,9 +122,9 @@ def export_tiff_slice(
 
                     tile_image.save(tile_tiff_path / tile_tiff_filename)
 
-            logging.debug("Saved tiles for slice %s", slice_name_number)
+            logger.debug("Saved tiles for slice %s", slice_name_number)
 
-    logging.debug("Saved all tiles of bbox %s", tiff_bbox)
+    logger.debug("Saved all tiles of bbox %s", tiff_bbox)
 
 
 def export_tiff_stack(
@@ -264,7 +266,7 @@ def main(
     bbox = BoundingBox.from_ndbbox(mag_view.bounding_box) if bbox is None else bbox
     bbox = bbox.align_with_mag(mag_view.mag)
 
-    logging.info("Starting tiff export for bounding box: %s", bbox)
+    logger.info("Starting tiff export for bounding box: %s", bbox)
     executor_args = Namespace(
         jobs=jobs,
         distribution_strategy=distribution_strategy.value,
@@ -273,7 +275,7 @@ def main(
     used_tile_size = None
     if tiles_per_dimension is not None:
         tile_size = tiles_per_dimension
-        logging.info(
+        logger.info(
             "Using tiling with %d,%d tiles in the dimensions.",
             tile_size[0],
             tile_size[1],
@@ -284,7 +286,7 @@ def main(
         )
 
     elif tile_size is not None:
-        logging.info("Using tiling with the size of %d,%d.", tile_size[0], tile_size[1])
+        logger.info("Using tiling with the size of %d,%d.", tile_size[0], tile_size[1])
         used_tile_size = tile_size
 
     export_tiff_stack(
diff --git a/webknossos/webknossos/dataset/_downsampling_utils.py b/webknossos/webknossos/dataset/_downsampling_utils.py
@@ -17,6 +17,8 @@
 from .layer_categories import LayerCategoryType
 from .view import View
 
+logger = logging.getLogger(__name__)
+
 
 class InterpolationModes(Enum):
     MEDIAN = 0
@@ -367,7 +369,7 @@ def downsample_cube_job(
         target_view.write(file_buffer, absolute_bounding_box=target_view.bounding_box)
 
     except Exception as exc:
-        logging.error(
+        logger.error(
             f"Downsampling of target {target_view.bounding_box} failed with {exc}"
         )
         raise exc
diff --git a/webknossos/webknossos/dataset/_upsampling_utils.py b/webknossos/webknossos/dataset/_upsampling_utils.py
@@ -6,6 +6,8 @@
 from .data_format import DataFormat
 from .view import View
 
+logger = logging.getLogger(__name__)
+
 
 def upsample_cube(cube_buffer: np.ndarray, factors: list[int]) -> np.ndarray:
     ds = cube_buffer.shape
@@ -69,7 +71,7 @@ def upsample_cube_job(
             target_view.write(file_buffer, absolute_bounding_box=chunk)
 
     except Exception as exc:
-        logging.error(
+        logger.error(
             f"Upsampling of target {target_view.bounding_box} failed with {exc}"
         )
         raise exc
diff --git a/webknossos/webknossos/dataset/_utils/buffered_slice_reader.py b/webknossos/webknossos/dataset/_utils/buffered_slice_reader.py
@@ -1,5 +1,5 @@
+import logging
 from collections.abc import Generator
-from logging import info
 from os import getpid
 from types import TracebackType
 from typing import TYPE_CHECKING
@@ -11,6 +11,8 @@
 
 from ...geometry import NDBoundingBox
 
+logger = logging.getLogger(__name__)
+
 
 class BufferedSliceReader:
     def __init__(
@@ -50,7 +52,7 @@ def _get_slice_generator(self) -> Generator[np.ndarray, None, None]:
 
         for chunk in self.bbox_current_mag.chunk(chunk_size):
             if self.use_logging:
-                info(f"({getpid()}) Reading data from bbox {chunk}.")
+                logger.info(f"({getpid()}) Reading data from bbox {chunk}.")
             data = self.view.read(
                 absolute_bounding_box=chunk.from_mag_to_mag1(self.view.mag)
             )
diff --git a/webknossos/webknossos/dataset/_utils/buffered_slice_writer.py b/webknossos/webknossos/dataset/_utils/buffered_slice_writer.py
@@ -1,8 +1,8 @@
+import logging
 import os
 import traceback
 import warnings
 from collections.abc import Generator
-from logging import error, info
 from os import getpid
 from types import TracebackType
 from typing import TYPE_CHECKING
@@ -16,10 +16,13 @@
     from ..view import View
 
 
+logger = logging.getLogger(__name__)
+
+
 def log_memory_consumption(additional_output: str = "") -> None:
     pid = os.getpid()
     process = psutil.Process(pid)
-    info(
+    logger.info(
         f"Currently consuming {process.memory_info().rss / 1024**3:.2f} GB of memory ({psutil.virtual_memory().available / 1024**3:.2f} GB still available) "
         f"in process {pid}. {additional_output}"
     )
@@ -105,7 +108,7 @@ def _flush_buffer(self) -> None:
         )
 
         if self._use_logging:
-            info(
+            logger.info(
                 f"({getpid()}) Writing {len(self._slices_to_write)} slices at position {self._buffer_start_slice}."
             )
             log_memory_consumption()
@@ -136,7 +139,7 @@ def _flush_buffer(self) -> None:
             ).moveaxis(-1, self.dimension)
             for chunk_bbox in bbox.chunk(chunk_size):
                 if self._use_logging:
-                    info(f"Writing chunk {chunk_bbox}.")
+                    logger.info(f"Writing chunk {chunk_bbox}.")
 
                 data = np.zeros(
                     (channel_count, *chunk_bbox.size),
@@ -199,12 +202,12 @@ def _flush_buffer(self) -> None:
                 del data
 
         except Exception as exc:
-            error(
+            logger.error(
                 f"({getpid()}) An exception occurred in BufferedSliceWriter._flush_buffer with {len(self._slices_to_write)} "
                 f"slices at position {self._buffer_start_slice}. Original error is:\n{type(exc).__name__}:{exc}\n\nTraceback:"
             )
             traceback.print_tb(exc.__traceback__)
-            error("\n")
+            logger.error("\n")
 
             raise exc
         finally:
diff --git a/webknossos/webknossos/dataset/dataset.py b/webknossos/webknossos/dataset/dataset.py
@@ -1989,7 +1989,7 @@ def add_layer_from_images(
                     if guessed_category != layer.category:
                         new_layer_properties: LayerProperties
                         if guessed_category == SEGMENTATION_CATEGORY:
-                            logging.info("The layer category is set to segmentation.")
+                            logger.info("The layer category is set to segmentation.")
                             new_layer_properties = SegmentationLayerProperties(
                                 **(
                                     attr.asdict(layer._properties, recurse=False)
@@ -2001,7 +2001,7 @@ def add_layer_from_images(
                                 self, new_layer_properties, read_only=False
                             )
                         else:
-                            logging.info("The layer category is set to color.")
+                            logger.info("The layer category is set to color.")
                             _properties = attr.asdict(layer._properties, recurse=False)
                             _properties.pop("largest_segment_id", None)
                             _properties.pop("mappings", None)
diff --git a/webknossos/webknossos/dataset/mag_view.py b/webknossos/webknossos/dataset/mag_view.py
@@ -31,6 +31,8 @@
 
 from .view import View
 
+logger = logging.getLogger(__name__)
+
 
 def _compress_cube_job(args: tuple[View, View, int]) -> None:
     source_view, target_view, _i = args
@@ -479,7 +481,7 @@ def compress(
         path = self._path
         if target_path is None:
             if self._is_compressed():
-                logging.info(f"Mag {self.name} is already compressed")
+                logger.info(f"Mag {self.name} is already compressed")
                 return
             else:
                 assert is_fs_path(path), (
@@ -515,7 +517,7 @@ def compress(
             compress=True,
         )
 
-        logging.info(f"Compressing mag {self.name} in '{str(uncompressed_full_path)}'")
+        logger.info(f"Compressing mag {self.name} in '{str(uncompressed_full_path)}'")
         with get_executor_for_args(None, executor) as executor:
             try:
                 bbox_iterator = self._array.list_bounding_boxes()
@@ -595,10 +597,10 @@ def merge_with_view(
             f"To merge two Views, both need the same mag: Own mag {self.mag} does not match other mag {other.mag}"
         )
 
-        logging.info("Scan disk for annotation shards.")
+        logger.info("Scan disk for annotation shards.")
         bboxes = list(bbox for bbox in other.get_bounding_boxes_on_disk())
 
-        logging.info("Grouping %s bboxes according to output shards.", len(bboxes))
+        logger.info("Grouping %s bboxes according to output shards.", len(bboxes))
         shards_with_bboxes = NDBoundingBox.group_boxes_with_aligned_mag(
             bboxes, Mag(self.info.shard_shape * self.mag)
         )
@@ -607,12 +609,12 @@ def merge_with_view(
         for shard_bbox in shards_with_bboxes.keys():
             new_bbox = new_bbox.extended_by(shard_bbox)
 
-        logging.info(f"Set mag layer bounding box to {new_bbox}")
+        logger.info(f"Set mag layer bounding box to {new_bbox}")
         self.layer.bounding_box = new_bbox
 
         args = [(other, shard, bboxes) for shard, bboxes in shards_with_bboxes.items()]
 
-        logging.info("Merging %s shards.", len(args))
+        logger.info("Merging %s shards.", len(args))
         wait_and_ensure_success(
             executor.map_to_futures(self.merge_chunk, args),
             executor,
diff --git a/webknossos/webknossos/utils.py b/webknossos/webknossos/utils.py
@@ -82,12 +82,12 @@ def call_with_retries(
 
 def time_start(identifier: str) -> None:
     times[identifier] = time.time()
-    logging.debug(f"{identifier} started")
+    logger.debug(f"{identifier} started")
 
 
 def time_stop(identifier: str) -> None:
     _time = times.pop(identifier)
-    logging.debug(f"{identifier} took {time.time() - _time:.8f}s")
+    logger.debug(f"{identifier} took {time.time() - _time:.8f}s")
 
 
 def get_executor_for_args(
@@ -103,7 +103,7 @@ def get_executor_for_args(
         # to these values:
         jobs = cpu_count()
         executor = get_executor("multiprocessing", max_workers=jobs)
-        logging.info(f"Using pool of {jobs} workers.")
+        logger.info(f"Using pool of {jobs} workers.")
     elif args.distribution_strategy == "multiprocessing":
         # Also accept "processes" instead of job to be compatible with segmentation-tools.
         # In the long run, the args should be unified and provided by the clustertools.
@@ -115,7 +115,7 @@ def get_executor_for_args(
             jobs = cpu_count()
 
         executor = get_executor("multiprocessing", max_workers=jobs)
-        logging.info(f"Using pool of {jobs} workers.")
+        logger.info(f"Using pool of {jobs} workers.")
     elif args.distribution_strategy in ("slurm", "kubernetes"):
         if args.job_resources is None:
             resources_example = (
@@ -133,15 +133,15 @@ def get_executor_for_args(
             keep_logs=True,
             job_resources=json.loads(args.job_resources),
         )
-        logging.info(f"Using {args.distribution_strategy} cluster.")
+        logger.info(f"Using {args.distribution_strategy} cluster.")
     elif args.distribution_strategy == "sequential":
         executor = get_executor(
             args.distribution_strategy,
             debug=True,
             keep_logs=True,
         )
     else:
-        logging.error(f"Unknown distribution strategy: {args.distribution_strategy}")
+        logger.error(f"Unknown distribution strategy: {args.distribution_strategy}")
 
     return executor
 
@@ -498,7 +498,6 @@ def check_version_in_thread() -> None:
 
             # Compare versions and log warning if needed
             if Version(current_version) < latest_version:
-                logger = logging.getLogger(__name__)
                 logger.warning(
                     f"Your current version {current_version} of the webknossos-libs is outdated. "
                     f"The latest version available on PyPI is {latest_version}. "
