Remove unnecessary logging. (#1124)

* Remove unnecessary logging.

* Update changelog.

* Update Changelog.md

* Remove parametrize from test_convert_with_all_params

* Adapt rules of filterwarnings.

Author: markbader

webknossos/Changelog.md

@@ -18,6 +18,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 - Added an implementation of padded_with_margins for NDBoundingBox class. [#1120](https://github.com/scalableminds/webknossos-libs/pull/1120)
 
 ### Changed
+- Removed additional logging messages during image conversion. [#1124](https://github.com/scalableminds/webknossos-libs/pull/1124)
 
 ### Fixed
 - Fixed an issue where cube jobs upsampling, downsampling and compress failed when performed on more than 3 dimensions. [#1095](https://github.com/scalableminds/webknossos-libs/pull/1095)

webknossos/tests/test_cli.py

@@ -202,16 +202,13 @@ def test_convert() -> None:
         assert (wkw_path / PROPERTIES_FILE_NAME).exists()
 
 
-@pytest.mark.parametrize(
-    "origin_path",
-    [TESTDATA_DIR / "tiff", TESTDATA_DIR / "tiff_with_different_shapes"],
-)
-def test_convert_with_all_params(origin_path: Path) -> None:
+def test_convert_with_all_params() -> None:
     """Tests the functionality of convert subcommand."""
 
     with tmp_cwd():
+        origin_path = TESTDATA_DIR / "tiff_with_different_shapes"
         wkw_path = Path(f"wkw_from_{origin_path.name}")
-        with pytest.warns(UserWarning):
+        with pytest.warns(UserWarning, match="Some images are larger than expected,"):
             result = runner.invoke(
                 app,
                 [

webknossos/webknossos/dataset/_utils/buffered_slice_writer.py

@@ -137,7 +137,8 @@ def _flush_buffer(self) -> None:
                 buffer_depth,
             ).moveaxis(-1, self.dimension)
             for chunk_bbox in bbox.chunk(chunk_size):
-                info(f"Writing chunk {chunk_bbox}.")
+                if self._use_logging:
+                    info(f"Writing chunk {chunk_bbox}.")
 
                 data = np.zeros(
                     (channel_count, *chunk_bbox.size),

webknossos/webknossos/dataset/dataset.py

@@ -628,9 +628,20 @@ def from_images(
             )
 
         if isinstance(map_filepath_to_layer_name, Dataset.ConversionLayerMapping):
-            map_filepath_to_layer_name = map_filepath_to_layer_name._to_callable(
-                input_upath, input_files=input_files, use_bioformats=use_bioformats
-            )
+            with warnings.catch_warnings():
+                warnings.filterwarnings(
+                    "ignore",
+                    category=UserWarning,
+                    module="pims",
+                )
+                warnings.filterwarnings(
+                    "once",
+                    category=UserWarning,
+                    module="pims_images",
+                )
+                map_filepath_to_layer_name = map_filepath_to_layer_name._to_callable(
+                    input_upath, input_files=input_files, use_bioformats=use_bioformats
+                )
 
         ds = cls(output_path, voxel_size=voxel_size, name=name)
 
@@ -666,7 +677,12 @@ def from_images(
                 warnings.filterwarnings(
                     "ignore",
                     category=UserWarning,
-                    message="Not all pims readers could be imported",
+                    module="pims_images",
+                )
+                warnings.filterwarnings(
+                    "ignore",
+                    category=UserWarning,
+                    module="pims",
                 )
                 for layer_name, filepaths in filepaths_per_layer.items():
                     filepaths.sort(key=z_slices_sort_key)