In pims tiff reader, leave chunks black that yield KeyError when accessing zarr store (#1388)

* In pims tiff reader, leave chunks black that yield KeyError when accessing zarr store

* changelog

* lint

* Revert "lint"

This reverts commit 28619db.

* disable linter rule for this line

Author: fm3

webknossos/Changelog.md

@@ -19,6 +19,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Changed
 
 ### Fixed
+- Fixed a bug where some tiff images could not be correctly converted to wkw/zarr, yielding KeyErrors. [#1388](https://github.com/scalableminds/webknossos-libs/pull/1388)
 
 
 ## [3.0.0](https://github.com/scalableminds/webknossos-libs/releases/tag/v3.0.0) - 2025-10-28

webknossos/webknossos/dataset/_utils/pims_tiff_reader.py

@@ -198,16 +198,21 @@ def get_frame_2D(self, **ind: int) -> np.ndarray:
             for chunk_projection in _chunk_indexing(
                 selection, array_shape, chunk_shape
             ):
-                # read data from zarr store
-                chunk_data = (
-                    zarr_store[".".join(map(str, chunk_projection.chunk_coords))]
-                    .ravel()
-                    .reshape(chunk_shape)
-                )
-                # write in output array
-                out[chunk_projection.out_selection] = chunk_data[
-                    chunk_projection.chunk_selection
-                ]
+                try:
+                    # read data from zarr store
+                    chunk_data = (
+                        zarr_store[".".join(map(str, chunk_projection.chunk_coords))]
+                        .ravel()
+                        .reshape(chunk_shape)
+                    )
+                    # write in output array
+                    out[chunk_projection.out_selection] = chunk_data[
+                        chunk_projection.chunk_selection
+                    ]
+                except KeyError:
+                    # chunk not present in zarr_store, leave black.
+                    # ruff: noqa: PERF203 try-catch is still faster than in for the ZarrStore
+                    pass
 
             return out