Pims normalize extensions for assertion (#865)

* Pims normalize extensions for assertion

* changelog

* update directly in class

---------

Co-authored-by: Jonathan Striebel <[email protected]>

Author: fm3

webknossos/Changelog.md

@@ -20,6 +20,8 @@ For upgrade instructions, please check the respective *Breaking Changes* section
 
 ### Fixed
 
+- Fixed a bug where some czi, dm3, dm4 images could not be converted to wkw due to a too-strict check. [#865](https://github.com/scalableminds/webknossos-libs/pull/865)
+
 
 ## [0.12.0](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.12.0) - 2023-02-10
 [Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.11.4...v0.12.0)

webknossos/webknossos/dataset/_utils/pims_czi_reader.py

@@ -37,7 +37,7 @@
 class PimsCziReader(FramesSequenceND):
     @classmethod
     def class_exts(cls) -> Set[str]:
-        return {".czi"}
+        return {"czi"}
 
     # class_priority is used in pims to pick the reader with the highest priority.
     # Default is 10, and bioformats priority (which is the only other reader supporting czi) is 2.

webknossos/webknossos/dataset/_utils/pims_dm_readers.py

@@ -20,7 +20,7 @@
 class PimsDm3Reader(FramesSequenceND):
     @classmethod
     def class_exts(cls) -> Set[str]:
-        return {".dm3"}
+        return {"dm3"}
 
     # class_priority is used in pims to pick the reader with the highest priority.
     # Default is 10, and bioformats priority is 2.
@@ -52,7 +52,7 @@ def _get_frame(self, **ind: int) -> np.ndarray:
 class PimsDm4Reader(FramesSequenceND):
     @classmethod
     def class_exts(cls) -> Set[str]:
-        return {".dm4"}
+        return {"dm4"}
 
     # class_priority is used in pims to pick the reader with the highest priority.
     # Default is 10, and bioformats priority is 2.

webknossos/webknossos/dataset/_utils/pims_images.py

@@ -567,7 +567,7 @@ def _get_all_pims_handlers() -> Iterable[
 def get_valid_pims_suffixes() -> Set[str]:
     valid_suffixes = set()
     for pims_handler in _get_all_pims_handlers():
-        valid_suffixes.update(pims_handler.class_exts())
+        valid_suffixes.update([ext.lstrip(".") for ext in pims_handler.class_exts()])
     return valid_suffixes