Improve knossos conversion (#271)

* make file listing in knossos conversion more precise

* format

Author: philippotto

wkcuber/convert_knossos.py

@@ -94,7 +94,9 @@ def convert_knossos(
         with get_executor_for_args(args) as executor:
             knossos_cubes = list(source_knossos.list_cubes())
             if len(knossos_cubes) == 0:
-                logging.error("No input KNOSSOS cubes found.")
+                logging.error(
+                    "No input KNOSSOS cubes found. Make sure to pass the path which points to a KNOSSOS magnification (e.g., testdata/knossos/color/1)."
+                )
                 exit(1)
 
             knossos_cubes.sort()

wkcuber/knossos.py

@@ -79,7 +79,7 @@ def __get_only_raw_file_path(self, cube_xyz: Tuple[int, ...]) -> Optional[str]:
         return raw_files[0] if len(raw_files) > 0 else None
 
     def list_files(self) -> Iterator[str]:
-        return iglob(path.join(self.root, "**", "*.raw"), recursive=True)
+        return iglob(path.join(self.root, "*", "*", "*", "*.raw"), recursive=True)
 
     def __parse_cube_file_name(self, filename: str) -> Optional[Tuple[int, int, int]]:
         m = CUBE_REGEX.search(filename)