webknossos-libs
webknossos-libs copied to clipboard
Dataset.from_images fails for some multipage tif files with IndexError: list index out of range
Saw exception in Dataset.from_images called with a tif file.
Stack trace:
Traceback (most recent call last):
File "/usr/local/lib/python3.11/concurrent/futures/process.py", line 261, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "site-packages/cluster_tools/executors/multiprocessing_.py", line 159, in _setup_logging_and_execute
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "site-packages/webknossos/dataset/_utils/pims_images.py", line 555, in copy_to_view
for image_slice in images[z_start:z_end]:
File "site-packages/slicerator/__init__.py", line 226, in <genexpr>
return (self._get(i) for i in self.indices)
^^^^^^^^^^^^
File "site-packages/slicerator/__init__.py", line 206, in _get
return self._ancestor[key]
~~~~~~~~~~~~~~^^^^^
File "site-packages/slicerator/__init__.py", line 187, in __getitem__
return self._get(indices)
^^^^^^^^^^^^^^^^^^
File "site-packages/pims/base_frames.py", line 100, in __getitem__
return self.get_frame(key)
^^^^^^^^^^^^^^^^^^^
File "site-packages/pims/base_frames.py", line 598, in get_frame
result = self._get_frame_wrapped(**coords)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "site-packages/webknossos/dataset/_utils/pims_tiff_reader.py", line 114, in get_frame_2D
page = _tiff.asarray(key=i)
^^^^^^^^^^^^^^^^^^^^
File "site-packages/tifffile/tifffile.py", line 12514, in asarray
result = self.parent.asarray(series=self, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "site-packages/tifffile/tifffile.py", line 4534, in asarray
pages = [pages[int(key)]]
~~~~~^^^^^^^^^^
File "site-packages/tifffile/tifffile.py", line 12641, in __getitem__
return self._getitem(int(key))
^^^^^^^^^^^^^^^^^^^^^^^
File "site-packages/tifffile/tifffile.py", line 12624, in _getitem
return self._pages[key]
~~~~~~~~~~~^^^^^
IndexError: list index out of range
Example images can be found in /srv/stores/webknossos.org/595d33d9f64a8589/.converting/