set_scene does not change scene when scene ids are duplicated

[jil24]

System and Software

• aicsimageio Version: 4.7.0
• Python Version 3.10.4
• Operating System: Mac OS 12.3.1 / M1

Description

When loading a file via bioformats (a leica LOF) with multiple scenes which are named identically, changing the scene via scene index does not work; no error occurs, but the active scene does not change.

I needed to update the bio formats jar to a more recent version manually since the packaged version does not have LOF support. I have no ability to control scene naming.

>>> import aicsimageio
>>> img = aicsimageio.AICSImage('example.lof', reader=aicsimageio.readers.bioformats_reader.BioformatsReader)
>>> img.scenes
('example-c1', 'example-c1', 'example-c1', 'example-c1')
>>> img.current_scene_index
0
img.set_scene(3)
img.current_scene_index
0

[evamaxfield]

I think this is because the function is simply misnamed? set_series instead of set_scene? cc @tlambert03 should I just quickly swap the function names?

[evamaxfield]

https://github.com/AllenCellModeling/aicsimageio/blob/main/aicsimageio/readers/bioformats_reader.py#L331

[evamaxfield]

We have tests but they only check shape 😬 https://github.com/AllenCellModeling/aicsimageio/blob/main/aicsimageio/tests/readers/test_bioformats_reader.py#L385

[tlambert03]

cc @tlambert03 should I just quickly swap the function names?

works for me!

[toloudis]

maybe run_image_file_checks should test scene index too?

[jil24]

So this has nothing to do with my scene/series name duplication at all?

[evamaxfield]

At the current moment, I do not believe so because you are providing an index and not name.

[jil24]

Hmm, I tried making the changes in those commits; there is no difference in the behavior

[evamaxfield]

Correction: this is likely because bioformats itself does not support multiple images (read: scenes in an AICSImageIO context) for Leica LOF: https://docs.openmicroscopy.org/bio-formats/6.9.1/supported-formats.html

[jil24]

Yet I can load multiple scenes via bio formats into FIJI from the same file?

[evamaxfield]

cc @joshmoore / someone from bioformats? Is the table out of date? Are LOF files actually supported?

[dgault]

Support for XLEF and LOF files was added in 6.9.0 as an external contribution from Leica Microsystems. So it should be supported if you are using the latest 6.9.1 release. The LOF reader will only read individual files
(https://docs.openmicroscopy.org/bio-formats/6.9.1/formats/leica-lof.html), whereas the XLEF reader will read the entire dataset (https://docs.openmicroscopy.org/bio-formats/6.9.1/formats/leica-xlef.html). So if you have an XLEF file you may want to point at it when opening the dataset.

[jil24]

I did a little more investigation; the problem seems to be not specific to LOF files. When opening a ome-tiff using bio-formats reader, I get the same silent failure to switch scenes. When using the ome_tiff_reader, everything works correctly.

[evamaxfield]

@tlambert03 would it be possible that the bioformats jar that ships with the python package simply doesn't have the latest version? Do you package that manually or is it auto pulled / built?

[tlambert03]

needs updating. but I've dragged my feet on that, since we should really be using scyjava. (see tlambert03/bioformats_jar#2)

I'll try to get on it soon

[tlambert03]

(it's '6.7.0')

[evamaxfield]

Support for XLEF and LOF files was added in 6.9.0 as an external contribution from Leica Microsystems. So it should be supported if you are using the latest 6.9.1 release.

[bioformats_jar is] '6.7.0'

Well now I am confused... It is opening a file format that it didn't officially support at that point

[evamaxfield]

needs updating. but I've dragged my feet on that, since we should really be using scyjava. (see tlambert03/bioformats_jar#2)

It never ceases to amaze me how complicated some issues are. As per usual, thanks for all you do

[evamaxfield]

I have found the bug and updated the PR. @jil24 could you attempt to install and use the branch again. There is a single bug that is maybe related but I will look into next week.

[evamaxfield]

This should now be fixed and released. pip install --upgrade aicsimageio should install 4.8.0