NGFF Testing

[dgault]

This is a placeholder issue for reports on testing of NGFF IDR datasets

[jburel]

image: 10648053

lower bound indicated as NaN

[will-moore]

That issue is not related to NGFF data but is due to float/double pixel type. Fixed at https://github.com/ome/omero-iviewer/pull/460

[jburel]

Exploring images with z section e.g. https://idr-testing.openmicroscopy.org/webclient/img_detail/2857886/ The loading of the planes is slow when scrolling through z (I assume the same is true for t) this means that the user will move the slider knob and won't see any change

[jburel]

https://idr-testing.openmicroscopy.org/webclient/img_detail/3193545/ missing thumbnails for some fields

[jburel]

See also https://idr-testing.openmicroscopy.org/webclient/?show=dataset-13751

[jburel]

Same https://idr-testing.openmicroscopy.org/webclient/?show=dataset-13751

[jburel]

https://idr-testing.openmicroscopy.org/webclient/img_detail/12555350/ Settings tab. It is stuck

Preview crash

Traceback (most recent call last):

  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/django/core/handlers/exception.py", line 47, in inner
    response = get_response(request)

  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/django/core/handlers/base.py", line 181, in _get_response
    response = wrapped_callback(request, *callback_args, **callback_kwargs)

  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/decorators.py", line 538, in wrapped
    retval = f(request, *args, **kwargs)

  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/decorators.py", line 597, in wrapper
    context = f(request, *args, **kwargs)

  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webclient/views.py", line 1776, in load_metadata_preview
    rdefId = manager.image.getRenderingDefId()

  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 7944, in wrapped
    if not self._prepareRenderingEngine() \

  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 8220, in _prepareRenderingEngine
    self._re = self._prepareRE(rdid=rdid)

  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 8199, in _prepareRE
    re.load(ctx)

  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 4859, in __call__
    return self.handle_exception(e, *args, **kwargs)

  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webclient/webclient_gateway.py", line 2123, in handle_exception
    super(OmeroWebSafeCallWrapper, self).handle_exception(e, *args, **kwargs)

  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 4856, in __call__
    return self.f(*args, **kwargs)

  File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero_api_RenderingEngine_ice.py", line 1192, in load
    return _M_omero.api.RenderingEngine._op_load.invoke(self, ((), _ctx))

Ice.UnknownLocalException: exception ::Ice::UnknownLocalException
{
    unknown = Network.cpp:2357: Ice::ConnectionRefusedException:
connection refused: Connection refused
}

<WSGIRequest: GET '/webclient/metadata_preview/well/2072079/?_=1700549940904'>

I successfully managed to view other images from the same study

[will-moore]

@jburel I think what has happened in https://github.com/ome/ZarrReader/issues/67#issuecomment-1820363750 is that I've saved new rendering settings to all images in the Plate while logged-in as demo user with "Save to All" in the webclient, but that has only requested new thumbnails for the first field of each Well. Now, when you view the images as public user, I think you don't have permissions to generate new thumbnails.

The reason I used "Save to All" as demo user was that this was a good test to check every (first field) Image in the Plate was valid, by regenerating thumbnails (and checking that they were the same as the thumbnails they replaced). However, this won't happen when we do this "for real" on IDR next.