Description
With our new use of NgffImageMeta, the Omero channels window appears to have become required in 0.12.0, while it's an optional thing for a user to enter in the web interface.
I don't fully understand how this issue arises to be honest though. Looking at the models, it looked like it should work. Why would an omero channel not have a window parameter? Don't we always set the min & max in the task based on the pixel bitrate? Or do we only do this when a user provides start & end?
In any case, we apparently get the following error when running the Yokogawa to OME-Zarr task (without setting window in the Create OME-Zarr step before):
2023-10-02 17:32:21,639; INFO; START yokogawa_to_ome_zarr task
2023-10-02 17:32:25,050; ERROR; Contents of /path/to/Hodgkin CV8000/Hodgkin CV8000 processed data fractal/Metastasis p146-1.zarr/F/04/0/ cannot be cast to NgffImageMeta.
Original error:
4 validation errors for NgffImageMeta
omero -> channels -> 0 -> window
field required (type=value_error.missing)
omero -> channels -> 1 -> window
field required (type=value_error.missing)
omero -> channels -> 2 -> window
field required (type=value_error.missing)
omero -> channels -> 3 -> window
field required (type=value_error.missing)
Traceback (most recent call last):
File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core0.12.0/venv/lib/python3.9/site-packages/fractal_tasks_core/tasks/yokogawa_to_ome_zarr.py", line 271, in <module>
run_fractal_task(
File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core0.12.0/venv/lib64/python3.9/site-packages/fractal_tasks_core/tasks/_utils.py", line 79, in run_fractal_task
metadata_update = task_function(**pars)
File "pydantic/decorator.py", line 40, in pydantic.decorator.validate_arguments.validate.wrapper_function
from contextlib import _GeneratorContextManager
File "pydantic/decorator.py", line 134, in pydantic.decorator.ValidatedFunction.call
File "pydantic/decorator.py", line 206, in pydantic.decorator.ValidatedFunction.execute
File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core0.12.0/venv/lib/python3.9/site-packages/fractal_tasks_core/tasks/yokogawa_to_ome_zarr.py", line 115, in yokogawa_to_ome_zarr
ngff_image_meta = load_NgffImageMeta(zarrurl)
File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core0.12.0/venv/lib64/python3.9/site-packages/fractal_tasks_core/lib_ngff.py", line 397, in load_NgffImageMeta
raise e
File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core0.12.0/venv/lib64/python3.9/site-packages/fractal_tasks_core/lib_ngff.py", line 391, in load_NgffImageMeta
return NgffImageMeta(**zarr_attrs)
File "pydantic/main.py", line 341, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 4 validation errors for NgffImageMeta
omero -> channels -> 0 -> window
field required (type=value_error.missing)
omero -> channels -> 1 -> window
field required (type=value_error.missing)
omero -> channels -> 2 -> window
field required (type=value_error.missing)
omero -> channels -> 3 -> window
field required (type=value_error.missing)
The relevant parameter in the Create OME-Zarr task looked like this (no window set):
"allowed_channels": [
{
"wavelength_id": "A01_C04",
"label": "DAPI",
"color": "0000FF",
"active": true,
"coefficient": 1,
"inverted": false
},
We should either revert this and make windows really optional again, or make it also required in the pydantic models we use for the web interface. This is a good example for the importance of #540
There is a good workaround for the moment: As long as one actually sets the window parameter in Omero channel, this issue does not arise.