A cell line shouldn't have an empty list of fields.

[zephyris]

It seems that there are cell lines which are expected to have image data, a list of fields, but have no entries in this list, zero fields, which suggests some kind of input data error(?). Having done full dataset analyses before, without getting similar exceptions, suggests a change associated with the BioImage Archive data source(?).

Not sure, but full error below:

"""
Traceback (most recent call last):
  File "/home/richard/miniconda3/lib/python3.13/site-packages/tryptag/datasource.py", line
    return self._fields[index]
           ~~~~~~~~~~~~^^^^^^^
KeyError: 0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/richard/miniconda3/lib/python3.13/concurrent/futures/process.py", line 254, 
    r = call_item.fn(*call_item.args, **call_item.kwargs)
  File "/home/richard/miniconda3/lib/python3.13/site-packages/tryptag/processing.py", line
    "result": analysis_function(
              ~~~~~~~~~~~~~~~~~^
        _tryptag_object,
        ^^^^^^^^^^^^^^^^
        _tryptag_object.gene_list[cell_line.gene_id][cell_line.terminus],
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    ),
    ^
  File "/mnt/f/Documents/GitHub/website-tryptag/generate_images.py", line 167, in tryptag_
    tmp_field = tryptag.open_field(cell_line, 0)
  File "/home/richard/miniconda3/lib/python3.13/site-packages/tryptag/tryptag.py", line 27
    cell_line.fields[field_index],
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "/home/richard/miniconda3/lib/python3.13/site-packages/tryptag/datasource.py", line
    raise FieldNotFoundError(index)
tryptag.datasource.FieldNotFoundError: 'No field with index 0 found.'
"""

        analysis_function,                f the following exception:
        ^^^^^^^^^^^^^^^^^^
        workers,
        ^^^^^^^^
        multiprocess_mode
        ^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/richard/miniconda3/lib/python3.13/site-packages/tryptag/processing.py", line 261, in analysis
    results.append(future.result())
                   ~~~~~~~~~~~~~^^
  File "/home/richard/miniconda3/lib/python3.13/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ~~~~~~~~~~~~~~~~~^^
  File "/home/richard/miniconda3/lib/python3.13/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
tryptag.datasource.FieldNotFoundError: 'No field with index No field with index 0 found. found.'

[zephyris]

This error came up in generating the images for the website. Reviewing the code, this may be a case which I haven't come across before, where I'm explicitly trying to access the zeroth field (for the purpose of grabbing contrast information) instead of iterating through all available fields or cells.

So, it likely is a source data weirdness, ie. localisation data but no images, but not a new source data weirdness. And, possibly not a bug(?).

[zephyris]

I've done a check and 25 cell lines have 0 fields, so a very isolated problem. Previously listed as 'localisation error' because it's some kind of technical failure leading to losing track of the images.