Make fractal-tasks-core library functions handle ngio ROI tables

[jluethi]

There was a minor change in how ngio writes masking ROI tables & maybe other ROI tables: The label column now is the index column of obs, not a column in the obs dataframe itself. Different tools like the masking functionality used in the Cellpose task rely on a column "label" being present in the obs dataframe.

For one of @nrepina 's tasks, we could work around this by changing the masked wrapper code here (

fractal-tasks-core/fractal_tasks_core/masked_loading.py

Line 107 in 1c87493

if column_name not in ROI_table.obs.columns:

) to:

# Check that ROI_table.obs has the right column and extract label_value
if column_name not in ROI_table.obs.columns:
    if ROI_table.obs.index.name == column_name:
        # Workaround for new ngio table
        ROI_table.obs[column_name] = ROI_table.obs.index
    else:
        raise ValueError(
            f"In _preprocess_input, {column_name=} "
            f" missing in {ROI_table.obs.columns=}"
        )
label_value = int(float(ROI_table.obs[column_name].iloc[ROI_positional_index]))

We should review whether it's simple to add this workaround to different places where this could occur to ensure our tasks keep working with the new ngio ROI tables without requiring an overall update to ngio yey.

cc @lorenzocerrone

[jluethi]

Ah actually, for that specific case, maybe there is an ngio workaround after all?

Let's think through the option of ngio writing the label column both in index & column "label".
It would be a bit ugly for sure, but then make it loadable from both...

Not sure I'm convinced, but something we can discuss