ngio for fractal-tasks-core: Overview

[jluethi]

This issue is meant as an overview for the effort to transition fractal-tasks-core to use ngio.

The overall strategy is:

1. Add an ngio dependency to fractal-tasks-core
2. Start using ngio in different tasks until all tasks depend on ngio for OME-Zarr reading & writing, label reading & writing & table reading & writing
3. Deprecate the respective library functions in fractal-tasks-core
4. Release a fractal-tasks-core 2.0.0 version where we remove those library functions

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Nomenclature below: Top-level TODOs are the tasks. Fix sub-items are must fix issues in the task: We want to see that the ngio refactor fixes this issue. Review sub-items are minor issues we may be able to tackle during the refactor.

Tasks to transition to using ngio:

Converters

• [ ] Convert Cellvoyager to OME-Zarr
  • [ ] Review https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/843
  • [ ] Review https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/823
• [ ] Convert Cellvoyager Multiplexing to OME-Zarr
  • [ ] Review https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/843
  • [ ] Review https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/845
  • [ ] Review https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/819

Tasks that write new OME-Zarr images

• [ ] Project Image (HCS Plate): in https://github.com/fractal-analytics-platform/fractal-tasks-core/blob/main/fractal_tasks_core/tasks/projection.py
  • [ ] Fix https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/840
  • [ ] Review https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/841
  • [ ] Review https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/823
  • [x] Overwrite false not supported correctly in ngio
  • [x] Improve how omero metadata is handled in ngio
  • [x] Replace use of NgffImageMeta usage with ngio (load_NgffImageMeta)
  • [x] Replace direct zarr operations (zarr.open_group etc.) with ngio
  • [x] Replace dask operations for array access with ngio
  • [x] Replace writing operations with ngio
  • [x] Replace pyramid building with ngio
• [ ] Illumination Correction
  • [ ] Should be simple
• [ ] Apply Registration to Image
  • [ ] Replace use of NgffImageMeta usage with ngio (load_NgffImageMeta)
  • [ ] In write_registered_zarr, replace metadata access & image loading & writing with ngio
  • [ ] In write_registered_zarr, replace pyramid building with ngio
  • [ ] Careful with race condition handling (=> @lorenzocerrone & @jluethi review together first)

Tasks that write tables

• [ ] Calculate Registration (image-based)
  • [ ] Review https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/851
  • [ ] Mostly simple, but complex well metadata parsing (ignore for initial transition)
• [ ] Find Registration Consensus
  • [ ] Should be simple

Other tasks:

• [ ] Import OME-Zarr
  • [ ] In _process_single_image: Replace use of NgffImageMeta usage with ngio
  • [ ] In _process_single_image: Replace ROI copying & table writing functionality with ngio

Not a goal for the moment: Handle the well & plate metadata with ngio

Currently blocked because we're waiting for feature X in ngio

Waiting for masking ROI writing

• [ ] Cellpose Segmentation
  • [ ] Fix https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/787
  • [ ] Review https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/742
  • [ ] Remove overlap check that only generates a warning: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/779

Task with other goals

• [ ] Napari Workflows Wrapper
  • [ ] Move napari workflows task into its own repo: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/849
  • [ ] Add a simpler scikit-image based measurement task to the fractal-tasks-core repo
  • [ ] Move these issue to new napari workflows repo:
    • [ ] https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/411
    • [ ] https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/356
    • [ ] https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/352
    • [ ] https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/349
    • [ ] https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/186
    • [ ] https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/183
    • [ ] https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/181

Additional issues:

• [ ] Review https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/833 & https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/463
• [ ] Test e.g. in the Cellpose task that label upsampling of a masking label image works when the dimensions don't easily match: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/771
• [ ] Review that table copying in illumination correction, apply registration etc. are now all using ngio features for this: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/725
• [ ] Review https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/681
• [ ] Review that we're not sensitive to trailing slashes in zarr_urls anymore: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/677 (maybe still an issue in some fractal-tasks-core helper functions?)
• [ ] Review how ROI tables & their indices now look: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/672
• [ ] Test core tasks with OME-Zarrs that have singleton T dimensions: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/663
• [ ] Review that try-except error handling for Zarr operations has been moved into ngio: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/541
• [ ] Review that tasks support actual workflows with time data (e.g. run cellpose & measurements across all timepoints of an existing OME-Zarr with timepoints): https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/169
• [ ] How are we handling global scale transformations in ngio? https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/50

Deprecate

• [ ] Deprecate prepare_label_group: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/634
• [ ] Deprecate is_ROI_table_valid: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/633
• [ ] Deprecate get_pixel_sizes_zyx: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/577

Issues Joel needs to review further

Not sure yet what exactly is needed now to close these issues

• [ ] https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/448
• [ ] Review that the masked loading now fulfills requirements described here: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/340
• [ ] Review mixed dimensionality support requirements: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/150

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Issues related to ngio that should get tackled later (e.g. after 2.0.0 release):

• Parallel processing of ROIs within tasks: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/44
• Parallelize illumination correction across channels: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/687 (either within the task or across a compound task)