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Add ROI tables, dimension separator & build_omero_channel_metadata changes #32

Merged
merged 42 commits into from
Sep 14, 2023
Merged

Add ROI tables, dimension separator & build_omero_channel_metadata changes #32

merged 42 commits into from
Sep 14, 2023

Commits on May 24, 2023

  1. Add write_roi_table function

    @jluethi
    jluethi committed May 24, 2023
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  2. Add ROI table calculation for 2D planes

    @jluethi
    jluethi committed May 24, 2023
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  3. Add basic scripts to process some test data (prototype for Fractal ta… 

    …sks)
    @jluethi
    jluethi committed May 24, 2023
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  4. Cleanup MetaSeriesUtils

    @jluethi
    jluethi committed May 24, 2023
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  5. Add ROI table generation to montage_stage_pos_image_YX and update tests

    @jluethi
    jluethi committed May 24, 2023
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  6. Update Zarr tests to also expect roi_tables

    @jluethi
    jluethi committed May 24, 2023
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Commits on May 25, 2023

  1. Add check to build_omero_channel_metadata for start & end values, cha… 

    …nge default upper quantile to 0.999
    @jluethi
    jluethi committed May 25, 2023
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Commits on Jun 2, 2023

  1. Improve 3D saving in Fractal tasks

    @jluethi
    jluethi committed Jun 2, 2023
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  2. Set the dimension_separator to / to make it work in napari

    @jluethi
    jluethi committed Jun 2, 2023
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  3. Change Fractal tasks to use mode instead of is_2D flag

    @jluethi
    jluethi committed Jun 2, 2023
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  4. Improve table metadata updates

    @jluethi
    jluethi committed Jun 2, 2023
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  5. Change create ome zarr into a Fractal task

    @jluethi
    jluethi committed Jun 2, 2023
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  6. Change fractal task filenames, organize them as actual task functions

    @jluethi
    jluethi committed Jun 2, 2023
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  7. Add main functions, update dependencies, add Fractal manifest

    @jluethi
    jluethi committed Jun 2, 2023
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Commits on Jun 5, 2023

  1. Add pydantic dependency for fractal-tasks extra

    @jluethi
    jluethi committed Jun 5, 2023
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  2. Add tasks manually to Fractal

    @jluethi
    jluethi committed Jun 5, 2023
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Commits on Jun 8, 2023

  1. Make Fractal tasks collectable by Fractal server

    @jluethi
    jluethi committed Jun 8, 2023
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  2. Fix bug: Channels have different z len => pick largest for ROI table

    @jluethi
    jluethi committed Jun 8, 2023
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  3. Add tests to check ROI table content

    @jluethi
    jluethi committed Jun 8, 2023
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  4. Update examples with roi tables

    @jluethi
    jluethi committed Jun 8, 2023
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  5. Update Fractal example to have relative paths

    @jluethi
    jluethi committed Jun 8, 2023
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  6. Add tests for Fractal tasks

    @jluethi
    jluethi committed Jun 8, 2023
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  7. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Jun 8, 2023
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  8. pre-commit cleanup

    @jluethi
    jluethi committed Jun 8, 2023
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Commits on Jun 13, 2023

  1. Remove all Fractal task parts from faim-hcs

    @jluethi
    jluethi committed Jun 13, 2023
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Commits on Jun 14, 2023

  1. Update anndata dependency & import from io, not experimental

    @jluethi
    jluethi committed Jun 14, 2023
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Commits on Jun 22, 2023

  1. Change Z step calculation

    @jluethi
    jluethi committed Jun 22, 2023
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  2. Update expected Z length in ROI table in MetaSeries tests

    @jluethi
    jluethi committed Jun 22, 2023
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  3. Parse the dimension_separator through all levels

    @jluethi
    jluethi committed Jun 22, 2023
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  4. Add lowest_res_target to _compute_chunk_size_cyx

    @jluethi
    jluethi committed Jun 22, 2023
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  5. Expose max_levels, max_size, lowest_res_target in top-level functions… 

    … (with defaults)
    @jluethi
    jluethi committed Jun 22, 2023
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  6. Simplify write_roi_table

    @jluethi
    jluethi committed Jun 22, 2023
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  7. Simplify montage_grid_image_YX

    @jluethi
    jluethi committed Jun 22, 2023
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Commits on Jun 23, 2023

  1. Merge branch 'main' into fractal-roi-tables

    @jluethi
    jluethi authored Jun 23, 2023
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  2. Refactor ROI table functions to have column names in a central place

    @jluethi
    jluethi committed Jun 23, 2023
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Commits on Jul 4, 2023

  1. Update src/faim_hcs/MetaSeriesUtils.py 

    Update docstring

Co-authored-by: Jan Eglinger <[email protected]>
    @jluethi @imagejan
    jluethi and imagejan authored Jul 4, 2023
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Commits on Jul 11, 2023

  1. Improve docstrings

    @jluethi
    jluethi committed Jul 11, 2023
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  2. Use column names as fixture in tests

    @jluethi
    jluethi committed Jul 11, 2023
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Commits on Sep 3, 2023

  1. Improve montage_stage_pos_image_YX docstring

    @jluethi
    jluethi committed Sep 3, 2023
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  2. Switch to kwargs for passing args for _compute_chunk_size_cyx

    @jluethi
    jluethi committed Sep 3, 2023
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Commits on Sep 4, 2023

  1. Fix fsspec & anndata dependencies

    @jluethi
    jluethi committed Sep 4, 2023
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  2. Increase compatible anndata version

    @jluethi
    jluethi committed Sep 4, 2023
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