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Caiman per plane processing #183

Merged
merged 65 commits into from
Feb 1, 2024
Merged

Caiman per plane processing #183

merged 65 commits into from
Feb 1, 2024

Commits on Aug 16, 2023

  1. support multiplane processing with CaImAn - per-plane basis

    Thinh Nguyen committed Aug 16, 2023
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Commits on Aug 23, 2023

  1. update pipeline to support per-plane processing with caiman

    Thinh Nguyen committed Aug 23, 2023
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  2. at Processing - generate new PerPlaneProcessingTask or confirm all Pe… 

    …rPlaneProcessing have completed
    Thinh Nguyen committed Aug 23, 2023
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  3. Update setup.py

    Thinh Nguyen committed Aug 23, 2023
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  4. bugfix

    Thinh Nguyen committed Aug 23, 2023
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Commits on Aug 24, 2023

  1. minor fix

    Thinh Nguyen committed Aug 24, 2023
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  2. Update attribute channel=' ' -> channel=null

    @kushalbakshi
    kushalbakshi committed Aug 24, 2023
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  3. Update aggr function with .proj()

    @kushalbakshi
    kushalbakshi committed Aug 24, 2023
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  4. Update key_source for Processing

    @kushalbakshi
    kushalbakshi committed Aug 24, 2023
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Commits on Aug 25, 2023

  1. update caiman results ingestion - use latest caiman loader

    Thinh Nguyen committed Aug 25, 2023
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  2. Update version.py

    Thinh Nguyen committed Aug 25, 2023
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  3. Revert Processing ker_source + fix output_dir error

    @kushalbakshi
    kushalbakshi committed Aug 25, 2023
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  4. Update key_source logic for Processing

    @kushalbakshi
    kushalbakshi committed Aug 25, 2023
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  5. Fix for str AttributeError

    @kushalbakshi
    kushalbakshi committed Aug 25, 2023
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  6. Fix TypeError for 'str' and 'str'

    @kushalbakshi
    kushalbakshi committed Aug 25, 2023
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  7. Debug mkdir AttributeError

    @kushalbakshi
    kushalbakshi committed Aug 25, 2023
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Commits on Aug 29, 2023

  1. Update caiman_loader keys for motion correction

    @kushalbakshi
    kushalbakshi committed Aug 29, 2023
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  2. Remove mask classification extraction from caiman loader

    @kushalbakshi
    kushalbakshi committed Aug 29, 2023
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  3. Merge branch 'per-plane-processing' of https://github.com/ttngu207/el… 

    …ement-calcium-imaging into per-plane-processing
    @kushalbakshi
    kushalbakshi committed Aug 29, 2023
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  4. Add exception to debug summary images

    @kushalbakshi
    kushalbakshi committed Aug 29, 2023
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  5. Refine summary image loading

    @kushalbakshi
    kushalbakshi committed Aug 29, 2023
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  6. Internal variable fkey -> field_key

    @kushalbakshi
    kushalbakshi committed Aug 29, 2023
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  7. Append to summary image list

    @kushalbakshi
    kushalbakshi committed Aug 29, 2023
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  8. fix incorrect shape in summary images retrieval

    Thinh Nguyen committed Aug 29, 2023
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Commits on Aug 30, 2023

  1. Manually merge changes from Thinh's branch

    @kushalbakshi
    kushalbakshi committed Aug 30, 2023
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  2. Update element_calcium_imaging/imaging_no_curation.py 

    Co-authored-by: Thinh Nguyen <thinh@datajoint.com>
    @kushalbakshi @ttngu207
    kushalbakshi and ttngu207 committed Aug 30, 2023
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  3. Merge pull request #2 from kushalbakshi/per-plane-processing

    @ttngu207
    ttngu207 committed Aug 30, 2023
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Commits on Sep 5, 2023

  1. Merge pull request #161 from ttngu207/per-plane-processing 

    Per plane processing
    @kushalbakshi
    kushalbakshi committed Sep 5, 2023
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  2. Merge branch 'main' of https://github.com/datajoint/element-calcium-i… 

    …maging into per-plane-processing
    Thinh Nguyen committed Sep 5, 2023
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  3. Merge pull request #163 from ttngu207/per-plane-processing 

    pull from upsteam main
    @sidhulyalkar
    sidhulyalkar committed Sep 5, 2023
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Commits on Sep 6, 2023

  1. update get_calcium_imaging_files parameter

    @sidhulyalkar
    sidhulyalkar committed Sep 6, 2023
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  2. Merge branch 'main' of https://github.com/sidhulyalkar/element-calciu… 

    …m-imaging into caiman_per_plane_processing
    @sidhulyalkar
    sidhulyalkar committed Sep 6, 2023
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  3. Merge branch 'main' into per-plane-processing

    Thinh Nguyen committed Sep 6, 2023
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  4. code cleanup

    Thinh Nguyen committed Sep 6, 2023
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  5. Merge pull request #165 from ttngu207/per-plane-processing 

    bugfix in infer_output_dir
    @kushalbakshi
    kushalbakshi committed Sep 6, 2023
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  6. Update setup.py

    Thinh Nguyen committed Sep 6, 2023
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Commits on Sep 7, 2023

  1. Fix PrairieViewMeta import statements

    @kushalbakshi
    kushalbakshi committed Sep 7, 2023
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  2. Black formatting

    @kushalbakshi
    kushalbakshi committed Sep 7, 2023
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  3. Merge pull request #166 from kushalbakshi/per-plane-processing 

    Fix `PrairieViewMeta` import statements
    @sidhulyalkar
    sidhulyalkar committed Sep 7, 2023
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  4. hard set force_sktiff to true

    @sidhulyalkar
    sidhulyalkar committed Sep 7, 2023
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  5. merge upstream

    @sidhulyalkar
    sidhulyalkar committed Sep 7, 2023
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  6. bump version

    @sidhulyalkar
    sidhulyalkar committed Sep 7, 2023
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  7. Merge pull request #167 from sidhulyalkar/caiman_per_plane_processing 

    Hard fix 'force_sktiff' suite2p parameter
    @kushalbakshi
    kushalbakshi committed Sep 7, 2023
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Commits on Oct 12, 2023

  1. Add motion correction indicies to caiman params

    @kushalbakshi
    kushalbakshi committed Oct 12, 2023
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  2. Black formatting

    @kushalbakshi
    kushalbakshi committed Oct 12, 2023
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Commits on Oct 16, 2023

  1. Merge branch 'caiman_per_plane_processing' of https://github.com/data… 

    …joint/element-calcium-imaging into per-plane-processing
    @kushalbakshi
    kushalbakshi committed Oct 16, 2023
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  2. Fix typo indicies -> indices

    @kushalbakshi
    kushalbakshi committed Oct 16, 2023
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  3. Merge pull request #171 from kushalbakshi/per-plane-processing 

    Formatting + Fix typo indicies -> indices
    @sidhulyalkar
    sidhulyalkar committed Oct 16, 2023
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  4. Revert old slice commit

    @kushalbakshi
    kushalbakshi committed Oct 16, 2023
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  5. Merge pull request #172 from kushalbakshi/per-plane-processing 

    Revert old `slice` commit
    @sidhulyalkar
    sidhulyalkar committed Oct 16, 2023
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Commits on Nov 28, 2023

  1. Merge branch 'staging' into caiman_per_plane_processing

    @kushalbakshi
    kushalbakshi committed Nov 28, 2023
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Commits on Jan 29, 2024

  1. feat(imaging): write bigtiff for caiman processing for bruker files

    Thinh Nguyen committed Jan 29, 2024
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  2. Merge remote-tracking branch 'upstream/caiman_per_plane_processing' i… 

    …nto per-plane-processing
    Thinh Nguyen committed Jan 29, 2024
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  3. style(imaging)

    Thinh Nguyen committed Jan 29, 2024
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  4. update(setup): revert bad merge conflict

    Thinh Nguyen committed Jan 29, 2024
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  5. Merge pull request #178 from ttngu207/per-plane-processing 

    feat(imaging): write bigtiff for caiman processing for bruker files
    @kushalbakshi
    kushalbakshi committed Jan 29, 2024
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Commits on Feb 1, 2024

  1. Fix - Remove plane_idx from write_single_bigtiff() for caiman pro… 

    …cessing
    @kushalbakshi
    kushalbakshi committed Feb 1, 2024
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  2. Update requirements in setup.py

    @kushalbakshi
    kushalbakshi committed Feb 1, 2024
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  3. Update element-interface requirement to staging branch

    @kushalbakshi
    kushalbakshi committed Feb 1, 2024
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  4. Merge pull request #180 from kushalbakshi/per-plane-processing 

    Fix - Remove `plane_idx` from `write_single_bigtiff()`
    Thinh Nguyen committed Feb 1, 2024
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  5. Merge pull request #4 from datajoint/caiman_per_plane_processing 

    pull from upstream
    Thinh Nguyen committed Feb 1, 2024
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  6. Merge branch 'main' of https://github.com/datajoint/element-calcium-i… 

    …maging into per-plane-processing
    Thinh Nguyen committed Feb 1, 2024
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  7. fix(setup): fix incorrect merge conflict resolution

    Thinh Nguyen committed Feb 1, 2024
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  8. fix(setting): black formatting

    Thinh Nguyen committed Feb 1, 2024
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  9. Merge pull request #182 from ttngu207/per-plane-processing 

    Fix merge conflict
    Thinh Nguyen committed Feb 1, 2024
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