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Add decoding functionality to Polaris #36

Merged
merged 71 commits into from
Feb 7, 2023
Merged

Add decoding functionality to Polaris #36

merged 71 commits into from
Feb 7, 2023

Commits on Nov 11, 2022

  1. Add latest decoding function as is

    @xuefei-wang
    xuefei-wang committed Nov 11, 2022
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  2. Remove redundent code in decoding function

    @xuefei-wang
    xuefei-wang committed Nov 11, 2022
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Commits on Nov 18, 2022

  1. Add liscence for decoding_functions file

    @xuefei-wang
    xuefei-wang committed Nov 18, 2022
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  2. Fix typo: polaris predict image channel should be 1

    @xuefei-wang
    xuefei-wang committed Nov 18, 2022
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  3. Initialize spot_decoding model

    @xuefei-wang
    xuefei-wang committed Nov 18, 2022
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  4. Deprecate old functions in multiplex.py

    @xuefei-wang
    xuefei-wang committed Nov 18, 2022
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Commits on Nov 22, 2022

  1. Add new utils functions for decoding

    @xuefei-wang
    xuefei-wang committed Nov 22, 2022
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  2. Refactor decoding functions

    @xuefei-wang
    xuefei-wang committed Nov 22, 2022
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  3. Implement spot decoding application

    @xuefei-wang
    xuefei-wang committed Nov 22, 2022
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  4. Add decoding functionality to Polaris app; format output

    @xuefei-wang
    xuefei-wang committed Nov 22, 2022
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  5. Add comment about cell_id=0 case: background

    @xuefei-wang
    xuefei-wang committed Nov 22, 2022
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  6. Make maxpool_extra_picel_num default to 0

    @xuefei-wang
    xuefei-wang committed Nov 22, 2022
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  7. Copy df_barcodes so that it does not modify input data

    @xuefei-wang
    xuefei-wang committed Nov 22, 2022
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  8. Update analysis notebooks

    @xuefei-wang
    xuefei-wang committed Nov 22, 2022
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  9. Specify url for torch packages to use cpu-only ones

    @xuefei-wang
    xuefei-wang committed Nov 22, 2022
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  10. Use a larger fov for multiplex example

    @xuefei-wang
    xuefei-wang committed Nov 22, 2022
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  11. Update requirements.txt (option: extra index url)

    @xuefei-wang
    xuefei-wang committed Nov 22, 2022
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Commits on Nov 23, 2022

  1. PEP8 formatted

    @xuefei-wang
    xuefei-wang committed Nov 23, 2022
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  2. PEP8 formating continued

    @xuefei-wang
    xuefei-wang committed Nov 23, 2022
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  3. PEP8 continued

    @xuefei-wang
    xuefei-wang committed Nov 23, 2022
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  4. PEP8 continued again

    @xuefei-wang
    xuefei-wang committed Nov 23, 2022
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Commits on Nov 24, 2022

  1. PEP8 continued again * 2

    @xuefei-wang
    xuefei-wang committed Nov 24, 2022
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  2. Point users to notebook for formatting df_barcodes

    @xuefei-wang
    xuefei-wang committed Nov 24, 2022
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  3. PEP8 rm trailing white spaces

    @xuefei-wang
    xuefei-wang committed Nov 24, 2022
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  4. Initialize tests to decoding related functions

    @xuefei-wang
    xuefei-wang committed Nov 24, 2022
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Commits on Dec 2, 2022

  1. Revert PEP8 too short wrapped lines

    @xuefei-wang
    xuefei-wang committed Dec 2, 2022
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  2. Implement tests for decoding

    @xuefei-wang
    xuefei-wang committed Dec 2, 2022
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Commits on Dec 5, 2022

  1. Fix bug: import missing package name

    @xuefei-wang
    xuefei-wang committed Dec 5, 2022
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  2. Fix bug: replace range with np.arange

    @xuefei-wang
    xuefei-wang committed Dec 5, 2022
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Commits on Dec 6, 2022

  1. Lint test files for decoding

    @xuefei-wang
    xuefei-wang committed Dec 6, 2022
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Commits on Dec 8, 2022

  1. Fix typo: extra comma

    @xuefei-wang
    xuefei-wang committed Dec 8, 2022
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Commits on Jan 3, 2023

  1. fix test bug: class_probs has #barcodes dim

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  2. Fix test bug: type error instead of value error

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  3. Fix test bug: format file

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  4. Fix test bug: missing one dim

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  5. Fix test bug: format (rm blank lines)

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  6. Fix test bug: redundant extra dim in index for barcodes

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  7. Fix test bug: missing num_image dim & add more rigorous tests

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  8. Fix test bug: redundant extra dim in index for barcodes (cont'd)

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  9. Fix test bug: formating

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  10. FIx test bug: not nesting arrays

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  11. Comment out unpassed test for now

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  12. Fix test bug: numpy.int does not exist due to version upgrade

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  13. Fix test bug: assert list equal

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  14. Fix test bug: slice_annotated_image bug found, np.int does not exist

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  15. Fix test bug: typo

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  16. fix test bug: formating

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  17. Fix test bug: barcode index starts from 1

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  18. Fix test bug: multiple tests got crosswired

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  19. Comment out test_slice_annotated_image for now

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  20. Fix test bug: rm ambiguity in test data

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  21. Test pining python version for tests

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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  22. Test pining python version for tests cont'd

    @xuefei-wang
    xuefei-wang committed Jan 3, 2023
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Commits on Jan 4, 2023

  1. Apply suggestions from code review and revert python version back 

    Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
    @xuefei-wang @rossbar
    xuefei-wang and rossbar authored Jan 4, 2023
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  2. Apply suggestions from code review and revert python version back cont'd

    @xuefei-wang
    xuefei-wang committed Jan 4, 2023
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Commits on Feb 2, 2023

  1. Clips probabilities before decoding (#39) 

    * Clip probability values
    @elaubsch
    elaubsch authored Feb 2, 2023
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  2. Merge branch 'master' into decoding

    @elaubsch
    elaubsch authored Feb 2, 2023
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Commits on Feb 7, 2023

  1. Doctoring formatting 

    Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
    @elaubsch @rossbar
    elaubsch and rossbar authored Feb 7, 2023
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  2. Remove code-block 

    Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
    @elaubsch @rossbar
    elaubsch and rossbar authored Feb 7, 2023
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  3. Add code-block 

    Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
    @elaubsch @rossbar
    elaubsch and rossbar authored Feb 7, 2023
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  4. Docstring formatting 

    Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
    @elaubsch @rossbar
    elaubsch and rossbar authored Feb 7, 2023
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  5. Unpin python 3.10 version 

    Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
    @elaubsch @rossbar
    elaubsch and rossbar authored Feb 7, 2023
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  6. Remove code-block directive from all scripts

    @elaubsch
    elaubsch committed Feb 7, 2023
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  7. Refactor r and c to rounds and channels

    @elaubsch
    elaubsch committed Feb 7, 2023
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  8. Fix misspelling of singleplex

    @elaubsch
    elaubsch committed Feb 7, 2023
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  9. Remove empty dictionary as default

    @elaubsch
    elaubsch committed Feb 7, 2023
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  10. Remove split empty parens

    @elaubsch
    elaubsch committed Feb 7, 2023
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  11. Add deprecation warnings

    @elaubsch
    elaubsch committed Feb 7, 2023
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  12. Rewrite slicing in _predict_spots_image for clarity

    @elaubsch
    elaubsch committed Feb 7, 2023
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  13. Refactor r and c to rounds and channels in tests and revert indexing … 

    …error
    @elaubsch
    elaubsch committed Feb 7, 2023
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  14. Remove dim calculation in reshape_torch_array

    @elaubsch
    elaubsch committed Feb 7, 2023
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