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Top-down Centered-instance Pipeline #16

Merged
merged 61 commits into from
Sep 19, 2023
Merged

Top-down Centered-instance Pipeline #16

merged 61 commits into from
Sep 19, 2023

Commits on Aug 3, 2023

  1. added make_centered_bboxes & normalize_bboxes

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    alckasoc committed Aug 3, 2023
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Commits on Aug 6, 2023

  1. added make_centered_bboxes & normalize_bboxes

    @alckasoc
    alckasoc committed Aug 6, 2023
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  2. created test_instance_cropping.py

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    alckasoc committed Aug 6, 2023
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  3. added test normalize bboxes; added find_global_peaks_rough

    @alckasoc
    alckasoc committed Aug 6, 2023
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  4. black formatted

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    alckasoc committed Aug 6, 2023
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  5. fixed merges

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    alckasoc committed Aug 6, 2023
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  6. black formatted peak_finding

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    alckasoc committed Aug 6, 2023
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Commits on Aug 10, 2023

  1. added make_grid_vectors, normalize_bboxes, integral_regression, added… 

    … docstring to make_centered_bboxes, fixed find_global_peaks_rough; added crop_bboxes
    @alckasoc
    alckasoc committed Aug 10, 2023
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  2. finished find_global_peaks with integral regression over centroid crops!

    @alckasoc
    alckasoc committed Aug 10, 2023
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  3. reformatted with pydocstyle & black

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    alckasoc committed Aug 10, 2023
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  4. Merge remote-tracking branch 'origin/main' into vincent/find_peaks

    @alckasoc
    alckasoc committed Aug 10, 2023
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  5. moved make_grid_vectors to data/utils

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    alckasoc committed Aug 10, 2023
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  6. removed normalize_bboxes

    @alckasoc
    alckasoc committed Aug 10, 2023
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  7. added tests docstrings

    @alckasoc
    alckasoc committed Aug 10, 2023
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  8. sorted imports with isort

    @alckasoc
    alckasoc committed Aug 10, 2023
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  9. remove unused imports

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    alckasoc committed Aug 10, 2023
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  10. updated test cases for instance cropping

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    alckasoc committed Aug 10, 2023
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Commits on Aug 11, 2023

  1. added minimal_cms.pt fixture + unit tests

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    alckasoc committed Aug 11, 2023
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  2. added minimal_bboxes fixture; added unit tests for crop_bboxes & inte… 

    …gral_regression
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  3. added find_global_peaks unit tests

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    alckasoc committed Aug 11, 2023
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Commits on Aug 17, 2023

  1. finished find_local_peaks_rough!

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    alckasoc committed Aug 17, 2023
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  2. finished find_local_peaks!

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    alckasoc committed Aug 17, 2023
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  3. added unit tests for find_local_peaks and find_local_peaks_rough

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    alckasoc committed Aug 17, 2023
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  4. updated test cases

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    alckasoc committed Aug 17, 2023
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  5. added more test cases for find_local_peaks

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    alckasoc committed Aug 17, 2023
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  6. updated test cases

    @alckasoc
    alckasoc committed Aug 17, 2023
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  7. added architectures folder

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    alckasoc committed Aug 17, 2023
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  8. added maxpool2d same padding, get_act_fn; added simpleconvblock, simp… 

    …leupsamplingblock, encoder, decoder; added unet
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    alckasoc committed Aug 17, 2023
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Commits on Aug 18, 2023

  1. added test_unet_reference

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    alckasoc committed Aug 18, 2023
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  2. black formatted common.py & test_unet.py

    @alckasoc
    alckasoc committed Aug 18, 2023
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  3. fixed merge conflicts

    @alckasoc
    alckasoc committed Aug 18, 2023
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  4. Merge branch 'main' into vincent/unet

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    alckasoc authored Aug 18, 2023
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  5. Merge branch 'vincent/unet' of https://github.com/talmolab/sleap-nn i… 

    …nto vincent/unet
    @alckasoc
    alckasoc committed Aug 18, 2023
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  6. deleted tmp nb

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    alckasoc committed Aug 18, 2023
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Commits on Aug 19, 2023

  1. _calc_same_pad returns int

    @alckasoc
    alckasoc committed Aug 19, 2023
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  2. fixed test case

    @alckasoc
    alckasoc committed Aug 19, 2023
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  3. added simpleconvblock tests

    @alckasoc
    alckasoc committed Aug 19, 2023
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  4. added tests

    @alckasoc
    alckasoc committed Aug 19, 2023
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  5. added tests for simple upsampling block

    @alckasoc
    alckasoc committed Aug 19, 2023
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Commits on Aug 28, 2023

  1. updated test_unet

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    alckasoc committed Aug 28, 2023
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Commits on Aug 30, 2023

  1. removed unnecessary variables

    @alckasoc
    alckasoc committed Aug 30, 2023
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  2. updated augmentation random erase default values

    @alckasoc
    alckasoc committed Aug 30, 2023
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  3. created data/pipelines.py

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    alckasoc committed Aug 30, 2023
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Commits on Aug 31, 2023

  1. added base config in config/data; temporary till config system settled

    @alckasoc
    alckasoc committed Aug 31, 2023
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  2. updated variable defaults to 0 and edited variable names in augmentation

    @alckasoc
    alckasoc committed Aug 31, 2023
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  3. updated parameter names in data/instance_cropping

    @alckasoc
    alckasoc committed Aug 31, 2023
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  4. added data/pipelines topdown pipeline make_base_pipeline

    @alckasoc
    alckasoc committed Aug 31, 2023
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  5. added test_pipelines

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    alckasoc committed Aug 31, 2023
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Commits on Sep 5, 2023

  1. removed configs

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    alckasoc committed Sep 5, 2023
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Commits on Sep 6, 2023

  1. updated augmentation class

    @alckasoc
    alckasoc committed Sep 6, 2023
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  2. modified test

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    alckasoc committed Sep 6, 2023
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  3. updated pipelines docstring

    @alckasoc
    alckasoc committed Sep 6, 2023
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  4. removed make_base_pipeline and updated tests

    @alckasoc
    alckasoc committed Sep 6, 2023
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  5. removed empty_cache in SleapDataset

    @alckasoc
    alckasoc committed Sep 6, 2023
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Commits on Sep 7, 2023

  1. Merge branch 'main' into vincent/topdownpipeline

    @alckasoc
    alckasoc authored Sep 7, 2023
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  2. updated test_pipelines

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    alckasoc committed Sep 7, 2023
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Commits on Sep 12, 2023

  1. updated sleapdataset to return a dict

    @alckasoc
    alckasoc committed Sep 12, 2023
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  2. added key filter transformer block, removed sleap dataset, added type… 

    … hinting
    @alckasoc
    alckasoc committed Sep 12, 2023
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  3. updated type hints

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    alckasoc committed Sep 12, 2023
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  4. added coderabbit suggestions

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    alckasoc committed Sep 12, 2023
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  5. fixed small squeeze issue

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    alckasoc committed Sep 12, 2023
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