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Binary segmentation #28

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Binary segmentation #28

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Commits on May 15, 2021

  1. Refactored DataManagerMixin as LightningDataModule

    @nathanpainchaud
    nathanpainchaud committed May 15, 2021
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Commits on May 27, 2021

  1. working on hydra to replace argparse

    @ThierryJudge
    ThierryJudge committed May 27, 2021
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  2. working training for mnist with "python runner.py +data=mnist +system… 

    …=classification +module=mlp"
    @ThierryJudge
    ThierryJudge committed May 27, 2021
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  3. Merge branch 'dev' of https://github.com/nathanpainchaud/vital into t… 

    …mp/refactor/hydra
    @ThierryJudge
    ThierryJudge committed May 27, 2021
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  4. working training for acdc

    @ThierryJudge
    ThierryJudge committed May 27, 2021
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Commits on May 28, 2021

  1. Add callbacks

    @ThierryJudge
    ThierryJudge committed May 28, 2021
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Commits on Jun 3, 2021

  1. change callbacks from list to dict

    @ThierryJudge
    ThierryJudge committed Jun 3, 2021
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Commits on Jun 4, 2021

  1. add check_cfg method

    @ThierryJudge
    ThierryJudge committed Jun 4, 2021
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Commits on Jun 8, 2021

  1. add check for default root dir

    @ThierryJudge
    ThierryJudge committed Jun 8, 2021
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  2. implement yaml configs

    @ThierryJudge
    ThierryJudge committed Jun 8, 2021
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  3. change config dir name, 

    log hparams
    @ThierryJudge
    ThierryJudge committed Jun 8, 2021
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Commits on Jun 9, 2021

  1. callbacks and config

    @ThierryJudge
    ThierryJudge committed Jun 9, 2021
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  2. fix callbacks and loggers 

    add arguments for system instantiate
add missing params to camus config
    @ThierryJudge
    ThierryJudge committed Jun 9, 2021
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  3. Fix pre-commit

    @ThierryJudge
    ThierryJudge committed Jun 9, 2021
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  4. merge dev

    @ThierryJudge
    ThierryJudge committed Jun 9, 2021
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  5. add hydra to requirements.txt 

    fix camus labels
    @ThierryJudge
    ThierryJudge committed Jun 9, 2021
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Commits on Jun 11, 2021

  1. allow more configurable callbacks

    @ThierryJudge
    ThierryJudge committed Jun 11, 2021
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  2. fix loading from checkpoint path, add hydra and dotenv to requirement… 

    …s.txt
    @ThierryJudge
    ThierryJudge committed Jun 11, 2021
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  3. Merge branch 'tmp/hydra/yaml' of https://github.com/nathanpainchaud/v… 

    …ital into tmp/hydra/yaml
    @ThierryJudge
    ThierryJudge committed Jun 11, 2021
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Commits on Jun 14, 2021

  1. allow model saving if not checkpoint if used

    @ThierryJudge
    ThierryJudge committed Jun 14, 2021
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Commits on Jun 15, 2021

  1. fix loggers

    @ThierryJudge
    ThierryJudge committed Jun 15, 2021
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Commits on Jun 16, 2021

  1. Move module configs in system folder to allow system config to overri… 

    …de module parameters
    @ThierryJudge
    ThierryJudge committed Jun 16, 2021
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  2. Work in progress: 

    * Add softmax and mcdropout system
* Add evaluation pipeline (Seg metrics, calibration overlap)
    @ThierryJudge
    ThierryJudge committed Jun 16, 2021
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Commits on Jun 17, 2021

  1. change unet dropout parameter name to be uniform with enet

    @ThierryJudge
    ThierryJudge committed Jun 17, 2021
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Commits on Jun 18, 2021

  1. Add resolvers for num_workers and gpus

    @ThierryJudge
    ThierryJudge committed Jun 18, 2021
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Commits on Jun 21, 2021

  1. add workers=True to seed_everything in runner.py

    @ThierryJudge
    ThierryJudge committed Jun 21, 2021
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  2. Merge dev.

    @ThierryJudge
    ThierryJudge committed Jun 21, 2021
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  3. Remove argparse methods.

    @ThierryJudge
    ThierryJudge committed Jun 21, 2021
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Commits on Jun 23, 2021

  1. Minor fixes and PR comment fixes

    @ThierryJudge
    ThierryJudge committed Jun 23, 2021
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Commits on Jul 9, 2021

  1. Remove test_step from computation. 

    Remove resume/train/ckpt_path errors from runner
Change default name to remove error.
    @ThierryJudge
    ThierryJudge committed Jul 9, 2021
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Commits on Jul 13, 2021

  1. minor fixes

    @ThierryJudge
    ThierryJudge committed Jul 13, 2021
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  2. Merge branch 'feature/refactor-hydra-yaml' of https://github.com/nath… 

    …anpainchaud/vital into feature/refactor-hydra-yaml
    @ThierryJudge
    ThierryJudge committed Jul 13, 2021
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Commits on Jul 20, 2021

  1. Remove log images 

    Update gitignore
add monitor to model_checkpoint.yaml to avoid warning
    @ThierryJudge
    ThierryJudge committed Jul 20, 2021
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Commits on Jul 21, 2021

  1. Merge dev

    @ThierryJudge
    ThierryJudge committed Jul 21, 2021
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Commits on Jul 22, 2021

  1. Loading checkpoint from Comet model registry

    @nathanpainchaud
    nathanpainchaud committed Jul 22, 2021
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  2. Refactored checkpoint CLI to document Comet model registry option

    @nathanpainchaud
    nathanpainchaud committed Jul 22, 2021
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  3. Fixed minimum Comet version to make both version and stage optional

    @nathanpainchaud
    nathanpainchaud committed Jul 22, 2021
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  4. Implemented caching logic for Comet checkpoints

    @nathanpainchaud
    nathanpainchaud committed Jul 22, 2021
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  5. Changed comet integration to rely on env vars instead of config file

    @nathanpainchaud
    nathanpainchaud committed Jul 22, 2021
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Commits on Jul 23, 2021

  1. Refactored Comet API init to support any API key setting method recog… 

    …nised by Comet
    @nathanpainchaud
    nathanpainchaud committed Jul 23, 2021
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  2. Merge feature/comet-model-registry into hydra refactor

    @ThierryJudge
    ThierryJudge committed Jul 23, 2021
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  3. Add comet tags and logging .hydra dir to comet. 

    Add comment regarding use of local ckpt with relative path
    @ThierryJudge
    ThierryJudge committed Jul 23, 2021
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Commits on Aug 3, 2021

  1. Add softmax parameter to Dice

    @ThierryJudge
    ThierryJudge committed Aug 3, 2021
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  2. Update segmentation metric for dice for binary segmentation 

    Update networks for 1 class output
    @ThierryJudge
    ThierryJudge committed Aug 3, 2021
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  3. Add image loggind to segmentation.py and classification system.

    @ThierryJudge
    ThierryJudge committed Aug 3, 2021
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  4. Almost functioning binary dice

    @ThierryJudge
    ThierryJudge committed Aug 3, 2021
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Commits on Aug 9, 2021

  1. minor improvements

    @ThierryJudge
    ThierryJudge committed Aug 9, 2021
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Commits on Aug 11, 2021

  1. Refactor Hydra to use yaml configuration (#22) 

    Co-authored-by: Nathan Painchaud <[email protected]>
    @ThierryJudge @nathanpainchaud
    ThierryJudge and nathanpainchaud authored Aug 11, 2021
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Commits on Aug 14, 2021

  1. minor change

    @ThierryJudge
    ThierryJudge committed Aug 14, 2021
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Commits on Aug 17, 2021

  1. Work in progress, fix comet TAGS

    @ThierryJudge
    ThierryJudge committed Aug 17, 2021
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Commits on Aug 18, 2021

  1. Merge hydra dev into feature/binary seg

    @ThierryJudge
    ThierryJudge committed Aug 18, 2021
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  2. change weights_only to weights to avoid passing 2 argument when loadi… 

    …ng weights.
    @ThierryJudge
    ThierryJudge committed Aug 18, 2021
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Commits on Aug 20, 2021

  1. Fix dropout for Unet

    @ThierryJudge
    ThierryJudge committed Aug 20, 2021
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  2. WIP learning sample confidence

    @ThierryJudge
    ThierryJudge committed Aug 20, 2021
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  3. Add dropout attribute

    @ThierryJudge
    ThierryJudge committed Aug 20, 2021
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Commits on Aug 24, 2021

  1. Add fix registry name for serialization.py

    @ThierryJudge
    ThierryJudge committed Aug 24, 2021
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Commits on Aug 31, 2021

  1. Fix binary dice with pred.squeeze() and clean up.

    @ThierryJudge
    ThierryJudge committed Aug 31, 2021
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  2. Fix typos in docstring

    @ThierryJudge
    ThierryJudge committed Aug 31, 2021
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Commits on Oct 20, 2021

  1. Merge dev into hydra-dev

    @ThierryJudge
    ThierryJudge committed Oct 20, 2021
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Commits on Nov 9, 2021

  1. Typo fix for MLP

    @ThierryJudge
    ThierryJudge committed Nov 9, 2021
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  2. Merge branch 'hydra-dev' of github.com:nathanpainchaud/vital into fea… 

    …ture/binary-segmentation
    @ThierryJudge
    ThierryJudge committed Nov 9, 2021
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Commits on Nov 11, 2021

  1. Refactor Hydra to use yaml configuration (#22) 

    Co-authored-by: Nathan Painchaud <[email protected]>
    @ThierryJudge @nathanpainchaud
    ThierryJudge and nathanpainchaud committed Nov 11, 2021
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  2. Typo fix for MLP

    @ThierryJudge
    ThierryJudge committed Nov 11, 2021
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  3. Merge branch 'hydra-dev' of github.com:nathanpainchaud/vital into hyd… 

    …ra-dev
    @ThierryJudge
    ThierryJudge committed Nov 11, 2021
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  4. Merge branch 'hydra-dev' of github.com:nathanpainchaud/vital into fea… 

    …ture/binary-segmentation
    @ThierryJudge
    ThierryJudge committed Nov 11, 2021
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  5. Remove comment from unet.

    @ThierryJudge
    ThierryJudge committed Nov 11, 2021
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