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Rhoadesj/dev #21

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wants to merge 44 commits into from
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Rhoadesj/dev #21

wants to merge 44 commits into from

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rhoadesScholar and others added 30 commits August 26, 2023 16:06
@rhoadesScholar
feat: better tqdm, training reloading
68258d7
@rhoadesScholar
feat: numpy version requirement (1.22.3); watershed
9eee5a7 
Watershed bug fixes for float64, bias hyperparameter, & npi.remap usage
@rhoadesScholar
feat: improve training logging
703a31d
@rhoadesScholar
Merge branch 'master' into rhoadesj/dev
b97f3d7
@rhoadesScholar
feat: stdout logging, version
8a03a57
@rhoadesScholar
feat: validation logging, keep best validation
9626922
@rhoadesScholar
WIP: apply.py
8212b8b
@rhoadesScholar
feat: keep actual best scoring dataset
8326400
@rhoadesScholar
feat: ready to debug apply.py
663fe0f
@rhoadesScholar
feat!: add cli for applying models
beeed60
@rhoadesScholar
feat!: add cli for applying models
8553b5a
@rhoadesScholar
feat: apply.py roi
273ecb7
@rhoadesScholar
feat: postprocess parameter parsing
2622b94
@rhoadesScholar
feat: overwrite option for predict & postprocess
bd192e5
@rhoadesScholar
bugfix!?: removed odd zarr creation
6421bd1 
already handled by funlib.persistence.prepare_ds
@rhoadesScholar
!: attempts to fix roi mismatch failed.
8198648 
committing for reference
@rhoadesScholar
bugfix: prediction works with zarrs
ed0d4ad 
bug seems specific to n5
@rhoadesScholar
feat: backlogged updates and wip
ae23179
@rhoadesScholar
feat: zarr fix dimension detection, simple augment config kwargs, val…
53b3556 
…idation bug hanging
@rhoadesScholar
bugfix: simple augment config
8e6dfa3
@rhoadesScholar
bugfix: simple augment config
0869015
@rhoadesScholar
feat: black format, iou score
922ba62
@rhoadesScholar
bugfix: remove array overspecification
7d954f9
@mzouink
hot distance loss function
ec1b0d8
@rhoadesScholar
feat: hotdistance predictor, model/target
be0f6db
@mzouink
hot distance task
da48612
@rhoadesScholar
Merge branch 'hot_distance' of github.com:janelia-cellmap/dacapo into…
a6714c0 
… hot_distance
@rhoadesScholar
feat: hot_distance_predictor target/weight
9567ec4
@rhoadesScholar
bugfix: temporarily remove IOU
bfcc339
@rhoadesScholar
feat: avg_iou
d8c8517
rhoadesScholar
rhoadesScholar commented Feb 8, 2024
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dacapo/experiments/tasks/evaluators/evaluator.py Outdated
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now in dev/validation

rhoadesScholar
rhoadesScholar commented Feb 8, 2024
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dacapo/experiments/tasks/evaluators/instance_evaluation_scores.py Outdated
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now in dev/validation

rhoadesScholar
rhoadesScholar commented Feb 8, 2024
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dacapo/experiments/tasks/evaluators/instance_evaluator.py Outdated
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now in dev/validation

rhoadesScholar
rhoadesScholar commented Feb 8, 2024
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dacapo/experiments/trainers/gp_augments/__init__.py Outdated
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now in dev/augmentations

rhoadesScholar
rhoadesScholar commented Feb 8, 2024
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dacapo/experiments/trainers/gp_augments/gaussian_noise_config.py Outdated
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now in dev/augmentations

rhoadesScholar
rhoadesScholar commented Feb 8, 2024
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dacapo/experiments/trainers/gp_augments/simple_config.py Outdated
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now in dev/augmentations

rhoadesScholar
rhoadesScholar commented Feb 8, 2024
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dacapo/experiments/validation_scores.py Outdated
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@rhoadesScholar rhoadesScholar Feb 8, 2024 •
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now in dev/validation

rhoadesScholar
rhoadesScholar commented Feb 8, 2024
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dacapo/gp/elastic_augment_fuse.py Outdated
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now in dev/augmentations

rhoadesScholar
rhoadesScholar commented Feb 8, 2024
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remove this change

rhoadesScholar
rhoadesScholar commented Feb 8, 2024
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dacapo/store/local_array_store.py Outdated
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remove comment

rhoadesScholar
rhoadesScholar commented Feb 8, 2024
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dacapo/validate.py
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now in dev/validation

rhoadesScholar
rhoadesScholar commented Feb 8, 2024
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dacapo/gp/dacapo_create_target.py Outdated
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dismiss comment until bug happens ;)

rhoadesScholar
rhoadesScholar commented Feb 9, 2024
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dacapo/experiments/tasks/hot_distance_task.py Outdated
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now in rhoadesj/hot_distance

rhoadesScholar
rhoadesScholar commented Feb 9, 2024
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dacapo/experiments/tasks/hot_distance_task_config.py Outdated
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now in rhoadesj/hot_distance

rhoadesScholar
rhoadesScholar commented Feb 9, 2024
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dacapo/experiments/tasks/losses/__init__.py Outdated
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now in rhoadesj/hot_distance

rhoadesScholar
rhoadesScholar commented Feb 9, 2024
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dacapo/experiments/tasks/losses/hot_distance_loss.py Outdated
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now in rhoadesj/hot_distance

rhoadesScholar
rhoadesScholar commented Feb 9, 2024
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dacapo/experiments/tasks/predictors/hot_distance_predictor.py Outdated
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now in rhoadesj/hot_distance

rhoadesScholar
rhoadesScholar commented Feb 11, 2024
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dacapo/experiments/tasks/post_processors/argmax_post_processor.py Outdated
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added to dev/post-process

rhoadesScholar
rhoadesScholar commented Feb 11, 2024
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dacapo/experiments/tasks/post_processors/dummy_post_processor.py Outdated
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added to dev/post-process

rhoadesScholar
rhoadesScholar commented Feb 11, 2024
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added to dev/post-process

rhoadesScholar
rhoadesScholar commented Feb 11, 2024
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dacapo/experiments/tasks/post_processors/threshold_post_processor.py Outdated
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added to dev/post-process

rhoadesScholar
rhoadesScholar commented Feb 11, 2024
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dacapo/experiments/tasks/post_processors/watershed_post_processor.py Outdated
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added to dev/post-process

rhoadesScholar
rhoadesScholar commented Feb 11, 2024
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dacapo/experiments/trainers/gunpowder_trainer.py Outdated
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added to dev/trainers

rhoadesScholar
rhoadesScholar commented Feb 11, 2024
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dacapo/experiments/trainers/gunpowder_trainer_config.py Outdated
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added to dev/trainers

rhoadesScholar
rhoadesScholar commented Feb 11, 2024
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added to dev/trainers

rhoadesScholar
rhoadesScholar commented Feb 11, 2024
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All changes have been split to separate branches for merging. This branch is now derelict.

@rhoadesScholar rhoadesScholar deleted the rhoadesj/dev branch March 11, 2024 02:33
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