Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Lightning backend #109

Merged
merged 255 commits into from
Apr 30, 2024
Merged

Lightning backend #109

merged 255 commits into from
Apr 30, 2024

Conversation

jdeschamps
Copy link
Member

We decided to use PyTorch Lightning as back-end to benefit from the various advantages it can bring (e.g. multi GPU training) and avoid supporting an entire pure PyTorch training engine.

This PR is the fruit of a lot of refactoring, and the current features are the following:

  • Full Pydantic configuration
  • Train and predict using Noise2Void, N2V, structN2V, CARE and N2N
  • Train on array or files
  • Tiled prediction
  • Export to the BMZ format
  • Plug-in your own function to read specific file formats

CatEek and others added 30 commits November 13, 2023 17:07
@CatEek
running norm draft
6774540
@CatEek
running stats(bug)
7297494
@CatEek
comments
3b0d0c2
@CatEek
prints
dd1927c
@CatEek
docstings
63c3929
@CatEek
noise model base
a72c927
@CatEek
nm wip
f3d0bda
@CatEek
loss_algo_draft
e40aded
@CatEek
add targets patching draft
8316da0
@CatEek
masking strat validation draft
12d3436
@CatEek
supervised roi
e4ef9ae
@CatEek
conf, noise model, pixel masking
3787585
@CatEek
care/n2n working in principle
d109fdc
@CatEek
config validation and test wip
383b06d
@CatEek
segm training wip
28119e4
@CatEek
load from ckpt fix
db0111c
@CatEek
seq patching logging update
70a1bc4
@CatEek
aug wrappers, smoke tests, patching, tiling
9c0a401
@CatEek
blurpool draft
8fb7500
@CatEek
n2v2 mvp
72e26d3
@CatEek
blurpool3d
caab647
@CatEek
clear todos
a2aa2ff
@CatEek
model factrory refac
1bf2771
@CatEek
lightning test
badc965
@CatEek
notebook+preds
c7bb2ab
@CatEek
structn2v test
0a31194
@CatEek
structn2v mve
2de057d
@CatEek
struct mask, normalize in mem
ca62687
@jdeschamps
Some API (WIP)
5aa451c
@CatEek
segm norm fix
74e2f1e
CatEek and others added 28 commits April 27, 2024 17:19
@CatEek
Export to BMZ and other changes (#108)
6405066
@CatEek
channel tests fix
de2b915
@jdeschamps
Revert "ci(dependabot): bump codecov/codecov-action from 3 to 4 (#100)"
af7dd8e 
This reverts commit e7fc8fc, reversing
changes made to b325df9.
@jdeschamps
Revert "Update README.md"
f390696 
This reverts commit b325df9.
@jdeschamps
Revert "ci(dependabot): bump styfle/cancel-workflow-action from 0.12.…
9e2b649 
…0 to 0.12.1 (#99)"

This reverts commit 6e773eb, reversing
changes made to 01df574.
@jdeschamps
Revert "ci(pre-commit.ci): autoupdate (#98)"
0e0ee00 
This reverts commit 01df574, reversing
changes made to e0595df.
@jdeschamps
Revert "Refactor BioImage.io Export/Import (#97)"
84f1b5b 
This reverts commit e0595df, reversing
changes made to a9b450f.
@jdeschamps
Revert "ci(dependabot): bump actions/setup-python from 4 to 5 (#96)"
3ca49a3 
This reverts commit a9b450f, reversing
changes made to 641cad4.
@jdeschamps
Revert "ci(pre-commit.ci): autoupdate (#95)"
620f114 
This reverts commit 641cad4, reversing
changes made to b21bfba.
@jdeschamps
Revert "ci(pre-commit.ci): autoupdate (#93)"
c952f4f 
This reverts commit b21bfba, reversing
changes made to 8e0b9b1.
@jdeschamps
Revert "ci(dependabot): bump styfle/cancel-workflow-action from 0.11.…
4d57b80 
…0 to 0.12.0 (#92)"

This reverts commit 8e0b9b1, reversing
changes made to 3380346.
@jdeschamps
Revert "ci(dependabot): bump actions/checkout from 3 to 4 (#91)"
bc4c3a3 
This reverts commit 3380346, reversing
changes made to 947c799.
@jdeschamps
Revert "Clean-up README"
b66d745 
This reverts commit 947c799.
@jdeschamps
Revert "Github templates and publishing (#90)"
0fd82d3 
This reverts commit cd2c2d6, reversing
changes made to 1d1fec9.
@jdeschamps
Merge branch 'dl4mia' into revert_divergence
72eb9f5
@jdeschamps
Merge remote-tracking branch 'origin/dl4mia_prep' into revert_divergence
1a3d039
@jdeschamps
Replace tuples by lists (yaml export issue)
95711de
@jdeschamps
Add single int check
cdc5727
@jdeschamps
Fix model_validators signature in config
6c28dfd
@jdeschamps
Fix error in axes - BMZ prediction
6699140
@pre-commit-ci
style(pre-commit.ci): auto fixes [...]
d1b8ae6
@jdeschamps
Add torch dependency
c361b55
@jdeschamps
Add torchvision
c0d9020
@jdeschamps
Remove non-sensical version
dc6c5a6
@jdeschamps
Prevent torch 2.3.0 on macOS intel
ffb91dd
@jdeschamps
Prevent different number of channels in N2V and N2N
54b622b
@jdeschamps
Merge branch 'configuration_fixes' into lightning_backend
5216d57
@jdeschamps
Use macOs intel runners on Github CI
381bce8
@jdeschamps jdeschamps merged commit 5ffdd5f into main Apr 30, 2024
14 of 15 checks passed
@jdeschamps jdeschamps deleted the lightning_backend branch April 30, 2024 13:16
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@jdeschamps @CatEek