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Addition of super-resolution in 2D notebooks to the generation folder #1842

Merged
merged 39 commits into from
Sep 25, 2024
Merged

Addition of super-resolution in 2D notebooks to the generation folder #1842

merged 39 commits into from
Sep 25, 2024

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virginiafdez
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Description

Addition of notebooks for 2D super-resolution using MedNIST. One of them uses normal PyTorch and the other uses PyTorch Lightning.
Added them to the README file within generation.

Checks

  • Avoid including large-size files in the PR.
  • Clean up long text outputs from code cells in the notebook.
  • For security purposes, please check the contents and remove any sensitive info such as user names and private key.
  • Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the ./figure folder
  • Notebook runs automatically ./runner.sh -t <path to .ipynb file>

Virginia Fernandez and others added 30 commits September 4, 2024 17:49
Porting of 2D ControlNet tutorial using DDPM and ControlNet to guide …
36b7247 
…the synthetic process. We used BraTS and conditioning on binary brain masks.

Signed-off-by: Virginia Fernandez <[email protected]>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
f1dbc6c 
for more information, see https://pre-commit.ci
Removing blank line at end of file.
5e0059b 
Signed-off-by: Virginia Fernandez <[email protected]>
Merge remote-tracking branch 'origin/main' into main
65bc4c6
Removing blank line at end of file.
bfa92c9 
Signed-off-by: Virginia Fernandez <[email protected]>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
536745a 
for more information, see https://pre-commit.ci
Fix flake8 issues to ControlNet.
906fb05 
Signed-off-by: Virginia Fernandez <[email protected]>
Merge remote-tracking branch 'origin/main' into main
cf723c8 
# Conflicts:
#	generation/controlnet/2d_controlnet.ipynb
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
4f139d8 
for more information, see https://pre-commit.ci
Set download to True.
bd0d765 
Signed-off-by: Virginia Fernandez <[email protected]>
@KumoLiu
Merge branch 'main' into main
ee99e97
Change call to autocast.
ef6c972 
Signed-off-by: Virginia Fernandez <[email protected]>
Merge remote-tracking branch 'origin/main' into main
fbbd937
@virginiafdez
Merge branch 'Project-MONAI:main' into main
b63c863
Change call to autocast.
fa99612 
Signed-off-by: Virginia Fernandez <[email protected]>
@KumoLiu
Merge branch 'main' into main
95e0026
Addition of ControlNet to the README.
079532c 
Signed-off-by: Virginia Fernandez <[email protected]>
Addition of tutorials for the 2D and 3D autoencoderkl.
8491dfa 
Signed-off-by: Virginia Fernandez <[email protected]>
@virginiafdez
Merge branch 'Project-MONAI:main' into main
14fa31f
Addition of tutorials for the 2D and 3D autoencoderkl tutorials. Pass…
d6aec13 
…ed PEP8 compliance.

Signed-off-by: Virginia Fernandez <[email protected]>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
8eec20d 
for more information, see https://pre-commit.ci
Incorporate suggestions made by Eric (fix of tempfile import and use,…
c7a243e 
… typo).

Signed-off-by: Virginia Fernandez <[email protected]>
Re-run 3D models to ensure that losses go down.
e5fba2b 
Signed-off-by: Virginia Fernandez <[email protected]>
@virginiafdez
Merge branch 'Project-MONAI:main' into main
c01dacb
Adding autoencoder info to README.
433fd62 
Signed-off-by: Virginia Fernandez <[email protected]>
@virginiafdez
Merge branch 'Project-MONAI:main' into main
524ef2f
Fix issue with the plots for autoencoder tutorials. Add anomaly detec…
f9f329c 
…tion nbs to the README.

Signed-off-by: Virginia Fernandez <[email protected]>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
5145843 
for more information, see https://pre-commit.ci
Add download = True to 3D NB.
57ab963 
Signed-off-by: Virginia Fernandez <[email protected]>
@ericspod
Tweak for the number of samples to render
dfc1ebf 
Signed-off-by: Eric Kerfoot <[email protected]>
ericspod and others added 4 commits September 20, 2024 21:14
@ericspod
Fix
699446d 
Signed-off-by: Eric Kerfoot <[email protected]>
@ericspod
Fix
92bee49 
Signed-off-by: Eric Kerfoot <[email protected]>
@virginiafdez
Merge branch 'Project-MONAI:main' into main
b8df6c9
Addition of 2D super-resolution notebook using normal PyTorch and PyT…
019a40e 
…orch Lightning. Addition of notebook descriptions to README.md file within generation.

Signed-off-by: Virginia Fernandez <[email protected]>
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@ericspod ericspod enabled auto-merge (squash) September 25, 2024 17:26
@ericspod ericspod merged commit c29337a into Project-MONAI:main Sep 25, 2024
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@virginiafdez @ericspod @KumoLiu