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6676 port generative networks autoencoderkl #7260

Merged
merged 14 commits into from
Dec 5, 2023
Merged

6676 port generative networks autoencoderkl #7260

merged 14 commits into from
Dec 5, 2023

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marksgraham
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Partially fixes #6676

Description

Implements the AutoencoderKL network from MONAI Generative.

NB this network is subject to a planned refactor once the porting is complete, see here.

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • New tests added to cover the changes.
  • Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

@marksgraham
Adds network and tests
d99044b
@marksgraham
Mypy fixes
9d16b48 
Signed-off-by: Mark Graham <markgraham539@gmail.com>
@marksgraham
Fix doc
fbfd8f5 
Signed-off-by: Mark Graham <markgraham539@gmail.com>
@ericspod
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Looks good to me since we've already used this code a lot and reviewed it elsewhere. The fails are from the arguments for checkpoint being different in older versions of Pytorch. We could define a separate checkpoint function which adapts the interface depending on the version of Pytorch we're dealing with. I see checkpoint being used in other parts of MONAI with this argument so it seems it's not well tested.

@ericspod ericspod mentioned this pull request Nov 28, 2023
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KumoLiu
KumoLiu reviewed Nov 29, 2023
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marksgraham and others added 8 commits November 29, 2023 08:27
@marksgraham @ericspod
Update monai/networks/nets/autoencoderkl.py
cd60374 
Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Signed-off-by: Mark Graham <markgraham539@gmail.com>
@marksgraham @KumoLiu
Update monai/networks/nets/autoencoderkl.py
b9798b3 
Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: Mark Graham <markgraham539@gmail.com>
@marksgraham
Rename num_channels to channels
a6bb925
@marksgraham
Use optional import
4caafe0
@marksgraham
DCO Remediation Commit for Mark Graham <markgraham539@gmail.com>
2bf0169 
I, Mark Graham <markgraham539@gmail.com>, hereby add my Signed-off-by to this commit: d99044b
I, Mark Graham <markgraham539@gmail.com>, hereby add my Signed-off-by to this commit: a6bb925
I, Mark Graham <markgraham539@gmail.com>, hereby add my Signed-off-by to this commit: 4caafe0

Signed-off-by: Mark Graham <markgraham539@gmail.com>
@marksgraham
Updates use_checkpointing to use_checkpoint
6a9f657 
Signed-off-by: Mark Graham <markgraham539@gmail.com>
@marksgraham
Checkpoint fixes
3e7dc6c 
Signed-off-by: Mark Graham <markgraham539@gmail.com>
@marksgraham
Change decorator order so test skipping works
d4302d9 
Signed-off-by: Mark Graham <markgraham539@gmail.com>
@KumoLiu KumoLiu requested a review from Nic-Ma November 29, 2023 15:37
@marksgraham
Version fix
6817179 
Signed-off-by: Mark Graham <markgraham539@gmail.com>
@Nic-Ma
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Nic-Ma commented Dec 1, 2023

@KumoLiu please create a seperate branch for Generative AI development, for example "gen-ai-dev", then let's merge the PR to that branch as we discussed.

Thanks.

@KumoLiu
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KumoLiu commented Dec 1, 2023

please create a seperate branch for Generative AI development, for example "gen-ai-dev", then let's merge the PR to that branch as we discussed.

Have created.

@marksgraham marksgraham changed the base branch from dev to gen-ai-dev December 4, 2023 12:15
@marksgraham
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please create a seperate branch for Generative AI development, for example "gen-ai-dev", then let's merge the PR to that branch as we discussed.

Have created.

Hi @Nic-Ma - have changed the PR to merge to gen-ai-dev

@KumoLiu KumoLiu requested a review from ericspod December 5, 2023 08:47
@KumoLiu
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KumoLiu commented Dec 5, 2023

/build

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KumoLiu commented Dec 5, 2023

Hi @ericspod, and @Nic-Ma, do you have any other concerns on this PR?

@KumoLiu KumoLiu mentioned this pull request Dec 5, 2023
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ericspod commented Dec 5, 2023

Looks good, we shall consider refactorings later once the porting is complete.

@marksgraham marksgraham merged commit fac754d into Project-MONAI:gen-ai-dev Dec 5, 2023
28 checks passed
marksgraham added a commit to marksgraham/MONAI that referenced this pull request Jan 30, 2024
@marksgraham @ericspod @KumoLiu
6676 port generative networks autoencoderkl (Project-MONAI#7260)
039ee21 
Partially fixes Project-MONAI#6676

### Description
Implements the AutoencoderKL network from MONAI Generative.

NB this network is subject to a planned refactor once the porting is
complete, [see
here](Project-MONAI#7227).

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [x] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: Mark Graham <markgraham539@gmail.com>
Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: Mark Graham <markgraham539@gmail.com>
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@KumoLiu KumoLiu KumoLiu left review comments

@ericspod ericspod ericspod approved these changes

@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma

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Move MONAI Generative into core
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@marksgraham @ericspod @Nic-Ma @KumoLiu