Merge genaidev Into Dev #7886
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Merge genaidev Into Dev #7886
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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](#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>
Partially fixes #6676 ### Description Implements the VQ-VAE network, including the vector quantizer block, from MONAI Generative. ### 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. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: KumoLiu <yunl@nvidia.com> Signed-off-by: Mark Graham <markgraham539@gmail.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: KumoLiu <yunl@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Towards #6676 . ### Description Adds a simple decoder-only transformer architecture. ### 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. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] 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>
Towards #6676 . ### Description Adds a DDPM unet. Refactoring for some of the blocks here is scheduled [here](#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. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Part of #6676 . ### Description Ports the ControlNet. ### 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. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] 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>
Part of #6676 . ### Description Adds a patchgan-style discriminator, both single scale and multiscale. ### 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. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Towards #6676 . ### Description This adds SPADE-enabled autoencoder and diffusion_model_unet architectures. They are new implementations for each network, rather than options in the existing network, because @virginiafdez and I felt that adding additional options to the existing networks to enable spade compatibility significantly reduced the readability of them for users who were not interested in SPADE functionality. These are the last networks to be ported over. ### 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. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] 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> Signed-off-by: Mark Graham <mark@Marks-MacBook-Pro.local> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Towards #6676 . ### Description This adds some base classes for DDPM noise schedulers + three scheduler types. ### 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. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] 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>
This is an update to PR #7332 - I addressed the comments but failed to push the changes before it was merged! Changes are very minor. ### Description A few sentences describing the changes proposed in this pull request. ### 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). - [ ] 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. --------- Signed-off-by: Mark Graham <markgraham539@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Towards #6676 . ### Description This ordering util got missed out my previous PR for the Generative utils. ### 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. - [ ] 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. - [x] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Mark Graham <markgraham539@gmail.com>
Part of #6676 . ### Description Adds Inferers to assist with training and sampling from diffusion models and controllers. Also takes the opportunity to make two changes which slipped through the previous PRs: - rename the `num_channels` arg in the spade diffusion unet to `channels` to be consistent with all the other models added from Generative - this slipped through in the networks PR. - add the `Ordering` class to `__init__.py` for easier import ### 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. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes #7356 ### Description Add relative positinoal embedding in attention block as described in https://arxiv.org/pdf/2112.01526.pdf Largely inspired by https://github.com/facebookresearch/segment-anything/blob/main/segment_anything/modeling/image_encoder.py Can be useful for #6357 ### 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). - [ ] 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`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: vgrau98 <victor.grau93@gmail.com> Signed-off-by: vgrau98 <35843843+vgrau98@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Part of #6676 . ### Description A few sentences describing the changes proposed in this pull request. ### 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. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Mark Graham <markgraham539@gmail.com> Signed-off-by: dongy <dongy@nvidia.com> Signed-off-by: KumoLiu <yunl@nvidia.com> Signed-off-by: myron <amyronenko@nvidia.com> Signed-off-by: kaibo <ktang@unc.edu> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: elitap <elias.tappeiner@gmx.at> Signed-off-by: Felix Schnabel <f.schnabel@tum.de> Signed-off-by: YanxuanLiu <yanxuanl@nvidia.com> Signed-off-by: ytl0623 <david89062388@gmail.com> Signed-off-by: Dženan Zukić <dzenan.zukic@kitware.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Ishan Dutta <ishandutta0098@gmail.com> Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: Mark Graham <mark@Marks-MacBook-Pro.local> Signed-off-by: vgrau98 <victor.grau93@gmail.com> Signed-off-by: vgrau98 <35843843+vgrau98@users.noreply.github.com> Signed-off-by: heyufan1995 <heyufan1995@gmail.com> Signed-off-by: binliu <binliu@nvidia.com> Signed-off-by: axel.vlaminck <axel.vlaminck@gmail.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> Co-authored-by: Dong Yang <don.yang.mech@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: myron <myron@users.noreply.github.com> Co-authored-by: Kaibo Tang <99367900+kvttt@users.noreply.github.com> Co-authored-by: monai-bot <64792179+monai-bot@users.noreply.github.com> Co-authored-by: elitap <elitap@users.noreply.github.com> Co-authored-by: Felix Schnabel <f.schnabel@tum.de> Co-authored-by: YanxuanLiu <104543031+YanxuanLiu@users.noreply.github.com> Co-authored-by: ytl0623 <david89062388@gmail.com> Co-authored-by: Dženan Zukić <dzenan.zukic@kitware.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Ishan Dutta <ishandutta0098@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: KumoLiu <yunl@nvidia.com> Co-authored-by: Kaibo Tang <ktang@unc.edu> Co-authored-by: vgrau98 <35843843+vgrau98@users.noreply.github.com> Co-authored-by: Yufan He <59374597+heyufan1995@users.noreply.github.com> Co-authored-by: binliunls <107988372+binliunls@users.noreply.github.com> Co-authored-by: Ben Murray <ben.murray@gmail.com> Co-authored-by: axel.vlaminck <axel.vlaminck@gmail.com>
Part of the refactoring in #7227 ### Description Refactors autoencoderkl. Changes are: - Introduce `CastToTempType` class for upsampling - `Downsample` block removed and replaced by a `Sequential` - The attention block now uses MONAI's `SABlock`, allowing a lot of code to be removed - Added a `load_old_state_dict` that allows for models trained on MONAI Generative to be loaded in to this model, especially important given some of the MONAI Generative's [model zoo](https://github.com/Project-MONAI/GenerativeModels/tree/main/model-zoo) uses this model. I have tested this works locally. I discussed with @ericspod inheriting from `AutoEncoder` but after experimentation have decided against it as it introduced changes that made it very hard to ensure we could load model's trained in MONAI Generative. ### 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). - [ ] New tests added to cover the changes. - [x] 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. --------- Signed-off-by: KumoLiu <yunl@nvidia.com> Signed-off-by: kaibo <ktang@unc.edu> Signed-off-by: heyufan1995 <heyufan1995@gmail.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: binliu <binliu@nvidia.com> Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: axel.vlaminck <axel.vlaminck@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Ibrahim Hadzic <ibrahimhadzic45@gmail.com> Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Signed-off-by: Timothy Baker <bakertim@umich.edu> Signed-off-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Signed-off-by: Fabian Klopfer <fabian.klopfer@ieee.org> Signed-off-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Signed-off-by: Lucas Robinet <67736918+Lucas-rbnt@users.noreply.github.com> Signed-off-by: chaoliu <chaoliu@nvidia.com> Signed-off-by: cxlcl <chaoliucxl@gmail.com> Signed-off-by: chaoliu <chaoliucxl@gmail.com> Signed-off-by: Suraj Pai <b.pai@maastrichtuniversity.nl> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com> Signed-off-by: elitap <elias.tappeiner@gmx.at> Signed-off-by: Felix Schnabel <f.schnabel@tum.de> Signed-off-by: YanxuanLiu <yanxuanl@nvidia.com> Signed-off-by: ytl0623 <david89062388@gmail.com> Signed-off-by: Dženan Zukić <dzenan.zukic@kitware.com> Signed-off-by: Ishan Dutta <ishandutta0098@gmail.com> Signed-off-by: John Zielke <j.l.zielke@gmail.com> Signed-off-by: Mingxin Zheng <mingxinz@nvidia.com> Signed-off-by: Vladimir Chernyi <57420464+scalyvladimir@users.noreply.github.com> Signed-off-by: Yiheng Wang <vennw@nvidia.com> Signed-off-by: Szabolcs Botond Lorincz Molnar <szabolcs.lorincz@mvision.ai> Signed-off-by: Mark Graham <markgraham539@gmail.com> Signed-off-by: Lucas Robinet <luca.robinet@gmail.com> Signed-off-by: Mingxin <mingxinz@nvidia.com> Signed-off-by: Han Wang <freddie.wanah@gmail.com> Signed-off-by: Konstantin Sukharev <k.sukharev@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Kaibo Tang <ktang@unc.edu> Co-authored-by: Yufan He <59374597+heyufan1995@users.noreply.github.com> Co-authored-by: binliunls <107988372+binliunls@users.noreply.github.com> Co-authored-by: Ben Murray <ben.murray@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: axel.vlaminck <axel.vlaminck@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: monai-bot <64792179+monai-bot@users.noreply.github.com> Co-authored-by: Ibrahim Hadzic <ibrahimhadzic45@gmail.com> Co-authored-by: Dr. Behrooz Hashemian <3968947+drbeh@users.noreply.github.com> Co-authored-by: Timothy J. Baker <62781117+tim-the-baker@users.noreply.github.com> Co-authored-by: Mathijs de Boer <8137653+MathijsdeBoer@users.noreply.github.com> Co-authored-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Co-authored-by: Fabian Klopfer <fabian.klopfer@ieee.org> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Lucas Robinet <67736918+Lucas-rbnt@users.noreply.github.com> Co-authored-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Co-authored-by: cxlcl <chaoliucxl@gmail.com> Co-authored-by: Suraj Pai <b.pai@maastrichtuniversity.nl> Co-authored-by: Juampa <1523654+juampatronics@users.noreply.github.com> Co-authored-by: elitap <elitap@users.noreply.github.com> Co-authored-by: Felix Schnabel <f.schnabel@tum.de> Co-authored-by: YanxuanLiu <104543031+YanxuanLiu@users.noreply.github.com> Co-authored-by: ytl0623 <david89062388@gmail.com> Co-authored-by: Dženan Zukić <dzenan.zukic@kitware.com> Co-authored-by: Ishan Dutta <ishandutta0098@gmail.com> Co-authored-by: johnzielke <j.l.zielke@gmail.com> Co-authored-by: Vladimir Chernyi <57420464+scalyvladimir@users.noreply.github.com> Co-authored-by: Lőrincz-Molnár Szabolcs-Botond <lorincz_szabolcs@yahoo.com> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: Lucas Robinet <luca.robinet@gmail.com> Co-authored-by: Han Wang <freddie.wanah@gmail.com> Co-authored-by: Konstantin Sukharev <50718389+k-sukharev@users.noreply.github.com>
Part of #7227 . ### Description A few sentences describing the changes proposed in this pull request. ### 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). - [ ] 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. --------- Signed-off-by: KumoLiu <yunl@nvidia.com> Signed-off-by: kaibo <ktang@unc.edu> Signed-off-by: heyufan1995 <heyufan1995@gmail.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: binliu <binliu@nvidia.com> Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: axel.vlaminck <axel.vlaminck@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Ibrahim Hadzic <ibrahimhadzic45@gmail.com> Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Signed-off-by: Timothy Baker <bakertim@umich.edu> Signed-off-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Signed-off-by: Fabian Klopfer <fabian.klopfer@ieee.org> Signed-off-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Signed-off-by: Lucas Robinet <67736918+Lucas-rbnt@users.noreply.github.com> Signed-off-by: chaoliu <chaoliu@nvidia.com> Signed-off-by: cxlcl <chaoliucxl@gmail.com> Signed-off-by: chaoliu <chaoliucxl@gmail.com> Signed-off-by: Suraj Pai <b.pai@maastrichtuniversity.nl> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com> Signed-off-by: elitap <elias.tappeiner@gmx.at> Signed-off-by: Felix Schnabel <f.schnabel@tum.de> Signed-off-by: YanxuanLiu <yanxuanl@nvidia.com> Signed-off-by: ytl0623 <david89062388@gmail.com> Signed-off-by: Dženan Zukić <dzenan.zukic@kitware.com> Signed-off-by: Ishan Dutta <ishandutta0098@gmail.com> Signed-off-by: John Zielke <j.l.zielke@gmail.com> Signed-off-by: Mingxin Zheng <mingxinz@nvidia.com> Signed-off-by: Vladimir Chernyi <57420464+scalyvladimir@users.noreply.github.com> Signed-off-by: Yiheng Wang <vennw@nvidia.com> Signed-off-by: Szabolcs Botond Lorincz Molnar <szabolcs.lorincz@mvision.ai> Signed-off-by: Lucas Robinet <luca.robinet@gmail.com> Signed-off-by: Mingxin <mingxinz@nvidia.com> Signed-off-by: Han Wang <freddie.wanah@gmail.com> Signed-off-by: Konstantin Sukharev <k.sukharev@gmail.com> Signed-off-by: Ben Murray <ben.murray@gmail.com> Signed-off-by: Matthew Vine <32849887+MattTheCuber@users.noreply.github.com> Signed-off-by: Mark Graham <markgraham539@gmail.com> Signed-off-by: Peter Kaplinsky <peterkaplinsky@gmail.com> Signed-off-by: Simon Jensen <61684806+simojens@users.noreply.github.com> Signed-off-by: NabJa <nabil.jabareen@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Kaibo Tang <ktang@unc.edu> Co-authored-by: Yufan He <59374597+heyufan1995@users.noreply.github.com> Co-authored-by: binliunls <107988372+binliunls@users.noreply.github.com> Co-authored-by: Ben Murray <ben.murray@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: axel.vlaminck <axel.vlaminck@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: monai-bot <64792179+monai-bot@users.noreply.github.com> Co-authored-by: Ibrahim Hadzic <ibrahimhadzic45@gmail.com> Co-authored-by: Dr. Behrooz Hashemian <3968947+drbeh@users.noreply.github.com> Co-authored-by: Timothy J. Baker <62781117+tim-the-baker@users.noreply.github.com> Co-authored-by: Mathijs de Boer <8137653+MathijsdeBoer@users.noreply.github.com> Co-authored-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Co-authored-by: Fabian Klopfer <fabian.klopfer@ieee.org> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Lucas Robinet <67736918+Lucas-rbnt@users.noreply.github.com> Co-authored-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Co-authored-by: cxlcl <chaoliucxl@gmail.com> Co-authored-by: Suraj Pai <b.pai@maastrichtuniversity.nl> Co-authored-by: Juampa <1523654+juampatronics@users.noreply.github.com> Co-authored-by: elitap <elitap@users.noreply.github.com> Co-authored-by: Felix Schnabel <f.schnabel@tum.de> Co-authored-by: YanxuanLiu <104543031+YanxuanLiu@users.noreply.github.com> Co-authored-by: ytl0623 <david89062388@gmail.com> Co-authored-by: Dženan Zukić <dzenan.zukic@kitware.com> Co-authored-by: Ishan Dutta <ishandutta0098@gmail.com> Co-authored-by: johnzielke <j.l.zielke@gmail.com> Co-authored-by: Vladimir Chernyi <57420464+scalyvladimir@users.noreply.github.com> Co-authored-by: Lőrincz-Molnár Szabolcs-Botond <lorincz_szabolcs@yahoo.com> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: Lucas Robinet <luca.robinet@gmail.com> Co-authored-by: Han Wang <freddie.wanah@gmail.com> Co-authored-by: Konstantin Sukharev <50718389+k-sukharev@users.noreply.github.com> Co-authored-by: Matthew Vine <32849887+MattTheCuber@users.noreply.github.com> Co-authored-by: Pkaps25 <43655728+Pkaps25@users.noreply.github.com> Co-authored-by: Peter Kaplinsky <peterkaplinsky@gmail.com> Co-authored-by: Simon Jensen <61684806+simojens@users.noreply.github.com> Co-authored-by: NabJa <32510324+NabJa@users.noreply.github.com>
Part of #7227 . ### Description A few sentences describing the changes proposed in this pull request. ### 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). - [ ] 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. Signed-off-by: Mark Graham <markgraham539@gmail.com>
Towards #7227 . ### Description There were lots of contigous calls in the DiffusionModelUnet. It turns out these are necessary after attention blocks, as the einops operation sometimes leads to non-contigous tensors that can cause errors. I've tidied the code up so the .contiguous calls are only after attention calls. A few sentences describing the changes proposed in this pull request. ### 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). - [ ] 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. --------- Signed-off-by: Mark Graham <markgraham539@gmail.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Part of #7227 . ### Description Tidies up some of controlnet A few sentences describing the changes proposed in this pull request. ### 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). - [ ] 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. --------- Signed-off-by: Mark Graham <markgraham539@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
…tion (#7775) - spade_network, and SPADENet (VAE-GAN) - test_spade_vaegan (to test previously mentioned model) Modification of: - spade_diffusion_model_unet.py to change namings. - SPADE normalisation layer, to use get_norm_layer function instead of defining such layers directly. Fixes # . ### Description A few sentences describing the changes proposed in this pull request. ### 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. - [] 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. --------- Signed-off-by: Mark Graham <markgraham539@gmail.com> Signed-off-by: virginiafdez <virginia.fernandez@kcl.ac.uk> Co-authored-by: virginiafdez <virginia.fernandez@kcl.ac.uk> Co-authored-by: Mark Graham <markgraham539@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes # . ### Description Fixes a bug in the inferer and adds clipping parameters to the DDIM/DDPM schedulers. ### 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). - [ ] 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. --------- Signed-off-by: virginiafdez <virginia.fernandez@kcl.ac.uk> Co-authored-by: virginiafdez <virginia.fernandez@kcl.ac.uk>
### Description This merges `dev` into `gen-ai-dev` and modifies/fixes some places in code to remove undeclared variable errors raised by pylint. This should all be non-breaking and not changing anything functional in this branch. When completed, the branch should be ready for merging into `dev`. This also resolves various conflicts which need to be checked for correctness. ### 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). - [ ] 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. --------- Signed-off-by: KumoLiu <yunl@nvidia.com> Signed-off-by: kaibo <ktang@unc.edu> Signed-off-by: heyufan1995 <heyufan1995@gmail.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: binliu <binliu@nvidia.com> Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: axel.vlaminck <axel.vlaminck@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Ibrahim Hadzic <ibrahimhadzic45@gmail.com> Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Signed-off-by: Timothy Baker <bakertim@umich.edu> Signed-off-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Signed-off-by: Fabian Klopfer <fabian.klopfer@ieee.org> Signed-off-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Signed-off-by: Lucas Robinet <67736918+Lucas-rbnt@users.noreply.github.com> Signed-off-by: chaoliu <chaoliu@nvidia.com> Signed-off-by: cxlcl <chaoliucxl@gmail.com> Signed-off-by: chaoliu <chaoliucxl@gmail.com> Signed-off-by: Suraj Pai <b.pai@maastrichtuniversity.nl> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com> Signed-off-by: elitap <elias.tappeiner@gmx.at> Signed-off-by: Felix Schnabel <f.schnabel@tum.de> Signed-off-by: YanxuanLiu <yanxuanl@nvidia.com> Signed-off-by: ytl0623 <david89062388@gmail.com> Signed-off-by: Dženan Zukić <dzenan.zukic@kitware.com> Signed-off-by: Ishan Dutta <ishandutta0098@gmail.com> Signed-off-by: John Zielke <j.l.zielke@gmail.com> Signed-off-by: Mingxin Zheng <mingxinz@nvidia.com> Signed-off-by: Vladimir Chernyi <57420464+scalyvladimir@users.noreply.github.com> Signed-off-by: Yiheng Wang <vennw@nvidia.com> Signed-off-by: Szabolcs Botond Lorincz Molnar <szabolcs.lorincz@mvision.ai> Signed-off-by: Lucas Robinet <luca.robinet@gmail.com> Signed-off-by: Mingxin <mingxinz@nvidia.com> Signed-off-by: Han Wang <freddie.wanah@gmail.com> Signed-off-by: Konstantin Sukharev <k.sukharev@gmail.com> Signed-off-by: Ben Murray <ben.murray@gmail.com> Signed-off-by: Matthew Vine <32849887+MattTheCuber@users.noreply.github.com> Signed-off-by: Peter Kaplinsky <peterkaplinsky@gmail.com> Signed-off-by: Simon Jensen <61684806+simojens@users.noreply.github.com> Signed-off-by: NabJa <nabil.jabareen@gmail.com> Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Kaibo Tang <ktang@unc.edu> Co-authored-by: Yufan He <59374597+heyufan1995@users.noreply.github.com> Co-authored-by: binliunls <107988372+binliunls@users.noreply.github.com> Co-authored-by: Ben Murray <ben.murray@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: axel.vlaminck <axel.vlaminck@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: monai-bot <64792179+monai-bot@users.noreply.github.com> Co-authored-by: Ibrahim Hadzic <ibrahimhadzic45@gmail.com> Co-authored-by: Dr. Behrooz Hashemian <3968947+drbeh@users.noreply.github.com> Co-authored-by: Timothy J. Baker <62781117+tim-the-baker@users.noreply.github.com> Co-authored-by: Mathijs de Boer <8137653+MathijsdeBoer@users.noreply.github.com> Co-authored-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Co-authored-by: Fabian Klopfer <fabian.klopfer@ieee.org> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Lucas Robinet <67736918+Lucas-rbnt@users.noreply.github.com> Co-authored-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Co-authored-by: cxlcl <chaoliucxl@gmail.com> Co-authored-by: Suraj Pai <b.pai@maastrichtuniversity.nl> Co-authored-by: Juampa <1523654+juampatronics@users.noreply.github.com> Co-authored-by: elitap <elitap@users.noreply.github.com> Co-authored-by: Felix Schnabel <f.schnabel@tum.de> Co-authored-by: YanxuanLiu <104543031+YanxuanLiu@users.noreply.github.com> Co-authored-by: ytl0623 <david89062388@gmail.com> Co-authored-by: Dženan Zukić <dzenan.zukic@kitware.com> Co-authored-by: Ishan Dutta <ishandutta0098@gmail.com> Co-authored-by: johnzielke <j.l.zielke@gmail.com> Co-authored-by: Vladimir Chernyi <57420464+scalyvladimir@users.noreply.github.com> Co-authored-by: Lőrincz-Molnár Szabolcs-Botond <lorincz_szabolcs@yahoo.com> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: Lucas Robinet <luca.robinet@gmail.com> Co-authored-by: Han Wang <freddie.wanah@gmail.com> Co-authored-by: Konstantin Sukharev <50718389+k-sukharev@users.noreply.github.com> Co-authored-by: Matthew Vine <32849887+MattTheCuber@users.noreply.github.com> Co-authored-by: Pkaps25 <43655728+Pkaps25@users.noreply.github.com> Co-authored-by: Peter Kaplinsky <peterkaplinsky@gmail.com> Co-authored-by: Simon Jensen <61684806+simojens@users.noreply.github.com> Co-authored-by: NabJa <32510324+NabJa@users.noreply.github.com> Co-authored-by: Yu <146002968+Yu0610@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
…ply.github.com> I, Eric Kerfoot <17726042+ericspod@users.noreply.github.com>, hereby add my Signed-off-by to this commit: 15ff663 Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
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I've set DCO to pass again. My email should be configured correctly now. I attempted the remediation commit but that added a second remediation entry for myself instead. The given instructions are perhaps incorrect? |
ericspod
commented
Jul 18, 2024
ericspod
commented
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ericspod
commented
Jul 18, 2024
ericspod
commented
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ericspod
commented
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ericspod
commented
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ericspod
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ericspod
requested review from
KumoLiu,
aylward,
Warvito,
marksgraham and
Nic-Ma
|
Hi @KumoLiu I have gone through the PR with @virginiafdez and we're happy with it and all tests pass. A number of changes I did were to do with mypy code checking. The issue is that variables need to always exist in every code path, in many places variables are only assigned in one or another |
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/build |
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Hi @ericspod @virginiafdez, remaining issue in the blossom ci. |
This should just be a matter of changing the alias |
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/build |
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/build |
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@KumoLiu I think we're good now if you wanted to review anything I've commented on above. |
KumoLiu
approved these changes
Jul 19, 2024
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May need @virginiafdez approve to merge the PR. |
virginiafdez
approved these changes
Jul 19, 2024
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Done! I didn't add any comment because I checked this with Eric yesterday.
…________________________________
From: YunLiu ***@***.***>
Sent: 19 July 2024 16:31
To: Project-MONAI/MONAI ***@***.***>
Cc: Virginia Fernandez ***@***.***>; Mention ***@***.***>
Subject: Re: [Project-MONAI/MONAI] Merge genaidev Into Dev (PR #7886)
May need @virginiafdez<https://github.com/virginiafdez> approve to merge the PR.
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Reply to this email directly, view it on GitHub<#7886 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AOVQGV3UHPTQ4QTHYMDGTMDZNEWLXAVCNFSM6AAAAABKB6GR4GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZZGQ3DMNRRHE>.
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Fixes #6676 .
Description
This merges the Generative Models code into dev. Everything has been checked by the generative team, tests all pass, and the changes that have been done recently are integrated. This is ready to merge.
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.