From 5ea7dce4abda33872f547babb9a367bfa12eb4c7 Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Fri, 20 Dec 2024 16:59:16 +0800 Subject: [PATCH 1/3] Increase duration in nsys profile (#1906) Fixes #1905 Increase the profiling duration in nsys, as the KeyError seems to occur because the profile did not have sufficient time to reach the post-processing step. ### 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 ` Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .../tumor_detection/ignite/profiling_camelyon_pipeline.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pathology/tumor_detection/ignite/profiling_camelyon_pipeline.ipynb b/pathology/tumor_detection/ignite/profiling_camelyon_pipeline.ipynb index 33b826838..25ec13eb8 100644 --- a/pathology/tumor_detection/ignite/profiling_camelyon_pipeline.ipynb +++ b/pathology/tumor_detection/ignite/profiling_camelyon_pipeline.ipynb @@ -159,7 +159,7 @@ "!nsys profile \\\n", " --trace nvtx,osrt,cudnn,cuda, \\\n", " --delay 5 \\\n", - " --duration 10 \\\n", + " --duration 20 \\\n", " --show-output true \\\n", " --force-overwrite true \\\n", " --output profile_report.nsys-rep \\\n", From 48e59500df4b3a7ec5a705a417d5d9dc53940e4f Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 7 Jan 2025 11:02:30 +0800 Subject: [PATCH 2/3] [pre-commit.ci] pre-commit suggestions (#1917) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.6.0...v5.0.0) - [github.com/psf/black: 24.4.2 → 24.10.0](https://github.com/psf/black/compare/24.4.2...24.10.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a6f73e321..17555c58d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,7 +9,7 @@ ci: repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + rev: v5.0.0 hooks: - id: end-of-file-fixer - id: trailing-whitespace @@ -23,7 +23,7 @@ repos: - id: detect-private-key - repo: https://github.com/psf/black - rev: "24.4.2" + rev: "24.10.0" hooks: - id: black - id: black-jupyter From 476d2fce5ba4cac1de3046cc9701159d5bd61795 Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Tue, 7 Jan 2025 12:59:39 +0800 Subject: [PATCH 3/3] Fix broken link for 2d GAN (#1916) Fix broken link for 2d GAN ### 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 ` Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> --- generation/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/generation/README.md b/generation/README.md index df50ed899..6c4fe96aa 100644 --- a/generation/README.md +++ b/generation/README.md @@ -43,7 +43,7 @@ Example shows the use cases of using MONAI to evaluate the performance of a gene ## [Training a 2D VQ-VAE + Autoregressive Transformers](./2d_vqvae_transformer/2d_vqvae_transformer_tutorial.ipynb): Example shows how to train a Vector-Quantized Variation Autoencoder + Transformers on the MedNIST dataset. -## Training VQ-VAEs and VQ-GANs: [2D VAE](./2d_vqvae/2d_vqvae_tutorial.ipynb), [3D VAE](./3d_vqvae/3d_vqvae_tutorial.ipynb) and [2D GAN](./3d_autoencoderkl/2d_vqgan_tutorial.ipynb) +## Training VQ-VAEs and VQ-GANs: [2D VAE](./2d_vqvae/2d_vqvae_tutorial.ipynb), [3D VAE](./3d_vqvae/3d_vqvae_tutorial.ipynb) and [2D GAN](./2d_vqgan/2d_vqgan_tutorial.ipynb) Examples show how to train Vector Quantized Variation Autoencoder on [2D](./2d_vqvae/2d_vqvae_tutorial.ipynb) and [3D](./3d_vqvae/3d_vqvae_tutorial.ipynb), and how to use the PatchDiscriminator class to train a [VQ-GAN](./2d_vqgan/2d_vqgan_tutorial.ipynb) and improve the quality of the generated images. ## [Training a 2D Denoising Diffusion Probabilistic Model](./2d_ddpm/2d_ddpm_tutorial.ipynb):