From 63fb8688b049a7e0260a8e0994d912d8b5a1ca9a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fernando=20P=C3=A9rez-Garc=C3=ADa?= Date: Mon, 14 Mar 2022 16:50:29 +0000 Subject: [PATCH] Update TorchIO version (#677) * Update TorchIO version Resolves #672. --- CHANGELOG.md | 8 ++++++-- environment.yml | 2 +- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 81f258b65..91350ede7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,8 @@ created. ## Upcoming ### Added --([#671](https://github.com/microsoft/InnerEye-DeepLearning/pull/671)) Remove sequence models and unused variables. Simplify README. + +- ([#671](https://github.com/microsoft/InnerEye-DeepLearning/pull/671)) Remove sequence models and unused variables. Simplify README. - ([#678](https://github.com/microsoft/InnerEye-DeepLearning/pull/678)) Add function to get log level name and use it for logging. - ([#666](https://github.com/microsoft/InnerEye-DeepLearning/pull/666)) Replace RadIO with TorchIO for patch-based inference. - ([#643](https://github.com/microsoft/InnerEye-DeepLearning/pull/643)) Test for recovery of SSL job. Tracks learning rate and train @@ -35,7 +36,7 @@ jobs that run in AzureML. - ([#554](https://github.com/microsoft/InnerEye-DeepLearning/pull/554)) Added a parameter `pretraining_dataset_id` to `NIH_COVID_BYOL` to specify the name of the SSL training dataset. - ([#560](https://github.com/microsoft/InnerEye-DeepLearning/pull/560)) Added pre-commit hooks. --([#619](https://github.com/microsoft/InnerEye-DeepLearning/pull/619)) Add DeepMIL PANDA +- ([#619](https://github.com/microsoft/InnerEye-DeepLearning/pull/619)) Add DeepMIL PANDA - ([#559](https://github.com/microsoft/InnerEye-DeepLearning/pull/559)) Adding the accompanying code for the ["Active label cleaning: Improving dataset quality under resource constraints"](https://arxiv.org/abs/2109.00574) paper. The code can be found in the [InnerEye-DataQuality](InnerEye-DataQuality/README.md) subfolder. It provides tools for training noise robust models, running label cleaning simulation and loading our label cleaning benchmark datasets. - ([#589](https://github.com/microsoft/InnerEye-DeepLearning/pull/589)) Add `LightningContainer.update_azure_config()` hook to enable overriding `AzureConfig` parameters from a container (e.g. `experiment_name`, `cluster`, `num_nodes`). @@ -55,6 +56,9 @@ jobs that run in AzureML. - ([#679](https://github.com/microsoft/InnerEye-DeepLearning/pull/679)) Add FP and TN slides/tiles to DeepMIL outputs and extend outputs to multi-class problems. ### Changed + +- ([#677](https://github.com/microsoft/InnerEye-DeepLearning/pull/677)) Update TorchIO version to include the recent bug fix related to patch-based inference. +- ([#666](https://github.com/microsoft/InnerEye-DeepLearning/pull/666)) Replace RadIO with TorchIO for patch-based inference. - ([#659](https://github.com/microsoft/InnerEye-DeepLearning/pull/659)) Update cudatoolkit version from 11.1 to 11.3. - ([#588](https://github.com/microsoft/InnerEye-DeepLearning/pull/588)) Replace SciPy with PIL.PngImagePlugin.PngImageFile to load png files. - ([#585](https://github.com/microsoft/InnerEye-DeepLearning/pull/585)) Switching to PyTorch 1.10.0 and torchvision 0.11.1 diff --git a/environment.yml b/environment.yml index 46f127b08..d4b80ff2a 100644 --- a/environment.yml +++ b/environment.yml @@ -69,7 +69,7 @@ dependencies: - tabulate==0.8.7 - tensorboard==2.3.0 - tensorboardX==2.1 - - torchio==0.18.73 + - torchio==0.18.74 - torchmetrics==0.6.0 - umap-learn==0.5.2 - yacs==0.1.8