Fernando Pérez-García
Fernando Pérez-García
This will avoid e.g. https://github.com/microsoft/InnerEye-DeepLearning/pull/769#issuecomment-1193686392.
From https://github.com/readthedocs/recommonmark: > **Warning:** recommonmark is now deprecated. We recommend using [MyST](https://github.com/executablebooks/MyST-Parser) for a docutils bridge going forward. See [this issue](https://github.com/readthedocs/recommonmark/issues/221) for background and discussion. [AB#5336](https://innereye.visualstudio.com/60ce1777-00d6-4015-82bc-488a0c00202f/_workitems/edit/5336)
Assuming #660 has been fixed: ```shell $ make html python preprocess.py Running Sphinx v3.1.1 making output directory... done WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0...
The run ID [`refs_pull_633_merge_1642019743_f212b068`](https://ml.azure.com/runs/refs_pull_633_merge_1642019743_f212b068?wsid=/subscriptions/a85ceddd-892e-4637-ae4b-67d15ddf5f2b/resourceGroups/innereye-deeplearning/providers/Microsoft.MachineLearningServices/workspaces/InnerEye-DeepLearning&tid=72f988bf-86f1-41af-91ab-2d7cd011db47) failed. This causes multiple tests to fail, e.g., https://github.com/microsoft/InnerEye-DeepLearning/blob/1600ef3ddfa83328ec35d179533c3a4e95f88a69/Tests/AfterTraining/test_after_training.py#L147-L150 This test is skipped in CI, therefore this is missed: https://github.com/microsoft/InnerEye-DeepLearning/blob/1600ef3ddfa83328ec35d179533c3a4e95f88a69/Tests/AfterTraining/test_after_training.py#L143-L147 If the run ID is replaced...
If the patch size is larger than the image size during inference with TorchIO, an error is raised. This implies that this situation wasn't being covered by the tests. To...
There are some quantitative differences in inference depending on whether RadIO or TorchIO are used: - https://github.com/microsoft/InnerEye-DeepLearning/pull/666#issuecomment-1048104234 I suspect that the little differences might happen because overlapping patches are cropped...
[pytorch-lightning < 1.5.8 is vulnerable to Deserialization of Untrusted Data](https://github.com/advisories/GHSA-2vj5-px25-gjrp). We are using 1.5.5: https://github.com/microsoft/InnerEye-DeepLearning/blob/914a89383d3275cb3304bde9c6cdd6050357f3f7/environment.yml#L57 Should we use a newer version? [AB#4978](https://innereye.visualstudio.com/60ce1777-00d6-4015-82bc-488a0c00202f/_workitems/edit/4978)
Stubs for `tqdm` are now available: https://github.com/tqdm/tqdm/issues/260#issuecomment-1176245901
**🚀 Feature** Add support to transform images in GPU devices. **Motivation** Some transforms would benefit a lot from hardware acceleration. I suspect the two main sources of improvement would be...
As in https://github.com/NifTK/NiftyNet/commit/a91644b881192fb68e7faabc2065129f09d5bdd5#diff-5b79901b7b2f56394aca30c562e9e186