* Fix shell lexer name
* Update CHANGELOG
* Fix CHANGELOG
* Fix "html_static_path entry '_static' does not exist"
* Clean up preprocess script
* Fix link to InnerEye-DataQuality
* Use shutil.copy to copy files
* Remove extra info from CHANGELOG
* Fix broken link to LICENSE
* Fix lexer name for YAML
* Remove colons from headers
* Fix InnerEye module not being found
This PR contains some changes needed to make the SSLContainer compatible with new datasets and allow a user to run by simply creating a new augmentation config or defining a child class
* _get_transforms has been changed to accept new datasets without the need to touch the class
* get_cxr_ssl_transform has been changed to avoid the hidden channel expansion and make that optional. It has been also renamed to get_ssl_transform because it has nothing specific to cxr
* drop_last is now set as parameter of the InnerEyeVisionDataModule and the SSLContainer - that means it can be changed when initializing a new SSLContainer
* documentation about bringing your own SSL model has been updated
* Some additions and fix to the docs describing how to setup the environment. The new version should be a little more clear.
* A small change in the logging info when submitting azureml - the workspace name is now reporte
* Fixing unit test
My approach was wrong, since it only tested the first time the mocked function was called.
I've swapped to Anton's suggestion by adding return values so that the mock can be called
multiple times in a test execution.
* Missing documentation
Inference should become more flexible to work also on datasets where we do not have segmentations yet, or only some of the structures segmented. This will prove especially useful for partners like UCLH. Done by adding `allow_incomplete_labels` to the relevant methods.
Allows cross validation with 'bring your own' Lightning models (without ensemble building).
Moved the code dealing with hyperdrive config retrieval from ModelConfigBase into it's base class WorkflowParams
so that it is available (and implemented) in LightningContainer
Removed the exception thrown in runner when trying to use cross validation with LightningContainer.
Added cross validation to HelloContainer (and especially its HelloDataModule) as exemplar code, and documentation to point to this change.
Three new unit tests:
1) That cross validation is handled correctly for LightningContainer in runner
2) That LightningContainer converts ScriptRunConfig into HyperDriveConfig
3) The cross validation functionality in HelloDataModule
- The regresssion test code in #492 missed out files in AzureML, because the wrong function was called in the main workflow.
- Cleaner folder structure for regression test results
Jobs got stuck if they used PyTorch Lightning built-in metrics objects, which were then trying to synchronize across GPUs. Resolved by shutting down torch.distributed
Add test that a boolean command line parameter is one of: 'on', 't', 'true', 'y', 'yes', '1' (for true) or 'off', 'f', 'false', 'n', 'no', '0' (for false) after lower()
If a flag default is False, then allow --flag to set it to True (so the ==True is unnecessary)
If a flag default is True, then allow --no-flag to set it to False (so the ==False is unnecessary)
The current documentation uses the submodule setup at many places. However, we found that it can easily mislead users. Switching to suggesting plain forking.
* Refractor augmentations initial commit
* Test custom transforms and transform pipeline
* Make transforms independent of config
* Add placeholder to doc as reminder
* Update tests
* Update tests
* Add test for affine
* Add tests for color transform
* Add a todo list
* Adding new test and simplifying the transforms API further
* New tests for new custom transforms
* Remove deprecated file
* Update all transforms
* Add test for custom pipeline transform
* Fix the full pipeline test
* Rename
* SImplify feeding in transforms
* Updating CHANGELOG.md
* Updating CHANGELOG.md
* Flake8
* Simplify more
* Fixes
* Fixes
* Flake8
* Fix few things
* Fix few things
* Updating tests for new API
* Simplify image versus sample
* Update
* Update
* Update
* Update
* Error in test copy paste
* Style
* Add augmentation doc
* Add augmentation doc
* Doc strings
* Flake8
* Flake8
* Mypy
* Fix test and docstring
* Put back skipif windows
* flake8
* mypy
* Skip if OOM
* Skip if OOM
* Import was missing
* Separate transform pipeline from ScalarItem management.
* Update documentation to new API
* Accidental commit
* PR suggestion
* Make test for elastic human checkable
* Make test for elastic human checkable
* Update with p=0
* Update with p=0
* Add human readable test output for gamma transform
* Solve OOM, remove duplicate test input definitions
* Flake8
* Mypy
* Fix config
* Add check PR comment
* PR comment
Add necessary tooling and examples for running fastMRI reconstruction models.
- Script to create and run an Azure Data Factory to download the raw data, and place them into a storage account
- Detailed examples to run the VarNet model from the fastMRI github repo
- Ability to work with fixed mounting points for datasets
- This PR adds support for multilabel classification models. Multiclass models (where labels are mutually exclusive) are not supported. Changes made:
- `dataset.csv` can include multiple labels per sample
- Loss functions changed to support multilabel classification tasks
- Extra report for multilabel classification tasks
- Add support for png images
Co-authored-by: Shruthi42 <13177030+Shruthi42@users.noreply.github.com>
Co-authored-by: melanibe <32590828+melanibe@users.noreply.github.com>
Co-authored-by: Anton Schwaighofer <antonsc@microsoft.com>
* Renamed HeadAndNeckBase to HeadAndNeckPaper, and ProstateBase to ProstatePaper;
* Added new extensions of SegmentationModelBases HeadAndNeckBase and ProstateBase;
* Delete unused ProstatePaperBase.py;
* Added validation for SliceExclusionRule and SummedProbabilityRule.
* test
* fix test
* download fix
* create separate model folder
* fixing tests
* making HD check better
* Tests
* inverted logic
* registering on parent run
* docu
Peter Hessey
Anton Schwaighofer
Fernando Pérez-García
Javier
maxilse
Jonathan Tripp
vale-salvatelli
Shruthi42
Tim Regan
Alberto Santamaria-Pang
melanibe
Steve Haigh
Clemens Siebler
Ivan Tarapov