Hi-ml

Added

- ([227](https://github.com/microsoft/hi-ml/pull/227)) Add TransformerPooling.
- ([179](https://github.com/microsoft/hi-ml/pull/179)) Add GaussianBlur and RotationByMultiplesOf90 augmentations. Added torchvision and opencv to
the environment file since it is necessary for the augmentations.
- ([193](https://github.com/microsoft/hi-ml/pull/193)) Add transformation adaptor to hi-ml-histopathology.
- ([178](https://github.com/microsoft/hi-ml/pull/178)) Add runner script for running ML experiments.
- ([181](https://github.com/microsoft/hi-ml/pull/181)) Add computational pathology tools in hi-ml-histopathology folder.
- ([187](https://github.com/microsoft/hi-ml/pull/187)) Add mean pooling layer for MIL.
- ([186](https://github.com/microsoft/hi-ml/pull/186)) Add inference to hi-ml runner.
- ([198](https://github.com/microsoft/hi-ml/pull/198)) Add cross-validation to hi-ml runner.
- ([198](https://github.com/microsoft/hi-ml/pull/198)) Improved editor setup for VSCode.

Changed

- ([227](https://github.com/microsoft/hi-ml/pull/227)) Pooling constructor is outside of DeepMIL and inside of BaseMIL now.
- ([198](https://github.com/microsoft/hi-ml/pull/198)) Model config loader is now more flexible, can accept fully qualified class name or just top-level module name and class (like histopathology.DeepSMILECrck)
- ([198](https://github.com/microsoft/hi-ml/pull/198)) Runner raises an error when Conda environment file contains a pip include (-r) statement

- ([196](https://github.com/microsoft/hi-ml/pull/196)) Show current workspace name in error message.

Fixed
- ([267]https://github.com/microsoft/hi-ml/pull/267)) Correct PYTHONPATH for Windows in VS Code settings
- ([266]https://github.com/microsoft/hi-ml/pull/266)) Pin jinja2 package to avoid 'No attribute Markup' bug in version 3.1.0
- ([246](https://github.com/microsoft/hi-ml/pull/246)) Added tolerance to `test_attentionlayers.py`.
- ([198](https://github.com/microsoft/hi-ml/pull/198)) Dependencies for histopathology folder are no longer specified in `test_requirements.txt`, but correctly in the histopathology Conda environment.
- ([188](https://github.com/microsoft/hi-ml/pull/188)) Updated DeepSMILES models. Now they are uptodate with innereye-dl.
- ([179](https://github.com/microsoft/hi-ml/pull/179)) HEDJitter was jittering the D channel as well. StainNormalization was relying on skimage.
- ([195](https://github.com/microsoft/hi-ml/pull/195)) Fix DeepMIL metrics bug whereby hard labels were used instead of probabilities.


Removed

Deprecated

Added

- ([170](https://github.com/microsoft/hi-ml/pull/170)) Add utils including bag sampling, bounding boxes, HEDJitter, StainNormalisation and add attention layers

Changed

- ([173](https://github.com/microsoft/hi-ml/pull/173)) Improve report tool: allow lists of tables, option for zipping report folder, option for base64 encoding images

Fixed

- ([169](https://github.com/microsoft/hi-ml/pull/169)) Fix a test that was failing occasionally

Removed

Deprecated

Added

- ([159](https://github.com/microsoft/hi-ml/pull/159)) Add profiling for loading png image files as numpy arrays.
- ([152](https://github.com/microsoft/hi-ml/pull/152)) Add a custom HTML reporting tool
- ([167](https://github.com/microsoft/hi-ml/pull/167)) Ability to log to an AzureML run when outside of AzureML

Changed

- ([164](https://github.com/microsoft/hi-ml/pull/164)) Look in more locations for std out from AzureML run.
- ([167](https://github.com/microsoft/hi-ml/pull/167)) The AzureMLLogger has one mandatory argument now, that controls
whether it should log to AzureML also when running on a VM.

Fixed

- ([161](https://github.com/microsoft/hi-ml/pull/161)) Empty string as target folder for a dataset creates an invalid mounting path for the dataset in AzureML (fixes #160)
- ([167](https://github.com/microsoft/hi-ml/pull/167)) Fix bugs in logging hyperparameters: logging as name/value
table, rather than one column per hyperparameter. Use string logging for all hyperparameters
- ([174](https://github.com/microsoft/hi-ml/pull/174)) Fix bugs in returned local_checkpoint_path when downloading checkpoints from AML run

Removed

Deprecated

Added

- ([145](https://github.com/microsoft/hi-ml/pull/145)) Add ability to mount datasets when running locally.
- ([149](https://github.com/microsoft/hi-ml/pull/149)) Add a k-fold cross validation wrapper around HyperDrive
- ([132](https://github.com/microsoft/hi-ml/pull/132)) Profile methods for loading png image files.

Changed

Fixed

- ([156](https://github.com/microsoft/hi-ml/pull/156) AzureML Runs should use registered environment after retrieval)

Removed

Deprecated

Added

- ([142](https://github.com/microsoft/hi-ml/pull/142)) Adding AzureML progress bar and diagnostics for batch loading
- ([138](https://github.com/microsoft/hi-ml/pull/138)) Guidelines and profiling for whole slide images.

Changed

- ([129])<https://github.com/microsoft/hi-ml/pull/129>)) Refactor command line tools' arguments. Refactor health_azure.utils' various get_run functions. Replace
argparsing with parametrized classes.

Fixed

Removed

Deprecated

Added

- ([133](https://github.com/microsoft/hi-ml/pull/133)) PyTorch Lightning logger for AzureML. Helper functions for consistent logging
- ([136](https://github.com/microsoft/hi-ml/pull/136)) Documentation for using low priority nodes

Changed

- ([133](https://github.com/microsoft/hi-ml/pull/133)) Made _**large breaking changes**_ to module names,
from `health.azure` to `health_azure`.
- ([141])(https://github.com/microsoft/hi-ml/pull/141)) Update changelog for release and increase scope of test_register_environment to ensure that by default environments are registered with a version number

Fixed

- ([134](https://github.com/microsoft/hi-ml/pull/134)) Fixed repo references and added pyright to enforce global checking
- ([139](https://github.com/microsoft/hi-ml/pull/139) Fix register_environment, which was ignoring existing environemnts
previously. Also ensure that the environment is given version 1 by default instead of "autosave")