69a64d1df5
Update README.md ( #847 )
2024-03-21 09:43:17 +00:00
2877002d50
Update README.md
2023-03-23 09:36:07 +00:00
03b4cc3f2a
BUG: Rename pretraining_run_checkpoints ( #841 )
...
"Parameter `extra_downloaded_run_id` has been renamed to
`pretraining_run_checkpoints`" (According to CHANGELOG.md) but is still
in used in SSLClassifierContainer class (in
InnerEye/ML/SSL/lightning_containers/ssl_image_classifier.py).
It will raise an AttributeError: 'SSLClassifierCIFAR' object has no
attribute 'extra_downloaded_run_id' when trying to run python
InnerEyeML/runner.py --model=CXRImageClassifier
--pretraining_run_recovery_id={THE_ID_TO_YOUR_SSL_TRAINING_JOB}.
So renamed it to `pretraining_run_checkpoints` there too.
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2023-02-16 12:09:45 +00:00
d902e02fc6
ENH: Adapt HelloWorld to run using the Inference Service ( #837 )
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Closes #696 .
Changes the HelloWorld model to only use a single channel, as this is
the format that the [Inference
Service](https://github.com/microsoft/InnerEye-Inference/ ) expects for
its inputs.
As many tests require the 2-channel data, this PR also creates a new
class, `HelloWorld2Channel`, which inherits from `HelloWorld` but uses 2
channels and can be used for testing. This avoids the pain of having to
alter all unit and regression tests that relied on the 2-channel data
and model.
Both models can be trained on the same data, but now the `HelloWorld`
model can be run by the Inference Service.
2022-11-22 11:00:04 +00:00
8f9d823101
DEL: Remove `environment_win.yml` ( #836 )
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Closes #822 .
Removes the outdated and difficult-to-maintain locked windows
environment and updates documentation accordingly.
2022-11-17 12:24:34 +00:00
9083966673
ENH: Improve regression tests ( #827 )
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Closes #740 . Updates the lung model regression test to use the latest
parameters and train for a substantial number of steps to ensure
training is progressing as expecting. The small number of epochs and
smaller data subset is used as running a full training run isn't
feasible. The new test runs in < 30 minutes but on real data.
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Bypassing branch protections for failing PyTest as the test that is failing is `Tests/SSL/test_ssl_containers.py::test_innereye_ssl_container_cifar10_resnet_simclr` as the URL for CIFAR seems to be broken currently (returning 500 server error).
2022-11-16 15:05:46 +00:00
4aadd0d0f7
DOC: Update sample tasks docs ( #833 )
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Closes #761
2022-11-16 11:11:13 +00:00
70fbd758eb
DOC: Update `HeadAndNeckBase` docs ( #821 )
...
Closes #730
2022-11-11 11:06:46 +00:00
acfa812408
BUG: Patch imports for `move_model.py` ( #831 )
...
Closes #830
2022-11-11 10:17:25 +00:00
f66c61bb28
DOC: Add documentation on monitoring jobs in AzureML portal ( #826 )
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Closes #254
2022-11-10 22:18:42 +00:00
ca48126414
DOC: Hotfix doc links ( #823 )
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Some of the doc links in the pre-trained model page are broken, this is
quick hotfix to remedy that.
2022-11-07 13:57:23 +00:00
657530439c
ENH: Publish lung segmentation model ( #808 )
...
This PR contains the hyperparameter updates for training and running
inference on InnerEye Lung segmentation model on a Standard_NC24rs_v3
Azure cluster (4 x V100).
It also includes all the documentation of the model will be released in
a tagged version in the same fashion as the [hippocampus
model](https://github.com/microsoft/InnerEye-DeepLearning/releases/tag/v0.5 ).
I will tag and release the model after this PR is merged to ensure that
the source code in the main branch is correct at the time of release
(docs currently include a link to v0.8 which doesn't yet exist).
2022-11-07 13:04:02 +00:00
12f78f34f5
DOC: Fix doc typo ( #820 )
...
Closes #781
2022-11-02 15:10:59 +00:00
33ae7c20e7
DOC: Correct RTD version ( #815 )
...
Closes #810
2022-10-28 14:37:01 +01:00
f2e0a98429
ENH: Improve `rtconvert` log visibility ( #814 )
...
Closes #813
2022-10-28 09:21:59 +01:00
02e7d9a91d
ENH: Upgrade DICOM-RT Version to 1.1.0 ( #807 )
...
Upgrading DICOM-RT to incorporate fixes to various DICOM issues.
2022-10-14 10:04:29 +01:00
78b7de2b5f
ENH: Fix logging + model registration for Amulet runs ( #804 )
...
Adds functionality to properly log IE-DL outputs and register trained
models when running jobs through amulet.
2022-09-30 11:42:38 +01:00
a6dcef0252
DOC: Typo fix ( #803 )
2022-09-27 10:41:31 +01:00
5b21840df4
ENH: Upgrading package versions for security patches ( #757 )
...
* 🚧 💥 Update to secure versions of packages
* ⬆️ Upgrade hi-ml version
* 🏷️ Fix mypy and update windows env
* ✅ Update current epoch value in lightning tests
* 🐛 Fix wnidows line endings
* ✅ Remove checkpoint load epoch check
* 📌 Lock env anew
* 🎨 🐛 Add merge_conda_files() to common_util
* ✅ Add logging to tests
* 🚧 Update VarINetWithImageLogging logger syntax
* ✅ Fix Train2Nodes tests
* ✅ Remove cwd change, update CIFAR SSL metrics
* ⚰️ Remove unnecessary PL backwards compatibility
* 📌 Lock env
* 📌 Upgrade to hi-ml v0.2.5
* 📌 Testing lightning 1.6.5
* ♻️ Resolve PR comments
2022-09-14 16:33:17 +00:00
7894498635
DOC: Fix dead TRE links ( #798 )
...
* 📝 Fix broken link
* 📝 Update TRE documentation
2022-09-13 13:29:24 +01:00
57489686c5
DOC: Add `InnerEye/Common` docstrings to RTD ( #797 )
...
* 📝 Create basic for ML API
* 📝 Add ML/configs base doc files
* 📝 Finish ML/configs API
* 📝 Update augmentations
* 📝 Add ML/dataset API docs
* 📝 Add rst skeleton for ML/models
* 📝 Fix docstring missing newlines
* Remove script
* 📝 Finish ML/models API docs
* 📝 Start ML/SSL API. Fix some formatting issues
* 📝 Correct whitespace issues in `:param`
* 📝 Fix whitespace errors on `:return` statements
* 📝 Fix :return: statements
* 📝 Finish ML/SSL API
* 📝 Add ML/utils API docs
* 📝 Add visualizer docs, fix `:raise` indents
* 📝 Fix more issues with the `:raises:` formatting
* ♻️ Restructuring folders
* 📝 Limit API `toctree` depth
* 📝 Add primary InnerEye/ML files API to docs
* 📝 Fix and add `InnerEye/ML/*.py` docs
* ⚰️ Remove weird `settings.json` change
* 📌 Switch recommonmark to MyST-parser
* 📌 Add myst-parser to `environment.yml`, lock env
* 🚧 Add Common docs
* 📝 Add common docstrings fixes
* 🐛 Remove git artifacts
2022-09-13 13:20:27 +01:00
bb0ec8a2d9
DOC: Add `InnerEye/Azure` docstrings to RTD ( #788 )
...
* 📝 Create basic for ML API
* 📝 Add ML/configs base doc files
* 📝 Finish ML/configs API
* 📝 Update augmentations
* 📝 Add ML/dataset API docs
* 📝 Add rst skeleton for ML/models
* 📝 Fix docstring missing newlines
* Remove script
* 📝 Finish ML/models API docs
* 📝 Start ML/SSL API. Fix some formatting issues
* 📝 Correct whitespace issues in `:param`
* 📝 Fix whitespace errors on `:return` statements
* 📝 Fix :return: statements
* 📝 Finish ML/SSL API
* 📝 Add ML/utils API docs
* 📝 Add visualizer docs, fix `:raise` indents
* 📝 Fix more issues with the `:raises:` formatting
* ♻️ Restructuring folders
* 📝 Limit API `toctree` depth
* 📝 Add primary InnerEye/ML files API to docs
* 📝 Fix and add `InnerEye/ML/*.py` docs
* ⚰️ Remove weird `settings.json` change
* 📌 Switch recommonmark to MyST-parser
* 📝 Add InnerEye/Azure docstrings to RTD
* 💡 ♻️ Address review comments
* 📝 Update Azure title
* 📝 ♻️ Address review comments
2022-09-12 11:48:03 +01:00
879cb5f6ad
DOC: Add scripts to RTD ( #793 )
2022-09-06 13:19:25 +01:00
c7b2051836
DOC: Add AML notes for how ACR is used ( #795 )
2022-09-06 10:30:59 +00:00
8cf63c8e7a
BUG: Dont update multi-node env vars for single node training ( #796 )
...
Update environment variables for multi-node jobs
2022-09-02 16:22:14 +00:00
8ffab94d46
ENH: Switch recommonmark to MyST-parser ( #787 )
...
* 📝 Create basic for ML API
* 📝 Add ML/configs base doc files
* 📝 Finish ML/configs API
* 📝 Update augmentations
* 📝 Add ML/dataset API docs
* 📝 Add rst skeleton for ML/models
* 📝 Fix docstring missing newlines
* Remove script
* 📝 Finish ML/models API docs
* 📝 Start ML/SSL API. Fix some formatting issues
* 📝 Correct whitespace issues in `:param`
* 📝 Fix whitespace errors on `:return` statements
* 📝 Fix :return: statements
* 📝 Finish ML/SSL API
* 📝 Add ML/utils API docs
* 📝 Add visualizer docs, fix `:raise` indents
* 📝 Fix more issues with the `:raises:` formatting
* ♻️ Restructuring folders
* 📝 Limit API `toctree` depth
* 📝 Add primary InnerEye/ML files API to docs
* 📝 Fix and add `InnerEye/ML/*.py` docs
* ⚰️ Remove weird `settings.json` change
* 📌 Switch recommonmark to MyST-parser
* 📌 Add myst-parser to `environment.yml`, lock env
2022-08-18 13:39:49 +01:00
e6b24063ef
DOC: Add a copy of the software dev document from hi-ml ( #789 )
2022-08-18 09:02:44 +01:00
59214c268e
DOC: Add all `InnerEye/ML` docstrings to ReadTheDocs ( #783 )
...
* 📝 Create basic for ML API
* 📝 Add ML/configs base doc files
* 📝 Finish ML/configs API
* 📝 Update augmentations
* 📝 Add ML/dataset API docs
* 📝 Add rst skeleton for ML/models
* 📝 Fix docstring missing newlines
* Remove script
* 📝 Finish ML/models API docs
* 📝 Start ML/SSL API. Fix some formatting issues
* 📝 Correct whitespace issues in `:param`
* 📝 Fix whitespace errors on `:return` statements
* 📝 Fix :return: statements
* 📝 Finish ML/SSL API
* 📝 Add ML/utils API docs
* 📝 Add visualizer docs, fix `:raise` indents
* 📝 Fix more issues with the `:raises:` formatting
* ♻️ Restructuring folders
* 📝 Limit API `toctree` depth
* 📝 Add primary InnerEye/ML files API to docs
* 📝 Fix and add `InnerEye/ML/*.py` docs
* ⚰️ Remove weird `settings.json` change
* ♻️ 💡 Address review comments
2022-08-16 08:58:38 +00:00
c1b363e158
ENH: Move docs to ReadTheDocs ( #768 )
...
* 📝 Move docs folder to sphinx-docs
* Trigger build for new URL
* 📝 Fix build to include README + CHANGLOG
* 📝 Add back in link fixing
* 🐛 Fix docs links
* 🚨 📝 Fix markdown linting
* 📝 Change relative links to GitHub ones permanently
* 📝 Replace more relative paths
* ⚡ ️ 📝 Switch to symlinks
* 📝 Replace README in toctree
* 📝 Update README
* 🐛 Attempt to fix images not rendering
* 🐛 Fix broken links
* Remove IDE settings from gitignore
* ⚡ ️ Move docs to `docs/` and add Makefile back
* 🙈 Update gitignore
* ♻️ ⚡ ️ Resolve review comments and change theme
* 📝 🔀 Rebase + markdown linting
* 🔥 Remove build files (again)
* 🙈 Remove pieline-breaking symlink
* ➕ Add furo to sphinx dependencies
* 📌 Move sphinx deps to environment.yml + lock
* 📝 Improve doc folder structure
* Return to copying instead of symlink
* 📝 Update indexing and titles
* 📝 Address review comments
2022-08-04 09:15:19 +01:00
4e12cec106
DOC: Update installation guide in /docs/WSL.md ( #769 )
...
* Update installation guide in WSL.md
- Removed long installation guide
- Included new shorter guide to install WSL
* Update WSL.md with given suggestions
- More clear language
* Update docs/WSL.md
* Update docs/WSL.md
* Update docs/WSL.md
* Trim trailing whitespace in WSL.md
- Trimmed trailing whitespace to pass the CI checks
Co-authored-by: Anton Schwaighofer <antonsc@microsoft.com>
2022-08-01 09:14:33 +01:00
7c283f744a
DEL: Delete empty grad cam file ( #775 )
...
Delete empty grad cam file
2022-07-27 09:03:47 +01:00
e4a0b38c8b
DOC: Improve hippocampus model documentation ( #772 )
...
* Add hippocampus docs
* Update docs/building_models.md
* update documentation
* Update docs/hippocampus_model.md
Co-authored-by: Fernando Pérez-García <fperezgarcia@microsoft.com>
* Address PR comments
* Incorporate model card in docu
* update docu
* update documentation
* Update hippocampus docs
Co-authored-by: Anton Schwaighofer <antonsc@microsoft.com>
Co-authored-by: Fernando Pérez-García <fperezgarcia@microsoft.com>
2022-07-26 18:32:11 +01:00
aec9e28e3f
DOC: Add hippocampus docs ( #756 )
...
Add documentation on evaluating the trained Hippocampus model.
2022-07-25 16:20:37 +00:00
48a6332569
BUG: Add sys.path changes to inference script ( #771 )
...
* 🐛 Add sys.path changes to inference script
* Update InnerEye/Scripts/submit_for_inference.py
Co-authored-by: Fernando Pérez-García <fperezgarcia@microsoft.com>
Co-authored-by: Fernando Pérez-García <fperezgarcia@microsoft.com>
2022-07-22 16:57:17 +01:00
ca9286c8a6
BUG: Regex for fastMRI matches more URLs than desired ( #762 )
2022-07-19 14:17:31 +01:00
88a805ee01
DOC: Add Read the Docs config file ( #720 )
...
* Add ReadTheDocs config file
* Update versions of docs requirements
* Move pip requirements to text file
* Add package requirements to RTD config
* Remove comments
* Add hi-ml-azure to docs requirements
* Move torchvision to docs requirements
* Fix requirement syntax
* Remove requirements file
* Update Python version
* Install requirements with conda
* Update Python version
* Update RTD config
* Specify Python 3
* Update RTD config
* Try installing conda manually
* Fix job name
* Specify conda Python
* Revert removing docs requirements
* Update Sphinx requirements
* Undo some changes
2022-07-07 16:06:29 +01:00
75d07b96e8
ENH: Autoupdate hooks [pre-commit.ci] ( #737 )
...
* [pre-commit.ci] pre-commit autoupdate
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.3.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.0.1...v4.3.0 )
- [github.com/PyCQA/flake8: 3.9.2 → 4.0.1](https://github.com/PyCQA/flake8/compare/3.9.2...4.0.1 )
- [github.com/pre-commit/mirrors-autopep8: v1.5.7 → v1.6.0](https://github.com/pre-commit/mirrors-autopep8/compare/v1.5.7...v1.6.0 )
* Update .pre-commit-config.yaml
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Fernando Pérez-García <fperezgarcia@microsoft.com>
2022-07-07 16:03:39 +01:00
cf8bd5e906
BUG: Ensemble HeadAndNeck model encounters 'CUDA out of memory' ( #754 )
...
Fix cuda out of memory for ensembles
2022-06-30 17:00:59 +01:00
38f830374e
ENH: Move hi-ml and fastMRI to PyPI packages ( #752 )
...
* 🔥 💥 Remove submodules
* ➕ Add packages to primary dependencies
* 📌 ⬆️ Upgrade python to 3.8 and lock
* ✅ Fix fastMRI test
* 💚 ✅ Fix tests and CI workflows
* 🏷️ Fix MyPy and Flake8 issues
* ⬆️ Update windows dependencies
* 📝 Add fastMRI reference
* ⚰️ Remove references to old submodules
2022-06-23 09:44:54 +01:00
69a5e8cd2c
DOC: Update environment documentation ( #748 )
...
* 📝 Update environment documentation
* 📝 Add quick setup, add review comment changes
2022-06-22 10:57:30 +00:00
b42043f31a
ENH: Remove cucim + change lock script line endings ( #750 )
...
📌 Remove cucim + change lock script line endings
2022-06-21 22:45:23 +01:00
106c101ff7
DOC: Improve doc for checkpointing ( #747 )
2022-06-21 17:09:24 +01:00
6a103f14ea
ENH: Sample all classes with equal probability in hippocampus config ( #746 )
2022-06-20 15:40:33 +01:00
cf1de78ae5
ENH: Add hippocampus segmentation config file ( #739 )
...
* Adding hippocampus segmentation config file
2022-06-14 11:50:06 +01:00
a9fd52c2c9
BUG: Fix missing channels dimension in normalization ( #701 )
...
* Fix missing channels dimension in normalization
* Update CHANGELOG
* Add test for 3D and 4D input images
* Move conversion to NumPy array
2022-06-13 13:47:27 +01:00
edc72eda8c
STYLE: Fix pre-commit errors ( #736 )
...
* STYLE: Apply some autopep8 fixes
* Fix more pre-commit errors
2022-06-07 09:14:00 +01:00
ad9aac5413
DOC: Improve documentation for dataset creation ( #723 )
2022-06-06 16:12:10 +00:00
796594f6f7
STYLE: Disable pre-commit CI autofixes
2022-06-01 21:46:49 +01:00
92d94799f2
ENH: Add Environment Locking ( #735 )
...
* ✨ Add environment locking script
* 📝 ✨ Finish script, add documentation
* 🐛 Change Windows env file in workflow
* 📝 🐛 Add review changes + fixes
* 🚧 Temporarily alter tests and conda channels
* 🚧 Add logging
* ✅ Fix TestSubmodule env file
* 🔥 Delete env test
* 🧑💻 Add warning to environment.yml
* 📝 ⚰️ Update based on review comments
* 📝 Add final changes
2022-06-01 10:05:54 +00:00
c7e4a3e945
Auto add issues to GitHub Project ( #721 )
...
Adds a new workflow that automatically adds any new issues to the InnerEye-OSS GitHub Project
2022-05-26 09:19:48 +01:00
Anton Schwaighofer
Peter Hessey
Eran
Sarthak Pati
Dr Kenji Takeda
Melissa Bristow
arsenkhy
Fernando Pérez-García
pre-commit-ci[bot]
Anna Schroder