merge master

.github/workflows/blossom-ci.yml

@@ -29,9 +29,12 @@ jobs:
       args: ${{ env.args }}
 
     # This job only runs for pull request comments
-    if: |
-         contains( 'Nic-Ma,wyli,pxLi,', format('{0},', github.actor)) &&
-         github.event.comment.body == '/build'
+    if: contains('\
+      Nic-Ma,\
+      wyli,\
+      pxLi,\
+      YanxuanLiu,\
+      ', format('{0},', github.actor)) && github.event.comment.body == '/build'
     steps:
       - name: Check if comment is issued by authorized person
         run: blossom-ci

.github/workflows/cron.yml

@@ -50,7 +50,7 @@ jobs:
         python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
         BUILD_MONAI=1 ./runtests.sh --build --coverage --unittests --disttests  # unit tests with coverage report
         BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
-        coverage xml
+        coverage xml --ignore-errors
         if pgrep python; then pkill python; fi
     - name: Upload coverage
       uses: codecov/codecov-action@v1
@@ -62,7 +62,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.06"]  # 21.02, 21.10 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.07"]  # 21.02, 21.10 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -93,7 +93,7 @@ jobs:
         python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
         BUILD_MONAI=1 ./runtests.sh --build --coverage --unittests --disttests  # unit tests with coverage report
         BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
-        coverage xml
+        coverage xml --ignore-errors
         if pgrep python; then pkill python; fi
     - name: Upload coverage
       uses: codecov/codecov-action@v1
@@ -106,7 +106,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.06"]  # 21.02, 21.10 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.07"]  # 21.02, 21.10 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -192,7 +192,7 @@ jobs:
         ngc --version
         BUILD_MONAI=1 ./runtests.sh --build --coverage --pytype --unittests --disttests  # unit tests with pytype checks, coverage report
         BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
-        coverage xml
+        coverage xml --ignore-errors
         if pgrep python; then pkill python; fi
     - name: Upload coverage
       uses: codecov/codecov-action@v1
@@ -204,7 +204,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     needs: cron-gpu  # so that monai itself is verified first
     container:
-      image: nvcr.io/nvidia/pytorch:22.06-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:22.07-py3  # testing with the latest pytorch base image
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, common]
     steps:

.github/workflows/pythonapp-gpu.yml

@@ -23,7 +23,7 @@ jobs:
           - "PT17+CUDA102"
           - "PT18+CUDA102"
           - "PT18+CUDA112"
-          - "PT112+CUDA116"
+          - "PT112+CUDA117"
           - "PT110+CUDA102"
           - "PT112+CUDA102"
         include:
@@ -45,11 +45,11 @@ jobs:
             # 21.10: 1.10.0a0+0aef44c
             pytorch: "-h"
             base: "nvcr.io/nvidia/pytorch:21.10-py3"
-          - environment: PT112+CUDA116
+          - environment: PT112+CUDA117
             # we explicitly set pytorch to -h to avoid pip install error
-            # 22.06: 1.13.0a0+340c412
+            # 22.07: 1.13.0a0+08820cb
             pytorch: "-h"
-            base: "nvcr.io/nvidia/pytorch:22.06-py3"
+            base: "nvcr.io/nvidia/pytorch:22.07-py3"
           - environment: PT110+CUDA102
             pytorch: "torch==1.10.2 torchvision==0.11.3"
             base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
@@ -142,7 +142,7 @@ jobs:
           # test the clang-format tool downloading once
           coverage run -m tests.clang_format_utils
         fi
-        coverage xml
+        coverage xml --ignore-errors
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage

.github/workflows/pythonapp.yml

@@ -222,5 +222,6 @@ jobs:
         cd docs/
         make clean
         make html 2>&1 | tee tmp_log
+        if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "found errors"; grep "ERROR:" tmp_log; exit 1; fi
         if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; grep "WARNING:" tmp_log; exit 1; fi
       shell: bash

.github/workflows/release.yml

@@ -79,7 +79,7 @@ jobs:
 
     - if: matrix.python-version == '3.8' && startsWith(github.ref, 'refs/tags/')
       name: Publish to Test PyPI
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         password: ${{ secrets.TEST_PYPI }}
         repository_url: https://test.pypi.org/legacy/

.github/workflows/setupapp.yml

@@ -61,7 +61,7 @@ jobs:
         python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
         BUILD_MONAI=1 ./runtests.sh --build --coverage --unittests --disttests  # unit tests with coverage report
         BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
-        coverage xml
+        coverage xml --ignore-errors
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
@@ -105,7 +105,7 @@ jobs:
         python -m pip list
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
         BUILD_MONAI=1 ./runtests.sh --build --quick --unittests --disttests
-        coverage xml
+        coverage xml --ignore-errors
     - name: Upload coverage
       uses: codecov/codecov-action@v1
       with:

.gitignore

@@ -131,6 +131,8 @@ tests/testing_data/MedNIST*
 tests/testing_data/*Hippocampus*
 tests/testing_data/*.tiff
 tests/testing_data/schema.json
+tests/testing_data/endo.mp4
+tests/testing_data/ultrasound.avi
 *.svg
 
 # clang format tool

CHANGELOG.md

@@ -1,11 +1,38 @@
 # Changelog
 All notable changes to MONAI are documented in this file.
 
-The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
-and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [0.9.1] - 2022-07-22
+### Added
+* Support of `monai.data.MetaTensor` as core data structure across the modules
+* Support of `inverse` in array-based transforms
+* `monai.apps.TciaDataset` APIs for The Cancer Imaging Archive (TCIA) datasets, including a pydicom-backend reader
+* Initial release of components for MRI reconstruction in `monai.apps.reconstruction`, including various FFT utilities
+* New metrics and losses, including mean IoU and structural similarity index
+* `monai.utils.StrEnum` class to simplify Enum-based type annotations
+### Changed
+* Base Docker image upgraded to `nvcr.io/nvidia/pytorch:22.06-py3` from `nvcr.io/nvidia/pytorch:22.04-py3`
+* Optionally depend on PyTorch-Ignite v0.4.9 instead of v0.4.8
+### Fixed
+* Fixed issue of not skipping post activations in `Convolution` when input arguments are None
+* Fixed issue of ignoring dropout arguments in `DynUNet`
+* Fixed issue of hard-coded non-linear function in ViT classification head
+* Fixed issue of in-memory config overriding with `monai.bundle.ConfigParser.update`
+* 2D SwinUNETR incompatible shapes
+* Fixed issue with `monai.bundle.verify_metadata` not raising exceptions
+* Fixed issue with `monai.transforms.GridPatch` returns inconsistent type location when padding
+* Wrong generalized Dice score metric when denominator is 0 but prediction is non-empty
+* Docker image build error due to NGC CLI upgrade
+* Optional default value when parsing id unavailable in a ConfigParser instance
+* Immutable data input for the patch-based WSI datasets
+### Deprecated
+* `*_transforms` and `*_meta_dict` fields in dictionary-based transforms in favor of MetaTensor
+* `meta_keys`, `meta_key_postfix`, `src_affine` arguments in various transforms, in favor of MetaTensor
+* `AsChannelFirst` and `AddChannel`, in favor of `EnsureChannelFirst` transform
+
 ## [0.9.0] - 2022-06-08
 ### Added
 * `monai.bundle` primary module with a `ConfigParser` and command-line interfaces for configuration-based workflows
@@ -534,7 +561,8 @@ the postprocessing steps should be used before calling the metrics methods
 
 [highlights]: https://github.com/Project-MONAI/MONAI/blob/master/docs/source/highlights.md
 
-[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/0.9.0...HEAD
+[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/0.9.1...HEAD
+[0.9.1]: https://github.com/Project-MONAI/MONAI/compare/0.9.0...0.9.1
 [0.9.0]: https://github.com/Project-MONAI/MONAI/compare/0.8.1...0.9.0
 [0.8.1]: https://github.com/Project-MONAI/MONAI/compare/0.8.0...0.8.1
 [0.8.0]: https://github.com/Project-MONAI/MONAI/compare/0.7.0...0.8.0

CITATION.cff

@@ -6,8 +6,8 @@ title: "MONAI: Medical Open Network for AI"
 abstract: "AI Toolkit for Healthcare Imaging"
 authors:
   - name: "MONAI Consortium"
-date-released: 2022-06-13
-version: "0.9.0"
+date-released: 2022-07-25
+version: "0.9.1"
 identifiers:
   - description: "This DOI represents all versions of MONAI, and will always resolve to the latest one."
     type: doi

CONTRIBUTING.md

@@ -283,10 +283,25 @@ for example, ``import monai.transforms.Spacing`` is the equivalent of ``monai.tr
 For string definition, [f-string](https://www.python.org/dev/peps/pep-0498/) is recommended to use over `%-print` and `format-print`. So please try to use `f-string` if you need to define any string object.
 
 #### Backwards compatibility
-MONAI is currently under active development, and with major version zero (following the [Semantic Versioning](https://semver.org/)).
-The backwards compatibility of the API is not always guaranteed at this initial development stage.
-However, utility functions are provided in the `monai.utils.deprecated` modules to help users migrate to the new API.
-The use of these functions is encouraged.
+MONAI in general follows [PyTorch's policy for backward compatibility](https://github.com/pytorch/pytorch/wiki/PyTorch's-Python-Frontend-Backward-and-Forward-Compatibility-Policy).
+Utility functions are provided in `monai.utils.deprecated` to help migrate from the deprecated to new APIs. The use of these utilities is encouraged.
+The pull request [template contains checkboxes](https://github.com/Project-MONAI/MONAI/blame/dev/.github/pull_request_template.md#L11-L12) that
+the contributor should use accordingly to clearly indicate breaking changes.
+
+The process of releasing backwards incompatible API changes is as follows:
+1. discuss the breaking changes during pull requests or in dev meetings with a feature proposal if needed.
+1. add a warning message in the upcoming release (version `X.Y`), the warning message should include a forecast of removing the deprecated API in:
+   1. `X+1.0` -- major version `X+1` and minor version `0` the next major version if it's a significant change,
+   1. `X.Y+2` -- major version `X` and minor version `Y+2` (the minor version after the next one), if it's a minor API change.
+   1. Note that the versioning policy is similar to PyTorch's approach which does not precisely follow [the semantic versioning](https://semver.org/) definition.
+      Major version numbers are instead used to represent major product version (which is currently not planned to be greater than 1),
+      minor version for both compatible and incompatible, and patch version for bug fixes.
+   1. when recommending new API to use in place of a deprecated API, the recommended version should
+      provide exact feature-like behaviour otherwise users will have a harder time migrating.
+1. add new test cases by extending the existing unit tests to cover both the deprecated and updated APIs.
+1. collect feedback from the users during the subsequent few releases, and reconsider step 1 if needed.
+1. before each release, review the deprecating APIs and relevant tests, and clean up the removed APIs described in step 2.
+
 
 
 ### Submitting pull requests
@@ -349,12 +364,11 @@ When major features are ready for a milestone, to prepare for a new release:
 - Merge `releasing/[version number]` to `dev`, this step must make sure that the tagging commit unchanged on `dev`.
 - Publish the release note.
 
-Note that the release should be tagged with a [PEP440](https://www.python.org/dev/peps/pep-0440/) compliant
-[semantic versioning](https://semver.org/spec/v2.0.0.html) number.
+Note that the release should be tagged with a [PEP440](https://www.python.org/dev/peps/pep-0440/) compliant version number.
 
 If any error occurs during the release process, first check out a new hotfix branch from the `releasing/[version number]`,
 then make PRs to the `releasing/[version number]` to fix the bugs via the regular contribution procedure.
 
 If any error occurs after the release process, first check out a new hotfix branch from the `main` branch,
-make a minor version release following the semantic versioning, for example, `releasing/0.1.1`.
+make a patch version release following the semantic versioning, for example, `releasing/0.1.1`.
 Make sure the `releasing/0.1.1` is merged back into both `dev` and `main` and all the test pipelines succeed.

Dockerfile

@@ -11,7 +11,7 @@
 
 # To build with a different base image
 # please run `docker build` using the `--build-arg PYTORCH_IMAGE=...` flag.
-ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:22.06-py3
+ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:22.07-py3
 FROM ${PYTORCH_IMAGE}
 
 LABEL maintainer="monai.contact@gmail.com"

docs/requirements.txt

@@ -30,3 +30,4 @@ fire
 jsonschema
 pynrrd
 pydicom
+h5py

docs/source/api.rst

@@ -7,6 +7,7 @@ API Reference
    :maxdepth: 1
 
    apps
+   fl
    bundle
    transforms
    losses

docs/source/apps.rst

@@ -15,6 +15,9 @@ Applications
 .. autoclass:: DecathlonDataset
     :members:
 
+.. autoclass:: TciaDataset
+    :members:
+
 .. autoclass:: CrossValidation
     :members:
 
@@ -184,3 +187,26 @@ Applications
     :members:
 .. automodule:: monai.apps.detection.metrics.matching
     :members:
+
+`Reconstruction`
+----------------
+
+`ConvertToTensorComplex`
+~~~~~~~~~~~~~~~~~~~~~~~~
+.. autofunction:: monai.apps.reconstruction.complex_utils.convert_to_tensor_complex
+
+`ComplexAbs`
+~~~~~~~~~~~~
+.. autofunction:: monai.apps.reconstruction.complex_utils.complex_abs
+
+`RootSumOfSquares`
+~~~~~~~~~~~~~~~~~~
+.. autofunction:: monai.apps.reconstruction.mri_utils.root_sum_of_squares
+
+`ComplexMul`
+~~~~~~~~~~~~
+.. autofunction:: monai.apps.reconstruction.complex_utils.complex_mul
+
+`ComplexConj`
+~~~~~~~~~~~~~
+.. autofunction:: monai.apps.reconstruction.complex_utils.complex_conj

docs/source/conf.py

@@ -40,6 +40,7 @@
     "engines",
     "data",
     "apps",
+    "fl",
     "bundle",
     "config",
     "handlers",

docs/source/config_syntax.md

@@ -15,7 +15,7 @@ Content:
   - [`@` to reference Python objects in configurations](#to-reference-python-objects-in-configurations)
   - [`$` to evaluate as Python expressions](#to-evaluate-as-python-expressions)
   - [`%` to textually replace configuration elements](#to-textually-replace-configuration-elements)
-  - [`_target_` (`_disabled_` and `_requires_`) to instantiate a Python object](#instantiate-a-python-object)
+  - [`_target_` (`_disabled_`, `_desc_`, and `_requires_`) to instantiate a Python object](#instantiate-a-python-object)
 - [The command line interface](#the-command-line-interface)
 - [Recommendations](#recommendations)
 
@@ -67,7 +67,7 @@ or additionally, tune the input parameters then instantiate the component:
 BasicUNet features: (32, 32, 32, 64, 64, 64).
 ```
 
-For more details on the `ConfigParser` API, please see https://docs.monai.io/en/latest/bundle.html#config-parser.
+For more details on the `ConfigParser` API, please see [`monai.bundle.ConfigParser`](https://docs.monai.io/en/latest/bundle.html#config-parser).
 
 ## Syntax examples explained
 
@@ -141,17 +141,19 @@ This dictionary will be instantiated as a Pytorch object at runtime.
 {
   "component_name": {
     "_target_": "my.module.Class",
+    "_desc_": "this is a customized class which also triggers 'cudnn_opt' reference",
     "_requires_": "@cudnn_opt",
     "_disabled_": "true"}
 }
 ```
 
-_Description:_ `_requires_` and `_disabled_` are optional keys.
-`_requires_` specifies references (string starts with `@`) or
-Python expression that will be evaluated/instantiated before `_target_` object is instantiated.
-It is useful when the component does not explicitly depend on the other ConfigItems via
-its arguments, but requires the dependencies to be instantiated/evaluated beforehand.
-`_disabled_` specifies a flag to indicate whether to skip the instantiation.
+_Description:_ `_requires_`, `_disabled_`, and `_desc_` are optional keys.
+- `_requires_` specifies references (string starts with `@`) or
+  Python expression that will be evaluated/instantiated before `_target_` object is instantiated.
+  It is useful when the component does not explicitly depend on the other ConfigItems via
+  its arguments, but requires the dependencies to be instantiated/evaluated beforehand.
+- `_disabled_` specifies a flag to indicate whether to skip the instantiation.
+- `_desc_` can be used for providing free text descriptions.
 
 ## The command line interface