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merge master#157

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Nic-Ma merged 410 commits intoNic-Ma:2495-enhance-net-blockfrom
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Jul 1, 2021
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merge master#157
Nic-Ma merged 410 commits intoNic-Ma:2495-enhance-net-blockfrom
Project-MONAI:dev

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@Nic-Ma Nic-Ma commented Jul 1, 2021

Fixes # .

Description

A few sentences describing the changes proposed in this pull request.

Status

Ready/Work in progress/Hold

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • New tests added to cover the changes.
  • Integration tests passed locally by running ./runtests.sh --codeformat --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

Nic-Ma and others added 30 commits April 7, 2021 16:36
* [DLMED] add support for addtional events

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add unit tests

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix typehints

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* fixes typos

Signed-off-by: Wenqi Li <[email protected]>

Co-authored-by: monai-bot <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
* fixes #1965

Signed-off-by: Wenqi Li <[email protected]>

* adds docstring

Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance doc-strings

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

Co-authored-by: monai-bot <[email protected]>
* adding init efficientnet support

Signed-off-by: masadcv <[email protected]>

* fixing flake8 and further refactoring

Signed-off-by: masadcv <[email protected]>

* adding unittests for efficiennet

Signed-off-by: masadcv <[email protected]>

* making unittests backwards compatible python<3.8

Signed-off-by: masadcv <[email protected]>

* fixed kitty unittests file path

Signed-off-by: masadcv <[email protected]>

* adding docstrings and minor refactoring

Signed-off-by: masadcv <[email protected]>

* fix flake8-py3 failing test

Signed-off-by: masadcv <[email protected]>

* generalize drop_connect for n-dim, fix/add unittests, remove assert

Signed-off-by: masadcv <[email protected]>

* fix failing unittest, CC0-license image for test

Signed-off-by: masadcv <[email protected]>

* refactoring code for review

Signed-off-by: masadcv <[email protected]>

* WIP fix mypy type hint errors

Signed-off-by: masadcv <[email protected]>

* fix cuda test error

Signed-off-by: masadcv <[email protected]>

* WIP fix test errors

Signed-off-by: masadcv <[email protected]>

* adding non-default shape tests

Signed-off-by: masadcv <[email protected]>

* remove 3d case from non-default shape test

Signed-off-by: masadcv <[email protected]>

* refactoring and updating docs

Signed-off-by: masadcv <[email protected]>

Co-authored-by: Yiheng Wang <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] add TransformInverter handler

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix typo

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add support in SegmentationSaver handler

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8 issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8 issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix CI test

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

Co-authored-by: monai-bot <[email protected]>
* changelog for 0.5.0

Signed-off-by: Wenqi Li <[email protected]>

* update changelog

Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add TransformInverter handler

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix typo

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add support in SegmentationSaver handler

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8 issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8 issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix CI test

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] save mode into inverse dict

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add unit tests

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix ToTensor inverse issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] change the replacement logic into util function

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add more tests

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

Co-authored-by: monai-bot <[email protected]>
* [DLMED] update highlights for 0.5

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add invert transforms

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add more highlights

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add checkpointloader

Signed-off-by: Nic Ma <[email protected]>

* downscale image

Signed-off-by: Wenqi Li <[email protected]>

* downscale image

Signed-off-by: Wenqi Li <[email protected]>

* update docs

Signed-off-by: Wenqi Li <[email protected]>

* update desc

Signed-off-by: Wenqi Li <[email protected]>

* update

Signed-off-by: Wenqi Li <[email protected]>

Co-authored-by: Wenqi Li <[email protected]>
* update convs docstrings

Signed-off-by: Wenqi Li <[email protected]>

* increase tol for cuda crf

Signed-off-by: Wenqi Li <[email protected]>

* update requirements according to docs/requirements

Signed-off-by: Wenqi Li <[email protected]>

* prune image

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>

Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] metrics support a list of tensor

Signed-off-by: Nic Ma <[email protected]>

* update workflow test

Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] fix engine.state.output dict copy issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add num_workers

Signed-off-by: Nic Ma <[email protected]>

* fixes typos

Signed-off-by: Wenqi Li <[email protected]>

* update tests

Signed-off-by: Wenqi Li <[email protected]>

* update docstrings

Signed-off-by: Wenqi Li <[email protected]>

* tests

Signed-off-by: Wenqi Li <[email protected]>

Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* handling error

Signed-off-by: Wenqi Li <[email protected]>

* temp test

Signed-off-by: Wenqi Li <[email protected]>

* fixes tests

Signed-off-by: Wenqi Li <[email protected]>

* Revert "temp test"

This reverts commit 60661ae.

Signed-off-by: Wenqi Li <[email protected]>
* update dev version

Signed-off-by: Wenqi Li <[email protected]>

* typo fix

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
TTA progress bar, use torch for mode, add label meta_data
* follow up of #1992

Signed-off-by: Wenqi Li <[email protected]>

* update spacing inverse

Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] update TransformInverter

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix deepcopy

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

Co-authored-by: monai-bot <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add more tests

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add nearest test cases

Signed-off-by: Nic Ma <[email protected]>
* adds a what's new page

Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add SaliencyInferer

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] enhance CAM logic

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add unit tests

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix typo

Co-authored-by: Richard Brown <[email protected]>
Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8 issue

Signed-off-by: Nic Ma <[email protected]>

Co-authored-by: Richard Brown <[email protected]>
* [DLMED] enhance unit tests

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

Co-authored-by: monai-bot <[email protected]>
* [DLMED] add warning

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

Co-authored-by: monai-bot <[email protected]>
* Jupyter and other additions

Signed-off-by: Eric Kerfoot <[email protected]>
* allow slicing with SpatialCrop(d)

Signed-off-by: Richard Brown <[email protected]>
* fixes docstring

Signed-off-by: Wenqi Li <[email protected]>

* update example

Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add alias

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] add unit tests

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

Co-authored-by: monai-bot <[email protected]>
myron and others added 29 commits June 23, 2021 18:13
* [DLMED] add TorchVisionClassificationModel

Signed-off-by: Nic Ma <[email protected]>

Co-authored-by: monai-bot <[email protected]>
* Add parameter unpacking for transforms

Signed-off-by: Sebastian Penhouet <[email protected]>
* [DLMED] add copy logic

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8

Signed-off-by: Nic Ma <[email protected]>
* Add query to NGC to get matched model URL and version.
Allow mmar download with latest version or a specific version.

Signed-off-by: Isaac Yang <[email protected]>
no need for default orig_size stored for invertible transforms
Signed-off-by: Yiheng Wang <[email protected]>
* [DLMED] enhance ToTensor

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>
#2455)

* add clara_train_covid19_3d_ct_classification and clara_train_covid19_annotation_ct_lung_1

point to pt version of covid19 lung annotation model

Signed-off-by: Holger Roth <[email protected]>
* [DLMED] add pad options

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add to dict transforms

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>

Co-authored-by: monai-bot <[email protected]>
* [DLMED] update ignite to 0.4.5

Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add dynamic data list in CacheDataset

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add support to PersistentDataset

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8 issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix CI tests

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] enhance dataset

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update_data -> set_data

Signed-off-by: Nic Ma <[email protected]>
…2315)

* [WIP] 2220 Decollate batch into list of tensors after model forward (#2244)

* [DLMED] add support for Activation transform

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] change all the array level post transforms to channel-first

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update all the IO, utility, post transforms

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update engines for list of dict

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update all the event handlers

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] support non-batch data

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update based on the latest APIs

Signed-off-by: Nic Ma <[email protected]>

Co-authored-by: monai-bot <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] fix all the unit tests

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix unit tests

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8 issues

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] remove unused import

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8 issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix integration test

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix integration tests

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] fix integration tests

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] fix flake8 issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add support to copy scalar

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8 issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix wrong unit tests

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix doc issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix broken tests

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix unit tests

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] simplify CSV saver

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add copy_scalar_to_batch util

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8 issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] change to preprocessing and postprocessing

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] change file name to postprocessing

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix typo in doc-string

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add Decollated back

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update to use ignite v0.4.5 metrics API

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix flake8 issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix conflicts

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* fixes #2452

Signed-off-by: Wenqi Li <[email protected]>

Co-authored-by: monai-bot <[email protected]>
* deprecation fixes

Signed-off-by: Eric Kerfoot <[email protected]>

* deprecation fixes

Signed-off-by: Eric Kerfoot <[email protected]>

* deprecation fixes

Signed-off-by: Eric Kerfoot <[email protected]>

* deprecation fixes

Signed-off-by: Eric Kerfoot <[email protected]>

* deprecation fixes

Signed-off-by: Eric Kerfoot <[email protected]>

* deprecation fixes

Signed-off-by: Eric Kerfoot <[email protected]>

* deprecation fixes

Signed-off-by: Eric Kerfoot <[email protected]>
* enhance version compare

Signed-off-by: Wenqi Li <[email protected]>

* update

Signed-off-by: Wenqi Li <[email protected]>

* remove unused

Signed-off-by: Wenqi Li <[email protected]>

* remove unused vars

Signed-off-by: Wenqi Li <[email protected]>

* update debug info

Signed-off-by: Wenqi Li <[email protected]>

* temp tests

Signed-off-by: Wenqi Li <[email protected]>

* non integer comparison

Signed-off-by: Wenqi Li <[email protected]>

* adds tests

Signed-off-by: Wenqi Li <[email protected]>

* no temp tests

Signed-off-by: Wenqi Li <[email protected]>

* update test

Signed-off-by: Wenqi Li <[email protected]>

Co-authored-by: Nic Ma <[email protected]>
* [DLMED] add deprecated decorator

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] enhance doc-string

Signed-off-by: Nic Ma <[email protected]>

Co-authored-by: monai-bot <[email protected]>
* [DLMED] add support to compare metrics

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>
* add UNETR, ViT

Signed-off-by: ahatamizadeh <[email protected]>

* add UNETR, ViT

Signed-off-by: ahatamizadeh <[email protected]>

* add UNETR, ViT

Signed-off-by: ahatamizadeh <[email protected]>

* add UNETR, ViT

Signed-off-by: ahatamizadeh <[email protected]>

* add UNETR, ViT

Signed-off-by: ahatamizadeh <[email protected]>

* add UNETR, ViT

Signed-off-by: ahatamizadeh <[email protected]>

* add UNETR, ViT

Signed-off-by: ahatamizadeh <[email protected]>
@Nic-Ma Nic-Ma merged commit 8410443 into Nic-Ma:2495-enhance-net-block Jul 1, 2021
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