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merge master#411

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Nic-Ma:4217-update-pytorchfrom
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May 3, 2022
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merge master#411
Nic-Ma merged 50 commits into
Nic-Ma:4217-update-pytorchfrom
Project-MONAI:dev

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@Nic-Ma Nic-Ma commented May 3, 2022

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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 -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

ericspod and others added 30 commits April 4, 2022 19:38
* Adding discussion on format to bundle specification

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updates:
- [github.com/asottile/pyupgrade: v2.31.0 → v2.31.1](asottile/pyupgrade@v2.31.0...v2.31.1)

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* [DLMED] change PatchIter to be a transform

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* [DLMED] add dict transform

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* [DLMED] add unit tests

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* [DLMED] store coords in dict

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* [DLMED] update according to comments

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* [DLMED] restore the doc-string

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* [DLMED] store more info

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* [DLMED] update according to comments

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* Fix a logical error in level verification

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* Refactor `if` expression

* update clang format

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* SplitDim

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* fix

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* fixes

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* fix update meta

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* update docs

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* update mmar tests

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* fixes pylint error

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* extend mlp

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* 0 mlp_dim

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* update based on comments

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* added 2D (normalized) surface dice metric

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* exclude from min tests

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* more detailled docstring

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* Fix doc strings error

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* remove duplicate places

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* update sys req

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* temp test

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* update code for torch>=1.7

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* temp tests

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* fixes tests

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* autofix

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* fixes import

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* clear cache

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* update based on comments

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* remove temp cmd

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* Update the existing functionality to comply with the `torchscript.jit.script` function.

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* meta tensor

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* [DLMED] add kwargs for to() API

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* [DLMED] fix typo

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* update meta tensor api

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* no skip if before pytorch 1.7

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* fix

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* fix

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* [DLMED] fix typo in bundle scripts

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… and iterating across batches (#4137)

`MetaTensor`: collate; decollate; dataset; dataloader; out=; indexing and iterating across batches (#4137)
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* [DLMED] update all the engines

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* [DLMED] fix flake8

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* [DLMED] fix flake8

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* Implement WSIReader with OpenSlide backend .

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* Add unittest for openslide

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* Add docs

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* formatting

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* Update imports and few fixes

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* Fix x,y in docstrings

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* Address comments

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* Remove x and y

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* Implement PatchWSIDataset

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* Add unittests

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* Add docs

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* Reorder imports

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* formatting:

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* Address comments

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* Update to be compatible with Dataset

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* Update reader to accept str, class, object

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* Add test cases for various reader and level arguments

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* Update comment about OpenSlide cache

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* Rename reader_name to backend

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* Add unittests for openslide

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* sorts

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* Add docstring for kwargs

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* draft download

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* update bundle download

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* add url and load

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* rename args and remove a few places

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* fix flake8 issue

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* enhance with reviews

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* add instantiate for load

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* fix black error

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* add skip

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* add schemaerror

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* fix partial places

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* download zip bundle

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* update ts features

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* add config_files test case

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* workaround

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* [DLMED] fix tifffile issue

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dongyang0122 and others added 20 commits April 23, 2022 16:37
… layer options (#4157)

* fixed a bug

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* autofix

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* update test case

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* Redesign whole slide image reading (#4107)

* Redesign BaseWSIReader,  WSIReader, CuCIMWSIReader

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* Add image mode for output validation

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* Update references to new WSIReader

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* sort imports

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* Clean up imports

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* Update docs and docstrings

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* Make workaround for CuImage objects

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* Update a note about cucim

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* Update type hints and docstrings

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* Implement Split transform

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* Implement SplitDict

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* Address all comments

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* Revert references to new wsireader

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* Add missing comma

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* Support new temp dgx runner

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* atol 1e-5

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* [DLMED] enhance CLI runner_id

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* [DLMED] optimize config logic

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* [DLMED] fix list order

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* fixes #4172 aggregate with no in-place buffer change

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* update reduction option

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* fixes flake8

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* update

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* Add DeepEdit transforms and interaction

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* Remove unused global variable
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* Make all transforms optional

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* temp tests

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* update

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* workaround

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* fixes typo

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@Nic-Ma Nic-Ma merged commit a82b38e into Nic-Ma:4217-update-pytorch May 3, 2022
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