Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

merge master #429

Merged
merged 183 commits into from
Jul 8, 2022
Merged

merge master #429

merged 183 commits into from
Jul 8, 2022

Conversation

Nic-Ma
Copy link
Owner

@Nic-Ma Nic-Ma commented Jul 8, 2022

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
@ericspod @pre-commit-ci
Adding discussion on format to bundle specification (#4047)
dc7a5b2 
* Adding discussion on format to bundle specification

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit suggestions (#4072)
c5bf120 
updates:
- [github.com/asottile/pyupgrade: v2.31.0 → v2.31.1](asottile/pyupgrade@v2.31.0...v2.31.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@Nic-Ma @pre-commit-ci
4060 Add PatchIter and PatchIterd transform (#4061)
c51d85e 
* [DLMED] change PatchIter to be a transform

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add dict transform

Signed-off-by: Nic Ma <nma@nvidia.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* [DLMED] add unit tests

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] store coords in dict

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] restore the doc-string

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] store more info

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@bhashemian
Fix a logical error in level verification (#4075)
b229e9c 
* Fix a logical error in level verification

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@Nic-Ma
[DLMED] add allow_missing_reference (#4079)
b5e7fe1 
Signed-off-by: Nic Ma <nma@nvidia.com>
@deepsource-autofix @monai-bot
autofixes: Refactor if expression and clangformat (#4081)
e8146e9 
* Refactor `if` expression

* update clang format

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [MONAI] python code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@rijobro @wyli
SplitDim (#3884)
b6b2cfb 
* SplitDim

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* fix

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* fixes

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* fix update meta

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* update docs

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@wyli @pre-commit-ci
update mmar tests (#4091)
d68554e 
* update mmar tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fixes pylint error

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@wyli
extending the mlp module (#4089)
17529e7 
* extend mlp

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* 0 mlp_dim

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@SilviaSeidlitz
added 2D (normalized) surface dice metric (#4050)
6602303 
* added 2D (normalized) surface dice metric

Signed-off-by: Silvia Seidlitz <s.seidlitz@dkfz-heidelberg.de>

* exclude from min tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* more detailled docstring

Signed-off-by: Silvia Seidlitz <s.seidlitz@dkfz-heidelberg.de>
@yiheng-wang-nv
4073 Enhance DynUNet doc-strings (#4102)
af6560a 
* Fix doc strings error

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* remove duplicate places

Signed-off-by: Yiheng Wang <vennw@nvidia.com>
@wyli
4105 drops pt16 support (#4106)
9c0a538 
* update sys req

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp test

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update code for torch>=1.7

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* autofix

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes import

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* clear cache

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* remove temp cmd

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@ramonemiliani93
Make pixelshuffle scriptable (#4109)
4e7ca44 
* Update the existing functionality to comply with the `torchscript.jit.script` function.

Signed-off-by: Ramon Emiliani <ramon@afxmedical.com>
@rijobro
meta tensor (#4077)
1880d38 
* meta tensor

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@Nic-Ma @monai-bot
4084 Add kwargs for Tensor.to() in engines (#4112)
f8c2655 
* [DLMED] add kwargs for to() API

Signed-off-by: Nic Ma <nma@nvidia.com>

* [MONAI] python code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] fix typo

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix flake8

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@wyli
fixes pytorch version tests (#4127)
ccac5ff 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
update meta tensor api (#4131)
137164d 
* update meta tensor api

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
runtests.sh isort (#4134)
5e180c6 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@wyli
update citation (#4133)
8544d9e 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
ToMetaTensor and FromMetaTensor transforms (#4115)
443fc0c 
to and from meta
@rijobro
no skip if before pytorch 1.7 (#4139)
cc9c066 
* no skip if before pytorch 1.7

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* fix

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* fix

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@Nic-Ma
[DLMED] fix file name in meta (#4145)
e1a62f2 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma @monai-bot
4116 Add support for advanced args of AMP (#4132)
4a8f815 
* [DLMED] fix typo in bundle scripts

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add support for AMP args

Signed-off-by: Nic Ma <nma@nvidia.com>

* [MONAI] python code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] fix flake8

Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@bhashemian
New wsireader (#4147)
cb9040e
@rijobro
MetaTensor: collate; decollate; dataset; dataloader; out=; indexing…
6dfb6a8 
… and iterating across batches (#4137)

`MetaTensor`: collate; decollate; dataset; dataloader; out=; indexing and iterating across batches (#4137)
@Nic-Ma @pre-commit-ci
4148 Enhance engine iteration logic and the typehints (#4150)
ed1c281 
* [DLMED] update Workflow.py

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update all the engines

Signed-off-by: Nic Ma <nma@nvidia.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* [DLMED] fix flake8

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix flake8

Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@bhashemian
Add OpenSlide support for new WSIReader (#4155)
ed70e11 
* Implement WSIReader with OpenSlide backend .

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add unittest for openslide

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add docs

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* formatting

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update imports and few fixes

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Fix x,y in docstrings

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Address comments

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Remove x and y

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Redesign PatchWSIDataset (#4152)
65d7296 
* Implement PatchWSIDataset

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add unittests

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add docs

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Reorder imports

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* formatting:

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Address comments

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update to be compatible with Dataset

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update reader to accept str, class, object

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add test cases for various reader and level arguments

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update comment about OpenSlide cache

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Rename reader_name to backend

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add new test cases

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add unittests for openslide

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add new test cases

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* sorts

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add docstring for kwargs

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@yiheng-wang-nv @pre-commit-ci @Nic-Ma
4095 Add bundle download (#4114)
e0e2e65 
* draft download

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* update bundle download

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* add url and load

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* rename args and remove a few places

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix flake8 issue

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* enhance with reviews

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* add instantiate for load

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* fix black error

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* add unittest

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* add load to docs

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* add skip

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* add schemaerror

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* fix partial places

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* download zip bundle

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* [DLMED] restore Exception for test

Signed-off-by: Nic Ma <nma@nvidia.com>

* update ts features

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* add config_files test case

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* enhance docstring example for args_file

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
Disable pylint error and fix CI tests of new tifffile (#4162)
710781b 
* workaround

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix tifffile issue

Signed-off-by: Nic Ma <nma@nvidia.com>
rijobro and others added 29 commits June 20, 2022 21:13
@rijobro
MetaTensor non-breaking changes (#4539)
8b5ddf5 
* MetaTensor non-breaking changes

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@wyli
4530 optional SummaryWriter (#4546)
1f07913 
fixes #4530

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
Enhance type conversion of MetaTensor (#4549)
d34fa14 
* [DLMED] update type conversion

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add unit tests

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix flake8

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix typo

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli @pre-commit-ci
4351 - adds StrEnum (#4556)
6c095a8 
* adds strenum

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@Nic-Ma
Move metatensor support into dev (update inverse, runtests.sh) (#4557)
669bddf 
* [DLMED] update inverse for MetaTensor

Signed-off-by: Nic Ma <nma@nvidia.com>
@function2-llx
Wrap Type to the typing of writer parameter of SaveImage (#4561)
d6b4593 
* wrap `Type` to the typing of `writer` parameter of `SaveImage`

Signed-off-by: function2 <luolx21@mails.tsinghua.edu.cn>
@dyollb
add TORCH backend for RandHistogramShift (#4567)
ca165d8 
* add TORCH backend for RandHistogramShift

Signed-off-by: Bryn Lloyd <lloyd@itis.swiss>
@Can-Zhao
correct code examples in box_utils docstring (#4572)
9d23698 
* clean up code examle in box_utils docstring

Signed-off-by: Can Zhao <canz@nvidia.com>

* clean up code examle in box_utils docstring

Signed-off-by: Can Zhao <canz@nvidia.com>
@mueller-franzes @pre-commit-ci
Fix incorrect documentation for ResampleToMatch (#4576)
9c47101 
* fix documentation for ResampleToMatch

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Co-authored-by: Gustav Müller-Franzes <gustav.mueller-franzes@rwth-aachen.de>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@Can-Zhao
correct a bug in convert_mask_to_box (#4583)
f9b038a
@Nic-Ma
Fix error in the bundle script (#4584)
4c5c388 
[DLMED] fix error in script

Signed-off-by: Nic Ma <nma@nvidia.com>
@JohnMasoner
Add Unified Focal Loss (#4488)
78f8e74 
* Add Unified Focal Loss

Signed-off-by: JohnMasoner <masoner6429@gmail.com>
@yiheng-wang-nv @monai-bot @wyli
4502-implement-pydicomreader (#4550)
ff9ff55 
* implement pydicomreader

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* [MONAI] code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

* modify read function to return obj

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* enhance docstrings and fix errors

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* add unittest

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* adds deps

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* optional meta

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* adds consistency

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com>
@wyli
4589 enable dropout in dynunet (#4590)
d4c6521 
* 4589 enable dropout

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes docstring typo

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@deepsource-autofix @monai-bot
Move dictionary inserts to its definition (#4594)
23d9b52 
* Move dictionary inserts to its definition

* [MONAI] code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@Nic-Ma @pre-commit-ci
4578 add default return for ConfigParser (#4601)
040a4ce 
* [DLMED] add default value

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@mersad95zd @Can-Zhao @pre-commit-ci
mri utils added (#4552)
25d6208 
* mri utils added

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* fft_utils with its unit test added

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* fft_utils updated with monai data converter

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* updated fft_util's docstring

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* apps.rst updated with fft_utils docstrings under the reconstruction module

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* fft_utils docstring updated by adding dimension hins

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* fft_utils docstring updated by removing redundant output type

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* test_fft_utils.py moved to the tests folder

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* created fft_utils_t, the torch-only version of fft_utils

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fft_utils_t updated with type ignore for  mypy

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* docs/source/networks.rst updated with fft_utils_t

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* manual fix for fft_utils_t output data types

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* added support for older pytorch versions

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

* fixes mypy

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update to remove assert

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Co-authored-by: Can Zhao <69829124+Can-Zhao@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@JHancox
Hovernet and associated test script added (#4602)
91ec2b5 
* Hovernet and associated test script added

Signed-off-by: JHancox <jhancox@nvidia.com>
@vale-salvatelli
Fix the location type returned in GridPatch when padding (#4598)
112d36c 
* Fix the location type returned in GridPatch when padding

This PR fixes this issue #4597

* signing and fixing docstring

Signed-off-by: Valentina Salvatelli <vsalvatelli@microsoft.com>
@Can-Zhao
debug device conflict (#4614)
7f80288 
* debug device conflict

Signed-off-by: Can Zhao <canz@nvidia.com>

* debug device conflict

Signed-off-by: Can Zhao <canz@nvidia.com>
@wyli
4531 test/update deps versions (#4605)
edf3b74 
* ignite 0.4.9

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* pytorch docker 22.05

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* pytorch 1.8.2, 1.12.0

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update install command 1.8.2

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes mypy

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Revert "temp tests"

This reverts commit 5167d65.

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* test 22.06

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes unit tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@upupming
fix: avoid duplicate log when multiple DataStats are used (#4623)
b45794a 
* fix: avoid duplicate log when multiple DataStats are used

Signed-off-by: upupming <yimingli.cs@gmail.com>
@pre-commit-ci
[pre-commit.ci] pre-commit suggestions (#4631)
564c6be 
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.1.0 → v4.3.0](pre-commit/pre-commit-hooks@v4.1.0...v4.3.0)
- [github.com/asottile/pyupgrade: v2.31.1 → v2.34.0](asottile/pyupgrade@v2.31.1...v2.34.0)
- [github.com/hadialqattan/pycln: v1.3.3 → v1.3.5](hadialqattan/pycln@v1.3.3...v1.3.5)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@Nic-Ma @pre-commit-ci @wyli
Move metatensor support into dev branch (crop/pad) (#4548)
a2d6346 
* [DLMED] adapt Pad transform for MetaTensor

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] format code

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update inverse and spatial_pad

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update border pad

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update divisible pad

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update spatial crop

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] make thread safe

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update CenterSpatialCrop

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update scale crop

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix flake8

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update random spatial crop

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update random scale crop

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update random spatial crop samples

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] adjust Pad design

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update CropForeground

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update random weighted crop

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update RandCropPosNeg

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update rand crop by label classes

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update ResizeCropOrPad

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] restore numpy pad

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update dict spatial pad

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update border pad and divisible pad

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update spatial crop dict

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update center spatial crop

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update rand scale crop dict

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update rand spatial crop samples dict

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update crop foreground dict

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update rand weighted crop dict

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update pos neg crop dict

Signed-off-by: Nic Ma <nma@nvidia.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* [DLMED] update crop by labels dict

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update resize with pad or crop dict

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update format

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix all the mypy errors

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add crop / pad base tests

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update border pad test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update spatial crop

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update pad transforms

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update samples crop

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update crop tests

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add test for deepcopy

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix typo

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update docs

Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@wyli
Move metatensor support into dev branch (#4562)
24cf761
@wyli
compat. torch 1.7/1.8 sw integration
99b9dd7 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
4641 PadListDataCollate for metatensor (#4642)
6638abf 
fixes #4641 inverse padlist

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@vale-salvatelli
Fix casting of location dtype in GridPatch (#4635)
4ddd2bc 
Signed-off-by: vale-salvatelli <vsalvatelli@microsoft.com>
@wyli
4636 4637 backward compatible types (#4638)
e270741 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma Nic-Ma merged commit ca62306 into Nic-Ma:main Jul 8, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.