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merge master #32

Merged
merged 31 commits into from
Feb 24, 2021
Merged

merge master #32

merged 31 commits into from
Feb 24, 2021

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Nic-Ma
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@Nic-Ma Nic-Ma commented Feb 24, 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.

wyli and others added 30 commits February 2, 2021 09:32
@wyli
1534 type hints numpy 1 20 (#1536)
c415509 
* numpy dtype alias

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

* is_tensor => isinstance

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

* type of dtype

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

* relaxes some typing constraints

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

* fixes unit tests

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

* update based on the comments

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

* fixes docstring typos

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
1512 rand_gaussian_noised with multiple keys (#1530)
5e8d2a9 
* rand_gaussian_noised with multiple keys

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

* update key names

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

* clear list of noise before randomising

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

* add type

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

* bug fix

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

* use ensure_tuple_rep

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@Nic-Ma
1478 Fix TorchScript issue in AHNet with PyTorch 1.5 (#1538)
97ff1e0 
* [DLMED] fix TorchScript issue in AHNet

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

* [DLMED] add test cases

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

* [DLMED] fix torchscript issue in PyTorch 1.5

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma @monai-bot
1533 Fix distributed data parallel issue in ClassificationSaver (#1535)
26581a0 
* [DLMED] fix distirbuted data parallel issue in ClassificationSaver

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

* [MONAI] python code formatting

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

* [DLMED] fix min test

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

* [DLMED] add @SkipIfBeforePyTorchVersion((1, 7))

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

* [DLMED] update according to comments

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

* [DLMED] fix typo

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

* [MONAI] python code formatting

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@Nic-Ma @wyli
1539 Add warning message to SmartCache (#1540)
fbab554 
* [DLMED] update SmartCacheDataset docs and warning

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

* isAlive => is_alive

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

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
1531 Fix evenly divisible issue in the AUC metric (#1532)
f7565bf 
* [DLMED] fix evenly divisible issue in AUC metric

Signed-off-by: Nic Ma <nma@nvidia.com>
@kate-sann5100
1525 add MultiScaleLoss (#1544)
2021f24
@Nic-Ma @monai-bot @wyli
1542 Add RandLambdad transform (#1546)
bcdee8c 
* [DLMED] add RandLambdad transform

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

* [DLMED] add doc-strings

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

* [MONAI] python code formatting

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

* [DLMED] update according to comments

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

* [DLMED] fix typo

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

* [DLMED] change to rtol=1e-05

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

* [MONAI] python code formatting

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

* fixes seeds

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>
@Nic-Ma
1555 Fix typo in SegResNet doc-string (#1563)
5a237c6 
* [DLMED] fix typo in the doc-string of SegResNet

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

* [DLMED] update according to Yiheng's comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] Enhance doc-string of transforms (#1562)
aab702a 
Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
extention -> extension (#1565)
866d53d 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma @monai-bot
1570 Fix distributed issue in ClassificationSaver (#1571)
8d70890 
* [DLMED] fix classification saver issue

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

* [DLMED] enhance distributed tests

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

* [MONAI] python code formatting

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@Nic-Ma
1556 Optimize the numpy computation for spatial axes (#1572)
910b1d4 
* [DLMED] Enhance doc-string of transforms

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

* [DLMED] optimize the numpy computation

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

* [DLMED] fix flake8 issue

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

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma @monai-bot
Add base class for TensorBoard handlers (#1573)
af1ffd6 
* [DLMED] add base class for TensorBoard handlers

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

* [MONAI] python code formatting

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

* [DLMED] enhance integration test with TensorBoard writer

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

* [MONAI] python code formatting

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

* [DLMED] add close method

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

* [DLMED] Enhance MetricsSaver doc-strings

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@kate-sann5100 @wyli
1559 add DVF2DDF (#1566)
3bdf0c8 
* 1559 add DVF2DDF

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1559 add gradient test

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* update docs; test cases

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

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@yiheng-wang-nv
Modify dynunet forward function (#1596)
3f16c21 
Signed-off-by: Yiheng Wang <vennw@nvidia.com>
@YuanTingHsieh
Add deepgrow dataset (#1581)
1b170d8 
* Add deepgrow dataset

Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com>

* Fix CI/CD issue

Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com>

* Fix issues based on review

Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com>
@Nic-Ma @monai-bot
1568 Enhance tests to use self random state (#1599)
181f633 
* [DLMED] change tests to use self random state

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

* [MONAI] python code formatting

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

* [DLMED] fix CI tests

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@wyli
Revert "1568 Enhance tests to use self random state (#1599)" (#1607)
19a9f05 
This reverts commit 181f633.

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@adamaji
Update minimum ITK version to 5.0 (#1609)
5b72d05 
Signed-off-by: Adam Aji <3487395+adamaji@users.noreply.github.com>
@adamaji
Throw warning when reading NRRD05 files to upgrade to ITK >= 5.2 (#1602)
e9bf574 
Signed-off-by: Adam Aji <3487395+adamaji@users.noreply.github.com>
@YuanTingHsieh
Add deepgrow interaction (#1582)
5dffc11 
* Add deepgrow interaction

Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com>

* Fix review comments

Signed-off-by: Sachidanand Alle <salle@nvidia.com>
@YuanTingHsieh
Add deepgrow training transforms (#1579)
46cc0e5 
* Add DeepGrow 2D/3D transforms

Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com>

* Fix docstrings

Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com>

* Remove inference transform for smaller PR

Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com>

* Remove unused imports

Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com>

* Fix review comments

Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com>

* Fix review comments

Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com>
@Nic-Ma
1575 Add SaveImage and SaveImaged transforms (#1612)
a664506 
* [DLMED] add SaveImage and SaveImaged transforms

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

* [DLMED] fix typo

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

* [DLMED] fix flake8 issues

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

* [DLMED] update according to comments

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

* [DLMED] fix CI tests

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

* [DLMED] update according to comments

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

* [DLMED] add ignore

Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
1545 upgrade base image to pytorch 20.12 (#1613)
75b78cd 
* test new image

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

* temp no cron

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

* fixes unit tests

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

* adds base docker test

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

* undo temp tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma @monai-bot
1578 Add support to resume previous best metrics in CheckpointSaver (#…
cb5f899 
…1608)

* [DLMED] add support to resume metrics in CheckpointSaver

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

* [MONAI] python code formatting

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

* [DLMED] fix doc-string

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@wyli
1618 Fixes Dockerfile (#1619)
d22c112 
* update dockerfile

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

* temp tests

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

* Revert "temp tests"

This reverts commit 9cbfaa9.

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
determine if is_quick without using decorator (#1620)
3e7f53f 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro
make random inverse affine matrix (#1621)
a894adc 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro
Compose len (#1622)
6bdc8c6 
* Compose len

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

* Compose.flatten()

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro
unify progress bar for datasets (#1625)
db2dbb0 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@Nic-Ma Nic-Ma merged commit cd16a13 into Nic-Ma:master Feb 24, 2021
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7 participants
@Nic-Ma @wyli @rijobro @kate-sann5100 @yiheng-wang-nv @YuanTingHsieh @adamaji