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Merged
merged 59 commits into from
Jan 5, 2022
Merged

rebase dev and add box utils #3586

merged 59 commits into from
Jan 5, 2022

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Can-Zhao
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@Can-Zhao Can-Zhao commented Jan 5, 2022

Fixes # .

Description

rebase dev
add box utils

Status

Work in progress

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.

bhashemian and others added 30 commits December 2, 2021 09:20
@bhashemian @Nic-Ma
3415 Update WSIReader (Project-MONAI#3417)
ad0f866 
* Update WSIReader level/location/size calculation

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

* Update location downsampling

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

* Update tests and add a new test case

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

* Update few names and logics

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

* Fix the dependency issue

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

* Check for imagecodecs + tifffile

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

* Remove new test case that uses too much memory

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

* Add new case and ignore level=0 for TiffFile

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

* Address comments

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

Co-authored-by: Nic Ma <nma@nvidia.com>
@wyli
update create_file_basename (Project-MONAI#3436)
035f91c 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@bhashemian
Update TiffFile backend in WSIReader (Project-MONAI#3438)
f6a0c87 
* Update TiffFile backend to read only the entire image

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@Nic-Ma
3429 Enhance the scalar write logic of TensorBoardStatsHandler (Proje…
0935d5a 
…ct-MONAI#3431)

* [DLMED] extract write logic

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>
@Nic-Ma @monai-bot
3430 support dataframes and streams in CSVDataset (Project-MONAI#3440)
f3e7cc0 
* [DLMED] add dataframe

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

* [DLMED] enhance CSV iterable dataset

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

* [DLMED] add unit tests

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

* [DLMED] fix typehints

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

* [DLMED] add comment

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] fix file close issue

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

* [DLMED] fix doc

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 @monai-bot
Add base class for workflows (Project-MONAI#3445)
8a47227 
* [DLMED] add BaseWorkflow

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>

* [DLMED] add *args, **kwargs

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@Nic-Ma @monai-bot
Enhance deprecated arg for kwargs in CSV datasets (Project-MONAI#3446)
a17813b 
* [DLMED] fix deprecated arg

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>
@yiheng-wang-nv
3293 Remove extra deep supervision modules of DynUNet (Project-MONAI#…
98c1c43 
…3427)

* enhance dynunet

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

* fix black issue

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

* use strict=False

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

* fix black 21.12 error

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

* enhance code and update docstring

Signed-off-by: Yiheng Wang <vennw@nvidia.com>
@wyli
471- fixes deprecated args (Project-MONAI#3447)
29e9ab3 
* fixes deprecated args

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

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
improve error message if reader nott available (Project-MONAI#3457)
a7bc4a3 
improve error message if reader nott available
@wyli
adds the missing imports (Project-MONAI#3462)
d2543ad 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
revise MILModel docstring (Project-MONAI#3459)
82576e7 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
deprecate reduction (Project-MONAI#3464)
4b5ad0b 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma @monai-bot
3444 Add DatasetFunc (Project-MONAI#3456)
5b36d02 
* [DLMED] add dataset generator

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

* [DLMED] add DatasetGenerator

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

* [DLMED] update according to comments

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

* [MONAI] python code formatting

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

* [DLMED] fix wrong test

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

* [DLMED] simplify according to comments

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

* [DLMED] remove return

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

* [DLMED] update rtol for CI

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@Nic-Ma
Add missing components to API doc (Project-MONAI#3468)
89f0bd4 
* [DLMED] add missing docs

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

* [DLMED] add missing components

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

* [DLMED] fix test

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma @monai-bot
3466 3467 Add channel_wise and correct doc-string (Project-MONAI#3469)
d386213 
* [DLMED] add channel-wise

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

* [DLMED] update according to comments

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

* [DLMED] fix typo

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* [DLMED] skip test if before 1.7

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* [MONAI] python code formatting

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@Nic-Ma
[DLMED] remove cls (Project-MONAI#3475)
a4c1300 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
Add Iteration base class (Project-MONAI#3472)
360c52f 
* [DLMED] add Iteration base class

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

* [DLMED] update according to comments

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* [DLMED] update according to comments

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@yiheng-wang-nv
fix link error (Project-MONAI#3488)
cb70e13 
Signed-off-by: Yiheng Wang <vennw@nvidia.com>
@Nic-Ma
3465 Support string as dtype (Project-MONAI#3478)
9ef0070 
* [DLMED] support string dtype

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

* [DLMED] fix typo

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

* [DLMED] enhance dtype in ToCupy

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] update to 0.4.7 (Project-MONAI#3483)
7a66f18 
Signed-off-by: Nic Ma <nma@nvidia.com>
@bhashemian
Improve NVTX Range Naming (Project-MONAI#3484)
f6648a3 
* Update to not include number for the name of the first range

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

* Update CuCIM and TorchVision wrappers to include name

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

* Update nvtx range to append undelying class for wrapper tranforms

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

* Add new test cases to cover changes

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* Update cucim and torchvision check

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@Nic-Ma
3471 3491 Add example images for intensity transforms (Project-MONAI#…
9927691 
…3494)

* [DLMED] add missing images

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

* [DLMED] fix 3471

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

* [DLMED] fix AsDiscrete

Signed-off-by: Nic Ma <nma@nvidia.com>
@ebrahimebrahim
Make bending energy loss invariant to resolution (Project-MONAI#3493)
88d91d6 
* make bending energy loss invariant to resolution

fixes Project-MONAI#3485

Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com>

* set BendingEnergyLoss default normalize to False

Maybe it's more important that the default behavior match usage of the
term "bending energy" elsewhere, rather than that it be the most
convenient behavior.

Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com>
@wyli
Removes redundant casting -- ensure tuple (Project-MONAI#3495)
3761ee0 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
3498 Correct kwargs arg for convert_to_torchscript (Project-MONAI…
a255648 
…#3499)

* [DLMED] correct kwargs

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

* [DLMED] fix grammar

Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
update tests with 1.10.1 (Project-MONAI#3500)
531c276 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
3501 Add dict version SavitzkyGolaySmoothd (Project-MONAI#3502)
d663d78 
* [DLMED] add SavitzkyGolaySmoothd

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

* [DLMED] fix typo

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

* [DLMED] update according to comments

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@wyli
remove file (Project-MONAI#3507)
d2861a2 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
avoid 60.0.0 (Project-MONAI#3514)
29779d1 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
ericspod and others added 27 commits December 21, 2021 00:05
@ericspod @pre-commit-ci
@monai-bot @Nic-Ma
Adding Torchscript utility functions (Project-MONAI#3138)
9734478 
* Adding Torchscript utility functions

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

* [MONAI] python code formatting

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* Adding Torchscript utility functions

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* Added test for extra files

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

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* Update

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@Nic-Ma
3517 Refine AddCoordinateChannels transform (Project-MONAI#3524)
8e2ade5 
* [DLMED] change to utility transforms

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

* [DLMED] enhance args

Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
3521 Copyright header update (Project-MONAI#3522)
1516ca7 
* adds missing item

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

* update the contributing guide

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

* update copyright headers

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
3521 - adds a util to check the licence info (Project-MONAI#3523)
299a0d1 
* util to check the licence info

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

* update flags

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

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
3350 Remove PyTorch 1.5.x related logic and mark versions for all new…
58ded72 
… APIs (Project-MONAI#3526)

* [DLMED] clarify old APIs

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

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
3533 Update PyTorch docker to 21.12 (Project-MONAI#3534)
08f9bac 
* [DLMED] update to 21.12

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

* [DLMED] update according to comments

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* [DLMED] add PyTorch 1.9 test

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@Nic-Ma
3531 Add args to subclass of CacheDataset (Project-MONAI#3532)
9caa1d0 
* [DLMED] add missing args

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

* [DLMED] update according to comments

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* [DLMED] update progress arg

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@Nic-Ma
3525 Fix invertible issue in OneOf compose (Project-MONAI#3530)
6767959 
* [DLMED] fix oneof

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

* [DLMED] add more unit tests

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* [DLMED] update index

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* [DLMED] update according to comments

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* Revert "[DLMED] update according to comments"

This reverts commit c6c3a35.

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* Revert "[DLMED] update index"

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@wyli
3535 - drop python 36 support (Project-MONAI#3536)
e655b4e 
* drop py36 support

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* drop 20.09 test because of python min version 3.6

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* update tests

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* error->warning, revise copyright

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@wyli
3541 has cupy check (Project-MONAI#3544)
21c5f6d 
* has cupy check

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

* update based on comments

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@wyli
3053 release *_dist.py tests memory to avoid OOM (Project-MONAI#3537)
7f23f38 
* adds min. memory testing utils

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* include valueerror for robust outcome

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* ensure float

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* msg improvements

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* update threshold

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* remove ref

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* separate disttests

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@Nic-Ma
3539 Remove decollate warning (Project-MONAI#3545)
29bc93b 
* [DLMED] remove warning

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

* [DLMED] fix typo

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@Nic-Ma @wyli
[DLMED] enhance set_determinism (Project-MONAI#3547)
df75199 
Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@ericspod @pre-commit-ci @monai-bot
Smooth Deform (Project-MONAI#3551)
2e492a9 
* Adding smooth deform transform

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

* Update

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* Updates

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* Type fixing

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* Fix

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* Fix for moveaxis

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* Fix for moveaxis

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* Adding example images, random field sized reduced to (10,10,10)

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* Changed backend

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@wyli @ericspod
3552 - runtest.sh defaults to no build/install (Project-MONAI#3555)
05f8219 
* runtest.sh defaults to no build/install

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

* following test case conventions for multiprocessing

- adding `_dist` to multiprocessing test cases
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* exclude lmdbdataset tests in min_tests

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Remove apply_same_field (Project-MONAI#3556)
c8e7fe1 
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@wyli
skipping pretraining network loading when downloading is unsuccessful (…
885d5b9 
…Project-MONAI#3558)

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[DLMED] fix mypy errors (Project-MONAI#3562)
ba23afd 
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3559 Enhance DatasetSummary for several points (Project-MONAI#3560)
adca1bb 
* [DLMED] update dataset summary

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* [DLMED] enhance data type

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* [DLMED] fix pickle issue

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@Can-Zhao
add box util in monai/data
06ae905
@Can-Zhao
add box util in monai/data
60bf24d
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[pre-commit.ci] pre-commit suggestions (Project-MONAI#3568)
9417ff2 
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3565 - adds metadata when loading dicom series (Project-MONAI#3566)
a7835ab 
* adds metadata when loading dicom series

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* fixes timed tests

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* update based on comments

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3580 - create codeql-analysis.yml (Project-MONAI#3579)
bb4ad5f 
* Create codeql-analysis.yml

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* build cpp

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

* fixes Multiplication result converted to larger type

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

* fixes url parsing

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
498 Add logger_handler to LrScheduleHandler (Project-MONAI#3570)
4bd13fe 
* [DLMED] add log handler

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

* [DLMED] fix CI tests

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

* [DLMED] fix CI test

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

* [DLMED] test CI

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

* [DLMED] fix logging

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

* [DLMED] temp test

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

* [DLMED] fix wrong unit test

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

* [DLMED] fix wrong test cases

Signed-off-by: Nic Ma <nma@nvidia.com>
@Can-Zhao
Merge pull request #1 from Can-Zhao/box_util
564cd2a 
Box util
@Can-Zhao
Merge branch 'Project-MONAI:dev' into detection
69a667f
@Can-Zhao Can-Zhao merged commit dd74c59 into Project-MONAI:feature/1741-detection Jan 5, 2022
Can-Zhao added a commit that referenced this pull request Jan 5, 2022
@Can-Zhao
Revert "rebase dev and add box utils (#3586)"
d1addce 
This reverts commit dd74c59.
Can-Zhao added a commit that referenced this pull request Jan 5, 2022
@Can-Zhao
Revert "rebase dev and add box utils (#3586)" (#3587)
397a661 
This reverts commit dd74c59.
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8 participants
@Can-Zhao @bhashemian @wyli @Nic-Ma @yiheng-wang-nv @rijobro @ebrahimebrahim @ericspod