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rebase dev and add box utils#3586

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Can-Zhao merged 59 commits intoProject-MONAI:feature/1741-detectionfrom
Can-Zhao:detection
Jan 5, 2022
Merged

rebase dev and add box utils#3586
Can-Zhao merged 59 commits intoProject-MONAI:feature/1741-detectionfrom
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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
* Update WSIReader level/location/size calculation

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

* Update location downsampling

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

* Update tests and add a new test case

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

* Update few names and logics

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

* Fix the dependency issue

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

* Check for imagecodecs + tifffile

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

* Remove new test case that uses too much memory

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

* Add new case and ignore level=0 for TiffFile

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

* Address comments

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

Co-authored-by: Nic Ma <[email protected]>
* Update TiffFile backend to read only the entire image

Signed-off-by: Behrooz <[email protected]>
…ct-MONAI#3431)

* [DLMED] extract write logic

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 according to comments

Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add dataframe

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

* [DLMED] enhance CSV iterable dataset

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]>

* [DLMED] add comment

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 according to comments

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

* [DLMED] fix file close issue

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

* [DLMED] fix doc

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 BaseWorkflow

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

* [DLMED] fix typo

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

* [MONAI] python code formatting

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

* [DLMED] add *args, **kwargs

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

Co-authored-by: monai-bot <[email protected]>
* [DLMED] fix deprecated arg

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]>
…3427)

* enhance dynunet

Signed-off-by: Yiheng Wang <[email protected]>

* fix black issue

Signed-off-by: Yiheng Wang <[email protected]>

* use strict=False

Signed-off-by: Yiheng Wang <[email protected]>

* fix black 21.12 error

Signed-off-by: Yiheng Wang <[email protected]>

* enhance code and update docstring

Signed-off-by: Yiheng Wang <[email protected]>
* fixes deprecated args

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

* update based on comments

Signed-off-by: Wenqi Li <[email protected]>
improve error message if reader nott available
* [DLMED] add dataset generator

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

* [DLMED] add DatasetGenerator

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

* [DLMED] update according to comments

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

* [MONAI] python code formatting

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

* [DLMED] fix wrong test

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

* [DLMED] simplify according to comments

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

* [DLMED] remove return

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

* [DLMED] update rtol for CI

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

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

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

* [DLMED] add missing components

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

* [DLMED] fix test

Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add channel-wise

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

* [DLMED] update according to comments

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

* [DLMED] fix typo

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

* [DLMED] skip test if before 1.7

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 Iteration base class

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] support string dtype

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

* [DLMED] fix typo

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

* [DLMED] enhance dtype in ToCupy

Signed-off-by: Nic Ma <[email protected]>
* Update to not include number for the name of the first range

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

* Update CuCIM and TorchVision wrappers to include name

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

* Update nvtx range to append undelying class for wrapper tranforms

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

* Add new test cases to cover changes

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

* Update cucim and torchvision check

Signed-off-by: Behrooz <[email protected]>
…3494)

* [DLMED] add missing images

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

* [DLMED] fix 3471

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

* [DLMED] fix AsDiscrete

Signed-off-by: Nic Ma <[email protected]>
* make bending energy loss invariant to resolution

fixes Project-MONAI#3485

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

* 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 <[email protected]>
…#3499)

* [DLMED] correct kwargs

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

* [DLMED] fix grammar

Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add SavitzkyGolaySmoothd

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

* [DLMED] fix typo

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

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>
ericspod and others added 27 commits December 21, 2021 00:05
* Adding Torchscript utility functions

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

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

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

* [MONAI] python code formatting

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

* Adding Torchscript utility functions

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

* Added test for extra files

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

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

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

* Update

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

* Update

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

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

* Update

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* Update

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* Updates

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

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

* Updates

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

* Updates

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

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: monai-bot <[email protected]>
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* [DLMED] change to utility transforms

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

* [DLMED] enhance args

Signed-off-by: Nic Ma <[email protected]>
* adds missing item

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

* update the contributing guide

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

* update copyright headers

Signed-off-by: Wenqi Li <[email protected]>
* util to check the licence info

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

* update flags

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

* update based on comments

Signed-off-by: Wenqi Li <[email protected]>
… APIs (Project-MONAI#3526)

* [DLMED] clarify old APIs

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

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>
* [DLMED] update to 21.12

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

* [DLMED] update according to comments

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

* [DLMED] add PyTorch 1.9 test

Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add missing args

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

* [DLMED] update according to comments

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

* [DLMED] update progress arg

Signed-off-by: Nic Ma <[email protected]>
* [DLMED] fix oneof

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

* [DLMED] add more unit tests

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

* [DLMED] update index

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

* [DLMED] update according to comments

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

* Revert "[DLMED] update according to comments"

This reverts commit c6c3a35.

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

* Revert "[DLMED] update index"

This reverts commit 649a7c5.

Signed-off-by: Nic Ma <[email protected]>
* drop py36 support

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

* drop 20.09 test because of python min version 3.6

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

* update tests

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

* error->warning, revise copyright

Signed-off-by: Wenqi Li <[email protected]>
* has cupy check

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

* update based on comments

Signed-off-by: Wenqi Li <[email protected]>
* adds min. memory testing utils

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

* include valueerror for robust outcome

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

* ensure float

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

* msg improvements

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

* update threshold

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

* remove ref

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

* separate disttests

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

* update based on comments

Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] remove warning

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

* [DLMED] fix typo

Signed-off-by: Nic Ma <[email protected]>
* Adding smooth deform transform

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

* Update

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

* Updates

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

* Docs update

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

* Type fixing

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

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

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

* [MONAI] python code formatting

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

* Fix

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

* Fix

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

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

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

* Fix for moveaxis

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

* Fix for moveaxis

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

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

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

* Changed backend

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

* [MONAI] python code formatting

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

* Tweak

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: monai-bot <[email protected]>
* runtest.sh defaults to no build/install

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

* following test case conventions for multiprocessing

- adding `_dist` to multiprocessing test cases
- decouple multiprocessing LMDB tests from `test_lmdbdataset`

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

* exclude lmdbdataset tests in min_tests

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

Co-authored-by: Eric Kerfoot <[email protected]>
* [DLMED] update dataset summary

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

* [DLMED] enhance data type

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

* [DLMED] fix pickle issue

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

Co-authored-by: Wenqi Li <[email protected]>
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.1.0](pre-commit/pre-commit-hooks@v4.0.1...v4.1.0)
- [github.com/asottile/pyupgrade: v2.29.0 → v2.31.0](asottile/pyupgrade@v2.29.0...v2.31.0)
- [github.com/asottile/yesqa: v1.2.3 → v1.3.0](asottile/yesqa@v1.2.3...v1.3.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* adds metadata when loading dicom series

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

* fixes timed tests

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

* update based on comments

Signed-off-by: Wenqi Li <[email protected]>
* Create codeql-analysis.yml

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

* build cpp

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

* fixes Multiplication result converted to larger type

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

* fixes url parsing

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

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

* [DLMED] fix CI tests

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

* [DLMED] fix CI test

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

* [DLMED] test CI

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

* [DLMED] fix logging

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

* [DLMED] temp test

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

* [DLMED] fix wrong unit test

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* [DLMED] fix wrong test cases

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@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 added a commit that referenced this pull request Jan 5, 2022
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8 participants