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merge master #192

Merged
merged 22 commits into from
Aug 10, 2021
Merged

merge master #192

merged 22 commits into from
Aug 10, 2021

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Nic-Ma
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@Nic-Ma Nic-Ma commented Aug 10, 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 -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

wyli and others added 22 commits July 23, 2021 09:52
@wyli
fixes randbiasfield (#2645)
a566dc6 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
1979 Enhance TTA to align with Invertd args and support no label (#2654)
325775b 
* [DLMED] enhance TTA

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

* [DLMED] fix typo

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma @yiheng-wang-nv @wyli
2635 Enhance doc-string of UNet for spatial size (#2641)
141e9db 
* [DLMED] enhance doc-string for spatial shape

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

* [DLMED] add ill test case

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

* [DLMED] update test error

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

* update docstring and add more test cases

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

* [DLMED] add link to doc-string

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

* [DLMED] enhance doc-string

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

Co-authored-by: Yiheng Wang <vennw@nvidia.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@wyli
new theme (#2657)
8d4f45f 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
2635 enhance UNet doc for the typical use case (#2659)
aaeebd6 
* [DLMED] enhance doc-string

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

* [DLMED] enhance the sanity check

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

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma @wyli
2648 add RandCoarseDropout transform (#2658)
c4833f5 
* [DLMED] add RandCoarseDropout

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

* [DLMED] fix typo

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

* [DLMED] add dict version transform

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

* [DLMED] updated according to comments

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

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@wyli
add citation metadata (#2663)
35e45df 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
2648 Add LongestRescale transform (#2662)
d8613b2 
* [DLMED] init the transform

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

* [DLMED] update doc-string

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

* [DLMED] complete array transform

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

* [DLMED] add unit tests

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

* [DLMED] add dict transform and inverse tests

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

* [DLMED] fix mypy type

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

* [DLMED] change to enhance Resize transform

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] fix TTA

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

* [DLMED] remove tests

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

* [DLMED] fix mypy error

Signed-off-by: Nic Ma <nma@nvidia.com>
@drbeh @nsrivathsa
Stain normalization (#2666)
30ce63d 
* added stain norm and tests

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* import changes

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* changed stain extraction tests

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* edited stain norm tests

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* convert floats to float32

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* added uint8 assumption to docstring

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* add error case

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* formatting change

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* modify tests wrt cupy import

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* minor change to pass lint test

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* import changes

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* refactored classes

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* Restructure and rename transforms

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

* added dict transform

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* Move stain_extractor to init

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

* Exclude pathology transform tests from mini tests

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

* Fix type checking for cupy ndarray

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

* Include pathology transform tests

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

* Update to cupy 9.0.0

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

* Remove exact version for cupy

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

* add to docs

Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com>

* Organize into stain dir

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

* Add/update init files

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

* Transit all from cupy to numpy

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

* Update imports

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

* Update test cases for numpy

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

* Rename to NormalizeHEStains and NormalizeHEStainsD

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

* Add dictionary variant names

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

* Fix typing and formatting

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

* Fix docs

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

* Update test cases

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

* Fix clip max

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

* Fix var typing

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

* Fix a typing issue

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

* Update default values, and change D to d

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

* Update docs

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

* Add image value check

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

* Add test cases for negative and invalid values

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

Co-authored-by: Neha Srivathsa <nsrivathsa@nvidia.com>
Co-authored-by: nsrivathsa <81264348+nsrivathsa@users.noreply.github.com>
@yiheng-wang-nv
2583 Add DatasetCalculator (#2616)
390fe7f 
* Add DatasetCalculator

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

* update docstring

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

* use multiprocessing

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

* update to use dataset and other places

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

* update to support array return

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

* update with new testcases and change name

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

* update min test

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

* update unittest

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

* fix vstack error

Signed-off-by: Yiheng Wang <vennw@nvidia.com>
@Nic-Ma
2648 Enhance RandLambda to execute deterministic transforms for rando…
607a31a 
…m part of dataset (#2667)

* [DLMED] add RandCompose

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

* [DLMED] add unit tests

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

* [DLMED] change to enhance RandLambda

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

* [DLMED] remove RandCompose

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

* [DLMED] fix format

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

* [DLMED] enhance doc

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

* [DLMED] add inverse operation

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

* [DLMED] add more tests

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

* [DLMED] fix subprogress issue

Signed-off-by: Nic Ma <nma@nvidia.com>
@drbeh
Restructure pathology transforms (#2671)
7f42efe 
* Restructure transforms into a directory

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

* Fix a typo

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

Co-authored-by: Behrooz <3968947+behxyz@users.noreply.github.com>
@yanielc
Updated RandKSpaceSpikeNoised. Collected Fourier mappings. (#2665)
4f7371a 
* Moved fourier functions to their own class. Modified RandKSpaceSpikeNoised.

1. Allow RandKSpaceSpikeNoised to work with arbitrary keys.
2. Introduced Fourier transform to keep the forward/backward fourier mappings.

Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>

* removed old code

Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>

* Ignore torch.fft tests if not present

Ignore tests with versions of Pytorch which lack the module fft.

Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>

* update

Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>

* typing update

Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>

* added unit test for Fourier

Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>

* added unit test for Fourier

Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>

* fixing black

Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>
@tvercaut
Change MONAI author from a person to en entity (#2690)
9ecb0e1 
This is to address an issue in the bibtex conversion.

Signed-off-by: Tom Vercauteren <tom.vercauteren@kcl.ac.uk>
@Nic-Ma @monai-bot
2679 Add IntensityStats transform to record intensity statistics into…
482ff5d 
… meta data (#2685)

* [DLMED] add IntensityStats transform

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

* [DLMED] add unit tests

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

* [DLMED] add dict version transform

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

* [DLMED] enhance ShiftIntensity transform

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

* [DLMED] fix typo

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

* [DLMED] change to utility

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

* [DLMED] adjust to look_up_option

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

* [DLMED] add multi-processing test

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

* [DLMED] add mask option

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] fix pickle issue

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

* [DLMED] enhance error message

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

* [DLMED] add pickle test

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

* [MONAI] python code formatting

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

* [DLMED] enhance pickle test

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@Nic-Ma
2687 2688 Enhance doc-strings of Affine related transforms (#2693)
f6ad4ba 
* [DLMED] update doc-strings of Affine transforms

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

* [DLMED] fix format issue

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

* [DLMED] update according to comments

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

* [DLMED] remove coord link

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] update int method (#2696)
03a8372 
Signed-off-by: Nic Ma <nma@nvidia.com>
@madil90
Increase timeout of tests (#2711)
4298b14 
Signed-off-by: Mohammad Adil <madil@nvidia.com>
@wyli
2499 adds 2d/3d support of patchembedding, ViT, and unetr model (#2698)
62425d7 
* 2d/3d patchembedding

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

* minor updates for selfattention

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

* 2d vit

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

* fixes type hint

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

* update unetr

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

* fixes unit test

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Spenhouet
[2678] Add transform to fill holes and to filter (#2692)
945e21c 
* Add transform to fill holes and to filter (#2678)

Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de>

* Change name of label filter class (#2678)

Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de>

* Change fill holes to growing logic (#2678)

Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de>

* Fix missing entry in min_tests (#2678)

Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de>

* Fix review comments (#2678)

Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de>

* Remove batch dim and add one-hot handling (#2678)

Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de>

* [MONAI] python code formatting

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

Co-authored-by: Sebastian Penhouet <sebastian.penhouet@airamed.de>
@deepsource-autofix @monai-bot
Remove unnecessary use of comprehension (#2719)
1ffa909 
* Remove unnecessary use of comprehension

* Remove unnecessary comprehension (#2718)

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>

* Refactor unnecessary `else` / `elif` when `if` block has a `return` statement (#2717)

* Refactor unnecessary `else` / `elif` when `if` block has a `return` statement

* Unnecessary `else`/`elif` used after `raise` PYL-R1720

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

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* Replace ternary syntax with if expression (#2716)

* Replace ternary syntax with if expression

* fixes Duplicate dictionary keys PYL-W0109

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

* remove Unused variable data_

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

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [MONAI] python code formatting

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

* fixes scaler type

Signed-off-by: Wenqi Li <wenqil@nvidia.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
[DLMED] add select_fn for MaskIntensity (#2726)
2f1c7a5 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma Nic-Ma merged commit ed6b846 into Nic-Ma:2691-histogram-intensity Aug 10, 2021
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8 participants
@Nic-Ma @wyli @drbeh @yiheng-wang-nv @yanielc @tvercaut @madil90 @Spenhouet