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merge master #3

Merged
merged 19 commits into from
Jan 11, 2021
Merged

merge master #3

merged 19 commits into from
Jan 11, 2021

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Nic-Ma
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@Nic-Ma Nic-Ma commented Jan 11, 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.

Nic-Ma and others added 19 commits December 17, 2020 11:59
@Nic-Ma
[DLMED] add missing import (#1376)
09638a7 
Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
adds jpeg (#1379)
1608b10 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
[DLMED] add missing arg in GANTrainer (#1383)
b7ecd7b 
Signed-off-by: Nic Ma <nma@nvidia.com>
@charliebudd
1198 efficient differentiable bilateral filter (#1375)
70be9ab 
* Initial cpu implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* hue speed increase moving away from torch tensors

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* allowing generic channel dimension size

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* allowing generic dimensionality

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* manual testing script for bilateral filter

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* Initial commit of CRF using permutohedral lattice to optimise message passing, implementation from https://github.com/SamuelJoutard/Permutohedral_attention_module

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* temporary example scripts demonstrating the usage of crf and phl, and some data to process

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* alternate phl implementation using a more efficient cuda hashtable, code currently untested due to windows build issues, implementation from https://github.com/SamuelJoutard/Permutohedral_attention_module

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* c++ cpu permutohedral lattice implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* comparison script

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* cleaning

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* backwards pass

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* initial cuda brute force kernel

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* reverting setup.py

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* working cuda kernel for brute force 2d kernel

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing unresolved symbols when compiling without cuda

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* removing macros file

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* placeholder cuda phl implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* changing test case color sigma

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* Initial import of reference cuda phl implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing cuda kernel color weight error

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* initial edits to cuda phl code

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing errors in cuda phl implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* removing logging from cuda phl

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* using template data_ptr function

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixed cpu phl implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* updating cpu phl to run on arbitrary input dimensions and channles

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* 2d and 3d testing scripts

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* Generalising permutohedral implementation to remove independance on width and height

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* removing width and height from permutohedral filter function and implementing templated feature creation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixed typo

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* exteneding 3d testing script

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* generalising bruteforce cuda implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* updating testing scripts

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* file organisiation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing weight error in cpu bruteforce implementation, also inlineing functions

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* some refactoring and introducing proper batch handling

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing indexing error at border

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing some artifacts in cuda phl for high color sigmas

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* fixing gaussian kernel function for cpu and cuda bruteforce

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* ensuring kernel is an odd numbered size

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* adding tests for precised implementation

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* adding approximate imlpementation test

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* templating implementations based on scalar_type

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* cleaning up

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* code formatting

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* removing half precision implementation for permutohedral due to errors caused on windows

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* skipping cuda tests if cuda missing

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* reformating

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* adding unit test skip based on cpp extention availablility

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* removing unused import

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* changing to  use of THCatomic add

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* adding missing licenses

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* clang reformat

Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>
@rijobro
update contributing and normalis* -> normaliz* (#1388)
36b8302 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@Nic-Ma
[DLMED] add output_dtype (#1394)
f20e132 
Signed-off-by: Nic Ma <nma@nvidia.com>
@rijobro
with eval_mode(net): (#1384)
a4b1144 
* eval_mode

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

* DynUnetSupervision unittest shouldnt use eval_mode

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

* move to device

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@Nic-Ma
1390 Enhance DynUNet with get_feature_maps API (#1393)
e2c0ed2 
* [DLMED] add get_feature_maps API to dynunet

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

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
adds missing desc (#1403)
0c2411e 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli @Nic-Ma @IsaacYangSLA
part of #926 (#1368)
1924b43 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Co-authored-by: Nic Ma <nma@nvidia.com>
Co-authored-by: Isaac Yang <isaacy@nvidia.com>
@yiheng-wang-nv
Implement dice cross entropy loss (#1409)
115f146 
Signed-off-by: yiheng-wang-nv <vennw@nvidia.com>
@rijobro
Unify visualisation (#1381)
a74fef9 
* unify visualisation
@kate-sann5100
1405 add bending energy loss (#1408)
5aa5e16 
* 1405 add bending energy loss

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
@danielschulz
Fix failures from many pulls from hub.docker.com (Done) (#1406)
db831ae 
* changed year 2020 in copyright to "2020 - 2021" for both occurences

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* added SHA256 check before unpacking downloaded artifacts
added list of Nvidia maintainers
resolves: "docker image tests failed due to dockerhub limitation #1380"

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* added danielschulz-specific changes for GitHu Actions to work properly

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* added test

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* revoked test line

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* migrated code to local registry instead of hub.docker.com to circumvent rate limiting on it
remark: do not use it as pull-through cache as this would not work with static labels and docker images would diverge from one another

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* reverted back local-only changes

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* improved checking integrity of NGC CLI

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* removed typo in GH repository variable

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* added remark

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>

* improved MAINTAINER label
got rid of "as base" extension in FROM -- seems not be be pickup downwards (is no multi-stage Docker build -- hence: removed)

Signed-off-by: Daniel Schulz danielschulz2005@hotmail.com <danielschulz2005@hotmail.com>
@wyli
fixes dockerfile (#1413)
db7bf89 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
Wildcard import (#1411)
1f74ca2 
add `__all__` and `remove import *`. Update CONTRIBUTING.md
@wyli @IsaacYangSLA
Fixes ci (#1416)
53c145d 
* temp tests

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

* fixes typo

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

* temp tests

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

* fixes docker login warning

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

* Revert "temp tests"

This reverts commit 99c6d20.

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

* Revert "temp tests"

This reverts commit c529bf9.

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

Co-authored-by: Isaac Yang <isaacy@nvidia.com>
@IsaacYangSLA
Improve docker build process (#1419)
a4ef691 
* Improve docker build process, fixes #1276
@kate-sann5100
1412 local normalized cross correlation (#1415)
1544d0c 
* 1412 add local normalized cross correlation

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
@Nic-Ma Nic-Ma merged commit 60639e3 into Nic-Ma:1420-enhance-infer-doc Jan 11, 2021
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8 participants
@Nic-Ma @wyli @yiheng-wang-nv @charliebudd @rijobro @kate-sann5100 @danielschulz @IsaacYangSLA