merge master #8
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Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Nic Ma <nma@nvidia.com>
* 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>
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Signed-off-by: Nic Ma <nma@nvidia.com>
* 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>
* [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>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: yiheng-wang-nv <vennw@nvidia.com>
* unify visualisation
* 1405 add bending energy loss Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
* 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>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
add `__all__` and `remove import *`. Update CONTRIBUTING.md
* 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>
* Improve docker build process, fixes #1276
* 1412 add local normalized cross correlation Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
* Add .deepsource.toml Signed-off-by: Devdutt Shenoi <devdutt@outlook.in> * Remove unnecessary use of comprehension Signed-off-by: Devdutt Shenoi <devdutt@outlook.in> * Use literal syntax instead of function calls to create data structure Signed-off-by: Devdutt Shenoi <devdutt@outlook.in> * Pass string format arguments as logging method parameters Signed-off-by: Devdutt Shenoi <devdutt@outlook.in>
Signed-off-by: Nic Ma <nma@nvidia.com>
People are asking for 0.4.0+ functionality, so by making the master installation instructions a section, we can easily copy a link pointing to the relevant bit of code. Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* Remove unnecessary lambda expression * fixes compatible attributes in config printing 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>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* [DLMED] enhance the arg of rotate90 transform Signed-off-by: Nic Ma <nma@nvidia.com>
* update Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * use mask_size rather than margin Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * use mask_size instead of margin Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix index typo Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * remove postprocessing and fix docstring Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * update for code review Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * autofix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
…tatement (#1434) * Refactor unnecessary `else` / `elif` when `if` block has a `return` statement * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
* 1412 add global mutual information Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
…atement (#1438) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
* fix bug Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * autofix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
* [DLMED] add TorchVision transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests 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] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com>
* [DLMED] refine Brats transform and add missing docs 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>
* add aliases to import Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * all-> __all__; resolves built-in name conficts Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> * exit -> sys.exit Signed-off-by: Wenqi Li <wenqil@nvidia.com> * maintainer field deprecated https://docs.docker.com/engine/reference/builder/\#maintainer-deprecated Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
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Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
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Types of changes
./runtests.sh --codeformat --coverage../runtests.sh --quick.make htmlcommand in thedocs/folder.