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Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* Initial cpu implementation Signed-off-by: charliebudd <[email protected]> * hue speed increase moving away from torch tensors Signed-off-by: charliebudd <[email protected]> * allowing generic channel dimension size Signed-off-by: charliebudd <[email protected]> * allowing generic dimensionality Signed-off-by: charliebudd <[email protected]> * manual testing script for bilateral filter Signed-off-by: charliebudd <[email protected]> * Initial commit of CRF using permutohedral lattice to optimise message passing, implementation from https://github.com/SamuelJoutard/Permutohedral_attention_module Signed-off-by: charliebudd <[email protected]> * temporary example scripts demonstrating the usage of crf and phl, and some data to process Signed-off-by: charliebudd <[email protected]> * 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 <[email protected]> * c++ cpu permutohedral lattice implementation Signed-off-by: charliebudd <[email protected]> * comparison script Signed-off-by: charliebudd <[email protected]> * cleaning Signed-off-by: charliebudd <[email protected]> * backwards pass Signed-off-by: charliebudd <[email protected]> * initial cuda brute force kernel Signed-off-by: charliebudd <[email protected]> * reverting setup.py Signed-off-by: charliebudd <[email protected]> * working cuda kernel for brute force 2d kernel Signed-off-by: charliebudd <[email protected]> * fixing unresolved symbols when compiling without cuda Signed-off-by: charliebudd <[email protected]> * removing macros file Signed-off-by: charliebudd <[email protected]> * placeholder cuda phl implementation Signed-off-by: charliebudd <[email protected]> * changing test case color sigma Signed-off-by: charliebudd <[email protected]> * Initial import of reference cuda phl implementation Signed-off-by: charliebudd <[email protected]> * fixing cuda kernel color weight error Signed-off-by: charliebudd <[email protected]> * initial edits to cuda phl code Signed-off-by: charliebudd <[email protected]> * fixing errors in cuda phl implementation Signed-off-by: charliebudd <[email protected]> * removing logging from cuda phl Signed-off-by: charliebudd <[email protected]> * using template data_ptr function Signed-off-by: charliebudd <[email protected]> * fixed cpu phl implementation Signed-off-by: charliebudd <[email protected]> * updating cpu phl to run on arbitrary input dimensions and channles Signed-off-by: charliebudd <[email protected]> * 2d and 3d testing scripts Signed-off-by: charliebudd <[email protected]> * Generalising permutohedral implementation to remove independance on width and height Signed-off-by: charliebudd <[email protected]> * removing width and height from permutohedral filter function and implementing templated feature creation Signed-off-by: charliebudd <[email protected]> * fixed typo Signed-off-by: charliebudd <[email protected]> * exteneding 3d testing script Signed-off-by: charliebudd <[email protected]> * generalising bruteforce cuda implementation Signed-off-by: charliebudd <[email protected]> * updating testing scripts Signed-off-by: charliebudd <[email protected]> * file organisiation Signed-off-by: charliebudd <[email protected]> * fixing weight error in cpu bruteforce implementation, also inlineing functions Signed-off-by: charliebudd <[email protected]> * some refactoring and introducing proper batch handling Signed-off-by: charliebudd <[email protected]> * fixing indexing error at border Signed-off-by: charliebudd <[email protected]> * fixing some artifacts in cuda phl for high color sigmas Signed-off-by: charliebudd <[email protected]> * fixing gaussian kernel function for cpu and cuda bruteforce Signed-off-by: charliebudd <[email protected]> * ensuring kernel is an odd numbered size Signed-off-by: charliebudd <[email protected]> * adding tests for precised implementation Signed-off-by: charliebudd <[email protected]> * adding approximate imlpementation test Signed-off-by: charliebudd <[email protected]> * templating implementations based on scalar_type Signed-off-by: charliebudd <[email protected]> * cleaning up Signed-off-by: charliebudd <[email protected]> * code formatting Signed-off-by: charliebudd <[email protected]> * removing half precision implementation for permutohedral due to errors caused on windows Signed-off-by: charliebudd <[email protected]> * skipping cuda tests if cuda missing Signed-off-by: charliebudd <[email protected]> * reformating Signed-off-by: charliebudd <[email protected]> * adding unit test skip based on cpp extention availablility Signed-off-by: charliebudd <[email protected]> * removing unused import Signed-off-by: charliebudd <[email protected]> * changing to use of THCatomic add Signed-off-by: charliebudd <[email protected]> * adding missing licenses Signed-off-by: charliebudd <[email protected]> * clang reformat Signed-off-by: charliebudd <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* eval_mode Signed-off-by: Richard Brown <[email protected]> * DynUnetSupervision unittest shouldnt use eval_mode Signed-off-by: Richard Brown <[email protected]> * move to device Signed-off-by: Richard Brown <[email protected]>
* [DLMED] add get_feature_maps API to dynunet Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: Isaac Yang <[email protected]>
Signed-off-by: yiheng-wang-nv <[email protected]>
* unify visualisation
* 1405 add bending energy loss Signed-off-by: kate-sann5100 <[email protected]>
* changed year 2020 in copyright to "2020 - 2021" for both occurences Signed-off-by: Daniel Schulz [email protected] <[email protected]> * 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 [email protected] <[email protected]> * added danielschulz-specific changes for GitHu Actions to work properly Signed-off-by: Daniel Schulz [email protected] <[email protected]> * added test Signed-off-by: Daniel Schulz [email protected] <[email protected]> * revoked test line Signed-off-by: Daniel Schulz [email protected] <[email protected]> * 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 [email protected] <[email protected]> * reverted back local-only changes Signed-off-by: Daniel Schulz [email protected] <[email protected]> * improved checking integrity of NGC CLI Signed-off-by: Daniel Schulz [email protected] <[email protected]> * removed typo in GH repository variable Signed-off-by: Daniel Schulz [email protected] <[email protected]> * added remark Signed-off-by: Daniel Schulz [email protected] <[email protected]> * 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 [email protected] <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
add `__all__` and `remove import *`. Update CONTRIBUTING.md
* temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes docker login warning Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 99c6d20. Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit c529bf9. Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Isaac Yang <[email protected]>
* Improve docker build process, fixes #1276
* 1412 add local normalized cross correlation Signed-off-by: kate-sann5100 <[email protected]>
* Add .deepsource.toml Signed-off-by: Devdutt Shenoi <[email protected]> * Remove unnecessary use of comprehension Signed-off-by: Devdutt Shenoi <[email protected]> * Use literal syntax instead of function calls to create data structure Signed-off-by: Devdutt Shenoi <[email protected]> * Pass string format arguments as logging method parameters Signed-off-by: Devdutt Shenoi <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
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 <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* Remove unnecessary lambda expression * fixes compatible attributes in config printing Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance the arg of rotate90 transform Signed-off-by: Nic Ma <[email protected]>
* update Signed-off-by: Richard Brown <[email protected]> * use mask_size rather than margin Signed-off-by: Richard Brown <[email protected]> * use mask_size instead of margin Signed-off-by: Richard Brown <[email protected]> * fix index typo Signed-off-by: Richard Brown <[email protected]> * remove postprocessing and fix docstring Signed-off-by: Richard Brown <[email protected]> * update for code review Signed-off-by: Richard Brown <[email protected]> * autofix Signed-off-by: Richard Brown <[email protected]>
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 <[email protected]> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
* [DLMED] remove deprecated APIs in IO transforms Signed-off-by: Nic Ma <[email protected]>
* Remove length check in favour of truthiness of the object * fixes The truth value of an array with more than one element is ambiguous Signed-off-by: Wenqi Li <[email protected]> * fixes indices types Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <[email protected]>
* 1442 add localnet Signed-off-by: kate-sann5100 <[email protected]> * 1442 add test Signed-off-by: kate-sann5100 <[email protected]> * 1442 add documentation Signed-off-by: kate-sann5100 <[email protected]> * 1442 add typing Signed-off-by: kate-sann5100 <[email protected]> * 1442 reformat Signed-off-by: kate-sann5100 <[email protected]> * 1442 reformat Signed-off-by: kate-sann5100 <[email protected]> * 1442 reformat Signed-off-by: kate-sann5100 <[email protected]> * 1442 remove initializsation Signed-off-by: kate-sann5100 <[email protected]> * 1442 update factory calls Signed-off-by: kate-sann5100 <[email protected]>
* faster amazon download Signed-off-by: Richard Brown <[email protected]> * remove unused imports Signed-off-by: Richard Brown <[email protected]>
* Remove assert statement from non-test files * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * fixes assertion conditions Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
…th() (#1418) * Added new simplelayer SavitskyGolayFilter() Signed-off-by: Christian Baker <[email protected]> * Unit tests written for SavitskyGolayFilter() Signed-off-by: Christian Baker <[email protected]> * New array transform SavitskyGolaySmooth() written that wraps SavitskyGolayFilter() simplelayer Signed-off-by: Christian Baker <[email protected]> * Tests added for SavitskyGolaySmooth() Signed-off-by: Christian Baker <[email protected]> * Added to Sphinx .rst files and rebuilt docs Signed-off-by: Christian Baker <[email protected]>
* exposing permutohedral lattice filter in python api Signed-off-by: charliebudd <[email protected]> * unit tests for phl filter Co-authored-by: monai-bot <[email protected]>
* [DLMED] change NiftiDataset to ImageDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] update CI tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]>
* 1452 add Warp layer and test Signed-off-by: kate-sann5100 <[email protected]> * 1452 add documentation Signed-off-by: kate-sann5100 <[email protected]> * 1452 enforce same image and ddf size, add test case Signed-off-by: kate-sann5100 <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
* 1442 add initialization Signed-off-by: kate-sann5100 <[email protected]> * 1442 fix typing and add test cases Signed-off-by: kate-sann5100 <[email protected]>
* [DLMED] fix TorchScript issue in AHNet Signed-off-by: Nic Ma <[email protected]> * [DLMED] add test cases Signed-off-by: Nic Ma <[email protected]>
* Fix for device config script Signed-off-by: Eric Kerfoot <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add IterationHandler refer to the EpochHandler in ignite Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix the multi-gpu issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix distributed tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
Stop build if the tag format is wrong Signed-off-by: Isaac Yang <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
learning rate finder and corresponding test
* test new action for quick test; add temp tests Signed-off-by: Wenqi Li <[email protected]> * testing action Signed-off-by: Wenqi Li <[email protected]> * remove temp test Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add more Events Signed-off-by: Nic Ma <[email protected]> * [DLMED] add 3 Events Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[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]> Co-authored-by: monai-bot <[email protected]>
* 1442 use pull-grid only for above linear interpolation Signed-off-by: kate-sann5100 <[email protected]>
Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
…1497) * [DLMED] add IterationHandler refer to the EpochHandler in ignite Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix the multi-gpu issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix distributed tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add engine to metrics Signed-off-by: Nic Ma <[email protected]> * [DLMED] share metric details in engine Signed-off-by: Nic Ma <[email protected]> * [DLMED] add metrics report Signed-off-by: Nic Ma <[email protected]> * [DLMED] add average value to report Signed-off-by: Nic Ma <[email protected]> * [DLMED] add summary report Signed-off-by: Nic Ma <[email protected]> * [DLMED] add docs Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add unit tests and distributed tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove from min_tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove useless var Signed-off-by: Nic Ma <[email protected]> * [DLMED] add skip flag Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add dist tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance some unit tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] remove from min_tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] change to standlone APIs to write files Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add file type check Signed-off-by: Nic Ma <[email protected]> * [DLMED] add output_type arg Signed-off-by: Nic Ma <[email protected]> * [DLMED] develop standlone API Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 error Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix min test Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
* fixes #1526 Signed-off-by: Wenqi Li <[email protected]> * fixes Useless inheritance from object https://deepsource.io/gh/Project-MONAI/MONAI/issue/PYL-R0205 Signed-off-by: Wenqi Li <[email protected]> * fixes https://github.com/Project-MONAI/MONAI/pull/1527/checks?check_run_id=1794062607#step:10:7763 Signed-off-by: Wenqi Li <[email protected]>
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Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
Status
Ready/Work in progress/Hold
Types of changes
./runtests.sh --codeformat --coverage../runtests.sh --quick.make htmlcommand in thedocs/folder.