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Merged
Nic-Ma
merged 5 commits into
Nic-Ma:1378-add-niftisaver-data-type
from
Project-MONAI:master
Dec 23, 2020
Merged
merge mater #2
Nic-Ma
merged 5 commits into
Nic-Ma:1378-add-niftisaver-data-type
from
Project-MONAI:master
Dec 23, 2020
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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>
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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.